--- /dev/null
+.bundle
+.rvmrc
+*~
+*.pyc
+docker/*/generated
+docker/config.yml
+doc/.site
+doc/sdk/python/arvados
+sdk/perl/MYMETA.*
+sdk/perl/Makefile
+sdk/perl/blib
+sdk/perl/pm_to_blib
+*/vendor/bundle
+sdk/java/target
+*.class
+apps/workbench/vendor/bundle
+services/api/vendor/bundle
+sdk/java/log
+sdk/cli/vendor
--- /dev/null
+Server-side components of Arvados contained in the apps/ and services/
+directories, including the API Server, Workbench, and Crunch, are licenced
+under the GNU Affero General Public License version 3 (see agpl-3.0.txt)
+
+The Arvados client Software Development Kits contained in the sdk/ directory,
+example scripts in the crunch_scripts/ directory, and code samples in the
+Aravados documentation are licensed under the Apache License, Version 2.0 (see
+LICENSE-2.0.txt)
+
+The Arvados Documentation located in the doc/ directory is licensed under the
+Creative Commons Attribution-Share Alike 3.0 United States (see by-sa-3.0.txt)
\ No newline at end of file
--- /dev/null
+
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-Run a web service from Arvados.
+Welcome to Arvados!
-usage: arv-web.py [-h] --project PROJECT [--port PORT] --image IMAGE
+The main Arvados web site is
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-This queries an Arvados project and FUSE mounts the most recently modified
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+For support see
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+Installation documentation is located at
+ http://doc.arvados.org/install
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+If you wish to build the documentation yourself, follow the instructions in
+doc/README to build the documentation, then consult the "Install Guide".
-To build the Docker image:
-
-$ docker build -t arvados/arv-web .
+See COPYING for information about Arvados Free Software licenses.
--- /dev/null
+ GNU AFFERO GENERAL PUBLIC LICENSE
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+ requiring that modified versions of such material be marked in
+ reasonable ways as different from the original version; or
+
+ d) Limiting the use for publicity purposes of names of licensors or
+ authors of the material; or
+
+ e) Declining to grant rights under trademark law for use of some
+ trade names, trademarks, or service marks; or
+
+ f) Requiring indemnification of licensors and authors of that
+ material by anyone who conveys the material (or modified versions of
+ it) with contractual assumptions of liability to the recipient, for
+ any liability that these contractual assumptions directly impose on
+ those licensors and authors.
+
+ All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term. If a license document contains
+a further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms
+of that license document, provided that the further restriction does
+not survive such relicensing or conveying.
+
+ If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.
+
+ Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
+
+ 8. Termination.
+
+ You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+ However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+ Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+ Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+
+ 10. Automatic Licensing of Downstream Recipients.
+
+ Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.
+
+ An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.
+
+ You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.
+
+ Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+ In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+ If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Remote Network Interaction; Use with the GNU General Public License.
+
+ Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
+Source of your version by providing access to the Corresponding Source
+from a network server at no charge, through some standard or customary
+means of facilitating copying of software. This Corresponding Source
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<http://www.gnu.org/licenses/>.
--- /dev/null
+Run a web service from Arvados.
+
+usage: arv-web.py [-h] --project PROJECT [--port PORT] --image IMAGE
+
+optional arguments:
+ -h, --help show this help message and exit
+ --project PROJECT Project to watch
+ --port PORT Local bind port
+ --image IMAGE Docker image to run
+
+
+This queries an Arvados project and FUSE mounts the most recently modified
+collection into a temporary directory. It then runs the supplied Docker image
+with the collection bind mounted to /mnt inside the container.
+
+When a new collection is added to the project, or an existing project is
+updated, it will detect the change, it will stop the running Docker container,
+unmount the old collection, mount the new most recently modified collection,
+and restart the Docker container with the new mount.
+
+The supplied Dockerfile builds a Docker image that runs Apache with /mnt as the
+DocumentRoot. It is configured to run web applications based on Python WSGI,
+Ruby Rack, CGI, to serve static HTML, or simply browse the contents of the
+/public subdirectory of the collection using Apache's default index pages.
+
+To build the Docker image:
+
+$ docker build -t arvados/arv-web .
--- /dev/null
+# Ignore the default SQLite database.
+/db/*.sqlite3
+
+# Ignore all logfiles and tempfiles.
+/log/*.log
+/tmp
+
+/config/.secret_token
+/config/initializers/secret_token.rb
+
+/public/assets
+
+/config/environments/development.rb
+/config/environments/production.rb
+/config/application.yml
+
+# Workbench doesn't need one anyway, so this shouldn't come up, but...
+/config/database.yml
+
+/config/piwik.yml
+
+# Capistrano files are coming from another repo
+/Capfile*
+/config/deploy*
+
+# Themes are coming from another repo
+/themes/*
+
+# This can be a symlink to ../../../doc/.site in dev setups
+/public/doc
+
+# SimpleCov reports
+/coverage
+
+# Dev/test SSL certificates
+/self-signed.key
+/self-signed.pem
--- /dev/null
+source 'https://rubygems.org'
+
+gem 'rails', '~> 4.1.0'
+gem 'minitest', '>= 5.0.0'
+
+gem 'arvados', '>= 0.1.20141114230720'
+
+# Bundle edge Rails instead:
+# gem 'rails', :git => 'git://github.com/rails/rails.git'
+
+gem 'sqlite3'
+
+gem 'multi_json'
+gem 'oj'
+gem 'sass'
+
+# Note: keeping this out of the "group :assets" section "may" allow us
+# to use Coffescript for UJS responses. It also prevents a
+# warning/problem when running tests: "WARN: tilt autoloading
+# 'coffee_script' in a non thread-safe way; explicit require
+# 'coffee_script' suggested."
+gem 'coffee-rails'
+
+# Gems used only for assets and not required
+# in production environments by default.
+group :assets do
+ gem 'sass-rails', '~> 4.0.4'
+
+ # See https://github.com/sstephenson/execjs#readme for more supported runtimes
+ gem 'therubyracer', :platforms => :ruby
+
+ gem 'uglifier', '>= 1.0.3'
+end
+
+group :development do
+ gem 'byebug'
+ gem 'ruby-debug-passenger'
+end
+
+group :test, :diagnostics do
+ gem 'selenium-webdriver'
+ gem 'capybara'
+ gem 'poltergeist'
+ gem 'headless'
+end
+
+group :test, :performance do
+ gem 'rails-perftest'
+ gem 'ruby-prof'
+end
+
+group :test do
+ gem 'rvm-capistrano'
+ # Note: "require: false" here tells bunder not to automatically
+ # 'require' the packages during application startup. Installation is
+ # still mandatory.
+ gem 'simplecov', '~> 0.7.1', require: false
+ gem 'simplecov-rcov', require: false
+ gem 'mocha', require: false
+end
+
+gem 'jquery-rails'
+gem 'bootstrap-sass', '~> 3.1.0'
+gem 'bootstrap-x-editable-rails'
+gem 'bootstrap-tab-history-rails'
+
+gem 'angularjs-rails'
+
+gem 'less'
+gem 'less-rails'
+gem 'wiselinks'
+gem 'sshkey'
+
+# To use ActiveModel has_secure_password
+# gem 'bcrypt-ruby', '~> 3.0.0'
+
+# To use Jbuilder templates for JSON
+# gem 'jbuilder'
+
+# Use unicorn as the app server
+# gem 'unicorn'
+
+# Deploy with Capistrano
+# gem 'capistrano'
+
+# To use debugger
+#gem 'byebug'
+
+gem 'passenger', :group => :production
+gem 'andand'
+gem 'RedCloth'
+
+gem 'piwik_analytics'
+gem 'httpclient', '~> 2.5.0'
+
+# This fork has Rails 4 compatible routes
+gem 'themes_for_rails', git: 'https://github.com/holtkampw/themes_for_rails', ref: '1fd2d7897d75ae0d6375f4c390df87b8e91ad417'
+
+gem "deep_merge", :require => 'deep_merge/rails_compat'
+
+gem 'morrisjs-rails'
+gem 'raphael-rails'
--- /dev/null
+GIT
+ remote: https://github.com/holtkampw/themes_for_rails
+ revision: 1fd2d7897d75ae0d6375f4c390df87b8e91ad417
+ ref: 1fd2d7897d75ae0d6375f4c390df87b8e91ad417
+ specs:
+ themes_for_rails (0.5.1)
+ rails (>= 3.0.0)
+
+GEM
+ remote: https://rubygems.org/
+ specs:
+ RedCloth (4.2.9)
+ actionmailer (4.1.8)
+ actionpack (= 4.1.8)
+ actionview (= 4.1.8)
+ mail (~> 2.5, >= 2.5.4)
+ actionpack (4.1.8)
+ actionview (= 4.1.8)
+ activesupport (= 4.1.8)
+ rack (~> 1.5.2)
+ rack-test (~> 0.6.2)
+ actionview (4.1.8)
+ activesupport (= 4.1.8)
+ builder (~> 3.1)
+ erubis (~> 2.7.0)
+ activemodel (4.1.8)
+ activesupport (= 4.1.8)
+ builder (~> 3.1)
+ activerecord (4.1.8)
+ activemodel (= 4.1.8)
+ activesupport (= 4.1.8)
+ arel (~> 5.0.0)
+ activesupport (4.1.8)
+ i18n (~> 0.6, >= 0.6.9)
+ json (~> 1.7, >= 1.7.7)
+ minitest (~> 5.1)
+ thread_safe (~> 0.1)
+ tzinfo (~> 1.1)
+ addressable (2.3.6)
+ andand (1.3.3)
+ angularjs-rails (1.3.3)
+ arel (5.0.1.20140414130214)
+ arvados (0.1.20141114230720)
+ activesupport (>= 3.2.13)
+ andand (~> 1.3, >= 1.3.3)
+ google-api-client (~> 0.6.3, >= 0.6.3)
+ json (~> 1.7, >= 1.7.7)
+ jwt (>= 0.1.5, < 1.0.0)
+ autoparse (0.3.3)
+ addressable (>= 2.3.1)
+ extlib (>= 0.9.15)
+ multi_json (>= 1.0.0)
+ bootstrap-sass (3.1.1.1)
+ sass (~> 3.2)
+ bootstrap-tab-history-rails (0.1.0)
+ railties (>= 3.1)
+ bootstrap-x-editable-rails (1.5.1.1)
+ railties (>= 3.0)
+ builder (3.2.2)
+ byebug (3.5.1)
+ columnize (~> 0.8)
+ debugger-linecache (~> 1.2)
+ slop (~> 3.6)
+ capistrano (2.15.5)
+ highline
+ net-scp (>= 1.0.0)
+ net-sftp (>= 2.0.0)
+ net-ssh (>= 2.0.14)
+ net-ssh-gateway (>= 1.1.0)
+ capybara (2.4.4)
+ mime-types (>= 1.16)
+ nokogiri (>= 1.3.3)
+ rack (>= 1.0.0)
+ rack-test (>= 0.5.4)
+ xpath (~> 2.0)
+ childprocess (0.5.5)
+ ffi (~> 1.0, >= 1.0.11)
+ cliver (0.3.2)
+ coffee-rails (4.1.0)
+ coffee-script (>= 2.2.0)
+ railties (>= 4.0.0, < 5.0)
+ coffee-script (2.3.0)
+ coffee-script-source
+ execjs
+ coffee-script-source (1.8.0)
+ columnize (0.8.9)
+ commonjs (0.2.7)
+ daemon_controller (1.2.0)
+ debugger-linecache (1.2.0)
+ deep_merge (1.0.1)
+ erubis (2.7.0)
+ execjs (2.2.2)
+ extlib (0.9.16)
+ faraday (0.8.9)
+ multipart-post (~> 1.2.0)
+ ffi (1.9.6)
+ google-api-client (0.6.4)
+ addressable (>= 2.3.2)
+ autoparse (>= 0.3.3)
+ extlib (>= 0.9.15)
+ faraday (~> 0.8.4)
+ jwt (>= 0.1.5)
+ launchy (>= 2.1.1)
+ multi_json (>= 1.0.0)
+ signet (~> 0.4.5)
+ uuidtools (>= 2.1.0)
+ headless (1.0.2)
+ highline (1.6.21)
+ hike (1.2.3)
+ httpclient (2.5.3.3)
+ i18n (0.6.11)
+ jquery-rails (3.1.2)
+ railties (>= 3.0, < 5.0)
+ thor (>= 0.14, < 2.0)
+ json (1.8.1)
+ jwt (0.1.13)
+ multi_json (>= 1.5)
+ launchy (2.4.3)
+ addressable (~> 2.3)
+ less (2.6.0)
+ commonjs (~> 0.2.7)
+ less-rails (2.6.0)
+ actionpack (>= 3.1)
+ less (~> 2.6.0)
+ libv8 (3.16.14.7)
+ mail (2.6.3)
+ mime-types (>= 1.16, < 3)
+ metaclass (0.0.4)
+ mime-types (2.4.3)
+ mini_portile (0.6.1)
+ minitest (5.4.3)
+ mocha (1.1.0)
+ metaclass (~> 0.0.1)
+ morrisjs-rails (0.5.1)
+ railties (> 3.1, < 5)
+ multi_json (1.10.1)
+ multipart-post (1.2.0)
+ net-scp (1.2.1)
+ net-ssh (>= 2.6.5)
+ net-sftp (2.1.2)
+ net-ssh (>= 2.6.5)
+ net-ssh (2.9.1)
+ net-ssh-gateway (1.2.0)
+ net-ssh (>= 2.6.5)
+ nokogiri (1.6.4.1)
+ mini_portile (~> 0.6.0)
+ oj (2.11.1)
+ passenger (4.0.53)
+ daemon_controller (>= 1.2.0)
+ rack
+ rake (>= 0.8.1)
+ piwik_analytics (1.0.2)
+ actionpack
+ activesupport
+ rails (>= 3.0.0)
+ poltergeist (1.5.1)
+ capybara (~> 2.1)
+ cliver (~> 0.3.1)
+ multi_json (~> 1.0)
+ websocket-driver (>= 0.2.0)
+ rack (1.5.2)
+ rack-test (0.6.2)
+ rack (>= 1.0)
+ rails (4.1.8)
+ actionmailer (= 4.1.8)
+ actionpack (= 4.1.8)
+ actionview (= 4.1.8)
+ activemodel (= 4.1.8)
+ activerecord (= 4.1.8)
+ activesupport (= 4.1.8)
+ bundler (>= 1.3.0, < 2.0)
+ railties (= 4.1.8)
+ sprockets-rails (~> 2.0)
+ rails-perftest (0.0.5)
+ railties (4.1.8)
+ actionpack (= 4.1.8)
+ activesupport (= 4.1.8)
+ rake (>= 0.8.7)
+ thor (>= 0.18.1, < 2.0)
+ rake (10.4.0)
+ raphael-rails (2.1.2)
+ ref (1.0.5)
+ ruby-debug-passenger (0.2.0)
+ ruby-prof (0.15.2)
+ rubyzip (1.1.6)
+ rvm-capistrano (1.5.5)
+ capistrano (~> 2.15.4)
+ sass (3.2.19)
+ sass-rails (4.0.4)
+ railties (>= 4.0.0, < 5.0)
+ sass (~> 3.2.2)
+ sprockets (~> 2.8, < 2.12)
+ sprockets-rails (~> 2.0)
+ selenium-webdriver (2.44.0)
+ childprocess (~> 0.5)
+ multi_json (~> 1.0)
+ rubyzip (~> 1.0)
+ websocket (~> 1.0)
+ signet (0.4.5)
+ addressable (>= 2.2.3)
+ faraday (~> 0.8.1)
+ jwt (>= 0.1.5)
+ multi_json (>= 1.0.0)
+ simplecov (0.7.1)
+ multi_json (~> 1.0)
+ simplecov-html (~> 0.7.1)
+ simplecov-html (0.7.1)
+ simplecov-rcov (0.2.3)
+ simplecov (>= 0.4.1)
+ slop (3.6.0)
+ sprockets (2.11.3)
+ hike (~> 1.2)
+ multi_json (~> 1.0)
+ rack (~> 1.0)
+ tilt (~> 1.1, != 1.3.0)
+ sprockets-rails (2.2.0)
+ actionpack (>= 3.0)
+ activesupport (>= 3.0)
+ sprockets (>= 2.8, < 4.0)
+ sqlite3 (1.3.10)
+ sshkey (1.6.1)
+ therubyracer (0.12.1)
+ libv8 (~> 3.16.14.0)
+ ref
+ thor (0.19.1)
+ thread_safe (0.3.4)
+ tilt (1.4.1)
+ tzinfo (1.2.2)
+ thread_safe (~> 0.1)
+ uglifier (2.5.3)
+ execjs (>= 0.3.0)
+ json (>= 1.8.0)
+ uuidtools (2.1.5)
+ websocket (1.2.1)
+ websocket-driver (0.4.0)
+ wiselinks (1.2.1)
+ xpath (2.0.0)
+ nokogiri (~> 1.3)
+
+PLATFORMS
+ ruby
+
+DEPENDENCIES
+ RedCloth
+ andand
+ angularjs-rails
+ arvados (>= 0.1.20141114230720)
+ bootstrap-sass (~> 3.1.0)
+ bootstrap-tab-history-rails
+ bootstrap-x-editable-rails
+ byebug
+ capybara
+ coffee-rails
+ deep_merge
+ headless
+ httpclient (~> 2.5.0)
+ jquery-rails
+ less
+ less-rails
+ minitest (>= 5.0.0)
+ mocha
+ morrisjs-rails
+ multi_json
+ oj
+ passenger
+ piwik_analytics
+ poltergeist
+ rails (~> 4.1.0)
+ rails-perftest
+ raphael-rails
+ ruby-debug-passenger
+ ruby-prof
+ rvm-capistrano
+ sass
+ sass-rails (~> 4.0.4)
+ selenium-webdriver
+ simplecov (~> 0.7.1)
+ simplecov-rcov
+ sqlite3
+ sshkey
+ themes_for_rails!
+ therubyracer
+ uglifier (>= 1.0.3)
+ wiselinks
--- /dev/null
+h1. Developing Workbench
+
+This document includes information to help developers who would like to contribute to Workbench. If you just want to install it, please refer to our "Workbench installation guide":http://doc.arvados.org/install/install-workbench-app.html.
+
+h2. Running tests
+
+The Workbench application includes a series of integration tests. When you run these, it starts the API server in a test environment, with all of its fixtures loaded, then tests Workbench by starting that server and making requests against it.
+
+In order for this to work, you must have Firefox installed (or Iceweasel, if you're running Debian), as well as the X Virtual Frame Buffer driver.
+
+<pre>
+$ sudo apt-get install iceweasel xvfb
+</pre>
+
+If you install the Workbench Bundle in deployment mode, you must also install the API server Bundle in deployment mode, and vice versa. If your Bundle installs have mismatched modes, the integration tests will fail with "Gem not found" errors.
+
+h2. Writing tests
+
+Integration tests are written with Capybara, which drives a fully-featured Web browser to interact with Workbench exactly as a user would.
+
+If your test requires JavaScript support, your test method should start with the line @Capybara.current_driver = Capybara.javascript_driver@. Otherwise, Capybara defaults to a simpler browser for speed.
+
+In most tests, you can directly call "Capybara's Session methods":http://rubydoc.info/github/jnicklas/capybara/Capybara/Session to drive the browser and check its state. If you need finer-grained control, refer to the "full Capybara documentation":http://rubydoc.info/github/jnicklas/capybara/Capybara.
--- /dev/null
+#!/usr/bin/env rake
+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
+
+require File.expand_path('../config/application', __FILE__)
+
+ArvadosWorkbench::Application.load_tasks
--- /dev/null
+// Compile any new HTML content that was loaded via jQuery.ajax().
+// Currently this only works for tabs, and only because they emit an
+// arv:pane:loaded event after updating the DOM.
+
+$(document).on('arv:pane:loaded', function(event, $updatedElement) {
+ if (angular && $updatedElement) {
+ angular.element($updatedElement).injector().invoke([
+ '$compile', function($compile) {
+ var scope = angular.element($updatedElement).scope();
+ $compile($updatedElement)(scope);
+ }]);
+ }
+});
--- /dev/null
+// This is a manifest file that'll be compiled into application.js, which will include all the files
+// listed below.
+//
+// Any JavaScript/Coffee file within this directory, lib/assets/javascripts, vendor/assets/javascripts,
+// or vendor/assets/javascripts of plugins, if any, can be referenced here using a relative path.
+//
+// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
+// the compiled file.
+//
+// WARNING: THE FIRST BLANK LINE MARKS THE END OF WHAT'S TO BE PROCESSED, ANY BLANK LINE SHOULD
+// GO AFTER THE REQUIRES BELOW.
+//
+//= require jquery
+//= require jquery_ujs
+//= require bootstrap
+//= require bootstrap/dropdown
+//= require bootstrap/tab
+//= require bootstrap/tooltip
+//= require bootstrap/popover
+//= require bootstrap/collapse
+//= require bootstrap/modal
+//= require bootstrap/button
+//= require bootstrap3-editable/bootstrap-editable
+//= require bootstrap-tab-history
+//= require wiselinks
+//= require angular
+//= require raphael
+//= require morris
+//= require jquery.number.min
+//= require_tree .
+
+jQuery(function($){
+ $(document).ajaxStart(function(){
+ $('.modal-with-loading-spinner .spinner').show();
+ }).ajaxStop(function(){
+ $('.modal-with-loading-spinner .spinner').hide();
+ });
+
+ $('[data-toggle=tooltip]').tooltip();
+
+ $('.expand-collapse-row').on('click', function(event) {
+ var targets = $('#' + $(this).attr('data-id'));
+ if (targets.css('display') == 'none') {
+ $(this).addClass('icon-minus-sign');
+ $(this).removeClass('icon-plus-sign');
+ } else {
+ $(this).addClass('icon-plus-sign');
+ $(this).removeClass('icon-minus-sign');
+ }
+ targets.fadeToggle(200);
+ });
+
+ var ajaxCount = 0;
+
+ $(document).
+ on('ajax:send', function(e, xhr) {
+ ajaxCount += 1;
+ if (ajaxCount == 1) {
+ $('.loading').fadeTo('fast', 1);
+ }
+ }).
+ on('ajax:complete', function(e, status) {
+ ajaxCount -= 1;
+ if (ajaxCount == 0) {
+ $('.loading').fadeOut('fast', 0);
+ }
+ }).
+ on('ajaxSend', function(e, xhr) {
+ // jQuery triggers 'ajaxSend' event when starting an ajax call, but
+ // rails-generated ajax triggers generate 'ajax:send'. Workbench
+ // event listeners currently expect 'ajax:send', so trigger the
+ // rails event in response to the jQuery one.
+ $(document).trigger('ajax:send');
+ }).
+ on('ajaxComplete', function(e, xhr) {
+ // See comment above about ajaxSend/ajax:send
+ $(document).trigger('ajax:complete');
+ }).
+ on('click', '.removable-tag a', function(e) {
+ var tag_span = $(this).parents('[data-tag-link-uuid]').eq(0)
+ tag_span.fadeTo('fast', 0.2);
+ $.ajax('/links/' + tag_span.attr('data-tag-link-uuid'),
+ {dataType: 'json',
+ type: 'POST',
+ data: { '_method': 'DELETE' },
+ context: tag_span}).
+ done(function(data, status, jqxhr) {
+ this.remove();
+ }).
+ fail(function(jqxhr, status, error) {
+ this.addClass('label-danger').fadeTo('fast', '1');
+ });
+ return false;
+ }).
+ on('click', 'a.add-tag-button', function(e) {
+ var jqxhr;
+ var new_tag_uuid = 'new-tag-' + Math.random();
+ var tag_head_uuid = $(this).parents('tr').attr('data-object-uuid');
+ var new_tag = window.prompt("Add tag for collection "+
+ tag_head_uuid,
+ "");
+ if (new_tag == null)
+ return false;
+ var new_tag_span =
+ $('<span class="label label-info removable-tag"></span>').
+ attr('data-tag-link-uuid', new_tag_uuid).
+ text(new_tag).
+ css('opacity', '0.2').
+ append(' <span class="removable-tag"><a title="Delete tag"><i class="fa fa-fw fa-trash-o"></i></a></span>');
+ $(this).
+ parent().
+ find('>span').
+ append(new_tag_span).
+ append(' ');
+ $.ajax($(this).attr('data-remote-href'),
+ {dataType: 'json',
+ type: $(this).attr('data-remote-method'),
+ data: {
+ 'link[head_uuid]': tag_head_uuid,
+ 'link[link_class]': 'tag',
+ 'link[name]': new_tag
+ },
+ context: new_tag_span}).
+ done(function(data, status, jqxhr) {
+ this.attr('data-tag-link-uuid', data.uuid).
+ fadeTo('fast', '1');
+ }).
+ fail(function(jqxhr, status, error) {
+ this.addClass('label-danger').fadeTo('fast', '1');
+ });
+ return false;
+ });
+
+ $(document).
+ on('ajax:complete ready', function() {
+ // See http://getbootstrap.com/javascript/#buttons
+ $('.btn').button();
+ }).
+ on('ready ajax:complete', function() {
+ $('[data-toggle~=tooltip]').tooltip({container:'body'});
+ }).
+ on('ready ajax:complete', function() {
+ // This makes the dialog close on Esc key, obviously.
+ $('.modal').attr('tabindex', '-1')
+ });
+
+ HeaderRowFixer = function(selector) {
+ this.duplicateTheadTr = function() {
+ $(selector).each(function() {
+ var the_table = this;
+ if ($('>tbody>tr:first>th', the_table).length > 0)
+ return;
+ $('>tbody', the_table).
+ prepend($('>thead>tr', the_table).
+ clone().
+ css('opacity', 0));
+ });
+ }
+ this.fixThead = function() {
+ $(selector).each(function() {
+ var widths = [];
+ $('> tbody > tr:eq(1) > td', this).each( function(i,v){
+ widths.push($(v).width());
+ });
+ for(i=0;i<widths.length;i++) {
+ $('thead th:eq('+i+')', this).width(widths[i]);
+ }
+ });
+ }
+ }
+
+ var fixer = new HeaderRowFixer('.table-fixed-header-row');
+ fixer.duplicateTheadTr();
+ fixer.fixThead();
+ $(window).resize(function(){
+ fixer.fixThead();
+ });
+ $(document).on('ajax:complete', function(e, status) {
+ fixer.duplicateTheadTr();
+ fixer.fixThead();
+ });
+
+ $(document).ready(function() {
+ /* When wiselinks is initialized, selection.js is not working. Since we want to stop
+ using selection.js in the near future, let's not initialize wiselinks for now. */
+
+ // window.wiselinks = new Wiselinks();
+
+ $(document).off('page:loading').on('page:loading', function(event, $target, render, url){
+ $("#page-wrapper").fadeOut(200);
+ });
+
+ $(document).off('page:redirected').on('page:redirected', function(event, $target, render, url){
+ });
+
+ $(document).off('page:always').on('page:always', function(event, xhr, settings){
+ $("#page-wrapper").fadeIn(200);
+ });
+
+ $(document).off('page:done').on('page:done', function(event, $target, status, url, data){
+ });
+
+ $(document).off('page:fail').on('page:fail', function(event, $target, status, url, error, code){
+ });
+ });
+
+ $(document).on('click', '.compute-detail', function(e) {
+ $(e.target).collapse('hide');
+ });
+
+ $(document).on('click', '.compute-node-summary', function(e) {
+ $(e.target.href).collapse('toggle');
+ });
+
+ $(document).on('click', '.force-cache-reload', function(e) {
+ history.replaceState( { nocache: true }, '' );
+ });
+});
+
+window.addEventListener("DOMContentLoaded", function(e) {
+ if(history.state) {
+ if(history.state.nocache) {
+ showLoadingModal();
+ history.replaceState( {}, '' );
+ location.reload(true);
+ }
+ }
+});
+
+function showLoadingModal() {
+ $('#loading-modal').modal('show');
+}
+
+function hideLoadingModal() {
+ $('#loading-modal').modal('hide');
+}
+
+function hasHTML5History() {
+ return !!(window.history && window.history.pushState);
+}
--- /dev/null
+angular.
+ module('Arvados', []).
+ service('ArvadosClient', ArvadosClient);
+
+ArvadosClient.$inject = ['arvadosApiToken', 'arvadosDiscoveryUri']
+function ArvadosClient(arvadosApiToken, arvadosDiscoveryUri) {
+ $.extend(this, {
+ apiPromise: apiPromise,
+ uniqueNameForManifest: uniqueNameForManifest
+ });
+ return this;
+ ////////////////////////////////
+
+ var that = this;
+ var promiseDiscovery;
+ var discoveryDoc;
+
+ function apiPromise(controller, action, params) {
+ // Start an API call. Return a promise that will resolve with
+ // the API response.
+ return getDiscoveryDoc().then(function() {
+ var meth = discoveryDoc.resources[controller].methods[action];
+ var data = $.extend({}, params, {_method: meth.httpMethod});
+ $.each(data, function(k, v) {
+ if (typeof(v) === 'object') {
+ data[k] = JSON.stringify(v);
+ }
+ });
+ var path = meth.path.replace(/{(.*?)}/, function(_, key) {
+ var val = data[key];
+ delete data[key];
+ return encodeURIComponent(val);
+ });
+ return $.ajax({
+ url: discoveryDoc.baseUrl + path,
+ type: 'POST',
+ crossDomain: true,
+ dataType: 'json',
+ data: data,
+ headers: {
+ Authorization: 'OAuth2 ' + arvadosApiToken
+ }
+ });
+ });
+ }
+
+ function uniqueNameForManifest(manifest, newStreamName, origName) {
+ // Return an (escaped) filename starting with (unescaped)
+ // origName that won't conflict with any existing names in the
+ // manifest if saved under newStreamName. newStreamName must
+ // be exactly as given in the manifest, e.g., "." or "./foo"
+ // or "./foo/bar".
+ //
+ // Example:
+ //
+ // uniqueNameForManifest('./foo [...] 0:0:bar\\040baz.txt\n', '.',
+ // 'foo/bar baz.txt')
+ // =>
+ // 'foo/bar\\040baz\\040(1).txt'
+ var newName;
+ var nameStub = origName;
+ var suffixInt = null;
+ var ok = false;
+ var lineMatch, linesRe = /(\S+).*/gm;
+ var fileTokenMatch, fileTokensRe = / \d+:\d+:(\S+)/g;
+ while (!ok) {
+ ok = true;
+ // Add ' (N)' before the filename extension, if any.
+ newName = (!suffixInt ? nameStub :
+ nameStub.replace(/(\.[^.]*)?$/, ' ('+suffixInt+')$1')).
+ replace(/ /g, '\\040');
+ while (ok && null !==
+ (lineMatch = linesRe.exec(manifest))) {
+ // lineMatch is [theEntireLine, streamName]
+ while (ok && null !==
+ (fileTokenMatch = fileTokensRe.exec(lineMatch[0]))) {
+ // fileTokenMatch is [theEntireToken, fileName]
+ if (lineMatch[1] + '/' + fileTokenMatch[1]
+ ===
+ newStreamName + '/' + newName) {
+ ok = false;
+ }
+ }
+ }
+ suffixInt = (suffixInt || 0) + 1;
+ }
+ return newName;
+ }
+
+ function getDiscoveryDoc() {
+ if (!promiseDiscovery) {
+ promiseDiscovery = $.ajax({
+ url: arvadosDiscoveryUri,
+ crossDomain: true
+ }).then(function(data, status, xhr) {
+ discoveryDoc = data;
+ });
+ }
+ return promiseDiscovery;
+ }
+}
--- /dev/null
+jQuery ->
+ $("a[rel=popover]").popover()
+ $(".tooltip").tooltip()
+ $("a[rel=tooltip]").tooltip()
\ No newline at end of file
--- /dev/null
+jQuery(function($){
+ $(document).on('click', '.toggle-persist button', function() {
+ var toggle_group = $(this).parents('[data-remote-href]').first();
+ var want_persist = !toggle_group.find('button').hasClass('active');
+ var want_state = want_persist ? 'persistent' : 'cache';
+ toggle_group.find('button').
+ toggleClass('active', want_persist).
+ html(want_persist ? 'Persistent' : 'Cache');
+ $.ajax(toggle_group.attr('data-remote-href'),
+ {dataType: 'json',
+ type: 'POST',
+ data: {
+ value: want_state
+ },
+ context: {
+ toggle_group: toggle_group,
+ want_state: want_state,
+ button: this
+ }
+ }).
+ done(function(data, status, jqxhr) {
+ var context = this;
+ // Remove "danger" status in case a previous action failed
+ $('.btn-danger', context.toggle_group).
+ addClass('btn-info').
+ removeClass('btn-danger');
+ // Update last-saved-state
+ context.toggle_group.
+ attr('data-persistent-state', context.want_state);
+ }).
+ fail(function(jqxhr, status, error) {
+ var context = this;
+ var saved_state;
+ // Add a visual indication that something failed
+ $(context.button).
+ addClass('btn-danger').
+ removeClass('btn-info');
+ // Change to the last-saved-state
+ saved_state = context.toggle_group.attr('data-persistent-state');
+ $(context.button).
+ toggleClass('active', saved_state == 'persistent').
+ html(saved_state == 'persistent' ? 'Persistent' : 'Cache');
+
+ if (jqxhr.readyState == 0 || jqxhr.status == 0) {
+ // Request cancelled due to page reload.
+ // Displaying an alert would be rather annoying.
+ } else if (jqxhr.responseJSON && jqxhr.responseJSON.errors) {
+ window.alert("Request failed: " +
+ jqxhr.responseJSON.errors.join("; "));
+ } else {
+ window.alert("Request failed.");
+ }
+ });
+ });
+});
--- /dev/null
+jQuery(function($){
+$(document).on('ajax:complete arv:pane:loaded ready', function() {
+ $('[data-utc-date]').each(function(i, elm) {
+ // Try matching the date using a couple of different formats.
+ var v = $(elm).attr('data-utc-date').match(/(\d\d\d\d)-(\d\d)-(\d\d) (\d\d):(\d\d):(\d\d) UTC/);
+ if (!v) {
+ v = $(elm).attr('data-utc-date').match(/(\d\d\d\d)-(\d\d)-(\d\d)T(\d\d):(\d\d):(\d\d)Z/);
+ }
+
+ if (v) {
+ // Create a new date object from the timestamp so the browser can
+ // render the date based on the locale/timezone.
+ var ts = new Date(Date.UTC(v[1], v[2]-1, v[3], v[4], v[5], v[6]));
+ if ($(elm).attr('data-utc-date-opts') && $(elm).attr('data-utc-date-opts').match(/noseconds/)) {
+ $(elm).text((ts.getHours() > 12 ? (ts.getHours()-12) : ts.getHours())
+ + ":" + (ts.getMinutes() < 10 ? '0' : '') + ts.getMinutes()
+ + (ts.getHours() >= 12 ? " PM " : " AM ")
+ + ts.toLocaleDateString());
+ } else {
+ $(elm).text(ts.toLocaleTimeString() + " " + ts.toLocaleDateString());
+ }
+ }
+ });
+});
+});
--- /dev/null
+$.fn.editable.defaults.ajaxOptions = {type: 'post', dataType: 'json'};
+$.fn.editable.defaults.send = 'always';
+
+// Default for editing is popup. I experimented with inline which is a little
+// nicer in that it shows up right under the mouse instead of nearby. However,
+// the inline box is taller than the regular content, which causes the page
+// layout to shift unless we make the table rows tall, which leaves a lot of
+// wasted space when not editing. Also inline can get cut off if the page is
+// too narrow, when the popup box will just move to do the right thing.
+//$.fn.editable.defaults.mode = 'inline';
+
+$.fn.editable.defaults.success = function (response, newValue) {
+ $(document).trigger('editable:success', [this, response, newValue]);
+};
+
+$.fn.editable.defaults.params = function (params) {
+ var a = {};
+ var key = params.pk.key;
+ a.id = $(this).attr('data-object-uuid') || params.pk.id;
+ a[key] = params.pk.defaults || {};
+ // Remove null values. Otherwise they get transmitted as empty
+ // strings in request params.
+ for (i in a[key]) {
+ if (a[key][i] == null)
+ delete a[key][i];
+ }
+ a[key][params.name] = params.value;
+ if (!a.id) {
+ a['_method'] = 'post';
+ } else {
+ a['_method'] = 'put';
+ }
+ return a;
+};
+
+$.fn.editable.defaults.validate = function (value) {
+ if (value == "***invalid***") {
+ return "Invalid selection";
+ }
+}
+
+$(document).
+ on('ready ajax:complete', function() {
+ $('.editable').
+ not('.editable-done-setup').
+ addClass('editable-done-setup').
+ editable({
+ success: function(response, newValue) {
+ // If we just created a new object, stash its UUID
+ // so we edit it next time instead of creating
+ // another new object.
+ if (!$(this).attr('data-object-uuid') && response.uuid) {
+ $(this).attr('data-object-uuid', response.uuid);
+ }
+ if (response.href) {
+ $(this).editable('option', 'url', response.href);
+ }
+ if ($(this).attr('data-name')) {
+ var textileAttr = $(this).attr('data-name') + 'Textile';
+ if (response[textileAttr]) {
+ $(this).attr('data-textile', response[textileAttr]);
+ }
+ }
+ return;
+ },
+ error: function(response, newValue) {
+ var errlist = response.responseJSON.errors;
+ var errmsg;
+ if (Array.isArray(errlist)) {
+ errmsg = errlist.join();
+ } else {
+ errmsg = ("The server returned an error when making " +
+ "this update (status " + response.status +
+ ": " + errlist + ").");
+ }
+ return errmsg;
+ }
+ }).
+ on('hidden', function(e, reason) {
+ // After saving a new attribute, update the same
+ // information if it appears elsewhere on the page.
+ if (reason != 'save') return;
+ var html = $(this).html();
+ if( $(this).attr('data-textile') ) {
+ html = $(this).attr('data-textile');
+ $(this).html(html);
+ }
+ var uuid = $(this).attr('data-object-uuid');
+ var attr = $(this).attr('data-name');
+ var edited = this;
+ if (uuid && attr) {
+ $("[data-object-uuid='" + uuid + "']" +
+ "[data-name='" + attr + "']").each(function() {
+ if (this != edited)
+ $(this).html(html);
+ });
+ }
+ });
+ }).
+ on('ready ajax:complete', function() {
+ $("[data-toggle~='x-editable']").
+ not('.editable-done-setup').
+ addClass('editable-done-setup').
+ click(function(e) {
+ e.stopPropagation();
+ $($(this).attr('data-toggle-selector')).editable('toggle');
+ });
+ });
+
+$.fn.editabletypes.text.defaults.tpl = '<input type="text" name="editable-text">'
+
+$.fn.editableform.buttons = '\
+<button type="submit" class="btn btn-primary btn-sm editable-submit" \
+ id="editable-submit"><i class="glyphicon glyphicon-ok"></i></button>\
+<button type="button" class="btn btn-default btn-sm editable-cancel" \
+ id="editable-cancel"><i class="glyphicon glyphicon-remove"></i></button>\
+'
--- /dev/null
+/*
+ * This js establishes a websockets connection with the API Server.
+ */
+
+/* Subscribe to websockets event log. Do nothing if already connected. */
+function subscribeToEventLog () {
+ // if websockets are not supported by browser, do not subscribe for events
+ websocketsSupported = ('WebSocket' in window);
+ if (websocketsSupported == false) {
+ return;
+ }
+
+ // check if websocket connection is already stored on the window
+ event_log_disp = $(window).data("arv-websocket");
+ if (event_log_disp == null) {
+ // need to create new websocket and event log dispatcher
+ websocket_url = $('meta[name=arv-websocket-url]').attr("content");
+ if (websocket_url == null)
+ return;
+
+ event_log_disp = new WebSocket(websocket_url);
+
+ event_log_disp.onopen = onEventLogDispatcherOpen;
+ event_log_disp.onmessage = onEventLogDispatcherMessage;
+
+ // store websocket in window to allow reuse when multiple divs subscribe for events
+ $(window).data("arv-websocket", event_log_disp);
+ }
+}
+
+/* Send subscribe message to the websockets server. Without any filters
+ arguments, this subscribes to all events */
+function onEventLogDispatcherOpen(event) {
+ this.send('{"method":"subscribe"}');
+}
+
+/* Trigger event for all applicable elements waiting for this event */
+function onEventLogDispatcherMessage(event) {
+ parsedData = JSON.parse(event.data);
+ object_uuid = parsedData.object_uuid;
+
+ if (!object_uuid) {
+ return;
+ }
+
+ // if there are any listeners for this object uuid or "all", trigger the event
+ matches = ".arv-log-event-listener[data-object-uuid=\"" + object_uuid + "\"],.arv-log-event-listener[data-object-uuids~=\"" + object_uuid + "\"],.arv-log-event-listener[data-object-uuid=\"all\"],.arv-log-event-listener[data-object-kind=\"" + parsedData.object_kind + "\"]";
+ $(matches).trigger('arv-log-event', parsedData);
+}
+
+/* Automatically connect if there are any elements on the page that want to
+ receive event log events. */
+$(document).on('ajax:complete ready', function() {
+ var a = $('.arv-log-event-listener');
+ if (a.length > 0) {
+ subscribeToEventLog();
+ }
+});
+
+/* Assumes existence of:
+ window.jobGraphData = [];
+ window.jobGraphSeries = [];
+ window.jobGraphSortedSeries = [];
+ window.jobGraphMaxima = {};
+ */
+function processLogLineForChart( logLine ) {
+ try {
+ var match = logLine.match(/^(\S+) (\S+) (\S+) (\S+) stderr crunchstat: (\S+) (.*)/);
+ if( !match ) {
+ match = logLine.match(/^((?:Sun|Mon|Tue|Wed|Thu|Fri|Sat) (?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec) \d{1,2} \d\d:\d\d:\d\d \d{4}) (\S+) (\S+) (\S+) stderr crunchstat: (\S+) (.*)/);
+ if( match ) {
+ match[1] = (new Date(match[1] + ' UTC')).toISOString().replace('Z','');
+ }
+ }
+ if( match ) {
+ var rawDetailData = '';
+ var datum = null;
+
+ // the timestamp comes first
+ var timestamp = match[1].replace('_','T') + 'Z';
+
+ // we are interested in "-- interval" recordings
+ var intervalMatch = match[6].match(/(.*) -- interval (.*)/);
+ if( intervalMatch ) {
+ var intervalData = intervalMatch[2].trim().split(' ');
+ var dt = parseFloat(intervalData[0]);
+ var dsum = 0.0;
+ for(var i=2; i < intervalData.length; i += 2 ) {
+ dsum += parseFloat(intervalData[i]);
+ }
+ datum = dsum/dt;
+
+ if( datum < 0 ) {
+ // not interested in negative deltas
+ return;
+ }
+
+ rawDetailData = intervalMatch[2];
+
+ // for the series name use the task number (4th term) and then the first word after 'crunchstat:'
+ var series = 'T' + match[4] + '-' + match[5];
+
+ // special calculation for cpus
+ if( /-cpu$/.test(series) ) {
+ // divide the stat by the number of cpus unless the time count is less than the interval length
+ if( dsum.toFixed(1) > dt.toFixed(1) ) {
+ var cpuCountMatch = intervalMatch[1].match(/(\d+) cpus/);
+ if( cpuCountMatch ) {
+ datum = datum / cpuCountMatch[1];
+ }
+ }
+ }
+
+ addJobGraphDatum( timestamp, datum, series, rawDetailData );
+ } else {
+ // we are also interested in memory ("mem") recordings
+ var memoryMatch = match[6].match(/(\d+) cache (\d+) swap (\d+) pgmajfault (\d+) rss/);
+ if( memoryMatch ) {
+ rawDetailData = match[6];
+ // one datapoint for rss and one for swap - only show the rawDetailData for rss
+ addJobGraphDatum( timestamp, parseInt(memoryMatch[4]), 'T' + match[4] + "-rss", rawDetailData );
+ addJobGraphDatum( timestamp, parseInt(memoryMatch[2]), 'T' + match[4] + "-swap", '' );
+ } else {
+ // not interested
+ return;
+ }
+ }
+
+ window.redraw = true;
+ }
+ } catch( err ) {
+ console.log( 'Ignoring error trying to process log line: ' + err);
+ }
+}
+
+function addJobGraphDatum(timestamp, datum, series, rawDetailData) {
+ // check for new series
+ if( $.inArray( series, jobGraphSeries ) < 0 ) {
+ var newIndex = jobGraphSeries.push(series) - 1;
+ jobGraphSortedSeries.push(newIndex);
+ jobGraphSortedSeries.sort( function(a,b) {
+ var matchA = jobGraphSeries[a].match(/^T(\d+)-(.*)/);
+ var matchB = jobGraphSeries[b].match(/^T(\d+)-(.*)/);
+ var termA = ('000000' + matchA[1]).slice(-6) + matchA[2];
+ var termB = ('000000' + matchB[1]).slice(-6) + matchB[2];
+ return termA > termB ? 1 : -1;
+ });
+ jobGraphMaxima[series] = null;
+ window.recreate = true;
+ }
+
+ if( datum !== 0 && ( jobGraphMaxima[series] === null || jobGraphMaxima[series] < datum ) ) {
+ if( isJobSeriesRescalable(series) ) {
+ // use old maximum to get a scale conversion
+ var scaleConversion = jobGraphMaxima[series]/datum;
+ // set new maximum and rescale the series
+ jobGraphMaxima[series] = datum;
+ rescaleJobGraphSeries( series, scaleConversion );
+ }
+ }
+
+ // scale
+ var scaledDatum = null;
+ if( isJobSeriesRescalable(series) && jobGraphMaxima[series] !== null && jobGraphMaxima[series] !== 0 ) {
+ scaledDatum = datum/jobGraphMaxima[series]
+ } else {
+ scaledDatum = datum;
+ }
+ // identify x axis point, searching from the end of the array (most recent)
+ var found = false;
+ for( var i = jobGraphData.length - 1; i >= 0; i-- ) {
+ if( jobGraphData[i]['t'] === timestamp ) {
+ found = true;
+ jobGraphData[i][series] = scaledDatum;
+ jobGraphData[i]['raw-'+series] = rawDetailData;
+ break;
+ } else if( jobGraphData[i]['t'] < timestamp ) {
+ // we've gone far enough back in time and this data is supposed to be sorted
+ break;
+ }
+ }
+ // index counter from previous loop will have gone one too far, so add one
+ var insertAt = i+1;
+ if(!found) {
+ // create a new x point for this previously unrecorded timestamp
+ var entry = { 't': timestamp };
+ entry[series] = scaledDatum;
+ entry['raw-'+series] = rawDetailData;
+ jobGraphData.splice( insertAt, 0, entry );
+ var shifted = [];
+ // now let's see about "scrolling" the graph, dropping entries that are too old (>10 minutes)
+ while( jobGraphData.length > 0
+ && (Date.parse( jobGraphData[0]['t'] ) + 10*60000 < Date.parse( jobGraphData[jobGraphData.length-1]['t'] )) ) {
+ shifted.push(jobGraphData.shift());
+ }
+ if( shifted.length > 0 ) {
+ // from those that we dropped, were any of them maxima? if so we need to rescale
+ jobGraphSeries.forEach( function(series) {
+ // test that every shifted entry in this series was either not a number (in which case we don't care)
+ // or else approximately (to 2 decimal places) smaller than the scaled maximum (i.e. 1),
+ // because otherwise we just scrolled off something that was a maximum point
+ // and so we need to recalculate a new maximum point by looking at all remaining displayed points in the series
+ if( isJobSeriesRescalable(series) && jobGraphMaxima[series] !== null
+ && !shifted.every( function(e) { return( !$.isNumeric(e[series]) || e[series].toFixed(2) < 1.0 ) } ) ) {
+ // check the remaining displayed points and find the new (scaled) maximum
+ var seriesMax = null;
+ jobGraphData.forEach( function(entry) {
+ if( $.isNumeric(entry[series]) && (seriesMax === null || entry[series] > seriesMax)) {
+ seriesMax = entry[series];
+ }
+ });
+ if( seriesMax !== null && seriesMax !== 0 ) {
+ // set new actual maximum using the new maximum as the conversion conversion and rescale the series
+ jobGraphMaxima[series] *= seriesMax;
+ var scaleConversion = 1/seriesMax;
+ rescaleJobGraphSeries( series, scaleConversion );
+ }
+ else {
+ // we no longer have any data points displaying for this series
+ jobGraphMaxima[series] = null;
+ }
+ }
+ });
+ }
+ // add a 10 minute old null data point to keep the chart honest if the oldest point is less than 9.9 minutes old
+ if( jobGraphData.length > 0 ) {
+ var earliestTimestamp = jobGraphData[0]['t'];
+ var mostRecentTimestamp = jobGraphData[jobGraphData.length-1]['t'];
+ if( (Date.parse( earliestTimestamp ) + 9.9*60000 > Date.parse( mostRecentTimestamp )) ) {
+ var tenMinutesBefore = (new Date(Date.parse( mostRecentTimestamp ) - 600*1000)).toISOString();
+ jobGraphData.unshift( { 't': tenMinutesBefore } );
+ }
+ }
+ }
+
+}
+
+function createJobGraph(elementName) {
+ delete jobGraph;
+ var emptyGraph = false;
+ if( jobGraphData.length === 0 ) {
+ // If there is no data we still want to show an empty graph,
+ // so add an empty datum and placeholder series to fool it into displaying itself.
+ // Note that when finally a new series is added, the graph will be recreated anyway.
+ jobGraphData.push( {} );
+ jobGraphSeries.push( '' );
+ emptyGraph = true;
+ }
+ var graphteristics = {
+ element: elementName,
+ data: jobGraphData,
+ ymax: 1.0,
+ yLabelFormat: function () { return ''; },
+ xkey: 't',
+ ykeys: jobGraphSeries,
+ labels: jobGraphSeries,
+ resize: true,
+ hideHover: 'auto',
+ parseTime: true,
+ hoverCallback: function(index, options, content) {
+ var s = "<div class='morris-hover-row-label'>";
+ s += options.data[index][options.xkey];
+ s += "</div> ";
+ for( i = 0; i < jobGraphSortedSeries.length; i++ ) {
+ var sortedIndex = jobGraphSortedSeries[i];
+ var series = options.ykeys[sortedIndex];
+ var datum = options.data[index][series];
+ var point = ''
+ point += "<div class='morris-hover-point' style='color: ";
+ point += options.lineColors[sortedIndex % options.lineColors.length];
+ point += "'>";
+ var labelMatch = options.labels[sortedIndex].match(/^T(\d+)-(.*)/);
+ point += 'Task ' + labelMatch[1] + ' ' + labelMatch[2];
+ point += ": ";
+ if ( datum !== undefined ) {
+ if( isJobSeriesRescalable( series ) ) {
+ datum *= jobGraphMaxima[series];
+ }
+ if( parseFloat(datum) !== 0 ) {
+ if( /-cpu$/.test(series) ){
+ datum = $.number(datum * 100, 1) + '%';
+ } else if( datum < 10 ) {
+ datum = $.number(datum, 2);
+ } else {
+ datum = $.number(datum);
+ }
+ if(options.data[index]['raw-'+series]) {
+ datum += ' (' + options.data[index]['raw-'+series] + ')';
+ }
+ }
+ point += datum;
+ } else {
+ continue;
+ }
+ point += "</div> ";
+ s += point;
+ }
+ return s;
+ }
+ }
+ if( emptyGraph ) {
+ graphteristics['axes'] = false;
+ graphteristics['parseTime'] = false;
+ graphteristics['hideHover'] = 'always';
+ }
+ window.jobGraph = Morris.Line( graphteristics );
+ if( emptyGraph ) {
+ jobGraphData = [];
+ jobGraphSeries = [];
+ }
+}
+
+function rescaleJobGraphSeries( series, scaleConversion ) {
+ if( isJobSeriesRescalable() ) {
+ $.each( jobGraphData, function( i, entry ) {
+ if( entry[series] !== null && entry[series] !== undefined ) {
+ entry[series] *= scaleConversion;
+ }
+ });
+ }
+}
+
+// that's right - we never do this for the 'cpu' series, which will always be between 0 and 1 anyway
+function isJobSeriesRescalable( series ) {
+ return !/-cpu$/.test(series);
+}
+
+$(document).on('arv-log-event', '#log_graph_div', function(event, eventData) {
+ if( eventData.properties.text ) {
+ eventData.properties.text.split('\n').forEach( function( logLine ) {
+ processLogLineForChart( logLine );
+ } );
+ }
+} );
+
+$(document).on('ready ajax:complete', function() {
+ $('#log_graph_div').not('.graph-is-setup').addClass('graph-is-setup').each( function( index, graph_div ) {
+ window.jobGraphData = [];
+ window.jobGraphSeries = [];
+ window.jobGraphSortedSeries = [];
+ window.jobGraphMaxima = {};
+ window.recreate = false;
+ window.redraw = false;
+
+ createJobGraph($(graph_div).attr('id'));
+ var object_uuid = $(graph_div).data('object-uuid');
+ // if there are any listeners for this object uuid or "all", we will trigger the event
+ var matches = ".arv-log-event-listener[data-object-uuid=\"" + object_uuid + "\"],.arv-log-event-listener[data-object-uuids~=\"" + object_uuid + "\"]";
+
+ $(document).trigger('ajax:send');
+ $.get('/jobs/' + $(graph_div).data('object-uuid') + '/logs.json', function(data) {
+ data.forEach( function( entry ) {
+ $(matches).trigger('arv-log-event', entry);
+ });
+ });
+
+ setInterval( function() {
+ if( recreate ) {
+ window.recreate = false;
+ window.redraw = false;
+ // series have changed, draw entirely new graph
+ $(graph_div).html('');
+ createJobGraph($(graph_div).attr('id'));
+ } else if( redraw ) {
+ window.redraw = false;
+ jobGraph.setData( jobGraphData );
+ }
+ }, 5000);
+ });
+});
--- /dev/null
+// filterable.js shows/hides content when the user operates
+// search/select widgets. For "infinite scroll" content, it passes the
+// filters to the server and retrieves new content. For other content,
+// it filters the existing DOM elements using jQuery show/hide.
+//
+// Usage:
+//
+// 1. Add the "filterable" class to each filterable content item.
+// Typically, each item is a 'tr' or a 'div class="row"'.
+//
+// <div id="results">
+// <div class="filterable row">First row</div>
+// <div class="filterable row">Second row</div>
+// </div>
+//
+// 2. Add the "filterable-control" class to each search/select widget.
+// Also add a data-filterable-target attribute with a jQuery selector
+// for an ancestor of the filterable items, i.e., the container in
+// which this widget should apply filtering.
+//
+// <input class="filterable-control" data-filterable-target="#results"
+// type="text" />
+//
+// Supported widgets:
+//
+// <input type="text" ... />
+//
+// The input value is used as a regular expression. Rows with content
+// matching the regular expression are shown.
+//
+// <select ... data-filterable-attribute="data-example-attr">
+// <option value="foo">Foo</option>
+// <option value="">Show all</option>
+// </select>
+//
+// When the user selects the "Foo" option, rows with
+// data-example-attr="foo" are shown, and all others are hidden. When
+// the user selects the "Show all" option, all rows are shown.
+//
+// Notes:
+//
+// When multiple filterable-control widgets operate on the same
+// data-filterable-target, items must pass _all_ filters in order to
+// be shown.
+//
+// If one data-filterable-target is the parent of another
+// data-filterable-target, results are undefined. Don't do this.
+//
+// Combining "select" filterable-controls with infinite-scroll is not
+// yet supported.
+
+function updateFilterableQueryNow($target) {
+ var newquery = $target.data('filterable-query-new');
+ var params = $target.data('infinite-content-params-filterable') || {};
+ params.filters = [['any', 'ilike', '%' + newquery + '%']];
+ $target.data('infinite-content-params-filterable', params);
+ $target.data('filterable-query', newquery);
+}
+
+$(document).
+ on('ready ajax:success', function() {
+ // Copy any initial input values into
+ // data-filterable-query[-new].
+ $('input[type=text].filterable-control').each(function() {
+ var $this = $(this);
+ var $target = $($this.attr('data-filterable-target'));
+ if ($target.data('filterable-query-new') === undefined) {
+ $target.data('filterable-query', $this.val());
+ $target.data('filterable-query-new', $this.val());
+ updateFilterableQueryNow($target);
+ }
+ });
+ $('[data-infinite-scroller]').on('refresh-content', '[data-filterable-query]', function(e) {
+ // If some other event causes a refresh-content event while there
+ // is a new query waiting to cooloff, we should use the new query
+ // right away -- otherwise we'd launch an extra ajax request that
+ // would have to be reloaded as soon as the cooloff period ends.
+ if (this != e.target)
+ return;
+ if ($(this).data('filterable-query') == $(this).data('filterable-query-new'))
+ return;
+ updateFilterableQueryNow($(this));
+ });
+ }).
+ on('paste keyup input', 'input[type=text].filterable-control', function(e) {
+ var regexp;
+ if (this != e.target) return;
+ var $target = $($(this).attr('data-filterable-target'));
+ var currentquery = $target.data('filterable-query');
+ if (currentquery === undefined) currentquery = '';
+ if ($target.is('[data-infinite-scroller]')) {
+ // We already know how to load content dynamically, so we
+ // can do all filtering on the server side.
+
+ if ($target.data('infinite-cooloff-timer') > 0) {
+ // Clear a stale refresh-after-delay timer.
+ clearTimeout($target.data('infinite-cooloff-timer'));
+ }
+ // Stash the new query string in the filterable container.
+ $target.data('filterable-query-new', $(this).val());
+ if (currentquery == $(this).val()) {
+ // Don't mess with existing results or queries in
+ // progress.
+ return;
+ }
+ $target.data('infinite-cooloff-timer', setTimeout(function() {
+ // If the user doesn't do any query-changing actions
+ // in the next 1/4 second (like type or erase
+ // characters in the search box), hide the stale
+ // content and ask the server for new results.
+ updateFilterableQueryNow($target);
+ $target.trigger('refresh-content');
+ }, 250));
+ } else {
+ // Target does not have infinite-scroll capability. Just
+ // filter the rows in the browser using a RegExp.
+ regexp = undefined;
+ try {
+ regexp = new RegExp($(this).val(), 'i');
+ } catch(e) {
+ if (e instanceof SyntaxError) {
+ // Invalid/partial regexp. See 'has-error' below.
+ } else {
+ throw e;
+ }
+ }
+ $target.
+ toggleClass('has-error', regexp === undefined).
+ addClass('filterable-container').
+ data('q', regexp).
+ trigger('refresh');
+ }
+ }).on('refresh', '.filterable-container', function() {
+ var $container = $(this);
+ var q = $(this).data('q');
+ var filters = $(this).data('filters');
+ $('.filterable', this).hide().filter(function() {
+ var $row = $(this);
+ var pass = true;
+ if (q && !$row.text().match(q))
+ return false;
+ if (filters) {
+ $.each(filters, function(filterby, val) {
+ if (!val) return;
+ if (!pass) return;
+ pass = false;
+ $.each(val.split(" "), function(i, e) {
+ if ($row.attr(filterby) == e)
+ pass = true;
+ });
+ });
+ }
+ return pass;
+ }).show();
+
+ // Show/hide each section heading depending on whether any
+ // content rows are visible in that section.
+ $('.row[data-section-heading]', this).each(function(){
+ $(this).toggle($('.row.filterable[data-section-name="' +
+ $(this).attr('data-section-name') +
+ '"]:visible').length > 0);
+ });
+
+ // Load more content if the last result is showing.
+ $('.infinite-scroller').add(window).trigger('scroll');
+ }).on('change', 'select.filterable-control', function() {
+ var val = $(this).val();
+ var filterby = $(this).attr('data-filterable-attribute');
+ var $target = $($(this).attr('data-filterable-target')).
+ addClass('filterable-container');
+ var filters = $target.data('filters') || {};
+ filters[filterby] = val;
+ $target.
+ data('filters', filters).
+ trigger('refresh');
+ }).on('ajax:complete', function() {
+ $('.filterable-control').trigger('input');
+ });
--- /dev/null
+function maybe_load_more_content(event) {
+ var scroller = this;
+ var $container = $(event.data.container);
+ var src; // url for retrieving content
+ var scrollHeight;
+ var spinner, colspan;
+ var serial = Date.now();
+ var params;
+ scrollHeight = scroller.scrollHeight || $('body')[0].scrollHeight;
+ if ($(scroller).scrollTop() + $(scroller).height()
+ >
+ scrollHeight - 50)
+ {
+ if (!$container.attr('data-infinite-content-href0')) {
+ // Remember the first page source url, so we can refresh
+ // from page 1 later.
+ $container.attr('data-infinite-content-href0',
+ $container.attr('data-infinite-content-href'));
+ }
+ src = $container.attr('data-infinite-content-href');
+ if (!src || !$container.is(':visible'))
+ // Finished
+ return;
+
+ // Don't start another request until this one finishes
+ $container.attr('data-infinite-content-href', null);
+ spinner = '<div class="spinner spinner-32px spinner-h-center"></div>';
+ if ($container.is('table,tbody,thead,tfoot')) {
+ // Hack to determine how many columns a new tr should have
+ // in order to reach full width.
+ colspan = $container.closest('table').
+ find('tr').eq(0).find('td,th').length;
+ if (colspan == 0)
+ colspan = '*';
+ spinner = ('<tr class="spinner"><td colspan="' + colspan + '">' +
+ spinner +
+ '</td></tr>');
+ }
+ $container.find(".spinner").detach();
+ $container.append(spinner);
+ $container.attr('data-infinite-serial', serial);
+
+ if (src == $container.attr('data-infinite-content-href0')) {
+ // If we're loading the first page, collect filters from
+ // various sources.
+ params = mergeInfiniteContentParams($container);
+ $.each(params, function(k,v) {
+ if (v instanceof Object) {
+ params[k] = JSON.stringify(v);
+ }
+ });
+ } else {
+ // If we're loading page >1, ignore other filtering
+ // mechanisms and just use the "next page" URI from the
+ // previous page's response. Aside from avoiding race
+ // conditions (where page 2 could have different filters
+ // than page 1), this allows the server to use filters in
+ // the "next page" URI to achieve paging. (To apply any
+ // new filters effectively, we need to load page 1 again
+ // anyway.)
+ params = {};
+ }
+
+ $.ajax(src,
+ {dataType: 'json',
+ type: 'GET',
+ data: params,
+ context: {container: $container, src: src, serial: serial}}).
+ fail(function(jqxhr, status, error) {
+ var $faildiv;
+ var $container = this.container;
+ if ($container.attr('data-infinite-serial') != this.serial) {
+ // A newer request is already in progress.
+ return;
+ }
+ if (jqxhr.readyState == 0 || jqxhr.status == 0) {
+ message = "Cancelled."
+ } else if (jqxhr.responseJSON && jqxhr.responseJSON.errors) {
+ message = jqxhr.responseJSON.errors.join("; ");
+ } else {
+ message = "Request failed.";
+ }
+ // TODO: report the message to the user.
+ console.log(message);
+ $faildiv = $('<div />').
+ attr('data-infinite-content-href', this.src).
+ addClass('infinite-retry').
+ append('<span class="fa fa-warning" /> Oops, request failed. <button class="btn btn-xs btn-primary">Retry</button>');
+ $container.find('div.spinner').replaceWith($faildiv);
+ }).
+ done(function(data, status, jqxhr) {
+ if ($container.attr('data-infinite-serial') != this.serial) {
+ // A newer request is already in progress.
+ return;
+ }
+ $container.find(".spinner").detach();
+ $container.append(data.content);
+ $container.attr('data-infinite-content-href', data.next_page_href);
+ });
+ }
+}
+
+function ping_all_scrollers() {
+ // Send a scroll event to all scroll listeners that might need
+ // updating. Adding infinite-scroller class to the window element
+ // doesn't work, so we add it explicitly here.
+ $('.infinite-scroller').add(window).trigger('scroll');
+}
+
+function mergeInfiniteContentParams($container) {
+ var params = {};
+ // Combine infiniteContentParams from multiple sources. This
+ // mechanism allows each of several components to set and
+ // update its own set of filters, without having to worry
+ // about stomping on some other component's filters.
+ //
+ // For example, filterable.js writes filters in
+ // infiniteContentParamsFilterable ("search for text foo")
+ // without worrying about clobbering the filters set up by the
+ // tab pane ("only show jobs and pipelines in this tab").
+ $.each($container.data(), function(datakey, datavalue) {
+ // Note: We attach these data to DOM elements using
+ // <element data-foo-bar="baz">. We store/retrieve them
+ // using $('element').data('foo-bar'), although
+ // .data('fooBar') would also work. The "all data" hash
+ // returned by $('element').data(), however, always has
+ // keys like 'fooBar'. In other words, where we have a
+ // choice, we stick with the 'foo-bar' style to be
+ // consistent with HTML. Here, our only option is
+ // 'fooBar'.
+ if (/^infiniteContentParams/.exec(datakey)) {
+ if (datavalue instanceof Object) {
+ $.each(datavalue, function(hkey, hvalue) {
+ if (hvalue instanceof Array) {
+ params[hkey] = (params[hkey] || []).
+ concat(hvalue);
+ } else if (hvalue instanceof Object) {
+ $.extend(params[hkey], hvalue);
+ } else {
+ params[hkey] = hvalue;
+ }
+ });
+ }
+ }
+ });
+ return params;
+}
+
+function setColumnSort( $container, $header, direction ) {
+ // $container should be the tbody or whatever has all the infinite table data attributes
+ // $header should be the th with a preset data-sort-order attribute
+ // direction should be "asc" or "desc"
+ // This function returns the order by clause for this column header as a string
+
+ // First reset all sort directions
+ $('th[data-sort-order]').removeData('sort-order-direction');
+ // set the current one
+ $header.data('sort-order-direction', direction);
+ // change the ordering parameter
+ var paramsAttr = 'infinite-content-params-' + $container.data('infinite-content-params-attr');
+ var params = $container.data(paramsAttr) || {};
+ params.order = $header.data('sort-order').split(",").join( ' ' + direction + ', ' ) + ' ' + direction;
+ $container.data(paramsAttr, params);
+ // show the correct icon next to the column header
+ $container.trigger('sort-icons');
+
+ return params.order;
+}
+
+$(document).
+ on('click', 'div.infinite-retry button', function() {
+ var $retry_div = $(this).closest('.infinite-retry');
+ var $container = $(this).closest('.infinite-scroller-ready')
+ $container.attr('data-infinite-content-href',
+ $retry_div.attr('data-infinite-content-href'));
+ $retry_div.
+ replaceWith('<div class="spinner spinner-32px spinner-h-center" />');
+ ping_all_scrollers();
+ }).
+ on('refresh-content', '[data-infinite-scroller]', function() {
+ // Clear all rows, reset source href to initial state, and
+ // (if the container is visible) start loading content.
+ var first_page_href = $(this).attr('data-infinite-content-href0');
+ if (!first_page_href)
+ first_page_href = $(this).attr('data-infinite-content-href');
+ $(this).
+ html('').
+ attr('data-infinite-content-href', first_page_href);
+ ping_all_scrollers();
+ }).
+ on('ready ajax:complete', function() {
+ $('[data-infinite-scroller]').each(function() {
+ if ($(this).hasClass('infinite-scroller-ready'))
+ return;
+ $(this).addClass('infinite-scroller-ready');
+
+ // deal with sorting if there is any, and if it was set on this page for this tab already
+ if( $('th[data-sort-order]').length ) {
+ var tabId = $(this).closest('div.tab-pane').attr('id');
+ if( hasHTML5History() && history.state !== undefined && history.state !== null && history.state.order !== undefined && history.state.order[tabId] !== undefined ) {
+ // we will use the list of one or more table columns associated with this header to find the right element
+ // see sortable_columns as it is passed to render_pane in the various tab .erbs (e.g. _show_jobs_and_pipelines.html.erb)
+ var strippedColumns = history.state.order[tabId].replace(/\s|\basc\b|\bdesc\b/g,'');
+ var sortDirection = history.state.order[tabId].split(" ")[1].replace(/,/,'');
+ $columnHeader = $(this).closest('table').find('[data-sort-order="'+ strippedColumns +'"]');
+ setColumnSort( $(this), $columnHeader, sortDirection );
+ } else {
+ // otherwise just reset the sort icons
+ $(this).trigger('sort-icons');
+ }
+ }
+
+ // $scroller is the DOM element that hears "scroll"
+ // events: sometimes it's a div, sometimes it's
+ // window. Here, "this" is the DOM element containing the
+ // result rows. We pass it to maybe_load_more_content in
+ // event.data.
+ var $scroller = $($(this).attr('data-infinite-scroller'));
+ if (!$scroller.hasClass('smart-scroll') &&
+ 'scroll' != $scroller.css('overflow-y'))
+ $scroller = $(window);
+ $scroller.
+ addClass('infinite-scroller').
+ on('scroll resize', { container: this }, maybe_load_more_content).
+ trigger('scroll');
+ });
+ }).
+ on('shown.bs.tab', 'a[data-toggle="tab"]', function(event) {
+ $(event.target.getAttribute('href') + ' [data-infinite-scroller]').
+ trigger('scroll');
+ }).
+ on('click', 'th[data-sort-order]', function() {
+ var direction = $(this).data('sort-order-direction');
+ // reverse the current direction, or do ascending if none
+ if( direction === undefined || direction === 'desc' ) {
+ direction = 'asc';
+ } else {
+ direction = 'desc';
+ }
+
+ var $container = $(this).closest('table').find('[data-infinite-content-params-attr]');
+
+ var order = setColumnSort( $container, $(this), direction );
+
+ // put it in the browser history state if browser allows it
+ if( hasHTML5History() ) {
+ var tabId = $(this).closest('div.tab-pane').attr('id');
+ var state = history.state || {};
+ if( state.order === undefined ) {
+ state.order = {};
+ }
+ state.order[tabId] = order;
+ history.replaceState( state, null, null );
+ }
+
+ $container.trigger('refresh-content');
+ }).
+ on('sort-icons', function() {
+ // set or reset the icon next to each sortable column header according to the current direction attribute
+ $('th[data-sort-order]').each(function() {
+ $(this).find('i').remove();
+ var direction = $(this).data('sort-order-direction');
+ if( direction !== undefined ) {
+ $(this).append('<i class="fa fa-sort-' + direction + '"/>');
+ } else {
+ $(this).append('<i class="fa fa-sort"/>');
+ }
+ });
+ });
--- /dev/null
+cache_age_in_days = (milliseconds_age) ->
+ ONE_DAY = 1000 * 60 * 60 * 24
+ milliseconds_age / ONE_DAY
+
+cache_age_hover = (milliseconds_age) ->
+ 'Cache age ' + cache_age_in_days(milliseconds_age).toFixed(1) + ' days.'
+
+cache_age_axis_label = (milliseconds_age) ->
+ cache_age_in_days(milliseconds_age).toFixed(0) + ' days'
+
+float_as_percentage = (proportion) ->
+ (proportion.toFixed(4) * 100) + '%'
+
+$.renderHistogram = (histogram_data) ->
+ Morris.Area({
+ element: 'cache-age-vs-disk-histogram',
+ pointSize: 0,
+ lineWidth: 0,
+ data: histogram_data,
+ xkey: 'age',
+ ykeys: ['persisted', 'cache'],
+ labels: ['Persisted Storage Disk Utilization', 'Cached Storage Disk Utilization'],
+ ymax: 1,
+ ymin: 0,
+ xLabelFormat: cache_age_axis_label,
+ yLabelFormat: float_as_percentage,
+ dateFormat: cache_age_hover
+ })
--- /dev/null
+;(function(){
+
+/**
+ * Require the given path.
+ *
+ * @param {String} path
+ * @return {Object} exports
+ * @api public
+ */
+
+function require(path, parent, orig) {
+ var resolved = require.resolve(path);
+
+ // lookup failed
+ if (null == resolved) {
+ orig = orig || path;
+ parent = parent || 'root';
+ var err = new Error('Failed to require "' + orig + '" from "' + parent + '"');
+ err.path = orig;
+ err.parent = parent;
+ err.require = true;
+ throw err;
+ }
+
+ var module = require.modules[resolved];
+
+ // perform real require()
+ // by invoking the module's
+ // registered function
+ if (!module._resolving && !module.exports) {
+ var mod = {};
+ mod.exports = {};
+ mod.client = mod.component = true;
+ module._resolving = true;
+ module.call(this, mod.exports, require.relative(resolved), mod);
+ delete module._resolving;
+ module.exports = mod.exports;
+ }
+
+ return module.exports;
+}
+
+/**
+ * Registered modules.
+ */
+
+require.modules = {};
+
+/**
+ * Registered aliases.
+ */
+
+require.aliases = {};
+
+/**
+ * Resolve `path`.
+ *
+ * Lookup:
+ *
+ * - PATH/index.js
+ * - PATH.js
+ * - PATH
+ *
+ * @param {String} path
+ * @return {String} path or null
+ * @api private
+ */
+
+require.resolve = function(path) {
+ if (path.charAt(0) === '/') path = path.slice(1);
+
+ var paths = [
+ path,
+ path + '.js',
+ path + '.json',
+ path + '/index.js',
+ path + '/index.json'
+ ];
+
+ for (var i = 0; i < paths.length; i++) {
+ var path = paths[i];
+ if (require.modules.hasOwnProperty(path)) return path;
+ if (require.aliases.hasOwnProperty(path)) return require.aliases[path];
+ }
+};
+
+/**
+ * Normalize `path` relative to the current path.
+ *
+ * @param {String} curr
+ * @param {String} path
+ * @return {String}
+ * @api private
+ */
+
+require.normalize = function(curr, path) {
+ var segs = [];
+
+ if ('.' != path.charAt(0)) return path;
+
+ curr = curr.split('/');
+ path = path.split('/');
+
+ for (var i = 0; i < path.length; ++i) {
+ if ('..' == path[i]) {
+ curr.pop();
+ } else if ('.' != path[i] && '' != path[i]) {
+ segs.push(path[i]);
+ }
+ }
+
+ return curr.concat(segs).join('/');
+};
+
+/**
+ * Register module at `path` with callback `definition`.
+ *
+ * @param {String} path
+ * @param {Function} definition
+ * @api private
+ */
+
+require.register = function(path, definition) {
+ require.modules[path] = definition;
+};
+
+/**
+ * Alias a module definition.
+ *
+ * @param {String} from
+ * @param {String} to
+ * @api private
+ */
+
+require.alias = function(from, to) {
+ if (!require.modules.hasOwnProperty(from)) {
+ throw new Error('Failed to alias "' + from + '", it does not exist');
+ }
+ require.aliases[to] = from;
+};
+
+/**
+ * Return a require function relative to the `parent` path.
+ *
+ * @param {String} parent
+ * @return {Function}
+ * @api private
+ */
+
+require.relative = function(parent) {
+ var p = require.normalize(parent, '..');
+
+ /**
+ * lastIndexOf helper.
+ */
+
+ function lastIndexOf(arr, obj) {
+ var i = arr.length;
+ while (i--) {
+ if (arr[i] === obj) return i;
+ }
+ return -1;
+ }
+
+ /**
+ * The relative require() itself.
+ */
+
+ function localRequire(path) {
+ var resolved = localRequire.resolve(path);
+ return require(resolved, parent, path);
+ }
+
+ /**
+ * Resolve relative to the parent.
+ */
+
+ localRequire.resolve = function(path) {
+ var c = path.charAt(0);
+ if ('/' == c) return path.slice(1);
+ if ('.' == c) return require.normalize(p, path);
+
+ // resolve deps by returning
+ // the dep in the nearest "deps"
+ // directory
+ var segs = parent.split('/');
+ var i = lastIndexOf(segs, 'deps') + 1;
+ if (!i) i = 0;
+ path = segs.slice(0, i + 1).join('/') + '/deps/' + path;
+ return path;
+ };
+
+ /**
+ * Check if module is defined at `path`.
+ */
+
+ localRequire.exists = function(path) {
+ return require.modules.hasOwnProperty(localRequire.resolve(path));
+ };
+
+ return localRequire;
+};
+require.register("component-classes/index.js", function(exports, require, module){
+/**
+ * Module dependencies.
+ */
+
+var index = require('indexof');
+
+/**
+ * Whitespace regexp.
+ */
+
+var re = /\s+/;
+
+/**
+ * toString reference.
+ */
+
+var toString = Object.prototype.toString;
+
+/**
+ * Wrap `el` in a `ClassList`.
+ *
+ * @param {Element} el
+ * @return {ClassList}
+ * @api public
+ */
+
+module.exports = function(el){
+ return new ClassList(el);
+};
+
+/**
+ * Initialize a new ClassList for `el`.
+ *
+ * @param {Element} el
+ * @api private
+ */
+
+function ClassList(el) {
+ if (!el) throw new Error('A DOM element reference is required');
+ this.el = el;
+ this.list = el.classList;
+}
+
+/**
+ * Add class `name` if not already present.
+ *
+ * @param {String} name
+ * @return {ClassList}
+ * @api public
+ */
+
+ClassList.prototype.add = function(name){
+ // classList
+ if (this.list) {
+ this.list.add(name);
+ return this;
+ }
+
+ // fallback
+ var arr = this.array();
+ var i = index(arr, name);
+ if (!~i) arr.push(name);
+ this.el.className = arr.join(' ');
+ return this;
+};
+
+/**
+ * Remove class `name` when present, or
+ * pass a regular expression to remove
+ * any which match.
+ *
+ * @param {String|RegExp} name
+ * @return {ClassList}
+ * @api public
+ */
+
+ClassList.prototype.remove = function(name){
+ if ('[object RegExp]' == toString.call(name)) {
+ return this.removeMatching(name);
+ }
+
+ // classList
+ if (this.list) {
+ this.list.remove(name);
+ return this;
+ }
+
+ // fallback
+ var arr = this.array();
+ var i = index(arr, name);
+ if (~i) arr.splice(i, 1);
+ this.el.className = arr.join(' ');
+ return this;
+};
+
+/**
+ * Remove all classes matching `re`.
+ *
+ * @param {RegExp} re
+ * @return {ClassList}
+ * @api private
+ */
+
+ClassList.prototype.removeMatching = function(re){
+ var arr = this.array();
+ for (var i = 0; i < arr.length; i++) {
+ if (re.test(arr[i])) {
+ this.remove(arr[i]);
+ }
+ }
+ return this;
+};
+
+/**
+ * Toggle class `name`, can force state via `force`.
+ *
+ * For browsers that support classList, but do not support `force` yet,
+ * the mistake will be detected and corrected.
+ *
+ * @param {String} name
+ * @param {Boolean} force
+ * @return {ClassList}
+ * @api public
+ */
+
+ClassList.prototype.toggle = function(name, force){
+ // classList
+ if (this.list) {
+ if ("undefined" !== typeof force) {
+ if (force !== this.list.toggle(name, force)) {
+ this.list.toggle(name); // toggle again to correct
+ }
+ } else {
+ this.list.toggle(name);
+ }
+ return this;
+ }
+
+ // fallback
+ if ("undefined" !== typeof force) {
+ if (!force) {
+ this.remove(name);
+ } else {
+ this.add(name);
+ }
+ } else {
+ if (this.has(name)) {
+ this.remove(name);
+ } else {
+ this.add(name);
+ }
+ }
+
+ return this;
+};
+
+/**
+ * Return an array of classes.
+ *
+ * @return {Array}
+ * @api public
+ */
+
+ClassList.prototype.array = function(){
+ var str = this.el.className.replace(/^\s+|\s+$/g, '');
+ var arr = str.split(re);
+ if ('' === arr[0]) arr.shift();
+ return arr;
+};
+
+/**
+ * Check if class `name` is present.
+ *
+ * @param {String} name
+ * @return {ClassList}
+ * @api public
+ */
+
+ClassList.prototype.has =
+ClassList.prototype.contains = function(name){
+ return this.list
+ ? this.list.contains(name)
+ : !! ~index(this.array(), name);
+};
+
+});
+require.register("segmentio-extend/index.js", function(exports, require, module){
+
+module.exports = function extend (object) {
+ // Takes an unlimited number of extenders.
+ var args = Array.prototype.slice.call(arguments, 1);
+
+ // For each extender, copy their properties on our object.
+ for (var i = 0, source; source = args[i]; i++) {
+ if (!source) continue;
+ for (var property in source) {
+ object[property] = source[property];
+ }
+ }
+
+ return object;
+};
+});
+require.register("component-indexof/index.js", function(exports, require, module){
+module.exports = function(arr, obj){
+ if (arr.indexOf) return arr.indexOf(obj);
+ for (var i = 0; i < arr.length; ++i) {
+ if (arr[i] === obj) return i;
+ }
+ return -1;
+};
+});
+require.register("component-event/index.js", function(exports, require, module){
+var bind = window.addEventListener ? 'addEventListener' : 'attachEvent',
+ unbind = window.removeEventListener ? 'removeEventListener' : 'detachEvent',
+ prefix = bind !== 'addEventListener' ? 'on' : '';
+
+/**
+ * Bind `el` event `type` to `fn`.
+ *
+ * @param {Element} el
+ * @param {String} type
+ * @param {Function} fn
+ * @param {Boolean} capture
+ * @return {Function}
+ * @api public
+ */
+
+exports.bind = function(el, type, fn, capture){
+ el[bind](prefix + type, fn, capture || false);
+ return fn;
+};
+
+/**
+ * Unbind `el` event `type`'s callback `fn`.
+ *
+ * @param {Element} el
+ * @param {String} type
+ * @param {Function} fn
+ * @param {Boolean} capture
+ * @return {Function}
+ * @api public
+ */
+
+exports.unbind = function(el, type, fn, capture){
+ el[unbind](prefix + type, fn, capture || false);
+ return fn;
+};
+});
+require.register("timoxley-to-array/index.js", function(exports, require, module){
+/**
+ * Convert an array-like object into an `Array`.
+ * If `collection` is already an `Array`, then will return a clone of `collection`.
+ *
+ * @param {Array | Mixed} collection An `Array` or array-like object to convert e.g. `arguments` or `NodeList`
+ * @return {Array} Naive conversion of `collection` to a new `Array`.
+ * @api public
+ */
+
+module.exports = function toArray(collection) {
+ if (typeof collection === 'undefined') return []
+ if (collection === null) return [null]
+ if (collection === window) return [window]
+ if (typeof collection === 'string') return [collection]
+ if (isArray(collection)) return collection
+ if (typeof collection.length != 'number') return [collection]
+ if (typeof collection === 'function' && collection instanceof Function) return [collection]
+
+ var arr = []
+ for (var i = 0; i < collection.length; i++) {
+ if (Object.prototype.hasOwnProperty.call(collection, i) || i in collection) {
+ arr.push(collection[i])
+ }
+ }
+ if (!arr.length) return []
+ return arr
+}
+
+function isArray(arr) {
+ return Object.prototype.toString.call(arr) === "[object Array]";
+}
+
+});
+require.register("javve-events/index.js", function(exports, require, module){
+var events = require('event'),
+ toArray = require('to-array');
+
+/**
+ * Bind `el` event `type` to `fn`.
+ *
+ * @param {Element} el, NodeList, HTMLCollection or Array
+ * @param {String} type
+ * @param {Function} fn
+ * @param {Boolean} capture
+ * @api public
+ */
+
+exports.bind = function(el, type, fn, capture){
+ el = toArray(el);
+ for ( var i = 0; i < el.length; i++ ) {
+ events.bind(el[i], type, fn, capture);
+ }
+};
+
+/**
+ * Unbind `el` event `type`'s callback `fn`.
+ *
+ * @param {Element} el, NodeList, HTMLCollection or Array
+ * @param {String} type
+ * @param {Function} fn
+ * @param {Boolean} capture
+ * @api public
+ */
+
+exports.unbind = function(el, type, fn, capture){
+ el = toArray(el);
+ for ( var i = 0; i < el.length; i++ ) {
+ events.unbind(el[i], type, fn, capture);
+ }
+};
+
+});
+require.register("javve-get-by-class/index.js", function(exports, require, module){
+/**
+ * Find all elements with class `className` inside `container`.
+ * Use `single = true` to increase performance in older browsers
+ * when only one element is needed.
+ *
+ * @param {String} className
+ * @param {Element} container
+ * @param {Boolean} single
+ * @api public
+ */
+
+module.exports = (function() {
+ if (document.getElementsByClassName) {
+ return function(container, className, single) {
+ if (single) {
+ return container.getElementsByClassName(className)[0];
+ } else {
+ return container.getElementsByClassName(className);
+ }
+ };
+ } else if (document.querySelector) {
+ return function(container, className, single) {
+ className = '.' + className;
+ if (single) {
+ return container.querySelector(className);
+ } else {
+ return container.querySelectorAll(className);
+ }
+ };
+ } else {
+ return function(container, className, single) {
+ var classElements = [],
+ tag = '*';
+ if (container == null) {
+ container = document;
+ }
+ var els = container.getElementsByTagName(tag);
+ var elsLen = els.length;
+ var pattern = new RegExp("(^|\\s)"+className+"(\\s|$)");
+ for (var i = 0, j = 0; i < elsLen; i++) {
+ if ( pattern.test(els[i].className) ) {
+ if (single) {
+ return els[i];
+ } else {
+ classElements[j] = els[i];
+ j++;
+ }
+ }
+ }
+ return classElements;
+ };
+ }
+})();
+
+});
+require.register("javve-get-attribute/index.js", function(exports, require, module){
+/**
+ * Return the value for `attr` at `element`.
+ *
+ * @param {Element} el
+ * @param {String} attr
+ * @api public
+ */
+
+module.exports = function(el, attr) {
+ var result = (el.getAttribute && el.getAttribute(attr)) || null;
+ if( !result ) {
+ var attrs = el.attributes;
+ var length = attrs.length;
+ for(var i = 0; i < length; i++) {
+ if (attr[i] !== undefined) {
+ if(attr[i].nodeName === attr) {
+ result = attr[i].nodeValue;
+ }
+ }
+ }
+ }
+ return result;
+}
+});
+require.register("javve-natural-sort/index.js", function(exports, require, module){
+/*
+ * Natural Sort algorithm for Javascript - Version 0.7 - Released under MIT license
+ * Author: Jim Palmer (based on chunking idea from Dave Koelle)
+ */
+
+module.exports = function(a, b, options) {
+ var re = /(^-?[0-9]+(\.?[0-9]*)[df]?e?[0-9]?$|^0x[0-9a-f]+$|[0-9]+)/gi,
+ sre = /(^[ ]*|[ ]*$)/g,
+ dre = /(^([\w ]+,?[\w ]+)?[\w ]+,?[\w ]+\d+:\d+(:\d+)?[\w ]?|^\d{1,4}[\/\-]\d{1,4}[\/\-]\d{1,4}|^\w+, \w+ \d+, \d{4})/,
+ hre = /^0x[0-9a-f]+$/i,
+ ore = /^0/,
+ options = options || {},
+ i = function(s) { return options.insensitive && (''+s).toLowerCase() || ''+s },
+ // convert all to strings strip whitespace
+ x = i(a).replace(sre, '') || '',
+ y = i(b).replace(sre, '') || '',
+ // chunk/tokenize
+ xN = x.replace(re, '\0$1\0').replace(/\0$/,'').replace(/^\0/,'').split('\0'),
+ yN = y.replace(re, '\0$1\0').replace(/\0$/,'').replace(/^\0/,'').split('\0'),
+ // numeric, hex or date detection
+ xD = parseInt(x.match(hre)) || (xN.length != 1 && x.match(dre) && Date.parse(x)),
+ yD = parseInt(y.match(hre)) || xD && y.match(dre) && Date.parse(y) || null,
+ oFxNcL, oFyNcL,
+ mult = options.desc ? -1 : 1;
+ // first try and sort Hex codes or Dates
+ if (yD)
+ if ( xD < yD ) return -1 * mult;
+ else if ( xD > yD ) return 1 * mult;
+ // natural sorting through split numeric strings and default strings
+ for(var cLoc=0, numS=Math.max(xN.length, yN.length); cLoc < numS; cLoc++) {
+ // find floats not starting with '0', string or 0 if not defined (Clint Priest)
+ oFxNcL = !(xN[cLoc] || '').match(ore) && parseFloat(xN[cLoc]) || xN[cLoc] || 0;
+ oFyNcL = !(yN[cLoc] || '').match(ore) && parseFloat(yN[cLoc]) || yN[cLoc] || 0;
+ // handle numeric vs string comparison - number < string - (Kyle Adams)
+ if (isNaN(oFxNcL) !== isNaN(oFyNcL)) { return (isNaN(oFxNcL)) ? 1 : -1; }
+ // rely on string comparison if different types - i.e. '02' < 2 != '02' < '2'
+ else if (typeof oFxNcL !== typeof oFyNcL) {
+ oFxNcL += '';
+ oFyNcL += '';
+ }
+ if (oFxNcL < oFyNcL) return -1 * mult;
+ if (oFxNcL > oFyNcL) return 1 * mult;
+ }
+ return 0;
+};
+
+/*
+var defaultSort = getSortFunction();
+
+module.exports = function(a, b, options) {
+ if (arguments.length == 1) {
+ options = a;
+ return getSortFunction(options);
+ } else {
+ return defaultSort(a,b);
+ }
+}
+*/
+});
+require.register("javve-to-string/index.js", function(exports, require, module){
+module.exports = function(s) {
+ s = (s === undefined) ? "" : s;
+ s = (s === null) ? "" : s;
+ s = s.toString();
+ return s;
+};
+
+});
+require.register("component-type/index.js", function(exports, require, module){
+/**
+ * toString ref.
+ */
+
+var toString = Object.prototype.toString;
+
+/**
+ * Return the type of `val`.
+ *
+ * @param {Mixed} val
+ * @return {String}
+ * @api public
+ */
+
+module.exports = function(val){
+ switch (toString.call(val)) {
+ case '[object Date]': return 'date';
+ case '[object RegExp]': return 'regexp';
+ case '[object Arguments]': return 'arguments';
+ case '[object Array]': return 'array';
+ case '[object Error]': return 'error';
+ }
+
+ if (val === null) return 'null';
+ if (val === undefined) return 'undefined';
+ if (val !== val) return 'nan';
+ if (val && val.nodeType === 1) return 'element';
+
+ return typeof val.valueOf();
+};
+
+});
+require.register("list.js/index.js", function(exports, require, module){
+/*
+ListJS with beta 1.0.0
+By Jonny Strömberg (www.jonnystromberg.com, www.listjs.com)
+*/
+(function( window, undefined ) {
+"use strict";
+
+var document = window.document,
+ getByClass = require('get-by-class'),
+ extend = require('extend'),
+ indexOf = require('indexof');
+
+var List = function(id, options, values) {
+
+ var self = this,
+ init,
+ Item = require('./src/item')(self),
+ addAsync = require('./src/add-async')(self),
+ parse = require('./src/parse')(self);
+
+ init = {
+ start: function() {
+ self.listClass = "list";
+ self.searchClass = "search";
+ self.sortClass = "sort";
+ self.page = 200;
+ self.i = 1;
+ self.items = [];
+ self.visibleItems = [];
+ self.matchingItems = [];
+ self.searched = false;
+ self.filtered = false;
+ self.handlers = { 'updated': [] };
+ self.plugins = {};
+ self.helpers = {
+ getByClass: getByClass,
+ extend: extend,
+ indexOf: indexOf
+ };
+
+ extend(self, options);
+
+ self.listContainer = (typeof(id) === 'string') ? document.getElementById(id) : id;
+ if (!self.listContainer) { return; }
+ self.list = getByClass(self.listContainer, self.listClass, true);
+
+ self.templater = require('./src/templater')(self);
+ self.search = require('./src/search')(self);
+ self.filter = require('./src/filter')(self);
+ self.sort = require('./src/sort')(self);
+
+ this.items();
+ self.update();
+ this.plugins();
+ },
+ items: function() {
+ parse(self.list);
+ if (values !== undefined) {
+ self.add(values);
+ }
+ },
+ plugins: function() {
+ for (var i = 0; i < self.plugins.length; i++) {
+ var plugin = self.plugins[i];
+ self[plugin.name] = plugin;
+ plugin.init(self);
+ }
+ }
+ };
+
+
+ /*
+ * Add object to list
+ */
+ this.add = function(values, callback) {
+ if (callback) {
+ addAsync(values, callback);
+ return;
+ }
+ var added = [],
+ notCreate = false;
+ if (values[0] === undefined){
+ values = [values];
+ }
+ for (var i = 0, il = values.length; i < il; i++) {
+ var item = null;
+ if (values[i] instanceof Item) {
+ item = values[i];
+ item.reload();
+ } else {
+ notCreate = (self.items.length > self.page) ? true : false;
+ item = new Item(values[i], undefined, notCreate);
+ }
+ self.items.push(item);
+ added.push(item);
+ }
+ self.update();
+ return added;
+ };
+
+ this.show = function(i, page) {
+ this.i = i;
+ this.page = page;
+ self.update();
+ return self;
+ };
+
+ /* Removes object from list.
+ * Loops through the list and removes objects where
+ * property "valuename" === value
+ */
+ this.remove = function(valueName, value, options) {
+ var found = 0;
+ for (var i = 0, il = self.items.length; i < il; i++) {
+ if (self.items[i].values()[valueName] == value) {
+ self.templater.remove(self.items[i], options);
+ self.items.splice(i,1);
+ il--;
+ i--;
+ found++;
+ }
+ }
+ self.update();
+ return found;
+ };
+
+ /* Gets the objects in the list which
+ * property "valueName" === value
+ */
+ this.get = function(valueName, value) {
+ var matchedItems = [];
+ for (var i = 0, il = self.items.length; i < il; i++) {
+ var item = self.items[i];
+ if (item.values()[valueName] == value) {
+ matchedItems.push(item);
+ }
+ }
+ return matchedItems;
+ };
+
+ /*
+ * Get size of the list
+ */
+ this.size = function() {
+ return self.items.length;
+ };
+
+ /*
+ * Removes all items from the list
+ */
+ this.clear = function() {
+ self.templater.clear();
+ self.items = [];
+ return self;
+ };
+
+ this.on = function(event, callback) {
+ self.handlers[event].push(callback);
+ return self;
+ };
+
+ this.off = function(event, callback) {
+ var e = self.handlers[event];
+ var index = indexOf(e, callback);
+ if (index > -1) {
+ e.splice(index, 1);
+ }
+ return self;
+ };
+
+ this.trigger = function(event) {
+ var i = self.handlers[event].length;
+ while(i--) {
+ self.handlers[event][i](self);
+ }
+ return self;
+ };
+
+ this.reset = {
+ filter: function() {
+ var is = self.items,
+ il = is.length;
+ while (il--) {
+ is[il].filtered = false;
+ }
+ return self;
+ },
+ search: function() {
+ var is = self.items,
+ il = is.length;
+ while (il--) {
+ is[il].found = false;
+ }
+ return self;
+ }
+ };
+
+ this.update = function() {
+ var is = self.items,
+ il = is.length;
+
+ self.visibleItems = [];
+ self.matchingItems = [];
+ self.templater.clear();
+ for (var i = 0; i < il; i++) {
+ if (is[i].matching() && ((self.matchingItems.length+1) >= self.i && self.visibleItems.length < self.page)) {
+ is[i].show();
+ self.visibleItems.push(is[i]);
+ self.matchingItems.push(is[i]);
+ } else if (is[i].matching()) {
+ self.matchingItems.push(is[i]);
+ is[i].hide();
+ } else {
+ is[i].hide();
+ }
+ }
+ self.trigger('updated');
+ return self;
+ };
+
+ init.start();
+};
+
+module.exports = List;
+
+})(window);
+
+});
+require.register("list.js/src/search.js", function(exports, require, module){
+var events = require('events'),
+ getByClass = require('get-by-class'),
+ toString = require('to-string');
+
+module.exports = function(list) {
+ var item,
+ text,
+ columns,
+ searchString,
+ customSearch;
+
+ var prepare = {
+ resetList: function() {
+ list.i = 1;
+ list.templater.clear();
+ customSearch = undefined;
+ },
+ setOptions: function(args) {
+ if (args.length == 2 && args[1] instanceof Array) {
+ columns = args[1];
+ } else if (args.length == 2 && typeof(args[1]) == "function") {
+ customSearch = args[1];
+ } else if (args.length == 3) {
+ columns = args[1];
+ customSearch = args[2];
+ }
+ },
+ setColumns: function() {
+ columns = (columns === undefined) ? prepare.toArray(list.items[0].values()) : columns;
+ },
+ setSearchString: function(s) {
+ s = toString(s).toLowerCase();
+ s = s.replace(/[-[\]{}()*+?.,\\^$|#]/g, "\\$&"); // Escape regular expression characters
+ searchString = s;
+ },
+ toArray: function(values) {
+ var tmpColumn = [];
+ for (var name in values) {
+ tmpColumn.push(name);
+ }
+ return tmpColumn;
+ }
+ };
+ var search = {
+ list: function() {
+ for (var k = 0, kl = list.items.length; k < kl; k++) {
+ search.item(list.items[k]);
+ }
+ },
+ item: function(item) {
+ item.found = false;
+ for (var j = 0, jl = columns.length; j < jl; j++) {
+ if (search.values(item.values(), columns[j])) {
+ item.found = true;
+ return;
+ }
+ }
+ },
+ values: function(values, column) {
+ if (values.hasOwnProperty(column)) {
+ text = toString(values[column]).toLowerCase();
+ if ((searchString !== "") && (text.search(searchString) > -1)) {
+ return true;
+ }
+ }
+ return false;
+ },
+ reset: function() {
+ list.reset.search();
+ list.searched = false;
+ }
+ };
+
+ var searchMethod = function(str) {
+ list.trigger('searchStart');
+
+ prepare.resetList();
+ prepare.setSearchString(str);
+ prepare.setOptions(arguments); // str, cols|searchFunction, searchFunction
+ prepare.setColumns();
+
+ if (searchString === "" ) {
+ search.reset();
+ } else {
+ list.searched = true;
+ if (customSearch) {
+ customSearch(searchString, columns);
+ } else {
+ search.list();
+ }
+ }
+
+ list.update();
+ list.trigger('searchComplete');
+ return list.visibleItems;
+ };
+
+ list.handlers.searchStart = list.handlers.searchStart || [];
+ list.handlers.searchComplete = list.handlers.searchComplete || [];
+
+ events.bind(getByClass(list.listContainer, list.searchClass), 'keyup', function(e) {
+ var target = e.target || e.srcElement, // IE have srcElement
+ alreadyCleared = (target.value === "" && !list.searched);
+ if (!alreadyCleared) { // If oninput already have resetted the list, do nothing
+ searchMethod(target.value);
+ }
+ });
+
+ // Used to detect click on HTML5 clear button
+ events.bind(getByClass(list.listContainer, list.searchClass), 'input', function(e) {
+ var target = e.target || e.srcElement;
+ if (target.value === "") {
+ searchMethod('');
+ }
+ });
+
+ list.helpers.toString = toString;
+ return searchMethod;
+};
+
+});
+require.register("list.js/src/sort.js", function(exports, require, module){
+var naturalSort = require('natural-sort'),
+ classes = require('classes'),
+ events = require('events'),
+ getByClass = require('get-by-class'),
+ getAttribute = require('get-attribute');
+
+module.exports = function(list) {
+ list.sortFunction = list.sortFunction || function(itemA, itemB, options) {
+ options.desc = options.order == "desc" ? true : false; // Natural sort uses this format
+ return naturalSort(itemA.values()[options.valueName], itemB.values()[options.valueName], options);
+ };
+
+ var buttons = {
+ els: undefined,
+ clear: function() {
+ for (var i = 0, il = buttons.els.length; i < il; i++) {
+ classes(buttons.els[i]).remove('asc');
+ classes(buttons.els[i]).remove('desc');
+ }
+ },
+ getOrder: function(btn) {
+ var predefinedOrder = getAttribute(btn, 'data-order');
+ if (predefinedOrder == "asc" || predefinedOrder == "desc") {
+ return predefinedOrder;
+ } else if (classes(btn).has('desc')) {
+ return "asc";
+ } else if (classes(btn).has('asc')) {
+ return "desc";
+ } else {
+ return "asc";
+ }
+ },
+ getInSensitive: function(btn, options) {
+ var insensitive = getAttribute(btn, 'data-insensitive');
+ if (insensitive === "true") {
+ options.insensitive = true;
+ } else {
+ options.insensitive = false;
+ }
+ },
+ setOrder: function(options) {
+ for (var i = 0, il = buttons.els.length; i < il; i++) {
+ var btn = buttons.els[i];
+ if (getAttribute(btn, 'data-sort') !== options.valueName) {
+ continue;
+ }
+ var predefinedOrder = getAttribute(btn, 'data-order');
+ if (predefinedOrder == "asc" || predefinedOrder == "desc") {
+ if (predefinedOrder == options.order) {
+ classes(btn).add(options.order);
+ }
+ } else {
+ classes(btn).add(options.order);
+ }
+ }
+ }
+ };
+ var sort = function() {
+ list.trigger('sortStart');
+ options = {};
+
+ var target = arguments[0].currentTarget || arguments[0].srcElement || undefined;
+
+ if (target) {
+ options.valueName = getAttribute(target, 'data-sort');
+ buttons.getInSensitive(target, options);
+ options.order = buttons.getOrder(target);
+ } else {
+ options = arguments[1] || options;
+ options.valueName = arguments[0];
+ options.order = options.order || "asc";
+ options.insensitive = (typeof options.insensitive == "undefined") ? true : options.insensitive;
+ }
+ buttons.clear();
+ buttons.setOrder(options);
+
+ options.sortFunction = options.sortFunction || list.sortFunction;
+ list.items.sort(function(a, b) {
+ return options.sortFunction(a, b, options);
+ });
+ list.update();
+ list.trigger('sortComplete');
+ };
+
+ // Add handlers
+ list.handlers.sortStart = list.handlers.sortStart || [];
+ list.handlers.sortComplete = list.handlers.sortComplete || [];
+
+ buttons.els = getByClass(list.listContainer, list.sortClass);
+ events.bind(buttons.els, 'click', sort);
+ list.on('searchStart', buttons.clear);
+ list.on('filterStart', buttons.clear);
+
+ // Helpers
+ list.helpers.classes = classes;
+ list.helpers.naturalSort = naturalSort;
+ list.helpers.events = events;
+ list.helpers.getAttribute = getAttribute;
+
+ return sort;
+};
+
+});
+require.register("list.js/src/item.js", function(exports, require, module){
+module.exports = function(list) {
+ return function(initValues, element, notCreate) {
+ var item = this;
+
+ this._values = {};
+
+ this.found = false; // Show if list.searched == true and this.found == true
+ this.filtered = false;// Show if list.filtered == true and this.filtered == true
+
+ var init = function(initValues, element, notCreate) {
+ if (element === undefined) {
+ if (notCreate) {
+ item.values(initValues, notCreate);
+ } else {
+ item.values(initValues);
+ }
+ } else {
+ item.elm = element;
+ var values = list.templater.get(item, initValues);
+ item.values(values);
+ }
+ };
+ this.values = function(newValues, notCreate) {
+ if (newValues !== undefined) {
+ for(var name in newValues) {
+ item._values[name] = newValues[name];
+ }
+ if (notCreate !== true) {
+ list.templater.set(item, item.values());
+ }
+ } else {
+ return item._values;
+ }
+ };
+ this.show = function() {
+ list.templater.show(item);
+ };
+ this.hide = function() {
+ list.templater.hide(item);
+ };
+ this.matching = function() {
+ return (
+ (list.filtered && list.searched && item.found && item.filtered) ||
+ (list.filtered && !list.searched && item.filtered) ||
+ (!list.filtered && list.searched && item.found) ||
+ (!list.filtered && !list.searched)
+ );
+ };
+ this.visible = function() {
+ return (item.elm.parentNode == list.list) ? true : false;
+ };
+ init(initValues, element, notCreate);
+ };
+};
+
+});
+require.register("list.js/src/templater.js", function(exports, require, module){
+var getByClass = require('get-by-class');
+
+var Templater = function(list) {
+ var itemSource = getItemSource(list.item),
+ templater = this;
+
+ function getItemSource(item) {
+ if (item === undefined) {
+ var nodes = list.list.childNodes,
+ items = [];
+
+ for (var i = 0, il = nodes.length; i < il; i++) {
+ // Only textnodes have a data attribute
+ if (nodes[i].data === undefined) {
+ return nodes[i];
+ }
+ }
+ return null;
+ } else if (item.indexOf("<") !== -1) { // Try create html element of list, do not work for tables!!
+ var div = document.createElement('div');
+ div.innerHTML = item;
+ return div.firstChild;
+ } else {
+ return document.getElementById(list.item);
+ }
+ }
+
+ /* Get values from element */
+ this.get = function(item, valueNames) {
+ templater.create(item);
+ var values = {};
+ for(var i = 0, il = valueNames.length; i < il; i++) {
+ var elm = getByClass(item.elm, valueNames[i], true);
+ values[valueNames[i]] = elm ? elm.innerHTML : "";
+ }
+ return values;
+ };
+
+ /* Sets values at element */
+ this.set = function(item, values) {
+ if (!templater.create(item)) {
+ for(var v in values) {
+ if (values.hasOwnProperty(v)) {
+ // TODO speed up if possible
+ var elm = getByClass(item.elm, v, true);
+ if (elm) {
+ /* src attribute for image tag & text for other tags */
+ if (elm.tagName === "IMG" && values[v] !== "") {
+ elm.src = values[v];
+ } else {
+ elm.innerHTML = values[v];
+ }
+ }
+ }
+ }
+ }
+ };
+
+ this.create = function(item) {
+ if (item.elm !== undefined) {
+ return false;
+ }
+ /* If item source does not exists, use the first item in list as
+ source for new items */
+ var newItem = itemSource.cloneNode(true);
+ newItem.removeAttribute('id');
+ item.elm = newItem;
+ templater.set(item, item.values());
+ return true;
+ };
+ this.remove = function(item) {
+ list.list.removeChild(item.elm);
+ };
+ this.show = function(item) {
+ templater.create(item);
+ list.list.appendChild(item.elm);
+ };
+ this.hide = function(item) {
+ if (item.elm !== undefined && item.elm.parentNode === list.list) {
+ list.list.removeChild(item.elm);
+ }
+ };
+ this.clear = function() {
+ /* .innerHTML = ''; fucks up IE */
+ if (list.list.hasChildNodes()) {
+ while (list.list.childNodes.length >= 1)
+ {
+ list.list.removeChild(list.list.firstChild);
+ }
+ }
+ };
+};
+
+module.exports = function(list) {
+ return new Templater(list);
+};
+
+});
+require.register("list.js/src/filter.js", function(exports, require, module){
+module.exports = function(list) {
+
+ // Add handlers
+ list.handlers.filterStart = list.handlers.filterStart || [];
+ list.handlers.filterComplete = list.handlers.filterComplete || [];
+
+ return function(filterFunction) {
+ list.trigger('filterStart');
+ list.i = 1; // Reset paging
+ list.reset.filter();
+ if (filterFunction === undefined) {
+ list.filtered = false;
+ } else {
+ list.filtered = true;
+ var is = list.items;
+ for (var i = 0, il = is.length; i < il; i++) {
+ var item = is[i];
+ if (filterFunction(item)) {
+ item.filtered = true;
+ } else {
+ item.filtered = false;
+ }
+ }
+ }
+ list.update();
+ list.trigger('filterComplete');
+ return list.visibleItems;
+ };
+};
+
+});
+require.register("list.js/src/add-async.js", function(exports, require, module){
+module.exports = function(list) {
+ return function(values, callback, items) {
+ var valuesToAdd = values.splice(0, 100);
+ items = items || [];
+ items = items.concat(list.add(valuesToAdd));
+ if (values.length > 0) {
+ setTimeout(function() {
+ addAsync(values, callback, items);
+ }, 10);
+ } else {
+ list.update();
+ callback(items);
+ }
+ };
+};
+});
+require.register("list.js/src/parse.js", function(exports, require, module){
+module.exports = function(list) {
+
+ var Item = require('./item')(list);
+
+ var getChildren = function(parent) {
+ var nodes = parent.childNodes,
+ items = [];
+ for (var i = 0, il = nodes.length; i < il; i++) {
+ // Only textnodes have a data attribute
+ if (nodes[i].data === undefined) {
+ items.push(nodes[i]);
+ }
+ }
+ return items;
+ };
+
+ var parse = function(itemElements, valueNames) {
+ for (var i = 0, il = itemElements.length; i < il; i++) {
+ list.items.push(new Item(valueNames, itemElements[i]));
+ }
+ };
+ var parseAsync = function(itemElements, valueNames) {
+ var itemsToIndex = itemElements.splice(0, 100); // TODO: If < 100 items, what happens in IE etc?
+ parse(itemsToIndex, valueNames);
+ if (itemElements.length > 0) {
+ setTimeout(function() {
+ init.items.indexAsync(itemElements, valueNames);
+ }, 10);
+ } else {
+ list.update();
+ // TODO: Add indexed callback
+ }
+ };
+
+ return function() {
+ var itemsToIndex = getChildren(list.list),
+ valueNames = list.valueNames;
+
+ if (list.indexAsync) {
+ parseAsync(itemsToIndex, valueNames);
+ } else {
+ parse(itemsToIndex, valueNames);
+ }
+ };
+};
+
+});
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+require.alias("component-classes/index.js", "list.js/deps/classes/index.js");
+require.alias("component-classes/index.js", "classes/index.js");
+require.alias("component-indexof/index.js", "component-classes/deps/indexof/index.js");
+
+require.alias("segmentio-extend/index.js", "list.js/deps/extend/index.js");
+require.alias("segmentio-extend/index.js", "extend/index.js");
+
+require.alias("component-indexof/index.js", "list.js/deps/indexof/index.js");
+require.alias("component-indexof/index.js", "indexof/index.js");
+
+require.alias("javve-events/index.js", "list.js/deps/events/index.js");
+require.alias("javve-events/index.js", "events/index.js");
+require.alias("component-event/index.js", "javve-events/deps/event/index.js");
+
+require.alias("timoxley-to-array/index.js", "javve-events/deps/to-array/index.js");
+
+require.alias("javve-get-by-class/index.js", "list.js/deps/get-by-class/index.js");
+require.alias("javve-get-by-class/index.js", "get-by-class/index.js");
+
+require.alias("javve-get-attribute/index.js", "list.js/deps/get-attribute/index.js");
+require.alias("javve-get-attribute/index.js", "get-attribute/index.js");
+
+require.alias("javve-natural-sort/index.js", "list.js/deps/natural-sort/index.js");
+require.alias("javve-natural-sort/index.js", "natural-sort/index.js");
+
+require.alias("javve-to-string/index.js", "list.js/deps/to-string/index.js");
+require.alias("javve-to-string/index.js", "list.js/deps/to-string/index.js");
+require.alias("javve-to-string/index.js", "to-string/index.js");
+require.alias("javve-to-string/index.js", "javve-to-string/index.js");
+require.alias("component-type/index.js", "list.js/deps/type/index.js");
+require.alias("component-type/index.js", "type/index.js");
+if (typeof exports == "object") {
+ module.exports = require("list.js");
+} else if (typeof define == "function" && define.amd) {
+ define(function(){ return require("list.js"); });
+} else {
+ this["List"] = require("list.js");
+}})();
\ No newline at end of file
--- /dev/null
+function newTaskState() {
+ return {"complete_count": 0,
+ "failure_count": 0,
+ "task_count": 0,
+ "incomplete_count": 0,
+ "nodes": []};
+}
+
+function addToLogViewer(logViewer, lines, taskState) {
+ var re = /((\d\d\d\d)-(\d\d)-(\d\d))_((\d\d):(\d\d):(\d\d)) ([a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}) (\d+) (\d+)? (.*)/;
+
+ var items = [];
+ var count = logViewer.items.length;
+ for (var a in lines) {
+ var v = lines[a].match(re);
+ if (v != null) {
+
+ var ts = new Date(Date.UTC(v[2], v[3]-1, v[4], v[6], v[7], v[8]));
+
+ v11 = v[11];
+ if (typeof v[11] === 'undefined') {
+ v11 = "";
+ } else {
+ v11 = Number(v11);
+ }
+
+ var message = v[12];
+ var type = "";
+ var node = "";
+ var slot = "";
+ if (v11 !== "") {
+ if (!taskState.hasOwnProperty(v11)) {
+ taskState[v11] = {};
+ taskState.task_count += 1;
+ }
+
+ if (/^stderr /.test(message)) {
+ message = message.substr(7);
+ if (/^crunchstat: /.test(message)) {
+ type = "crunchstat";
+ message = message.substr(12);
+ } else if (/^srun: /.test(message) || /^slurmd/.test(message)) {
+ type = "task-dispatch";
+ } else {
+ type = "task-print";
+ }
+ } else {
+ var m;
+ if (m = /^success in (\d+) second/.exec(message)) {
+ taskState[v11].outcome = "success";
+ taskState[v11].runtime = Number(m[1]);
+ taskState.complete_count += 1;
+ }
+ else if (m = /^failure \(\#\d+, (temporary|permanent)\) after (\d+) second/.exec(message)) {
+ taskState[v11].outcome = "failure";
+ taskState[v11].runtime = Number(m[2]);
+ taskState.failure_count += 1;
+ if (m[1] == "permanent") {
+ taskState.incomplete_count += 1;
+ }
+ }
+ else if (m = /^child \d+ started on ([^.]*)\.(\d+)/.exec(message)) {
+ taskState[v11].node = m[1];
+ taskState[v11].slot = m[2];
+ if (taskState.nodes.indexOf(m[1], 0) == -1) {
+ taskState.nodes.push(m[1]);
+ }
+ for (var i in items) {
+ if (i > 0) {
+ if (items[i].taskid === v11) {
+ items[i].node = m[1];
+ items[i].slot = m[2];
+ }
+ }
+ }
+ }
+ type = "task-dispatch";
+ }
+ node = taskState[v11].node;
+ slot = taskState[v11].slot;
+ } else {
+ type = "crunch";
+ }
+
+ items.push({
+ id: count,
+ ts: ts,
+ timestamp: ts.toLocaleDateString() + " " + ts.toLocaleTimeString(),
+ taskid: v11,
+ node: node,
+ slot: slot,
+ message: message.replace(/&/g, '&').replace(/</g, '<').replace(/>/g, '>'),
+ type: type
+ });
+ count += 1;
+ } else {
+ console.log("Did not parse line " + a + ": " + lines[a]);
+ }
+ }
+ logViewer.add(items);
+}
+
+function sortById(a, b, opt) {
+ a = a.values();
+ b = b.values();
+
+ if (a["id"] > b["id"]) {
+ return 1;
+ }
+ if (a["id"] < b["id"]) {
+ return -1;
+ }
+ return 0;
+}
+
+function sortByTask(a, b, opt) {
+ var aa = a.values();
+ var bb = b.values();
+
+ if (aa["taskid"] === "" && bb["taskid"] !== "") {
+ return -1;
+ }
+ if (aa["taskid"] !== "" && bb["taskid"] === "") {
+ return 1;
+ }
+
+ if (aa["taskid"] !== "" && bb["taskid"] !== "") {
+ if (aa["taskid"] > bb["taskid"]) {
+ return 1;
+ }
+ if (aa["taskid"] < bb["taskid"]) {
+ return -1;
+ }
+ }
+
+ return sortById(a, b, opt);
+}
+
+function sortByNode(a, b, opt) {
+ var aa = a.values();
+ var bb = b.values();
+
+ if (aa["node"] === "" && bb["node"] !== "") {
+ return -1;
+ }
+ if (aa["node"] !== "" && bb["node"] === "") {
+ return 1;
+ }
+
+ if (aa["node"] !== "" && bb["node"] !== "") {
+ if (aa["node"] > bb["node"]) {
+ return 1;
+ }
+ if (aa["node"] < bb["node"]) {
+ return -1;
+ }
+ }
+
+ if (aa["slot"] !== "" && bb["slot"] !== "") {
+ if (aa["slot"] > bb["slot"]) {
+ return 1;
+ }
+ if (aa["slot"] < bb["slot"]) {
+ return -1;
+ }
+ }
+
+ return sortById(a, b, opt);
+}
+
+
+function dumbPluralize(n, s, p) {
+ if (typeof p === 'undefined') {
+ p = "s";
+ }
+ if (n == 0 || n > 1) {
+ return n + " " + (s + p);
+ } else {
+ return n + " " + s;
+ }
+}
+
+function generateJobOverview(id, logViewer, taskState) {
+ var html = "";
+
+ if (logViewer.items.length > 2) {
+ var first = logViewer.items[1];
+ var last = logViewer.items[logViewer.items.length-1];
+ var duration = (last.values().ts.getTime() - first.values().ts.getTime()) / 1000;
+
+ var hours = 0;
+ var minutes = 0;
+ var seconds;
+
+ if (duration >= 3600) {
+ hours = Math.floor(duration / 3600);
+ duration -= (hours * 3600);
+ }
+ if (duration >= 60) {
+ minutes = Math.floor(duration / 60);
+ duration -= (minutes * 60);
+ }
+ seconds = duration;
+
+ var tcount = taskState.task_count;
+
+ html += "<p>";
+ html += "Started at " + first.values().timestamp + ". ";
+ html += "Ran " + dumbPluralize(tcount, " task") + " over ";
+ if (hours > 0) {
+ html += dumbPluralize(hours, " hour");
+ }
+ if (minutes > 0) {
+ html += " " + dumbPluralize(minutes, " minute");
+ }
+ if (seconds > 0) {
+ html += " " + dumbPluralize(seconds, " second");
+ }
+
+ html += " using " + dumbPluralize(taskState.nodes.length, " node");
+
+ html += ". " + dumbPluralize(taskState.complete_count, "task") + " completed";
+ html += ", " + dumbPluralize(taskState.incomplete_count, "task") + " incomplete";
+ html += " (" + dumbPluralize(taskState.failure_count, " failure") + ")";
+
+ html += ". Finished at " + last.values().timestamp + ".";
+ html += "</p>";
+ } else {
+ html = "<p>Job log is empty or failed to load.</p>";
+ }
+
+ $(id).html(html);
+}
+
+function gotoPage(n, logViewer, page, id) {
+ if (n < 0) { return; }
+ if (n*page > logViewer.matchingItems.length) { return; }
+ logViewer.page_offset = n;
+ logViewer.show(n*page, page);
+}
+
+function updatePaging(id, logViewer, page) {
+ var p = "";
+ var i = logViewer.matchingItems.length;
+ var n;
+ for (n = 0; (n*page) < i; n += 1) {
+ if (n == logViewer.page_offset) {
+ p += "<span class='log-viewer-page-num'>" + (n+1) + "</span> ";
+ } else {
+ p += "<a href=\"#\" class='log-viewer-page-num log-viewer-page-" + n + "'>" + (n+1) + "</a> ";
+ }
+ }
+ $(id).html(p);
+ for (n = 0; (n*page) < i; n += 1) {
+ (function(n) {
+ $(".log-viewer-page-" + n).on("click", function() {
+ gotoPage(n, logViewer, page, id);
+ return false;
+ });
+ })(n);
+ }
+
+ if (logViewer.page_offset == 0) {
+ $(".log-viewer-page-up").addClass("text-muted");
+ } else {
+ $(".log-viewer-page-up").removeClass("text-muted");
+ }
+
+ if (logViewer.page_offset == (n-1)) {
+ $(".log-viewer-page-down").addClass("text-muted");
+ } else {
+ $(".log-viewer-page-down").removeClass("text-muted");
+ }
+}
+
+function nextPage(logViewer, page, id) {
+ gotoPage(logViewer.page_offset+1, logViewer, page, id);
+}
+
+function prevPage(logViewer, page, id) {
+ gotoPage(logViewer.page_offset-1, logViewer, page, id);
+}
--- /dev/null
+$(document).
+ on('click', '[data-toggle-permission] input[type=checkbox]', function() {
+ var data = {};
+ var keys = ['data-permission-uuid',
+ 'data-permission-name',
+ 'data-permission-head',
+ 'data-permission-tail'];
+ var attr;
+ for(var i in keys) {
+ attr = keys[i];
+ data[attr] = $(this).closest('[' + attr + ']').attr(attr);
+ if (data[attr] === undefined) {
+ console.log(["Error: no " + attr + " established here.", this]);
+ return;
+ }
+ }
+ var is_checked = $(this).prop('checked');
+
+ if (is_checked) {
+ $.ajax('/links',
+ {dataType: 'json',
+ type: 'POST',
+ data: {'link[tail_uuid]': data['data-permission-tail'],
+ 'link[head_uuid]': data['data-permission-head'],
+ 'link[link_class]': 'permission',
+ 'link[name]': data['data-permission-name']},
+ context: this}).
+ fail(function(jqxhr, status, error) {
+ $(this).prop('checked', false);
+ }).
+ done(function(data, status, jqxhr) {
+ $(this).attr('data-permission-uuid', data['uuid']);
+ }).
+ always(function() {
+ $(this).prop('disabled', false);
+ });
+ }
+ else {
+ $.ajax('/links/' + data['data-permission-uuid'],
+ {dataType: 'json',
+ type: 'POST',
+ data: {'_method': 'DELETE'},
+ context: this}).
+ fail(function(jqxhr, status, error) {
+ $(this).prop('checked', true);
+ }).
+ done(function(data, status, jqxhr) {
+ $(this).attr('data-permission-uuid', 'x');
+ }).
+ always(function() {
+ $(this).prop('disabled', false);
+ });
+ }
+ $(this).prop('disabled', true);
+ });
--- /dev/null
+function run_pipeline_button_state() {
+ var a = $('a.editable.required.editable-empty,input.form-control.required[value=""]');
+ if (a.length > 0) {
+ $(".run-pipeline-button").addClass("disabled");
+ }
+ else {
+ $(".run-pipeline-button").removeClass("disabled");
+ }
+}
+
+$(document).on('editable:success', function(event, tag, response, newValue) {
+ var $tag = $(tag);
+ if ($('.run-pipeline-button').length == 0)
+ return;
+ if ($tag.hasClass("required")) {
+ if (newValue && newValue.trim() != "") {
+ $tag.removeClass("editable-empty");
+ $tag.parent().css("background-color", "");
+ $tag.parent().prev().css("background-color", "");
+ }
+ else {
+ $tag.addClass("editable-empty");
+ $tag.parent().css("background-color", "#ffdddd");
+ $tag.parent().prev().css("background-color", "#ffdddd");
+ }
+ }
+ if ($tag.attr('data-name')) {
+ // Update other inputs representing the same piece of data
+ $('.editable[data-name="' + $tag.attr('data-name') + '"]').
+ editable('setValue', newValue);
+ }
+ run_pipeline_button_state();
+});
+
+$(document).on('ready ajax:complete', function() {
+ $('a.editable.required').each(function() {
+ var $tag = $(this);
+ if ($tag.hasClass("editable-empty")) {
+ $tag.parent().css("background-color", "#ffdddd");
+ $tag.parent().prev().css("background-color", "#ffdddd");
+ }
+ else {
+ $tag.parent().css("background-color", "");
+ $tag.parent().prev().css("background-color", "");
+ }
+ });
+ run_pipeline_button_state();
+});
+
+$(document).on('arv-log-event', '.arv-refresh-on-state-change', function(event, eventData) {
+ if (this != event.target) {
+ // Not interested in events sent to child nodes.
+ return;
+ }
+ if (eventData.event_type == "update" &&
+ eventData.properties.old_attributes.state != eventData.properties.new_attributes.state)
+ {
+ $(event.target).trigger('arv:pane:reload');
+ }
+});
+
+$(document).on('arv-log-event', '.arv-log-event-subscribe-to-pipeline-job-uuids', function(event, eventData){
+ if (this != event.target) {
+ // Not interested in events sent to child nodes.
+ return;
+ }
+ if (!((eventData.object_kind == 'arvados#pipelineInstance') &&
+ (eventData.event_type == "create" ||
+ eventData.event_type == "update") &&
+ eventData.properties &&
+ eventData.properties.new_attributes &&
+ eventData.properties.new_attributes.components)) {
+ return;
+ }
+ var objs = "";
+ var components = eventData.properties.new_attributes.components;
+ for (a in components) {
+ if (components[a].job && components[a].job.uuid) {
+ objs += " " + components[a].job.uuid;
+ }
+ }
+ $(event.target).attr("data-object-uuids", eventData.object_uuid + objs);
+});
+
+$(document).on('ready ajax:success', function() {
+ $('.arv-log-refresh-control').each(function() {
+ var uuids = $(this).attr('data-object-uuids');
+ var $pane = $(this).closest('[data-pane-content-url]');
+ $pane.attr('data-object-uuids', uuids);
+ });
+});
+
+$(document).on('arv-log-event', '.arv-log-event-handler-append-logs', function(event, eventData){
+ if (this != event.target) {
+ // Not interested in events sent to child nodes.
+ return;
+ }
+ var wasatbottom = ($(this).scrollTop() + $(this).height() >= this.scrollHeight);
+
+ if (eventData.event_type == "stderr" || eventData.event_type == "stdout") {
+ if( eventData.prepend ) {
+ $(this).prepend(eventData.properties.text);
+ } else {
+ $(this).append(eventData.properties.text);
+ }
+ }
+
+ if (wasatbottom) {
+ this.scrollTop = this.scrollHeight;
+ }
+});
+
+// Set up all events for the pipeline instances compare button.
+(function() {
+ var compare_form = '#compare';
+ var compare_inputs = '#comparedInstances :checkbox[name="uuids[]"]';
+ var update_button = function(event) {
+ var $form = $(compare_form);
+ var $checked_inputs = $(compare_inputs).filter(':checked');
+ $(':submit', $form).prop('disabled', (($checked_inputs.length < 2) ||
+ ($checked_inputs.length > 3)));
+ $('input[name="uuids[]"]', $form).remove();
+ $form.append($checked_inputs.clone()
+ .removeAttr('id').attr('type', 'hidden'));
+ };
+ $(document)
+ .on('ready ajax:success', compare_form, update_button)
+ .on('change', compare_inputs, update_button);
+})();
--- /dev/null
+$(document).
+ on('click', "#report-issue-submit", function(e){
+ $(this).html('Sending');
+ $(this).prop('disabled', true);
+ var $cancelButton = $('#report-issue-cancel');
+ if ($cancelButton) {
+ $cancelButton.html('Close');
+ }
+ $('div').remove('.modal-footer-status');
+
+ $.ajax('/').
+ success(function(data, status, jqxhr) {
+ var $sendButton = $('#report-issue-submit');
+ $sendButton.html('Report sent');
+ $('div').remove('.modal-footer-status');
+ $('.modal-footer').append('<div><br/></div><div class="modal-footer-status alert alert-success"><p class="contain-align-left">Thanks for reporting this issue!</p></div>');
+ }).
+ fail(function(jqxhr, status, error) {
+ var $sendButton = $('#report-issue-submit');
+ if ($sendButton && $sendButton.prop('disabled')) {
+ $('div').remove('.modal-footer-status');
+ $('.modal-footer').append('<div><br/></div><div class="modal-footer-status alert alert-danger"><p class="contain-align-left">We are sorry. We could not submit your report! We really want this to work, though -- please try again.</p></div>');
+ $sendButton.html('Send problem report');
+ $sendButton.prop('disabled', false);
+ }
+ var $cancelButton = $('#report-issue-cancel');
+ $cancelButton.html('Cancel');
+ });
+
+ });
--- /dev/null
+$(document).on('click', '.selectable', function() {
+ var any;
+ var $this = $(this);
+ var $container = $(this).closest('.selectable-container');
+ if (!$container.hasClass('multiple')) {
+ $container.
+ find('.selectable').
+ removeClass('active');
+ }
+ $this.toggleClass('active');
+
+ if (!$this.hasClass('use-preview-selection')) {
+ any = ($container.
+ find('.selectable.active').length > 0)
+ }
+
+ if (!$container.hasClass('preview-selectable-container')) {
+ $this.
+ closest('.modal').
+ find('[data-enable-if-selection]').
+ prop('disabled', !any);
+
+ if ($this.hasClass('active')) {
+ var no_preview_available = '<div class="spinner-h-center spinner-v-center"><center>(No preview available)</center></div>';
+ if (!$this.attr('data-preview-href')) {
+ $(".modal-dialog-preview-pane").html(no_preview_available);
+ return;
+ }
+ $(".modal-dialog-preview-pane").html('<div class="spinner spinner-32px spinner-h-center spinner-v-center"></div>');
+ $.ajax($this.attr('data-preview-href'),
+ {dataType: "html"}).
+ done(function(data, status, jqxhr) {
+ $(".modal-dialog-preview-pane").html(data);
+ }).
+ fail(function(data, status, jqxhr) {
+ $(".modal-dialog-preview-pane").html(no_preview_available);
+ });
+ }
+ } else {
+ any = ($container.
+ find('.preview-selectable.active').length > 0)
+ $(this).
+ closest('.modal').
+ find('[data-enable-if-selection]').
+ prop('disabled', !any);
+ }
+
+}).on('click', '.modal button[data-action-href]', function() {
+ var selection = [];
+ var data = [];
+ var $modal = $(this).closest('.modal');
+ var http_method = $(this).attr('data-method').toUpperCase();
+ var action_data = $(this).data('action-data');
+ var action_data_from_params = $(this).data('action-data-from-params');
+ var selection_param = action_data.selection_param;
+ $modal.find('.modal-error').removeClass('hide').hide();
+
+ var $preview_selections = $modal.find('.preview-selectable.active');
+ if ($preview_selections.length > 0) {
+ data.push({name: selection_param, value: $preview_selections.first().attr('href')});
+ }
+
+ if (data.length == 0) { // not using preview selection option
+ $modal.find('.selectable.active[data-object-uuid]').each(function() {
+ var val = $(this).attr('data-object-uuid');
+ data.push({name: selection_param, value: val});
+ });
+ }
+ $.each($.extend({}, action_data, action_data_from_params),
+ function(key, value) {
+ if (value instanceof Array && key[-1] != ']') {
+ for (var i in value) {
+ data.push({name: key + '[]', value: value[i]});
+ }
+ } else {
+ data.push({name: key, value: value});
+ }
+ });
+ if (http_method === 'PATCH') {
+ // Some user agents do not support HTTP PATCH (notably,
+ // phantomjs silently ignores our "data" and sends an empty
+ // request body) so we use POST instead, and supply a
+ // _method=PATCH param to tell Rails what we really want.
+ data.push({name: '_method', value: http_method});
+ http_method = 'POST';
+ }
+ $.ajax($(this).attr('data-action-href'),
+ {dataType: 'json',
+ type: http_method,
+ data: data,
+ traditional: false,
+ context: {modal: $modal, action_data: action_data}}).
+ fail(function(jqxhr, status, error) {
+ if (jqxhr.readyState == 0 || jqxhr.status == 0) {
+ message = "Cancelled."
+ } else if (jqxhr.responseJSON && jqxhr.responseJSON.errors) {
+ message = jqxhr.responseJSON.errors.join("; ");
+ } else {
+ message = "Request failed.";
+ }
+ this.modal.find('.modal-error').
+ html('<div class="alert alert-danger">' + message + '</div>').
+ show();
+ }).
+ done(function(data, status, jqxhr) {
+ var event_name = this.action_data.success;
+ this.modal.find('.modal-error').hide();
+ $(document).trigger(event_name!=null ? event_name : 'page-refresh',
+ [data, status, jqxhr, this.action_data]);
+ });
+}).on('click', '.chooser-show-project', function() {
+ var params = {};
+ var project_uuid = $(this).attr('data-project-uuid');
+ $(this).attr('href', '#'); // Skip normal click handler
+ if (project_uuid) {
+ params = {'filters': [['owner_uuid',
+ '=',
+ project_uuid]],
+ 'project_uuid': project_uuid
+ };
+ }
+ // Use current selection as dropdown button label
+ $(this).
+ closest('.dropdown-menu').
+ prev('button').
+ html($(this).text() + ' <span class="caret"></span>');
+ // Set (or unset) filter params and refresh filterable rows
+ $($(this).closest('[data-filterable-target]').attr('data-filterable-target')).
+ data('infinite-content-params-from-project-dropdown', params).
+ trigger('refresh-content');
+}).on('ready', function() {
+ $('form[data-search-modal] a').on('click', function() {
+ $(this).closest('form').submit();
+ return false;
+ });
+ $('form[data-search-modal]').on('submit', function() {
+ // Ask the server for a Search modal. When it arrives, copy
+ // the search string from the top nav input into the modal's
+ // search query field.
+ var $form = $(this);
+ var searchq = $form.find('input').val();
+ var is_a_uuid = /^([0-9a-f]{32}(\+\S+)?|[0-9a-z]{5}-[0-9a-z]{5}-[0-9a-z]{15})$/;
+ if (searchq.trim().match(is_a_uuid)) {
+ window.location = '/actions?uuid=' + encodeURIComponent(searchq.trim());
+ // Show the "loading" indicator. TODO: better page transition hook
+ $(document).trigger('ajax:send');
+ return false;
+ }
+ if ($form.find('a[data-remote]').length > 0) {
+ // A search dialog is already loading.
+ return false;
+ }
+ $('<a />').
+ attr('href', $form.attr('data-search-modal')).
+ attr('data-remote', 'true').
+ attr('data-method', 'GET').
+ hide().
+ appendTo($form).
+ on('ajax:success', function(data, status, xhr) {
+ $('body > .modal-container input[type=text]').
+ val($form.find('input').val()).
+ focus();
+ $form.find('input').val('');
+ }).on('ajax:complete', function() {
+ $(this).detach();
+ }).
+ click();
+ return false;
+ });
+}).on('page-refresh', function(event, data, status, jqxhr, action_data) {
+ window.location.reload();
+}).on('tab-refresh', function(event, data, status, jqxhr, action_data) {
+ $(document).trigger('arv:pane:reload:all');
+ $('body > .modal-container .modal').modal('hide');
+}).on('redirect-to-created-object', function(event, data, status, jqxhr, action_data) {
+ window.location.href = data.href.replace(/^[^\/]*\/\/[^\/]*/, '');
+}).on('shown.bs.modal', 'body > .modal-container .modal', function() {
+ $('.focus-on-display', this).focus();
+});
--- /dev/null
+//= require jquery
+//= require jquery_ujs
+
+/** Javascript for selection. */
+
+jQuery(function($){
+ $(document).
+ on('change', '.persistent-selection:checkbox', function(e) {
+ $(document).trigger('selections-updated');
+ });
+});
+
+function dispatch_selection_action() {
+ // Build a new "href" attribute for this link by starting with the
+ // "data-href" attribute and appending ?foo[]=bar&foo[]=baz (or
+ // &foo=... as appropriate) to reflect the current object
+ // selections.
+ var data = [];
+ var param_name = $(this).attr('data-selection-param-name');
+ var href = $(this).attr('data-href');
+ if ($(this).closest('.disabled').length > 0) {
+ return false;
+ }
+ $(this).
+ closest('.selection-action-container').
+ find(':checkbox:checked:visible').
+ each(function() {
+ data.push({name: param_name, value: $(this).val()});
+ });
+ if (href.indexOf('?') >= 0)
+ href += '&';
+ else
+ href += '?';
+ href += $.param(data, true);
+ $(this).attr('href', href);
+ return true;
+}
+
+function enable_disable_selection_actions() {
+ var $container = $(this);
+ var $checked = $('.persistent-selection:checkbox:checked', $container);
+ $('[data-selection-action]', $container).
+ closest('div.btn-group-sm').
+ find('ul li').
+ toggleClass('disabled', ($checked.length == 0));
+ $('[data-selection-action=compare]', $container).
+ closest('li').
+ toggleClass('disabled',
+ ($checked.filter('[value*=-d1hrv-]').length < 2) ||
+ ($checked.not('[value*=-d1hrv-]').length > 0));
+ <% unless Group.copies_to_projects? %>
+ $('[data-selection-action=copy]', $container).
+ closest('li').
+ toggleClass('disabled',
+ ($checked.filter('[value*=-j7d0g-]').length > 0) ||
+ ($checked.length < 1));
+ <% end %>
+ $('[data-selection-action=combine-project-contents]', $container).
+ closest('li').
+ toggleClass('disabled',
+ ($checked.filter('[value*=-4zz18-]').length < 1) ||
+ ($checked.length != $checked.filter('[value*=-4zz18-]').length));
+}
+
+$(document).
+ on('selections-updated', function() {
+ $('.selection-action-container').each(enable_disable_selection_actions);
+ }).
+ on('ready ajax:complete', function() {
+ $('[data-selection-action]').
+ off('click', dispatch_selection_action).
+ on('click', dispatch_selection_action);
+ $(this).trigger('selections-updated');
+ });
--- /dev/null
+function graph_zoom(divId, svgId, scale) {
+ var pg = document.getElementById(divId);
+ vcenter = (pg.scrollTop + (pg.scrollHeight - pg.scrollTopMax)/2.0) / pg.scrollHeight;
+ hcenter = (pg.scrollLeft + (pg.scrollWidth - pg.scrollLeftMax)/2.0) / pg.scrollWidth;
+ var g = document.getElementById(svgId);
+ g.setAttribute("height", parseFloat(g.getAttribute("height")) * scale);
+ g.setAttribute("width", parseFloat(g.getAttribute("width")) * scale);
+ pg.scrollTop = (vcenter * pg.scrollHeight) - (pg.scrollHeight - pg.scrollTopMax)/2.0;
+ pg.scrollLeft = (hcenter * pg.scrollWidth) - (pg.scrollWidth - pg.scrollLeftMax)/2.0;
+ smart_scroll_fixup();
+}
+
+function smart_scroll_fixup(s) {
+
+ if (s != null && s.type == 'shown.bs.tab') {
+ s = [s.target];
+ }
+ else {
+ s = $(".smart-scroll");
+ }
+
+ s.each(function(i, a) {
+ a = $(a);
+ var h = window.innerHeight - a.offset().top - a.attr("data-smart-scroll-padding-bottom");
+ height = String(h) + "px";
+ a.css('max-height', height);
+ });
+}
+
+$(window).on('load ready resize scroll ajax:complete', smart_scroll_fixup);
+$(document).on('shown.bs.tab', 'ul.nav-tabs > li > a', smart_scroll_fixup);
--- /dev/null
+// Load tab panes on demand. See app/views/application/_content.html.erb
+
+// Fire when a tab is selected/clicked.
+$(document).on('shown.bs.tab', '[data-toggle="tab"]', function(event) {
+ // reload the pane (unless it's already loaded)
+ $($(event.target).attr('href')).
+ not('.pane-loaded').
+ trigger('arv:pane:reload');
+});
+
+// Ask a refreshable pane to reload via ajax.
+//
+// Target of this event is the DOM element to be updated. A reload
+// consists of an AJAX call to load the "data-pane-content-url" and
+// replace the content of the target element with the retrieved HTML.
+//
+// There are four CSS classes set on the element to indicate its state:
+// pane-loading, pane-stale, pane-loaded, pane-reload-pending
+//
+// There are five states based on the presence or absence of css classes:
+//
+// 1. Absence of any pane-* states means the pane is empty, and should
+// be loaded as soon as it becomes visible.
+//
+// 2. "pane-loading" means an AJAX call has been made to reload the
+// pane and we are waiting on a result.
+//
+// 3. "pane-loading pane-stale" means the pane is loading, but has
+// already been invalidated and should schedule a reload as soon as
+// possible after the current load completes. (This happens when there
+// is a cluster of events, where the reload is triggered by the first
+// event, but we want ensure that we eventually load the final
+// quiescent state).
+//
+// 4. "pane-loaded" means the pane is up to date.
+//
+// 5. "pane-loaded pane-reload-pending" means a reload is needed, and
+// has been scheduled, but has not started because the pane's
+// minimum-time-between-reloads throttle has not yet been reached.
+//
+$(document).on('arv:pane:reload', '[data-pane-content-url]', function(e) {
+ if (this != e.target) {
+ // An arv:pane:reload event was sent to an element (e.target)
+ // which happens to have an ancestor (this) matching the above
+ // '[data-pane-content-url]' selector. This happens because
+ // events bubble up the DOM on their way to document. However,
+ // here we only care about events delivered directly to _this_
+ // selected element (i.e., this==e.target), not ones delivered
+ // to its children. The event "e" is uninteresting here.
+ return;
+ }
+
+ // $pane, the event target, is an element whose content is to be
+ // replaced. Pseudoclasses on $pane (pane-loading, etc) encode the
+ // current loading state.
+ var $pane = $(this);
+
+ if ($pane.hasClass('pane-loading')) {
+ // Already loading, mark stale to schedule a reload after this one.
+ $pane.addClass('pane-stale');
+ return;
+ }
+
+ // The default throttle (mininum milliseconds between refreshes)
+ // can be overridden by an .arv-log-refresh-control element inside
+ // the pane -- or, failing that, the pane element itself -- with a
+ // data-load-throttle attribute. This allows the server to adjust
+ // the throttle depending on the pane content.
+ var throttle =
+ $pane.find('.arv-log-refresh-control').attr('data-load-throttle') ||
+ $pane.attr('data-load-throttle') ||
+ 15000;
+ var now = (new Date()).getTime();
+ var loaded_at = $pane.attr('data-loaded-at');
+ var since_last_load = now - loaded_at;
+ if (loaded_at && (since_last_load < throttle)) {
+ if (!$pane.hasClass('pane-reload-pending')) {
+ $pane.addClass('pane-reload-pending');
+ setTimeout((function() {
+ $pane.trigger('arv:pane:reload');
+ }), throttle - since_last_load);
+ }
+ return;
+ }
+
+ // We know this doesn't have 'pane-loading' because we tested for it above
+ $pane.removeClass('pane-reload-pending');
+ $pane.removeClass('pane-loaded');
+ $pane.removeClass('pane-stale');
+
+ if (!$pane.hasClass('active') &&
+ $pane.parent().hasClass('tab-content')) {
+ // $pane is one of the content areas in a bootstrap tabs
+ // widget, and it isn't the currently selected tab. If and
+ // when the user does select the corresponding tab, it will
+ // get a shown.bs.tab event, which will invoke this reload
+ // function again (see handler above). For now, we just insert
+ // a spinner, which will be displayed while the new content is
+ // loading.
+ $pane.html('<div class="spinner spinner-32px spinner-h-center"></div>');
+ return;
+ }
+
+ $pane.addClass('pane-loading');
+
+ var content_url = $pane.attr('data-pane-content-url');
+ $.ajax(content_url, {dataType: 'html', type: 'GET', context: $pane}).
+ done(function(data, status, jqxhr) {
+ // Preserve collapsed state
+ var $pane = this;
+ var collapsable = {};
+ $(".collapse", this).each(function(i, c) {
+ collapsable[c.id] = $(c).hasClass('in');
+ });
+ var tmp = $(data);
+ $(".collapse", tmp).each(function(i, c) {
+ if (collapsable[c.id]) {
+ $(c).addClass('in');
+ } else {
+ $(c).removeClass('in');
+ }
+ });
+ $pane.html(tmp);
+ $pane.removeClass('pane-loading');
+ $pane.addClass('pane-loaded');
+ $pane.attr('data-loaded-at', (new Date()).getTime());
+ $pane.trigger('arv:pane:loaded', [$pane]);
+
+ if ($pane.hasClass('pane-stale')) {
+ $pane.trigger('arv:pane:reload');
+ }
+ }).fail(function(jqxhr, status, error) {
+ var $pane = this;
+ var errhtml;
+ var contentType = jqxhr.getResponseHeader('Content-Type');
+ if (contentType && contentType.match(/\btext\/html\b/)) {
+ var $response = $(jqxhr.responseText);
+ var $wrapper = $('div#page-wrapper', $response);
+ if ($wrapper.length) {
+ errhtml = $wrapper.html();
+ } else {
+ errhtml = jqxhr.responseText;
+ }
+ } else {
+ errhtml = ("An error occurred: " +
+ (jqxhr.responseText || status)).
+ replace(/&/g, '&').
+ replace(/</g, '<').
+ replace(/>/g, '>');
+ }
+ $pane.html('<div><p>' +
+ '<a href="#" class="btn btn-primary tab_reload">' +
+ '<i class="fa fa-fw fa-refresh"></i> ' +
+ 'Reload tab</a></p><iframe style="width: 100%"></iframe></div>');
+ $('.tab_reload', $pane).click(function() {
+ $(this).
+ html('<div class="spinner spinner-32px spinner-h-center"></div>').
+ closest('.pane-loaded').
+ attr('data-loaded-at', 0).
+ trigger('arv:pane:reload');
+ });
+ // We want to render the error in an iframe, in order to
+ // avoid conflicts with the main page's element ids, etc.
+ // In order to do that dynamically, we have to set a
+ // timeout on the iframe window to load our HTML *after*
+ // the default source (e.g., about:blank) has loaded.
+ var iframe = $('iframe', $pane)[0];
+ iframe.contentWindow.setTimeout(function() {
+ $('body', iframe.contentDocument).html(errhtml);
+ iframe.height = iframe.contentDocument.body.scrollHeight + "px";
+ }, 1);
+ $pane.removeClass('pane-loading');
+ $pane.addClass('pane-loaded');
+ });
+});
+
+// Mark all panes as stale/dirty. Refresh any 'active' panes.
+$(document).on('arv:pane:reload:all', function() {
+ $('[data-pane-content-url]').trigger('arv:pane:reload');
+});
+
+$(document).on('arv-log-event', '.arv-refresh-on-log-event', function(event) {
+ if (this != event.target) {
+ // Not interested in events sent to child nodes.
+ return;
+ }
+ // Panes marked arv-refresh-on-log-event should be refreshed
+ $(event.target).trigger('arv:pane:reload');
+});
+
+// If there is a 'tab counts url' in the nav-tabs element then use it to get some javascript that will update them
+$(document).on('ready count-change', function() {
+ var tabCountsUrl = $('ul.nav-tabs').data('tab-counts-url');
+ if( tabCountsUrl && tabCountsUrl.length ) {
+ $.get( tabCountsUrl );
+ }
+});
--- /dev/null
+var app = angular.module('Workbench', ['Arvados']);
+app.controller('UploadToCollection', UploadToCollection);
+app.directive('arvUuid', arvUuid);
+
+function arvUuid() {
+ // Copy the given uuid into the current $scope.
+ return {
+ restrict: 'A',
+ link: function(scope, element, attributes) {
+ scope.uuid = attributes.arvUuid;
+ }
+ };
+}
+
+UploadToCollection.$inject = ['$scope', '$filter', '$q', '$timeout',
+ 'ArvadosClient', 'arvadosApiToken'];
+function UploadToCollection($scope, $filter, $q, $timeout,
+ ArvadosClient, arvadosApiToken) {
+ $.extend($scope, {
+ uploadQueue: [],
+ uploader: new QueueUploader(),
+ addFilesToQueue: function(files) {
+ // Angular binding doesn't work its usual magic for file
+ // inputs, so we need to $scope.$apply() this update.
+ $scope.$apply(function(){
+ var i, nItemsTodo;
+ // Add these new files after the items already waiting
+ // in the queue -- but before the items that are
+ // 'Done' and have therefore been pushed to the
+ // bottom.
+ for (nItemsTodo = 0;
+ (nItemsTodo < $scope.uploadQueue.length &&
+ $scope.uploadQueue[nItemsTodo].state !== 'Done'); ) {
+ nItemsTodo++;
+ }
+ for (i=0; i<files.length; i++) {
+ $scope.uploadQueue.splice(nItemsTodo+i, 0,
+ new FileUploader(files[i]));
+ }
+ });
+ },
+ go: function() {
+ $scope.uploader.go();
+ },
+ stop: function() {
+ $scope.uploader.stop();
+ },
+ removeFileFromQueue: function(index) {
+ var wasRunning = $scope.uploader.running;
+ $scope.uploadQueue[index].stop();
+ $scope.uploadQueue.splice(index, 1);
+ if (wasRunning)
+ $scope.go();
+ },
+ countInStates: function(want_states) {
+ var found = 0;
+ $.each($scope.uploadQueue, function() {
+ if (want_states.indexOf(this.state) >= 0) {
+ ++found;
+ }
+ });
+ return found;
+ }
+ });
+ ////////////////////////////////
+
+ var keepProxy;
+
+ function SliceReader(_slice) {
+ var that = this;
+ $.extend(this, {
+ go: go
+ });
+ ////////////////////////////////
+ var _deferred;
+ var _reader;
+ function go() {
+ // Return a promise, which will be resolved with the
+ // requested slice data.
+ _deferred = $.Deferred();
+ _reader = new FileReader();
+ _reader.onload = resolve;
+ _reader.onerror = _deferred.reject;
+ _reader.onprogress = _deferred.notify;
+ _reader.readAsArrayBuffer(_slice.blob);
+ return _deferred.promise();
+ }
+ function resolve() {
+ if (that._reader.result.length !== that._slice.size) {
+ // Sometimes we get an onload event even if the read
+ // did not return the desired number of bytes. We
+ // treat that as a fail.
+ _deferred.reject(
+ null, "Read error",
+ "Short read: wanted " + _slice.size +
+ ", received " + _reader.result.length);
+ return;
+ }
+ return _deferred.resolve(_reader.result);
+ }
+ }
+
+ function SliceUploader(_label, _data, _dataSize) {
+ $.extend(this, {
+ go: go,
+ stop: stop
+ });
+ ////////////////////////////////
+ var that = this;
+ var _deferred;
+ var _failCount = 0;
+ var _failMax = 3;
+ var _jqxhr;
+ function go() {
+ // Send data to the Keep proxy. Retry a few times on
+ // fail. Return a promise that will get resolved with
+ // resolve(locator) when the block is accepted by the
+ // proxy.
+ _deferred = $.Deferred();
+ goSend();
+ return _deferred.promise();
+ }
+ function stop() {
+ _failMax = 0;
+ _jqxhr.abort();
+ _deferred.reject({
+ textStatus: 'stopped',
+ err: 'interrupted at slice '+_label
+ });
+ }
+ function goSend() {
+ _jqxhr = $.ajax({
+ url: proxyUriBase(),
+ type: 'POST',
+ crossDomain: true,
+ headers: {
+ 'Authorization': 'OAuth2 '+arvadosApiToken,
+ 'Content-Type': 'application/octet-stream',
+ 'X-Keep-Desired-Replicas': '2'
+ },
+ xhr: function() {
+ // Make an xhr that reports upload progress
+ var xhr = $.ajaxSettings.xhr();
+ if (xhr.upload) {
+ xhr.upload.onprogress = onSendProgress;
+ }
+ return xhr;
+ },
+ processData: false,
+ data: _data
+ });
+ _jqxhr.then(onSendResolve, onSendReject);
+ }
+ function onSendProgress(xhrProgressEvent) {
+ _deferred.notify(xhrProgressEvent.loaded, _dataSize);
+ }
+ function onSendResolve(data, textStatus, jqxhr) {
+ _deferred.resolve(data, _dataSize);
+ }
+ function onSendReject(xhr, textStatus, err) {
+ if (++_failCount < _failMax) {
+ // TODO: nice to tell the user that retry is happening.
+ console.log('slice ' + _label + ': ' +
+ textStatus + ', retry ' + _failCount);
+ goSend();
+ } else {
+ _deferred.reject(
+ {xhr: xhr, textStatus: textStatus, err: err});
+ }
+ }
+ function proxyUriBase() {
+ return ((keepProxy.service_ssl_flag ? 'https' : 'http') +
+ '://' + keepProxy.service_host + ':' +
+ keepProxy.service_port + '/');
+ }
+ }
+
+ function FileUploader(file) {
+ $.extend(this, {
+ file: file,
+ locators: [],
+ progress: 0.0,
+ state: 'Queued', // Queued, Uploading, Paused, Uploaded, Done
+ statistics: null,
+ go: go,
+ stop: stop // User wants to stop.
+ });
+ ////////////////////////////////
+ var that = this;
+ var _currentUploader;
+ var _currentSlice;
+ var _deferred;
+ var _maxBlobSize = Math.pow(2,26);
+ var _bytesDone = 0;
+ var _queueTime = Date.now();
+ var _startTime;
+ var _startByte;
+ var _finishTime;
+ var _readPos = 0; // number of bytes confirmed uploaded
+ function go() {
+ if (_deferred)
+ _deferred.reject({textStatus: 'restarted'});
+ _deferred = $.Deferred();
+ that.state = 'Uploading';
+ _startTime = Date.now();
+ _startByte = _readPos;
+ setProgress();
+ goSlice();
+ return _deferred.promise().always(function() { _deferred = null; });
+ }
+ function stop() {
+ if (_deferred) {
+ that.state = 'Paused';
+ _deferred.reject({textStatus: 'stopped', err: 'interrupted'});
+ }
+ if (_currentUploader) {
+ _currentUploader.stop();
+ _currentUploader = null;
+ }
+ }
+ function goSlice() {
+ // Ensure this._deferred gets resolved or rejected --
+ // either right here, or when a new promise arranged right
+ // here is fulfilled.
+ _currentSlice = nextSlice();
+ if (!_currentSlice) {
+ // All slices have been uploaded, but the work won't
+ // be truly Done until the target collection has been
+ // updated by the QueueUploader. This state is called:
+ that.state = 'Uploaded';
+ setProgress(_readPos);
+ _currentUploader = null;
+ _deferred.resolve([that]);
+ return;
+ }
+ _currentUploader = new SliceUploader(
+ _readPos.toString(),
+ _currentSlice.blob,
+ _currentSlice.size);
+ _currentUploader.go().then(
+ onUploaderResolve,
+ onUploaderReject,
+ onUploaderProgress);
+ }
+ function onUploaderResolve(locator, dataSize) {
+ var sizeHint = (''+locator).split('+')[1];
+ if (!locator || parseInt(sizeHint) !== dataSize) {
+ console.log("onUploaderResolve, but locator '" + locator +
+ "' with size hint '" + sizeHint +
+ "' does not look right for dataSize=" + dataSize);
+ return onUploaderReject({
+ textStatus: "error",
+ err: "Bad response from slice upload"
+ });
+ }
+ that.locators.push(locator);
+ _readPos += dataSize;
+ _currentUploader = null;
+ goSlice();
+ }
+ function onUploaderReject(reason) {
+ that.state = 'Paused';
+ setProgress(_readPos);
+ _currentUploader = null;
+ if (_deferred)
+ _deferred.reject(reason);
+ }
+ function onUploaderProgress(sliceDone, sliceSize) {
+ setProgress(_readPos + sliceDone);
+ }
+ function nextSlice() {
+ var size = Math.min(
+ _maxBlobSize,
+ that.file.size - _readPos);
+ setProgress(_readPos);
+ if (size === 0) {
+ return false;
+ }
+ var blob = that.file.slice(
+ _readPos, _readPos+size,
+ 'application/octet-stream; charset=x-user-defined');
+ return {blob: blob, size: size};
+ }
+ function setProgress(bytesDone) {
+ var kBps;
+ if (that.file.size == 0)
+ that.progress = 100;
+ else
+ that.progress = Math.min(100, 100 * bytesDone / that.file.size);
+ if (bytesDone > _startByte) {
+ kBps = (bytesDone - _startByte) /
+ (Date.now() - _startTime);
+ that.statistics = (
+ '' + $filter('number')(bytesDone/1024, '0') + ' KiB ' +
+ 'at ~' + $filter('number')(kBps, '0') + ' KiB/s')
+ if (that.state === 'Paused') {
+ that.statistics += ', paused';
+ } else if (that.state === 'Uploading') {
+ that.statistics += ', ETA ' +
+ $filter('date')(
+ new Date(
+ Date.now() + (that.file.size - bytesDone) / kBps),
+ 'shortTime')
+ }
+ } else {
+ that.statistics = that.state;
+ }
+ if (that.state === 'Uploaded') {
+ // 'Uploaded' gets reported as 'finished', which is a
+ // little misleading because the collection hasn't
+ // been updated yet. But FileUploader's portion of the
+ // work (and the time when it makes sense to show
+ // speed and ETA) is finished.
+ that.statistics += ', finished ' +
+ $filter('date')(Date.now(), 'shortTime');
+ _finishTime = Date.now();
+ }
+ if (_deferred)
+ _deferred.notify();
+ }
+ }
+
+ function QueueUploader() {
+ $.extend(this, {
+ state: 'Idle', // Idle, Running, Stopped, Failed
+ stateReason: null,
+ statusSuccess: null,
+ go: go,
+ stop: stop
+ });
+ ////////////////////////////////
+ var that = this;
+ var _deferred; // the one we promise to go()'s caller
+ var _deferredAppend; // tracks current appendToCollection
+ function go() {
+ if (_deferred) return _deferred.promise();
+ if (_deferredAppend) return _deferredAppend.promise();
+ _deferred = $.Deferred();
+ that.state = 'Running';
+ ArvadosClient.apiPromise(
+ 'keep_services', 'list',
+ {filters: [['service_type','=','proxy']]}).
+ then(doQueueWithProxy);
+ onQueueProgress();
+ return _deferred.promise().always(function() { _deferred = null; });
+ }
+ function stop() {
+ that.state = 'Stopped';
+ if (_deferred) {
+ _deferred.reject({});
+ }
+ for (var i=0; i<$scope.uploadQueue.length; i++)
+ $scope.uploadQueue[i].stop();
+ onQueueProgress();
+ }
+ function doQueueWithProxy(data) {
+ keepProxy = data.items[0];
+ if (!keepProxy) {
+ that.state = 'Failed';
+ that.stateReason =
+ 'There seems to be no Keep proxy service available.';
+ _deferred.reject(null, 'error', that.stateReason);
+ return;
+ }
+ return doQueueWork();
+ }
+ function doQueueWork() {
+ // If anything is not Done, do it.
+ if ($scope.uploadQueue.length > 0 &&
+ $scope.uploadQueue[0].state !== 'Done') {
+ if (_deferred) {
+ that.stateReason = null;
+ return $scope.uploadQueue[0].go().
+ then(appendToCollection, null, onQueueProgress).
+ then(doQueueWork, onQueueReject);
+ } else {
+ // Queue work has been stopped. Just update the
+ // view.
+ onQueueProgress();
+ return;
+ }
+ }
+ // If everything is Done, resolve the promise and clean
+ // up. Note this can happen even after the _deferred
+ // promise has been rejected: specifically, when stop() is
+ // called too late to prevent completion of the last
+ // upload. In that case we want to update state to "Idle",
+ // rather than leave it at "Stopped".
+ onQueueResolve();
+ }
+ function onQueueReject(reason) {
+ if (!_deferred) {
+ // Outcome has already been decided (by stop()).
+ return;
+ }
+
+ that.state = 'Failed';
+ that.stateReason = (
+ (reason.textStatus || 'Error') +
+ (reason.xhr && reason.xhr.options
+ ? (' (from ' + reason.xhr.options.url + ')')
+ : '') +
+ ': ' +
+ (reason.err || ''));
+ if (reason.xhr && reason.xhr.responseText)
+ that.stateReason += ' -- ' + reason.xhr.responseText;
+ _deferred.reject(reason);
+ onQueueProgress();
+ }
+ function onQueueResolve() {
+ that.state = 'Idle';
+ that.stateReason = 'Done!';
+ if (_deferred)
+ _deferred.resolve();
+ onQueueProgress();
+ }
+ function onQueueProgress() {
+ // Ensure updates happen after FileUpload promise callbacks.
+ $timeout(function(){$scope.$apply();});
+ }
+ function appendToCollection(uploads) {
+ _deferredAppend = $.Deferred();
+ ArvadosClient.apiPromise(
+ 'collections', 'get',
+ { uuid: $scope.uuid }).
+ then(function(collection) {
+ var manifestText = '';
+ $.each(uploads, function(_, upload) {
+ var locators = upload.locators;
+ if (locators.length === 0) {
+ // Every stream must have at least one
+ // data locator, even if it is zero bytes
+ // long:
+ locators = ['d41d8cd98f00b204e9800998ecf8427e+0'];
+ }
+ filename = ArvadosClient.uniqueNameForManifest(
+ collection.manifest_text,
+ '.', upload.file.name);
+ collection.manifest_text += '. ' +
+ locators.join(' ') +
+ ' 0:' + upload.file.size.toString() + ':' +
+ filename +
+ '\n';
+ });
+ return ArvadosClient.apiPromise(
+ 'collections', 'update',
+ { uuid: $scope.uuid,
+ collection:
+ { manifest_text:
+ collection.manifest_text }
+ });
+ }).
+ then(function() {
+ // Mark the completed upload(s) as Done and push
+ // them to the bottom of the queue.
+ var i, qLen = $scope.uploadQueue.length;
+ for (i=0; i<qLen; i++) {
+ if (uploads.indexOf($scope.uploadQueue[i]) >= 0) {
+ $scope.uploadQueue[i].state = 'Done';
+ $scope.uploadQueue.push.apply(
+ $scope.uploadQueue,
+ $scope.uploadQueue.splice(i, 1));
+ --i;
+ --qLen;
+ }
+ }
+ }).
+ then(_deferredAppend.resolve,
+ _deferredAppend.reject);
+ return _deferredAppend.promise().
+ always(function() {
+ _deferredAppend = null;
+ });
+ }
+ }
+}
--- /dev/null
+function enable_okbutton() {
+ var $div = $('#open_user_agreement');
+ var allchecked = $('input[name="checked[]"]', $div).not(':checked').length == 0;
+ $('input[type=submit]', $div).prop('disabled', !allchecked);
+}
+$(document).on('click keyup input', '#open_user_agreement input', enable_okbutton);
+$(document).on('ready ajax:complete', enable_okbutton);
--- /dev/null
+$(document).
+ on('notifications:recount',
+ function() {
+ var menu = $('.notification-menu');
+ n = $('.notification', menu).not('.empty').length;
+ $('.notification-count', menu).html(n>0 ? n : '');
+ }).
+ on('ajax:success', 'form.new_authorized_key',
+ function(e, data, status, xhr) {
+ $(e.target).parents('.notification').eq(0).fadeOut('slow', function() {
+ $('<li class="alert alert-success daxalert">SSH key added.</li>').hide().replaceAll(this).fadeIn('slow');
+ $(document).trigger('notifications:recount');
+ });
+ }).
+ on('ajax:complete', 'form.new_authorized_key',
+ function(e, data, status, xhr) {
+ $($('input[name=disable_element]', e.target).val()).
+ fadeTo(200, 1.0);
+ }).
+ on('ajax:error', 'form.new_authorized_key',
+ function(e, xhr, status, error) {
+ var error_div;
+ response = $.parseJSON(xhr.responseText);
+ error_div = $(e.target).parent().find('div.ajax-errors');
+ if (error_div.length == 0) {
+ $(e.target).parent().append('<div class="alert alert-error ajax-errors"></div>');
+ error_div = $(e.target).parent().find('div.ajax-errors');
+ }
+ if (response.errors) {
+ error_div.html($('<p/>').text(response.errors).html());
+ } else {
+ error_div.html('<p>Sorry, request failed.');
+ }
+ error_div.show();
+ $($('input[name=disable_element]', e.target).val()).
+ fadeTo(200, 1.0);
+ }).
+ on('click', 'form[data-remote] input[type=submit]',
+ function(e) {
+ $(e.target).parents('form').eq(0).parent().find('div.ajax-errors').html('').hide();
+ $($(e.target).
+ parents('form').
+ find('input[name=disable_element]').
+ val()).
+ fadeTo(200, 0.3);
+ return true;
+ });
--- /dev/null
+// Place all the styles related to the ApiClientAuthorizations controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+/*
+ * This is a manifest file that'll be compiled into application.css, which will include all the files
+ * listed below.
+ *
+ * Any CSS and SCSS file within this directory, lib/assets/stylesheets, vendor/assets/stylesheets,
+ * or vendor/assets/stylesheets of plugins, if any, can be referenced here using a relative path.
+ *
+ * You're free to add application-wide styles to this file and they'll appear at the top of the
+ * compiled file, but it's generally better to create a new file per style scope.
+ *
+ *= require_self
+ *= require bootstrap
+ *= require bootstrap3-editable/bootstrap-editable
+ *= require morris
+ *= require_tree .
+ */
+
+.contain-align-left {
+ text-align: left;
+}
+table.topalign>tbody>tr>td {
+ vertical-align: top;
+}
+table.topalign>thead>tr>td {
+ vertical-align: bottom;
+}
+tr.cell-valign-center>td {
+ vertical-align: middle;
+}
+tr.cell-noborder>td,tr.cell-noborder>th {
+ border: none;
+}
+table.table-justforlayout>tr>td,
+table.table-justforlayout>tr>th,
+table.table-justforlayout>thead>tr>td,
+table.table-justforlayout>thead>tr>th,
+table.table-justforlayout>tbody>tr>td,
+table.table-justforlayout>tbody>tr>th{
+ border: none;
+}
+table.table-justforlayout {
+ margin-bottom: 0;
+}
+.smaller-text {
+ font-size: .8em;
+}
+.deemphasize {
+ font-size: .8em;
+ color: #888;
+}
+.lighten {
+ color: #888;
+}
+.arvados-filename,
+.arvados-uuid {
+ font-size: .8em;
+ font-family: monospace;
+}
+table .data-size, .table .data-size {
+ text-align: right;
+}
+body .editable-empty {
+ color: #999;
+}
+body .editable-empty:hover {
+ color: #0088cc;
+}
+table.arv-index tbody td.arv-object-AuthorizedKey.arv-attr-public_key {
+ overflow-x: hidden;
+ max-width: 120px;
+}
+table.arv-index > thead > tr > th {
+ border-top: none;
+}
+table.table-fixedlayout {
+ white-space: nowrap;
+ table-layout: fixed;
+}
+table.table-fixedlayout td {
+ overflow: hidden;
+ overflow-x: hidden;
+ text-overflow: ellipsis;
+}
+table.table-smallcontent td {
+ font-size: 85%;
+}
+form input.search-mini {
+ padding: 0 6px;
+}
+form.small-form-margin {
+ margin-bottom: 2px;
+}
+.nowrap {
+ white-space: nowrap;
+}
+
+/* top nav */
+$top-nav-bg: #3c163d;
+$top-nav-bg-bottom: #260027;
+nav.navbar-fixed-top .navbar-brand {
+ color: #79537a;
+ letter-spacing: 0.4em;
+}
+nav.navbar-fixed-top {
+ background: $top-nav-bg;
+ background: linear-gradient(to bottom, $top-nav-bg 0%,$top-nav-bg-bottom 100%);
+}
+.navbar.breadcrumbs {
+ line-height: 50px;
+ border-radius: 0;
+ margin-bottom: 0;
+ border-right: 0;
+ border-left: 0;
+}
+.navbar.breadcrumbs .nav > li > a,
+.navbar.breadcrumbs .nav > li {
+ color: #000;
+}
+.navbar.breadcrumbs .nav > li.nav-separator > i {
+ color: #bbb;
+}
+.navbar.breadcrumbs .navbar-form {
+ margin-top: 0px;
+ margin-bottom: 0px;
+}
+.navbar.breadcrumbs .navbar-text {
+ margin-top: 0px;
+ margin-bottom: 0px;
+}
+
+nav.navbar-fixed-top .navbar-nav.navbar-right > li.open > a,
+nav.navbar-fixed-top .navbar-nav.navbar-right > li.open > a:focus,
+nav.navbar-fixed-top .navbar-nav.navbar-right > li.open > a:hover {
+ background: lighten($top-nav-bg, 5%);
+}
+nav.navbar-fixed-top .navbar-nav.navbar-right > li > a,
+nav.navbar-fixed-top .navbar-nav.navbar-right > li > a:focus,
+nav.navbar-fixed-top .navbar-nav.navbar-right > li > a:hover {
+ color: #fff;
+}
+
+.dax {
+ max-width: 10%;
+ margin-right: 1em;
+ float: left
+}
+
+.smart-scroll {
+ overflow: auto;
+ margin-bottom: -15px;
+}
+
+.infinite-scroller .fa-warning {
+ color: #800;
+}
+
+th[data-sort-order] {
+ cursor: pointer;
+}
+
+.inline-progress-container div.progress {
+ margin-bottom: 0;
+}
+
+.inline-progress-container {
+ width: 100%;
+ display:inline-block;
+}
+
+td.add-tag-button {
+ white-space: normal;
+}
+td.add-tag-button .add-tag-button {
+ margin-right: 4px;
+ opacity: 0.2;
+}
+td.add-tag-button .add-tag-button:hover {
+ opacity: 1;
+}
+span.removable-tag-container {
+ line-height: 1.6;
+}
+.label.removable-tag a {
+ color: #fff;
+ cursor: pointer;
+}
+
+li.notification {
+ padding: 10px;
+}
+
+// See HeaderRowFixer in application.js
+table.table-fixed-header-row {
+ width: 100%;
+ border-spacing: 0px;
+ margin:0;
+}
+table.table-fixed-header-row thead {
+ position:fixed;
+ background: #fff;
+}
+table.table-fixed-header-row tbody {
+ position:relative;
+ top:1.5em;
+}
+
+.dropdown-menu {
+ max-height: 30em;
+ overflow-y: auto;
+}
+
+.row-fill-height, .row-fill-height>div[class*='col-'] {
+ display: flex;
+}
+.row-fill-height>div[class*='col-']>div {
+ width: 100%;
+}
+
+/* Show editable popover above side-nav */
+.editable-popup.popover {
+ z-index:1055;
+}
+
+/* Do not leave space for left-nav */
+div#wrapper {
+ padding-left: 0;
+}
+
+.arv-description-as-subtitle {
+ padding-bottom: 1em;
+}
+.arv-description-in-table {
+ height: 4em;
+ overflow-x: hidden;
+ overflow-y: hidden;
+}
+.arv-description-in-table:hover {
+ overflow-y: auto;
+}
+
+.btn.btn-nodecorate {
+ border: none;
+}
+svg text {
+ font-size: 6pt;
+}
+
+div.pane-content iframe {
+ width: 100%;
+ border: none;
+}
+span.editable-textile {
+ display: inline-block;
+}
+.text-overflow-ellipsis {
+ white-space: nowrap;
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+.time-label-divider {
+ font-size: 80%;
+ min-width: 1em;
+ padding: 0px 2px 0px 0px;
+}
+.task-summary-status {
+ font-size: 80%;
+}
+#page-wrapper > div > h2 {
+ margin-top: 0px;
+}
+
+.compute-summary-numbers td {
+ font-size: 150%;
+}
+
+.arv-log-refresh-control {
+ display: none;
+}
+
+[ng\:cloak], [ng-cloak], .ng-cloak {
+ display: none !important;
+}
--- /dev/null
+// Place all the styles related to the AuthorizedKeys controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
+form .table input[type=text] {
+ width: 600px;
+}
+form .table textarea {
+ width: 600px;
+ height: 10em;
+}
--- /dev/null
+/* Colors
+ * Contextual variations of badges
+ * Bootstrap 3.0 removed contexts for badges, we re-introduce them, based on what is done for labels
+ */
+
+.badge.badge-error {
+ background-color: #b94a48;
+}
+
+.badge.badge-warning {
+ background-color: #f89406;
+}
+
+.badge.badge-success {
+ background-color: #468847;
+}
+
+.badge.badge-info {
+ background-color: #3a87ad;
+}
+
+.badge.badge-inverse {
+ background-color: #333333;
+}
+
+.badge.badge-alert {
+ background: red;
+}
--- /dev/null
+.card {
+ padding-top: 20px;
+ margin: 10px 0 20px 0;
+ background-color: #ffffff;
+ border: 1px solid #d8d8d8;
+ border-top-width: 0;
+ border-bottom-width: 2px;
+ -webkit-border-radius: 3px;
+ -moz-border-radius: 3px;
+ border-radius: 3px;
+ -webkit-box-shadow: none;
+ -moz-box-shadow: none;
+ box-shadow: none;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+.card.arvados-object {
+ position: relative;
+ display: inline-block;
+ width: 170px;
+ height: 175px;
+ padding-top: 0;
+ margin-left: 20px;
+ overflow: hidden;
+ vertical-align: top;
+}
+.card.arvados-object .card-top.green {
+ background-color: #53a93f;
+}
+.card.arvados-object .card-top.blue {
+ background-color: #427fed;
+}
+.card.arvados-object .card-top {
+ position: absolute;
+ top: 0;
+ left: 0;
+ display: inline-block;
+ width: 170px;
+ height: 25px;
+ background-color: #ffffff;
+}
+.card.arvados-object .card-info {
+ position: absolute;
+ top: 25px;
+ display: inline-block;
+ width: 100%;
+ height: 101px;
+ overflow: hidden;
+ background: #ffffff;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+.card.arvados-object .card-info .title {
+ display: block;
+ margin: 8px 14px 0 14px;
+ overflow: hidden;
+ font-size: 16px;
+ font-weight: bold;
+ line-height: 18px;
+ color: #404040;
+}
+.card.arvados-object .card-info .desc {
+ display: block;
+ margin: 8px 14px 0 14px;
+ overflow: hidden;
+ font-size: 12px;
+ line-height: 16px;
+ color: #737373;
+ text-overflow: ellipsis;
+}
+.card.arvados-object .card-bottom {
+ position: absolute;
+ bottom: 0;
+ left: 0;
+ display: inline-block;
+ width: 100%;
+ padding: 10px 20px;
+ line-height: 29px;
+ text-align: center;
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
--- /dev/null
+/* Style for _show_files tree view. */
+
+ul#collection_files {
+ padding: 0 .5em;
+}
+
+ul.collection_files {
+ line-height: 2.5em;
+ list-style-type: none;
+ padding-left: 2.3em;
+}
+
+ul.collection_files li {
+ clear: both;
+}
+
+.collection_files_row {
+ padding: 1px; /* Replaced by border for :hover */
+}
+
+.collection_files_row:hover {
+ background-color: #D9EDF7;
+ padding: 0px;
+ border: 1px solid #BCE8F1;
+ border-radius: 3px;
+}
+
+.collection_files_inline {
+ clear: both;
+ width: 80%;
+ margin: 0 3em;
+}
+
+.collection_files_inline img {
+ max-height: 15em;
+}
+
+.collection_files_name {
+ padding-left: .5em;
+ white-space: nowrap;
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+
+.collection_files_name i.fa-fw:first-child {
+ width: 1.6em;
+}
+
+/*
+ "active" and "inactive" colors are too similar for a toggle switch
+ in the default bootstrap theme.
+ */
+
+$inactive-bg: #5bc0de;
+$active-bg: #39b3d7;
+
+.btn-group.toggle-persist .btn {
+ width: 6em;
+}
+.btn-group.toggle-persist .btn-info {
+ background-color: lighten($inactive-bg, 15%);
+}
+
+.btn-group.toggle-persist .btn-info.active {
+ background-color: $active-bg;
+}
--- /dev/null
+// Place all the styles related to the Groups controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Humans controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the JobTasks controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+.arv-job-log-window {
+ height: 40em;
+ white-space: pre;
+ overflow: scroll;
+ background: black;
+ color: white;
+ font-family: monospace;
+ font-size: .8em;
+ border: 2px solid black;
+}
+
+.morris-hover-point {
+ text-align: left;
+ width: 100%;
+}
\ No newline at end of file
--- /dev/null
+// Place all the styles related to the KeepDisks controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
+
+/* Margin allows us some space between the table above. */
+div.graph {
+ margin-top: 20px;
+}
+div.graph h3, div.graph h4 {
+ text-align: center;
+}
--- /dev/null
+// Place all the styles related to the Links controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+.loading {
+ opacity: 0;
+}
+
+.spinner {
+ /* placeholder for stuff like $.find('.spinner').detach() */
+}
+
+.spinner-32px {
+ background-image: url('<%= asset_path('spinner_32px.gif') %>');
+ background-repeat: no-repeat;
+ width: 32px;
+ height: 32px;
+}
+
+.spinner-h-center {
+ margin-left: auto;
+ margin-right: auto;
+}
+
+.spinner-v-center {
+ position: relative;
+ top: 45%;
+}
+
+.rotating {
+ color: #f00;
+ /* Chrome and Firefox, at least in Linux, render a horrible shaky
+ mess -- better not to bother.
+
+ animation-name: rotateThis;
+ animation-duration: 2s;
+ animation-iteration-count: infinite;
+ animation-timing-function: linear;
+ -moz-animation-name: rotateThis;
+ -moz-animation-duration: 2s;
+ -moz-animation-iteration-count: infinite;
+ -moz-animation-timing-function: linear;
+ -ms-animation-name: rotateThis;
+ -ms-animation-duration: 2s;
+ -ms-animation-iteration-count: infinite;
+ -ms-animation-timing-function: linear;
+ -webkit-animation-name: rotateThis;
+ -webkit-animation-duration: 2s;
+ -webkit-animation-iteration-count: infinite;
+ -webkit-animation-timing-function: linear;
+ */
+}
+
+@keyframes rotateThis {
+ from { transform: rotate( 0deg ); }
+ to { transform: rotate( 360deg ); }
+}
+
+@-webkit-keyframes rotateThis {
+ from { -webkit-transform: rotate( 0deg ); }
+ to { -webkit-transform: rotate( 360deg ); }
+}
+
+@-moz-keyframes rotateThis {
+ from { -moz-transform: rotate( 0deg ); }
+ to { -moz-transform: rotate( 360deg ); }
+}
+
+@-ms-keyframes rotateThis {
+ from { -ms-transform: rotate( 0deg ); }
+ to { -ms-transform: rotate( 360deg ); }
+}
--- /dev/null
+.log-viewer-table {
+ width: 100%;
+ font-family: "Lucida Console", Monaco, monospace;
+ font-size: 11px;
+ table-layout: fixed;
+ thead tr {
+ th {
+ padding-right: 1em;
+ }
+ th.id {
+ display: none;
+ }
+ th.timestamp {
+ width: 15em;
+ }
+ th.type {
+ width: 8em;
+ }
+ th.taskid {
+ width: 4em;
+ }
+ th.node {
+ width: 8em;
+ }
+ th.slot {
+ width: 3em;
+ }
+ th.message {
+ width: auto;
+ }
+ }
+ tbody tr {
+ vertical-align: top;
+ td {
+ padding-right: 1em;
+ }
+ td.id {
+ display: none;
+ }
+ td.taskid {
+ text-align: right;
+ }
+ td.slot {
+ text-align: right;
+ }
+ td.message {
+ word-wrap: break-word;
+ }
+ }
+}
+
+.log-viewer-button {
+ width: 12em;
+}
+
+.log-viewer-paging-div {
+ font-size: 18px;
+ text-align: center;
+}
+
+.log-viewer-page-num {
+ padding-left: .3em;
+ padding-right: .3em;
+}
\ No newline at end of file
--- /dev/null
+// Place all the styles related to the Logs controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Nodes controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the PipelineInstances controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
+
+.pipeline-compare-headrow div {
+ padding-top: .5em;
+ padding-bottom: .5em;
+}
+.pipeline-compare-headrow:first-child {
+ border-bottom: 1px solid black;
+}
+.pipeline-compare-row .notnormal {
+ background: #ffffaa;
+}
+
+.pipeline_color_legend {
+ margin-top: 0.2em;
+ padding: 0.2em 1em;
+ border: 1px solid #000;
+}
+.pipeline_color_legend a {
+ color: #000;
+}
+
+.col-md-1.pipeline-instance-spacing {
+ padding: 0px;
+ margin: 0px;
+}
+
+.col-md-3.pipeline-instance-spacing > .progress {
+ padding: 0px;
+ margin: 0px;
+}
\ No newline at end of file
--- /dev/null
+// Place all the styles related to the PipelineTemplates controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
+
+.pipeline_color_legend {
+ padding-left: 1em;
+ padding-right: 1em;
+}
+
+table.pipeline-components-table {
+ width: 100%;
+ table-layout: fixed;
+ overflow: hidden;
+}
+
+table.pipeline-components-table thead th {
+ text-align: bottom;
+}
+table.pipeline-components-table div.progress {
+ margin-bottom: 0;
+}
+
+table.pipeline-components-table td {
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+
+td.required {
+ background: #ffdddd;
+}
--- /dev/null
+.arv-project-list > .row {
+ padding-top: 5px;
+ padding-bottom: 5px;
+ padding-right: 1em;
+}
+.arv-project-list > .row.project:hover {
+ background: #d9edf7;
+}
+div.scroll-20em {
+ height: 20em;
+ overflow-y: scroll;
+}
+
+.compute-summary {
+ margin: 0.15em 0em 0.15em 0em;
+ display: inline-block;
+}
+
+.compute-summary-head {
+ margin-left: 0.3em;
+}
+
+.compute-detail {
+ border: 1px solid;
+ border-color: #DDD;
+ border-radius: 3px;
+ padding: 0.2em;
+ position: absolute;
+ z-index: 1;
+ background: white;
+}
+
+.compute-detail:hover {
+ cursor: pointer;
+}
+
+.compute-node-summary:hover {
+ cursor: pointer;
+}
+
+.compute-summary-numbers .panel {
+ margin-bottom: 0px;
+}
+
+.compute-summary-numbers table {
+ width: 100%;
+ td,th {
+ text-align: center;
+ }
+}
+
+.compute-summary-nodelist {
+ margin-bottom: 10px
+}
+
+.dashboard-panel-info-row {
+ padding: .5em;
+ border-radius: .3em;
+}
+
+.dashboard-panel-info-row:hover {
+ background-color: #D9EDF7;
+}
+
+.progress-bar.progress-bar-default {
+ background-color: #999;
+}
\ No newline at end of file
--- /dev/null
+// Place all the styles related to the Repositories controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+/*
+Author: Start Bootstrap - http://startbootstrap.com
+'SB Admin' HTML Template by Start Bootstrap
+
+All Start Bootstrap themes are licensed under Apache 2.0.
+For more info and more free Bootstrap 3 HTML themes, visit http://startbootstrap.com!
+*/
+
+/* ATTN: This is mobile first CSS - to update 786px and up screen width use the media query near the bottom of the document! */
+
+/* Global Styles */
+
+body {
+ margin-top: 50px;
+}
+
+#wrapper {
+ padding-left: 0;
+}
+
+#page-wrapper {
+ width: 100%;
+ padding: 5px 15px;
+}
+
+/* Nav Messages */
+
+.messages-dropdown .dropdown-menu .message-preview .avatar,
+.messages-dropdown .dropdown-menu .message-preview .name,
+.messages-dropdown .dropdown-menu .message-preview .message,
+.messages-dropdown .dropdown-menu .message-preview .time {
+ display: block;
+}
+
+.messages-dropdown .dropdown-menu .message-preview .avatar {
+ float: left;
+ margin-right: 15px;
+}
+
+.messages-dropdown .dropdown-menu .message-preview .name {
+ font-weight: bold;
+}
+
+.messages-dropdown .dropdown-menu .message-preview .message {
+ font-size: 12px;
+}
+
+.messages-dropdown .dropdown-menu .message-preview .time {
+ font-size: 12px;
+}
+
+
+/* Nav Announcements */
+
+.announcement-heading {
+ font-size: 50px;
+ margin: 0;
+}
+
+.announcement-text {
+ margin: 0;
+}
+
+/* Table Headers */
+
+table.tablesorter thead {
+ cursor: pointer;
+}
+
+table.tablesorter thead tr th:hover {
+ background-color: #f5f5f5;
+}
+
+/* Flot Chart Containers */
+
+.flot-chart {
+ display: block;
+ height: 400px;
+}
+
+.flot-chart-content {
+ width: 100%;
+ height: 100%;
+}
+
+/* Edit Below to Customize Widths > 768px */
+@media (min-width:768px) {
+
+ /* Wrappers */
+
+ #wrapper {
+ padding-left: 225px;
+ }
+
+ #page-wrapper {
+ padding: 15px 25px;
+ }
+
+ /* Side Nav */
+
+ .side-nav {
+ margin-left: -225px;
+ left: 225px;
+ width: 225px;
+ position: fixed;
+ top: 50px;
+ height: calc(100% - 50px);
+ border-radius: 0;
+ border: none;
+ background-color: #f8f8f8;
+ overflow-y: auto;
+ overflow-x: hidden; /* no left nav scroll bar */
+ }
+
+ /* Bootstrap Default Overrides - Customized Dropdowns for the Side Nav */
+
+ .side-nav>li.dropdown>ul.dropdown-menu {
+ position: relative;
+ min-width: 225px;
+ margin: 0;
+ padding: 0;
+ border: none;
+ border-radius: 0;
+ background-color: transparent;
+ box-shadow: none;
+ -webkit-box-shadow: none;
+ }
+
+ .side-nav>li.dropdown>ul.dropdown-menu>li>a {
+ color: #777777;
+ padding: 15px 15px 15px 25px;
+ }
+
+ .side-nav>li.dropdown>ul.dropdown-menu>li>a:hover,
+ .side-nav>li.dropdown>ul.dropdown-menu>li>a.active,
+ .side-nav>li.dropdown>ul.dropdown-menu>li>a:focus {
+ background-color: #ffffff;
+ }
+
+ .side-nav>li>a {
+ width: 225px;
+ }
+
+ .navbar-default .navbar-nav.side-nav>li>a:hover,
+ .navbar-default .navbar-nav.side-nav>li>a:focus {
+ background-color: #ffffff;
+ }
+
+ /* Nav Messages */
+
+ .messages-dropdown .dropdown-menu {
+ min-width: 300px;
+ }
+
+ .messages-dropdown .dropdown-menu li a {
+ white-space: normal;
+ }
+
+ .navbar-collapse {
+ padding-left: 15px !important;
+ padding-right: 15px !important;
+ }
+
+}
--- /dev/null
+/*
+ We don't want the default Rails CSS, so the rules are deleted. This
+ empty file is left here so Rails doesn't re-add it next time it
+ generates a scaffold.
+ */
--- /dev/null
+.selectable-container > .row {
+ padding-top: 5px;
+ padding-bottom: 5px;
+ padding-right: 1em;
+ color: #888;
+}
+.selectable-container > .row.selectable {
+ color: #000;
+}
+.selectable.active, .selectable:hover {
+ background: #d9edf7;
+ cursor: pointer;
+}
+.selectable.active,
+.selectable.active *,
+.selectable.active:hover,
+.selectable.active:hover * {
+ background: #428bca;
+ color: #fff;
+}
+.selectable-container > .row.class-separator {
+ background: #ddd;
+}
--- /dev/null
+// Place all the styles related to the Sessions controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Specimens controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Traits controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the user_agreements controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Users controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the VirtualMachines controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+class ActionsController < ApplicationController
+
+ skip_filter :require_thread_api_token, only: [:report_issue_popup, :report_issue]
+ skip_filter :check_user_agreements, only: [:report_issue_popup, :report_issue]
+
+ @@exposed_actions = {}
+ def self.expose_action method, &block
+ @@exposed_actions[method] = true
+ define_method method, block
+ end
+
+ def model_class
+ ArvadosBase::resource_class_for_uuid(params[:uuid])
+ end
+
+ def show
+ @object = model_class.andand.find(params[:uuid])
+ if @object.is_a? Link and
+ @object.link_class == 'name' and
+ ArvadosBase::resource_class_for_uuid(@object.head_uuid) == Collection
+ redirect_to collection_path(id: @object.uuid)
+ elsif @object
+ redirect_to @object
+ else
+ raise ActiveRecord::RecordNotFound
+ end
+ end
+
+ def post
+ params.keys.collect(&:to_sym).each do |param|
+ if @@exposed_actions[param]
+ return self.send(param)
+ end
+ end
+ redirect_to :back
+ end
+
+ expose_action :copy_selections_into_project do
+ move_or_copy :copy
+ end
+
+ expose_action :move_selections_into_project do
+ move_or_copy :move
+ end
+
+ def move_or_copy action
+ uuids_to_add = params["selection"]
+ uuids_to_add = [ uuids_to_add ] unless uuids_to_add.is_a? Array
+ uuids_to_add.
+ collect { |x| ArvadosBase::resource_class_for_uuid(x) }.
+ uniq.
+ each do |resource_class|
+ resource_class.filter([['uuid','in',uuids_to_add]]).each do |src|
+ if resource_class == Collection and not Collection.attribute_info.include?(:name)
+ dst = Link.new(owner_uuid: @object.uuid,
+ tail_uuid: @object.uuid,
+ head_uuid: src.uuid,
+ link_class: 'name',
+ name: src.uuid)
+ else
+ case action
+ when :copy
+ dst = src.dup
+ if dst.respond_to? :'name='
+ if dst.name
+ dst.name = "Copy of #{dst.name}"
+ else
+ dst.name = "Copy of unnamed #{dst.class_for_display.downcase}"
+ end
+ end
+ if resource_class == Collection
+ dst.manifest_text = Collection.select([:manifest_text]).where(uuid: src.uuid).first.manifest_text
+ end
+ when :move
+ dst = src
+ else
+ raise ArgumentError.new "Unsupported action #{action}"
+ end
+ dst.owner_uuid = @object.uuid
+ dst.tail_uuid = @object.uuid if dst.class == Link
+ end
+ begin
+ dst.save!
+ rescue
+ dst.name += " (#{Time.now.localtime})" if dst.respond_to? :name=
+ dst.save!
+ end
+ end
+ end
+ redirect_to @object
+ end
+
+ def arv_normalize mt, *opts
+ r = ""
+ env = Hash[ENV].
+ merge({'ARVADOS_API_HOST' =>
+ arvados_api_client.arvados_v1_base.
+ sub(/\/arvados\/v1/, '').
+ sub(/^https?:\/\//, ''),
+ 'ARVADOS_API_TOKEN' => 'x',
+ 'ARVADOS_API_HOST_INSECURE' =>
+ Rails.configuration.arvados_insecure_https ? 'true' : 'false'
+ })
+ IO.popen([env, 'arv-normalize'] + opts, 'w+b') do |io|
+ io.write mt
+ io.close_write
+ while buf = io.read(2**16)
+ r += buf
+ end
+ end
+ r
+ end
+
+ expose_action :combine_selected_files_into_collection do
+ uuids = []
+ pdhs = []
+ files = []
+ params["selection"].each do |s|
+ a = ArvadosBase::resource_class_for_uuid s
+ if a == Link
+ begin
+ if (m = CollectionsHelper.match(Link.find(s).head_uuid))
+ pdhs.append(m[1] + m[2])
+ files.append(m)
+ end
+ rescue
+ end
+ elsif (m = CollectionsHelper.match(s))
+ pdhs.append(m[1] + m[2])
+ files.append(m)
+ elsif (m = CollectionsHelper.match_uuid_with_optional_filepath(s))
+ uuids.append(m[1])
+ files.append(m)
+ end
+ end
+
+ pdhs = pdhs.uniq
+ uuids = uuids.uniq
+ chash = {}
+
+ Collection.select([:uuid, :manifest_text]).where(uuid: uuids).each do |c|
+ chash[c.uuid] = c
+ end
+
+ Collection.select([:portable_data_hash, :manifest_text]).where(portable_data_hash: pdhs).each do |c|
+ chash[c.portable_data_hash] = c
+ end
+
+ combined = ""
+ files.each do |m|
+ mt = chash[m[1]+m[2]].andand.manifest_text
+ if not m[4].nil? and m[4].size > 1
+ combined += arv_normalize mt, '--extract', ".#{m[4]}"
+ else
+ combined += mt
+ end
+ end
+
+ normalized = arv_normalize combined
+ newc = Collection.new({:manifest_text => normalized})
+ newc.name = newc.name || "Collection created at #{Time.now.localtime}"
+
+ # set owner_uuid to current project, provided it is writable
+ current_project_writable = false
+ action_data = JSON.parse(params['action_data']) if params['action_data']
+ if action_data && action_data['current_project_uuid']
+ current_project = Group.find(action_data['current_project_uuid']) rescue nil
+ if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
+ newc.owner_uuid = action_data['current_project_uuid']
+ current_project_writable = true
+ end
+ end
+
+ newc.save!
+
+ chash.each do |k,v|
+ l = Link.new({
+ tail_uuid: k,
+ head_uuid: newc.uuid,
+ link_class: "provenance",
+ name: "provided"
+ })
+ l.save!
+ end
+
+ msg = current_project_writable ?
+ "Created new collection in the project #{current_project.name}." :
+ "Created new collection in your Home project."
+
+ redirect_to newc, flash: {'message' => msg}
+ end
+
+ def report_issue_popup
+ respond_to do |format|
+ format.js
+ format.html
+ end
+ end
+
+ def report_issue
+ logger.warn "report_issue: #{params.inspect}"
+
+ respond_to do |format|
+ IssueReporter.send_report(current_user, params).deliver
+ format.js {render nothing: true}
+ end
+ end
+
+end
--- /dev/null
+class ApiClientAuthorizationsController < ApplicationController
+
+ def index_pane_list
+ %w(Recent Help)
+ end
+
+end
--- /dev/null
+class ApplicationController < ActionController::Base
+ include ArvadosApiClientHelper
+ include ApplicationHelper
+
+ respond_to :html, :json, :js
+ protect_from_forgery
+
+ ERROR_ACTIONS = [:render_error, :render_not_found]
+
+ around_filter :thread_clear
+ around_filter :set_thread_api_token
+ # Methods that don't require login should
+ # skip_around_filter :require_thread_api_token
+ around_filter :require_thread_api_token, except: ERROR_ACTIONS
+ before_filter :set_cache_buster
+ before_filter :accept_uuid_as_id_param, except: ERROR_ACTIONS
+ before_filter :check_user_agreements, except: ERROR_ACTIONS
+ before_filter :check_user_profile, except: ERROR_ACTIONS
+ before_filter :check_user_notifications, except: ERROR_ACTIONS
+ before_filter :load_filters_and_paging_params, except: ERROR_ACTIONS
+ before_filter :find_object_by_uuid, except: [:create, :index, :choose] + ERROR_ACTIONS
+ theme :select_theme
+
+ begin
+ rescue_from(ActiveRecord::RecordNotFound,
+ ActionController::RoutingError,
+ ActionController::UnknownController,
+ AbstractController::ActionNotFound,
+ with: :render_not_found)
+ rescue_from(Exception,
+ ActionController::UrlGenerationError,
+ with: :render_exception)
+ end
+
+ def set_cache_buster
+ response.headers["Cache-Control"] = "no-cache, no-store, max-age=0, must-revalidate"
+ response.headers["Pragma"] = "no-cache"
+ response.headers["Expires"] = "Fri, 01 Jan 1990 00:00:00 GMT"
+ end
+
+ def unprocessable(message=nil)
+ @errors ||= []
+
+ @errors << message if message
+ render_error status: 422
+ end
+
+ def render_error(opts={})
+ opts[:status] ||= 500
+ respond_to do |f|
+ # json must come before html here, so it gets used as the
+ # default format when js is requested by the client. This lets
+ # ajax:error callback parse the response correctly, even though
+ # the browser can't.
+ f.json { render opts.merge(json: {success: false, errors: @errors}) }
+ f.html { render({action: 'error'}.merge(opts)) }
+ end
+ end
+
+ def render_exception(e)
+ logger.error e.inspect
+ logger.error e.backtrace.collect { |x| x + "\n" }.join('') if e.backtrace
+ err_opts = {status: 422}
+ if e.is_a?(ArvadosApiClient::ApiError)
+ err_opts.merge!(action: 'api_error', locals: {api_error: e})
+ @errors = e.api_response[:errors]
+ elsif @object.andand.errors.andand.full_messages.andand.any?
+ @errors = @object.errors.full_messages
+ else
+ @errors = [e.to_s]
+ end
+ # Make user information available on the error page, falling back to the
+ # session cache if the API server is unavailable.
+ begin
+ load_api_token(session[:arvados_api_token])
+ rescue ArvadosApiClient::ApiError
+ unless session[:user].nil?
+ begin
+ Thread.current[:user] = User.new(session[:user])
+ rescue ArvadosApiClient::ApiError
+ # This can happen if User's columns are unavailable. Nothing to do.
+ end
+ end
+ end
+ # Preload projects trees for the template. If that's not doable, set empty
+ # trees so error page rendering can proceed. (It's easier to rescue the
+ # exception here than in a template.)
+ unless current_user.nil?
+ begin
+ build_project_trees
+ rescue ArvadosApiClient::ApiError
+ # Fall back to the default-setting code later.
+ end
+ end
+ @my_project_tree ||= []
+ @shared_project_tree ||= []
+ render_error(err_opts)
+ end
+
+ def render_not_found(e=ActionController::RoutingError.new("Path not found"))
+ logger.error e.inspect
+ @errors = ["Path not found"]
+ set_thread_api_token do
+ self.render_error(action: '404', status: 404)
+ end
+ end
+
+ # params[:order]:
+ #
+ # The order can be left empty to allow it to default.
+ # Or it can be a comma separated list of real database column names, one per model.
+ # Column names should always be qualified by a table name and a direction is optional, defaulting to asc
+ # (e.g. "collections.name" or "collections.name desc").
+ # If a column name is specified, that table will be sorted by that column.
+ # If there are objects from different models that will be shown (such as in Jobs and Pipelines tab),
+ # then a sort column name can optionally be specified for each model, passed as an comma-separated list (e.g. "jobs.script, pipeline_instances.name")
+ # Currently only one sort column name and direction can be specified for each model.
+ def load_filters_and_paging_params
+ if params[:order].blank?
+ @order = 'created_at desc'
+ elsif params[:order].is_a? Array
+ @order = params[:order]
+ else
+ begin
+ @order = JSON.load(params[:order])
+ rescue
+ @order = params[:order].split(',')
+ end
+ end
+ @order = [@order] unless @order.is_a? Array
+
+ @limit ||= 200
+ if params[:limit]
+ @limit = params[:limit].to_i
+ end
+
+ @offset ||= 0
+ if params[:offset]
+ @offset = params[:offset].to_i
+ end
+
+ @filters ||= []
+ if params[:filters]
+ filters = params[:filters]
+ if filters.is_a? String
+ filters = Oj.load filters
+ elsif filters.is_a? Array
+ filters = filters.collect do |filter|
+ if filter.is_a? String
+ # Accept filters[]=["foo","=","bar"]
+ Oj.load filter
+ else
+ # Accept filters=[["foo","=","bar"]]
+ filter
+ end
+ end
+ end
+ # After this, params[:filters] can be trusted to be an array of arrays:
+ params[:filters] = filters
+ @filters += filters
+ end
+ end
+
+ def find_objects_for_index
+ @objects ||= model_class
+ @objects = @objects.filter(@filters).limit(@limit).offset(@offset)
+ @objects.fetch_multiple_pages(false)
+ end
+
+ def render_index
+ respond_to do |f|
+ f.json {
+ if params[:partial]
+ @next_page_href = next_page_href(partial: params[:partial], filters: @filters.to_json)
+ render json: {
+ content: render_to_string(partial: "show_#{params[:partial]}",
+ formats: [:html]),
+ next_page_href: @next_page_href
+ }
+ else
+ render json: @objects
+ end
+ }
+ f.html {
+ if params[:tab_pane]
+ render_pane params[:tab_pane]
+ else
+ render
+ end
+ }
+ f.js { render }
+ end
+ end
+
+ helper_method :render_pane
+ def render_pane tab_pane, opts={}
+ render_opts = {
+ partial: 'show_' + tab_pane.downcase,
+ locals: {
+ comparable: self.respond_to?(:compare),
+ objects: @objects,
+ tab_pane: tab_pane
+ }.merge(opts[:locals] || {})
+ }
+ if opts[:to_string]
+ render_to_string render_opts
+ else
+ render render_opts
+ end
+ end
+
+ def index
+ find_objects_for_index if !@objects
+ render_index
+ end
+
+ helper_method :next_page_offset
+ def next_page_offset objects=nil
+ if !objects
+ objects = @objects
+ end
+ if objects.respond_to?(:result_offset) and
+ objects.respond_to?(:result_limit) and
+ objects.respond_to?(:items_available)
+ next_offset = objects.result_offset + objects.result_limit
+ if next_offset < objects.items_available
+ next_offset
+ else
+ nil
+ end
+ end
+ end
+
+ helper_method :next_page_href
+ def next_page_href with_params={}
+ if next_page_offset
+ url_for with_params.merge(offset: next_page_offset)
+ end
+ end
+
+ def show
+ if !@object
+ return render_not_found("object not found")
+ end
+ respond_to do |f|
+ f.json do
+ extra_attrs = { href: url_for(action: :show, id: @object) }
+ @object.textile_attributes.each do |textile_attr|
+ extra_attrs.merge!({ "#{textile_attr}Textile" => view_context.render_markup(@object.attributes[textile_attr]) })
+ end
+ render json: @object.attributes.merge(extra_attrs)
+ end
+ f.html {
+ if params['tab_pane']
+ render_pane(if params['tab_pane'].is_a? Hash then params['tab_pane']["name"] else params['tab_pane'] end)
+ elsif request.method.in? ['GET', 'HEAD']
+ render
+ else
+ redirect_to (params[:return_to] ||
+ polymorphic_url(@object,
+ anchor: params[:redirect_to_anchor]))
+ end
+ }
+ f.js { render }
+ end
+ end
+
+ def choose
+ params[:limit] ||= 40
+ respond_to do |f|
+ if params[:partial]
+ f.json {
+ find_objects_for_index if !@objects
+ render json: {
+ content: render_to_string(partial: "choose_rows.html",
+ formats: [:html]),
+ next_page_href: next_page_href(partial: params[:partial])
+ }
+ }
+ end
+ f.js {
+ find_objects_for_index if !@objects
+ render partial: 'choose', locals: {multiple: params[:multiple]}
+ }
+ end
+ end
+
+ def render_content
+ if !@object
+ return render_not_found("object not found")
+ end
+ end
+
+ def new
+ @object = model_class.new
+ end
+
+ def update
+ @updates ||= params[@object.resource_param_name.to_sym]
+ @updates.keys.each do |attr|
+ if @object.send(attr).is_a? Hash
+ if @updates[attr].is_a? String
+ @updates[attr] = Oj.load @updates[attr]
+ end
+ if params[:merge] || params["merge_#{attr}".to_sym]
+ # Merge provided Hash with current Hash, instead of
+ # replacing.
+ @updates[attr] = @object.send(attr).with_indifferent_access.
+ deep_merge(@updates[attr].with_indifferent_access)
+ end
+ end
+ end
+ if @object.update_attributes @updates
+ show
+ else
+ self.render_error status: 422
+ end
+ end
+
+ def create
+ @new_resource_attrs ||= params[model_class.to_s.underscore.singularize]
+ @new_resource_attrs ||= {}
+ @new_resource_attrs.reject! { |k,v| k.to_s == 'uuid' }
+ @object ||= model_class.new @new_resource_attrs, params["options"]
+
+ if @object.save
+ show
+ else
+ render_error status: 422
+ end
+ end
+
+ # Clone the given object, merging any attribute values supplied as
+ # with a create action.
+ def copy
+ @new_resource_attrs ||= params[model_class.to_s.underscore.singularize]
+ @new_resource_attrs ||= {}
+ @object = @object.dup
+ @object.update_attributes @new_resource_attrs
+ if not @new_resource_attrs[:name] and @object.respond_to? :name
+ if @object.name and @object.name != ''
+ @object.name = "Copy of #{@object.name}"
+ else
+ @object.name = ""
+ end
+ end
+ @object.save!
+ show
+ end
+
+ def destroy
+ if @object.destroy
+ respond_to do |f|
+ f.json { render json: @object }
+ f.html {
+ redirect_to(params[:return_to] || :back)
+ }
+ f.js { render }
+ end
+ else
+ self.render_error status: 422
+ end
+ end
+
+ def current_user
+ Thread.current[:user]
+ end
+
+ def model_class
+ controller_name.classify.constantize
+ end
+
+ def breadcrumb_page_name
+ (@breadcrumb_page_name ||
+ (@object.friendly_link_name if @object.respond_to? :friendly_link_name) ||
+ action_name)
+ end
+
+ def index_pane_list
+ %w(Recent)
+ end
+
+ def show_pane_list
+ %w(Attributes Advanced)
+ end
+
+ protected
+
+ def strip_token_from_path(path)
+ path.sub(/([\?&;])api_token=[^&;]*[&;]?/, '\1')
+ end
+
+ def redirect_to_login
+ respond_to do |f|
+ f.html {
+ if request.method.in? ['GET', 'HEAD']
+ redirect_to arvados_api_client.arvados_login_url(return_to: strip_token_from_path(request.url))
+ else
+ flash[:error] = "Either you are not logged in, or your session has timed out. I can't automatically log you in and re-attempt this request."
+ redirect_to :back
+ end
+ }
+ f.json {
+ @errors = ['You do not seem to be logged in. You did not supply an API token with this request, and your session (if any) has timed out.']
+ self.render_error status: 422
+ }
+ end
+ false # For convenience to return from callbacks
+ end
+
+ def using_specific_api_token(api_token, opts={})
+ start_values = {}
+ [:arvados_api_token, :user].each do |key|
+ start_values[key] = Thread.current[key]
+ end
+ if opts.fetch(:load_user, true)
+ load_api_token(api_token)
+ else
+ Thread.current[:arvados_api_token] = api_token
+ Thread.current[:user] = nil
+ end
+ begin
+ yield
+ ensure
+ start_values.each_key { |key| Thread.current[key] = start_values[key] }
+ end
+ end
+
+
+ def accept_uuid_as_id_param
+ if params[:id] and params[:id].match /\D/
+ params[:uuid] = params.delete :id
+ end
+ end
+
+ def find_object_by_uuid
+ begin
+ if not model_class
+ @object = nil
+ elsif not params[:uuid].is_a?(String)
+ @object = model_class.where(uuid: params[:uuid]).first
+ elsif params[:uuid].empty?
+ @object = nil
+ elsif (model_class != Link and
+ resource_class_for_uuid(params[:uuid]) == Link)
+ @name_link = Link.find(params[:uuid])
+ @object = model_class.find(@name_link.head_uuid)
+ else
+ @object = model_class.find(params[:uuid])
+ end
+ rescue ArvadosApiClient::NotFoundException, RuntimeError => error
+ if error.is_a?(RuntimeError) and (error.message !~ /^argument to find\(/)
+ raise
+ end
+ render_not_found(error)
+ return false
+ end
+ end
+
+ def thread_clear
+ load_api_token(nil)
+ Rails.cache.delete_matched(/^request_#{Thread.current.object_id}_/)
+ yield
+ Rails.cache.delete_matched(/^request_#{Thread.current.object_id}_/)
+ end
+
+ # Set up the thread with the given API token and associated user object.
+ def load_api_token(new_token)
+ Thread.current[:arvados_api_token] = new_token
+ if new_token.nil?
+ Thread.current[:user] = nil
+ else
+ Thread.current[:user] = User.current
+ end
+ end
+
+ # If there's a valid api_token parameter, set up the session with that
+ # user's information. Return true if the method redirects the request
+ # (usually a post-login redirect); false otherwise.
+ def setup_user_session
+ return false unless params[:api_token]
+ Thread.current[:arvados_api_token] = params[:api_token]
+ begin
+ user = User.current
+ rescue ArvadosApiClient::NotLoggedInException
+ false # We may redirect to login, or not, based on the current action.
+ else
+ session[:arvados_api_token] = params[:api_token]
+ # If we later have trouble contacting the API server, we still want
+ # to be able to render basic user information in the UI--see
+ # render_exception above. We store that in the session here. This is
+ # not intended to be used as a general-purpose cache. See #2891.
+ session[:user] = {
+ uuid: user.uuid,
+ email: user.email,
+ first_name: user.first_name,
+ last_name: user.last_name,
+ is_active: user.is_active,
+ is_admin: user.is_admin,
+ prefs: user.prefs
+ }
+
+ if !request.format.json? and request.method.in? ['GET', 'HEAD']
+ # Repeat this request with api_token in the (new) session
+ # cookie instead of the query string. This prevents API
+ # tokens from appearing in (and being inadvisedly copied
+ # and pasted from) browser Location bars.
+ redirect_to strip_token_from_path(request.fullpath)
+ true
+ else
+ false
+ end
+ ensure
+ Thread.current[:arvados_api_token] = nil
+ end
+ end
+
+ # Save the session API token in thread-local storage, and yield.
+ # This method also takes care of session setup if the request
+ # provides a valid api_token parameter.
+ # If a token is unavailable or expired, the block is still run, with
+ # a nil token.
+ def set_thread_api_token
+ if Thread.current[:arvados_api_token]
+ yield # An API token has already been found - pass it through.
+ return
+ elsif setup_user_session
+ return # A new session was set up and received a response.
+ end
+
+ begin
+ load_api_token(session[:arvados_api_token])
+ yield
+ rescue ArvadosApiClient::NotLoggedInException
+ # If we got this error with a token, it must've expired.
+ # Retry the request without a token.
+ unless Thread.current[:arvados_api_token].nil?
+ load_api_token(nil)
+ yield
+ end
+ ensure
+ # Remove token in case this Thread is used for anything else.
+ load_api_token(nil)
+ end
+ end
+
+ # Redirect to login/welcome if client provided expired API token (or none at all)
+ def require_thread_api_token
+ if Thread.current[:arvados_api_token]
+ yield
+ elsif session[:arvados_api_token]
+ # Expired session. Clear it before refreshing login so that,
+ # if this login procedure fails, we end up showing the "please
+ # log in" page instead of getting stuck in a redirect loop.
+ session.delete :arvados_api_token
+ redirect_to_login
+ else
+ redirect_to welcome_users_path(return_to: request.fullpath)
+ end
+ end
+
+ def ensure_current_user_is_admin
+ unless current_user and current_user.is_admin
+ @errors = ['Permission denied']
+ self.render_error status: 401
+ end
+ end
+
+ helper_method :unsigned_user_agreements
+ def unsigned_user_agreements
+ @signed_ua_uuids ||= UserAgreement.signatures.map &:head_uuid
+ @unsigned_user_agreements ||= UserAgreement.all.map do |ua|
+ if not @signed_ua_uuids.index ua.uuid
+ Collection.find(ua.uuid)
+ end
+ end.compact
+ end
+
+ def check_user_agreements
+ if current_user && !current_user.is_active
+ if not current_user.is_invited
+ return redirect_to inactive_users_path(return_to: request.fullpath)
+ end
+ if unsigned_user_agreements.empty?
+ # No agreements to sign. Perhaps we just need to ask?
+ current_user.activate
+ if !current_user.is_active
+ logger.warn "#{current_user.uuid.inspect}: " +
+ "No user agreements to sign, but activate failed!"
+ end
+ end
+ if !current_user.is_active
+ redirect_to user_agreements_path(return_to: request.fullpath)
+ end
+ end
+ true
+ end
+
+ def check_user_profile
+ if request.method.downcase != 'get' || params[:partial] ||
+ params[:tab_pane] || params[:action_method] ||
+ params[:action] == 'setup_popup'
+ return true
+ end
+
+ if missing_required_profile?
+ redirect_to profile_user_path(current_user.uuid, return_to: request.fullpath)
+ end
+ true
+ end
+
+ helper_method :missing_required_profile?
+ def missing_required_profile?
+ missing_required = false
+
+ profile_config = Rails.configuration.user_profile_form_fields
+ if current_user && profile_config
+ current_user_profile = current_user.prefs[:profile]
+ profile_config.kind_of?(Array) && profile_config.andand.each do |entry|
+ if entry['required']
+ if !current_user_profile ||
+ !current_user_profile[entry['key'].to_sym] ||
+ current_user_profile[entry['key'].to_sym].empty?
+ missing_required = true
+ break
+ end
+ end
+ end
+ end
+
+ missing_required
+ end
+
+ def select_theme
+ return Rails.configuration.arvados_theme
+ end
+
+ @@notification_tests = []
+
+ @@notification_tests.push lambda { |controller, current_user|
+ AuthorizedKey.limit(1).where(authorized_user_uuid: current_user.uuid).each do
+ return nil
+ end
+ return lambda { |view|
+ view.render partial: 'notifications/ssh_key_notification'
+ }
+ }
+
+ @@notification_tests.push lambda { |controller, current_user|
+ Collection.limit(1).where(created_by: current_user.uuid).each do
+ return nil
+ end
+ return lambda { |view|
+ view.render partial: 'notifications/collections_notification'
+ }
+ }
+
+ @@notification_tests.push lambda { |controller, current_user|
+ PipelineInstance.limit(1).where(created_by: current_user.uuid).each do
+ return nil
+ end
+ return lambda { |view|
+ view.render partial: 'notifications/pipelines_notification'
+ }
+ }
+
+ def check_user_notifications
+ return if params['tab_pane']
+
+ @notification_count = 0
+ @notifications = []
+
+ if current_user.andand.is_active
+ @showallalerts = false
+ @@notification_tests.each do |t|
+ a = t.call(self, current_user)
+ if a
+ @notification_count += 1
+ @notifications.push a
+ end
+ end
+ end
+
+ if @notification_count == 0
+ @notification_count = ''
+ end
+ end
+
+ helper_method :all_projects
+ def all_projects
+ @all_projects ||= Group.
+ filter([['group_class','=','project']]).order('name')
+ end
+
+ helper_method :my_projects
+ def my_projects
+ return @my_projects if @my_projects
+ @my_projects = []
+ root_of = {}
+ all_projects.each do |g|
+ root_of[g.uuid] = g.owner_uuid
+ @my_projects << g
+ end
+ done = false
+ while not done
+ done = true
+ root_of = root_of.each_with_object({}) do |(child, parent), h|
+ if root_of[parent]
+ h[child] = root_of[parent]
+ done = false
+ else
+ h[child] = parent
+ end
+ end
+ end
+ @my_projects = @my_projects.select do |g|
+ root_of[g.uuid] == current_user.uuid
+ end
+ end
+
+ helper_method :projects_shared_with_me
+ def projects_shared_with_me
+ my_project_uuids = my_projects.collect &:uuid
+ all_projects.reject { |x| x.uuid.in? my_project_uuids }
+ end
+
+ helper_method :recent_jobs_and_pipelines
+ def recent_jobs_and_pipelines
+ (Job.limit(10) |
+ PipelineInstance.limit(10)).
+ sort_by do |x|
+ (x.finished_at || x.started_at rescue nil) || x.modified_at || x.created_at
+ end.reverse
+ end
+
+ helper_method :running_pipelines
+ def running_pipelines
+ pi = PipelineInstance.order(["started_at asc", "created_at asc"]).filter([["state", "in", ["RunningOnServer", "RunningOnClient"]]])
+ jobs = {}
+ pi.each do |pl|
+ pl.components.each do |k,v|
+ if v.is_a? Hash and v[:job]
+ jobs[v[:job][:uuid]] = {}
+ end
+ end
+ end
+
+ if jobs.keys.any?
+ Job.filter([["uuid", "in", jobs.keys]]).each do |j|
+ jobs[j[:uuid]] = j
+ end
+
+ pi.each do |pl|
+ pl.components.each do |k,v|
+ if v.is_a? Hash and v[:job]
+ v[:job] = jobs[v[:job][:uuid]]
+ end
+ end
+ end
+ end
+
+ pi
+ end
+
+ helper_method :finished_pipelines
+ def finished_pipelines lim
+ PipelineInstance.limit(lim).order(["finished_at desc"]).filter([["state", "in", ["Complete", "Failed", "Paused"]], ["finished_at", "!=", nil]])
+ end
+
+ helper_method :recent_collections
+ def recent_collections lim
+ c = Collection.limit(lim).order(["modified_at desc"]).filter([["owner_uuid", "is_a", "arvados#group"]])
+ own = {}
+ Group.filter([["uuid", "in", c.map(&:owner_uuid)]]).each do |g|
+ own[g[:uuid]] = g
+ end
+ {collections: c, owners: own}
+ end
+
+ helper_method :my_project_tree
+ def my_project_tree
+ build_project_trees
+ @my_project_tree
+ end
+
+ helper_method :shared_project_tree
+ def shared_project_tree
+ build_project_trees
+ @shared_project_tree
+ end
+
+ def build_project_trees
+ return if @my_project_tree and @shared_project_tree
+ parent_of = {current_user.uuid => 'me'}
+ all_projects.each do |ob|
+ parent_of[ob.uuid] = ob.owner_uuid
+ end
+ children_of = {false => [], 'me' => [current_user]}
+ all_projects.each do |ob|
+ if ob.owner_uuid != current_user.uuid and
+ not parent_of.has_key? ob.owner_uuid
+ parent_of[ob.uuid] = false
+ end
+ children_of[parent_of[ob.uuid]] ||= []
+ children_of[parent_of[ob.uuid]] << ob
+ end
+ buildtree = lambda do |children_of, root_uuid=false|
+ tree = {}
+ children_of[root_uuid].andand.each do |ob|
+ tree[ob] = buildtree.call(children_of, ob.uuid)
+ end
+ tree
+ end
+ sorted_paths = lambda do |tree, depth=0|
+ paths = []
+ tree.keys.sort_by { |ob|
+ ob.is_a?(String) ? ob : ob.friendly_link_name
+ }.each do |ob|
+ paths << {object: ob, depth: depth}
+ paths += sorted_paths.call tree[ob], depth+1
+ end
+ paths
+ end
+ @my_project_tree =
+ sorted_paths.call buildtree.call(children_of, 'me')
+ @shared_project_tree =
+ sorted_paths.call({'Projects shared with me' =>
+ buildtree.call(children_of, false)})
+ end
+
+ helper_method :get_object
+ def get_object uuid
+ if @get_object.nil? and @objects
+ @get_object = @objects.each_with_object({}) do |object, h|
+ h[object.uuid] = object
+ end
+ end
+ @get_object ||= {}
+ @get_object[uuid]
+ end
+
+ helper_method :project_breadcrumbs
+ def project_breadcrumbs
+ crumbs = []
+ current = @name_link || @object
+ while current
+ # Halt if a group ownership loop is detected. API should refuse
+ # to produce this state, but it could still arise from a race
+ # condition when group ownership changes between our find()
+ # queries.
+ break if crumbs.collect(&:uuid).include? current.uuid
+
+ if current.is_a?(Group) and current.group_class == 'project'
+ crumbs.prepend current
+ end
+ if current.is_a? Link
+ current = Group.find?(current.tail_uuid)
+ else
+ current = Group.find?(current.owner_uuid)
+ end
+ end
+ crumbs
+ end
+
+ helper_method :current_project_uuid
+ def current_project_uuid
+ if @object.is_a? Group and @object.group_class == 'project'
+ @object.uuid
+ elsif @name_link.andand.tail_uuid
+ @name_link.tail_uuid
+ elsif @object and resource_class_for_uuid(@object.owner_uuid) == Group
+ @object.owner_uuid
+ else
+ nil
+ end
+ end
+
+ # helper method to get links for given object or uuid
+ helper_method :links_for_object
+ def links_for_object object_or_uuid
+ raise ArgumentError, 'No input argument' unless object_or_uuid
+ preload_links_for_objects([object_or_uuid])
+ uuid = object_or_uuid.is_a?(String) ? object_or_uuid : object_or_uuid.uuid
+ @all_links_for[uuid] ||= []
+ end
+
+ # helper method to preload links for given objects and uuids
+ helper_method :preload_links_for_objects
+ def preload_links_for_objects objects_and_uuids
+ @all_links_for ||= {}
+
+ raise ArgumentError, 'Argument is not an array' unless objects_and_uuids.is_a? Array
+ return @all_links_for if objects_and_uuids.empty?
+
+ uuids = objects_and_uuids.collect { |x| x.is_a?(String) ? x : x.uuid }
+
+ # if already preloaded for all of these uuids, return
+ if not uuids.select { |x| @all_links_for[x].nil? }.any?
+ return @all_links_for
+ end
+
+ uuids.each do |x|
+ @all_links_for[x] = []
+ end
+
+ # TODO: make sure we get every page of results from API server
+ Link.filter([['head_uuid', 'in', uuids]]).each do |link|
+ @all_links_for[link.head_uuid] << link
+ end
+ @all_links_for
+ end
+
+ # helper method to get a certain number of objects of a specific type
+ # this can be used to replace any uses of: "dataclass.limit(n)"
+ helper_method :get_n_objects_of_class
+ def get_n_objects_of_class dataclass, size
+ @objects_map_for ||= {}
+
+ raise ArgumentError, 'Argument is not a data class' unless dataclass.is_a? Class and dataclass < ArvadosBase
+ raise ArgumentError, 'Argument is not a valid limit size' unless (size && size>0)
+
+ # if the objects_map_for has a value for this dataclass, and the
+ # size used to retrieve those objects is equal, return it
+ size_key = "#{dataclass.name}_size"
+ if @objects_map_for[dataclass.name] && @objects_map_for[size_key] &&
+ (@objects_map_for[size_key] == size)
+ return @objects_map_for[dataclass.name]
+ end
+
+ @objects_map_for[size_key] = size
+ @objects_map_for[dataclass.name] = dataclass.limit(size)
+ end
+
+ # helper method to get collections for the given uuid
+ helper_method :collections_for_object
+ def collections_for_object uuid
+ raise ArgumentError, 'No input argument' unless uuid
+ preload_collections_for_objects([uuid])
+ @all_collections_for[uuid] ||= []
+ end
+
+ # helper method to preload collections for the given uuids
+ helper_method :preload_collections_for_objects
+ def preload_collections_for_objects uuids
+ @all_collections_for ||= {}
+
+ raise ArgumentError, 'Argument is not an array' unless uuids.is_a? Array
+ return @all_collections_for if uuids.empty?
+
+ # if already preloaded for all of these uuids, return
+ if not uuids.select { |x| @all_collections_for[x].nil? }.any?
+ return @all_collections_for
+ end
+
+ uuids.each do |x|
+ @all_collections_for[x] = []
+ end
+
+ # TODO: make sure we get every page of results from API server
+ Collection.where(uuid: uuids).each do |collection|
+ @all_collections_for[collection.uuid] << collection
+ end
+ @all_collections_for
+ end
+
+ # helper method to get log collections for the given log
+ helper_method :log_collections_for_object
+ def log_collections_for_object log
+ raise ArgumentError, 'No input argument' unless log
+
+ preload_log_collections_for_objects([log])
+
+ uuid = log
+ fixup = /([a-f0-9]{32}\+\d+)(\+?.*)/.match(log)
+ if fixup && fixup.size>1
+ uuid = fixup[1]
+ end
+
+ @all_log_collections_for[uuid] ||= []
+ end
+
+ # helper method to preload collections for the given uuids
+ helper_method :preload_log_collections_for_objects
+ def preload_log_collections_for_objects logs
+ @all_log_collections_for ||= {}
+
+ raise ArgumentError, 'Argument is not an array' unless logs.is_a? Array
+ return @all_log_collections_for if logs.empty?
+
+ uuids = []
+ logs.each do |log|
+ fixup = /([a-f0-9]{32}\+\d+)(\+?.*)/.match(log)
+ if fixup && fixup.size>1
+ uuids << fixup[1]
+ else
+ uuids << log
+ end
+ end
+
+ # if already preloaded for all of these uuids, return
+ if not uuids.select { |x| @all_log_collections_for[x].nil? }.any?
+ return @all_log_collections_for
+ end
+
+ uuids.each do |x|
+ @all_log_collections_for[x] = []
+ end
+
+ # TODO: make sure we get every page of results from API server
+ Collection.where(uuid: uuids).each do |collection|
+ @all_log_collections_for[collection.uuid] << collection
+ end
+ @all_log_collections_for
+ end
+
+ # helper method to get object of a given dataclass and uuid
+ helper_method :object_for_dataclass
+ def object_for_dataclass dataclass, uuid
+ raise ArgumentError, 'No input argument dataclass' unless (dataclass && uuid)
+ preload_objects_for_dataclass(dataclass, [uuid])
+ @objects_for[uuid]
+ end
+
+ # helper method to preload objects for given dataclass and uuids
+ helper_method :preload_objects_for_dataclass
+ def preload_objects_for_dataclass dataclass, uuids
+ @objects_for ||= {}
+
+ raise ArgumentError, 'Argument is not a data class' unless dataclass.is_a? Class
+ raise ArgumentError, 'Argument is not an array' unless uuids.is_a? Array
+
+ return @objects_for if uuids.empty?
+
+ # if already preloaded for all of these uuids, return
+ if not uuids.select { |x| @objects_for[x].nil? }.any?
+ return @objects_for
+ end
+
+ dataclass.where(uuid: uuids).each do |obj|
+ @objects_for[obj.uuid] = obj
+ end
+ @objects_for
+ end
+
+ def wiselinks_layout
+ 'body'
+ end
+end
--- /dev/null
+class AuthorizedKeysController < ApplicationController
+ def index_pane_list
+ %w(Recent Help)
+ end
+
+ def new
+ super
+ @object.authorized_user_uuid = current_user.uuid if current_user
+ @object.key_type = 'SSH'
+ end
+
+ def create
+ defaults = { authorized_user_uuid: current_user.uuid, key_type: 'SSH' }
+ @object = AuthorizedKey.new defaults.merge(params[:authorized_key] || {})
+ super
+ end
+end
--- /dev/null
+require "arvados/keep"
+
+class CollectionsController < ApplicationController
+ include ActionController::Live
+
+ skip_around_filter(:require_thread_api_token,
+ only: [:show_file, :show_file_links])
+ skip_before_filter(:find_object_by_uuid,
+ only: [:provenance, :show_file, :show_file_links])
+ # We depend on show_file to display the user agreement:
+ skip_before_filter :check_user_agreements, only: :show_file
+ skip_before_filter :check_user_profile, only: :show_file
+
+ RELATION_LIMIT = 5
+
+ def show_pane_list
+ panes = %w(Files Upload Provenance_graph Used_by Advanced)
+ panes = panes - %w(Upload) unless (@object.editable? rescue false)
+ panes
+ end
+
+ def set_persistent
+ case params[:value]
+ when 'persistent', 'cache'
+ persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
+ ['link_class', '=', 'resources'],
+ ['name', '=', 'wants'],
+ ['tail_uuid', '=', current_user.uuid],
+ ['head_uuid', '=', @object.uuid]])
+ logger.debug persist_links.inspect
+ else
+ return unprocessable "Invalid value #{value.inspect}"
+ end
+ if params[:value] == 'persistent'
+ if not persist_links.any?
+ Link.create(link_class: 'resources',
+ name: 'wants',
+ tail_uuid: current_user.uuid,
+ head_uuid: @object.uuid)
+ end
+ else
+ persist_links.each do |link|
+ link.destroy || raise
+ end
+ end
+
+ respond_to do |f|
+ f.json { render json: @object }
+ end
+ end
+
+ def index
+ # API server index doesn't return manifest_text by default, but our
+ # callers want it unless otherwise specified.
+ @select ||= Collection.columns.map(&:name)
+ base_search = Collection.select(@select)
+ if params[:search].andand.length.andand > 0
+ tags = Link.where(any: ['contains', params[:search]])
+ @objects = (base_search.where(uuid: tags.collect(&:head_uuid)) |
+ base_search.where(any: ['contains', params[:search]])).
+ uniq { |c| c.uuid }
+ else
+ if params[:limit]
+ limit = params[:limit].to_i
+ else
+ limit = 100
+ end
+
+ if params[:offset]
+ offset = params[:offset].to_i
+ else
+ offset = 0
+ end
+
+ @objects = base_search.limit(limit).offset(offset)
+ end
+ @links = Link.where(head_uuid: @objects.collect(&:uuid))
+ @collection_info = {}
+ @objects.each do |c|
+ @collection_info[c.uuid] = {
+ tag_links: [],
+ wanted: false,
+ wanted_by_me: false,
+ provenance: [],
+ links: []
+ }
+ end
+ @links.each do |link|
+ @collection_info[link.head_uuid] ||= {}
+ info = @collection_info[link.head_uuid]
+ case link.link_class
+ when 'tag'
+ info[:tag_links] << link
+ when 'resources'
+ info[:wanted] = true
+ info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
+ when 'provenance'
+ info[:provenance] << link.name
+ end
+ info[:links] << link
+ end
+ @request_url = request.url
+
+ render_index
+ end
+
+ def show_file_links
+ Thread.current[:reader_tokens] = [params[:reader_token]]
+ return if false.equal?(find_object_by_uuid)
+ render layout: false
+ end
+
+ def show_file
+ # We pipe from arv-get to send the file to the user. Before we start it,
+ # we ask the API server if the file actually exists. This serves two
+ # purposes: it lets us return a useful status code for common errors, and
+ # helps us figure out which token to provide to arv-get.
+ coll = nil
+ tokens = [Thread.current[:arvados_api_token], params[:reader_token]].compact
+ usable_token = find_usable_token(tokens) do
+ coll = Collection.find(params[:uuid])
+ end
+
+ file_name = params[:file].andand.sub(/^(\.\/|\/|)/, './')
+ if usable_token.nil?
+ return # Response already rendered.
+ elsif file_name.nil? or not coll.manifest.has_file?(file_name)
+ return render_not_found
+ end
+
+ opts = params.merge(arvados_api_token: usable_token)
+
+ # Handle Range requests. Currently we support only 'bytes=0-....'
+ if request.headers.include? 'HTTP_RANGE'
+ if m = /^bytes=0-(\d+)/.match(request.headers['HTTP_RANGE'])
+ opts[:maxbytes] = m[1]
+ size = params[:size] || '*'
+ self.response.status = 206
+ self.response.headers['Content-Range'] = "bytes 0-#{m[1]}/#{size}"
+ end
+ end
+
+ ext = File.extname(params[:file])
+ self.response.headers['Content-Type'] =
+ Rack::Mime::MIME_TYPES[ext] || 'application/octet-stream'
+ if params[:size]
+ size = params[:size].to_i
+ if opts[:maxbytes]
+ size = [size, opts[:maxbytes].to_i].min
+ end
+ self.response.headers['Content-Length'] = size.to_s
+ end
+ self.response.headers['Content-Disposition'] = params[:disposition] if params[:disposition]
+ begin
+ file_enumerator(opts).each do |bytes|
+ response.stream.write bytes
+ end
+ ensure
+ response.stream.close
+ end
+ end
+
+ def sharing_scopes
+ ["GET /arvados/v1/collections/#{@object.uuid}", "GET /arvados/v1/collections/#{@object.uuid}/", "GET /arvados/v1/keep_services/accessible"]
+ end
+
+ def search_scopes
+ begin
+ ApiClientAuthorization.filter([['scopes', '=', sharing_scopes]]).results
+ rescue ArvadosApiClient::AccessForbiddenException
+ nil
+ end
+ end
+
+ def find_object_by_uuid
+ if not Keep::Locator.parse params[:id]
+ super
+ end
+ end
+
+ def show
+ return super if !@object
+ if current_user
+ if Keep::Locator.parse params["uuid"]
+ @same_pdh = Collection.filter([["portable_data_hash", "=", @object.portable_data_hash]])
+ if @same_pdh.results.size == 1
+ redirect_to collection_path(@same_pdh[0]["uuid"])
+ return
+ end
+ owners = @same_pdh.map(&:owner_uuid).to_a.uniq
+ preload_objects_for_dataclass Group, owners
+ preload_objects_for_dataclass User, owners
+ render 'hash_matches'
+ return
+ else
+ jobs_with = lambda do |conds|
+ Job.limit(RELATION_LIMIT).where(conds)
+ .results.sort_by { |j| j.finished_at || j.created_at }
+ end
+ @output_of = jobs_with.call(output: @object.portable_data_hash)
+ @log_of = jobs_with.call(log: @object.portable_data_hash)
+ @project_links = Link.limit(RELATION_LIMIT).order("modified_at DESC")
+ .where(head_uuid: @object.uuid, link_class: 'name').results
+ project_hash = Group.where(uuid: @project_links.map(&:tail_uuid)).to_hash
+ @projects = project_hash.values
+
+ @permissions = Link.limit(RELATION_LIMIT).order("modified_at DESC")
+ .where(head_uuid: @object.uuid, link_class: 'permission',
+ name: 'can_read').results
+ @logs = Log.limit(RELATION_LIMIT).order("created_at DESC")
+ .where(object_uuid: @object.uuid).results
+ @is_persistent = Link.limit(1)
+ .where(head_uuid: @object.uuid, tail_uuid: current_user.uuid,
+ link_class: 'resources', name: 'wants')
+ .results.any?
+ @search_sharing = search_scopes
+
+ if params["tab_pane"] == "Provenance_graph"
+ @prov_svg = ProvenanceHelper::create_provenance_graph(@object.provenance, "provenance_svg",
+ {:request => request,
+ :direction => :bottom_up,
+ :combine_jobs => :script_only}) rescue nil
+ end
+ if params["tab_pane"] == "Used_by"
+ @used_by_svg = ProvenanceHelper::create_provenance_graph(@object.used_by, "used_by_svg",
+ {:request => request,
+ :direction => :top_down,
+ :combine_jobs => :script_only,
+ :pdata_only => true}) rescue nil
+ end
+ end
+ end
+ super
+ end
+
+ def sharing_popup
+ @search_sharing = search_scopes
+ render("sharing_popup.js", content_type: "text/javascript")
+ end
+
+ helper_method :download_link
+
+ def download_link
+ collections_url + "/download/#{@object.uuid}/#{@search_sharing.first.api_token}/"
+ end
+
+ def share
+ ApiClientAuthorization.create(scopes: sharing_scopes)
+ sharing_popup
+ end
+
+ def unshare
+ search_scopes.each do |s|
+ s.destroy
+ end
+ sharing_popup
+ end
+
+ protected
+
+ def find_usable_token(token_list)
+ # Iterate over every given token to make it the current token and
+ # yield the given block.
+ # If the block succeeds, return the token it used.
+ # Otherwise, render an error response based on the most specific
+ # error we encounter, and return nil.
+ most_specific_error = [401]
+ token_list.each do |api_token|
+ begin
+ # We can't load the corresponding user, because the token may not
+ # be scoped for that.
+ using_specific_api_token(api_token, load_user: false) do
+ yield
+ return api_token
+ end
+ rescue ArvadosApiClient::ApiError => error
+ if error.api_status >= most_specific_error.first
+ most_specific_error = [error.api_status, error]
+ end
+ end
+ end
+ case most_specific_error.shift
+ when 401, 403
+ redirect_to_login
+ when 404
+ render_not_found(*most_specific_error)
+ end
+ return nil
+ end
+
+ def file_enumerator(opts)
+ FileStreamer.new opts
+ end
+
+ class FileStreamer
+ include ArvadosApiClientHelper
+ def initialize(opts={})
+ @opts = opts
+ end
+ def each
+ return unless @opts[:uuid] && @opts[:file]
+
+ env = Hash[ENV].dup
+
+ require 'uri'
+ u = URI.parse(arvados_api_client.arvados_v1_base)
+ env['ARVADOS_API_HOST'] = "#{u.host}:#{u.port}"
+ env['ARVADOS_API_TOKEN'] = @opts[:arvados_api_token]
+ env['ARVADOS_API_HOST_INSECURE'] = "true" if Rails.configuration.arvados_insecure_https
+
+ bytesleft = @opts[:maxbytes].andand.to_i || 2**16
+ io = IO.popen([env, 'arv-get', "#{@opts[:uuid]}/#{@opts[:file]}"], 'rb')
+ while bytesleft > 0 && (buf = io.read([bytesleft, 2**16].min)) != nil
+ # shrink the bytesleft count, if we were given a maximum byte
+ # count to read
+ if @opts.include? :maxbytes
+ bytesleft = bytesleft - buf.length
+ end
+ yield buf
+ end
+ io.close
+ # "If ios is opened by IO.popen, close sets $?."
+ # http://www.ruby-doc.org/core-2.1.3/IO.html#method-i-close
+ Rails.logger.warn("#{@opts[:uuid]}/#{@opts[:file]}: #{$?}") if $? != 0
+ end
+ end
+end
--- /dev/null
+class GroupsController < ApplicationController
+ def index
+ @groups = Group.filter [['group_class', '!=', 'project']]
+ @group_uuids = @groups.collect &:uuid
+ @links_from = Link.where link_class: 'permission', tail_uuid: @group_uuids
+ @links_to = Link.where link_class: 'permission', head_uuid: @group_uuids
+ render_index
+ end
+
+ def show
+ if @object.group_class == 'project'
+ redirect_to(project_path(@object))
+ else
+ super
+ end
+ end
+end
--- /dev/null
+class HumansController < ApplicationController
+end
--- /dev/null
+class JobTasksController < ApplicationController
+end
--- /dev/null
+class JobsController < ApplicationController
+ include JobsHelper
+
+ def generate_provenance(jobs)
+ return if params['tab_pane'] != "Provenance"
+
+ nodes = {}
+ collections = []
+ hashes = []
+ jobs.each do |j|
+ nodes[j[:uuid]] = j
+ hashes << j[:output]
+ ProvenanceHelper::find_collections(j[:script_parameters]) do |hash, uuid|
+ collections << uuid if uuid
+ hashes << hash if hash
+ end
+ nodes[j[:script_version]] = {:uuid => j[:script_version]}
+ end
+
+ Collection.where(uuid: collections).each do |c|
+ nodes[c[:portable_data_hash]] = c
+ end
+
+ Collection.where(portable_data_hash: hashes).each do |c|
+ nodes[c[:portable_data_hash]] = c
+ end
+
+ @svg = ProvenanceHelper::create_provenance_graph nodes, "provenance_svg", {
+ :request => request,
+ :all_script_parameters => true,
+ :script_version_nodes => true}
+ end
+
+ def index
+ @svg = ""
+ if params[:uuid]
+ @objects = Job.where(uuid: params[:uuid])
+ generate_provenance(@objects)
+ render_index
+ else
+ @limit = 20
+ super
+ end
+ end
+
+ def cancel
+ @object.cancel
+ if params[:return_to]
+ redirect_to params[:return_to]
+ else
+ redirect_to @object
+ end
+ end
+
+ def show
+ generate_provenance([@object])
+ super
+ end
+
+ def logs
+ @logs = Log.select(%w(event_type object_uuid event_at properties))
+ .order('event_at DESC')
+ .filter([["event_type", "=", "stderr"],
+ ["object_uuid", "in", [@object.uuid]]])
+ .limit(500)
+ .results
+ .to_a
+ .map{ |e| e.serializable_hash.merge({ 'prepend' => true }) }
+ respond_to do |format|
+ format.json { render json: @logs }
+ end
+ end
+
+ def index_pane_list
+ if params[:uuid]
+ %w(Recent Provenance)
+ else
+ %w(Recent)
+ end
+ end
+
+ def show_pane_list
+ %w(Status Log Details Provenance Advanced)
+ end
+end
--- /dev/null
+class KeepDisksController < ApplicationController
+ def create
+ defaults = { is_readable: true, is_writable: true }
+ @object = KeepDisk.new defaults.merge(params[:keep_disk] || {})
+ super
+ end
+
+ def index
+ # Retrieve cache age histogram info from logs.
+
+ # In the logs we expect to find it in an ordered list with entries
+ # of the form (mtime, disk proportion free).
+
+ # An entry of the form (1388747781, 0.52) means that if we deleted
+ # the oldest non-presisted blocks until we had 52% of the disk
+ # free, then all blocks with an mtime greater than 1388747781
+ # would be preserved.
+
+ # The chart we want to produce, will tell us how much of the disk
+ # will be free if we use a cache age of x days. Therefore we will
+ # produce output specifying the age, cache and persisted. age is
+ # specified in milliseconds. cache is the size of the cache if we
+ # delete all blocks older than age. persistent is the size of the
+ # persisted blocks. It is constant regardless of age, but it lets
+ # us show a stacked graph.
+
+ # Finally each entry in cache_age_histogram is a dictionary,
+ # because that's what our charting package wats.
+
+ @cache_age_histogram = []
+ @histogram_pretty_date = nil
+ histogram_log = Log.
+ filter([[:event_type, '=', 'block-age-free-space-histogram']]).
+ order(:created_at => :desc).
+ limit(1)
+ histogram_log.each do |log_entry|
+ # We expect this block to only execute at most once since we
+ # specified limit(1)
+ @cache_age_histogram = log_entry['properties'][:histogram]
+ # Javascript wants dates in milliseconds.
+ histogram_date_ms = log_entry['event_at'].to_i * 1000
+ @histogram_pretty_date = log_entry['event_at'].strftime('%b %-d, %Y')
+
+ total_free_cache = @cache_age_histogram[-1][1]
+ persisted_storage = 1 - total_free_cache
+ @cache_age_histogram.map! { |x| {:age => histogram_date_ms - x[0]*1000,
+ :cache => total_free_cache - x[1],
+ :persisted => persisted_storage} }
+ end
+
+ # Do the regular control work needed.
+ super
+ end
+end
--- /dev/null
+class KeepServicesController < ApplicationController
+end
--- /dev/null
+class LinksController < ApplicationController
+ def show
+ if @object.link_class == 'name' and
+ Collection == ArvadosBase::resource_class_for_uuid(@object.head_uuid)
+ return redirect_to collection_path(@object.uuid)
+ end
+ super
+ end
+end
--- /dev/null
+class LogsController < ApplicationController
+ before_filter :ensure_current_user_is_admin
+end
--- /dev/null
+class NodesController < ApplicationController
+end
--- /dev/null
+class PipelineInstancesController < ApplicationController
+ skip_before_filter :find_object_by_uuid, only: :compare
+ before_filter :find_objects_by_uuid, only: :compare
+ include PipelineInstancesHelper
+ include PipelineComponentsHelper
+
+ def copy
+ template = PipelineTemplate.find?(@object.pipeline_template_uuid)
+
+ source = @object
+ @object = PipelineInstance.new
+ @object.pipeline_template_uuid = source.pipeline_template_uuid
+
+ if params['components'] == 'use_latest' and template
+ @object.components = template.components.deep_dup
+ @object.components.each do |cname, component|
+ # Go through the script parameters of each component
+ # that are marked as user input and copy them over.
+ # Skip any components that are not present in the
+ # source instance (there's nothing to copy)
+ if source.components.include? cname
+ component[:script_parameters].each do |pname, val|
+ if val.is_a? Hash and val[:dataclass]
+ # this is user-inputtable, so check the value from the source pipeline
+ srcvalue = source.components[cname][:script_parameters][pname]
+ if not srcvalue.nil?
+ component[:script_parameters][pname] = srcvalue
+ end
+ end
+ end
+ end
+ end
+ else
+ @object.components = source.components.deep_dup
+ end
+
+ if params['script'] == 'use_same'
+ # Go through each component and copy the script_version from each job.
+ @object.components.each do |cname, component|
+ if source.components.include? cname and source.components[cname][:job]
+ component[:script_version] = source.components[cname][:job][:script_version]
+ end
+ end
+ end
+
+ @object.components.each do |cname, component|
+ component.delete :job
+ end
+ @object.state = 'New'
+
+ # set owner_uuid to that of source, provided it is a project and wriable by current user
+ current_project = Group.find(source.owner_uuid) rescue nil
+ if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
+ @object.owner_uuid = source.owner_uuid
+ end
+
+ super
+ end
+
+ def update
+ @updates ||= params[@object.class.to_s.underscore.singularize.to_sym]
+ if (components = @updates[:components])
+ components.each do |cname, component|
+ if component[:script_parameters]
+ component[:script_parameters].each do |param, value_info|
+ if value_info.is_a? Hash
+ value_info_partitioned = value_info[:value].partition('/') if value_info[:value].andand.class.eql?(String)
+ value_info_value = value_info_partitioned ? value_info_partitioned[0] : value_info[:value]
+ value_info_class = resource_class_for_uuid value_info_value
+ if value_info_class == Link
+ # Use the link target, not the link itself, as script
+ # parameter; but keep the link info around as well.
+ link = Link.find value_info[:value]
+ value_info[:value] = link.head_uuid
+ value_info[:link_uuid] = link.uuid
+ value_info[:link_name] = link.name
+ else
+ # Delete stale link_uuid and link_name data.
+ value_info[:link_uuid] = nil
+ value_info[:link_name] = nil
+ end
+ if value_info_class == Collection
+ # to ensure reproducibility, the script_parameter for a
+ # collection should be the portable_data_hash
+ # keep the collection name and uuid for human-readability
+ obj = Collection.find value_info_value
+ if value_info_partitioned
+ value_info[:value] = obj.portable_data_hash + value_info_partitioned[1] + value_info_partitioned[2]
+ value_info[:selection_name] = obj.name ? obj.name + value_info_partitioned[1] + value_info_partitioned[2] : obj.name
+ else
+ value_info[:value] = obj.portable_data_hash
+ value_info[:selection_name] = obj.name
+ end
+ value_info[:selection_uuid] = obj.uuid
+ end
+ end
+ end
+ end
+ end
+ end
+ super
+ end
+
+ def graph(pipelines)
+ return nil, nil if params['tab_pane'] != "Graph"
+
+ provenance = {}
+ pips = {}
+ n = 1
+
+ # When comparing more than one pipeline, "pips" stores bit fields that
+ # indicates which objects are part of which pipelines.
+
+ pipelines.each do |p|
+ collections = []
+ hashes = []
+ jobs = []
+
+ p[:components].each do |k, v|
+ provenance["component_#{p[:uuid]}_#{k}"] = v
+
+ collections << v[:output_uuid] if v[:output_uuid]
+ jobs << v[:job][:uuid] if v[:job]
+ end
+
+ jobs = jobs.compact.uniq
+ if jobs.any?
+ Job.where(uuid: jobs).each do |j|
+ job_uuid = j.uuid
+
+ provenance[job_uuid] = j
+ pips[job_uuid] = 0 unless pips[job_uuid] != nil
+ pips[job_uuid] |= n
+
+ hashes << j[:output] if j[:output]
+ ProvenanceHelper::find_collections(j) do |hash, uuid|
+ collections << uuid if uuid
+ hashes << hash if hash
+ end
+
+ if j[:script_version]
+ script_uuid = j[:script_version]
+ provenance[script_uuid] = {:uuid => script_uuid}
+ pips[script_uuid] = 0 unless pips[script_uuid] != nil
+ pips[script_uuid] |= n
+ end
+ end
+ end
+
+ hashes = hashes.compact.uniq
+ if hashes.any?
+ Collection.where(portable_data_hash: hashes).each do |c|
+ hash_uuid = c.portable_data_hash
+ provenance[hash_uuid] = c
+ pips[hash_uuid] = 0 unless pips[hash_uuid] != nil
+ pips[hash_uuid] |= n
+ end
+ end
+
+ collections = collections.compact.uniq
+ if collections.any?
+ Collection.where(uuid: collections).each do |c|
+ collection_uuid = c.uuid
+ provenance[collection_uuid] = c
+ pips[collection_uuid] = 0 unless pips[collection_uuid] != nil
+ pips[collection_uuid] |= n
+ end
+ end
+
+ n = n << 1
+ end
+
+ return provenance, pips
+ end
+
+ def show
+ # the #show action can also be called by #compare, which does its own work to set up @pipelines
+ unless defined? @pipelines
+ @pipelines = [@object]
+ end
+
+ provenance, pips = graph(@pipelines)
+ if provenance
+ @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => request,
+ :all_script_parameters => true,
+ :combine_jobs => :script_and_version,
+ :pips => pips,
+ :only_components => true,
+ :no_docker => true,
+ :no_log => true}
+ end
+
+ super
+ end
+
+ def compare
+ @breadcrumb_page_name = 'compare'
+
+ @rows = [] # each is {name: S, components: [...]}
+
+ if params['tab_pane'] == "Compare" or params['tab_pane'].nil?
+ # Build a table: x=pipeline y=component
+ @objects.each_with_index do |pi, pi_index|
+ pipeline_jobs(pi).each do |component|
+ # Find a cell with the same name as this component but no
+ # entry for this pipeline
+ target_row = nil
+ @rows.each_with_index do |row, row_index|
+ if row[:name] == component[:name] and !row[:components][pi_index]
+ target_row = row
+ end
+ end
+ if !target_row
+ target_row = {name: component[:name], components: []}
+ @rows << target_row
+ end
+ target_row[:components][pi_index] = component
+ end
+ end
+
+ @rows.each do |row|
+ # Build a "normal" pseudo-component for this row by picking the
+ # most common value for each attribute. If all values are
+ # equally common, there is no "normal".
+ normal = {} # attr => most common value
+ highscore = {} # attr => how common "normal" is
+ score = {} # attr => { value => how common }
+ row[:components].each do |pj|
+ next if pj.nil?
+ pj.each do |k,v|
+ vstr = for_comparison v
+ score[k] ||= {}
+ score[k][vstr] = (score[k][vstr] || 0) + 1
+ highscore[k] ||= 0
+ if score[k][vstr] == highscore[k]
+ # tie for first place = no "normal"
+ normal.delete k
+ elsif score[k][vstr] == highscore[k] + 1
+ # more pipelines have v than anything else
+ highscore[k] = score[k][vstr]
+ normal[k] = vstr
+ end
+ end
+ end
+
+ # Add a hash in component[:is_normal]: { attr => is_the_value_normal? }
+ row[:components].each do |pj|
+ next if pj.nil?
+ pj[:is_normal] = {}
+ pj.each do |k,v|
+ pj[:is_normal][k] = (normal.has_key?(k) && normal[k] == for_comparison(v))
+ end
+ end
+ end
+ end
+
+ if params['tab_pane'] == "Graph"
+ @pipelines = @objects
+ end
+
+ @object = @objects.first
+
+ show
+ end
+
+ def show_pane_list
+ panes = %w(Components Log Graph Advanced)
+ if @object and @object.state.in? ['New', 'Ready']
+ panes = %w(Inputs) + panes - %w(Log)
+ end
+ if not @object.components.values.any? { |x| x[:job] rescue false }
+ panes -= ['Graph']
+ end
+ panes
+ end
+
+ def compare_pane_list
+ %w(Compare Graph)
+ end
+
+ protected
+ def for_comparison v
+ if v.is_a? Hash or v.is_a? Array
+ v.to_json
+ else
+ v.to_s
+ end
+ end
+
+ def load_filters_and_paging_params
+ params[:limit] = 20
+ super
+ end
+
+ def find_objects_by_uuid
+ @objects = model_class.where(uuid: params[:uuids])
+ end
+end
--- /dev/null
+class PipelineTemplatesController < ApplicationController
+ include PipelineComponentsHelper
+
+ def show
+ @objects = PipelineInstance.where(pipeline_template_uuid: @object.uuid)
+ super
+ end
+
+ def show_pane_list
+ %w(Components Pipelines Advanced)
+ end
+end
--- /dev/null
+class ProjectsController < ApplicationController
+ before_filter :set_share_links, if: -> { defined? @object }
+
+ def model_class
+ Group
+ end
+
+ def find_object_by_uuid
+ if current_user and params[:uuid] == current_user.uuid
+ @object = current_user.dup
+ @object.uuid = current_user.uuid
+ class << @object
+ def name
+ 'Home'
+ end
+ def description
+ ''
+ end
+ def attribute_editable? attr, *args
+ case attr
+ when 'description', 'name'
+ false
+ else
+ super
+ end
+ end
+ end
+ else
+ super
+ end
+ end
+
+ def set_share_links
+ @user_is_manager = false
+ @share_links = []
+ if @object.uuid != current_user.uuid
+ begin
+ @share_links = Link.permissions_for(@object)
+ @user_is_manager = true
+ rescue ArvadosApiClient::AccessForbiddenException,
+ ArvadosApiClient::NotFoundException
+ end
+ end
+ end
+
+ def index_pane_list
+ %w(Projects)
+ end
+
+ # Returning an array of hashes instead of an array of strings will allow
+ # us to tell the interface to get counts for each pane (using :filters).
+ # It also seems to me that something like these could be used to configure the contents of the panes.
+ def show_pane_list
+ pane_list = [
+ {
+ :name => 'Data_collections',
+ :filters => [%w(uuid is_a arvados#collection)]
+ },
+ {
+ :name => 'Jobs_and_pipelines',
+ :filters => [%w(uuid is_a) + [%w(arvados#job arvados#pipelineInstance)]]
+ },
+ {
+ :name => 'Pipeline_templates',
+ :filters => [%w(uuid is_a arvados#pipelineTemplate)]
+ },
+ {
+ :name => 'Subprojects',
+ :filters => [%w(uuid is_a arvados#group)]
+ },
+ { :name => 'Other_objects',
+ :filters => [%w(uuid is_a) + [%w(arvados#human arvados#specimen arvados#trait)]]
+ }
+ ]
+ pane_list << { :name => 'Sharing',
+ :count => @share_links.count } if @user_is_manager
+ pane_list << { :name => 'Advanced' }
+ end
+
+ # Called via AJAX and returns Javascript that populates tab counts into tab titles.
+ # References #show_pane_list action which should return an array of hashes each with :name
+ # and then optionally a :filters to run or a straight up :count
+ #
+ # This action could easily be moved to the ApplicationController to genericize the tab_counts behaviour,
+ # but one or more new routes would have to be created, the js.erb would also have to be moved
+ def tab_counts
+ @tab_counts = {}
+ show_pane_list.each do |pane|
+ if pane.is_a?(Hash)
+ if pane[:count]
+ @tab_counts[pane[:name]] = pane[:count]
+ elsif pane[:filters]
+ @tab_counts[pane[:name]] = @object.contents(filters: pane[:filters]).items_available
+ end
+ end
+ end
+ end
+
+ def remove_item
+ params[:item_uuids] = [params[:item_uuid]]
+ remove_items
+ render template: 'projects/remove_items'
+ end
+
+ def remove_items
+ @removed_uuids = []
+ links = []
+ params[:item_uuids].collect { |uuid| ArvadosBase.find uuid }.each do |item|
+ if (item.class == Link and
+ item.link_class == 'name' and
+ item.tail_uuid == @object.uuid)
+ # Given uuid is a name link, linking an object to this
+ # project. First follow the link to find the item we're removing,
+ # then delete the link.
+ links << item
+ item = ArvadosBase.find item.head_uuid
+ else
+ # Given uuid is an object. Delete all names.
+ links += Link.where(tail_uuid: @object.uuid,
+ head_uuid: item.uuid,
+ link_class: 'name')
+ end
+ links.each do |link|
+ @removed_uuids << link.uuid
+ link.destroy
+ end
+ if item.owner_uuid == @object.uuid
+ # Object is owned by this project. Remove it from the project by
+ # changing owner to the current user.
+ begin
+ item.update_attributes owner_uuid: current_user.uuid
+ @removed_uuids << item.uuid
+ rescue ArvadosApiClient::ApiErrorResponseException => e
+ if e.message.include? 'collection_owner_uuid_name_unique'
+ rename_to = item.name + ' removed from ' +
+ (@object.name ? @object.name : @object.uuid) +
+ ' at ' + Time.now.to_s
+ updates = {}
+ updates[:name] = rename_to
+ updates[:owner_uuid] = current_user.uuid
+ item.update_attributes updates
+ @removed_uuids << item.uuid
+ else
+ raise
+ end
+ end
+ end
+ end
+ end
+
+ def destroy
+ while (objects = Link.filter([['owner_uuid','=',@object.uuid],
+ ['tail_uuid','=',@object.uuid]])).any?
+ objects.each do |object|
+ object.destroy
+ end
+ end
+ while (objects = @object.contents(include_linked: false)).any?
+ objects.each do |object|
+ object.update_attributes! owner_uuid: current_user.uuid
+ end
+ end
+ if ArvadosBase::resource_class_for_uuid(@object.owner_uuid) == Group
+ params[:return_to] ||= group_path(@object.owner_uuid)
+ else
+ params[:return_to] ||= projects_path
+ end
+ super
+ end
+
+ def find_objects_for_index
+ @objects = all_projects
+ super
+ end
+
+ def load_contents_objects kinds=[]
+ kind_filters = @filters.select do |attr,op,val|
+ op == 'is_a' and val.is_a? Array and val.count > 1
+ end
+ if /^created_at\b/ =~ @order[0] and kind_filters.count == 1
+ # If filtering on multiple types and sorting by date: Get the
+ # first page of each type, sort the entire set, truncate to one
+ # page, and use the last item on this page as a filter for
+ # retrieving the next page. Ideally the API would do this for
+ # us, but it doesn't (yet).
+
+ # To avoid losing items that have the same created_at as the
+ # last item on this page, we retrieve an overlapping page with a
+ # "created_at <= last_created_at" filter, then remove duplicates
+ # with a "uuid not in [...]" filter (see below).
+ nextpage_operator = /\bdesc$/i =~ @order[0] ? '<=' : '>='
+
+ @objects = []
+ @name_link_for = {}
+ kind_filters.each do |attr,op,val|
+ (val.is_a?(Array) ? val : [val]).each do |type|
+ objects = @object.contents(order: @order,
+ limit: @limit,
+ include_linked: true,
+ filters: (@filters - kind_filters + [['uuid', 'is_a', type]]),
+ )
+ objects.each do |object|
+ @name_link_for[object.andand.uuid] = objects.links_for(object, 'name').first
+ end
+ @objects += objects
+ end
+ end
+ @objects = @objects.to_a.sort_by(&:created_at)
+ @objects.reverse! if nextpage_operator == '<='
+ @objects = @objects[0..@limit-1]
+ @next_page_filters = @filters.reject do |attr,op,val|
+ (attr == 'created_at' and op == nextpage_operator) or
+ (attr == 'uuid' and op == 'not in')
+ end
+
+ if @objects.any?
+ last_created_at = @objects.last.created_at
+
+ last_uuids = []
+ @objects.each do |obj|
+ last_uuids << obj.uuid if obj.created_at.eql?(last_created_at)
+ end
+
+ @next_page_filters += [['created_at',
+ nextpage_operator,
+ last_created_at]]
+ @next_page_filters += [['uuid', 'not in', last_uuids]]
+ @next_page_href = url_for(partial: :contents_rows,
+ limit: @limit,
+ filters: @next_page_filters.to_json)
+ else
+ @next_page_href = nil
+ end
+ else
+ @objects = @object.contents(order: @order,
+ limit: @limit,
+ include_linked: true,
+ filters: @filters,
+ offset: @offset)
+ @next_page_href = next_page_href(partial: :contents_rows,
+ filters: @filters.to_json,
+ order: @order.to_json)
+ end
+
+ preload_links_for_objects(@objects.to_a)
+ end
+
+ def show
+ if !@object
+ return render_not_found("object not found")
+ end
+
+ if params[:partial]
+ load_contents_objects
+ respond_to do |f|
+ f.json {
+ render json: {
+ content: render_to_string(partial: 'show_contents_rows.html',
+ formats: [:html]),
+ next_page_href: @next_page_href
+ }
+ }
+ end
+ else
+ @objects = []
+ super
+ end
+ end
+
+ def create
+ @new_resource_attrs = (params['project'] || {}).merge(group_class: 'project')
+ @new_resource_attrs[:name] ||= 'New project'
+ super
+ end
+
+ def update
+ @updates = params['project']
+ super
+ end
+
+ helper_method :get_objects_and_names
+ def get_objects_and_names(objects=nil)
+ objects = @objects if objects.nil?
+ objects_and_names = []
+ objects.each do |object|
+ if objects.respond_to? :links_for and
+ !(name_links = objects.links_for(object, 'name')).empty?
+ name_links.each do |name_link|
+ objects_and_names << [object, name_link]
+ end
+ elsif @name_link_for.andand[object.uuid]
+ objects_and_names << [object, @name_link_for[object.uuid]]
+ elsif object.respond_to? :name
+ objects_and_names << [object, object]
+ else
+ objects_and_names << [object,
+ Link.new(owner_uuid: @object.uuid,
+ tail_uuid: @object.uuid,
+ head_uuid: object.uuid,
+ link_class: "name",
+ name: "")]
+
+ end
+ end
+ objects_and_names
+ end
+
+ def share_with
+ if not params[:uuids].andand.any?
+ @errors = ["No user/group UUIDs specified to share with."]
+ return render_error(status: 422)
+ end
+ results = {"success" => [], "errors" => []}
+ params[:uuids].each do |shared_uuid|
+ begin
+ Link.create(tail_uuid: shared_uuid, link_class: "permission",
+ name: "can_read", head_uuid: @object.uuid)
+ rescue ArvadosApiClient::ApiError => error
+ error_list = error.api_response.andand[:errors]
+ if error_list.andand.any?
+ results["errors"] += error_list.map { |e| "#{shared_uuid}: #{e}" }
+ else
+ error_code = error.api_status || "Bad status"
+ results["errors"] << "#{shared_uuid}: #{error_code} response"
+ end
+ else
+ results["success"] << shared_uuid
+ end
+ end
+ if results["errors"].empty?
+ results.delete("errors")
+ status = 200
+ else
+ status = 422
+ end
+ respond_to do |f|
+ f.json { render(json: results, status: status) }
+ end
+ end
+end
--- /dev/null
+class RepositoriesController < ApplicationController
+ def index_pane_list
+ %w(recent help)
+ end
+end
--- /dev/null
+class SearchController < ApplicationController
+ def find_objects_for_index
+ search_what = Group
+ if params[:project_uuid]
+ # Special case for "search all things in project":
+ @filters = @filters.select do |attr, operator, operand|
+ not (attr == 'owner_uuid' and operator == '=')
+ end
+ # Special case for project_uuid is a user uuid:
+ if ArvadosBase::resource_class_for_uuid(params[:project_uuid]) == User
+ search_what = User.find params[:project_uuid]
+ else
+ search_what = Group.find params[:project_uuid]
+ end
+ end
+ @objects = search_what.contents(limit: @limit,
+ offset: @offset,
+ filters: @filters,
+ include_linked: true)
+ super
+ end
+
+ def next_page_href with_params={}
+ super with_params.merge(last_object_class: @objects.last.class.to_s,
+ project_uuid: params[:project_uuid],
+ filters: @filters.to_json)
+ end
+end
--- /dev/null
+class SessionsController < ApplicationController
+ skip_around_filter :require_thread_api_token, :only => [:destroy, :index]
+ skip_around_filter :set_thread_api_token, :only => [:destroy, :index]
+ skip_before_filter :find_object_by_uuid, :only => [:destroy, :index]
+
+ def destroy
+ session.clear
+ redirect_to arvados_api_client.arvados_logout_url(return_to: root_url)
+ end
+
+ def index
+ redirect_to root_url if session[:arvados_api_token]
+ render_index
+ end
+end
--- /dev/null
+class SpecimensController < ApplicationController
+end
--- /dev/null
+class TraitsController < ApplicationController
+end
--- /dev/null
+class UserAgreementsController < ApplicationController
+ skip_before_filter :check_user_agreements
+ skip_before_filter :find_object_by_uuid
+ skip_before_filter :check_user_profile
+
+ def index
+ if unsigned_user_agreements.empty?
+ redirect_to(params[:return_to] || :back)
+ end
+ end
+
+ def model_class
+ Collection
+ end
+
+ def sign
+ params[:checked].each do |checked|
+ if (r = CollectionsHelper.match_uuid_with_optional_filepath(checked))
+ UserAgreement.sign uuid: r[1]
+ end
+ end
+ current_user.activate
+ redirect_to(params[:return_to] || :back)
+ end
+end
--- /dev/null
+class UsersController < ApplicationController
+ skip_around_filter :require_thread_api_token, only: :welcome
+ skip_before_filter :check_user_agreements, only: [:welcome, :inactive]
+ skip_before_filter :check_user_profile, only: [:welcome, :inactive, :profile]
+ skip_before_filter :find_object_by_uuid, only: [:welcome, :activity, :storage]
+ before_filter :ensure_current_user_is_admin, only: [:sudo, :unsetup, :setup]
+
+ def show
+ if params[:uuid] == current_user.uuid
+ respond_to do |f|
+ f.html do
+ redirect_to(params[:return_to] || project_path(params[:uuid]))
+ end
+ end
+ else
+ super
+ end
+ end
+
+ def welcome
+ if current_user
+ redirect_to (params[:return_to] || '/')
+ end
+ end
+
+ def inactive
+ if current_user.andand.is_invited
+ redirect_to (params[:return_to] || '/')
+ end
+ end
+
+ def profile
+ params[:offer_return_to] ||= params[:return_to]
+ end
+
+ def activity
+ @breadcrumb_page_name = nil
+ @users = User.limit(params[:limit])
+ @user_activity = {}
+ @activity = {
+ logins: {},
+ jobs: {},
+ pipeline_instances: {}
+ }
+ @total_activity = {}
+ @spans = [['This week', Time.now.beginning_of_week, Time.now],
+ ['Last week',
+ Time.now.beginning_of_week.advance(weeks:-1),
+ Time.now.beginning_of_week],
+ ['This month', Time.now.beginning_of_month, Time.now],
+ ['Last month',
+ 1.month.ago.beginning_of_month,
+ Time.now.beginning_of_month]]
+ @spans.each do |span, threshold_start, threshold_end|
+ @activity[:logins][span] = Log.
+ filter([[:event_type, '=', 'login'],
+ [:object_kind, '=', 'arvados#user'],
+ [:created_at, '>=', threshold_start],
+ [:created_at, '<', threshold_end]])
+ @activity[:jobs][span] = Job.
+ filter([[:created_at, '>=', threshold_start],
+ [:created_at, '<', threshold_end]])
+ @activity[:pipeline_instances][span] = PipelineInstance.
+ filter([[:created_at, '>=', threshold_start],
+ [:created_at, '<', threshold_end]])
+ @activity.each do |type, act|
+ records = act[span]
+ @users.each do |u|
+ @user_activity[u.uuid] ||= {}
+ @user_activity[u.uuid][span + ' ' + type.to_s] ||= 0
+ end
+ records.each do |record|
+ @user_activity[record.modified_by_user_uuid] ||= {}
+ @user_activity[record.modified_by_user_uuid][span + ' ' + type.to_s] ||= 0
+ @user_activity[record.modified_by_user_uuid][span + ' ' + type.to_s] += 1
+ @total_activity[span + ' ' + type.to_s] ||= 0
+ @total_activity[span + ' ' + type.to_s] += 1
+ end
+ end
+ end
+ @users = @users.sort_by do |a|
+ [-@user_activity[a.uuid].values.inject(:+), a.full_name]
+ end
+ # Prepend a "Total" pseudo-user to the sorted list
+ @user_activity[nil] = @total_activity
+ @users = [OpenStruct.new(uuid: nil)] + @users
+ end
+
+ def storage
+ @breadcrumb_page_name = nil
+ @users = User.limit(params[:limit])
+ @user_storage = {}
+ total_storage = {}
+ @log_date = {}
+ @users.each do |u|
+ @user_storage[u.uuid] ||= {}
+ storage_log = Log.
+ filter([[:object_uuid, '=', u.uuid],
+ [:event_type, '=', 'user-storage-report']]).
+ order(:created_at => :desc).
+ limit(1)
+ storage_log.each do |log_entry|
+ # We expect this block to only execute once since we specified limit(1)
+ @user_storage[u.uuid] = log_entry['properties']
+ @log_date[u.uuid] = log_entry['event_at']
+ end
+ total_storage.merge!(@user_storage[u.uuid]) { |k,v1,v2| v1 + v2 }
+ end
+ @users = @users.sort_by { |u|
+ [-@user_storage[u.uuid].values.push(0).inject(:+), u.full_name]}
+ # Prepend a "Total" pseudo-user to the sorted list
+ @users = [OpenStruct.new(uuid: nil)] + @users
+ @user_storage[nil] = total_storage
+ end
+
+ def show_pane_list
+ if current_user.andand.is_admin
+ super | %w(Admin)
+ else
+ super
+ end
+ end
+
+ def index_pane_list
+ if current_user.andand.is_admin
+ super | %w(Activity)
+ else
+ super
+ end
+ end
+
+ def sudo
+ resp = arvados_api_client.api(ApiClientAuthorization, '', {
+ api_client_authorization: {
+ owner_uuid: @object.uuid
+ }
+ })
+ redirect_to root_url(api_token: resp[:api_token])
+ end
+
+ def home
+ @showallalerts = false
+ @my_ssh_keys = AuthorizedKey.where(authorized_user_uuid: current_user.uuid)
+ @my_tag_links = {}
+
+ @my_jobs = Job.
+ limit(10).
+ order('created_at desc').
+ where(created_by: current_user.uuid)
+
+ @my_collections = Collection.
+ limit(10).
+ order('created_at desc').
+ where(created_by: current_user.uuid)
+ collection_uuids = @my_collections.collect &:uuid
+
+ @persist_state = {}
+ collection_uuids.each do |uuid|
+ @persist_state[uuid] = 'cache'
+ end
+
+ Link.filter([['head_uuid', 'in', collection_uuids],
+ ['link_class', 'in', ['tag', 'resources']]]).
+ each do |link|
+ case link.link_class
+ when 'tag'
+ (@my_tag_links[link.head_uuid] ||= []) << link
+ when 'resources'
+ if link.name == 'wants'
+ @persist_state[link.head_uuid] = 'persistent'
+ end
+ end
+ end
+
+ @my_pipelines = PipelineInstance.
+ limit(10).
+ order('created_at desc').
+ where(created_by: current_user.uuid)
+
+ respond_to do |f|
+ f.js { render template: 'users/home.js' }
+ f.html { render template: 'users/home' }
+ end
+ end
+
+ def unsetup
+ if current_user.andand.is_admin
+ @object.unsetup
+ end
+ show
+ end
+
+ def setup
+ respond_to do |format|
+ if current_user.andand.is_admin
+ setup_params = {}
+ setup_params[:send_notification_email] = "#{Rails.configuration.send_user_setup_notification_email}"
+ if params['user_uuid'] && params['user_uuid'].size>0
+ setup_params[:uuid] = params['user_uuid']
+ end
+ if params['email'] && params['email'].size>0
+ user = {email: params['email']}
+ setup_params[:user] = user
+ end
+ if params['openid_prefix'] && params['openid_prefix'].size>0
+ setup_params[:openid_prefix] = params['openid_prefix']
+ end
+ if params['repo_name'] && params['repo_name'].size>0
+ setup_params[:repo_name] = params['repo_name']
+ end
+ if params['vm_uuid'] && params['vm_uuid'].size>0
+ setup_params[:vm_uuid] = params['vm_uuid']
+ end
+
+ if User.setup setup_params
+ format.js
+ else
+ self.render_error status: 422
+ end
+ else
+ self.render_error status: 422
+ end
+ end
+ end
+
+ def setup_popup
+ @vms = VirtualMachine.all.results
+
+ @current_selections = find_current_links @object
+
+ respond_to do |format|
+ format.html
+ format.js
+ end
+ end
+
+ def manage_account
+ # repositories current user can read / write
+ repo_links = Link.
+ filter([['head_uuid', 'is_a', 'arvados#repository'],
+ ['tail_uuid', '=', current_user.uuid],
+ ['link_class', '=', 'permission'],
+ ])
+ @my_repositories = Repository.where uuid: repo_links.collect(&:head_uuid)
+ @repo_writable = {}
+ repo_links.each do |link|
+ if link.name.in? ['can_write', 'can_manage']
+ @repo_writable[link.head_uuid] = true
+ end
+ end
+
+ # virtual machines the current user can login into
+ @my_vm_logins = {}
+ Link.where(tail_uuid: current_user.uuid,
+ link_class: 'permission',
+ name: 'can_login').
+ each do |perm_link|
+ if perm_link.properties.andand[:username]
+ @my_vm_logins[perm_link.head_uuid] ||= []
+ @my_vm_logins[perm_link.head_uuid] << perm_link.properties[:username]
+ end
+ end
+ @my_virtual_machines = VirtualMachine.where(uuid: @my_vm_logins.keys)
+
+ # current user's ssh keys
+ @my_ssh_keys = AuthorizedKey.where(key_type: 'SSH', owner_uuid: current_user.uuid)
+
+ respond_to do |f|
+ f.html { render template: 'users/manage_account' }
+ end
+ end
+
+ def add_ssh_key_popup
+ respond_to do |format|
+ format.html
+ format.js
+ end
+ end
+
+ def add_ssh_key
+ respond_to do |format|
+ key_params = {'key_type' => 'SSH'}
+ key_params['authorized_user_uuid'] = current_user.uuid
+
+ if params['name'] && params['name'].size>0
+ key_params['name'] = params['name'].strip
+ end
+ if params['public_key'] && params['public_key'].size>0
+ key_params['public_key'] = params['public_key'].strip
+ end
+
+ if !key_params['name'] && params['public_key'].andand.size>0
+ split_key = key_params['public_key'].split
+ key_params['name'] = split_key[-1] if (split_key.size == 3)
+ end
+
+ new_key = AuthorizedKey.create! key_params
+ if new_key
+ format.js
+ else
+ self.render_error status: 422
+ end
+ end
+ end
+
+ protected
+
+ def find_current_links user
+ current_selections = {}
+
+ if !user
+ return current_selections
+ end
+
+ # oid login perm
+ oid_login_perms = Link.where(tail_uuid: user.email,
+ head_kind: 'arvados#user',
+ link_class: 'permission',
+ name: 'can_login')
+
+ if oid_login_perms.any?
+ prefix_properties = oid_login_perms.first.properties
+ current_selections[:identity_url_prefix] = prefix_properties[:identity_url_prefix]
+ end
+
+ # repo perm
+ repo_perms = Link.where(tail_uuid: user.uuid,
+ head_kind: 'arvados#repository',
+ link_class: 'permission',
+ name: 'can_write')
+ if repo_perms.any?
+ repo_uuid = repo_perms.first.head_uuid
+ repos = Repository.where(head_uuid: repo_uuid)
+ if repos.any?
+ repo_name = repos.first.name
+ current_selections[:repo_name] = repo_name
+ end
+ end
+
+ # vm login perm
+ vm_login_perms = Link.where(tail_uuid: user.uuid,
+ head_kind: 'arvados#virtualMachine',
+ link_class: 'permission',
+ name: 'can_login')
+ if vm_login_perms.any?
+ vm_uuid = vm_login_perms.first.head_uuid
+ current_selections[:vm_uuid] = vm_uuid
+ end
+
+ return current_selections
+ end
+
+end
--- /dev/null
+class VirtualMachinesController < ApplicationController
+ def index
+ @objects ||= model_class.all
+ @vm_logins = {}
+ if @objects.andand.first
+ Link.where(tail_uuid: current_user.uuid,
+ head_uuid: @objects.collect(&:uuid),
+ link_class: 'permission',
+ name: 'can_login').
+ each do |perm_link|
+ if perm_link.properties.andand[:username]
+ @vm_logins[perm_link.head_uuid] ||= []
+ @vm_logins[perm_link.head_uuid] << perm_link.properties[:username]
+ end
+ end
+ @objects.each do |vm|
+ vm.current_user_logins = @vm_logins[vm.uuid].andand.compact || []
+ end
+ end
+ super
+ end
+end
--- /dev/null
+class WebsocketController < ApplicationController
+ skip_before_filter :find_objects_for_index
+
+ def index
+ end
+
+ def model_class
+ "Websocket"
+ end
+end
--- /dev/null
+module ApplicationHelper
+ def current_user
+ controller.current_user
+ end
+
+ def self.match_uuid(uuid)
+ /^([0-9a-z]{5})-([0-9a-z]{5})-([0-9a-z]{15})$/.match(uuid.to_s)
+ end
+
+ def current_api_host
+ Rails.configuration.arvados_v1_base.gsub /https?:\/\/|\/arvados\/v1/,''
+ end
+
+ def render_markup(markup)
+ raw RedCloth.new(markup.to_s).to_html(:refs_arvados, :textile) if markup
+ end
+
+ def human_readable_bytes_html(n)
+ return h(n) unless n.is_a? Fixnum
+ return "0 bytes" if (n == 0)
+
+ orders = {
+ 1 => "bytes",
+ 1024 => "KiB",
+ (1024*1024) => "MiB",
+ (1024*1024*1024) => "GiB",
+ (1024*1024*1024*1024) => "TiB"
+ }
+
+ orders.each do |k, v|
+ sig = (n.to_f/k)
+ if sig >=1 and sig < 1024
+ if v == 'bytes'
+ return "%i #{v}" % sig
+ else
+ return "%0.1f #{v}" % sig
+ end
+ end
+ end
+
+ return h(n)
+ #raw = n.to_s
+ #cooked = ''
+ #while raw.length > 3
+ # cooked = ',' + raw[-3..-1] + cooked
+ # raw = raw[0..-4]
+ #end
+ #cooked = raw + cooked
+ end
+
+ def resource_class_for_uuid(attrvalue, opts={})
+ ArvadosBase::resource_class_for_uuid(attrvalue, opts)
+ end
+
+ ##
+ # Returns HTML that links to the Arvados object specified in +attrvalue+
+ # Provides various output control and styling options.
+ #
+ # +attrvalue+ an Arvados model object or uuid
+ #
+ # +opts+ a set of flags to control output:
+ #
+ # [:link_text] the link text to use (may include HTML), overrides everything else
+ #
+ # [:friendly_name] whether to use the "friendly" name in the link text (by
+ # calling #friendly_link_name on the object), otherwise use the uuid
+ #
+ # [:with_class_name] prefix the link text with the class name of the model
+ #
+ # [:no_tags] disable tags in the link text (default is to show tags).
+ # Currently tags are only shown for Collections.
+ #
+ # [:thumbnail] if the object is a collection, show an image thumbnail if the
+ # collection consists of a single image file.
+ #
+ # [:no_link] don't create a link, just return the link text
+ #
+ # +style_opts+ additional HTML properties for the anchor tag, passed to link_to
+ #
+ def link_to_if_arvados_object(attrvalue, opts={}, style_opts={})
+ if (resource_class = resource_class_for_uuid(attrvalue, opts))
+ if attrvalue.is_a? ArvadosBase
+ object = attrvalue
+ link_uuid = attrvalue.uuid
+ else
+ object = nil
+ link_uuid = attrvalue
+ end
+ link_name = opts[:link_text]
+ tags = ""
+ if !link_name
+ link_name = object.andand.default_name || resource_class.default_name
+
+ if opts[:friendly_name]
+ if attrvalue.respond_to? :friendly_link_name
+ link_name = attrvalue.friendly_link_name opts[:lookup]
+ else
+ begin
+ if resource_class.name == 'Collection'
+ link_name = collections_for_object(link_uuid).andand.first.andand.friendly_link_name
+ else
+ link_name = object_for_dataclass(resource_class, link_uuid).andand.friendly_link_name
+ end
+ rescue ArvadosApiClient::NotFoundException
+ # If that lookup failed, the link will too. So don't make one.
+ return attrvalue
+ end
+ end
+ end
+ if link_name.nil? or link_name.empty?
+ link_name = attrvalue
+ end
+ if opts[:with_class_name]
+ link_name = "#{resource_class.to_s}: #{link_name}"
+ end
+ if !opts[:no_tags] and resource_class == Collection
+ links_for_object(link_uuid).each do |tag|
+ if tag.link_class.in? ["tag", "identifier"]
+ tags += ' <span class="label label-info">'
+ tags += link_to tag.name, controller: "links", filters: [["link_class", "=", "tag"], ["name", "=", tag.name]].to_json
+ tags += '</span>'
+ end
+ end
+ end
+ if opts[:thumbnail] and resource_class == Collection
+ # add an image thumbnail if the collection consists of a single image file.
+ collections_for_object(link_uuid).each do |c|
+ if c.files.length == 1 and CollectionsHelper::is_image c.files.first[1]
+ link_name += " "
+ link_name += image_tag "#{url_for c}/#{CollectionsHelper::file_path c.files.first}", style: "height: 4em; width: auto"
+ end
+ end
+ end
+ end
+ style_opts[:class] = (style_opts[:class] || '') + ' nowrap'
+ if opts[:no_link]
+ raw(link_name)
+ else
+ (link_to raw(link_name), { controller: resource_class.to_s.tableize, action: 'show', id: ((opts[:name_link].andand.uuid) || link_uuid) }, style_opts) + raw(tags)
+ end
+ else
+ # just return attrvalue if it is not recognizable as an Arvados object or uuid.
+ if attrvalue.nil? or (attrvalue.is_a? String and attrvalue.empty?)
+ "(none)"
+ else
+ attrvalue
+ end
+ end
+ end
+
+ def render_editable_attribute(object, attr, attrvalue=nil, htmloptions={})
+ attrvalue = object.send(attr) if attrvalue.nil?
+ if not object.attribute_editable?(attr)
+ if attrvalue && attrvalue.length > 0
+ return render_attribute_as_textile( object, attr, attrvalue, false )
+ else
+ return (attr == 'name' and object.andand.default_name) ||
+ '(none)'
+ end
+ end
+
+ input_type = 'text'
+ case object.class.attribute_info[attr.to_sym].andand[:type]
+ when 'text'
+ input_type = 'textarea'
+ when 'datetime'
+ input_type = 'date'
+ else
+ input_type = 'text'
+ end
+
+ attrvalue = attrvalue.to_json if attrvalue.is_a? Hash or attrvalue.is_a? Array
+ rendervalue = render_attribute_as_textile( object, attr, attrvalue, false )
+
+ ajax_options = {
+ "data-pk" => {
+ id: object.uuid,
+ key: object.class.to_s.underscore
+ }
+ }
+ if object.uuid
+ ajax_options['data-url'] = url_for(action: "update", id: object.uuid, controller: object.class.to_s.pluralize.underscore)
+ else
+ ajax_options['data-url'] = url_for(action: "create", controller: object.class.to_s.pluralize.underscore)
+ ajax_options['data-pk'][:defaults] = object.attributes
+ end
+ ajax_options['data-pk'] = ajax_options['data-pk'].to_json
+ @unique_id ||= (Time.now.to_f*1000000).to_i
+ span_id = object.uuid.to_s + '-' + attr.to_s + '-' + (@unique_id += 1).to_s
+
+ span_tag = content_tag 'span', rendervalue, {
+ "data-emptytext" => '(none)',
+ "data-placement" => "bottom",
+ "data-type" => input_type,
+ "data-title" => "Edit #{attr.to_s.gsub '_', ' '}",
+ "data-name" => attr,
+ "data-object-uuid" => object.uuid,
+ "data-toggle" => "manual",
+ "data-value" => attrvalue,
+ "id" => span_id,
+ :class => "editable #{is_textile?( object, attr ) ? 'editable-textile' : ''}"
+ }.merge(htmloptions).merge(ajax_options)
+ edit_button = raw('<a href="#" class="btn btn-xs btn-default btn-nodecorate" data-toggle="x-editable tooltip" data-toggle-selector="#' + span_id + '" data-placement="top" title="' + (htmloptions[:tiptitle] || 'edit') + '"><i class="fa fa-fw fa-pencil"></i></a>')
+ if htmloptions[:btnplacement] == :left
+ edit_button + ' ' + span_tag
+ else
+ span_tag + ' ' + edit_button
+ end
+ end
+
+ def render_pipeline_component_attribute(object, attr, subattr, value_info, htmloptions={})
+ datatype = nil
+ required = true
+ attrvalue = value_info
+
+ if value_info.is_a? Hash
+ if value_info[:output_of]
+ return raw("<span class='label label-default'>#{value_info[:output_of]}</span>")
+ end
+ if value_info[:dataclass]
+ dataclass = value_info[:dataclass]
+ end
+ if value_info[:optional] != nil
+ required = (value_info[:optional] != "true")
+ end
+ if value_info[:required] != nil
+ required = value_info[:required]
+ end
+
+ # Pick a suitable attrvalue to show as the current value (i.e.,
+ # the one that would be used if we ran the pipeline right now).
+ if value_info[:value]
+ attrvalue = value_info[:value]
+ elsif value_info[:default]
+ attrvalue = value_info[:default]
+ else
+ attrvalue = ''
+ end
+ preconfigured_search_str = value_info[:search_for]
+ end
+
+ if not object.andand.attribute_editable?(attr)
+ return link_to_if_arvados_object attrvalue
+ end
+
+ if dataclass
+ begin
+ dataclass = dataclass.constantize
+ rescue NameError
+ end
+ else
+ dataclass = ArvadosBase.resource_class_for_uuid(attrvalue)
+ end
+
+ id = "#{object.uuid}-#{subattr.join('-')}"
+ dn = "[#{attr}]"
+ subattr.each do |a|
+ dn += "[#{a}]"
+ end
+ if value_info.is_a? Hash
+ dn += '[value]'
+ end
+
+ if (dataclass == Collection) or (dataclass == File)
+ selection_param = object.class.to_s.underscore + dn
+ display_value = attrvalue
+ if value_info.is_a?(Hash)
+ if (link = Link.find? value_info[:link_uuid])
+ display_value = link.name
+ elsif value_info[:link_name]
+ display_value = value_info[:link_name]
+ elsif value_info[:selection_name]
+ display_value = value_info[:selection_name]
+ end
+ end
+ if (attr == :components) and (subattr.size > 2)
+ chooser_title = "Choose a #{dataclass == Collection ? 'dataset' : 'file'} for #{object.component_input_title(subattr[0], subattr[2])}:"
+ else
+ chooser_title = "Choose a #{dataclass == Collection ? 'dataset' : 'file'}:"
+ end
+ modal_path = choose_collections_path \
+ ({ title: chooser_title,
+ filters: [['owner_uuid', '=', object.owner_uuid]].to_json,
+ action_name: 'OK',
+ action_href: pipeline_instance_path(id: object.uuid),
+ action_method: 'patch',
+ preconfigured_search_str: (preconfigured_search_str || ""),
+ action_data: {
+ merge: true,
+ use_preview_selection: dataclass == File ? true : nil,
+ selection_param: selection_param,
+ success: 'page-refresh'
+ }.to_json,
+ })
+ return content_tag('div', :class => 'input-group') do
+ html = text_field_tag(dn, display_value,
+ :class =>
+ "form-control #{'required' if required}")
+ html + content_tag('span', :class => 'input-group-btn') do
+ link_to('Choose',
+ modal_path,
+ { :class => "btn btn-primary",
+ :remote => true,
+ :method => 'get',
+ })
+ end
+ end
+ end
+
+ if dataclass == 'number' or attrvalue.is_a? Fixnum or attrvalue.is_a? Float
+ datatype = 'number'
+ elsif attrvalue.is_a? String
+ datatype = 'text'
+ elsif attrvalue.is_a?(Array) or dataclass.andand.is_a?(Class)
+ # TODO: find a way to edit with x-editable
+ return attrvalue
+ end
+
+ # When datatype is a String or Fixnum, link_to the attrvalue
+ lt = link_to attrvalue, '#', {
+ "data-emptytext" => "none",
+ "data-placement" => "bottom",
+ "data-type" => datatype,
+ "data-url" => url_for(action: "update", id: object.uuid, controller: object.class.to_s.pluralize.underscore, merge: true),
+ "data-title" => "Set value for #{subattr[-1].to_s}",
+ "data-name" => dn,
+ "data-pk" => "{id: \"#{object.uuid}\", key: \"#{object.class.to_s.underscore}\"}",
+ "data-value" => attrvalue,
+ # "clear" button interferes with form-control's up/down arrows
+ "data-clear" => false,
+ :class => "editable #{'required' if required} form-control",
+ :id => id
+ }.merge(htmloptions)
+
+ lt
+ end
+
+ def render_arvados_object_list_start(list, button_text, button_href,
+ params={}, *rest, &block)
+ show_max = params.delete(:show_max) || 3
+ params[:class] ||= 'btn btn-xs btn-default'
+ list[0...show_max].each { |item| yield item }
+ unless list[show_max].nil?
+ link_to(h(button_text) +
+ raw(' <i class="fa fa-fw fa-arrow-circle-right"></i>'),
+ button_href, params, *rest)
+ end
+ end
+
+ def render_controller_partial partial, opts
+ cname = opts.delete :controller_name
+ begin
+ render opts.merge(partial: "#{cname}/#{partial}")
+ rescue ActionView::MissingTemplate
+ render opts.merge(partial: "application/#{partial}")
+ end
+ end
+
+ RESOURCE_CLASS_ICONS = {
+ "Collection" => "fa-archive",
+ "Group" => "fa-users",
+ "Human" => "fa-male", # FIXME: Use a more inclusive icon.
+ "Job" => "fa-gears",
+ "KeepDisk" => "fa-hdd-o",
+ "KeepService" => "fa-exchange",
+ "Link" => "fa-arrows-h",
+ "Node" => "fa-cloud",
+ "PipelineInstance" => "fa-gears",
+ "PipelineTemplate" => "fa-gears",
+ "Repository" => "fa-code-fork",
+ "Specimen" => "fa-flask",
+ "Trait" => "fa-clipboard",
+ "User" => "fa-user",
+ "VirtualMachine" => "fa-terminal",
+ }
+ DEFAULT_ICON_CLASS = "fa-cube"
+
+ def fa_icon_class_for_class(resource_class, default=DEFAULT_ICON_CLASS)
+ RESOURCE_CLASS_ICONS.fetch(resource_class.to_s, default)
+ end
+
+ def fa_icon_class_for_uuid(uuid, default=DEFAULT_ICON_CLASS)
+ fa_icon_class_for_class(resource_class_for_uuid(uuid), default)
+ end
+
+ def fa_icon_class_for_object(object, default=DEFAULT_ICON_CLASS)
+ case class_name = object.class.to_s
+ when "Group"
+ object.group_class ? 'fa-folder' : 'fa-users'
+ else
+ RESOURCE_CLASS_ICONS.fetch(class_name, default)
+ end
+ end
+
+ def chooser_preview_url_for object, use_preview_selection=false
+ case object.class.to_s
+ when 'Collection'
+ polymorphic_path(object, tab_pane: 'chooser_preview', use_preview_selection: use_preview_selection)
+ else
+ nil
+ end
+ end
+
+ def render_attribute_as_textile( object, attr, attrvalue, truncate )
+ if attrvalue && (is_textile? object, attr)
+ markup = render_markup attrvalue
+ markup = markup[0,markup.index('</p>')+4] if (truncate && markup.index('</p>'))
+ return markup
+ else
+ return attrvalue
+ end
+ end
+
+ def render_localized_date(date, opts="")
+ raw("<span class='utc-date' data-utc-date='#{date}' data-utc-date-opts='noseconds'>#{date}</span>")
+ end
+
+private
+ def is_textile?( object, attr )
+ is_textile = object.textile_attributes.andand.include?(attr)
+ end
+end
--- /dev/null
+module ArvadosApiClientHelper
+ def arvados_api_client
+ ArvadosApiClient.new_or_current
+ end
+end
+
+# For the benefit of themes that still expect $arvados_api_client to work:
+class ArvadosClientProxyHack
+ def method_missing *args
+ ArvadosApiClient.new_or_current.send *args
+ end
+end
+$arvados_api_client = ArvadosClientProxyHack.new
--- /dev/null
+module CollectionsHelper
+ def d3ify_links(links)
+ links.collect do |x|
+ {source: x.tail_uuid, target: x.head_uuid, type: x.name}
+ end
+ end
+
+ ##
+ # Regex match for collection portable data hash, returns a regex match object with the
+ # hash in group 1, (optional) size in group 2, (optional) subsequent uuid
+ # fields in group 3, and (optional) file path within the collection as group
+ # 4
+ # returns nil for no match.
+ #
+ # +pdh+ the portable data hash string to match
+ #
+ def self.match(pdh)
+ /^([a-f0-9]{32})(\+\d+)(\+[^+]+)*?(\/.*)?$/.match(pdh.to_s)
+ end
+
+ ##
+ # Regex match for collection UUIDs, returns a regex match object with the
+ # uuid in group 1, empty groups 2 and 3 (for consistency with the match
+ # method above), and (optional) file path within the collection as group
+ # 4.
+ # returns nil for no match.
+ #
+ def self.match_uuid_with_optional_filepath(uuid_with_optional_file)
+ /^([0-9a-z]{5}-4zz18-[0-9a-z]{15})()()(\/.*)?$/.match(uuid_with_optional_file.to_s)
+ end
+
+ ##
+ # Regex match for common image file extensions, returns a regex match object
+ # with the matched extension in group 1; or nil for no match.
+ #
+ # +file+ the file string to match
+ #
+ def self.is_image file
+ /\.(jpg|jpeg|gif|png|svg)$/i.match(file)
+ end
+
+ ##
+ # Generates a relative file path than can be appended to the URL of a
+ # collection to get a file download link without adding a spurious ./ at the
+ # beginning for files in the default stream.
+ #
+ # +file+ an entry in the Collection.files list in the form [stream, name, size]
+ #
+ def self.file_path file
+ f0 = file[0]
+ f0 = '' if f0 == '.'
+ f0 = f0[2..-1] if f0[0..1] == './'
+ f0 += '/' if not f0.empty?
+ file_path = "#{f0}#{file[1]}"
+ end
+end
--- /dev/null
+module JobsHelper
+ def stderr_log_history(job_uuids)
+ results = []
+
+ log_history = Log.where(event_type: 'stderr',
+ object_uuid: job_uuids).order('id DESC')
+ if !log_history.results.empty?
+ reversed_results = log_history.results.reverse
+ reversed_results.each do |entry|
+ if entry.andand.properties
+ properties = entry.properties
+ text = properties[:text]
+ if text
+ results = results.concat text.split("\n")
+ end
+ end
+ end
+ end
+ return results
+ end
+
+end
--- /dev/null
+module PipelineComponentsHelper
+ def render_pipeline_components(template_suffix, fallback=nil, locals={})
+ begin
+ render(partial: "pipeline_instances/show_components_#{template_suffix}",
+ locals: locals)
+ rescue => e
+ logger.error "#{e.inspect}"
+ logger.error "#{e.backtrace.join("\n\t")}"
+ case fallback
+ when :json
+ render(partial: "pipeline_instances/show_components_json",
+ locals: {error_name: e.inspect, backtrace: e.backtrace.join("\n\t")})
+ end
+ end
+ end
+end
--- /dev/null
+module PipelineInstancesHelper
+
+ def pipeline_jobs object=nil
+ object ||= @object
+ if object.components[:steps].is_a? Array
+ pipeline_jobs_oldschool object
+ elsif object.components.is_a? Hash
+ pipeline_jobs_newschool object
+ end
+ end
+
+ def render_pipeline_jobs
+ pipeline_jobs.collect do |pj|
+ render_pipeline_job pj
+ end
+ end
+
+ def render_pipeline_job pj
+ pj[:progress_bar] = render partial: 'job_progress', locals: {:j => pj[:job]}
+ pj[:output_link] = link_to_if_arvados_object pj[:output]
+ pj[:job_link] = link_to_if_arvados_object pj[:job][:uuid] if pj[:job]
+ pj
+ end
+
+ # Merge (started_at, finished_at) time range into the list of time ranges in
+ # timestamps (timestamps must be sorted and non-overlapping).
+ # return the updated timestamps list.
+ def merge_range timestamps, started_at, finished_at
+ # in the comments below, 'i' is the entry in the timestamps array and 'j'
+ # is the started_at, finished_at range which is passed in.
+ timestamps.each_index do |i|
+ if started_at
+ if started_at >= timestamps[i][0] and finished_at <= timestamps[i][1]
+ # 'j' started and ended during 'i'
+ return timestamps
+ end
+
+ if started_at < timestamps[i][0] and finished_at >= timestamps[i][0] and finished_at <= timestamps[i][1]
+ # 'j' started before 'i' and finished during 'i'
+ # re-merge range between when 'j' started and 'i' finished
+ finished_at = timestamps[i][1]
+ timestamps.delete_at i
+ return merge_range timestamps, started_at, finished_at
+ end
+
+ if started_at >= timestamps[i][0] and started_at <= timestamps[i][1]
+ # 'j' started during 'i' and finished sometime after
+ # move end time of 'i' back
+ # re-merge range between when 'i' started and 'j' finished
+ started_at = timestamps[i][0]
+ timestamps.delete_at i
+ return merge_range timestamps, started_at, finished_at
+ end
+
+ if finished_at < timestamps[i][0]
+ # 'j' finished before 'i' started, so insert before 'i'
+ timestamps.insert i, [started_at, finished_at]
+ return timestamps
+ end
+ end
+ end
+
+ timestamps << [started_at, finished_at]
+ end
+
+ # Accept a list of objects with [:started_at] and [:finshed_at] keys and
+ # merge overlapping ranges to compute the time spent running after periods of
+ # overlapping execution are factored out.
+ def determine_wallclock_runtime jobs
+ timestamps = []
+ jobs.each do |j|
+ insert_at = 0
+ started_at = j[:started_at]
+ finished_at = (if j[:finished_at] then j[:finished_at] else Time.now end)
+ if started_at
+ timestamps = merge_range timestamps, started_at, finished_at
+ end
+ end
+ timestamps.map { |t| t[1] - t[0] }.reduce(:+) || 0
+ end
+
+ protected
+
+ def pipeline_jobs_newschool object
+ ret = []
+ i = -1
+
+ jobuuids = object.components.values.map { |c|
+ c[:job][:uuid] if c.is_a?(Hash) and c[:job].is_a?(Hash)
+ }.compact
+ job = {}
+ Job.where(uuid: jobuuids).each do |j|
+ job[j[:uuid]] = j
+ end
+
+ object.components.each do |cname, c|
+ i += 1
+ pj = {index: i, name: cname}
+ if not c.is_a?(Hash)
+ ret << pj
+ next
+ end
+ if c[:job] and c[:job][:uuid] and job[c[:job][:uuid]]
+ pj[:job] = job[c[:job][:uuid]]
+ elsif c[:job].is_a?(Hash)
+ pj[:job] = c[:job]
+ if pj[:job][:started_at].is_a? String
+ pj[:job][:started_at] = Time.parse(pj[:job][:started_at])
+ end
+ if pj[:job][:finished_at].is_a? String
+ pj[:job][:finished_at] = Time.parse(pj[:job][:finished_at])
+ end
+ # If necessary, figure out the state based on the other fields.
+ pj[:job][:state] ||= if pj[:job][:cancelled_at]
+ "Cancelled"
+ elsif pj[:job][:success] == false
+ "Failed"
+ elsif pj[:job][:success] == true
+ "Complete"
+ elsif pj[:job][:running] == true
+ "Running"
+ else
+ "Queued"
+ end
+ else
+ pj[:job] = {}
+ end
+ pj[:percent_done] = 0
+ pj[:percent_running] = 0
+ if pj[:job][:success]
+ if pj[:job][:output]
+ pj[:progress] = 1.0
+ pj[:percent_done] = 100
+ else
+ pj[:progress] = 0.0
+ end
+ else
+ if pj[:job][:tasks_summary]
+ begin
+ ts = pj[:job][:tasks_summary]
+ denom = ts[:done].to_f + ts[:running].to_f + ts[:todo].to_f
+ pj[:progress] = (ts[:done].to_f + ts[:running].to_f/2) / denom
+ pj[:percent_done] = 100.0 * ts[:done].to_f / denom
+ pj[:percent_running] = 100.0 * ts[:running].to_f / denom
+ pj[:progress_detail] = "#{ts[:done]} done #{ts[:running]} run #{ts[:todo]} todo"
+ rescue
+ pj[:progress] = 0.5
+ pj[:percent_done] = 0.0
+ pj[:percent_running] = 100.0
+ end
+ else
+ pj[:progress] = 0.0
+ end
+ end
+
+ case pj[:job][:state]
+ when 'Complete'
+ pj[:result] = 'complete'
+ pj[:labeltype] = 'success'
+ pj[:complete] = true
+ pj[:progress] = 1.0
+ when 'Failed'
+ pj[:result] = 'failed'
+ pj[:labeltype] = 'danger'
+ pj[:failed] = true
+ when 'Cancelled'
+ pj[:result] = 'cancelled'
+ pj[:labeltype] = 'danger'
+ pj[:failed] = true
+ when 'Running'
+ pj[:result] = 'running'
+ pj[:labeltype] = 'primary'
+ when 'Queued'
+ pj[:result] = 'queued'
+ pj[:labeltype] = 'default'
+ else
+ pj[:result] = 'none'
+ pj[:labeltype] = 'default'
+ end
+
+ pj[:job_id] = pj[:job][:uuid]
+ pj[:script] = pj[:job][:script] || c[:script]
+ pj[:repository] = pj[:job][:script] || c[:repository]
+ pj[:script_parameters] = pj[:job][:script_parameters] || c[:script_parameters]
+ pj[:script_version] = pj[:job][:script_version] || c[:script_version]
+ pj[:nondeterministic] = pj[:job][:nondeterministic] || c[:nondeterministic]
+ pj[:output] = pj[:job][:output]
+ pj[:output_uuid] = c[:output_uuid]
+ pj[:finished_at] = pj[:job][:finished_at]
+ ret << pj
+ end
+ ret
+ end
+
+ def pipeline_jobs_oldschool object
+ ret = []
+ object.components[:steps].each_with_index do |step, i|
+ pj = {index: i, name: step[:name]}
+ if step[:complete] and step[:complete] != 0
+ if step[:output_data_locator]
+ pj[:progress] = 1.0
+ else
+ pj[:progress] = 0.0
+ end
+ else
+ if step[:progress] and
+ (re = step[:progress].match /^(\d+)\+(\d+)\/(\d+)$/)
+ pj[:progress] = (((re[1].to_f + re[2].to_f/2) / re[3].to_f) rescue 0.5)
+ else
+ pj[:progress] = 0.0
+ end
+ if step[:failed]
+ pj[:result] = 'failed'
+ pj[:failed] = true
+ end
+ end
+ if step[:warehousejob]
+ if step[:complete]
+ pj[:result] = 'complete'
+ pj[:complete] = true
+ pj[:progress] = 1.0
+ elsif step[:warehousejob][:finishtime]
+ pj[:result] = 'failed'
+ pj[:failed] = true
+ elsif step[:warehousejob][:starttime]
+ pj[:result] = 'running'
+ else
+ pj[:result] = 'queued'
+ end
+ end
+ pj[:progress_detail] = (step[:progress] rescue nil)
+ pj[:job_id] = (step[:warehousejob][:id] rescue nil)
+ pj[:job_link] = pj[:job_id]
+ pj[:script] = step[:function]
+ pj[:script_version] = (step[:warehousejob][:revision] rescue nil)
+ pj[:output] = step[:output_data_locator]
+ pj[:finished_at] = (Time.parse(step[:warehousejob][:finishtime]) rescue nil)
+ ret << pj
+ end
+ ret
+ end
+
+ MINUTE = 60
+ HOUR = 60 * MINUTE
+ DAY = 24 * HOUR
+
+ def render_runtime duration, use_words, round_to_min=true
+ days = 0
+ hours = 0
+ minutes = 0
+ seconds = 0
+
+ if duration >= DAY
+ days = (duration / DAY).floor
+ duration -= days * DAY
+ end
+
+ if duration >= HOUR
+ hours = (duration / HOUR).floor
+ duration -= hours * HOUR
+ end
+
+ if duration >= MINUTE
+ minutes = (duration / MINUTE).floor
+ duration -= minutes * MINUTE
+ end
+
+ seconds = duration.floor
+
+ if round_to_min and seconds >= 30
+ minutes += 1
+ end
+
+ if use_words
+ s = []
+ if days > 0 then
+ s << "#{days} day#{'s' if days != 1}"
+ end
+ if hours > 0 then
+ s << "#{hours} hour#{'s' if hours != 1}"
+ end
+ if minutes > 0 then
+ s << "#{minutes} minute#{'s' if minutes != 1}"
+ end
+ if not round_to_min or s.size == 0
+ s << "#{seconds} second#{'s' if seconds != 1}"
+ end
+ s = s * " "
+ else
+ s = ""
+ if days > 0
+ s += "#{days}<span class='time-label-divider'>d</span> "
+ end
+
+ if (hours > 0)
+ s += "#{hours}<span class='time-label-divider'>h</span>"
+ end
+
+ s += "#{minutes}<span class='time-label-divider'>m</span>"
+
+ if not round_to_min
+ s += "#{seconds}<span class='time-label-divider'>s</span>"
+ end
+ end
+
+ raw(s)
+ end
+
+end
--- /dev/null
+module ProvenanceHelper
+
+ class GenerateGraph
+ def initialize(pdata, opts)
+ @pdata = pdata
+ @opts = opts
+ @visited = {}
+ @jobs = {}
+ @node_extra = {}
+ end
+
+ def self.collection_uuid(uuid)
+ Keep::Locator.parse(uuid).andand.strip_hints.andand.to_s
+ end
+
+ def url_for u
+ p = { :host => @opts[:request].host,
+ :port => @opts[:request].port,
+ :protocol => @opts[:request].protocol }
+ p.merge! u
+ Rails.application.routes.url_helpers.url_for (p)
+ end
+
+ def determine_fillcolor(n)
+ fillcolor = %w(666666 669966 666699 666666 996666)[n || 0] || '666666'
+ "style=\"filled\",color=\"#ffffff\",fillcolor=\"##{fillcolor}\",fontcolor=\"#ffffff\""
+ end
+
+ def describe_node(uuid, describe_opts={})
+ bgcolor = determine_fillcolor (describe_opts[:pip] || @opts[:pips].andand[uuid])
+
+ rsc = ArvadosBase::resource_class_for_uuid uuid
+
+ if GenerateGraph::collection_uuid(uuid) || rsc == Collection
+ if Collection.is_empty_blob_locator? uuid.to_s
+ # special case
+ return "\"#{uuid}\" [label=\"(empty collection)\"];\n"
+ end
+
+ href = url_for ({:controller => Collection.to_s.tableize,
+ :action => :show,
+ :id => uuid.to_s })
+
+ return "\"#{uuid}\" [label=\"#{encode_quotes(describe_opts[:label] || (@pdata[uuid] and @pdata[uuid][:name]) || uuid)}\",shape=box,href=\"#{href}\",#{bgcolor}];\n"
+ else
+ href = ""
+ if describe_opts[:href]
+ href = ",href=\"#{url_for ({:controller => describe_opts[:href][:controller],
+ :action => :show,
+ :id => describe_opts[:href][:id] })}\""
+ end
+ return "\"#{uuid}\" [label=\"#{encode_quotes(describe_opts[:label] || uuid)}\",#{bgcolor},shape=#{describe_opts[:shape] || 'box'}#{href}];\n"
+ end
+ end
+
+ def job_uuid(job)
+ d = Digest::MD5.hexdigest(job[:script_parameters].to_json)
+ if @opts[:combine_jobs] == :script_only
+ uuid = "#{job[:script]}_#{d}"
+ elsif @opts[:combine_jobs] == :script_and_version
+ uuid = "#{job[:script]}_#{job[:script_version]}_#{d}"
+ else
+ uuid = "#{job[:uuid]}"
+ end
+
+ @jobs[uuid] = [] unless @jobs[uuid]
+ @jobs[uuid] << job unless @jobs[uuid].include? job
+
+ uuid
+ end
+
+ def edge(tail, head, extra)
+ if @opts[:direction] == :bottom_up
+ gr = "\"#{encode_quotes head}\" -> \"#{encode_quotes tail}\""
+ else
+ gr = "\"#{encode_quotes tail}\" -> \"#{encode_quotes head}\""
+ end
+
+ if extra.length > 0
+ gr += " ["
+ extra.each do |k, v|
+ gr += "#{k}=\"#{encode_quotes v}\","
+ end
+ gr += "]"
+ end
+ gr += ";\n"
+ gr
+ end
+
+ def script_param_edges(uuid, sp)
+ gr = ""
+
+ sp.each do |k, v|
+ if @opts[:all_script_parameters]
+ if v.is_a? Array or v.is_a? Hash
+ encv = JSON.pretty_generate(v).gsub("\n", "\\l") + "\\l"
+ else
+ encv = v.to_json
+ end
+ gr += "\"#{encode_quotes encv}\" [shape=box];\n"
+ gr += edge(encv, uuid, {:label => k})
+ end
+ end
+ gr
+ end
+
+ def job_edges job, edge_opts={}
+ uuid = job_uuid(job)
+ gr = ""
+
+ ProvenanceHelper::find_collections job[:script_parameters] do |collection_hash, collection_uuid, key|
+ if collection_uuid
+ gr += describe_node(collection_uuid)
+ gr += edge(collection_uuid, uuid, {:label => key})
+ else
+ gr += describe_node(collection_hash)
+ gr += edge(collection_hash, uuid, {:label => key})
+ end
+ end
+
+ if job[:docker_image_locator] and !@opts[:no_docker]
+ gr += describe_node(job[:docker_image_locator], {label: (job[:runtime_constraints].andand[:docker_image] || job[:docker_image_locator])})
+ gr += edge(job[:docker_image_locator], uuid, {label: "docker_image"})
+ end
+
+ if @opts[:script_version_nodes]
+ gr += describe_node(job[:script_version], {:label => "git:#{job[:script_version]}"})
+ gr += edge(job[:script_version], uuid, {:label => "script_version"})
+ end
+
+ if job[:output] and !edge_opts[:no_output]
+ gr += describe_node(job[:output])
+ gr += edge(uuid, job[:output], {label: "output" })
+ end
+
+ if job[:log] and !edge_opts[:no_log]
+ gr += describe_node(job[:log])
+ gr += edge(uuid, job[:log], {label: "log"})
+ end
+
+ gr
+ end
+
+ def generate_provenance_edges(uuid)
+ gr = ""
+ m = GenerateGraph::collection_uuid(uuid)
+ uuid = m if m
+
+ if uuid.nil? or uuid.empty? or @visited[uuid]
+ return ""
+ end
+
+ if @pdata[uuid].nil?
+ return ""
+ else
+ @visited[uuid] = true
+ end
+
+ if uuid.start_with? "component_"
+ # Pipeline component inputs
+ job = @pdata[@pdata[uuid][:job].andand[:uuid]]
+
+ if job
+ gr += describe_node(job_uuid(job), {label: uuid[38..-1], pip: @opts[:pips].andand[job[:uuid]], shape: "oval",
+ href: {controller: 'jobs', id: job[:uuid]}})
+ gr += job_edges job, {no_output: true, no_log: true}
+ end
+
+ # Pipeline component output
+ outuuid = @pdata[uuid][:output_uuid]
+ if outuuid
+ outcollection = @pdata[outuuid]
+ if outcollection
+ gr += edge(job_uuid(job), outcollection[:portable_data_hash], {label: "output"})
+ gr += describe_node(outcollection[:portable_data_hash], {label: outcollection[:name]})
+ end
+ elsif job and job[:output]
+ gr += describe_node(job[:output])
+ gr += edge(job_uuid(job), job[:output], {label: "output" })
+ end
+ else
+ rsc = ArvadosBase::resource_class_for_uuid uuid
+
+ if rsc == Job
+ job = @pdata[uuid]
+ gr += job_edges job if job
+ end
+ end
+
+ @pdata.each do |k, link|
+ if link[:head_uuid] == uuid.to_s and link[:link_class] == "provenance"
+ href = url_for ({:controller => Link.to_s.tableize,
+ :action => :show,
+ :id => link[:uuid] })
+
+ gr += describe_node(link[:tail_uuid])
+ gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => href})
+ gr += generate_provenance_edges(link[:tail_uuid])
+ end
+ end
+
+ gr
+ end
+
+ def describe_jobs
+ gr = ""
+ @jobs.each do |k, v|
+ href = url_for ({:controller => Job.to_s.tableize,
+ :action => :index })
+
+ gr += "\"#{k}\" [href=\"#{href}?"
+
+ n = 0
+ v.each do |u|
+ gr += ";" unless gr.end_with? "?"
+ gr += "uuid%5b%5d=#{u[:uuid]}"
+ n |= @opts[:pips][u[:uuid]] if @opts[:pips] and @opts[:pips][u[:uuid]]
+ end
+
+ gr += "\",label=\""
+
+ label = "#{v[0][:script]}"
+
+ if label == "run-command" and v[0][:script_parameters][:command].is_a? Array
+ label = v[0][:script_parameters][:command].join(' ')
+ end
+
+ if not @opts[:combine_jobs]
+ label += "\\n#{v[0][:finished_at]}"
+ end
+
+ gr += encode_quotes label
+
+ gr += "\",#{determine_fillcolor n}];\n"
+ end
+ gr
+ end
+
+ def encode_quotes value
+ value.to_s.gsub("\"", "\\\"").gsub("\n", "\\n")
+ end
+ end
+
+ def self.create_provenance_graph(pdata, svgId, opts={})
+ if pdata.is_a? Array or pdata.is_a? ArvadosResourceList
+ p2 = {}
+ pdata.each do |k|
+ p2[k[:uuid]] = k if k[:uuid]
+ end
+ pdata = p2
+ end
+
+ unless pdata.is_a? Hash
+ raise "create_provenance_graph accepts Array or Hash for pdata only, pdata is #{pdata.class}"
+ end
+
+ gr = """strict digraph {
+node [fontsize=10,fontname=\"Helvetica,Arial,sans-serif\"];
+edge [fontsize=10,fontname=\"Helvetica,Arial,sans-serif\"];
+"""
+
+ if opts[:direction] == :bottom_up
+ gr += "edge [dir=back];"
+ end
+
+ begin
+ pdata = pdata.stringify_keys
+
+ g = GenerateGraph.new(pdata, opts)
+
+ pdata.each do |k, v|
+ if !opts[:only_components] or k.start_with? "component_"
+ gr += g.generate_provenance_edges(k)
+ else
+ #gr += describe_node(k)
+ end
+ end
+
+ if !opts[:only_components]
+ gr += g.describe_jobs
+ end
+
+ rescue => e
+ Rails.logger.warn "#{e.inspect}"
+ Rails.logger.warn "#{e.backtrace.join("\n\t")}"
+ raise
+ end
+
+ gr += "}"
+ svg = ""
+
+ require 'open3'
+
+ Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
+ stdin.print(gr)
+ stdin.close
+ svg = stdout.read()
+ wait_thr.value
+ stdout.close()
+ end
+
+ svg = svg.sub(/<\?xml.*?\?>/m, "")
+ svg = svg.sub(/<!DOCTYPE.*?>/m, "")
+ svg = svg.sub(/<svg /, "<svg id=\"#{svgId}\" ")
+ end
+
+ # yields hash, uuid
+ # Position indicates whether it is a content hash or arvados uuid.
+ # One will hold a value, the other will always be nil.
+ def self.find_collections(sp, key=nil, &b)
+ case sp
+ when ArvadosBase
+ sp.class.columns.each do |c|
+ find_collections(sp[c.name.to_sym], nil, &b)
+ end
+ when Hash
+ sp.each do |k, v|
+ find_collections(v, key || k, &b)
+ end
+ when Array
+ sp.each do |v|
+ find_collections(v, key, &b)
+ end
+ when String
+ if m = /[a-f0-9]{32}\+\d+/.match(sp)
+ yield m[0], nil, key
+ elsif m = /[0-9a-z]{5}-4zz18-[0-9a-z]{15}/.match(sp)
+ yield nil, m[0], key
+ end
+ end
+ end
+end
--- /dev/null
+module VersionHelper
+ # api_version returns the git commit hash for the API server's
+ # current version. It is extracted from api_version_text, which
+ # returns the source_version provided by the discovery document and
+ # may have the word "-modified" appended to it (if the API server is
+ # running from a locally modified repository).
+
+ def api_version
+ api_version_text.sub(/[^[:xdigit:]].*/, '')
+ end
+
+ def api_version_text
+ arvados_api_client.discovery[:source_version]
+ end
+
+ # wb_version and wb_version_text provide the same strings for the
+ # code version that this Workbench is currently running.
+
+ def wb_version
+ Rails.configuration.source_version
+ end
+
+ def wb_version_text
+ wb_version + (Rails.configuration.local_modified or '')
+ end
+
+ def version_link_target version
+ "https://arvados.org/projects/arvados/repository/changes?rev=#{version}"
+ end
+end
--- /dev/null
+class IssueReporter < ActionMailer::Base
+ default from: Rails.configuration.issue_reporter_email_from
+ default to: Rails.configuration.issue_reporter_email_to
+
+ def send_report(user, params)
+ @user = user
+ @params = params
+ subject = 'Issue reported'
+ subject += " by #{@user.email}" if @user
+ mail(subject: subject)
+ end
+end
--- /dev/null
+class ApiClientAuthorization < ArvadosBase
+ def editable_attributes
+ %w(expires_at default_owner_uuid)
+ end
+ def self.creatable?
+ false
+ end
+end
--- /dev/null
+require 'httpclient'
+require 'thread'
+
+class ArvadosApiClient
+ class ApiError < StandardError
+ attr_reader :api_response, :api_response_s, :api_status, :request_url
+
+ def initialize(request_url, errmsg)
+ @request_url = request_url
+ @api_response ||= {}
+ errors = @api_response[:errors]
+ if not errors.is_a?(Array)
+ @api_response[:errors] = [errors || errmsg]
+ end
+ super(errmsg)
+ end
+ end
+
+ class NoApiResponseException < ApiError
+ def initialize(request_url, exception)
+ @api_response_s = exception.to_s
+ super(request_url,
+ "#{exception.class.to_s} error connecting to API server")
+ end
+ end
+
+ class InvalidApiResponseException < ApiError
+ def initialize(request_url, api_response)
+ @api_status = api_response.status_code
+ @api_response_s = api_response.content
+ super(request_url, "Unparseable response from API server")
+ end
+ end
+
+ class ApiErrorResponseException < ApiError
+ def initialize(request_url, api_response)
+ @api_status = api_response.status_code
+ @api_response_s = api_response.content
+ @api_response = Oj.load(@api_response_s, :symbol_keys => true)
+ errors = @api_response[:errors]
+ if errors.respond_to?(:join)
+ errors = errors.join("\n\n")
+ else
+ errors = errors.to_s
+ end
+ super(request_url, "#{errors} [API: #{@api_status}]")
+ end
+ end
+
+ class AccessForbiddenException < ApiErrorResponseException; end
+ class NotFoundException < ApiErrorResponseException; end
+ class NotLoggedInException < ApiErrorResponseException; end
+
+ ERROR_CODE_CLASSES = {
+ 401 => NotLoggedInException,
+ 403 => AccessForbiddenException,
+ 404 => NotFoundException,
+ }
+
+ @@profiling_enabled = Rails.configuration.profiling_enabled
+ @@discovery = nil
+
+ # An API client object suitable for handling API requests on behalf
+ # of the current thread.
+ def self.new_or_current
+ # If this thread doesn't have an API client yet, *or* this model
+ # has been reloaded since the existing client was created, create
+ # a new client. Otherwise, keep using the latest client created in
+ # the current thread.
+ unless Thread.current[:arvados_api_client].andand.class == self
+ Thread.current[:arvados_api_client] = new
+ end
+ Thread.current[:arvados_api_client]
+ end
+
+ def initialize *args
+ @api_client = nil
+ @client_mtx = Mutex.new
+ end
+
+ def api(resources_kind, action, data=nil, tokens={})
+
+ profile_checkpoint
+
+ if not @api_client
+ @client_mtx.synchronize do
+ @api_client = HTTPClient.new
+ if Rails.configuration.arvados_insecure_https
+ @api_client.ssl_config.verify_mode = OpenSSL::SSL::VERIFY_NONE
+ else
+ # Use system CA certificates
+ @api_client.ssl_config.add_trust_ca('/etc/ssl/certs')
+ end
+ end
+ end
+
+ resources_kind = class_kind(resources_kind).pluralize if resources_kind.is_a? Class
+ url = "#{self.arvados_v1_base}/#{resources_kind}#{action}"
+
+ # Clean up /arvados/v1/../../discovery/v1 to /discovery/v1
+ url.sub! '/arvados/v1/../../', '/'
+
+ query = {
+ 'api_token' => tokens[:arvados_api_token] || Thread.current[:arvados_api_token] || '',
+ 'reader_tokens' => (tokens[:reader_tokens] || Thread.current[:reader_tokens] || []).to_json,
+ }
+ if !data.nil?
+ data.each do |k,v|
+ if v.is_a? String or v.nil?
+ query[k] = v
+ elsif v == true
+ query[k] = 1
+ elsif v == false
+ query[k] = 0
+ else
+ query[k] = JSON.dump(v)
+ end
+ end
+ else
+ query["_method"] = "GET"
+ end
+ if @@profiling_enabled
+ query["_profile"] = "true"
+ end
+
+ header = {"Accept" => "application/json"}
+
+ profile_checkpoint { "Prepare request #{url} #{query[:uuid]} #{query[:where]} #{query[:filters]} #{query[:order]}" }
+ msg = @client_mtx.synchronize do
+ begin
+ @api_client.post(url, query, header: header)
+ rescue => exception
+ raise NoApiResponseException.new(url, exception)
+ end
+ end
+ profile_checkpoint 'API transaction'
+
+ begin
+ resp = Oj.load(msg.content, :symbol_keys => true)
+ rescue Oj::ParseError
+ resp = nil
+ end
+ if not resp.is_a? Hash
+ raise InvalidApiResponseException.new(url, msg)
+ elsif msg.status_code != 200
+ error_class = ERROR_CODE_CLASSES.fetch(msg.status_code,
+ ApiErrorResponseException)
+ raise error_class.new(url, msg)
+ end
+
+ if resp[:_profile]
+ Rails.logger.info "API client: " \
+ "#{resp.delete(:_profile)[:request_time]} request_time"
+ end
+ profile_checkpoint 'Parse response'
+ resp
+ end
+
+ def self.patch_paging_vars(ary, items_available, offset, limit, links=nil)
+ if items_available
+ (class << ary; self; end).class_eval { attr_accessor :items_available }
+ ary.items_available = items_available
+ end
+ if offset
+ (class << ary; self; end).class_eval { attr_accessor :offset }
+ ary.offset = offset
+ end
+ if limit
+ (class << ary; self; end).class_eval { attr_accessor :limit }
+ ary.limit = limit
+ end
+ if links
+ (class << ary; self; end).class_eval { attr_accessor :links }
+ ary.links = links
+ end
+ ary
+ end
+
+ def unpack_api_response(j, kind=nil)
+ if j.is_a? Hash and j[:items].is_a? Array and j[:kind].match(/(_list|List)$/)
+ ary = j[:items].collect { |x| unpack_api_response x, x[:kind] }
+ links = ArvadosResourceList.new Link
+ links.results = (j[:links] || []).collect do |x|
+ unpack_api_response x, x[:kind]
+ end
+ self.class.patch_paging_vars(ary, j[:items_available], j[:offset], j[:limit], links)
+ elsif j.is_a? Hash and (kind || j[:kind])
+ oclass = self.kind_class(kind || j[:kind])
+ if oclass
+ j.keys.each do |k|
+ childkind = j["#{k.to_s}_kind".to_sym]
+ if childkind
+ j[k] = self.unpack_api_response(j[k], childkind)
+ end
+ end
+ oclass.new.private_reload(j)
+ else
+ j
+ end
+ else
+ j
+ end
+ end
+
+ def arvados_login_url(params={})
+ if Rails.configuration.respond_to? :arvados_login_base
+ uri = Rails.configuration.arvados_login_base
+ else
+ uri = self.arvados_v1_base.sub(%r{/arvados/v\d+.*}, '/login')
+ end
+ if params.size > 0
+ uri += '?' << params.collect { |k,v|
+ CGI.escape(k.to_s) + '=' + CGI.escape(v.to_s)
+ }.join('&')
+ end
+ uri
+ end
+
+ def arvados_logout_url(params={})
+ arvados_login_url(params).sub('/login','/logout')
+ end
+
+ def arvados_v1_base
+ Rails.configuration.arvados_v1_base
+ end
+
+ def discovery
+ @@discovery ||= api '../../discovery/v1/apis/arvados/v1/rest', ''
+ end
+
+ def kind_class(kind)
+ kind.match(/^arvados\#(.+?)(_list|List)?$/)[1].pluralize.classify.constantize rescue nil
+ end
+
+ def class_kind(resource_class)
+ resource_class.to_s.underscore
+ end
+
+ def self.class_kind(resource_class)
+ resource_class.to_s.underscore
+ end
+
+ protected
+ def profile_checkpoint label=nil
+ return if !@@profiling_enabled
+ label = yield if block_given?
+ t = Time.now
+ if label and @profile_t0
+ Rails.logger.info "API client: #{t - @profile_t0} #{label}"
+ end
+ @profile_t0 = t
+ end
+end
--- /dev/null
+class ArvadosBase < ActiveRecord::Base
+ self.abstract_class = true
+ attr_accessor :attribute_sortkey
+ attr_accessor :create_params
+
+ def self.arvados_api_client
+ ArvadosApiClient.new_or_current
+ end
+
+ def arvados_api_client
+ ArvadosApiClient.new_or_current
+ end
+
+ def self.uuid_infix_object_kind
+ @@uuid_infix_object_kind ||=
+ begin
+ infix_kind = {}
+ arvados_api_client.discovery[:schemas].each do |name, schema|
+ if schema[:uuidPrefix]
+ infix_kind[schema[:uuidPrefix]] =
+ 'arvados#' + name.to_s.camelcase(:lower)
+ end
+ end
+
+ # Recognize obsolete types.
+ infix_kind.
+ merge('mxsvm' => 'arvados#pipelineTemplate', # Pipeline
+ 'uo14g' => 'arvados#pipelineInstance', # PipelineInvocation
+ 'ldvyl' => 'arvados#group') # Project
+ end
+ end
+
+ def initialize raw_params={}, create_params={}
+ super self.class.permit_attribute_params(raw_params)
+ @create_params = create_params
+ @attribute_sortkey ||= {
+ 'id' => nil,
+ 'name' => '000',
+ 'owner_uuid' => '002',
+ 'event_type' => '100',
+ 'link_class' => '100',
+ 'group_class' => '100',
+ 'tail_uuid' => '101',
+ 'head_uuid' => '102',
+ 'object_uuid' => '102',
+ 'summary' => '104',
+ 'description' => '104',
+ 'properties' => '150',
+ 'info' => '150',
+ 'created_at' => '200',
+ 'modified_at' => '201',
+ 'modified_by_user_uuid' => '202',
+ 'modified_by_client_uuid' => '203',
+ 'uuid' => '999',
+ }
+ end
+
+ def self.columns
+ return @columns if @columns.andand.any?
+ @columns = []
+ @attribute_info ||= {}
+ schema = arvados_api_client.discovery[:schemas][self.to_s.to_sym]
+ return @columns if schema.nil?
+ schema[:properties].each do |k, coldef|
+ case k
+ when :etag, :kind
+ attr_reader k
+ else
+ if coldef[:type] == coldef[:type].downcase
+ # boolean, integer, etc.
+ @columns << column(k, coldef[:type].to_sym)
+ else
+ # Hash, Array
+ @columns << column(k, :text)
+ serialize k, coldef[:type].constantize
+ end
+ @attribute_info[k] = coldef
+ end
+ end
+ @columns
+ end
+
+ def self.column(name, sql_type = nil, default = nil, null = true)
+ ActiveRecord::ConnectionAdapters::Column.new(name.to_s, default, sql_type.to_s, null)
+ end
+
+ def self.attribute_info
+ self.columns
+ @attribute_info
+ end
+
+ def self.find(uuid, opts={})
+ if uuid.class != String or uuid.length < 27 then
+ raise 'argument to find() must be a uuid string. Acceptable formats: warehouse locator or string with format xxxxx-xxxxx-xxxxxxxxxxxxxxx'
+ end
+
+ if self == ArvadosBase
+ # Determine type from uuid and defer to the appropriate subclass.
+ return resource_class_for_uuid(uuid).find(uuid, opts)
+ end
+
+ # Only do one lookup on the API side per {class, uuid, workbench
+ # request} unless {cache: false} is given via opts.
+ cache_key = "request_#{Thread.current.object_id}_#{self.to_s}_#{uuid}"
+ if opts[:cache] == false
+ Rails.cache.write cache_key, arvados_api_client.api(self, '/' + uuid)
+ end
+ hash = Rails.cache.fetch cache_key do
+ arvados_api_client.api(self, '/' + uuid)
+ end
+ new.private_reload(hash)
+ end
+
+ def self.find?(*args)
+ find(*args) rescue nil
+ end
+
+ def self.order(*args)
+ ArvadosResourceList.new(self).order(*args)
+ end
+
+ def self.filter(*args)
+ ArvadosResourceList.new(self).filter(*args)
+ end
+
+ def self.where(*args)
+ ArvadosResourceList.new(self).where(*args)
+ end
+
+ def self.limit(*args)
+ ArvadosResourceList.new(self).limit(*args)
+ end
+
+ def self.select(*args)
+ ArvadosResourceList.new(self).select(*args)
+ end
+
+ def self.eager(*args)
+ ArvadosResourceList.new(self).eager(*args)
+ end
+
+ def self.all
+ ArvadosResourceList.new(self)
+ end
+
+ def self.permit_attribute_params raw_params
+ # strong_parameters does not provide security in Workbench: anyone
+ # who can get this far can just as well do a call directly to our
+ # database (Arvados) with the same credentials we use.
+ #
+ # The following permit! is necessary even with
+ # "ActionController::Parameters.permit_all_parameters = true",
+ # because permit_all does not permit nested attributes.
+ ActionController::Parameters.new(raw_params).permit!
+ end
+
+ def self.create raw_params={}, create_params={}
+ x = super(permit_attribute_params(raw_params))
+ x.create_params = create_params
+ x
+ end
+
+ def update_attributes raw_params={}
+ super(self.class.permit_attribute_params(raw_params))
+ end
+
+ def save
+ obdata = {}
+ self.class.columns.each do |col|
+ unless self.send(col.name.to_sym).nil? and !self.changed.include?(col.name)
+ obdata[col.name.to_sym] = self.send(col.name.to_sym)
+ end
+ end
+ obdata.delete :id
+ postdata = { self.class.to_s.underscore => obdata }
+ if etag
+ postdata['_method'] = 'PUT'
+ obdata.delete :uuid
+ resp = arvados_api_client.api(self.class, '/' + uuid, postdata)
+ else
+ postdata.merge!(@create_params) if @create_params
+ resp = arvados_api_client.api(self.class, '', postdata)
+ end
+ return false if !resp[:etag] || !resp[:uuid]
+
+ # set read-only non-database attributes
+ @etag = resp[:etag]
+ @kind = resp[:kind]
+
+ # attributes can be modified during "save" -- we should update our copies
+ resp.keys.each do |attr|
+ if self.respond_to? "#{attr}=".to_sym
+ self.send(attr.to_s + '=', resp[attr.to_sym])
+ end
+ end
+
+ @new_record = false
+
+ self
+ end
+
+ def save!
+ self.save or raise Exception.new("Save failed")
+ end
+
+ def destroy
+ if etag || uuid
+ postdata = { '_method' => 'DELETE' }
+ resp = arvados_api_client.api(self.class, '/' + uuid, postdata)
+ resp[:etag] && resp[:uuid] && resp
+ else
+ true
+ end
+ end
+
+ def links(*args)
+ o = {}
+ o.merge!(args.pop) if args[-1].is_a? Hash
+ o[:link_class] ||= args.shift
+ o[:name] ||= args.shift
+ o[:tail_uuid] = self.uuid
+ if all_links
+ return all_links.select do |m|
+ ok = true
+ o.each do |k,v|
+ if !v.nil?
+ test_v = m.send(k)
+ if (v.respond_to?(:uuid) ? v.uuid : v.to_s) != (test_v.respond_to?(:uuid) ? test_v.uuid : test_v.to_s)
+ ok = false
+ end
+ end
+ end
+ ok
+ end
+ end
+ @links = arvados_api_client.api Link, '', { _method: 'GET', where: o, eager: true }
+ @links = arvados_api_client.unpack_api_response(@links)
+ end
+
+ def all_links
+ return @all_links if @all_links
+ res = arvados_api_client.api Link, '', {
+ _method: 'GET',
+ where: {
+ tail_kind: self.kind,
+ tail_uuid: self.uuid
+ },
+ eager: true
+ }
+ @all_links = arvados_api_client.unpack_api_response(res)
+ end
+
+ def reload
+ private_reload(self.uuid)
+ end
+
+ def private_reload(uuid_or_hash)
+ raise "No such object" if !uuid_or_hash
+ if uuid_or_hash.is_a? Hash
+ hash = uuid_or_hash
+ else
+ hash = arvados_api_client.api(self.class, '/' + uuid_or_hash)
+ end
+ hash.each do |k,v|
+ if self.respond_to?(k.to_s + '=')
+ self.send(k.to_s + '=', v)
+ else
+ # When ArvadosApiClient#schema starts telling us what to expect
+ # in API responses (not just the server side database
+ # columns), this sort of awfulness can be avoided:
+ self.instance_variable_set('@' + k.to_s, v)
+ if !self.respond_to? k
+ singleton = class << self; self end
+ singleton.send :define_method, k, lambda { instance_variable_get('@' + k.to_s) }
+ end
+ end
+ end
+ @all_links = nil
+ @new_record = false
+ self
+ end
+
+ def to_param
+ uuid
+ end
+
+ def initialize_copy orig
+ super
+ forget_uuid!
+ end
+
+ def attributes_for_display
+ self.attributes.reject { |k,v|
+ attribute_sortkey.has_key?(k) and !attribute_sortkey[k]
+ }.sort_by { |k,v|
+ attribute_sortkey[k] or k
+ }
+ end
+
+ def class_for_display
+ self.class.to_s.underscore.humanize
+ end
+
+ def self.class_for_display
+ self.to_s.underscore.humanize
+ end
+
+ # Array of strings that are names of attributes that should be rendered as textile.
+ def textile_attributes
+ []
+ end
+
+ def self.creatable?
+ current_user
+ end
+
+ def self.goes_in_projects?
+ false
+ end
+
+ # can this class of object be copied into a project?
+ # override to false on indivudal model classes for which this should not be true
+ def self.copies_to_projects?
+ self.goes_in_projects?
+ end
+
+ def editable?
+ (current_user and current_user.is_active and
+ (current_user.is_admin or
+ current_user.uuid == self.owner_uuid or
+ new_record? or
+ (respond_to?(:writable_by) ?
+ writable_by.include?(current_user.uuid) :
+ (ArvadosBase.find(owner_uuid).writable_by.include? current_user.uuid rescue false)))) or false
+ end
+
+ # Array of strings that are the names of attributes that can be edited
+ # with X-Editable.
+ def editable_attributes
+ self.class.columns.map(&:name) -
+ %w(created_at modified_at modified_by_user_uuid modified_by_client_uuid updated_at)
+ end
+
+ def attribute_editable?(attr, ever=nil)
+ if not editable_attributes.include?(attr.to_s)
+ false
+ elsif not (current_user.andand.is_active)
+ false
+ elsif attr == 'uuid'
+ current_user.is_admin
+ elsif ever
+ true
+ else
+ editable?
+ end
+ end
+
+ def self.resource_class_for_uuid(uuid, opts={})
+ if uuid.is_a? ArvadosBase
+ return uuid.class
+ end
+ unless uuid.is_a? String
+ return nil
+ end
+ if opts[:class].is_a? Class
+ return opts[:class]
+ end
+ if uuid.match /^[0-9a-f]{32}(\+[^,]+)*(,[0-9a-f]{32}(\+[^,]+)*)*$/
+ return Collection
+ end
+ resource_class = nil
+ uuid.match /^[0-9a-z]{5}-([0-9a-z]{5})-[0-9a-z]{15}$/ do |re|
+ resource_class ||= arvados_api_client.
+ kind_class(self.uuid_infix_object_kind[re[1]])
+ end
+ if opts[:referring_object] and
+ opts[:referring_attr] and
+ opts[:referring_attr].match /_uuid$/
+ resource_class ||= arvados_api_client.
+ kind_class(opts[:referring_object].
+ attributes[opts[:referring_attr].
+ sub(/_uuid$/, '_kind')])
+ end
+ resource_class
+ end
+
+ def resource_param_name
+ self.class.to_s.underscore
+ end
+
+ def friendly_link_name lookup=nil
+ (name if self.respond_to? :name) || default_name
+ end
+
+ def content_summary
+ self.class_for_display
+ end
+
+ def selection_label
+ friendly_link_name
+ end
+
+ def self.default_name
+ self.to_s.underscore.humanize
+ end
+
+ def controller
+ (self.class.to_s.pluralize + 'Controller').constantize
+ end
+
+ def controller_name
+ self.class.to_s.tableize
+ end
+
+ # Placeholder for name when name is missing or empty
+ def default_name
+ if self.respond_to? :name
+ "New #{class_for_display.downcase}"
+ else
+ uuid
+ end
+ end
+
+ def owner
+ ArvadosBase.find(owner_uuid) rescue nil
+ end
+
+ protected
+
+ def forget_uuid!
+ self.uuid = nil
+ @etag = nil
+ self
+ end
+
+ def self.current_user
+ Thread.current[:user] ||= User.current if Thread.current[:arvados_api_token]
+ Thread.current[:user]
+ end
+ def current_user
+ self.class.current_user
+ end
+end
--- /dev/null
+class ArvadosResourceList
+ include ArvadosApiClientHelper
+ include Enumerable
+
+ attr_reader :resource_class
+
+ def initialize resource_class=nil
+ @resource_class = resource_class
+ @fetch_multiple_pages = true
+ @arvados_api_token = Thread.current[:arvados_api_token]
+ @reader_tokens = Thread.current[:reader_tokens]
+ end
+
+ def eager(bool=true)
+ @eager = bool
+ self
+ end
+
+ def limit(max_results)
+ if not max_results.nil? and not max_results.is_a? Integer
+ raise ArgumentError("argument to limit() must be an Integer or nil")
+ end
+ @limit = max_results
+ self
+ end
+
+ def offset(skip)
+ @offset = skip
+ self
+ end
+
+ def order(orderby_spec)
+ @orderby_spec = orderby_spec
+ self
+ end
+
+ def select(columns=nil)
+ # If no column arguments were given, invoke Enumerable#select.
+ if columns.nil?
+ super()
+ else
+ @select ||= []
+ @select += columns
+ self
+ end
+ end
+
+ def filter _filters
+ @filters ||= []
+ @filters += _filters
+ self
+ end
+
+ def where(cond)
+ @cond = cond.dup
+ @cond.keys.each do |uuid_key|
+ if @cond[uuid_key] and (@cond[uuid_key].is_a? Array or
+ @cond[uuid_key].is_a? ArvadosBase)
+ # Coerce cond[uuid_key] to an array of uuid strings. This
+ # allows caller the convenience of passing an array of real
+ # objects and uuids in cond[uuid_key].
+ if !@cond[uuid_key].is_a? Array
+ @cond[uuid_key] = [@cond[uuid_key]]
+ end
+ @cond[uuid_key] = @cond[uuid_key].collect do |item|
+ if item.is_a? ArvadosBase
+ item.uuid
+ else
+ item
+ end
+ end
+ end
+ end
+ @cond.keys.select { |x| x.match /_kind$/ }.each do |kind_key|
+ if @cond[kind_key].is_a? Class
+ @cond = @cond.merge({ kind_key => 'arvados#' + arvados_api_client.class_kind(@cond[kind_key]) })
+ end
+ end
+ self
+ end
+
+ def fetch_multiple_pages(f)
+ @fetch_multiple_pages = f
+ self
+ end
+
+ def results
+ if !@results
+ @results = []
+ self.each_page do |r|
+ @results.concat r
+ end
+ end
+ @results
+ end
+
+ def results=(r)
+ @results = r
+ @items_available = r.items_available if r.respond_to? :items_available
+ @result_limit = r.limit if r.respond_to? :limit
+ @result_offset = r.offset if r.respond_to? :offset
+ @results
+ end
+
+ def to_ary
+ results
+ end
+
+ def each(&block)
+ if not @results.nil?
+ @results.each &block
+ else
+ self.each_page do |items|
+ items.each do |i|
+ block.call i
+ end
+ end
+ end
+ self
+ end
+
+ def first
+ results.first
+ end
+
+ def last
+ results.last
+ end
+
+ def [](*x)
+ results.send('[]', *x)
+ end
+
+ def |(x)
+ if x.is_a? Hash
+ self.to_hash | x
+ else
+ results | x.to_ary
+ end
+ end
+
+ def to_hash
+ Hash[self.collect { |x| [x.uuid, x] }]
+ end
+
+ def empty?
+ self.first.nil?
+ end
+
+ def items_available
+ results
+ @items_available
+ end
+
+ def result_limit
+ results
+ @result_limit
+ end
+
+ def result_offset
+ results
+ @result_offset
+ end
+
+ # Obsolete method retained during api transition.
+ def links_for item_or_uuid, link_class=false
+ []
+ end
+
+ protected
+
+ def each_page
+ api_params = {
+ _method: 'GET'
+ }
+ api_params[:where] = @cond if @cond
+ api_params[:eager] = '1' if @eager
+ api_params[:select] = @select if @select
+ api_params[:order] = @orderby_spec if @orderby_spec
+ api_params[:filters] = @filters if @filters
+
+
+ item_count = 0
+ offset = @offset || 0
+ @result_limit = nil
+ @result_offset = nil
+
+ begin
+ api_params[:offset] = offset
+ api_params[:limit] = (@limit - item_count) if @limit
+
+ res = arvados_api_client.api(@resource_class, '', api_params,
+ arvados_api_token: @arvados_api_token,
+ reader_tokens: @reader_tokens)
+ items = arvados_api_client.unpack_api_response res
+
+ @items_available = items.items_available if items.respond_to?(:items_available)
+ @result_limit = items.limit if (@fetch_multiple_pages == false) and items.respond_to?(:limit)
+ @result_offset = items.offset if (@fetch_multiple_pages == false) and items.respond_to?(:offset)
+
+ break if items.nil? or not items.any?
+
+ item_count += items.size
+ if items.respond_to?(:offset)
+ offset = items.offset + items.size
+ else
+ offset = item_count
+ end
+
+ yield items
+
+ break if @limit and item_count >= @limit
+ break if items.respond_to? :items_available and offset >= items.items_available
+ end while @fetch_multiple_pages
+ self
+ end
+
+end
--- /dev/null
+class AuthorizedKey < ArvadosBase
+ def attribute_editable?(attr, ever=nil)
+ if (attr.to_s == 'authorized_user_uuid') and (not ever)
+ current_user.andand.is_admin
+ else
+ super
+ end
+ end
+end
--- /dev/null
+require "arvados/keep"
+
+class Collection < ArvadosBase
+ MD5_EMPTY = 'd41d8cd98f00b204e9800998ecf8427e'
+
+ def default_name
+ if Collection.is_empty_blob_locator? self.uuid
+ "Empty Collection"
+ else
+ super
+ end
+ end
+
+ # Return true if the given string is the locator of a zero-length blob
+ def self.is_empty_blob_locator? locator
+ !!locator.to_s.match("^#{MD5_EMPTY}(\\+.*)?\$")
+ end
+
+ def self.goes_in_projects?
+ true
+ end
+
+ def manifest
+ if @manifest.nil? or manifest_text_changed?
+ @manifest = Keep::Manifest.new(manifest_text || "")
+ end
+ @manifest
+ end
+
+ def files
+ # This method provides backwards compatibility for code that relied on
+ # the old files field in API results. New code should use manifest
+ # methods directly.
+ manifest.files
+ end
+
+ def content_summary
+ ApplicationController.helpers.human_readable_bytes_html(total_bytes) + " " + super
+ end
+
+ def total_bytes
+ manifest.files.inject(0) { |sum, filespec| sum + filespec.last }
+ end
+
+ def files_tree
+ tree = manifest.files.group_by do |file_spec|
+ File.split(file_spec.first)
+ end
+ return [] if tree.empty?
+ # Fill in entries for empty directories.
+ tree.keys.map { |basedir, _| File.split(basedir) }.each do |splitdir|
+ until tree.include?(splitdir)
+ tree[splitdir] = []
+ splitdir = File.split(splitdir.first)
+ end
+ end
+ dir_to_tree = lambda do |dirname|
+ # First list subdirectories, with their files inside.
+ subnodes = tree.keys.select { |bd, td| (bd == dirname) and (td != '.') }
+ .sort.flat_map do |parts|
+ [parts + [nil]] + dir_to_tree.call(File.join(parts))
+ end
+ # Then extend that list with files in this directory.
+ subnodes + tree[File.split(dirname)]
+ end
+ dir_to_tree.call('.')
+ end
+
+ def editable_attributes
+ %w(name description manifest_text)
+ end
+
+ def self.creatable?
+ false
+ end
+
+ def provenance
+ arvados_api_client.api "collections/#{self.uuid}/", "provenance"
+ end
+
+ def used_by
+ arvados_api_client.api "collections/#{self.uuid}/", "used_by"
+ end
+
+ def uuid
+ if self[:uuid].nil?
+ return self[:portable_data_hash]
+ else
+ super
+ end
+ end
+
+ def friendly_link_name lookup=nil
+ name || portable_data_hash
+ end
+
+ def textile_attributes
+ [ 'description' ]
+ end
+
+end
--- /dev/null
+class Group < ArvadosBase
+ def self.goes_in_projects?
+ true
+ end
+
+ def self.copies_to_projects?
+ false
+ end
+
+ def self.contents params={}
+ res = arvados_api_client.api self, "/contents", {
+ _method: 'GET'
+ }.merge(params)
+ ret = ArvadosResourceList.new
+ ret.results = arvados_api_client.unpack_api_response(res)
+ ret
+ end
+
+ def contents params={}
+ res = arvados_api_client.api self.class, "/#{self.uuid}/contents", {
+ _method: 'GET'
+ }.merge(params)
+ ret = ArvadosResourceList.new
+ ret.results = arvados_api_client.unpack_api_response(res)
+ ret
+ end
+
+ def class_for_display
+ group_class == 'project' ? 'Project' : super
+ end
+
+ def textile_attributes
+ [ 'description' ]
+ end
+end
--- /dev/null
+class Human < ArvadosBase
+ def self.goes_in_projects?
+ true
+ end
+end
--- /dev/null
+class Job < ArvadosBase
+ def self.goes_in_projects?
+ true
+ end
+
+ def content_summary
+ "#{script} job"
+ end
+
+ def editable_attributes
+ %w(description)
+ end
+
+ def self.creatable?
+ false
+ end
+
+ def default_name
+ if script
+ x = "\"#{script}\" job"
+ else
+ x = super
+ end
+ if finished_at
+ x += " finished #{finished_at.strftime('%b %-d')}"
+ elsif started_at
+ x += " started #{started_at.strftime('%b %-d')}"
+ elsif created_at
+ x += " submitted #{created_at.strftime('%b %-d')}"
+ end
+ end
+
+ def cancel
+ arvados_api_client.api "jobs/#{self.uuid}/", "cancel", {}
+ end
+
+ def self.queue_size
+ arvados_api_client.api("jobs/", "queue_size", {"_method"=> "GET"})[:queue_size] rescue 0
+ end
+
+ def self.queue
+ arvados_api_client.unpack_api_response arvados_api_client.api("jobs/", "queue", {"_method"=> "GET"})
+ end
+
+ def textile_attributes
+ [ 'description' ]
+ end
+end
--- /dev/null
+class JobTask < ArvadosBase
+end
--- /dev/null
+class KeepDisk < ArvadosBase
+ def self.creatable?
+ current_user and current_user.is_admin
+ end
+end
--- /dev/null
+class KeepService < ArvadosBase
+ def self.creatable?
+ current_user and current_user.is_admin
+ end
+end
--- /dev/null
+class Link < ArvadosBase
+ attr_accessor :head
+ attr_accessor :tail
+ def self.by_tail(t, opts={})
+ where(opts.merge :tail_uuid => t.uuid)
+ end
+
+ def default_name
+ self.class.resource_class_for_uuid(head_uuid).default_name rescue super
+ end
+
+ def self.permissions_for(thing)
+ if thing.respond_to? :uuid
+ uuid = thing.uuid
+ else
+ uuid = thing
+ end
+ result = arvados_api_client.api("permissions", "/#{uuid}")
+ arvados_api_client.unpack_api_response(result)
+ end
+end
--- /dev/null
+class Log < ArvadosBase
+ attr_accessor :object
+ def self.creatable?
+ # Technically yes, but not worth offering: it will be empty, and
+ # you won't be able to edit it.
+ false
+ end
+end
--- /dev/null
+class Node < ArvadosBase
+ def self.creatable?
+ current_user and current_user.is_admin
+ end
+ def friendly_link_name lookup=nil
+ (hostname && !hostname.empty?) ? hostname : uuid
+ end
+end
--- /dev/null
+class PipelineInstance < ArvadosBase
+ attr_accessor :pipeline_template
+
+ def self.goes_in_projects?
+ true
+ end
+
+ def friendly_link_name lookup=nil
+ pipeline_name = self.name
+ if pipeline_name.nil? or pipeline_name.empty?
+ template = if lookup and lookup[self.pipeline_template_uuid]
+ lookup[self.pipeline_template_uuid]
+ else
+ PipelineTemplate.where(uuid: self.pipeline_template_uuid).first
+ end
+ if template
+ template.name
+ else
+ self.uuid
+ end
+ else
+ pipeline_name
+ end
+ end
+
+ def content_summary
+ begin
+ PipelineTemplate.find(pipeline_template_uuid).name
+ rescue
+ super
+ end
+ end
+
+ def update_job_parameters(new_params)
+ self.components[:steps].each_with_index do |step, i|
+ step[:params].each do |param|
+ if new_params.has_key?(new_param_name = "#{i}/#{param[:name]}") or
+ new_params.has_key?(new_param_name = "#{step[:name]}/#{param[:name]}") or
+ new_params.has_key?(new_param_name = param[:name])
+ param_type = :value
+ %w(hash data_locator).collect(&:to_sym).each do |ptype|
+ param_type = ptype if param.has_key? ptype
+ end
+ param[param_type] = new_params[new_param_name]
+ end
+ end
+ end
+ end
+
+ def editable_attributes
+ %w(name description components)
+ end
+
+ def attribute_editable?(name, ever=nil)
+ if name.to_s == "components"
+ (ever or %w(New Ready).include?(state)) and super
+ else
+ super
+ end
+ end
+
+ def attributes_for_display
+ super.reject { |k,v| k == 'components' }
+ end
+
+ def self.creatable?
+ false
+ end
+
+ def component_input_title(component_name, input_name)
+ component = components[component_name]
+ return nil if component.nil?
+ param_info = component[:script_parameters].andand[input_name.to_sym]
+ if param_info.is_a?(Hash) and param_info[:title]
+ param_info[:title]
+ else
+ "\"#{input_name.to_s}\" parameter for #{component[:script]} script in #{component_name} component"
+ end
+ end
+
+ def textile_attributes
+ [ 'description' ]
+ end
+end
--- /dev/null
+class PipelineTemplate < ArvadosBase
+ def self.goes_in_projects?
+ true
+ end
+
+ def self.creatable?
+ false
+ end
+
+ def textile_attributes
+ [ 'description' ]
+ end
+end
--- /dev/null
+class Repository < ArvadosBase
+ def self.creatable?
+ current_user and current_user.is_admin
+ end
+ def attributes_for_display
+ super.reject { |x| x[0] == 'fetch_url' }
+ end
+end
--- /dev/null
+class Specimen < ArvadosBase
+ def self.goes_in_projects?
+ true
+ end
+end
--- /dev/null
+class Trait < ArvadosBase
+ def self.goes_in_projects?
+ true
+ end
+end
--- /dev/null
+class User < ArvadosBase
+ def initialize(*args)
+ super(*args)
+ @attribute_sortkey['first_name'] = '050'
+ @attribute_sortkey['last_name'] = '051'
+ end
+
+ def self.current
+ res = arvados_api_client.api self, '/current'
+ arvados_api_client.unpack_api_response(res)
+ end
+
+ def self.system
+ @@arvados_system_user ||= begin
+ res = arvados_api_client.api self, '/system'
+ arvados_api_client.unpack_api_response(res)
+ end
+ end
+
+ def full_name
+ (self.first_name || "") + " " + (self.last_name || "")
+ end
+
+ def activate
+ self.private_reload(arvados_api_client.api(self.class,
+ "/#{self.uuid}/activate",
+ {}))
+ end
+
+ def contents params={}
+ Group.contents params.merge(uuid: self.uuid)
+ end
+
+ def attributes_for_display
+ super.reject { |k,v| %w(owner_uuid default_owner_uuid identity_url prefs).index k }
+ end
+
+ def attribute_editable?(attr, ever=nil)
+ (ever or not (self.uuid.andand.match(/000000000000000$/) and
+ self.is_admin)) and super
+ end
+
+ def friendly_link_name lookup=nil
+ [self.first_name, self.last_name].compact.join ' '
+ end
+
+ def unsetup
+ self.private_reload(arvados_api_client.api(self.class,
+ "/#{self.uuid}/unsetup",
+ {}))
+ end
+
+ def self.setup params
+ arvados_api_client.api(self, "/setup", params)
+ end
+
+ def update_profile params
+ self.private_reload(arvados_api_client.api(self.class,
+ "/#{self.uuid}/profile",
+ params))
+ end
+
+end
--- /dev/null
+class UserAgreement < ArvadosBase
+ def self.signatures
+ res = arvados_api_client.api self, '/signatures'
+ arvados_api_client.unpack_api_response(res)
+ end
+ def self.sign(params)
+ res = arvados_api_client.api self, '/sign', params
+ arvados_api_client.unpack_api_response(res)
+ end
+end
--- /dev/null
+class VirtualMachine < ArvadosBase
+ attr_accessor :current_user_logins
+ def self.creatable?
+ current_user.andand.is_admin
+ end
+ def attributes_for_display
+ super.append ['current_user_logins', @current_user_logins]
+ end
+ def editable_attributes
+ super - %w(current_user_logins)
+ end
+ def self.attribute_info
+ merger = ->(k,a,b) { a.merge(b, &merger) }
+ merger [nil,
+ {current_user_logins: {column_heading: "logins", type: 'array'}},
+ super]
+ end
+ def friendly_link_name lookup=nil
+ (hostname && !hostname.empty?) ? hostname : uuid
+ end
+end
--- /dev/null
+<pre>
+### Pasting the following lines at a shell prompt will allow Arvados SDKs
+### to authenticate to your account, <%= current_user.email %>
+
+read ARVADOS_API_TOKEN <<EOF
+<%= Thread.current[:arvados_api_token] %>
+EOF
+export ARVADOS_API_TOKEN ARVADOS_API_HOST=<%= current_api_host %>
+<% if Rails.configuration.arvados_insecure_https %>
+export ARVADOS_API_HOST_INSECURE=true
+<% else %>
+unset ARVADOS_API_HOST_INSECURE
+<% end %>
+</pre>
--- /dev/null
+<%
+ if (controller.andand.action_name == 'show') and params[:uuid]
+ class_name = controller.model_class.to_s.underscore
+ class_name_h = class_name.humanize(capitalize: false)
+ req_item = safe_join([class_name_h, " with UUID ",
+ raw("<code>"), params[:uuid], raw("</code>")], "")
+ req_item_plain_text = safe_join([class_name_h, " with UUID ", params[:uuid]])
+ else
+ req_item = "page you requested"
+ req_item_plain_text = "page you requested"
+ end
+%>
+
+<h2>Not Found</h2>
+
+<p>The <%= req_item %> was not found.
+
+<% if class_name %>
+Perhaps you'd like to
+<%= link_to("browse all #{class_name_h.pluralize}", action: :index, controller: class_name.tableize) %>?
+<% end %>
+
+</p>
+
+<% error_message = "The #{req_item_plain_text} was not found." %>
+<%= render :partial => "report_error", :locals => {error_message: error_message, error_type: '404'} %>
--- /dev/null
+{"errors":<%= raw @errors.to_json %>}
\ No newline at end of file
--- /dev/null
+<% if attrvalue.is_a? Array and attrvalue.collect(&:class).uniq.compact == [String] %>
+ <% attrvalue.each do |message| %>
+ <%= message %><br />
+ <% end %>
+<% else %>
+ <% if attr and obj.attribute_editable?(attr) and (!defined?(editable) || editable) %>
+ <% if resource_class_for_uuid(attrvalue, {referring_object: obj, referring_attr: attr}) %>
+ <%= link_to_if_arvados_object attrvalue, {referring_attr: attr, referring_object: obj, with_class_name: true, friendly_name: true} %>
+ <br>
+ <% end %>
+ <%= render_editable_attribute obj, attr %>
+ <% elsif attr == 'uuid' %>
+ <%= link_to_if_arvados_object attrvalue, {referring_attr: attr, referring_object: obj, with_class_name: false, friendly_name: false} %>
+ <% else %>
+ <%= link_to_if_arvados_object attrvalue, {referring_attr: attr, referring_object: obj, with_class_name: true, friendly_name: true, thumbnail: true} %>
+ <% end %>
+ <!--
+ <% if resource_class_for_uuid(attrvalue, {referring_object: obj, referring_attr: attr}) %>
+ <%= link_to_if_arvados_object(attrvalue, { referring_object: obj, link_text: raw('<span class="glyphicon glyphicon-hand-right"></span>'), referring_attr: attr }) %>
+ <% end %>
+ -->
+<% end %>
--- /dev/null
+<% content_for :arvados_object_table do %>
+
+<% end %>
+
+<% if content_for? :page_content %>
+<%= yield :page_content %>
+<% else %>
+<%= yield :arvados_object_table %>
+<% end %>
+
+<div>
+ <ul class="nav nav-tabs">
+ <% if content_for? :page_content %>
+ <li><a href="#arvados-object-table" data-toggle="tab">Table</a></li>
+ <% end %>
+ <li class="active"><a href="#arvados-object-json" data-toggle="tab">API response JSON</a></li>
+ <% if @object.andand.uuid %>
+ <li><a href="#arvados-object-curl" data-toggle="tab">curl update example</a></li>
+ <li><a href="#arvados-object-arv" data-toggle="tab">“arv” CLI examples</a></li>
+ <li><a href="#arvados-object-python" data-toggle="tab">Python example</a></li>
+ <% end %>
+ </ul>
+
+ <div class="tab-content">
+ <% if content_for? :page_content %>
+ <div id="arvados-object-table" class="tab-pane fade">
+ <%= yield :arvados_object_table %>
+ </div>
+ <% end %>
+ <div id="arvados-object-json" class="tab-pane fade in active">
+
+ </div>
+
+
+ </div>
+</div>
--- /dev/null
+<% object ||= @object %>
+<% if attrvalue.is_a? Hash then attrvalue.each do |infokey, infocontent| %>
+<tr class="info">
+ <td><%= attr %>[<%= infokey %>]</td>
+ <td>
+ <%= render partial: 'application/arvados_attr_value', locals: { obj: object, attr: nil, attrvalue: infocontent } %>
+ </td>
+</tr>
+<% end %>
+<% elsif attrvalue.is_a? String or attrvalue.respond_to? :to_s %>
+<tr class="<%= 'info' if %w(uuid owner_uuid created_at modified_at modified_by_user_uuid modified_by_client_uuid updated_at).include?(attr.to_s) %>">
+ <td><%= attr %></td>
+ <td>
+ <%= render partial: 'application/arvados_attr_value', locals: { obj: object, attr: attr, attrvalue: attrvalue } %>
+ </td>
+</tr>
+<% end %>
--- /dev/null
+<div class="modal arv-choose modal-with-loading-spinner">
+ <div class="modal-dialog" style="width:80%">
+ <div class="modal-content">
+ <div class="modal-header">
+ <button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
+ <h4 class="modal-title"><%= params[:title] || "Choose #{@objects.resource_class.andand.class_for_display}" %></h4>
+ </div>
+
+ <div class="modal-body">
+ <% project_filters, chooser_filters = (params[:filters] || []).partition do |attr, op, val|
+ attr == "owner_uuid" and op == "="
+ end %>
+ <div class="input-group">
+ <% if params[:by_project].to_s != "false" %>
+ <% if project_filters.empty?
+ selected_project_name = 'All projects'
+ else
+ val = project_filters.last.last
+ if val == current_user.uuid
+ selected_project_name = "Home"
+ else
+ selected_project_name = Group.find(val).name rescue val
+ end
+ end
+ %>
+ <div class="input-group-btn" data-filterable-target=".modal.arv-choose .selectable-container">
+ <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">
+ <%= selected_project_name %> <span class="caret"></span>
+ </button>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <%= link_to '#', class: 'chooser-show-project' do %>
+ All projects
+ <% end %>
+ </li>
+ <li class="divider" />
+ <%= render partial: "projects_tree_menu", locals: {
+ :project_link_to => Proc.new do |pnode, &block|
+ link_to "#", {
+ class: "chooser-show-project",
+ data: {'project_uuid' => pnode[:object].uuid},
+ }, &block
+ end,
+ :top_button => nil
+ } %>
+ </ul>
+ </div>
+ <% end %>
+ <input type="text" value="<%=params[:preconfigured_search_str] || ''%>" class="form-control filterable-control focus-on-display" placeholder="Search" data-filterable-target=".modal.arv-choose .selectable-container"/>
+ </div>
+ <div style="height: 1em" />
+
+ <% preview_pane = (params[:preview_pane].to_s != "false")
+ pane_col_class = preview_pane ? "col-md-6" : "col-md-12" %>
+ <div class="row" style="height: 20em">
+ <div class="<%= pane_col_class %> arv-filterable-list selectable-container <%= 'multiple' if multiple %>"
+ style="height: 100%; overflow-y: scroll"
+ data-infinite-scroller="#choose-scroll"
+ id="choose-scroll"
+ data-infinite-content-params-from-chooser="<%= {filters: chooser_filters}.to_json %>"
+ <% if project_filters.any? %>
+ data-infinite-content-params-from-project-dropdown="<%= {filters: project_filters, project_uuid: project_filters.last.last}.to_json %>"
+ <% end %>
+ <%
+ action_data = JSON.parse params['action_data'] if params['action_data']
+ use_preview_sel = action_data ? action_data['use_preview_selection'] : false
+ %>
+ data-infinite-content-href="<%= url_for partial: true,
+ use_preview_selection: use_preview_sel %>">
+ </div>
+ <% if preview_pane %>
+ <div class="col-md-6 hidden-xs hidden-sm modal-dialog-preview-pane" style="height: 100%; overflow-y: scroll">
+ </div>
+ <% end %>
+ </div>
+
+ <div class="modal-footer">
+ <button class="btn btn-default" data-dismiss="modal" aria-hidden="true">Cancel</button>
+ <button class="btn btn-primary" aria-hidden="true" data-enable-if-selection disabled><%= raw(params[:action_name]) || 'Select' %></button>
+ <div class="modal-error hide" style="text-align: left; margin-top: 1em;">
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+</div>
--- /dev/null
+<%
+=begin
+
+Parameters received from the caller/requestor of the modal are
+attached to the action button (.btn-primary) as follows:
+
+action_class -- string -- added as a pseudoclass to the action button.
+
+action_href -- string -- will be available at $(btn).attr('data-action-href')
+
+action_data -- json-encoded object -- will be at $(btn).data('action-data')
+
+action_data_form_params -- array -- for each X in this array, the
+value of params[X] during this "show chooser" request will be in
+$(btn).data('action-data-from-params')[X].
+
+=end
+%>
+
+$('body > .modal-container').html("<%= escape_javascript(render partial: 'choose.html', locals: {multiple: multiple}) %>");
+$('body > .modal-container .modal').modal('show');
+$('body > .modal-container .modal .modal-footer .btn-primary').
+ addClass('<%= j params[:action_class] %>').
+ attr('data-action-href', '<%= j params[:action_href] %>').
+ attr('data-method', '<%= j params[:action_method] %>').
+ data('action-data', <%= raw params[:action_data] %>).
+ data('action-data-from-params', <%= raw params.select { |k,v| k.in?(params[:action_data_from_params] || []) }.to_json %>);
--- /dev/null
+<% content_for :tab_panes do %>
+
+ <% comparable = controller.respond_to? :compare %>
+
+ <ul class="nav nav-tabs" data-tab-counts-url="<%= url_for(action: :tab_counts) rescue '' %>">
+ <% pane_list.each_with_index do |pane, i| %>
+ <% pane_name = (pane.is_a?(Hash) ? pane[:name] : pane) %>
+ <li class="<%= 'active' if i==0 %>">
+ <a href="#<%= pane_name %>"
+ id="<%= pane_name %>-tab"
+ data-toggle="tab"
+ data-tab-history=true
+ data-tab-history-update-url=true
+ >
+ <%= pane_name.gsub('_', ' ') %> <span id="<%= pane_name %>-count"></span>
+ </a>
+ </li>
+ <% end %>
+ </ul>
+
+ <div class="tab-content">
+ <% pane_list.each_with_index do |pane, i| %>
+ <% pane_name = (pane.is_a?(Hash) ? pane[:name] : pane) %>
+ <div id="<%= pane_name %>"
+ class="tab-pane fade <%= 'in active pane-loaded' if i==0 %> arv-log-event-listener arv-refresh-on-log-event arv-log-event-subscribe-to-pipeline-job-uuids"
+ <% if controller.action_name == "index" %>
+ data-object-kind="arvados#<%= ArvadosApiClient.class_kind controller.model_class %>"
+ <% else %>
+ data-object-uuid="<%= @object.uuid %>"
+ <% end %>
+ data-pane-content-url="<%= url_for(params.merge(tab_pane: pane_name)) %>"
+ style="margin-top:0.5em;"
+ >
+ <div class="pane-content">
+ <% if i == 0 %>
+ <%= render_pane pane_name, to_string: true %>
+ <% else %>
+ <div class="spinner spinner-32px spinner-h-center"></div>
+ <% end %>
+ </div>
+ </div>
+ <% end %>
+ </div>
+
+<% end %>
--- /dev/null
+<div class="clearfix">
+ <%= content_for :content_top %>
+ <div class="pull-right">
+ <%= content_for :tab_line_buttons %>
+ </div>
+</div>
+
+<%= content_for :tab_panes %>
+
+<%= render :partial => 'loading_modal' %>
--- /dev/null
+<% if object.editable? %>
+ <%= link_to({action: 'destroy', id: object.uuid}, method: :delete, remote: true, data: {confirm: "Really delete #{object.class_for_display.downcase} '#{object.friendly_link_name}'?"}) do %>
+ <i class="glyphicon glyphicon-trash"></i>
+ <% end %>
+<% end %>
--- /dev/null
+<% if (j.andand[:state] == "Running" or defined? scaleby) and (not defined? show_progress_bar or show_progress_bar) %>
+ <%
+ failed = j[:tasks_summary][:failed] || 0 rescue 0
+ done = j[:tasks_summary][:done] || 0 rescue 0
+ running = j[:tasks_summary][:running] || 0 rescue 0
+ todo = j[:tasks_summary][:todo] || 0 rescue 0
+
+ if done + running + failed + todo == 0
+ # No tasks were ever created for this job;
+ # render an empty progress bar.
+ done_percent = 0
+ else
+ percent_total_tasks = 100.0 / (done + running + failed + todo)
+ if defined? scaleby
+ percent_total_tasks *= scaleby
+ end
+ done_percent = (done+failed) * percent_total_tasks
+ end
+ %>
+
+ <% if not defined? scaleby %>
+ <div class="progress" style="margin-bottom: 0px">
+ <% end %>
+
+ <span class="progress-bar <%= if failed == 0 then 'progress-bar-success' else 'progress-bar-warning' end %>" style="width: <%= done_percent %>%;">
+ </span>
+
+ <% if not defined? scaleby %>
+ </div>
+ <% end %>
+
+<% else %>
+
+<% to_label = {
+ "Cancelled" => "danger",
+ "Complete" => "success",
+ "Running" => "info",
+ "Failed" => "danger",
+ "Queued" => "default",
+ nil => "default"
+ } %>
+
+ <span class="label label-<%= to_label[j.andand[:state]] %>">
+ <%= if defined? title
+ title
+ else
+ if j.andand[:state] then j[:state].downcase else "Not ready" end
+ end
+ %></span>
+
+<% end %>
--- /dev/null
+<div class="socket">
+ <div class="gel center-gel">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c1 r1">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c2 r1">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c3 r1">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c4 r1">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c5 r1">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c6 r1">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+
+ <div class="gel c7 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+
+ <div class="gel c8 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c9 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c10 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c11 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c12 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c13 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c14 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c15 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c16 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c17 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c18 r2">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c19 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c20 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c21 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c22 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c23 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c24 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c25 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c26 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c28 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c29 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c30 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c31 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c32 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c33 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c34 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c35 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c36 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+ <div class="gel c37 r3">
+ <div class="hex-brick h1"></div>
+ <div class="hex-brick h2"></div>
+ <div class="hex-brick h3"></div>
+ </div>
+
+</div>
--- /dev/null
+<div id="loading-modal" class="modal fade">
+ <div class="modal-dialog">
+ <div class="modal-content">
+ <div class="modal-header">
+ <h3>Refreshing...</h3>
+ </div>
+ <div class="modal-body">
+ <p>Content may have changed.</p>
+ </div>
+ </div>
+ </div>
+</div>
--- /dev/null
+<% if @object.respond_to? :name %>
+ <h2>
+ <%= render_editable_attribute @object, 'name', nil, { 'data-emptytext' => "New #{controller.model_class.to_s.underscore.gsub("_"," ")}" } %>
+ </h2>
+<% end %>
+
+<% if @object.respond_to? :description %>
+ <div class="arv-description-as-subtitle">
+ <%= render_editable_attribute @object, 'description', nil, { 'data-emptytext' => "(No description provided)", 'data-toggle' => 'manual' } %>
+ </div>
+<% end %>
+
--- /dev/null
+<% content_for :css do %>
+.index-paging {
+text-align: center;
+padding-left: 1em;
+padding-right: 1em;
+background-color: whitesmoke;
+}
+.paging-number {
+display: inline-block;
+min-width: 1.2em;
+}
+<% end %>
+
+<% results.fetch_multiple_pages(false) %>
+
+<% if results.respond_to? :result_offset and
+ results.respond_to? :result_limit and
+ results.respond_to? :items_available and
+ results.result_offset != nil and
+ results.result_limit != nil and
+ results.items_available != nil
+%>
+<div class="index-paging">
+ Displaying <%= results.result_offset+1 %> –
+ <%= if results.result_offset + results.result_limit > results.items_available
+ results.items_available
+ else
+ results.result_offset + results.result_limit
+ end %>
+ out of <%= results.items_available %>
+</div>
+
+<% if not (results.result_offset == 0 and results.items_available <= results.result_limit) %>
+
+<div class="index-paging">
+
+<% if results.result_offset > 0 %>
+ <% if results.result_offset > results.result_limit %>
+ <% prev_offset = results.result_offset - results.result_limit %>
+ <% else %>
+ <% prev_offset = 0 %>
+ <% end %>
+<% else %>
+ <% prev_offset = nil %>
+<% end %>
+
+<% this_offset = results.result_offset %>
+
+<% if (results.result_offset + results.result_limit) < results.items_available %>
+ <% next_offset = results.result_offset + results.result_limit %>
+<% else %>
+ <% next_offset = nil %>
+<% end %>
+
+<span class="pull-left">
+<% if results.result_offset > 0 %>
+ <%= link_to raw("<span class='glyphicon glyphicon-fast-backward'></span>"), {:id => object, :offset => 0, :limit => results.result_limit} %>
+<% else %>
+ <span class='glyphicon glyphicon-fast-backward text-muted'></span>
+<% end %>
+
+<% if prev_offset %>
+ <%= link_to raw("<span class='glyphicon glyphicon-step-backward'></span>"), {:id => object, :offset => prev_offset, :limit => results.result_limit} %>
+<% else %>
+<span class='glyphicon glyphicon-step-backward text-muted'></span>
+<% end %>
+</span>
+
+<% first = this_offset - (10 * results.result_limit) %>
+<% last = this_offset + (11 * results.result_limit) %>
+
+<% lastpage_offset = (results.items_available / results.result_limit) * results.result_limit %>
+
+<% if last > results.items_available %>
+ <% first -= (last - lastpage_offset) %>
+ <% last -= (last - results.items_available) %>
+<% end %>
+
+<% if first < 0 %>
+ <% d = -first %>
+ <% first += d %>
+ <% last += d %>
+<% end %>
+
+<% last = results.items_available if last > results.items_available %>
+
+<% i = first %>
+<% n = first / results.result_limit %>
+
+<% if first > 0 %>
+…
+<% end %>
+
+<% while i < last %>
+<% if i != this_offset %>
+ <%= link_to "#{n+1}", {:id => @object, :offset => i, :limit => results.result_limit}, class: 'paging-number' %>
+<% else %>
+ <span class="paging-number" style="font-weight: bold;"><%= n+1 %></span>
+<% end %>
+<% i += results.result_limit %>
+<% n += 1 %>
+<% end %>
+
+<% if last < results.items_available %>
+…
+<% end %>
+
+<span class="pull-right">
+<% if next_offset %>
+ <%= link_to raw("<span class='glyphicon glyphicon-step-forward'></span>"), {:id => @object, :offset => next_offset, :limit => results.result_limit} %>
+<% else %>
+<span class='glyphicon glyphicon-forward text-muted'></span>
+<% end %>
+
+<% if (results.items_available - results.result_offset) >= results.result_limit %>
+ <%= link_to raw("<span class='glyphicon glyphicon-fast-forward'></span>"), {:id => @object, :offset => results.items_available - (results.items_available % results.result_limit),
+ :limit => results.result_limit} %>
+<% else %>
+ <span class='glyphicon glyphicon-fast-forward text-muted'></span>
+<% end %>
+
+</span>
+
+</div>
+
+<% end %>
+
+<% end %>
--- /dev/null
+<% component_frac = 1.0 / p.components.length %>
+<div class="progress">
+ <% p.components.each do |k,c| %>
+ <% if c.is_a?(Hash) and c[:job] %>
+ <%= render partial: "job_progress", locals: {:j => c[:job], :scaleby => component_frac } %>
+ <% end %>
+ <% end %>
+</div>
--- /dev/null
+<% if p.state == 'Complete' %>
+ <span class="label label-success">complete</span>
+<% elsif p.state == 'Failed' %>
+ <span class="label label-danger">failed</span>
+<% elsif p.state == 'RunningOnServer' || p.state == 'RunningOnClient' %>
+ <span class="label label-info">running</span>
+<% elsif p.state == 'Paused' %>
+ <span class="label label-default">paused</span>
+<% else %>
+ <% if not p.components.values.any? { |c| c[:job] rescue false } %>
+ <span class="label label-default">not started</span>
+ <% else %>
+ <span class="label label-default">not running</span>
+ <% end %>
+<% end %>
--- /dev/null
+<li>
+ <%= project_link_to.call({object: current_user, depth: 0}) do %>
+ <span style="padding-left: 0">Home</span>
+ <% end %>
+</li>
+<% my_project_tree.each do |pnode| %>
+ <% next if pnode[:object].class != Group %>
+ <li>
+ <%= project_link_to.call pnode do %>
+ <span style="padding-left: <%= pnode[:depth] %>em"></span><%= pnode[:object].name %>
+ <% end %>
+ </li>
+<% end %>
+<li class="divider" />
+<li role="presentation" class="dropdown-header">
+ Projects shared with me
+</li>
+<% shared_project_tree.each do |pnode| %>
+ <% next if pnode[:object].class != Group %>
+ <li>
+ <%= project_link_to.call pnode do %>
+ <span style="padding-left: <%= pnode[:depth]-1 %>em"></span><i class="fa fa-fw fa-share-alt" style="color:#aaa"></i> <%= pnode[:object].name %>
+ <% end %>
+ </li>
+<% end %>
--- /dev/null
+<p>
+<br/><strong>If you suspect this is a bug, you can help us fix it by sending us a problem report:</strong><br/><br/>
+<% if error_type == 'api' %>
+ <%
+ api_request_url = api_error.andand.request_url ? api_error.request_url : ''
+ api_error_response = api_error.andand.api_response ? api_error.api_response : ''
+ %>
+ Send a problem report right here. <%= link_to report_issue_popup_path(popup_type: 'report', current_location: request.url, current_path: request.fullpath, action_method: 'post', api_error_request_url: api_request_url, api_error_response: api_error_response),
+ {class: 'btn btn-primary report-issue-modal-window', :remote => true, return_to: request.url} do %>
+ <i class="fa fa-fw fa-support"></i> Report problem
+ <% end %>
+<% else %>
+ Send a problem report right here. <%= link_to report_issue_popup_path(popup_type: 'report', current_location: request.url, current_path: request.fullpath, action_method: 'post', error_message: error_message),
+ {class: 'btn btn-primary report-issue-modal-window', :remote => true, return_to: request.url} do %>
+ <i class="fa fa-fw fa-support"></i> Report problem
+ <% end %>
+<% end %>
+<% support_email = Rails.configuration.support_email_address%>
+<br/><br/>
+ If you prefer, send email to: <a href="mailto:<%=support_email%>?subject=Workbench problem report&body=Problem while viewing page <%=request.url%>"><%=support_email%></a>
+</p>
--- /dev/null
+<%
+ generated_at = arvados_api_client.discovery[:generatedAt]
+ arvados_base = Rails.configuration.arvados_v1_base
+ support_email = Rails.configuration.support_email_address
+
+ api_version_link = link_to api_version_text, version_link_target(api_version)
+ wb_version_link = link_to wb_version_text, version_link_target(wb_version)
+
+ additional_info = {}
+ additional_info['Current location'] = params[:current_location]
+ additional_info['User UUID'] = current_user.uuid if current_user
+
+ additional_info_str = additional_info.map {|k,v| "#{k}=#{v}"}.join("\n")
+
+ additional_info['api_version'] = api_version_text
+ additional_info['generated_at'] = generated_at
+ additional_info['workbench_version'] = wb_version_text
+ additional_info['arvados_base'] = arvados_base
+ additional_info['support_email'] = support_email
+ additional_info['error_message'] = params[:error_message] if params[:error_message]
+ additional_info['api_error_request_url'] = params[:api_error_request_url] if params[:api_error_request_url]
+ additional_info['api_error_response'] = params[:api_error_response] if params[:api_error_response]
+%>
+
+<div class="modal">
+ <div class="modal-dialog modal-with-loading-spinner">
+ <div class="modal-content">
+
+ <%= form_tag report_issue_path, {name: 'report-issue-form', method: 'post',
+ class: 'form-horizontal', remote: true} do %>
+
+ <%
+ title = 'Version / debugging info'
+ title = 'Report a problem' if params[:popup_type] == 'report'
+ %>
+
+ <div class="modal-header">
+ <button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
+ <div>
+ <div class="col-sm-8"> <h4 class="modal-title"><%=title%></h4> </div>
+ <div class="spinner spinner-32px spinner-h-center col-sm-1" hidden="true"></div>
+ </div>
+ <br/>
+ </div>
+
+ <div class="modal-body" style="height: 25em; overflow-y: scroll">
+ <div class="form-group">
+ <label for="support_email" class="col-sm-4 control-label"> Support email </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" name="support_version"><a href="mailto:<%=support_email%>?subject=Workbench problem report&body=Problem while viewing page <%=params[:current_location]%>"><%=support_email%></a></p>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="current_page" class="col-sm-4 control-label"> Current page </label>
+ <div class="col-sm-8">
+ <p class="form-control-static text-overflow-ellipsis" name="current_page"><%=params[:current_path]%></a></p>
+ </div>
+ </div>
+
+ <% if params[:popup_type] == 'report' %>
+ <div class="form-group">
+ <label for="report_text_label" class="col-sm-4 control-label"> Describe the problem </label>
+ <div class="col-sm-8">
+ <textarea class="form-control" rows="4" id="report_issue_text" name="report_issue_text" type="text" placeholder="Describe the problem"/>
+ </div>
+ <input type="hidden" name="report_additional_info" value="<%=additional_info.to_json%>">
+ </div>
+ <% end %>
+
+ <div class="form-group">
+ <label for="wb_version" class="col-sm-4 control-label"> Workbench version </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" name="wb_version"><%= wb_version_link %></p>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="server_version" class="col-sm-4 control-label"> API version </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" name="server_version"><%= api_version_link %></p>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="generated_at" class="col-sm-4 control-label"> API startup time </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" name="generated_at"><%=generated_at%></p>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="arvados_base" class="col-sm-4 control-label"> API address </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" name="arvados_base"><%=arvados_base%></p>
+ </div>
+ </div>
+
+ <% if current_user %>
+ <div class="form-group">
+ <label for="user_uuid" class="col-sm-4 control-label"> User UUID </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" name="user_uuid"><%=current_user.uuid%></p>
+ </div>
+ </div>
+ <% end %>
+
+ <% if params[:error_message] %>
+ <div class="form-group">
+ <label for="error_message" class="col-sm-4 control-label"> Error message </label>
+ <div class="col-sm-8">
+ <p class="form-control-static text-overflow-ellipsis" name="error_message"><%=params[:error_message]%></p>
+ </div>
+ </div>
+ <% end %>
+
+ <% if params[:api_error_request_url] %>
+ <div class="form-group">
+ <label for="api_error_url" class="col-sm-4 control-label"> API error request URL </label>
+ <div class="col-sm-8">
+ <p class="form-control-static text-overflow-ellipsis" name="api_error_url"><%=params[:api_error_request_url]%></p>
+ </div>
+ </div>
+ <% end %>
+
+ <% if params[:api_error_response] %>
+ <div class="form-group">
+ <label for="api_error_response" class="col-sm-4 control-label"> API error response </label>
+ <div class="col-sm-8">
+ <p class="form-control-static text-overflow-ellipsis" name="api_error_response"><%=params[:api_error_response]%></p>
+ </div>
+ </div>
+ <% end %>
+ </div>
+
+ <div class="modal-footer">
+ <% if params[:popup_type] == 'report' %>
+ <button class="btn btn-default report-issue-cancel" id="report-issue-cancel" data-dismiss="modal" aria-hidden="true">Cancel</button>
+ <button type="submit" id="report-issue-submit" class="btn btn-primary report-issue-submit" autofocus>Send problem report</button>
+ <% else %>
+ <button class="btn btn-default" data-dismiss="modal" aria-hidden="true">Close</button>
+ <% end %>
+ </div>
+ <% end #form %>
+ </div>
+ </div>
+</div>
--- /dev/null
+<%if object and object.uuid and (object.class.goes_in_projects? or (object.is_a?(Link) and ArvadosBase::resource_class_for_uuid(object.head_uuid).to_s == 'Collection')) %>
+ <% fn = if defined? friendly_name and not friendly_name.nil?
+ friendly_name
+ else
+ link_to_if_arvados_object object, {no_link: true}
+ end
+ %>
+ <% # This 'fn' string may contain embedded HTML which is already marked html_safe.
+ # Since we are putting it into a tag attribute, we need to copy into an
+ # unsafe string so that rails will escape it for us.
+ fn = String.new fn %>
+<%= check_box_tag 'uuids[]', object.uuid, false, {
+ :class => 'persistent-selection',
+ :friendly_type => object.class.name,
+ :friendly_name => fn,
+ :href => "#{url_for controller: object.class.name.tableize, action: 'show', id: object.uuid }",
+ :title => "Click to add this item to your selection list"
+} %>
+<% end %>
--- /dev/null
+<div class="panel-group" id="arv-adv-accordion">
+ <% ['API response',
+ 'Metadata',
+ 'Python example',
+ 'CLI example',
+ 'curl example'].each do |section| %>
+ <% section_id = section.gsub(" ","_").downcase %>
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <h4 class="panel-title">
+ <a data-toggle="collapse" data-parent="#arv-adv-accordion" href="#advanced_<%=section_id%>">
+ <%= section %>
+ </a>
+ </h4>
+ </div>
+ <div id="advanced_<%=section_id%>" class="panel-collapse collapse <%#= 'in' if section == 'API response'%>">
+ <div class="panel-body">
+ <%= render partial: "show_advanced_#{section_id}", locals: {object: @object} %>
+ </div>
+ </div>
+ </div>
+ <% end %>
+</div>
--- /dev/null
+<pre>
+<%= JSON.pretty_generate(object.attributes.reject { |k,v| k == 'id' }) rescue nil %>
+</pre>
--- /dev/null
+An example arv command to get a <%= object.class.to_s.underscore %> using its uuid:
+<pre>
+arv <%= object.class.to_s.underscore %> get \
+ --uuid <%= object.uuid %>
+</pre>
+
+An example arv command to update the "<%= object.attributes.keys[-3] %>" attribute for the current <%= object.class.to_s.underscore %>:
+<pre>
+arv <%= object.class.to_s.underscore %> update \
+ --uuid <%= object.uuid %> \
+ --<%= object.class.to_s.underscore.gsub '_', '-' %> '<%= JSON.generate({object.attributes.keys[-3] => object.attributes.values[-3]}).gsub("'","'\''") %>'
+</pre>
--- /dev/null
+An example curl command to update the "<%= object.attributes.keys[-3] %>" attribute for the current <%= object.class.to_s.underscore %>:
+<pre>
+curl -X PUT \
+ -H "Authorization: OAuth2 $ARVADOS_API_TOKEN" \
+ --data-urlencode <%= object.class.to_s.underscore %>@/dev/stdin \
+ https://$ARVADOS_API_HOST/arvados/v1/<%= object.class.to_s.pluralize.underscore %>/<%= object.uuid %> \
+ <<EOF
+<%= JSON.pretty_generate({object.attributes.keys[-3] => object.attributes.values[-3]}) %>
+EOF
+</pre>
--- /dev/null
+<% outgoing = Link.where(tail_uuid: @object.uuid) %>
+<% incoming = Link.where(head_uuid: @object.uuid) %>
+
+<%
+ preload_uuids = []
+ preload_head_uuids = []
+ outgoing.results.each do |link|
+ preload_uuids << link.uuid
+ preload_uuids << link.head_uuid
+ preload_head_uuids << link.head_uuid
+ end
+ preload_collections_for_objects preload_uuids
+ preload_links_for_objects preload_head_uuids
+%>
+
+<% if (outgoing | incoming).any? %>
+<table class="table topalign">
+ <colgroup>
+ <col width="20%" />
+ <col width="10%" />
+ <col width="10%" />
+ <col width="20%" />
+ <col width="20%" />
+ <col width="20%" />
+ </colgroup>
+ <thead>
+ <tr>
+ <th></th>
+ <th>link_class</th>
+ <th>name</th>
+ <th>tail</th>
+ <th>head</th>
+ <th>properties</th>
+ </tr>
+ </thead>
+ <tbody>
+ <% (outgoing | incoming).each do |link| %>
+ <tr>
+ <td>
+ <%= render partial: 'show_object_button', locals: { object: link, size: 'xs' } %>
+ <span class="arvados-uuid"><%= link.uuid %></span>
+ </td>
+ <td><%= link.link_class %></td>
+ <td><%= link.name %></td>
+ <td><%= link.tail_uuid == object.uuid ? 'this' : (render partial: 'application/arvados_attr_value', locals: { obj: link, attr: "tail_uuid", attrvalue: link.tail_uuid, editable: false }) %></td>
+ <td><%= link.head_uuid == object.uuid ? 'this' : (render partial: 'application/arvados_attr_value', locals: { obj: link, attr: "head_uuid", attrvalue: link.head_uuid, editable: false }) %></td>
+ <td><%= render partial: 'application/arvados_attr_value', locals: { obj: link, attr: "properties", attrvalue: link.properties, editable: false } %></td>
+ </tr>
+ <% end %>
+ </tbody>
+</table>
+<% else %>
+<span class="deemphasize">
+ (No metadata links found)
+</span>
+<% end %>
--- /dev/null
+An example python command to get a <%= object.class.to_s.underscore %> using its uuid:
+<pre>
+import arvados
+
+x = arvados.api().<%= object.class.to_s.pluralize.underscore %>().get(uuid='<%= object.uuid %>').execute()
+</pre>
--- /dev/null
+<% if @object.andand.uuid %>
+
+<div class="panel panel-default">
+ <div class="panel-heading">curl</div>
+ <div class="panel-body">
+ <pre>
+curl -X PUT \
+ -H "Authorization: OAuth2 $ARVADOS_API_TOKEN" \
+ --data-urlencode <%= @object.class.to_s.underscore %>@/dev/stdin \
+ https://$ARVADOS_API_HOST/arvados/v1/<%= @object.class.to_s.pluralize.underscore %>/<%= @object.uuid %> \
+ <<EOF
+<%= JSON.pretty_generate({@object.attributes.keys[-3] => @object.attributes.values[-3]}) %>
+EOF
+ </pre>
+ </div>
+</div>
+
+<div class="panel panel-default">
+ <div class="panel-heading"><b>arv</b> command line tool</div>
+ <div class="panel-body">
+ <pre>
+arv <%= @object.class.to_s.underscore %> get \
+ --uuid <%= @object.uuid %>
+
+arv <%= @object.class.to_s.underscore %> update \
+ --uuid <%= @object.uuid %> \
+ --<%= @object.class.to_s.underscore.gsub '_', '-' %> '<%= JSON.generate({@object.attributes.keys[-3] => @object.attributes.values[-3]}).gsub("'","'\''") %>'
+ </pre>
+ </div>
+</div>
+
+<div class="panel panel-default">
+ <div class="panel-heading"><b>Python</b> SDK</div>
+ <div class="panel-body">
+ <pre>
+import arvados
+
+x = arvados.api().<%= @object.class.to_s.pluralize.underscore %>().get(uuid='<%= @object.uuid %>').execute()
+ </pre>
+<% end %>
+ </div>
+</div>
--- /dev/null
+<%= form_for @object do |f| %>
+<table class="table topalign">
+ <thead>
+ </thead>
+ <tbody>
+ <% @object.attributes_for_display.each do |attr, attrvalue| %>
+ <%= render partial: 'application/arvados_object_attr', locals: { attr: attr, attrvalue: attrvalue } %>
+ <% end %>
+ </tbody>
+</table>
+
+<% end %>
+
--- /dev/null
+<% htmloptions = {class: ''}.merge(htmloptions || {})
+ htmloptions[:class] += " btn-#{size}" rescue nil
+ link_text = 'Show' unless defined?(link_text) and link_text
+ %>
+<%= link_to_if_arvados_object object, {
+ link_text: raw('<i class="fa fa-fw ' + fa_icon_class_for_object(object) + '"></i> ' + link_text),
+ name_link: (defined?(name_link) && name_link && name_link.uuid) ? name_link : nil
+ }, {
+ data: {
+ toggle: 'tooltip',
+ placement: 'top'
+ },
+ title: 'show ' + object.class_for_display.downcase,
+ class: 'btn btn-default ' + htmloptions[:class],
+ } %>
--- /dev/null
+<%= object.content_summary %>
+
--- /dev/null
+<% if objects.empty? %>
+<br/>
+<p style="text-align: center">
+ No <%= controller.controller_name.humanize.downcase %> to display.
+</p>
+
+<% else %>
+
+<% attr_blacklist = ' created_at modified_at modified_by_user_uuid modified_by_client_uuid updated_at owner_uuid group_class properties' %>
+
+<%= render partial: "paging", locals: {results: objects, object: @object} %>
+
+<%= form_tag do |f| %>
+
+<table class="table table-condensed arv-index">
+ <thead>
+ <tr>
+ <% if objects.first and objects.first.class.goes_in_projects? %>
+ <th></th>
+ <% end %>
+ <th></th>
+ <% objects.first.attributes_for_display.each do |attr, attrvalue| %>
+ <% next if attr_blacklist.index(" "+attr) %>
+ <th class="arv-attr-<%= attr %>">
+ <%= controller.model_class.attribute_info[attr.to_sym].andand[:column_heading] or attr.sub /_uuid/, '' %>
+ </th>
+ <% end %>
+ <th>
+ <!-- a column for delete buttons -->
+ </th>
+ </tr>
+ </thead>
+
+ <tbody>
+ <% objects.each do |object| %>
+ <tr data-object-uuid="<%= object.uuid %>">
+ <% if objects.first.class.goes_in_projects? %>
+ <td>
+ <%= render :partial => "selection_checkbox", :locals => {:object => object} %>
+ </td>
+ <% end %>
+ <td>
+ <%= render :partial => "show_object_button", :locals => {object: object, size: 'xs'} %>
+ </td>
+
+ <% object.attributes_for_display.each do |attr, attrvalue| %>
+ <% next if attr_blacklist.index(" "+attr) %>
+ <td class="arv-object-<%= object.class.to_s %> arv-attr-<%= attr %>">
+ <% if attr == 'uuid' %>
+ <span class="arvados-uuid"><%= attrvalue %></span>
+ <% else %>
+ <%= link_to_if_arvados_object attrvalue, {referring_attr: attr, referring_object: object, with_class_name: true, friendly_name: true} %>
+ <% end %>
+ </td>
+ <% end %>
+ <td>
+ <%= render partial: 'delete_object_button', locals: {object:object} %>
+ </td>
+ </tr>
+ <% end %>
+ </tbody>
+
+ <tfoot>
+ </tfoot>
+</table>
+
+<% end %>
+
+<%= render partial: "paging", locals: {results: objects, object: @object} %>
+
+<% end %>
--- /dev/null
+<%= content_for :css do %>
+/* Need separate style for each instance of svg div because javascript will manipulate the properties. */
+#<%= divId %> {
+ padding-left: 3px;
+ overflow: auto;
+ border: solid;
+ border-width: 1px;
+ border-color: gray;
+ position: absolute;
+ left: 25px;
+ right: 25px;
+}
+path:hover {
+stroke-width: 5;
+}
+path {
+stroke-linecap: round;
+}
+<% end %>
+
+<%= content_for :js do %>
+ $(window).on('load', function() {
+ $(window).on('load resize scroll', function () { graph_zoom("<%= divId %>","<%=svgId %>", 1) } );
+ });
+<% end %>
+
+<div id="_<%= divId %>_container">
+ <div style="text-align: right">
+ <a style="cursor: pointer"><span class="glyphicon glyphicon-zoom-out" onclick="graph_zoom('<%= divId %>', '<%= svgId %>', .9)"></span></a>
+ <a style="cursor: pointer"><span class="glyphicon glyphicon-zoom-in" onclick="graph_zoom('<%= divId %>', '<%= svgId %>', 1./.9)"></span></a>
+ </div>
+
+ <div id="<%= divId %>" class="smart-scroll">
+ <span id="_<%= divId %>_center" style="padding-left: 0px"></span>
+ <%= raw(svg) %>
+ </div>
+</div>
--- /dev/null
+<% object_class = @object.class_for_display.downcase %>
+<% content_for :page_title do %>
+ <%= (@object.respond_to?(:properties) and !@object.properties.nil? ? @object.properties[:page_title] : nil) ||
+ @name_link.andand.name ||
+ @object.friendly_link_name %>
+<% end %>
+
+<% content_for :content_top do %>
+ <% if !['Group','User', 'Collection'].include? @object.class.to_s # projects and collections handle it themselves %>
+ <%= render partial: 'name_and_description' %>
+ <% end %>
+<% end %>
+
+<% if @object.class.goes_in_projects? && @object.uuid != current_user.uuid # Not the "Home" project %>
+ <% content_for :tab_line_buttons do %>
+ <% if @object.class.copies_to_projects? %>
+ <%= link_to(
+ choose_projects_path(
+ title: "Copy this #{object_class} to:",
+ action_name: 'Copy',
+ action_href: actions_path,
+ action_method: 'post',
+ action_data: {
+ copy_selections_into_project: true,
+ selection: @name_link.andand.uuid || @object.uuid,
+ selection_param: 'uuid',
+ success: 'redirect-to-created-object'
+ }.to_json),
+ { class: "btn btn-sm btn-primary", remote: true, method: 'get',
+ title: "Make a copy this #{object_class}" }) do %>
+ <i class="fa fa-fw fa-copy"></i> Copy to project...
+ <% end %>
+ <% end %>
+ <% if (ArvadosBase.find(@object.owner_uuid).writable_by.include?(current_user.uuid) rescue nil) %>
+ <%= link_to(
+ choose_projects_path(
+ title: "Move this #{object_class} to:",
+ action_name: 'Move',
+ action_href: actions_path,
+ action_method: 'post',
+ action_data: {
+ move_selections_into_project: true,
+ selection: @name_link.andand.uuid || @object.uuid,
+ selection_param: 'uuid',
+ success: 'redirect-to-created-object'
+ }.to_json),
+ { class: "btn btn-sm btn-primary force-cache-reload", remote: true, method: 'get',
+ title: "Move this #{object_class} to a different project"}) do %>
+ <i class="fa fa-fw fa-truck"></i> Move <%=object_class%>...
+ <% end %>
+ <% end %>
+ <% end %>
+<% end %>
+
+<%
+ # Display any flash messages in an alert. If there is any entry with "error" key, alert-danger is used.
+ flash_msg = ''
+ flash_msg_is_error = false
+ flash.each do |msg|
+ flash_msg_is_error ||= (msg[0]=='error')
+ flash_msg += ('<p class="contain-align-left">' + msg[1] + '</p>')
+ end
+ if flash_msg != ''
+%>
+<div class="flash-message alert <%= flash_msg_is_error ? 'alert-danger' : 'alert-warning' %>"><%=flash_msg.html_safe%></div>
+<% end %>
--- /dev/null
+<h2>Oh... fiddlesticks.</h2>
+
+<p>An error occurred when Workbench sent a request to the Arvados API server. Try reloading this page. If the problem is temporary, your request might go through next time.
+
+<% if not api_error %>
+</p>
+<% else %>
+If that doesn't work, the information below can help system administrators track down the problem.
+</p>
+
+<dl>
+ <dt>API request URL</dt>
+ <dd><code><%= api_error.request_url %></code></dd>
+
+ <% if api_error.api_response.empty? %>
+ <dt>Invalid API response</dt>
+ <dd><%= api_error.api_response_s %></dd>
+ <% else %>
+ <dt>API response</dt>
+ <dd><pre><%= Oj.dump(api_error.api_response, indent: 2) %></pre></dd>
+ <% end %>
+</dl>
+<% end %>
+
+<%= render :partial => "report_error", :locals => {api_error: api_error, error_type: 'api'} %>
--- /dev/null
+{"errors":<%= raw @errors.to_json %>}
\ No newline at end of file
--- /dev/null
+$(document).trigger('count-change');
+$('[data-object-uuid=<%= @object.uuid %>]').hide('slow', function() {
+ $(this).remove();
+});
--- /dev/null
+<h2>Oh... fiddlesticks.</h2>
+
+<p>Sorry, I had some trouble handling your request.</p>
+
+<ul>
+<% if @errors.is_a? Array then @errors.each do |error| %>
+<li><%= error %></li>
+<% end end %>
+</ul>
--- /dev/null
+{"errors":<%= raw @errors.to_json %>}
\ No newline at end of file
--- /dev/null
+<% content_for :page_title do %>
+<%= controller.controller_name.humanize.capitalize %>
+<% end %>
+
+<% content_for :tab_line_buttons do %>
+
+ <% if controller.model_class.creatable? %>
+
+ <% if controller.model_class.name == 'User' %>
+ <%= link_to setup_user_popup_path,
+ {class: 'btn btn-sm btn-primary', :remote => true, 'data-toggle' => "modal",
+ 'data-target' => '#user-setup-modal-window', return_to: request.url} do %>
+ <i class="fa fa-fw fa-plus"></i> Add a new user
+ <% end %>
+ <div id="user-setup-modal-window" class="modal fade" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true"></div>
+ <% elsif controller.controller_name == 'manage_account' %>
+ <%# No add button is needed %>
+ <% else %>
+ <%= button_to({action: 'create'}, {class: 'btn btn-sm btn-primary'}) do %>
+ <i class="fa fa-fw fa-plus"></i>
+ Add a new
+ <%= controller.controller_name.singularize.humanize.downcase %>
+ <% end %>
+ <% end %>
+
+ <% end %>
+
+<% end %>
+
+<%= render partial: 'content', layout: 'content_layout', locals: {pane_list: controller.index_pane_list }%>
--- /dev/null
+$("#report-issue-modal-window").html("<%= escape_javascript(render partial: 'report_issue_popup') %>");
+$("#report-issue-modal-window .modal").modal('show');
+
+// Disable the submit button on modal loading
+$submit = $('#report-issue-submit');
+$submit.prop('disabled', true);
+
+// capture events to enable submit button when applicable
+$('#report_issue_text').bind('input propertychange', function() {
+ var problem_desc = document.forms["report-issue-form"]["report_issue_text"].value;
+ $submit.prop('disabled', (problem_desc === null) || (problem_desc === ""));
+});
--- /dev/null
+<%= render partial: 'title_and_buttons' %>
+<%= render partial: 'content', layout: 'content_layout', locals: {pane_list: controller.show_pane_list }%>
--- /dev/null
+<%= render partial: 'form' %>
--- /dev/null
+../application/_choose.js.erb
\ No newline at end of file
--- /dev/null
+<% @objects.each do |object| %>
+ <div class="row filterable selectable <%= 'use-preview-selection' if params['use_preview_selection']%>" data-object-uuid="<%= object.uuid %>"
+ data-preview-href="<%= chooser_preview_url_for object, params['use_preview_selection'] %>"
+ style="margin-left: 1em; border-bottom-style: solid; border-bottom-width: 1px; border-bottom-color: #DDDDDD">
+ <i class="fa fa-fw fa-archive"></i>
+ <% if object.respond_to? :name %>
+ <% if not (object.name.nil? or object.name.empty?) %>
+ <%= object.name %>
+ <% elsif object.is_a? Collection and object.files.length > 0 %>
+ <%= object.files[0][1] %>
+ <%= "+ #{object.files.length-1} more" if object.files.length > 1 %>
+ <% else %>
+ <%= object.uuid %>
+ <% end %>
+ <% else %>
+ <%= object.uuid %>
+ <% end %>
+ <% links_for_object(object).each do |tag| %>
+ <% if tag.link_class == 'tag' %>
+ <span class="label label-info"><%= tag.name %></span>
+ <% end %>
+ <% end %>
+ </div>
+<% end %>
--- /dev/null
+<% @objects.each do |c| %>
+
+<tr class="collection" data-object-uuid="<%= c.uuid %>">
+ <td>
+ <%=
+ friendly_name = c.friendly_link_name
+ @collection_info[c.uuid][:tag_links].each do |tag_link|
+ friendly_name += raw(" <span class='label label-info'>#{tag_link.name}</span>")
+ end
+ render partial: "selection_checkbox", locals: {
+ object: c,
+ friendly_name: friendly_name
+ }
+ %>
+
+ <%= render :partial => "show_object_button", :locals => {object: c, size: 'xs'} %>
+ </td>
+ <td>
+ <%= c.uuid %>
+ </td>
+ <td>
+ <% i = 0 %>
+ <% while i < 3 and i < c.files.length %>
+ <% file = c.files[i] %>
+ <% file_path = "#{file[0]}/#{file[1]}" %>
+ <%= link_to file[1], {controller: 'collections', action: 'show_file', uuid: c.uuid, file: file_path, size: file[2], disposition: 'inline'}, {title: 'View in browser'} %><br />
+ <% i += 1 %>
+ <% end %>
+ <% if i < c.files.length %>
+ ⋮
+ <% end %>
+ </td>
+ <td>
+ <%= c.created_at.to_s if c.created_at %>
+ </td>
+ <td class="add-tag-button">
+ <a class="btn btn-xs btn-info add-tag-button pull-right" data-remote-href="<%= url_for(controller: 'links', action: 'create') %>" data-remote-method="post"><i class="glyphicon glyphicon-plus"></i> Add</a>
+ <span class="removable-tag-container">
+ <% if @collection_info[c.uuid] %>
+ <% @collection_info[c.uuid][:tag_links].each do |tag_link| %>
+ <span class="label label-info removable-tag" data-tag-link-uuid="<%= tag_link.uuid %>"><%= tag_link.name %>
+ <% if tag_link.owner_uuid == current_user.uuid %>
+ <a title="Delete tag"><i class="glyphicon glyphicon-trash"></i></a>
+ <% end %>
+ </span>
+ <% end %>
+ <% end %>
+ </span>
+ </td>
+</tr>
+
+<% end %>
--- /dev/null
+<% button_attrs = {
+ class: 'btn btn-xs btn-info',
+ remote: true,
+ method: :post,
+ } %>
+<% if @search_sharing.nil? %>
+ <p>Your API token is not authorized to manage collection sharing links.</p>
+<% elsif @search_sharing.empty? %>
+ <%= button_to("Create sharing link", {action: "share"}, button_attrs) %>
+<% else %>
+ <div>
+ <% button_attrs[:class] += " pull-right" %>
+ <%= button_to("Unshare", {action: "unshare"}, button_attrs) %>
+ Shared at:
+ <div class="smaller-text" style="clear: both; word-break: break-all"><%= link_to download_link, download_link %></div>
+ </div>
+<% end %>
--- /dev/null
+<%= render partial: "show_source_summary" %>
+<%= render partial: "show_files", locals: {no_checkboxes: true, use_preview_selection: params['use_preview_selection']} %>
--- /dev/null
+<script>
+function select_all_files() {
+ $("#collection_files :checkbox").filter(":visible").prop("checked", true).trigger("change");
+}
+
+function unselect_all_files() {
+ $("#collection_files :checkbox").filter(":visible").prop("checked", false).trigger("change");
+}
+</script>
+
+<%
+ preview_selectable_container = ''
+ preview_selectable = ''
+ padding_left = '1em'
+ if !params['use_preview_selection'].nil? and params['use_preview_selection'] == 'true'
+ preview_selectable_container = 'preview-selectable-container selectable-container'
+ preview_selectable = 'preview-selectable selectable'
+ padding_left = '0em'
+ end
+%>
+
+<div class="selection-action-container" style="padding-left: <%=padding_left%>">
+ <% if !defined? no_checkboxes or !no_checkboxes %>
+ <div class="row">
+ <div class="pull-left">
+ <div class="btn-group btn-group-sm">
+ <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">Selection... <span class="caret"></span></button>
+ <ul class="dropdown-menu" role="menu">
+ <li><%= link_to "Create new collection with selected files", '#',
+ method: :post,
+ 'data-href' => combine_selected_path(
+ action_data: {current_project_uuid: @object.owner_uuid}.to_json
+ ),
+ 'data-selection-param-name' => 'selection[]',
+ 'data-selection-action' => 'combine-collections',
+ 'data-toggle' => 'dropdown'
+ %></li>
+ </ul>
+ </div>
+ <div class="btn-group btn-group-sm">
+ <button id="select-all" type="button" class="btn btn-default" onClick="select_all_files()">Select all</button>
+ <button id="unselect-all" type="button" class="btn btn-default" onClick="unselect_all_files()">Unselect all</button>
+ </div>
+ </div>
+ <div class="pull-right">
+ <input class="form-control filterable-control" data-filterable-target="ul#collection_files" id="file_regex" name="file_regex" placeholder="filename regex" type="text"/>
+ </div>
+ </div>
+ <p/>
+ <% end %>
+
+<% file_tree = @object.andand.files_tree %>
+<% if file_tree.nil? or file_tree.empty? %>
+ <p>This collection is empty.</p>
+<% else %>
+ <ul id="collection_files" class="collection_files <%=preview_selectable_container%>">
+ <% dirstack = [file_tree.first.first] %>
+ <% file_tree.take(10000).each_with_index do |(dirname, filename, size), index| %>
+ <% file_path = CollectionsHelper::file_path([dirname, filename]) %>
+ <% while dirstack.any? and (dirstack.last != dirname) %>
+ <% dirstack.pop %></ul></li>
+ <% end %>
+ <li>
+ <% if size.nil? # This is a subdirectory. %>
+ <% dirstack.push(File.join(dirname, filename)) %>
+ <div class="collection_files_row">
+ <div class="collection_files_name"><i class="fa fa-fw fa-folder-open"></i> <%= filename %></div>
+ </div>
+ <ul class="collection_files">
+ <% else %>
+ <% link_params = {controller: 'collections', action: 'show_file',
+ uuid: @object.portable_data_hash, file: file_path, size: size} %>
+ <div class="collection_files_row filterable <%=preview_selectable%>" href="<%=@object.uuid%>/<%=file_path%>">
+ <div class="collection_files_buttons pull-right">
+ <%= raw(human_readable_bytes_html(size)) %>
+ <% disable_search = (Rails.configuration.filename_suffixes_with_view_icon.include? file_path.split('.')[-1]) ? false : true %>
+ <%= link_to(raw('<i class="fa fa-search"></i>'),
+ link_params.merge(disposition: 'inline'),
+ {title: "View #{file_path}", class: "btn btn-info btn-sm", disabled: disable_search}) %>
+ <%= link_to(raw('<i class="fa fa-download"></i>'),
+ link_params.merge(disposition: 'attachment'),
+ {title: "Download #{file_path}", class: "btn btn-info btn-sm"}) %>
+ </div>
+
+ <div class="collection_files_name">
+ <% if !defined? no_checkboxes or !no_checkboxes %>
+ <%= check_box_tag 'uuids[]', "#{@object.uuid}/#{file_path}", false, {
+ :class => "persistent-selection",
+ :friendly_type => "File",
+ :friendly_name => "#{@object.uuid}/#{file_path}",
+ :href => url_for(controller: 'collections', action: 'show_file',
+ uuid: @object.portable_data_hash, file: file_path),
+ :title => "Include #{file_path} in your selections",
+ } %>
+ <span> </span>
+ <% end %>
+ <% if CollectionsHelper::is_image(filename) %>
+ <i class="fa fa-fw fa-bar-chart-o"></i> <%= filename %></div>
+ <div class="collection_files_inline">
+ <%= link_to(image_tag("#{url_for @object}/#{file_path}"),
+ link_params.merge(disposition: 'inline'),
+ {title: file_path}) %>
+ </div>
+ </div>
+ <% else %>
+ <i class="fa fa-fw fa-file" href="<%=@object.uuid%>/<%=file_path%>" ></i> <%= filename %></div>
+ </div>
+ <% end %>
+ </li>
+ <% end # if file or directory %>
+ <% end # file_tree.each %>
+ <%= raw(dirstack.map { |_| "</ul>" }.join("</li>")) %>
+<% end # if file_tree %>
+
+<% content_for :footer_html do %>
+<div id="collection-sharing-modal-window" class="modal fade" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true"></div>
+<% end %>
+
+</div>
--- /dev/null
+<%= render partial: 'application/svg_div', locals: {
+ divId: "provenance_graph_div",
+ svgId: "provenance_svg",
+ svg: @prov_svg } %>
--- /dev/null
+<div class="selection-action-container" style="padding-left: 1em">
+ <div class="row">
+ <div class="pull-left">
+ <div class="btn-group btn-group-sm">
+ <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">Selection... <span class="caret"></span></button>
+ <ul class="dropdown-menu" role="menu">
+ <li><%= link_to "Create new collection with selected collections", '#',
+ method: :post,
+ 'data-href' => combine_selected_path,
+ 'data-selection-param-name' => 'selection[]',
+ 'data-selection-action' => 'combine-collections',
+ 'data-toggle' => 'dropdown'
+ %></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+ <p/>
+
+<%= render partial: "paging", locals: {results: @objects, object: @object} %>
+
+<div style="padding-right: 1em">
+
+<%= form_tag do |f| %>
+
+<table id="collections-index" class="topalign table table-condensed table-fixedlayout"> <!-- table-fixed-header-row -->
+ <colgroup>
+ <col width="10%" />
+ <col width="10%" />
+ <col width="40%" />
+ <col width="10%" />
+ <col width="30%" />
+ </colgroup>
+ <thead>
+ <tr class="contain-align-left">
+ <th></th>
+ <th>uuid</th>
+ <th>contents</th>
+ <th>created at</th>
+ <th>tags</th>
+ </tr>
+ </thead>
+ <tbody>
+ <%= render partial: 'index_tbody' %>
+ </tbody>
+</table>
+
+<% end %>
+
+</div>
+
+<%= render partial: "paging", locals: {results: @objects, object: @object} %>
+
+<% content_for :footer_js do %>
+$(document).on('click', 'form[data-remote] input[type=submit]', function() {
+ $('table#collections-index tbody').fadeTo(200, 0.3);
+ return true;
+});
+<% end %>
+
+</div>
--- /dev/null
+<% if not (@output_of.andand.any? or @log_of.andand.any?) %>
+ <p><i>No source information available.</i></p>
+<% end %>
+
+<% if @output_of.andand.any? %>
+ <p><i>This collection was the output of:</i><br />
+ <% pipelines = PipelineInstance.filter([["components", "like", "%#{@object.uuid}%"]]).each do |pipeline| %>
+ <% pipeline.components.each do |cname, c| %>
+ <% if c[:output_uuid] == @object.uuid %>
+ <b><%= cname %></b> component of <b><%= link_to_if_arvados_object(pipeline, friendly_name: true) %></b>
+ <% if c.andand[:job].andand[:finished_at] %>
+ finished at <%= render_localized_date(c[:job][:finished_at]) %>
+ <% end %>
+ <br>
+ <% end %>
+ <% end %>
+ <% end %>
+ </p>
+<% end %>
+
+<% if @log_of.andand.any? %>
+ <p><i>This collection contains log messages from:</i><br />
+ <%= render_arvados_object_list_start(@log_of, 'Show all jobs',
+ jobs_path(filters: [['log', '=', @object.uuid]].to_json)) do |job| %>
+ <%= link_to_if_arvados_object(job, friendly_name: true) %><br />
+ <% end %>
+ </p>
+<% end %>
--- /dev/null
+<div class="arv-log-refresh-control"
+ data-load-throttle="86486400000" <%# 1001 nights (in milliseconds) %>
+ ></div>
+<div ng-cloak ng-controller="UploadToCollection" arv-uuid="<%= @object.uuid %>">
+ <div class="panel panel-primary">
+ <div class="panel-body">
+ <div class="row">
+ <div class="col-sm-4">
+ <input type="file" multiple id="file_selector" ng-model="incoming" onchange="angular.element(this).scope().addFilesToQueue(this.files); $(this).val('');">
+ <div class="btn-group btn-group-sm" role="group" style="margin-top: 1.5em">
+ <button type="button" class="btn btn-default" ng-click="stop()" ng-disabled="uploader.state !== 'Running'"><i class="fa fa-fw fa-pause"></i> Pause</button>
+ <button type="button" class="btn btn-primary" ng-click="go()" ng-disabled="uploader.state === 'Running' || countInStates(['Paused', 'Queued']) === 0"><i class="fa fa-fw fa-play"></i> Start</button>
+ </div>
+ </div>
+ <div class="col-sm-8">
+ <div ng-show="uploader.state === 'Running'"
+ class="alert alert-info"
+ ><i class="fa fa-gear"></i>
+ Upload in progress.
+ <span ng-show="countInStates(['Done']) > 0">
+ {{countInStates(['Done'])}} file{{countInStates(['Done'])>1?'s':''}} finished.
+ </span>
+ </div>
+ <div ng-show="uploader.state === 'Idle' && uploader.stateReason"
+ class="alert alert-success"
+ ><i class="fa fa-fw fa-flag-checkered"></i> {{uploader.stateReason}}
+ </div>
+ <div ng-show="uploader.state === 'Failed'"
+ class="alert alert-danger"
+ ><i class="fa fa-fw fa-warning"></i> {{uploader.stateReason}}
+ </div>
+ <div ng-show="uploader.state === 'Stopped'"
+ class="alert alert-info"
+ ><i class="fa fa-fw fa-info"></i> Paused. Click the Start button to resume uploading.
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div ng-repeat="upload in uploadQueue" class="row" ng-class="{lighten: upload.state==='Done'}">
+ <div class="col-sm-1">
+ <button class="btn btn-xs btn-default"
+ ng-show="upload.state!=='Done'"
+ ng-click="removeFileFromQueue($index)"
+ title="cancel"><i class="fa fa-fw fa-times"></i></button>
+ <span class="label label-success label-info"
+ ng-show="upload.state==='Done'">finished</span>
+ </div>
+ <div class="col-sm-4 nowrap" style="overflow-x:hidden;text-overflow:ellipsis">
+ <span title="{{upload.file.name}}">
+ {{upload.file.name}}
+ </span>
+ </div>
+ <div class="col-sm-1" style="text-align: right">
+ {{upload.file.size/1024 | number:0}} KiB
+ </div>
+ <div class="col-sm-2">
+ <div class="progress">
+ <span class="progress-bar" style="width: {{upload.progress}}%"></span>
+ </div>
+ </div>
+ <div class="col-sm-4" ng-class="{lighten: upload.state !== 'Uploading'}">
+ {{upload.statistics}}
+ </div>
+ </div>
+</div>
--- /dev/null
+<%= render partial: 'application/svg_div', locals: {
+ divId: "used_by_graph",
+ svgId: "used_by_svg",
+ svg: @used_by_svg } %>
+
--- /dev/null
+<%#= render :partial => 'nav' %>
+<table class="table table-bordered">
+ <tbody>
+ <tr>
+ <td class="d3">
+ </td>
+ </tr>
+ </tbody>
+</table>
+
+<% content_for :head do %>
+<%= javascript_include_tag '/d3.v3.min.js' %>
+
+ <style type="text/css">
+
+path.link {
+ fill: none;
+ stroke: #666;
+ stroke-width: 1.5px;
+}
+
+path.link.derived_from {
+ stroke: green;
+ stroke-dasharray: 0,4 1;
+}
+
+path.link.can_write {
+ stroke: green;
+}
+
+path.link.member_of {
+ stroke: blue;
+ stroke-dasharray: 0,4 1;
+}
+
+path.link.created {
+ stroke: red;
+}
+
+circle.node {
+ fill: #ccc;
+ stroke: #333;
+ stroke-width: 1.5px;
+}
+
+edgetext {
+ font: 12px sans-serif;
+ pointer-events: none;
+ text-align: center;
+}
+
+text {
+ font: 12px sans-serif;
+ pointer-events: none;
+}
+
+text.shadow {
+ stroke: #fff;
+ stroke-width: 3px;
+ stroke-opacity: .8;
+}
+
+ </style>
+<% end %>
+
+<% content_for :js do %>
+
+jQuery(function($){
+
+ var links = <%= raw d3ify_links(@links).to_json %>;
+
+ var nodes = {};
+
+ // Compute the distinct nodes from the links.
+ links.forEach(function(link) {
+ link.source = nodes[link.source] || (nodes[link.source] = {name: link.source});
+ link.target = nodes[link.target] || (nodes[link.target] = {name: link.target});
+ });
+
+ var fill_for = {'ldvyl': 'green',
+ 'j58dm': 'red',
+ '4zz18': 'blue'};
+ jQuery.each(nodes, function(i, node) {
+ var m = node.name.match(/-([a-z0-9]{5})-/)
+ if (m)
+ node.fill = fill_for[m[1]] || '#ccc';
+ else if (node.name.match(/^[0-9a-f]{32}/))
+ node.fill = fill_for['4zz18'];
+ else
+ node.fill = '#ccc';
+ });
+
+ var w = 960,
+ h = 600;
+
+ var force = d3.layout.force()
+ .nodes(d3.values(nodes))
+ .links(links)
+ .size([w, h])
+ .linkDistance(150)
+ .charge(-300)
+ .on("tick", tick)
+ .start();
+
+ var svg = d3.select("td.d3").append("svg:svg")
+ .attr("width", w)
+ .attr("height", h);
+
+ // Per-type markers, as they don't inherit styles.
+ svg.append("svg:defs").selectAll("marker")
+ .data(["member_of", "owner", "derived_from"])
+ .enter().append("svg:marker")
+ .attr("id", String)
+ .attr("viewBox", "0 -5 10 10")
+ .attr("refX", 15)
+ .attr("refY", -1.5)
+ .attr("markerWidth", 6)
+ .attr("markerHeight", 6)
+ .attr("orient", "auto")
+ .append("svg:path")
+ .attr("d", "M0,-5L10,0L0,5");
+
+ var path = svg.append("svg:g").selectAll("path")
+ .data(force.links())
+ .enter().append("svg:path")
+ .attr("class", function(d) { return "link " + d.type; })
+ .attr("marker-end", function(d) { return "url(#" + d.type + ")"; });
+
+ var circle = svg.append("svg:g").selectAll("circle")
+ .data(force.nodes())
+ .enter().append("svg:circle")
+ .attr("r", 6)
+ .style("fill", function(d) { return d.fill; })
+ .call(force.drag);
+
+ var text = svg.append("svg:g").selectAll("g")
+ .data(force.nodes())
+ .enter().append("svg:g");
+
+ // A copy of the text with a thick white stroke for legibility.
+ text.append("svg:text")
+ .attr("x", 8)
+ .attr("y", ".31em")
+ .attr("class", "shadow")
+ .text(function(d) { return d.name.replace(/^([0-9a-z]{5}-){2}/,''); });
+
+ text.append("svg:text")
+ .attr("x", 8)
+ .attr("y", ".31em")
+ .text(function(d) { return d.name.replace(/^([0-9a-z]{5}-){2}/,''); });
+
+ var edgetext = svg.append("svg:g").selectAll("g")
+ .data(force.links())
+ .enter().append("svg:g");
+
+ edgetext
+ .append("svg:text")
+ .attr("x","-5em")
+ .attr("y","-0.2em")
+ .text(function(d) { return d.type; });
+
+ // Use elliptical arc path segments to doubly-encode directionality.
+ function tick() {
+ path.attr("d", function(d) {
+ var dx = d.target.x - d.source.x,
+ dy = d.target.y - d.source.y,
+ // dr = Math.sqrt(dx * dx + dy * dy);
+ dr = 0;
+ return "M" + d.source.x + "," + d.source.y + "A" + dr + "," + dr + " 0 0,1 " + d.target.x + "," + d.target.y;
+ });
+
+ circle.attr("transform", function(d) {
+ return "translate(" + d.x + "," + d.y + ")";
+ });
+
+ text.attr("transform", function(d) {
+ return "translate(" + d.x + "," + d.y + ")";
+ });
+
+ edgetext.attr("transform", function(d) {
+ return "translate(" +
+ (d.source.x + d.target.x)/2 + "," +
+ (d.source.y + d.target.y)/2 +
+ ")rotate(" +
+ (Math.atan2(d.target.y - d.source.y, d.target.x - d.source.x) * 180 / Math.PI) +
+ ")";
+ });
+ }
+
+})(jQuery);
+<% end %>
--- /dev/null
+<div class="row">
+ <div class="col-md-10 col-md-offset-1">
+ <div class="panel panel-info">
+ <div class="panel-heading">
+ <h3 class="panel-title"><%= params["uuid"] %></h3>
+ </div>
+ <div class="panel-body">
+ <p><i>The following collections have this content:</i></p>
+ <% @same_pdh.sort { |a,b| b.created_at <=> a.created_at }.each do |c| %>
+ <div class="row">
+ <div class="col-md-8">
+ <% owner = object_for_dataclass(Group, c.owner_uuid) || object_for_dataclass(User, c.owner_uuid) %>
+ <%= link_to_if_arvados_object owner, {:friendly_name => true} %> / <%= link_to_if_arvados_object c, {:friendly_name => true} %><br>
+ </div>
+ <div class="col-md-4">
+ <%= render_localized_date c.created_at %>
+ </div>
+ </div>
+ <% end %>
+ </div>
+ </div>
+ </div>
+</div>
--- /dev/null
+<% content_for :tab_line_buttons do %>
+ <%= form_tag collections_path, method: 'get', remote: true, class: 'form-search' do %>
+ <div class="input-group">
+ <%= text_field_tag :search, params[:search], class: 'form-control', placeholder: 'Search collections' %>
+ <span class="input-group-btn">
+ <%= button_tag(class: 'btn btn-info') do %>
+ <span class="glyphicon glyphicon-search"></span>
+ <% end %>
+ </span>
+ </div>
+ <% end %>
+<% end %>
+
+<%= render file: 'application/index.html.erb', locals: local_assigns %>
--- /dev/null
+if(history.replaceState)
+ history.replaceState(null, null, "<%= escape_javascript(@request_url) %>");
+$('table#collections-index tbody').html("<%= escape_javascript(render partial: 'index_tbody') %>");
+$('table#collections-index tbody').fadeTo(200, 1.0);
--- /dev/null
+$("#sharing-button").html("<%= escape_javascript(render partial: 'sharing_button') %>");
--- /dev/null
+<div class="row row-fill-height">
+ <div class="col-md-6">
+ <div class="panel panel-info">
+ <div class="panel-heading">
+ <h3 class="panel-title">
+ <% if @name_link.nil? and @object.uuid.match /[0-9a-f]{32}/ %>
+ Content hash <%= @object.portable_data_hash %>
+ <% else %>
+ <%= if @object.respond_to? :name
+ render_editable_attribute @object, :name
+ else
+ @name_link.andand.name || @object.uuid
+ end %>
+ <% end %>
+ </h3>
+ </div>
+ <div class="panel-body">
+ <div class="arv-description-as-subtitle">
+ <%= render_editable_attribute @object, 'description', nil, { 'data-emptytext' => "(No description provided)", 'data-toggle' => 'manual' } %>
+ </div>
+ <img src="/favicon.ico" class="pull-right" alt="" style="opacity: 0.3"/>
+ <p><i>Content hash:</i><br />
+ <span class="arvados-uuid"><%= link_to @object.portable_data_hash, collection_path(@object.portable_data_hash) %></span>
+ </p>
+ <%= render partial: "show_source_summary" %>
+ </div>
+ </div>
+ </div>
+ <div class="col-md-3">
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <h3 class="panel-title">
+ Activity
+ </h3>
+ </div>
+ <div class="panel-body smaller-text">
+ <!--
+ <input type="text" class="form-control" placeholder="Search"/>
+ -->
+ <div style="height:0.5em;"></div>
+ <% name_or_object = @name_link.andand.uuid ? @name_link : @object %>
+ <% if name_or_object.created_at and not @logs.andand.any? %>
+ <p>
+ Created: <%= name_or_object.created_at.to_s(:long) if name_or_object.created_at %>
+ </p>
+ <p>
+ Last modified: <%= name_or_object.modified_at.to_s(:long) if name_or_object.modified_at %> by <%= link_to_if_arvados_object name_or_object.modified_by_user_uuid, friendly_name: true %>
+ </p>
+ <% else %>
+ <%= render_arvados_object_list_start(@logs, 'Show all activity',
+ logs_path(filters: [['object_uuid','=',name_or_object.uuid]].to_json)) do |log| %>
+ <p>
+ <%= time_ago_in_words(log.event_at) rescue 'unknown time' %> ago: <%= log.summary %>
+ <% if log.object_uuid %>
+ <%= link_to_if_arvados_object log.object_uuid, link_text: raw('<i class="fa fa-hand-o-right"></i>') %>
+ <% end %>
+ </p>
+ <% end %>
+ <% end %>
+ </div>
+ </div>
+ </div>
+ <div class="col-md-3">
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <h3 class="panel-title">
+ Sharing and permissions
+ </h3>
+ </div>
+ <div class="panel-body">
+ <!--
+ <input type="text" class="form-control" placeholder="Search"/>
+ -->
+
+ <div id="sharing-button">
+ <%= render partial: 'sharing_button' %>
+ </div>
+
+ <div style="height:0.5em;"></div>
+ <% if @projects.andand.any? %>
+ <p>Included in projects:<br />
+ <%= render_arvados_object_list_start(@projects, 'Show all projects',
+ links_path(filters: [['head_uuid', '=', @object.uuid],
+ ['link_class', '=', 'name']].to_json)) do |project| %>
+ <%= link_to_if_arvados_object(project, friendly_name: true) %><br />
+ <% end %>
+ </p>
+ <% end %>
+ <% if @permissions.andand.any? %>
+ <p>Readable by:<br />
+ <%= render_arvados_object_list_start(@permissions, 'Show all permissions',
+ links_path(filters: [['head_uuid', '=', @object.uuid],
+ ['link_class', '=', 'permission']].to_json)) do |link| %>
+ <%= link_to_if_arvados_object(link.tail_uuid, friendly_name: true) %><br />
+ <% end %>
+ </p>
+ <% end %>
+
+ </div>
+ </div>
+ </div>
+</div>
+
+<%= render file: 'application/show.html.erb', locals: local_assigns %>
--- /dev/null
+<!DOCTYPE html>
+<html>
+<% coll_name = "Collection #{@object.uuid}" %>
+<% link_opts = {controller: 'collections', action: 'show_file',
+ uuid: @object.uuid, reader_token: params[:reader_token]} %>
+<head>
+ <meta charset="utf-8">
+ <title>
+ <%= coll_name %> / <%= Rails.configuration.site_name %>
+ </title>
+ <meta name="description" content="">
+ <meta name="author" content="">
+ <meta name="robots" content="NOINDEX">
+ <style type="text/css">
+body {
+ margin: 1.5em;
+}
+pre {
+ background-color: #D9EDF7;
+ border-radius: .25em;
+ padding: .75em;
+ overflow: auto;
+}
+.footer {
+ font-size: 82%;
+}
+.footer h2 {
+ font-size: 1.2em;
+}
+ </style>
+</head>
+<body>
+
+<h1><%= coll_name %></h1>
+
+<p>This collection of data files is being shared with you through
+Arvados. You can download individual files listed below. To download
+the entire collection with wget, try:</p>
+
+<pre>$ wget --mirror --no-parent --no-host --cut-dirs=3 <%=
+ url_for(link_opts.merge(action: 'show_file_links', only_path: false,
+ trailing_slash: true))
+ %></pre>
+
+<h2>File Listing</h2>
+
+<% file_tree = @object.andand.files_tree %>
+<% if file_tree.andand.any? %>
+ <ul id="collection_files" class="collection_files">
+ <% dirstack = [file_tree.first.first] %>
+ <% file_tree.take(10000).each_with_index do |(dirname, filename, size), index| %>
+ <% file_path = CollectionsHelper::file_path([dirname, filename]) %>
+ <% while dirstack.any? and (dirstack.last != dirname) %>
+ <% dirstack.pop %></ul></li>
+ <% end %>
+ <li>
+ <% if size.nil? # This is a subdirectory. %>
+ <% dirstack.push(File.join(dirname, filename)) %>
+ <%= filename %>
+ <ul class="collection_files">
+ <% else %>
+ <%= link_to(filename,
+ link_opts.merge(file: file_path),
+ {title: "Download #{file_path}"}) %>
+ </li>
+ <% end %>
+ <% end %>
+ <%= raw(dirstack.map { |_| "</ul>" }.join("</li>")) %>
+<% else %>
+ <p>No files in this collection.</p>
+<% end %>
+
+<div class="footer">
+<h2>About Arvados</h2>
+
+<p>Arvados is a free and open source software bioinformatics platform.
+To learn more, visit arvados.org.
+Arvados is not responsible for the files listed on this page.</p>
+</div>
+
+</body>
+</html>
--- /dev/null
+<% icon_class = fa_icon_class_for_class(Group) %>
+<% @objects.each do |object| %>
+ <div class="row filterable selectable" data-object-uuid="<%= object.uuid %>">
+ <div class="col-sm-12" style="overflow-x:hidden">
+ <i class="fa fa-fw <%= icon_class %>"></i>
+ <%= object.name %>
+ </div>
+ </div>
+<% end %>
--- /dev/null
+<%= render partial: "paging", locals: {results: @groups, object: @object} %>
+
+<table class="table table-hover">
+ <thead>
+ <tr class="contain-align-left">
+ <th>
+ Group
+ </th><th>
+ Owner
+ </th><th>
+ Incoming permissions
+ </th><th>
+ Outgoing permissions
+ </th><th>
+ <!-- column for delete buttons -->
+ </th>
+ </tr>
+ </thead>
+ <tbody>
+
+ <% @groups.sort_by { |g| g[:created_at] }.reverse.each do |g| %>
+
+ <tr>
+ <td>
+ <%= link_to_if_arvados_object g, friendly_name: true %>
+ </td><td>
+ <%= link_to_if_arvados_object g.owner_uuid, friendly_name: true %>
+ </td><td>
+ <%= @links_to.select { |x| x.head_uuid == g.uuid }.collect(&:tail_uuid).uniq.count %>
+ </td><td>
+ <%= @links_from.select { |x| x.tail_uuid == g.uuid }.collect(&:head_uuid).uniq.count %>
+ </td><td>
+ <%= render partial: 'delete_object_button', locals: {object:g} %>
+ </td>
+ </tr>
+
+ <% end %>
+
+ </tbody>
+</table>
+
+<%= render partial: "paging", locals: {results: @groups, object: @object} %>
--- /dev/null
+<% if @user %>
+Issue reported by user <%=@user.email%>
+<% else %>
+Issue reported
+<% end %>
+
+Details of the report:
+<% if @params['report_additional_info'] %>
+<% map_to_s = JSON.parse(@params['report_additional_info']).map {|k,v| "#{k}=#{v}"}.join("\n") %>
+<%= map_to_s %>
+<% end %>
+Report text=<%=@params['report_issue_text'] %>
--- /dev/null
+<%= render partial: 'application/show_attributes' %>
--- /dev/null
+<% if @object.state != "Running" %>
+ <%= form_tag '/jobs', style: "display:inline; padding-left: 1em" do |f| %>
+ <% [:script, :script_version, :repository, :supplied_script_version, :nondeterministic].each do |d| %>
+ <%= hidden_field :job, d, :value => @object[d] %>
+ <% end %>
+ <% [:script_parameters, :runtime_constraints].each do |d| %>
+ <%= hidden_field :job, d, :value => JSON.dump(@object[d]) %>
+ <% end %>
+ <%= button_tag ({class: 'btn btn-sm btn-primary', id: "re-run-same-job-button",
+ title: 'Re-run job using the same script version as this run'}) do %>
+ <i class="fa fa-fw fa-gear"></i> Re-run same version
+ <% end %>
+ <% end %>
+ <% if @object.respond_to? :supplied_script_version and !@object.supplied_script_version.nil? and !@object.supplied_script_version.empty? and @object.script_version != @object.supplied_script_version%>
+ <%= form_tag '/jobs', style: "display:inline" do |f| %>
+ <% [:script, :repository, :supplied_script_version, :nondeterministic].each do |d| %>
+ <%= hidden_field :job, d, :value => @object[d] %>
+ <% end %>
+ <%= hidden_field :job, :script_version, :value => @object[:supplied_script_version] %>
+ <% [:script_parameters, :runtime_constraints].each do |d| %>
+ <%= hidden_field :job, d, :value => JSON.dump(@object[d]) %>
+ <% end %>
+ <%= button_tag ({class: 'btn btn-sm btn-primary', id: "re-run-latest-job-button",
+ title: 'Re-run job using the latest script version'}) do%>
+ <i class="fa fa-fw fa-gear"></i> Re-run latest version
+ <% end %>
+ <% end %>
+ <% end %>
+<% end %>
--- /dev/null
+<% if !@object.log %>
+
+<div id="log_graph_div"
+ class="arv-log-event-listener"
+ data-object-uuid="<%= @object.uuid %>"></div>
+
+<div id="event_log_div"
+ class="arv-log-event-listener arv-log-event-handler-append-logs arv-job-log-window"
+ data-object-uuid="<%= @object.uuid %>"
+ ></div>
+
+<%# Applying a long throttle suppresses the auto-refresh of this
+ partial that would normally be triggered by arv-log-event. %>
+<div class="arv-log-refresh-control"
+ data-load-throttle="86486400000" <%# 1001 nights %>
+ ></div>
+
+<% else %>
+
+<script>
+(function() {
+var pagesize = 1000;
+var logViewer = new List('log-viewer', {
+ valueNames: [ 'id', 'timestamp', 'taskid', 'message', 'type'],
+ page: pagesize
+});
+
+logViewer.page_offset = 0;
+logViewer.on("updated", function() { updatePaging(".log-viewer-paging", logViewer, pagesize) } );
+$(".log-viewer-page-up").on("click", function() { prevPage(logViewer, pagesize, ".log-viewer-paging"); return false; });
+$(".log-viewer-page-down").on("click", function() { nextPage(logViewer, pagesize, ".log-viewer-paging"); return false; });
+
+var taskState = newTaskState();
+
+var makeFilter = function() {
+ var pass = [];
+ $(".toggle-filter, .radio-filter").each(function(i, e) {
+ if (e.checked) {
+ pass.push(e.id.substr(5));
+ }
+ });
+
+ return (function(item) {
+ var v = false;
+ if (item.values().taskid !== "") {
+ for (a in pass) {
+ if (pass[a] == "all-tasks") { v = true; }
+ else if (pass[a] == "successful-tasks" && taskState[item.values().taskid].outcome == "success") { v = true; }
+ else if (pass[a] == "failed-tasks" && taskState[item.values().taskid].outcome == "failure") { v = true; }
+ }
+ } else {
+ v = true;
+ }
+ for (a in pass) {
+ if (pass[a] == item.values().type) { return v; }
+ }
+ return false;
+ });
+}
+
+<% if @object.log and !@object.log.empty? %>
+ <% logcollection = Collection.find @object.log %>
+ <% if logcollection %>
+ log_size = <%= logcollection.files[0][2] %>
+ log_maxbytes = <%= Rails.configuration.log_viewer_max_bytes %>;
+ logcollection_url = '<%=j url_for logcollection %>/<%=j logcollection.files[0][1] %>';
+ $("#log-viewer-download-url").attr('href', logcollection_url);
+ $("#log-viewer-download-pane").show();
+ if (log_size > log_maxbytes) {
+ range_header = { 'Range': 'bytes=0-' + log_maxbytes };
+ } else {
+ range_header = null;
+ }
+ $.ajax(logcollection_url, { headers: range_header }).
+ done(function(data, status, jqxhr) {
+ logViewer.filter();
+ addToLogViewer(logViewer, data.split("\n"), taskState);
+ logViewer.filter(makeFilter());
+ content_range_hdr = jqxhr.getResponseHeader('Content-Range');
+ var v = content_range_hdr && content_range_hdr.match(/bytes \d+-(\d+)\/(.+)/);
+ short_log = v && (v[2] == '*' || parseInt(v[1]) + 1 < v[2]);
+ if (jqxhr.status == 206 && short_log) {
+ $("#log-viewer-overview").html(
+ '<p>Showing only ' + data.length + ' bytes of this log.' +
+ ' Timing information is unavailable since' +
+ ' the full log was not retrieved.</p>'
+ );
+ } else {
+ generateJobOverview("#log-viewer-overview", logViewer, taskState);
+ }
+ $("#log-viewer .spinner").detach();
+ }).
+ fail(function(jqxhr, status, error) {
+ $("#log-viewer .spinner").detach();
+ });
+ <% end %>
+<% else %>
+ <%# Live log loading not implemented yet. %>
+<% end %>
+
+$(".toggle-filter, .radio-filter").on("change", function() {
+ logViewer.filter(makeFilter());
+});
+
+$("#filter-all").on("click", function() {
+ $(".toggle-filter").each(function(i, f) { f.checked = true; });
+ logViewer.filter(makeFilter());
+});
+
+$("#filter-none").on("click", function() {
+ $(".toggle-filter").each(function(i, f) { f.checked = false; console.log(f); });
+ logViewer.filter(makeFilter());
+});
+
+$("#sort-by-time").on("change", function() {
+ logViewer.sort("id", {sortFunction: sortById});
+});
+
+$("#sort-by-task").on("change", function() {
+ logViewer.sort("taskid", {sortFunction: sortByTask});
+});
+
+$("#sort-by-node").on("change", function() {
+ logViewer.sort("node", {sortFunction: sortByNode});
+});
+
+$("#set-show-failed-only").on("click", function() {
+ $("#sort-by-task").prop("checked", true);
+ $("#show-failed-tasks").prop("checked", true);
+ $("#show-crunch").prop("checked", false);
+ $("#show-task-dispatch").prop("checked", true);
+ $("#show-script-print").prop("checked", true);
+ $("#show-crunchstat").prop("checked", false);
+ logViewer.filter(makeFilter());
+ logViewer.sort("taskid", {sortFunction: sortByTask});
+});
+
+})();
+
+</script>
+
+<div id="log-viewer">
+
+ <h3>Summary</h3>
+ <p id="log-viewer-overview">
+ <% if !logcollection %>
+ The collection containing the job log was not found.
+ <% end %>
+ </p>
+
+ <p id="log-viewer-download-pane" style="display:none">
+ <a id="log-viewer-download-url" href="">Download the full log</a>
+ </p>
+
+ <div class="h3">Log
+
+ <span class="pull-right">
+ <% if @object.andand.tasks_summary.andand[:failed] and @object.tasks_summary[:failed] > 0 %>
+ <button id="set-show-failed-only" class="btn btn-danger">
+ Show failed task diagnostics only
+ </button>
+ <% end %>
+
+ <button id="filter-all" class="btn">
+ Select all
+ </button>
+ <button id="filter-none" class="btn">
+ Select none
+ </button>
+ </span>
+ </div>
+
+ <input class="search pull-right" style="margin-top: 1em" placeholder="Search" />
+
+ <div>
+ <div class="radio-inline log-viewer-button" style="margin-left: 10px">
+ <label><input id="sort-by-time" type="radio" name="sort-radio" checked> Sort by time</label>
+ </div>
+ <div class="radio-inline log-viewer-button">
+ <label><input id="sort-by-node" type="radio" name="sort-radio" > Sort by node</label>
+ </div>
+
+ <div class="radio-inline log-viewer-button">
+ <label><input id="sort-by-task" type="radio" name="sort-radio" > Sort by task</label>
+ </div>
+ </div>
+
+ <div>
+ <div class="radio-inline log-viewer-button" style="margin-left: 10px">
+ <label><input id="show-all-tasks" type="radio" name="show-tasks-group" checked="true" class="radio-filter"> Show all tasks</label>
+ </div>
+ <div class="radio-inline log-viewer-button">
+ <label><input id="show-successful-tasks" type="radio" name="show-tasks-group" class="radio-filter"> Only successful tasks</label>
+ </div>
+ <div class="radio-inline log-viewer-button">
+ <label><input id="show-failed-tasks" type="radio" name="show-tasks-group" class="radio-filter"> Only failed tasks</label>
+ </div>
+ </div>
+
+ <div>
+ <div class="checkbox-inline log-viewer-button" style="margin-left: 10px">
+ <label><input id="show-crunch" type="checkbox" checked="true" class="toggle-filter"> Show crunch diagnostics</label>
+ </div>
+ <div class="checkbox-inline log-viewer-button">
+ <label><input id="show-task-dispatch" type="checkbox" checked="true" class="toggle-filter"> Show task dispatch</label>
+ </div>
+ <div class="checkbox-inline log-viewer-button">
+ <label><input id="show-task-print" type="checkbox" checked="true" class="toggle-filter"> Show task diagnostics</label>
+ </div>
+ <div class="checkbox-inline log-viewer-button">
+ <label><input id="show-crunchstat" type="checkbox" checked="true" class="toggle-filter"> Show compute usage</label>
+ </div>
+
+ </div>
+
+ <div class="smart-scroll" data-smart-scroll-padding-bottom="50" style="margin-bottom: 0px">
+ <table class="log-viewer-table">
+ <thead>
+ <tr>
+ <th class="id" data-sort="id"></th>
+ <th class="timestamp" data-sort="timestamp">Timestamp</th>
+ <th class="node" data-sort="node">Node</th>
+ <th class="slot" data-sort="slot">Slot</th>
+ <th class="type" data-sort="type">Log type</th>
+ <th class="taskid" data-sort="taskid">Task</th>
+ <th class="message" data-sort="message">Message</th>
+ </tr>
+ </thead>
+ <tbody class="list">
+ <tr>
+ <td class="id"></td>
+ <td class="timestamp"></td>
+ <td class="node"></td>
+ <td class="slot"></td>
+ <td class="type"></td>
+ <td class="taskid"></td>
+ <td class="message"></td>
+ </tr>
+ </tbody>
+ </table>
+
+ <% if @object.log and logcollection %>
+ <div class="spinner spinner-32px"></div>
+ <% end %>
+
+ </div>
+
+ <div class="log-viewer-paging-div" style="margin-bottom: -15px">
+ <a href="#" class="log-viewer-page-up"><span class='glyphicon glyphicon-arrow-up'></span></a>
+ <span class="log-viewer-paging"></span>
+ <a href="#" class="log-viewer-page-down"><span class='glyphicon glyphicon-arrow-down'></span></a>
+ </div>
+
+</div>
+
+<% end %>
--- /dev/null
+<div class="nowrap">
+ <div class="row">
+ <div class="col-sm-2 inline-progress-container">
+ <%= render partial: 'job_progress', locals: {j: object} %>
+ </div>
+ <div class="col-sm-10">
+ <%= object.script %>
+ <span class="deemphasize">
+ job
+ using <%= object.script_version %> commit
+ from <%= object.repository %> repository
+ </span>
+ </div>
+ </div>
+</div>
--- /dev/null
+<%= render partial: 'application/svg_div', locals: {
+ divId: "provenance_graph",
+ svgId: "provenance_svg",
+ svg: @svg } %>
--- /dev/null
+<% content_for :css do %>
+ table.topalign>tbody>tr>td {
+ vertical-align: top;
+ }
+ table.topalign>thead>tr>td {
+ vertical-align: bottom;
+ }
+<% end %>
+
+<%= render partial: "paging", locals: {results: objects, object: @object} %>
+
+<table class="topalign table">
+ <thead>
+ <tr class="contain-align-left">
+ <th>
+ </th><th>
+ status
+ </th><th>
+ uuid
+ </th><th>
+ script
+ </th><th>
+ version
+ </th><th>
+ output
+ </th>
+ </tr>
+ </thead>
+ <tbody>
+
+ <% @objects.sort_by { |j| j[:created_at] }.reverse.each do |j| %>
+
+ <tr class="cell-noborder">
+ <td>
+ <i class="icon-plus-sign expand-collapse-row" data-id="<%= j.uuid %>" style="cursor: pointer"></i>
+ </td>
+ <td>
+ <div class="inline-progress-container">
+ <%= render partial: 'job_progress', locals: {:j => j} %>
+ </div>
+ </td>
+ <td>
+ <%= link_to_if_arvados_object j %>
+ </td>
+ <td>
+ <%= j.script %>
+ </td>
+ <td>
+ <%= j.script_version.andand[0..8] %>
+ </td>
+ <td>
+ <%= link_to_if_arvados_object j.output %>
+ </td>
+ </tr>
+ <tr class="cell-noborder" id="<%= j.uuid %>" style="display:none">
+ <td colspan="7"><table class="table table-justforlayout"><tr>
+ <td style="border-left: 1px solid black">
+ <table class="table table-condensed">
+ <tr>
+ <td>
+ queued
+ </td>
+ <td>
+ ✉ <span title="<%= j.created_at %>"><%= raw distance_of_time_in_words(Time.now, j.created_at).sub('about ','~').sub(' ',' ') + ' ago' if j.created_at %></span>
+ </td>
+ <td>
+ <%= raw('for ' + distance_of_time_in_words(j.started_at, j.created_at).sub('about ','~').sub(' ',' ')) if j.created_at and j.started_at %>
+ </td>
+ </tr>
+ <% if j.started_at.is_a? Time %>
+ <tr>
+ <td>
+ started
+ </td>
+ <td>
+ ✈ <span title="<%= j.created_at %>"><%= raw distance_of_time_in_words(j.started_at, Time.now).sub('about ','~').sub(' ',' ') + ' ago' if j.started_at %></span>
+ </td>
+ <td>
+ <% if j.finished_at.is_a? Time %>
+ <%= raw('ran ' + distance_of_time_in_words(j.finished_at, j.started_at).sub('about ','~').sub(' ',' ')) %>
+ <% elsif j.state == "Running" %>
+ <span class="badge badge-success" title="tasks finished">✔ <%= j.tasks_summary[:done] %></span>
+ <span class="badge badge-info" title="tasks running">✈ <%= j.tasks_summary[:running] %></span>
+ <span class="badge" title="tasks todo">✉ <%= j.tasks_summary[:todo] %></span>
+ <% if j.tasks_summary[:failed] %>
+ <span class="badge badge-warning" title="task failures">✖ <%= j.tasks_summary[:failed] %></span>
+ <% end %>
+ <% end %>
+ </td>
+ </tr>
+ <% end %>
+ </table>
+ </td><td>
+ <table class="table table-condensed">
+ <tr><td colspan="2">
+ <%= j.script %> <%= j.script_version %>
+ </td></tr>
+ <% j.script_parameters.sort.each do |k,v| %>
+ <tr>
+ <td><%= k %></td><td><%= link_to_if_arvados_object v %></td>
+ </tr>
+ <% end %>
+ <tr>
+ <td>output</td><td><%= link_to_if_arvados_object j.output %></td>
+ </tr>
+ </table>
+ </td><td>
+ <table class="table table-condensed">
+ <% j.runtime_constraints.sort.each do |k,v| %>
+ <tr><td><%= v %></td><td><%= k %></td></tr>
+ <% end %>
+ </table>
+ </td>
+ </tr></table></td>
+ </tr>
+
+ <% end %>
+
+ </tbody>
+</table>
--- /dev/null
+<div class="arv-log-refresh-control"
+ data-load-throttle="15000"
+ ></div>
+<%=
+ pj = {}
+ pj[:job] = @object
+ pj[:name] = @object[:name] || "this job"
+ pj[:progress_bar] = render(partial: "job_progress",
+ locals: {:j => @object })
+ tasks = JobTask.filter([['job_uuid', '=', @object.uuid]]).results
+ render(partial: 'pipeline_instances/running_component',
+ locals: { tasks: tasks, pj: pj, i: 0, expanded: true})
+%>
+
+<div class="panel panel-default">
+ <div class="panel-heading">
+ <span class="panel-title">Used in pipelines</span>
+ </div>
+ <div class="panel-body">
+ <% pi = PipelineInstance.order("created_at desc").filter([["components", "like", "%#{@object.uuid}%"]]) %>
+
+ <% pi.each do |pipeline| %>
+ <% pipeline.components.each do |k, v| %>
+ <% if v[:job] and v[:job][:uuid] == @object.uuid %>
+ <div>
+ <b><%= k %></b>
+ component of
+ <%= link_to_if_arvados_object pipeline, friendly_name: true %>
+ created at
+ <%= render_localized_date(pipeline.created_at) %>.
+ </div>
+ <% end %>
+ <% end %>
+ <% end %>
+ </div>
+</div>
--- /dev/null
+<% content_for :tab_line_buttons do %>
+ <div class="pane-loaded arv-log-event-listener arv-refresh-on-state-change"
+ data-pane-content-url="<%= url_for(params.merge(tab_pane: "job_buttons")) %>"
+ data-object-uuid="<%= @object.uuid %>"
+ style="display: inline">
+ <%= render partial: 'show_job_buttons', locals: {object: @object}%>
+ </div>
+<% end %>
+
+<%= render partial: 'title_and_buttons' %>
+<%= render partial: 'content', layout: 'content_layout', locals: {pane_list: controller.show_pane_list }%>
--- /dev/null
+<% unless @histogram_pretty_date.nil? %>
+ <% content_for :tab_panes do %>
+ <script type="text/javascript">
+ $(document).ready(function(){
+ $.renderHistogram(<%= raw @cache_age_histogram.to_json %>);
+ });
+ </script>
+ <div class='graph'>
+ <h3>Cache Age vs. Disk Utilization</h3>
+ <h4>circa <%= @histogram_pretty_date %></h4>
+ <div id='cache-age-vs-disk-histogram'>
+ </div>
+ </div>
+ <% end %>
+<% end %>
+<%= content_for :content_top %>
+<div class="pull-right">
+ <%= content_for :tab_line_buttons %>
+</div>
+<%= content_for :tab_panes %>
--- /dev/null
+<!DOCTYPE html>
+<html ng-app="Workbench">
+<head>
+ <meta charset="utf-8">
+ <title>
+ <% if content_for? :page_title %>
+ <%= yield :page_title %> / <%= Rails.configuration.site_name %>
+ <% else %>
+ <%= Rails.configuration.site_name %>
+ <% end %>
+ </title>
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <link rel="icon" href="/favicon.ico" type="image/x-icon">
+ <link rel="shortcut icon" href="/favicon.ico" type="image/x-icon">
+ <meta name="description" content="">
+ <meta name="author" content="">
+ <% if current_user and $arvados_api_client.discovery[:websocketUrl] %>
+ <meta name="arv-websocket-url" content="<%=$arvados_api_client.discovery[:websocketUrl]%>?api_token=<%=Thread.current[:arvados_api_token]%>">
+ <% end %>
+ <meta name="robots" content="NOINDEX, NOFOLLOW">
+ <%= stylesheet_link_tag "application", :media => "all" %>
+ <%= javascript_include_tag "application" %>
+ <%= csrf_meta_tags %>
+ <%= yield :head %>
+ <%= javascript_tag do %>
+ angular.module('Arvados').value('arvadosApiToken', '<%=Thread.current[:arvados_api_token]%>');
+ angular.module('Arvados').value('arvadosDiscoveryUri', '<%= Rails.configuration.arvados_v1_base.sub '/arvados/v1', '/discovery/v1/apis/arvados/v1/rest' %>');
+ <%= yield :js %>
+ <% end %>
+ <style>
+ <%= yield :css %>
+ body {
+ min-height: 100%;
+ height: 100%;
+ }
+
+ @media (max-width: 979px) { body { padding-top: 0; } }
+
+ @media (max-width: 767px) {
+ .breadcrumbs {
+ display: none;
+ }
+ }
+ </style>
+ <link href="//netdna.bootstrapcdn.com/font-awesome/4.1.0/css/font-awesome.css" rel="stylesheet">
+ <%= piwik_tracking_tag if (PiwikAnalytics.configuration.url != 'localhost' rescue false) %>
+</head>
+<body>
+<%= render template: 'layouts/body' %>
+<%= javascript_tag do %>
+<%= yield :footer_js %>
+<% end %>
+</body>
+</html>
--- /dev/null
+ <div id="wrapper" class="container-fluid">
+ <nav class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="/" data-push=true><%= Rails.configuration.site_name.downcase rescue Rails.application.class.parent_name %></a>
+ </div>
+
+ <div class="collapse navbar-collapse">
+ <ul class="nav navbar-nav navbar-right">
+
+ <li>
+ <a><i class="rotating loading glyphicon glyphicon-refresh"></i></a>
+ </li>
+
+ <% if current_user %>
+ <% if current_user.is_active %>
+ <li>
+ <form class="navbar-form" role="search"
+ data-search-modal=
+ "<%= url_for(
+ action: 'choose',
+ controller: 'search',
+ title: 'Search',
+ action_name: 'Show',
+ action_href: url_for(controller: :actions, action: :show),
+ action_method: 'get',
+ action_data: {selection_param: 'uuid', success: 'redirect-to-created-object', copy_from_search_box: true}.to_json)
+ %>">
+ <div class="input-group" style="width: 220px">
+ <input type="text" class="form-control" placeholder="search">
+ <a class="input-group-addon"><span class="glyphicon glyphicon-search"></span></a>
+ </div>
+ </form>
+ </li>
+ <% end %>
+
+ <li class="dropdown notification-menu">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="notifications-menu">
+ <span class="badge badge-alert notification-count"><%= @notification_count %></span>
+ <%= current_user.email %> <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <% if current_user.is_active %>
+ <li role="menuitem"><a href="/manage_account" role="menuitem"><i class="fa fa-key fa-fw"></i> Manage account</a></li>
+ <% if Rails.configuration.user_profile_form_fields %>
+ <li role="menuitem"><a href="/users/<%=current_user.uuid%>/profile" role="menuitem"><i class="fa fa-key fa-fw"></i> Manage profile</a></li>
+ <% end %>
+ <% end %>
+ <li role="menuitem"><a href="<%= logout_path %>" role="menuitem"><i class="fa fa-sign-out fa-fw"></i> Log out</a></li>
+ <% if current_user.is_active and
+ (@notifications || []).length > 0 %>
+ <li role="presentation" class="divider"></li>
+ <% @notifications.each_with_index do |n, i| %>
+ <% if i > 0 %><li class="divider"></li><% end %>
+ <li class="notification"><%= n.call(self) %></li>
+ <% end %>
+ <% end %>
+ </ul>
+ </li>
+
+ <% if current_user.is_admin %>
+ <li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="system-menu">
+ <span class="fa fa-lg fa-gear"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li role="presentation" class="dropdown-header">
+ Settings
+ </li>
+ <li role="menuitem"><a href="/repositories">
+ <i class="fa fa-lg fa-code-fork fa-fw"></i> Repositories
+ </a></li>
+ <li role="menuitem"><a href="/virtual_machines">
+ <i class="fa fa-lg fa-terminal fa-fw"></i> Virtual machines
+ </a></li>
+ <li role="menuitem"><a href="/authorized_keys">
+ <i class="fa fa-lg fa-key fa-fw"></i> SSH keys
+ </a></li>
+ <li role="menuitem"><a href="/api_client_authorizations">
+ <i class="fa fa-lg fa-ticket fa-fw"></i> API tokens
+ </a></li>
+ <li role="menuitem"><a href="/links">
+ <i class="fa fa-lg fa-arrows-h fa-fw"></i> Links
+ </a></li>
+ <li role="menuitem"><a href="/users">
+ <i class="fa fa-lg fa-user fa-fw"></i> Users
+ </a></li>
+ <li role="menuitem"><a href="/groups">
+ <i class="fa fa-lg fa-users fa-fw"></i> Groups
+ </a></li>
+ <li role="menuitem"><a href="/nodes">
+ <i class="fa fa-lg fa-cloud fa-fw"></i> Compute nodes
+ </a></li>
+ <li role="menuitem"><a href="/keep_services">
+ <i class="fa fa-lg fa-exchange fa-fw"></i> Keep services
+ </a></li>
+ <li role="menuitem"><a href="/keep_disks">
+ <i class="fa fa-lg fa-hdd-o fa-fw"></i> Keep disks
+ </a></li>
+ </ul>
+ </li>
+ <% end %>
+ <% else %>
+ <li><a href="<%= arvados_api_client.arvados_login_url(return_to: root_url) %>">Log in</a></li>
+ <% end %>
+
+ <li class="dropdown help-menu">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="arv-help">
+ <span class="fa fa-lg fa-question-circle"></span>
+ </a>
+ <ul class="dropdown-menu">
+ <li><%= link_to raw('<i class="fa fa-book fa-fw"></i> Tutorials and User guide'), "#{Rails.configuration.arvados_docsite}/user", target: "_blank" %></li>
+ <li><%= link_to raw('<i class="fa fa-book fa-fw"></i> API Reference'), "#{Rails.configuration.arvados_docsite}/api", target: "_blank" %></li>
+ <li><%= link_to raw('<i class="fa fa-book fa-fw"></i> SDK Reference'), "#{Rails.configuration.arvados_docsite}/sdk", target: "_blank" %></li>
+ <li role="presentation" class="divider"></li>
+ <li> <%= link_to report_issue_popup_path(popup_type: 'version', current_location: request.url, current_path: request.fullpath, action_method: 'post'),
+ {class: 'report-issue-modal-window', remote: true, return_to: request.url} do %>
+ <i class="fa fa-fw fa-support"></i> Show version / debugging info ...
+ <% end %>
+ </li>
+ <li> <%= link_to report_issue_popup_path(popup_type: 'report', current_location: request.url, current_path: request.fullpath, action_method: 'post'),
+ {class: 'report-issue-modal-window', remote: true, return_to: request.url} do %>
+ <i class="fa fa-fw fa-support"></i> Report a problem ...
+ <% end %>
+ </li>
+ </ul>
+ </li>
+ </ul>
+ </div><!-- /.navbar-collapse -->
+ </nav>
+
+ <% if current_user.andand.is_active %>
+ <nav class="navbar navbar-default breadcrumbs" role="navigation">
+ <ul class="nav navbar-nav navbar-left">
+ <li>
+ <a href="/">
+ <i class="fa fa-lg fa-fw fa-dashboard"></i>
+ Dashboard
+ </a>
+ </li>
+ <li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="projects-menu">
+ Projects
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" style="min-width: 20em" role="menu">
+ <li>
+ <%= link_to projects_path(options: {ensure_unique_name: true}), method: :post, class: 'btn btn-xs btn-default pull-right' do %>
+ <i class="fa fa-plus"></i> Add a new project
+ <% end %>
+ </li>
+ <%= render partial: "projects_tree_menu", locals: {
+ :project_link_to => Proc.new do |pnode, &block|
+ link_to(project_path(pnode[:object].uuid),
+ data: { 'object-uuid' => pnode[:object].uuid,
+ 'name' => 'name' },
+ &block)
+ end,
+ } %>
+ </ul>
+ </li>
+ <% if @name_link or @object %>
+ <li class="nav-separator">
+ <i class="fa fa-lg fa-angle-double-right"></i>
+ </li>
+ <li>
+ <%= link_to project_path(current_user.uuid) do %>
+ Home
+ <% end %>
+ </li>
+ <% project_breadcrumbs.each do |p| %>
+ <li class="nav-separator">
+ <i class="fa fa-lg fa-angle-double-right"></i>
+ </li>
+ <li>
+ <%= link_to(p.name, project_path(p.uuid), data: {object_uuid: p.uuid, name: 'name'}) %>
+ </li>
+ <% end %>
+ <% end %>
+ </ul>
+ </nav>
+ <% end %>
+
+ <div id="page-wrapper">
+ <%= yield %>
+ </div>
+ </div>
+
+ <%= yield :footer_html %>
+
+<div class="modal-container"></div>
+<div id="report-issue-modal-window"></div>
--- /dev/null
+<% if @object %>
+(<%= @object.link_class %>)
+<%= @object.name %>:
+<%= @object.tail_kind.andand.sub 'arvados#', '' %>
+→
+<%= @object.head_kind.andand.sub 'arvados#', '' %>
+<% end %>
+
--- /dev/null
+ <%= image_tag "dax.png", class: "dax" %>
+ <p>
+ Hi, I noticed you haven't uploaded a new collection yet.
+ <%= link_to "Click here to learn how to upload data to Arvados Keep.",
+ "#{Rails.configuration.arvados_docsite}/user/tutorials/tutorial-keep.html",
+ style: "font-weight: bold", target: "_blank" %>
+ </p>
--- /dev/null
+ <p><%= image_tag "dax.png", class: "dax" %>
+ Hi, I noticed you haven't run a job yet.
+ <%= link_to "Click here to learn how to run an Arvados Crunch job.",
+ "#{Rails.configuration.arvados_docsite}/user/tutorials/tutorial-job1.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ </p>
+
--- /dev/null
+ <p><%= image_tag "dax.png", class: "dax" %>
+ Hi, I noticed you haven't run a pipeline yet.
+ <%= link_to "Click here to learn how to run an Arvados Crunch pipeline.",
+ "#{Rails.configuration.arvados_docsite}/user/tutorials/tutorial-pipeline-workbench.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ </p>
--- /dev/null
+ <%= image_tag "dax.png", class: "dax" %>
+ <div>
+ Hi, I noticed that you have not yet set up an SSH public key for use with Arvados.
+ <%= link_to "Click here to set up an SSH public key for use with Arvados.",
+ "/manage_account", style: "font-weight: bold" %>
+ </div>
--- /dev/null
+<% pipeline_jobs(object).each do |pj| %>
+ <span class="label label-<%= pj[:labeltype] %>">
+ <%= pj[:name] %>
+ </span>
+<% end %>
--- /dev/null
+<% current_job = pj[:job] if pj[:job] != {} and pj[:job][:uuid] %>
+<div class="panel panel-default">
+ <div class="panel-heading">
+ <div class="container-fluid">
+ <div class="row-fluid">
+ <%# column offset 0 %>
+ <div class="col-md-3" style="word-break:break-all;">
+ <h4 class="panel-title">
+ <a data-toggle="collapse" href="#collapse<%= i %>">
+ <%= pj[:name] %> <span class="caret"></span>
+ </a>
+ </h4>
+ </div>
+
+ <%# column offset 3 %>
+ <div class="col-md-2 pipeline-instance-spacing">
+ <%= pj[:progress_bar] %>
+ </div>
+
+ <% if current_job %>
+ <%# column offset 5 %>
+ <% if current_job[:state] != "Queued" %>
+ <div class="col-md-3">
+ <% if current_job[:started_at] %>
+ <% walltime = ((if current_job[:finished_at] then current_job[:finished_at] else Time.now() end) - current_job[:started_at]) %>
+ <% cputime = tasks.map { |task|
+ if task.started_at and task.job_uuid == current_job[:uuid]
+ (if task.finished_at then task.finished_at else Time.now() end) - task.started_at
+ else
+ 0
+ end
+ }.reduce(:+) || 0 %>
+ <%= render_runtime(walltime, false, false) %>
+ <% if cputime > 0 %> / <%= render_runtime(cputime, false, false) %> (<%= (cputime/walltime).round(1) %>⨯)<% end %>
+ <% end %>
+ </div>
+ <% end %>
+
+ <% if current_job[:state] == "Queued" %>
+ <%# column offset 5 %>
+ <div class="col-md-6">
+ <% queuetime = Time.now - current_job[:created_at] %>
+ Queued for <%= render_runtime(queuetime, true) %>.
+ <% begin %>
+ <% if current_job[:queue_position] == 0 %>
+ This job is next in the queue to run.
+ <% elsif current_job[:queue_position] == 1 %>
+ There is 1 job in the queue ahead of this one.
+ <% elsif current_job[:queue_position] %>
+ There are <%= current_job[:queue_position] %> jobs in the queue ahead of this one.
+ <% end %>
+ <% rescue %>
+ <% end %>
+ </div>
+ <% elsif current_job[:state] == "Running" %>
+ <%# column offset 8 %>
+ <div class="col-md-3">
+ <span class="task-summary-status">
+ <%= current_job[:tasks_summary][:done] %> <%= "task".pluralize(current_job[:tasks_summary][:done]) %> done,
+ <%= current_job[:tasks_summary][:failed] %> failed,
+ <%= current_job[:tasks_summary][:running] %> running,
+ <%= current_job[:tasks_summary][:todo] %> pending
+ </span>
+ </div>
+ <% elsif current_job[:state].in? ["Complete", "Failed", "Cancelled"] %>
+ <%# column offset 8 %>
+ <div class="col-md-4 text-overflow-ellipsis">
+ <% if pj[:output_uuid] %>
+ <%= link_to_if_arvados_object pj[:output_uuid], friendly_name: true %>
+ <% elsif current_job[:output] %>
+ <%= link_to_if_arvados_object current_job[:output], link_text: "Output of #{pj[:name]}" %>
+ <% else %>
+ No output.
+ <% end %>
+ </div>
+ <% end %>
+
+ <% if current_job[:state].in? ["Queued", "Running"] %>
+ <%# column offset 11 %>
+ <div class="col-md-1 pipeline-instance-spacing">
+ <%= form_tag "/jobs/#{current_job[:uuid]}/cancel", remote: true, style: "display:inline; padding-left: 1em" do |f| %>
+ <%= hidden_field_tag :return_to, url_for(@object) %>
+ <%= button_tag "Cancel", {class: 'btn btn-xs btn-danger', id: "cancel-job-button"} %>
+ <% end %>
+ </div>
+ <% end %>
+ <% end %>
+ </div>
+ </div>
+ </div>
+
+ <div id="collapse<%= i %>" class="panel-collapse collapse <%= if expanded then 'in' end %>">
+ <div class="panel-body">
+ <div class="container">
+ <% current_component = (if current_job then current_job else pj end) %>
+ <div class="row">
+ <div class="col-md-6">
+ <table>
+ <% [:script, :repository, :script_version, :supplied_script_version, :nondeterministic].each do |k| %>
+ <tr>
+ <td style="padding-right: 1em">
+ <%= k.to_s %>:
+ </td>
+ <td>
+ <% if current_component[k].nil? %>
+ (none)
+ <% else %>
+ <%= current_component[k] %>
+ <% end %>
+ </td>
+ </tr>
+ <% end %>
+ <% if current_component[:runtime_constraints].andand[:docker_image] and current_component[:docker_image_locator] %>
+ <tr>
+ <td style="padding-right: 1em">
+ docker_image:
+ </td>
+ <td>
+ <%= current_component[:runtime_constraints][:docker_image] %>
+ </td>
+ </tr>
+ <tr>
+ <td style="padding-right: 1em">
+ docker_image_locator:
+ </td>
+ <td>
+ <%= link_to_if_arvados_object current_component[:docker_image_locator], friendly_name: true %>
+ </td>
+ </tr>
+ <% else %>
+ <tr>
+ <td style="padding-right: 1em">
+ docker_image:
+ </td>
+ <td>
+ Not run in Docker
+ </td>
+ </tr>
+ <% end %>
+ </table>
+ </div>
+ <div class="col-md-5">
+ <table>
+ <% [:uuid, :modified_by_user_uuid, :priority, :created_at, :started_at, :finished_at].each do |k| %>
+ <tr>
+ <td style="padding-right: 1em">
+ <%= k.to_s %>:
+ </td>
+ <td>
+ <% if k == :uuid %>
+ <%= link_to_if_arvados_object current_component[k], link_text: current_component[k] %>
+ <% elsif k.to_s.end_with? 'uuid' %>
+ <%= link_to_if_arvados_object current_component[k], friendly_name: true %>
+ <% elsif k.to_s.end_with? '_at' %>
+ <%= render_localized_date(current_component[k]) %>
+ <% else %>
+ <%= current_component[k] %>
+ <% end %>
+ </td>
+ </tr>
+ <% end %>
+ </table>
+ </div>
+ </div>
+ <div class="row">
+ <div class="col-md-6">
+ <p>script_parameters:</p>
+ <pre><%= JSON.pretty_generate(current_component[:script_parameters]) rescue nil %></pre>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+</div>
--- /dev/null
+<% pi_span = [(10.0/[@objects.count,1].max).floor,1].max %>
+
+<div class="headrow pipeline-compare-headrow">
+ <div class="row">
+ <div class="col-sm-2">
+ <%# label %>
+ </div>
+ <% @objects.each do |object| %>
+ <div class="col-sm-<%= pi_span %>" style="overflow-x: hidden; text-overflow: ellipsis;">
+ <%= render :partial => "show_object_button", :locals => {object: object, size: 'sm' } %>
+ <%= object.name || "unnamed #{object.class_for_display.downcase}" %>
+ <br />
+ <span class="deemphasize">Template:</span> <%= link_to_if_arvados_object object.pipeline_template_uuid, friendly_name: true %>
+ </div>
+ <% end %>
+ </div>
+</div>
+
+<% @rows.each do |row| %>
+<div class="row pipeline-compare-row">
+ <div class="col-sm-2">
+ <%= row[:name] %>
+ </div>
+ <% @objects.each_with_index do |_, x| %>
+ <div class="col-sm-<%= pi_span %>">
+ <div class="row">
+ <div class="col-sm-12">
+
+ <% if row[:components][x] %>
+ <% pj = render_pipeline_job row[:components][x] %>
+
+ <%= link_to_if_arvados_object pj[:job_id], {friendly_name: true, with_class_name: true}, {class: 'deemphasize'} %>
+ <br />
+
+ <% %w(script script_version script_parameters output).each do |key| %>
+ <% unless key=='output' and pj[:result] != 'complete' %>
+ <% val = pj[key.to_sym] || pj[:job].andand[key.to_sym] %>
+ <% link_name = case
+ when !val
+ val = ''
+ when key == 'script_version' && val.match(/^[0-9a-f]{7,}$/)
+ val = val[0..7] # TODO: leave val alone, make link_to handle git commits
+ when key == 'output'
+ val.sub! /\+K.*$/, ''
+ val[0..12]
+ when key == 'script_parameters'
+ val = val.keys.sort.join(', ')
+ end
+ %>
+ <span class="deemphasize"><%= key %>:</span> <span class="<%= 'notnormal' if !pj[:is_normal][key.to_sym] %>"><%= link_to_if_arvados_object val, {friendly_name: true, link_text: link_name} %></span>
+ <% end %>
+ <br />
+ <% end %>
+ <% else %>
+ None
+ <% end %>
+ </div>
+ </div>
+ </div>
+ <% end %>
+</div>
+<div class="row" style="padding: .5em">
+</div>
+<% end %>
+
+
--- /dev/null
+<% if !@object.state.in? ['New', 'Ready'] %>
+
+ <%
+ job_uuids = @object.components.map { |k,j| j.is_a? Hash and j[:job].andand[:uuid] }.compact
+ throttle = @object.state.start_with?('Running') ? 5000 : 15000
+ %>
+ <div class="arv-log-refresh-control"
+ data-load-throttle="<%= throttle %>"
+ data-object-uuids="<%= @object.uuid %> <%= job_uuids.join(' ') %>"
+ ></div>
+
+ <%= render_pipeline_components("running", :json) %>
+
+<% else %>
+ <%# state is either New or Ready %>
+ <p><i>Here are all of the pipeline's components (jobs that will need to run in order to complete the pipeline). If you know what you're doing (or you're experimenting) you can modify these parameters before starting the pipeline. Usually, you only need to edit the settings presented on the "Inputs" tab above.</i></p>
+
+ <%= render_pipeline_components("editable", :json, editable: true) %>
+<% end %>
--- /dev/null
+<table class="table pipeline-components-table" style="margin-top: -.1em">
+ <colgroup>
+ <col style="width: 20%" />
+ <col style="width: 20%" />
+ <col style="width: 20%" />
+ <col style="width: 40%" />
+ </colgroup>
+
+ <thead>
+ <tr>
+ <th>
+ component
+ </th><th>
+ script
+ </th><th>
+ parameter
+ </th><th>
+ value
+ </th>
+ </tr>
+ </thead>
+ <tbody>
+ <% @object.components.each do |k, component| %>
+ <% next if !component %>
+ <tr>
+ <td><%= k %></td>
+
+ <td><%= component[:script] %></td>
+
+ <td>script version</td>
+
+ <td>
+ <%= render_pipeline_component_attribute (editable && @object), :components, [k, :script_version], component[:script_version] %>
+ </td>
+ </tr>
+
+ <% component[:script_parameters].andand.each do |p, tv| %>
+ <tr>
+ <td style="border-top: none"></td>
+ <td style="border-top: none"></td>
+
+ <td class="property-edit-row"><%= p %></td>
+ <td class="property-edit-row"><%= render_pipeline_component_attribute (editable && @object), :components, [k, :script_parameters, p.to_sym], tv %></td>
+ </tr>
+ <% end %>
+ <% end %>
+ </tbody>
+</table>
--- /dev/null
+<p>The components of this pipeline are in a format that Workbench does not recognize.</p>
+
+<p>Error encountered: <b><%= error_name %></b></p>
+
+ <div id="components-accordion" class="panel panel-default">
+ <div class="panel-heading">
+ <h4 class="panel-title">
+ <a data-toggle="collapse" data-parent="#components-accordion" href="#components-json">
+ Show components JSON
+ </a>
+ </h4>
+ </div>
+ <div id="components-json" class="panel-collapse collapse">
+ <div class="panel-body">
+ <pre><%= Oj.dump(@object.components, indent: 2) %></pre>
+ </div>
+ </div>
+ <div class="panel-heading">
+ <h4 class="panel-title">
+ <a data-toggle="collapse" data-parent="#components-accordion" href="#components-backtrace">
+ Show backtrace
+ </a>
+ </h4>
+ </div>
+ <div id="components-backtrace" class="panel-collapse collapse">
+ <div class="panel-body">
+ <pre><%= backtrace %></pre>
+ </div>
+ </div>
+ </div>
--- /dev/null
+<%# Summary %>
+
+<div class="pull-right" style="padding-left: 1em">
+ Current state: <span class="badge badge-info" data-pipeline-state="<%= @object.state %>">
+ <% if @object.state == "RunningOnServer" %>
+ Active
+ <% else %>
+ <%= @object.state %>
+ <% end %>
+ </span>
+</div>
+
+<% pipeline_jobs = render_pipeline_jobs %>
+<% job_uuids = pipeline_jobs.map { |j| j[:job].andand[:uuid] }.compact %>
+
+<% if @object.state == 'Paused' %>
+ <p>
+ This pipeline is paused. Jobs that are
+ already running will continue to run, but no new jobs will be submitted.
+ </p>
+<% end %>
+
+<% tasks = JobTask.filter([['job_uuid', 'in', job_uuids]]).results %>
+<% runningtime = determine_wallclock_runtime(pipeline_jobs.map {|j| j[:job]}.compact) %>
+
+<p>
+ <% if @object.started_at %>
+ This pipeline started at <%= render_localized_date(@object.started_at) %>.
+ It
+ <% if @object.state == 'Complete' %>
+ completed in
+ <% elsif @object.state == 'Failed' %>
+ failed after
+ <% else %>
+ has been active for
+ <% end %>
+
+ <% walltime = if @object.finished_at then
+ @object.finished_at - @object.started_at
+ else
+ Time.now - @object.started_at
+ end %>
+
+ <%= if walltime > runningtime
+ render_runtime(walltime, true, false)
+ else
+ render_runtime(runningtime, true, false)
+ end %><% if @object.finished_at %> at <%= render_localized_date(@object.finished_at) %><% end %>.
+ <% else %>
+ This pipeline is <%= if @object.state.start_with? 'Running' then 'active' else @object.state.downcase end %>.
+ <% walltime = 0%>
+ <% end %>
+
+ <% if @object.state == 'Failed' %>
+ Check the Log tab for more detail about why this pipeline failed.
+ <% end %>
+</p>
+
+<p>
+ This pipeline
+ <% if @object.state.start_with? 'Running' %>
+ has run
+ <% else %>
+ ran
+ <% end %>
+ for
+ <% cputime = tasks.map { |task|
+ if task.started_at
+ (if task.finished_at then task.finished_at else Time.now() end) - task.started_at
+ else
+ 0
+ end
+ }.reduce(:+) || 0 %>
+ <%= render_runtime(runningtime, true, false) %><% if (walltime - runningtime) > 0 %>
+ (<%= render_runtime(walltime - runningtime, true, false) %> queued)<% end %><% if cputime == 0 %>.<% else %>
+ and used
+ <%= render_runtime(cputime, true, false) %>
+ of CPU time (<%= (cputime/runningtime).round(1) %>⨯ scaling).
+ <% end %>
+</p>
+
+<%# Components %>
+
+<% pipeline_jobs.each_with_index do |pj, i| %>
+ <%= render partial: 'running_component', locals: {tasks: tasks, pj: pj, i: i, expanded: false} %>
+<% end %>
--- /dev/null
+<% if @pipelines.count > 1 %>
+ <div style="text-align: center; padding-top: 0.5em">
+ <span class="pipeline_color_legend" style="background: #aaffaa"><%= link_to_if_arvados_object @pipelines[0], friendly_name: true %></span>
+ <span class="pipeline_color_legend" style="background: #aaaaff"><%= link_to_if_arvados_object @pipelines[1], friendly_name: true %></span>
+ <% if @pipelines.count > 2 %>
+ <span class="pipeline_color_legend" style="background: #ffaaaa"><%= link_to_if_arvados_object @pipelines[2], friendly_name: true %></span>
+ <% end %>
+ <span class="pipeline_color_legend" style="background: #aaaaaa">Common to <%= @pipelines.count > 2 ? 'multiple' : 'both' %> pipelines</span>
+ </div>
+<% end %>
+
+<%= render partial: 'application/svg_div', locals: {
+ divId: "provenance_graph",
+ svgId: "provenance_svg",
+ svg: @prov_svg } %>
--- /dev/null
+<% n_inputs = 0 %>
+
+<% content_for :pi_input_form do %>
+<form role="form" style="width:60%">
+ <div class="form-group">
+ <% @object.components.each do |cname, component| %>
+ <% next if !component %>
+ <% component[:script_parameters].andand.each do |pname, pvalue_spec| %>
+ <% if pvalue_spec.is_a? Hash %>
+ <% if pvalue_spec[:description] or
+ pvalue_spec[:required] or pvalue_spec[:optional] == false %>
+ <% n_inputs += 1 %>
+ <label for="<% "#{cname}-#{pname}" %>">
+ <%= @object.component_input_title(cname, pname) %>
+ </label>
+ <div>
+ <p class="form-control-static">
+ <%= render_pipeline_component_attribute @object, :components, [cname, :script_parameters, pname.to_sym], pvalue_spec %>
+ </p>
+ </div>
+ <p class="help-block">
+ <%= pvalue_spec[:description] %>
+ </p>
+ <% end %>
+ <% end %>
+ <% end %>
+ <% end %>
+ </div>
+</form>
+<% end %>
+
+<% if n_inputs == 0 %>
+ <p>This pipeline does not need any further inputs specified. You can start it by clicking the "Run" button whenever you're ready. (It's not too late to change existing settings, though.)</p>
+<% else %>
+ <p><i>Provide <%= n_inputs > 1 ? 'values' : 'a value' %> for the following <%= n_inputs > 1 ? 'parameters' : 'parameter' %>, then click the "Run" button to start the pipeline.</i></p>
+ <%= content_for :pi_input_form %>
+
+ <%= link_to(url_for('pipeline_instance[state]' => 'RunningOnServer'),
+ class: 'btn btn-primary run-pipeline-button',
+ method: :patch
+ ) do %>
+ Run <i class="fa fa-fw fa-play"></i>
+ <% end %>
+
+<% end %>
+
+<div style="margin-top: 1em;">
+ <p>Click the "Components" tab above to see a full list of pipeline settings.</p>
+</div>
--- /dev/null
+<% log_uuids = [@object.uuid] + pipeline_jobs(@object).collect{|x|x[:job].andand[:uuid]}.compact %>
+<% log_history = stderr_log_history(log_uuids) %>
+<div id="event_log_div"
+ class="arv-log-event-listener arv-log-event-handler-append-logs arv-log-event-subscribe-to-pipeline-job-uuids arv-job-log-window"
+ data-object-uuids="<%= log_uuids.join(' ') %>"
+ ><%= log_history.join("\n") %></div>
+
+<%# Applying a long throttle suppresses the auto-refresh of this
+ partial that would normally be triggered by arv-log-event. %>
+<div class="arv-log-refresh-control"
+ data-load-throttle="86486400000" <%# 1001 nights %>
+ ></div>
--- /dev/null
+<div class="nowrap">
+ <%= object.content_summary %><br />
+ <%= render partial: 'pipeline_instances/component_labels', locals: {object: object} %>
+</div>
--- /dev/null
+<%= form_tag({}, {id: "comparedInstances"}) do |f| %>
+
+<table class="table table-condensed table-fixedlayout arv-recent-pipeline-instances">
+ <colgroup>
+ <col width="5%" />
+ <col width="15%" />
+ <col width="25%" />
+ <col width="20%" />
+ <col width="15%" />
+ <col width="15%" />
+ <col width="5%" />
+ </colgroup>
+ <thead>
+ <tr class="contain-align-left">
+ <th>
+ </th><th>
+ Status
+ </th><th>
+ Instance
+ </th><th>
+ Template
+ </th><th>
+ Owner
+ </th><th>
+ Created at
+ </th><th>
+ </th>
+ </tr>
+ </thead>
+
+ <tbody data-infinite-scroller="#recent-pipeline-instances" id="recent-pipeline-instances"
+ data-infinite-content-href="<%= url_for partial: :recent_rows %>" >
+ </tbody>
+
+</table>
+
+<% end %>
--- /dev/null
+<% @objects.sort_by { |ob| ob.created_at }.reverse.each do |ob| %>
+ <tr data-object-uuid="<%= ob.uuid %>" data-kind="<%= ob.kind %>" >
+ <td>
+ <%= check_box_tag 'uuids[]', ob.uuid, false, :class => 'persistent-selection' %>
+ </td><td>
+ <%= render partial: 'pipeline_status_label', locals: {:p => ob} %>
+ </td><td colspan="1">
+ <%= link_to_if_arvados_object ob, friendly_name: true %>
+ </td><td>
+ <%= link_to_if_arvados_object ob.pipeline_template_uuid, friendly_name: true %>
+ </td><td>
+ <%= link_to_if_arvados_object ob.owner_uuid, friendly_name: true %>
+ </td><td>
+ <%= ob.created_at.to_s %>
+ </td><td>
+ <%= render partial: 'delete_object_button', locals: {object:ob} %>
+ </td>
+ </tr>
+ <tr data-object-uuid="<%= ob.uuid %>">
+ <td style="border-top: 0;" colspan="2">
+ </td>
+ <td style="border-top: 0; opacity: 0.5;" colspan="6">
+ <% ob.components.each do |cname, c| %>
+ <% if c.is_a?(Hash) and c[:job] %>
+ <%= render partial: "job_progress", locals: {:j => c[:job], :title => cname.to_s, :show_progress_bar => false } %>
+ <% else %>
+ <span class="label label-default"><%= cname.to_s %></span>
+ <% end %>
+ <% end %>
+ </td>
+ </tr>
+<% end %>
--- /dev/null
+ <% if @object.state.in? ['Complete', 'Failed', 'Cancelled', 'Paused'] %>
+
+ <%= link_to(copy_pipeline_instance_path('id' => @object.uuid, 'script' => "use_latest", "components" => "use_latest", "pipeline_instance[state]" => "RunningOnServer"),
+ class: 'btn btn-primary',
+ title: 'Re-run with latest options',
+ #data: {toggle: :tooltip, placement: :top}, title: 'Re-run',
+ method: :post,
+ ) do %>
+ <i class="fa fa-fw fa-play"></i> Re-run with latest
+ <% end %>
+
+ <%= link_to raw('<i class="fa fa-fw fa-cogs"></i> Re-run options...'),
+ "#",
+ {class: 'btn btn-primary', 'data-toggle' => "modal",
+ 'data-target' => '#clone-and-edit-modal-window',
+ title: 'Re-run with options'} %>
+ <% end %>
+
+ <% if @object.state.in? ['New', 'Ready'] %>
+ <%= link_to(url_for('pipeline_instance[state]' => 'RunningOnServer'),
+ class: 'btn btn-primary run-pipeline-button',
+ title: 'Run this pipeline',
+ method: :patch
+ ) do %>
+ <i class="fa fa-fw fa-play"></i> Run
+ <% end %>
+ <% else %>
+ <% if @object.state.in? ['RunningOnClient', 'RunningOnServer'] %>
+ <%= link_to(url_for('pipeline_instance[state]' => 'Paused'),
+ class: 'btn btn-primary run-pipeline-button',
+ title: 'Pause this pipeline',
+ method: :patch
+ ) do %>
+ <i class="fa fa-fw fa-pause"></i> Pause
+ <% end %>
+ <% elsif @object.state == 'Paused' %>
+ <%= link_to(url_for('pipeline_instance[state]' => 'RunningOnServer'),
+ class: 'btn btn-primary run-pipeline-button',
+ title: 'Resume this pipeline',
+ method: :patch
+ ) do %>
+ <i class="fa fa-fw fa-play"></i> Resume
+ <% end %>
+ <% end %>
+ <% end %>
--- /dev/null
+<% if (o = Group.find?(@objects.first.owner_uuid)) %>
+ <% content_for :breadcrumbs do %>
+ <li class="nav-separator"><span class="glyphicon glyphicon-arrow-right"></span></li>
+ <li>
+ <%= link_to(o.name, project_path(o.uuid)) %>
+ </li>
+ <li class="nav-separator">
+ <span class="glyphicon glyphicon-arrow-right"></span>
+ </li>
+ <li>
+ <%= link_to '#' do %>compare pipelines<% end %>
+ </li>
+ <% end %>
+<% end %>
+<%= render partial: 'content', layout: 'content_layout', locals: {pane_list: controller.compare_pane_list } %>
--- /dev/null
+<% content_for :tab_line_buttons do %>
+ <div class="input-group">
+ <input type="text" class="form-control filterable-control recent-pipeline-instances-filterable-control"
+ placeholder="Search pipeline instances"
+ data-filterable-target="#recent-pipeline-instances"
+ <%# Just for the double-load test in FilterableInfiniteScrollTest: %>
+ value="<%= params[:search] %>"
+ />
+ </div>
+
+ <%= form_tag({action: 'compare', controller: params[:controller], method: 'get'}, {method: 'get', id: 'compare', class: 'pull-right small-form-margin'}) do |f| %>
+ <%= submit_tag 'Compare 2 or 3 selected', {class: 'btn btn-primary', disabled: true} %>
+ <% end rescue nil %>
+
+<% end %>
+
+<%= render file: 'application/index.html.erb', locals: local_assigns %>
--- /dev/null
+<% template = PipelineTemplate.find?(@object.pipeline_template_uuid) %>
+<%= content_for :content_top do %>
+ <div class="row">
+ <div class="col-sm-6">
+ <%= render partial: 'name_and_description' %>
+ </div>
+ <% if template %>
+ <div class="alert alert-info col-sm-6">
+ This pipeline was created from the template <%= link_to_if_arvados_object template, friendly_name: true %><br />
+ <% if template.modified_at && (template.modified_at > @object.created_at) %>
+ Note: This template has been modified since this instance was created.
+ <% end %>
+ </div>
+ <% end %>
+ </div>
+<% end %>
+
+<% content_for :tab_line_buttons do %>
+
+ <div id="pipeline-instance-tab-buttons"
+ class="pane-loaded arv-log-event-listener arv-refresh-on-state-change"
+ data-pane-content-url="<%= url_for(params.merge(tab_pane: "tab_buttons")) %>"
+ data-object-uuid="<%= @object.uuid %>"
+ >
+ <%= render partial: 'show_tab_buttons', locals: {object: @object}%>
+ </div>
+
+<% end %>
+
+<%= render partial: 'content', layout: 'content_layout', locals: {pane_list: controller.show_pane_list }%>
+
+<div id="clone-and-edit-modal-window" class="modal fade" role="dialog"
+ aria-labelledby="myModalLabel" aria-hidden="true">
+ <div class="modal-dialog">
+ <div class="modal-content">
+
+ <%= form_tag copy_pipeline_instance_path do |f| %>
+
+ <div class="modal-header">
+ <button type="button" class="close" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">×</button>
+ <div>
+ <div class="col-sm-6"> <h4 class="modal-title">Re-run pipeline</h4> </div>
+ </div>
+ <br/>
+ </div>
+
+ <div class="modal-body">
+ <%= radio_button_tag(:script, "use_latest", true) %>
+ <%= label_tag(:script_use_latest, "Use latest script versions") %>
+ <br>
+ <%= radio_button_tag(:script, "use_same") %>
+ <%= label_tag(:script_use_same, "Use same script versions as this run") %>
+ <br>
+ <% if template %>
+ <br>
+ <%= radio_button_tag(:components, "use_latest", true) %>
+ <%= label_tag(:components_use_latest, "Update components against template") %>
+ <br>
+ <%= radio_button_tag(:components, "use_same") %>
+ <%= label_tag(:components_use_same, "Use same components as this run") %>
+ <% end %>
+ </div>
+
+ <div class="modal-footer">
+ <button type="submit" class="btn btn-primary" name="pipeline_instance[state]" value="New">Copy and edit inputs</button>
+ <button type="submit" class="btn btn-primary" name="pipeline_instance[state]" value="RunningOnServer">Run now</button>
+ <button class="btn btn-default" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">Cancel</button>
+ </div>
+
+ </div>
+ <% end %>
+ </div>
+</div>
--- /dev/null
+<% self.formats = [:html] %>
+var new_content = "<%= escape_javascript(render template: 'pipeline_instances/show') %>";
+var selected_tab_hrefs = [];
+if ($('div#page-wrapper').html() != new_content) {
+ $('.nav-tabs li.active a').each(function() {
+ selected_tab_hrefs.push($(this).attr('href'));
+ });
+
+ $('div#page-wrapper').html(new_content);
+
+ // Show the same tabs that were active before we rewrote page-wrapper
+ $.each(selected_tab_hrefs, function(i, href) {
+ $('.nav-tabs li a[href="' + href + '"]').tab('show');
+ });
+}
--- /dev/null
+../application/_choose.js.erb
\ No newline at end of file
--- /dev/null
+<% @objects.each do |object| %>
+ <div class="row filterable selectable" data-object-uuid="<%= object.uuid %>" data-preview-href="<%= url_for object %>?tab_pane=chooser_preview">
+ <div class="col-sm-12" style="overflow-x:hidden">
+ <i class="fa fa-fw fa-gear"></i>
+ <%= object.name %>
+ </div>
+ </div>
+<% end %>
--- /dev/null
+<%= content_for :content_top do %>
+ <h2>Template '<%= @object.name %>'</h2>
+<% end %>
+
+<table class="table topalign">
+ <thead>
+ </thead>
+ <tbody>
+ <% @object.attributes_for_display.each do |attr, attrvalue| %>
+ <% if attr != 'components' %>
+ <%= render partial: 'application/arvados_object_attr', locals: { attr: attr, attrvalue: attrvalue } %>
+ <% end %>
+ <% end %>
+ </tbody>
+</table>
--- /dev/null
+<div class="col-sm-11 col-sm-push-1 arv-description-in-table">
+ <%= @object.description %>
+</div>
+<%= render partial: 'show_components' %>
--- /dev/null
+<%= render_pipeline_components("editable", :json, editable: false) %>
--- /dev/null
+
+ <%= render partial: 'pipeline_instances/show_recent' %>
--- /dev/null
+<%= render partial: "paging", locals: {results: @objects, object: @object} %>
+
+<table class="table table-condensed arv-index">
+ <colgroup>
+ <col width="8%" />
+ <col width="10%" />
+ <col width="22%" />
+ <col width="45%" />
+ <col width="15%" />
+ </colgroup>
+ <thead>
+ <tr class="contain-align-left">
+ <th>
+ </th><th>
+ </th><th>
+ name
+ </th><th>
+ description/components
+ </th><th>
+ owner
+ </th>
+ </tr>
+ </thead>
+ <tbody>
+
+ <% @objects.sort_by { |ob| ob[:created_at] }.reverse.each do |ob| %>
+
+ <tr>
+ <td>
+ <%= button_to(choose_projects_path(id: "run-pipeline-button",
+ title: 'Choose project',
+ editable: true,
+ action_name: 'Choose',
+ action_href: pipeline_instances_path,
+ action_method: 'post',
+ action_data: {selection_param: 'pipeline_instance[owner_uuid]',
+ 'pipeline_instance[pipeline_template_uuid]' => ob.uuid,
+ 'pipeline_instance[description]' => "Created at #{Time.now.localtime}" + (ob.name.andand.size.andand>0 ? " using the pipeline template *#{ob.name}*" : ""),
+ 'success' => 'redirect-to-created-object'
+ }.to_json),
+ { class: "btn btn-default btn-xs", title: "Run #{ob.name}", remote: true, method: :get }
+ ) do %>
+ <i class="fa fa-fw fa-play"></i> Run
+ <% end %>
+ </td>
+ <td>
+ <%= render :partial => "show_object_button", :locals => {object: ob, size: 'xs'} %>
+ </td><td>
+ <%= render_editable_attribute ob, 'name' %>
+ </td><td>
+ <% if ob.respond_to?(:description) and ob.description %>
+ <%= render_attribute_as_textile(ob, "description", ob.description, false) %>
+ <br />
+ <% end %>
+ <% ob.components.collect { |k,v| k.to_s }.each do |k| %>
+ <span class="label label-default"><%= k %></span>
+ <% end %>
+ </td><td>
+ <%= link_to_if_arvados_object ob.owner_uuid, friendly_name: true %>
+ </td>
+ </tr>
+
+ <% end %>
+
+ </tbody>
+</table>
+
+<%= render partial: "paging", locals: {results: @objects, object: @object} %>
--- /dev/null
+<% content_for :tab_line_buttons do %>
+ <%= link_to(choose_projects_path(id: "run-pipeline-button",
+ title: 'Choose project',
+ editable: true,
+ action_name: 'Choose',
+ action_href: pipeline_instances_path,
+ action_method: 'post',
+ action_data: {selection_param: 'pipeline_instance[owner_uuid]',
+ 'pipeline_instance[pipeline_template_uuid]' => @object.uuid,
+ 'pipeline_instance[description]' => "Created at #{Time.now.localtime}" + (@object.name.andand.size.andand>0 ? " using the pipeline template *#{@object.name}*" : ""),
+ 'success' => 'redirect-to-created-object'
+ }.to_json),
+ { class: "btn btn-primary btn-sm", remote: true, title: 'Run this pipeline' }
+ ) do %>
+ <i class="fa fa-gear"></i> Run this pipeline
+ <% end %>
+<% end %>
+
+<%= render file: 'application/show.html.erb', locals: local_assigns %>
--- /dev/null
+<div class="modal modal-with-loading-spinner">
+ <div class="modal-dialog">
+ <div class="modal-content">
+
+ <div class="modal-header">
+ <button type="button" class="close" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">×</button>
+ <div>
+ <div class="col-sm-6"> <h4 class="modal-title"><%= params[:title] || 'Choose project' %></h4> </div>
+ <div class="spinner spinner-32px spinner-h-center col-sm-1" hidden="true"></div>
+ </div>
+ <br/>
+ </div>
+
+ <div class="modal-body">
+ <div class="selectable-container" style="height: 15em; overflow-y: scroll">
+ <% [my_project_tree, shared_project_tree].each do |tree| %>
+ <% tree.each do |projectnode| %>
+ <% if projectnode[:object].is_a? String %>
+ <div class="row" style="padding-left: <%= 1 + projectnode[:depth] %>em; margin-right: 0px">
+ <i class="fa fa-fw fa-share-alt"></i>
+ <%= projectnode[:object] %>
+ </div>
+ <% else
+ row_selectable = !params[:editable] || projectnode[:object].editable?
+ if projectnode[:object].uuid == current_user.uuid
+ row_name = "Home"
+ row_selectable = true
+ else
+ row_name = projectnode[:object].friendly_link_name || 'New project'
+ end %>
+ <div class="<%= 'selectable project' if row_selectable %> row"
+ style="padding-left: <%= 1 + projectnode[:depth] %>em; margin-right: 0px" data-object-uuid="<%= projectnode[:object].uuid %>">
+ <i class="fa fa-fw fa-folder-o"></i> <%= row_name %>
+ </div>
+ <% end %>
+ <% end %>
+ <% end %>
+ </div>
+ </div>
+
+ <div class="modal-footer">
+ <button class="btn btn-default" data-dismiss="modal" aria-hidden="true">Cancel</button>
+ <button class="btn btn-primary" aria-hidden="true" data-enable-if-selection disabled><%= params[:action_name] || 'Select' %></button>
+ <div class="modal-error hide" style="text-align: left; margin-top: 1em;">
+ </div>
+ </div>
+ </div>
+ </div>
+</div>
--- /dev/null
+../application/_choose.js.erb
\ No newline at end of file
--- /dev/null
+<h4>Queue</h4>
+<% queue = Job.queue %>
+<% if queue.any? %>
+
+<% queue.each do |j| %>
+ <div class="row">
+ <div class="col-md-3 text-overflow-ellipsis">
+ <%= link_to_if_arvados_object j, friendly_name: true %>
+ </div>
+ <div class="col-md-4">
+ <%= render_localized_date(j[:created_at]) %>
+ </div>
+ <div class="col-md-3">
+ <%= render_runtime(Time.now - j[:created_at], false) %>
+ </div>
+ <div class="col-md-2">
+ <%= j[:priority] %>
+ </div>
+ </div>
+<% end %>
+ <div class="row">
+ <div class="col-md-3">
+ <b>Job</b>
+ </div>
+ <div class="col-md-4">
+ <b>Submitted</b>
+ </div>
+ <div class="col-md-3">
+ <b>Queued</b>
+ </div>
+ <div class="col-md-2">
+ <b>Priority</b>
+ </div>
+ </div>
+ <% if Job.queue_size > queue.size %>
+ <i>Note: some items in the queue are not visible to you.</i>
+ <% end %>
+ <div>
+ </div>
+<% else %>
+ There are currently no jobs in your queue.
+<% end %>
+
+<h4>Node status</h4>
+<div class="compute-summary-nodelist">
+ <% nodes.sort_by { |n| n.hostname || "" }.each do |n| %>
+ <% if n.crunch_worker_state.in? ["busy", "idle"] and (Time.now - n[:last_ping_at]) < 3600 %>
+ <div class="compute-summary">
+ <a data-toggle="collapse" href="#detail_<%= n.hostname %>" class="compute-summary-head label label-<%= if n.crunch_worker_state == 'busy' then 'primary' else 'default' end %>">
+ <%= n.hostname %>
+ </a>
+ <div id="detail_<%= n.hostname %>" class="collapse compute-detail">
+ state: <%= n.crunch_worker_state %><br>
+ <% [:total_cpu_cores, :total_ram_mb, :total_scratch_mb].each do |i| %>
+ <%= i.to_s.gsub '_', ' ' %>: <%= n.info[i] %><br>
+ <% end %>
+ </div>
+ </div>
+ <% end %>
+ <% end %>
+</div>
--- /dev/null
+<div class="compute-summary-numbers">
+ <table>
+ <colgroup>
+ <col width="25%">
+ <col width="25%">
+ <col width="25%">
+ </colgroup>
+ <tr>
+ <td><%= Job.queue_size %></td>
+ <td><%= nodes.select {|n| n.crunch_worker_state == "busy" }.size %></td>
+ <td><%= nodes.select {|n| n.crunch_worker_state == "idle" }.size %></td>
+ </tr>
+ <tr>
+ <th>Queued jobs</th>
+ <th>Busy nodes</th>
+ <th>Idle nodes</th>
+ </tr>
+ </table>
+</div>
--- /dev/null
+<div>
+ <% any = false %>
+ <% recent_jobs_and_pipelines[0..9].each do |object| %>
+ <% any = true %>
+ <div class="row" style="height: 4.5em">
+ <div class="col-sm-4">
+ <%= render :partial => "show_object_button", :locals => {object: object, size: 'xs'} %>
+ <% if object.respond_to?(:name) %>
+ <%= render_editable_attribute object, 'name', nil, {tiptitle: 'rename'} %>
+ <% else %>
+ <%= object.class_for_display %> <%= object.uuid %>
+ <% end %>
+ </div>
+ <div class="col-sm-8 arv-description-in-table">
+ <%= render_controller_partial(
+ 'show_object_description_cell.html',
+ controller_name: object.controller_name,
+ locals: {object: object})
+ %>
+ </div>
+ </div>
+ <% end %>
+ <% if not any %>
+ <span class="deemphasize">No jobs or pipelines to display.</span>
+ <% end %>
+</div>
--- /dev/null
+<div class="container-fluid arv-project-list">
+ <% tree.each do |projectnode| %>
+ <% rowtype = projectnode[:object].class %>
+ <% next if rowtype != Group and !show_root_node %>
+ <div class="<%= 'project' if rowtype.in?([Group,User]) %> row">
+ <div class="col-md-4" style="padding-left: <%= projectnode[:depth] - (show_root_node ? 0 : 1) %>em;">
+ <% if show_root_node and rowtype == String %>
+ <i class="fa fa-fw fa-share-alt"></i>
+ <%= projectnode[:object] %>
+ <% elsif show_root_node and rowtype == User %>
+ <% if projectnode[:object].uuid == current_user.andand.uuid %>
+ <i class="fa fa-fw fa-folder-o"></i>
+ <%= link_to project_path(id: projectnode[:object].uuid) do %>
+ Home
+ <% end %>
+ <% else %>
+ <i class="fa fa-fw fa-folder-o"></i>
+ <%= projectnode[:object].friendly_link_name %>
+ <% end %>
+ <% elsif rowtype == Group %>
+ <i class="fa fa-fw fa-folder-o"></i>
+ <%= link_to projectnode[:object] do %>
+ <%= projectnode[:object].friendly_link_name %>
+ <% end %>
+ <% end %>
+ </div>
+ <% if projectnode[:object].respond_to?(:description) and not projectnode[:object].description.blank? %>
+ <div class="col-md-8 small"><%= render_attribute_as_textile(projectnode[:object], "description", projectnode[:object].description, true) %></div>
+ <% end %>
+ </div>
+ <% end %>
+</div>
--- /dev/null
+<% get_objects_and_names.each do |object, name_link| %>
+ <% name_object = (object.respond_to?(:name) || !name_link) ? object : name_link %>
+ <tr class="filterable"
+ data-object-uuid="<%= name_object.uuid %>"
+ data-kind="<%= object.kind %>"
+ data-object-created-at="<%= object.created_at %>"
+ >
+ <td>
+ <div style="width:1em; display:inline-block;">
+ <%= render partial: 'selection_checkbox', locals: {object: name_object, friendly_name: ((name_object.name rescue '') || '')} %>
+ </div>
+ </td>
+
+ <td>
+ <% if @object.editable? %>
+ <%= link_to({action: 'remove_item', id: @object.uuid, item_uuid: ((name_link && name_link.uuid) || object.uuid)}, method: :delete, remote: true, data: {confirm: "Remove #{object.class_for_display.downcase} #{name_object.name rescue object.uuid} from this project?", toggle: 'tooltip', placement: 'top'}, class: 'btn btn-sm btn-default btn-nodecorate', title: 'remove') do %>
+ <i class="fa fa-fw fa-trash-o"></i>
+ <% end %>
+ <% else %>
+ <i class="fa fa-fw"></i><%# placeholder %>
+ <% end %>
+ </td>
+
+ <td>
+ <%= render :partial => "show_object_button", :locals => {object: object, size: 'sm', name_link: name_link} %>
+ </td>
+
+ <td>
+ <%= render_editable_attribute (name_link || object), 'name', nil, {tiptitle: 'rename'} %>
+ </td>
+
+ <td class="arv-description-in-table">
+ <%= render_controller_partial(
+ 'show_object_description_cell.html',
+ controller_name: object.controller_name,
+ locals: {object: object})
+ %>
+ </td>
+ </tr>
+<% end %>
--- /dev/null
+
+ <div class="row">
+ <div class="col-md-6">
+ <div class="panel panel-default" style="min-height: 10.5em">
+ <div class="panel-heading"><span class="panel-title">Active pipelines</span>
+ <span class="pull-right">
+ <%= link_to(
+ choose_pipeline_templates_path(
+ title: 'Choose a pipeline to run:',
+ action_name: 'Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i>',
+ action_href: pipeline_instances_path,
+ action_method: 'post',
+ action_data: {'selection_param' => 'pipeline_instance[pipeline_template_uuid]', 'pipeline_instance[owner_uuid]' => current_user.uuid, 'success' => 'redirect-to-created-object'}.to_json),
+ { class: "btn btn-primary btn-xs", remote: true }) do %>
+ <i class="fa fa-fw fa-gear"></i> Run a pipeline...
+ <% end %>
+ </span>
+ </div>
+
+ <% _running_pipelines = running_pipelines %>
+ <% _finished_pipelines = finished_pipelines(8) %>
+ <% lookup = preload_objects_for_dataclass PipelineTemplate, (_running_pipelines.map(&:pipeline_template_uuid) + _finished_pipelines.map(&:pipeline_template_uuid)) %>
+
+ <div class="panel-body">
+ <% if _running_pipelines.empty? %>
+ No pipelines are currently running.
+ <% else %>
+ <% _running_pipelines.each do |p| %>
+ <div class="dashboard-panel-info-row">
+ <div class="clearfix">
+ <%= link_to_if_arvados_object p, {friendly_name: true, lookup: lookup} %>
+
+ <div class="pull-right" style="width: 40%">
+ <div class="progress" style="margin-bottom: 0px">
+ <% p.components.each do |k, v| %>
+ <% if v.is_a? Hash and v[:job] %>
+ <%= render partial: 'job_progress', locals: {:j => v[:job], :scaleby => (1.0/p.components.size)} %>
+ <% end %>
+ <% end %>
+ </div>
+ </div>
+ </div>
+
+ <%
+ running = p.components.select { |k, c| c.is_a? Hash and c[:job].andand[:state] == "Running" }
+ queued = p.components.select { |k, c| c.is_a? Hash and c[:job].andand[:state] == "Queued" }
+ %>
+
+ <div class="clearfix">
+ Started at <%= render_localized_date(p[:started_at] || p[:created_at], "noseconds") %>.
+ <% pipeline_time = Time.now - (p[:started_at] || p[:created_at]) %>
+ Active for <%= render_runtime(pipeline_time, false) %>.
+
+ <div class="pull-right">
+ <% running.each do |k,v| %>
+ <%= render partial: 'job_progress', locals: {:j => v[:job], :show_progress_bar => false, :title => k} %>
+ <% end %>
+ <% queued.each do |k,v| %>
+ <%= render partial: 'job_progress', locals: {:j => v[:job], :show_progress_bar => false, :title => k} %>
+ <% end %>
+ </div>
+ </div>
+ </div>
+ <% end %>
+ <% end %>
+ </div>
+ </div>
+
+ <div class="panel panel-default">
+ <div class="panel-heading"><span class="panel-title">Recently finished pipelines</span>
+ <span class="pull-right">
+ <%= link_to pipeline_instances_path, class: 'btn btn-default btn-xs' do %>
+ All pipelines <i class="fa fa-fw fa-arrow-circle-right"></i>
+ <% end %>
+ </span>
+ </div>
+ <div class="panel-body">
+ <% _finished_pipelines.each do |p| %>
+ <div class="dashboard-panel-info-row">
+ <div class="row">
+ <div class="col-md-6 text-overflow-ellipsis">
+ <%= link_to_if_arvados_object p, {friendly_name: true, lookup: lookup} %>
+ </div>
+ <div class="col-md-2">
+ <%= render partial: "pipeline_status_label", locals: {p: p}%>
+ </div>
+ <div class="col-md-4">
+ <%= render_localized_date(p[:finished_at] || p[:modified_at], "noseconds") %>
+ </div>
+ </div>
+ <div class="row">
+ <div class="col-md-12">
+ <% if p[:started_at] and p[:finished_at] %>
+ <% pipeline_time = p[:finished_at] - p[:started_at] %>
+ Active for <%= render_runtime(pipeline_time, false) %>
+ <% end %>
+
+ <span class="pull-right text-overflow-ellipsis" style="max-width: 100%">
+ <% outputs = [] %>
+ <% p.components.each do |k, c| %>
+ <% outputs << c[:output_uuid] if c[:output_uuid] %>
+ <% end %>
+ <% if outputs.size == 0 %>
+ No output.
+ <% elsif outputs.size == 1 %>
+ <i class="fa fa-fw fa-archive"></i> <%= link_to_if_arvados_object outputs[0], friendly_name: true %>
+ <% else %>
+ <a href="#<%= p[:uuid] %>-outputs" data-toggle="collapse">Outputs <span class="caret"></span></a>
+ <% end %>
+ </span>
+ </div>
+ </div>
+
+ <div class="row collapse" id="<%= p[:uuid] %>-outputs" >
+ <div class="col-md-12">
+ <div class="pull-right" style="max-width: 100%">
+ <% outputs.each do |out| %>
+ <div class="text-overflow-ellipsis">
+ <i class="fa fa-fw fa-archive"></i> <%= link_to_if_arvados_object out, friendly_name: true %>
+ </div>
+ <% end %>
+ </div>
+ </div>
+ </div>
+ </div>
+ <% end %>
+ </div>
+ </div>
+ </div>
+
+ <div class="col-md-6">
+ <% nodes = Node.all %>
+ <div class="panel panel-default" style="min-height: 10.5em">
+ <div class="panel-heading"><span class="panel-title">Compute and job status</span>
+ <span class="pull-right">
+ <%= link_to jobs_path, class: 'btn btn-default btn-xs' do %>
+ All jobs <i class="fa fa-fw fa-arrow-circle-right"></i>
+ <% end %>
+ </span>
+ </div>
+ <div class="panel-body">
+ <div>
+ <%= render partial: 'compute_node_summary', locals: {nodes: nodes} %>
+ <div style="text-align: center">
+ <a data-toggle="collapse" href="#compute_node_status">Details <span class="caret"></span></a>
+ </div>
+ </div>
+ <div id="compute_node_status" class="collapse">
+ <%= render partial: 'compute_node_status', locals: {nodes: nodes} %>
+ </div>
+ </div>
+ </div>
+ <div class="panel panel-default">
+ <div class="panel-heading"><span class="panel-title">Recent collections</span>
+ <span class="pull-right">
+ <%= link_to collections_path, class: 'btn btn-default btn-xs' do %>
+ All collections <i class="fa fa-fw fa-arrow-circle-right"></i>
+ <% end %>
+ </span>
+ </div>
+ <div class="panel-body">
+ <% r = recent_collections(8) %>
+ <% r[:collections].each do |p| %>
+ <div class="dashboard-panel-info-row">
+ <div>
+ <i class="fa fa-fw fa-folder-o"></i><%= link_to_if_arvados_object r[:owners][p[:owner_uuid]], friendly_name: true %>/
+ <span class="pull-right"><%= render_localized_date(p[:modified_at], "noseconds") %></span>
+ </div>
+ <div class="text-overflow-ellipsis" style="margin-left: 1em; width: 100%"><%= link_to_if_arvados_object p, {friendly_name: true, no_tags: true} %>
+ </div>
+ </div>
+ <% end %>
+ </div>
+ </div>
+ </div>
+ </div>
+
+</div>
--- /dev/null
+<%= render_pane 'tab_contents', to_string: true, locals: {
+ filters: [['uuid', 'is_a', "arvados#collection"]],
+ sortable_columns: { 'name' => 'collections.name', 'description' => 'collections.description' }
+ }.merge(local_assigns) %>
--- /dev/null
+<div class="row">
+ <% @objects[0..3].each do |object| %>
+ <div class="card arvados-object">
+ <div class="card-top blue">
+ <a href="#">
+ <img src="/favicon.ico" alt=""/>
+ </a>
+ </div>
+ <div class="card-info">
+ <span class="title"><%= @objects.name_for(object) || object.class_for_display %></span>
+ <div class="desc"><%= object.respond_to?(:description) ? object.description : object.uuid %></div>
+ </div>
+ <div class="card-bottom">
+ <%= render :partial => "show_object_button", :locals => {object: object, htmloptions: {class: 'btn-default btn-block'}} %>
+ </div>
+ </div>
+ <% end %>
+</div>
--- /dev/null
+<%= render_pane 'tab_contents', to_string: true, locals: {
+ limit: 50,
+ filters: [['uuid', 'is_a', ["arvados#job", "arvados#pipelineInstance"]]],
+ sortable_columns: { 'name' => 'jobs.script, pipeline_instances.name', 'description' => 'jobs.description, pipeline_instances.description' }
+ }.merge(local_assigns) %>
--- /dev/null
+<%= render_pane 'tab_contents', to_string: true, locals: {
+ filters: [['uuid', 'is_a', ["arvados#human", "arvados#specimen", "arvados#trait"]]],
+ sortable_columns: { 'name' => 'humans.uuid, specimens.uuid, traits.name' }
+ }.merge(local_assigns) %>
--- /dev/null
+<%= render_pane 'tab_contents', to_string: true, locals: {
+ filters: [['uuid', 'is_a', ["arvados#pipelineTemplate"]]],
+ sortable_columns: { 'name' => 'pipeline_templates.name', 'description' => 'pipeline_templates.description' }
+ }.merge(local_assigns) %>
--- /dev/null
+<%
+ uuid_map = {}
+ if @share_links
+ [User, Group].each do |type|
+ type
+ .filter([['uuid','in',@share_links.collect(&:tail_uuid)]])
+ .each do |o|
+ uuid_map[o.uuid] = o
+ end
+ end
+ end
+ perm_name_desc_map = {}
+ perm_desc_name_map = {}
+ perms_json = []
+ ['Read', 'Write', 'Manage'].each do |link_desc|
+ link_name = "can_#{link_desc.downcase}"
+ perm_name_desc_map[link_name] = link_desc
+ perm_desc_name_map[link_desc] = link_name
+ perms_json << {value: link_name, text: link_desc}
+ end
+ perms_json = perms_json.to_json
+ choose_filters = {
+ "groups" => [["group_class", "=", "role"]],
+ }
+ choose_filters.default = []
+ owner_icon = fa_icon_class_for_uuid(@object.owner_uuid)
+ if owner_icon == "fa-users"
+ owner_icon = "fa-folder"
+ owner_type = "parent project"
+ else
+ owner_type = "owning user"
+ end
+%>
+
+<div class="pull-right">
+ <% ["users", "groups"].each do |share_class| %>
+
+ <%= link_to(send("choose_#{share_class}_path",
+ title: "Share with #{share_class}",
+ by_project: false,
+ preview_pane: false,
+ multiple: true,
+ filters: choose_filters[share_class].to_json,
+ action_method: 'post',
+ action_href: share_with_project_path,
+ action_name: 'Add',
+ action_data: {selection_param: 'uuids[]', success: 'tab-refresh'}.to_json),
+ class: "btn btn-primary btn-sm", remote: true) do %>
+ <i class="fa fa-fw fa-plus"></i> Share with <%= share_class %>…
+ <% end %>
+
+ <% end %>
+</div>
+
+<p>Permissions for this project are inherited from the <%= owner_type %>
+ <i class="fa fa-fw <%= owner_icon %>"></i>
+ <%= link_to_if_arvados_object @object.owner_uuid, friendly_name: true %>.
+</p>
+
+<table id="project_sharing" class="topalign table" style="clear: both; margin-top: 1em;">
+ <tr>
+ <th>User/Group Name</th>
+ <th>Email Address</th>
+ <th colspan="2">Project Access</th>
+ </tr>
+
+ <% @share_links.andand.each do |link|
+ shared_with = uuid_map[link.tail_uuid]
+ if shared_with.nil?
+ link_name = link.tail_uuid
+ elsif shared_with.respond_to?(:full_name)
+ link_name = shared_with.full_name
+ else
+ link_name = shared_with.name
+ end
+ if shared_with && shared_with.respond_to?(:email)
+ email = shared_with.email
+ end
+ %>
+ <tr data-object-uuid="<%= link.uuid %>">
+ <td>
+ <i class="fa fa-fw <%= fa_icon_class_for_uuid(link.tail_uuid) %>"></i>
+ <%= link_to_if_arvados_object(link.tail_uuid, link_text: link_name) %>
+ </td>
+ <td>
+ <%= email %>
+ </td>
+ <td><%= link_to perm_name_desc_map[link.name], '#', {
+ "data-emptytext" => "Read",
+ "data-placement" => "bottom",
+ "data-type" => "select",
+ "data-url" => url_for(action: "update", id: link.uuid, controller: "links", merge: true),
+ "data-title" => "Set #{link_name}'s access level",
+ "data-name" => "[name]",
+ "data-pk" => {id: link.tail_uuid, key: "link"}.to_json,
+ "data-value" => link.name,
+ "data-clear" => false,
+ "data-source" => perms_json,
+ "data-tpl" => "<select id=\"share_change_level\"></select>",
+ "class" => "editable form-control",
+ } %>
+ </td>
+ <td>
+ <%= link_to(
+ {action: 'destroy', id: link.uuid, controller: "links"},
+ {title: 'Revoke', class: 'btn btn-default btn-nodecorate', method: :delete,
+ data: {confirm: "Revoke #{link_name}'s access to this project?",
+ remote: true}}) do %>
+ <i class="fa fa-fw fa-trash-o"></i>
+ <% end %>
+ </td>
+ </tr>
+ <% end %>
+</table>
--- /dev/null
+<%= render_pane 'tab_contents', to_string: true, locals: {
+ filters: [['uuid', 'is_a', ["arvados#group"]]],
+ sortable_columns: { 'name' => 'groups.name', 'description' => 'groups.description' }
+ }.merge(local_assigns) %>
--- /dev/null
+<% sortable_columns = {} if local_assigns[:sortable_columns].nil? %>
+<div class="selection-action-container">
+ <div class="row">
+ <div class="col-sm-5">
+ <div class="btn-group btn-group-sm">
+ <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">Selection <span class="caret"></span></button>
+ <ul class="dropdown-menu" role="menu">
+ <li><%= link_to "Create new collection with selected collections", '#',
+ 'data-href' => combine_selected_path(
+ action_data: {current_project_uuid: @object.uuid}.to_json
+ ),
+ 'id' => 'combine_selections_button',
+ method: :post,
+ 'data-selection-param-name' => 'selection[]',
+ 'data-selection-action' => 'combine-project-contents',
+ 'data-toggle' => 'dropdown'
+ %></li>
+ <li><%= link_to "Compare selected", 'action',
+ 'data-href' => compare_pipeline_instances_path,
+ 'data-selection-param-name' => 'uuids[]',
+ 'data-selection-action' => 'compare'
+ %></li>
+ <li><%= link_to "Copy selected...", '#',
+ 'data-href' => choose_projects_path(
+ title: 'Copy selected items to...',
+ editable: true,
+ action_name: 'Copy',
+ action_href: actions_path,
+ action_method: 'post',
+ action_data_from_params: ['selection'],
+ action_data: {
+ copy_selections_into_project: true,
+ selection_param: 'uuid',
+ success: 'page-refresh'}.to_json),
+ 'data-remote' => true,
+ 'data-selection-param-name' => 'selection[]',
+ 'data-selection-action' => 'copy'
+ %></li>
+ <% if @object.editable? %>
+ <li><%= link_to "Move selected...", '#',
+ 'data-href' => choose_projects_path(
+ title: 'Move selected items to...',
+ editable: true,
+ action_name: 'Move',
+ action_href: actions_path,
+ action_method: 'post',
+ action_data_from_params: ['selection'],
+ action_data: {
+ move_selections_into_project: true,
+ selection_param: 'uuid',
+ success: 'page-refresh'}.to_json),
+ 'data-remote' => true,
+ 'data-selection-param-name' => 'selection[]',
+ 'data-selection-action' => 'move'
+ %></li>
+ <li><%= link_to "Remove selected", '#',
+ method: :delete,
+ 'data-href' => url_for(action: :remove_items),
+ 'data-selection-param-name' => 'item_uuids[]',
+ 'data-selection-action' => 'remove',
+ 'data-remote' => true,
+ 'data-toggle' => 'dropdown'
+ %></li>
+ <% end %>
+ </ul>
+ </div>
+ </div>
+ <div class="col-sm-4 pull-right">
+ <input type="text" class="form-control filterable-control" placeholder="Search project contents" data-filterable-target="table.arv-index.arv-project-<%= tab_pane %> tbody"/>
+ </div>
+ </div>
+
+ <table class="table table-condensed arv-index arv-project-<%= tab_pane %>">
+ <colgroup>
+ <col width="0*" style="max-width: fit-content;" />
+ <col width="0*" style="max-width: fit-content;" />
+ <col width="0*" style="max-width: fit-content;" />
+ <col width="60%" style="width: 60%;" />
+ <col width="40%" style="width: 40%;" />
+ </colgroup>
+ <tbody data-infinite-scroller="#<%= tab_pane %>-scroll" data-infinite-content-href="<%= url_for partial: :contents_rows %>" data-infinite-content-params-projecttab="<%= local_assigns.select{|k| [:order, :limit, :filters].include? k }.to_json %>" data-infinite-content-params-attr="projecttab">
+ </tbody>
+ <thead>
+ <tr>
+ <th></th>
+ <th></th>
+ <th></th>
+ <% sort_order = sortable_columns['name'].gsub(/\s/,'') if sortable_columns['name'] %>
+ <th <% if !sort_order.nil? %>
+ data-sort-order='<%= sort_order %>'
+ <% end %> >
+ name
+ </th>
+ <% sort_order = sortable_columns['description'].gsub(/\s/,'') if sortable_columns['description'] %>
+ <th <% if !sort_order.nil? %>
+ data-sort-order='<%= sort_order %>'
+ <% end %> >
+ description
+ </th>
+ </tr>
+ </thead>
+ </table>
+</div>
--- /dev/null
+<div class="pane-loaded arv-log-event-listener arv-refresh-on-log-event"
+ data-pane-content-url="<%= root_url tab_pane: "dashboard" %>"
+ data-object-uuid="all"
+ data-load-throttle="15000"
+ >
+ <%= render partial: 'show_dashboard' %>
+</div>
--- /dev/null
+$(document).trigger('count-change');
+<% @removed_uuids.each do |uuid| %>
+ $('[data-object-uuid=<%= uuid %>]').hide('slow', function() {
+ $(this).remove();
+ });
+<% end %>
--- /dev/null
+<% if @object.uuid != current_user.uuid # Not the "Home" project %>
+<% content_for :content_top do %>
+ <%= render partial: 'name_and_description' %>
+<% end %>
+<% end %>
+
+<% content_for :tab_line_buttons do %>
+ <% if @object.editable? %>
+ <div class="btn-group btn-group-sm">
+ <button type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown"><i class="fa fa-fw fa-plus"></i> Add data <span class="caret"></span></button>
+ <ul class="dropdown-menu pull-right" role="menu">
+ <li>
+ <%= link_to(
+ choose_collections_path(
+ title: 'Choose a collection to copy into this project:',
+ multiple: true,
+ action_name: 'Copy',
+ action_href: actions_path(id: @object.uuid),
+ action_method: 'post',
+ action_data: {selection_param: 'selection[]', copy_selections_into_project: @object.uuid, success: 'page-refresh'}.to_json),
+ { remote: true, data: {'event-after-select' => 'page-refresh', 'toggle' => 'dropdown'} }) do %>
+ <i class="fa fa-fw fa-clipboard"></i> Copy data from another project
+ <% end %>
+ </li>
+ <li>
+ <%= link_to(collections_path(options: {ensure_unique_name: true}, collection: {manifest_text: "", name: "New collection", owner_uuid: @object.uuid}, redirect_to_anchor: 'Upload'), {
+ method: 'post',
+ data: {toggle: 'dropdown'}}) do %>
+ <i class="fa fa-fw fa-upload"></i> Upload files from my computer
+ <% end %>
+ </li>
+ </ul>
+ </div>
+ <%= link_to(
+ choose_pipeline_templates_path(
+ title: 'Choose a pipeline to run:',
+ action_name: 'Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i>',
+ action_href: pipeline_instances_path,
+ action_method: 'post',
+ action_data: {'selection_param' => 'pipeline_instance[pipeline_template_uuid]', 'pipeline_instance[owner_uuid]' => @object.uuid, 'success' => 'redirect-to-created-object'}.to_json),
+ { class: "btn btn-primary btn-sm", remote: true, title: "Run a pipeline in this project" }) do %>
+ <i class="fa fa-fw fa-gear"></i> Run a pipeline...
+ <% end %>
+ <%= link_to projects_path({'project[owner_uuid]' => @object.uuid, 'options' => {'ensure_unique_name' => true}}), method: :post, title: "Add a subproject to this project", class: 'btn btn-sm btn-primary' do %>
+ <i class="fa fa-fw fa-plus"></i>
+ Add a subproject
+ <% end %>
+ <% end %>
+<% end %>
+
+<%= render file: 'application/show.html.erb', locals: local_assigns %>
--- /dev/null
+<% @tab_counts.each do |pane_name, tab_count| %>
+ $('span#<%= pane_name %>-count').html('(<%= tab_count %>)');
+<% end %>
\ No newline at end of file
--- /dev/null
+<% if (example = @objects.select(&:push_url).first) %>
+
+<p>
+Sample git quick start:
+</p>
+
+<pre>
+git clone <%= example.push_url %> <%= example.name unless example.push_url.match(/:(\S+)\.git$/).andand[1] == example.name %>
+cd <%= example.name %>
+# edit files
+git add the/files/you/changed
+git commit
+git push
+</pre>
+
+<% end %>
+
+<p>
+ See also:
+ <%= link_to raw('Arvados Docs → User Guide → SSH access'),
+ "#{Rails.configuration.arvados_docsite}/user/getting_started/ssh-access-unix.html",
+ target: "_blank"%> and
+ <%= link_to raw('Arvados Docs → User Guide → Writing a Crunch
+ Script'),
+ "#{Rails.configuration.arvados_docsite}/user/tutorials/tutorial-firstscript.html",
+ target: "_blank"%>.
+</p>
--- /dev/null
+<% current_class = params[:last_object_class] %>
+<% @objects.each do |object| %>
+ <% icon_class = fa_icon_class_for_class(object.class) %>
+ <% if object.class.to_s != current_class %>
+ <% current_class = object.class.to_s %>
+ <div class="row class-separator" data-section-heading="true" data-section-name="<%= object.class.to_s %>">
+ <div class="col-sm-12">
+ <%= object.class_for_display.pluralize.downcase %>
+ </div>
+ </div>
+ <% end %>
+ <div class="row filterable selectable" data-section-name="<%= object.class.to_s %>" data-object-uuid="<%= object.uuid %>" data-preview-href="<%= chooser_preview_url_for object %>">
+ <div class="col-sm-12" style="overflow-x:hidden; white-space: nowrap">
+ <i class="fa fa-fw <%= icon_class %>"></i>
+ <% if (name_link = @objects.links_for(object, 'name').first) %>
+ <%= name_link.name %>
+ <span style="display:none"><%= object.uuid %></span>
+ <% elsif object.respond_to?(:name) and object.name and object.name.length > 0 %>
+ <%= object.name %>
+ <span style="display:none"><%= object.uuid %></span>
+ <% else %>
+ <span class="arvados-uuid"><%= object.uuid %></span>
+ <% end %>
+ </div>
+ </div>
+<% end %>
--- /dev/null
+<p>You have logged out.</p>
--- /dev/null
+<% content_for :breadcrumbs do raw '<!-- -->' end %>
+
+<% n_files = unsigned_user_agreements.collect(&:files).flatten(1).count %>
+<% content_for :page_title do %>
+<% if n_files == 1 %>
+<%= unsigned_user_agreements.first.files.first[1].sub(/\.[a-z]{3,4}$/,'') %>
+<% else %>
+User agreements
+<% end %>
+<% end %>
+
+<%= form_for(unsigned_user_agreements.first, {url: {action: 'sign', controller: 'user_agreements'}, method: :post}) do |f| %>
+<%= hidden_field_tag :return_to, request.url %>
+<div id="open_user_agreement">
+ <div class="alert alert-info">
+ <strong>Please check <%= n_files > 1 ? 'each' : 'the' %> box below</strong> to indicate that you have read and accepted the user agreement<%= 's' if n_files > 1 %>.
+ </div>
+ <% if n_files == 1 and (Rails.configuration.show_user_agreement_inline rescue false) %>
+ <% ua = unsigned_user_agreements.first; file = ua.files.first %>
+ <object data="<%= url_for(controller: 'collections', action: 'show_file', uuid: ua.uuid, file: "#{file[0]}/#{file[1]}") %>" type="<%= Rack::Mime::MIME_TYPES[file[1].match(/\.\w+$/)[0]] rescue '' %>" width="100%" height="400px">
+ </object>
+ <% end %>
+ <div>
+ <% unsigned_user_agreements.each do |ua| %>
+ <% ua.files.each do |file| %>
+ <div class="checkbox">
+ <%= f.label 'checked[]' do %>
+ <%= check_box_tag 'checked[]', "#{ua.uuid}/#{file[0]}/#{file[1]}", false %>
+ Accept <%= file[1].sub(/\.[a-z]{3,4}$/,'') %>
+ <%= link_to 'View agreement', {controller: 'collections', action: 'show_file', uuid: ua.uuid, file: "#{file[0]}/#{file[1]}"}, {target: '_blank', class: 'btn btn-xs btn-info'} %>
+ <% end %>
+ </div>
+ <% end %>
+ <% end %>
+ </div>
+ <div style="height: 1em"></div>
+ <div>
+ <%= f.submit 'Continue', {class: 'btn btn-primary'} %>
+ </div>
+</div>
+<% end %>
--- /dev/null
+<div class="modal-dialog modal-with-loading-spinner">
+ <div class="modal-content">
+
+ <%= form_tag add_ssh_key_path, {method: 'get', id: 'add_new_key_form', name: 'add_new_key_form', class: 'form-search, new_authorized_key', remote: true} do %>
+
+ <div class="modal-header">
+ <button type="button" class="close" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">×</button>
+ <div>
+ <div class="col-sm-6"> <h4 class="modal-title">Add SSH Key</h4> </div>
+ <div class="spinner spinner-32px spinner-h-center col-sm-1" hidden="true"></div>
+ </div>
+ <br/>
+ </div>
+
+ <div class="modal-body">
+ <div> <%= link_to "Click here to learn about SSH keys in Arvados.",
+ "#{Rails.configuration.arvados_docsite}/user/getting_started/ssh-access-unix.html",
+ style: "font-weight: bold",
+ target: "_blank" %>
+ </div>
+ <div class="form-group">
+ <label for="public_key">Public Key</label>
+ <textarea class="form-control" id="public_key" rows="4" name="public_key" type="text"/>
+ </div>
+ <div class="form-group">
+ <label for="name">Name</label>
+ <input class="form-control" id="name" maxlength="250" name="name" type="text"/>
+ </div>
+ </div>
+
+ <div class="modal-footer">
+ <button type="submit" class="btn btn-primary" autofocus>Submit</button>
+ <button class="btn btn-default" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">Cancel</button>
+ </div>
+
+ <% end #form %>
+ </div>
+</div>
--- /dev/null
+<% icon_class = fa_icon_class_for_class(User) %>
+<% @objects.each do |object| %>
+ <div class="row filterable selectable" data-object-uuid="<%= object.uuid %>">
+ <div class="col-sm-12" style="overflow-x:hidden">
+ <i class="fa fa-fw <%= icon_class %>"></i>
+ <%= object.full_name %> <<%= object.email %>>
+ </div>
+ </div>
+<% end %>
--- /dev/null
+<% content_for :breadcrumbs do raw '<!-- -->' end %>
+<% content_for :css do %>
+ .dash-list {
+ padding: 9px 0;
+ }
+ .dash-list>ul>li>a>span {
+ min-width: 1.5em;
+ margin-left: auto;
+ margin-right: auto;
+ }
+ .centerme {
+ margin-left: auto;
+ margin-right: auto;
+ text-align: center;
+ }
+ .bigfatnumber {
+ font-size: 4em;
+ font-weight: bold;
+ }
+ .dax {
+ max-width: 10%;
+ margin-right: 1em;
+ float: left
+ }
+ .daxalert {
+ overflow: hidden;
+ }
+<% end %>
+
+<div id="home-tables">
+
+ <%= render :partial => 'tables' %>
+
+</div>
--- /dev/null
+<div class="col-sm-6">
+ <div class="panel-group" id="arv-adv-accordion">
+ <% ['Virtual Machines',
+ 'Repositories'].each do |section| %>
+ <% section_id = section.gsub(" ","_").downcase %>
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <h4 class="panel-title">
+ <a data-parent="#arv-adv-accordion" href="#manage_<%=section_id%>">
+ <%= section %>
+ </a>
+ </h4>
+ </div>
+ <div id="manage_<%=section_id%>">
+ <div class="panel-body">
+ <%= render partial: "manage_#{section_id}" %>
+ </div>
+ </div>
+ </div>
+ <% end %>
+ </div>
+</div>
+<div class="col-sm-6">
+ <div class="panel-group" id="arv-adv-accordion">
+ <% ['SSH Keys',
+ 'Current Token'].each do |section| %>
+ <% section_id = section.gsub(" ","_").downcase %>
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <% if section_id == 'ssh_keys' %>
+ <div class="pull-right">
+ <%= link_to raw('<i class="fa fa-plus"></i>' " Add new SSH key"), add_ssh_key_popup_url,
+ {class: 'btn btn-xs btn-primary', :remote => true, 'data-toggle' => "modal",
+ 'data-target' => '#add-ssh-key-modal-window'} %>
+ </div>
+ <% end %>
+ <h4 class="panel-title">
+ <a data-parent="#arv-adv-accordion" href="#manage_<%=section_id%>">
+ <%= section %>
+ </a>
+ </h4>
+ </div>
+ <div id="manage_<%=section_id%>">
+ <div class="panel-body">
+ <%= render partial: "manage_#{section_id}" %>
+ </div>
+ </div>
+ </div>
+ <% end %>
+ </div>
+ <div id="add-ssh-key-modal-window" class="modal fade" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true"></div>
+</div>
--- /dev/null
+<p>The Arvados API token is a secret key that enables the Arvados SDKs to access Arvados with the proper permissions. For more information see <%= link_to raw('Getting an API token'), "#{Rails.configuration.arvados_docsite}/user/reference/api-tokens.html", target: "_blank"%>.</p>
+<p>Paste the following lines at a shell prompt to set up the necessary environment for Arvados SDKs to authenticate to your account, <b><%= current_user.email %></b></p>
+
+<pre>
+HISTIGNORE=$HISTIGNORE:'export ARVADOS_API_TOKEN=*'
+export ARVADOS_API_TOKEN=<%= Thread.current[:arvados_api_token] %>
+export ARVADOS_API_HOST=<%= current_api_host %>
+<% if Rails.configuration.arvados_insecure_https %>
+export ARVADOS_API_HOST_INSECURE=true
+<% else %>
+unset ARVADOS_API_HOST_INSECURE
+<% end %>
+</pre>
--- /dev/null
+<div>
+ <p>
+ For more information see <%= link_to raw('Writing a pipeline'),
+ "#{Rails.configuration.arvados_docsite}/user/tutorials/tutorial-firstscript.html", target: "_blank"%>.
+ </p>
+
+ <% if !@my_repositories.any? %>
+ You do not seem to have access to any repositories. If you would like to request access, please contact your system admin.
+ <% else %>
+ <table class="table repositories-table">
+ <colgroup>
+ <col style="width: 30%" />
+ <col style="width: 10%" />
+ <col style="width: 60%" />
+ </colgroup>
+ <thead>
+ <tr>
+ <th> Name </th>
+ <th> Read/Write </th>
+ <th> URL </th>
+ </tr>
+ </thead>
+ <tbody>
+ <% @my_repositories.andand.each do |repo| %>
+ <% writable = @repo_writable[repo.uuid] %>
+ <tr>
+ <td style="word-break:break-all;">
+ <%= repo[:name] %>
+ </td>
+ <td>
+ <%= writable ? 'writable' : 'read-only' %>
+ </td>
+ <td style="word-break:break-all;">
+ <code><%= writable ? repo[:push_url] : repo[:fetch_url] %></code>
+ </td>
+ </tr>
+ <% end %>
+ </tbody>
+ </table>
+ <% end %>
+</div>
--- /dev/null
+<div>
+ <% if !@my_ssh_keys.any? %>
+ <p> You have not yet set up an SSH public key for use with Arvados. </p>
+ <p> <%= link_to "Click here",
+ "#{Rails.configuration.arvados_docsite}/user/getting_started/ssh-access-unix.html",
+ style: "font-weight: bold",
+ target: "_blank" %> to learn about SSH keys in Arvados.
+ </p>
+ <p> When you have an SSH key you would like to use, add it using the <b>Add</b> button. </p>
+ <% else %>
+ <table class="table manage-ssh-keys-table">
+ <colgroup>
+ <col style="width: 35%" />
+ <col style="width: 55%" />
+ <col style="width: 10%" />
+ </colgroup>
+ <thead>
+ <tr>
+ <th> Name </th>
+ <th> Key Fingerprint </th>
+ <th> </th>
+ </tr>
+ </thead>
+ <tbody>
+ <% @my_ssh_keys.andand.each do |key| %>
+ <tr style="word-break:break-all;">
+ <td>
+ <%= key[:name] %>
+ </td>
+ <td style="word-break:break-all;">
+ <% if key[:public_key] && key[:public_key].size > 0 %>
+ <div>
+ <span title="<%=key[:public_key]%>"> <%=
+ begin
+ SSHKey.fingerprint key[:public_key]
+ rescue
+ "INVALID KEY: " + key[:public_key]
+ end
+ %> </span>
+ </div>
+ <% else %>
+ <%= key[:public_key] %>
+ <% end %>
+ </td>
+ <td>
+ <%= link_to(authorized_key_path(id: key[:uuid]), method: :delete, class: 'btn btn-sm', data: {confirm: "Really delete key?"}) do %>
+ <i class="fa fa-fw fa-trash-o"></i>
+ <% end %>
+ </td>
+ </tr>
+ <% end %>
+ </tbody>
+ </table>
+ <% end %>
+</div>
--- /dev/null
+<div>
+ <p>
+ For more information see <%= link_to raw('Arvados Docs → User Guide → SSH access'),
+ "#{Rails.configuration.arvados_docsite}/user/getting_started/ssh-access-unix.html",
+ target: "_blank"%>. A sample <i>~/.ssh/config</i> entry is provided below.
+ </p>
+
+ <% if !@my_virtual_machines.any? %>
+ You do not seem to have access to any virtual machines. If you would like to request access, please contact your system admin.
+ <% else %>
+ <table class="table virtual-machines-table">
+ <colgroup>
+ <col style="width: 25%" />
+ <col style="width: 25%" />
+ <col style="width: 50%" />
+ </colgroup>
+ <thead>
+ <tr>
+ <th> Host name </th>
+ <th> Login name </th>
+ <th> Command line </th>
+ </tr>
+ </thead>
+ <tbody>
+ <% @my_virtual_machines.andand.each do |vm| %>
+ <tr>
+ <td style="word-break:break-all;">
+ <%= vm[:hostname] %>
+ </td>
+ <td style="word-break:break-all;">
+ <%= @my_vm_logins[vm[:uuid]].andand.compact.andand.join(", ") %>
+ </td>
+ <td style="word-break:break-all;">
+ <% if @my_vm_logins[vm[:uuid]] %>
+ <% @my_vm_logins[vm[:uuid]].each do |login| %>
+ <code>ssh <%= login %>@<%= vm[:hostname] %>.arvados</code>
+ <% end %>
+ <% end %>
+ </td>
+ </tr>
+ <% end %>
+ </tbody>
+ </table>
+
+ <p><i>~/.ssh/config:</i></p>
+ <pre>Host *.arvados
+ TCPKeepAlive yes
+ ServerAliveInterval 60
+ ProxyCommand ssh -p2222 turnout@switchyard.<%= current_api_host || 'xyzzy.arvadosapi.com' %> -x -a $SSH_PROXY_FLAGS %h
+ </pre>
+ <% end %>
+</div>
--- /dev/null
+<div class="modal-dialog modal-with-loading-spinner">
+ <div class="modal-content">
+
+ <%= form_tag setup_user_path, {id: 'setup_form', name: 'setup_form', method: 'get',
+ class: 'form-search', remote: true} do %>
+
+ <div class="modal-header">
+ <button type="button" class="close" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">×</button>
+ <div>
+ <div class="col-sm-6"> <h4 class="modal-title">Setup User</h4> </div>
+ <div class="spinner spinner-32px spinner-h-center col-sm-1" hidden="true"></div>
+ </div>
+ <br/>
+ </div>
+
+ <div class="modal-body">
+ <% if @object%>
+ <% uuid = @object.uuid %>
+ <% email = @object.email %>
+ <% end %>
+ <% disable_email = uuid != nil %>
+ <% identity_url_prefix = @current_selections[:identity_url_prefix] %>
+ <% disable_url_prefix = identity_url_prefix != nil %>
+ <% selected_repo = @current_selections[:repo_name] %>
+ <% selected_vm = @current_selections[:vm_uuid] %>
+
+ <input id="user_uuid" maxlength="250" name="user_uuid" type="hidden" value="<%=uuid%>">
+ <div class="form-group">
+ <label for="email">Email</label>
+ <% if disable_email %>
+ <input class="form-control" id="email" maxlength="250" name="email" type="text" value="<%=email%>" disabled>
+ <% else %>
+ <input class="form-control" id="email" maxlength="250" name="email" type="text">
+ <% end %>
+ </div>
+ <div class="form-group">
+ <label for="openid_prefix">Identity URL Prefix</label>
+ <% if disable_url_prefix %>
+ <input class="form-control" id="openid_prefix" maxlength="250" name="openid_prefix" type="text"
+ value="<%=identity_url_prefix%>" disabled=true>
+ <% else %>
+ <input class="form-control" id="openid_prefix" maxlength="250" name="openid_prefix" type="text"
+ value="<%= Rails.configuration.default_openid_prefix %>">
+ <% end %>
+ </div>
+ <div class="form-group">
+ <label for="repo_name">Repository Name and Shell Login</label>
+ <input class="form-control" id="repo_name" maxlength="250" name="repo_name" type="text" value="<%=selected_repo%>">
+ </div>
+ <div class="form-group">
+ <label for="vm_uuid">Virtual Machine</label>
+ <select class="form-control" name="vm_uuid">
+ <option value="" <%= 'selected' unless selected_vm %>>
+ Choose One:
+ </option>
+ <% @vms.each do |vm| %>
+ <option value="<%=vm.uuid%>"
+ <%= 'selected' if selected_vm == vm.uuid %>>
+ <%= vm.hostname %>
+ </option>
+ <% end %>
+ </select>
+ </div>
+ </div>
+
+ <div class="modal-footer">
+ <button type="submit" id="register" class="btn btn-primary" autofocus>Submit</button>
+ <button class="btn btn-default" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">Cancel</button>
+ </div>
+
+ <% end #form %>
+ </div>
+</div>
--- /dev/null
+<p>
+ As an admin user, you can <%= link_to "view recent user activity", activity_users_url %> and <%= link_to "view user storage activity", storage_users_url %>.
+</p>
+
--- /dev/null
+<div class="row">
+ <div class="col-md-6">
+ <p>
+ As an admin, you can log in as this user. When you’ve
+ finished, you will need to log out and log in again with your
+ own account.
+ </p>
+
+ <blockquote>
+ <%= button_to "Log in as #{@object.full_name}", sudo_user_url(id: @object.uuid), class: 'btn btn-primary' %>
+ </blockquote>
+
+ <p>
+ As an admin, you can setup this user. Please input a VM and
+ repository for the user. If you had previously provided any of
+ these items, they are pre-filled for you and you can leave them
+ as is if you would like to reuse them.
+ </p>
+
+ <blockquote>
+ <%= link_to "Setup #{@object.full_name}", setup_popup_user_url(id: @object.uuid), {class: 'btn btn-primary', :remote => true, 'data-toggle' => "modal", 'data-target' => '#user-setup-modal-window'} %>
+ </blockquote>
+
+ <p>
+ As an admin, you can deactivate and reset this user. This will
+ remove all repository/VM permissions for the user. If you
+ "setup" the user again, the user will have to sign the user
+ agreement again.
+ </p>
+
+ <blockquote>
+ <%= button_to "Deactivate #{@object.full_name}", unsetup_user_url(id: @object.uuid), class: 'btn btn-primary', data: {confirm: "Are you sure you want to deactivate #{@object.full_name}?"} %>
+ </blockquote>
+ </div>
+ <div class="col-md-6">
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ Group memberships
+ </div>
+ <div class="panel-body">
+ <div class="alert alert-info">
+ <b>Tip:</b> in most cases, you want <i>both permissions at once</i> for a given group.
+ <br/>
+ The user→group permission is can_manage.
+ <br/>
+ The group→user permission is can_read.
+ </div>
+ <form>
+ <% permitted_group_perms = {}
+ Link.filter([
+ ['tail_uuid', '=', @object.uuid],
+ ['head_uuid', 'is_a', 'arvados#group'],
+ ['link_class', '=', 'permission'],
+ ]).each do |perm|
+ permitted_group_perms[perm.head_uuid] = perm.uuid
+ end %>
+ <% member_group_perms = {}
+ Link.permissions_for(@object).each do |perm|
+ member_group_perms[perm.tail_uuid] = perm.uuid
+ end %>
+ <% Group.order(['name']).where(group_class: 'role').each do |group| %>
+ <div>
+ <label class="checkbox-inline" data-toggle-permission="true" data-permission-tail="<%= @object.uuid %>" data-permission-name="can_manage">
+ <%= check_box_tag(
+ 'group_uuids[]',
+ group.uuid,
+ permitted_group_perms[group.uuid],
+ disabled: (group.owner_uuid == @object.uuid),
+ data: {
+ permission_head: group.uuid,
+ permission_uuid: permitted_group_perms[group.uuid]}) %>
+ <small>user→group</small>
+ </label>
+ <label class="checkbox-inline" data-toggle-permission="true" data-permission-head="<%= @object.uuid %>" data-permission-name="can_read">
+ <%= check_box_tag(
+ 'group_uuids[]',
+ group.uuid,
+ member_group_perms[group.uuid],
+ disabled: (group.owner_uuid == @object.uuid),
+ data: {
+ permission_tail: group.uuid,
+ permission_uuid: member_group_perms[group.uuid]}) %>
+ <small>group→user</small>
+ </label>
+ <label class="checkbox-inline">
+ <%= group.name || '(unnamed)' %> <span class="deemphasize">(owned by <%= User.find?(group.owner_uuid).andand.full_name %>)</span>
+ </label>
+ </div>
+ <% end.empty? and begin %>
+ <div>
+ (No groups defined.)
+ </div>
+ <% end %>
+ </form>
+ </div>
+ <div class="panel-footer">
+ To manage these groups (roles), use:
+ <ul>
+ <li><code>arv group create \<br/>--group '{"group_class":"role","name":"New group"}'</code></li>
+ <li><code>arv group list \<br/>--filters '[["group_class","=","role"]]' \<br/>--select '["uuid","name"]'</code></li>
+ <li><code>arv edit <i>uuid</i></code></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+</div>
+
+<div id="user-setup-modal-window" class="modal fade" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true"></div>
--- /dev/null
+<% if current_user.andand.is_active %>
+ <div>
+ <strong>Recent jobs</strong>
+ <%= link_to '(refresh)', {format: :js}, {class: 'refresh', remote: true} %>
+ <%= link_to raw("Show all jobs →"), jobs_path, class: 'pull-right' %>
+ <% if not current_user.andand.is_active or @my_jobs.empty? %>
+ <p>(None)</p>
+ <% else %>
+ <table class="table table-bordered table-condensed table-fixedlayout">
+ <colgroup>
+ <col width="20%" />
+ <col width="20%" />
+ <col width="20%" />
+ <col width="13%" />
+ <col width="13%" />
+ <col width="20%" />
+ </colgroup>
+
+ <tr>
+ <th>Script</th>
+ <th>Output</th>
+ <th>Log</th>
+ <th>Created at</th>
+ <th>Status</th>
+ </tr>
+
+ <%# Preload collections, logs, and pipeline instance objects %>
+ <%
+ collection_uuids = []
+ log_uuids = []
+ @my_jobs[0..6].each do |j|
+ collection_uuids << j.output
+ log_uuids << j.log
+ end
+
+ @my_collections[0..6].each do |c|
+ collection_uuids << c.uuid
+ end
+
+ preload_collections_for_objects collection_uuids
+ preload_log_collections_for_objects log_uuids
+
+ pi_uuids = []
+ @my_pipelines[0..6].each do |p|
+ pi_uuids << p.uuid
+ end
+ resource_class = resource_class_for_uuid(pi_uuids.first, friendly_name: true)
+ preload_objects_for_dataclass resource_class, pi_uuids
+ %>
+
+ <% @my_jobs[0..6].each do |j| %>
+ <tr data-object-uuid="<%= j.uuid %>">
+ <td>
+ <small>
+ <%= link_to((j.script.andand[0..31] || j.uuid), job_path(j.uuid)) %>
+ </small>
+ </td>
+
+ <td>
+ <small>
+ <% if j.state == "Complete" and j.output %>
+ <a href="<%= collection_path(j.output) %>">
+ <% collections = collections_for_object(j.output) %>
+ <% if collections && !collections.empty? %>
+ <% c = collections.first %>
+ <% c.files.each do |file| %>
+ <%= file[0] == '.' ? file[1] : "#{file[0]}/#{file[1]}" %>
+ <% end %>
+ <% end %>
+ </a>
+ <% end %>
+ </small>
+ </td>
+
+<td>
+ <small>
+ <% if j.log %>
+ <% log_collections = log_collections_for_object(j.log) %>
+ <% if log_collections && !log_collections.empty? %>
+ <% c = log_collections.first %>
+ <% c.files.each do |file| %>
+ <a href="<%= collection_path(j.log) %>/<%= file[1] %>?disposition=inline&size=<%= file[2] %>">Log</a>
+ <% end %>
+ <% end %>
+ <% elsif j.respond_to? :log_buffer and j.log_buffer.is_a? String %>
+ <% buf = j.log_buffer.strip.split("\n").last %>
+ <span title="<%= buf %>"><%= buf %></span>
+ <% end %>
+ </small>
+</td>
+
+<td>
+ <small>
+ <%= j.created_at.to_s if j.created_at %>
+ </small>
+</td>
+
+<td>
+ <div class="inline-progress-container">
+ <%= render partial: 'job_progress', locals: {:j => j} %>
+ </div>
+</td>
+
+</tr>
+<% end %>
+</table>
+<% end %>
+</div>
+
+<div>
+ <strong>Recent pipeline instances</strong>
+ <%= link_to '(refresh)', {format: :js}, {class: 'refresh', remote: true} %>
+ <%= link_to raw("Show all pipeline instances →"), pipeline_instances_path, class: 'pull-right' %>
+ <% if not current_user.andand.is_active or @my_pipelines.empty? %>
+ <p>(None)</p>
+ <% else %>
+ <table class="table table-bordered table-condensed table-fixedlayout">
+ <colgroup>
+ <col width="30%" />
+ <col width="30%" />
+ <col width="13%" />
+ <col width="13%" />
+ <col width="20%" />
+ </colgroup>
+
+ <tr>
+ <th>Instance</th>
+ <th>Template</th>
+ <th>Created at</th>
+ <th>Status</th>
+ <th>Progress</th>
+ </tr>
+
+ <% @my_pipelines[0..6].each do |p| %>
+ <tr data-object-uuid="<%= p.uuid %>">
+ <td>
+ <small>
+ <%= link_to_if_arvados_object p.uuid, friendly_name: true %>
+ </small>
+ </td>
+
+ <td>
+ <small>
+ <%= link_to_if_arvados_object p.pipeline_template_uuid, friendly_name: true %>
+ </small>
+ </td>
+
+ <td>
+ <small>
+ <%= (p.created_at.to_s) if p.created_at %>
+ </small>
+ </td>
+
+ <td>
+ <%= render partial: 'pipeline_status_label', locals: {:p => p} %>
+ </td>
+
+ <td>
+ <div class="inline-progress-container">
+ <%= render partial: 'pipeline_progress', locals: {:p => p} %>
+ </div>
+ </td>
+ </tr>
+ <% end %>
+ </table>
+ <% end %>
+</div>
+
+<div>
+ <strong>Recent collections</strong>
+ <%= link_to '(refresh)', {format: :js}, {class: 'refresh', remote: true} %>
+ <%= link_to raw("Show all collections →"), collections_path, class: 'pull-right' %>
+ <div class="pull-right" style="padding-right: 1em; width: 30%;">
+ <%= form_tag collections_path,
+ method: 'get',
+ class: 'form-search small-form-margin' do %>
+ <div class="input-group input-group-sm">
+ <%= text_field_tag :search, params[:search], class: 'form-control', placeholder: 'Search' %>
+ <span class="input-group-btn">
+ <%= button_tag(class: 'btn btn-info') do %>
+ <span class="glyphicon glyphicon-search"></span>
+ <% end %>
+ </span>
+ </div>
+ <% end %>
+ </div>
+ <% if not current_user.andand.is_active or @my_collections.empty? %>
+ <p>(None)</p>
+ <% else %>
+ <table class="table table-bordered table-condensed table-fixedlayout">
+ <colgroup>
+ <col width="46%" />
+ <col width="32%" />
+ <col width="10%" />
+ <col width="12%" />
+ </colgroup>
+
+ <tr>
+ <th>Contents</th>
+ <th>Tags</th>
+ <th>Age</th>
+ <th>Storage</th>
+ </tr>
+
+ <% @my_collections[0..6].each do |c| %>
+ <tr data-object-uuid="<%= c.uuid %>">
+ <td>
+ <small>
+ <a href="<%= collection_path(c.uuid) %>">
+ <% c.files.each do |file| %>
+ <%= file[0] == '.' ? file[1] : "#{file[0]}/#{file[1]}" %>
+ <% end %>
+ </a>
+ </small>
+ </td>
+ <td>
+ <% if @my_tag_links[c.uuid] %>
+ <small>
+ <%= @my_tag_links[c.uuid].collect(&:name).join(", ") %>
+ </small>
+ <% end %>
+ </td>
+ <td>
+ <small>
+ <%= c.created_at.to_s if c.created_at %>
+ </small>
+ </td>
+ <td>
+ <%= render partial: 'collections/toggle_persist', locals: { uuid: c.uuid, current_state: @persist_state[c.uuid] } %>
+ </td>
+ </tr>
+ <% end %>
+ </table>
+ <% end %>
+</div>
+
+<% else %>
+
+ <div class="row-fluid">
+ <div class="col-sm-4">
+ <%= image_tag "dax.png", style: "max-width:100%" %>
+ </div>
+ <div class="col-sm-8">
+ <h2>Welcome to Arvados, <%= current_user.first_name %>!</h2>
+ <div class="well">
+ <p>
+ Your account must be activated by an Arvados administrator. If this
+ is your first time accessing Arvados and would like to request
+ access, or you believe you are seeing the page in error, please
+ <%= link_to "contact us", Rails.configuration.activation_contact_link %>.
+ You should receive an email at the address you used to log in when
+ your account is activated. In the mean time, you can
+ <%= link_to "learn more about Arvados", "https://arvados.org/projects/arvados/wiki/Introduction_to_Arvados" %>,
+ and <%= link_to "read the Arvados user guide", "http://doc.arvados.org/user" %>.
+ </p>
+ <p style="padding-bottom: 1em">
+ <%= link_to raw('Contact us ✉'),
+ Rails.configuration.activation_contact_link, class: "pull-right btn btn-primary" %></p>
+ </div>
+ </div>
+ </div>
+<% end %>
+
+<% content_for :js do %>
+setInterval(function(){$('a.refresh:eq(0)').click()}, 60000);
+<% end %>
--- /dev/null
+<% content_for :css do %>
+table#users-activity-table th {
+ overflow-x: hidden;
+}
+table#users-activity-table .cell-for-span-This-month,
+table#users-activity-table .cell-for-span-Last-month {
+ background: #eee;
+}
+<% end %>
+<table class="table table-condensed arv-index" id="users-activity-table">
+ <colgroup>
+ <col width="28%" />
+ </colgroup>
+ <% @spans.each do |_| %>
+ <colgroup>
+ <% 3.times do %>
+ <col width="<%= (72 / @spans.count / 3).floor %>%" />
+ <% end %>
+ </colgroup>
+ <% end %>
+
+ <tr>
+ <th rowspan="2">User</th>
+ <% @spans.each do |span, start_at, end_at| %>
+ <th colspan="3" class="cell-for-span-<%= span.gsub ' ','-' %>">
+ <%= span %>
+ <br />
+ <%= start_at.strftime('%b %-d') %>
+ -
+ <%= (end_at-1.second).strftime('%b %-d') %>
+ </th>
+ <% end %>
+ </tr>
+ <tr>
+ <% @spans.each do |span, _| %>
+ <th class="cell-for-span-<%= span.gsub ' ','-' %>">Logins</th>
+ <th class="cell-for-span-<%= span.gsub ' ','-' %>">Jobs</th>
+ <th class="cell-for-span-<%= span.gsub ' ','-' %>">Pipelines</th>
+ <% end %>
+ </tr>
+
+ <% @users.each do |user| %>
+ <tr>
+ <td>
+ <small>
+ <% if user.uuid %>
+ <%= link_to_if_arvados_object user, friendly_name: true %>
+ <% else %>
+ <b>Total</b>
+ <% end %>
+ </small>
+ </td>
+
+ <% @spans.each do |span, _| %>
+ <% ['logins', 'jobs', 'pipeline_instances'].each do |type| %>
+ <td class="cell-for-span-<%= span.gsub ' ','-' %>">
+ <small>
+ <%= @user_activity[user.uuid][span + " " + type].to_s %>
+ </small>
+ </td>
+ <% end %>
+ <% end %>
+ </tr>
+ <% end %>
+</table>
+
+<% content_for :footer_js do %>
+$('#users-activity-table td small').each(function(){
+ if ($(this).html().trim() == '0')
+ $(this).css('opacity', '0.3');
+});
+<% end %>
--- /dev/null
+$("#add-ssh-key-modal-window").modal("hide");
+document.location.reload();
--- /dev/null
+$("#add-ssh-key-modal-window").html("<%= escape_javascript(render partial: 'add_ssh_key_popup') %>");
+
+// reset form input fields, for the next time around
+function reset_form() {
+ $('#name').val("");
+ $('#public_key').val("");
+ $('select').val('')
+}
--- /dev/null
+<%= render :partial => 'home' %>
--- /dev/null
+var new_content = "<%= escape_javascript(render partial: 'tables') %>";
+if ($('div#home-tables').html() != new_content)
+ $('div#home-tables').html(new_content);
--- /dev/null
+<% content_for :breadcrumbs do raw '<!-- -->' end %>
+
+<div class="row">
+ <div class="col-sm-8 col-sm-push-4" style="margin-top: 1em">
+ <div class="well clearfix">
+ <%= image_tag "dax.png", style: "width: 147px; height: 197px; max-width: 25%; margin-right: 2em", class: 'pull-left' %>
+
+ <h3>Hi! You're logged in, but...</h3>
+
+ <p>
+
+ Your account is inactive.
+
+ </p><p>
+
+ An administrator must activate your account before you can get
+ any further.
+
+ </p><p>
+
+ <%= link_to 'Retry', (params[:return_to] || '/'), class: 'btn btn-primary' %>
+
+ </p>
+ </div>
+ </div>
+</div>
--- /dev/null
+<%= render :partial => 'manage_account' %>
--- /dev/null
+<%
+ profile_config = Rails.configuration.user_profile_form_fields
+ current_user_profile = current_user.prefs[:profile]
+ show_save_button = false
+
+ profile_message = Rails.configuration.user_profile_form_message
+%>
+
+<div>
+ <div class="panel panel-default">
+ <div class="panel-heading">
+ <h4 class="panel-title">
+ Profile
+ </h4>
+ </div>
+ <div class="panel-body">
+ <% if !missing_required_profile? && params[:offer_return_to] %>
+ <div class="alert alert-success">
+ <p>Thank you for filling in your profile. <%= link_to 'Back to work!', params[:offer_return_to], class: 'btn btn-sm btn-primary' %></p>
+ </div>
+ <% else %>
+ <div class="alert alert-info">
+ <p><%=raw(profile_message)%></p>
+ </div>
+ <% end %>
+
+ <%= form_for current_user, html: {id: 'save_profile_form', name: 'save_profile_form', class: 'form-horizontal'} do %>
+ <%= hidden_field_tag :offer_return_to, params[:offer_return_to] %>
+ <%= hidden_field_tag :return_to, profile_user_path(current_user.uuid, offer_return_to: params[:offer_return_to]) %>
+ <div class="form-group">
+ <label for="email" class="col-sm-3 control-label"> Email </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" id="email" name="email"><%=current_user.email%></p>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="first_name" class="col-sm-3 control-label"> First name </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" id="first_name" name="first_name"><%=current_user.first_name%></p>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="last_name" class="col-sm-3 control-label"> Last name </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" id="last_name" name="last_name"><%=current_user.last_name%></p>
+ </div>
+ </div>
+ <div class="form-group">
+ <label for="identity_url" class="col-sm-3 control-label"> Identity URL </label>
+ <div class="col-sm-8">
+ <p class="form-control-static" id="identity_url" name="identity_url"><%=current_user.andand.identity_url%></p>
+ </div>
+ </div>
+
+ <% profile_config.kind_of?(Array) && profile_config.andand.each do |entry| %>
+ <% if entry['key'] %>
+ <%
+ show_save_button = true
+ label = entry['required'] ? '* ' : ''
+ label += entry['form_field_title']
+ value = current_user_profile[entry['key'].to_sym] if current_user_profile
+ %>
+ <div class="form-group">
+ <label for="<%=entry['key']%>"
+ class="col-sm-3 control-label"
+ style=<%="color:red" if entry['required']&&(!value||value.empty?)%>> <%=label%>
+ </label>
+ <% if entry['type'] == 'select' %>
+ <div class="col-sm-8">
+ <select class="form-control" name="user[prefs][:profile][:<%=entry['key']%>]">
+ <% entry['options'].each do |option| %>
+ <option value="<%=option%>" <%='selected' if option==value%>><%=option%></option>
+ <% end %>
+ </select>
+ </div>
+ <% else %>
+ <div class="col-sm-8">
+ <input type="text" class="form-control" name="user[prefs][:profile][:<%=entry['key']%>]" placeholder="<%=entry['form_field_description']%>" value="<%=value%>" ></input>
+ </div>
+ <% end %>
+ </div>
+ <% end %>
+ <% end %>
+
+ <% if show_save_button %>
+ <div class="form-group">
+ <div class="col-sm-offset-3 col-sm-8">
+ <button type="submit" class="btn btn-primary">Save profile</button>
+ </div>
+ </div>
+ <% end %>
+ <% end %>
+ </div>
+ </div>
+</div>
--- /dev/null
+$("#user-setup-modal-window").modal("hide");
+document.location.reload();
--- /dev/null
+$("#user-setup-modal-window").html("<%= escape_javascript(render partial: 'setup_popup') %>");
+
+// disable the submit button on load
+var $input = $('input:text'),
+$register = $('#register');
+
+var email_disabled = document.forms["setup_form"]["email"].disabled;
+var email_value = document.forms["setup_form"]["email"].value;
+var prefix_value = document.forms["setup_form"]["openid_prefix"].value;
+if ((email_disabled == false) && (email_value == null || email_value == "" ||
+ prefix_value == null || prefix_value == "")) {
+ $register.prop('disabled', true);
+}
+
+// capture events to enable submit button when applicable
+$input.on('keyup paste mouseleave', function() {
+ var trigger = false;
+
+ var email_disabled = document.forms["setup_form"]["email"].disabled;
+ var email_value = document.forms["setup_form"]["email"].value;
+ var prefix_value = document.forms["setup_form"]["openid_prefix"].value;
+
+ var emailRegExp = /^([\w-\.]+@([\w-]+\.)+[\w-]{2,4})?$/;
+ var validEmail = false;
+
+ if (emailRegExp.test(email_value )) {
+ validEmail = true;
+ }
+
+ if ((email_disabled == false) && (!validEmail || email_value == null ||
+ email_value == "" || prefix_value == null || prefix_value == "")){
+ trigger = true;
+ }
+
+ $register.prop('disabled', trigger);
+});
+
+// reset form input fields, for the next time around
+function reset_form() {
+ $('#email').val("");
+ $('#openid_prefix').val("");
+ $('#repo_name').val("");
+ $('select').val('')
+}
--- /dev/null
+<% content_for :css do %>
+table#users-storage-table th {
+ overflow-x: hidden;
+ text-align: center;
+}
+table#users-storage-table .byte-value {
+ text-align: right;
+}
+<% end %>
+<table class="table table-condensed arv-index" id="users-storage-table">
+ <colgroup>
+ <col />
+ </colgroup>
+
+ <tr>
+ <th rowspan="2">User</th>
+ <th colspan="2">
+ Collections Read Size
+ </th>
+ <th colspan="2">
+ Collections Persisted Storage
+ </th>
+ <th rowspan="2">Measured At</th>
+ </tr>
+ <tr>
+ <% 2.times do %>
+ <th class="byte-value">
+ Total (unweighted)
+ </th>
+ <th class="byte-value">
+ Shared (weighted)
+ </th>
+ <% end %>
+ </tr>
+
+ <% @users.each do |user| %>
+ <tr>
+ <td>
+ <% if user.uuid %>
+ <small>
+ <%= link_to_if_arvados_object user, friendly_name: true %>
+ </small>
+ <% else %>
+ <b>Total</b>
+ <% end %>
+ </td>
+ <% [:read_collections_total_bytes, :read_collections_weighted_bytes, :persisted_collections_total_bytes, :persisted_collections_weighted_bytes].each do |key| %>
+ <td class="byte-value">
+ <%= human_readable_bytes_html(@user_storage[user.uuid].fetch(key,0).floor) %>
+ </td>
+ <% end %>
+ <% if @log_date.key?(user.uuid) %>
+ <td class="date" title="<%= @log_date[user.uuid] %>">
+ <%= @log_date[user.uuid].strftime('%F') %>
+ </td>
+ <% end %>
+ </tr>
+ <% end %>
+</table>
+
+<% content_for :footer_js do %>
+$('#users-storage-table td small').each(function(){
+ if ($(this).html().trim() == '0')
+ $(this).css('opacity', '0.3');
+});
+<% end %>
--- /dev/null
+<% content_for :breadcrumbs do raw '<!-- -->' end %>
+
+<div class="row">
+ <div class="col-sm-8 col-sm-push-4" style="margin-top: 1em">
+ <div class="well clearfix">
+ <%= image_tag "dax.png", style: "width: 147px; height: 197px; max-width: 25%; margin-right: 2em", class: 'pull-left' %>
+
+ <h3>Please log in.</h3>
+
+ <p>
+
+ The "Log in" button below will show you a Google sign-in page.
+ After you assure Google that you want to log in here with your
+ Google account, you will be redirected back here to
+ <%= Rails.configuration.site_name %>.
+
+ </p><p>
+
+ If you have never used <%= Rails.configuration.site_name %>
+ before, logging in for the first time will automatically
+ create a new account.
+
+ </p><p>
+
+ <i><%= Rails.configuration.site_name %> uses your name and
+ email address only for identification, and does not retrieve
+ any other personal information from Google.</i>
+
+ </p>
+ <%# Todo: add list of external authentications providers to
+ discovery document, then generate the option list here. Right
+ now, don't provide 'auth_provider' to get the default one. %>
+ <div class="pull-right">
+ <%= link_to arvados_api_client.arvados_login_url(return_to: request.url), class: "btn btn-primary" do %>
+ Log in to <%= Rails.configuration.site_name %>
+ <i class="fa fa-fw fa-arrow-circle-right"></i>
+ <% end %>
+ </div>
+ </div>
+ </div>
+</div>
--- /dev/null
+<p>
+Sample <code>~/.ssh/config</code> section:
+</p>
+
+<pre>
+Host *.arvados
+ ProxyCommand ssh -p2222 turnout@switchyard.<%= current_api_host || 'xyzzy.arvadosapi.com' %> -x -a $SSH_PROXY_FLAGS %h
+<% if @objects.first.andand.current_user_logins.andand.first %>
+ User <%= @objects.first.current_user_logins.andand.first %>
+<% end %>
+</pre>
+
+<p>
+Sample login command:
+</p>
+
+<pre>
+ssh <%= @objects.first.andand.hostname.andand.sub('.'+current_api_host,'') or 'vm-hostname' %>.arvados
+</pre>
+
+<p>
+ See also:
+ <%= link_to raw('Arvados Docs → User Guide → SSH access'),
+ "#{Rails.configuration.arvados_docsite}/user/getting_started/ssh-access-unix.html",
+ target: "_blank"%>.
+</p>
--- /dev/null
+<% content_for :page_title do %>
+ Event bus debugging page
+<% end %>
+<h1>Event bus debugging page</h1>
+
+<form>
+<textarea style="width:100%; height: 10em" id="websocket-message-content"></textarea>
+<button type="button" id="send-to-websocket">Send</button>
+</form>
+
+<br>
+
+<p id="PutStuffHere"></p>
+
+<script>
+$(function() {
+putStuffThere = function (content) {
+ $("#PutStuffHere").append(content + "<br>");
+};
+
+var dispatcher = new WebSocket('<%= arvados_api_client.discovery[:websocketUrl] %>?api_token=<%= Thread.current[:arvados_api_token] %>');
+dispatcher.onmessage = function(event) {
+ //putStuffThere(JSON.parse(event.data));
+ putStuffThere(event.data);
+};
+
+sendStuff = function () {
+ dispatcher.send($("#websocket-message-content").val());
+};
+
+$("#send-to-websocket").click(sendStuff);
+});
+
+</script>
--- /dev/null
+# This file is used by Rack-based servers to start the application.
+
+require ::File.expand_path('../config/environment', __FILE__)
+run ArvadosWorkbench::Application
--- /dev/null
+# Do not use this file for site configuration. Create application.yml
+# instead (see application.yml.example).
+
+# Below is a sample setting for diagnostics testing.
+# Configure workbench URL as "arvados_workbench_url"
+# Configure test user tokens as "user_tokens".
+# At this time the tests need an "active" user token.
+# Also, configure the pipelines to be executed as "pipelines_to_test".
+# For each of the pipelines identified by the name of your choice
+# ("pipeline_1" and "pipeline_2" in this sample), provide the following:
+# template_uuid: is the uuid of the template to be executed
+# input_paths: an array of inputs for the pipeline. Use either a collection's "uuid"
+# or a file's "uuid/file_name" path in this array. If the pipeline does not require
+# any inputs, this can be omitted.
+# max_wait_seconds: max time in seconds to wait for the pipeline run to complete.
+# Default value of 30 seconds is used when this value is not provided.
+diagnostics:
+ arvados_workbench_url: https://localhost:3031
+ user_tokens:
+ active: eu33jurqntstmwo05h1jr3eblmi961e802703y6657s8zb14r
+ pipelines_to_test:
+ pipeline_1:
+ template_uuid: zzzzz-p5p6p-rxj8d71854j9idn
+ input_paths: [zzzzz-4zz18-nz98douzhaa3jh2]
+ max_wait_seconds: 10
+ pipeline_2:
+ template_uuid: zzzzz-p5p6p-1xbobfobk94ppbv
+ input_paths: [zzzzz-4zz18-nz98douzhaa3jh2, zzzzz-4zz18-gpw9o5wpcti3nib]
+
+# Below is a sample setting for performance testing.
+# Configure workbench URL as "arvados_workbench_url"
+# Configure test user token as "user_token".
+performance:
+ arvados_workbench_url: https://localhost:3031
+ user_token: eu33jurqntstmwo05h1jr3eblmi961e802703y6657s8zb14r
+
+development:
+ cache_classes: false
+ eager_load: true
+ consider_all_requests_local: true
+ action_controller.perform_caching: false
+ action_mailer.raise_delivery_errors: false
+ active_support.deprecation: :log
+ action_dispatch.best_standards_support: :builtin
+ assets.debug: true
+ profiling_enabled: true
+ site_name: Arvados Workbench (dev)
+ local_modified: "<%= '-modified' if `git status -s` != '' %>"
+
+ # API server configuration
+ arvados_login_base: ~
+ arvados_v1_base: ~
+ arvados_insecure_https: ~
+
+production:
+ force_ssl: true
+ cache_classes: true
+ eager_load: true
+ consider_all_requests_local: false
+ action_controller.perform_caching: true
+ serve_static_assets: false
+ assets.compile: false
+ assets.digest: true
+ i18n.fallbacks: true
+ active_support.deprecation: :notify
+ profiling_enabled: false
+
+ arvados_insecure_https: false
+
+ data_import_dir: /data/arvados-workbench-upload/data
+ data_export_dir: /data/arvados-workbench-download/data
+
+ # API server configuration
+ arvados_login_base: ~
+ arvados_v1_base: ~
+ arvados_insecure_https: ~
+
+ site_name: Arvados Workbench
+
+test:
+ cache_classes: true
+ eager_load: false
+ serve_static_assets: true
+ static_cache_control: public, max-age=3600
+ consider_all_requests_local: true
+ action_controller.perform_caching: false
+ action_dispatch.show_exceptions: false
+ action_controller.allow_forgery_protection: false
+ action_mailer.delivery_method: :test
+ active_support.deprecation: :stderr
+ profiling_enabled: false
+ secret_token: <%= rand(2**256).to_s(36) %>
+ secret_key_base: <%= rand(2**256).to_s(36) %>
+
+ # When you run the Workbench's integration tests, it starts the API
+ # server as a dependency. These settings should match the API
+ # server's Rails defaults. If you adjust those, change these
+ # settings in application.yml to match.
+ arvados_login_base: https://localhost:3000/login
+ arvados_v1_base: https://localhost:3000/arvados/v1
+ arvados_insecure_https: true
+
+ site_name: Workbench:test
+
+ # Enable user profile with one required field
+ user_profile_form_fields:
+ - key: organization
+ type: text
+ form_field_title: Institution
+ form_field_description: Your organization
+ required: true
+ - key: role
+ type: select
+ form_field_title: Your role
+ form_field_description: Choose the category that best describes your role in your organization.
+ options:
+ - Bio-informatician
+ - Computational biologist
+ - Biologist or geneticist
+ - Software developer
+ - IT
+ - Other
+
+common:
+ assets.js_compressor: false
+ assets.css_compressor: false
+ data_import_dir: /tmp/arvados-workbench-upload
+ data_export_dir: /tmp/arvados-workbench-download
+ arvados_login_base: https://arvados.local/login
+ arvados_v1_base: https://arvados.local/arvados/v1
+ arvados_insecure_https: true
+ activation_contact_link: mailto:info@arvados.org
+ arvados_docsite: http://doc.arvados.org
+ arvados_theme: default
+ show_user_agreement_inline: false
+ secret_token: ~
+ secret_key_base: false
+ default_openid_prefix: https://www.google.com/accounts/o8/id
+ send_user_setup_notification_email: true
+
+ # Set user_profile_form_fields to enable and configure the user profile page.
+ # Default is set to false. A commented setting with full description is provided below.
+ user_profile_form_fields: false
+
+ # Below is a sample setting of user_profile_form_fields config parameter.
+ # This configuration parameter should be set to either false (to disable) or
+ # to an array as shown below.
+ # Configure the list of input fields to be displayed in the profile page
+ # using the attribute "key" for each of the input fields.
+ # This sample shows configuration with one required and one optional form fields.
+ # For each of these input fields:
+ # You can specify "type" as "text" or "select".
+ # List the "options" to be displayed for each of the "select" menu.
+ # Set "required" as "true" for any of these fields to make them required.
+ # If any of the required fields are missing in the user's profile, the user will be
+ # redirected to the profile page before they can access any Workbench features.
+ #user_profile_form_fields:
+ # - key: organization
+ # type: text
+ # form_field_title: Institution/Company
+ # form_field_description: Your organization
+ # required: true
+ # - key: role
+ # type: select
+ # form_field_title: Your role
+ # form_field_description: Choose the category that best describes your role in your organization.
+ # options:
+ # - Bio-informatician
+ # - Computational biologist
+ # - Biologist or geneticist
+ # - Software developer
+ # - IT
+ # - Other
+
+ # Use "user_profile_form_message" to configure the message you want to display on
+ # the profile page.
+ user_profile_form_message: Welcome to Arvados. All <span style="color:red">required fields</span> must be completed before you can proceed.
+
+ # source_version
+ source_version: "<%= `git log -n 1 --format=%h`.strip %>"
+ local_modified: false
+
+ # report notification to and from addresses
+ issue_reporter_email_from: arvados@example.com
+ issue_reporter_email_to: arvados@example.com
+ support_email_address: arvados@example.com
+
+ # filename suffixes for which view icon would be shown in collection show page
+ filename_suffixes_with_view_icon: [txt, gif, jpeg, jpg, png, html, htm, pdf]
+
+ # the maximum number of bytes to load in the log viewer
+ log_viewer_max_bytes: 1000000
--- /dev/null
+require File.expand_path('../boot', __FILE__)
+
+require 'rails/all'
+
+Bundler.require(:default, Rails.env)
+
+module ArvadosWorkbench
+ class Application < Rails::Application
+ # Settings in config/environments/* take precedence over those specified here.
+ # Application configuration should go into files in config/initializers
+ # -- all .rb files in that directory are automatically loaded.
+
+ # Custom directories with classes and modules you want to be autoloadable.
+ # config.autoload_paths += %W(#{config.root}/extras)
+
+ # Only load the plugins named here, in the order given (default is alphabetical).
+ # :all can be used as a placeholder for all plugins not explicitly named.
+ # config.plugins = [ :exception_notification, :ssl_requirement, :all ]
+
+ # Activate observers that should always be running.
+ # config.active_record.observers = :cacher, :garbage_collector, :forum_observer
+
+ # Set Time.zone default to the specified zone and make Active Record auto-convert to this zone.
+ # Run "rake -D time" for a list of tasks for finding time zone names. Default is UTC.
+ # config.time_zone = 'Central Time (US & Canada)'
+
+ # The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
+ # config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
+ # config.i18n.default_locale = :de
+
+ # Configure the default encoding used in templates for Ruby 1.9.
+ config.encoding = "utf-8"
+
+ # Configure sensitive parameters which will be filtered from the log file.
+ config.filter_parameters += [:password]
+
+ # Enable escaping HTML in JSON.
+ config.active_support.escape_html_entities_in_json = true
+
+ # Use SQL instead of Active Record's schema dumper when creating the database.
+ # This is necessary if your schema can't be completely dumped by the schema dumper,
+ # like if you have constraints or database-specific column types
+ # config.active_record.schema_format = :sql
+
+ # Enable the asset pipeline
+ config.assets.enabled = true
+
+ # Version of your assets, change this if you want to expire all your assets
+ config.assets.version = '1.0'
+ end
+end
+
+require File.expand_path('../load_config', __FILE__)
--- /dev/null
+# Copy this file to application.yml and edit to suit.
+#
+# Consult application.default.yml for the full list of configuration
+# settings.
+#
+# The order of precedence is:
+# 1. config/environments/{RAILS_ENV}.rb (deprecated)
+# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
+# 3. Section in application.yml called "common"
+# 4. Section in application.default.yml corresponding to RAILS_ENV
+# 5. Section in application.default.yml called "common"
+
+development:
+ # At minimum, you need a nice long randomly generated secret_token here.
+ secret_token: ~
+
+ # You probably also want to point to your API server.
+ arvados_login_base: https://arvados.local:3030/login
+ arvados_v1_base: https://arvados.local:3030/arvados/v1
+ arvados_insecure_https: true
+
+production:
+ # At minimum, you need a nice long randomly generated secret_token here.
+ secret_token: ~
+
+ # You probably also want to point to your API server.
+ arvados_login_base: https://arvados.local:3030/login
+ arvados_v1_base: https://arvados.local:3030/arvados/v1
+ arvados_insecure_https: false
--- /dev/null
+require 'rubygems'
+
+# Set up gems listed in the Gemfile.
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+
+require 'bundler/setup' if File.exists?(ENV['BUNDLE_GEMFILE'])
+
+# Use ARVADOS_API_TOKEN environment variable (if set) in console
+require 'rails'
+module ArvadosApiClientConsoleMode
+ class Railtie < Rails::Railtie
+ console do
+ Thread.current[:arvados_api_token] ||= ENV['ARVADOS_API_TOKEN']
+ end
+ end
+end
--- /dev/null
+# SQLite version 3.x
+# gem install sqlite3
+#
+# Ensure the SQLite 3 gem is defined in your Gemfile
+# gem 'sqlite3'
+development:
+ adapter: sqlite3
+ database: db/development.sqlite3
+ pool: 5
+ timeout: 5000
+
+# Warning: The database defined as "test" will be erased and
+# re-generated from your development database when you run "rake".
+# Do not set this db to the same as development or production.
+test:
+ adapter: sqlite3
+ database: db/test.sqlite3
+ pool: 5
+ timeout: 5000
+
+production:
+ adapter: sqlite3
+ database: db/production.sqlite3
+ pool: 5
+ timeout: 5000
+
+# Note: The "diagnostics" database configuration is not actually used.
+diagnostics:
+ adapter: sqlite3
+ database: db/diagnostics.sqlite3
+ pool: 5
+ timeout: 5000
+
+# Note: The "performance" database configuration is not actually used.
+performance:
+ adapter: sqlite3
+ database: db/diagnostics.sqlite3
+ pool: 5
+ timeout: 5000
--- /dev/null
+# Load the rails application
+require File.expand_path('../application', __FILE__)
+
+# Initialize the rails application
+ArvadosWorkbench::Application.initialize!
--- /dev/null
+ArvadosWorkbench::Application.configure do
+ # Settings specified here will take precedence over those in config/application.rb
+
+ # In the development environment your application's code is reloaded on
+ # every request. This slows down response time but is perfect for development
+ # since you don't have to restart the web server when you make code changes.
+ config.cache_classes = false
+
+ # Show full error reports and disable caching
+ config.consider_all_requests_local = true
+ config.action_controller.perform_caching = false
+
+ # Don't care if the mailer can't send
+ config.action_mailer.raise_delivery_errors = false
+
+ # Print deprecation notices to the Rails logger
+ config.active_support.deprecation = :log
+
+ # Only use best-standards-support built into browsers
+ config.action_dispatch.best_standards_support = :builtin
+
+ # Do not compress assets
+ config.assets.js_compressor = false
+
+ # Expands the lines which load the assets
+ config.assets.debug = true
+
+end
--- /dev/null
+ArvadosWorkbench::Application.configure do
+ # Settings specified here will take precedence over those in config/application.rb
+
+ # Code is not reloaded between requests
+ config.cache_classes = true
+
+ # Full error reports are disabled and caching is turned on
+ config.consider_all_requests_local = false
+ config.action_controller.perform_caching = true
+
+ # Disable Rails's static asset server (Apache or nginx will already do this)
+ config.serve_static_assets = false
+
+ # Compress JavaScripts and CSS
+ config.assets.js_compressor = :uglifier
+
+ # Don't fallback to assets pipeline if a precompiled asset is missed
+ config.assets.compile = false
+
+ # Generate digests for assets URLs
+ config.assets.digest = true
+
+ # Defaults to nil and saved in location specified by config.assets.prefix
+ # config.assets.manifest = YOUR_PATH
+
+ # Specifies the header that your server uses for sending files
+ # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
+ # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
+
+ # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
+ # config.force_ssl = true
+
+ # See everything in the log (default is :info)
+ # config.log_level = :debug
+
+ # Prepend all log lines with the following tags
+ # config.log_tags = [ :subdomain, :uuid ]
+
+ # Use a different logger for distributed setups
+ # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
+
+ # Use a different cache store in production
+ # config.cache_store = :mem_cache_store
+
+ # Enable serving of images, stylesheets, and JavaScripts from an asset server
+ # config.action_controller.asset_host = "http://assets.example.com"
+
+ # Precompile additional assets (application.js, application.css, and all non-JS/CSS are already added)
+ # config.assets.precompile += %w( search.js )
+
+ # Disable delivery errors, bad email addresses will be ignored
+ # config.action_mailer.raise_delivery_errors = false
+
+ # Enable threaded mode
+ # config.threadsafe!
+
+ # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
+ # the I18n.default_locale when a translation can not be found)
+ config.i18n.fallbacks = true
+
+ # Send deprecation notices to registered listeners
+ config.active_support.deprecation = :notify
+
+ # Log timing data for API transactions
+ config.profiling_enabled = false
+
+end
--- /dev/null
+test.rb.example
\ No newline at end of file
--- /dev/null
+ArvadosWorkbench::Application.configure do
+ # Settings specified here will take precedence over those in config/application.rb
+
+ # The test environment is used exclusively to run your application's
+ # test suite. You never need to work with it otherwise. Remember that
+ # your test database is "scratch space" for the test suite and is wiped
+ # and recreated between test runs. Don't rely on the data there!
+ config.cache_classes = true
+
+ # Configure static asset server for tests with Cache-Control for performance
+ config.serve_static_assets = true
+ config.static_cache_control = "public, max-age=3600"
+
+ # Show full error reports and disable caching
+ config.consider_all_requests_local = true
+ config.action_controller.perform_caching = false
+
+ # Raise exceptions instead of rendering exception templates
+ config.action_dispatch.show_exceptions = false
+
+ # Disable request forgery protection in test environment
+ config.action_controller.allow_forgery_protection = false
+
+ # Tell Action Mailer not to deliver emails to the real world.
+ # The :test delivery method accumulates sent emails in the
+ # ActionMailer::Base.deliveries array.
+ config.action_mailer.delivery_method = :test
+
+ # Print deprecation notices to the stderr
+ config.active_support.deprecation = :stderr
+
+ # Log timing data for API transactions
+ config.profiling_enabled = false
+
+end
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
+# Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
+
+# You can also remove all the silencers if you're trying to debug a problem that might stem from framework code.
+# Rails.backtrace_cleaner.remove_silencers!
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# Add new inflection rules using the following format
+# (all these examples are active by default):
+# ActiveSupport::Inflector.inflections do |inflect|
+# inflect.plural /^(ox)$/i, '\1en'
+# inflect.singular /^(ox)en/i, '\1'
+# inflect.irregular 'person', 'people'
+# inflect.uncountable %w( fish sheep )
+# end
+#
+# These inflection rules are supported but not enabled by default:
+# ActiveSupport::Inflector.inflections do |inflect|
+# inflect.acronym 'RESTful'
+# end
+
+ActiveSupport::Inflector.inflections do |inflect|
+ inflect.plural /^([Ss]pecimen)$/i, '\1s'
+ inflect.singular /^([Ss]pecimen)s?/i, '\1'
+ inflect.plural /^([Hh]uman)$/i, '\1s'
+ inflect.singular /^([Hh]uman)s?/i, '\1'
+end
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# Add new mime types for use in respond_to blocks:
+# Mime::Type.register "text/richtext", :rtf
+# Mime::Type.register_alias "text/html", :iphone
--- /dev/null
+module RedClothArvadosLinkExtension
+
+ class RedClothViewBase < ActionView::Base
+ include ApplicationHelper
+ include ActionView::Helpers::UrlHelper
+ include Rails.application.routes.url_helpers
+
+ def helper_link_to_if_arvados_object(link, opts)
+ link_to_if_arvados_object(link, opts)
+ end
+ end
+
+ def refs_arvados(text)
+ text.gsub!(/"(?!\s)([^"]*\S)":(\S+)/) do
+ text, link = $~[1..2]
+ arvados_link = RedClothViewBase.new.helper_link_to_if_arvados_object(link, { :link_text => text })
+ # if it's not an arvados_link the helper will return the link unprocessed and so we will reconstruct the textile link string so it can be processed normally
+ (arvados_link == link) ? "\"#{text}\":#{link}" : arvados_link
+ end
+ end
+end
+
+RedCloth.send(:include, RedClothArvadosLinkExtension)
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# Your secret key for verifying the integrity of signed cookies.
+# If you change this key, all old signed cookies will become invalid!
+# Make sure the secret is at least 30 characters and all random,
+# no regular words or you'll be exposed to dictionary attacks.
+ArvadosWorkbench::Application.config.secret_token ||= rand(2**256).to_s(36)
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+ArvadosWorkbench::Application.config.session_store :cookie_store, key: '_arvados_workbench_session'
+
+# Use the database for sessions instead of the cookie-based default,
+# which shouldn't be used to store highly confidential information
+# (create the session table with "rails generate session_migration")
+# ArvadosWorkbench::Application.config.session_store :active_record_store
--- /dev/null
+# Be sure to restart your server when you modify this file.
+#
+# This file contains settings for ActionController::ParamsWrapper which
+# is enabled by default.
+
+# Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
+ActiveSupport.on_load(:action_controller) do
+ wrap_parameters format: [:json]
+end
+
+# Disable root element in JSON by default.
+ActiveSupport.on_load(:active_record) do
+ self.include_root_in_json = false
+end
--- /dev/null
+# This file must be loaded _after_ secret_token.rb if secret_token is
+# defined there instead of in config/application.yml.
+
+$application_config = {}
+
+%w(application.default application).each do |cfgfile|
+ path = "#{::Rails.root.to_s}/config/#{cfgfile}.yml"
+ if File.exists? path
+ yaml = ERB.new(IO.read path).result(binding)
+ confs = YAML.load(yaml)
+ $application_config.merge!(confs['common'] || {})
+ $application_config.merge!(confs[::Rails.env.to_s] || {})
+ end
+end
+
+ArvadosWorkbench::Application.configure do
+ nils = []
+ $application_config.each do |k, v|
+ # "foo.bar: baz" --> { config.foo.bar = baz }
+ cfg = config
+ ks = k.split '.'
+ k = ks.pop
+ ks.each do |kk|
+ cfg = cfg.send(kk)
+ end
+ if cfg.respond_to?(k.to_sym) and !cfg.send(k).nil?
+ # Config must have been set already in environments/*.rb.
+ #
+ # After config files have been migrated, this mechanism should
+ # be deprecated, then removed.
+ elsif v.nil?
+ # Config variables are not allowed to be nil. Make a "naughty"
+ # list, and present it below.
+ nils << k
+ else
+ cfg.send "#{k}=", v
+ end
+ end
+ if !nils.empty?
+ raise <<EOS
+Refusing to start in #{::Rails.env.to_s} mode with missing configuration.
+
+The following configuration settings must be specified in
+config/application.yml:
+* #{nils.join "\n* "}
+
+EOS
+ end
+end
--- /dev/null
+# Sample localization file for English. Add more files in this directory for other locales.
+# See https://github.com/svenfuchs/rails-i18n/tree/master/rails%2Flocale for starting points.
+
+en:
+ helpers:
+ actions: "Actions"
+ links:
+ back: "Back"
+ cancel: "Cancel"
+ confirm: "Are you sure?"
+ destroy: "Delete"
+ new: "New"
+ edit: "Edit"
+ titles:
+ edit: "Edit"
+ save: "Save"
+ new: "New"
+ delete: "Delete"
--- /dev/null
+# Sample localization file for English. Add more files in this directory for other locales.
+# See https://github.com/svenfuchs/rails-i18n/tree/master/rails%2Flocale for starting points.
+
+en:
+ hello: "Hello world"
--- /dev/null
+# Configuration:
+#
+# disabled
+# false if tracking tag should be shown
+# use_async
+# Set to true if you want to use asynchronous tracking
+# url
+# The url of your piwik instance (e.g. localhost/piwik/
+# id_site
+# The id of your website inside Piwik
+#
+production:
+ piwik:
+ id_site: 1
+ url: localhost
+ use_async: false
+ disabled: false
+
+development:
+ piwik:
+ id_site: 1
+ url: localhost
+ disabled: true
+ use_async: false
+ hostname: localhost
+
+test:
+ piwik:
+ id_site: 1
+ url: localhost
+ disabled: true
+ use_async: false
+ hostname: localhost
--- /dev/null
+ArvadosWorkbench::Application.routes.draw do
+ themes_for_rails
+
+ resources :keep_disks
+ resources :keep_services
+ resources :user_agreements do
+ post 'sign', on: :collection
+ get 'signatures', on: :collection
+ end
+ get '/user_agreements/signatures' => 'user_agreements#signatures'
+ get "users/setup_popup" => 'users#setup_popup', :as => :setup_user_popup
+ get "users/setup" => 'users#setup', :as => :setup_user
+ get "report_issue_popup" => 'actions#report_issue_popup', :as => :report_issue_popup
+ post "report_issue" => 'actions#report_issue', :as => :report_issue
+ resources :nodes
+ resources :humans
+ resources :traits
+ resources :api_client_authorizations
+ resources :repositories
+ resources :virtual_machines
+ resources :authorized_keys
+ resources :job_tasks
+ resources :jobs do
+ post 'cancel', :on => :member
+ get 'logs', :on => :member
+ end
+ match '/logout' => 'sessions#destroy', via: [:get, :post]
+ get '/logged_out' => 'sessions#index'
+ resources :users do
+ get 'choose', :on => :collection
+ get 'home', :on => :member
+ get 'welcome', :on => :collection
+ get 'inactive', :on => :collection
+ get 'activity', :on => :collection
+ get 'storage', :on => :collection
+ post 'sudo', :on => :member
+ post 'unsetup', :on => :member
+ get 'setup_popup', :on => :member
+ get 'profile', :on => :member
+ end
+ get '/manage_account' => 'users#manage_account'
+ get "/add_ssh_key_popup" => 'users#add_ssh_key_popup', :as => :add_ssh_key_popup
+ get "/add_ssh_key" => 'users#add_ssh_key', :as => :add_ssh_key
+ resources :logs
+ resources :factory_jobs
+ resources :uploaded_datasets
+ resources :groups do
+ get 'choose', on: :collection
+ end
+ resources :specimens
+ resources :pipeline_templates do
+ get 'choose', on: :collection
+ end
+ resources :pipeline_instances do
+ get 'compare', on: :collection
+ post 'copy', on: :member
+ end
+ resources :links
+ get '/collections/graph' => 'collections#graph'
+ resources :collections do
+ post 'set_persistent', on: :member
+ get 'sharing_popup', :on => :member
+ post 'share', :on => :member
+ post 'unshare', :on => :member
+ get 'choose', on: :collection
+ end
+ get('/collections/download/:uuid/:reader_token/*file' => 'collections#show_file',
+ format: false)
+ get '/collections/download/:uuid/:reader_token' => 'collections#show_file_links'
+ get '/collections/:uuid/*file' => 'collections#show_file', :format => false
+ resources :projects do
+ match 'remove/:item_uuid', on: :member, via: :delete, action: :remove_item
+ match 'remove_items', on: :member, via: :delete, action: :remove_items
+ get 'choose', on: :collection
+ post 'share_with', on: :member
+ get 'tab_counts', on: :member
+ end
+ resources :search do
+ get 'choose', :on => :collection
+ end
+
+ post 'actions' => 'actions#post'
+ get 'actions' => 'actions#show'
+ get 'websockets' => 'websocket#index'
+ post "combine_selected" => 'actions#combine_selected_files_into_collection'
+
+ root :to => 'projects#index'
+
+ # Send unroutable requests to an arbitrary controller
+ # (ends up at ApplicationController#render_not_found)
+ match '*a', to: 'links#render_not_found', via: [:get, :post]
+end
--- /dev/null
+# encoding: UTF-8
+# This file is auto-generated from the current state of the database. Instead
+# of editing this file, please use the migrations feature of Active Record to
+# incrementally modify your database, and then regenerate this schema definition.
+#
+# Note that this schema.rb definition is the authoritative source for your
+# database schema. If you need to create the application database on another
+# system, you should be using db:schema:load, not running all the migrations
+# from scratch. The latter is a flawed and unsustainable approach (the more migrations
+# you'll amass, the slower it'll run and the greater likelihood for issues).
+#
+# It's strongly recommended to check this file into your version control system.
+
+ActiveRecord::Schema.define(:version => 0) do
+
+end
--- /dev/null
+# This file should contain all the record creation needed to seed the database with its default values.
+# The data can then be loaded with the rake db:seed (or created alongside the db with db:setup).
+#
+# Examples:
+#
+# cities = City.create([{ name: 'Chicago' }, { name: 'Copenhagen' }])
+# Mayor.create(name: 'Emanuel', city: cities.first)
--- /dev/null
+namespace :config do
+ desc 'Ensure site configuration has all required settings'
+ task check: :environment do
+ $application_config.sort.each do |k, v|
+ if ENV.has_key?('QUIET') then
+ # Make sure we still check for the variable to exist
+ eval("Rails.configuration.#{k}")
+ else
+ if /(password|secret)/.match(k) then
+ # Make sure we still check for the variable to exist, but don't print the value
+ eval("Rails.configuration.#{k}")
+ $stderr.puts "%-32s %s" % [k, '*********']
+ else
+ $stderr.puts "%-32s %s" % [k, eval("Rails.configuration.#{k}")]
+ end
+ end
+ end
+ end
+end
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+ <title>The page you were looking for doesn't exist (404)</title>
+ <style type="text/css">
+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+ div.dialog {
+ width: 25em;
+ padding: 0 4em;
+ margin: 4em auto 0 auto;
+ border: 1px solid #ccc;
+ border-right-color: #999;
+ border-bottom-color: #999;
+ }
+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+ </style>
+</head>
+
+<body>
+ <!-- This file lives in public/404.html -->
+ <div class="dialog">
+ <h1>The page you were looking for doesn't exist.</h1>
+ <p>You may have mistyped the address or the page may have moved.</p>
+ </div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+ <title>The change you wanted was rejected (422)</title>
+ <style type="text/css">
+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+ div.dialog {
+ width: 25em;
+ padding: 0 4em;
+ margin: 4em auto 0 auto;
+ border: 1px solid #ccc;
+ border-right-color: #999;
+ border-bottom-color: #999;
+ }
+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+ </style>
+</head>
+
+<body>
+ <!-- This file lives in public/422.html -->
+ <div class="dialog">
+ <h1>The change you wanted was rejected.</h1>
+ <p>Maybe you tried to change something you didn't have access to.</p>
+ </div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+ <title>We're sorry, but something went wrong (500)</title>
+ <style type="text/css">
+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+ div.dialog {
+ width: 25em;
+ padding: 0 4em;
+ margin: 4em auto 0 auto;
+ border: 1px solid #ccc;
+ border-right-color: #999;
+ border-bottom-color: #999;
+ }
+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+ </style>
+</head>
+
+<body>
+ <!-- This file lives in public/500.html -->
+ <div class="dialog">
+ <h1>We're sorry, but something went wrong.</h1>
+ </div>
+</body>
+</html>
--- /dev/null
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u=t[r],a=n[0],o=n[1],c=u[0],l=u[1],s=a[0],f=a[1],h=o[0],d=o[1],g=Math.abs(h-s),p=d-f;if(Pu>Math.abs(p)){var m=f>l?-e:e;n.push([-e,m],[e,m])}else if(Pu>g){var v=s>c?-e:e;n.push([v,-e],[v,e])}else{var m=(s-c)*(d-f)>(h-s)*(f-l)?e:-e,y=Math.abs(p)-g;Pu>Math.abs(y)?n.push([0>p?m:-m,m]):(y>0&&(m*=-1),n.push([-e,m],[e,m]))}}}),n};var _o={l:"r",r:"l"};d3.geom.delaunay=function(t){var n=t.map(function(){return[]}),e=[];return $i(t,function(e){n[e.region.l.index].push(t[e.region.r.index])}),n.forEach(function(n,r){var i=t[r],u=i[0],a=i[1];n.forEach(function(t){t.angle=Math.atan2(t[0]-u,t[1]-a)}),n.sort(function(t,n){return t.angle-n.angle});for(var o=0,c=n.length-1;c>o;o++)e.push([i,n[o],n[o+1]])}),e},d3.geom.quadtree=function(t,n,e,r,i){function u(t,n,e,r,i,u){if(!isNaN(n.x)&&!isNaN(n.y))if(t.leaf){var o=t.point;o?.01>Math.abs(o.x-n.x)+Math.abs(o.y-n.y)?a(t,n,e,r,i,u):(t.point=null,a(t,o,e,r,i,u),a(t,n,e,r,i,u)):t.point=n}else a(t,n,e,r,i,u)}function a(t,n,e,r,i,a){var o=.5*(e+i),c=.5*(r+a),l=n.x>=o,s=n.y>=c,f=(s<<1)+l;t.leaf=!1,t=t.nodes[f]||(t.nodes[f]=Ji()),l?e=o:i=o,s?r=c:a=c,u(t,n,e,r,i,a)}var o,c=-1,l=t.length;if(5>arguments.length)if(3===arguments.length)i=e,r=n,e=n=0;else for(n=e=1/0,r=i=-1/0;l>++c;)o=t[c],n>o.x&&(n=o.x),e>o.y&&(e=o.y),o.x>r&&(r=o.x),o.y>i&&(i=o.y);var s=r-n,f=i-e;s>f?i=e+s:r=n+f;var h=Ji();return h.add=function(t){u(h,t,n,e,r,i)},h.visit=function(t){Gi(t,h,n,e,r,i)},t.forEach(h.add),h},d3.time={};var wo=Date,So=["Sunday","Monday","Tuesday","Wednesday","Thursday","Friday","Saturday"];Ki.prototype={getDate:function(){return this._.getUTCDate()},getDay:function(){return this._.getUTCDay()},getFullYear:function(){return this._.getUTCFullYear()},getHours:function(){return this._.getUTCHours()},getMilliseconds:function(){return this._.getUTCMilliseconds()},getMinutes:function(){return this._.getUTCMinutes()},getMonth:function(){return this._.getUTCMonth()},getSeconds:function(){return this._.getUTCSeconds()},getTime:function(){return this._.getTime()},getTimezoneOffset:function(){return 0},valueOf:function(){return this._.valueOf()},setDate:function(){ko.setUTCDate.apply(this._,arguments)},setDay:function(){ko.setUTCDay.apply(this._,arguments)},setFullYear:function(){ko.setUTCFullYear.apply(this._,arguments)},setHours:function(){ko.setUTCHours.apply(this._,arguments)},setMilliseconds:function(){ko.setUTCMilliseconds.apply(this._,arguments)},setMinutes:function(){ko.setUTCMinutes.apply(this._,arguments)},setMonth:function(){ko.setUTCMonth.apply(this._,arguments)},setSeconds:function(){ko.setUTCSeconds.apply(this._,arguments)},setTime:function(){ko.setTime.apply(this._,arguments)}};var ko=Date.prototype,Eo="%a %b %e %X %Y",Ao="%m/%d/%Y",No="%H:%M:%S",To=["Sunday","Monday","Tuesday","Wednesday","Thursday","Friday","Saturday"],qo=["Sun","Mon","Tue","Wed","Thu","Fri","Sat"],Co=["January","February","March","April","May","June","July","August","September","October","November","December"],zo=["Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec"];d3.time.format=function(t){function n(n){for(var r,i,u,a=[],o=-1,c=0;e>++o;)37===t.charCodeAt(o)&&(a.push(t.substring(c,o)),null!=(i=jo[r=t.charAt(++o)])&&(r=t.charAt(++o)),(u=Oo[r])&&(r=u(n,null==i?"e"===r?" ":"0":i)),a.push(r),c=o+1);return a.push(t.substring(c,o)),a.join("")}var e=t.length;return n.parse=function(n){var e={y:1900,m:0,d:1,H:0,M:0,S:0,L:0},r=Wi(e,t,n,0);if(r!=n.length)return null;"p"in e&&(e.H=e.H%12+12*e.p);var i=new wo;return i.setFullYear(e.y,e.m,e.d),i.setHours(e.H,e.M,e.S,e.L),i},n.toString=function(){return t},n};var Do=Qi(To),Lo=Qi(qo),Fo=Qi(Co),Ho=tu(Co),Ro=Qi(zo),Po=tu(zo),jo={"-":"",_:" ",0:"0"},Oo={a:function(t){return qo[t.getDay()]},A:function(t){return To[t.getDay()]},b:function(t){return zo[t.getMonth()]},B:function(t){return Co[t.getMonth()]},c:d3.time.format(Eo),d:function(t,n){return nu(t.getDate(),n,2)},e:function(t,n){return nu(t.getDate(),n,2)},H:function(t,n){return nu(t.getHours(),n,2)},I:function(t,n){return nu(t.getHours()%12||12,n,2)},j:function(t,n){return nu(1+d3.time.dayOfYear(t),n,3)},L:function(t,n){return nu(t.getMilliseconds(),n,3)},m:function(t,n){return nu(t.getMonth()+1,n,2)},M:function(t,n){return nu(t.getMinutes(),n,2)},p:function(t){return t.getHours()>=12?"PM":"AM"},S:function(t,n){return nu(t.getSeconds(),n,2)},U:function(t,n){return nu(d3.time.sundayOfYear(t),n,2)},w:function(t){return t.getDay()},W:function(t,n){return nu(d3.time.mondayOfYear(t),n,2)},x:d3.time.format(Ao),X:d3.time.format(No),y:function(t,n){return nu(t.getFullYear()%100,n,2)},Y:function(t,n){return nu(t.getFullYear()%1e4,n,4)},Z:Mu,"%":function(){return"%"}},Yo={a:eu,A:ru,b:iu,B:uu,c:au,d:du,e:du,H:gu,I:gu,L:vu,m:hu,M:pu,p:yu,S:mu,x:ou,X:cu,y:su,Y:lu},Uo=/^\s*\d+/,Io=d3.map({am:0,pm:1});d3.time.format.utc=function(t){function n(t){try{wo=Ki;var n=new wo;return n._=t,e(n)}finally{wo=Date}}var e=d3.time.format(t);return n.parse=function(t){try{wo=Ki;var n=e.parse(t);return n&&n._}finally{wo=Date}},n.toString=e.toString,n};var Vo=d3.time.format.utc("%Y-%m-%dT%H:%M:%S.%LZ");d3.time.format.iso=Date.prototype.toISOString?bu:Vo,bu.parse=function(t){var n=new Date(t);return isNaN(n)?null:n},bu.toString=Vo.toString,d3.time.second=xu(function(t){return new wo(1e3*Math.floor(t/1e3))},function(t,n){t.setTime(t.getTime()+1e3*Math.floor(n))},function(t){return t.getSeconds()}),d3.time.seconds=d3.time.second.range,d3.time.seconds.utc=d3.time.second.utc.range,d3.time.minute=xu(function(t){return new wo(6e4*Math.floor(t/6e4))},function(t,n){t.setTime(t.getTime()+6e4*Math.floor(n))},function(t){return t.getMinutes()}),d3.time.minutes=d3.time.minute.range,d3.time.minutes.utc=d3.time.minute.utc.range,d3.time.hour=xu(function(t){var n=t.getTimezoneOffset()/60;return new wo(36e5*(Math.floor(t/36e5-n)+n))},function(t,n){t.setTime(t.getTime()+36e5*Math.floor(n))},function(t){return t.getHours()}),d3.time.hours=d3.time.hour.range,d3.time.hours.utc=d3.time.hour.utc.range,d3.time.day=xu(function(t){var n=new wo(1970,0);return n.setFullYear(t.getFullYear(),t.getMonth(),t.getDate()),n},function(t,n){t.setDate(t.getDate()+n)},function(t){return 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t.getMonth()}),d3.time.months=d3.time.month.range,d3.time.months.utc=d3.time.month.utc.range,d3.time.year=xu(function(t){return t=d3.time.day(t),t.setMonth(0,1),t},function(t,n){t.setFullYear(t.getFullYear()+n)},function(t){return t.getFullYear()}),d3.time.years=d3.time.year.range,d3.time.years.utc=d3.time.year.utc.range;var Xo=[1e3,5e3,15e3,3e4,6e4,3e5,9e5,18e5,36e5,108e5,216e5,432e5,864e5,1728e5,6048e5,2592e6,7776e6,31536e6],Zo=[[d3.time.second,1],[d3.time.second,5],[d3.time.second,15],[d3.time.second,30],[d3.time.minute,1],[d3.time.minute,5],[d3.time.minute,15],[d3.time.minute,30],[d3.time.hour,1],[d3.time.hour,3],[d3.time.hour,6],[d3.time.hour,12],[d3.time.day,1],[d3.time.day,2],[d3.time.week,1],[d3.time.month,1],[d3.time.month,3],[d3.time.year,1]],Bo=[[d3.time.format("%Y"),o],[d3.time.format("%B"),function(t){return t.getMonth()}],[d3.time.format("%b %d"),function(t){return 1!=t.getDate()}],[d3.time.format("%a %d"),function(t){return t.getDay()&&1!=t.getDate()}],[d3.time.format("%I %p"),function(t){return t.getHours()}],[d3.time.format("%I:%M"),function(t){return t.getMinutes()}],[d3.time.format(":%S"),function(t){return t.getSeconds()}],[d3.time.format(".%L"),function(t){return t.getMilliseconds()}]],$o=d3.scale.linear(),Jo=Eu(Bo);Zo.year=function(t,n){return $o.domain(t.map(Nu)).ticks(n).map(Au)},d3.time.scale=function(){return wu(d3.scale.linear(),Zo,Jo)};var Go=Zo.map(function(t){return[t[0].utc,t[1]]}),Ko=[[d3.time.format.utc("%Y"),o],[d3.time.format.utc("%B"),function(t){return t.getUTCMonth()}],[d3.time.format.utc("%b %d"),function(t){return 1!=t.getUTCDate()}],[d3.time.format.utc("%a %d"),function(t){return t.getUTCDay()&&1!=t.getUTCDate()}],[d3.time.format.utc("%I %p"),function(t){return t.getUTCHours()}],[d3.time.format.utc("%I:%M"),function(t){return t.getUTCMinutes()}],[d3.time.format.utc(":%S"),function(t){return t.getUTCSeconds()}],[d3.time.format.utc(".%L"),function(t){return t.getUTCMilliseconds()}]],Wo=Eu(Ko);Go.year=function(t,n){return $o.domain(t.map(qu)).ticks(n).map(Tu)},d3.time.scale.utc=function(){return wu(d3.scale.linear(),Go,Wo)}})();
\ No newline at end of file
--- /dev/null
+<!DOCTYPE html>
+<!-- from http://bl.ocks.org/1153292 -->
+<html>
+ <head>
+ <meta http-equiv="Content-type" content="text/html; charset=utf-8">
+ <title>Object graph example</title>
+ <script src="d3.v3.min.js"></script>
+ <style type="text/css">
+
+path.link {
+ fill: none;
+ stroke: #666;
+ stroke-width: 1.5px;
+}
+
+marker#can_read {
+ fill: green;
+}
+
+path.link.can_read {
+ stroke: green;
+ stroke-dasharray: 0,4 1;
+}
+
+path.link.can_write {
+ stroke: green;
+}
+
+path.link.member_of {
+ stroke: blue;
+ stroke-dasharray: 0,4 1;
+}
+
+path.link.created {
+ stroke: red;
+}
+
+circle {
+ fill: #ccc;
+ stroke: #333;
+ stroke-width: 1.5px;
+}
+
+edgetext {
+ font: 12px sans-serif;
+ pointer-events: none;
+ text-align: center;
+}
+
+text {
+ font: 12px sans-serif;
+ pointer-events: none;
+}
+
+text.shadow {
+ stroke: #fff;
+ stroke-width: 3px;
+ stroke-opacity: .8;
+}
+
+ </style>
+ </head>
+ <body>
+ <script type="text/javascript">
+
+var links = [
+ {source: "user: customer", target: "project: customer_project", type: "can_read"},
+ {source: "user: import robot", target: "project: customer_project", type: "can_read"},
+ {source: "user: pipeline robot", target: "project: customer_project", type: "can_read"},
+ {source: "user: uploader", target: "collection: w3anr2hk2wgfpuo", type: "created"},
+ {source: "user: uploader", target: "project: customer_project", type: "created"},
+ {source: "collection: w3anr2hk2wgfpuo", target: "project: customer_project", type: "member_of"}
+];
+
+var nodes = {};
+
+// Compute the distinct nodes from the links.
+links.forEach(function(link) {
+ link.source = nodes[link.source] || (nodes[link.source] = {name: link.source});
+ link.target = nodes[link.target] || (nodes[link.target] = {name: link.target});
+});
+
+var w = 960,
+ h = 500;
+
+var force = d3.layout.force()
+ .nodes(d3.values(nodes))
+ .links(links)
+ .size([w, h])
+ .linkDistance(250)
+ .charge(-300)
+ .on("tick", tick)
+ .start();
+
+var svg = d3.select("body").append("svg:svg")
+ .attr("width", w)
+ .attr("height", h);
+
+// Per-type markers, as they don't inherit styles.
+svg.append("svg:defs").selectAll("marker")
+ .data(["created", "member_of", "can_read", "can_write"])
+ .enter().append("svg:marker")
+ .attr("id", String)
+ .attr("viewBox", "0 -5 10 10")
+ .attr("refX", 15)
+ .attr("refY", -1.5)
+ .attr("markerWidth", 6)
+ .attr("markerHeight", 6)
+ .attr("orient", "auto")
+ .append("svg:path")
+ .attr("d", "M0,-5L10,0L0,5");
+
+var path = svg.append("svg:g").selectAll("path")
+ .data(force.links())
+ .enter().append("svg:path")
+ .attr("class", function(d) { return "link " + d.type; })
+ .attr("marker-end", function(d) { return "url(#" + d.type + ")"; });
+
+var circle = svg.append("svg:g").selectAll("circle")
+ .data(force.nodes())
+ .enter().append("svg:circle")
+ .attr("r", 6)
+ .call(force.drag);
+
+var text = svg.append("svg:g").selectAll("g")
+ .data(force.nodes())
+ .enter().append("svg:g");
+
+// A copy of the text with a thick white stroke for legibility.
+text.append("svg:text")
+ .attr("x", 8)
+ .attr("y", ".31em")
+ .attr("class", "shadow")
+ .text(function(d) { return d.name; });
+
+text.append("svg:text")
+ .attr("x", 8)
+ .attr("y", ".31em")
+ .text(function(d) { return d.name; });
+
+var edgetext = svg.append("svg:g").selectAll("g")
+ .data(force.links())
+ .enter().append("svg:g");
+
+edgetext
+ .append("svg:text")
+ .attr("x",0)
+ .attr("y","-0.2em")
+ .text(function(d) { return d.type; });
+
+// Use elliptical arc path segments to doubly-encode directionality.
+function tick() {
+ path.attr("d", function(d) {
+ var dx = d.target.x - d.source.x,
+ dy = d.target.y - d.source.y,
+ // dr = Math.sqrt(dx * dx + dy * dy);
+ dr = 0;
+ return "M" + d.source.x + "," + d.source.y + "A" + dr + "," + dr + " 0 0,1 " + d.target.x + "," + d.target.y;
+ });
+
+ circle.attr("transform", function(d) {
+ return "translate(" + d.x + "," + d.y + ")";
+ });
+
+ text.attr("transform", function(d) {
+ return "translate(" + d.x + "," + d.y + ")";
+ });
+
+ edgetext.attr("transform", function(d) {
+ return "translate(" +
+ (d.source.x + d.target.x)/2 + "," +
+ (d.source.y + d.target.y)/2 +
+ ")rotate(" +
+ (Math.atan2(d.target.y - d.source.y, d.target.x - d.source.x) * 180 / Math.PI) +
+ ")";
+ });
+}
+
+ </script>
+ </body>
+</html>
--- /dev/null
+#!/usr/bin/env ruby
+# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
+
+APP_PATH = File.expand_path('../../config/application', __FILE__)
+require File.expand_path('../../config/boot', __FILE__)
+require 'rails/commands'
--- /dev/null
+require 'test_helper'
+
+class ActionsControllerTest < ActionController::TestCase
+
+ test "send report" do
+ post :report_issue, {format: 'js'}, session_for(:admin)
+ assert_response :success
+
+ found_email = false
+ ActionMailer::Base.deliveries.andand.each do |email|
+ if email.subject.include? "Issue reported by admin"
+ found_email = true
+ break
+ end
+ end
+ assert_equal true, found_email, 'Expected email after issue reported'
+ end
+
+ test "combine files into new collection" do
+ post(:combine_selected_files_into_collection, {
+ selection: ['zzzzz-4zz18-znfnqtbbv4spc3w/foo',
+ 'zzzzz-4zz18-ehbhgtheo8909or/bar',
+ 'zzzzz-4zz18-y9vne9npefyxh8g/baz',
+ '1fd08fc162a5c6413070a8bd0bffc818+150'],
+ format: "json"},
+ session_for(:active))
+
+ assert_response 302 # collection created and redirected to new collection page
+
+ assert response.headers['Location'].include? '/collections/'
+ new_collection_uuid = response.headers['Location'].split('/')[-1]
+
+ use_token :active
+ collection = Collection.select([:uuid, :manifest_text]).where(uuid: new_collection_uuid).first
+ manifest_text = collection['manifest_text']
+ assert manifest_text.include?('foo'), 'Not found foo in new collection manifest text'
+ assert manifest_text.include?('bar'), 'Not found bar in new collection manifest text'
+ assert manifest_text.include?('baz'), 'Not found baz in new collection manifest text'
+ assert manifest_text.include?('0:0:file1 0:0:file2 0:0:file3'),
+ 'Not found 0:0:file1 0:0:file2 0:0:file3 in new collection manifest text'
+ assert manifest_text.include?('dir1/subdir'), 'Not found dir1/subdir in new collection manifest text'
+ assert manifest_text.include?('dir2'), 'Not found dir2 in new collection manifest text'
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class ApiClientAuthorizationsControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class ApplicationControllerTest < ActionController::TestCase
+ # These tests don't do state-changing API calls. Save some time by
+ # skipping the database reset.
+ reset_api_fixtures :after_each_test, false
+ reset_api_fixtures :after_suite, true
+
+ setup do
+ @user_dataclass = ArvadosBase.resource_class_for_uuid(api_fixture('users')['active']['uuid'])
+ end
+
+ test "links for object" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ link_head_uuid = api_fixture('links')['foo_file_readable_by_active']['head_uuid']
+
+ links = ac.send :links_for_object, link_head_uuid
+
+ assert links, 'Expected links'
+ assert links.is_a?(Array), 'Expected an array'
+ assert links.size > 0, 'Expected at least one link'
+ assert links[0][:uuid], 'Expected uuid for the head_link'
+ end
+
+ test "preload links for objects and uuids" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ link1_head_uuid = api_fixture('links')['foo_file_readable_by_active']['head_uuid']
+ link2_uuid = api_fixture('links')['bar_file_readable_by_active']['uuid']
+ link3_head_uuid = api_fixture('links')['bar_file_readable_by_active']['head_uuid']
+
+ link2_object = User.find(api_fixture('users')['active']['uuid'])
+ link2_object_uuid = link2_object['uuid']
+
+ uuids = [link1_head_uuid, link2_object, link3_head_uuid]
+ links = ac.send :preload_links_for_objects, uuids
+
+ assert links, 'Expected links'
+ assert links.is_a?(Hash), 'Expected a hash'
+ assert links.size == 3, 'Expected two objects in the preloaded links hash'
+ assert links[link1_head_uuid], 'Expected links for the passed in link head_uuid'
+ assert links[link2_object_uuid], 'Expected links for the passed in object uuid'
+ assert links[link3_head_uuid], 'Expected links for the passed in link head_uuid'
+
+ # invoke again for this same input. this time, the preloaded data will be returned
+ links = ac.send :preload_links_for_objects, uuids
+ assert links, 'Expected links'
+ assert links.is_a?(Hash), 'Expected a hash'
+ assert links.size == 3, 'Expected two objects in the preloaded links hash'
+ assert links[link1_head_uuid], 'Expected links for the passed in link head_uuid'
+ end
+
+ [ [:preload_links_for_objects, [] ],
+ [:preload_collections_for_objects, [] ],
+ [:preload_log_collections_for_objects, [] ],
+ [:preload_objects_for_dataclass, [] ],
+ ].each do |input|
+ test "preload data for empty array input #{input}" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ if input[0] == :preload_objects_for_dataclass
+ objects = ac.send input[0], @user_dataclass, input[1]
+ else
+ objects = ac.send input[0], input[1]
+ end
+
+ assert objects, 'Expected objects'
+ assert objects.is_a?(Hash), 'Expected a hash'
+ assert objects.size == 0, 'Expected no objects in the preloaded hash'
+ end
+ end
+
+ [ [:preload_links_for_objects, 'input not an array'],
+ [:preload_links_for_objects, nil],
+ [:links_for_object, nil],
+ [:preload_collections_for_objects, 'input not an array'],
+ [:preload_collections_for_objects, nil],
+ [:collections_for_object, nil],
+ [:preload_log_collections_for_objects, 'input not an array'],
+ [:preload_log_collections_for_objects, nil],
+ [:log_collections_for_object, nil],
+ [:preload_objects_for_dataclass, 'input not an array'],
+ [:preload_objects_for_dataclass, nil],
+ [:object_for_dataclass, 'some_dataclass', nil],
+ [:object_for_dataclass, nil, 'some_uuid'],
+ ].each do |input|
+ test "preload data for wrong type input #{input}" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ if input[0] == :object_for_dataclass
+ assert_raise ArgumentError do
+ ac.send input[0], input[1], input[2]
+ end
+ else
+ assert_raise ArgumentError do
+ ac.send input[0], input[1]
+ end
+ end
+ end
+ end
+
+ [ [:links_for_object, 'no-such-uuid' ],
+ [:collections_for_object, 'no-such-uuid' ],
+ [:log_collections_for_object, 'no-such-uuid' ],
+ [:object_for_dataclass, 'no-such-uuid' ],
+ ].each do |input|
+ test "get data for no such uuid #{input}" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ if input[0] == :object_for_dataclass
+ object = ac.send input[0], @user_dataclass, input[1]
+ assert_not object, 'Expected no object'
+ else
+ objects = ac.send input[0], input[1]
+ assert objects, 'Expected objects'
+ assert objects.is_a?(Array), 'Expected a array'
+ end
+ end
+ end
+
+ test "get 10 objects of data class user" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ objects = ac.send :get_n_objects_of_class, @user_dataclass, 10
+
+ assert objects, 'Expected objects'
+ assert objects.is_a?(ArvadosResourceList), 'Expected an ArvadosResourceList'
+
+ first_object = objects.first
+ assert first_object, 'Expected at least one object'
+ assert_equal 'User', first_object.class.name, 'Expected user object'
+
+ # invoke it again. this time, the preloaded info will be returned
+ objects = ac.send :get_n_objects_of_class, @user_dataclass, 10
+ assert objects, 'Expected objects'
+ assert_equal 'User', objects.first.class.name, 'Expected user object'
+ end
+
+ [ ['User', 10],
+ [nil, 10],
+ [@user_dataclass, 0],
+ [@user_dataclass, -1],
+ [@user_dataclass, nil] ].each do |input|
+ test "get_n_objects for incorrect input #{input}" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ assert_raise ArgumentError do
+ ac.send :get_n_objects_of_class, input[0], input[1]
+ end
+ end
+ end
+
+ test "collections for object" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ uuid = api_fixture('collections')['foo_file']['uuid']
+
+ collections = ac.send :collections_for_object, uuid
+
+ assert collections, 'Expected collections'
+ assert collections.is_a?(Array), 'Expected an array'
+ assert collections.size == 1, 'Expected one collection object'
+ assert_equal collections[0][:uuid], uuid, 'Expected uuid not found in collections'
+ end
+
+ test "preload collections for given uuids" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ uuid1 = api_fixture('collections')['foo_file']['uuid']
+ uuid2 = api_fixture('collections')['bar_file']['uuid']
+
+ uuids = [uuid1, uuid2]
+ collections = ac.send :preload_collections_for_objects, uuids
+
+ assert collections, 'Expected collection'
+ assert collections.is_a?(Hash), 'Expected a hash'
+ assert collections.size == 2, 'Expected two objects in the preloaded collection hash'
+ assert collections[uuid1], 'Expected collections for the passed in uuid'
+ assert_equal collections[uuid1].size, 1, 'Expected one collection for the passed in uuid'
+ assert collections[uuid2], 'Expected collections for the passed in uuid'
+ assert_equal collections[uuid2].size, 1, 'Expected one collection for the passed in uuid'
+
+ # invoke again for this same input. this time, the preloaded data will be returned
+ collections = ac.send :preload_collections_for_objects, uuids
+ assert collections, 'Expected collection'
+ assert collections.is_a?(Hash), 'Expected a hash'
+ assert collections.size == 2, 'Expected two objects in the preloaded collection hash'
+ assert collections[uuid1], 'Expected collections for the passed in uuid'
+ end
+
+ test "log collections for object" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ uuid = api_fixture('logs')['log4']['object_uuid']
+
+ collections = ac.send :log_collections_for_object, uuid
+
+ assert collections, 'Expected collections'
+ assert collections.is_a?(Array), 'Expected an array'
+ assert collections.size == 1, 'Expected one collection object'
+ assert_equal collections[0][:uuid], uuid, 'Expected uuid not found in collections'
+ end
+
+ test "preload log collections for given uuids" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ uuid1 = api_fixture('logs')['log4']['object_uuid']
+ uuid2 = api_fixture('collections')['bar_file']['uuid']
+
+ uuids = [uuid1, uuid2]
+ collections = ac.send :preload_log_collections_for_objects, uuids
+
+ assert collections, 'Expected collection'
+ assert collections.is_a?(Hash), 'Expected a hash'
+ assert collections.size == 2, 'Expected two objects in the preloaded collection hash'
+ assert collections[uuid1], 'Expected collections for the passed in uuid'
+ assert_equal collections[uuid1].size, 1, 'Expected one collection for the passed in uuid'
+ assert collections[uuid2], 'Expected collections for the passed in uuid'
+ assert_equal collections[uuid2].size, 1, 'Expected one collection for the passed in uuid'
+
+ # invoke again for this same input. this time, the preloaded data will be returned
+ collections = ac.send :preload_log_collections_for_objects, uuids
+ assert collections, 'Expected collection'
+ assert collections.is_a?(Hash), 'Expected a hash'
+ assert collections.size == 2, 'Expected two objects in the preloaded collection hash'
+ assert collections[uuid1], 'Expected collections for the passed in uuid'
+ end
+
+ test "object for dataclass" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ dataclass = ArvadosBase.resource_class_for_uuid(api_fixture('jobs')['running']['uuid'])
+ uuid = api_fixture('jobs')['running']['uuid']
+
+ obj = ac.send :object_for_dataclass, dataclass, uuid
+
+ assert obj, 'Expected object'
+ assert 'Job', obj.class
+ assert_equal uuid, obj['uuid'], 'Expected uuid not found'
+ assert_equal api_fixture('jobs')['running']['script_version'], obj['script_version'],
+ 'Expected script_version not found'
+ end
+
+ test "preload objects for dataclass" do
+ use_token :active
+
+ ac = ApplicationController.new
+
+ dataclass = ArvadosBase.resource_class_for_uuid(api_fixture('jobs')['running']['uuid'])
+
+ uuid1 = api_fixture('jobs')['running']['uuid']
+ uuid2 = api_fixture('jobs')['running_cancelled']['uuid']
+
+ uuids = [uuid1, uuid2]
+ users = ac.send :preload_objects_for_dataclass, dataclass, uuids
+
+ assert users, 'Expected objects'
+ assert users.is_a?(Hash), 'Expected a hash'
+
+ assert users.size == 2, 'Expected two objects in the preloaded hash'
+ assert users[uuid1], 'Expected user object for the passed in uuid'
+ assert users[uuid2], 'Expected user object for the passed in uuid'
+
+ # invoke again for this same input. this time, the preloaded data will be returned
+ users = ac.send :preload_objects_for_dataclass, dataclass, uuids
+ assert users, 'Expected objects'
+ assert users.is_a?(Hash), 'Expected a hash'
+ assert users.size == 2, 'Expected two objects in the preloaded hash'
+
+ # invoke again for this with one more uuid
+ uuids << api_fixture('jobs')['foobar']['uuid']
+ users = ac.send :preload_objects_for_dataclass, dataclass, uuids
+ assert users, 'Expected objects'
+ assert users.is_a?(Hash), 'Expected a hash'
+ assert users.size == 3, 'Expected two objects in the preloaded hash'
+ end
+
+ test "requesting a nonexistent object returns 404" do
+ # We're really testing ApplicationController's find_object_by_uuid.
+ # It's easiest to do that by instantiating a concrete controller.
+ @controller = NodesController.new
+ get(:show, {id: "zzzzz-zzzzz-zzzzzzzzzzzzzzz"}, session_for(:admin))
+ assert_response 404
+ end
+
+ test "Workbench returns 4xx when API server is unreachable" do
+ # We're really testing ApplicationController's render_exception.
+ # Our primary concern is that it doesn't raise an error and
+ # return 500.
+ orig_api_server = Rails.configuration.arvados_v1_base
+ begin
+ # The URL should look valid in all respects, and avoid talking over a
+ # network. 100::/64 is the IPv6 discard prefix, so it's perfect.
+ Rails.configuration.arvados_v1_base = "https://[100::f]:1/"
+ @controller = NodesController.new
+ get(:index, {}, session_for(:active))
+ assert_includes(405..422, @response.code.to_i,
+ "bad response code when API server is unreachable")
+ ensure
+ Rails.configuration.arvados_v1_base = orig_api_server
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class AuthorizedKeysControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class CollectionsControllerTest < ActionController::TestCase
+ # These tests don't do state-changing API calls. Save some time by
+ # skipping the database reset.
+ reset_api_fixtures :after_each_test, false
+ reset_api_fixtures :after_suite, true
+
+ include PipelineInstancesHelper
+
+ NONEXISTENT_COLLECTION = "ffffffffffffffffffffffffffffffff+0"
+
+ def stub_file_content
+ # For the duration of the current test case, stub file download
+ # content with a randomized (but recognizable) string. Return the
+ # string, the test case can use it in assertions.
+ txt = 'the quick brown fox ' + rand(2**32).to_s
+ @controller.stubs(:file_enumerator).returns([txt])
+ txt
+ end
+
+ def collection_params(collection_name, file_name=nil)
+ uuid = api_fixture('collections')[collection_name.to_s]['uuid']
+ params = {uuid: uuid, id: uuid}
+ params[:file] = file_name if file_name
+ params
+ end
+
+ def assert_hash_includes(actual_hash, expected_hash, msg=nil)
+ expected_hash.each do |key, value|
+ assert_equal(value, actual_hash[key], msg)
+ end
+ end
+
+ def assert_no_session
+ assert_hash_includes(session, {arvados_api_token: nil},
+ "session includes unexpected API token")
+ end
+
+ def assert_session_for_auth(client_auth)
+ api_token =
+ api_fixture('api_client_authorizations')[client_auth.to_s]['api_token']
+ assert_hash_includes(session, {arvados_api_token: api_token},
+ "session token does not belong to #{client_auth}")
+ end
+
+ def show_collection(params, session={}, response=:success)
+ params = collection_params(params) if not params.is_a? Hash
+ session = session_for(session) if not session.is_a? Hash
+ get(:show, params, session)
+ assert_response response
+ end
+
+ test "viewing a collection" do
+ show_collection(:foo_file, :active)
+ assert_equal([['.', 'foo', 3]], assigns(:object).files)
+ end
+
+ test "viewing a collection fetches related projects" do
+ show_collection({id: api_fixture('collections')["foo_file"]['portable_data_hash']}, :active)
+ assert_includes(assigns(:same_pdh).map(&:owner_uuid),
+ api_fixture('groups')['aproject']['uuid'],
+ "controller did not find linked project")
+ end
+
+ test "viewing a collection fetches related permissions" do
+ show_collection(:bar_file, :active)
+ assert_includes(assigns(:permissions).map(&:uuid),
+ api_fixture('links')['bar_file_readable_by_active']['uuid'],
+ "controller did not find permission link")
+ end
+
+ test "viewing a collection fetches jobs that output it" do
+ show_collection(:bar_file, :active)
+ assert_includes(assigns(:output_of).map(&:uuid),
+ api_fixture('jobs')['foobar']['uuid'],
+ "controller did not find output job")
+ end
+
+ test "viewing a collection fetches jobs that logged it" do
+ show_collection(:baz_file, :active)
+ assert_includes(assigns(:log_of).map(&:uuid),
+ api_fixture('jobs')['foobar']['uuid'],
+ "controller did not find logger job")
+ end
+
+ test "viewing a collection fetches logs about it" do
+ show_collection(:foo_file, :active)
+ assert_includes(assigns(:logs).map(&:uuid),
+ api_fixture('logs')['log4']['uuid'],
+ "controller did not find related log")
+ end
+
+ test "sharing auths available to admin" do
+ show_collection("collection_owned_by_active", "admin_trustedclient")
+ assert_not_nil assigns(:search_sharing)
+ end
+
+ test "sharing auths available to owner" do
+ show_collection("collection_owned_by_active", "active_trustedclient")
+ assert_not_nil assigns(:search_sharing)
+ end
+
+ test "sharing auths available to reader" do
+ show_collection("foo_collection_in_aproject",
+ "project_viewer_trustedclient")
+ assert_not_nil assigns(:search_sharing)
+ end
+
+ test "viewing collection files with a reader token" do
+ params = collection_params(:foo_file)
+ params[:reader_token] = api_fixture("api_client_authorizations",
+ "active_all_collections", "api_token")
+ get(:show_file_links, params)
+ assert_response :success
+ assert_equal([['.', 'foo', 3]], assigns(:object).files)
+ assert_no_session
+ end
+
+ test "fetching collection file with reader token" do
+ expected = stub_file_content
+ params = collection_params(:foo_file, "foo")
+ params[:reader_token] = api_fixture("api_client_authorizations",
+ "active_all_collections", "api_token")
+ get(:show_file, params)
+ assert_response :success
+ assert_equal(expected, @response.body,
+ "failed to fetch a Collection file with a reader token")
+ assert_no_session
+ end
+
+ test "reader token Collection links end with trailing slash" do
+ # Testing the fix for #2937.
+ session = session_for(:active_trustedclient)
+ post(:share, collection_params(:foo_file), session)
+ assert(@controller.download_link.ends_with? '/',
+ "Collection share link does not end with slash for wget")
+ end
+
+ test "getting a file from Keep" do
+ params = collection_params(:foo_file, 'foo')
+ sess = session_for(:active)
+ expect_content = stub_file_content
+ get(:show_file, params, sess)
+ assert_response :success
+ assert_equal(expect_content, @response.body,
+ "failed to get a correct file from Keep")
+ end
+
+ test "can't get a file from Keep without permission" do
+ params = collection_params(:foo_file, 'foo')
+ sess = session_for(:spectator)
+ get(:show_file, params, sess)
+ assert_response 404
+ end
+
+ test "trying to get a nonexistent file from Keep returns a 404" do
+ params = collection_params(:foo_file, 'gone')
+ sess = session_for(:admin)
+ get(:show_file, params, sess)
+ assert_response 404
+ end
+
+ test "getting a file from Keep with a good reader token" do
+ params = collection_params(:foo_file, 'foo')
+ read_token = api_fixture('api_client_authorizations')['active']['api_token']
+ params[:reader_token] = read_token
+ expect_content = stub_file_content
+ get(:show_file, params)
+ assert_response :success
+ assert_equal(expect_content, @response.body,
+ "failed to get a correct file from Keep using a reader token")
+ assert_not_equal(read_token, session[:arvados_api_token],
+ "using a reader token set the session's API token")
+ end
+
+ test "trying to get from Keep with an unscoped reader token prompts login" do
+ params = collection_params(:foo_file, 'foo')
+ params[:reader_token] =
+ api_fixture('api_client_authorizations')['active_noscope']['api_token']
+ get(:show_file, params)
+ assert_response :redirect
+ end
+
+ test "can get a file with an unpermissioned auth but in-scope reader token" do
+ params = collection_params(:foo_file, 'foo')
+ sess = session_for(:expired)
+ read_token = api_fixture('api_client_authorizations')['active']['api_token']
+ params[:reader_token] = read_token
+ expect_content = stub_file_content
+ get(:show_file, params, sess)
+ assert_response :success
+ assert_equal(expect_content, @response.body,
+ "failed to get a correct file from Keep using a reader token")
+ assert_not_equal(read_token, session[:arvados_api_token],
+ "using a reader token set the session's API token")
+ end
+
+ test "inactive user can retrieve user agreement" do
+ ua_collection = api_fixture('collections')['user_agreement']
+ # Here we don't test whether the agreement can be retrieved from
+ # Keep. We only test that show_file decides to send file content,
+ # so we use the file content stub.
+ stub_file_content
+ get :show_file, {
+ uuid: ua_collection['uuid'],
+ file: ua_collection['manifest_text'].match(/ \d+:\d+:(\S+)/)[1]
+ }, session_for(:inactive)
+ assert_nil(assigns(:unsigned_user_agreements),
+ "Did not skip check_user_agreements filter " +
+ "when showing the user agreement.")
+ assert_response :success
+ end
+
+ test "requesting nonexistent Collection returns 404" do
+ show_collection({uuid: NONEXISTENT_COLLECTION, id: NONEXISTENT_COLLECTION},
+ :active, 404)
+ end
+
+ test "use a reasonable read buffer even if client requests a huge range" do
+ fakefiledata = mock
+ IO.expects(:popen).returns(fakefiledata)
+ fakefiledata.expects(:read).twice.with() do |length|
+ # Fail the test if read() is called with length>1MiB:
+ length < 2**20
+ ## Force the ActionController::Live thread to lose the race to
+ ## verify that @response.body.length actually waits for the
+ ## response (see below):
+ # sleep 3
+ end.returns("foo\n", nil)
+ fakefiledata.expects(:close)
+ foo_file = api_fixture('collections')['foo_file']
+ @request.headers['Range'] = 'bytes=0-4294967296/*'
+ get :show_file, {
+ uuid: foo_file['uuid'],
+ file: foo_file['manifest_text'].match(/ \d+:\d+:(\S+)/)[1]
+ }, session_for(:active)
+ # Wait for the whole response to arrive before deciding whether
+ # mocks' expectations were met. Otherwise, Mocha will fail the
+ # test depending on how slowly the ActionController::Live thread
+ # runs.
+ @response.body.length
+ end
+
+ test "show file in a subdirectory of a collection" do
+ params = collection_params(:collection_with_files_in_subdir, 'subdir2/subdir3/subdir4/file1_in_subdir4.txt')
+ expect_content = stub_file_content
+ get(:show_file, params, session_for(:user1_with_load))
+ assert_response :success
+ assert_equal(expect_content, @response.body, "failed to get a correct file from Keep")
+ end
+
+ test 'provenance graph' do
+ use_token 'admin'
+
+ obj = find_fixture Collection, "graph_test_collection3"
+
+ provenance = obj.provenance.stringify_keys
+
+ [obj[:portable_data_hash]].each do |k|
+ assert_not_nil provenance[k], "Expected key #{k} in provenance set"
+ end
+
+ prov_svg = ProvenanceHelper::create_provenance_graph(provenance, "provenance_svg",
+ {:request => RequestDuck,
+ :direction => :bottom_up,
+ :combine_jobs => :script_only})
+
+ stage1 = find_fixture Job, "graph_stage1"
+ stage3 = find_fixture Job, "graph_stage3"
+ previous_job_run = find_fixture Job, "previous_job_run"
+
+ obj_id = obj.portable_data_hash.gsub('+', '\\\+')
+ stage1_out = stage1.output.gsub('+', '\\\+')
+ stage1_id = "#{stage1.script}_#{Digest::MD5.hexdigest(stage1[:script_parameters].to_json)}"
+ stage3_id = "#{stage3.script}_#{Digest::MD5.hexdigest(stage3[:script_parameters].to_json)}"
+
+ assert /#{obj_id}->#{stage3_id}/.match(prov_svg)
+
+ assert /#{stage3_id}->#{stage1_out}/.match(prov_svg)
+
+ assert /#{stage1_out}->#{stage1_id}/.match(prov_svg)
+
+ end
+
+ test 'used_by graph' do
+ use_token 'admin'
+ obj = find_fixture Collection, "graph_test_collection1"
+
+ used_by = obj.used_by.stringify_keys
+
+ used_by_svg = ProvenanceHelper::create_provenance_graph(used_by, "used_by_svg",
+ {:request => RequestDuck,
+ :direction => :top_down,
+ :combine_jobs => :script_only,
+ :pdata_only => true})
+
+ stage2 = find_fixture Job, "graph_stage2"
+ stage3 = find_fixture Job, "graph_stage3"
+
+ stage2_id = "#{stage2.script}_#{Digest::MD5.hexdigest(stage2[:script_parameters].to_json)}"
+ stage3_id = "#{stage3.script}_#{Digest::MD5.hexdigest(stage3[:script_parameters].to_json)}"
+
+ obj_id = obj.portable_data_hash.gsub('+', '\\\+')
+ stage3_out = stage3.output.gsub('+', '\\\+')
+
+ assert /#{obj_id}->#{stage2_id}/.match(used_by_svg)
+
+ assert /#{obj_id}->#{stage3_id}/.match(used_by_svg)
+
+ assert /#{stage3_id}->#{stage3_out}/.match(used_by_svg)
+
+ assert /#{stage3_id}->#{stage3_out}/.match(used_by_svg)
+
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class ProjectsControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class HumansControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class JobTasksControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class JobsControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class KeepDisksControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class MetadataControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class LogsControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class NodesControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineInstancesControllerTest < ActionController::TestCase
+ include PipelineInstancesHelper
+
+ def create_instance_long_enough_to(instance_attrs={})
+ # create 'two_part' pipeline with the given instance attributes
+ pt_fixture = api_fixture('pipeline_templates')['two_part']
+ post :create, {
+ pipeline_instance: instance_attrs.merge({
+ pipeline_template_uuid: pt_fixture['uuid']
+ }),
+ format: :json
+ }, session_for(:active)
+ assert_response :success
+ pi_uuid = assigns(:object).uuid
+ assert_not_nil assigns(:object)
+
+ # yield
+ yield pi_uuid, pt_fixture
+
+ # delete the pipeline instance
+ use_token :active
+ PipelineInstance.where(uuid: pi_uuid).first.destroy
+ end
+
+ test "pipeline instance components populated after create" do
+ create_instance_long_enough_to do |new_instance_uuid, template_fixture|
+ assert_equal(template_fixture['components'].to_json,
+ assigns(:object).components.to_json)
+ end
+ end
+
+ test "can render pipeline instance with tagged collections" do
+ # Make sure to pass in a tagged collection to test that part of the rendering behavior.
+ get(:show,
+ {id: api_fixture("pipeline_instances")["pipeline_with_tagged_collection_input"]["uuid"]},
+ session_for(:active))
+ assert_response :success
+ end
+
+ test "update script_parameters one at a time using merge param" do
+ template_fixture = api_fixture('pipeline_templates')['two_part']
+ post :update, {
+ id: api_fixture("pipeline_instances")["pipeline_to_merge_params"]["uuid"],
+ pipeline_instance: {
+ components: {
+ "part-two" => {
+ script_parameters: {
+ integer_with_value: {
+ value: 9
+ },
+ plain_string: {
+ value: 'quux'
+ },
+ }
+ }
+ }
+ },
+ merge: true,
+ format: :json
+ }, session_for(:active)
+ assert_response :success
+ assert_not_nil assigns(:object)
+ orig_params = template_fixture['components']['part-two']['script_parameters']
+ new_params = assigns(:object).components[:'part-two'][:script_parameters]
+ orig_params.keys.each do |k|
+ unless %w(integer_with_value plain_string).index(k)
+ assert_equal orig_params[k].to_json, new_params[k.to_sym].to_json
+ end
+ end
+ end
+
+ test "component rendering copes with unexpected components format" do
+ get(:show,
+ {id: api_fixture("pipeline_instances")["components_is_jobspec"]["uuid"]},
+ session_for(:active))
+ assert_response :success
+ end
+
+ test "dates in JSON components are parsed" do
+ get(:show,
+ {id: api_fixture('pipeline_instances')['has_component_with_completed_jobs']['uuid']},
+ session_for(:active))
+ assert_response :success
+ assert_not_nil assigns(:object)
+ assert_not_nil assigns(:object).components[:foo][:job]
+ assert assigns(:object).components[:foo][:job][:started_at].is_a? Time
+ assert assigns(:object).components[:foo][:job][:finished_at].is_a? Time
+ end
+
+ # The next two tests ensure that a pipeline instance can be copied
+ # when the template has components that do not exist in the
+ # instance (ticket #4000).
+
+ test "copy pipeline instance with components=use_latest" do
+ post(:copy,
+ {
+ id: api_fixture('pipeline_instances')['pipeline_with_newer_template']['uuid'],
+ components: 'use_latest',
+ script: 'use_latest',
+ pipeline_instance: {
+ state: 'RunningOnServer'
+ }
+ },
+ session_for(:active))
+ assert_response 302
+ assert_not_nil assigns(:object)
+
+ # Component 'foo' has script parameters only in the pipeline instance.
+ # Component 'bar' is present only in the pipeline_template.
+ # Test that the copied pipeline instance includes parameters for
+ # component 'foo' from the source instance, and parameters for
+ # component 'bar' from the source template.
+ #
+ assert_not_nil assigns(:object).components[:foo]
+ foo = assigns(:object).components[:foo]
+ assert_not_nil foo[:script_parameters]
+ assert_not_nil foo[:script_parameters][:input]
+ assert_equal 'foo instance input', foo[:script_parameters][:input][:title]
+
+ assert_not_nil assigns(:object).components[:bar]
+ bar = assigns(:object).components[:bar]
+ assert_not_nil bar[:script_parameters]
+ assert_not_nil bar[:script_parameters][:input]
+ assert_equal 'bar template input', bar[:script_parameters][:input][:title]
+ end
+
+ test "copy pipeline instance on newer template works with script=use_same" do
+ post(:copy,
+ {
+ id: api_fixture('pipeline_instances')['pipeline_with_newer_template']['uuid'],
+ components: 'use_latest',
+ script: 'use_same',
+ pipeline_instance: {
+ state: 'RunningOnServer'
+ }
+ },
+ session_for(:active))
+ assert_response 302
+ assert_not_nil assigns(:object)
+
+ # Test that relevant component parameters were copied from both
+ # the source instance and source template, respectively (see
+ # previous test)
+ #
+ assert_not_nil assigns(:object).components[:foo]
+ foo = assigns(:object).components[:foo]
+ assert_not_nil foo[:script_parameters]
+ assert_not_nil foo[:script_parameters][:input]
+ assert_equal 'foo instance input', foo[:script_parameters][:input][:title]
+
+ assert_not_nil assigns(:object).components[:bar]
+ bar = assigns(:object).components[:bar]
+ assert_not_nil bar[:script_parameters]
+ assert_not_nil bar[:script_parameters][:input]
+ assert_equal 'bar template input', bar[:script_parameters][:input][:title]
+ end
+
+ test "generate graph" do
+
+ use_token 'admin'
+
+ pipeline_for_graph = {
+ state: 'Complete',
+ uuid: 'zzzzz-d1hrv-9fm8l10i9z2kqc9',
+ components: {
+ stage1: {
+ repository: 'foo',
+ script: 'hash',
+ script_version: 'master',
+ job: {uuid: 'zzzzz-8i9sb-graphstage10000'},
+ output_uuid: 'zzzzz-4zz18-bv31uwvy3neko22'
+ },
+ stage2: {
+ repository: 'foo',
+ script: 'hash2',
+ script_version: 'master',
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45'
+ },
+ job: {uuid: 'zzzzz-8i9sb-graphstage20000'},
+ output_uuid: 'zzzzz-4zz18-uukreo9rbgwsujx'
+ }
+ }
+ }
+
+ @controller.params['tab_pane'] = "Graph"
+ provenance, pips = @controller.graph([pipeline_for_graph])
+
+ graph_test_collection1 = find_fixture Collection, "graph_test_collection1"
+ stage1 = find_fixture Job, "graph_stage1"
+ stage2 = find_fixture Job, "graph_stage2"
+
+ ['component_zzzzz-d1hrv-9fm8l10i9z2kqc9_stage1',
+ 'component_zzzzz-d1hrv-9fm8l10i9z2kqc9_stage2',
+ stage1.uuid,
+ stage2.uuid,
+ stage1.output,
+ stage2.output,
+ pipeline_for_graph[:components][:stage1][:output_uuid],
+ pipeline_for_graph[:components][:stage2][:output_uuid]
+ ].each do |k|
+
+ assert_not_nil provenance[k], "Expected key #{k} in provenance set"
+ assert_equal 1, pips[k], "Expected key #{k} in pips set" if !k.start_with? "component_"
+ end
+
+ prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => RequestDuck,
+ :all_script_parameters => true,
+ :combine_jobs => :script_and_version,
+ :pips => pips,
+ :only_components => true }
+
+ stage1_id = "#{stage1[:script]}_#{stage1[:script_version]}_#{Digest::MD5.hexdigest(stage1[:script_parameters].to_json)}"
+ stage2_id = "#{stage2[:script]}_#{stage2[:script_version]}_#{Digest::MD5.hexdigest(stage2[:script_parameters].to_json)}"
+
+ stage1_out = stage1[:output].gsub('+','\\\+')
+
+ assert_match /#{stage1_id}->#{stage1_out}/, prov_svg
+
+ assert_match /#{stage1_out}->#{stage2_id}/, prov_svg
+
+ end
+
+ test "generate graph compare" do
+
+ use_token 'admin'
+
+ pipeline_for_graph1 = {
+ state: 'Complete',
+ uuid: 'zzzzz-d1hrv-9fm8l10i9z2kqc9',
+ components: {
+ stage1: {
+ repository: 'foo',
+ script: 'hash',
+ script_version: 'master',
+ job: {uuid: 'zzzzz-8i9sb-graphstage10000'},
+ output_uuid: 'zzzzz-4zz18-bv31uwvy3neko22'
+ },
+ stage2: {
+ repository: 'foo',
+ script: 'hash2',
+ script_version: 'master',
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45'
+ },
+ job: {uuid: 'zzzzz-8i9sb-graphstage20000'},
+ output_uuid: 'zzzzz-4zz18-uukreo9rbgwsujx'
+ }
+ }
+ }
+
+ pipeline_for_graph2 = {
+ state: 'Complete',
+ uuid: 'zzzzz-d1hrv-9fm8l10i9z2kqc0',
+ components: {
+ stage1: {
+ repository: 'foo',
+ script: 'hash',
+ script_version: 'master',
+ job: {uuid: 'zzzzz-8i9sb-graphstage10000'},
+ output_uuid: 'zzzzz-4zz18-bv31uwvy3neko22'
+ },
+ stage2: {
+ repository: 'foo',
+ script: 'hash2',
+ script_version: 'master',
+ script_parameters: {
+ },
+ job: {uuid: 'zzzzz-8i9sb-graphstage30000'},
+ output_uuid: 'zzzzz-4zz18-uukreo9rbgwsujj'
+ }
+ }
+ }
+
+ @controller.params['tab_pane'] = "Graph"
+ provenance, pips = @controller.graph([pipeline_for_graph1, pipeline_for_graph2])
+
+ collection1 = find_fixture Collection, "graph_test_collection1"
+
+ stage1 = find_fixture Job, "graph_stage1"
+ stage2 = find_fixture Job, "graph_stage2"
+ stage3 = find_fixture Job, "graph_stage3"
+
+ [['component_zzzzz-d1hrv-9fm8l10i9z2kqc9_stage1', nil],
+ ['component_zzzzz-d1hrv-9fm8l10i9z2kqc9_stage2', nil],
+ ['component_zzzzz-d1hrv-9fm8l10i9z2kqc0_stage1', nil],
+ ['component_zzzzz-d1hrv-9fm8l10i9z2kqc0_stage2', nil],
+ [stage1.uuid, 3],
+ [stage2.uuid, 1],
+ [stage3.uuid, 2],
+ [stage1.output, 3],
+ [stage2.output, 1],
+ [stage3.output, 2],
+ [pipeline_for_graph1[:components][:stage1][:output_uuid], 3],
+ [pipeline_for_graph1[:components][:stage2][:output_uuid], 1],
+ [pipeline_for_graph2[:components][:stage2][:output_uuid], 2]
+ ].each do |k|
+ assert_not_nil provenance[k[0]], "Expected key #{k[0]} in provenance set"
+ assert_equal k[1], pips[k[0]], "Expected key #{k} in pips" if !k[0].start_with? "component_"
+ end
+
+ prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => RequestDuck,
+ :all_script_parameters => true,
+ :combine_jobs => :script_and_version,
+ :pips => pips,
+ :only_components => true }
+
+ collection1_id = collection1.portable_data_hash.gsub('+','\\\+')
+
+ stage2_id = "#{stage2[:script]}_#{stage2[:script_version]}_#{Digest::MD5.hexdigest(stage2[:script_parameters].to_json)}"
+ stage3_id = "#{stage3[:script]}_#{stage3[:script_version]}_#{Digest::MD5.hexdigest(stage3[:script_parameters].to_json)}"
+
+ stage2_out = stage2[:output].gsub('+','\\\+')
+ stage3_out = stage3[:output].gsub('+','\\\+')
+
+ assert_match /#{collection1_id}->#{stage2_id}/, prov_svg
+ assert_match /#{collection1_id}->#{stage3_id}/, prov_svg
+
+ assert_match /#{stage2_id}->#{stage2_out}/, prov_svg
+ assert_match /#{stage3_id}->#{stage3_out}/, prov_svg
+
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineTemplatesControllerTest < ActionController::TestCase
+ test "component rendering copes with unexpeceted components format" do
+ get(:show,
+ {id: api_fixture("pipeline_templates")["components_is_jobspec"]["uuid"]},
+ session_for(:active))
+ assert_response :success
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class ProjectsControllerTest < ActionController::TestCase
+ test "invited user is asked to sign user agreements on front page" do
+ get :index, {}, session_for(:inactive)
+ assert_response :redirect
+ assert_match(/^#{Regexp.escape(user_agreements_url)}\b/,
+ @response.redirect_url,
+ "Inactive user was not redirected to user_agreements page")
+ end
+
+ test "uninvited user is asked to wait for activation" do
+ get :index, {}, session_for(:inactive_uninvited)
+ assert_response :redirect
+ assert_match(/^#{Regexp.escape(inactive_users_url)}\b/,
+ @response.redirect_url,
+ "Uninvited user was not redirected to inactive user page")
+ end
+
+ [[:active, true],
+ [:project_viewer, false]].each do |which_user, should_show|
+ test "create subproject button #{'not ' unless should_show} shown to #{which_user}" do
+ readonly_project_uuid = api_fixture('groups')['aproject']['uuid']
+ get :show, {
+ id: readonly_project_uuid
+ }, session_for(which_user)
+ buttons = css_select('[data-method=post]').select do |el|
+ el.attributes['href'].match /project.*owner_uuid.*#{readonly_project_uuid}/
+ end
+ if should_show
+ assert_not_empty(buttons, "did not offer to create a subproject")
+ else
+ assert_empty(buttons.collect(&:to_s),
+ "offered to create a subproject in a non-writable project")
+ end
+ end
+ end
+
+ test "sharing a project with a user and group" do
+ uuid_list = [api_fixture("groups")["future_project_viewing_group"]["uuid"],
+ api_fixture("users")["future_project_user"]["uuid"]]
+ post(:share_with, {
+ id: api_fixture("groups")["asubproject"]["uuid"],
+ uuids: uuid_list,
+ format: "json"},
+ session_for(:active))
+ assert_response :success
+ assert_equal(uuid_list, json_response["success"])
+ end
+
+ test "user with project read permission can't add permissions" do
+ share_uuid = api_fixture("users")["spectator"]["uuid"]
+ post(:share_with, {
+ id: api_fixture("groups")["aproject"]["uuid"],
+ uuids: [share_uuid],
+ format: "json"},
+ session_for(:project_viewer))
+ assert_response 422
+ assert(json_response["errors"].andand.
+ any? { |msg| msg.start_with?("#{share_uuid}: ") },
+ "JSON response missing properly formatted sharing error")
+ end
+
+ def user_can_manage(user_sym, group_key)
+ get(:show, {id: api_fixture("groups")[group_key]["uuid"]},
+ session_for(user_sym))
+ is_manager = assigns(:user_is_manager)
+ assert_not_nil(is_manager, "user_is_manager flag not set")
+ if not is_manager
+ assert_empty(assigns(:share_links),
+ "non-manager has share links set")
+ end
+ is_manager
+ end
+
+ test "admin can_manage aproject" do
+ assert user_can_manage(:admin, "aproject")
+ end
+
+ test "owner can_manage aproject" do
+ assert user_can_manage(:active, "aproject")
+ end
+
+ test "owner can_manage asubproject" do
+ assert user_can_manage(:active, "asubproject")
+ end
+
+ test "viewer can't manage aproject" do
+ refute user_can_manage(:project_viewer, "aproject")
+ end
+
+ test "viewer can't manage asubproject" do
+ refute user_can_manage(:project_viewer, "asubproject")
+ end
+
+ test "subproject_admin can_manage asubproject" do
+ assert user_can_manage(:subproject_admin, "asubproject")
+ end
+
+ test "detect ownership loop in project breadcrumbs" do
+ # This test has an arbitrary time limit -- otherwise we'd just sit
+ # here forever instead of reporting that the loop was not
+ # detected. The test passes quickly, but fails slowly.
+ Timeout::timeout 10 do
+ get(:show,
+ { id: api_fixture("groups")["project_owns_itself"]["uuid"] },
+ session_for(:admin))
+ end
+ assert_response :success
+ end
+
+ test "project admin can remove items from the project" do
+ coll_key = "collection_to_remove_from_subproject"
+ coll_uuid = api_fixture("collections")[coll_key]["uuid"]
+ delete(:remove_item,
+ { id: api_fixture("groups")["asubproject"]["uuid"],
+ item_uuid: coll_uuid,
+ format: "js" },
+ session_for(:subproject_admin))
+ assert_response :success
+ assert_match(/\b#{coll_uuid}\b/, @response.body,
+ "removed object not named in response")
+ end
+
+ test 'projects#show tab infinite scroll partial obeys limit' do
+ get_contents_rows(limit: 1, filters: [['uuid','is_a',['arvados#job']]])
+ assert_response :success
+ assert_equal(1, json_response['content'].scan('<tr').count,
+ "Did not get exactly one row")
+ end
+
+ ['', ' asc', ' desc'].each do |direction|
+ test "projects#show tab partial orders correctly by #{direction}" do
+ _test_tab_content_order direction
+ end
+ end
+
+ def _test_tab_content_order direction
+ get_contents_rows(limit: 100,
+ order: "created_at#{direction}",
+ filters: [['uuid','is_a',['arvados#job',
+ 'arvados#pipelineInstance']]])
+ assert_response :success
+ not_grouped_by_kind = nil
+ last_timestamp = nil
+ last_kind = nil
+ found_kind = {}
+ json_response['content'].scan /<tr[^>]+>/ do |tr_tag|
+ found_timestamps = 0
+ tr_tag.scan(/\ data-object-created-at=\"(.*?)\"/).each do |t,|
+ if last_timestamp
+ correct_operator = / desc$/ =~ direction ? :>= : :<=
+ assert_operator(last_timestamp, correct_operator, t,
+ "Rows are not sorted by created_at#{direction}")
+ end
+ last_timestamp = t
+ found_timestamps += 1
+ end
+ assert_equal(1, found_timestamps,
+ "Content row did not have exactly one timestamp")
+
+ # Confirm that the test for timestamp ordering couldn't have
+ # passed merely because the test fixtures have convenient
+ # timestamps (e.g., there is only one pipeline and one job in
+ # the project being tested, or there are no pipelines at all in
+ # the project being tested):
+ tr_tag.scan /\ data-kind=\"(.*?)\"/ do |kind|
+ if last_kind and last_kind != kind and found_kind[kind]
+ # We saw this kind before, then a different kind, then
+ # this kind again. That means objects are not grouped by
+ # kind.
+ not_grouped_by_kind = true
+ end
+ found_kind[kind] ||= 0
+ found_kind[kind] += 1
+ last_kind = kind
+ end
+ end
+ assert_equal(true, not_grouped_by_kind,
+ "Could not confirm that results are not grouped by kind")
+ end
+
+ def get_contents_rows params
+ params = {
+ id: api_fixture('users')['active']['uuid'],
+ partial: :contents_rows,
+ format: :json,
+ }.merge(params)
+ encoded_params = Hash[params.map { |k,v|
+ [k, (v.is_a?(Array) || v.is_a?(Hash)) ? v.to_json : v]
+ }]
+ get :show, encoded_params, session_for(:active)
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class RepositoriesControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class SearchControllerTest < ActionController::TestCase
+ # These tests don't do state-changing API calls. Save some time by
+ # skipping the database reset.
+ reset_api_fixtures :after_each_test, false
+ reset_api_fixtures :after_suite, true
+
+ include Rails.application.routes.url_helpers
+
+ test 'Get search dialog' do
+ xhr :get, :choose, {
+ format: :js,
+ title: 'Search',
+ action_name: 'Show',
+ action_href: url_for(host: 'localhost', controller: :actions, action: :show),
+ action_data: {}.to_json,
+ }, session_for(:active)
+ assert_response :success
+ end
+
+ test 'Get search results for all projects' do
+ xhr :get, :choose, {
+ format: :json,
+ partial: true,
+ }, session_for(:active)
+ assert_response :success
+ assert_not_empty(json_response['content'],
+ 'search results for all projects should not be empty')
+ end
+
+ test 'Get search results for empty project' do
+ xhr :get, :choose, {
+ format: :json,
+ partial: true,
+ project_uuid: api_fixture('groups')['empty_project']['uuid'],
+ }, session_for(:active)
+ assert_response :success
+ assert_empty(json_response['content'],
+ 'search results for empty project should be empty')
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class SessionsControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class SpecimensControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class TraitsControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class UserAgreementsControllerTest < ActionController::TestCase
+ test 'User agreements page shows form if some user agreements are not signed' do
+ get :index, {}, session_for(:inactive)
+ assert_response 200
+ end
+
+ test 'User agreements page redirects if all user agreements signed' do
+ get :index, {return_to: root_path}, session_for(:active)
+ assert_response :redirect
+ assert_equal(root_url,
+ @response.redirect_url,
+ "Active user was not redirected to :return_to param")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class UsersControllerTest < ActionController::TestCase
+ test "valid token works in controller test" do
+ get :index, {}, session_for(:active)
+ assert_response :success
+ end
+
+ test "ignore previously valid token (for deleted user), don't crash" do
+ get :activity, {}, session_for(:valid_token_deleted_user)
+ assert_response :redirect
+ assert_match /^#{Rails.configuration.arvados_login_base}/, @response.redirect_url
+ assert_nil assigns(:my_jobs)
+ assert_nil assigns(:my_ssh_keys)
+ end
+
+ test "expired token redirects to api server login" do
+ get :show, {
+ id: api_fixture('users')['active']['uuid']
+ }, session_for(:expired_trustedclient)
+ assert_response :redirect
+ assert_match /^#{Rails.configuration.arvados_login_base}/, @response.redirect_url
+ assert_nil assigns(:my_jobs)
+ assert_nil assigns(:my_ssh_keys)
+ end
+
+ test "show welcome page if no token provided" do
+ get :index, {}
+ assert_response :redirect
+ assert_match /\/users\/welcome/, @response.redirect_url
+ end
+
+ test "show repositories with read, write, or manage permission" do
+ get :manage_account, {}, session_for(:active)
+ assert_response :success
+ repos = assigns(:my_repositories)
+ assert repos
+ assert_not_empty repos, "my_repositories should not be empty"
+ editables = repos.collect { |r| !!assigns(:repo_writable)[r.uuid] }
+ assert_includes editables, true, "should have a writable repository"
+ assert_includes editables, false, "should have a readonly repository"
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class VirtualMachinesControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'diagnostics_test_helper'
+
+class PipelineTest < DiagnosticsTest
+ pipelines_to_test = Rails.configuration.pipelines_to_test.andand.keys
+
+ setup do
+ need_selenium 'to make websockets work'
+ end
+
+ pipelines_to_test.andand.each do |pipeline_to_test|
+ test "run pipeline: #{pipeline_to_test}" do
+ visit_page_with_token 'active'
+ pipeline_config = Rails.configuration.pipelines_to_test[pipeline_to_test]
+
+ # Search for tutorial template
+ find '.navbar-fixed-top'
+ within('.navbar-fixed-top') do
+ page.find_field('search').set pipeline_config['template_uuid']
+ page.find('.glyphicon-search').click
+ end
+
+ # Run the pipeline
+ assert_triggers_dom_event 'shown.bs.modal' do
+ find('a,button', text: 'Run').click
+ end
+
+ # Choose project
+ within('.modal-dialog') do
+ find('.selectable', text: 'Home').click
+ find('button', text: 'Choose').click
+ end
+
+ page.assert_selector('a.disabled,button.disabled', text: 'Run') if pipeline_config['input_paths'].any?
+
+ # Choose input for the pipeline
+ pipeline_config['input_paths'].each do |look_for|
+ select_input look_for
+ end
+ wait_for_ajax
+
+ # All needed input are filled in. Run this pipeline now
+ find('a,button', text: 'Run').click
+
+ # Pipeline is running. We have a "Stop" button instead now.
+ page.assert_selector 'a,button', text: 'Pause'
+
+ # Wait for pipeline run to complete
+ wait_until_page_has 'Complete', pipeline_config['max_wait_seconds']
+ end
+ end
+
+ def select_input look_for
+ inputs_needed = page.all('.btn', text: 'Choose')
+ return if (!inputs_needed || !inputs_needed.any?)
+
+ look_for_uuid = nil
+ look_for_file = nil
+ if look_for.andand.index('/').andand.>0
+ partitions = look_for.partition('/')
+ look_for_uuid = partitions[0]
+ look_for_file = partitions[2]
+ else
+ look_for_uuid = look_for
+ look_for_file = nil
+ end
+
+ assert_triggers_dom_event 'shown.bs.modal' do
+ inputs_needed[0].click
+ end
+
+ within('.modal-dialog') do
+ if look_for_uuid
+ fill_in('Search', with: look_for_uuid, exact: true)
+ wait_for_ajax
+ end
+
+ page.all('.selectable').first.click
+ wait_for_ajax
+ # ajax reload is wiping out input selection after search results; so, select again.
+ page.all('.selectable').first.click
+ wait_for_ajax
+
+ if look_for_file
+ wait_for_ajax
+ within('.collection_files_name', text: look_for_file) do
+ find('.fa-file').click
+ end
+ end
+
+ find('button', text: 'OK').click
+ wait_for_ajax
+ end
+ end
+end
--- /dev/null
+require 'integration_helper'
+require 'yaml'
+
+# Diagnostics tests are executed when "RAILS_ENV=diagnostics" is used.
+# When "RAILS_ENV=test" is used, tests in the "diagnostics" directory
+# will not be executed.
+
+# Command to run diagnostics tests:
+# RAILS_ENV=diagnostics bundle exec rake TEST=test/diagnostics/**/*.rb
+
+class DiagnosticsTest < ActionDispatch::IntegrationTest
+
+ # Prepends workbench URL to the path provided and visits that page
+ # Expects path parameters such as "/collections/<uuid>"
+ def visit_page_with_token token_name, path='/'
+ workbench_url = Rails.configuration.arvados_workbench_url
+ if workbench_url.end_with? '/'
+ workbench_url = workbench_url[0, workbench_url.size-1]
+ end
+ tokens = Rails.configuration.user_tokens
+ visit page_with_token(tokens[token_name], (workbench_url + path))
+ end
+
+ # Looks for the text_to_look_for for up to the max_time provided
+ def wait_until_page_has text_to_look_for, max_time=30
+ max_time = 30 if (!max_time || (max_time.to_s != max_time.to_i.to_s))
+ Timeout.timeout(max_time) do
+ loop until page.has_text?(text_to_look_for)
+ end
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineInstancesHelperTest < ActionView::TestCase
+ test "one" do
+ r = [{started_at: 1, finished_at: 3}]
+ assert_equal 2, determine_wallclock_runtime(r)
+
+ r = [{started_at: 1, finished_at: 5}]
+ assert_equal 4, determine_wallclock_runtime(r)
+
+ r = [{started_at: 1, finished_at: 2}, {started_at: 3, finished_at: 5}]
+ assert_equal 3, determine_wallclock_runtime(r)
+
+ r = [{started_at: 3, finished_at: 5}, {started_at: 1, finished_at: 2}]
+ assert_equal 3, determine_wallclock_runtime(r)
+
+ r = [{started_at: 3, finished_at: 5}, {started_at: 1, finished_at: 2},
+ {started_at: 2, finished_at: 4}]
+ assert_equal 4, determine_wallclock_runtime(r)
+
+ r = [{started_at: 1, finished_at: 5}, {started_at: 2, finished_at: 3}]
+ assert_equal 4, determine_wallclock_runtime(r)
+
+ r = [{started_at: 3, finished_at: 5}, {started_at: 1, finished_at: 4}]
+ assert_equal 4, determine_wallclock_runtime(r)
+
+ r = [{started_at: 1, finished_at: 4}, {started_at: 3, finished_at: 5}]
+ assert_equal 4, determine_wallclock_runtime(r)
+
+ r = [{started_at: 1, finished_at: 4}, {started_at: 3, finished_at: 5},
+ {started_at: 5, finished_at: 8}]
+ assert_equal 7, determine_wallclock_runtime(r)
+
+ r = [{started_at: 1, finished_at: 4}, {started_at: 3, finished_at: 5},
+ {started_at: 6, finished_at: 8}]
+ assert_equal 6, determine_wallclock_runtime(r)
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class SearchHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'integration_helper'
+
+class ApplicationLayoutTest < ActionDispatch::IntegrationTest
+ # These tests don't do state-changing API calls. Save some time by
+ # skipping the database reset.
+ reset_api_fixtures :after_each_test, false
+ reset_api_fixtures :after_suite, true
+
+ setup do
+ need_javascript
+ end
+
+ def verify_homepage user, invited, has_profile
+ profile_config = Rails.configuration.user_profile_form_fields
+
+ if !user
+ assert page.has_text?('Please log in'), 'Not found text - Please log in'
+ assert page.has_text?('The "Log in" button below will show you a Google sign-in page'), 'Not found text - google sign in page'
+ assert page.has_no_text?('My projects'), 'Found text - My projects'
+ assert page.has_link?("Log in to #{Rails.configuration.site_name}"), 'Not found text - log in to'
+ elsif user['is_active']
+ if profile_config && !has_profile
+ assert page.has_text?('Save profile'), 'No text - Save profile'
+ else
+ assert page.has_link?("Projects"), 'Not found link - Projects'
+ page.find("#projects-menu").click
+ assert page.has_text?('Projects shared with me'), 'Not found text - Project shared with me'
+ end
+ elsif invited
+ assert page.has_text?('Please check the box below to indicate that you have read and accepted the user agreement'), 'Not found text - Please check the box below . . .'
+ else
+ assert page.has_text?('Your account is inactive'), 'Not found text - Your account is inactive'
+ end
+
+ within('.navbar-fixed-top') do
+ if !user
+ assert page.has_link?('Log in'), 'Not found link - Log in'
+ else
+ # my account menu
+ assert page.has_link?("#{user['email']}"), 'Not found link - email'
+ find('a', text: "#{user['email']}").click
+ within('.dropdown-menu') do
+ if user['is_active']
+ assert page.has_no_link?('Not active'), 'Found link - Not active'
+ assert page.has_no_link?('Sign agreements'), 'Found link - Sign agreements'
+
+ assert page.has_link?('Manage account'), 'No link - Manage account'
+
+ if profile_config
+ assert page.has_link?('Manage profile'), 'No link - Manage profile'
+ else
+ assert page.has_no_link?('Manage profile'), 'Found link - Manage profile'
+ end
+ else
+ assert page.has_no_link?('Manage account'), 'Found link - Manage account'
+ assert page.has_no_link?('Manage profile'), 'Found link - Manage profile'
+ end
+ assert page.has_link?('Log out'), 'No link - Log out'
+ end
+ end
+ end
+ end
+
+ # test the help menu
+ def check_help_menu
+ within('.navbar-fixed-top') do
+ page.find("#arv-help").click
+ within('.dropdown-menu') do
+ assert page.has_link?('Tutorials and User guide'), 'No link - Tutorials and User guide'
+ assert page.has_link?('API Reference'), 'No link - API Reference'
+ assert page.has_link?('SDK Reference'), 'No link - SDK Reference'
+ assert page.has_link?('Show version / debugging info ...'), 'No link - Show version / debugging info'
+ assert page.has_link?('Report a problem ...'), 'No link - Report a problem'
+ # Version info and Report a problem are tested in "report_issue_test.rb"
+ end
+ end
+ end
+
+ def verify_system_menu user
+ if user && user['is_admin']
+ assert page.has_link?('system-menu'), 'No link - system menu'
+ within('.navbar-fixed-top') do
+ page.find("#system-menu").click
+ within('.dropdown-menu') do
+ assert page.has_text?('Groups'), 'No text - Groups'
+ assert page.has_link?('Repositories'), 'No link - Repositories'
+ assert page.has_link?('Virtual machines'), 'No link - Virtual machines'
+ assert page.has_link?('SSH keys'), 'No link - SSH keys'
+ assert page.has_link?('API tokens'), 'No link - API tokens'
+ find('a', text: 'Users').click
+ end
+ end
+ assert page.has_text? 'Add a new user'
+ else
+ assert page.has_no_link?('system-menu'), 'Found link - system menu'
+ end
+ end
+
+ [
+ [nil, nil, false, false],
+ ['inactive', api_fixture('users')['inactive'], true, false],
+ ['inactive_uninvited', api_fixture('users')['inactive_uninvited'], false, false],
+ ['active', api_fixture('users')['active'], true, true],
+ ['admin', api_fixture('users')['admin'], true, true],
+ ['active_no_prefs', api_fixture('users')['active_no_prefs'], true, false],
+ ['active_no_prefs_profile', api_fixture('users')['active_no_prefs_profile'], true, false],
+ ].each do |token, user, invited, has_profile|
+
+ test "visit home page for user #{token}" do
+ if !token
+ visit ('/')
+ else
+ visit page_with_token(token)
+ end
+
+ verify_homepage user, invited, has_profile
+ end
+
+ test "check help for user #{token}" do
+ if !token
+ visit ('/')
+ else
+ visit page_with_token(token)
+ end
+
+ check_help_menu
+ end
+
+ test "test system menu for user #{token}" do
+ if !token
+ visit ('/')
+ else
+ visit page_with_token(token)
+ end
+
+ verify_system_menu user
+ end
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class CollectionUploadTest < ActionDispatch::IntegrationTest
+ setup do
+ testfiles.each do |filename, content|
+ open(testfile_path(filename), 'w') do |io|
+ io.write content
+ end
+ end
+ end
+
+ teardown do
+ testfiles.each do |filename, _|
+ File.unlink(testfile_path filename)
+ end
+ end
+
+ test "Create new collection using upload button" do
+ need_javascript
+ visit page_with_token 'active', aproject_path
+ find('.btn', text: 'Add data').click
+ click_link 'Upload files from my computer'
+ # Should be looking at a new empty collection.
+ assert_text 'New collection'
+ assert_text 'd41d8cd98f00b204e9800998ecf8427e+0'
+ # The "Upload" tab should be active and loaded.
+ assert_selector 'div#Upload.active div.panel'
+ end
+
+ test "No Upload tab on non-writable collection" do
+ need_javascript
+ visit(page_with_token 'active',
+ '/collections/'+api_fixture('collections')['user_agreement']['uuid'])
+ assert_no_selector '.nav-tabs Upload'
+ end
+
+ test "Upload two empty files with the same name" do
+ need_selenium "to make file uploads work"
+ visit page_with_token 'active', sandbox_path
+ find('.nav-tabs a', text: 'Upload').click
+ attach_file 'file_selector', testfile_path('empty.txt')
+ assert_selector 'div', text: 'empty.txt'
+ attach_file 'file_selector', testfile_path('empty.txt')
+ assert_selector 'div.row div span[title]', text: 'empty.txt', count: 2
+ click_button 'Start'
+ assert_text :visible, 'Done!'
+ visit sandbox_path+'.json'
+ assert_match /_text":"\. d41d8\S+ 0:0:empty.txt\\n\. d41d8\S+ 0:0:empty\\\\040\(1\).txt\\n"/, body
+ end
+
+ test "Upload non-empty files, report errors" do
+ need_selenium "to make file uploads work"
+ visit page_with_token 'active', sandbox_path
+ find('.nav-tabs a', text: 'Upload').click
+ attach_file 'file_selector', testfile_path('a')
+ attach_file 'file_selector', testfile_path('foo.txt')
+ assert_selector 'button:not([disabled])', text: 'Start'
+ click_button 'Start'
+ if "test environment does not have a keepproxy yet, see #4534" != "fixed"
+ using_wait_time 20 do
+ assert_text :visible, 'error'
+ end
+ else
+ assert_text :visible, 'Done!'
+ visit sandbox_path+'.json'
+ assert_match /_text":"\. 0cc1\S+ 0:1:a\\n\. acbd\S+ 0:3:foo.txt\\n"/, body
+ end
+ end
+
+ protected
+
+ def aproject_path
+ '/projects/' + api_fixture('groups')['aproject']['uuid']
+ end
+
+ def sandbox_uuid
+ api_fixture('collections')['upload_sandbox']['uuid']
+ end
+
+ def sandbox_path
+ '/collections/' + sandbox_uuid
+ end
+
+ def testfiles
+ {
+ 'empty.txt' => '',
+ 'a' => 'a',
+ 'foo.txt' => 'foo'
+ }
+ end
+
+ def testfile_path filename
+ # Must be an absolute path. https://github.com/jnicklas/capybara/issues/621
+ File.join Dir.getwd, 'tmp', filename
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class CollectionsTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ # check_checkboxes_state asserts that the page holds at least one
+ # checkbox matching 'selector', and that all matching checkboxes
+ # are in state 'checkbox_status' (i.e. checked if true, unchecked otherwise)
+ def assert_checkboxes_state(selector, checkbox_status, msg=nil)
+ assert page.has_selector?(selector)
+ page.all(selector).each do |checkbox|
+ assert(checkbox.checked? == checkbox_status, msg)
+ end
+ end
+
+ test "Can copy a collection to a project" do
+ collection_uuid = api_fixture('collections')['foo_file']['uuid']
+ collection_name = api_fixture('collections')['foo_file']['name']
+ project_uuid = api_fixture('groups')['aproject']['uuid']
+ project_name = api_fixture('groups')['aproject']['name']
+ visit page_with_token('active', "/collections/#{collection_uuid}")
+ click_link 'Copy to project...'
+ find('.selectable', text: project_name).click
+ find('.modal-footer a,button', text: 'Copy').click
+ wait_for_ajax
+ # It should navigate to the project after copying...
+ assert(page.has_text?(project_name))
+ assert(page.has_text?("Copy of #{collection_name}"))
+ end
+
+ test "Collection page renders name" do
+ Capybara.current_driver = :rack_test
+ uuid = api_fixture('collections')['foo_file']['uuid']
+ coll_name = api_fixture('collections')['foo_file']['name']
+ visit page_with_token('active', "/collections/#{uuid}")
+ assert(page.has_text?(coll_name), "Collection page did not include name")
+ # Now check that the page is otherwise normal, and the collection name
+ # isn't only showing up in an error message.
+ assert(page.has_link?('foo'), "Collection page did not include file link")
+ end
+
+ def check_sharing(want_state, link_regexp)
+ # We specifically want to click buttons. See #4291.
+ if want_state == :off
+ click_button "Unshare"
+ text_assertion = :assert_no_text
+ link_assertion = :assert_empty
+ else
+ click_button "Create sharing link"
+ text_assertion = :assert_text
+ link_assertion = :refute_empty
+ end
+ using_wait_time(Capybara.default_wait_time * 3) do
+ send(text_assertion, "Shared at:")
+ end
+ send(link_assertion, all("a").select { |a| a[:href] =~ link_regexp })
+ end
+
+ test "creating and uncreating a sharing link" do
+ coll_uuid = api_fixture("collections", "collection_owned_by_active", "uuid")
+ download_link_re =
+ Regexp.new(Regexp.escape("/collections/download/#{coll_uuid}/"))
+ visit page_with_token("active_trustedclient", "/collections/#{coll_uuid}")
+ within "#sharing-button" do
+ check_sharing(:on, download_link_re)
+ check_sharing(:off, download_link_re)
+ end
+ end
+
+ test "can download an entire collection with a reader token" do
+ Capybara.current_driver = :rack_test
+ CollectionsController.any_instance.
+ stubs(:file_enumerator).returns(["foo\n", "file\n"])
+ uuid = api_fixture('collections')['foo_file']['uuid']
+ token = api_fixture('api_client_authorizations')['active_all_collections']['api_token']
+ url_head = "/collections/download/#{uuid}/#{token}/"
+ visit url_head
+ # It seems that Capybara can't inspect tags outside the body, so this is
+ # a very blunt approach.
+ assert_no_match(/<\s*meta[^>]+\bnofollow\b/i, page.html,
+ "wget prohibited from recursing the collection page")
+ # Look at all the links that wget would recurse through using our
+ # recommended options, and check that it's exactly the file list.
+ hrefs = page.all('a').map do |anchor|
+ link = anchor[:href] || ''
+ if link.start_with? url_head
+ link[url_head.size .. -1]
+ elsif link.start_with? '/'
+ nil
+ else
+ link
+ end
+ end
+ assert_equal(['foo'], hrefs.compact.sort,
+ "download page did provide strictly file links")
+ within "#collection_files" do
+ click_link "foo"
+ assert_equal("foo\nfile\n", page.html)
+ end
+ end
+
+ test "can view empty collection" do
+ Capybara.current_driver = :rack_test
+ uuid = 'd41d8cd98f00b204e9800998ecf8427e+0'
+ visit page_with_token('active', "/collections/#{uuid}")
+ assert page.has_text?(/This collection is empty|The following collections have this content/)
+ end
+
+ test "combine selected collections into new collection" do
+ foo_collection = api_fixture('collections')['foo_file']
+ bar_collection = api_fixture('collections')['bar_file']
+
+ visit page_with_token('active', "/collections")
+
+ assert(page.has_text?(foo_collection['uuid']), "Collection page did not include foo file")
+ assert(page.has_text?(bar_collection['uuid']), "Collection page did not include bar file")
+
+ within('tr', text: foo_collection['uuid']) do
+ find('input[type=checkbox]').click
+ end
+
+ within('tr', text: bar_collection['uuid']) do
+ find('input[type=checkbox]').click
+ end
+
+ click_button 'Selection...'
+ within('.selection-action-container') do
+ click_link 'Create new collection with selected collections'
+ end
+
+ # now in the newly created collection page
+ assert(page.has_text?('Copy to project'), "Copy to project text not found in new collection page")
+ assert(page.has_no_text?(foo_collection['name']), "Collection page did not include foo file")
+ assert(page.has_text?('foo'), "Collection page did not include foo file")
+ assert(page.has_no_text?(bar_collection['name']), "Collection page did not include foo file")
+ assert(page.has_text?('bar'), "Collection page did not include bar file")
+ assert(page.has_text?('Created new collection in your Home project'),
+ 'Not found flash message that new collection is created in Home project')
+ end
+
+ [
+ ['active', 'foo_file', false],
+ ['active', 'foo_collection_in_aproject', true],
+ ['project_viewer', 'foo_file', false],
+ ['project_viewer', 'foo_collection_in_aproject', false], #aproject not writable
+ ].each do |user, collection, expect_collection_in_aproject|
+ test "combine selected collection files into new collection #{user} #{collection} #{expect_collection_in_aproject}" do
+ my_collection = api_fixture('collections')[collection]
+
+ visit page_with_token(user, "/collections")
+
+ # choose file from foo collection
+ within('tr', text: my_collection['uuid']) do
+ click_link 'Show'
+ end
+
+ # now in collection page
+ find('input[type=checkbox]').click
+
+ click_button 'Selection...'
+ within('.selection-action-container') do
+ click_link 'Create new collection with selected files'
+ end
+
+ # now in the newly created collection page
+ assert(page.has_text?('Copy to project'), "Copy to project text not found in new collection page")
+ assert(page.has_no_text?(my_collection['name']), "Collection page did not include foo file")
+ assert(page.has_text?('foo'), "Collection page did not include foo file")
+ if expect_collection_in_aproject
+ aproject = api_fixture('groups')['aproject']
+ assert page.has_text?("Created new collection in the project #{aproject['name']}"),
+ 'Not found flash message that new collection is created in aproject'
+ else
+ assert page.has_text?("Created new collection in your Home project"),
+ 'Not found flash message that new collection is created in Home project'
+ end
+ end
+ end
+
+ test "combine selected collection files from collection subdirectory" do
+ visit page_with_token('user1_with_load', "/collections/zzzzz-4zz18-filesinsubdir00")
+
+ # now in collection page
+ input_files = page.all('input[type=checkbox]')
+ (0..input_files.count-1).each do |i|
+ input_files[i].click
+ end
+
+ click_button 'Selection...'
+ within('.selection-action-container') do
+ click_link 'Create new collection with selected files'
+ end
+
+ # now in the newly created collection page
+ assert(page.has_text?('file_in_subdir1'), 'file not found - file_in_subdir1')
+ assert(page.has_text?('file1_in_subdir3.txt'), 'file not found - file1_in_subdir3.txt')
+ assert(page.has_text?('file2_in_subdir3.txt'), 'file not found - file2_in_subdir3.txt')
+ assert(page.has_text?('file1_in_subdir4.txt'), 'file not found - file1_in_subdir4.txt')
+ assert(page.has_text?('file2_in_subdir4.txt'), 'file not found - file1_in_subdir4.txt')
+ end
+
+ test "Collection portable data hash redirect" do
+ di = api_fixture('collections')['docker_image']
+ visit page_with_token('active', "/collections/#{di['portable_data_hash']}")
+
+ # check redirection
+ assert current_path.end_with?("/collections/#{di['uuid']}")
+ assert page.has_text?("docker_image")
+ assert page.has_text?("Activity")
+ assert page.has_text?("Sharing and permissions")
+ end
+
+ test "Collection portable data hash with multiple matches" do
+ pdh = api_fixture('collections')['baz_file']['portable_data_hash']
+ visit page_with_token('admin', "/collections/#{pdh}")
+
+ matches = api_fixture('collections').select {|k,v| v["portable_data_hash"] == pdh}
+ assert matches.size > 1
+
+ matches.each do |k,v|
+ assert page.has_link?(v["name"]), "Page /collections/#{pdh} should contain link '#{v['name']}'"
+ end
+ assert page.has_no_text?("Activity")
+ assert page.has_no_text?("Sharing and permissions")
+ end
+
+ test "Filtering collection files by regexp" do
+ col = api_fixture('collections', 'multilevel_collection_1')
+ visit page_with_token('active', "/collections/#{col['uuid']}")
+
+ # Filter file list to some but not all files in the collection
+ page.find_field('file_regex').set('file[12]')
+ assert page.has_text?("file1")
+ assert page.has_text?("file2")
+ assert page.has_no_text?("file3")
+
+ # Filter file list with a regex matching all files
+ page.find_field('file_regex').set('.*')
+ assert page.has_text?("file1")
+ assert page.has_text?("file2")
+ assert page.has_text?("file3")
+
+ # Filter file list to a regex matching no files
+ page.find_field('file_regex').set('file9')
+ assert page.has_no_text?("file1")
+ assert page.has_no_text?("file2")
+ assert page.has_no_text?("file3")
+ # make sure that we actually are looking at the collections
+ # page and not e.g. a fiddlesticks
+ assert page.has_text?("multilevel_collection_1")
+ assert page.has_text?(col['portable_data_hash'])
+
+ # Set filename filter to a syntactically invalid regex
+ # Page loads, but stops filtering after the last valid regex parse
+ page.find_field('file_regex').set('file[2')
+ assert page.has_text?("multilevel_collection_1")
+ assert page.has_text?(col['portable_data_hash'])
+ assert page.has_text?("file1")
+ assert page.has_text?("file2")
+ assert page.has_text?("file3")
+
+ # Test the "Select all" button
+
+ # Note: calling .set('') on a Selenium element is not sufficient
+ # to reset the field for this test, as it does not send any key
+ # events to the browser. To clear the field, we must instead send
+ # a backspace character.
+ # See https://selenium.googlecode.com/svn/trunk/docs/api/rb/Selenium/WebDriver/Element.html#clear-instance_method
+ page.find_field('file_regex').set("\b") # backspace
+ find('button#select-all').click
+ assert_checkboxes_state('input[type=checkbox]', true, '"select all" should check all checkboxes')
+
+ # Test the "Unselect all" button
+ page.find_field('file_regex').set("\b") # backspace
+ find('button#unselect-all').click
+ assert_checkboxes_state('input[type=checkbox]', false, '"unselect all" should clear all checkboxes')
+
+ # Filter files, then "select all", then unfilter
+ page.find_field('file_regex').set("\b") # backspace
+ find('button#unselect-all').click
+ page.find_field('file_regex').set('file[12]')
+ find('button#select-all').click
+ page.find_field('file_regex').set("\b") # backspace
+
+ # all "file1" and "file2" checkboxes must be selected
+ # all "file3" checkboxes must be clear
+ assert_checkboxes_state('[value*="file1"]', true, 'checkboxes for file1 should be selected after filtering')
+ assert_checkboxes_state('[value*="file2"]', true, 'checkboxes for file2 should be selected after filtering')
+ assert_checkboxes_state('[value*="file3"]', false, 'checkboxes for file3 should be clear after filtering')
+
+ # Select all files, then filter, then "unselect all", then unfilter
+ page.find_field('file_regex').set("\b") # backspace
+ find('button#select-all').click
+ page.find_field('file_regex').set('file[12]')
+ find('button#unselect-all').click
+ page.find_field('file_regex').set("\b") # backspace
+
+ # all "file1" and "file2" checkboxes must be clear
+ # all "file3" checkboxes must be selected
+ assert_checkboxes_state('[value*="file1"]', false, 'checkboxes for file1 should be clear after filtering')
+ assert_checkboxes_state('[value*="file2"]', false, 'checkboxes for file2 should be clear after filtering')
+ assert_checkboxes_state('[value*="file3"]', true, 'checkboxes for file3 should be selected after filtering')
+ end
+
+ test "Creating collection from list of filtered files" do
+ col = api_fixture('collections', 'collection_with_files_in_subdir')
+ visit page_with_token('user1_with_load', "/collections/#{col['uuid']}")
+ assert page.has_text?('file_in_subdir1'), 'expected file_in_subdir1 not found'
+ assert page.has_text?('file1_in_subdir3'), 'expected file1_in_subdir3 not found'
+ assert page.has_text?('file2_in_subdir3'), 'expected file2_in_subdir3 not found'
+ assert page.has_text?('file1_in_subdir4'), 'expected file1_in_subdir4 not found'
+ assert page.has_text?('file2_in_subdir4'), 'expected file2_in_subdir4 not found'
+
+ # Select all files but then filter them to files in subdir1, subdir2 or subdir3
+ find('button#select-all').click
+ page.find_field('file_regex').set('_in_subdir[123]')
+ assert page.has_text?('file_in_subdir1'), 'expected file_in_subdir1 not in filtered files'
+ assert page.has_text?('file1_in_subdir3'), 'expected file1_in_subdir3 not in filtered files'
+ assert page.has_text?('file2_in_subdir3'), 'expected file2_in_subdir3 not in filtered files'
+ assert page.has_no_text?('file1_in_subdir4'), 'file1_in_subdir4 found in filtered files'
+ assert page.has_no_text?('file2_in_subdir4'), 'file2_in_subdir4 found in filtered files'
+
+ # Create a new collection
+ click_button 'Selection...'
+ within('.selection-action-container') do
+ click_link 'Create new collection with selected files'
+ end
+
+ # now in the newly created collection page
+ assert page.has_text?('Content hash:'), 'not on new collection page'
+ assert page.has_no_text?(col['uuid']), 'new collection page has old collection uuid'
+ assert page.has_no_text?(col['portable_data_hash']), 'new collection page has old portable_data_hash'
+
+ # must have files in subdir1 and subdir3 but not subdir4
+ assert page.has_text?('file_in_subdir1'), 'file_in_subdir1 missing from new collection'
+ assert page.has_text?('file1_in_subdir3'), 'file1_in_subdir3 missing from new collection'
+ assert page.has_text?('file2_in_subdir3'), 'file2_in_subdir3 missing from new collection'
+ assert page.has_no_text?('file1_in_subdir4'), 'file1_in_subdir4 found in new collection'
+ assert page.has_no_text?('file2_in_subdir4'), 'file2_in_subdir4 found in new collection'
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class ErrorsTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ BAD_UUID = "ffffffffffffffffffffffffffffffff+0"
+
+ test "error page renders user navigation" do
+ visit(page_with_token("active", "/collections/#{BAD_UUID}"))
+ assert(page.has_text?(api_fixture("users")["active"]["email"]),
+ "User information missing from error page")
+ assert(page.has_no_text?(/log ?in/i),
+ "Logged in user prompted to log in on error page")
+ end
+
+ test "no user navigation with expired token" do
+ visit(page_with_token("expired", "/collections/#{BAD_UUID}"))
+ assert(page.has_no_text?(api_fixture("users")["active"]["email"]),
+ "Page visited with expired token included user information")
+ assert(page.has_selector?("a", text: /log ?in/i),
+ "Login prompt missing on expired token error page")
+ end
+
+ test "error page renders without login" do
+ visit "/collections/download/#{BAD_UUID}/#{@@API_AUTHS['active']['api_token']}"
+ assert(page.has_no_text?(/\b500\b/),
+ "Error page without login returned 500")
+ end
+
+ test "'object not found' page includes search link" do
+ visit(page_with_token("active", "/collections/#{BAD_UUID}"))
+ assert(all("a").any? { |a| a[:href] =~ %r{/collections/?(\?|$)} },
+ "no search link found on 404 page")
+ end
+
+ def now_timestamp
+ Time.now.utc.to_i
+ end
+
+ def page_has_error_token?(start_stamp)
+ matching_stamps = (start_stamp .. now_timestamp).to_a.join("|")
+ # Check the page HTML because we really don't care how it's presented.
+ # I think it would even be reasonable to put it in a comment.
+ page.html =~ /\b(#{matching_stamps})\+[0-9A-Fa-f]{8}\b/
+ end
+
+ # We use API tokens with limited scopes as the quickest way to get the API
+ # server to return an error. If Workbench gets smarter about coping when
+ # it has a too-limited token, these tests will need to be adjusted.
+ test "API error page includes error token" do
+ start_stamp = now_timestamp
+ visit(page_with_token("active_readonly", "/authorized_keys"))
+ click_on "Add a new authorized key"
+ assert(page.has_text?(/fiddlesticks/i),
+ "Not on an error page after making an SSH key out of scope")
+ assert(page_has_error_token?(start_stamp), "no error token on 404 page")
+ end
+
+ test "showing a bad UUID returns 404" do
+ visit(page_with_token("active", "/pipeline_templates/zzz"))
+ assert(page.has_no_text?(/fiddlesticks/i),
+ "trying to show a bad UUID rendered a fiddlesticks page, not 404")
+ end
+
+ test "404 page includes information about missing object" do
+ visit(page_with_token("active", "/groups/zazazaz"))
+ assert(page.has_text?(/group with UUID zazazaz/i),
+ "name of searched group missing from 404 page")
+ end
+
+ test "unrouted 404 page works" do
+ visit(page_with_token("active", "/__asdf/ghjk/zxcv"))
+ assert(page.has_text?(/not found/i),
+ "unrouted page missing 404 text")
+ assert(page.has_no_text?(/fiddlesticks/i),
+ "unrouted request returned a generic error page, not 404")
+ end
+
+ test "API error page has Report problem button" do
+ original_arvados_v1_base = Rails.configuration.arvados_v1_base
+
+ begin
+ # point to a bad api server url to generate fiddlesticks error
+ Rails.configuration.arvados_v1_base = "https://[100::f]:1/"
+
+ visit page_with_token("active")
+
+ assert(page.has_text?(/fiddlesticks/i), 'Expected to be in error page')
+
+ # reset api server base config to let the popup rendering to work
+ Rails.configuration.arvados_v1_base = original_arvados_v1_base
+
+ # check the "Report problem" button
+ assert page.has_link? 'Report problem', 'Report problem link not found'
+
+ click_link 'Report problem'
+ within '.modal-content' do
+ assert page.has_text?('Report a problem'), 'Report a problem text not found'
+ assert page.has_no_text?('Version / debugging info'), 'Version / debugging info is not expected'
+ assert page.has_text?('Describe the problem'), 'Describe the problem text not found'
+ assert page.has_text?('Send problem report'), 'Send problem report button text is not found'
+ assert page.has_no_button?('Send problem report'), 'Send problem report button is not disabled before entering problem description'
+ assert page.has_button?('Cancel'), 'Cancel button not found'
+
+ # enter a report text and click on report
+ page.find_field('report_issue_text').set 'my test report text'
+ assert page.has_button?('Send problem report'), 'Send problem report button not enabled after entering text'
+ click_button 'Send problem report'
+
+ # ajax success updated button texts and added footer message
+ assert page.has_no_text?('Send problem report'), 'Found button - Send problem report'
+ assert page.has_no_button?('Cancel'), 'Found button - Cancel'
+ assert page.has_text?('Report sent'), 'No text - Report sent'
+ assert page.has_button?('Close'), 'No button - Close'
+ assert page.has_text?('Thanks for reporting this issue'), 'No text - Thanks for reporting this issue'
+
+ click_button 'Close'
+ end
+
+ # out of the popup now and should be back in the error page
+ assert(page.has_text?(/fiddlesticks/i), 'Expected to be in error page after closing report issue popup')
+ ensure
+ Rails.configuration.arvados_v1_base = original_arvados_v1_base
+ end
+ end
+
+end
--- /dev/null
+require 'integration_helper'
+
+class FilterableInfiniteScrollTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ # Chrome remembers what you had in the text field when you hit
+ # "back". Here, we simulate the same effect by sending an otherwise
+ # unused ?search=foo param to pre-populate the search field.
+ test 'no double-load if text input has a value at page load time' do
+ visit page_with_token('admin', '/pipeline_instances')
+ assert_text 'pipeline_2'
+ visit page_with_token('admin', '/pipeline_instances?search=pipeline_1')
+ # Horrible hack to ensure the search results can't load correctly
+ # on the second attempt.
+ assert_selector '#recent-pipeline-instances'
+ assert page.evaluate_script('$("#recent-pipeline-instances[data-infinite-content-href0]").attr("data-infinite-content-href0","/give-me-an-error").length == 1')
+ # Wait for the first page of results to appear.
+ assert_text 'pipeline_1'
+ # Make sure the results are filtered.
+ assert_no_text 'pipeline_2'
+ # Make sure pipeline_2 didn't disappear merely because the results
+ # were replaced with an error message.
+ assert_text 'pipeline_1'
+ end
+end
--- /dev/null
+require 'fileutils'
+require 'tmpdir'
+
+require 'integration_helper'
+
+class JobsTest < ActionDispatch::IntegrationTest
+
+ def fakepipe_with_log_data
+ content =
+ "2014-01-01_12:00:01 zzzzz-8i9sb-0vsrcqi7whchuil 0 log message 1\n" +
+ "2014-01-01_12:00:02 zzzzz-8i9sb-0vsrcqi7whchuil 0 log message 2\n" +
+ "2014-01-01_12:00:03 zzzzz-8i9sb-0vsrcqi7whchuil 0 log message 3\n"
+ StringIO.new content, 'r'
+ end
+
+ test "add job description" do
+ need_javascript
+ visit page_with_token("active", "/jobs")
+
+ # go to job running the script "doesnotexist"
+ within first('tr', text: 'doesnotexist') do
+ find("a").click
+ end
+
+ # edit job description
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('*Textile description for job* - "Go to dashboard":/')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+
+ # Verify edited description
+ assert page.has_no_text? '*Textile description for job*'
+ assert page.has_text? 'Textile description for job'
+ assert page.has_link? 'Go to dashboard'
+ click_link 'Go to dashboard'
+ assert page.has_text? 'Active pipelines'
+ end
+
+ test "view job log" do
+ need_javascript
+ job = api_fixture('jobs')['job_with_real_log']
+
+ IO.expects(:popen).returns(fakepipe_with_log_data)
+
+ visit page_with_token("active", "/jobs/#{job['uuid']}")
+ assert page.has_text? job['script_version']
+
+ click_link 'Log'
+ wait_for_ajax
+ assert page.has_text? 'Started at'
+ assert page.has_text? 'Finished at'
+ assert page.has_text? 'log message 1'
+ assert page.has_text? 'log message 2'
+ assert page.has_text? 'log message 3'
+ assert page.has_no_text? 'Showing only 100 bytes of this log'
+ end
+
+ test 'view partial job log' do
+ need_javascript
+ # This config will be restored during teardown by ../test_helper.rb:
+ Rails.configuration.log_viewer_max_bytes = 100
+
+ IO.expects(:popen).returns(fakepipe_with_log_data)
+ job = api_fixture('jobs')['job_with_real_log']
+
+ visit page_with_token("active", "/jobs/#{job['uuid']}")
+ assert page.has_text? job['script_version']
+
+ click_link 'Log'
+ wait_for_ajax
+ assert page.has_text? 'Showing only 100 bytes of this log'
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class LoginsTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ test "login with api_token works after redirect" do
+ visit page_with_token('active_trustedclient')
+ assert page.has_text?('Active pipelines'), "Missing 'Active pipelines' from page"
+ assert_no_match(/\bapi_token=/, current_path)
+ end
+
+ test "trying to use expired token redirects to login page" do
+ visit page_with_token('expired_trustedclient')
+ buttons = all("a.btn", text: /Log in/)
+ assert_equal(1, buttons.size, "Failed to find one login button")
+ login_link = buttons.first[:href]
+ assert_match(%r{//[^/]+/login}, login_link)
+ assert_no_match(/\bapi_token=/, login_link)
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class PipelineInstancesTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ test 'Create and run a pipeline' do
+ visit page_with_token('active_trustedclient')
+
+ visit '/pipeline_templates'
+ within('tr', text: 'Two Part Pipeline Template') do
+ find('a,button', text: 'Run').click
+ end
+
+ # project chooser
+ within('.modal-dialog') do
+ find('.selectable', text: 'A Project').click
+ find('button', text: 'Choose').click
+ end
+
+ # This pipeline needs input. So, Run should be disabled
+ page.assert_selector 'a.disabled,button.disabled', text: 'Run'
+
+ instance_page = current_path
+
+ # Add this collection to the project
+ visit '/projects'
+ find("#projects-menu").click
+ find('.dropdown-menu a,button', text: 'A Project').click
+ find('.btn', text: 'Add data').click
+ find('.dropdown-menu a,button', text: 'Copy data from another project').click
+ within('.modal-dialog') do
+ wait_for_ajax
+ first('span', text: 'foo_tag').click
+ find('.btn', text: 'Copy').click
+ end
+ using_wait_time(Capybara.default_wait_time * 3) do
+ wait_for_ajax
+ end
+
+ click_link 'Jobs and pipelines'
+ find('tr[data-kind="arvados#pipelineInstance"]', text: '(none)').
+ find('a', text: 'Show').
+ click
+
+ assert find('p', text: 'Provide a value')
+
+ find('div.form-group', text: 'Foo/bar pair').
+ find('.btn', text: 'Choose').
+ click
+
+ within('.modal-dialog') do
+ assert(has_text?("Foo/bar pair"),
+ "pipeline input picker missing name of input")
+ wait_for_ajax
+ first('span', text: 'foo_tag').click
+ find('button', text: 'OK').click
+ end
+ wait_for_ajax
+
+ # The input, after being specified, should still be displayed (#3382)
+ assert find('div.form-group', text: 'Foo/bar pair')
+
+ # The input, after being specified, should still be editable (#3382)
+ find('div.form-group', text: 'Foo/bar pair').
+ find('.btn', text: 'Choose').click
+
+ within('.modal-dialog') do
+ assert(has_text?("Foo/bar pair"),
+ "pipeline input picker missing name of input")
+ wait_for_ajax
+ first('span', text: 'foo_tag').click
+ find('button', text: 'OK').click
+ end
+
+ # For good measure, check one last time that the input, after being specified twice, is still be displayed (#3382)
+ assert find('div.form-group', text: 'Foo/bar pair')
+
+ # Ensure that the collection's portable_data_hash, uuid and name
+ # are saved in the desired places. (#4015)
+
+ # foo_collection_in_aproject is the collection tagged with foo_tag.
+ collection = api_fixture('collections', 'foo_collection_in_aproject')
+ click_link 'Advanced'
+ click_link 'API response'
+ api_response = JSON.parse(find('div#advanced_api_response pre').text)
+ input_params = api_response['components']['part-one']['script_parameters']['input']
+ assert_equal input_params['value'], collection['portable_data_hash']
+ assert_equal input_params['selection_name'], collection['name']
+ assert_equal input_params['selection_uuid'], collection['uuid']
+
+ # "Run" button is now enabled
+ page.assert_no_selector 'a.disabled,button.disabled', text: 'Run'
+
+ first('a,button', text: 'Run').click
+
+ # Pipeline is running. We have a "Pause" button instead now.
+ page.assert_selector 'a,button', text: 'Pause'
+ find('a,button', text: 'Pause').click
+
+ # Pipeline is stopped. It should now be in paused state and Runnable again.
+ assert page.has_text? 'Paused'
+ page.assert_no_selector 'a.disabled,button.disabled', text: 'Resume'
+ page.assert_selector 'a,button', text: 'Re-run with latest'
+ page.assert_selector 'a,button', text: 'Re-run options'
+
+ # Since it is test env, no jobs are created to run. So, graph not visible
+ assert_not page.has_text? 'Graph'
+ end
+
+ # Create a pipeline instance from within a project and run
+ test 'Create pipeline inside a project and run' do
+ visit page_with_token('active_trustedclient')
+
+ # Add this collection to the project using collections menu from top nav
+ visit '/projects'
+ find("#projects-menu").click
+ find('.dropdown-menu a,button', text: 'A Project').click
+ find('.btn', text: 'Add data').click
+ find('.dropdown-menu a,button', text: 'Copy data from another project').click
+ within('.modal-dialog') do
+ wait_for_ajax
+ first('span', text: 'foo_tag').click
+ find('.btn', text: 'Copy').click
+ end
+ using_wait_time(Capybara.default_wait_time * 3) do
+ wait_for_ajax
+ end
+
+ create_and_run_pipeline_in_aproject true, 'Two Part Pipeline Template', 'foo_collection_in_aproject', false
+ end
+
+ # Create a pipeline instance from outside of a project
+ test 'Run a pipeline from dashboard' do
+ visit page_with_token('active_trustedclient')
+ create_and_run_pipeline_in_aproject false, 'Two Part Pipeline Template', 'foo_collection_in_aproject', false
+ end
+
+ test 'view pipeline with job and see graph' do
+ visit page_with_token('active_trustedclient')
+
+ visit '/pipeline_instances'
+ assert page.has_text? 'pipeline_with_job'
+
+ find('a', text: 'pipeline_with_job').click
+
+ # since the pipeline component has a job, expect to see the graph
+ assert page.has_text? 'Graph'
+ click_link 'Graph'
+ page.assert_selector "#provenance_graph"
+ end
+
+ test 'pipeline description' do
+ visit page_with_token('active_trustedclient')
+
+ visit '/pipeline_instances'
+ assert page.has_text? 'pipeline_with_job'
+
+ find('a', text: 'pipeline_with_job').click
+
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('*Textile description for pipeline instance*')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+
+ # verify description
+ assert page.has_no_text? '*Textile description for pipeline instance*'
+ assert page.has_text? 'Textile description for pipeline instance'
+ end
+
+ test "JSON popup available for strange components" do
+ uuid = api_fixture("pipeline_instances")["components_is_jobspec"]["uuid"]
+ visit page_with_token("active", "/pipeline_instances/#{uuid}")
+ click_on "Components"
+ assert(page.has_no_text?("script_parameters"),
+ "components JSON visible without popup")
+ click_on "Show components JSON"
+ assert(page.has_text?("script_parameters"),
+ "components JSON not found")
+ end
+
+ PROJECT_WITH_SEARCH_COLLECTION = "A Subproject"
+ def check_parameter_search(proj_name)
+ template = api_fixture("pipeline_templates")["parameter_with_search"]
+ search_text = template["components"]["with-search"]["script_parameters"]["input"]["search_for"]
+ visit page_with_token("active", "/pipeline_templates/#{template['uuid']}")
+ click_on "Run this pipeline"
+ within(".modal-dialog") do # Set project for the new pipeline instance
+ find(".selectable", text: proj_name).click
+ click_on "Choose"
+ end
+ assert(has_text?("This pipeline was created from the template"), "did not land on pipeline instance page")
+ first("a.btn,button", text: "Choose").click
+ within(".modal-body") do
+ if (proj_name != PROJECT_WITH_SEARCH_COLLECTION)
+ # Switch finder modal to Subproject to find the Collection.
+ click_on proj_name
+ click_on PROJECT_WITH_SEARCH_COLLECTION
+ end
+ assert_equal(search_text, first("input").value,
+ "parameter search not preseeded")
+ assert(has_text?(api_fixture("collections")["baz_collection_name_in_asubproject"]["name"]),
+ "baz Collection not in preseeded search results")
+ end
+ end
+
+ test "Workbench respects search_for parameter in templates" do
+ check_parameter_search(PROJECT_WITH_SEARCH_COLLECTION)
+ end
+
+ test "Workbench preserves search_for parameter after project switch" do
+ check_parameter_search("A Project")
+ end
+
+ [
+ [true, 'Two Part Pipeline Template', 'foo_collection_in_aproject', false],
+ [false, 'Two Part Pipeline Template', 'foo_collection_in_aproject', false],
+ [true, 'Two Part Template with dataclass File', 'foo_collection_in_aproject', true],
+ [false, 'Two Part Template with dataclass File', 'foo_collection_in_aproject', true],
+ [true, 'Two Part Pipeline Template', 'collection_with_no_name_in_aproject', false],
+ ].each do |in_aproject, template_name, collection, choose_file|
+ test "Run pipeline instance in #{in_aproject} with #{template_name} with #{collection} file #{choose_file}" do
+ if in_aproject
+ visit page_with_token 'active', \
+ '/projects/'+api_fixture('groups')['aproject']['uuid']
+ else
+ visit page_with_token 'active', '/'
+ end
+
+ # need bigger modal size when choosing a file from collection
+ if Capybara.current_driver == :selenium
+ Capybara.current_session.driver.browser.manage.window.resize_to(1200, 800)
+ end
+
+ create_and_run_pipeline_in_aproject in_aproject, template_name, collection, choose_file
+ instance_path = current_path
+
+ # Pause the pipeline
+ find('a,button', text: 'Pause').click
+ assert page.has_text? 'Paused'
+ page.assert_no_selector 'a.disabled,button.disabled', text: 'Resume'
+ page.assert_selector 'a,button', text: 'Re-run with latest'
+ page.assert_selector 'a,button', text: 'Re-run options'
+
+ # Verify that the newly created instance is created in the right project.
+ assert page.has_text? 'Home'
+ if in_aproject
+ assert page.has_text? 'A Project'
+ else
+ assert page.has_no_text? 'A Project'
+ end
+ end
+ end
+
+ [
+ ['active', false, false, false],
+ ['active', false, false, true],
+ ['active', true, false, false],
+ ['active', true, true, false],
+ ['active', true, false, true],
+ ['active', true, true, true],
+ ['project_viewer', false, false, true],
+ ['project_viewer', true, true, true],
+ ].each do |user, with_options, choose_options, in_aproject|
+ test "Rerun pipeline instance as #{user} using options #{with_options} #{choose_options} in #{in_aproject}" do
+ if in_aproject
+ visit page_with_token 'active', \
+ '/projects/'+api_fixture('groups')['aproject']['uuid']
+ else
+ visit page_with_token 'active', '/'
+ end
+
+ # need bigger modal size when choosing a file from collection
+ if Capybara.current_driver == :selenium
+ Capybara.current_session.driver.browser.manage.window.resize_to(1200, 800)
+ end
+
+ create_and_run_pipeline_in_aproject in_aproject, 'Two Part Pipeline Template', 'foo_collection_in_aproject'
+ instance_path = current_path
+
+ # Pause the pipeline
+ find('a,button', text: 'Pause').click
+ assert page.has_text? 'Paused'
+ page.assert_no_selector 'a.disabled,button.disabled', text: 'Resume'
+ page.assert_selector 'a,button', text: 'Re-run with latest'
+ page.assert_selector 'a,button', text: 'Re-run options'
+
+ # Pipeline can be re-run now. Access it as the specified user, and re-run
+ if user == 'project_viewer'
+ visit page_with_token(user, instance_path)
+ assert page.has_text? 'A Project'
+ page.assert_no_selector 'a.disabled,button.disabled', text: 'Resume'
+ page.assert_selector 'a,button', text: 'Re-run with latest'
+ page.assert_selector 'a,button', text: 'Re-run options'
+ end
+
+ # Now re-run the pipeline
+ if with_options
+ assert_triggers_dom_event 'shown.bs.modal' do
+ find('a,button', text: 'Re-run options').click
+ end
+ within('.modal-dialog') do
+ page.assert_selector 'a,button', text: 'Copy and edit inputs'
+ page.assert_selector 'a,button', text: 'Run now'
+ if choose_options
+ find('button', text: 'Copy and edit inputs').click
+ else
+ find('button', text: 'Run now').click
+ end
+ end
+ else
+ find('a,button', text: 'Re-run with latest').click
+ end
+
+ # Verify that the newly created instance is created in the right
+ # project. In case of project_viewer user, since the user cannot
+ # write to the project, the pipeline should have been created in
+ # the user's Home project.
+ assert_not_equal instance_path, current_path, 'Rerun instance path expected to be different'
+ assert_text 'Home'
+ if in_aproject && (user != 'project_viewer')
+ assert_text 'A Project'
+ else
+ assert_no_text 'A Project'
+ end
+ end
+ end
+
+ # Create and run a pipeline for 'Two Part Pipeline Template' in 'A Project'
+ def create_and_run_pipeline_in_aproject in_aproject, template_name, collection_fixture, choose_file=false
+ # collection in aproject to be used as input
+ collection = api_fixture('collections', collection_fixture)
+
+ # create a pipeline instance
+ find('.btn', text: 'Run a pipeline').click
+ within('.modal-dialog') do
+ find('.selectable', text: template_name).click
+ find('.btn', text: 'Next: choose inputs').click
+ end
+
+ assert find('p', text: 'Provide a value')
+
+ find('div.form-group', text: 'Foo/bar pair').
+ find('.btn', text: 'Choose').
+ click
+
+ within('.modal-dialog') do
+ if in_aproject
+ assert_selector 'button.dropdown-toggle', text: 'A Project'
+ wait_for_ajax
+ else
+ assert_selector 'button.dropdown-toggle', text: 'Home'
+ wait_for_ajax
+ click_button "Home"
+ click_link "A Project"
+ wait_for_ajax
+ end
+
+ if collection_fixture == 'foo_collection_in_aproject'
+ first('span', text: 'foo_tag').click
+ elsif collection['name']
+ first('span', text: "#{collection['name']}").click
+ else
+ collection_uuid = collection['uuid']
+ find("div[data-object-uuid=#{collection_uuid}]").click
+ end
+
+ if choose_file
+ wait_for_ajax
+ find('.preview-selectable', text: 'foo').click
+ end
+ find('button', text: 'OK').click
+ end
+
+ # The input, after being specified, should still be displayed (#3382)
+ assert find('div.form-group', text: 'Foo/bar pair')
+
+ # Ensure that the collection's portable_data_hash, uuid and name
+ # are saved in the desired places. (#4015)
+ click_link 'Advanced'
+ click_link 'API response'
+
+ api_response = JSON.parse(find('div#advanced_api_response pre').text)
+ input_params = api_response['components']['part-one']['script_parameters']['input']
+ assert_equal(input_params['selection_uuid'], collection['uuid'], "Not found expected input param uuid")
+ if choose_file
+ assert_equal(input_params['value'], collection['portable_data_hash']+'/foo', "Not found expected input file param value")
+ assert_equal(input_params['selection_name'], collection['name']+'/foo', "Not found expected input file param name")
+ else
+ assert_equal(input_params['value'], collection['portable_data_hash'], "Not found expected input param value")
+ assert_equal(input_params['selection_name'], collection['name'], "Not found expected input selection name")
+ end
+
+ # "Run" button present and enabled
+ page.assert_no_selector 'a.disabled,button.disabled', text: 'Run'
+ first('a,button', text: 'Run').click
+
+ # Pipeline is running. We have a "Pause" button instead now.
+ page.assert_no_selector 'a,button', text: 'Run'
+ page.assert_no_selector 'a.disabled,button.disabled', text: 'Resume'
+ page.assert_selector 'a,button', text: 'Pause'
+
+ # Since it is test env, no jobs are created to run. So, graph not visible
+ assert_not page.has_text? 'Graph'
+ end
+
+ [
+ [1, 0], # run time 0 minutes
+ [10, 17*60*60 + 51*60], # run time 17 hours and 51 minutes
+ ].each do |index, run_time|
+ test "pipeline start and finish time display #{index}" do
+ visit page_with_token("user1_with_load", "/pipeline_instances/zzzzz-d1hrv-10pipelines0#{index.to_s.rjust(3, '0')}")
+
+ assert page.has_text? 'This pipeline started at'
+ page_text = page.text
+
+ match = /This pipeline started at (.*)\. It failed after (.*) seconds at (.*)\. Check the Log/.match page_text
+ assert_not_nil(match, 'Did not find text - This pipeline started at . . . ')
+
+ start_at = match[1]
+ finished_at = match[3]
+ assert_not_nil(start_at, 'Did not find start_at time')
+ assert_not_nil(finished_at, 'Did not find finished_at time')
+
+ # start and finished time display is of the format '2:20 PM 10/20/2014'
+ start_time = DateTime.strptime(start_at, '%H:%M %p %m/%d/%Y').to_time
+ finished_time = DateTime.strptime(finished_at, '%H:%M %p %m/%d/%Y').to_time
+ assert_equal(run_time, finished_time-start_time,
+ "Time difference did not match for start_at #{start_at}, finished_at #{finished_at}, ran_for #{match[2]}")
+ end
+ end
+
+ [
+ ['fuse', nil, 2, 20], # has 2 as of 11-07-2014
+ ['fuse', 'FUSE project', 1, 1], # 1 with this name
+ ['user1_with_load', nil, 30, 100], # has 37 as of 11-07-2014
+ ['user1_with_load', 'pipeline_10', 2, 2], # 2 with this name
+ ['user1_with_load', '000010pipelines', 10, 10], # owned_by the project zzzzz-j7d0g-000010pipelines
+ ['user1_with_load', '000025pipelines', 25, 25], # owned_by the project zzzzz-j7d0g-000025pipelines, two pages
+ ['admin', nil, 40, 200],
+ ['admin', 'FUSE project', 1, 1],
+ ['admin', 'pipeline_10', 2, 2],
+ ['active', 'containing at least two', 2, 100], # component description
+ ['admin', 'containing at least two', 2, 100],
+ ['active', nil, 10, 100],
+ ['active', 'no such match', 0, 0],
+ ].each do |user, search_filter, expected_min, expected_max|
+ test "scroll pipeline instances page for #{user} with search filter #{search_filter}
+ and expect #{expected_min} <= found_items <= #{expected_max}" do
+ visit page_with_token(user, "/pipeline_instances")
+
+ if search_filter
+ find('.recent-pipeline-instances-filterable-control').set(search_filter)
+ # Wait for 250ms debounce timer (see filterable.js)
+ sleep 0.350
+ wait_for_ajax
+ end
+
+ page_scrolls = expected_max/20 + 2 # scroll num_pages+2 times to test scrolling is disabled when it should be
+ within('.arv-recent-pipeline-instances') do
+ (0..page_scrolls).each do |i|
+ page.driver.scroll_to 0, 999000
+ begin
+ wait_for_ajax
+ rescue
+ end
+ end
+ end
+
+ # Verify that expected number of pipeline instances are found
+ found_items = page.all('tr[data-kind="arvados#pipelineInstance"]')
+ found_count = found_items.count
+ if expected_min == expected_max
+ assert_equal(true, found_count == expected_min,
+ "Not found expected number of items. Expected #{expected_min} and found #{found_count}")
+ assert page.has_no_text? 'request failed'
+ else
+ assert_equal(true, found_count>=expected_min,
+ "Found too few items. Expected at least #{expected_min} and found #{found_count}")
+ assert_equal(true, found_count<=expected_max,
+ "Found too many items. Expected at most #{expected_max} and found #{found_count}")
+ end
+ end
+ end
+
+end
--- /dev/null
+require 'integration_helper'
+
+class PipelineTemplatesTest < ActionDispatch::IntegrationTest
+ test "JSON popup available for strange components" do
+ need_javascript
+ uuid = api_fixture("pipeline_templates")["components_is_jobspec"]["uuid"]
+ visit page_with_token("active", "/pipeline_templates/#{uuid}")
+ click_on "Components"
+ assert(page.has_no_text?("script_parameters"),
+ "components JSON visible without popup")
+ click_on "Show components JSON"
+ assert(page.has_text?("script_parameters"),
+ "components JSON not found")
+ end
+
+ test "pipeline template description" do
+ need_javascript
+ visit page_with_token("active", "/pipeline_templates")
+
+ # go to Two Part pipeline template
+ within first('tr', text: 'Two Part Pipeline Template') do
+ find(".fa-gears").click
+ end
+
+ # edit template description
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('*Textile description for pipeline template* - "Go to dashboard":/')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+
+ # Verfiy edited description
+ assert page.has_no_text? '*Textile description for pipeline template*'
+ assert page.has_text? 'Textile description for pipeline template'
+ assert page.has_link? 'Go to dashboard'
+ click_link 'Go to dashboard'
+ assert page.has_text? 'Active pipelines'
+
+ # again visit recent templates page and verify edited description
+ visit page_with_token("active", "/pipeline_templates")
+ assert page.has_no_text? '*Textile description for pipeline template*'
+ assert page.has_text? 'Textile description for pipeline template'
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class ProjectsTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ test 'Check collection count for A Project in the tab pane titles' do
+ project_uuid = api_fixture('groups')['aproject']['uuid']
+ visit page_with_token 'active', '/projects/' + project_uuid
+ wait_for_ajax
+ collection_count = page.all("[data-pk*='collection']").count
+ assert_selector '#Data_collections-tab span', text: "(#{collection_count})"
+ end
+
+ test 'Find a project and edit its description' do
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: "A Project").click
+ within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
+ find('span', text: api_fixture('groups')['aproject']['name']).click
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('I just edited this.')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+ end
+ visit current_path
+ assert(find?('.container-fluid', text: 'I just edited this.'),
+ "Description update did not survive page refresh")
+ end
+
+ test 'Find a project and edit description to textile description' do
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: "A Project").click
+ within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
+ find('span', text: api_fixture('groups')['aproject']['name']).click
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('<p>*Textile description for A project* - "take me home":/ </p><p>And a new paragraph in description.</p>')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+ end
+
+ # visit project page
+ visit current_path
+ assert_no_text '*Textile description for A project*'
+ assert(find?('.container-fluid', text: 'Textile description for A project'),
+ "Description update did not survive page refresh")
+ assert(find?('.container-fluid', text: 'And a new paragraph in description'),
+ "Description did not contain the expected new paragraph")
+ assert(page.has_link?("take me home"), "link not found in description")
+
+ click_link 'take me home'
+
+ # now in dashboard
+ assert(page.has_text?('Active pipelines'), 'Active pipelines - not found on dashboard')
+ end
+
+ test 'Find a project and edit description to html description' do
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: "A Project").click
+ within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
+ find('span', text: api_fixture('groups')['aproject']['name']).click
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('<br>Textile description for A project</br> - <a href="/">take me home</a>')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+ end
+ visit current_path
+ assert(find?('.container-fluid', text: 'Textile description for A project'),
+ "Description update did not survive page refresh")
+ assert(!find?('.container-fluid', text: '<br>Textile description for A project</br>'),
+ "Textile description is displayed with uninterpreted formatting characters")
+ assert(page.has_link?("take me home"),"link not found in description")
+ click_link 'take me home'
+ assert page.has_text?('Active pipelines')
+ end
+
+ test 'Find a project and edit description to textile description with link to object' do
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: "A Project").click
+ within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
+ find('span', text: api_fixture('groups')['aproject']['name']).click
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('*Textile description for A project* - "go to sub-project":' + api_fixture('groups')['asubproject']['uuid'] + "'")
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+ end
+ visit current_path
+ assert(find?('.container-fluid', text: 'Textile description for A project'),
+ "Description update did not survive page refresh")
+ assert(!find?('.container-fluid', text: '*Textile description for A project*'),
+ "Textile description is displayed with uninterpreted formatting characters")
+ assert(page.has_link?("go to sub-project"), "link not found in description")
+ click_link 'go to sub-project'
+ assert(page.has_text?(api_fixture('groups')['asubproject']['name']), 'sub-project name not found after clicking link')
+ end
+
+ test 'Add a new name, then edit it, without creating a duplicate' do
+ project_uuid = api_fixture('groups')['aproject']['uuid']
+ specimen_uuid = api_fixture('traits')['owned_by_aproject_with_no_name']['uuid']
+ visit page_with_token 'active', '/projects/' + project_uuid
+ click_link 'Other objects'
+ within '.selection-action-container' do
+ # Wait for the tab to load:
+ assert_selector 'tr[data-kind="arvados#trait"]'
+ within first('tr', text: 'Trait') do
+ find(".fa-pencil").click
+ find('.editable-input input').set('Now I have a name.')
+ find('.glyphicon-ok').click
+ assert_selector '.editable', text: 'Now I have a name.'
+ find(".fa-pencil").click
+ find('.editable-input input').set('Now I have a new name.')
+ find('.glyphicon-ok').click
+ end
+ wait_for_ajax
+ assert_selector '.editable', text: 'Now I have a new name.'
+ end
+ visit current_path
+ click_link 'Other objects'
+ within '.selection-action-container' do
+ find '.editable', text: 'Now I have a new name.'
+ assert_no_selector '.editable', text: 'Now I have a name.'
+ end
+ end
+
+ test 'Create a project and move it into a different project' do
+ visit page_with_token 'active', '/projects'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: "Home").click
+ find('.btn', text: "Add a subproject").click
+
+ within('h2') do
+ find('.fa-pencil').click
+ find('.editable-input input').set('Project 1234')
+ find('.glyphicon-ok').click
+ end
+ wait_for_ajax
+
+ visit '/projects'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: "Home").click
+ find('.btn', text: "Add a subproject").click
+ within('h2') do
+ find('.fa-pencil').click
+ find('.editable-input input').set('Project 5678')
+ find('.glyphicon-ok').click
+ end
+ wait_for_ajax
+
+ click_link 'Move project...'
+ find('.selectable', text: 'Project 1234').click
+ find('.modal-footer a,button', text: 'Move').click
+ wait_for_ajax
+
+ # Wait for the page to refresh and show the new parent in Sharing panel
+ click_link 'Sharing'
+ assert(page.has_link?("Project 1234"),
+ "Project 5678 should now be inside project 1234")
+ end
+
+ def show_project_using(auth_key, proj_key='aproject')
+ project_uuid = api_fixture('groups')[proj_key]['uuid']
+ visit(page_with_token(auth_key, "/projects/#{project_uuid}"))
+ assert(page.has_text?("A Project"), "not on expected project page")
+ end
+
+ def share_rows
+ find('#project_sharing').all('tr')
+ end
+
+ def add_share_and_check(share_type, name, obj=nil)
+ assert(page.has_no_text?(name), "project is already shared with #{name}")
+ start_share_count = share_rows.size
+ click_on("Share with #{share_type}")
+ within(".modal-container") do
+ # Order is important here: we should find something that appears in the
+ # modal before we make any assertions about what's not in the modal.
+ # Otherwise, the not-included assertions might falsely pass because
+ # the modal hasn't loaded yet.
+ find(".selectable", text: name).click
+ assert(has_no_selector?(".modal-dialog-preview-pane"),
+ "preview pane available in sharing dialog")
+ if share_type == 'users' and obj and obj['email']
+ assert(page.has_text?(obj['email']), "Did not find user's email")
+ end
+ assert_raises(Capybara::ElementNotFound,
+ "Projects pulldown available from sharing dialog") do
+ click_on "All projects"
+ end
+ click_on "Add"
+ end
+ using_wait_time(Capybara.default_wait_time * 3) do
+ assert(page.has_link?(name),
+ "new share was not added to sharing table")
+ assert_equal(start_share_count + 1, share_rows.size,
+ "new share did not add row to sharing table")
+ end
+ end
+
+ def modify_share_and_check(name)
+ start_rows = share_rows
+ link_row = start_rows.select { |row| row.has_text?(name) }
+ assert_equal(1, link_row.size, "row with new permission not found")
+ within(link_row.first) do
+ click_on("Read")
+ select("Write", from: "share_change_level")
+ click_on("editable-submit")
+ assert(has_link?("Write"),
+ "failed to change access level on new share")
+ click_on "Revoke"
+ if Capybara.current_driver == :selenium
+ page.driver.browser.switch_to.alert.accept
+ else
+ # poltergeist returns true for confirm(), so we don't need to accept.
+ end
+ end
+ wait_for_ajax
+ using_wait_time(Capybara.default_wait_time * 3) do
+ assert(page.has_no_text?(name),
+ "new share row still exists after being revoked")
+ assert_equal(start_rows.size - 1, share_rows.size,
+ "revoking share did not remove row from sharing table")
+ end
+ end
+
+ test "project viewer can't see project sharing tab" do
+ show_project_using("project_viewer")
+ assert(page.has_no_link?("Sharing"),
+ "read-only project user sees sharing tab")
+ end
+
+ test "project owner can manage sharing for another user" do
+ add_user = api_fixture('users')['future_project_user']
+ new_name = ["first_name", "last_name"].map { |k| add_user[k] }.join(" ")
+
+ show_project_using("active")
+ click_on "Sharing"
+ add_share_and_check("users", new_name, add_user)
+ modify_share_and_check(new_name)
+ end
+
+ test "project owner can manage sharing for another group" do
+ new_name = api_fixture('groups')['future_project_viewing_group']['name']
+
+ show_project_using("active")
+ click_on "Sharing"
+ add_share_and_check("groups", new_name)
+ modify_share_and_check(new_name)
+ end
+
+ test "'share with group' listing does not offer projects" do
+ show_project_using("active")
+ click_on "Sharing"
+ click_on "Share with groups"
+ good_uuid = api_fixture("groups")["private"]["uuid"]
+ assert(page.has_selector?(".selectable[data-object-uuid=\"#{good_uuid}\"]"),
+ "'share with groups' listing missing owned user group")
+ bad_uuid = api_fixture("groups")["asubproject"]["uuid"]
+ assert(page.has_no_selector?(".selectable[data-object-uuid=\"#{bad_uuid}\"]"),
+ "'share with groups' listing includes project")
+ end
+
+ [
+ ['Move',api_fixture('collections')['collection_to_move_around_in_aproject'],
+ api_fixture('groups')['aproject'],api_fixture('groups')['asubproject']],
+ ['Remove',api_fixture('collections')['collection_to_move_around_in_aproject'],
+ api_fixture('groups')['aproject']],
+ ['Copy',api_fixture('collections')['collection_to_move_around_in_aproject'],
+ api_fixture('groups')['aproject'],api_fixture('groups')['asubproject']],
+ ['Remove',api_fixture('collections')['collection_in_aproject_with_same_name_as_in_home_project'],
+ api_fixture('groups')['aproject'],nil,true],
+ ].each do |action, my_collection, src, dest=nil, expect_name_change=nil|
+ test "selection #{action} -> #{expect_name_change.inspect} for project" do
+ perform_selection_action src, dest, my_collection, action
+
+ case action
+ when 'Copy'
+ assert page.has_text?(my_collection['name']), 'Collection not found in src project after copy'
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: dest['name']).click
+ assert page.has_text?(my_collection['name']), 'Collection not found in dest project after copy'
+
+ when 'Move'
+ assert page.has_no_text?(my_collection['name']), 'Collection still found in src project after move'
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: dest['name']).click
+ assert page.has_text?(my_collection['name']), 'Collection not found in dest project after move'
+
+ when 'Remove'
+ assert page.has_no_text?(my_collection['name']), 'Collection still found in src project after remove'
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: "Home").click
+ assert page.has_text?(my_collection['name']), 'Collection not found in home project after remove'
+ if expect_name_change
+ assert page.has_text?(my_collection['name']+' removed from ' + src['name']),
+ 'Collection with update name is not found in home project after remove'
+ end
+ end
+ end
+ end
+
+ def perform_selection_action src, dest, item, action
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: src['name']).click
+ assert page.has_text?(item['name']), 'Collection not found in src project'
+
+ within('tr', text: item['name']) do
+ find('input[type=checkbox]').click
+ end
+
+ click_button 'Selection'
+
+ within('.selection-action-container') do
+ assert page.has_text?("Compare selected"), "Compare selected link text not found"
+ assert page.has_link?("Copy selected"), "Copy selected link not found"
+ assert page.has_link?("Move selected"), "Move selected link not found"
+ assert page.has_link?("Remove selected"), "Remove selected link not found"
+
+ click_link "#{action} selected"
+ end
+
+ # select the destination project if a Copy or Move action is being performed
+ if action == 'Copy' || action == 'Move'
+ within(".modal-container") do
+ find('.selectable', text: dest['name']).click
+ find('.modal-footer a,button', text: action).click
+ wait_for_ajax
+ end
+ end
+ end
+
+ # Test copy action state. It should not be available when a subproject is selected.
+ test "copy action is disabled when a subproject is selected" do
+ my_project = api_fixture('groups')['aproject']
+ my_collection = api_fixture('collections')['collection_to_move_around_in_aproject']
+ my_subproject = api_fixture('groups')['asubproject']
+
+ # verify that selection options are disabled on the project until an item is selected
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: my_project['name']).click
+
+ click_button 'Selection'
+ within('.selection-action-container') do
+ assert_selector 'li.disabled', text: 'Create new collection with selected collections'
+ assert_selector 'li.disabled', text: 'Compare selected'
+ assert_selector 'li.disabled', text: 'Copy selected'
+ assert_selector 'li.disabled', text: 'Move selected'
+ assert_selector 'li.disabled', text: 'Remove selected'
+ end
+
+ # select collection and verify links are enabled
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: my_project['name']).click
+ assert page.has_text?(my_collection['name']), 'Collection not found in project'
+
+ within('tr', text: my_collection['name']) do
+ find('input[type=checkbox]').click
+ end
+
+ click_button 'Selection'
+ within('.selection-action-container') do
+ assert_no_selector 'li.disabled', text: 'Create new collection with selected collections'
+ assert_selector 'li', text: 'Create new collection with selected collections'
+ assert_selector 'li.disabled', text: 'Compare selected'
+ assert_no_selector 'li.disabled', text: 'Copy selected'
+ assert_selector 'li', text: 'Copy selected'
+ assert_no_selector 'li.disabled', text: 'Move selected'
+ assert_selector 'li', text: 'Move selected'
+ assert_no_selector 'li.disabled', text: 'Remove selected'
+ assert_selector 'li', text: 'Remove selected'
+ end
+
+ # select subproject and verify that copy action is disabled
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: my_project['name']).click
+
+ click_link 'Subprojects'
+ assert page.has_text?(my_subproject['name']), 'Subproject not found in project'
+
+ within('tr', text: my_subproject['name']) do
+ find('input[type=checkbox]').click
+ end
+
+ click_button 'Selection'
+ within('.selection-action-container') do
+ assert_selector 'li.disabled', text: 'Create new collection with selected collections'
+ assert_selector 'li.disabled', text: 'Compare selected'
+ assert_selector 'li.disabled', text: 'Copy selected'
+ assert_no_selector 'li.disabled', text: 'Move selected'
+ assert_selector 'li', text: 'Move selected'
+ assert_no_selector 'li.disabled', text: 'Remove selected'
+ assert_selector 'li', text: 'Remove selected'
+ end
+
+ # select subproject and a collection and verify that copy action is still disabled
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: my_project['name']).click
+
+ click_link 'Subprojects'
+ assert page.has_text?(my_subproject['name']), 'Subproject not found in project'
+
+ within('tr', text: my_subproject['name']) do
+ find('input[type=checkbox]').click
+ end
+
+ click_link 'Data collections'
+ assert page.has_text?(my_collection['name']), 'Collection not found in project'
+
+ within('tr', text: my_collection['name']) do
+ find('input[type=checkbox]').click
+ end
+
+ click_link 'Subprojects'
+ click_button 'Selection'
+ within('.selection-action-container') do
+ assert_selector 'li.disabled', text: 'Create new collection with selected collections'
+ assert_selector 'li.disabled', text: 'Compare selected'
+ assert_selector 'li.disabled', text: 'Copy selected'
+ assert_no_selector 'li.disabled', text: 'Move selected'
+ assert_selector 'li', text: 'Move selected'
+ assert_no_selector 'li.disabled', text: 'Remove selected'
+ assert_selector 'li', text: 'Remove selected'
+ end
+ end
+
+ # When project tabs are switched, only options applicable to the current tab's selections are enabled.
+ test "verify selection options when tabs are switched" do
+ my_project = api_fixture('groups')['aproject']
+ my_collection = api_fixture('collections')['collection_to_move_around_in_aproject']
+ my_subproject = api_fixture('groups')['asubproject']
+
+ # select subproject and a collection and verify that copy action is still disabled
+ visit page_with_token 'active', '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: my_project['name']).click
+
+ # Select a sub-project
+ click_link 'Subprojects'
+ assert page.has_text?(my_subproject['name']), 'Subproject not found in project'
+
+ within('tr', text: my_subproject['name']) do
+ find('input[type=checkbox]').click
+ end
+
+ # Select a collection
+ click_link 'Data collections'
+ assert page.has_text?(my_collection['name']), 'Collection not found in project'
+
+ within('tr', text: my_collection['name']) do
+ find('input[type=checkbox]').click
+ end
+
+ # Go back to Subprojects tab
+ click_link 'Subprojects'
+ click_button 'Selection'
+ within('.selection-action-container') do
+ assert_selector 'li.disabled', text: 'Create new collection with selected collections'
+ assert_selector 'li.disabled', text: 'Compare selected'
+ assert_selector 'li.disabled', text: 'Copy selected'
+ assert_no_selector 'li.disabled', text: 'Move selected'
+ assert_selector 'li', text: 'Move selected'
+ assert_no_selector 'li.disabled', text: 'Remove selected'
+ assert_selector 'li', text: 'Remove selected'
+ end
+
+ # Close the dropdown by clicking outside it.
+ find('.dropdown-toggle', text: 'Selection').find(:xpath, '..').click
+
+ # Go back to Data collections tab
+ find('.nav-tabs a', text: 'Data collections').click
+ click_button 'Selection'
+ within('.selection-action-container') do
+ assert_no_selector 'li.disabled', text: 'Create new collection with selected collections'
+ assert_selector 'li', text: 'Create new collection with selected collections'
+ assert_selector 'li.disabled', text: 'Compare selected'
+ assert_no_selector 'li.disabled', text: 'Copy selected'
+ assert_selector 'li', text: 'Copy selected'
+ assert_no_selector 'li.disabled', text: 'Move selected'
+ assert_selector 'li', text: 'Move selected'
+ assert_no_selector 'li.disabled', text: 'Remove selected'
+ assert_selector 'li', text: 'Remove selected'
+ end
+ end
+
+ # "Move selected" and "Remove selected" options should not be available when current user cannot write to the project
+ test "move selected and remove selected actions not available when current user cannot write to project" do
+ my_project = api_fixture('groups')['anonymously_accessible_project']
+ visit page_with_token 'active', "/projects/#{my_project['uuid']}"
+
+ click_button 'Selection'
+ within('.selection-action-container') do
+ assert_selector 'li', text: 'Create new collection with selected collections'
+ assert_selector 'li', text: 'Compare selected'
+ assert_selector 'li', text: 'Copy selected'
+ assert_no_selector 'li', text: 'Move selected'
+ assert_no_selector 'li', text: 'Remove selected'
+ end
+ end
+
+ [
+ ['active', true],
+ ['project_viewer', false],
+ ].each do |user, expect_collection_in_aproject|
+ test "combine selected collections into new collection #{user} #{expect_collection_in_aproject}" do
+ my_project = api_fixture('groups')['aproject']
+ my_collection = api_fixture('collections')['collection_to_move_around_in_aproject']
+
+ visit page_with_token user, '/'
+ find("#projects-menu").click
+ find(".dropdown-menu a", text: my_project['name']).click
+ assert page.has_text?(my_collection['name']), 'Collection not found in project'
+
+ within('tr', text: my_collection['name']) do
+ find('input[type=checkbox]').click
+ end
+
+ click_button 'Selection'
+ within('.selection-action-container') do
+ click_link 'Create new collection with selected collections'
+ end
+
+ # now in the new collection page
+ if expect_collection_in_aproject
+ assert page.has_text?("Created new collection in the project #{my_project['name']}"),
+ 'Not found flash message that new collection is created in aproject'
+ else
+ assert page.has_text?("Created new collection in your Home project"),
+ 'Not found flash message that new collection is created in Home project'
+ end
+ assert page.has_text?('Content hash'), 'Not found content hash in collection page'
+ end
+ end
+
+ [
+ ["jobs", "/jobs"],
+ ["pipelines", "/pipeline_instances"],
+ ["collections", "/collections"]
+ ].each do |target,path|
+ test "Test dashboard button all #{target}" do
+ visit page_with_token 'active', '/'
+ click_link "All #{target}"
+ assert_equal path, current_path
+ end
+ end
+
+ def scroll_setup(project_name,
+ total_nbr_items,
+ item_list_parameter,
+ sorted = false,
+ sort_parameters = nil)
+ project_uuid = api_fixture('groups')[project_name]['uuid']
+ visit page_with_token 'user1_with_load', '/projects/' + project_uuid
+
+ assert(page.has_text?("#{item_list_parameter.humanize} (#{total_nbr_items})"), "Number of #{item_list_parameter.humanize} did not match the input amount")
+
+ click_link item_list_parameter.humanize
+ wait_for_ajax
+
+ if sorted
+ find("th[data-sort-order='#{sort_parameters.gsub(/\s/,'')}']").click
+ wait_for_ajax
+ end
+ end
+
+ def scroll_items_check(nbr_items,
+ fixture_prefix,
+ item_list_parameter,
+ item_selector,
+ sorted = false)
+ items = []
+ for i in 1..nbr_items
+ items << "#{fixture_prefix}#{i}"
+ end
+
+ verify_items = items.dup
+ unexpected_items = []
+ item_count = 0
+ within(".arv-project-#{item_list_parameter}") do
+ page.execute_script "window.scrollBy(0,999000)"
+ begin
+ wait_for_ajax
+ rescue
+ end
+
+ # Visit all rows. If not all expected items are found, retry
+ found_items = page.all(item_selector)
+ item_count = found_items.count
+
+ previous = nil
+ (0..item_count-1).each do |i|
+ # Found row text using the fixture string e.g. "Show Collection_#{n} "
+ item_name = found_items[i].text.split[1]
+ if !items.include? item_name
+ unexpected_items << item_name
+ else
+ verify_items.delete item_name
+ end
+ if sorted
+ # check sort order
+ assert_operator( previous.downcase, :<=, item_name.downcase) if previous
+ previous = item_name
+ end
+ end
+
+ assert_equal true, unexpected_items.empty?, "Found unexpected #{item_list_parameter.humanize} #{unexpected_items.inspect}"
+ assert_equal nbr_items, item_count, "Found different number of #{item_list_parameter.humanize}"
+ assert_equal true, verify_items.empty?, "Did not find all the #{item_list_parameter.humanize}"
+ end
+ end
+
+ [
+ ['project_with_10_collections', 10],
+ ['project_with_201_collections', 201], # two pages of data
+ ].each do |project_name, nbr_items|
+ test "scroll collections tab for #{project_name} with #{nbr_items} objects" do
+ item_list_parameter = "Data_collections"
+ scroll_setup project_name,
+ nbr_items,
+ item_list_parameter
+ scroll_items_check nbr_items,
+ "Collection_",
+ item_list_parameter,
+ 'tr[data-kind="arvados#collection"]'
+ end
+ end
+
+ [
+ ['project_with_10_collections', 10],
+ ['project_with_201_collections', 201], # two pages of data
+ ].each do |project_name, nbr_items|
+ test "scroll collections tab for #{project_name} with #{nbr_items} objects with ascending sort (case insensitive)" do
+ item_list_parameter = "Data_collections"
+ scroll_setup project_name,
+ nbr_items,
+ item_list_parameter,
+ true,
+ "collections.name"
+ scroll_items_check nbr_items,
+ "Collection_",
+ item_list_parameter,
+ 'tr[data-kind="arvados#collection"]',
+ true
+ end
+ end
+
+ [
+ ['project_with_10_pipelines', 10, 0],
+ ['project_with_2_pipelines_and_60_jobs', 2, 60],
+ ['project_with_25_pipelines', 25, 0],
+ ].each do |project_name, num_pipelines, num_jobs|
+ test "scroll pipeline instances tab for #{project_name} with #{num_pipelines} pipelines and #{num_jobs} jobs" do
+ item_list_parameter = "Jobs_and_pipelines"
+ scroll_setup project_name,
+ num_pipelines + num_jobs,
+ item_list_parameter
+ # check the general scrolling and the pipelines
+ scroll_items_check num_pipelines,
+ "pipeline_",
+ item_list_parameter,
+ 'tr[data-kind="arvados#pipelineInstance"]'
+ # Check job count separately
+ jobs_found = page.all('tr[data-kind="arvados#job"]')
+ found_job_count = jobs_found.count
+ assert_equal num_jobs, found_job_count, 'Did not find expected number of jobs'
+ end
+ end
+
+ # Move button accessibility
+ [
+ ['admin', true],
+ ['active', true], # project owner
+ ['project_viewer', false],
+ ].each do |user, can_move|
+ test "#{user} can move subproject under another user's Home #{can_move}" do
+ project = api_fixture('groups')['aproject']
+ collection = api_fixture('collections')['collection_to_move_around_in_aproject']
+
+ # verify the project move button
+ visit page_with_token user, "/projects/#{project['uuid']}"
+ if can_move
+ assert page.has_link? 'Move project...'
+ else
+ assert page.has_no_link? 'Move project...'
+ end
+ end
+ end
+
+ test "error while loading tab" do
+ original_arvados_v1_base = Rails.configuration.arvados_v1_base
+
+ visit page_with_token 'active', '/projects/' + api_fixture('groups')['aproject']['uuid']
+
+ # Point to a bad api server url to generate error
+ Rails.configuration.arvados_v1_base = "https://[100::f]:1/"
+ click_link 'Other objects'
+ within '#Other_objects' do
+ # Error
+ assert_selector('a', text: 'Reload tab')
+
+ # Now point back to the orig api server and reload tab
+ Rails.configuration.arvados_v1_base = original_arvados_v1_base
+ click_link 'Reload tab'
+ assert_no_selector('a', text: 'Reload tab')
+ assert_selector('button', text: 'Selection')
+ within '.selection-action-container' do
+ assert_selector 'tr[data-kind="arvados#trait"]'
+ end
+ end
+ end
+
+ test "add new project using projects dropdown" do
+ # verify that selection options are disabled on the project until an item is selected
+ visit page_with_token 'active', '/'
+
+ # Add a new project
+ find("#projects-menu").click
+ click_link 'Add a new project'
+ assert_text 'New project'
+ assert_text 'No description provided'
+
+ # Add one more new project
+ find("#projects-menu").click
+ click_link 'Add a new project'
+ match = /New project \(\d\)/.match page.text
+ assert match, 'Expected project name not found'
+ assert_text 'No description provided'
+ end
+
+ test "first tab loads data when visiting other tab directly" do
+ # As of 2014-12-19, the first tab of project#show uses infinite scrolling.
+ # Make sure that it loads data even if we visit another tab directly.
+ need_selenium 'to land on specified tab using {url}#Advanced'
+ project = api_fixture("groups", "aproject")
+ visit(page_with_token("active_trustedclient",
+ "/projects/#{project['uuid']}#Advanced"))
+ assert_text("API response")
+ find("#page-wrapper .nav-tabs :first-child a").click
+ assert_text("bytes Collection")
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class ReportIssueTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ @user_profile_form_fields = Rails.configuration.user_profile_form_fields
+ end
+
+ teardown do
+ Rails.configuration.user_profile_form_fields = @user_profile_form_fields
+ end
+
+ # test version info and report issue from help menu
+ def check_version_info_and_report_issue_from_help_menu
+ within '.navbar-fixed-top' do
+ find('.help-menu > a').click
+ within '.help-menu .dropdown-menu' do
+ assert page.has_link?('Tutorials and User guide'), 'No link - Tutorials and User guide'
+ assert page.has_link?('API Reference'), 'No link - API Reference'
+ assert page.has_link?('SDK Reference'), 'No link - SDK Reference'
+ assert page.has_link?('Show version / debugging info ...'), 'No link - Show version / debugging info'
+ assert page.has_link?('Report a problem ...'), 'No link - Report a problem'
+
+ # check show version info link
+ click_link 'Show version / debugging info ...'
+ end
+ end
+
+ within '.modal-content' do
+ assert page.has_text?('Version / debugging info'), 'No text - Version / debugging info'
+ assert page.has_no_text?('Report a problem'), 'Found text - Report a problem'
+ assert page.has_no_text?('Describe the problem?'), 'Found text - Describe the problem'
+ assert page.has_button?('Close'), 'No button - Close'
+ assert page.has_no_button?('Send problem report'), 'Found button - Send problem report'
+ history_links = all('a').select do |a|
+ a[:href] =~ %r!^https://arvados.org/projects/arvados/repository/changes\?rev=[0-9a-f]+$!
+ end
+ assert_operator(2, :<=, history_links.count,
+ "Should have found two links to revision history " +
+ "in #{history_links.inspect}")
+ click_button 'Close'
+ end
+
+ # check report issue link
+ within '.navbar-fixed-top' do
+ find('.help-menu > a').click
+ find('.help-menu .dropdown-menu a', text: 'Report a problem ...').click
+ end
+
+ within '.modal-content' do
+ assert page.has_text?('Report a problem'), 'No text - Report a problem'
+ assert page.has_no_text?('Version / debugging info'), 'Found text - Version / debugging info'
+ assert page.has_text?('Describe the problem'), 'No text - Describe the problem'
+ assert page.has_no_button?('Close'), 'Found button - Close'
+ assert page.has_text?('Send problem report'), 'Send problem report button text is not found'
+ assert page.has_no_button?('Send problem report'), 'Send problem report button is not disabled before entering problem description'
+ assert page.has_button?('Cancel'), 'No button - Cancel'
+
+ # enter a report text and click on report
+ page.find_field('report_issue_text').set 'my test report text'
+ assert page.has_button?('Send problem report'), 'Send problem report button not enabled after entering text'
+ click_button 'Send problem report'
+
+ # ajax success updated button texts and added footer message
+ assert page.has_no_text?('Send problem report'), 'Found button - Send problem report'
+ assert page.has_no_button?('Cancel'), 'Found button - Cancel'
+ assert page.has_text?('Report sent'), 'No text - Report sent'
+ assert page.has_button?('Close'), 'No text - Close'
+ assert page.has_text?('Thanks for reporting this issue'), 'No text - Thanks for reporting this issue'
+
+ click_button 'Close'
+ end
+ end
+
+ [
+ [nil, nil],
+ ['inactive', api_fixture('users')['inactive']],
+ ['inactive_uninvited', api_fixture('users')['inactive_uninvited']],
+ ['active', api_fixture('users')['active']],
+ ['admin', api_fixture('users')['admin']],
+ ['active_no_prefs', api_fixture('users')['active_no_prefs']],
+ ['active_no_prefs_profile', api_fixture('users')['active_no_prefs_profile']],
+ ].each do |token, user|
+
+ test "check version info and report issue for user #{token}" do
+ if !token
+ visit ('/')
+ else
+ visit page_with_token(token)
+ end
+
+ check_version_info_and_report_issue_from_help_menu
+ end
+
+ end
+
+end
--- /dev/null
+require 'integration_helper'
+
+class SearchBoxTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ # test the search box
+ def verify_search_box user
+ if user && user['is_active']
+ # let's search for a valid uuid
+ within('.navbar-fixed-top') do
+ page.has_field?('search')
+ page.find_field('search').set user['uuid']
+ page.find('.glyphicon-search').click
+ end
+
+ # we should now be in the user's home project as a result of search
+ assert_selector "#Data_collections[data-object-uuid='#{user['uuid']}']", "Expected to be in user page after search click"
+
+ # let's search again for an invalid valid uuid
+ within('.navbar-fixed-top') do
+ search_for = String.new user['uuid']
+ search_for[0]='1'
+ page.find_field('search').set search_for
+ page.find('.glyphicon-search').click
+ end
+
+ # we should see 'not found' error page
+ assert page.has_text?('Not Found'), 'No text - Not Found'
+ assert page.has_link?('Report problem'), 'No text - Report problem'
+ click_link 'Report problem'
+ within '.modal-content' do
+ assert page.has_text?('Report a problem'), 'No text - Report a problem'
+ assert page.has_no_text?('Version / debugging info'), 'No text - Version / debugging info'
+ assert page.has_text?('Describe the problem'), 'No text - Describe the problem'
+ assert page.has_text?('Send problem report'), 'Send problem report button text is not found'
+ assert page.has_no_button?('Send problem report'), 'Send problem report button is not disabled before entering problem description'
+ assert page.has_button?('Cancel'), 'No button - Cancel'
+
+ # enter a report text and click on report
+ page.find_field('report_issue_text').set 'my test report text'
+ assert page.has_button?('Send problem report'), 'Send problem report button not enabled after entering text'
+ click_button 'Send problem report'
+
+ # ajax success updated button texts and added footer message
+ assert page.has_no_text?('Send problem report'), 'Found button - Send problem report'
+ assert page.has_no_button?('Cancel'), 'Found button - Cancel'
+ assert page.has_text?('Report sent'), 'No text - Report sent'
+ assert page.has_button?('Close'), 'No text - Close'
+ assert page.has_text?('Thanks for reporting this issue'), 'No text - Thanks for reporting this issue'
+
+ click_button 'Close'
+ end
+
+ # let's search for the anonymously accessible project
+ publicly_accessible_project = api_fixture('groups')['anonymously_accessible_project']
+
+ within('.navbar-fixed-top') do
+ # search again for the anonymously accessible project
+ page.find_field('search').set publicly_accessible_project['name'][0,10]
+ page.find('.glyphicon-search').click
+ end
+
+ within '.modal-content' do
+ assert page.has_text?('All projects'), 'No text - All projects'
+ assert page.has_text?('Search'), 'No text - Search'
+ assert page.has_text?('Cancel'), 'No text - Cancel'
+ assert_selector('div', text: publicly_accessible_project['name'])
+ find(:xpath, '//div[./span[contains(.,publicly_accessible_project["uuid"])]]').click
+
+ click_button 'Show'
+ end
+
+ # seeing "Unrestricted public data" now
+ assert page.has_text?(publicly_accessible_project['name']), 'No text - publicly accessible project name'
+ assert page.has_text?(publicly_accessible_project['description']), 'No text - publicly accessible project description'
+ else
+ within('.navbar-fixed-top') do
+ page.has_no_field?('search')
+ end
+ end
+ end
+
+ [
+ [nil, nil],
+ ['inactive', api_fixture('users')['inactive']],
+ ['inactive_uninvited', api_fixture('users')['inactive_uninvited']],
+ ['active', api_fixture('users')['active']],
+ ['admin', api_fixture('users')['admin']],
+ ].each do |token, user|
+
+ test "test search box for user #{token}" do
+ visit page_with_token(token)
+
+ verify_search_box user
+ end
+
+ end
+
+end
--- /dev/null
+require 'integration_helper'
+require 'uri'
+
+class SmokeTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ def assert_visit_success(allowed=[200])
+ assert_includes(allowed, status_code,
+ "#{current_url} returned #{status_code}, not one of " +
+ allowed.inspect)
+ end
+
+ def all_links_in(find_spec, text_regexp=//)
+ all(find_spec + ' a').collect { |tag|
+ if tag[:href].nil? or tag[:href].empty? or (tag.text !~ text_regexp)
+ nil
+ elsif tag[:'data-remote']
+ # these don't necessarily work with format=html
+ nil
+ else
+ url = URI(tag[:href])
+ url.host.nil? ? url.path : nil
+ end
+ }.compact
+ end
+
+ test "all first-level links succeed" do
+ visit page_with_token('active_trustedclient', '/')
+ assert_visit_success
+ click_link 'notifications-menu'
+ urls = [all_links_in('nav'),
+ all_links_in('.navbar', /^Manage /)].flatten
+ seen_urls = ['/']
+ while not (url = urls.shift).nil?
+ next if seen_urls.include? url
+ visit url
+ seen_urls << url
+ assert_visit_success
+ # Uncommenting the line below lets you crawl the entire site for a
+ # more thorough test.
+ # urls += all_links_in('body')
+ end
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class UserAgreementsTest < ActionDispatch::IntegrationTest
+
+ setup do
+ need_javascript
+ end
+
+ def continuebutton_selector
+ 'input[type=submit][disabled][value=Continue]'
+ end
+
+ test "cannot click continue without ticking checkbox" do
+ visit page_with_token('inactive')
+ assert_selector continuebutton_selector
+ end
+
+ test "continue button is enabled after ticking checkbox" do
+ visit page_with_token('inactive')
+ assert_selector continuebutton_selector
+ find('input[type=checkbox]').click
+ assert_no_selector continuebutton_selector
+ assert_nil(find_button('Continue')[:disabled],
+ 'Continue button did not become enabled')
+ end
+
+end
--- /dev/null
+require 'integration_helper'
+
+class UserManageAccountTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ end
+
+ # test manage_account page
+ def verify_manage_account user
+ if user['is_active']
+ within('.navbar-fixed-top') do
+ find('a', text: "#{user['email']}").click
+ within('.dropdown-menu') do
+ find('a', text: 'Manage account').click
+ end
+ end
+
+ # now in manage account page
+ assert page.has_text?('Virtual Machines'), 'No text - Virtual Machines'
+ assert page.has_text?('Repositories'), 'No text - Repositories'
+ assert page.has_text?('SSH Keys'), 'No text - SSH Keys'
+ assert page.has_text?('Current Token'), 'No text - Current Token'
+ assert page.has_text?('The Arvados API token is a secret key that enables the Arvados SDKs to access Arvados'), 'No text - Arvados API token'
+ add_and_verify_ssh_key
+ else # inactive user
+ within('.navbar-fixed-top') do
+ find('a', text: "#{user['email']}").click
+ within('.dropdown-menu') do
+ assert page.has_no_link?('Manage profile'), 'Found link - Manage profile'
+ end
+ end
+ end
+ end
+
+ def add_and_verify_ssh_key
+ click_link 'Add new SSH key'
+
+ within '.modal-content' do
+ assert page.has_text?('Public Key'), 'No text - Public Key'
+ assert page.has_button?('Cancel'), 'No button - Cancel'
+ assert page.has_button?('Submit'), 'No button - Submit'
+
+ page.find_field('public_key').set 'first test with an incorrect ssh key value'
+ click_button 'Submit'
+ assert page.has_text?('Public key does not appear to be a valid ssh-rsa or dsa public key'), 'No text - Public key does not appear to be a valid'
+
+ public_key_str = api_fixture('authorized_keys')['active']['public_key']
+ page.find_field('public_key').set public_key_str
+ page.find_field('name').set 'added_in_test'
+ click_button 'Submit'
+ assert page.has_text?('Public key already exists in the database, use a different key.'), 'No text - Public key already exists'
+
+ new_key = SSHKey.generate
+ page.find_field('public_key').set new_key.ssh_public_key
+ page.find_field('name').set 'added_in_test'
+ click_button 'Submit'
+ end
+
+ # key must be added. look for it in the refreshed page
+ assert page.has_text?('added_in_test'), 'No text - added_in_test'
+ end
+
+ [
+ ['inactive', api_fixture('users')['inactive']],
+ ['inactive_uninvited', api_fixture('users')['inactive_uninvited']],
+ ['active', api_fixture('users')['active']],
+ ['admin', api_fixture('users')['admin']],
+ ].each do |token, user|
+ test "test manage account for user #{token}" do
+ visit page_with_token(token)
+ verify_manage_account user
+ end
+ end
+
+ [
+ ['inactive_but_signed_user_agreement', true],
+ ['active', false],
+ ].each do |user, notifications|
+ test "test manage account for #{user} with notifications #{notifications}" do
+ visit page_with_token(user)
+ click_link 'notifications-menu'
+ if notifications
+ assert_selector('a', text: 'Click here to set up an SSH public key for use with Arvados')
+ assert_selector('a', text: 'Click here to learn how to run an Arvados Crunch pipeline')
+ click_link('Click here to set up an SSH public key for use with Arvados')
+ assert_selector('a', text: 'Add new SSH key')
+
+ add_and_verify_ssh_key
+
+ # No more SSH notification
+ click_link 'notifications-menu'
+ assert_no_selector('a', text: 'Click here to set up an SSH public key for use with Arvados')
+ assert_selector('a', text: 'Click here to learn how to run an Arvados Crunch pipeline')
+ else
+ assert_no_selector('a', text: 'Click here to set up an SSH public key for use with Arvados')
+ assert_no_selector('a', text: 'Click here to learn how to run an Arvados Crunch pipeline')
+ end
+ end
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class UserProfileTest < ActionDispatch::IntegrationTest
+ setup do
+ need_javascript
+ @user_profile_form_fields = Rails.configuration.user_profile_form_fields
+ end
+
+ teardown do
+ Rails.configuration.user_profile_form_fields = @user_profile_form_fields
+ end
+
+ def verify_homepage_with_profile user, invited, has_profile
+ profile_config = Rails.configuration.user_profile_form_fields
+
+ if !user
+ assert page.has_text?('Please log in'), 'Not found text - Please log in'
+ elsif user['is_active']
+ if profile_config && !has_profile
+ assert page.has_text?('Save profile'), 'No text - Save profile'
+ add_profile user
+ else
+ assert page.has_text?('Active pipelines'), 'Not found text - Active pipelines'
+ assert page.has_no_text?('Save profile'), 'Found text - Save profile'
+ end
+ elsif invited
+ assert page.has_text?('Please check the box below to indicate that you have read and accepted the user agreement'), 'Not found text - Please check the box below . . .'
+ assert page.has_no_text?('Save profile'), 'Found text - Save profile'
+ else
+ assert page.has_text?('Your account is inactive'), 'Not found text - Your account is inactive'
+ assert page.has_no_text?('Save profile'), 'Found text - Save profile'
+ end
+
+ within('.navbar-fixed-top') do
+ if !user
+ assert page.has_link?('Log in'), 'Not found link - Log in'
+ else
+ # my account menu
+ assert page.has_link?("#{user['email']}"), 'Not found link - email'
+ find('a', text: "#{user['email']}").click
+ within('.dropdown-menu') do
+ if user['is_active']
+ assert page.has_no_link?('Not active'), 'Found link - Not active'
+ assert page.has_no_link?('Sign agreements'), 'Found link - Sign agreements'
+
+ assert page.has_link?('Manage account'), 'No link - Manage account'
+
+ if profile_config
+ assert page.has_link?('Manage profile'), 'No link - Manage profile'
+ else
+ assert page.has_no_link?('Manage profile'), 'Found link - Manage profile'
+ end
+ end
+ assert page.has_link?('Log out'), 'No link - Log out'
+ end
+ end
+ end
+ end
+
+ # Check manage profile page and add missing profile to the user
+ def add_profile user
+ assert page.has_no_text?('My projects'), 'Found text - My projects'
+ assert page.has_no_text?('Projects shared with me'), 'Found text - Projects shared with me'
+
+ assert page.has_text?('Profile'), 'No text - Profile'
+ assert page.has_text?('First name'), 'No text - First name'
+ assert page.has_text?('Last name'), 'No text - Last name'
+ assert page.has_text?('Identity URL'), 'No text - Identity URL'
+ assert page.has_text?('Email'), 'No text - Email'
+ assert page.has_text?(user['email']), 'No text - user email'
+
+ # Using the default profile which has message and one required field
+
+ # Save profile without filling in the required field. Expect to be back in this profile page again
+ click_button "Save profile"
+ assert page.has_text?('Profile'), 'No text - Profile'
+ assert page.has_text?('First name'), 'No text - First name'
+ assert page.has_text?('Last name'), 'No text - Last name'
+ assert page.has_text?('Save profile'), 'No text - Save profile'
+
+ # This time fill in required field and then save. Expect to go to requested page after that.
+ profile_message = Rails.configuration.user_profile_form_message
+ required_field_title = ''
+ required_field_key = ''
+ profile_config = Rails.configuration.user_profile_form_fields
+ profile_config.andand.each do |entry|
+ if entry['required']
+ required_field_key = entry['key']
+ required_field_title = entry['form_field_title']
+ end
+ end
+
+ assert page.has_text? profile_message.gsub(/<.*?>/,'')
+ assert page.has_text?(required_field_title), 'No text - configured required field title'
+
+ page.find_field('user[prefs][:profile][:'+required_field_key+']').set 'value to fill required field'
+
+ click_button "Save profile"
+ # profile saved and in profile page now with success
+ assert page.has_text?('Thank you for filling in your profile'), 'No text - Thank you for filling'
+ click_link 'Back to work!'
+
+ # profile saved and in home page now
+ assert page.has_text?('Active pipelines'), 'No text - Active pipelines'
+ end
+
+ [
+ [nil, nil, false, false],
+ ['inactive', api_fixture('users')['inactive'], true, false],
+ ['inactive_uninvited', api_fixture('users')['inactive_uninvited'], false, false],
+ ['active', api_fixture('users')['active'], true, true],
+ ['admin', api_fixture('users')['admin'], true, true],
+ ['active_no_prefs', api_fixture('users')['active_no_prefs'], true, false],
+ ['active_no_prefs_profile', api_fixture('users')['active_no_prefs_profile'], true, false],
+ ].each do |token, user, invited, has_profile|
+
+ test "visit home page when profile is configured for user #{token}" do
+ # Our test config enabled profile by default. So, no need to update config
+ if !token
+ visit ('/')
+ else
+ visit page_with_token(token)
+ end
+
+ verify_homepage_with_profile user, invited, has_profile
+ end
+
+ test "visit home page when profile not configured for user #{token}" do
+ Rails.configuration.user_profile_form_fields = false
+
+ if !token
+ visit ('/')
+ else
+ visit page_with_token(token)
+ end
+
+ verify_homepage_with_profile user, invited, has_profile
+ end
+
+ end
+
+end
--- /dev/null
+require 'integration_helper'
+
+class UsersTest < ActionDispatch::IntegrationTest
+
+ test "login as active user but not admin" do
+ need_javascript
+ visit page_with_token('active_trustedclient')
+
+ assert page.has_no_link? 'Users' 'Found Users link for non-admin user'
+ end
+
+ test "login as admin user and verify active user data" do
+ need_javascript
+ visit page_with_token('admin_trustedclient')
+
+ # go to Users list page
+ find('#system-menu').click
+ click_link 'Users'
+
+ # check active user attributes in the list page
+ page.within(:xpath, '//tr[@data-object-uuid="zzzzz-tpzed-xurymjxw79nv3jz"]') do
+ assert (text.include? 'true false'), 'Expected is_active'
+ end
+
+ find('tr', text: 'zzzzz-tpzed-xurymjxw79nv3jz').
+ find('a', text: 'Show').
+ click
+ assert page.has_text? 'Attributes'
+ assert page.has_text? 'Advanced'
+ assert page.has_text? 'Admin'
+
+ # go to the Attributes tab
+ click_link 'Attributes'
+ assert page.has_text? 'modified_by_user_uuid'
+ page.within(:xpath, '//span[@data-name="is_active"]') do
+ assert_equal "true", text, "Expected user's is_active to be true"
+ end
+ page.within(:xpath, '//span[@data-name="is_admin"]') do
+ assert_equal "false", text, "Expected user's is_admin to be false"
+ end
+
+ end
+
+ test "create a new user" do
+ need_javascript
+
+ visit page_with_token('admin_trustedclient')
+
+ find('#system-menu').click
+ click_link 'Users'
+
+ assert page.has_text? 'zzzzz-tpzed-d9tiejq69daie8f'
+
+ click_link 'Add a new user'
+
+ within '.modal-content' do
+ find 'label', text: 'Virtual Machine'
+ fill_in "email", :with => "foo@example.com"
+ fill_in "repo_name", :with => "test_repo"
+ click_button "Submit"
+ wait_for_ajax
+ end
+
+ visit '/users'
+
+ # verify that the new user showed up in the users page and find
+ # the new user's UUID
+ new_user_uuid =
+ find('tr[data-object-uuid]', text: 'foo@example.com')['data-object-uuid']
+ assert new_user_uuid, "Expected new user uuid not found"
+
+ # go to the new user's page
+ find('tr', text: new_user_uuid).
+ find('a', text: 'Show').
+ click
+
+ assert page.has_text? 'modified_by_user_uuid'
+ page.within(:xpath, '//span[@data-name="is_active"]') do
+ assert_equal "false", text, "Expected new user's is_active to be false"
+ end
+
+ click_link 'Advanced'
+ click_link 'Metadata'
+ assert page.has_text? 'Repository: test_repo'
+ assert !(page.has_text? 'VirtualMachine:')
+ end
+
+ test "setup the active user" do
+ need_javascript
+ visit page_with_token('admin_trustedclient')
+
+ find('#system-menu').click
+ click_link 'Users'
+
+ # click on active user
+ find('tr', text: 'zzzzz-tpzed-xurymjxw79nv3jz').
+ find('a', text: 'Show').
+ click
+ user_url = page.current_url
+
+ # Setup user
+ click_link 'Admin'
+ assert page.has_text? 'As an admin, you can setup'
+
+ click_link 'Setup Active User'
+
+ within '.modal-content' do
+ find 'label', text: 'Virtual Machine'
+ fill_in "repo_name", :with => "test_repo"
+ click_button "Submit"
+ end
+
+ visit user_url
+ assert page.has_text? 'modified_by_client_uuid'
+
+ click_link 'Advanced'
+ click_link 'Metadata'
+ assert page.has_text? 'Repository: test_repo'
+ assert !(page.has_text? 'VirtualMachine:')
+
+ # Click on Setup button again and this time also choose a VM
+ click_link 'Admin'
+ click_link 'Setup Active User'
+
+ within '.modal-content' do
+ fill_in "repo_name", :with => "second_test_repo"
+ select("testvm.shell", :from => 'vm_uuid')
+ click_button "Submit"
+ end
+
+ visit user_url
+ find '#Attributes', text: 'modified_by_client_uuid'
+
+ click_link 'Advanced'
+ click_link 'Metadata'
+ assert page.has_text? 'Repository: second_test_repo'
+ assert page.has_text? 'VirtualMachine: testvm.shell'
+ end
+
+ test "unsetup active user" do
+ need_javascript
+
+ visit page_with_token('admin_trustedclient')
+
+ find('#system-menu').click
+ click_link 'Users'
+
+ # click on active user
+ find('tr', text: 'zzzzz-tpzed-xurymjxw79nv3jz').
+ find('a', text: 'Show').
+ click
+ user_url = page.current_url
+
+ # Verify that is_active is set
+ find('a,button', text: 'Attributes').click
+ assert page.has_text? 'modified_by_user_uuid'
+ page.within(:xpath, '//span[@data-name="is_active"]') do
+ assert_equal "true", text, "Expected user's is_active to be true"
+ end
+
+ # go to Admin tab
+ click_link 'Admin'
+ assert page.has_text? 'As an admin, you can deactivate and reset this user'
+
+ # unsetup user and verify all the above links are deleted
+ click_link 'Admin'
+ click_button 'Deactivate Active User'
+
+ if Capybara.current_driver == :selenium
+ sleep(0.1)
+ page.driver.browser.switch_to.alert.accept
+ else
+ # poltergeist returns true for confirm(), so we don't need to accept.
+ end
+
+ # Should now be back in the Attributes tab for the user
+ assert page.has_text? 'modified_by_user_uuid'
+ page.within(:xpath, '//span[@data-name="is_active"]') do
+ assert_equal "false", text, "Expected user's is_active to be false after unsetup"
+ end
+
+ click_link 'Advanced'
+ click_link 'Metadata'
+ assert !(page.has_text? 'Repository: test_repo')
+ assert !(page.has_text? 'Repository: second_test_repo')
+ assert !(page.has_text? 'VirtualMachine: testvm.shell')
+
+ # setup user again and verify links present
+ click_link 'Admin'
+ click_link 'Setup Active User'
+
+ within '.modal-content' do
+ fill_in "repo_name", :with => "second_test_repo"
+ select("testvm.shell", :from => 'vm_uuid')
+ click_button "Submit"
+ end
+
+ visit user_url
+ assert page.has_text? 'modified_by_client_uuid'
+
+ click_link 'Advanced'
+ click_link 'Metadata'
+ assert page.has_text? 'Repository: second_test_repo'
+ assert page.has_text? 'VirtualMachine: testvm.shell'
+ end
+
+end
--- /dev/null
+require 'integration_helper'
+
+class VirtualMachinesTest < ActionDispatch::IntegrationTest
+ test "make and name a new virtual machine" do
+ need_javascript
+ visit page_with_token('admin_trustedclient')
+ find('#system-menu').click
+ click_link 'Virtual machines'
+ assert page.has_text? 'testvm.shell'
+ click_on 'Add a new virtual machine'
+ find('tr', text: 'hostname').
+ find('a[data-original-title=edit]').click
+ assert page.has_text? 'Edit hostname'
+ fill_in 'editable-text', with: 'testname'
+ click_button 'editable-submit'
+ assert page.has_text? 'testname'
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class WebsocketTest < ActionDispatch::IntegrationTest
+ setup do
+ need_selenium "to make websockets work"
+ end
+
+ test "test page" do
+ visit(page_with_token("admin", "/websockets"))
+ fill_in("websocket-message-content", :with => "Stuff")
+ click_button("Send")
+ assert_text '"status":400'
+ end
+
+ test "test live logging" do
+ visit(page_with_token("admin", "/pipeline_instances/zzzzz-d1hrv-9fm8l10i9z2kqc6"))
+ click_link("Log")
+ assert_no_text '123 hello'
+
+ api = ArvadosApiClient.new
+
+ Thread.current[:arvados_api_token] = @@API_AUTHS["admin"]['api_token']
+ api.api("logs", "", {log: {
+ object_uuid: "zzzzz-d1hrv-9fm8l10i9z2kqc6",
+ event_type: "stderr",
+ properties: {"text" => "123 hello"}}})
+ assert_text '123 hello'
+ Thread.current[:arvados_api_token] = nil
+ end
+
+
+ [["pipeline_instances", api_fixture("pipeline_instances")['pipeline_with_newer_template']['uuid']],
+ ["jobs", api_fixture("jobs")['running']['uuid']]].each do |c|
+ test "test live logging scrolling #{c[0]}" do
+
+ controller = c[0]
+ uuid = c[1]
+
+ visit(page_with_token("admin", "/#{controller}/#{uuid}"))
+ click_link("Log")
+ assert_no_text '123 hello'
+
+ api = ArvadosApiClient.new
+
+ text = ""
+ (1..1000).each do |i|
+ text << "#{i} hello\n"
+ end
+
+ Thread.current[:arvados_api_token] = @@API_AUTHS["admin"]['api_token']
+ api.api("logs", "", {log: {
+ object_uuid: uuid,
+ event_type: "stderr",
+ properties: {"text" => text}}})
+ assert_text '1000 hello'
+
+ # First test that when we're already at the bottom of the page, it scrolls down
+ # when a new line is added.
+ old_top = page.evaluate_script("$('#event_log_div').scrollTop()")
+
+ api.api("logs", "", {log: {
+ object_uuid: uuid,
+ event_type: "stderr",
+ properties: {"text" => "1001 hello\n"}}})
+ assert_text '1001 hello'
+
+ # Check that new value of scrollTop is greater than the old one
+ assert page.evaluate_script("$('#event_log_div').scrollTop()") > old_top
+
+ # Now scroll to 30 pixels from the top
+ page.execute_script "$('#event_log_div').scrollTop(30)"
+ assert_equal 30, page.evaluate_script("$('#event_log_div').scrollTop()")
+
+ api.api("logs", "", {log: {
+ object_uuid: uuid,
+ event_type: "stderr",
+ properties: {"text" => "1002 hello\n"}}})
+ assert_text '1002 hello'
+
+ # Check that we haven't changed scroll position
+ assert_equal 30, page.evaluate_script("$('#event_log_div').scrollTop()")
+
+ Thread.current[:arvados_api_token] = nil
+ end
+ end
+
+ test "pipeline instance arv-refresh-on-log-event" do
+ Thread.current[:arvados_api_token] = @@API_AUTHS["admin"]['api_token']
+ # Do something and check that the pane reloads.
+ p = PipelineInstance.create({state: "RunningOnServer",
+ components: {
+ c1: {
+ script: "test_hash.py",
+ script_version: "1de84a854e2b440dc53bf42f8548afa4c17da332"
+ }
+ }
+ })
+
+ visit(page_with_token("admin", "/pipeline_instances/#{p.uuid}"))
+
+ assert_text 'Active'
+ assert page.has_link? 'Pause'
+ assert_no_text 'Complete'
+ assert page.has_no_link? 'Re-run with latest'
+
+ p.state = "Complete"
+ p.save!
+
+ assert_no_text 'Active'
+ assert page.has_no_link? 'Pause'
+ assert_text 'Complete'
+ assert page.has_link? 'Re-run with latest'
+
+ Thread.current[:arvados_api_token] = nil
+ end
+
+ test "job arv-refresh-on-log-event" do
+ Thread.current[:arvados_api_token] = @@API_AUTHS["admin"]['api_token']
+ # Do something and check that the pane reloads.
+ p = Job.where(uuid: api_fixture('jobs')['running_will_be_completed']['uuid']).results.first
+
+ visit(page_with_token("admin", "/jobs/#{p.uuid}"))
+
+ assert_no_text 'complete'
+ assert_no_text 'Re-run same version'
+
+ p.state = "Complete"
+ p.save!
+
+ assert_text 'complete'
+ assert_text 'Re-run same version'
+
+ Thread.current[:arvados_api_token] = nil
+ end
+
+ test "dashboard arv-refresh-on-log-event" do
+ Thread.current[:arvados_api_token] = @@API_AUTHS["admin"]['api_token']
+
+ visit(page_with_token("admin", "/"))
+
+ assert_no_text 'test dashboard arv-refresh-on-log-event'
+
+ # Do something and check that the pane reloads.
+ p = PipelineInstance.create({state: "RunningOnServer",
+ name: "test dashboard arv-refresh-on-log-event",
+ components: {
+ }
+ })
+
+ assert_text 'test dashboard arv-refresh-on-log-event'
+
+ Thread.current[:arvados_api_token] = nil
+ end
+
+ test "live log charting" do
+ uuid = api_fixture("jobs")['running']['uuid']
+
+ visit page_with_token "admin", "/jobs/#{uuid}"
+ click_link "Log"
+
+ api = ArvadosApiClient.new
+
+ # should give 45.3% or (((36.39+0.86)/10.0002)/8)*100 rounded to 1 decimal place
+ text = "2014-11-07_23:33:51 #{uuid} 31708 1 stderr crunchstat: cpu 1970.8200 user 60.2700 sys 8 cpus -- interval 10.0002 seconds 35.3900 user 0.8600 sys"
+
+ Thread.current[:arvados_api_token] = @@API_AUTHS["admin"]['api_token']
+ api.api("logs", "", {log: {
+ object_uuid: uuid,
+ event_type: "stderr",
+ properties: {"text" => text}}})
+ wait_for_ajax
+
+ # using datapoint 1 instead of datapoint 0 because there will be a "dummy" datapoint with no actual stats 10 minutes previous to the one we're looking for, for the sake of making the x-axis of the graph show a full 10 minutes of time even though there is only a single real datapoint
+ cpu_stat = page.evaluate_script("jobGraphData[1]['T1-cpu']")
+
+ assert_equal 45.3, (cpu_stat.to_f*100).round(1)
+
+ Thread.current[:arvados_api_token] = nil
+ end
+
+ test "live log charting from replayed log" do
+ uuid = api_fixture("jobs")['running']['uuid']
+
+ visit page_with_token "admin", "/jobs/#{uuid}"
+ click_link "Log"
+
+ ApiServerForTests.new.run_rake_task("replay_job_log", "test/job_logs/crunchstatshort.log,1.0,#{uuid}")
+ wait_for_ajax
+
+ # see above comment as to why we use datapoint 1 rather than 0
+ cpu_stat = page.evaluate_script("jobGraphData[1]['T1-cpu']")
+
+ assert_equal 45.3, (cpu_stat.to_f*100).round(1)
+ end
+
+end
--- /dev/null
+require 'test_helper'
+require 'capybara/rails'
+require 'capybara/poltergeist'
+require 'uri'
+require 'yaml'
+
+Capybara.register_driver :poltergeist do |app|
+ Capybara::Poltergeist::Driver.new app, {
+ window_size: [1200, 800],
+ phantomjs_options: ['--ignore-ssl-errors=true'],
+ inspector: true,
+ }
+end
+
+module WaitForAjax
+ Capybara.default_wait_time = 5
+ def wait_for_ajax
+ Timeout.timeout(Capybara.default_wait_time) do
+ loop until finished_all_ajax_requests?
+ end
+ end
+
+ def finished_all_ajax_requests?
+ page.evaluate_script('jQuery.active').zero?
+ end
+end
+
+module AssertDomEvent
+ # Yield the supplied block, then wait for an event to arrive at a
+ # DOM element.
+ def assert_triggers_dom_event events, target='body'
+ magic = 'received-dom-event-' + rand(2**30).to_s(36)
+ page.evaluate_script <<eos
+ $('#{target}').one('#{events}', function() {
+ $('body').addClass('#{magic}');
+ });
+eos
+ yield
+ assert_selector "body.#{magic}"
+ page.evaluate_script "$('body').removeClass('#{magic}');";
+ end
+end
+
+module HeadlessHelper
+ class HeadlessSingleton
+ def self.get
+ @headless ||= Headless.new reuse: false
+ end
+ end
+
+ Capybara.default_driver = :rack_test
+
+ def self.included base
+ base.class_eval do
+ setup do
+ Capybara.use_default_driver
+ @headless = false
+ end
+
+ teardown do
+ if @headless
+ @headless.stop
+ @headless = false
+ end
+ end
+ end
+ end
+
+ def need_selenium reason=nil
+ Capybara.current_driver = :selenium
+ unless ENV['ARVADOS_TEST_HEADFUL'] or @headless
+ @headless = HeadlessSingleton.get
+ @headless.start
+ end
+ end
+
+ def need_javascript reason=nil
+ unless Capybara.current_driver == :selenium
+ Capybara.current_driver = :poltergeist
+ end
+ end
+end
+
+class ActionDispatch::IntegrationTest
+ # Make the Capybara DSL available in all integration tests
+ include Capybara::DSL
+ include ApiFixtureLoader
+ include WaitForAjax
+ include AssertDomEvent
+ include HeadlessHelper
+
+ @@API_AUTHS = self.api_fixture('api_client_authorizations')
+
+ def page_with_token(token, path='/')
+ # Generate a page path with an embedded API token.
+ # Typical usage: visit page_with_token('token_name', page)
+ # The token can be specified by the name of an api_client_authorizations
+ # fixture, or passed as a raw string.
+ api_token = ((@@API_AUTHS.include? token) ?
+ @@API_AUTHS[token]['api_token'] : token)
+ path_parts = path.partition("#")
+ sep = (path_parts.first.include? '?') ? '&' : '?'
+ q_string = URI.encode_www_form('api_token' => api_token)
+ path_parts.insert(1, "#{sep}#{q_string}")
+ path_parts.join("")
+ end
+
+ # Find a page element, but return false instead of raising an
+ # exception if not found. Use this with assertions to explain that
+ # the error signifies a failed test rather than an unexpected error
+ # during a testing procedure.
+ def find? *args
+ begin
+ find *args
+ rescue Capybara::ElementNotFound
+ false
+ end
+ end
+
+ @@screenshot_count = 1
+ def screenshot
+ image_file = "./tmp/workbench-fail-#{@@screenshot_count}.png"
+ begin
+ page.save_screenshot image_file
+ rescue Capybara::NotSupportedByDriverError
+ # C'est la vie.
+ else
+ puts "Saved #{image_file}"
+ @@screenshot_count += 1
+ end
+ end
+
+ teardown do
+ if not passed?
+ screenshot
+ end
+ if Capybara.current_driver == :selenium
+ page.execute_script("window.localStorage.clear()")
+ end
+ Capybara.reset_sessions!
+ end
+end
--- /dev/null
+# http://guides.rubyonrails.org/v3.2.13/performance_testing.html
+
+require 'test_helper'
+require 'rails/performance_test_help'
+require 'performance_test_helper'
+require 'selenium-webdriver'
+require 'headless'
+
+class BrowsingTest < WorkbenchPerformanceTest
+ self.profile_options = { :runs => 5,
+ :metrics => [:wall_time],
+ :output => 'tmp/performance',
+ :formats => [:flat] }
+
+ setup do
+ need_javascript
+ end
+
+ test "home page" do
+ visit_page_with_token
+ wait_for_ajax
+ assert_text 'Dashboard'
+ assert_selector 'a', text: 'Run a pipeline'
+ end
+
+ test "search for hash" do
+ visit_page_with_token
+ wait_for_ajax
+ assert_text 'Dashboard'
+
+ within('.navbar-fixed-top') do
+ page.find_field('search').set('hash')
+ wait_for_ajax
+ page.find('.glyphicon-search').click
+ end
+
+ # In the search dialog now. Expect at least one item in the result display.
+ within '.modal-content' do
+ wait_for_ajax
+ assert_text 'All projects'
+ assert_text 'Search'
+ assert(page.has_selector?(".selectable[data-object-uuid]"))
+ click_button 'Cancel'
+ end
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+# Performance test can run in two two different ways:
+#
+# 1. Similar to other integration tests using the command:
+# RAILS_ENV=test bundle exec rake test:benchmark
+#
+# 2. Against a configured workbench url using "RAILS_ENV=performance".
+# RAILS_ENV=performance bundle exec rake test:benchmark
+
+class WorkbenchPerformanceTest < ActionDispatch::PerformanceTest
+
+ # When running in "RAILS_ENV=performance" mode, uses performance
+ # config params. In this mode, prepends workbench URL to the given
+ # path provided, and visits that page using the configured
+ # "user_token".
+ def visit_page_with_token path='/'
+ if Rails.env == 'performance'
+ token = Rails.configuration.user_token
+ workbench_url = Rails.configuration.arvados_workbench_url
+ if workbench_url.end_with? '/'
+ workbench_url = workbench_url[0, workbench_url.size-1]
+ end
+ else
+ token = 'active'
+ workbench_url = ''
+ end
+
+ visit page_with_token(token, (workbench_url + path))
+ end
+
+end
--- /dev/null
+ENV["RAILS_ENV"] = "test" if (ENV["RAILS_ENV"] != "diagnostics" and ENV["RAILS_ENV"] != "performance")
+
+unless ENV["NO_COVERAGE_TEST"]
+ begin
+ require 'simplecov'
+ require 'simplecov-rcov'
+ class SimpleCov::Formatter::MergedFormatter
+ def format(result)
+ SimpleCov::Formatter::HTMLFormatter.new.format(result)
+ SimpleCov::Formatter::RcovFormatter.new.format(result)
+ end
+ end
+ SimpleCov.formatter = SimpleCov::Formatter::MergedFormatter
+ SimpleCov.start do
+ add_filter '/test/'
+ add_filter 'initializers/secret_token'
+ end
+ rescue Exception => e
+ $stderr.puts "SimpleCov unavailable (#{e}). Proceeding without."
+ end
+end
+
+require File.expand_path('../../config/environment', __FILE__)
+require 'rails/test_help'
+require 'mocha/mini_test'
+
+class ActiveSupport::TestCase
+ # Setup all fixtures in test/fixtures/*.(yml|csv) for all tests in
+ # alphabetical order.
+ #
+ # Note: You'll currently still have to declare fixtures explicitly
+ # in integration tests -- they do not yet inherit this setting
+ fixtures :all
+ def use_token token_name
+ auth = api_fixture('api_client_authorizations')[token_name.to_s]
+ Thread.current[:arvados_api_token] = auth['api_token']
+ end
+
+ teardown do
+ Thread.current[:arvados_api_token] = nil
+ Thread.current[:user] = nil
+ Thread.current[:reader_tokens] = nil
+ # Diagnostics suite doesn't run a server, so there's no cache to clear.
+ Rails.cache.clear unless (Rails.env == "diagnostics")
+ # Restore configuration settings changed during tests
+ $application_config.each do |k,v|
+ if k.match /^[^.]*$/
+ Rails.configuration.send (k + '='), v
+ end
+ end
+ end
+end
+
+module ApiFixtureLoader
+ def self.included(base)
+ base.extend(ClassMethods)
+ end
+
+ module ClassMethods
+ @@api_fixtures = {}
+ def api_fixture(name, *keys)
+ # Returns the data structure from the named API server test fixture.
+ @@api_fixtures[name] ||= \
+ begin
+ path = File.join(ApiServerForTests::ARV_API_SERVER_DIR,
+ 'test', 'fixtures', "#{name}.yml")
+ file = IO.read(path)
+ trim_index = file.index('# Test Helper trims the rest of the file')
+ file = file[0, trim_index] if trim_index
+ YAML.load(file)
+ end
+ keys.inject(@@api_fixtures[name]) { |hash, key| hash[key] }
+ end
+ end
+ def api_fixture(name, *keys)
+ self.class.api_fixture(name, *keys)
+ end
+
+ def find_fixture(object_class, name)
+ object_class.find(api_fixture(object_class.to_s.pluralize.underscore,
+ name, "uuid"))
+ end
+end
+
+class ActiveSupport::TestCase
+ include ApiFixtureLoader
+ def session_for api_client_auth_name
+ {
+ arvados_api_token: api_fixture('api_client_authorizations')[api_client_auth_name.to_s]['api_token']
+ }
+ end
+ def json_response
+ Oj.load(@response.body)
+ end
+end
+
+class ApiServerForTests
+ ARV_API_SERVER_DIR = File.expand_path('../../../../services/api', __FILE__)
+ SERVER_PID_PATH = File.expand_path('tmp/pids/wbtest-server.pid', ARV_API_SERVER_DIR)
+ WEBSOCKET_PID_PATH = File.expand_path('tmp/pids/wstest-server.pid', ARV_API_SERVER_DIR)
+ @main_process_pid = $$
+
+ def _system(*cmd)
+ $stderr.puts "_system #{cmd.inspect}"
+ Bundler.with_clean_env do
+ if not system({'RAILS_ENV' => 'test', "ARVADOS_WEBSOCKETS" => (if @websocket then "ws-only" end)}, *cmd)
+ raise RuntimeError, "#{cmd[0]} returned exit code #{$?.exitstatus}"
+ end
+ end
+ end
+
+ def make_ssl_cert
+ unless File.exists? './self-signed.key'
+ _system('openssl', 'req', '-new', '-x509', '-nodes',
+ '-out', './self-signed.pem',
+ '-keyout', './self-signed.key',
+ '-days', '3650',
+ '-subj', '/CN=localhost')
+ end
+ end
+
+ def kill_server
+ if (pid = find_server_pid)
+ $stderr.puts "Sending TERM to API server, pid #{pid}"
+ Process.kill 'TERM', pid
+ end
+ end
+
+ def find_server_pid
+ pid = nil
+ begin
+ pid = IO.read(@pidfile).to_i
+ $stderr.puts "API server is running, pid #{pid.inspect}"
+ rescue Errno::ENOENT
+ end
+ return pid
+ end
+
+ def run(args=[])
+ ::MiniTest.after_run do
+ self.kill_server
+ end
+
+ @websocket = args.include?("--websockets")
+
+ @pidfile = if @websocket
+ WEBSOCKET_PID_PATH
+ else
+ SERVER_PID_PATH
+ end
+
+ # Kill server left over from previous test run
+ self.kill_server
+
+ Capybara.javascript_driver = :poltergeist
+ Dir.chdir(ARV_API_SERVER_DIR) do |apidir|
+ ENV["NO_COVERAGE_TEST"] = "1"
+ if @websocket
+ _system('bundle', 'exec', 'passenger', 'start', '-d', '-p3333',
+ '--pid-file', @pidfile)
+ else
+ make_ssl_cert
+ _system('bundle', 'exec', 'rake', 'db:test:load')
+ _system('bundle', 'exec', 'rake', 'db:fixtures:load')
+ _system('bundle', 'exec', 'passenger', 'start', '-d', '-p3000',
+ '--pid-file', @pidfile,
+ '--ssl',
+ '--ssl-certificate', 'self-signed.pem',
+ '--ssl-certificate-key', 'self-signed.key')
+ end
+ timeout = Time.now.tv_sec + 10
+ good_pid = false
+ while (not good_pid) and (Time.now.tv_sec < timeout)
+ sleep 0.2
+ server_pid = find_server_pid
+ good_pid = (server_pid and
+ (server_pid > 0) and
+ (Process.kill(0, server_pid) rescue false))
+ end
+ if not good_pid
+ raise RuntimeError, "could not find API server Rails pid"
+ end
+ end
+ end
+
+ def run_rake_task(task_name, arg_string)
+ Dir.chdir(ARV_API_SERVER_DIR) do
+ _system('bundle', 'exec', 'rake', "#{task_name}[#{arg_string}]")
+ end
+ end
+end
+
+class ActionController::TestCase
+ setup do
+ @counter = 0
+ end
+
+ def check_counter action
+ @counter += 1
+ if @counter == 2
+ assert_equal 1, 2, "Multiple actions in controller test"
+ end
+ end
+
+ [:get, :post, :put, :patch, :delete].each do |method|
+ define_method method do |action, *args|
+ check_counter action
+ super action, *args
+ end
+ end
+end
+
+# Test classes can call reset_api_fixtures(when_to_reset,flag) to
+# override the default. Example:
+#
+# class MySuite < ActionDispatch::IntegrationTest
+# reset_api_fixtures :after_each_test, false
+# reset_api_fixtures :after_suite, true
+# ...
+# end
+#
+# The default behavior is reset_api_fixtures(:after_each_test,true).
+#
+class ActiveSupport::TestCase
+
+ def self.inherited subclass
+ subclass.class_eval do
+ class << self
+ attr_accessor :want_reset_api_fixtures
+ end
+ @want_reset_api_fixtures = {
+ after_each_test: true,
+ after_suite: false,
+ before_suite: false,
+ }
+ end
+ super
+ end
+ # Existing subclasses of ActiveSupport::TestCase (ones that already
+ # existed before we set up the self.inherited hook above) will not
+ # get their own instance variable. They're not real test cases
+ # anyway, so we give them a "don't reset anywhere" stub.
+ def self.want_reset_api_fixtures
+ {}
+ end
+
+ def self.reset_api_fixtures where, t=true
+ if not want_reset_api_fixtures.has_key? where
+ raise ArgumentError, "There is no #{where.inspect} hook"
+ end
+ self.want_reset_api_fixtures[where] = t
+ end
+
+ def self.run *args
+ reset_api_fixtures_now if want_reset_api_fixtures[:before_suite]
+ result = super
+ reset_api_fixtures_now if want_reset_api_fixtures[:after_suite]
+ result
+ end
+
+ def after_teardown
+ if self.class.want_reset_api_fixtures[:after_each_test]
+ self.class.reset_api_fixtures_now
+ end
+ super
+ end
+
+ protected
+ def self.reset_api_fixtures_now
+ # Never try to reset fixtures when we're just using test
+ # infrastructure to run performance/diagnostics suites.
+ return unless Rails.env == 'test'
+
+ auth = api_fixture('api_client_authorizations')['admin_trustedclient']
+ Thread.current[:arvados_api_token] = auth['api_token']
+ ArvadosApiClient.new.api(nil, '../../database/reset', {})
+ Thread.current[:arvados_api_token] = nil
+ end
+end
+
+# If it quacks like a duck, it must be a HTTP request object.
+class RequestDuck
+ def self.host
+ "localhost"
+ end
+
+ def self.port
+ 8080
+ end
+
+ def self.protocol
+ "http"
+ end
+end
+
+# Example:
+#
+# apps/workbench$ RAILS_ENV=test bundle exec irb -Ilib:test
+# > load 'test/test_helper.rb'
+# > singletest 'integration/collection_upload_test.rb', 'Upload two empty files'
+#
+def singletest test_class_file, test_name
+ load File.join('test', test_class_file)
+ Minitest.run ['-v', '-n', "test_#{test_name.gsub ' ', '_'}"]
+ Object.send(:remove_const,
+ test_class_file.gsub(/.*\/|\.rb$/, '').camelize.to_sym)
+ ::Minitest::Runnable.runnables.reject! { true }
+end
+
+if ENV["RAILS_ENV"].eql? 'test'
+ ApiServerForTests.new.run
+ ApiServerForTests.new.run ["--websockets"]
+end
--- /dev/null
+require 'test_helper'
+
+class ResourceListTest < ActiveSupport::TestCase
+
+ test 'links_for on a resource list that does not return links' do
+ use_token :active
+ results = Specimen.all
+ assert_equal [], results.links_for(api_fixture('users')['active']['uuid'])
+ end
+
+ test 'get all items by default' do
+ use_token :admin
+ a = 0
+ Collection.where(owner_uuid: 'zzzzz-j7d0g-0201collections').each do
+ a += 1
+ end
+ assert_equal 201, a
+ end
+
+ test 'prefetch all items' do
+ use_token :admin
+ a = 0
+ Collection.where(owner_uuid: 'zzzzz-j7d0g-0201collections').each do
+ a += 1
+ end
+ assert_equal 201, a
+ end
+
+ test 'get limited items' do
+ use_token :admin
+ a = 0
+ Collection.where(owner_uuid: 'zzzzz-j7d0g-0201collections').limit(51).each do
+ a += 1
+ end
+ assert_equal 51, a
+ end
+
+ test 'get limited items, limit % page_size != 0' do
+ skip "Requires server MAX_LIMIT < 200 which is not currently the default"
+
+ use_token :admin
+ max_page_size = Collection.
+ where(owner_uuid: 'zzzzz-j7d0g-0201collections').
+ limit(1000000000).
+ fetch_multiple_pages(false).
+ count
+ # Conditions necessary for this test to be valid:
+ assert_operator 200, :>, max_page_size
+ assert_operator 1, :<, max_page_size
+ # Verify that the server really sends max_page_size when asked for max_page_size+1
+ assert_equal max_page_size, Collection.
+ where(owner_uuid: 'zzzzz-j7d0g-0201collections').
+ limit(max_page_size+1).
+ fetch_multiple_pages(false).
+ results.
+ count
+ # Now that we know the max_page_size+1 is in the middle of page 2,
+ # make sure #each returns page 1 and only the requested part of
+ # page 2.
+ a = 0
+ saw_uuid = {}
+ Collection.where(owner_uuid: 'zzzzz-j7d0g-0201collections').limit(max_page_size+1).each do |item|
+ a += 1
+ saw_uuid[item.uuid] = true
+ end
+ assert_equal max_page_size+1, a
+ # Ensure no overlap between pages
+ assert_equal max_page_size+1, saw_uuid.size
+ end
+
+ test 'get single page of items' do
+ use_token :admin
+ a = 0
+ c = Collection.where(owner_uuid: 'zzzzz-j7d0g-0201collections').fetch_multiple_pages(false)
+ c.each do
+ a += 1
+ end
+
+ assert_operator a, :<, 201
+ assert_equal c.result_limit, a
+ end
+
+ test 'get empty set' do
+ use_token :admin
+ c = Collection.
+ where(owner_uuid: 'doesn-texis-tdoesntexistdoe').
+ fetch_multiple_pages(false)
+ # Important: check c.result_offset before calling c.results here.
+ assert_equal 0, c.result_offset
+ assert_equal 0, c.items_available
+ assert_empty c.results
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class CollectionTest < ActiveSupport::TestCase
+ test 'recognize empty blob locator' do
+ ['d41d8cd98f00b204e9800998ecf8427e+0',
+ 'd41d8cd98f00b204e9800998ecf8427e',
+ 'd41d8cd98f00b204e9800998ecf8427e+0+Xyzzy'].each do |x|
+ assert_equal true, Collection.is_empty_blob_locator?(x)
+ end
+ ['d41d8cd98f00b204e9800998ecf8427e0',
+ 'acbd18db4cc2f85cedef654fccc4a4d8+3',
+ 'acbd18db4cc2f85cedef654fccc4a4d8+0'].each do |x|
+ assert_equal false, Collection.is_empty_blob_locator?(x)
+ end
+ end
+
+ def get_files_tree(coll_name)
+ use_token :admin
+ Collection.find(api_fixture('collections')[coll_name]['uuid']).files_tree
+ end
+
+ test "easy files_tree" do
+ files_in = lambda do |dirname|
+ (1..3).map { |n| [dirname, "file#{n}", 0] }
+ end
+ assert_equal([['.', 'dir1', nil], ['./dir1', 'subdir', nil]] +
+ files_in['./dir1/subdir'] + files_in['./dir1'] +
+ [['.', 'dir2', nil]] + files_in['./dir2'] + files_in['.'],
+ get_files_tree('multilevel_collection_1'),
+ "Collection file tree was malformed")
+ end
+
+ test "files_tree with files deep in subdirectories" do
+ # This test makes sure files_tree generates synthetic directory entries.
+ # The manifest doesn't list directories with no files.
+ assert_equal([['.', 'dir1', nil], ['./dir1', 'sub1', nil],
+ ['./dir1/sub1', 'a', 0], ['./dir1/sub1', 'b', 0],
+ ['.', 'dir2', nil], ['./dir2', 'sub2', nil],
+ ['./dir2/sub2', 'c', 0], ['./dir2/sub2', 'd', 0]],
+ get_files_tree('multilevel_collection_2'),
+ "Collection file tree was malformed")
+ end
+
+ test "portable_data_hash never editable" do
+ refute(Collection.new.attribute_editable?("portable_data_hash", :ever))
+ end
+
+ test "admin can edit name" do
+ use_token :admin
+ assert(find_fixture(Collection, "foo_file").attribute_editable?("name"),
+ "admin not allowed to edit collection name")
+ end
+
+ test "project owner can edit name" do
+ use_token :active
+ assert(find_fixture(Collection, "foo_collection_in_aproject")
+ .attribute_editable?("name"),
+ "project owner not allowed to edit collection name")
+ end
+
+ test "project admin can edit name" do
+ use_token :subproject_admin
+ assert(find_fixture(Collection, "baz_file_in_asubproject")
+ .attribute_editable?("name"),
+ "project admin not allowed to edit collection name")
+ end
+
+ test "project viewer cannot edit name" do
+ use_token :project_viewer
+ refute(find_fixture(Collection, "foo_collection_in_aproject")
+ .attribute_editable?("name"),
+ "project viewer allowed to edit collection name")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class GroupTest < ActiveSupport::TestCase
+ test "get contents with names" do
+ use_token :active
+ oi = Group.
+ find(api_fixture('groups')['asubproject']['uuid']).
+ contents()
+ assert_operator(0, :<, oi.count,
+ "Expected to find some items belonging to :active user")
+ assert_operator(0, :<, oi.items_available,
+ "Expected contents response to have items_available > 0")
+ oi_uuids = oi.collect { |i| i['uuid'] }
+
+ expect_uuid = api_fixture('specimens')['in_asubproject']['uuid']
+ assert_includes(oi_uuids, expect_uuid,
+ "Expected '#{expect_uuid}' in asubproject's contents")
+ end
+
+ test "can select specific group columns" do
+ use_token :admin
+ Group.select(["uuid", "name"]).limit(5).each do |user|
+ assert_not_nil user.uuid
+ assert_not_nil user.name
+ assert_nil user.owner_uuid
+ end
+ end
+
+ test "project editable by its admin" do
+ use_token :subproject_admin
+ project = Group.find(api_fixture("groups")["asubproject"]["uuid"])
+ assert(project.editable?, "project not editable by admin")
+ end
+
+ test "project not editable by reader" do
+ use_token :project_viewer
+ project = Group.find(api_fixture("groups")["aproject"]["uuid"])
+ refute(project.editable?, "project editable by reader")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class ApiClientAuthorizationsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class AuthorizedKeysHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class CollectionsHelperTest < ActionView::TestCase
+ test "file_path generates short names" do
+ assert_equal('foo', CollectionsHelper.file_path(['.', 'foo', 0]),
+ "wrong result for filename in collection root")
+ assert_equal('foo/bar', CollectionsHelper.file_path(['foo', 'bar', 0]),
+ "wrong result for filename in directory without leading .")
+ assert_equal('foo/bar', CollectionsHelper.file_path(['./foo', 'bar', 0]),
+ "wrong result for filename in directory with leading .")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class ProjectsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class HumansHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class JobTasksHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class JobsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class KeepDisksHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class MetadataHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class LogsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class NodesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineInstancesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineTemplatesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class ProjectsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class RepositoriesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class SessionsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class SpecimensHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class TraitsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class UserAgreementsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class UsersHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class VirtualMachinesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class JobTest < ActiveSupport::TestCase
+ test "admin can edit description" do
+ use_token :admin
+ assert(find_fixture(Job, "job_in_subproject")
+ .attribute_editable?("description"),
+ "admin not allowed to edit job description")
+ end
+
+ test "project owner can edit description" do
+ use_token :active
+ assert(find_fixture(Job, "job_in_subproject")
+ .attribute_editable?("description"),
+ "project owner not allowed to edit job description")
+ end
+
+ test "project admin can edit description" do
+ use_token :subproject_admin
+ assert(find_fixture(Job, "job_in_subproject")
+ .attribute_editable?("description"),
+ "project admin not allowed to edit job description")
+ end
+
+ test "project viewer cannot edit description" do
+ use_token :project_viewer
+ refute(find_fixture(Job, "job_in_subproject")
+ .attribute_editable?("description"),
+ "project viewer allowed to edit job description")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class LinkTest < ActiveSupport::TestCase
+ def uuid_for(fixture_name, object_name)
+ api_fixture(fixture_name)[object_name]["uuid"]
+ end
+
+ test "active user can get permissions for owned project object" do
+ use_token :active
+ project = Group.find(uuid_for("groups", "aproject"))
+ refute_empty(Link.permissions_for(project),
+ "no permissions found for managed project")
+ end
+
+ test "active user can get permissions for owned project by UUID" do
+ use_token :active
+ refute_empty(Link.permissions_for(uuid_for("groups", "aproject")),
+ "no permissions found for managed project")
+ end
+
+ test "admin can get permissions for project object" do
+ use_token :admin
+ project = Group.find(uuid_for("groups", "aproject"))
+ refute_empty(Link.permissions_for(project),
+ "no permissions found for managed project")
+ end
+
+ test "admin can get permissions for project by UUID" do
+ use_token :admin
+ refute_empty(Link.permissions_for(uuid_for("groups", "aproject")),
+ "no permissions found for managed project")
+ end
+
+ test "project viewer can't get permissions for readable project object" do
+ use_token :project_viewer
+ project = Group.find(uuid_for("groups", "aproject"))
+ assert_raises(ArvadosApiClient::AccessForbiddenException) do
+ Link.permissions_for(project)
+ end
+ end
+
+ test "project viewer can't get permissions for readable project by UUID" do
+ use_token :project_viewer
+ assert_raises(ArvadosApiClient::AccessForbiddenException) do
+ Link.permissions_for(uuid_for("groups", "aproject"))
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineInstanceTest < ActiveSupport::TestCase
+ def attribute_editable_for?(token_name, pi_name, attr_name, ever=nil)
+ use_token token_name
+ find_fixture(PipelineInstance, pi_name).attribute_editable?(attr_name, ever)
+ end
+
+ test "admin can edit name" do
+ assert(attribute_editable_for?(:admin, "new_pipeline_in_subproject",
+ "name"),
+ "admin not allowed to edit pipeline instance name")
+ end
+
+ test "project owner can edit name" do
+ assert(attribute_editable_for?(:active, "new_pipeline_in_subproject",
+ "name"),
+ "project owner not allowed to edit pipeline instance name")
+ end
+
+ test "project admin can edit name" do
+ assert(attribute_editable_for?(:subproject_admin,
+ "new_pipeline_in_subproject", "name"),
+ "project admin not allowed to edit pipeline instance name")
+ end
+
+ test "project viewer cannot edit name" do
+ refute(attribute_editable_for?(:project_viewer,
+ "new_pipeline_in_subproject", "name"),
+ "project viewer allowed to edit pipeline instance name")
+ end
+
+ test "name editable on completed pipeline" do
+ assert(attribute_editable_for?(:active, "has_component_with_completed_jobs",
+ "name"),
+ "name not editable on complete pipeline")
+ end
+
+ test "components editable on new pipeline" do
+ assert(attribute_editable_for?(:active, "new_pipeline", "components"),
+ "components not editable on new pipeline")
+ end
+
+ test "components not editable on completed pipeline" do
+ refute(attribute_editable_for?(:active, "has_component_with_completed_jobs",
+ "components"),
+ "components not editable on new pipeline")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class UserTest < ActiveSupport::TestCase
+ test "can select specific user columns" do
+ use_token :admin
+ User.select(["uuid", "is_active"]).limit(5).each do |user|
+ assert_not_nil user.uuid
+ assert_not_nil user.is_active
+ assert_nil user.first_name
+ end
+ end
+end
--- /dev/null
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--- /dev/null
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+ Creative Commons may be contacted at http://creativecommons.org/.
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import os
+import re
+
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True)
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+gatk_path = arvados.util.tarball_extract(
+ tarball = this_job['script_parameters']['gatk_binary_tarball'],
+ path = 'gatk')
+bundle_path = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['gatk_bundle'],
+ path = 'gatk-bundle',
+ files = ['human_g1k_v37.dict', 'human_g1k_v37.fasta', 'human_g1k_v37.fasta.fai'])
+this_task_input = this_task['parameters']['input']
+
+input_file = list(arvados.CollectionReader(this_task_input).all_files())[0]
+
+# choose vcf temporary file names
+vcf_in = os.path.join(arvados.current_task().tmpdir,
+ os.path.basename(input_file.name()))
+vcf_out = re.sub('(.*)\\.vcf', '\\1-filtered.vcf', vcf_in)
+
+# fetch the unfiltered data
+vcf_in_file = open(vcf_in, 'w')
+for buf in input_file.readall():
+ vcf_in_file.write(buf)
+vcf_in_file.close()
+
+stdoutdata, stderrdata = arvados.util.run_command(
+ ['java', '-Xmx1g',
+ '-jar', os.path.join(gatk_path,'GenomeAnalysisTK.jar'),
+ '-T', 'VariantFiltration', '--variant', vcf_in,
+ '--out', vcf_out,
+ '--filterExpression', 'QD < 2.0',
+ '--filterName', 'GATK_QD',
+ '--filterExpression', 'MQ < 40.0',
+ '--filterName', 'GATK_MQ',
+ '--filterExpression', 'FS > 60.0',
+ '--filterName', 'GATK_FS',
+ '--filterExpression', 'MQRankSum < -12.5',
+ '--filterName', 'GATK_MQRankSum',
+ '--filterExpression', 'ReadPosRankSum < -8.0',
+ '--filterName', 'GATK_ReadPosRankSum',
+ '-R', os.path.join(bundle_path, 'human_g1k_v37.fasta')],
+ cwd=arvados.current_task().tmpdir)
+
+# store the filtered data
+with open(vcf_out, 'rb') as f:
+ out = arvados.CollectionWriter()
+ while True:
+ buf = f.read()
+ if len(buf) == 0:
+ break
+ out.write(buf)
+out.set_current_file_name(os.path.basename(vcf_out))
+
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import os
+import re
+import arvados
+import arvados_gatk2
+import arvados_samtools
+from arvados_ipc import *
+
+class InvalidArgumentError(Exception):
+ pass
+
+arvados_samtools.one_task_per_bam_file(if_sequence=0, and_end_task=True)
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+tmpdir = arvados.current_task().tmpdir
+arvados.util.clear_tmpdir()
+
+known_sites_files = arvados.getjobparam(
+ 'known_sites',
+ ['dbsnp_137.b37.vcf',
+ 'Mills_and_1000G_gold_standard.indels.b37.vcf',
+ ])
+bundle_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['gatk_bundle'],
+ files = [
+ 'human_g1k_v37.dict',
+ 'human_g1k_v37.fasta',
+ 'human_g1k_v37.fasta.fai'
+ ] + known_sites_files + [v + '.idx' for v in known_sites_files],
+ path = 'gatk_bundle')
+ref_fasta_files = [os.path.join(bundle_dir, f)
+ for f in os.listdir(bundle_dir)
+ if re.search(r'\.fasta(\.gz)?$', f)]
+
+input_collection = this_task['parameters']['input']
+input_dir = arvados.util.collection_extract(
+ collection = input_collection,
+ path = os.path.join(this_task.tmpdir, 'input'))
+input_bam_files = []
+for f in arvados.util.listdir_recursive(input_dir):
+ if re.search(r'\.bam$', f):
+ input_stream_name, input_file_name = os.path.split(f)
+ input_bam_files += [os.path.join(input_dir, f)]
+if len(input_bam_files) != 1:
+ raise InvalidArgumentError("Expected exactly one bam file per task.")
+
+known_sites_args = []
+for f in known_sites_files:
+ known_sites_args += ['-knownSites', os.path.join(bundle_dir, f)]
+
+recal_file = os.path.join(tmpdir, 'recal.csv')
+
+children = {}
+pipes = {}
+
+arvados_gatk2.run(
+ args=[
+ '-nct', arvados_gatk2.cpus_on_this_node(),
+ '-T', 'BaseRecalibrator',
+ '-R', ref_fasta_files[0],
+ '-I', input_bam_files[0],
+ '-o', recal_file,
+ ] + known_sites_args)
+
+pipe_setup(pipes, 'BQSR')
+if 0 == named_fork(children, 'BQSR'):
+ pipe_closeallbut(pipes, ('BQSR', 'w'))
+ arvados_gatk2.run(
+ args=[
+ '-T', 'PrintReads',
+ '-R', ref_fasta_files[0],
+ '-I', input_bam_files[0],
+ '-o', '/dev/fd/' + str(pipes['BQSR','w']),
+ '-BQSR', recal_file,
+ '--disable_bam_indexing',
+ ],
+ close_fds=False)
+ os._exit(0)
+os.close(pipes.pop(('BQSR','w'), None))
+
+out = arvados.CollectionWriter()
+out.start_new_stream(input_stream_name)
+
+out.start_new_file(input_file_name + '.recal.csv')
+out.write(open(recal_file, 'rb'))
+
+out.start_new_file(input_file_name)
+while True:
+ buf = os.read(pipes['BQSR','r'], 2**20)
+ if len(buf) == 0:
+ break
+ out.write(buf)
+pipe_closeallbut(pipes)
+
+if waitpid_and_check_children(children):
+ this_task.set_output(out.finish())
+else:
+ sys.exit(1)
--- /dev/null
+#!/usr/bin/env python
+
+import os
+import re
+import string
+import threading
+import arvados
+import arvados_gatk2
+import arvados_picard
+from arvados_ipc import *
+
+class InvalidArgumentError(Exception):
+ pass
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+tmpdir = arvados.current_task().tmpdir
+arvados.util.clear_tmpdir()
+
+bundle_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['gatk_bundle'],
+ files = [
+ 'human_g1k_v37.dict',
+ 'human_g1k_v37.fasta',
+ 'human_g1k_v37.fasta.fai',
+ 'dbsnp_137.b37.vcf',
+ 'dbsnp_137.b37.vcf.idx',
+ ],
+ path = 'gatk_bundle')
+ref_fasta_files = [os.path.join(bundle_dir, f)
+ for f in os.listdir(bundle_dir)
+ if re.search(r'\.fasta(\.gz)?$', f)]
+regions_args = []
+if 'regions' in this_job['script_parameters']:
+ regions_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['regions'],
+ path = 'regions')
+ region_padding = int(this_job['script_parameters']['region_padding'])
+ for f in os.listdir(regions_dir):
+ if re.search(r'\.bed$', f):
+ regions_args += [
+ '--intervals', os.path.join(regions_dir, f),
+ '--interval_padding', str(region_padding)
+ ]
+
+
+# Start a child process for each input file, feeding data to picard.
+
+input_child_names = []
+children = {}
+pipes = {}
+
+input_collection = this_job['script_parameters']['input']
+input_index = 0
+for s in arvados.CollectionReader(input_collection).all_streams():
+ for f in s.all_files():
+ if not re.search(r'\.bam$', f.name()):
+ continue
+ input_index += 1
+ childname = 'input-' + str(input_index)
+ input_child_names += [childname]
+ pipe_setup(pipes, childname)
+ childpid = named_fork(children, childname)
+ if childpid == 0:
+ pipe_closeallbut(pipes, (childname, 'w'))
+ for s in f.readall():
+ os.write(pipes[childname, 'w'], s)
+ os.close(pipes[childname, 'w'])
+ os._exit(0)
+ sys.stderr.write("pid %d writing %s to fd %d->%d\n" %
+ (childpid,
+ s.name()+'/'+f.name(),
+ pipes[childname, 'w'],
+ pipes[childname, 'r']))
+ pipe_closeallbut(pipes, *[(childname, 'r')
+ for childname in input_child_names])
+
+
+# Merge-sort the input files to merge.bam
+
+arvados_picard.run(
+ 'MergeSamFiles',
+ args=[
+ 'I=/dev/fd/' + str(pipes[childname, 'r'])
+ for childname in input_child_names
+ ],
+ params={
+ 'o': 'merge.bam',
+ 'quiet': 'true',
+ 'so': 'coordinate',
+ 'use_threading': 'true',
+ 'create_index': 'true',
+ 'validation_stringency': 'LENIENT',
+ },
+ close_fds=False,
+ )
+pipe_closeallbut(pipes)
+
+
+# Run CoverageBySample on merge.bam
+
+pipe_setup(pipes, 'stats_log')
+pipe_setup(pipes, 'stats_out')
+if 0 == named_fork(children, 'GATK'):
+ pipe_closeallbut(pipes,
+ ('stats_log', 'w'),
+ ('stats_out', 'w'))
+ arvados_gatk2.run(
+ args=[
+ '-T', 'CoverageBySample',
+ '-R', ref_fasta_files[0],
+ '-I', 'merge.bam',
+ '-o', '/dev/fd/' + str(pipes['stats_out', 'w']),
+ '--log_to_file', '/dev/fd/' + str(pipes['stats_log', 'w']),
+ ]
+ + regions_args,
+ close_fds=False)
+ pipe_closeallbut(pipes)
+ os._exit(0)
+pipe_closeallbut(pipes, ('stats_log', 'r'), ('stats_out', 'r'))
+
+
+# Start two threads to read from CoverageBySample pipes
+
+class ExceptionPropagatingThread(threading.Thread):
+ """
+ If a subclassed thread calls _raise(e) in run(), running join() on
+ the thread will raise e in the thread that calls join().
+ """
+ def __init__(self, *args, **kwargs):
+ super(ExceptionPropagatingThread, self).__init__(*args, **kwargs)
+ self.__exception = None
+ def join(self, *args, **kwargs):
+ ret = super(ExceptionPropagatingThread, self).join(*args, **kwargs)
+ if self.__exception:
+ raise self.__exception
+ return ret
+ def _raise(self, exception):
+ self.__exception = exception
+
+class StatsLogReader(ExceptionPropagatingThread):
+ def __init__(self, **kwargs):
+ super(StatsLogReader, self).__init__()
+ self.args = kwargs
+ def run(self):
+ try:
+ for logline in self.args['infile']:
+ x = re.search('Processing (\d+) bp from intervals', logline)
+ if x:
+ self._total_bp = int(x.group(1))
+ except Exception as e:
+ self._raise(e)
+ def total_bp(self):
+ self.join()
+ return self._total_bp
+stats_log_thr = StatsLogReader(infile=os.fdopen(pipes.pop(('stats_log', 'r'))))
+stats_log_thr.start()
+
+class StatsOutReader(ExceptionPropagatingThread):
+ """
+ Read output of CoverageBySample and collect a histogram of
+ coverage (last column) -> number of loci (number of rows).
+ """
+ def __init__(self, **kwargs):
+ super(StatsOutReader, self).__init__()
+ self.args = kwargs
+ def run(self):
+ try:
+ hist = [0]
+ histtot = 0
+ for line in self.args['infile']:
+ try:
+ i = int(string.split(line)[-1])
+ except ValueError:
+ continue
+ if i >= 1:
+ if len(hist) <= i:
+ hist.extend([0 for x in range(1+i-len(hist))])
+ hist[i] += 1
+ histtot += 1
+ hist[0] = stats_log_thr.total_bp() - histtot
+ self._histogram = hist
+ except Exception as e:
+ self._raise(e)
+ def histogram(self):
+ self.join()
+ return self._histogram
+stats_out_thr = StatsOutReader(infile=os.fdopen(pipes.pop(('stats_out', 'r'))))
+stats_out_thr.start()
+
+
+# Run UnifiedGenotyper on merge.bam
+
+arvados_gatk2.run(
+ args=[
+ '-nt', arvados_gatk2.cpus_on_this_node(),
+ '-T', 'UnifiedGenotyper',
+ '-R', ref_fasta_files[0],
+ '-I', 'merge.bam',
+ '-o', os.path.join(tmpdir, 'out.vcf'),
+ '--dbsnp', os.path.join(bundle_dir, 'dbsnp_137.b37.vcf'),
+ '-metrics', 'UniGenMetrics',
+ '-A', 'DepthOfCoverage',
+ '-A', 'AlleleBalance',
+ '-A', 'QualByDepth',
+ '-A', 'HaplotypeScore',
+ '-A', 'MappingQualityRankSumTest',
+ '-A', 'ReadPosRankSumTest',
+ '-A', 'FisherStrand',
+ '-glm', 'both',
+ ]
+ + regions_args
+ + arvados.getjobparam('GATK2_UnifiedGenotyper_args',[]))
+
+# Copy the output VCF file to Keep
+
+out = arvados.CollectionWriter()
+out.start_new_stream()
+out.start_new_file('out.vcf')
+out.write(open(os.path.join(tmpdir, 'out.vcf'), 'rb'))
+
+
+# Write statistics to Keep
+
+out.start_new_file('mincoverage_nlocus.csv')
+sofar = 0
+hist = stats_out_thr.histogram()
+total_bp = stats_log_thr.total_bp()
+for i in range(len(hist)):
+ out.write("%d,%d,%f\n" %
+ (i,
+ total_bp - sofar,
+ 100.0 * (total_bp - sofar) / total_bp))
+ sofar += hist[i]
+
+if waitpid_and_check_children(children):
+ this_task.set_output(out.finish())
+else:
+ sys.exit(1)
--- /dev/null
+#!/usr/bin/env python
+
+import os
+import re
+import arvados
+import arvados_gatk2
+import arvados_picard
+import arvados_samtools
+from arvados_ipc import *
+
+class InvalidArgumentError(Exception):
+ pass
+
+arvados_samtools.one_task_per_bam_file(if_sequence=0, and_end_task=True)
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+tmpdir = arvados.current_task().tmpdir
+arvados.util.clear_tmpdir()
+
+known_sites_files = arvados.getjobparam(
+ 'known_sites',
+ ['dbsnp_137.b37.vcf',
+ 'Mills_and_1000G_gold_standard.indels.b37.vcf',
+ ])
+bundle_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['gatk_bundle'],
+ files = [
+ 'human_g1k_v37.dict',
+ 'human_g1k_v37.fasta',
+ 'human_g1k_v37.fasta.fai'
+ ] + known_sites_files + [v + '.idx' for v in known_sites_files],
+ path = 'gatk_bundle')
+ref_fasta_files = [os.path.join(bundle_dir, f)
+ for f in os.listdir(bundle_dir)
+ if re.search(r'\.fasta(\.gz)?$', f)]
+regions_args = []
+if 'regions' in this_job['script_parameters']:
+ regions_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['regions'],
+ path = 'regions')
+ region_padding = int(this_job['script_parameters']['region_padding'])
+ for f in os.listdir(regions_dir):
+ if re.search(r'\.bed$', f):
+ regions_args += [
+ '--intervals', os.path.join(regions_dir, f),
+ '--interval_padding', str(region_padding)
+ ]
+
+input_collection = this_task['parameters']['input']
+input_dir = arvados.util.collection_extract(
+ collection = input_collection,
+ path = os.path.join(this_task.tmpdir, 'input'))
+input_bam_files = []
+for f in arvados.util.listdir_recursive(input_dir):
+ if re.search(r'\.bam$', f):
+ input_stream_name, input_file_name = os.path.split(f)
+ input_bam_files += [os.path.join(input_dir, f)]
+if len(input_bam_files) != 1:
+ raise InvalidArgumentError("Expected exactly one bam file per task.")
+
+known_sites_args = []
+for f in known_sites_files:
+ known_sites_args += ['-known', os.path.join(bundle_dir, f)]
+
+children = {}
+pipes = {}
+
+arvados_gatk2.run(
+ args=[
+ '-nt', arvados_gatk2.cpus_per_task(),
+ '-T', 'RealignerTargetCreator',
+ '-R', ref_fasta_files[0],
+ '-I', input_bam_files[0],
+ '-o', os.path.join(tmpdir, 'intervals.list')
+ ] + known_sites_args + regions_args)
+
+pipe_setup(pipes, 'IndelRealigner')
+if 0 == named_fork(children, 'IndelRealigner'):
+ pipe_closeallbut(pipes, ('IndelRealigner', 'w'))
+ arvados_gatk2.run(
+ args=[
+ '-T', 'IndelRealigner',
+ '-R', ref_fasta_files[0],
+ '-targetIntervals', os.path.join(tmpdir, 'intervals.list'),
+ '-I', input_bam_files[0],
+ '-o', '/dev/fd/' + str(pipes['IndelRealigner','w']),
+ '--disable_bam_indexing',
+ ] + known_sites_args + regions_args,
+ close_fds=False)
+ os._exit(0)
+os.close(pipes.pop(('IndelRealigner','w'), None))
+
+pipe_setup(pipes, 'bammanifest')
+pipe_setup(pipes, 'bam')
+if 0==named_fork(children, 'bammanifest'):
+ pipe_closeallbut(pipes,
+ ('IndelRealigner', 'r'),
+ ('bammanifest', 'w'),
+ ('bam', 'w'))
+ out = arvados.CollectionWriter()
+ out.start_new_stream(input_stream_name)
+ out.start_new_file(input_file_name)
+ while True:
+ buf = os.read(pipes['IndelRealigner','r'], 2**20)
+ if len(buf) == 0:
+ break
+ os.write(pipes['bam','w'], buf)
+ out.write(buf)
+ os.write(pipes['bammanifest','w'], out.manifest_text())
+ os.close(pipes['bammanifest','w'])
+ os._exit(0)
+
+pipe_setup(pipes, 'index')
+if 0==named_fork(children, 'index'):
+ pipe_closeallbut(pipes, ('bam', 'r'), ('index', 'w'))
+ arvados_picard.run(
+ 'BuildBamIndex',
+ params={
+ 'i': '/dev/fd/' + str(pipes['bam','r']),
+ 'o': '/dev/fd/' + str(pipes['index','w']),
+ 'quiet': 'true',
+ 'validation_stringency': 'LENIENT'
+ },
+ close_fds=False)
+ os._exit(0)
+
+pipe_setup(pipes, 'indexmanifest')
+if 0==named_fork(children, 'indexmanifest'):
+ pipe_closeallbut(pipes, ('index', 'r'), ('indexmanifest', 'w'))
+ out = arvados.CollectionWriter()
+ out.start_new_stream(input_stream_name)
+ out.start_new_file(re.sub('\.bam$', '.bai', input_file_name))
+ while True:
+ buf = os.read(pipes['index','r'], 2**20)
+ if len(buf) == 0:
+ break
+ out.write(buf)
+ os.write(pipes['indexmanifest','w'], out.manifest_text())
+ os.close(pipes['indexmanifest','w'])
+ os._exit(0)
+
+pipe_closeallbut(pipes, ('bammanifest', 'r'), ('indexmanifest', 'r'))
+outmanifest = ''
+for which in ['bammanifest', 'indexmanifest']:
+ with os.fdopen(pipes[which,'r'], 'rb', 2**20) as f:
+ while True:
+ buf = f.read()
+ if buf == '':
+ break
+ outmanifest += buf
+
+all_ok = True
+for (childname, pid) in children.items():
+ all_ok = all_ok and waitpid_and_check_exit(pid, childname)
+
+if all_ok:
+ this_task.set_output(outmanifest)
+else:
+ sys.exit(1)
--- /dev/null
+#!/usr/bin/python
+
+import arvados
+import subprocess
+import crunchutil.subst as subst
+import shutil
+import os
+import sys
+import time
+
+if len(arvados.current_task()['parameters']) > 0:
+ p = arvados.current_task()['parameters']
+else:
+ p = arvados.current_job()['script_parameters']
+
+t = arvados.current_task().tmpdir
+
+os.unlink("/usr/local/share/bcbio-nextgen/galaxy")
+os.mkdir("/usr/local/share/bcbio-nextgen/galaxy")
+shutil.copy("/usr/local/share/bcbio-nextgen/config/bcbio_system.yaml", "/usr/local/share/bcbio-nextgen/galaxy")
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool_data_table_conf.xml", "w") as f:
+ f.write('''<tables>
+ <!-- Locations of indexes in the BWA mapper format -->
+ <table name="bwa_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bwa_index.loc" />
+ </table>
+ <!-- Locations of indexes in the Bowtie2 mapper format -->
+ <table name="bowtie2_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bowtie2_indices.loc" />
+ </table>
+ <!-- Locations of indexes in the Bowtie2 mapper format for TopHat2 to use -->
+ <table name="tophat2_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bowtie2_indices.loc" />
+ </table>
+ <!-- Location of SAMTools indexes and other files -->
+ <table name="sam_fa_indexes" comment_char="#">
+ <columns>index, value, path</columns>
+ <file path="tool-data/sam_fa_indices.loc" />
+ </table>
+ <!-- Location of Picard dict file and other files -->
+ <table name="picard_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/picard_index.loc" />
+ </table>
+ <!-- Location of Picard dict files valid for GATK -->
+ <table name="gatk_picard_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/gatk_sorted_picard_index.loc" />
+ </table>
+</tables>
+''')
+
+os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/tool-data")
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bowtie2_indices.loc", "w") as f:
+ f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(dir $(bowtie2_indices))\n"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bwa_index.loc", "w") as f:
+ f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(bwa_index))\n"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/gatk_sorted_picard_index.loc", "w") as f:
+ f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(gatk_sorted_picard_index))\n"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/picard_index.loc", "w") as f:
+ f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(picard_index))\n"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc", "w") as f:
+ f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))\n"))
+
+with open("/tmp/crunch-job/freebayes-variant.yaml", "w") as f:
+ f.write('''
+# Template for whole genome Illumina variant calling with FreeBayes
+# This is a GATK-free pipeline without post-alignment BAM pre-processing
+# (recalibration and realignment)
+---
+details:
+ - analysis: variant2
+ genome_build: GRCh37
+ # to do multi-sample variant calling, assign samples the same metadata / batch
+ # metadata:
+ # batch: your-arbitrary-batch-name
+ algorithm:
+ aligner: bwa
+ mark_duplicates: true
+ recalibrate: false
+ realign: false
+ variantcaller: freebayes
+ platform: illumina
+ quality_format: Standard
+ # for targetted projects, set the region
+ # variant_regions: /path/to/your.bed
+''')
+
+os.unlink("/usr/local/share/bcbio-nextgen/gemini_data")
+os.symlink(arvados.get_job_param_mount("gemini_data"), "/usr/local/share/bcbio-nextgen/gemini_data")
+
+os.chdir(arvados.current_task().tmpdir)
+
+rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/freebayes-variant.yaml", "project1",
+ subst.do_substitution(p, "$(file $(R1))"),
+ subst.do_substitution(p, "$(file $(R2))")])
+
+os.chdir("project1/work")
+
+os.symlink("/usr/local/share/bcbio-nextgen/galaxy/tool-data", "tool-data")
+
+rcode = subprocess.call(["bcbio_nextgen.py", "../config/project1.yaml", "-n", os.environ['CRUNCH_NODE_SLOTS']])
+
+print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
+
+if rcode == 0:
+ os.chdir("../final")
+
+ print("arvados-bcbio-nextgen: the follow output files will be saved to keep:")
+
+ subprocess.call(["find", ".", "-type", "f", "-printf", "arvados-bcbio-nextgen: %12.12s %h/%f\\n"])
+
+ print("arvados-bcbio-nextgen: start writing output to keep")
+
+ done = False
+ api = arvados.api('v1')
+ while not done:
+ try:
+ out = arvados.CollectionWriter()
+ out.write_directory_tree(".", max_manifest_depth=0)
+ outuuid = out.finish()
+ api.job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={
+ 'output':outuuid,
+ 'success': (rcode == 0),
+ 'progress':1.0
+ }).execute()
+ done = True
+ except Exception as e:
+ print("arvados-bcbio-nextgen: caught exception: {}".format(e))
+ time.sleep(5)
+
+sys.exit(rcode)
--- /dev/null
+import arvados
+import re
+import os
+import sys
+import fcntl
+import subprocess
+
+bwa_install_path = None
+
+def install_path():
+ """
+ Extract the bwa source tree, build the bwa binary, and return the
+ path to the source tree.
+ """
+ global bwa_install_path
+ if bwa_install_path:
+ return bwa_install_path
+
+ bwa_install_path = arvados.util.tarball_extract(
+ tarball = arvados.current_job()['script_parameters']['bwa_tbz'],
+ path = 'bwa')
+
+ # build "bwa" binary
+ lockfile = open(os.path.split(bwa_install_path)[0] + '.bwa-make.lock',
+ 'w')
+ fcntl.flock(lockfile, fcntl.LOCK_EX)
+ arvados.util.run_command(['make', '-j16'], cwd=bwa_install_path)
+ lockfile.close()
+
+ return bwa_install_path
+
+def bwa_binary():
+ """
+ Return the path to the bwa executable.
+ """
+ return os.path.join(install_path(), 'bwa')
+
+def run(command, command_args, **kwargs):
+ """
+ Build and run the bwa binary.
+
+ command is the bwa module, e.g., "index" or "aln".
+
+ command_args is a list of additional command line arguments, e.g.,
+ ['-a', 'bwtsw', 'ref.fasta']
+
+ It is assumed that we are running in a Crunch job environment, and
+ the job's "bwa_tbz" parameter is a collection containing the bwa
+ source tree in a .tbz file.
+ """
+ execargs = [bwa_binary(),
+ command]
+ execargs += command_args
+ sys.stderr.write("%s.run: exec %s\n" % (__name__, str(execargs)))
+ arvados.util.run_command(
+ execargs,
+ cwd=arvados.current_task().tmpdir,
+ stderr=sys.stderr,
+ stdin=kwargs.get('stdin', subprocess.PIPE),
+ stdout=kwargs.get('stdout', sys.stderr))
+
+def one_task_per_pair_input_file(if_sequence=0, and_end_task=True):
+ """
+ Queue one task for each pair of fastq files in this job's input
+ collection.
+
+ Each new task will have two parameters, named "input_1" and
+ "input_2", each being a manifest containing a single fastq file.
+
+ A matching pair of files in the input collection is assumed to
+ have names "x_1.y" and "x_2.y".
+
+ Files in the input collection that are not part of a matched pair
+ are silently ignored.
+
+ if_sequence and and_end_task arguments have the same significance
+ as in arvados.job_setup.one_task_per_input_file().
+ """
+ if if_sequence != arvados.current_task()['sequence']:
+ return
+ job_input = arvados.current_job()['script_parameters']['input']
+ cr = arvados.CollectionReader(job_input)
+ all_files = []
+ for s in cr.all_streams():
+ all_files += list(s.all_files())
+ for s in cr.all_streams():
+ for left_file in s.all_files():
+ left_name = left_file.name()
+ right_file = None
+ right_name = re.sub(r'(.*_)1\.', '\g<1>2.', left_name)
+ if right_name == left_name:
+ continue
+ for f2 in s.all_files():
+ if right_name == f2.name():
+ right_file = f2
+ if right_file != None:
+ new_task_attrs = {
+ 'job_uuid': arvados.current_job()['uuid'],
+ 'created_by_job_task_uuid': arvados.current_task()['uuid'],
+ 'sequence': if_sequence + 1,
+ 'parameters': {
+ 'input_1':left_file.as_manifest(),
+ 'input_2':right_file.as_manifest()
+ }
+ }
+ arvados.api().job_tasks().create(body=new_task_attrs).execute()
+ if and_end_task:
+ arvados.api().job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={'success':True}
+ ).execute()
+ exit(0)
--- /dev/null
+import arvados
+import re
+import os
+import sys
+import fcntl
+import subprocess
+
+gatk2_install_path = None
+
+def install_path():
+ global gatk2_install_path
+ if gatk2_install_path:
+ return gatk2_install_path
+ gatk2_install_path = arvados.util.tarball_extract(
+ tarball = arvados.current_job()['script_parameters']['gatk_tbz'],
+ path = 'gatk2')
+ return gatk2_install_path
+
+def memory_limit():
+ taskspernode = int(os.environ.get('CRUNCH_NODE_SLOTS', '1'))
+ with open('/proc/meminfo', 'r') as f:
+ ram = int(re.search(r'MemTotal:\s*(\d+)', f.read()).group(1)) / 1024
+ if taskspernode > 1:
+ ram = ram / taskspernode
+ return max(ram-700, 500)
+
+def cpus_on_this_node():
+ with open('/proc/cpuinfo', 'r') as cpuinfo:
+ return max(int(os.environ.get('SLURM_CPUS_ON_NODE', 1)),
+ len(re.findall(r'^processor\s*:\s*\d',
+ cpuinfo.read(),
+ re.MULTILINE)))
+
+def cpus_per_task():
+ return max(1, (cpus_on_this_node()
+ / int(os.environ.get('CRUNCH_NODE_SLOTS', 1))))
+
+def run(**kwargs):
+ kwargs.setdefault('cwd', arvados.current_task().tmpdir)
+ kwargs.setdefault('stdout', sys.stderr)
+ execargs = ['java',
+ '-Xmx%dm' % memory_limit(),
+ '-Djava.io.tmpdir=' + arvados.current_task().tmpdir,
+ '-jar', os.path.join(install_path(), 'GenomeAnalysisTK.jar')]
+ execargs += [str(arg) for arg in kwargs.pop('args', [])]
+ sys.stderr.write("%s.run: exec %s\n" % (__name__, str(execargs)))
+ return arvados.util.run_command(execargs, **kwargs)
+
--- /dev/null
+import os
+import re
+import sys
+import subprocess
+
+def pipe_setup(pipes, name):
+ pipes[name,'r'], pipes[name,'w'] = os.pipe()
+
+def pipe_closeallbut(pipes, *keepus):
+ for n,m in pipes.keys():
+ if (n,m) not in keepus:
+ os.close(pipes.pop((n,m), None))
+
+def named_fork(children, name):
+ children[name] = os.fork()
+ return children[name]
+
+def waitpid_and_check_children(children):
+ """
+ Given a dict of childname->pid, wait for each child process to
+ finish, and report non-zero exit status on stderr. Return True if
+ all children exited 0.
+ """
+ all_ok = True
+ for (childname, pid) in children.items():
+ # all_ok must be on RHS here -- we need to call waitpid() on
+ # every child, even if all_ok is already False.
+ all_ok = waitpid_and_check_exit(pid, childname) and all_ok
+ return all_ok
+
+def waitpid_and_check_exit(pid, childname=''):
+ """
+ Wait for a child process to finish. If it exits non-zero, report
+ exit status on stderr (mentioning the given childname) and return
+ False. If it exits zero, return True.
+ """
+ _, childstatus = os.waitpid(pid, 0)
+ exitvalue = childstatus >> 8
+ signal = childstatus & 127
+ dumpedcore = childstatus & 128
+ if childstatus != 0:
+ sys.stderr.write("%s child %d failed: exit %d signal %d core %s\n"
+ % (childname, pid, exitvalue, signal,
+ ('y' if dumpedcore else 'n')))
+ return False
+ return True
+
--- /dev/null
+import arvados
+import re
+import os
+import sys
+import fcntl
+import subprocess
+
+picard_install_path = None
+
+def install_path():
+ global picard_install_path
+ if picard_install_path:
+ return picard_install_path
+ zipball = arvados.current_job()['script_parameters']['picard_zip']
+ extracted = arvados.util.zipball_extract(
+ zipball = zipball,
+ path = 'picard')
+ for f in os.listdir(extracted):
+ if (re.search(r'^picard-tools-[\d\.]+$', f) and
+ os.path.exists(os.path.join(extracted, f, '.'))):
+ picard_install_path = os.path.join(extracted, f)
+ break
+ if not picard_install_path:
+ raise Exception("picard-tools-{version} directory not found in %s" %
+ zipball)
+ return picard_install_path
+
+def run(module, **kwargs):
+ kwargs.setdefault('cwd', arvados.current_task().tmpdir)
+ execargs = ['java',
+ '-Xmx1500m',
+ '-Djava.io.tmpdir=' + arvados.current_task().tmpdir,
+ '-jar', os.path.join(install_path(), module + '.jar')]
+ execargs += [str(arg) for arg in kwargs.pop('args', [])]
+ for key, value in kwargs.pop('params', {}).items():
+ execargs += [key.upper() + '=' + str(value)]
+ sys.stderr.write("%s.run: exec %s\n" % (__name__, str(execargs)))
+ return arvados.util.run_command(execargs, **kwargs)
--- /dev/null
+import arvados
+import re
+import os
+import sys
+import fcntl
+import subprocess
+
+samtools_path = None
+
+def samtools_install_path():
+ """
+ Extract the samtools source tree, build the samtools binary, and
+ return the path to the source tree.
+ """
+ global samtools_path
+ if samtools_path:
+ return samtools_path
+ samtools_path = arvados.util.tarball_extract(
+ tarball = arvados.current_job()['script_parameters']['samtools_tgz'],
+ path = 'samtools')
+
+ # build "samtools" binary
+ lockfile = open(os.path.split(samtools_path)[0] + '.samtools-make.lock',
+ 'w')
+ fcntl.flock(lockfile, fcntl.LOCK_EX)
+ arvados.util.run_command(['make', '-j16'], cwd=samtools_path)
+ lockfile.close()
+
+ return samtools_path
+
+def samtools_binary():
+ """
+ Return the path to the samtools executable.
+ """
+ return os.path.join(samtools_install_path(), 'samtools')
+
+def run(command, command_args, **kwargs):
+ """
+ Build and run the samtools binary.
+
+ command is the samtools subcommand, e.g., "view" or "sort".
+
+ command_args is a list of additional command line arguments, e.g.,
+ ['-bt', 'ref_list.txt', '-o', 'aln.bam', 'aln.sam.gz']
+
+ It is assumed that we are running in a Crunch job environment, and
+ the job's "samtools_tgz" parameter is a collection containing the
+ samtools source tree in a .tgz file.
+ """
+ execargs = [samtools_binary(),
+ command]
+ execargs += command_args
+ sys.stderr.write("%s.run: exec %s\n" % (__name__, str(execargs)))
+ arvados.util.run_command(
+ execargs,
+ cwd=arvados.current_task().tmpdir,
+ stdin=kwargs.get('stdin', subprocess.PIPE),
+ stderr=kwargs.get('stderr', sys.stderr),
+ stdout=kwargs.get('stdout', sys.stderr))
+
+def one_task_per_bam_file(if_sequence=0, and_end_task=True):
+ """
+ Queue one task for each bam file in this job's input collection.
+
+ Each new task will have an "input" parameter: a manifest
+ containing one .bam file and (if available) the corresponding .bai
+ index file.
+
+ Files in the input collection that are not named *.bam or *.bai
+ (as well as *.bai files that do not match any .bam file present)
+ are silently ignored.
+
+ if_sequence and and_end_task arguments have the same significance
+ as in arvados.job_setup.one_task_per_input_file().
+ """
+ if if_sequence != arvados.current_task()['sequence']:
+ return
+ job_input = arvados.current_job()['script_parameters']['input']
+ cr = arvados.CollectionReader(job_input)
+ bam = {}
+ bai = {}
+ for s in cr.all_streams():
+ for f in s.all_files():
+ if re.search(r'\.bam$', f.name()):
+ bam[s.name(), f.name()] = f
+ elif re.search(r'\.bai$', f.name()):
+ bai[s.name(), f.name()] = f
+ for ((s_name, f_name), bam_f) in bam.items():
+ bai_f = bai.get((s_name, re.sub(r'bam$', 'bai', f_name)), None)
+ task_input = bam_f.as_manifest()
+ if bai_f:
+ task_input += bai_f.as_manifest()
+ new_task_attrs = {
+ 'job_uuid': arvados.current_job()['uuid'],
+ 'created_by_job_task_uuid': arvados.current_task()['uuid'],
+ 'sequence': if_sequence + 1,
+ 'parameters': {
+ 'input': task_input
+ }
+ }
+ arvados.api().job_tasks().create(body=new_task_attrs).execute()
+ if and_end_task:
+ arvados.api().job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={'success':True}
+ ).execute()
+ exit(0)
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import arvados_bwa
+import arvados_samtools
+import os
+import re
+import sys
+import subprocess
+
+arvados_bwa.one_task_per_pair_input_file(if_sequence=0, and_end_task=True)
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+ref_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['reference_index'],
+ path = 'reference',
+ decompress = False)
+
+ref_basename = None
+for f in os.listdir(ref_dir):
+ basename = re.sub(r'\.bwt$', '', f)
+ if basename != f:
+ ref_basename = os.path.join(ref_dir, basename)
+if ref_basename == None:
+ raise Exception("Could not find *.bwt in reference collection.")
+
+tmp_dir = arvados.current_task().tmpdir
+
+class Aligner:
+ def input_filename(self):
+ for s in arvados.CollectionReader(self.collection).all_streams():
+ for f in s.all_files():
+ return f.decompressed_name()
+ def generate_input(self):
+ for s in arvados.CollectionReader(self.collection).all_streams():
+ for f in s.all_files():
+ for s in f.readall_decompressed():
+ yield s
+ def aln(self, input_param):
+ self.collection = this_task['parameters'][input_param]
+ reads_filename = os.path.join(tmp_dir, self.input_filename())
+ aln_filename = os.path.join(tmp_dir, self.input_filename() + '.sai')
+ reads_pipe_r, reads_pipe_w = os.pipe()
+ if os.fork() == 0:
+ os.close(reads_pipe_r)
+ reads_file = open(reads_filename, 'wb')
+ for s in self.generate_input():
+ if len(s) != os.write(reads_pipe_w, s):
+ raise Exception("short write")
+ reads_file.write(s)
+ reads_file.close()
+ os.close(reads_pipe_w)
+ sys.exit(0)
+ os.close(reads_pipe_w)
+
+ aln_file = open(aln_filename, 'wb')
+ bwa_proc = subprocess.Popen(
+ [arvados_bwa.bwa_binary(),
+ 'aln', '-t', '16',
+ ref_basename,
+ '-'],
+ stdin=os.fdopen(reads_pipe_r, 'rb', 2**20),
+ stdout=aln_file)
+ aln_file.close()
+ return reads_filename, aln_filename
+
+reads_1, alignments_1 = Aligner().aln('input_1')
+reads_2, alignments_2 = Aligner().aln('input_2')
+pid1, exit1 = os.wait()
+pid2, exit2 = os.wait()
+if exit1 != 0 or exit2 != 0:
+ raise Exception("bwa aln exited non-zero (0x%x, 0x%x)" % (exit1, exit2))
+
+# output alignments in sam format to pipe
+sam_pipe_r, sam_pipe_w = os.pipe()
+sam_pid = os.fork()
+if sam_pid != 0:
+ # parent
+ os.close(sam_pipe_w)
+else:
+ # child
+ os.close(sam_pipe_r)
+ arvados_bwa.run('sampe',
+ [ref_basename,
+ alignments_1, alignments_2,
+ reads_1, reads_2],
+ stdout=os.fdopen(sam_pipe_w, 'wb', 2**20))
+ sys.exit(0)
+
+# convert sam (sam_pipe_r) to bam (bam_pipe_w)
+bam_pipe_r, bam_pipe_w = os.pipe()
+bam_pid = os.fork()
+if bam_pid != 0:
+ # parent
+ os.close(bam_pipe_w)
+ os.close(sam_pipe_r)
+else:
+ # child
+ os.close(bam_pipe_r)
+ arvados_samtools.run('view',
+ ['-S', '-b',
+ '-'],
+ stdin=os.fdopen(sam_pipe_r, 'rb', 2**20),
+ stdout=os.fdopen(bam_pipe_w, 'wb', 2**20))
+ sys.exit(0)
+
+# copy bam (bam_pipe_r) to Keep
+out_bam_filename = os.path.split(reads_1)[-1] + '.bam'
+out = arvados.CollectionWriter()
+out.start_new_stream()
+out.start_new_file(out_bam_filename)
+out.write(os.fdopen(bam_pipe_r, 'rb', 2**20))
+
+# make sure everyone exited nicely
+pid3, exit3 = os.waitpid(sam_pid, 0)
+if exit3 != 0:
+ raise Exception("bwa sampe exited non-zero (0x%x)" % exit3)
+pid4, exit4 = os.waitpid(bam_pid, 0)
+if exit4 != 0:
+ raise Exception("samtools view exited non-zero (0x%x)" % exit4)
+
+# proclaim success
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import arvados_bwa
+import os
+import re
+import sys
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+ref_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['input'],
+ path = 'reference',
+ decompress = False)
+
+ref_fasta_files = (os.path.join(ref_dir, f)
+ for f in os.listdir(ref_dir)
+ if re.search(r'\.fasta(\.gz)?$', f))
+
+# build reference index
+arvados_bwa.run('index',
+ ['-a', 'bwtsw'] + list(ref_fasta_files))
+
+# move output files to new empty directory
+out_dir = os.path.join(arvados.current_task().tmpdir, 'out')
+arvados.util.run_command(['rm', '-rf', out_dir], stderr=sys.stderr)
+os.mkdir(out_dir)
+for f in os.listdir(ref_dir):
+ if re.search(r'\.(amb|ann|bwt|pac|rbwt|rpac|rsa|sa)$', f):
+ sys.stderr.write("bwa output: %s (%d)\n" %
+ (f, os.stat(os.path.join(ref_dir, f)).st_size))
+ os.rename(os.path.join(ref_dir, f),
+ os.path.join(out_dir, f))
+
+# store output
+out = arvados.CollectionWriter()
+out.write_directory_tree(out_dir, max_manifest_depth=0)
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+# collection-merge
+#
+# Merge two or more collections together. Can also be used to extract specific
+# files from a collection to produce a new collection.
+#
+# input:
+# An array of collections or collection/file paths in script_parameter["input"]
+#
+# output:
+# A manifest with the collections merged. Duplicate file names will
+# have their contents concatenated in the order that they appear in the input
+# array.
+
+import arvados
+import md5
+import crunchutil.subst as subst
+import subprocess
+import os
+import hashlib
+
+p = arvados.current_job()['script_parameters']
+
+merged = ""
+src = []
+for c in p["input"]:
+ c = subst.do_substitution(p, c)
+ i = c.find('/')
+ if i == -1:
+ src.append(c)
+ merged += arvados.CollectionReader(c).manifest_text()
+ else:
+ src.append(c[0:i])
+ cr = arvados.CollectionReader(c[0:i])
+ j = c.rfind('/')
+ stream = c[i+1:j]
+ if stream == "":
+ stream = "."
+ fn = c[(j+1):]
+ for s in cr.all_streams():
+ if s.name() == stream:
+ if fn in s.files():
+ merged += s.files()[fn].as_manifest()
+
+arvados.current_task().set_output(merged)
--- /dev/null
+import arvados
+import arvados.commands.put as put
+import os
+import logging
+import time
+
+def machine_progress(bytes_written, bytes_expected):
+ return "upload wrote {} total {}\n".format(
+ bytes_written, -1 if (bytes_expected is None) else bytes_expected)
+
+class Args(object):
+ def __init__(self, fn):
+ self.filename = None
+ self.paths = [fn]
+ self.max_manifest_depth = 0
+
+# Upload to Keep with error recovery.
+# Return a uuid or raise an exception if there are too many failures.
+def upload(source_dir, logger=None):
+ if logger is None:
+ logger = logging.getLogger("arvados")
+
+ source_dir = os.path.abspath(source_dir)
+ done = False
+ if 'TASK_WORK' in os.environ:
+ resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
+ else:
+ resume_cache = put.ResumeCache(put.ResumeCache.make_path(Args(source_dir)))
+ reporter = put.progress_writer(machine_progress)
+ bytes_expected = put.expected_bytes_for([source_dir])
+ backoff = 1
+ outuuid = None
+ while not done:
+ try:
+ out = put.ArvPutCollectionWriter.from_cache(resume_cache, reporter, bytes_expected)
+ out.do_queued_work()
+ out.write_directory_tree(source_dir, max_manifest_depth=0)
+ outuuid = out.finish()
+ done = True
+ except KeyboardInterrupt as e:
+ logger.critical("caught interrupt signal 2")
+ raise e
+ except Exception as e:
+ logger.exception("caught exception:")
+ backoff *= 2
+ if backoff > 256:
+ logger.critical("Too many upload failures, giving up")
+ raise e
+ else:
+ logger.warning("Sleeping for %s seconds before trying again" % backoff)
+ time.sleep(backoff)
+ return outuuid
--- /dev/null
+import os
+import glob
+import stat
+
+class SubstitutionError(Exception):
+ pass
+
+def search(c):
+ DEFAULT = 0
+ DOLLAR = 1
+
+ i = 0
+ state = DEFAULT
+ start = None
+ depth = 0
+ while i < len(c):
+ if c[i] == '\\':
+ i += 1
+ elif state == DEFAULT:
+ if c[i] == '$':
+ state = DOLLAR
+ if depth == 0:
+ start = i
+ elif c[i] == ')':
+ if depth == 1:
+ return [start, i]
+ if depth > 0:
+ depth -= 1
+ elif state == DOLLAR:
+ if c[i] == '(':
+ depth += 1
+ state = DEFAULT
+ i += 1
+ if depth != 0:
+ raise SubstitutionError("Substitution error, mismatched parentheses {}".format(c))
+ return None
+
+def sub_file(v):
+ path = os.path.join(os.environ['TASK_KEEPMOUNT'], v)
+ st = os.stat(path)
+ if st and stat.S_ISREG(st.st_mode):
+ return path
+ else:
+ raise SubstitutionError("$(file {}) is not accessible or is not a regular file".format(path))
+
+def sub_dir(v):
+ d = os.path.dirname(v)
+ if d == '':
+ d = v
+ path = os.path.join(os.environ['TASK_KEEPMOUNT'], d)
+ st = os.stat(path)
+ if st and stat.S_ISDIR(st.st_mode):
+ return path
+ else:
+ raise SubstitutionError("$(dir {}) is not accessible or is not a directory".format(path))
+
+def sub_basename(v):
+ return os.path.splitext(os.path.basename(v))[0]
+
+def sub_glob(v):
+ l = glob.glob(v)
+ if len(l) == 0:
+ raise SubstitutionError("$(glob {}) no match fonud".format(v))
+ else:
+ return l[0]
+
+default_subs = {"file ": sub_file,
+ "dir ": sub_dir,
+ "basename ": sub_basename,
+ "glob ": sub_glob}
+
+def do_substitution(p, c, subs=default_subs):
+ while True:
+ m = search(c)
+ if m is None:
+ return c
+
+ v = do_substitution(p, c[m[0]+2 : m[1]])
+ var = True
+ for sub in subs:
+ if v.startswith(sub):
+ r = subs[sub](v[len(sub):])
+ var = False
+ break
+ if var:
+ if v in p:
+ r = p[v]
+ else:
+ raise SubstitutionError("Unknown variable or function '%s' while performing substitution on '%s'" % (v, c))
+ if r is None:
+ raise SubstitutionError("Substitution for '%s' is null while performing substitution on '%s'" % (v, c))
+ if not isinstance(r, basestring):
+ raise SubstitutionError("Substitution for '%s' must be a string while performing substitution on '%s'" % (v, c))
+
+ c = c[:m[0]] + r + c[m[1]+1:]
--- /dev/null
+import arvados
+import os
+import robust_put
+import stat
+
+# Implements "Virtual Working Directory"
+# Provides a way of emulating a shared writable directory in Keep based
+# on a "check out, edit, check in, merge" model.
+# At the moment, this only permits adding new files, applications
+# cannot modify or delete existing files.
+
+# Create a symlink tree rooted at target_dir mirroring arv-mounted
+# source_collection. target_dir must be empty, and will be created if it
+# doesn't exist.
+def checkout(source_collection, target_dir, keepmount=None):
+ # create symlinks
+ if keepmount is None:
+ keepmount = os.environ['TASK_KEEPMOUNT']
+
+ if not os.path.exists(target_dir):
+ os.makedirs(target_dir)
+
+ l = os.listdir(target_dir)
+ if len(l) > 0:
+ raise Exception("target_dir must be empty before checkout, contains %s" % l)
+
+ stem = os.path.join(keepmount, source_collection)
+ for root, dirs, files in os.walk(os.path.join(keepmount, source_collection), topdown=True):
+ rel = root[len(stem)+1:]
+ for d in dirs:
+ os.mkdir(os.path.join(target_dir, rel, d))
+ for f in files:
+ os.symlink(os.path.join(root, f), os.path.join(target_dir, rel, f))
+
+# Delete all symlinks and check in any remaining normal files.
+# If merge == True, merge the manifest with source_collection and return a
+# CollectionReader for the combined collection.
+def checkin(source_collection, target_dir, merge=True):
+ # delete symlinks, commit directory, merge manifests and return combined
+ # collection.
+ for root, dirs, files in os.walk(target_dir):
+ for f in files:
+ s = os.lstat(os.path.join(root, f))
+ if stat.S_ISLNK(s.st_mode):
+ os.unlink(os.path.join(root, f))
+
+ uuid = robust_put.upload(target_dir)
+ if merge:
+ cr1 = arvados.CollectionReader(source_collection)
+ cr2 = arvados.CollectionReader(uuid)
+ combined = arvados.CollectionReader(cr1.manifest_text() + cr2.manifest_text())
+ return combined
+ else:
+ return arvados.CollectionReader(uuid)
--- /dev/null
+#!/usr/bin/env python
+
+#
+# decompress-all.py
+#
+# Decompress all compressed files in the collection using the "dtrx" tool and
+# produce a new collection with the contents. Uncompressed files
+# are passed through.
+#
+# input:
+# A collection at script_parameters["input"]
+#
+# output:
+# A manifest of the uncompressed contents of the input collection.
+
+import arvados
+import re
+import subprocess
+import os
+import sys
+import crunchutil.robust_put as robust_put
+
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True,
+ input_as_path=True)
+
+task = arvados.current_task()
+
+input_file = task['parameters']['input']
+
+infile_parts = re.match(r"(^[a-f0-9]{32}\+\d+)(\+\S+)*(/.*)?(/[^/]+)$", input_file)
+
+outdir = os.path.join(task.tmpdir, "output")
+os.makedirs(outdir)
+os.chdir(outdir)
+
+if infile_parts is None:
+ print >>sys.stderr, "Failed to parse input filename '%s' as a Keep file\n" % input_file
+ sys.exit(1)
+
+cr = arvados.CollectionReader(infile_parts.group(1))
+streamname = infile_parts.group(3)[1:]
+filename = infile_parts.group(4)[1:]
+
+if streamname is not None:
+ subprocess.call(["mkdir", "-p", streamname])
+ os.chdir(streamname)
+else:
+ streamname = '.'
+
+m = re.match(r'.*\.(gz|Z|bz2|tgz|tbz|zip|rar|7z|cab|deb|rpm|cpio|gem)$', arvados.get_task_param_mount('input'), re.IGNORECASE)
+
+if m is not None:
+ rc = subprocess.call(["dtrx", "-r", "-n", "-q", arvados.get_task_param_mount('input')])
+ if rc == 0:
+ task.set_output(robust_put.upload(outdir))
+ else:
+ sys.exit(rc)
+else:
+ streamreader = filter(lambda s: s.name() == streamname, cr.all_streams())[0]
+ filereader = streamreader.files()[filename]
+ task.set_output(streamname + filereader.as_manifest()[1:])
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import os
+import re
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+this_job_input = this_job['script_parameters']['input']
+manifest_text = ""
+for f in arvados.CollectionReader(this_job_input).all_files():
+ if f.name() in this_job['script_parameters']['names']:
+ manifest_text += f.as_manifest()
+
+this_task.set_output(arvados.Keep.put(manifest_text))
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import re
+
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True)
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+this_task_input = this_task['parameters']['input']
+pattern = re.compile(this_job['script_parameters']['pattern'])
+
+input_file = list(arvados.CollectionReader(this_task_input).all_files())[0]
+out = arvados.CollectionWriter()
+out.set_current_file_name(input_file.decompressed_name())
+out.set_current_stream_name(input_file.stream_name())
+for line in input_file.readlines():
+ if pattern.search(line):
+ out.write(line)
+
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import hashlib
+import os
+
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=True)
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+
+if 'algorithm' in this_job['script_parameters']:
+ alg = this_job['script_parameters']['algorithm']
+else:
+ alg = 'md5'
+digestor = hashlib.new(alg)
+
+input_file = arvados.get_task_param_mount('input')
+
+with open(input_file) as f:
+ while True:
+ buf = f.read(2**20)
+ if len(buf) == 0:
+ break
+ digestor.update(buf)
+
+hexdigest = digestor.hexdigest()
+
+file_name = '/'.join(this_task['parameters']['input'].split('/')[1:])
+
+out = arvados.CollectionWriter()
+out.set_current_file_name("md5sum.txt")
+out.write("%s %s\n" % (hexdigest, file_name))
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import string
+import json
+import UserDict
+import sys
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+this_job_input = this_job['script_parameters']['input']
+
+out = arvados.CollectionWriter()
+out.set_current_file_name("arvados_objects.json")
+out.write("[\n")
+separator = ""
+
+traits = {}
+done_bytes = 0
+done_ratio = 0
+for input_file in arvados.CollectionReader(this_job_input).all_files():
+ for line_number, line in enumerate(input_file.readlines()):
+
+ done_bytes += len(line)
+ new_done_ratio = 1.0 * done_bytes / input_file.size()
+ if line_number == 2 or new_done_ratio - done_ratio > 0.05:
+ sys.stderr.write("progress: %d%% after %d lines\n" % (int(done_ratio * 100), line_number+1))
+ done_ratio = new_done_ratio
+
+ words = string.split(string.strip(line), "\t")
+ if line_number == 0:
+ headings = words
+ for t in arvados.api('v1').traits().list(
+ where={'name':words},
+ limit=1000
+ ).execute()['items']:
+ traits[t['name']] = t
+ for i, trait_name in enumerate(words[3:], start=3):
+ # find or create trait
+ if trait_name not in traits:
+ traits_match = arvados.api('v1').traits().list(
+ where={'name':trait_name}
+ ).execute()['items']
+ if len(traits_match) > 0:
+ traits[trait_name] = traits_match[0]
+ else:
+ traits[trait_name] = arvados.api('v1').traits().create(
+ trait={'name':trait_name}).execute()
+ out.write(separator)
+ out.write(json.dumps(traits[trait_name]))
+ separator = ",\n"
+ else:
+ huID_links_match = arvados.api('v1').links().list(
+ where={'link_class':'identifier','name':words[0]}
+ ).execute()['items']
+ if len(huID_links_match) > 0:
+ human_uuid = huID_links_match[0]['head_uuid']
+ else:
+ human = arvados.api('v1').humans().create(
+ body={}
+ ).execute()
+ huID_link = arvados.api('v1').links().create(
+ body={
+ 'link_class':'identifier',
+ 'name':words[0],
+ 'head_kind':'arvados#human',
+ 'head_uuid':human['uuid']
+ }
+ ).execute()
+ human_uuid = human['uuid']
+ human_trait = {}
+ for t in arvados.api('v1').links().list(
+ limit=10000,
+ where={
+ 'tail_uuid':human_uuid,
+ 'tail_kind':'arvados#human',
+ 'head_kind':'arvados#trait',
+ 'link_class':'human_trait',
+ 'name':'pgp-survey-response'
+ }
+ ).execute()['items']:
+ human_trait[t['head_uuid']] = t
+ for i, trait_value in enumerate(words[3:], start=3):
+ trait_uuid = traits[headings[i]]['uuid']
+ if trait_uuid in human_trait:
+ trait_link = human_trait[trait_uuid]
+ if trait_link['properties']['value'] != trait_value:
+ # update database value to match survey response
+ trait_link['properties']['value'] = trait_value
+ arvados.api('v1').links().update(
+ uuid=trait_link['uuid'],
+ body={'properties':trait_link['properties']}
+ ).execute()
+ out.write(",\n")
+ out.write(json.dumps(trait_link))
+ elif trait_value == '':
+ # nothing in database, nothing in input
+ pass
+ else:
+ trait_link = {
+ 'tail_uuid':human_uuid,
+ 'tail_kind':'arvados#human',
+ 'head_uuid':traits[headings[i]]['uuid'],
+ 'head_kind':'arvados#trait',
+ 'link_class':'human_trait',
+ 'name':'pgp-survey-response',
+ 'properties': { 'value': trait_value }
+ }
+ arvados.api('v1').links().create(
+ body=trait_link
+ ).execute()
+ out.write(",\n")
+ out.write(json.dumps(trait_link))
+
+out.write("\n]\n")
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+parser_path = arvados.util.git_checkout(
+ url = this_job['script_parameters']['parser_url'],
+ version = this_job['script_parameters']['parser_version'],
+ path = 'parser')
+
+stdoutdata, stderrdata = arvados.util.run_command(
+ ["python", "demo.py"],
+ cwd=parser_path)
+
+out = arvados.CollectionWriter()
+out.write(stdoutdata)
+out.set_current_file_name('participant_traits.tsv')
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import os
+import re
+import sys
+import subprocess
+import arvados_picard
+from arvados_ipc import *
+
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True)
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+ref_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['reference'],
+ path = 'reference',
+ decompress = True)
+ref_fasta_files = [os.path.join(ref_dir, f)
+ for f in os.listdir(ref_dir)
+ if re.search(r'\.fasta(\.gz)?$', f)]
+input_collection = this_task['parameters']['input']
+
+for s in arvados.CollectionReader(input_collection).all_streams():
+ for f in s.all_files():
+ input_stream_name = s.name()
+ input_file_name = f.name()
+ break
+
+# Unfortunately, picard FixMateInformation cannot read from a pipe. We
+# must copy the input to a temporary file before running picard.
+input_bam_path = os.path.join(this_task.tmpdir, input_file_name)
+with open(input_bam_path, 'wb') as bam:
+ for s in arvados.CollectionReader(input_collection).all_streams():
+ for f in s.all_files():
+ for s in f.readall():
+ bam.write(s)
+
+children = {}
+pipes = {}
+
+pipe_setup(pipes, 'fixmate')
+if 0==named_fork(children, 'fixmate'):
+ pipe_closeallbut(pipes, ('fixmate', 'w'))
+ arvados_picard.run(
+ 'FixMateInformation',
+ params={
+ 'i': input_bam_path,
+ 'o': '/dev/stdout',
+ 'quiet': 'true',
+ 'so': 'coordinate',
+ 'validation_stringency': 'LENIENT',
+ 'compression_level': 0
+ },
+ stdout=os.fdopen(pipes['fixmate','w'], 'wb', 2**20))
+ os._exit(0)
+os.close(pipes.pop(('fixmate','w'), None))
+
+pipe_setup(pipes, 'sortsam')
+if 0==named_fork(children, 'sortsam'):
+ pipe_closeallbut(pipes, ('fixmate', 'r'), ('sortsam', 'w'))
+ arvados_picard.run(
+ 'SortSam',
+ params={
+ 'i': '/dev/stdin',
+ 'o': '/dev/stdout',
+ 'quiet': 'true',
+ 'so': 'coordinate',
+ 'validation_stringency': 'LENIENT',
+ 'compression_level': 0
+ },
+ stdin=os.fdopen(pipes['fixmate','r'], 'rb', 2**20),
+ stdout=os.fdopen(pipes['sortsam','w'], 'wb', 2**20))
+ os._exit(0)
+
+pipe_setup(pipes, 'reordersam')
+if 0==named_fork(children, 'reordersam'):
+ pipe_closeallbut(pipes, ('sortsam', 'r'), ('reordersam', 'w'))
+ arvados_picard.run(
+ 'ReorderSam',
+ params={
+ 'i': '/dev/stdin',
+ 'o': '/dev/stdout',
+ 'reference': ref_fasta_files[0],
+ 'quiet': 'true',
+ 'validation_stringency': 'LENIENT',
+ 'compression_level': 0
+ },
+ stdin=os.fdopen(pipes['sortsam','r'], 'rb', 2**20),
+ stdout=os.fdopen(pipes['reordersam','w'], 'wb', 2**20))
+ os._exit(0)
+
+pipe_setup(pipes, 'addrg')
+if 0==named_fork(children, 'addrg'):
+ pipe_closeallbut(pipes, ('reordersam', 'r'), ('addrg', 'w'))
+ arvados_picard.run(
+ 'AddOrReplaceReadGroups',
+ params={
+ 'i': '/dev/stdin',
+ 'o': '/dev/stdout',
+ 'quiet': 'true',
+ 'rglb': this_job['script_parameters'].get('rglb', 0),
+ 'rgpl': this_job['script_parameters'].get('rgpl', 'illumina'),
+ 'rgpu': this_job['script_parameters'].get('rgpu', 0),
+ 'rgsm': this_job['script_parameters'].get('rgsm', 0),
+ 'validation_stringency': 'LENIENT'
+ },
+ stdin=os.fdopen(pipes['reordersam','r'], 'rb', 2**20),
+ stdout=os.fdopen(pipes['addrg','w'], 'wb', 2**20))
+ os._exit(0)
+
+pipe_setup(pipes, 'bammanifest')
+pipe_setup(pipes, 'bam')
+pipe_setup(pipes, 'casm_in')
+if 0==named_fork(children, 'bammanifest'):
+ pipe_closeallbut(pipes,
+ ('addrg', 'r'),
+ ('bammanifest', 'w'),
+ ('bam', 'w'),
+ ('casm_in', 'w'))
+ out = arvados.CollectionWriter()
+ out.start_new_stream(input_stream_name)
+ out.start_new_file(input_file_name)
+ while True:
+ buf = os.read(pipes['addrg','r'], 2**20)
+ if len(buf) == 0:
+ break
+ os.write(pipes['bam','w'], buf)
+ os.write(pipes['casm_in','w'], buf)
+ out.write(buf)
+ os.write(pipes['bammanifest','w'], out.manifest_text())
+ os.close(pipes['bammanifest','w'])
+ os._exit(0)
+
+pipe_setup(pipes, 'casm')
+if 0 == named_fork(children, 'casm'):
+ pipe_closeallbut(pipes, ('casm_in', 'r'), ('casm', 'w'))
+ arvados_picard.run(
+ 'CollectAlignmentSummaryMetrics',
+ params={
+ 'input': '/dev/fd/' + str(pipes['casm_in','r']),
+ 'output': '/dev/fd/' + str(pipes['casm','w']),
+ 'reference_sequence': ref_fasta_files[0],
+ 'validation_stringency': 'LENIENT',
+ },
+ close_fds=False)
+ os._exit(0)
+
+pipe_setup(pipes, 'index')
+if 0==named_fork(children, 'index'):
+ pipe_closeallbut(pipes, ('bam', 'r'), ('index', 'w'))
+ arvados_picard.run(
+ 'BuildBamIndex',
+ params={
+ 'i': '/dev/stdin',
+ 'o': '/dev/stdout',
+ 'quiet': 'true',
+ 'validation_stringency': 'LENIENT'
+ },
+ stdin=os.fdopen(pipes['bam','r'], 'rb', 2**20),
+ stdout=os.fdopen(pipes['index','w'], 'wb', 2**20))
+ os._exit(0)
+
+pipe_setup(pipes, 'indexmanifest')
+if 0==named_fork(children, 'indexmanifest'):
+ pipe_closeallbut(pipes, ('index', 'r'), ('indexmanifest', 'w'))
+ out = arvados.CollectionWriter()
+ out.start_new_stream(input_stream_name)
+ out.start_new_file(re.sub('\.bam$', '.bai', input_file_name))
+ while True:
+ buf = os.read(pipes['index','r'], 2**20)
+ if len(buf) == 0:
+ break
+ out.write(buf)
+ os.write(pipes['indexmanifest','w'], out.manifest_text())
+ os.close(pipes['indexmanifest','w'])
+ os._exit(0)
+
+pipe_closeallbut(pipes,
+ ('bammanifest', 'r'),
+ ('indexmanifest', 'r'),
+ ('casm', 'r'))
+
+outmanifest = ''
+
+for which in ['bammanifest', 'indexmanifest']:
+ with os.fdopen(pipes[which,'r'], 'rb', 2**20) as f:
+ while True:
+ buf = f.read()
+ if buf == '':
+ break
+ outmanifest += buf
+
+casm_out = arvados.CollectionWriter()
+casm_out.start_new_stream(input_stream_name)
+casm_out.start_new_file(input_file_name + '.casm.tsv')
+casm_out.write(os.fdopen(pipes.pop(('casm','r'))))
+
+outmanifest += casm_out.manifest_text()
+
+all_ok = True
+for (childname, pid) in children.items():
+ all_ok = all_ok and waitpid_and_check_exit(pid, childname)
+
+if all_ok:
+ this_task.set_output(outmanifest)
+else:
+ sys.exit(1)
--- /dev/null
+import arvados
+import re
+import os
+import sys
+
+rtg_install_path = None
+
+def setup():
+ global rtg_install_path
+ if rtg_install_path:
+ return rtg_install_path
+ rtg_path = arvados.util.zipball_extract(
+ zipball = arvados.current_job()['script_parameters']['rtg_binary_zip'],
+ path = 'rtg')
+ rtg_license_path = arvados.util.collection_extract(
+ collection = arvados.current_job()['script_parameters']['rtg_license'],
+ path = 'license',
+ decompress = False)
+
+ # symlink to rtg-license.txt
+ license_txt_path = os.path.join(rtg_license_path, 'rtg-license.txt')
+ try:
+ os.symlink(license_txt_path, os.path.join(rtg_path,'rtg-license.txt'))
+ except OSError:
+ if not os.path.exists(os.path.join(rtg_path,'rtg-license.txt')):
+ os.symlink(license_txt_path, os.path.join(rtg_path,'rtg-license.txt'))
+
+ rtg_install_path = rtg_path
+ return rtg_path
+
+def run_rtg(command, output_dir, command_args, **kwargs):
+ global rtg_install_path
+ execargs = [os.path.join(rtg_install_path, 'rtg'),
+ command,
+ '-o', output_dir]
+ execargs += command_args
+ sys.stderr.write("run_rtg: exec %s\n" % str(execargs))
+ arvados.util.run_command(
+ execargs,
+ cwd=arvados.current_task().tmpdir,
+ stderr=sys.stderr,
+ stdout=sys.stderr)
+
+ # Exit status cannot be trusted in rtg 1.1.1.
+ assert_done(output_dir)
+
+ # Copy log files to stderr and delete them to avoid storing them
+ # in Keep with the output data.
+ for dirent in arvados.util.listdir_recursive(output_dir):
+ if is_log_file(dirent):
+ log_file = os.path.join(output_dir, dirent)
+ sys.stderr.write(' '.join(['==>', dirent, '<==\n']))
+ with open(log_file, 'rb') as f:
+ while True:
+ buf = f.read(2**20)
+ if len(buf) == 0:
+ break
+ sys.stderr.write(buf)
+ sys.stderr.write('\n') # in case log does not end in newline
+ os.unlink(log_file)
+
+def assert_done(output_dir):
+ # Sanity-check exit code.
+ done_file = os.path.join(output_dir, 'done')
+ if not os.path.exists(done_file):
+ raise Exception("rtg exited 0 but %s does not exist. abort.\n" % done_file)
+
+def is_log_file(filename):
+ return re.search(r'^(.*/)?(progress|done|\S+.log)$', filename)
+
+setup()
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import os
+import re
+import sys
+import pyrtg
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+fasta_path = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['input'],
+ path = 'fasta',
+ decompress = False)
+fasta_files = filter(lambda f: f != '.locator', os.listdir(fasta_path))
+out_dir = os.path.join(arvados.current_task().tmpdir, 'ref-sdf')
+arvados.util.run_command(['rm', '-rf', out_dir], stderr=sys.stderr)
+
+pyrtg.run_rtg('format', out_dir,
+ map(lambda f: os.path.join(fasta_path, f), fasta_files))
+
+out = arvados.CollectionWriter()
+out.write_directory_tree(out_dir, max_manifest_depth=0)
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import os
+import re
+import sys
+import pyrtg
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+fastq_path = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['input'],
+ path = 'fastq')
+fastq_files = filter(lambda f: f != '.locator', os.listdir(fastq_path))
+tmp_dir_base = os.path.join(arvados.current_task().tmpdir, 'tmp')
+out_dir = os.path.join(arvados.current_task().tmpdir, 'reads')
+
+arvados.util.run_command(['rm', '-rf', tmp_dir_base], stderr=sys.stderr)
+arvados.util.run_command(['rm', '-rf', out_dir], stderr=sys.stderr)
+os.mkdir(tmp_dir_base)
+
+# convert fastq to sdf
+tmp_dirs = []
+for leftarm in fastq_files:
+ if re.search(r'_1.f(ast)?q(.gz)?$', leftarm):
+ rightarm = re.sub(r'_1(.f(ast)?q(.gz)?)$', '_2\\1', leftarm)
+ if rightarm in fastq_files:
+ tmp_dirs += ['%s/%08d' % (tmp_dir_base, len(tmp_dirs))]
+ pyrtg.run_rtg('format', tmp_dirs[-1],
+ ['-f', 'fastq',
+ '-q', 'sanger',
+ '-l', os.path.join(fastq_path, leftarm),
+ '-r', os.path.join(fastq_path, rightarm)])
+
+# split sdf
+pyrtg.run_rtg('sdfsplit', out_dir,
+ ['-n', '1500000'] + tmp_dirs)
+
+# store output
+out = arvados.CollectionWriter()
+out.write_directory_tree(out_dir, max_manifest_depth=1)
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import os
+import re
+import sys
+import pyrtg
+
+arvados.job_setup.one_task_per_input_stream(if_sequence=0, and_end_task=True)
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+in_dir = os.path.join(this_task.tmpdir, 'input')
+arvados.util.run_command(['rm', '-rf', in_dir], stderr=sys.stderr)
+in_dir = arvados.util.stream_extract(
+ stream = arvados.StreamReader(this_task['parameters']['input']),
+ path = in_dir,
+ decompress = False)
+ref_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['reference'],
+ path = 'reference',
+ decompress = False)
+
+out_dir = os.path.join(arvados.current_task().tmpdir, 'out')
+arvados.util.run_command(['rm', '-rf', out_dir], stderr=sys.stderr)
+
+# map reads
+pyrtg.run_rtg('map', out_dir,
+ ['-i', in_dir,
+ '-t', ref_dir,
+ '-a', '2',
+ '-b', '1',
+ '--sam-rg', '@RG\\tID:NA\\tSM:NA\\tPL:ILLUMINA'])
+
+# store output
+out = arvados.CollectionWriter()
+out.write_directory_tree(out_dir, this_task['parameters']['input'][0], 0)
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import os
+import re
+import sys
+import pyrtg
+
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+ref_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['reference'],
+ path = 'reference',
+ decompress = False)
+input_dir = arvados.util.collection_extract(
+ collection = this_job['script_parameters']['input'],
+ path = 'input')
+bam_files = map(lambda f: os.path.join(input_dir, f),
+ filter(lambda f: re.search(r'^(.*/)?alignments.bam$', f),
+ arvados.util.listdir_recursive(input_dir)))
+out_dir = os.path.join(arvados.current_task().tmpdir, 'out')
+arvados.util.run_command(['rm', '-rf', out_dir], stderr=sys.stderr)
+
+# call sequence variants
+pyrtg.run_rtg('snp', out_dir,
+ ['-t', ref_dir] + bam_files)
+
+# store output
+out = arvados.CollectionWriter()
+out.write_directory_tree(out_dir, max_manifest_depth=0)
+this_task.set_output(out.finish())
--- /dev/null
+#!/usr/bin/env python
+
+import logging
+
+logger = logging.getLogger('run-command')
+log_handler = logging.StreamHandler()
+log_handler.setFormatter(logging.Formatter("run-command: %(message)s"))
+logger.addHandler(log_handler)
+logger.setLevel(logging.INFO)
+
+import arvados
+import re
+import os
+import subprocess
+import sys
+import shutil
+import crunchutil.subst as subst
+import time
+import arvados.commands.put as put
+import signal
+import stat
+import copy
+import traceback
+import pprint
+import multiprocessing
+import crunchutil.robust_put as robust_put
+import crunchutil.vwd as vwd
+import argparse
+import json
+import tempfile
+import errno
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--dry-run', action='store_true')
+parser.add_argument('--script-parameters', type=str, default="{}")
+args = parser.parse_args()
+
+os.umask(0077)
+
+if not args.dry_run:
+ api = arvados.api('v1')
+ t = arvados.current_task().tmpdir
+ os.chdir(arvados.current_task().tmpdir)
+ os.mkdir("tmpdir")
+ os.mkdir("output")
+
+ os.chdir("output")
+
+ outdir = os.getcwd()
+
+ taskp = None
+ jobp = arvados.current_job()['script_parameters']
+ if len(arvados.current_task()['parameters']) > 0:
+ taskp = arvados.current_task()['parameters']
+else:
+ outdir = "/tmp"
+ jobp = json.loads(args.script_parameters)
+ os.environ['JOB_UUID'] = 'zzzzz-8i9sb-1234567890abcde'
+ os.environ['TASK_UUID'] = 'zzzzz-ot0gb-1234567890abcde'
+ os.environ['CRUNCH_SRC'] = '/tmp/crunche-src'
+ if 'TASK_KEEPMOUNT' not in os.environ:
+ os.environ['TASK_KEEPMOUNT'] = '/keep'
+
+links = []
+
+def sub_tmpdir(v):
+ return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
+
+def sub_outdir(v):
+ return outdir
+
+def sub_cores(v):
+ return str(multiprocessing.cpu_count())
+
+def sub_jobid(v):
+ return os.environ['JOB_UUID']
+
+def sub_taskid(v):
+ return os.environ['TASK_UUID']
+
+def sub_jobsrc(v):
+ return os.environ['CRUNCH_SRC']
+
+subst.default_subs["task.tmpdir"] = sub_tmpdir
+subst.default_subs["task.outdir"] = sub_outdir
+subst.default_subs["job.srcdir"] = sub_jobsrc
+subst.default_subs["node.cores"] = sub_cores
+subst.default_subs["job.uuid"] = sub_jobid
+subst.default_subs["task.uuid"] = sub_taskid
+
+class SigHandler(object):
+ def __init__(self):
+ self.sig = None
+
+ def send_signal(self, subprocesses, signum):
+ for sp in subprocesses:
+ sp.send_signal(signum)
+ self.sig = signum
+
+# http://rightfootin.blogspot.com/2006/09/more-on-python-flatten.html
+def flatten(l, ltypes=(list, tuple)):
+ ltype = type(l)
+ l = list(l)
+ i = 0
+ while i < len(l):
+ while isinstance(l[i], ltypes):
+ if not l[i]:
+ l.pop(i)
+ i -= 1
+ break
+ else:
+ l[i:i + 1] = l[i]
+ i += 1
+ return ltype(l)
+
+def add_to_group(gr, match):
+ m = match.groups()
+ if m not in gr:
+ gr[m] = []
+ gr[m].append(match.group(0))
+
+class EvaluationError(Exception):
+ pass
+
+# Return the name of variable ('var') that will take on each value in 'items'
+# when performing an inner substitution
+def var_items(p, c, key):
+ if key not in c:
+ raise EvaluationError("'%s' was expected in 'p' but is missing" % key)
+
+ if "var" in c:
+ if not isinstance(c["var"], basestring):
+ raise EvaluationError("Value of 'var' must be a string")
+ # Var specifies the variable name for inner parameter substitution
+ return (c["var"], get_items(p, c[key]))
+ else:
+ # The component function ('key') value is a list, so return the list
+ # directly with no parameter selected.
+ if isinstance(c[key], list):
+ return (None, get_items(p, c[key]))
+ elif isinstance(c[key], basestring):
+ # check if c[key] is a string that looks like a parameter
+ m = re.match("^\$\((.*)\)$", c[key])
+ if m and m.group(1) in p:
+ return (m.group(1), get_items(p, c[key]))
+ else:
+ # backwards compatible, foreach specifies bare parameter name to use
+ return (c[key], get_items(p, p[c[key]]))
+ else:
+ raise EvaluationError("Value of '%s' must be a string or list" % key)
+
+# "p" is the parameter scope, "c" is the item to be expanded.
+# If "c" is a dict, apply function expansion.
+# If "c" is a list, recursively expand each item and return a new list.
+# If "c" is a string, apply parameter substitution
+def expand_item(p, c):
+ if isinstance(c, dict):
+ if "foreach" in c and "command" in c:
+ # Expand a command template for each item in the specified user
+ # parameter
+ var, items = var_items(p, c, "foreach")
+ if var is None:
+ raise EvaluationError("Must specify 'var' in foreach")
+ r = []
+ for i in items:
+ params = copy.copy(p)
+ params[var] = i
+ r.append(expand_item(params, c["command"]))
+ return r
+ elif "list" in c and "index" in c and "command" in c:
+ # extract a single item from a list
+ var, items = var_items(p, c, "list")
+ if var is None:
+ raise EvaluationError("Must specify 'var' in list")
+ params = copy.copy(p)
+ params[var] = items[int(c["index"])]
+ return expand_item(params, c["command"])
+ elif "regex" in c:
+ pattern = re.compile(c["regex"])
+ if "filter" in c:
+ # filter list so that it only includes items that match a
+ # regular expression
+ _, items = var_items(p, c, "filter")
+ return [i for i in items if pattern.match(i)]
+ elif "group" in c:
+ # generate a list of lists, where items are grouped on common
+ # subexpression match
+ _, items = var_items(p, c, "group")
+ groups = {}
+ for i in items:
+ match = pattern.match(i)
+ if match:
+ add_to_group(groups, match)
+ return [groups[k] for k in groups]
+ elif "extract" in c:
+ # generate a list of lists, where items are split by
+ # subexpression match
+ _, items = var_items(p, c, "extract")
+ r = []
+ for i in items:
+ match = pattern.match(i)
+ if match:
+ r.append(list(match.groups()))
+ return r
+ elif "batch" in c and "size" in c:
+ # generate a list of lists, where items are split into a batch size
+ _, items = var_items(p, c, "batch")
+ sz = int(c["size"])
+ r = []
+ for j in xrange(0, len(items), sz):
+ r.append(items[j:j+sz])
+ return r
+ raise EvaluationError("Missing valid list context function")
+ elif isinstance(c, list):
+ return [expand_item(p, arg) for arg in c]
+ elif isinstance(c, basestring):
+ m = re.match("^\$\((.*)\)$", c)
+ if m and m.group(1) in p:
+ return expand_item(p, p[m.group(1)])
+ else:
+ return subst.do_substitution(p, c)
+ else:
+ raise EvaluationError("expand_item() unexpected parameter type %s" % type(c))
+
+# Evaluate in a list context
+# "p" is the parameter scope, "value" will be evaluated
+# if "value" is a list after expansion, return that
+# if "value" is a path to a directory, return a list consisting of each entry in the directory
+# if "value" is a path to a file, return a list consisting of each line of the file
+def get_items(p, value):
+ value = expand_item(p, value)
+ if isinstance(value, list):
+ return value
+ elif isinstance(value, basestring):
+ mode = os.stat(value).st_mode
+ prefix = value[len(os.environ['TASK_KEEPMOUNT'])+1:]
+ if mode is not None:
+ if stat.S_ISDIR(mode):
+ items = [os.path.join(value, l) for l in os.listdir(value)]
+ elif stat.S_ISREG(mode):
+ with open(value) as f:
+ items = [line.rstrip("\r\n") for line in f]
+ return items
+ raise EvaluationError("get_items did not yield a list")
+
+stdoutname = None
+stdoutfile = None
+stdinname = None
+stdinfile = None
+
+# Construct the cross product of all values of each variable listed in fvars
+def recursive_foreach(params, fvars):
+ var = fvars[0]
+ fvars = fvars[1:]
+ items = get_items(params, params[var])
+ logger.info("parallelizing on %s with items %s" % (var, items))
+ if items is not None:
+ for i in items:
+ params = copy.copy(params)
+ params[var] = i
+ if len(fvars) > 0:
+ recursive_foreach(params, fvars)
+ else:
+ if not args.dry_run:
+ arvados.api().job_tasks().create(body={
+ 'job_uuid': arvados.current_job()['uuid'],
+ 'created_by_job_task_uuid': arvados.current_task()['uuid'],
+ 'sequence': 1,
+ 'parameters': params
+ }).execute()
+ else:
+ if isinstance(params["command"][0], list):
+ for c in params["command"]:
+ logger.info(flatten(expand_item(params, c)))
+ else:
+ logger.info(flatten(expand_item(params, params["command"])))
+ else:
+ logger.error("parameter %s with value %s in task.foreach yielded no items" % (var, params[var]))
+ sys.exit(1)
+
+try:
+ if "task.foreach" in jobp:
+ if args.dry_run or arvados.current_task()['sequence'] == 0:
+ # This is the first task to start the other tasks and exit
+ fvars = jobp["task.foreach"]
+ if isinstance(fvars, basestring):
+ fvars = [fvars]
+ if not isinstance(fvars, list) or len(fvars) == 0:
+ logger.error("value of task.foreach must be a string or non-empty list")
+ sys.exit(1)
+ recursive_foreach(jobp, jobp["task.foreach"])
+ if not args.dry_run:
+ if "task.vwd" in jobp:
+ # Set output of the first task to the base vwd collection so it
+ # will be merged with output fragments from the other tasks by
+ # crunch.
+ arvados.current_task().set_output(subst.do_substitution(jobp, jobp["task.vwd"]))
+ else:
+ arvados.current_task().set_output(None)
+ sys.exit(0)
+ else:
+ # This is the only task so taskp/jobp are the same
+ taskp = jobp
+except Exception as e:
+ logger.exception("caught exception")
+ logger.error("job parameters were:")
+ logger.error(pprint.pformat(jobp))
+ sys.exit(1)
+
+try:
+ if not args.dry_run:
+ if "task.vwd" in taskp:
+ # Populate output directory with symlinks to files in collection
+ vwd.checkout(subst.do_substitution(taskp, taskp["task.vwd"]), outdir)
+
+ if "task.cwd" in taskp:
+ os.chdir(subst.do_substitution(taskp, taskp["task.cwd"]))
+
+ cmd = []
+ if isinstance(taskp["command"][0], list):
+ for c in taskp["command"]:
+ cmd.append(flatten(expand_item(taskp, c)))
+ else:
+ cmd.append(flatten(expand_item(taskp, taskp["command"])))
+
+ if "task.stdin" in taskp:
+ stdinname = subst.do_substitution(taskp, taskp["task.stdin"])
+ if not args.dry_run:
+ stdinfile = open(stdinname, "rb")
+
+ if "task.stdout" in taskp:
+ stdoutname = subst.do_substitution(taskp, taskp["task.stdout"])
+ if not args.dry_run:
+ stdoutfile = open(stdoutname, "wb")
+
+ logger.info("{}{}{}".format(' | '.join([' '.join(c) for c in cmd]), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else ""))
+
+ if args.dry_run:
+ sys.exit(0)
+except subst.SubstitutionError as e:
+ logger.error(str(e))
+ logger.error("task parameters were:")
+ logger.error(pprint.pformat(taskp))
+ sys.exit(1)
+except Exception as e:
+ logger.exception("caught exception")
+ logger.error("task parameters were:")
+ logger.error(pprint.pformat(taskp))
+ sys.exit(1)
+
+# rcode holds the return codes produced by each subprocess
+rcode = {}
+try:
+ subprocesses = []
+ close_streams = []
+ if stdinfile:
+ close_streams.append(stdinfile)
+ next_stdin = stdinfile
+
+ for i in xrange(len(cmd)):
+ if i == len(cmd)-1:
+ # this is the last command in the pipeline, so its stdout should go to stdoutfile
+ next_stdout = stdoutfile
+ else:
+ # this is an intermediate command in the pipeline, so its stdout should go to a pipe
+ next_stdout = subprocess.PIPE
+
+ sp = subprocess.Popen(cmd[i], shell=False, stdin=next_stdin, stdout=next_stdout)
+
+ # Need to close the FDs on our side so that subcommands will get SIGPIPE if the
+ # consuming process ends prematurely.
+ if sp.stdout:
+ close_streams.append(sp.stdout)
+
+ # Send this processes's stdout to to the next process's stdin
+ next_stdin = sp.stdout
+
+ subprocesses.append(sp)
+
+ # File descriptors have been handed off to the subprocesses, so close them here.
+ for s in close_streams:
+ s.close()
+
+ # Set up signal handling
+ sig = SigHandler()
+
+ # Forward terminate signals to the subprocesses.
+ signal.signal(signal.SIGINT, lambda signum, frame: sig.send_signal(subprocesses, signum))
+ signal.signal(signal.SIGTERM, lambda signum, frame: sig.send_signal(subprocesses, signum))
+ signal.signal(signal.SIGQUIT, lambda signum, frame: sig.send_signal(subprocesses, signum))
+
+ active = 1
+ pids = set([s.pid for s in subprocesses])
+ while len(pids) > 0:
+ (pid, status) = os.wait()
+ pids.discard(pid)
+ if not taskp.get("task.ignore_rcode"):
+ rcode[pid] = (status >> 8)
+ else:
+ rcode[pid] = 0
+
+ if sig.sig is not None:
+ logger.critical("terminating on signal %s" % sig.sig)
+ sys.exit(2)
+ else:
+ for i in xrange(len(cmd)):
+ r = rcode[subprocesses[i].pid]
+ logger.info("%s completed with exit code %i (%s)" % (cmd[i][0], r, "success" if r == 0 else "failed"))
+
+except Exception as e:
+ logger.exception("caught exception")
+
+# restore default signal handlers.
+signal.signal(signal.SIGINT, signal.SIG_DFL)
+signal.signal(signal.SIGTERM, signal.SIG_DFL)
+signal.signal(signal.SIGQUIT, signal.SIG_DFL)
+
+for l in links:
+ os.unlink(l)
+
+logger.info("the following output files will be saved to keep:")
+
+subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr)
+
+logger.info("start writing output to keep")
+
+if "task.vwd" in taskp:
+ if "task.foreach" in jobp:
+ # This is a subtask, so don't merge with the original collection, that will happen at the end
+ outcollection = vwd.checkin(subst.do_substitution(taskp, taskp["task.vwd"]), outdir, merge=False).manifest_text()
+ else:
+ # Just a single task, so do merge with the original collection
+ outcollection = vwd.checkin(subst.do_substitution(taskp, taskp["task.vwd"]), outdir, merge=True).manifest_text()
+else:
+ outcollection = robust_put.upload(outdir, logger)
+
+# Success if we ran any subprocess, and they all exited 0.
+success = rcode and all(status == 0 for status in rcode.itervalues())
+
+api.job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={
+ 'output': outcollection,
+ 'success': success,
+ 'progress':1.0
+ }).execute()
+
+sys.exit(0 if success else 1)
--- /dev/null
+#!/usr/bin/python
+
+import arvados
+import re
+import hashlib
+import string
+
+api = arvados.api('v1')
+
+piece = 0
+manifest_text = ""
+
+# Look for paired reads
+
+inp = arvados.CollectionReader(arvados.getjobparam('reads'))
+
+manifest_list = []
+
+chunking = False #arvados.getjobparam('chunking')
+
+def nextline(reader, start):
+ n = -1
+ while True:
+ r = reader.readfrom(start, 128)
+ if r == '':
+ break
+ n = string.find(r, "\n")
+ if n > -1:
+ break
+ else:
+ start += 128
+ return n
+
+# Chunk a fastq into approximately 64 MiB chunks. Requires that the input data
+# be decompressed ahead of time, such as using decompress-all.py. Generates a
+# new manifest, but doesn't actually move any data around. Handles paired
+# reads by ensuring that each chunk of a pair gets the same number of records.
+#
+# This works, but in practice is so slow that potential gains in alignment
+# performance are lost in the prep time, which is why it is currently disabled.
+#
+# A better algorithm would seek to a file position a bit less than the desired
+# chunk size and then scan ahead for the next record, making sure that record
+# was matched by the read pair.
+def splitfastq(p):
+ for i in xrange(0, len(p)):
+ p[i]["start"] = 0
+ p[i]["end"] = 0
+
+ count = 0
+ recordsize = [0, 0]
+
+ global piece
+ finish = False
+ while not finish:
+ for i in xrange(0, len(p)):
+ recordsize[i] = 0
+
+ # read next 4 lines
+ for i in xrange(0, len(p)):
+ for ln in xrange(0, 4):
+ r = nextline(p[i]["reader"], p[i]["end"]+recordsize[i])
+ if r == -1:
+ finish = True
+ break
+ recordsize[i] += (r+1)
+
+ splitnow = finish
+ for i in xrange(0, len(p)):
+ if ((p[i]["end"] - p[i]["start"]) + recordsize[i]) >= (64*1024*1024):
+ splitnow = True
+
+ if splitnow:
+ for i in xrange(0, len(p)):
+ global manifest_list
+ print >>sys.stderr, "Finish piece ./_%s/%s (%s %s)" % (piece, p[i]["reader"].name(), p[i]["start"], p[i]["end"])
+ manifest = []
+ manifest.extend(["./_" + str(piece)])
+ manifest.extend([d[arvados.LOCATOR] for d in p[i]["reader"]._stream._data_locators])
+ manifest.extend(["{}:{}:{}".format(seg[arvados.LOCATOR]+seg[arvados.OFFSET], seg[arvados.SEGMENTSIZE], p[i]["reader"].name().replace(' ', '\\040')) for seg in arvados.locators_and_ranges(p[i]["reader"].segments, p[i]["start"], p[i]["end"] - p[i]["start"])])
+ manifest_list.append(manifest)
+ p[i]["start"] = p[i]["end"]
+ piece += 1
+ else:
+ for i in xrange(0, len(p)):
+ p[i]["end"] += recordsize[i]
+ count += 1
+ if count % 10000 == 0:
+ print >>sys.stderr, "Record %s at %s" % (count, p[i]["end"])
+
+prog = re.compile(r'(.*?)(_[12])?\.fastq(\.gz)?$')
+
+# Look for fastq files
+for s in inp.all_streams():
+ for f in s.all_files():
+ name_pieces = prog.match(f.name())
+ if name_pieces is not None:
+ if s.name() != ".":
+ # The downstream tool (run-command) only iterates over the top
+ # level of directories so if there are fastq files in
+ # directories in the input, the choice is either to forget
+ # there are directories (which might lead to name conflicts) or
+ # just fail.
+ print >>sys.stderr, "fastq must be at the root of the collection"
+ sys.exit(1)
+
+ p = None
+ if name_pieces.group(2) is not None:
+ if name_pieces.group(2) == "_1":
+ p = [{}, {}]
+ p[0]["reader"] = s.files()[name_pieces.group(0)]
+ p[1]["reader"] = s.files()[name_pieces.group(1) + "_2.fastq" + (name_pieces.group(3) if name_pieces.group(3) else '')]
+ else:
+ p = [{}]
+ p[0]["reader"] = s.files()[name_pieces.group(0)]
+
+ if p is not None:
+ if chunking:
+ splitfastq(p)
+ else:
+ for i in xrange(0, len(p)):
+ m = p[i]["reader"].as_manifest().split()
+ m[0] = "./_" + str(piece)
+ manifest_list.append(m)
+ piece += 1
+
+manifest_text = "\n".join(" ".join(m) for m in manifest_list) + "\n"
+
+arvados.current_task().set_output(manifest_text)
--- /dev/null
+source 'https://rubygems.org'
+
+gem 'zenweb'
+gem 'liquid'
+gem 'RedCloth'
+gem 'colorize'
--- /dev/null
+GEM
+ remote: https://rubygems.org/
+ specs:
+ RedCloth (4.2.9)
+ coderay (1.1.0)
+ colorize (0.6.0)
+ kramdown (1.3.1)
+ less (1.2.21)
+ mutter (>= 0.4.2)
+ treetop (>= 1.4.2)
+ liquid (2.6.1)
+ makerakeworkwell (1.0.3)
+ rake (>= 0.9.2, < 11)
+ mutter (0.5.3)
+ polyglot (0.3.3)
+ rake (10.1.1)
+ treetop (1.4.15)
+ polyglot
+ polyglot (>= 0.3.1)
+ zenweb (3.3.1)
+ coderay (~> 1.0)
+ kramdown (~> 1.0)
+ less (~> 1.2)
+ makerakeworkwell (~> 1.0)
+ rake (>= 0.9, < 11)
+
+PLATFORMS
+ ruby
+
+DEPENDENCIES
+ RedCloth
+ colorize
+ liquid
+ zenweb
--- /dev/null
+h1. Arvados documentation
+
+This is the source code for "doc.arvados.org":http://doc.arvados.org.
+
+Here's how to build the HTML pages locally so you can preview your updates before you commit and push.
+
+Additional information is available on the "'Documentation' page on the Arvados wiki":https://arvados.org/projects/arvados/wiki/Documentation.
+
+h2. Install dependencies
+
+<pre>
+arvados/doc$ bundle install
+</pre>
+
+h2. Generate HTML pages
+
+<pre>
+arvados/doc$ rake
+</pre>
+
+Alternately, to make the documentation browsable on the local filesystem:
+
+<pre>
+arvados/doc$ rake generate baseurl=$PWD/.site
+</pre>
+
+h2. Run linkchecker
+
+If you have "Linkchecker":http://wummel.github.io/linkchecker/ installed on
+your system, you can run it against the documentation:
+
+<pre>
+arvados/doc$ rake linkchecker baseurl=file://$PWD/.site
+</pre>
+
+Please note that this will regenerate your $PWD/.site directory.
+
+h2. Preview HTML pages
+
+<pre>
+arvados/doc$ rake run
+[2014-03-10 09:03:41] INFO WEBrick 1.3.1
+[2014-03-10 09:03:41] INFO ruby 2.1.1 (2014-02-24) [x86_64-linux]
+[2014-03-10 09:03:41] INFO WEBrick::HTTPServer#start: pid=8926 port=8000
+</pre>
+
+Preview the rendered pages at "http://localhost:8000":http://localhost:8000.
+
+h2. Publish HTML pages inside Workbench
+
+(or some other web site)
+
+You can set @baseurl@ (the URL prefix for all internal links), @arvados_api_host@ and @arvados_workbench_host@ without changing @_config.yml@:
+
+<pre>
+arvados/doc$ rake generate baseurl=/doc arvados_api_host=xyzzy.arvadosapi.com
+</pre>
+
+Make the docs appear at {workbench_host}/doc by creating a symbolic link in Workbench's @public@ directory, pointing to the generated HTML tree.
+
+<pre>
+arvados/doc$ ln -sn ../../../doc/.site ../apps/workbench/public/doc
+</pre>
+
+h2. Delete generated files
+
+<pre>
+arvados/doc$ rake realclean
+</pre>
--- /dev/null
+#!/usr/bin/env rake
+
+require "rubygems"
+require "colorize"
+
+task :generate => [ :realclean, 'sdk/python/arvados/index.html' ] do
+ vars = ['baseurl', 'arvados_api_host', 'arvados_workbench_host']
+ vars.each do |v|
+ if ENV[v]
+ website.config.h[v] = ENV[v]
+ end
+ end
+end
+
+file "sdk/python/arvados/index.html" do |t|
+ `which epydoc`
+ if $? == 0
+ `epydoc --html --parse-only -o sdk/python/arvados ../sdk/python/arvados/`
+ else
+ puts "Warning: epydoc not found, Python documentation will not be generated".colorize(:light_red)
+ end
+end
+
+task :linkchecker => [ :generate ] do
+ Dir.chdir(".site") do
+ `which linkchecker`
+ if $? == 0
+ system "linkchecker index.html --ignore-url='!file://'" or exit $?.exitstatus
+ else
+ puts "Warning: linkchecker not found, skipping run".colorize(:light_red)
+ end
+ end
+end
+
+task :clean do
+ rm_rf "sdk/python/arvados"
+end
+
+require "zenweb/tasks"
+load "zenweb-textile.rb"
+load "zenweb-liquid.rb"
+
+task :extra_wirings do
+ $website.pages["sdk/python/python.html.textile.liquid"].depends_on("sdk/python/arvados/index.html")
+end
--- /dev/null
+# baseurl is the location of the generated site from the browser's
+# perspective (e.g., http://doc.arvados.org or
+# file:///tmp/arvados/doc/.site). To make docs show up inside
+# workbench, use /doc here and add a symlink at
+# apps/workbench/public/doc pointing to ../../../doc/.site
+# You can also set these on the command line:
+# $ rake generate baseurl=/example arvados_api_host=example.com
+
+baseurl:
+arvados_api_host: localhost
+arvados_workbench_host: localhost
+
+exclude: ["Rakefile", "tmp", "vendor"]
+
+navbar:
+ userguide:
+ - Getting Started:
+ - user/index.html.textile.liquid
+ - user/getting_started/community.html.textile.liquid
+ - Run a pipeline using Workbench:
+ - user/getting_started/workbench.html.textile.liquid
+ - user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+ - Access an Arvados virtual machine:
+ - user/getting_started/ssh-access-unix.html.textile.liquid
+ - user/getting_started/ssh-access-windows.html.textile.liquid
+ - user/getting_started/check-environment.html.textile.liquid
+ - user/reference/api-tokens.html.textile.liquid
+ - Working with data sets:
+ - user/tutorials/tutorial-keep.html.textile.liquid
+ - user/tutorials/tutorial-keep-get.html.textile.liquid
+ - user/tutorials/tutorial-keep-mount.html.textile.liquid
+ - user/topics/keep.html.textile.liquid
+ - Run a pipeline on the command line:
+ - user/topics/running-pipeline-command-line.html.textile.liquid
+ - user/topics/arv-run.html.textile.liquid
+ - Develop a new pipeline:
+ - user/tutorials/intro-crunch.html.textile.liquid
+ - user/tutorials/running-external-program.html.textile.liquid
+ - user/tutorials/tutorial-firstscript.html.textile.liquid
+ - user/tutorials/tutorial-submit-job.html.textile.liquid
+ - user/topics/tutorial-parallel.html.textile.liquid
+ - user/topics/arv-docker.html.textile.liquid
+ - Reference:
+ - user/topics/run-command.html.textile.liquid
+ - user/reference/job-pipeline-ref.html.textile.liquid
+ - user/examples/crunch-examples.html.textile.liquid
+ - Query the metadata database:
+ - user/topics/tutorial-trait-search.html.textile.liquid
+ - Arvados License:
+ - user/copying/copying.html.textile.liquid
+ - user/copying/agpl-3.0.html
+ - user/copying/LICENSE-2.0.html
+ - user/copying/by-sa-3.0.html
+ sdk:
+ - Overview:
+ - sdk/index.html.textile.liquid
+ - Python:
+ - sdk/python/sdk-python.html.textile.liquid
+ - sdk/python/python.html.textile.liquid
+ - sdk/python/crunch-utility-libraries.html.textile.liquid
+ - Perl:
+ - sdk/perl/index.html.textile.liquid
+ - Ruby:
+ - sdk/ruby/index.html.textile.liquid
+ - Java:
+ - sdk/java/index.html.textile.liquid
+ - Go:
+ - sdk/go/index.html.textile.liquid
+ - CLI:
+ - sdk/cli/index.html.textile.liquid
+ - sdk/cli/install.html.textile.liquid
+ - sdk/cli/reference.html.textile.liquid
+ - sdk/cli/subcommands.html.textile.liquid
+ api:
+ - Concepts:
+ - api/index.html.textile.liquid
+ - api/authentication.html.textile.liquid
+ - api/methods.html.textile.liquid
+ - api/resources.html.textile.liquid
+ - api/crunch-scripts.html.textile.liquid
+ - api/permission-model.html.textile.liquid
+ - API Methods:
+ - api/methods/api_client_authorizations.html.textile.liquid
+ - api/methods/api_clients.html.textile.liquid
+ - api/methods/authorized_keys.html.textile.liquid
+ - api/methods/collections.html.textile.liquid
+ - api/methods/groups.html.textile.liquid
+ - api/methods/humans.html.textile.liquid
+ - api/methods/jobs.html.textile.liquid
+ - api/methods/job_tasks.html.textile.liquid
+ - api/methods/keep_disks.html.textile.liquid
+ - api/methods/keep_services.html.textile.liquid
+ - api/methods/links.html.textile.liquid
+ - api/methods/logs.html.textile.liquid
+ - api/methods/nodes.html.textile.liquid
+ - api/methods/pipeline_instances.html.textile.liquid
+ - api/methods/pipeline_templates.html.textile.liquid
+ - api/methods/repositories.html.textile.liquid
+ - api/methods/specimens.html.textile.liquid
+ - api/methods/traits.html.textile.liquid
+ - api/methods/users.html.textile.liquid
+ - api/methods/virtual_machines.html.textile.liquid
+ - Schema:
+ - api/schema/ApiClientAuthorization.html.textile.liquid
+ - api/schema/ApiClient.html.textile.liquid
+ - api/schema/AuthorizedKey.html.textile.liquid
+ - api/schema/Collection.html.textile.liquid
+ - api/schema/Group.html.textile.liquid
+ - api/schema/Human.html.textile.liquid
+ - api/schema/Job.html.textile.liquid
+ - api/schema/JobTask.html.textile.liquid
+ - api/schema/KeepDisk.html.textile.liquid
+ - api/schema/KeepService.html.textile.liquid
+ - api/schema/Link.html.textile.liquid
+ - api/schema/Log.html.textile.liquid
+ - api/schema/Node.html.textile.liquid
+ - api/schema/PipelineInstance.html.textile.liquid
+ - api/schema/PipelineTemplate.html.textile.liquid
+ - api/schema/Repository.html.textile.liquid
+ - api/schema/Specimen.html.textile.liquid
+ - api/schema/Trait.html.textile.liquid
+ - api/schema/User.html.textile.liquid
+ - api/schema/VirtualMachine.html.textile.liquid
+ admin:
+ - Admin:
+ - admin/index.html.md.liquid
+ - admin/cheat_sheet.html.textile.liquid
+ installguide:
+ - Overview:
+ - install/index.html.textile.liquid
+ - Docker:
+ - install/install-docker.html.textile.liquid
+ - Manual installation:
+ - install/install-manual-overview.html.textile.liquid
+ - install/install-manual-prerequisites.html.textile.liquid
+ - install/install-api-server.html.textile.liquid
+ - install/install-workbench-app.html.textile.liquid
+ - install/install-shell-server.html.textile.liquid
+ - install/create-standard-objects.html.textile.liquid
+ - install/install-keepstore.html.textile.liquid
+ - install/install-keepproxy.html.textile.liquid
+ - install/install-crunch-dispatch.html.textile.liquid
+ - install/install-compute-node.html.textile.liquid
+ - Software prerequisites:
+ - install/install-manual-prerequisites-ruby.html.textile.liquid
+ - install/install-sso.html.textile.liquid
--- /dev/null
+#!/usr/bin/env python
+
+# Import the Arvados sdk module
+import arvados
+
+# Get information about the task from the environment
+this_task = arvados.current_task()
+
+this_task_input = arvados.current_job()['script_parameters']['input']
+
+# Create the object access to the collection referred to in the input
+collection = arvados.CollectionReader(this_task_input)
+
+# Create an object to write a new collection as output
+out = arvados.CollectionWriter()
+
+# Create a new file in the output collection
+with out.open('0-filter.txt') as out_file:
+ # Iterate over every input file in the input collection
+ for input_file in collection.all_files():
+ # Output every line in the file that starts with '0'
+ out_file.writelines(line for line in input_file if line.startswith('0'))
+
+# Commit the output to Keep.
+output_locator = out.finish()
+
+# Use the resulting locator as the output for this task.
+this_task.set_output(output_locator)
+
+# Done!
--- /dev/null
+<div class="alert alert-block alert-info">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <h4>Hi!</h4>
+ <P>This section is incomplete. Please be patient with us as we fill in the blanks — or <A href="https://arvados.org/projects/arvados/wiki/Documentation#Contributing">contribute to the documentation project.</A></P>
+</div>
--- /dev/null
+<div class="alert alert-block alert-info">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <h4>Hi!</h4>
+ <p>This section is incomplete. Please be patient with us as we fill in the blanks — or <A href="https://arvados.org/projects/arvados/wiki/Documentation#Contributing">contribute to the documentation project.</A></p>
+</div>
--- /dev/null
+#!/usr/bin/env python
+
+import hashlib
+import os
+import arvados
+
+# Jobs consist of one or more tasks. A task is a single invocation of
+# a crunch script.
+
+# Get the current task
+this_task = arvados.current_task()
+
+# Tasks have a sequence number for ordering. All tasks
+# with the current sequence number must finish successfully
+# before tasks in the next sequence are started.
+# The first task has sequence number 0
+if this_task['sequence'] == 0:
+ # Get the "input" field from "script_parameters" on the task object
+ job_input = arvados.current_job()['script_parameters']['input']
+
+ # Create a collection reader to read the input
+ cr = arvados.CollectionReader(job_input)
+
+ # Loop over each stream in the collection (a stream is a subset of
+ # files that logically represents a directory)
+ for s in cr.all_streams():
+
+ # Loop over each file in the stream
+ for f in s.all_files():
+
+ # Synthesize a manifest for just this file
+ task_input = f.as_manifest()
+
+ # Set attributes for a new task:
+ # 'job_uuid' the job that this task is part of
+ # 'created_by_job_task_uuid' this task that is creating the new task
+ # 'sequence' the sequence number of the new task
+ # 'parameters' the parameters to be passed to the new task
+ new_task_attrs = {
+ 'job_uuid': arvados.current_job()['uuid'],
+ 'created_by_job_task_uuid': arvados.current_task()['uuid'],
+ 'sequence': 1,
+ 'parameters': {
+ 'input':task_input
+ }
+ }
+
+ # Ask the Arvados API server to create a new task, running the same
+ # script as the parent task specified in 'created_by_job_task_uuid'
+ arvados.api().job_tasks().create(body=new_task_attrs).execute()
+
+ # Now tell the Arvados API server that this task executed successfully,
+ # even though it doesn't have any output.
+ this_task.set_output(None)
+else:
+ # The task sequence was not 0, so it must be a parallel worker task
+ # created by the first task
+
+ # Instead of getting "input" from the "script_parameters" field of
+ # the job object, we get it from the "parameters" field of the
+ # task object
+ this_task_input = this_task['parameters']['input']
+
+ collection = arvados.CollectionReader(this_task_input)
+
+ # There should only be one file in the collection, so get the
+ # first one from the all files iterator.
+ input_file = next(collection.all_files())
+ output_path = os.path.normpath(os.path.join(input_file.stream_name(),
+ input_file.name))
+
+ # Everything after this is the same as the first tutorial.
+ digestor = hashlib.new('md5')
+ for buf in input_file.readall():
+ digestor.update(buf)
+
+ out = arvados.CollectionWriter()
+ with out.open('md5sum.txt') as out_file:
+ out_file.write("{} {}\n".format(digestor.hexdigest(), output_path))
+
+ this_task.set_output(out.finish())
+
+# Done!
--- /dev/null
+{
+ "name": "Example using R in a custom Docker image",
+ "components": {
+ "Rscript": {
+ "script": "run-command",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "Rscript",
+ "$(glob $(file $(myscript))/*.r)",
+ "$(glob $(dir $(mydata))/*.csv)"
+ ],
+ "myscript": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "mydata": {
+ "required": true,
+ "dataclass": "Collection"
+ }
+ },
+ "runtime_constraints": {
+ "docker_image": "arvados/jobs-with-r"
+ }
+ }
+ }
+}
--- /dev/null
+package main
+
+
+// *******************
+// Import the modules.
+//
+// Our examples don't use keepclient, but they do use fmt and log to
+// display output.
+
+import (
+ "fmt"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "log"
+)
+
+func main() {
+
+
+ // ********************************
+ // Set up an API client user agent.
+ //
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ if err != nil {
+ log.Fatalf("Error setting up arvados client %s", err.Error())
+ }
+
+
+ // *****************************************
+ // Print the full name of the current user.
+ //
+
+ type user struct {
+ Uuid string `json:"uuid"`
+ FullName string `json:"full_name"`
+ }
+
+ var u user
+ err = arv.Call("GET", "users", "", "current", nil, &u)
+
+ if err != nil {
+ log.Fatalf("error querying current user", err.Error())
+ }
+
+ log.Printf("Logged in as %s (uuid %s)", u.FullName, u.Uuid)
+
+
+ // ********************************************************
+ // Print all fields from the first five collections returned.
+ //
+ // Note that some fields, are not returned by default and have to be
+ // requested. See below for an example.
+
+ var results map[string]interface{}
+
+ params := arvadosclient.Dict{"limit": 5}
+
+ err = arv.List("collections", params, &results)
+ if err != nil {
+ log.Fatalf("error querying collections", err.Error())
+ }
+
+ printArvadosResults(results)
+
+
+ // *********************************************************
+ // Print some fields from the first two collections returned.
+ //
+ // We also print manifest_test, which has to be explicitly requested.
+ //
+
+ collection_fields_wanted := []string{"manifest_text", "owner_uuid", "uuid"}
+ params = arvadosclient.Dict{"limit": 2, "select": collection_fields_wanted}
+
+ err = arv.List("collections", params, &results)
+ if err != nil {
+ log.Fatalf("error querying collections", err.Error())
+ }
+
+ printArvadosResults(results)
+}
+
+
+// A helper method which will print out a result map returned by
+// arvadosclient.
+func printArvadosResults(results map[string]interface{}) {
+ for key, value := range results {
+ // "items", if it exists, holds a map.
+ // So we print it prettily below.
+ if key != "items" {
+ fmt.Println(key, ":", value)
+ }
+ }
+
+ if value, ok := results["items"]; ok {
+ items := value.([]interface{})
+ for index, item := range items {
+ fmt.Println("=========== ", index, " ===========")
+ item_map := item.(map[string]interface{})
+ if len(item_map) == 0 {
+ fmt.Println("item", index, ": empty map")
+ } else {
+ for k, v := range item_map {
+ fmt.Println(index, k, ":", v)
+ }
+ }
+ }
+ }
+}
--- /dev/null
+import (
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/keepclient"
+)
--- /dev/null
+<div class="col-sm-3">
+ <div class="well">
+ <ol class="nav nav-list">
+ {% for section in site.navbar[page.navsection] %}
+ {% for entry in section %}
+ <li><span class="nav-header">{{ entry[0] }}</span>
+ <ol class="nav nav-list">
+ {% for item in entry[1] %}
+ {% assign p = site.pages[item] %}
+ <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}>
+ <a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
+ {% endfor %}
+ </ol>
+ {% endfor %}
+ {% endfor %}
+ </ol>
+ </div>
+</div>
--- /dev/null
+<div class="navbar navbar-default navbar-fixed-top">
+ <div class="container-fluid">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#bs-navbar-collapse">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="{{ site.baseurl }}/">Arvados Docs</a>
+ </div>
+ <div class="collapse navbar-collapse" id="bs-navbar-collapse">
+ <ul class="nav navbar-nav">
+ <li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/index.html">User Guide</a></li>
+ <li {% if page.navsection == 'sdk' %} class="active" {% endif %}><a href="{{ site.baseurl }}/sdk/index.html">SDK Reference</a></li>
+ <li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/index.html">API Reference</a></li>
+ <li {% if page.navsection == 'adminguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/admin/index.html">Admin Guide</a></li>
+ <li {% if page.navsection == 'installguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/install/index.html">Install Guide</a></li>
+ <li><a href="https://arvados.org/" style="padding-left: 2em">arvados.org »</a></li>
+ </ul>
+ </div>
+ </div>
+</div>
--- /dev/null
+<div class="alert alert-block alert-info">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <h4>Note:</h4>
--- /dev/null
+{
+ "name":"run-command example pipeline",
+ "components":{
+ "bwa-mem": {
+ "script": "run-command",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "bwa",
+ "mem",
+ "-t",
+ "$(node.cores)",
+ "$(glob $(dir $(reference_collection))/*.fasta)",
+ {
+ "foreach": "read_pair",
+ "command": "$(read_pair)"
+ }
+ ],
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
+ "task.foreach": ["sample_subdir", "read_pair"],
+ "reference_collection": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "sample": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "sample_subdir": "$(dir $(samples))",
+ "read_pair": {
+ "value": {
+ "group": "sample_subdir",
+ "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
+ }
+ }
+ }
+ }
+ }
+}
--- /dev/null
+{
+ "name":"run-command example pipeline",
+ "components":{
+ "bwa-mem": {
+ "script": "run-command",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "bwa",
+ "mem",
+ "-t",
+ "$(node.cores)",
+ "$(glob $(dir $(reference_collection))/*.fasta)",
+ "$(glob $(dir $(sample))/*_1.fastq)",
+ "$(glob $(dir $(sample))/*_2.fastq)"
+ ],
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
+ "reference_collection": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "sample": {
+ "required": true,
+ "dataclass": "Collection"
+ }
+ }
+ }
+ }
+}
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+
+# Automatically parallelize this job by running one task per file.
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True,
+ input_as_path=True)
+
+# Get the input file for the task
+input_file = arvados.get_task_param_mount('input')
+
+# Run the external 'md5sum' program on the input file
+stdoutdata, stderrdata = arvados.util.run_command(['md5sum', input_file])
+
+# Save the standard output (stdoutdata) to "md5sum.txt" in the output collection
+out = arvados.CollectionWriter()
+with out.open('md5sum.txt') as out_file:
+ out_file.write(stdoutdata)
+arvados.current_task().set_output(out.finish())
--- /dev/null
+<div class="alert alert-block alert-info">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <h4>Note!</h4>
+ <p>The SSO server codebase currently uses OpenID 2.0 to talk to Google's authentication service. Google <a href="https://developers.google.com/accounts/docs/OpenID2">has deprecated that protocol</a>. This means that new clients will not be allowed to talk to Google's authentication services anymore over OpenID 2.0, and they will phase out the use of OpenID 2.0 completely in the coming monts. We are working on upgrading the SSO server codebase to a newer protocol. That work should be complete by the end of November 2014. In the mean time, anyone is free to use the existing Curoverse SSO server for any local Arvados installation. Instructions to do so are provided on the "API server":install-api-server.html page.</p>
+ <p><strong>Recommendation: skip this step</strong></p>
+</div>
--- /dev/null
+
+You may now proceed to "adding your key to the Arvados Workbench.":#workbench
+
+h1(#workbench). Adding your key to Arvados Workbench
+
+h3. From the Workbench dashboard
+
+If you have no SSH keys registered, there should be a notification asking you to provide your SSH public key. In the Workbench top navigation menu, look for a dropdown menu with your email address in upper right corner. It will have an icon such as <span class="badge badge-alert">1</span> (the number indicates there are new notifications). Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Paste your public key into the text area provided and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
+
+h3. Alternate way to add SSH keys
+
+Click on the link with your _email address_ in the upper right corner to access the user settings menu, and click on the menu item *Manage account* to go to the account management page.
+
+On the *Manage account* page, click on the button <span class="btn btn-primary">*+* Add new SSH key</span> button in the upper right corner of the page in the SSH Keys panel.
+
+This will open a popup as shown in this screenshot:
+
+!{{ site.baseurl }}/images/ssh-adding-public-key.png!
+
+Paste the public key that you copied to the cliboard in the previous section into the popup text box labeled *Public Key* and click on the <span class="btn btn-primary">Submit</span> button to save it. This should refresh the Manage account page with the fingerprint of the public key that you just added in the SSH Keys panel. You are now ready to "log into an Arvados VM":#login.
+
+h1(#login). Using SSH to log into an Arvados VM
+
+To see a list of virtual machines that you have access to and determine the name and login information, click on the link with your _email address_ in the upper right corner and click on the menu item *Manage account* to go to the account management page. On this page, you will see a *Virtual Machines* panel, which lists the virtual machines you can access. The *hostname* column lists the name of each available VM. The *logins* column will have a list of comma separated values of the form @you@. In this guide the hostname will be *_shell_* and the login will be *_you_*. Replace these with your hostname and login name as appropriate.
+
+
--- /dev/null
+
+Arvados requires a public SSH key in order to securely log in to an Arvados VM instance, or to access an Arvados Git repository. The three sections below help you get started:
+
+# "Getting your SSH key":#gettingkey
+# "Adding your key to Arvados Workbench":#workbench
+# "Using SSH to log into an Arvados VM instance":#login
+
--- /dev/null
+{
+ "name": "Tutorial align using bwa mem and SortSam",
+ "components": {
+ "bwa-mem": {
+ "script": "run-command",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "bwa",
+ "mem",
+ "-t",
+ "$(node.cores)",
+ "-R",
+ "@RG\\tID:group_id\\tPL:illumina\\tSM:sample_id",
+ "$(glob $(dir $(reference_collection))/*.fasta)",
+ "$(glob $(dir $(sample))/*_1.fastq)",
+ "$(glob $(dir $(sample))/*_2.fastq)"
+ ],
+ "reference_collection": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "sample": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
+ },
+ "runtime_constraints": {
+ "docker_image": "arvados/jobs-java-bwa-samtools"
+ }
+ },
+ "SortSam": {
+ "script": "run-command",
+ "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "java",
+ "-Xmx4g",
+ "-Djava.io.tmpdir=$(tmpdir)",
+ "-jar",
+ "$(dir $(picard))/SortSam.jar",
+ "CREATE_INDEX=True",
+ "SORT_ORDER=coordinate",
+ "VALIDATION_STRINGENCY=LENIENT",
+ "INPUT=$(glob $(dir $(input))/*.sam)",
+ "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam"
+ ],
+ "input": {
+ "output_of": "bwa-mem"
+ },
+ "picard": {
+ "required": true,
+ "dataclass": "Collection",
+ "default": "88447c464574ad7f79e551070043f9a9+1970"
+ }
+ },
+ "runtime_constraints": {
+ "docker_image": "arvados/jobs-java-bwa-samtools"
+ }
+ }
+ }
+}
--- /dev/null
+{% include 'notebox_begin' %}
+This tutorial assumes either that you are logged into an Arvados VM instance (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login) or you have installed the Arvados "Command line SDK":{{site.baseurl}}/sdk/cli/install.html and "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html on your workstation and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html
+{% include 'notebox_end' %}
--- /dev/null
+#!/usr/bin/env python
+
+import hashlib # Import the hashlib module to compute MD5.
+import os # Import the os module for basic path manipulation
+import arvados # Import the Arvados sdk module
+
+# Automatically parallelize this job by running one task per file.
+# This means that if the input consists of many files, each file will
+# be processed in parallel on different nodes enabling the job to
+# be completed quicker.
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True,
+ input_as_path=True)
+
+# Get object representing the current task
+this_task = arvados.current_task()
+
+# Create the message digest object that will compute the MD5 hash
+digestor = hashlib.new('md5')
+
+# Get the input file for the task
+input_id, input_path = this_task['parameters']['input'].split('/', 1)
+
+# Open the input collection
+input_collection = arvados.CollectionReader(input_id)
+
+# Open the input file for reading
+with input_collection.open(input_path) as input_file:
+ for buf in input_file.readall(): # Iterate the file's data blocks
+ digestor.update(buf) # Update the MD5 hash object
+
+# Write a new collection as output
+out = arvados.CollectionWriter()
+
+# Write an output file with one line: the MD5 value and input path
+with out.open('md5sum.txt') as out_file:
+ out_file.write("{} {}/{}\n".format(digestor.hexdigest(), input_id,
+ os.path.normpath(input_path)))
+
+# Commit the output to Keep.
+output_locator = out.finish()
+
+# Use the resulting locator as the output for this task.
+this_task.set_output(output_locator)
+
+# Done!
--- /dev/null
+{
+ "name":"My md5 pipeline",
+ "components":{
+ "do_hash":{
+ "repository":"$USER",
+ "script":"hash.py",
+ "script_version":"master",
+ "runtime_constraints":{
+ "docker_image":"arvados/jobs-java-bwa-samtools"
+ },
+ "script_parameters":{
+ "input":{
+ "required": true,
+ "dataclass": "Collection"
+ }
+ }
+ }
+ }
+}
--- /dev/null
+{% assign n = 0 %}
+{% assign prev = "" %}
+{% assign nx = 0 %}
+{% for section in site.navbar[page.navsection] %}
+ {% for entry in section %}
+ {% for item in entry[1] %}
+ {% assign p = site.pages[item] %}
+ {% if nx == 1 %}
+ <hr>
+ {% if prev != "" %}
+ <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a>
+ {% endif %}
+ <a href="{{ site.baseurl }}{{ p.url }}" class="pull-right">Next: {{ p.title }}</a>
+ {% assign nx = 0 %}
+ {% assign n = 1 %}
+ {% endif %}
+ {% if p.url == page.url %}
+ {% assign nx = 1 %}
+ {% else %}
+ {% assign prev = p %}
+ {% endif %}
+ {% endfor %}
+ {% endfor %}
+{% endfor %}
+{% if n == 0 && prev != "" %}
+ <hr>
+ <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a>
+ {% assign n = 1 %}
+{% endif %}
\ No newline at end of file
--- /dev/null
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+ <title>{% unless page.title == "Arvados | Documentation" %} Arvados | Documentation | {% endunless %}{{ page.title }}</title>
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <meta name="description" content="">
+ <meta name="author" content="">
+ <link rel="icon" href="{{ site.baseurl }}/images/favicon.ico" type="image/x-icon">
+ <link rel="shortcut icon" href="{{ site.baseurl }}/images/favicon.ico" type="image/x-icon">
+ <link href="{{ site.baseurl }}/css/bootstrap.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/nav-list.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/badges.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/code.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/font-awesome.css" rel="stylesheet">
+ <style>
+ html {
+ height:100%;
+ }
+ body {
+ padding-top: 61px;
+ height: 90%; /* If calc() is not supported */
+ height: calc(100% - 46px); /* Sets the body full height minus the padding for the menu bar */
+ }
+ @media (max-width: 979px) {
+ div.frontpagehero {
+ margin-left: -20px;
+ margin-right: -20px;
+ padding-left: 20px;
+ }
+ }
+ .sidebar-nav {
+ padding: 9px 0;
+ }
+ .section-block {
+ background: #eeeeee;
+ padding: 1em;
+ -webkit-border-radius: 12px;
+ -moz-border-radius: 12px;
+ border-radius: 12px;
+ margin: 0 2em;
+ }
+ .row-fluid :first-child .section-block {
+ margin-left: 0;
+ }
+ .row-fluid :last-child .section-block {
+ margin-right: 0;
+ }
+ .rarr {
+ font-size: 1.5em;
+ }
+ .darr {
+ font-size: 4em;
+ text-align: center;
+ margin-bottom: 1em;
+ }
+ :target {
+ padding-top: 61px;
+ margin-top: -61px;
+ }
+ </style>
+
+ <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
+ <!--[if lt IE 9]>
+ <script src="../assets/js/html5shiv.js"></script>
+ <![endif]-->
+ </head>
+ <body class="nopad">
+ {% include 'navbar_top' %}
+
+ {% if page.navsection == 'top' or page.no_nav_left %}
+ {{ content }}
+ {% else %}
+
+ <div class="container-fluid">
+ <div class="row">
+ {% include 'navbar_left' %}
+ <div class="col-sm-9">
+ <h1>{{ page.title }}</h1>
+ {{ content }}
+ {% include 'webring' %}
+ </div>
+ </div>
+
+ <div style="height: 2em"></div>
+
+ </div>
+ {% endif %}
+ <script src="{{ site.baseurl }}/js/jquery.min.js"></script>
+ <script src="{{ site.baseurl }}/js/bootstrap.min.js"></script>
+ <script>
+ (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+ m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+ })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
+
+ ga('create', 'UA-40055979-1', 'arvados.org');
+ ga('send', 'pageview');
+
+ </script>
+
+<p style="text-align: center"><small>
+The content of this documentation is licensed under the
+<a href="{{ site.baseurl }}/user/copying/by-sa-3.0.html">Creative
+ Commons Attribution-Share Alike 3.0 United States</a> licence.<br>
+Code samples in this documentation are licensed under the
+<a href="{{ site.baseurl }}/user/copying/LICENSE-2.0.html">Apache License, Version 2.0.</a></small>
+</p>
+
+ </body>
+</html>
--- /dev/null
+---
+layout: default
+navsection: admin
+title: Cheat Sheet
+...
+
+
+
+h3. CLI setup
+
+<pre>
+ARVADOS_API_HOST={{ site.arvados_api_host }}
+ARVADOS_API_TOKEN=1234567890qwertyuiopasdfghjklzxcvbnm1234567890zzzz
+</pre>
+
+h3. Create VM
+
+<pre>
+arv virtual_machine create --virtual-machine '{"hostname":"xxxxxxxchangeme.example.com"}'
+</pre>
+
+h3. Activate user
+
+<pre>
+user_uuid=xxxxxxxchangeme
+
+arv user update --uuid "$user_uuid" --user '{"is_active":true}'
+</pre>
+
+h3. User → VM
+
+Give @$user_uuid@ permission to log in to @$vm_uuid@ as @$target_username@
+
+<pre>
+user_uuid=xxxxxxxchangeme
+vm_uuid=xxxxxxxchangeme
+target_username=xxxxxxxchangeme
+
+read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
+{
+"tail_uuid":"$user_uuid",
+"head_uuid":"$vm_uuid",
+"link_class":"permission",
+"name":"can_login",
+"properties":{"username":"$target_username"}
+}
+EOF
+</pre>
+
+h3. User → repo
+
+Give @$user_uuid@ permission to commit to @$repo_uuid@ as @$repo_username@
+
+<pre>
+user_uuid=xxxxxxxchangeme
+repo_uuid=xxxxxxxchangeme
+repo_username=xxxxxxxchangeme
+
+read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
+{
+"tail_uuid":"$user_uuid",
+"head_uuid":"$repo_uuid",
+"link_class":"permission",
+"name":"can_write",
+"properties":{"username":"$repo_username"}
+}
+EOF
+</pre>
--- /dev/null
+---
+layout: default
+navsection: admin
+title: Overview
+...
+
+{% include 'alert_stub' %}
+
+# Administration Overview
+
+Unlike other users, administrators
+
+* can see and modify all user-created objects regardless of permission settings
+* can directly create and modify system objects like Nodes and ApiClients
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Concepts
+title: Authentication
+
+...
+
+
+
+Every API request (except the authentication API itself) includes an @access_token@ parameter.
+
+table(table table-bordered table-condensed).
+|Name|Type|Description|
+|access_token|string|Access token returned by OAuth 2.0 authorization procedure|
+
+Many resources contain "actor" attributes like @modified_by@. An @access_token@ uniquely identifies a client (application or project) and an end-user.
+
+table(table table-bordered table-condensed).
+|Name|Type|Description|
+|modified_by_client_uuid|string|ID of API client|
+|modified_by_user_uuid|string|ID of authenticated user|
+
+h2. Authorizing a client application
+
+The Arvados API uses the "OAuth 2.0 protocol":http://tools.ietf.org/html/draft-ietf-oauth-v2-22 for authentication and authorization.
+
+h3. Register your client application
+
+Before an application can run on an Arvados cloud, it needs to be registered with the cloud.
+
+That registration yields a @client_id@ and a @client_secret@.
+
+h3. Obtain an access code
+
+A client obtains an access code by means of a standard Oauth 2.0 flow. The access code is granted to it by an authorized user. The client requests one or more scopes, which translate to a set of requested permissions (reading, writing, etc). Unless the access is to be short-lived, a refresh token is also granted to the application.
+
+h3. Refresh the access code (optional)
+
+Access codes have a limited lifetime. A refresh token allows an application to request a new access token.
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Concepts
+title: Crunch scripts
+
+...
+
+h2. Crunch scripts
+
+A crunch script is responsible for completing a single JobTask. In doing so, it will:
+
+* (optionally) read some input from Keep
+* (optionally) store some output in Keep
+* (optionally) create some new JobTasks and add them to the current Job
+* (optionally) update the current JobTask record with the "output" attribute set to a Keep locator or a fragment of a manifest
+* update the current JobTask record with the "success" attribute set to True
+
+A task's context is provided in environment variables.
+
+table(table table-bordered table-condensed).
+|Environment variable|Description|
+|@JOB_UUID@|UUID of the current "Job":schema/Job.html|
+|@TASK_UUID@|UUID of the current "JobTask":schema/JobTask.html|
+|@ARVADOS_API_HOST@|Hostname and port number of API server|
+|@ARVADOS_API_TOKEN@|Authentication token to use with API calls made by the current task|
+
+The crunch script typically uses the Python SDK (or another suitable client library / SDK) to connect to the Arvados service and retrieve the rest of the details about the current job and task.
+
+The Python SDK has some shortcuts for common operations.
+
+In general, a crunch script can access information about the current job and task like this:
+
+<pre>
+import arvados
+import os
+
+job = arvados.api().jobs().get(uuid=os.environ['JOB_UUID']).execute()
+$sys.stderr.write("script_parameters['foo'] == %s"
+ % job['script_parameters']['foo'])
+
+task = arvados.api().job_tasks().get(uuid=os.environ['TASK_UUID']).execute()
+$sys.stderr.write("current task sequence number is %d"
+ % task['sequence'])
+</pre>
+
--- /dev/null
+---
+layout: default
+navsection: api
+title: API Reference
+
+...
+
+
+
+h2. Concepts
+
+* Each API uses the same "authentication mechanism":authentication.html.
+* Resources in requests and responses adhere to a "common structure":resources.html.
+* API transactions use common "REST methods":methods.html.
+* API transactions are subject to a "permission model":permission-model.html.
+* "Job tasks":schema/JobTask.html use some special API features.
+
+h2. Resources
+
+h3. Generic Resources
+
+* "Collection":schema/Collection.html
+* "Job":schema/Job.html
+* "JobTask":schema/JobTask.html
+* "Link":schema/Link.html
+* "Log":schema/Log.html
+* "PipelineTemplate":schema/PipelineTemplate.html
+* "PipelineInstance":schema/PipelineInstance.html
+* "Group":schema/Group.html
+* "Human":schema/Human.html
+* "Specimen":schema/Specimen.html
+* "Trait":schema/Trait.html
+* "User":schema/User.html
+
+h3. Authentication
+
+These Arvados resources govern authorization and "authentication":authentication.html:
+
+* "ApiClient":schema/ApiClient.html
+* "ApiClientAuthorization":schema/ApiClientAuthorization.html
+* "AuthorizedKey":schema/AuthorizedKey.html
+
+h3. Arvados Infrastructure
+
+These resources govern the Arvados infrastructure itself: Git repositories, Keep disks, active nodes, etc.
+
+* "KeepDisk":schema/KeepDisk.html
+* "Node":schema/Node.html
+* "Repository":schema/Repository.html
+* "VirtualMachine":schema/VirtualMachine.html
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Concepts
+title: REST methods
+
+...
+
+
+
+(using Group as an example)
+
+h2(#index). Index, list, search
+
+<pre>
+GET https://{{ site.arvados_api_host }}/arvados/v1/groups?filters=[["owner_uuid","=","xyzzy-tpzed-a4lcehql0dv2u25"]]
+
+POST https://{{ site.arvados_api_host }}/arvados/v1/groups
+_method=GET
+filters=[["owner_uuid","=","xyzzy-tpzed-a4lcehql0dv2u25"]]
+</pre>
+
+→ Group resource list
+
+table(table table-bordered table-condensed).
+|*Parameter name*|*Value*|*Description*|
+|limit |integer|Maximum number of resources to return.|
+|offset |integer|Skip the first 'offset' resources that match the given filter conditions.|
+|filters |array |Conditions for selecting resources to return (see below).|
+|order |array |Attributes to use as sort keys to determine the order resources are returned, each optionally followed by @asc@ or @desc@ to indicate ascending or descending order.
+Example: @["head_uuid asc","modified_at desc"]@
+Default: @["created_at desc"]@|
+|select |array |Set of attributes to include in the response.
+Example: @["head_uuid","tail_uuid"]@
+Default: all available attributes, minus "manifest_text" in the case of collections.|
+|distinct|boolean|@true@: (default) do not return duplicate objects
+@false@: permitted to return duplicates|
+
+h3. Filters
+
+The value of the @filters@ parameter is an array of conditions. The @list@ method returns only the resources that satisfy all of the given conditions. In other words, the conjunction @AND@ is implicit.
+
+Each condition is expressed as an array with three elements: @[attribute, operator, operand]@.
+
+table(table table-bordered table-condensed).
+|_. Index|_. Element|_. Type|_. Description|_. Examples|
+|0|attribute|string|Name of the attribute to compare (or "any" to return resources with any matching attribute)|@script_version@, @head_uuid@, @any@|
+|1|operator|string|Comparison operator|@>@, @>=@, @like@, @not in@|
+|2|operand|string, array, or null|Value to compare with the resource attribute|@"d00220fb%"@, @"1234"@, @["foo","bar"]@, @nil@|
+
+The following operators are available.
+
+table(table table-bordered table-condensed).
+|_. Operator|_. Operand type|_. Example|
+|@<@, @<=@, @>=@, @>@, @like@, @ilike@|string|@["script_version","like","d00220fb%"]@|
+|@=@, @!=@|string or null|@["tail_uuid","=","xyzzy-j7d0g-fffffffffffffff"]@
+@["tail_uuid","!=",null]@|
+|@in@, @not in@|array of strings|@["script_version","in",["master","d00220fb38d4b85ca8fc28a8151702a2b9d1dec5"]]@|
+|@is_a@|string|@["head_uuid","is_a","arvados#pipelineInstance"]@|
+
+h2. Create
+
+<pre>
+POST https://{{ site.arvados_api_host }}/arvados/v1/groups
+group={"name":"fresh new group"}
+</pre>
+
+→ Group resource
+
+h2. Delete
+
+<pre>
+DELETE https://{{ site.arvados_api_host }}/arvados/v1/groups/xyzzy-ldvyl-vyydjeplwaa6emg
+</pre>
+
+→ Group resource
+
+h2. Update
+
+<pre>
+PUT https://{{ site.arvados_api_host }}/arvados/v1/groups/xyzzy-ldvyl-vyydjeplwaa6emg
+group={"uuid":"xyzzy-ldvyl-vyydjeplwaa6emg", "name":"Important group"}
+</pre>
+
+→ Group resource
+
+<pre>
+PUT https://{{ site.arvados_api_host }}/arvados/v1/groups/xyzzy-ldvyl-vyydjeplwaa6emg
+group[uuid]=xyzzy-ldvyl-vyydjeplwaa6emg
+group[name]=Important group
+</pre>
+
+→ Group resource
+
+More appropriate (but not yet implemented):
+
+<pre>
+PATCH https://{{ site.arvados_api_host }}/arvados/v1/groups/xyzzy-ldvyl-vyydjeplwaa6emg
+group={"uuid":"xyzzy-ldvyl-vyydjeplwaa6emg", "name":"Important group"}
+</pre>
+
+→ Group resource
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "api_client_authorizations"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client_authorizations@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new ApiClientAuthorization.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|api_client_authorization|object||query||
+
+h2. create_system_auth
+
+create_system_auth api_client_authorizations
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|api_client_id|integer||query||
+|scopes|array||query||
+
+h2. delete
+
+Delete an existing ApiClientAuthorization.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the ApiClientAuthorization in question.|path||
+
+h2. get
+
+Gets a ApiClientAuthorization's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the ApiClientAuthorization in question.|path||
+
+h2. list
+
+List api_client_authorizations.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of api_client_authorizations to return.|query||
+|order|string|Order in which to return matching api_client_authorizations.|query||
+|filters|array|Conditions for filtering api_client_authorizations.|query||
+
+h2. update
+
+Update attributes of an existing ApiClientAuthorization.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the ApiClientAuthorization in question.|path||
+|api_client_authorization|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "api_clients"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_clients@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+h2. create
+
+Create a new ApiClient.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|api_client|object||query||
+
+h2. delete
+
+Delete an existing ApiClient.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the ApiClient in question.|path||
+
+h2. get
+
+Gets a ApiClient's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the ApiClient in question.|path||
+
+h2. list
+
+List api_clients.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of api_clients to return.|query||
+|order|string|Order in which to return matching api_clients.|query||
+|filters|array|Conditions for filtering api_clients.|query||
+
+h2. update
+
+Update attributes of an existing ApiClient.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the ApiClient in question.|path||
+|api_client|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "authorized_keys"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/authorized_keys@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new AuthorizedKey.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|authorized_key|object||query||
+
+h2. delete
+
+Delete an existing AuthorizedKey.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the AuthorizedKey in question.|path||
+
+h2. get
+
+Gets a AuthorizedKey's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the AuthorizedKey in question.|path||
+
+h2. list
+
+List authorized_keys.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of authorized_keys to return.|query||
+|order|string|Order in which to return matching authorized_keys.|query||
+|filters|array|Conditions for filtering authorized_keys.|query||
+
+h2. update
+
+Update attributes of an existing AuthorizedKey.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the AuthorizedKey in question.|path||
+|authorized_key|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "collections"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/collections@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+h2. create
+
+Create a new Collection.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|collection|object||query||
+
+h2. delete
+
+Delete an existing Collection.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Collection in question.|path||
+
+h2. get
+
+Gets a Collection's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Collection in question.|path||
+
+h2. list
+
+List collections.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of collections to return.|query||
+|order|string|Order in which to return matching collections.|query||
+|filters|array|Conditions for filtering collections.|query||
+|select|array|Data fields to return in the result list.|query|@["uuid", "manifest_text"]@|
+
+N.B.: Because adding access tokens to manifests can be computationally expensive, the @manifest_text@ field is not included in results by default. If you need it, pass a @select@ parameter that includes @manifest_text@.
+
+h2. update
+
+Update attributes of an existing Collection.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Collection in question.|path||
+|collection|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "groups"
+
+...
+
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/groups@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. contents
+
+Retrieve a list of items which are associated with the given group by ownership (i.e., the group owns the item) or a "name" link (i.e., a "name" link referencing the item).
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the group in question.|path||
+|include_linked|boolean|If false, results will only include items whose @owner_uuid@ attribute is the specified group. If true, results will additionally include items for which a "name" link exists.|path|{white-space:nowrap}. @false@ (default)
+@true@|
+
+If @include_linked@ is @true@, the @"links"@ field in the response will contain the "name" links referencing the objects in the @"items"@ field.
+
+h2. create
+
+Create a new Group.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|group|object||query||
+
+h2. delete
+
+Delete an existing Group.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Group in question.|path||
+
+h2. get
+
+Gets a Group's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Group in question.|path||
+
+h2. list
+
+List groups.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of groups to return.|query||
+|order|string|Order in which to return matching groups.|query||
+|filters|array|Conditions for filtering groups.|query||
+
+h2. show
+
+show groups
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string||path||
+
+h2. update
+
+Update attributes of an existing Group.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Group in question.|path||
+|group|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "humans"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/humans@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new Human.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|human|object||query||
+
+h2. delete
+
+Delete an existing Human.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Human in question.|path||
+
+h2. get
+
+Gets a Human's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Human in question.|path||
+
+h2. list
+
+List humans.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of humans to return.|query||
+|order|string|Order in which to return matching humans.|query||
+|filters|array|Conditions for filtering humans.|query||
+
+h2. update
+
+Update attributes of an existing Human.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Human in question.|path||
+|human|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "job_tasks"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_tasks@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new JobTask.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|job_task|object||query||
+
+h2. delete
+
+Delete an existing JobTask.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the JobTask in question.|path||
+
+h2. get
+
+Gets a JobTask's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the JobTask in question.|path||
+
+h2. list
+
+List job_tasks.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of job_tasks to return.|query||
+|order|string|Order in which to return matching job_tasks.|query||
+|filters|array|Conditions for filtering job_tasks.|query||
+
+h2. update
+
+Update attributes of an existing JobTask.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the JobTask in question.|path||
+|job_task|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "jobs"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/jobs@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+h2. cancel
+
+Cancel a job that is queued or running.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string||path||
+
+h2(#create). create
+
+Create a new Job.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|job|object|See "Job resource":{{site.baseurl}}/api/schema/Job.html|request body||
+|minimum_script_version |string |Git branch, tag, or commit hash specifying the minimum acceptable script version (earliest ancestor) to consider when deciding whether to re-use a past job.[1]|query|@"c3e86c9"@|
+|exclude_script_versions|array of strings|Git commit branches, tags, or hashes to exclude when deciding whether to re-use a past job.|query|@["8f03c71","8f03c71"]@
+@["badtag1","badtag2"]@|
+|filters|array|Conditions to find Jobs to reuse.|query||
+|find_or_create |boolean |Before creating, look for an existing job that has identical script, script_version, and script_parameters to those in the present job, has nondeterministic=false, and did not fail (it could be queued, running, or completed). If such a job exists, respond with the existing job instead of submitting a new one.|query|@false@|
+
+When a job is submitted to the queue using the **create** method, the @script_version@ attribute is updated to a full 40-character Git commit hash based on the current content of the specified repository. If @script_version@ cannot be resolved, the job submission is rejected.
+
+fn1. See the "note about specifying Git commits on the Job resource page":{{site.baseurl}}/api/schema/Job.html#script_version for more detail.
+
+h3. Specialized filters
+
+Special filter operations are available for specific Job columns.
+
+* @script_version@ @in git@ @REFSPEC@, @arvados_sdk_version@ @in git@ @REFSPEC@<br>Resolve @REFSPEC@ to a list of Git commits, and match jobs with a @script_version@ or @arvados_sdk_version@ in that list. When creating a job and filtering @script_version@, the search will find commits between @REFSPEC@ and the submitted job's @script_version@; all other searches will find commits between @REFSPEC@ and HEAD. This list may include parallel branches if there is more than one path between @REFSPEC@ and the end commit in the graph. Use @not in@ or @not in git@ filters (below) to blacklist specific commits.
+
+* @script_version@ @not in git@ @REFSPEC@, @arvados_sdk_version@ @not in git@ @REFSPEC@<br>Resolve @REFSPEC@ to a list of Git commits, and match jobs with a @script_version@ or @arvados_sdk_version@ not in that list.
+
+* @docker_image_locator@ @in docker@ @SEARCH@<br>@SEARCH@ can be a Docker image hash, a repository name, or a repository name and tag separated by a colon (@:@). The server will find collections that contain a Docker image that match that search criteria, then match jobs with a @docker_image_locator@ in that list.
+
+* @docker_image_locator@ @not in docker@ @SEARCH@<br>Negate the @in docker@ filter.
+
+h3. Reusing jobs
+
+Because Arvados records the exact version of the script, input parameters, and runtime environment that was used to run the job, if the script is deterministic (meaning that the same code version is guaranteed to produce the same outputs from the same inputs) then it is possible to re-use the results of past jobs, and avoid re-running the computation to save time. Arvados uses the following algorithm to determine if a past job can be re-used:
+
+notextile. <div class="spaced-out">
+
+# If @find_or_create@ is false or omitted, create a new job and skip the rest of these steps.
+# If @filters@ are specified, find jobs that match those filters. Filters *must* be specified to limit the @repository@ and @script@ attributes. An error is returned if they are missing.
+# If @filters@ are not specified, find jobs with the same @repository@ and @script@, with a @script_version@ between @minimum_script_version@ and @script_version@ (excluding @excluded_script_versions@), and a @docker_image_locator@ with the latest Collection that matches the submitted job's @docker_image@ constraint. If the submitted job includes an @arvados_sdk_version@ constraint, jobs must have an @arvados_sdk_version@ between that refspec and HEAD to be found.
+# If the found jobs include a completed job, and all found completed jobs have consistent output, return one of them. Which specific job is returned is undefined.
+# If the found jobs only include incomplete jobs, return one of them. Which specific job is returned is undefined.
+# If no job has been returned so far, create and return a new job.
+
+</div>
+
+h3. Examples
+
+Run the script "crunch_scripts/hash.py" in the repository "you" using the "master" commit. Arvados should re-use a previous job if the script_version of the previous job is the same as the current "master" commit. This works irrespective of whether the previous job was submitted using the name "master", a different branch name or tag indicating the same commit, a SHA-1 commit hash, etc.
+
+<notextile><pre>
+{
+ "job": {
+ "script": "hash.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+ },
+ "find_or_create": true
+}
+</pre></notextile>
+
+Run using exactly the version "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5". Arvados should re-use a previous job if the "script_version" of that job is also "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5".
+
+<notextile><pre>
+{
+ "job": {
+ "script": "hash.py",
+ "repository": "<b>you</b>",
+ "script_version": "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+ },
+ "find_or_create": true
+}
+</pre></notextile>
+
+Arvados should re-use a previous job if the "script_version" of the previous job is between "earlier_version_tag" and the "master" commit (inclusive), but not the commit indicated by "blacklisted_version_tag". If there are no previous jobs matching these criteria, run the job using the "master" commit.
+
+<notextile><pre>
+{
+ "job": {
+ "script": "hash.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+ },
+ "minimum_script_version": "earlier_version_tag",
+ "exclude_script_versions": ["blacklisted_version_tag"],
+ "find_or_create": true
+}
+</pre></notextile>
+
+The same behavior, using filters:
+
+<notextile><pre>
+{
+ "job": {
+ "script": "hash.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+ },
+ "filters": [["script", "=", "hash.py"],
+ ["repository", "=", "<b>you</b>"],
+ ["script_version", "in git", "earlier_version_tag"],
+ ["script_version", "not in git", "blacklisted_version_tag"]],
+ "find_or_create": true
+}
+</pre></notextile>
+
+Run the script "crunch_scripts/monte-carlo.py" in the repository "you" using the current "master" commit. Because it is marked as "nondeterministic", this job will not be considered as a suitable candidate for future job submissions that use the "find_or_create" feature.
+
+<notextile><pre>
+{
+ "job": {
+ "script": "monte-carlo.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "nondeterministic": true,
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+ }
+}
+</pre></notextile>
+
+h2. delete
+
+Delete an existing Job.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Job in question.|path||
+
+h2. get
+
+Gets a Job's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Job in question.|path||
+
+h2. list
+
+List jobs.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of jobs to return.|query||
+|order|string|Order in which to return matching jobs.|query||
+|filters|array|Conditions for filtering jobs.|query||
+
+See the create method documentation for more information about Job-specific filters.
+
+h2. log_tail_follow
+
+log_tail_follow jobs
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string||path||
+|buffer_size|integer (default 8192)||query||
+
+h2. queue
+
+Get the current job queue.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|order|string||query||
+|filters|array||query||
+
+This method is equivalent to the "list method":#list, except that the results are restricted to queued jobs (i.e., jobs that have not yet been started or cancelled) and order defaults to queue priority.
+
+h2. update
+
+Update attributes of an existing Job.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Job in question.|path||
+|job|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "keep_disks"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/keep_disks@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+h2. create
+
+Create a new KeepDisk.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|keep_disk|object||query||
+
+h2. delete
+
+Delete an existing KeepDisk.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the KeepDisk in question.|path||
+
+h2. get
+
+Gets a KeepDisk's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the KeepDisk in question.|path||
+
+h2. list
+
+List keep_disks.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of keep_disks to return.|query||
+|order|string|Order in which to return matching keep_disks.|query||
+|filters|array|Conditions for filtering keep_disks.|query||
+
+h2. ping
+
+ping keep_disks
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|ping_secret|string||query||
+{background:#ccffcc}.|service_port|string||query||
+{background:#ccffcc}.|service_ssl_flag|string||query||
+|filesystem_uuid|string||query||
+|node_uuid|string||query||
+|service_host|string||query||
+|uuid|string||query||
+
+h2. update
+
+Update attributes of an existing KeepDisk.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the KeepDisk in question.|path||
+|keep_disk|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "keep_services"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/keep_services@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+h2. accessible
+
+Get a list of keep services that are accessible to the requesting client. This
+is context-sensitive, for example providing the list of actual Keep servers
+when inside the cluster, but providing a proxy service if client contacts
+Arvados from outside the cluster.
+
+Takes no arguments.
+
+h2. create
+
+Create a new KeepService.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|keep_disk|object||query||
+
+h2. delete
+
+Delete an existing KeepService.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the KeepService in question.|path||
+
+h2. get
+
+Gets a KeepService's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the KeepService in question.|path||
+
+h2. list
+
+List keep_services.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of keep_services to return.|query||
+|order|string|Order in which to return matching keep_services.|query||
+|filters|array|Conditions for filtering keep_services.|query||
+
+h2. update
+
+Update attributes of an existing KeepService.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the KeepService in question.|path||
+|keep_service|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "links"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/links@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+h2. create
+
+Create a new Link.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|link|object||query||
+
+h2. delete
+
+Delete an existing Link.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Link in question.|path||
+
+h2. get
+
+Gets a Link's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Link in question.|path||
+
+h2. list
+
+List links.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of links to return.|query||
+|order|string|Order in which to return matching links.|query||
+|filters|array|Conditions for filtering links.|query||
+
+h2. render_not_found
+
+render_not_found links
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|a|string||path||
+
+h2. update
+
+Update attributes of an existing Link.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Link in question.|path||
+|link|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "logs"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/logs@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new log entry.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|log|object||query||
+
+h2. delete
+
+Delete an existing log entry. This method can only be used by privileged (system administrator) users.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the log entry in question.|path||
+
+h2. get
+
+Retrieve a log entry.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the log entry in question.|path||
+
+h2. list
+
+List log entries.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of log entries to return.|query||
+|order|string|Order in which to return matching log entries.|query||
+|filters|array|Conditions for filtering log entries.|query||
+
+h2. update
+
+Update attributes of an existing log entry. This method can only be used by privileged (system administrator) users.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the log entry in question.|path||
+|log|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "nodes"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/nodes@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new Node.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|node|object||query||
+
+h2. delete
+
+Delete an existing Node.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Node in question.|path||
+
+h2. get
+
+Gets a Node's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Node in question.|path||
+
+h2. list
+
+List nodes.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of nodes to return.|query||
+|order|string|Order in which to return matching nodes.|query||
+|filters|array|Conditions for filtering nodes.|query||
+
+h2. ping
+
+ping nodes
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|ping_secret|string||query||
+{background:#ccffcc}.|uuid|string||path||
+
+h2. update
+
+Update attributes of an existing Node.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Node in question.|path||
+|node|object||query||
+
+To remove a node's job assignment, update the node object's @job_uuid@ to null.
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "pipeline_instances"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_instances@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new PipelineInstance.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|pipeline_instance|object||query||
+
+h2. delete
+
+Delete an existing PipelineInstance.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the PipelineInstance in question.|path||
+
+h2. get
+
+Gets a PipelineInstance's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the PipelineInstance in question.|path||
+
+h2. list
+
+List pipeline_instances.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of pipeline_instances to return.|query||
+|order|string|Order in which to return matching pipeline_instances.|query||
+|filters|array|Conditions for filtering pipeline_instances.|query||
+
+h2. update
+
+Update attributes of an existing PipelineInstance.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the PipelineInstance in question.|path||
+|pipeline_instance|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "pipeline_templates"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_templates@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new PipelineTemplate.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|pipeline_template|object||query||
+
+h2. delete
+
+Delete an existing PipelineTemplate.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the PipelineTemplate in question.|path||
+
+h2. get
+
+Gets a PipelineTemplate's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the PipelineTemplate in question.|path||
+
+h2. list
+
+List pipeline_templates.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of pipeline_templates to return.|query||
+|order|string|Order in which to return matching pipeline_templates.|query||
+|filters|array|Conditions for filtering pipeline_templates.|query||
+
+h2. update
+
+Update attributes of an existing PipelineTemplate.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the PipelineTemplate in question.|path||
+|pipeline_template|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "repositories"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/repositories@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new Repository.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|repository|object||query||
+
+h2. delete
+
+Delete an existing Repository.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Repository in question.|path||
+
+h2. get
+
+Gets a Repository's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Repository in question.|path||
+
+h2. get_all_permissions
+
+get_all_permissions repositories
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+
+h2. list
+
+List repositories.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of repositories to return.|query||
+|order|string|Order in which to return matching repositories.|query||
+|filters|array|Conditions for filtering repositories.|query||
+
+h2. update
+
+Update attributes of an existing Repository.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Repository in question.|path||
+|repository|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "specimens"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/specimens@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new Specimen.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|specimen|object||query||
+
+h2. delete
+
+Delete an existing Specimen.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Specimen in question.|path||
+
+h2. get
+
+Gets a Specimen's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Specimen in question.|path||
+
+h2. list
+
+List specimens.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of specimens to return.|query||
+|order|string|Order in which to return matching specimens.|query||
+|filters|array|Conditions for filtering specimens.|query||
+
+h2. update
+
+Update attributes of an existing Specimen.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Specimen in question.|path||
+|specimen|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "traits"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/traits@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new Trait.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|trait|object||query||
+
+h2. delete
+
+Delete an existing Trait.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Trait in question.|path||
+
+h2. get
+
+Gets a Trait's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Trait in question.|path||
+
+h2. list
+
+List traits.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of traits to return.|query||
+|order|string|Order in which to return matching traits.|query||
+|filters|array|Conditions for filtering traits.|query||
+
+h2. update
+
+Update attributes of an existing Trait.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the Trait in question.|path||
+|trait|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "users"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/users@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new User.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|user|object||query||
+
+h2. current
+
+current users
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+
+h2. delete
+
+Delete an existing User.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the User in question.|path||
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string||path||
+
+h2. get
+
+Gets a User's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the User in question.|path||
+
+h2. list
+
+List users.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of users to return.|query||
+|order|string|Order in which to return matching users.|query||
+|filters|array|Conditions for filtering users.|query||
+
+h2. show
+
+show users
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string||path||
+
+h2. system
+
+system users
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+
+h2. update
+
+Update attributes of an existing User.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the User in question.|path||
+|user|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "virtual_machines"
+
+...
+
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
+
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/virtual_machines@
+
+Required arguments are displayed in %{background:#ccffcc}green%.
+
+
+h2. create
+
+Create a new VirtualMachine.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|virtual_machine|object||query||
+
+h2. delete
+
+Delete an existing VirtualMachine.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the VirtualMachine in question.|path||
+
+h2. get
+
+Gets a VirtualMachine's metadata by UUID.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the VirtualMachine in question.|path||
+
+h2(#logins). logins
+
+Get a list of SSH keys and account names that should be able to log in to a given virtual machine.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string||path||
+
+The response is a "resource list":{{site.baseurl}}/api/resources.html#resourceList with @kind@ set to @"arvados#HashList"@. Each item is a hash with the following keys:
+
+table(table table-bordered table-condensed).
+|_. Key|_. Value type|_. Description|_. Example|
+|username|string|Name of the Unix login account to which the user should be able to log in|@"jsmith"@|
+|hostname|string|Hostname of the virtual machine|@"shell.xyzzy.arvadosapi.com"@|
+|public_key|string|SSH public key|@"ssh-rsa AAAAB3NzaC1yc2E..."@|
+|user_uuid|string|UUID of the user who should be able to log in|@"xyzzy-tpzed-mv4d7dy7n91te11"@|
+|virtual_machine_uuid|string|UUID of the "VirtualMachine resource":{{site.baseurl}}/api/schema/VirtualMachine.html|@"xyzzy-2x53u-kvszmclnbjuv8xc"@|
+|authorized_key_uuid|string|UUID of the "AuthorizedKey resource":{{site.baseurl}}/api/schema/AuthorizedKey.html|@"xyzzy-fngyi-v9p0cyfmjxbio64"@|
+
+h2. get_all_logins
+
+Get a list, for every virtual machine in the system, of SSH keys and account names that should be able to log in.
+
+Arguments: none.
+
+The response has the same format as the response to the "logins method":#logins above.
+
+h2. list
+
+List virtual_machines.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+|limit|integer (default 100)|Maximum number of virtual_machines to return.|query||
+|order|string|Order in which to return matching virtual_machines.|query||
+|filters|array|Conditions for filtering virtual_machines.|query||
+
+h2. update
+
+Update attributes of an existing VirtualMachine.
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+{background:#ccffcc}.|uuid|string|The UUID of the VirtualMachine in question.|path||
+|virtual_machine|object||query||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Concepts
+title: "Permission model"
+
+...
+
+
+
+Each API transaction (read, write, create, etc.) is done on behalf of a person.
+
+* An end user, via a web app
+* The owner of an installed app
+
+A user (person) is permitted to act on an object if there is a path (series of permission Links) from the acting user to the object in which
+
+* Every intervening object is a Group, and
+* Every intervening permission Link allows the current action
+
+Special case: A permission path can also include intervening User objects if the links _to_ the Users are "can_manage" links.
+
+Each object has exactly one _owner_, which can be either a User or a Group.
+
+* If the owner of X is A, then A is permitted to do any action on X.
+
+h3. Tokens
+
+An authorization token is issued at a user's request, and supplied to an API client using some suitable mechanism (_e.g._, cookie or application config file for a web app; environment variable or .rc-file for a CLI app).
+
+A user can have multiple valid tokens at a given time. At the user's option, a token can be restricted to a combination of
+
+* API client program
+* time interval
+* transaction type
+
+h3. System pseudo-user
+
+A privileged user account exists for the use of built-in Arvados system components. This user manages system-wide shared objects which can't really be "owned" by any particular user, like
+
+* Jobs and job steps (because a given job can be "wanted" by multiple users)
+* Provenance metadata (because no user should be able to modify this directly)
+* Storage metadata like
+** redundancy verified as N× at time Y
+** contents of collections A and B are identical
+
+The system pseudo-user's uuid is @{siteprefix}-tpzed-000000000000000@.
+
+h2. Example scenarios
+
+h3. 1. Private objects
+
+Alfred stores 3 data Collections in Keep and adds them to a new Group.
+
+The Collections and the Group can only be seen by Alfred, administrators, and the system user.
+
+The data in the Collections can only be retrieved by Alfred, administrators, and the system user.
+
+h3. 2. Public objects
+
+George creates a "PGP public data" Group, and grants "read" permission to all users.
+
+* ...by adding a Link: "All users" Group _can_read_→ "PGP public data" Group
+
+George stores 4 data Collections in Keep and adds them to the "PGP public data" Group
+
+* ...by adding a Link: Group _can_read_→ Collection
+
+Anyone who can connect to Arvados can log in with a Google/OpenID account and read the data.
+
+h3. 3. Group-managed objects
+
+Three lab members are working together on a project. All Specimens, Links, Jobs, etc. can be modified by any of the three lab members. _Other_ lab members, who are not working on this project, can view but not modify these objects.
+
+h3. 4. Group-level administrator
+
+The Ashton Lab administrator, Alison, manages user accounts within her lab. She can enable and disable accounts, and exercise any permission that her lab members have.
+
+George has read-only access to the same set of accounts. This lets him see things like user activity and resource usage reports, without worrying about accidentally messing up anyone's data.
+
+table(table table-bordered table-condensed).
+|Tail |Permission |Head |Effect|
+|Group: Ashton Lab Admin|can_manage |User: Lab Member 1 |Lab member 1 is in this administrative group|
+|Group: Ashton Lab Admin|can_manage |User: Lab Member 2 |Lab member 2 is in this administrative group|
+|Group: Ashton Lab Admin|can_manage |User: Lab Member 3 |Lab member 3 is in this administrative group|
+|Group: Ashton Lab Admin|can_manage |User: Alison |Alison is in this administrative group|
+|Group: Ashton Lab Admin|can_manage |User: George |George is in this administrative group|
+|Alison |can_manage |Group: Ashton Lab Admin |Alison can do everything the above lab members can do|
+|George |can_read |Group: Ashton Lab Admin |George can read everything the above lab members can read|
+
+h3. 5. Segregated roles
+
+Granwyth, at the Hulatberi Lab, sets up a Factory Robot which uses a hosted Arvados site to do work for the Hulatberi Lab.
+
+Frank uploads a data Collection using Factory Robot's upload interface. Factory Robot sets data owner to Hulatberi Lab.
+
+Factory Robot processes the data using a pipeline.
+
+Factory Robot grants permission for anyone in the Ingeborg Lab (a Hulateberi Lab customer) to read the output of the pipeline, as well as the pipeline invocation details. (Say, Ingeborg and Jill.)
+
+During and after processing, all members of the Hulatberi Lab (_e.g._, Mike) can inspect pipeline progress, read source/intermediate/output data, and modify objects.
+
+Possible encoding:
+
+table(table table-bordered table-condensed).
+|Tail |Permission |Head |Effect|
+|Frank |(none) | |Factory Robot uses only its own credentials during upload|
+|Granwyth |can_manage |User: Factory Robot |can revoke tokens, view activity... (needed?)|
+|Granwyth |can_manage |Group: Hulatberi Lab |can grant group-write permission to Factory Robot|
+|Factory Robot |can_write |Group: Hulatberi Lab |can add data, pipelines, jobs, etc. to the Lab group|
+|Mike |can_write |Group: Hulatberi Lab |can edit/annotate/delete objects that belong to the Lab|
+
+h3. Actions governed by permissions
+
+table(table table-bordered table-condensed).
+|_Action_|_Permissions needed_|
+|Retrieve data from Keep|can_read (system-wide?)|
+|Store data in Keep|can_write (system-wide?)|
+|Add a Collection to Arvados|can_write (system-wide?)|
+|Run a job|can_run (system-wide?)|
+|See progress/result of a job|can_read (on job)|
+|Give group permissions to a user/group|can_manage (on group)|
+|Revoke group permissions from a user/group|can_manage (on group)|
+|Change owner of an object|can_manage (on object)|
+|Add an object to a group|can_write (on group)|
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Concepts
+title: Resources
+
+...
+
+
+
+This page describes the common attributes of Arvados resources.
+
+The list of resource types is on the "front page of the API Reference":./.
+
+h2. Object IDs
+
+Object IDs are alphanumeric strings, unique across all installations (each installation has a unique prefix to prevent collisions).
+
+h2(#resource). Attributes of resources
+
+table(table table-bordered table-condensed).
+|*Attribute*|*Type*|*Description*|*Example*|
+|uuid|string|universally unique object identifier|@mk2qn-4zz18-w3anr2hk2wgfpuo@|
+|href|string|a URL that can be used to address this resource||
+|kind|string|@arvados#{resource_type}@|@arvados#collection@|
+|etag|string|The ETag[1] of the resource|@1xlmizzjq7wro3dlb2dirf505@|
+|self_link|string|||
+|owner_uuid|string|UUID of owner (typically User or Project)|@mk2qn-tpzed-a4lcehql0dv2u25@|
+|created_at|datetime|When resource was created|@2013-01-21T22:17:39Z@|
+|modified_by_client_uuid|string|API client software which most recently modified the resource|@mk2qn-ozdt8-vq8l5qkzj7pr7h7@|
+|modified_by_user_uuid|string|Authenticated user, on whose behalf the client was acting when modifying the resource|@mk2qn-tpzed-a4lcehql0dv2u25@|
+|modified_at|datetime|When resource was last modified|@2013-01-25T22:29:32Z@|
+
+h2(#resourceList). Attributes of resource lists
+
+table(table table-bordered table-condensed).
+|*Attribute*|*Type*|*Description*|*Example*|
+|kind|string|@arvados#{resource_type}List@|@arvados#projectList@|
+|etag|string|The ETag[1] of the resource list|@cd3o1wi9sf934saajykawrz2e@|
+|self_link|string|||
+|next_page_token|string|||
+|next_link|string|||
+|items[]|list|List of resources||
+
+
+h2. ETags
+
+fn1. Each response includes an ETag, a string which changes when the resource changes. Clients can use this to check whether a resource has changed since they last retrieved it. If a previous ETag is provided along with a request, and the resource has not changed since, the server may return a "not modified" response.
+
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: ApiClient
+
+...
+
+
+An **ApiClient** represents a client program that can issue requests to the API server.
+
+h2. Methods
+
+See "api_clients":{{site.baseurl}}/api/methods/api_clients.html
+
+h2. Resource
+
+Each ApiClient has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|name|string|||
+|url_prefix|string|||
+|is_trusted|boolean|Trusted by users to handle their API tokens (ApiClientAuthorizations).||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: ApiClientAuthorization
+
+...
+
+An **ApiClientAuthorization** represents an API client's authorization to make API requests on a user's behalf.
+
+h2. Methods
+
+See "api_client_authorizations":{{site.baseurl}}/api/methods/api_client_authorizations.html
+
+h2. Resource
+
+An ApiClientAuthorization is not a generic Arvados resource. The full list of properties that belong to an ApiClientAuthorization is:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|api_token|string|||
+|api_client_id|integer|||
+|user_id|integer|||
+|created_by_ip_address|string|||
+|last_used_by_ip_address|string|||
+|last_used_at|datetime|||
+|expires_at|datetime|||
+|default_owner_uuid|string|||
+|scopes|array|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: AuthorizedKey
+...
+
+An **AuthorizedKey** represents the public part of an SSH authentication key which can be used to authorize transactions on behalf of the user.
+
+h2. Methods
+
+See "authorized_keys":{{site.baseurl}}/api/methods/authorized_keys.html
+
+h2. Resource
+
+Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|name|string|||
+|key_type|string|||
+|authorized_user_uuid|string|||
+|public_key|text|||
+|expires_at|datetime|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Collection
+
+...
+
+Note: This resource concerns indexing, usage accounting, and integrity checks for data stored in Arvados. Reading and writing the data _per se_ is achieved by the "Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html storage system.
+
+h2. Methods
+
+See "collections":{{site.baseurl}}/api/methods/collections.html
+
+h3. Conditions of creating a Collection
+
+The @uuid@ and @manifest_text@ attributes must be provided when creating a Collection. The cryptographic digest of the supplied @manifest_text@ must match the supplied @uuid@.
+
+h3. Side effects of creating a Collection
+
+Referenced data can be protected from garbage collection. See the section about "resources" links on the "Links":Link.html page.
+
+Data can be shared with other users via the Arvados permission model.
+
+Clients can request checks of data integrity and storage redundancy.
+
+h2. Resource
+
+Each collection has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|locator|string|||
+|portable_data_hash|string|||
+|name|string|||
+|redundancy|number|||
+|redundancy_confirmed_by_client_uuid|string|API client||
+|redundancy_confirmed_at|datetime|||
+|redundancy_confirmed_as|number|||
+|manifest_text|text|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Group
+
+...
+
+A **Group** represents a set of objects. Groups allow you to organize content, define user roles, and apply permissions to sets of objects.
+
+h2. Methods
+
+See "groups":{{site.baseurl}}/api/methods/groups.html
+
+h2. Resource
+
+Each Group has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|name|string|||
+|group_class|string|Type of group. This does not affect behavior, but determines how the group is presented in the user interface. For example, @project@ indicates that the group should be displayed by Workbench and arv-mount as a project for organizing and naming objects.|@"project"@
+null|
+|description|text|||
+|writable_by|array|List of UUID strings identifying Users and other Groups that have write permission for this Group. Only users who are allowed to administer the Group will receive a full list. Other users will receive a partial list that includes the Group's owner_uuid and (if applicable) their own user UUID.||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Human
+
+...
+
+h2. Methods
+
+See "humans":{{site.baseurl}}/api/methods/humans.html
+
+h2. Resource
+
+Each Human has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|properties|hash|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Job
+
+...
+
+Applications submit compute jobs when:
+* Provenance is important, i.e., it is worth recording how the output was produced; or
+* Computation time is significant; or
+* The job management features are convenient (failure detection/recovery, regression testing, etc).
+
+h2. Methods
+
+See "jobs":{{site.baseurl}}/api/methods/jobs.html
+
+h2. Resource
+
+Each job has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Notes|
+|script|string|The filename of the job script.|This program will be invoked by Crunch for each job task. It is given as a path to an executable file, relative to the @/crunch_scripts@ directory in the Git tree specified by the _repository_ and _script_version_ attributes.|
+|script_parameters|hash|The input parameters for the job.|Conventionally, one of the parameters is called @"input"@. Typically, some parameter values are collection UUIDs. Ultimately, though, the significance of parameters is left entirely up to the script itself.|
+|repository|string|Git repository|Given as the name of a locally hosted Git repository.|
+|script_version|string|Git commit|During a **create** transaction, this is the Git branch, tag, or hash supplied by the client. Before the job starts, Arvados updates it to the full 40-character SHA-1 hash of the commit used by the job.
+See "Specifying Git versions":#script_version below for more detail about acceptable ways to specify a commit.|
+|cancelled_by_client_uuid|string|API client ID|Is null if job has not been cancelled|
+|cancelled_by_user_uuid|string|Authenticated user ID|Is null if job has not been cancelled|
+|cancelled_at|datetime|When job was cancelled|Is null if job has not been cancelled|
+|started_at|datetime|When job started running|Is null if job has not [yet] started|
+|finished_at|datetime|When job finished running|Is null if job has not [yet] finished|
+|running|boolean|Whether the job is running||
+|success|boolean|Whether the job indicated successful completion|Is null if job has not finished|
+|is_locked_by_uuid|string|UUID of the user who has locked this job|Is null if job is not locked. The system user locks the job when starting the job, in order to prevent job attributes from being altered.|
+|node_uuids|array|List of UUID strings for node objects that have been assigned to this job||
+|log|string|Collection UUID|Is null if the job has not finished. After the job runs, the given collection contains a text file with log messages provided by the @arv-crunch-job@ task scheduler as well as the standard error streams provided by the task processes.|
+|tasks_summary|hash|Summary of task completion states.|Example: @{"done":0,"running":4,"todo":2,"failed":0}@|
+|output|string|Collection UUID|Is null if the job has not finished.|
+|nondeterministic|boolean|The job is expected to produce different results if run more than once.|If true, this job will not be considered as a candidate for automatic re-use when submitting subsequent identical jobs.|
+|submit_id|string|Unique ID provided by client when job was submitted|Optional. This can be used by a client to make the "jobs.create":{{site.baseurl}}/api/methods/jobs.html#create method idempotent.|
+|priority|string|||
+|arvados_sdk_version|string|Git commit hash that specifies the SDK version to use from the Arvados repository|This is set by searching the Arvados repository for a match for the arvados_sdk_version runtime constraint.|
+|docker_image_locator|string|Portable data hash of the collection that contains the Docker image to use|This is set by searching readable collections for a match for the docker_image runtime constraint.|
+|runtime_constraints|hash|Constraints that must be satisfied by the job/task scheduler in order to run the job.|See below.|
+
+h3(#script_version). Specifying Git versions
+
+The script_version attribute and arvados_sdk_version runtime constraint are typically given as a branch, tag, or commit hash, but there are many more ways to specify a Git commit. The "specifying revisions" section of the "gitrevisions manual page":http://git-scm.com/docs/gitrevisions.html has a definitive list. Arvados accepts Git versions in any format listed there that names a single commit (not a tree, a blob, or a range of commits). However, some kinds of names can be expected to resolve differently in Arvados than they do in your local repository. For example, <code>HEAD@{1}</code> refers to the local reflog, and @origin/master@ typically refers to a remote branch: neither is likely to work as desired if given as a Git version.
+
+h3. Runtime constraints
+
+table(table table-bordered table-condensed).
+|_. Key|_. Type|_. Description|_. Implemented|
+|arvados_sdk_version|string|The Git version of the SDKs to use from the Arvados git repository. See "Specifying Git versions":#script_version for more detail about acceptable ways to specify a commit. If you use this, you must also specify a @docker_image@ constraint (see below). In order to install the Python SDK successfully, Crunch must be able to find and run virtualenv inside the container.|✓|
+|docker_image|string|The Docker image that this Job needs to run. If specified, Crunch will create a Docker container from this image, and run the Job's script inside that. The Keep mount and work directories will be available as volumes inside this container. The image must be uploaded to Arvados using @arv keep docker@. You may specify the image in any format that Docker accepts, such as @arvados/jobs@, @debian:latest@, or the Docker image id. Alternatively, you may specify the UUID or portable data hash of the image Collection, returned by @arv keep docker@.|✓|
+|min_nodes|integer||✓|
+|max_nodes|integer|||
+|min_cores_per_node|integer|Require that each node assigned to this Job have the specified number of CPU cores|✓|
+|min_ram_mb_per_node|integer|Require that each node assigned to this Job have the specified amount of real memory (in MiB)|✓|
+|min_scratch_mb_per_node|integer|Require that each node assigned to this Job have the specified amount of scratch storage available (in MiB)|✓|
+|max_tasks_per_node|integer|Maximum simultaneous tasks on a single node|✓|
+|min_ram_per_task|integer|Minimum real memory (KiB) per task||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: JobTask
+
+...
+
+A Job Task is a well defined independently-computable portion of a "Job":Job.html.
+
+Job tasks are created two ways:
+* When a job starts, it is seeded with a job task with @sequence=0@ and an empty @parameters{}@ list.
+* Job task A can create additional job tasks B, C, D, which will belong to the same job. Tasks B, C, D will not be performed until job task A is complete. If job task A fails, tasks B, C, D will be deleted.
+
+Job tasks have particular update semantics:
+* Progress reporting: A job task should only be <code>PATCH</code>ed by a worker process which has been dispatched to work on that task and is reporting progress or completion status — and by the job manager itself.
+* Completion: When a job task process terminates, the task is considered complete only if its most recent @PATCH@ transaction had @progress=1.0@ and @success=true@.
+* Temporary failure: If a job task process terminates without updating @success@ to @true@ or @false@, it is assumed that the task failed but is worth re-attempting (at a different time, on a different node, etc).
+
+
+h2. Methods
+
+See "job_tasks":{{site.baseurl}}/api/methods/job_tasks.html
+
+h2. Resource
+
+Each JobTask has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|sequence|integer|Execution sequence.
+A step cannot be run until all steps with lower sequence numbers have completed.
+Job steps with the same sequence number can be run in any order.||
+|parameters|hash|||
+|output|text|||
+|progress|float|||
+|success|boolean|Is null if the task has neither completed successfully nor failed permanently.||
+
+The following attributes should not be updated by anyone other than the job manager:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Notes|
+|qsequence|integer|Order of arrival|0-based|
+|job_uuid|string|||
+|created_by_job_task_uuid|string|||
+
+
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: KeepDisk
+
+...
+
+A **KeepDisk** is a filesystem volume used by a Keep storage server to store data blocks.
+
+h2. Methods
+
+See "keep_disks":{{site.baseurl}}/api/methods/keep_disks.html
+
+h2. Resource
+
+Each KeepDisk has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|ping_secret|string|||
+|node_uuid|string|||
+|filesystem_uuid|string|||
+|bytes_total|integer|||
+|bytes_free|integer|||
+|is_readable|boolean|||
+|is_writable|boolean|||
+|last_read_at|datetime|||
+|last_write_at|datetime|||
+|last_ping_at|datetime|||
+|keep_service_uuid|string|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: KeepService
+
+...
+
+A **KeepService** is a service endpoint that supports the Keep protocol.
+
+h2. Methods
+
+See "keep_services":{{site.baseurl}}/api/methods/keep_services.html
+
+h2. Resource
+
+Each KeepService has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|service_host|string|||
+|service_port|integer|||
+|service_ssl_flag|boolean|||
+|service_type|string|||
\ No newline at end of file
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Link
+
+...
+
+**Links** describe relationships between Arvados objects, and from objects to primitives.
+
+Links are directional: each metadata object has a tail (the "subject" being described), class, name, properties, and head (the "object" that describes the "subject"). A Link may describe a relationship between two objects in an Arvados database: e.g. a _permission_ link between a User and a Group defines the permissions that User has to read or modify the Group. Other Links simply represent metadata for a single object, e.g. the _identifier_ Link, in which the _name_ property represents a human-readable identifier for the object at the link's head.
+
+For links that don't make sense to share between API clients, a _link_class_ that begins with @client@ (like @client.my_app_id@ or @client.my_app_id.anythinghere@) should be used.
+
+h2. Methods
+
+See "links":{{site.baseurl}}/api/methods/links.html
+
+h2. Resource
+
+Each link has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|
+|tail_uuid|string|Object UUID at the tail (start, source, origin) of this link|
+|link_class|string|Class (see below)|
+|name|string|Link type (see below)|
+|head_uuid|string|Object UUID at the head (end, destination, target) of this link|
+|properties|hash|Additional information, expressed as a key→value hash. Key: string. Value: string, number, array, or hash.|
+
+h2. Link classes
+
+Some classes are pre-defined by convention and have standard meanings attached to names.
+
+h3. provenance
+
+table(table table-bordered table-condensed).
+|_. tail_type→head_type|_. name→head_uuid {properties}|_. Notes|
+|→Collection |provided → _collection uuid_
+{url→http://example.com/foo.tgz, retrieved_at→1352616640.000}||
+|Job→Collection |provided → _collection uuid_||
+|Specimen→Collection|provided → _collection uuid_||
+|Human→Specimen |provided → _specimen uuid_||
+|Human→Collection |provided → _collection uuid_||
+
+h3. permission
+
+table(table table-bordered table-condensed).
+|_. tail_type→head_type|_. name→head_uuid {properties}|_. Notes|
+|User→Group |{white-space:nowrap}. can_manage → _group uuid_|The User can read, write, and control permissions on the Group itself, every object owned by the Group, and every object on which the Group has _can_manage_ permission.|
+|User→Group |can_read → _group uuid_ |The User can retrieve the Group itself and every object that is readable by the Group.|
+|User→Job|can_write → _job uuid_ |The User can read and update the Job. (This works for all objects, not just jobs.)|
+|User→Job|can_manage → _job uuid_ |The User can read, update, and change permissions for the Job. (This works for all objects, not just jobs.)|
+|Group→Job|can_manage → _job uuid_ |Anyone with _can_manage_ permission on the Group can also read, update, and change permissions for the Job. Anyone with _can_read_ permission on the Group can read the Job. (This works for all objects, not just jobs.)|
+
+h3. resources
+
+table(table table-bordered table-condensed).
+|_. tail_type→head_type|_. name→head_uuid {properties}|_. Notes|
+|User→Collection|wants → _collection uuid_ |Determines whether data can be deleted|
+|User→Job |wants → _job uuid_ |Determines whether a job can be cancelled|
+
+h3. tag
+
+A **tag** link describes an object using an unparsed plain text string. Tags can be used to annotate objects that are not editable, like collections and objects shared as read-only.
+
+table(table table-bordered table-condensed).
+|_. tail_type→head_type|_. name→head_uuid {properties}|
+|→Collection | _tag name_ → _collection uuid_|
+|→Job | _tag name_ → _job uuid_|
+
+h3. human_trait
+
+table(table table-bordered table-condensed).
+|_. tail_type→head_type|_. name→head_uuid {properties}|_. Notes|
+|Human→Trait |measured → _trait uuid_ {value→1.83, unit→metre, measured_at→1352616640.000}||
+
+h3. identifier
+
+table(table table-bordered table-condensed).
+|_. tail_type→head_type|_. name→head_uuid {properties}|_. Notes|
+|→Human |hu123456 → _human uuid_||
+
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Log
+
+...
+
+**Log** objects record events that occur in an Arvados cluster. Both user-written pipelines and the Arvados system itself may generate Log events.
+
+h2. Methods
+
+See "logs":{{site.baseurl}}/api/methods/logs.html
+
+h2. Creation
+
+Any user may create Log entries for any event they find useful. User-generated Logs have no intrinsic meaning to other users or to the Arvados system itself; it is up to each user to choose appropriate log event types and summaries for their project.
+
+h3. System Logs
+
+Arvados uses Logs to record creation, deletion, and updates of other Arvados resources.
+
+h2. Resource
+
+Each Log has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|object_uuid|string|||
+|event_at|datetime|||
+|event_type|string|A user-defined category or type for this event.|@LOGIN@|
+|summary|text|||
+|properties|hash|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Node
+
+...
+
+A **Node** represents a host that can be used to run Crunch job tasks.
+
+h2. Methods
+
+See "nodes":{{site.baseurl}}/api/methods/nodes.html
+
+h2. Resource
+
+Each Node has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|slot_number|integer|||
+|hostname|string|||
+|domain|string|||
+|ip_address|string|||
+|job_uuid|string|The UUID of the job that this node is assigned to work on. If you do not have permission to read the job, this will be null.||
+|first_ping_at|datetime|||
+|last_ping_at|datetime|||
+|info|hash|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: PipelineInstance
+
+...
+
+A **PipelineInstance** is the act or record of applying a pipeline template to a specific set of inputs; generally, a pipeline instance refers to a set of jobs that have been run to satisfy the pipeline components.
+
+h2. Methods
+
+See "pipeline_instances":{{site.baseurl}}/api/methods/pipeline_instances.html
+
+h2. Resource
+
+Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|pipeline_template_uuid|string|||
+|name|string|||
+|components|hash|||
+|success|boolean|||
+|active|boolean|||
+|properties|Hash|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: PipelineTemplate
+...
+
+The pipeline template consists of "name" and "components".
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type |_. Accepted values |_. Required|_. Description|
+|name |string |any |yes |The human-readable name of the pipeline template.|
+|components |object |JSON object containing job submission objects|yes |The component jobs that make up the pipeline, with the component name as the key. |
+
+h3. Components
+
+The components field of the pipeline template is a JSON object which describes the individual steps that make up the pipeline. Each component is an Arvados job submission. "Parameters for job submissions are described on the job method page.":{{site.baseurl}}/api/methods/jobs.html#create In addition, a component can have the following parameters:
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type |_. Accepted values |_. Required|_. Description|
+|output_name |string or boolean|string or false |no |If a string is provided, use this name for the output collection of this component. If the value is false, do not create a permanent output collection (an temporary intermediate collection will still be created). If not provided, a default name will be assigned to the output.|
+
+h3. Script parameters
+
+When used in a pipeline, each parameter in the 'script_parameters' attribute of a component job can specify that the input parameter must be supplied by the user, or the input parameter should be linked to the output of another component. To do this, the value of the parameter should be JSON object containing one of the following attributes:
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type |_. Accepted values |_. Description|
+|default |any |any |The default value for this parameter.|
+|required |boolean |true or false |Specifies whether the parameter is required to have a value or not.|
+|dataclass |string |One of 'Collection', 'File' [1], 'number', or 'text' |Data type of this parameter.|
+|search_for |string |any string |Substring to use as a default search string when choosing inputs.|
+|output_of |string |the name of another component in the pipeline |Specifies that the value of this parameter should be set to the 'output' attribute of the job that corresponds to the specified component.|
+|title |string |any string |User friendly title to display when choosing parameter values|
+|description |string |any string |Extended text description for describing expected/valid values for the script parameter|
+|link_name |string |any string |User friendly name to display for the parameter value instead of the actual parameter value|
+
+The 'output_of' parameter is especially important, as this is how components are actually linked together to form a pipeline. Component jobs that depend on the output of other components do not run until the parent job completes and has produced output. If the parent job fails, the entire pipeline fails.
+
+fn1. The 'File' type refers to a specific file within a Keep collection in the form 'collection_hash/filename', for example '887cd41e9c613463eab2f0d885c6dd96+83/bob.txt'.
+
+The 'search_for' parameter is meaningful only when input dataclass of type Collection or File is used. If a value is provided, this will be preloaded into the input data chooser dialog in Workbench. For example, if your input dataclass is a File and you are interested in a certain filename extention, you can preconfigure it in this attribute.
+
+h3. Examples
+
+This is a pipeline named "Filter MD5 hash values" with two components, "do_hash" and "filter". The "input" script parameter of the "do_hash" component is required to be filled in by the user, and the expected data type is "Collection". This also specifies that the "input" script parameter of the "filter" component is the output of "do_hash", so "filter" will not run until "do_hash" completes successfully. When the pipeline runs, past jobs that meet the criteria described above may be substituted for either or both components to avoid redundant computation.
+
+<notextile><pre>
+{
+ "name": "Filter MD5 hash values",
+ "components": {
+ "do_hash": {
+ "script": "hash.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "required": true,
+ "dataclass": "Collection",
+ "search_for": ".fastq.gz",
+ "title":"Please select a fastq file"
+ }
+ },
+ },
+ "filter": {
+ "script": "0-filter.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "do_hash"
+ }
+ },
+ }
+ }
+}
+</pre></notextile>
+
+This pipeline consists of three components. The components "thing1" and "thing2" both depend on "cat_in_the_hat". Once the "cat_in_the_hat" job is complete, both "thing1" and "thing2" can run in parallel, because they do not depend on each other.
+
+<notextile><pre>
+{
+ "name": "Wreck the house",
+ "components": {
+ "cat_in_the_hat": {
+ "script": "cat.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "thing1": {
+ "script": "thing1.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "cat_in_the_hat"
+ }
+ },
+ },
+ "thing2": {
+ "script": "thing2.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "cat_in_the_hat"
+ }
+ },
+ },
+ }
+}
+</pre></notextile>
+
+This pipeline consists of three components. The component "cleanup" depends on "thing1" and "thing2". Both "thing1" and "thing2" are started immediately and can run in parallel, because they do not depend on each other, but "cleanup" cannot begin until both "thing1" and "thing2" have completed.
+
+<notextile><pre>
+{
+ "name": "Clean the house",
+ "components": {
+ "thing1": {
+ "script": "thing1.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "thing2": {
+ "script": "thing2.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "cleanup": {
+ "script": "cleanup.py",
+ "repository": "<b>you</b>",
+ "script_version": "master",
+ "script_parameters": {
+ "mess1": {
+ "output_of": "thing1"
+ },
+ "mess2": {
+ "output_of": "thing2"
+ }
+ }
+ }
+ }
+}
+</pre></notextile>
+
+h2. Methods
+
+See "pipeline_templates":{{site.baseurl}}/api/methods/pipeline_templates.html
+
+h2. Resource
+
+Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|name|string|||
+|components|hash|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Repository
+
+...
+
+A **Repository** represents a git repository hosted in an Arvados installation.
+
+h2. Methods
+
+See "repositories":{{site.baseurl}}/api/methods/repositories.html
+
+h2. Resource
+
+Each Repository has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|name|string|||
+|fetch_url|string|||
+|push_url|string|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Specimen
+
+...
+
+A **Specimen** represents a tissue sample or similar material obtained from a human that has some biomedical significance or interest.
+
+h2. Methods
+
+See "specimens":{{site.baseurl}}/api/methods/specimens.html
+
+h2. Resource
+
+Each Specimen has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|material|string|||
+|properties|hash|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: Trait
+
+...
+
+A **Trait** represents a measured or observed characteristic of a human.
+
+h2. Methods
+
+See "traits":{{site.baseurl}}/api/methods/traits.html
+
+h2. Resource
+
+Each Trait has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|name|string|||
+|properties|hash|||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: User
+
+...
+
+A **User** represents a person who interacts with Arvados via an ApiClient.
+
+h2. Methods
+
+See "users":{{site.baseurl}}/api/methods/users.html
+
+h2. Resource
+
+Each User has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|email|string|||
+|first_name|string|||
+|last_name|string|||
+|identity_url|string|||
+|is_admin|boolean|||
+|prefs|hash|||
+|default_owner_uuid|string|||
+|is_active|boolean|||
+|writable_by|array|List of UUID strings identifying Groups and other Users that can modify this User object. This will include the user's owner_uuid and, for administrators and users requesting their own User object, the requesting user's UUID.||
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: Schema
+title: VirtualMachine
+
+...
+
+A **VirtualMachine** represents a network host, running within an Arvados installation, on which Arvados users are given login accounts.
+
+h2. Methods
+
+See "virtual_machines":{{site.baseurl}}/api/methods/virtual_machines.html
+
+h2. Resource
+
+Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+|hostname|string|||
--- /dev/null
+/* Colors
+ * Contextual variations of badges
+ * Bootstrap 3.0 removed contexts for badges, we re-introduce them, based on what is done for labels
+ */
+
+.badge.badge-error {
+ background-color: #b94a48;
+}
+
+.badge.badge-warning {
+ background-color: #f89406;
+}
+
+.badge.badge-success {
+ background-color: #468847;
+}
+
+.badge.badge-info {
+ background-color: #3a87ad;
+}
+
+.badge.badge-inverse {
+ background-color: #333333;
+}
+
+.badge.badge-alert {
+ background: red;
+}
--- /dev/null
+/*!
+ * Bootstrap v3.1.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+.btn-default,
+.btn-primary,
+.btn-success,
+.btn-info,
+.btn-warning,
+.btn-danger {
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, .2);
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075);
+}
+.btn-default:active,
+.btn-primary:active,
+.btn-success:active,
+.btn-info:active,
+.btn-warning:active,
+.btn-danger:active,
+.btn-default.active,
+.btn-primary.active,
+.btn-success.active,
+.btn-info.active,
+.btn-warning.active,
+.btn-danger.active {
+ -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+ box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+}
+.btn:active,
+.btn.active {
+ background-image: none;
+}
+.btn-default {
+ text-shadow: 0 1px 0 #fff;
+ background-image: -webkit-linear-gradient(top, #fff 0%, #e0e0e0 100%);
+ background-image: linear-gradient(to bottom, #fff 0%, #e0e0e0 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe0e0e0', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #dbdbdb;
+ border-color: #ccc;
+}
+.btn-default:hover,
+.btn-default:focus {
+ background-color: #e0e0e0;
+ background-position: 0 -15px;
+}
+.btn-default:active,
+.btn-default.active {
+ background-color: #e0e0e0;
+ border-color: #dbdbdb;
+}
+.btn-primary {
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #2d6ca2 100%);
+ background-image: linear-gradient(to bottom, #428bca 0%, #2d6ca2 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff2d6ca2', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #2b669a;
+}
+.btn-primary:hover,
+.btn-primary:focus {
+ background-color: #2d6ca2;
+ background-position: 0 -15px;
+}
+.btn-primary:active,
+.btn-primary.active {
+ background-color: #2d6ca2;
+ border-color: #2b669a;
+}
+.btn-success {
+ background-image: -webkit-linear-gradient(top, #5cb85c 0%, #419641 100%);
+ background-image: linear-gradient(to bottom, #5cb85c 0%, #419641 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff419641', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #3e8f3e;
+}
+.btn-success:hover,
+.btn-success:focus {
+ background-color: #419641;
+ background-position: 0 -15px;
+}
+.btn-success:active,
+.btn-success.active {
+ background-color: #419641;
+ border-color: #3e8f3e;
+}
+.btn-info {
+ background-image: -webkit-linear-gradient(top, #5bc0de 0%, #2aabd2 100%);
+ background-image: linear-gradient(to bottom, #5bc0de 0%, #2aabd2 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff2aabd2', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #28a4c9;
+}
+.btn-info:hover,
+.btn-info:focus {
+ background-color: #2aabd2;
+ background-position: 0 -15px;
+}
+.btn-info:active,
+.btn-info.active {
+ background-color: #2aabd2;
+ border-color: #28a4c9;
+}
+.btn-warning {
+ background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #eb9316 100%);
+ background-image: linear-gradient(to bottom, #f0ad4e 0%, #eb9316 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffeb9316', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #e38d13;
+}
+.btn-warning:hover,
+.btn-warning:focus {
+ background-color: #eb9316;
+ background-position: 0 -15px;
+}
+.btn-warning:active,
+.btn-warning.active {
+ background-color: #eb9316;
+ border-color: #e38d13;
+}
+.btn-danger {
+ background-image: -webkit-linear-gradient(top, #d9534f 0%, #c12e2a 100%);
+ background-image: linear-gradient(to bottom, #d9534f 0%, #c12e2a 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc12e2a', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-color: #b92c28;
+}
+.btn-danger:hover,
+.btn-danger:focus {
+ background-color: #c12e2a;
+ background-position: 0 -15px;
+}
+.btn-danger:active,
+.btn-danger.active {
+ background-color: #c12e2a;
+ border-color: #b92c28;
+}
+.thumbnail,
+.img-thumbnail {
+ -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+ box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+}
+.dropdown-menu > li > a:hover,
+.dropdown-menu > li > a:focus {
+ background-color: #e8e8e8;
+ background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
+ background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0);
+ background-repeat: repeat-x;
+}
+.dropdown-menu > .active > a,
+.dropdown-menu > .active > a:hover,
+.dropdown-menu > .active > a:focus {
+ background-color: #357ebd;
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #357ebd 100%);
+ background-image: linear-gradient(to bottom, #428bca 0%, #357ebd 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff357ebd', GradientType=0);
+ background-repeat: repeat-x;
+}
+.navbar-default {
+ background-image: -webkit-linear-gradient(top, #fff 0%, #f8f8f8 100%);
+ background-image: linear-gradient(to bottom, #fff 0%, #f8f8f8 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#fff8f8f8', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075);
+}
+.navbar-default .navbar-nav > .active > a {
+ background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f3f3f3 100%);
+ background-image: linear-gradient(to bottom, #ebebeb 0%, #f3f3f3 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffebebeb', endColorstr='#fff3f3f3', GradientType=0);
+ background-repeat: repeat-x;
+ -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075);
+}
+.navbar-brand,
+.navbar-nav > li > a {
+ text-shadow: 0 1px 0 rgba(255, 255, 255, .25);
+}
+.navbar-inverse {
+ background-image: -webkit-linear-gradient(top, #3c3c3c 0%, #222 100%);
+ background-image: linear-gradient(to bottom, #3c3c3c 0%, #222 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3c3c3c', endColorstr='#ff222222', GradientType=0);
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+ background-repeat: repeat-x;
+}
+.navbar-inverse .navbar-nav > .active > a {
+ background-image: -webkit-linear-gradient(top, #222 0%, #282828 100%);
+ background-image: linear-gradient(to bottom, #222 0%, #282828 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff222222', endColorstr='#ff282828', GradientType=0);
+ background-repeat: repeat-x;
+ -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25);
+ box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25);
+}
+.navbar-inverse .navbar-brand,
+.navbar-inverse .navbar-nav > li > a {
+ text-shadow: 0 -1px 0 rgba(0, 0, 0, .25);
+}
+.navbar-static-top,
+.navbar-fixed-top,
+.navbar-fixed-bottom {
+ border-radius: 0;
+}
+.alert {
+ text-shadow: 0 1px 0 rgba(255, 255, 255, .2);
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05);
+}
+.alert-success {
+ background-image: -webkit-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%);
+ background-image: linear-gradient(to bottom, #dff0d8 0%, #c8e5bc 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffc8e5bc', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #b2dba1;
+}
+.alert-info {
+ background-image: -webkit-linear-gradient(top, #d9edf7 0%, #b9def0 100%);
+ background-image: linear-gradient(to bottom, #d9edf7 0%, #b9def0 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffb9def0', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #9acfea;
+}
+.alert-warning {
+ background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%);
+ background-image: linear-gradient(to bottom, #fcf8e3 0%, #f8efc0 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fff8efc0', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #f5e79e;
+}
+.alert-danger {
+ background-image: -webkit-linear-gradient(top, #f2dede 0%, #e7c3c3 100%);
+ background-image: linear-gradient(to bottom, #f2dede 0%, #e7c3c3 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffe7c3c3', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #dca7a7;
+}
+.progress {
+ background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%);
+ background-image: linear-gradient(to bottom, #ebebeb 0%, #f5f5f5 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffebebeb', endColorstr='#fff5f5f5', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar {
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #3071a9 100%);
+ background-image: linear-gradient(to bottom, #428bca 0%, #3071a9 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff3071a9', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-success {
+ background-image: -webkit-linear-gradient(top, #5cb85c 0%, #449d44 100%);
+ background-image: linear-gradient(to bottom, #5cb85c 0%, #449d44 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff449d44', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-info {
+ background-image: -webkit-linear-gradient(top, #5bc0de 0%, #31b0d5 100%);
+ background-image: linear-gradient(to bottom, #5bc0de 0%, #31b0d5 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff31b0d5', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-warning {
+ background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #ec971f 100%);
+ background-image: linear-gradient(to bottom, #f0ad4e 0%, #ec971f 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffec971f', GradientType=0);
+ background-repeat: repeat-x;
+}
+.progress-bar-danger {
+ background-image: -webkit-linear-gradient(top, #d9534f 0%, #c9302c 100%);
+ background-image: linear-gradient(to bottom, #d9534f 0%, #c9302c 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc9302c', GradientType=0);
+ background-repeat: repeat-x;
+}
+.list-group {
+ border-radius: 4px;
+ -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+ box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+}
+.list-group-item.active,
+.list-group-item.active:hover,
+.list-group-item.active:focus {
+ text-shadow: 0 -1px 0 #3071a9;
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #3278b3 100%);
+ background-image: linear-gradient(to bottom, #428bca 0%, #3278b3 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff3278b3', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #3278b3;
+}
+.panel {
+ -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .05);
+ box-shadow: 0 1px 2px rgba(0, 0, 0, .05);
+}
+.panel-default > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
+ background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-primary > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #428bca 0%, #357ebd 100%);
+ background-image: linear-gradient(to bottom, #428bca 0%, #357ebd 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff428bca', endColorstr='#ff357ebd', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-success > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%);
+ background-image: linear-gradient(to bottom, #dff0d8 0%, #d0e9c6 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffd0e9c6', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-info > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%);
+ background-image: linear-gradient(to bottom, #d9edf7 0%, #c4e3f3 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffc4e3f3', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-warning > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%);
+ background-image: linear-gradient(to bottom, #fcf8e3 0%, #faf2cc 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fffaf2cc', GradientType=0);
+ background-repeat: repeat-x;
+}
+.panel-danger > .panel-heading {
+ background-image: -webkit-linear-gradient(top, #f2dede 0%, #ebcccc 100%);
+ background-image: linear-gradient(to bottom, #f2dede 0%, #ebcccc 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffebcccc', GradientType=0);
+ background-repeat: repeat-x;
+}
+.well {
+ background-image: -webkit-linear-gradient(top, #e8e8e8 0%, #f5f5f5 100%);
+ background-image: linear-gradient(to bottom, #e8e8e8 0%, #f5f5f5 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffe8e8e8', endColorstr='#fff5f5f5', GradientType=0);
+ background-repeat: repeat-x;
+ border-color: #dcdcdc;
+ -webkit-box-shadow: inset 0 1px 3px rgba(0, 0, 0, .05), 0 1px 0 rgba(255, 255, 255, .1);
+ box-shadow: inset 0 1px 3px rgba(0, 0, 0, .05), 0 1px 0 rgba(255, 255, 255, .1);
+}
+/*# sourceMappingURL=bootstrap-theme.css.map */
--- /dev/null
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@end-color: darken(@btn-color, 12%));\n .reset-filter(); // Disable gradients for IE9 because filter bleeds through rounded corners\n background-repeat: repeat-x;\n border-color: darken(@btn-color, 14%);\n\n &:hover,\n &:focus {\n background-color: darken(@btn-color, 12%);\n background-position: 0 -15px;\n }\n\n &:active,\n &.active {\n background-color: darken(@btn-color, 12%);\n border-color: darken(@btn-color, 14%);\n }\n}\n\n// Common styles\n.btn {\n // Remove the gradient for the pressed/active state\n &:active,\n &.active {\n background-image: none;\n }\n}\n\n// Apply the mixin to the buttons\n.btn-default { .btn-styles(@btn-default-bg); text-shadow: 0 1px 0 #fff; border-color: #ccc; }\n.btn-primary { .btn-styles(@btn-primary-bg); }\n.btn-success { .btn-styles(@btn-success-bg); }\n.btn-info { .btn-styles(@btn-info-bg); }\n.btn-warning { .btn-styles(@btn-warning-bg); }\n.btn-danger { .btn-styles(@btn-danger-bg); }\n\n\n\n//\n// Images\n// --------------------------------------------------\n\n.thumbnail,\n.img-thumbnail {\n .box-shadow(0 1px 2px rgba(0,0,0,.075));\n}\n\n\n\n//\n// Dropdowns\n// --------------------------------------------------\n\n.dropdown-menu > li > a:hover,\n.dropdown-menu > li > a:focus {\n #gradient > .vertical(@start-color: @dropdown-link-hover-bg; @end-color: darken(@dropdown-link-hover-bg, 5%));\n background-color: darken(@dropdown-link-hover-bg, 5%);\n}\n.dropdown-menu > .active > a,\n.dropdown-menu > .active > a:hover,\n.dropdown-menu > .active > a:focus {\n #gradient > .vertical(@start-color: @dropdown-link-active-bg; @end-color: darken(@dropdown-link-active-bg, 5%));\n background-color: darken(@dropdown-link-active-bg, 5%);\n}\n\n\n\n//\n// Navbar\n// --------------------------------------------------\n\n// Default navbar\n.navbar-default {\n #gradient > .vertical(@start-color: lighten(@navbar-default-bg, 10%); @end-color: @navbar-default-bg);\n .reset-filter(); // Remove gradient in IE<10 to fix bug where dropdowns don't get triggered\n border-radius: @navbar-border-radius;\n @shadow: inset 0 1px 0 rgba(255,255,255,.15), 0 1px 5px rgba(0,0,0,.075);\n .box-shadow(@shadow);\n\n .navbar-nav > .active > a {\n #gradient > .vertical(@start-color: darken(@navbar-default-bg, 5%); @end-color: darken(@navbar-default-bg, 2%));\n .box-shadow(inset 0 3px 9px rgba(0,0,0,.075));\n }\n}\n.navbar-brand,\n.navbar-nav > li > a {\n text-shadow: 0 1px 0 rgba(255,255,255,.25);\n}\n\n// Inverted navbar\n.navbar-inverse {\n #gradient > .vertical(@start-color: lighten(@navbar-inverse-bg, 10%); @end-color: @navbar-inverse-bg);\n .reset-filter(); // Remove gradient in IE<10 to fix bug where dropdowns don't get triggered\n\n .navbar-nav > .active > a {\n #gradient > .vertical(@start-color: @navbar-inverse-bg; @end-color: lighten(@navbar-inverse-bg, 2.5%));\n .box-shadow(inset 0 3px 9px rgba(0,0,0,.25));\n }\n\n .navbar-brand,\n .navbar-nav > li > a {\n text-shadow: 0 -1px 0 rgba(0,0,0,.25);\n }\n}\n\n// Undo rounded corners in static and fixed navbars\n.navbar-static-top,\n.navbar-fixed-top,\n.navbar-fixed-bottom {\n border-radius: 0;\n}\n\n\n\n//\n// Alerts\n// --------------------------------------------------\n\n// Common styles\n.alert {\n text-shadow: 0 1px 0 rgba(255,255,255,.2);\n @shadow: inset 0 1px 0 rgba(255,255,255,.25), 0 1px 2px rgba(0,0,0,.05);\n .box-shadow(@shadow);\n}\n\n// Mixin for generating new styles\n.alert-styles(@color) {\n #gradient > .vertical(@start-color: @color; @end-color: darken(@color, 7.5%));\n border-color: darken(@color, 15%);\n}\n\n// Apply the mixin to the alerts\n.alert-success { .alert-styles(@alert-success-bg); }\n.alert-info { .alert-styles(@alert-info-bg); }\n.alert-warning { .alert-styles(@alert-warning-bg); }\n.alert-danger { .alert-styles(@alert-danger-bg); }\n\n\n\n//\n// Progress bars\n// --------------------------------------------------\n\n// Give the progress background some depth\n.progress {\n #gradient > .vertical(@start-color: darken(@progress-bg, 4%); @end-color: @progress-bg)\n}\n\n// Mixin for generating new styles\n.progress-bar-styles(@color) {\n #gradient > .vertical(@start-color: @color; @end-color: darken(@color, 10%));\n}\n\n// Apply the mixin to the progress bars\n.progress-bar { .progress-bar-styles(@progress-bar-bg); }\n.progress-bar-success { .progress-bar-styles(@progress-bar-success-bg); }\n.progress-bar-info { .progress-bar-styles(@progress-bar-info-bg); }\n.progress-bar-warning { .progress-bar-styles(@progress-bar-warning-bg); }\n.progress-bar-danger { .progress-bar-styles(@progress-bar-danger-bg); }\n\n\n\n//\n// List groups\n// --------------------------------------------------\n\n.list-group {\n border-radius: @border-radius-base;\n .box-shadow(0 1px 2px rgba(0,0,0,.075));\n}\n.list-group-item.active,\n.list-group-item.active:hover,\n.list-group-item.active:focus {\n text-shadow: 0 -1px 0 darken(@list-group-active-bg, 10%);\n #gradient > .vertical(@start-color: @list-group-active-bg; @end-color: darken(@list-group-active-bg, 7.5%));\n border-color: darken(@list-group-active-border, 7.5%);\n}\n\n\n\n//\n// Panels\n// --------------------------------------------------\n\n// Common styles\n.panel {\n .box-shadow(0 1px 2px rgba(0,0,0,.05));\n}\n\n// Mixin for generating new styles\n.panel-heading-styles(@color) {\n #gradient > .vertical(@start-color: @color; @end-color: darken(@color, 5%));\n}\n\n// Apply the mixin to the panel headings only\n.panel-default > .panel-heading { .panel-heading-styles(@panel-default-heading-bg); }\n.panel-primary > .panel-heading { .panel-heading-styles(@panel-primary-heading-bg); }\n.panel-success > .panel-heading { .panel-heading-styles(@panel-success-heading-bg); }\n.panel-info > .panel-heading { .panel-heading-styles(@panel-info-heading-bg); }\n.panel-warning > .panel-heading { .panel-heading-styles(@panel-warning-heading-bg); }\n.panel-danger > .panel-heading { .panel-heading-styles(@panel-danger-heading-bg); }\n\n\n\n//\n// Wells\n// --------------------------------------------------\n\n.well {\n #gradient > .vertical(@start-color: darken(@well-bg, 5%); @end-color: @well-bg);\n border-color: darken(@well-bg, 10%);\n @shadow: inset 0 1px 3px rgba(0,0,0,.05), 0 1px 0 rgba(255,255,255,.1);\n .box-shadow(@shadow);\n}\n","//\n// Mixins\n// --------------------------------------------------\n\n\n// Utilities\n// -------------------------\n\n// Clearfix\n// Source: http://nicolasgallagher.com/micro-clearfix-hack/\n//\n// For modern browsers\n// 1. The space content is one way to avoid an Opera bug when the\n// contenteditable attribute is included anywhere else in the document.\n// Otherwise it causes space to appear at the top and bottom of elements\n// that are clearfixed.\n// 2. The use of `table` rather than `block` is only necessary if using\n// `:before` to contain the top-margins of child elements.\n.clearfix() {\n &:before,\n &:after {\n content: \" \"; // 1\n display: table; // 2\n }\n &:after {\n clear: both;\n }\n}\n\n// WebKit-style focus\n.tab-focus() {\n // Default\n outline: thin dotted;\n // WebKit\n outline: 5px auto -webkit-focus-ring-color;\n outline-offset: -2px;\n}\n\n// Center-align a block level element\n.center-block() {\n display: block;\n margin-left: auto;\n margin-right: auto;\n}\n\n// Sizing shortcuts\n.size(@width; @height) {\n width: @width;\n height: @height;\n}\n.square(@size) {\n .size(@size; @size);\n}\n\n// Placeholder text\n.placeholder(@color: @input-color-placeholder) {\n &:-moz-placeholder { color: @color; } // Firefox 4-18\n &::-moz-placeholder { color: @color; // Firefox 19+\n opacity: 1; } // See https://github.com/twbs/bootstrap/pull/11526\n &:-ms-input-placeholder { color: @color; } // Internet Explorer 10+\n &::-webkit-input-placeholder { color: @color; } // Safari and Chrome\n}\n\n// Text overflow\n// Requires inline-block or block for proper styling\n.text-overflow() {\n overflow: hidden;\n text-overflow: ellipsis;\n white-space: nowrap;\n}\n\n// CSS image replacement\n//\n// Heads up! v3 launched with with only `.hide-text()`, but per our pattern for\n// mixins being reused as classes with the same name, this doesn't hold up. As\n// of v3.0.1 we have added `.text-hide()` and deprecated `.hide-text()`. Note\n// that we cannot chain the mixins together in Less, so they are repeated.\n//\n// Source: https://github.com/h5bp/html5-boilerplate/commit/aa0396eae757\n\n// Deprecated as of v3.0.1 (will be removed in v4)\n.hide-text() {\n font: ~\"0/0\" a;\n color: transparent;\n text-shadow: none;\n background-color: transparent;\n border: 0;\n}\n// New mixin to use as of v3.0.1\n.text-hide() {\n .hide-text();\n}\n\n\n\n// CSS3 PROPERTIES\n// --------------------------------------------------\n\n// Single side border-radius\n.border-top-radius(@radius) {\n border-top-right-radius: @radius;\n border-top-left-radius: @radius;\n}\n.border-right-radius(@radius) {\n border-bottom-right-radius: @radius;\n border-top-right-radius: @radius;\n}\n.border-bottom-radius(@radius) {\n border-bottom-right-radius: @radius;\n border-bottom-left-radius: @radius;\n}\n.border-left-radius(@radius) {\n border-bottom-left-radius: @radius;\n border-top-left-radius: @radius;\n}\n\n// Drop shadows\n//\n// Note: Deprecated `.box-shadow()` as of v3.1.0 since all of Bootstrap's\n// supported browsers that have box shadow capabilities now support the\n// standard `box-shadow` property.\n.box-shadow(@shadow) {\n -webkit-box-shadow: @shadow; // iOS <4.3 & Android <4.1\n box-shadow: @shadow;\n}\n\n// Transitions\n.transition(@transition) {\n -webkit-transition: @transition;\n transition: @transition;\n}\n.transition-property(@transition-property) {\n -webkit-transition-property: @transition-property;\n transition-property: @transition-property;\n}\n.transition-delay(@transition-delay) {\n -webkit-transition-delay: @transition-delay;\n transition-delay: @transition-delay;\n}\n.transition-duration(@transition-duration) {\n -webkit-transition-duration: @transition-duration;\n transition-duration: @transition-duration;\n}\n.transition-transform(@transition) {\n -webkit-transition: -webkit-transform @transition;\n -moz-transition: -moz-transform @transition;\n -o-transition: -o-transform @transition;\n transition: transform @transition;\n}\n\n// Transformations\n.rotate(@degrees) {\n -webkit-transform: rotate(@degrees);\n -ms-transform: rotate(@degrees); // IE9 only\n transform: rotate(@degrees);\n}\n.scale(@ratio; @ratio-y...) {\n -webkit-transform: scale(@ratio, @ratio-y);\n -ms-transform: scale(@ratio, @ratio-y); // IE9 only\n transform: scale(@ratio, @ratio-y);\n}\n.translate(@x; @y) {\n -webkit-transform: translate(@x, @y);\n -ms-transform: translate(@x, @y); // IE9 only\n transform: translate(@x, @y);\n}\n.skew(@x; @y) {\n -webkit-transform: skew(@x, @y);\n -ms-transform: skewX(@x) skewY(@y); // See https://github.com/twbs/bootstrap/issues/4885; IE9+\n transform: skew(@x, @y);\n}\n.translate3d(@x; @y; @z) {\n -webkit-transform: translate3d(@x, @y, @z);\n transform: translate3d(@x, @y, @z);\n}\n\n.rotateX(@degrees) {\n -webkit-transform: rotateX(@degrees);\n -ms-transform: rotateX(@degrees); // IE9 only\n transform: rotateX(@degrees);\n}\n.rotateY(@degrees) {\n -webkit-transform: rotateY(@degrees);\n -ms-transform: rotateY(@degrees); // IE9 only\n transform: rotateY(@degrees);\n}\n.perspective(@perspective) {\n -webkit-perspective: @perspective;\n -moz-perspective: @perspective;\n perspective: @perspective;\n}\n.perspective-origin(@perspective) {\n -webkit-perspective-origin: @perspective;\n -moz-perspective-origin: @perspective;\n perspective-origin: @perspective;\n}\n.transform-origin(@origin) {\n -webkit-transform-origin: @origin;\n -moz-transform-origin: @origin;\n -ms-transform-origin: @origin; // IE9 only\n transform-origin: @origin;\n}\n\n// Animations\n.animation(@animation) {\n -webkit-animation: @animation;\n animation: @animation;\n}\n.animation-name(@name) {\n -webkit-animation-name: @name;\n animation-name: @name;\n}\n.animation-duration(@duration) {\n -webkit-animation-duration: @duration;\n animation-duration: @duration;\n}\n.animation-timing-function(@timing-function) {\n -webkit-animation-timing-function: @timing-function;\n animation-timing-function: @timing-function;\n}\n.animation-delay(@delay) {\n -webkit-animation-delay: @delay;\n animation-delay: @delay;\n}\n.animation-iteration-count(@iteration-count) {\n -webkit-animation-iteration-count: @iteration-count;\n animation-iteration-count: @iteration-count;\n}\n.animation-direction(@direction) {\n -webkit-animation-direction: @direction;\n animation-direction: @direction;\n}\n\n// Backface visibility\n// Prevent browsers from flickering when using CSS 3D transforms.\n// Default value is `visible`, but can be changed to `hidden`\n.backface-visibility(@visibility){\n -webkit-backface-visibility: @visibility;\n -moz-backface-visibility: @visibility;\n backface-visibility: @visibility;\n}\n\n// Box sizing\n.box-sizing(@boxmodel) {\n -webkit-box-sizing: @boxmodel;\n -moz-box-sizing: @boxmodel;\n box-sizing: @boxmodel;\n}\n\n// User select\n// For selecting text on the page\n.user-select(@select) {\n -webkit-user-select: @select;\n -moz-user-select: @select;\n -ms-user-select: @select; // IE10+\n -o-user-select: @select;\n user-select: @select;\n}\n\n// Resize anything\n.resizable(@direction) {\n resize: @direction; // Options: horizontal, vertical, both\n overflow: auto; // Safari fix\n}\n\n// CSS3 Content Columns\n.content-columns(@column-count; @column-gap: @grid-gutter-width) {\n -webkit-column-count: @column-count;\n -moz-column-count: @column-count;\n column-count: @column-count;\n -webkit-column-gap: @column-gap;\n -moz-column-gap: @column-gap;\n column-gap: @column-gap;\n}\n\n// Optional hyphenation\n.hyphens(@mode: auto) {\n word-wrap: break-word;\n -webkit-hyphens: @mode;\n -moz-hyphens: @mode;\n -ms-hyphens: @mode; // IE10+\n -o-hyphens: @mode;\n hyphens: @mode;\n}\n\n// Opacity\n.opacity(@opacity) {\n opacity: @opacity;\n // IE8 filter\n @opacity-ie: (@opacity * 100);\n filter: ~\"alpha(opacity=@{opacity-ie})\";\n}\n\n\n\n// GRADIENTS\n// --------------------------------------------------\n\n#gradient {\n\n // Horizontal gradient, from left to right\n //\n // Creates two color stops, start and end, by specifying a color and position for each color stop.\n // Color stops are not available in IE9 and below.\n .horizontal(@start-color: #555; @end-color: #333; @start-percent: 0%; @end-percent: 100%) {\n background-image: -webkit-linear-gradient(left, color-stop(@start-color @start-percent), color-stop(@end-color @end-percent)); // Safari 5.1-6, Chrome 10+\n background-image: linear-gradient(to right, @start-color @start-percent, @end-color @end-percent); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n background-repeat: repeat-x;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)\",argb(@start-color),argb(@end-color))); // IE9 and down\n }\n\n // Vertical gradient, from top to bottom\n //\n // Creates two color stops, start and end, by specifying a color and position for each color stop.\n // Color stops are not available in IE9 and below.\n .vertical(@start-color: #555; @end-color: #333; @start-percent: 0%; @end-percent: 100%) {\n background-image: -webkit-linear-gradient(top, @start-color @start-percent, @end-color @end-percent); // Safari 5.1-6, Chrome 10+\n background-image: linear-gradient(to bottom, @start-color @start-percent, @end-color @end-percent); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n background-repeat: repeat-x;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)\",argb(@start-color),argb(@end-color))); // IE9 and down\n }\n\n .directional(@start-color: #555; @end-color: #333; @deg: 45deg) {\n background-repeat: repeat-x;\n background-image: -webkit-linear-gradient(@deg, @start-color, @end-color); // Safari 5.1-6, Chrome 10+\n background-image: linear-gradient(@deg, @start-color, @end-color); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n }\n .horizontal-three-colors(@start-color: #00b3ee; @mid-color: #7a43b6; @color-stop: 50%; @end-color: #c3325f) {\n background-image: -webkit-linear-gradient(left, @start-color, @mid-color @color-stop, @end-color);\n background-image: linear-gradient(to right, @start-color, @mid-color @color-stop, @end-color);\n background-repeat: no-repeat;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)\",argb(@start-color),argb(@end-color))); // IE9 and down, gets no color-stop at all for proper fallback\n }\n .vertical-three-colors(@start-color: #00b3ee; @mid-color: #7a43b6; @color-stop: 50%; @end-color: #c3325f) {\n background-image: -webkit-linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-image: linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-repeat: no-repeat;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)\",argb(@start-color),argb(@end-color))); // IE9 and down, gets no color-stop at all for proper fallback\n }\n .radial(@inner-color: #555; @outer-color: #333) {\n background-image: -webkit-radial-gradient(circle, @inner-color, @outer-color);\n background-image: radial-gradient(circle, @inner-color, @outer-color);\n background-repeat: no-repeat;\n }\n .striped(@color: rgba(255,255,255,.15); @angle: 45deg) {\n background-image: -webkit-linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n background-image: linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n }\n}\n\n// Reset filters for IE\n//\n// When you need to remove a gradient background, do not forget to use this to reset\n// the IE filter for IE9 and below.\n.reset-filter() {\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(enabled = false)\"));\n}\n\n\n\n// Retina images\n//\n// Short retina mixin for setting background-image and -size\n\n.img-retina(@file-1x; @file-2x; @width-1x; @height-1x) {\n background-image: url(\"@{file-1x}\");\n\n @media\n only screen and (-webkit-min-device-pixel-ratio: 2),\n only screen and ( min--moz-device-pixel-ratio: 2),\n only screen and ( -o-min-device-pixel-ratio: 2/1),\n only screen and ( min-device-pixel-ratio: 2),\n only screen and ( min-resolution: 192dpi),\n only screen and ( min-resolution: 2dppx) {\n background-image: url(\"@{file-2x}\");\n background-size: @width-1x @height-1x;\n }\n}\n\n\n// Responsive image\n//\n// Keep images from scaling beyond the width of their parents.\n\n.img-responsive(@display: block) {\n display: @display;\n max-width: 100%; // Part 1: Set a maximum relative to the parent\n height: auto; // Part 2: Scale the height according to the width, otherwise you get stretching\n}\n\n\n// COMPONENT MIXINS\n// --------------------------------------------------\n\n// Horizontal dividers\n// -------------------------\n// Dividers (basically an hr) within dropdowns and nav lists\n.nav-divider(@color: #e5e5e5) {\n height: 1px;\n margin: ((@line-height-computed / 2) - 1) 0;\n overflow: hidden;\n background-color: @color;\n}\n\n// Panels\n// -------------------------\n.panel-variant(@border; @heading-text-color; @heading-bg-color; @heading-border) {\n border-color: @border;\n\n & > .panel-heading {\n color: @heading-text-color;\n background-color: @heading-bg-color;\n border-color: @heading-border;\n\n + .panel-collapse .panel-body {\n border-top-color: @border;\n }\n }\n & > .panel-footer {\n + .panel-collapse .panel-body {\n border-bottom-color: @border;\n }\n }\n}\n\n// Alerts\n// -------------------------\n.alert-variant(@background; @border; @text-color) {\n background-color: @background;\n border-color: @border;\n color: @text-color;\n\n hr {\n border-top-color: darken(@border, 5%);\n }\n .alert-link {\n color: darken(@text-color, 10%);\n }\n}\n\n// Tables\n// -------------------------\n.table-row-variant(@state; @background) {\n // Exact selectors below required to override `.table-striped` and prevent\n // inheritance to nested tables.\n .table > thead > tr,\n .table > tbody > tr,\n .table > tfoot > tr {\n > td.@{state},\n > th.@{state},\n &.@{state} > td,\n &.@{state} > th {\n background-color: @background;\n }\n }\n\n // Hover states for `.table-hover`\n // Note: this is not available for cells or rows within `thead` or `tfoot`.\n .table-hover > tbody > tr {\n > td.@{state}:hover,\n > th.@{state}:hover,\n &.@{state}:hover > td,\n &.@{state}:hover > th {\n background-color: darken(@background, 5%);\n }\n }\n}\n\n// List Groups\n// -------------------------\n.list-group-item-variant(@state; @background; @color) {\n .list-group-item-@{state} {\n color: @color;\n background-color: @background;\n\n a& {\n color: @color;\n\n .list-group-item-heading { color: inherit; }\n\n &:hover,\n &:focus {\n color: @color;\n background-color: darken(@background, 5%);\n }\n &.active,\n &.active:hover,\n &.active:focus {\n color: #fff;\n background-color: @color;\n border-color: @color;\n }\n }\n }\n}\n\n// Button variants\n// -------------------------\n// Easily pump out default styles, as well as :hover, :focus, :active,\n// and disabled options for all buttons\n.button-variant(@color; @background; @border) {\n color: @color;\n background-color: @background;\n border-color: @border;\n\n &:hover,\n &:focus,\n &:active,\n &.active,\n .open .dropdown-toggle& {\n color: @color;\n background-color: darken(@background, 8%);\n border-color: darken(@border, 12%);\n }\n &:active,\n &.active,\n .open .dropdown-toggle& {\n background-image: none;\n }\n &.disabled,\n &[disabled],\n fieldset[disabled] & {\n &,\n &:hover,\n &:focus,\n &:active,\n &.active {\n background-color: @background;\n border-color: @border;\n }\n }\n\n .badge {\n color: @background;\n background-color: @color;\n }\n}\n\n// Button sizes\n// -------------------------\n.button-size(@padding-vertical; @padding-horizontal; @font-size; @line-height; @border-radius) {\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n line-height: @line-height;\n border-radius: @border-radius;\n}\n\n// Pagination\n// -------------------------\n.pagination-size(@padding-vertical; @padding-horizontal; @font-size; @border-radius) {\n > li {\n > a,\n > span {\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n }\n &:first-child {\n > a,\n > span {\n .border-left-radius(@border-radius);\n }\n }\n &:last-child {\n > a,\n > span {\n .border-right-radius(@border-radius);\n }\n }\n }\n}\n\n// Labels\n// -------------------------\n.label-variant(@color) {\n background-color: @color;\n &[href] {\n &:hover,\n &:focus {\n background-color: darken(@color, 10%);\n }\n }\n}\n\n// Contextual backgrounds\n// -------------------------\n.bg-variant(@color) {\n background-color: @color;\n a&:hover {\n background-color: darken(@color, 10%);\n }\n}\n\n// Typography\n// -------------------------\n.text-emphasis-variant(@color) {\n color: @color;\n a&:hover {\n color: darken(@color, 10%);\n }\n}\n\n// Navbar vertical align\n// -------------------------\n// Vertically center elements in the navbar.\n// Example: an element has a height of 30px, so write out `.navbar-vertical-align(30px);` to calculate the appropriate top margin.\n.navbar-vertical-align(@element-height) {\n margin-top: ((@navbar-height - @element-height) / 2);\n margin-bottom: ((@navbar-height - @element-height) / 2);\n}\n\n// Progress bars\n// -------------------------\n.progress-bar-variant(@color) {\n background-color: @color;\n .progress-striped & {\n #gradient > .striped();\n }\n}\n\n// Responsive utilities\n// -------------------------\n// More easily include all the states for responsive-utilities.less.\n.responsive-visibility() {\n display: block !important;\n table& { display: table; }\n tr& { display: table-row !important; }\n th&,\n td& { display: table-cell !important; }\n}\n\n.responsive-invisibility() {\n &,\n tr&,\n th&,\n td& { display: none !important; }\n}\n\n\n// Grid System\n// -----------\n\n// Centered container element\n.container-fixed() {\n margin-right: auto;\n margin-left: auto;\n padding-left: (@grid-gutter-width / 2);\n padding-right: (@grid-gutter-width / 2);\n &:extend(.clearfix all);\n}\n\n// Creates a wrapper for a series of columns\n.make-row(@gutter: @grid-gutter-width) {\n margin-left: (@gutter / -2);\n margin-right: (@gutter / -2);\n &:extend(.clearfix all);\n}\n\n// Generate the extra small columns\n.make-xs-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n float: left;\n width: percentage((@columns / @grid-columns));\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n}\n.make-xs-column-offset(@columns) {\n @media (min-width: @screen-xs-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-xs-column-push(@columns) {\n @media (min-width: @screen-xs-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-xs-column-pull(@columns) {\n @media (min-width: @screen-xs-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n\n// Generate the small columns\n.make-sm-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-sm-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-offset(@columns) {\n @media (min-width: @screen-sm-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-push(@columns) {\n @media (min-width: @screen-sm-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-pull(@columns) {\n @media (min-width: @screen-sm-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n\n// Generate the medium columns\n.make-md-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-md-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-offset(@columns) {\n @media (min-width: @screen-md-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-push(@columns) {\n @media (min-width: @screen-md-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-pull(@columns) {\n @media (min-width: @screen-md-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n\n// Generate the large columns\n.make-lg-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-lg-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-offset(@columns) {\n @media (min-width: @screen-lg-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-push(@columns) {\n @media (min-width: @screen-lg-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-pull(@columns) {\n @media (min-width: @screen-lg-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n\n// Framework grid generation\n//\n// Used only by Bootstrap to generate the correct number of grid classes given\n// any value of `@grid-columns`.\n\n.make-grid-columns() {\n // Common styles for all sizes of grid columns, widths 1-12\n .col(@index) when (@index = 1) { // initial\n @item: ~\".col-xs-@{index}, .col-sm-@{index}, .col-md-@{index}, .col-lg-@{index}\";\n .col((@index + 1), @item);\n }\n .col(@index, @list) when (@index =< @grid-columns) { // general; \"=<\" isn't a typo\n @item: ~\".col-xs-@{index}, .col-sm-@{index}, .col-md-@{index}, .col-lg-@{index}\";\n .col((@index + 1), ~\"@{list}, @{item}\");\n }\n .col(@index, @list) when (@index > @grid-columns) { // terminal\n @{list} {\n position: relative;\n // Prevent columns from collapsing when empty\n min-height: 1px;\n // Inner gutter via padding\n padding-left: (@grid-gutter-width / 2);\n padding-right: (@grid-gutter-width / 2);\n }\n }\n .col(1); // kickstart it\n}\n\n.make-grid-columns-float(@class) {\n .col(@index) when (@index = 1) { // initial\n @item: ~\".col-@{class}-@{index}\";\n .col((@index + 1), @item);\n }\n .col(@index, @list) when (@index =< @grid-columns) { // general\n @item: ~\".col-@{class}-@{index}\";\n .col((@index + 1), ~\"@{list}, @{item}\");\n }\n .col(@index, @list) when (@index > @grid-columns) { // terminal\n @{list} {\n float: left;\n }\n }\n .col(1); // kickstart it\n}\n\n.calc-grid(@index, @class, @type) when (@type = width) and (@index > 0) {\n .col-@{class}-@{index} {\n width: percentage((@index / @grid-columns));\n }\n}\n.calc-grid(@index, @class, @type) when (@type = push) {\n .col-@{class}-push-@{index} {\n left: percentage((@index / @grid-columns));\n }\n}\n.calc-grid(@index, @class, @type) when (@type = pull) {\n .col-@{class}-pull-@{index} {\n right: percentage((@index / @grid-columns));\n }\n}\n.calc-grid(@index, @class, @type) when (@type = offset) {\n .col-@{class}-offset-@{index} {\n margin-left: percentage((@index / @grid-columns));\n }\n}\n\n// Basic looping in LESS\n.make-grid(@index, @class, @type) when (@index >= 0) {\n .calc-grid(@index, @class, @type);\n // next iteration\n .make-grid((@index - 1), @class, @type);\n}\n\n\n// Form validation states\n//\n// Used in forms.less to generate the form validation CSS for warnings, errors,\n// and successes.\n\n.form-control-validation(@text-color: #555; @border-color: #ccc; @background-color: #f5f5f5) {\n // Color the label and help text\n .help-block,\n .control-label,\n .radio,\n .checkbox,\n .radio-inline,\n .checkbox-inline {\n color: @text-color;\n }\n // Set the border and box shadow on specific inputs to match\n .form-control {\n border-color: @border-color;\n .box-shadow(inset 0 1px 1px rgba(0,0,0,.075)); // Redeclare so transitions work\n &:focus {\n border-color: darken(@border-color, 10%);\n @shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 6px lighten(@border-color, 20%);\n .box-shadow(@shadow);\n }\n }\n // Set validation states also for addons\n .input-group-addon {\n color: @text-color;\n border-color: @border-color;\n background-color: @background-color;\n }\n // Optional feedback icon\n .form-control-feedback {\n color: @text-color;\n }\n}\n\n// Form control focus state\n//\n// Generate a customized focus state and for any input with the specified color,\n// which defaults to the `@input-focus-border` variable.\n//\n// We highly encourage you to not customize the default value, but instead use\n// this to tweak colors on an as-needed basis. This aesthetic change is based on\n// WebKit's default styles, but applicable to a wider range of browsers. Its\n// usability and accessibility should be taken into account with any change.\n//\n// Example usage: change the default blue border and shadow to white for better\n// contrast against a dark gray background.\n\n.form-control-focus(@color: @input-border-focus) {\n @color-rgba: rgba(red(@color), green(@color), blue(@color), .6);\n &:focus {\n border-color: @color;\n outline: 0;\n .box-shadow(~\"inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px @{color-rgba}\");\n }\n}\n\n// Form control sizing\n//\n// Relative text size, padding, and border-radii changes for form controls. For\n// horizontal sizing, wrap controls in the predefined grid classes. `<select>`\n// element gets special love because it's special, and that's a fact!\n\n.input-size(@input-height; @padding-vertical; @padding-horizontal; @font-size; @line-height; @border-radius) {\n height: @input-height;\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n line-height: @line-height;\n border-radius: @border-radius;\n\n select& {\n height: @input-height;\n line-height: @input-height;\n }\n\n textarea&,\n select[multiple]& {\n height: auto;\n }\n}\n"]}
\ No newline at end of file
--- /dev/null
+/*!
+ * Bootstrap v3.1.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+.btn-default,.btn-primary,.btn-success,.btn-info,.btn-warning,.btn-danger{text-shadow:0 -1px 0 rgba(0,0,0,.2);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075)}.btn-default:active,.btn-primary:active,.btn-success:active,.btn-info:active,.btn-warning:active,.btn-danger:active,.btn-default.active,.btn-primary.active,.btn-success.active,.btn-info.active,.btn-warning.active,.btn-danger.active{-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,.125);box-shadow:inset 0 3px 5px rgba(0,0,0,.125)}.btn:active,.btn.active{background-image:none}.btn-default{background-image:-webkit-linear-gradient(top,#fff 0,#e0e0e0 100%);background-image:linear-gradient(to bottom,#fff 0,#e0e0e0 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe0e0e0', 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\ No newline at end of file
--- /dev/null
+/*!
+ * Bootstrap v3.1.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+/*! normalize.css v3.0.0 | MIT License | git.io/normalize */
+html {
+ font-family: sans-serif;
+ -webkit-text-size-adjust: 100%;
+ -ms-text-size-adjust: 100%;
+}
+body {
+ margin: 0;
+}
+article,
+aside,
+details,
+figcaption,
+figure,
+footer,
+header,
+hgroup,
+main,
+nav,
+section,
+summary {
+ display: block;
+}
+audio,
+canvas,
+progress,
+video {
+ display: inline-block;
+ vertical-align: baseline;
+}
+audio:not([controls]) {
+ display: none;
+ height: 0;
+}
+[hidden],
+template {
+ display: none;
+}
+a {
+ background: transparent;
+}
+a:active,
+a:hover {
+ outline: 0;
+}
+abbr[title] {
+ border-bottom: 1px dotted;
+}
+b,
+strong {
+ font-weight: bold;
+}
+dfn {
+ font-style: italic;
+}
+h1 {
+ margin: .67em 0;
+ font-size: 2em;
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+mark {
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+ background: #ff0;
+}
+small {
+ font-size: 80%;
+}
+sub,
+sup {
+ position: relative;
+ font-size: 75%;
+ line-height: 0;
+ vertical-align: baseline;
+}
+sup {
+ top: -.5em;
+}
+sub {
+ bottom: -.25em;
+}
+img {
+ border: 0;
+}
+svg:not(:root) {
+ overflow: hidden;
+}
+figure {
+ margin: 1em 40px;
+}
+hr {
+ height: 0;
+ -moz-box-sizing: content-box;
+ box-sizing: content-box;
+}
+pre {
+ overflow: auto;
+}
+code,
+kbd,
+pre,
+samp {
+ font-family: monospace, monospace;
+ font-size: 1em;
+}
+button,
+input,
+optgroup,
+select,
+textarea {
+ margin: 0;
+ font: inherit;
+ color: inherit;
+}
+button {
+ overflow: visible;
+}
+button,
+select {
+ text-transform: none;
+}
+button,
+html input[type="button"],
+input[type="reset"],
+input[type="submit"] {
+ -webkit-appearance: button;
+ cursor: pointer;
+}
+button[disabled],
+html input[disabled] {
+ cursor: default;
+}
+button::-moz-focus-inner,
+input::-moz-focus-inner {
+ padding: 0;
+ border: 0;
+}
+input {
+ line-height: normal;
+}
+input[type="checkbox"],
+input[type="radio"] {
+ box-sizing: border-box;
+ padding: 0;
+}
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+input[type="number"]::-webkit-outer-spin-button {
+ height: auto;
+}
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+ -moz-box-sizing: content-box;
+ box-sizing: content-box;
+ -webkit-appearance: textfield;
+}
+input[type="search"]::-webkit-search-cancel-button,
+input[type="search"]::-webkit-search-decoration {
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+}
+fieldset {
+ padding: .35em .625em .75em;
+ margin: 0 2px;
+ border: 1px solid #c0c0c0;
+}
+legend {
+ padding: 0;
+ border: 0;
+}
+textarea {
+ overflow: auto;
+}
+optgroup {
+ font-weight: bold;
+}
+table {
+ border-spacing: 0;
+ border-collapse: collapse;
+}
+td,
+th {
+ padding: 0;
+}
+@media print {
+ * {
+ color: #000 !important;
+ text-shadow: none !important;
+ background: transparent !important;
+ box-shadow: none !important;
+ }
+ a,
+ a:visited {
+ text-decoration: underline;
+ }
+ a[href]:after {
+ content: " (" attr(href) ")";
+ }
+ abbr[title]:after {
+ content: " (" attr(title) ")";
+ }
+ a[href^="javascript:"]:after,
+ a[href^="#"]:after {
+ content: "";
+ }
+ pre,
+ blockquote {
+ border: 1px solid #999;
+
+ page-break-inside: avoid;
+ }
+ thead {
+ display: table-header-group;
+ }
+ tr,
+ img {
+ page-break-inside: avoid;
+ }
+ img {
+ max-width: 100% !important;
+ }
+ p,
+ h2,
+ h3 {
+ orphans: 3;
+ widows: 3;
+ }
+ h2,
+ h3 {
+ page-break-after: avoid;
+ }
+ select {
+ background: #fff !important;
+ }
+ .navbar {
+ display: none;
+ }
+ .table td,
+ .table th {
+ background-color: #fff !important;
+ }
+ .btn > .caret,
+ .dropup > .btn > .caret {
+ border-top-color: #000 !important;
+ }
+ .label {
+ border: 1px solid #000;
+ }
+ .table {
+ border-collapse: collapse !important;
+ }
+ .table-bordered th,
+ .table-bordered td {
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+ }
+}
+* {
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+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+*:before,
+*:after {
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+html {
+ font-size: 62.5%;
+
+ -webkit-tap-highlight-color: rgba(0, 0, 0, 0);
+}
+body {
+ font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
+ font-size: 14px;
+ line-height: 1.428571429;
+ color: #333;
+ background-color: #fff;
+}
+input,
+button,
+select,
+textarea {
+ font-family: inherit;
+ font-size: inherit;
+ line-height: inherit;
+}
+a {
+ color: #428bca;
+ text-decoration: none;
+}
+a:hover,
+a:focus {
+ color: #2a6496;
+ text-decoration: underline;
+}
+a:focus {
+ outline: thin dotted;
+ outline: 5px auto -webkit-focus-ring-color;
+ outline-offset: -2px;
+}
+figure {
+ margin: 0;
+}
+img {
+ vertical-align: middle;
+}
+.img-responsive {
+ display: block;
+ max-width: 100%;
+ height: auto;
+}
+.img-rounded {
+ border-radius: 6px;
+}
+.img-thumbnail {
+ display: inline-block;
+ max-width: 100%;
+ height: auto;
+ padding: 4px;
+ line-height: 1.428571429;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ border-radius: 4px;
+ -webkit-transition: all .2s ease-in-out;
+ transition: all .2s ease-in-out;
+}
+.img-circle {
+ border-radius: 50%;
+}
+hr {
+ margin-top: 20px;
+ margin-bottom: 20px;
+ border: 0;
+ border-top: 1px solid #eee;
+}
+.sr-only {
+ position: absolute;
+ width: 1px;
+ height: 1px;
+ padding: 0;
+ margin: -1px;
+ overflow: hidden;
+ clip: rect(0, 0, 0, 0);
+ border: 0;
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+h1,
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+ font-family: inherit;
+ font-weight: 500;
+ line-height: 1.1;
+ color: inherit;
+}
+h1 small,
+h2 small,
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+h6 small,
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+ color: #999;
+}
+h1,
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+h2,
+.h2,
+h3,
+.h3 {
+ margin-top: 20px;
+ margin-bottom: 10px;
+}
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+h1 .small,
+.h1 .small,
+h2 .small,
+.h2 .small,
+h3 .small,
+.h3 .small {
+ font-size: 65%;
+}
+h4,
+.h4,
+h5,
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+h6,
+.h6 {
+ margin-top: 10px;
+ margin-bottom: 10px;
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+h4 small,
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+.h4 .small,
+h5 .small,
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+h6 .small,
+.h6 .small {
+ font-size: 75%;
+}
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+.h1 {
+ font-size: 36px;
+}
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+ font-size: 30px;
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+ font-size: 24px;
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+p {
+ margin: 0 0 10px;
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+ margin-bottom: 20px;
+ font-size: 16px;
+ font-weight: 200;
+ line-height: 1.4;
+}
+@media (min-width: 768px) {
+ .lead {
+ font-size: 21px;
+ }
+}
+small,
+.small {
+ font-size: 85%;
+}
+cite {
+ font-style: normal;
+}
+.text-left {
+ text-align: left;
+}
+.text-right {
+ text-align: right;
+}
+.text-center {
+ text-align: center;
+}
+.text-justify {
+ text-align: justify;
+}
+.text-muted {
+ color: #999;
+}
+.text-primary {
+ color: #428bca;
+}
+a.text-primary:hover {
+ color: #3071a9;
+}
+.text-success {
+ color: #3c763d;
+}
+a.text-success:hover {
+ color: #2b542c;
+}
+.text-info {
+ color: #31708f;
+}
+a.text-info:hover {
+ color: #245269;
+}
+.text-warning {
+ color: #8a6d3b;
+}
+a.text-warning:hover {
+ color: #66512c;
+}
+.text-danger {
+ color: #a94442;
+}
+a.text-danger:hover {
+ color: #843534;
+}
+.bg-primary {
+ color: #fff;
+ background-color: #428bca;
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+a.bg-primary:hover {
+ background-color: #3071a9;
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+ background-color: #dff0d8;
+}
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+ background-color: #c1e2b3;
+}
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+ background-color: #d9edf7;
+}
+a.bg-info:hover {
+ background-color: #afd9ee;
+}
+.bg-warning {
+ background-color: #fcf8e3;
+}
+a.bg-warning:hover {
+ background-color: #f7ecb5;
+}
+.bg-danger {
+ background-color: #f2dede;
+}
+a.bg-danger:hover {
+ background-color: #e4b9b9;
+}
+.page-header {
+ padding-bottom: 9px;
+ margin: 40px 0 20px;
+ border-bottom: 1px solid #eee;
+}
+ul,
+ol {
+ margin-top: 0;
+ margin-bottom: 10px;
+}
+ul ul,
+ol ul,
+ul ol,
+ol ol {
+ margin-bottom: 0;
+}
+.list-unstyled {
+ padding-left: 0;
+ list-style: none;
+}
+.list-inline {
+ padding-left: 0;
+ list-style: none;
+}
+.list-inline > li {
+ display: inline-block;
+ padding-right: 5px;
+ padding-left: 5px;
+}
+.list-inline > li:first-child {
+ padding-left: 0;
+}
+dl {
+ margin-top: 0;
+ margin-bottom: 20px;
+}
+dt,
+dd {
+ line-height: 1.428571429;
+}
+dt {
+ font-weight: bold;
+}
+dd {
+ margin-left: 0;
+}
+@media (min-width: 768px) {
+ .dl-horizontal dt {
+ float: left;
+ width: 160px;
+ overflow: hidden;
+ clear: left;
+ text-align: right;
+ text-overflow: ellipsis;
+ white-space: nowrap;
+ }
+ .dl-horizontal dd {
+ margin-left: 180px;
+ }
+}
+abbr[title],
+abbr[data-original-title] {
+ cursor: help;
+ border-bottom: 1px dotted #999;
+}
+.initialism {
+ font-size: 90%;
+ text-transform: uppercase;
+}
+blockquote {
+ padding: 10px 20px;
+ margin: 0 0 20px;
+ font-size: 17.5px;
+ border-left: 5px solid #eee;
+}
+blockquote p:last-child,
+blockquote ul:last-child,
+blockquote ol:last-child {
+ margin-bottom: 0;
+}
+blockquote footer,
+blockquote small,
+blockquote .small {
+ display: block;
+ font-size: 80%;
+ line-height: 1.428571429;
+ color: #999;
+}
+blockquote footer:before,
+blockquote small:before,
+blockquote .small:before {
+ content: '\2014 \00A0';
+}
+.blockquote-reverse,
+blockquote.pull-right {
+ padding-right: 15px;
+ padding-left: 0;
+ text-align: right;
+ border-right: 5px solid #eee;
+ border-left: 0;
+}
+.blockquote-reverse footer:before,
+blockquote.pull-right footer:before,
+.blockquote-reverse small:before,
+blockquote.pull-right small:before,
+.blockquote-reverse .small:before,
+blockquote.pull-right .small:before {
+ content: '';
+}
+.blockquote-reverse footer:after,
+blockquote.pull-right footer:after,
+.blockquote-reverse small:after,
+blockquote.pull-right small:after,
+.blockquote-reverse .small:after,
+blockquote.pull-right .small:after {
+ content: '\00A0 \2014';
+}
+blockquote:before,
+blockquote:after {
+ content: "";
+}
+address {
+ margin-bottom: 20px;
+ font-style: normal;
+ line-height: 1.428571429;
+}
+code,
+kbd,
+pre,
+samp {
+ font-family: Menlo, Monaco, Consolas, "Courier New", monospace;
+}
+code {
+ padding: 2px 4px;
+ font-size: 90%;
+ color: #c7254e;
+ white-space: nowrap;
+ background-color: #f9f2f4;
+ border-radius: 4px;
+}
+kbd {
+ padding: 2px 4px;
+ font-size: 90%;
+ color: #fff;
+ background-color: #333;
+ border-radius: 3px;
+ box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .25);
+}
+pre {
+ display: block;
+ padding: 9.5px;
+ margin: 0 0 10px;
+ font-size: 13px;
+ line-height: 1.428571429;
+ color: #333;
+ word-break: break-all;
+ word-wrap: break-word;
+ background-color: #f5f5f5;
+ border: 1px solid #ccc;
+ border-radius: 4px;
+}
+pre code {
+ padding: 0;
+ font-size: inherit;
+ color: inherit;
+ white-space: pre-wrap;
+ background-color: transparent;
+ border-radius: 0;
+}
+.pre-scrollable {
+ max-height: 340px;
+ overflow-y: scroll;
+}
+.container {
+ padding-right: 15px;
+ padding-left: 15px;
+ margin-right: auto;
+ margin-left: auto;
+}
+@media (min-width: 768px) {
+ .container {
+ width: 750px;
+ }
+}
+@media (min-width: 992px) {
+ .container {
+ width: 970px;
+ }
+}
+@media (min-width: 1200px) {
+ .container {
+ width: 1170px;
+ }
+}
+.container-fluid {
+ padding-right: 15px;
+ padding-left: 15px;
+ margin-right: auto;
+ margin-left: auto;
+}
+.row {
+ margin-right: -15px;
+ margin-left: -15px;
+}
+.col-xs-1, .col-sm-1, .col-md-1, .col-lg-1, .col-xs-2, .col-sm-2, .col-md-2, .col-lg-2, .col-xs-3, .col-sm-3, .col-md-3, .col-lg-3, .col-xs-4, .col-sm-4, .col-md-4, .col-lg-4, .col-xs-5, .col-sm-5, .col-md-5, .col-lg-5, .col-xs-6, .col-sm-6, .col-md-6, .col-lg-6, .col-xs-7, .col-sm-7, .col-md-7, .col-lg-7, .col-xs-8, .col-sm-8, .col-md-8, .col-lg-8, .col-xs-9, .col-sm-9, .col-md-9, .col-lg-9, .col-xs-10, .col-sm-10, .col-md-10, .col-lg-10, .col-xs-11, .col-sm-11, .col-md-11, .col-lg-11, .col-xs-12, .col-sm-12, .col-md-12, .col-lg-12 {
+ position: relative;
+ min-height: 1px;
+ padding-right: 15px;
+ padding-left: 15px;
+}
+.col-xs-1, .col-xs-2, .col-xs-3, .col-xs-4, .col-xs-5, .col-xs-6, .col-xs-7, .col-xs-8, .col-xs-9, .col-xs-10, .col-xs-11, .col-xs-12 {
+ float: left;
+}
+.col-xs-12 {
+ width: 100%;
+}
+.col-xs-11 {
+ width: 91.66666666666666%;
+}
+.col-xs-10 {
+ width: 83.33333333333334%;
+}
+.col-xs-9 {
+ width: 75%;
+}
+.col-xs-8 {
+ width: 66.66666666666666%;
+}
+.col-xs-7 {
+ width: 58.333333333333336%;
+}
+.col-xs-6 {
+ width: 50%;
+}
+.col-xs-5 {
+ width: 41.66666666666667%;
+}
+.col-xs-4 {
+ width: 33.33333333333333%;
+}
+.col-xs-3 {
+ width: 25%;
+}
+.col-xs-2 {
+ width: 16.666666666666664%;
+}
+.col-xs-1 {
+ width: 8.333333333333332%;
+}
+.col-xs-pull-12 {
+ right: 100%;
+}
+.col-xs-pull-11 {
+ right: 91.66666666666666%;
+}
+.col-xs-pull-10 {
+ right: 83.33333333333334%;
+}
+.col-xs-pull-9 {
+ right: 75%;
+}
+.col-xs-pull-8 {
+ right: 66.66666666666666%;
+}
+.col-xs-pull-7 {
+ right: 58.333333333333336%;
+}
+.col-xs-pull-6 {
+ right: 50%;
+}
+.col-xs-pull-5 {
+ right: 41.66666666666667%;
+}
+.col-xs-pull-4 {
+ right: 33.33333333333333%;
+}
+.col-xs-pull-3 {
+ right: 25%;
+}
+.col-xs-pull-2 {
+ right: 16.666666666666664%;
+}
+.col-xs-pull-1 {
+ right: 8.333333333333332%;
+}
+.col-xs-pull-0 {
+ right: 0;
+}
+.col-xs-push-12 {
+ left: 100%;
+}
+.col-xs-push-11 {
+ left: 91.66666666666666%;
+}
+.col-xs-push-10 {
+ left: 83.33333333333334%;
+}
+.col-xs-push-9 {
+ left: 75%;
+}
+.col-xs-push-8 {
+ left: 66.66666666666666%;
+}
+.col-xs-push-7 {
+ left: 58.333333333333336%;
+}
+.col-xs-push-6 {
+ left: 50%;
+}
+.col-xs-push-5 {
+ left: 41.66666666666667%;
+}
+.col-xs-push-4 {
+ left: 33.33333333333333%;
+}
+.col-xs-push-3 {
+ left: 25%;
+}
+.col-xs-push-2 {
+ left: 16.666666666666664%;
+}
+.col-xs-push-1 {
+ left: 8.333333333333332%;
+}
+.col-xs-push-0 {
+ left: 0;
+}
+.col-xs-offset-12 {
+ margin-left: 100%;
+}
+.col-xs-offset-11 {
+ margin-left: 91.66666666666666%;
+}
+.col-xs-offset-10 {
+ margin-left: 83.33333333333334%;
+}
+.col-xs-offset-9 {
+ margin-left: 75%;
+}
+.col-xs-offset-8 {
+ margin-left: 66.66666666666666%;
+}
+.col-xs-offset-7 {
+ margin-left: 58.333333333333336%;
+}
+.col-xs-offset-6 {
+ margin-left: 50%;
+}
+.col-xs-offset-5 {
+ margin-left: 41.66666666666667%;
+}
+.col-xs-offset-4 {
+ margin-left: 33.33333333333333%;
+}
+.col-xs-offset-3 {
+ margin-left: 25%;
+}
+.col-xs-offset-2 {
+ margin-left: 16.666666666666664%;
+}
+.col-xs-offset-1 {
+ margin-left: 8.333333333333332%;
+}
+.col-xs-offset-0 {
+ margin-left: 0;
+}
+@media (min-width: 768px) {
+ .col-sm-1, .col-sm-2, .col-sm-3, .col-sm-4, .col-sm-5, .col-sm-6, .col-sm-7, .col-sm-8, .col-sm-9, .col-sm-10, .col-sm-11, .col-sm-12 {
+ float: left;
+ }
+ .col-sm-12 {
+ width: 100%;
+ }
+ .col-sm-11 {
+ width: 91.66666666666666%;
+ }
+ .col-sm-10 {
+ width: 83.33333333333334%;
+ }
+ .col-sm-9 {
+ width: 75%;
+ }
+ .col-sm-8 {
+ width: 66.66666666666666%;
+ }
+ .col-sm-7 {
+ width: 58.333333333333336%;
+ }
+ .col-sm-6 {
+ width: 50%;
+ }
+ .col-sm-5 {
+ width: 41.66666666666667%;
+ }
+ .col-sm-4 {
+ width: 33.33333333333333%;
+ }
+ .col-sm-3 {
+ width: 25%;
+ }
+ .col-sm-2 {
+ width: 16.666666666666664%;
+ }
+ .col-sm-1 {
+ width: 8.333333333333332%;
+ }
+ .col-sm-pull-12 {
+ right: 100%;
+ }
+ .col-sm-pull-11 {
+ right: 91.66666666666666%;
+ }
+ .col-sm-pull-10 {
+ right: 83.33333333333334%;
+ }
+ .col-sm-pull-9 {
+ right: 75%;
+ }
+ .col-sm-pull-8 {
+ right: 66.66666666666666%;
+ }
+ .col-sm-pull-7 {
+ right: 58.333333333333336%;
+ }
+ .col-sm-pull-6 {
+ right: 50%;
+ }
+ .col-sm-pull-5 {
+ right: 41.66666666666667%;
+ }
+ .col-sm-pull-4 {
+ right: 33.33333333333333%;
+ }
+ .col-sm-pull-3 {
+ right: 25%;
+ }
+ .col-sm-pull-2 {
+ right: 16.666666666666664%;
+ }
+ .col-sm-pull-1 {
+ right: 8.333333333333332%;
+ }
+ .col-sm-pull-0 {
+ right: 0;
+ }
+ .col-sm-push-12 {
+ left: 100%;
+ }
+ .col-sm-push-11 {
+ left: 91.66666666666666%;
+ }
+ .col-sm-push-10 {
+ left: 83.33333333333334%;
+ }
+ .col-sm-push-9 {
+ left: 75%;
+ }
+ .col-sm-push-8 {
+ left: 66.66666666666666%;
+ }
+ .col-sm-push-7 {
+ left: 58.333333333333336%;
+ }
+ .col-sm-push-6 {
+ left: 50%;
+ }
+ .col-sm-push-5 {
+ left: 41.66666666666667%;
+ }
+ .col-sm-push-4 {
+ left: 33.33333333333333%;
+ }
+ .col-sm-push-3 {
+ left: 25%;
+ }
+ .col-sm-push-2 {
+ left: 16.666666666666664%;
+ }
+ .col-sm-push-1 {
+ left: 8.333333333333332%;
+ }
+ .col-sm-push-0 {
+ left: 0;
+ }
+ .col-sm-offset-12 {
+ margin-left: 100%;
+ }
+ .col-sm-offset-11 {
+ margin-left: 91.66666666666666%;
+ }
+ .col-sm-offset-10 {
+ margin-left: 83.33333333333334%;
+ }
+ .col-sm-offset-9 {
+ margin-left: 75%;
+ }
+ .col-sm-offset-8 {
+ margin-left: 66.66666666666666%;
+ }
+ .col-sm-offset-7 {
+ margin-left: 58.333333333333336%;
+ }
+ .col-sm-offset-6 {
+ margin-left: 50%;
+ }
+ .col-sm-offset-5 {
+ margin-left: 41.66666666666667%;
+ }
+ .col-sm-offset-4 {
+ margin-left: 33.33333333333333%;
+ }
+ .col-sm-offset-3 {
+ margin-left: 25%;
+ }
+ .col-sm-offset-2 {
+ margin-left: 16.666666666666664%;
+ }
+ .col-sm-offset-1 {
+ margin-left: 8.333333333333332%;
+ }
+ .col-sm-offset-0 {
+ margin-left: 0;
+ }
+}
+@media (min-width: 992px) {
+ .col-md-1, .col-md-2, .col-md-3, .col-md-4, .col-md-5, .col-md-6, .col-md-7, .col-md-8, .col-md-9, .col-md-10, .col-md-11, .col-md-12 {
+ float: left;
+ }
+ .col-md-12 {
+ width: 100%;
+ }
+ .col-md-11 {
+ width: 91.66666666666666%;
+ }
+ .col-md-10 {
+ width: 83.33333333333334%;
+ }
+ .col-md-9 {
+ width: 75%;
+ }
+ .col-md-8 {
+ width: 66.66666666666666%;
+ }
+ .col-md-7 {
+ width: 58.333333333333336%;
+ }
+ .col-md-6 {
+ width: 50%;
+ }
+ .col-md-5 {
+ width: 41.66666666666667%;
+ }
+ .col-md-4 {
+ width: 33.33333333333333%;
+ }
+ .col-md-3 {
+ width: 25%;
+ }
+ .col-md-2 {
+ width: 16.666666666666664%;
+ }
+ .col-md-1 {
+ width: 8.333333333333332%;
+ }
+ .col-md-pull-12 {
+ right: 100%;
+ }
+ .col-md-pull-11 {
+ right: 91.66666666666666%;
+ }
+ .col-md-pull-10 {
+ right: 83.33333333333334%;
+ }
+ .col-md-pull-9 {
+ right: 75%;
+ }
+ .col-md-pull-8 {
+ right: 66.66666666666666%;
+ }
+ .col-md-pull-7 {
+ right: 58.333333333333336%;
+ }
+ .col-md-pull-6 {
+ right: 50%;
+ }
+ .col-md-pull-5 {
+ right: 41.66666666666667%;
+ }
+ .col-md-pull-4 {
+ right: 33.33333333333333%;
+ }
+ .col-md-pull-3 {
+ right: 25%;
+ }
+ .col-md-pull-2 {
+ right: 16.666666666666664%;
+ }
+ .col-md-pull-1 {
+ right: 8.333333333333332%;
+ }
+ .col-md-pull-0 {
+ right: 0;
+ }
+ .col-md-push-12 {
+ left: 100%;
+ }
+ .col-md-push-11 {
+ left: 91.66666666666666%;
+ }
+ .col-md-push-10 {
+ left: 83.33333333333334%;
+ }
+ .col-md-push-9 {
+ left: 75%;
+ }
+ .col-md-push-8 {
+ left: 66.66666666666666%;
+ }
+ .col-md-push-7 {
+ left: 58.333333333333336%;
+ }
+ .col-md-push-6 {
+ left: 50%;
+ }
+ .col-md-push-5 {
+ left: 41.66666666666667%;
+ }
+ .col-md-push-4 {
+ left: 33.33333333333333%;
+ }
+ .col-md-push-3 {
+ left: 25%;
+ }
+ .col-md-push-2 {
+ left: 16.666666666666664%;
+ }
+ .col-md-push-1 {
+ left: 8.333333333333332%;
+ }
+ .col-md-push-0 {
+ left: 0;
+ }
+ .col-md-offset-12 {
+ margin-left: 100%;
+ }
+ .col-md-offset-11 {
+ margin-left: 91.66666666666666%;
+ }
+ .col-md-offset-10 {
+ margin-left: 83.33333333333334%;
+ }
+ .col-md-offset-9 {
+ margin-left: 75%;
+ }
+ .col-md-offset-8 {
+ margin-left: 66.66666666666666%;
+ }
+ .col-md-offset-7 {
+ margin-left: 58.333333333333336%;
+ }
+ .col-md-offset-6 {
+ margin-left: 50%;
+ }
+ .col-md-offset-5 {
+ margin-left: 41.66666666666667%;
+ }
+ .col-md-offset-4 {
+ margin-left: 33.33333333333333%;
+ }
+ .col-md-offset-3 {
+ margin-left: 25%;
+ }
+ .col-md-offset-2 {
+ margin-left: 16.666666666666664%;
+ }
+ .col-md-offset-1 {
+ margin-left: 8.333333333333332%;
+ }
+ .col-md-offset-0 {
+ margin-left: 0;
+ }
+}
+@media (min-width: 1200px) {
+ .col-lg-1, .col-lg-2, .col-lg-3, .col-lg-4, .col-lg-5, .col-lg-6, .col-lg-7, .col-lg-8, .col-lg-9, .col-lg-10, .col-lg-11, .col-lg-12 {
+ float: left;
+ }
+ .col-lg-12 {
+ width: 100%;
+ }
+ .col-lg-11 {
+ width: 91.66666666666666%;
+ }
+ .col-lg-10 {
+ width: 83.33333333333334%;
+ }
+ .col-lg-9 {
+ width: 75%;
+ }
+ .col-lg-8 {
+ width: 66.66666666666666%;
+ }
+ .col-lg-7 {
+ width: 58.333333333333336%;
+ }
+ .col-lg-6 {
+ width: 50%;
+ }
+ .col-lg-5 {
+ width: 41.66666666666667%;
+ }
+ .col-lg-4 {
+ width: 33.33333333333333%;
+ }
+ .col-lg-3 {
+ width: 25%;
+ }
+ .col-lg-2 {
+ width: 16.666666666666664%;
+ }
+ .col-lg-1 {
+ width: 8.333333333333332%;
+ }
+ .col-lg-pull-12 {
+ right: 100%;
+ }
+ .col-lg-pull-11 {
+ right: 91.66666666666666%;
+ }
+ .col-lg-pull-10 {
+ right: 83.33333333333334%;
+ }
+ .col-lg-pull-9 {
+ right: 75%;
+ }
+ .col-lg-pull-8 {
+ right: 66.66666666666666%;
+ }
+ .col-lg-pull-7 {
+ right: 58.333333333333336%;
+ }
+ .col-lg-pull-6 {
+ right: 50%;
+ }
+ .col-lg-pull-5 {
+ right: 41.66666666666667%;
+ }
+ .col-lg-pull-4 {
+ right: 33.33333333333333%;
+ }
+ .col-lg-pull-3 {
+ right: 25%;
+ }
+ .col-lg-pull-2 {
+ right: 16.666666666666664%;
+ }
+ .col-lg-pull-1 {
+ right: 8.333333333333332%;
+ }
+ .col-lg-pull-0 {
+ right: 0;
+ }
+ .col-lg-push-12 {
+ left: 100%;
+ }
+ .col-lg-push-11 {
+ left: 91.66666666666666%;
+ }
+ .col-lg-push-10 {
+ left: 83.33333333333334%;
+ }
+ .col-lg-push-9 {
+ left: 75%;
+ }
+ .col-lg-push-8 {
+ left: 66.66666666666666%;
+ }
+ .col-lg-push-7 {
+ left: 58.333333333333336%;
+ }
+ .col-lg-push-6 {
+ left: 50%;
+ }
+ .col-lg-push-5 {
+ left: 41.66666666666667%;
+ }
+ .col-lg-push-4 {
+ left: 33.33333333333333%;
+ }
+ .col-lg-push-3 {
+ left: 25%;
+ }
+ .col-lg-push-2 {
+ left: 16.666666666666664%;
+ }
+ .col-lg-push-1 {
+ left: 8.333333333333332%;
+ }
+ .col-lg-push-0 {
+ left: 0;
+ }
+ .col-lg-offset-12 {
+ margin-left: 100%;
+ }
+ .col-lg-offset-11 {
+ margin-left: 91.66666666666666%;
+ }
+ .col-lg-offset-10 {
+ margin-left: 83.33333333333334%;
+ }
+ .col-lg-offset-9 {
+ margin-left: 75%;
+ }
+ .col-lg-offset-8 {
+ margin-left: 66.66666666666666%;
+ }
+ .col-lg-offset-7 {
+ margin-left: 58.333333333333336%;
+ }
+ .col-lg-offset-6 {
+ margin-left: 50%;
+ }
+ .col-lg-offset-5 {
+ margin-left: 41.66666666666667%;
+ }
+ .col-lg-offset-4 {
+ margin-left: 33.33333333333333%;
+ }
+ .col-lg-offset-3 {
+ margin-left: 25%;
+ }
+ .col-lg-offset-2 {
+ margin-left: 16.666666666666664%;
+ }
+ .col-lg-offset-1 {
+ margin-left: 8.333333333333332%;
+ }
+ .col-lg-offset-0 {
+ margin-left: 0;
+ }
+}
+table {
+ max-width: 100%;
+ background-color: transparent;
+}
+th {
+ text-align: left;
+}
+.table {
+ width: 100%;
+ margin-bottom: 20px;
+}
+.table > thead > tr > th,
+.table > tbody > tr > th,
+.table > tfoot > tr > th,
+.table > thead > tr > td,
+.table > tbody > tr > td,
+.table > tfoot > tr > td {
+ padding: 8px;
+ line-height: 1.428571429;
+ vertical-align: top;
+ border-top: 1px solid #ddd;
+}
+.table > thead > tr > th {
+ vertical-align: bottom;
+ border-bottom: 2px solid #ddd;
+}
+.table > caption + thead > tr:first-child > th,
+.table > colgroup + thead > tr:first-child > th,
+.table > thead:first-child > tr:first-child > th,
+.table > caption + thead > tr:first-child > td,
+.table > colgroup + thead > tr:first-child > td,
+.table > thead:first-child > tr:first-child > td {
+ border-top: 0;
+}
+.table > tbody + tbody {
+ border-top: 2px solid #ddd;
+}
+.table .table {
+ background-color: #fff;
+}
+.table-condensed > thead > tr > th,
+.table-condensed > tbody > tr > th,
+.table-condensed > tfoot > tr > th,
+.table-condensed > thead > tr > td,
+.table-condensed > tbody > tr > td,
+.table-condensed > tfoot > tr > td {
+ padding: 5px;
+}
+.table-bordered {
+ border: 1px solid #ddd;
+}
+.table-bordered > thead > tr > th,
+.table-bordered > tbody > tr > th,
+.table-bordered > tfoot > tr > th,
+.table-bordered > thead > tr > td,
+.table-bordered > tbody > tr > td,
+.table-bordered > tfoot > tr > td {
+ border: 1px solid #ddd;
+}
+.table-bordered > thead > tr > th,
+.table-bordered > thead > tr > td {
+ border-bottom-width: 2px;
+}
+.table-striped > tbody > tr:nth-child(odd) > td,
+.table-striped > tbody > tr:nth-child(odd) > th {
+ background-color: #f9f9f9;
+}
+.table-hover > tbody > tr:hover > td,
+.table-hover > tbody > tr:hover > th {
+ background-color: #f5f5f5;
+}
+table col[class*="col-"] {
+ position: static;
+ display: table-column;
+ float: none;
+}
+table td[class*="col-"],
+table th[class*="col-"] {
+ position: static;
+ display: table-cell;
+ float: none;
+}
+.table > thead > tr > td.active,
+.table > tbody > tr > td.active,
+.table > tfoot > tr > td.active,
+.table > thead > tr > th.active,
+.table > tbody > tr > th.active,
+.table > tfoot > tr > th.active,
+.table > thead > tr.active > td,
+.table > tbody > tr.active > td,
+.table > tfoot > tr.active > td,
+.table > thead > tr.active > th,
+.table > tbody > tr.active > th,
+.table > tfoot > tr.active > th {
+ background-color: #f5f5f5;
+}
+.table-hover > tbody > tr > td.active:hover,
+.table-hover > tbody > tr > th.active:hover,
+.table-hover > tbody > tr.active:hover > td,
+.table-hover > tbody > tr.active:hover > th {
+ background-color: #e8e8e8;
+}
+.table > thead > tr > td.success,
+.table > tbody > tr > td.success,
+.table > tfoot > tr > td.success,
+.table > thead > tr > th.success,
+.table > tbody > tr > th.success,
+.table > tfoot > tr > th.success,
+.table > thead > tr.success > td,
+.table > tbody > tr.success > td,
+.table > tfoot > tr.success > td,
+.table > thead > tr.success > th,
+.table > tbody > tr.success > th,
+.table > tfoot > tr.success > th {
+ background-color: #dff0d8;
+}
+.table-hover > tbody > tr > td.success:hover,
+.table-hover > tbody > tr > th.success:hover,
+.table-hover > tbody > tr.success:hover > td,
+.table-hover > tbody > tr.success:hover > th {
+ background-color: #d0e9c6;
+}
+.table > thead > tr > td.info,
+.table > tbody > tr > td.info,
+.table > tfoot > tr > td.info,
+.table > thead > tr > th.info,
+.table > tbody > tr > th.info,
+.table > tfoot > tr > th.info,
+.table > thead > tr.info > td,
+.table > tbody > tr.info > td,
+.table > tfoot > tr.info > td,
+.table > thead > tr.info > th,
+.table > tbody > tr.info > th,
+.table > tfoot > tr.info > th {
+ background-color: #d9edf7;
+}
+.table-hover > tbody > tr > td.info:hover,
+.table-hover > tbody > tr > th.info:hover,
+.table-hover > tbody > tr.info:hover > td,
+.table-hover > tbody > tr.info:hover > th {
+ background-color: #c4e3f3;
+}
+.table > thead > tr > td.warning,
+.table > tbody > tr > td.warning,
+.table > tfoot > tr > td.warning,
+.table > thead > tr > th.warning,
+.table > tbody > tr > th.warning,
+.table > tfoot > tr > th.warning,
+.table > thead > tr.warning > td,
+.table > tbody > tr.warning > td,
+.table > tfoot > tr.warning > td,
+.table > thead > tr.warning > th,
+.table > tbody > tr.warning > th,
+.table > tfoot > tr.warning > th {
+ background-color: #fcf8e3;
+}
+.table-hover > tbody > tr > td.warning:hover,
+.table-hover > tbody > tr > th.warning:hover,
+.table-hover > tbody > tr.warning:hover > td,
+.table-hover > tbody > tr.warning:hover > th {
+ background-color: #faf2cc;
+}
+.table > thead > tr > td.danger,
+.table > tbody > tr > td.danger,
+.table > tfoot > tr > td.danger,
+.table > thead > tr > th.danger,
+.table > tbody > tr > th.danger,
+.table > tfoot > tr > th.danger,
+.table > thead > tr.danger > td,
+.table > tbody > tr.danger > td,
+.table > tfoot > tr.danger > td,
+.table > thead > tr.danger > th,
+.table > tbody > tr.danger > th,
+.table > tfoot > tr.danger > th {
+ background-color: #f2dede;
+}
+.table-hover > tbody > tr > td.danger:hover,
+.table-hover > tbody > tr > th.danger:hover,
+.table-hover > tbody > tr.danger:hover > td,
+.table-hover > tbody > tr.danger:hover > th {
+ background-color: #ebcccc;
+}
+@media (max-width: 767px) {
+ .table-responsive {
+ width: 100%;
+ margin-bottom: 15px;
+ overflow-x: scroll;
+ overflow-y: hidden;
+ -webkit-overflow-scrolling: touch;
+ -ms-overflow-style: -ms-autohiding-scrollbar;
+ border: 1px solid #ddd;
+ }
+ .table-responsive > .table {
+ margin-bottom: 0;
+ }
+ .table-responsive > .table > thead > tr > th,
+ .table-responsive > .table > tbody > tr > th,
+ .table-responsive > .table > tfoot > tr > th,
+ .table-responsive > .table > thead > tr > td,
+ .table-responsive > .table > tbody > tr > td,
+ .table-responsive > .table > tfoot > tr > td {
+ white-space: nowrap;
+ }
+ .table-responsive > .table-bordered {
+ border: 0;
+ }
+ .table-responsive > .table-bordered > thead > tr > th:first-child,
+ .table-responsive > .table-bordered > tbody > tr > th:first-child,
+ .table-responsive > .table-bordered > tfoot > tr > th:first-child,
+ .table-responsive > .table-bordered > thead > tr > td:first-child,
+ .table-responsive > .table-bordered > tbody > tr > td:first-child,
+ .table-responsive > .table-bordered > tfoot > tr > td:first-child {
+ border-left: 0;
+ }
+ .table-responsive > .table-bordered > thead > tr > th:last-child,
+ .table-responsive > .table-bordered > tbody > tr > th:last-child,
+ .table-responsive > .table-bordered > tfoot > tr > th:last-child,
+ .table-responsive > .table-bordered > thead > tr > td:last-child,
+ .table-responsive > .table-bordered > tbody > tr > td:last-child,
+ .table-responsive > .table-bordered > tfoot > tr > td:last-child {
+ border-right: 0;
+ }
+ .table-responsive > .table-bordered > tbody > tr:last-child > th,
+ .table-responsive > .table-bordered > tfoot > tr:last-child > th,
+ .table-responsive > .table-bordered > tbody > tr:last-child > td,
+ .table-responsive > .table-bordered > tfoot > tr:last-child > td {
+ border-bottom: 0;
+ }
+}
+fieldset {
+ min-width: 0;
+ padding: 0;
+ margin: 0;
+ border: 0;
+}
+legend {
+ display: block;
+ width: 100%;
+ padding: 0;
+ margin-bottom: 20px;
+ font-size: 21px;
+ line-height: inherit;
+ color: #333;
+ border: 0;
+ border-bottom: 1px solid #e5e5e5;
+}
+label {
+ display: inline-block;
+ margin-bottom: 5px;
+ font-weight: bold;
+}
+input[type="search"] {
+ -webkit-box-sizing: border-box;
+ -moz-box-sizing: border-box;
+ box-sizing: border-box;
+}
+input[type="radio"],
+input[type="checkbox"] {
+ margin: 4px 0 0;
+ margin-top: 1px \9;
+ /* IE8-9 */
+ line-height: normal;
+}
+input[type="file"] {
+ display: block;
+}
+input[type="range"] {
+ display: block;
+ width: 100%;
+}
+select[multiple],
+select[size] {
+ height: auto;
+}
+input[type="file"]:focus,
+input[type="radio"]:focus,
+input[type="checkbox"]:focus {
+ outline: thin dotted;
+ outline: 5px auto -webkit-focus-ring-color;
+ outline-offset: -2px;
+}
+output {
+ display: block;
+ padding-top: 7px;
+ font-size: 14px;
+ line-height: 1.428571429;
+ color: #555;
+}
+.form-control {
+ display: block;
+ width: 100%;
+ height: 34px;
+ padding: 6px 12px;
+ font-size: 14px;
+ line-height: 1.428571429;
+ color: #555;
+ background-color: #fff;
+ background-image: none;
+ border: 1px solid #ccc;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ -webkit-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
+ transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
+}
+.form-control:focus {
+ border-color: #66afe9;
+ outline: 0;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, .6);
+ box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, .6);
+}
+.form-control:-moz-placeholder {
+ color: #999;
+}
+.form-control::-moz-placeholder {
+ color: #999;
+ opacity: 1;
+}
+.form-control:-ms-input-placeholder {
+ color: #999;
+}
+.form-control::-webkit-input-placeholder {
+ color: #999;
+}
+.form-control[disabled],
+.form-control[readonly],
+fieldset[disabled] .form-control {
+ cursor: not-allowed;
+ background-color: #eee;
+ opacity: 1;
+}
+textarea.form-control {
+ height: auto;
+}
+input[type="date"] {
+ line-height: 34px;
+}
+.form-group {
+ margin-bottom: 15px;
+}
+.radio,
+.checkbox {
+ display: block;
+ min-height: 20px;
+ padding-left: 20px;
+ margin-top: 10px;
+ margin-bottom: 10px;
+}
+.radio label,
+.checkbox label {
+ display: inline;
+ font-weight: normal;
+ cursor: pointer;
+}
+.radio input[type="radio"],
+.radio-inline input[type="radio"],
+.checkbox input[type="checkbox"],
+.checkbox-inline input[type="checkbox"] {
+ float: left;
+ margin-left: -20px;
+}
+.radio + .radio,
+.checkbox + .checkbox {
+ margin-top: -5px;
+}
+.radio-inline,
+.checkbox-inline {
+ display: inline-block;
+ padding-left: 20px;
+ margin-bottom: 0;
+ font-weight: normal;
+ vertical-align: middle;
+ cursor: pointer;
+}
+.radio-inline + .radio-inline,
+.checkbox-inline + .checkbox-inline {
+ margin-top: 0;
+ margin-left: 10px;
+}
+input[type="radio"][disabled],
+input[type="checkbox"][disabled],
+.radio[disabled],
+.radio-inline[disabled],
+.checkbox[disabled],
+.checkbox-inline[disabled],
+fieldset[disabled] input[type="radio"],
+fieldset[disabled] input[type="checkbox"],
+fieldset[disabled] .radio,
+fieldset[disabled] .radio-inline,
+fieldset[disabled] .checkbox,
+fieldset[disabled] .checkbox-inline {
+ cursor: not-allowed;
+}
+.input-sm {
+ height: 30px;
+ padding: 5px 10px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+select.input-sm {
+ height: 30px;
+ line-height: 30px;
+}
+textarea.input-sm,
+select[multiple].input-sm {
+ height: auto;
+}
+.input-lg {
+ height: 46px;
+ padding: 10px 16px;
+ font-size: 18px;
+ line-height: 1.33;
+ border-radius: 6px;
+}
+select.input-lg {
+ height: 46px;
+ line-height: 46px;
+}
+textarea.input-lg,
+select[multiple].input-lg {
+ height: auto;
+}
+.has-feedback {
+ position: relative;
+}
+.has-feedback .form-control {
+ padding-right: 42.5px;
+}
+.has-feedback .form-control-feedback {
+ position: absolute;
+ top: 25px;
+ right: 0;
+ display: block;
+ width: 34px;
+ height: 34px;
+ line-height: 34px;
+ text-align: center;
+}
+.has-success .help-block,
+.has-success .control-label,
+.has-success .radio,
+.has-success .checkbox,
+.has-success .radio-inline,
+.has-success .checkbox-inline {
+ color: #3c763d;
+}
+.has-success .form-control {
+ border-color: #3c763d;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+}
+.has-success .form-control:focus {
+ border-color: #2b542c;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #67b168;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #67b168;
+}
+.has-success .input-group-addon {
+ color: #3c763d;
+ background-color: #dff0d8;
+ border-color: #3c763d;
+}
+.has-success .form-control-feedback {
+ color: #3c763d;
+}
+.has-warning .help-block,
+.has-warning .control-label,
+.has-warning .radio,
+.has-warning .checkbox,
+.has-warning .radio-inline,
+.has-warning .checkbox-inline {
+ color: #8a6d3b;
+}
+.has-warning .form-control {
+ border-color: #8a6d3b;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+}
+.has-warning .form-control:focus {
+ border-color: #66512c;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #c0a16b;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #c0a16b;
+}
+.has-warning .input-group-addon {
+ color: #8a6d3b;
+ background-color: #fcf8e3;
+ border-color: #8a6d3b;
+}
+.has-warning .form-control-feedback {
+ color: #8a6d3b;
+}
+.has-error .help-block,
+.has-error .control-label,
+.has-error .radio,
+.has-error .checkbox,
+.has-error .radio-inline,
+.has-error .checkbox-inline {
+ color: #a94442;
+}
+.has-error .form-control {
+ border-color: #a94442;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075);
+}
+.has-error .form-control:focus {
+ border-color: #843534;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #ce8483;
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .075), 0 0 6px #ce8483;
+}
+.has-error .input-group-addon {
+ color: #a94442;
+ background-color: #f2dede;
+ border-color: #a94442;
+}
+.has-error .form-control-feedback {
+ color: #a94442;
+}
+.form-control-static {
+ margin-bottom: 0;
+}
+.help-block {
+ display: block;
+ margin-top: 5px;
+ margin-bottom: 10px;
+ color: #737373;
+}
+@media (min-width: 768px) {
+ .form-inline .form-group {
+ display: inline-block;
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .form-inline .form-control {
+ display: inline-block;
+ width: auto;
+ vertical-align: middle;
+ }
+ .form-inline .control-label {
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .form-inline .radio,
+ .form-inline .checkbox {
+ display: inline-block;
+ padding-left: 0;
+ margin-top: 0;
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .form-inline .radio input[type="radio"],
+ .form-inline .checkbox input[type="checkbox"] {
+ float: none;
+ margin-left: 0;
+ }
+ .form-inline .has-feedback .form-control-feedback {
+ top: 0;
+ }
+}
+.form-horizontal .control-label,
+.form-horizontal .radio,
+.form-horizontal .checkbox,
+.form-horizontal .radio-inline,
+.form-horizontal .checkbox-inline {
+ padding-top: 7px;
+ margin-top: 0;
+ margin-bottom: 0;
+}
+.form-horizontal .radio,
+.form-horizontal .checkbox {
+ min-height: 27px;
+}
+.form-horizontal .form-group {
+ margin-right: -15px;
+ margin-left: -15px;
+}
+.form-horizontal .form-control-static {
+ padding-top: 7px;
+}
+@media (min-width: 768px) {
+ .form-horizontal .control-label {
+ text-align: right;
+ }
+}
+.form-horizontal .has-feedback .form-control-feedback {
+ top: 0;
+ right: 15px;
+}
+.btn {
+ display: inline-block;
+ padding: 6px 12px;
+ margin-bottom: 0;
+ font-size: 14px;
+ font-weight: normal;
+ line-height: 1.428571429;
+ text-align: center;
+ white-space: nowrap;
+ vertical-align: middle;
+ cursor: pointer;
+ -webkit-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ -o-user-select: none;
+ user-select: none;
+ background-image: none;
+ border: 1px solid transparent;
+ border-radius: 4px;
+}
+.btn:focus {
+ outline: thin dotted;
+ outline: 5px auto -webkit-focus-ring-color;
+ outline-offset: -2px;
+}
+.btn:hover,
+.btn:focus {
+ color: #333;
+ text-decoration: none;
+}
+.btn:active,
+.btn.active {
+ background-image: none;
+ outline: 0;
+ -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+ box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+}
+.btn.disabled,
+.btn[disabled],
+fieldset[disabled] .btn {
+ pointer-events: none;
+ cursor: not-allowed;
+ filter: alpha(opacity=65);
+ -webkit-box-shadow: none;
+ box-shadow: none;
+ opacity: .65;
+}
+.btn-default {
+ color: #333;
+ background-color: #fff;
+ border-color: #ccc;
+}
+.btn-default:hover,
+.btn-default:focus,
+.btn-default:active,
+.btn-default.active,
+.open .dropdown-toggle.btn-default {
+ color: #333;
+ background-color: #ebebeb;
+ border-color: #adadad;
+}
+.btn-default:active,
+.btn-default.active,
+.open .dropdown-toggle.btn-default {
+ background-image: none;
+}
+.btn-default.disabled,
+.btn-default[disabled],
+fieldset[disabled] .btn-default,
+.btn-default.disabled:hover,
+.btn-default[disabled]:hover,
+fieldset[disabled] .btn-default:hover,
+.btn-default.disabled:focus,
+.btn-default[disabled]:focus,
+fieldset[disabled] .btn-default:focus,
+.btn-default.disabled:active,
+.btn-default[disabled]:active,
+fieldset[disabled] .btn-default:active,
+.btn-default.disabled.active,
+.btn-default[disabled].active,
+fieldset[disabled] .btn-default.active {
+ background-color: #fff;
+ border-color: #ccc;
+}
+.btn-default .badge {
+ color: #fff;
+ background-color: #333;
+}
+.btn-primary {
+ color: #fff;
+ background-color: #428bca;
+ border-color: #357ebd;
+}
+.btn-primary:hover,
+.btn-primary:focus,
+.btn-primary:active,
+.btn-primary.active,
+.open .dropdown-toggle.btn-primary {
+ color: #fff;
+ background-color: #3276b1;
+ border-color: #285e8e;
+}
+.btn-primary:active,
+.btn-primary.active,
+.open .dropdown-toggle.btn-primary {
+ background-image: none;
+}
+.btn-primary.disabled,
+.btn-primary[disabled],
+fieldset[disabled] .btn-primary,
+.btn-primary.disabled:hover,
+.btn-primary[disabled]:hover,
+fieldset[disabled] .btn-primary:hover,
+.btn-primary.disabled:focus,
+.btn-primary[disabled]:focus,
+fieldset[disabled] .btn-primary:focus,
+.btn-primary.disabled:active,
+.btn-primary[disabled]:active,
+fieldset[disabled] .btn-primary:active,
+.btn-primary.disabled.active,
+.btn-primary[disabled].active,
+fieldset[disabled] .btn-primary.active {
+ background-color: #428bca;
+ border-color: #357ebd;
+}
+.btn-primary .badge {
+ color: #428bca;
+ background-color: #fff;
+}
+.btn-success {
+ color: #fff;
+ background-color: #5cb85c;
+ border-color: #4cae4c;
+}
+.btn-success:hover,
+.btn-success:focus,
+.btn-success:active,
+.btn-success.active,
+.open .dropdown-toggle.btn-success {
+ color: #fff;
+ background-color: #47a447;
+ border-color: #398439;
+}
+.btn-success:active,
+.btn-success.active,
+.open .dropdown-toggle.btn-success {
+ background-image: none;
+}
+.btn-success.disabled,
+.btn-success[disabled],
+fieldset[disabled] .btn-success,
+.btn-success.disabled:hover,
+.btn-success[disabled]:hover,
+fieldset[disabled] .btn-success:hover,
+.btn-success.disabled:focus,
+.btn-success[disabled]:focus,
+fieldset[disabled] .btn-success:focus,
+.btn-success.disabled:active,
+.btn-success[disabled]:active,
+fieldset[disabled] .btn-success:active,
+.btn-success.disabled.active,
+.btn-success[disabled].active,
+fieldset[disabled] .btn-success.active {
+ background-color: #5cb85c;
+ border-color: #4cae4c;
+}
+.btn-success .badge {
+ color: #5cb85c;
+ background-color: #fff;
+}
+.btn-info {
+ color: #fff;
+ background-color: #5bc0de;
+ border-color: #46b8da;
+}
+.btn-info:hover,
+.btn-info:focus,
+.btn-info:active,
+.btn-info.active,
+.open .dropdown-toggle.btn-info {
+ color: #fff;
+ background-color: #39b3d7;
+ border-color: #269abc;
+}
+.btn-info:active,
+.btn-info.active,
+.open .dropdown-toggle.btn-info {
+ background-image: none;
+}
+.btn-info.disabled,
+.btn-info[disabled],
+fieldset[disabled] .btn-info,
+.btn-info.disabled:hover,
+.btn-info[disabled]:hover,
+fieldset[disabled] .btn-info:hover,
+.btn-info.disabled:focus,
+.btn-info[disabled]:focus,
+fieldset[disabled] .btn-info:focus,
+.btn-info.disabled:active,
+.btn-info[disabled]:active,
+fieldset[disabled] .btn-info:active,
+.btn-info.disabled.active,
+.btn-info[disabled].active,
+fieldset[disabled] .btn-info.active {
+ background-color: #5bc0de;
+ border-color: #46b8da;
+}
+.btn-info .badge {
+ color: #5bc0de;
+ background-color: #fff;
+}
+.btn-warning {
+ color: #fff;
+ background-color: #f0ad4e;
+ border-color: #eea236;
+}
+.btn-warning:hover,
+.btn-warning:focus,
+.btn-warning:active,
+.btn-warning.active,
+.open .dropdown-toggle.btn-warning {
+ color: #fff;
+ background-color: #ed9c28;
+ border-color: #d58512;
+}
+.btn-warning:active,
+.btn-warning.active,
+.open .dropdown-toggle.btn-warning {
+ background-image: none;
+}
+.btn-warning.disabled,
+.btn-warning[disabled],
+fieldset[disabled] .btn-warning,
+.btn-warning.disabled:hover,
+.btn-warning[disabled]:hover,
+fieldset[disabled] .btn-warning:hover,
+.btn-warning.disabled:focus,
+.btn-warning[disabled]:focus,
+fieldset[disabled] .btn-warning:focus,
+.btn-warning.disabled:active,
+.btn-warning[disabled]:active,
+fieldset[disabled] .btn-warning:active,
+.btn-warning.disabled.active,
+.btn-warning[disabled].active,
+fieldset[disabled] .btn-warning.active {
+ background-color: #f0ad4e;
+ border-color: #eea236;
+}
+.btn-warning .badge {
+ color: #f0ad4e;
+ background-color: #fff;
+}
+.btn-danger {
+ color: #fff;
+ background-color: #d9534f;
+ border-color: #d43f3a;
+}
+.btn-danger:hover,
+.btn-danger:focus,
+.btn-danger:active,
+.btn-danger.active,
+.open .dropdown-toggle.btn-danger {
+ color: #fff;
+ background-color: #d2322d;
+ border-color: #ac2925;
+}
+.btn-danger:active,
+.btn-danger.active,
+.open .dropdown-toggle.btn-danger {
+ background-image: none;
+}
+.btn-danger.disabled,
+.btn-danger[disabled],
+fieldset[disabled] .btn-danger,
+.btn-danger.disabled:hover,
+.btn-danger[disabled]:hover,
+fieldset[disabled] .btn-danger:hover,
+.btn-danger.disabled:focus,
+.btn-danger[disabled]:focus,
+fieldset[disabled] .btn-danger:focus,
+.btn-danger.disabled:active,
+.btn-danger[disabled]:active,
+fieldset[disabled] .btn-danger:active,
+.btn-danger.disabled.active,
+.btn-danger[disabled].active,
+fieldset[disabled] .btn-danger.active {
+ background-color: #d9534f;
+ border-color: #d43f3a;
+}
+.btn-danger .badge {
+ color: #d9534f;
+ background-color: #fff;
+}
+.btn-link {
+ font-weight: normal;
+ color: #428bca;
+ cursor: pointer;
+ border-radius: 0;
+}
+.btn-link,
+.btn-link:active,
+.btn-link[disabled],
+fieldset[disabled] .btn-link {
+ background-color: transparent;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+.btn-link,
+.btn-link:hover,
+.btn-link:focus,
+.btn-link:active {
+ border-color: transparent;
+}
+.btn-link:hover,
+.btn-link:focus {
+ color: #2a6496;
+ text-decoration: underline;
+ background-color: transparent;
+}
+.btn-link[disabled]:hover,
+fieldset[disabled] .btn-link:hover,
+.btn-link[disabled]:focus,
+fieldset[disabled] .btn-link:focus {
+ color: #999;
+ text-decoration: none;
+}
+.btn-lg {
+ padding: 10px 16px;
+ font-size: 18px;
+ line-height: 1.33;
+ border-radius: 6px;
+}
+.btn-sm {
+ padding: 5px 10px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+.btn-xs {
+ padding: 1px 5px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+.btn-block {
+ display: block;
+ width: 100%;
+ padding-right: 0;
+ padding-left: 0;
+}
+.btn-block + .btn-block {
+ margin-top: 5px;
+}
+input[type="submit"].btn-block,
+input[type="reset"].btn-block,
+input[type="button"].btn-block {
+ width: 100%;
+}
+.fade {
+ opacity: 0;
+ -webkit-transition: opacity .15s linear;
+ transition: opacity .15s linear;
+}
+.fade.in {
+ opacity: 1;
+}
+.collapse {
+ display: none;
+}
+.collapse.in {
+ display: block;
+}
+.collapsing {
+ position: relative;
+ height: 0;
+ overflow: hidden;
+ -webkit-transition: height .35s ease;
+ transition: height .35s ease;
+}
+@font-face {
+ font-family: 'Glyphicons Halflings';
+
+ src: url('../fonts/glyphicons-halflings-regular.eot');
+ src: url('../fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('../fonts/glyphicons-halflings-regular.woff') format('woff'), url('../fonts/glyphicons-halflings-regular.ttf') format('truetype'), url('../fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg');
+}
+.glyphicon {
+ position: relative;
+ top: 1px;
+ display: inline-block;
+ font-family: 'Glyphicons Halflings';
+ font-style: normal;
+ font-weight: normal;
+ line-height: 1;
+
+ -webkit-font-smoothing: antialiased;
+ -moz-osx-font-smoothing: grayscale;
+}
+.glyphicon-asterisk:before {
+ content: "\2a";
+}
+.glyphicon-plus:before {
+ content: "\2b";
+}
+.glyphicon-euro:before {
+ content: "\20ac";
+}
+.glyphicon-minus:before {
+ content: "\2212";
+}
+.glyphicon-cloud:before {
+ content: "\2601";
+}
+.glyphicon-envelope:before {
+ content: "\2709";
+}
+.glyphicon-pencil:before {
+ content: "\270f";
+}
+.glyphicon-glass:before {
+ content: "\e001";
+}
+.glyphicon-music:before {
+ content: "\e002";
+}
+.glyphicon-search:before {
+ content: "\e003";
+}
+.glyphicon-heart:before {
+ content: "\e005";
+}
+.glyphicon-star:before {
+ content: "\e006";
+}
+.glyphicon-star-empty:before {
+ content: "\e007";
+}
+.glyphicon-user:before {
+ content: "\e008";
+}
+.glyphicon-film:before {
+ content: "\e009";
+}
+.glyphicon-th-large:before {
+ content: "\e010";
+}
+.glyphicon-th:before {
+ content: "\e011";
+}
+.glyphicon-th-list:before {
+ content: "\e012";
+}
+.glyphicon-ok:before {
+ content: "\e013";
+}
+.glyphicon-remove:before {
+ content: "\e014";
+}
+.glyphicon-zoom-in:before {
+ content: "\e015";
+}
+.glyphicon-zoom-out:before {
+ content: "\e016";
+}
+.glyphicon-off:before {
+ content: "\e017";
+}
+.glyphicon-signal:before {
+ content: "\e018";
+}
+.glyphicon-cog:before {
+ content: "\e019";
+}
+.glyphicon-trash:before {
+ content: "\e020";
+}
+.glyphicon-home:before {
+ content: "\e021";
+}
+.glyphicon-file:before {
+ content: "\e022";
+}
+.glyphicon-time:before {
+ content: "\e023";
+}
+.glyphicon-road:before {
+ content: "\e024";
+}
+.glyphicon-download-alt:before {
+ content: "\e025";
+}
+.glyphicon-download:before {
+ content: "\e026";
+}
+.glyphicon-upload:before {
+ content: "\e027";
+}
+.glyphicon-inbox:before {
+ content: "\e028";
+}
+.glyphicon-play-circle:before {
+ content: "\e029";
+}
+.glyphicon-repeat:before {
+ content: "\e030";
+}
+.glyphicon-refresh:before {
+ content: "\e031";
+}
+.glyphicon-list-alt:before {
+ content: "\e032";
+}
+.glyphicon-lock:before {
+ content: "\e033";
+}
+.glyphicon-flag:before {
+ content: "\e034";
+}
+.glyphicon-headphones:before {
+ content: "\e035";
+}
+.glyphicon-volume-off:before {
+ content: "\e036";
+}
+.glyphicon-volume-down:before {
+ content: "\e037";
+}
+.glyphicon-volume-up:before {
+ content: "\e038";
+}
+.glyphicon-qrcode:before {
+ content: "\e039";
+}
+.glyphicon-barcode:before {
+ content: "\e040";
+}
+.glyphicon-tag:before {
+ content: "\e041";
+}
+.glyphicon-tags:before {
+ content: "\e042";
+}
+.glyphicon-book:before {
+ content: "\e043";
+}
+.glyphicon-bookmark:before {
+ content: "\e044";
+}
+.glyphicon-print:before {
+ content: "\e045";
+}
+.glyphicon-camera:before {
+ content: "\e046";
+}
+.glyphicon-font:before {
+ content: "\e047";
+}
+.glyphicon-bold:before {
+ content: "\e048";
+}
+.glyphicon-italic:before {
+ content: "\e049";
+}
+.glyphicon-text-height:before {
+ content: "\e050";
+}
+.glyphicon-text-width:before {
+ content: "\e051";
+}
+.glyphicon-align-left:before {
+ content: "\e052";
+}
+.glyphicon-align-center:before {
+ content: "\e053";
+}
+.glyphicon-align-right:before {
+ content: "\e054";
+}
+.glyphicon-align-justify:before {
+ content: "\e055";
+}
+.glyphicon-list:before {
+ content: "\e056";
+}
+.glyphicon-indent-left:before {
+ content: "\e057";
+}
+.glyphicon-indent-right:before {
+ content: "\e058";
+}
+.glyphicon-facetime-video:before {
+ content: "\e059";
+}
+.glyphicon-picture:before {
+ content: "\e060";
+}
+.glyphicon-map-marker:before {
+ content: "\e062";
+}
+.glyphicon-adjust:before {
+ content: "\e063";
+}
+.glyphicon-tint:before {
+ content: "\e064";
+}
+.glyphicon-edit:before {
+ content: "\e065";
+}
+.glyphicon-share:before {
+ content: "\e066";
+}
+.glyphicon-check:before {
+ content: "\e067";
+}
+.glyphicon-move:before {
+ content: "\e068";
+}
+.glyphicon-step-backward:before {
+ content: "\e069";
+}
+.glyphicon-fast-backward:before {
+ content: "\e070";
+}
+.glyphicon-backward:before {
+ content: "\e071";
+}
+.glyphicon-play:before {
+ content: "\e072";
+}
+.glyphicon-pause:before {
+ content: "\e073";
+}
+.glyphicon-stop:before {
+ content: "\e074";
+}
+.glyphicon-forward:before {
+ content: "\e075";
+}
+.glyphicon-fast-forward:before {
+ content: "\e076";
+}
+.glyphicon-step-forward:before {
+ content: "\e077";
+}
+.glyphicon-eject:before {
+ content: "\e078";
+}
+.glyphicon-chevron-left:before {
+ content: "\e079";
+}
+.glyphicon-chevron-right:before {
+ content: "\e080";
+}
+.glyphicon-plus-sign:before {
+ content: "\e081";
+}
+.glyphicon-minus-sign:before {
+ content: "\e082";
+}
+.glyphicon-remove-sign:before {
+ content: "\e083";
+}
+.glyphicon-ok-sign:before {
+ content: "\e084";
+}
+.glyphicon-question-sign:before {
+ content: "\e085";
+}
+.glyphicon-info-sign:before {
+ content: "\e086";
+}
+.glyphicon-screenshot:before {
+ content: "\e087";
+}
+.glyphicon-remove-circle:before {
+ content: "\e088";
+}
+.glyphicon-ok-circle:before {
+ content: "\e089";
+}
+.glyphicon-ban-circle:before {
+ content: "\e090";
+}
+.glyphicon-arrow-left:before {
+ content: "\e091";
+}
+.glyphicon-arrow-right:before {
+ content: "\e092";
+}
+.glyphicon-arrow-up:before {
+ content: "\e093";
+}
+.glyphicon-arrow-down:before {
+ content: "\e094";
+}
+.glyphicon-share-alt:before {
+ content: "\e095";
+}
+.glyphicon-resize-full:before {
+ content: "\e096";
+}
+.glyphicon-resize-small:before {
+ content: "\e097";
+}
+.glyphicon-exclamation-sign:before {
+ content: "\e101";
+}
+.glyphicon-gift:before {
+ content: "\e102";
+}
+.glyphicon-leaf:before {
+ content: "\e103";
+}
+.glyphicon-fire:before {
+ content: "\e104";
+}
+.glyphicon-eye-open:before {
+ content: "\e105";
+}
+.glyphicon-eye-close:before {
+ content: "\e106";
+}
+.glyphicon-warning-sign:before {
+ content: "\e107";
+}
+.glyphicon-plane:before {
+ content: "\e108";
+}
+.glyphicon-calendar:before {
+ content: "\e109";
+}
+.glyphicon-random:before {
+ content: "\e110";
+}
+.glyphicon-comment:before {
+ content: "\e111";
+}
+.glyphicon-magnet:before {
+ content: "\e112";
+}
+.glyphicon-chevron-up:before {
+ content: "\e113";
+}
+.glyphicon-chevron-down:before {
+ content: "\e114";
+}
+.glyphicon-retweet:before {
+ content: "\e115";
+}
+.glyphicon-shopping-cart:before {
+ content: "\e116";
+}
+.glyphicon-folder-close:before {
+ content: "\e117";
+}
+.glyphicon-folder-open:before {
+ content: "\e118";
+}
+.glyphicon-resize-vertical:before {
+ content: "\e119";
+}
+.glyphicon-resize-horizontal:before {
+ content: "\e120";
+}
+.glyphicon-hdd:before {
+ content: "\e121";
+}
+.glyphicon-bullhorn:before {
+ content: "\e122";
+}
+.glyphicon-bell:before {
+ content: "\e123";
+}
+.glyphicon-certificate:before {
+ content: "\e124";
+}
+.glyphicon-thumbs-up:before {
+ content: "\e125";
+}
+.glyphicon-thumbs-down:before {
+ content: "\e126";
+}
+.glyphicon-hand-right:before {
+ content: "\e127";
+}
+.glyphicon-hand-left:before {
+ content: "\e128";
+}
+.glyphicon-hand-up:before {
+ content: "\e129";
+}
+.glyphicon-hand-down:before {
+ content: "\e130";
+}
+.glyphicon-circle-arrow-right:before {
+ content: "\e131";
+}
+.glyphicon-circle-arrow-left:before {
+ content: "\e132";
+}
+.glyphicon-circle-arrow-up:before {
+ content: "\e133";
+}
+.glyphicon-circle-arrow-down:before {
+ content: "\e134";
+}
+.glyphicon-globe:before {
+ content: "\e135";
+}
+.glyphicon-wrench:before {
+ content: "\e136";
+}
+.glyphicon-tasks:before {
+ content: "\e137";
+}
+.glyphicon-filter:before {
+ content: "\e138";
+}
+.glyphicon-briefcase:before {
+ content: "\e139";
+}
+.glyphicon-fullscreen:before {
+ content: "\e140";
+}
+.glyphicon-dashboard:before {
+ content: "\e141";
+}
+.glyphicon-paperclip:before {
+ content: "\e142";
+}
+.glyphicon-heart-empty:before {
+ content: "\e143";
+}
+.glyphicon-link:before {
+ content: "\e144";
+}
+.glyphicon-phone:before {
+ content: "\e145";
+}
+.glyphicon-pushpin:before {
+ content: "\e146";
+}
+.glyphicon-usd:before {
+ content: "\e148";
+}
+.glyphicon-gbp:before {
+ content: "\e149";
+}
+.glyphicon-sort:before {
+ content: "\e150";
+}
+.glyphicon-sort-by-alphabet:before {
+ content: "\e151";
+}
+.glyphicon-sort-by-alphabet-alt:before {
+ content: "\e152";
+}
+.glyphicon-sort-by-order:before {
+ content: "\e153";
+}
+.glyphicon-sort-by-order-alt:before {
+ content: "\e154";
+}
+.glyphicon-sort-by-attributes:before {
+ content: "\e155";
+}
+.glyphicon-sort-by-attributes-alt:before {
+ content: "\e156";
+}
+.glyphicon-unchecked:before {
+ content: "\e157";
+}
+.glyphicon-expand:before {
+ content: "\e158";
+}
+.glyphicon-collapse-down:before {
+ content: "\e159";
+}
+.glyphicon-collapse-up:before {
+ content: "\e160";
+}
+.glyphicon-log-in:before {
+ content: "\e161";
+}
+.glyphicon-flash:before {
+ content: "\e162";
+}
+.glyphicon-log-out:before {
+ content: "\e163";
+}
+.glyphicon-new-window:before {
+ content: "\e164";
+}
+.glyphicon-record:before {
+ content: "\e165";
+}
+.glyphicon-save:before {
+ content: "\e166";
+}
+.glyphicon-open:before {
+ content: "\e167";
+}
+.glyphicon-saved:before {
+ content: "\e168";
+}
+.glyphicon-import:before {
+ content: "\e169";
+}
+.glyphicon-export:before {
+ content: "\e170";
+}
+.glyphicon-send:before {
+ content: "\e171";
+}
+.glyphicon-floppy-disk:before {
+ content: "\e172";
+}
+.glyphicon-floppy-saved:before {
+ content: "\e173";
+}
+.glyphicon-floppy-remove:before {
+ content: "\e174";
+}
+.glyphicon-floppy-save:before {
+ content: "\e175";
+}
+.glyphicon-floppy-open:before {
+ content: "\e176";
+}
+.glyphicon-credit-card:before {
+ content: "\e177";
+}
+.glyphicon-transfer:before {
+ content: "\e178";
+}
+.glyphicon-cutlery:before {
+ content: "\e179";
+}
+.glyphicon-header:before {
+ content: "\e180";
+}
+.glyphicon-compressed:before {
+ content: "\e181";
+}
+.glyphicon-earphone:before {
+ content: "\e182";
+}
+.glyphicon-phone-alt:before {
+ content: "\e183";
+}
+.glyphicon-tower:before {
+ content: "\e184";
+}
+.glyphicon-stats:before {
+ content: "\e185";
+}
+.glyphicon-sd-video:before {
+ content: "\e186";
+}
+.glyphicon-hd-video:before {
+ content: "\e187";
+}
+.glyphicon-subtitles:before {
+ content: "\e188";
+}
+.glyphicon-sound-stereo:before {
+ content: "\e189";
+}
+.glyphicon-sound-dolby:before {
+ content: "\e190";
+}
+.glyphicon-sound-5-1:before {
+ content: "\e191";
+}
+.glyphicon-sound-6-1:before {
+ content: "\e192";
+}
+.glyphicon-sound-7-1:before {
+ content: "\e193";
+}
+.glyphicon-copyright-mark:before {
+ content: "\e194";
+}
+.glyphicon-registration-mark:before {
+ content: "\e195";
+}
+.glyphicon-cloud-download:before {
+ content: "\e197";
+}
+.glyphicon-cloud-upload:before {
+ content: "\e198";
+}
+.glyphicon-tree-conifer:before {
+ content: "\e199";
+}
+.glyphicon-tree-deciduous:before {
+ content: "\e200";
+}
+.caret {
+ display: inline-block;
+ width: 0;
+ height: 0;
+ margin-left: 2px;
+ vertical-align: middle;
+ border-top: 4px solid;
+ border-right: 4px solid transparent;
+ border-left: 4px solid transparent;
+}
+.dropdown {
+ position: relative;
+}
+.dropdown-toggle:focus {
+ outline: 0;
+}
+.dropdown-menu {
+ position: absolute;
+ top: 100%;
+ left: 0;
+ z-index: 1000;
+ display: none;
+ float: left;
+ min-width: 160px;
+ padding: 5px 0;
+ margin: 2px 0 0;
+ font-size: 14px;
+ list-style: none;
+ background-color: #fff;
+ background-clip: padding-box;
+ border: 1px solid #ccc;
+ border: 1px solid rgba(0, 0, 0, .15);
+ border-radius: 4px;
+ -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, .175);
+ box-shadow: 0 6px 12px rgba(0, 0, 0, .175);
+}
+.dropdown-menu.pull-right {
+ right: 0;
+ left: auto;
+}
+.dropdown-menu .divider {
+ height: 1px;
+ margin: 9px 0;
+ overflow: hidden;
+ background-color: #e5e5e5;
+}
+.dropdown-menu > li > a {
+ display: block;
+ padding: 3px 20px;
+ clear: both;
+ font-weight: normal;
+ line-height: 1.428571429;
+ color: #333;
+ white-space: nowrap;
+}
+.dropdown-menu > li > a:hover,
+.dropdown-menu > li > a:focus {
+ color: #262626;
+ text-decoration: none;
+ background-color: #f5f5f5;
+}
+.dropdown-menu > .active > a,
+.dropdown-menu > .active > a:hover,
+.dropdown-menu > .active > a:focus {
+ color: #fff;
+ text-decoration: none;
+ background-color: #428bca;
+ outline: 0;
+}
+.dropdown-menu > .disabled > a,
+.dropdown-menu > .disabled > a:hover,
+.dropdown-menu > .disabled > a:focus {
+ color: #999;
+}
+.dropdown-menu > .disabled > a:hover,
+.dropdown-menu > .disabled > a:focus {
+ text-decoration: none;
+ cursor: not-allowed;
+ background-color: transparent;
+ background-image: none;
+ filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+}
+.open > .dropdown-menu {
+ display: block;
+}
+.open > a {
+ outline: 0;
+}
+.dropdown-menu-right {
+ right: 0;
+ left: auto;
+}
+.dropdown-menu-left {
+ right: auto;
+ left: 0;
+}
+.dropdown-header {
+ display: block;
+ padding: 3px 20px;
+ font-size: 12px;
+ line-height: 1.428571429;
+ color: #999;
+}
+.dropdown-backdrop {
+ position: fixed;
+ top: 0;
+ right: 0;
+ bottom: 0;
+ left: 0;
+ z-index: 990;
+}
+.pull-right > .dropdown-menu {
+ right: 0;
+ left: auto;
+}
+.dropup .caret,
+.navbar-fixed-bottom .dropdown .caret {
+ content: "";
+ border-top: 0;
+ border-bottom: 4px solid;
+}
+.dropup .dropdown-menu,
+.navbar-fixed-bottom .dropdown .dropdown-menu {
+ top: auto;
+ bottom: 100%;
+ margin-bottom: 1px;
+}
+@media (min-width: 768px) {
+ .navbar-right .dropdown-menu {
+ right: 0;
+ left: auto;
+ }
+ .navbar-right .dropdown-menu-left {
+ right: auto;
+ left: 0;
+ }
+}
+.btn-group,
+.btn-group-vertical {
+ position: relative;
+ display: inline-block;
+ vertical-align: middle;
+}
+.btn-group > .btn,
+.btn-group-vertical > .btn {
+ position: relative;
+ float: left;
+}
+.btn-group > .btn:hover,
+.btn-group-vertical > .btn:hover,
+.btn-group > .btn:focus,
+.btn-group-vertical > .btn:focus,
+.btn-group > .btn:active,
+.btn-group-vertical > .btn:active,
+.btn-group > .btn.active,
+.btn-group-vertical > .btn.active {
+ z-index: 2;
+}
+.btn-group > .btn:focus,
+.btn-group-vertical > .btn:focus {
+ outline: none;
+}
+.btn-group .btn + .btn,
+.btn-group .btn + .btn-group,
+.btn-group .btn-group + .btn,
+.btn-group .btn-group + .btn-group {
+ margin-left: -1px;
+}
+.btn-toolbar {
+ margin-left: -5px;
+}
+.btn-toolbar .btn-group,
+.btn-toolbar .input-group {
+ float: left;
+}
+.btn-toolbar > .btn,
+.btn-toolbar > .btn-group,
+.btn-toolbar > .input-group {
+ margin-left: 5px;
+}
+.btn-group > .btn:not(:first-child):not(:last-child):not(.dropdown-toggle) {
+ border-radius: 0;
+}
+.btn-group > .btn:first-child {
+ margin-left: 0;
+}
+.btn-group > .btn:first-child:not(:last-child):not(.dropdown-toggle) {
+ border-top-right-radius: 0;
+ border-bottom-right-radius: 0;
+}
+.btn-group > .btn:last-child:not(:first-child),
+.btn-group > .dropdown-toggle:not(:first-child) {
+ border-top-left-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.btn-group > .btn-group {
+ float: left;
+}
+.btn-group > .btn-group:not(:first-child):not(:last-child) > .btn {
+ border-radius: 0;
+}
+.btn-group > .btn-group:first-child > .btn:last-child,
+.btn-group > .btn-group:first-child > .dropdown-toggle {
+ border-top-right-radius: 0;
+ border-bottom-right-radius: 0;
+}
+.btn-group > .btn-group:last-child > .btn:first-child {
+ border-top-left-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.btn-group .dropdown-toggle:active,
+.btn-group.open .dropdown-toggle {
+ outline: 0;
+}
+.btn-group-xs > .btn {
+ padding: 1px 5px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+.btn-group-sm > .btn {
+ padding: 5px 10px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+.btn-group-lg > .btn {
+ padding: 10px 16px;
+ font-size: 18px;
+ line-height: 1.33;
+ border-radius: 6px;
+}
+.btn-group > .btn + .dropdown-toggle {
+ padding-right: 8px;
+ padding-left: 8px;
+}
+.btn-group > .btn-lg + .dropdown-toggle {
+ padding-right: 12px;
+ padding-left: 12px;
+}
+.btn-group.open .dropdown-toggle {
+ -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+ box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
+}
+.btn-group.open .dropdown-toggle.btn-link {
+ -webkit-box-shadow: none;
+ box-shadow: none;
+}
+.btn .caret {
+ margin-left: 0;
+}
+.btn-lg .caret {
+ border-width: 5px 5px 0;
+ border-bottom-width: 0;
+}
+.dropup .btn-lg .caret {
+ border-width: 0 5px 5px;
+}
+.btn-group-vertical > .btn,
+.btn-group-vertical > .btn-group,
+.btn-group-vertical > .btn-group > .btn {
+ display: block;
+ float: none;
+ width: 100%;
+ max-width: 100%;
+}
+.btn-group-vertical > .btn-group > .btn {
+ float: none;
+}
+.btn-group-vertical > .btn + .btn,
+.btn-group-vertical > .btn + .btn-group,
+.btn-group-vertical > .btn-group + .btn,
+.btn-group-vertical > .btn-group + .btn-group {
+ margin-top: -1px;
+ margin-left: 0;
+}
+.btn-group-vertical > .btn:not(:first-child):not(:last-child) {
+ border-radius: 0;
+}
+.btn-group-vertical > .btn:first-child:not(:last-child) {
+ border-top-right-radius: 4px;
+ border-bottom-right-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.btn-group-vertical > .btn:last-child:not(:first-child) {
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+ border-bottom-left-radius: 4px;
+}
+.btn-group-vertical > .btn-group:not(:first-child):not(:last-child) > .btn {
+ border-radius: 0;
+}
+.btn-group-vertical > .btn-group:first-child:not(:last-child) > .btn:last-child,
+.btn-group-vertical > .btn-group:first-child:not(:last-child) > .dropdown-toggle {
+ border-bottom-right-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.btn-group-vertical > .btn-group:last-child:not(:first-child) > .btn:first-child {
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+}
+.btn-group-justified {
+ display: table;
+ width: 100%;
+ table-layout: fixed;
+ border-collapse: separate;
+}
+.btn-group-justified > .btn,
+.btn-group-justified > .btn-group {
+ display: table-cell;
+ float: none;
+ width: 1%;
+}
+.btn-group-justified > .btn-group .btn {
+ width: 100%;
+}
+[data-toggle="buttons"] > .btn > input[type="radio"],
+[data-toggle="buttons"] > .btn > input[type="checkbox"] {
+ display: none;
+}
+.input-group {
+ position: relative;
+ display: table;
+ border-collapse: separate;
+}
+.input-group[class*="col-"] {
+ float: none;
+ padding-right: 0;
+ padding-left: 0;
+}
+.input-group .form-control {
+ float: left;
+ width: 100%;
+ margin-bottom: 0;
+}
+.input-group-lg > .form-control,
+.input-group-lg > .input-group-addon,
+.input-group-lg > .input-group-btn > .btn {
+ height: 46px;
+ padding: 10px 16px;
+ font-size: 18px;
+ line-height: 1.33;
+ border-radius: 6px;
+}
+select.input-group-lg > .form-control,
+select.input-group-lg > .input-group-addon,
+select.input-group-lg > .input-group-btn > .btn {
+ height: 46px;
+ line-height: 46px;
+}
+textarea.input-group-lg > .form-control,
+textarea.input-group-lg > .input-group-addon,
+textarea.input-group-lg > .input-group-btn > .btn,
+select[multiple].input-group-lg > .form-control,
+select[multiple].input-group-lg > .input-group-addon,
+select[multiple].input-group-lg > .input-group-btn > .btn {
+ height: auto;
+}
+.input-group-sm > .form-control,
+.input-group-sm > .input-group-addon,
+.input-group-sm > .input-group-btn > .btn {
+ height: 30px;
+ padding: 5px 10px;
+ font-size: 12px;
+ line-height: 1.5;
+ border-radius: 3px;
+}
+select.input-group-sm > .form-control,
+select.input-group-sm > .input-group-addon,
+select.input-group-sm > .input-group-btn > .btn {
+ height: 30px;
+ line-height: 30px;
+}
+textarea.input-group-sm > .form-control,
+textarea.input-group-sm > .input-group-addon,
+textarea.input-group-sm > .input-group-btn > .btn,
+select[multiple].input-group-sm > .form-control,
+select[multiple].input-group-sm > .input-group-addon,
+select[multiple].input-group-sm > .input-group-btn > .btn {
+ height: auto;
+}
+.input-group-addon,
+.input-group-btn,
+.input-group .form-control {
+ display: table-cell;
+}
+.input-group-addon:not(:first-child):not(:last-child),
+.input-group-btn:not(:first-child):not(:last-child),
+.input-group .form-control:not(:first-child):not(:last-child) {
+ border-radius: 0;
+}
+.input-group-addon,
+.input-group-btn {
+ width: 1%;
+ white-space: nowrap;
+ vertical-align: middle;
+}
+.input-group-addon {
+ padding: 6px 12px;
+ font-size: 14px;
+ font-weight: normal;
+ line-height: 1;
+ color: #555;
+ text-align: center;
+ background-color: #eee;
+ border: 1px solid #ccc;
+ border-radius: 4px;
+}
+.input-group-addon.input-sm {
+ padding: 5px 10px;
+ font-size: 12px;
+ border-radius: 3px;
+}
+.input-group-addon.input-lg {
+ padding: 10px 16px;
+ font-size: 18px;
+ border-radius: 6px;
+}
+.input-group-addon input[type="radio"],
+.input-group-addon input[type="checkbox"] {
+ margin-top: 0;
+}
+.input-group .form-control:first-child,
+.input-group-addon:first-child,
+.input-group-btn:first-child > .btn,
+.input-group-btn:first-child > .btn-group > .btn,
+.input-group-btn:first-child > .dropdown-toggle,
+.input-group-btn:last-child > .btn:not(:last-child):not(.dropdown-toggle),
+.input-group-btn:last-child > .btn-group:not(:last-child) > .btn {
+ border-top-right-radius: 0;
+ border-bottom-right-radius: 0;
+}
+.input-group-addon:first-child {
+ border-right: 0;
+}
+.input-group .form-control:last-child,
+.input-group-addon:last-child,
+.input-group-btn:last-child > .btn,
+.input-group-btn:last-child > .btn-group > .btn,
+.input-group-btn:last-child > .dropdown-toggle,
+.input-group-btn:first-child > .btn:not(:first-child),
+.input-group-btn:first-child > .btn-group:not(:first-child) > .btn {
+ border-top-left-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.input-group-addon:last-child {
+ border-left: 0;
+}
+.input-group-btn {
+ position: relative;
+ font-size: 0;
+ white-space: nowrap;
+}
+.input-group-btn > .btn {
+ position: relative;
+}
+.input-group-btn > .btn + .btn {
+ margin-left: -1px;
+}
+.input-group-btn > .btn:hover,
+.input-group-btn > .btn:focus,
+.input-group-btn > .btn:active {
+ z-index: 2;
+}
+.input-group-btn:first-child > .btn,
+.input-group-btn:first-child > .btn-group {
+ margin-right: -1px;
+}
+.input-group-btn:last-child > .btn,
+.input-group-btn:last-child > .btn-group {
+ margin-left: -1px;
+}
+.nav {
+ padding-left: 0;
+ margin-bottom: 0;
+ list-style: none;
+}
+.nav > li {
+ position: relative;
+ display: block;
+}
+.nav > li > a {
+ position: relative;
+ display: block;
+ padding: 10px 15px;
+}
+.nav > li > a:hover,
+.nav > li > a:focus {
+ text-decoration: none;
+ background-color: #eee;
+}
+.nav > li.disabled > a {
+ color: #999;
+}
+.nav > li.disabled > a:hover,
+.nav > li.disabled > a:focus {
+ color: #999;
+ text-decoration: none;
+ cursor: not-allowed;
+ background-color: transparent;
+}
+.nav .open > a,
+.nav .open > a:hover,
+.nav .open > a:focus {
+ background-color: #eee;
+ border-color: #428bca;
+}
+.nav .nav-divider {
+ height: 1px;
+ margin: 9px 0;
+ overflow: hidden;
+ background-color: #e5e5e5;
+}
+.nav > li > a > img {
+ max-width: none;
+}
+.nav-tabs {
+ border-bottom: 1px solid #ddd;
+}
+.nav-tabs > li {
+ float: left;
+ margin-bottom: -1px;
+}
+.nav-tabs > li > a {
+ margin-right: 2px;
+ line-height: 1.428571429;
+ border: 1px solid transparent;
+ border-radius: 4px 4px 0 0;
+}
+.nav-tabs > li > a:hover {
+ border-color: #eee #eee #ddd;
+}
+.nav-tabs > li.active > a,
+.nav-tabs > li.active > a:hover,
+.nav-tabs > li.active > a:focus {
+ color: #555;
+ cursor: default;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ border-bottom-color: transparent;
+}
+.nav-tabs.nav-justified {
+ width: 100%;
+ border-bottom: 0;
+}
+.nav-tabs.nav-justified > li {
+ float: none;
+}
+.nav-tabs.nav-justified > li > a {
+ margin-bottom: 5px;
+ text-align: center;
+}
+.nav-tabs.nav-justified > .dropdown .dropdown-menu {
+ top: auto;
+ left: auto;
+}
+@media (min-width: 768px) {
+ .nav-tabs.nav-justified > li {
+ display: table-cell;
+ width: 1%;
+ }
+ .nav-tabs.nav-justified > li > a {
+ margin-bottom: 0;
+ }
+}
+.nav-tabs.nav-justified > li > a {
+ margin-right: 0;
+ border-radius: 4px;
+}
+.nav-tabs.nav-justified > .active > a,
+.nav-tabs.nav-justified > .active > a:hover,
+.nav-tabs.nav-justified > .active > a:focus {
+ border: 1px solid #ddd;
+}
+@media (min-width: 768px) {
+ .nav-tabs.nav-justified > li > a {
+ border-bottom: 1px solid #ddd;
+ border-radius: 4px 4px 0 0;
+ }
+ .nav-tabs.nav-justified > .active > a,
+ .nav-tabs.nav-justified > .active > a:hover,
+ .nav-tabs.nav-justified > .active > a:focus {
+ border-bottom-color: #fff;
+ }
+}
+.nav-pills > li {
+ float: left;
+}
+.nav-pills > li > a {
+ border-radius: 4px;
+}
+.nav-pills > li + li {
+ margin-left: 2px;
+}
+.nav-pills > li.active > a,
+.nav-pills > li.active > a:hover,
+.nav-pills > li.active > a:focus {
+ color: #fff;
+ background-color: #428bca;
+}
+.nav-stacked > li {
+ float: none;
+}
+.nav-stacked > li + li {
+ margin-top: 2px;
+ margin-left: 0;
+}
+.nav-justified {
+ width: 100%;
+}
+.nav-justified > li {
+ float: none;
+}
+.nav-justified > li > a {
+ margin-bottom: 5px;
+ text-align: center;
+}
+.nav-justified > .dropdown .dropdown-menu {
+ top: auto;
+ left: auto;
+}
+@media (min-width: 768px) {
+ .nav-justified > li {
+ display: table-cell;
+ width: 1%;
+ }
+ .nav-justified > li > a {
+ margin-bottom: 0;
+ }
+}
+.nav-tabs-justified {
+ border-bottom: 0;
+}
+.nav-tabs-justified > li > a {
+ margin-right: 0;
+ border-radius: 4px;
+}
+.nav-tabs-justified > .active > a,
+.nav-tabs-justified > .active > a:hover,
+.nav-tabs-justified > .active > a:focus {
+ border: 1px solid #ddd;
+}
+@media (min-width: 768px) {
+ .nav-tabs-justified > li > a {
+ border-bottom: 1px solid #ddd;
+ border-radius: 4px 4px 0 0;
+ }
+ .nav-tabs-justified > .active > a,
+ .nav-tabs-justified > .active > a:hover,
+ .nav-tabs-justified > .active > a:focus {
+ border-bottom-color: #fff;
+ }
+}
+.tab-content > .tab-pane {
+ display: none;
+}
+.tab-content > .active {
+ display: block;
+}
+.nav-tabs .dropdown-menu {
+ margin-top: -1px;
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+}
+.navbar {
+ position: relative;
+ min-height: 50px;
+ margin-bottom: 20px;
+ border: 1px solid transparent;
+}
+@media (min-width: 768px) {
+ .navbar {
+ border-radius: 4px;
+ }
+}
+@media (min-width: 768px) {
+ .navbar-header {
+ float: left;
+ }
+}
+.navbar-collapse {
+ max-height: 340px;
+ padding-right: 15px;
+ padding-left: 15px;
+ overflow-x: visible;
+ -webkit-overflow-scrolling: touch;
+ border-top: 1px solid transparent;
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1);
+}
+.navbar-collapse.in {
+ overflow-y: auto;
+}
+@media (min-width: 768px) {
+ .navbar-collapse {
+ width: auto;
+ border-top: 0;
+ box-shadow: none;
+ }
+ .navbar-collapse.collapse {
+ display: block !important;
+ height: auto !important;
+ padding-bottom: 0;
+ overflow: visible !important;
+ }
+ .navbar-collapse.in {
+ overflow-y: visible;
+ }
+ .navbar-fixed-top .navbar-collapse,
+ .navbar-static-top .navbar-collapse,
+ .navbar-fixed-bottom .navbar-collapse {
+ padding-right: 0;
+ padding-left: 0;
+ }
+}
+.container > .navbar-header,
+.container-fluid > .navbar-header,
+.container > .navbar-collapse,
+.container-fluid > .navbar-collapse {
+ margin-right: -15px;
+ margin-left: -15px;
+}
+@media (min-width: 768px) {
+ .container > .navbar-header,
+ .container-fluid > .navbar-header,
+ .container > .navbar-collapse,
+ .container-fluid > .navbar-collapse {
+ margin-right: 0;
+ margin-left: 0;
+ }
+}
+.navbar-static-top {
+ z-index: 1000;
+ border-width: 0 0 1px;
+}
+@media (min-width: 768px) {
+ .navbar-static-top {
+ border-radius: 0;
+ }
+}
+.navbar-fixed-top,
+.navbar-fixed-bottom {
+ position: fixed;
+ right: 0;
+ left: 0;
+ z-index: 1030;
+}
+@media (min-width: 768px) {
+ .navbar-fixed-top,
+ .navbar-fixed-bottom {
+ border-radius: 0;
+ }
+}
+.navbar-fixed-top {
+ top: 0;
+ border-width: 0 0 1px;
+}
+.navbar-fixed-bottom {
+ bottom: 0;
+ margin-bottom: 0;
+ border-width: 1px 0 0;
+}
+.navbar-brand {
+ float: left;
+ height: 20px;
+ padding: 15px 15px;
+ font-size: 18px;
+ line-height: 20px;
+}
+.navbar-brand:hover,
+.navbar-brand:focus {
+ text-decoration: none;
+}
+@media (min-width: 768px) {
+ .navbar > .container .navbar-brand,
+ .navbar > .container-fluid .navbar-brand {
+ margin-left: -15px;
+ }
+}
+.navbar-toggle {
+ position: relative;
+ float: right;
+ padding: 9px 10px;
+ margin-top: 8px;
+ margin-right: 15px;
+ margin-bottom: 8px;
+ background-color: transparent;
+ background-image: none;
+ border: 1px solid transparent;
+ border-radius: 4px;
+}
+.navbar-toggle:focus {
+ outline: none;
+}
+.navbar-toggle .icon-bar {
+ display: block;
+ width: 22px;
+ height: 2px;
+ border-radius: 1px;
+}
+.navbar-toggle .icon-bar + .icon-bar {
+ margin-top: 4px;
+}
+@media (min-width: 768px) {
+ .navbar-toggle {
+ display: none;
+ }
+}
+.navbar-nav {
+ margin: 7.5px -15px;
+}
+.navbar-nav > li > a {
+ padding-top: 10px;
+ padding-bottom: 10px;
+ line-height: 20px;
+}
+@media (max-width: 767px) {
+ .navbar-nav .open .dropdown-menu {
+ position: static;
+ float: none;
+ width: auto;
+ margin-top: 0;
+ background-color: transparent;
+ border: 0;
+ box-shadow: none;
+ }
+ .navbar-nav .open .dropdown-menu > li > a,
+ .navbar-nav .open .dropdown-menu .dropdown-header {
+ padding: 5px 15px 5px 25px;
+ }
+ .navbar-nav .open .dropdown-menu > li > a {
+ line-height: 20px;
+ }
+ .navbar-nav .open .dropdown-menu > li > a:hover,
+ .navbar-nav .open .dropdown-menu > li > a:focus {
+ background-image: none;
+ }
+}
+@media (min-width: 768px) {
+ .navbar-nav {
+ float: left;
+ margin: 0;
+ }
+ .navbar-nav > li {
+ float: left;
+ }
+ .navbar-nav > li > a {
+ padding-top: 15px;
+ padding-bottom: 15px;
+ }
+ .navbar-nav.navbar-right:last-child {
+ margin-right: -15px;
+ }
+}
+@media (min-width: 768px) {
+ .navbar-left {
+ float: left !important;
+ }
+ .navbar-right {
+ float: right !important;
+ }
+}
+.navbar-form {
+ padding: 10px 15px;
+ margin-top: 8px;
+ margin-right: -15px;
+ margin-bottom: 8px;
+ margin-left: -15px;
+ border-top: 1px solid transparent;
+ border-bottom: 1px solid transparent;
+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 0 rgba(255, 255, 255, .1);
+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, .1), 0 1px 0 rgba(255, 255, 255, .1);
+}
+@media (min-width: 768px) {
+ .navbar-form .form-group {
+ display: inline-block;
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .navbar-form .form-control {
+ display: inline-block;
+ width: auto;
+ vertical-align: middle;
+ }
+ .navbar-form .control-label {
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .navbar-form .radio,
+ .navbar-form .checkbox {
+ display: inline-block;
+ padding-left: 0;
+ margin-top: 0;
+ margin-bottom: 0;
+ vertical-align: middle;
+ }
+ .navbar-form .radio input[type="radio"],
+ .navbar-form .checkbox input[type="checkbox"] {
+ float: none;
+ margin-left: 0;
+ }
+ .navbar-form .has-feedback .form-control-feedback {
+ top: 0;
+ }
+}
+@media (max-width: 767px) {
+ .navbar-form .form-group {
+ margin-bottom: 5px;
+ }
+}
+@media (min-width: 768px) {
+ .navbar-form {
+ width: auto;
+ padding-top: 0;
+ padding-bottom: 0;
+ margin-right: 0;
+ margin-left: 0;
+ border: 0;
+ -webkit-box-shadow: none;
+ box-shadow: none;
+ }
+ .navbar-form.navbar-right:last-child {
+ margin-right: -15px;
+ }
+}
+.navbar-nav > li > .dropdown-menu {
+ margin-top: 0;
+ border-top-left-radius: 0;
+ border-top-right-radius: 0;
+}
+.navbar-fixed-bottom .navbar-nav > li > .dropdown-menu {
+ border-bottom-right-radius: 0;
+ border-bottom-left-radius: 0;
+}
+.navbar-btn {
+ margin-top: 8px;
+ margin-bottom: 8px;
+}
+.navbar-btn.btn-sm {
+ margin-top: 10px;
+ margin-bottom: 10px;
+}
+.navbar-btn.btn-xs {
+ margin-top: 14px;
+ margin-bottom: 14px;
+}
+.navbar-text {
+ margin-top: 15px;
+ margin-bottom: 15px;
+}
+@media (min-width: 768px) {
+ .navbar-text {
+ float: left;
+ margin-right: 15px;
+ margin-left: 15px;
+ }
+ .navbar-text.navbar-right:last-child {
+ margin-right: 0;
+ }
+}
+.navbar-default {
+ background-color: #f8f8f8;
+ border-color: #e7e7e7;
+}
+.navbar-default .navbar-brand {
+ color: #777;
+}
+.navbar-default .navbar-brand:hover,
+.navbar-default .navbar-brand:focus {
+ color: #5e5e5e;
+ background-color: transparent;
+}
+.navbar-default .navbar-text {
+ color: #777;
+}
+.navbar-default .navbar-nav > li > a {
+ color: #777;
+}
+.navbar-default .navbar-nav > li > a:hover,
+.navbar-default .navbar-nav > li > a:focus {
+ color: #333;
+ background-color: transparent;
+}
+.navbar-default .navbar-nav > .active > a,
+.navbar-default .navbar-nav > .active > a:hover,
+.navbar-default .navbar-nav > .active > a:focus {
+ color: #555;
+ background-color: #e7e7e7;
+}
+.navbar-default .navbar-nav > .disabled > a,
+.navbar-default .navbar-nav > .disabled > a:hover,
+.navbar-default .navbar-nav > .disabled > a:focus {
+ color: #ccc;
+ background-color: transparent;
+}
+.navbar-default .navbar-toggle {
+ border-color: #ddd;
+}
+.navbar-default .navbar-toggle:hover,
+.navbar-default .navbar-toggle:focus {
+ background-color: #ddd;
+}
+.navbar-default .navbar-toggle .icon-bar {
+ background-color: #888;
+}
+.navbar-default .navbar-collapse,
+.navbar-default .navbar-form {
+ border-color: #e7e7e7;
+}
+.navbar-default .navbar-nav > .open > a,
+.navbar-default .navbar-nav > .open > a:hover,
+.navbar-default .navbar-nav > .open > a:focus {
+ color: #555;
+ background-color: #e7e7e7;
+}
+@media (max-width: 767px) {
+ .navbar-default .navbar-nav .open .dropdown-menu > li > a {
+ color: #777;
+ }
+ .navbar-default .navbar-nav .open .dropdown-menu > li > a:hover,
+ .navbar-default .navbar-nav .open .dropdown-menu > li > a:focus {
+ color: #333;
+ background-color: transparent;
+ }
+ .navbar-default .navbar-nav .open .dropdown-menu > .active > a,
+ .navbar-default .navbar-nav .open .dropdown-menu > .active > a:hover,
+ .navbar-default .navbar-nav .open .dropdown-menu > .active > a:focus {
+ color: #555;
+ background-color: #e7e7e7;
+ }
+ .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a,
+ .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a:hover,
+ .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a:focus {
+ color: #ccc;
+ background-color: transparent;
+ }
+}
+.navbar-default .navbar-link {
+ color: #777;
+}
+.navbar-default .navbar-link:hover {
+ color: #333;
+}
+.navbar-inverse {
+ background-color: #222;
+ border-color: #080808;
+}
+.navbar-inverse .navbar-brand {
+ color: #999;
+}
+.navbar-inverse .navbar-brand:hover,
+.navbar-inverse .navbar-brand:focus {
+ color: #fff;
+ background-color: transparent;
+}
+.navbar-inverse .navbar-text {
+ color: #999;
+}
+.navbar-inverse .navbar-nav > li > a {
+ color: #999;
+}
+.navbar-inverse .navbar-nav > li > a:hover,
+.navbar-inverse .navbar-nav > li > a:focus {
+ color: #fff;
+ background-color: transparent;
+}
+.navbar-inverse .navbar-nav > .active > a,
+.navbar-inverse .navbar-nav > .active > a:hover,
+.navbar-inverse .navbar-nav > .active > a:focus {
+ color: #fff;
+ background-color: #080808;
+}
+.navbar-inverse .navbar-nav > .disabled > a,
+.navbar-inverse .navbar-nav > .disabled > a:hover,
+.navbar-inverse .navbar-nav > .disabled > a:focus {
+ color: #444;
+ background-color: transparent;
+}
+.navbar-inverse .navbar-toggle {
+ border-color: #333;
+}
+.navbar-inverse .navbar-toggle:hover,
+.navbar-inverse .navbar-toggle:focus {
+ background-color: #333;
+}
+.navbar-inverse .navbar-toggle .icon-bar {
+ background-color: #fff;
+}
+.navbar-inverse .navbar-collapse,
+.navbar-inverse .navbar-form {
+ border-color: #101010;
+}
+.navbar-inverse .navbar-nav > .open > a,
+.navbar-inverse .navbar-nav > .open > a:hover,
+.navbar-inverse .navbar-nav > .open > a:focus {
+ color: #fff;
+ background-color: #080808;
+}
+@media (max-width: 767px) {
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .dropdown-header {
+ border-color: #080808;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu .divider {
+ background-color: #080808;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu > li > a {
+ color: #999;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu > li > a:hover,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > li > a:focus {
+ color: #fff;
+ background-color: transparent;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a:hover,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a:focus {
+ color: #fff;
+ background-color: #080808;
+ }
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a:hover,
+ .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a:focus {
+ color: #444;
+ background-color: transparent;
+ }
+}
+.navbar-inverse .navbar-link {
+ color: #999;
+}
+.navbar-inverse .navbar-link:hover {
+ color: #fff;
+}
+.breadcrumb {
+ padding: 8px 15px;
+ margin-bottom: 20px;
+ list-style: none;
+ background-color: #f5f5f5;
+ border-radius: 4px;
+}
+.breadcrumb > li {
+ display: inline-block;
+}
+.breadcrumb > li + li:before {
+ padding: 0 5px;
+ color: #ccc;
+ content: "/\00a0";
+}
+.breadcrumb > .active {
+ color: #999;
+}
+.pagination {
+ display: inline-block;
+ padding-left: 0;
+ margin: 20px 0;
+ border-radius: 4px;
+}
+.pagination > li {
+ display: inline;
+}
+.pagination > li > a,
+.pagination > li > span {
+ position: relative;
+ float: left;
+ padding: 6px 12px;
+ margin-left: -1px;
+ line-height: 1.428571429;
+ color: #428bca;
+ text-decoration: none;
+ background-color: #fff;
+ border: 1px solid #ddd;
+}
+.pagination > li:first-child > a,
+.pagination > li:first-child > span {
+ margin-left: 0;
+ border-top-left-radius: 4px;
+ border-bottom-left-radius: 4px;
+}
+.pagination > li:last-child > a,
+.pagination > li:last-child > span {
+ border-top-right-radius: 4px;
+ border-bottom-right-radius: 4px;
+}
+.pagination > li > a:hover,
+.pagination > li > span:hover,
+.pagination > li > a:focus,
+.pagination > li > span:focus {
+ color: #2a6496;
+ background-color: #eee;
+ border-color: #ddd;
+}
+.pagination > .active > a,
+.pagination > .active > span,
+.pagination > .active > a:hover,
+.pagination > .active > span:hover,
+.pagination > .active > a:focus,
+.pagination > .active > span:focus {
+ z-index: 2;
+ color: #fff;
+ cursor: default;
+ background-color: #428bca;
+ border-color: #428bca;
+}
+.pagination > .disabled > span,
+.pagination > .disabled > span:hover,
+.pagination > .disabled > span:focus,
+.pagination > .disabled > a,
+.pagination > .disabled > a:hover,
+.pagination > .disabled > a:focus {
+ color: #999;
+ cursor: not-allowed;
+ background-color: #fff;
+ border-color: #ddd;
+}
+.pagination-lg > li > a,
+.pagination-lg > li > span {
+ padding: 10px 16px;
+ font-size: 18px;
+}
+.pagination-lg > li:first-child > a,
+.pagination-lg > li:first-child > span {
+ border-top-left-radius: 6px;
+ border-bottom-left-radius: 6px;
+}
+.pagination-lg > li:last-child > a,
+.pagination-lg > li:last-child > span {
+ border-top-right-radius: 6px;
+ border-bottom-right-radius: 6px;
+}
+.pagination-sm > li > a,
+.pagination-sm > li > span {
+ padding: 5px 10px;
+ font-size: 12px;
+}
+.pagination-sm > li:first-child > a,
+.pagination-sm > li:first-child > span {
+ border-top-left-radius: 3px;
+ border-bottom-left-radius: 3px;
+}
+.pagination-sm > li:last-child > a,
+.pagination-sm > li:last-child > span {
+ border-top-right-radius: 3px;
+ border-bottom-right-radius: 3px;
+}
+.pager {
+ padding-left: 0;
+ margin: 20px 0;
+ text-align: center;
+ list-style: none;
+}
+.pager li {
+ display: inline;
+}
+.pager li > a,
+.pager li > span {
+ display: inline-block;
+ padding: 5px 14px;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ border-radius: 15px;
+}
+.pager li > a:hover,
+.pager li > a:focus {
+ text-decoration: none;
+ background-color: #eee;
+}
+.pager .next > a,
+.pager .next > span {
+ float: right;
+}
+.pager .previous > a,
+.pager .previous > span {
+ float: left;
+}
+.pager .disabled > a,
+.pager .disabled > a:hover,
+.pager .disabled > a:focus,
+.pager .disabled > span {
+ color: #999;
+ cursor: not-allowed;
+ background-color: #fff;
+}
+.label {
+ display: inline;
+ padding: .2em .6em .3em;
+ font-size: 75%;
+ font-weight: bold;
+ line-height: 1;
+ color: #fff;
+ text-align: center;
+ white-space: nowrap;
+ vertical-align: baseline;
+ border-radius: .25em;
+}
+.label[href]:hover,
+.label[href]:focus {
+ color: #fff;
+ text-decoration: none;
+ cursor: pointer;
+}
+.label:empty {
+ display: none;
+}
+.btn .label {
+ position: relative;
+ top: -1px;
+}
+.label-default {
+ background-color: #999;
+}
+.label-default[href]:hover,
+.label-default[href]:focus {
+ background-color: #808080;
+}
+.label-primary {
+ background-color: #428bca;
+}
+.label-primary[href]:hover,
+.label-primary[href]:focus {
+ background-color: #3071a9;
+}
+.label-success {
+ background-color: #5cb85c;
+}
+.label-success[href]:hover,
+.label-success[href]:focus {
+ background-color: #449d44;
+}
+.label-info {
+ background-color: #5bc0de;
+}
+.label-info[href]:hover,
+.label-info[href]:focus {
+ background-color: #31b0d5;
+}
+.label-warning {
+ background-color: #f0ad4e;
+}
+.label-warning[href]:hover,
+.label-warning[href]:focus {
+ background-color: #ec971f;
+}
+.label-danger {
+ background-color: #d9534f;
+}
+.label-danger[href]:hover,
+.label-danger[href]:focus {
+ background-color: #c9302c;
+}
+.badge {
+ display: inline-block;
+ min-width: 10px;
+ padding: 3px 7px;
+ font-size: 12px;
+ font-weight: bold;
+ line-height: 1;
+ color: #fff;
+ text-align: center;
+ white-space: nowrap;
+ vertical-align: baseline;
+ background-color: #999;
+ border-radius: 10px;
+}
+.badge:empty {
+ display: none;
+}
+.btn .badge {
+ position: relative;
+ top: -1px;
+}
+.btn-xs .badge {
+ top: 0;
+ padding: 1px 5px;
+}
+a.badge:hover,
+a.badge:focus {
+ color: #fff;
+ text-decoration: none;
+ cursor: pointer;
+}
+a.list-group-item.active > .badge,
+.nav-pills > .active > a > .badge {
+ color: #428bca;
+ background-color: #fff;
+}
+.nav-pills > li > a > .badge {
+ margin-left: 3px;
+}
+.jumbotron {
+ padding: 30px;
+ margin-bottom: 30px;
+ color: inherit;
+ background-color: #eee;
+}
+.jumbotron h1,
+.jumbotron .h1 {
+ color: inherit;
+}
+.jumbotron p {
+ margin-bottom: 15px;
+ font-size: 21px;
+ font-weight: 200;
+}
+.container .jumbotron {
+ border-radius: 6px;
+}
+.jumbotron .container {
+ max-width: 100%;
+}
+@media screen and (min-width: 768px) {
+ .jumbotron {
+ padding-top: 48px;
+ padding-bottom: 48px;
+ }
+ .container .jumbotron {
+ padding-right: 60px;
+ padding-left: 60px;
+ }
+ .jumbotron h1,
+ .jumbotron .h1 {
+ font-size: 63px;
+ }
+}
+.thumbnail {
+ display: block;
+ padding: 4px;
+ margin-bottom: 20px;
+ line-height: 1.428571429;
+ background-color: #fff;
+ border: 1px solid #ddd;
+ border-radius: 4px;
+ -webkit-transition: all .2s ease-in-out;
+ transition: all .2s ease-in-out;
+}
+.thumbnail > img,
+.thumbnail a > img {
+ display: block;
+ max-width: 100%;
+ height: auto;
+ margin-right: auto;
+ margin-left: auto;
+}
+a.thumbnail:hover,
+a.thumbnail:focus,
+a.thumbnail.active {
+ border-color: #428bca;
+}
+.thumbnail .caption {
+ padding: 9px;
+ color: #333;
+}
+.alert {
+ padding: 15px;
+ margin-bottom: 20px;
+ border: 1px solid transparent;
+ border-radius: 4px;
+}
+.alert h4 {
+ margin-top: 0;
+ color: inherit;
+}
+.alert .alert-link {
+ font-weight: bold;
+}
+.alert > p,
+.alert > ul {
+ margin-bottom: 0;
+}
+.alert > p + p {
+ margin-top: 5px;
+}
+.alert-dismissable {
+ padding-right: 35px;
+}
+.alert-dismissable .close {
+ position: relative;
+ top: -2px;
+ right: -21px;
+ color: inherit;
+}
+.alert-success {
+ color: #3c763d;
+ background-color: #dff0d8;
+ border-color: #d6e9c6;
+}
+.alert-success hr {
+ border-top-color: #c9e2b3;
+}
+.alert-success .alert-link {
+ color: #2b542c;
+}
+.alert-info {
+ color: #31708f;
+ background-color: #edf6fa;
+ border-color: #bce8f1;
+}
+.alert-info hr {
+ border-top-color: #a6e1ec;
+}
+.alert-info .alert-link {
+ color: #245269;
+ font-weight: bold;
+}
+.alert-info a {
+ font-weight: bold;
+}
+.alert-warning {
+ color: #8a6d3b;
+ background-color: #fcf8e3;
+ border-color: #faebcc;
+}
+.alert-warning hr {
+ border-top-color: #f7e1b5;
+}
+.alert-warning .alert-link {
+ color: #66512c;
+}
+.alert-danger {
+ color: #a94442;
+ background-color: #f2dede;
+ border-color: #ebccd1;
+}
+.alert-danger hr {
+ border-top-color: #e4b9c0;
+}
+.alert-danger .alert-link {
+ color: #843534;
+}
+@-webkit-keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+@keyframes progress-bar-stripes {
+ from {
+ background-position: 40px 0;
+ }
+ to {
+ background-position: 0 0;
+ }
+}
+.progress {
+ height: 20px;
+ margin-bottom: 20px;
+ overflow: hidden;
+ background-color: #f5f5f5;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, .1);
+ box-shadow: inset 0 1px 2px rgba(0, 0, 0, .1);
+}
+.progress-bar {
+ float: left;
+ width: 0;
+ height: 100%;
+ font-size: 12px;
+ line-height: 20px;
+ color: #fff;
+ text-align: center;
+ background-color: #428bca;
+ -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .15);
+ box-shadow: inset 0 -1px 0 rgba(0, 0, 0, .15);
+ -webkit-transition: width .6s ease;
+ transition: width .6s ease;
+}
+.progress-striped .progress-bar {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-size: 40px 40px;
+}
+.progress.active .progress-bar {
+ -webkit-animation: progress-bar-stripes 2s linear infinite;
+ animation: progress-bar-stripes 2s linear infinite;
+}
+.progress-bar-success {
+ background-color: #5cb85c;
+}
+.progress-striped .progress-bar-success {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.progress-bar-info {
+ background-color: #5bc0de;
+}
+.progress-striped .progress-bar-info {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.progress-bar-warning {
+ background-color: #f0ad4e;
+}
+.progress-striped .progress-bar-warning {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.progress-bar-danger {
+ background-color: #d9534f;
+}
+.progress-striped .progress-bar-danger {
+ background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+ background-image: linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+}
+.media,
+.media-body {
+ overflow: hidden;
+ zoom: 1;
+}
+.media,
+.media .media {
+ margin-top: 15px;
+}
+.media:first-child {
+ margin-top: 0;
+}
+.media-object {
+ display: block;
+}
+.media-heading {
+ margin: 0 0 5px;
+}
+.media > .pull-left {
+ margin-right: 10px;
+}
+.media > .pull-right {
+ margin-left: 10px;
+}
+.media-list {
+ padding-left: 0;
+ list-style: none;
+}
+.list-group {
+ padding-left: 0;
+ margin-bottom: 20px;
+}
+.list-group-item {
+ position: relative;
+ display: block;
+ padding: 10px 15px;
+ margin-bottom: -1px;
+ background-color: #fff;
+ border: 1px solid #ddd;
+}
+.list-group-item:first-child {
+ border-top-left-radius: 4px;
+ border-top-right-radius: 4px;
+}
+.list-group-item:last-child {
+ margin-bottom: 0;
+ border-bottom-right-radius: 4px;
+ border-bottom-left-radius: 4px;
+}
+.list-group-item > .badge {
+ float: right;
+}
+.list-group-item > .badge + .badge {
+ margin-right: 5px;
+}
+a.list-group-item {
+ color: #555;
+}
+a.list-group-item .list-group-item-heading {
+ color: #333;
+}
+a.list-group-item:hover,
+a.list-group-item:focus {
+ text-decoration: none;
+ background-color: #f5f5f5;
+}
+a.list-group-item.active,
+a.list-group-item.active:hover,
+a.list-group-item.active:focus {
+ z-index: 2;
+ color: #fff;
+ background-color: #428bca;
+ border-color: #428bca;
+}
+a.list-group-item.active .list-group-item-heading,
+a.list-group-item.active:hover .list-group-item-heading,
+a.list-group-item.active:focus .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item.active .list-group-item-text,
+a.list-group-item.active:hover .list-group-item-text,
+a.list-group-item.active:focus .list-group-item-text {
+ color: #e1edf7;
+}
+.list-group-item-success {
+ color: #3c763d;
+ background-color: #dff0d8;
+}
+a.list-group-item-success {
+ color: #3c763d;
+}
+a.list-group-item-success .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item-success:hover,
+a.list-group-item-success:focus {
+ color: #3c763d;
+ background-color: #d0e9c6;
+}
+a.list-group-item-success.active,
+a.list-group-item-success.active:hover,
+a.list-group-item-success.active:focus {
+ color: #fff;
+ background-color: #3c763d;
+ border-color: #3c763d;
+}
+.list-group-item-info {
+ color: #31708f;
+ background-color: #d9edf7;
+}
+a.list-group-item-info {
+ color: #31708f;
+}
+a.list-group-item-info .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item-info:hover,
+a.list-group-item-info:focus {
+ color: #31708f;
+ background-color: #c4e3f3;
+}
+a.list-group-item-info.active,
+a.list-group-item-info.active:hover,
+a.list-group-item-info.active:focus {
+ color: #fff;
+ background-color: #31708f;
+ border-color: #31708f;
+}
+.list-group-item-warning {
+ color: #8a6d3b;
+ background-color: #fcf8e3;
+}
+a.list-group-item-warning {
+ color: #8a6d3b;
+}
+a.list-group-item-warning .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item-warning:hover,
+a.list-group-item-warning:focus {
+ color: #8a6d3b;
+ background-color: #faf2cc;
+}
+a.list-group-item-warning.active,
+a.list-group-item-warning.active:hover,
+a.list-group-item-warning.active:focus {
+ color: #fff;
+ background-color: #8a6d3b;
+ border-color: #8a6d3b;
+}
+.list-group-item-danger {
+ color: #a94442;
+ background-color: #f2dede;
+}
+a.list-group-item-danger {
+ color: #a94442;
+}
+a.list-group-item-danger .list-group-item-heading {
+ color: inherit;
+}
+a.list-group-item-danger:hover,
+a.list-group-item-danger:focus {
+ color: #a94442;
+ background-color: #ebcccc;
+}
+a.list-group-item-danger.active,
+a.list-group-item-danger.active:hover,
+a.list-group-item-danger.active:focus {
+ color: #fff;
+ background-color: #a94442;
+ border-color: #a94442;
+}
+.list-group-item-heading {
+ margin-top: 0;
+ margin-bottom: 5px;
+}
+.list-group-item-text {
+ margin-bottom: 0;
+ line-height: 1.3;
+}
+.panel {
+ margin-bottom: 20px;
+ background-color: #fff;
+ border: 1px solid transparent;
+ border-radius: 4px;
+ -webkit-box-shadow: 0 1px 1px rgba(0, 0, 0, .05);
+ box-shadow: 0 1px 1px rgba(0, 0, 0, .05);
+}
+.panel-body {
+ padding: 15px;
+}
+.panel > .list-group {
+ margin-bottom: 0;
+}
+.panel > .list-group .list-group-item {
+ border-width: 1px 0;
+ border-radius: 0;
+}
+.panel > .list-group .list-group-item:first-child {
+ border-top: 0;
+}
+.panel > .list-group .list-group-item:last-child {
+ border-bottom: 0;
+}
+.panel > .list-group:first-child .list-group-item:first-child {
+ border-top-left-radius: 3px;
+ border-top-right-radius: 3px;
+}
+.panel > .list-group:last-child .list-group-item:last-child {
+ border-bottom-right-radius: 3px;
+ border-bottom-left-radius: 3px;
+}
+.panel-heading + .list-group .list-group-item:first-child {
+ border-top-width: 0;
+}
+.panel > .table,
+.panel > .table-responsive > .table {
+ margin-bottom: 0;
+}
+.panel > .table:first-child > thead:first-child > tr:first-child td:first-child,
+.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child td:first-child,
+.panel > .table:first-child > tbody:first-child > tr:first-child td:first-child,
+.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child td:first-child,
+.panel > .table:first-child > thead:first-child > tr:first-child th:first-child,
+.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child th:first-child,
+.panel > .table:first-child > tbody:first-child > tr:first-child th:first-child,
+.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child th:first-child {
+ border-top-left-radius: 3px;
+}
+.panel > .table:first-child > thead:first-child > tr:first-child td:last-child,
+.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child td:last-child,
+.panel > .table:first-child > tbody:first-child > tr:first-child td:last-child,
+.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child td:last-child,
+.panel > .table:first-child > thead:first-child > tr:first-child th:last-child,
+.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child th:last-child,
+.panel > .table:first-child > tbody:first-child > tr:first-child th:last-child,
+.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child th:last-child {
+ border-top-right-radius: 3px;
+}
+.panel > .table:last-child > tbody:last-child > tr:last-child td:first-child,
+.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child td:first-child,
+.panel > .table:last-child > tfoot:last-child > tr:last-child td:first-child,
+.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child td:first-child,
+.panel > .table:last-child > tbody:last-child > tr:last-child th:first-child,
+.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child th:first-child,
+.panel > .table:last-child > tfoot:last-child > tr:last-child th:first-child,
+.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child th:first-child {
+ border-bottom-left-radius: 3px;
+}
+.panel > .table:last-child > tbody:last-child > tr:last-child td:last-child,
+.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child td:last-child,
+.panel > .table:last-child > tfoot:last-child > tr:last-child td:last-child,
+.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child td:last-child,
+.panel > .table:last-child > tbody:last-child > tr:last-child th:last-child,
+.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child th:last-child,
+.panel > .table:last-child > tfoot:last-child > tr:last-child th:last-child,
+.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child th:last-child {
+ border-bottom-right-radius: 3px;
+}
+.panel > .panel-body + .table,
+.panel > .panel-body + .table-responsive {
+ border-top: 1px solid #ddd;
+}
+.panel > .table > tbody:first-child > tr:first-child th,
+.panel > .table > tbody:first-child > tr:first-child td {
+ border-top: 0;
+}
+.panel > .table-bordered,
+.panel > .table-responsive > .table-bordered {
+ border: 0;
+}
+.panel > .table-bordered > thead > tr > th:first-child,
+.panel > .table-responsive > .table-bordered > thead > tr > th:first-child,
+.panel > .table-bordered > tbody > tr > th:first-child,
+.panel > .table-responsive > .table-bordered > tbody > tr > th:first-child,
+.panel > .table-bordered > tfoot > tr > th:first-child,
+.panel > .table-responsive > .table-bordered > tfoot > tr > th:first-child,
+.panel > .table-bordered > thead > tr > td:first-child,
+.panel > .table-responsive > .table-bordered > thead > tr > td:first-child,
+.panel > .table-bordered > tbody > tr > td:first-child,
+.panel > .table-responsive > .table-bordered > tbody > tr > td:first-child,
+.panel > .table-bordered > tfoot > tr > td:first-child,
+.panel > .table-responsive > .table-bordered > tfoot > tr > td:first-child {
+ border-left: 0;
+}
+.panel > .table-bordered > thead > tr > th:last-child,
+.panel > .table-responsive > .table-bordered > thead > tr > th:last-child,
+.panel > .table-bordered > tbody > tr > th:last-child,
+.panel > .table-responsive > .table-bordered > tbody > tr > th:last-child,
+.panel > .table-bordered > tfoot > tr > th:last-child,
+.panel > .table-responsive > .table-bordered > tfoot > tr > th:last-child,
+.panel > .table-bordered > thead > tr > td:last-child,
+.panel > .table-responsive > .table-bordered > thead > tr > td:last-child,
+.panel > .table-bordered > tbody > tr > td:last-child,
+.panel > .table-responsive > .table-bordered > tbody > tr > td:last-child,
+.panel > .table-bordered > tfoot > tr > td:last-child,
+.panel > .table-responsive > .table-bordered > tfoot > tr > td:last-child {
+ border-right: 0;
+}
+.panel > .table-bordered > thead > tr:first-child > th,
+.panel > .table-responsive > .table-bordered > thead > tr:first-child > th,
+.panel > .table-bordered > tbody > tr:first-child > th,
+.panel > .table-responsive > .table-bordered > tbody > tr:first-child > th,
+.panel > .table-bordered > tfoot > tr:first-child > th,
+.panel > .table-responsive > .table-bordered > tfoot > tr:first-child > th,
+.panel > .table-bordered > thead > tr:first-child > td,
+.panel > .table-responsive > .table-bordered > thead > tr:first-child > td,
+.panel > .table-bordered > tbody > tr:first-child > td,
+.panel > .table-responsive > .table-bordered > tbody > tr:first-child > td,
+.panel > .table-bordered > tfoot > tr:first-child > td,
+.panel > .table-responsive > .table-bordered > tfoot > tr:first-child > td {
+ border-top: 0;
+}
+.panel > .table-bordered > thead > tr:last-child > th,
+.panel > .table-responsive > .table-bordered > thead > tr:last-child > th,
+.panel > .table-bordered > tbody > tr:last-child > th,
+.panel > .table-responsive > .table-bordered > tbody > tr:last-child > th,
+.panel > .table-bordered > tfoot > tr:last-child > th,
+.panel > .table-responsive > .table-bordered > tfoot > tr:last-child > th,
+.panel > .table-bordered > thead > tr:last-child > td,
+.panel > .table-responsive > .table-bordered > thead > tr:last-child > td,
+.panel > .table-bordered > tbody > tr:last-child > td,
+.panel > .table-responsive > .table-bordered > tbody > tr:last-child > td,
+.panel > .table-bordered > tfoot > tr:last-child > td,
+.panel > .table-responsive > .table-bordered > tfoot > tr:last-child > td {
+ border-bottom: 0;
+}
+.panel > .table-responsive {
+ margin-bottom: 0;
+ border: 0;
+}
+.panel-heading {
+ padding: 10px 15px;
+ border-bottom: 1px solid transparent;
+ border-top-left-radius: 3px;
+ border-top-right-radius: 3px;
+}
+.panel-heading > .dropdown .dropdown-toggle {
+ color: inherit;
+}
+.panel-title {
+ margin-top: 0;
+ margin-bottom: 0;
+ font-size: 16px;
+ color: inherit;
+}
+.panel-title > a {
+ color: inherit;
+}
+.panel-footer {
+ padding: 10px 15px;
+ background-color: #f5f5f5;
+ border-top: 1px solid #ddd;
+ border-bottom-right-radius: 3px;
+ border-bottom-left-radius: 3px;
+}
+.panel-group {
+ margin-bottom: 20px;
+}
+.panel-group .panel {
+ margin-bottom: 0;
+ overflow: hidden;
+ border-radius: 4px;
+}
+.panel-group .panel + .panel {
+ margin-top: 5px;
+}
+.panel-group .panel-heading {
+ border-bottom: 0;
+}
+.panel-group .panel-heading + .panel-collapse .panel-body {
+ border-top: 1px solid #ddd;
+}
+.panel-group .panel-footer {
+ border-top: 0;
+}
+.panel-group .panel-footer + .panel-collapse .panel-body {
+ border-bottom: 1px solid #ddd;
+}
+.panel-default {
+ border-color: #ddd;
+}
+.panel-default > .panel-heading {
+ color: #333;
+ background-color: #f5f5f5;
+ border-color: #ddd;
+}
+.panel-default > .panel-heading + .panel-collapse .panel-body {
+ border-top-color: #ddd;
+}
+.panel-default > .panel-footer + .panel-collapse .panel-body {
+ border-bottom-color: #ddd;
+}
+.panel-primary {
+ border-color: #428bca;
+}
+.panel-primary > .panel-heading {
+ color: #fff;
+ background-color: #428bca;
+ border-color: #428bca;
+}
+.panel-primary > .panel-heading + .panel-collapse .panel-body {
+ border-top-color: #428bca;
+}
+.panel-primary > .panel-footer + .panel-collapse .panel-body {
+ border-bottom-color: #428bca;
+}
+.panel-success {
+ border-color: #d6e9c6;
+}
+.panel-success > .panel-heading {
+ color: #3c763d;
+ background-color: #dff0d8;
+ border-color: #d6e9c6;
+}
+.panel-success > .panel-heading + .panel-collapse .panel-body {
+ border-top-color: #d6e9c6;
+}
+.panel-success > .panel-footer + .panel-collapse .panel-body {
+ border-bottom-color: #d6e9c6;
+}
+.panel-info {
+ border-color: #bce8f1;
+}
+.panel-info > .panel-heading {
+ color: #31708f;
+ background-color: #d9edf7;
+ border-color: #bce8f1;
+}
+.panel-info > .panel-heading + .panel-collapse .panel-body {
+ border-top-color: #bce8f1;
+}
+.panel-info > .panel-footer + .panel-collapse .panel-body {
+ border-bottom-color: #bce8f1;
+}
+.panel-warning {
+ border-color: #faebcc;
+}
+.panel-warning > .panel-heading {
+ color: #8a6d3b;
+ background-color: #fcf8e3;
+ border-color: #faebcc;
+}
+.panel-warning > .panel-heading + .panel-collapse .panel-body {
+ border-top-color: #faebcc;
+}
+.panel-warning > .panel-footer + .panel-collapse .panel-body {
+ border-bottom-color: #faebcc;
+}
+.panel-danger {
+ border-color: #ebccd1;
+}
+.panel-danger > .panel-heading {
+ color: #a94442;
+ background-color: #f2dede;
+ border-color: #ebccd1;
+}
+.panel-danger > .panel-heading + .panel-collapse .panel-body {
+ border-top-color: #ebccd1;
+}
+.panel-danger > .panel-footer + .panel-collapse .panel-body {
+ border-bottom-color: #ebccd1;
+}
+.well {
+ min-height: 20px;
+ padding: 19px;
+ margin-bottom: 20px;
+ background-color: #f5f5f5;
+ border: 1px solid #e3e3e3;
+ border-radius: 4px;
+ -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, .05);
+ box-shadow: inset 0 1px 1px rgba(0, 0, 0, .05);
+}
+.well blockquote {
+ border-color: #ddd;
+ border-color: rgba(0, 0, 0, .15);
+}
+.well-lg {
+ padding: 24px;
+ border-radius: 6px;
+}
+.well-sm {
+ padding: 9px;
+ border-radius: 3px;
+}
+.close {
+ float: right;
+ font-size: 21px;
+ font-weight: bold;
+ line-height: 1;
+ color: #000;
+ text-shadow: 0 1px 0 #fff;
+ filter: alpha(opacity=20);
+ opacity: .2;
+}
+.close:hover,
+.close:focus {
+ color: #000;
+ text-decoration: none;
+ cursor: pointer;
+ filter: alpha(opacity=50);
+ opacity: .5;
+}
+button.close {
+ -webkit-appearance: none;
+ padding: 0;
+ cursor: pointer;
+ background: transparent;
+ border: 0;
+}
+.modal-open {
+ overflow: hidden;
+}
+.modal {
+ position: fixed;
+ top: 0;
+ right: 0;
+ bottom: 0;
+ left: 0;
+ z-index: 1050;
+ display: none;
+ overflow: auto;
+ overflow-y: scroll;
+ -webkit-overflow-scrolling: touch;
+ outline: 0;
+}
+.modal.fade .modal-dialog {
+ -webkit-transition: -webkit-transform .3s ease-out;
+ -moz-transition: -moz-transform .3s ease-out;
+ -o-transition: -o-transform .3s ease-out;
+ transition: transform .3s ease-out;
+ -webkit-transform: translate(0, -25%);
+ -ms-transform: translate(0, -25%);
+ transform: translate(0, -25%);
+}
+.modal.in .modal-dialog {
+ -webkit-transform: translate(0, 0);
+ -ms-transform: translate(0, 0);
+ transform: translate(0, 0);
+}
+.modal-dialog {
+ position: relative;
+ width: auto;
+ margin: 10px;
+}
+.modal-content {
+ position: relative;
+ background-color: #fff;
+ background-clip: padding-box;
+ border: 1px solid #999;
+ border: 1px solid rgba(0, 0, 0, .2);
+ border-radius: 6px;
+ outline: none;
+ -webkit-box-shadow: 0 3px 9px rgba(0, 0, 0, .5);
+ box-shadow: 0 3px 9px rgba(0, 0, 0, .5);
+}
+.modal-backdrop {
+ position: fixed;
+ top: 0;
+ right: 0;
+ bottom: 0;
+ left: 0;
+ z-index: 1040;
+ background-color: #000;
+}
+.modal-backdrop.fade {
+ filter: alpha(opacity=0);
+ opacity: 0;
+}
+.modal-backdrop.in {
+ filter: alpha(opacity=50);
+ opacity: .5;
+}
+.modal-header {
+ min-height: 16.428571429px;
+ padding: 15px;
+ border-bottom: 1px solid #e5e5e5;
+}
+.modal-header .close {
+ margin-top: -2px;
+}
+.modal-title {
+ margin: 0;
+ line-height: 1.428571429;
+}
+.modal-body {
+ position: relative;
+ padding: 20px;
+}
+.modal-footer {
+ padding: 19px 20px 20px;
+ margin-top: 15px;
+ text-align: right;
+ border-top: 1px solid #e5e5e5;
+}
+.modal-footer .btn + .btn {
+ margin-bottom: 0;
+ margin-left: 5px;
+}
+.modal-footer .btn-group .btn + .btn {
+ margin-left: -1px;
+}
+.modal-footer .btn-block + .btn-block {
+ margin-left: 0;
+}
+@media (min-width: 768px) {
+ .modal-dialog {
+ width: 600px;
+ margin: 30px auto;
+ }
+ .modal-content {
+ -webkit-box-shadow: 0 5px 15px rgba(0, 0, 0, .5);
+ box-shadow: 0 5px 15px rgba(0, 0, 0, .5);
+ }
+ .modal-sm {
+ width: 300px;
+ }
+ .modal-lg {
+ width: 900px;
+ }
+}
+.tooltip {
+ position: absolute;
+ z-index: 1030;
+ display: block;
+ font-size: 12px;
+ line-height: 1.4;
+ visibility: visible;
+ filter: alpha(opacity=0);
+ opacity: 0;
+}
+.tooltip.in {
+ filter: alpha(opacity=90);
+ opacity: .9;
+}
+.tooltip.top {
+ padding: 5px 0;
+ margin-top: -3px;
+}
+.tooltip.right {
+ padding: 0 5px;
+ margin-left: 3px;
+}
+.tooltip.bottom {
+ padding: 5px 0;
+ margin-top: 3px;
+}
+.tooltip.left {
+ padding: 0 5px;
+ margin-left: -3px;
+}
+.tooltip-inner {
+ max-width: 200px;
+ padding: 3px 8px;
+ color: #fff;
+ text-align: center;
+ text-decoration: none;
+ background-color: #000;
+ border-radius: 4px;
+}
+.tooltip-arrow {
+ position: absolute;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+}
+.tooltip.top .tooltip-arrow {
+ bottom: 0;
+ left: 50%;
+ margin-left: -5px;
+ border-width: 5px 5px 0;
+ border-top-color: #000;
+}
+.tooltip.top-left .tooltip-arrow {
+ bottom: 0;
+ left: 5px;
+ border-width: 5px 5px 0;
+ border-top-color: #000;
+}
+.tooltip.top-right .tooltip-arrow {
+ right: 5px;
+ bottom: 0;
+ border-width: 5px 5px 0;
+ border-top-color: #000;
+}
+.tooltip.right .tooltip-arrow {
+ top: 50%;
+ left: 0;
+ margin-top: -5px;
+ border-width: 5px 5px 5px 0;
+ border-right-color: #000;
+}
+.tooltip.left .tooltip-arrow {
+ top: 50%;
+ right: 0;
+ margin-top: -5px;
+ border-width: 5px 0 5px 5px;
+ border-left-color: #000;
+}
+.tooltip.bottom .tooltip-arrow {
+ top: 0;
+ left: 50%;
+ margin-left: -5px;
+ border-width: 0 5px 5px;
+ border-bottom-color: #000;
+}
+.tooltip.bottom-left .tooltip-arrow {
+ top: 0;
+ left: 5px;
+ border-width: 0 5px 5px;
+ border-bottom-color: #000;
+}
+.tooltip.bottom-right .tooltip-arrow {
+ top: 0;
+ right: 5px;
+ border-width: 0 5px 5px;
+ border-bottom-color: #000;
+}
+.popover {
+ position: absolute;
+ top: 0;
+ left: 0;
+ z-index: 1010;
+ display: none;
+ max-width: 276px;
+ padding: 1px;
+ text-align: left;
+ white-space: normal;
+ background-color: #fff;
+ background-clip: padding-box;
+ border: 1px solid #ccc;
+ border: 1px solid rgba(0, 0, 0, .2);
+ border-radius: 6px;
+ -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, .2);
+ box-shadow: 0 5px 10px rgba(0, 0, 0, .2);
+}
+.popover.top {
+ margin-top: -10px;
+}
+.popover.right {
+ margin-left: 10px;
+}
+.popover.bottom {
+ margin-top: 10px;
+}
+.popover.left {
+ margin-left: -10px;
+}
+.popover-title {
+ padding: 8px 14px;
+ margin: 0;
+ font-size: 14px;
+ font-weight: normal;
+ line-height: 18px;
+ background-color: #f7f7f7;
+ border-bottom: 1px solid #ebebeb;
+ border-radius: 5px 5px 0 0;
+}
+.popover-content {
+ padding: 9px 14px;
+}
+.popover .arrow,
+.popover .arrow:after {
+ position: absolute;
+ display: block;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+}
+.popover .arrow {
+ border-width: 11px;
+}
+.popover .arrow:after {
+ content: "";
+ border-width: 10px;
+}
+.popover.top .arrow {
+ bottom: -11px;
+ left: 50%;
+ margin-left: -11px;
+ border-top-color: #999;
+ border-top-color: rgba(0, 0, 0, .25);
+ border-bottom-width: 0;
+}
+.popover.top .arrow:after {
+ bottom: 1px;
+ margin-left: -10px;
+ content: " ";
+ border-top-color: #fff;
+ border-bottom-width: 0;
+}
+.popover.right .arrow {
+ top: 50%;
+ left: -11px;
+ margin-top: -11px;
+ border-right-color: #999;
+ border-right-color: rgba(0, 0, 0, .25);
+ border-left-width: 0;
+}
+.popover.right .arrow:after {
+ bottom: -10px;
+ left: 1px;
+ content: " ";
+ border-right-color: #fff;
+ border-left-width: 0;
+}
+.popover.bottom .arrow {
+ top: -11px;
+ left: 50%;
+ margin-left: -11px;
+ border-top-width: 0;
+ border-bottom-color: #999;
+ border-bottom-color: rgba(0, 0, 0, .25);
+}
+.popover.bottom .arrow:after {
+ top: 1px;
+ margin-left: -10px;
+ content: " ";
+ border-top-width: 0;
+ border-bottom-color: #fff;
+}
+.popover.left .arrow {
+ top: 50%;
+ right: -11px;
+ margin-top: -11px;
+ border-right-width: 0;
+ border-left-color: #999;
+ border-left-color: rgba(0, 0, 0, .25);
+}
+.popover.left .arrow:after {
+ right: 1px;
+ bottom: -10px;
+ content: " ";
+ border-right-width: 0;
+ border-left-color: #fff;
+}
+.carousel {
+ position: relative;
+}
+.carousel-inner {
+ position: relative;
+ width: 100%;
+ overflow: hidden;
+}
+.carousel-inner > .item {
+ position: relative;
+ display: none;
+ -webkit-transition: .6s ease-in-out left;
+ transition: .6s ease-in-out left;
+}
+.carousel-inner > .item > img,
+.carousel-inner > .item > a > img {
+ display: block;
+ max-width: 100%;
+ height: auto;
+ line-height: 1;
+}
+.carousel-inner > .active,
+.carousel-inner > .next,
+.carousel-inner > .prev {
+ display: block;
+}
+.carousel-inner > .active {
+ left: 0;
+}
+.carousel-inner > .next,
+.carousel-inner > .prev {
+ position: absolute;
+ top: 0;
+ width: 100%;
+}
+.carousel-inner > .next {
+ left: 100%;
+}
+.carousel-inner > .prev {
+ left: -100%;
+}
+.carousel-inner > .next.left,
+.carousel-inner > .prev.right {
+ left: 0;
+}
+.carousel-inner > .active.left {
+ left: -100%;
+}
+.carousel-inner > .active.right {
+ left: 100%;
+}
+.carousel-control {
+ position: absolute;
+ top: 0;
+ bottom: 0;
+ left: 0;
+ width: 15%;
+ font-size: 20px;
+ color: #fff;
+ text-align: center;
+ text-shadow: 0 1px 2px rgba(0, 0, 0, .6);
+ filter: alpha(opacity=50);
+ opacity: .5;
+}
+.carousel-control.left {
+ background-image: -webkit-linear-gradient(left, color-stop(rgba(0, 0, 0, .5) 0%), color-stop(rgba(0, 0, 0, .0001) 100%));
+ background-image: linear-gradient(to right, rgba(0, 0, 0, .5) 0%, rgba(0, 0, 0, .0001) 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#80000000', endColorstr='#00000000', GradientType=1);
+ background-repeat: repeat-x;
+}
+.carousel-control.right {
+ right: 0;
+ left: auto;
+ background-image: -webkit-linear-gradient(left, color-stop(rgba(0, 0, 0, .0001) 0%), color-stop(rgba(0, 0, 0, .5) 100%));
+ background-image: linear-gradient(to right, rgba(0, 0, 0, .0001) 0%, rgba(0, 0, 0, .5) 100%);
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#00000000', endColorstr='#80000000', GradientType=1);
+ background-repeat: repeat-x;
+}
+.carousel-control:hover,
+.carousel-control:focus {
+ color: #fff;
+ text-decoration: none;
+ filter: alpha(opacity=90);
+ outline: none;
+ opacity: .9;
+}
+.carousel-control .icon-prev,
+.carousel-control .icon-next,
+.carousel-control .glyphicon-chevron-left,
+.carousel-control .glyphicon-chevron-right {
+ position: absolute;
+ top: 50%;
+ z-index: 5;
+ display: inline-block;
+}
+.carousel-control .icon-prev,
+.carousel-control .glyphicon-chevron-left {
+ left: 50%;
+}
+.carousel-control .icon-next,
+.carousel-control .glyphicon-chevron-right {
+ right: 50%;
+}
+.carousel-control .icon-prev,
+.carousel-control .icon-next {
+ width: 20px;
+ height: 20px;
+ margin-top: -10px;
+ margin-left: -10px;
+ font-family: serif;
+}
+.carousel-control .icon-prev:before {
+ content: '\2039';
+}
+.carousel-control .icon-next:before {
+ content: '\203a';
+}
+.carousel-indicators {
+ position: absolute;
+ bottom: 10px;
+ left: 50%;
+ z-index: 15;
+ width: 60%;
+ padding-left: 0;
+ margin-left: -30%;
+ text-align: center;
+ list-style: none;
+}
+.carousel-indicators li {
+ display: inline-block;
+ width: 10px;
+ height: 10px;
+ margin: 1px;
+ text-indent: -999px;
+ cursor: pointer;
+ background-color: #000 \9;
+ background-color: rgba(0, 0, 0, 0);
+ border: 1px solid #fff;
+ border-radius: 10px;
+}
+.carousel-indicators .active {
+ width: 12px;
+ height: 12px;
+ margin: 0;
+ background-color: #fff;
+}
+.carousel-caption {
+ position: absolute;
+ right: 15%;
+ bottom: 20px;
+ left: 15%;
+ z-index: 10;
+ padding-top: 20px;
+ padding-bottom: 20px;
+ color: #fff;
+ text-align: center;
+ text-shadow: 0 1px 2px rgba(0, 0, 0, .6);
+}
+.carousel-caption .btn {
+ text-shadow: none;
+}
+@media screen and (min-width: 768px) {
+ .carousel-control .glyphicons-chevron-left,
+ .carousel-control .glyphicons-chevron-right,
+ .carousel-control .icon-prev,
+ .carousel-control .icon-next {
+ width: 30px;
+ height: 30px;
+ margin-top: -15px;
+ margin-left: -15px;
+ font-size: 30px;
+ }
+ .carousel-caption {
+ right: 20%;
+ left: 20%;
+ padding-bottom: 30px;
+ }
+ .carousel-indicators {
+ bottom: 20px;
+ }
+}
+.clearfix:before,
+.clearfix:after,
+.container:before,
+.container:after,
+.container-fluid:before,
+.container-fluid:after,
+.row:before,
+.row:after,
+.form-horizontal .form-group:before,
+.form-horizontal .form-group:after,
+.btn-toolbar:before,
+.btn-toolbar:after,
+.btn-group-vertical > .btn-group:before,
+.btn-group-vertical > .btn-group:after,
+.nav:before,
+.nav:after,
+.navbar:before,
+.navbar:after,
+.navbar-header:before,
+.navbar-header:after,
+.navbar-collapse:before,
+.navbar-collapse:after,
+.pager:before,
+.pager:after,
+.panel-body:before,
+.panel-body:after,
+.modal-footer:before,
+.modal-footer:after {
+ display: table;
+ content: " ";
+}
+.clearfix:after,
+.container:after,
+.container-fluid:after,
+.row:after,
+.form-horizontal .form-group:after,
+.btn-toolbar:after,
+.btn-group-vertical > .btn-group:after,
+.nav:after,
+.navbar:after,
+.navbar-header:after,
+.navbar-collapse:after,
+.pager:after,
+.panel-body:after,
+.modal-footer:after {
+ clear: both;
+}
+.center-block {
+ display: block;
+ margin-right: auto;
+ margin-left: auto;
+}
+.pull-right {
+ float: right !important;
+}
+.pull-left {
+ float: left !important;
+}
+.hide {
+ display: none !important;
+}
+.show {
+ display: block !important;
+}
+.invisible {
+ visibility: hidden;
+}
+.text-hide {
+ font: 0/0 a;
+ color: transparent;
+ text-shadow: none;
+ background-color: transparent;
+ border: 0;
+}
+.hidden {
+ display: none !important;
+ visibility: hidden !important;
+}
+.affix {
+ position: fixed;
+}
+@-ms-viewport {
+ width: device-width;
+}
+.visible-xs,
+tr.visible-xs,
+th.visible-xs,
+td.visible-xs {
+ display: none !important;
+}
+@media (max-width: 767px) {
+ .visible-xs {
+ display: block !important;
+ }
+ table.visible-xs {
+ display: table;
+ }
+ tr.visible-xs {
+ display: table-row !important;
+ }
+ th.visible-xs,
+ td.visible-xs {
+ display: table-cell !important;
+ }
+}
+.visible-sm,
+tr.visible-sm,
+th.visible-sm,
+td.visible-sm {
+ display: none !important;
+}
+@media (min-width: 768px) and (max-width: 991px) {
+ .visible-sm {
+ display: block !important;
+ }
+ table.visible-sm {
+ display: table;
+ }
+ tr.visible-sm {
+ display: table-row !important;
+ }
+ th.visible-sm,
+ td.visible-sm {
+ display: table-cell !important;
+ }
+}
+.visible-md,
+tr.visible-md,
+th.visible-md,
+td.visible-md {
+ display: none !important;
+}
+@media (min-width: 992px) and (max-width: 1199px) {
+ .visible-md {
+ display: block !important;
+ }
+ table.visible-md {
+ display: table;
+ }
+ tr.visible-md {
+ display: table-row !important;
+ }
+ th.visible-md,
+ td.visible-md {
+ display: table-cell !important;
+ }
+}
+.visible-lg,
+tr.visible-lg,
+th.visible-lg,
+td.visible-lg {
+ display: none !important;
+}
+@media (min-width: 1200px) {
+ .visible-lg {
+ display: block !important;
+ }
+ table.visible-lg {
+ display: table;
+ }
+ tr.visible-lg {
+ display: table-row !important;
+ }
+ th.visible-lg,
+ td.visible-lg {
+ display: table-cell !important;
+ }
+}
+@media (max-width: 767px) {
+ .hidden-xs,
+ tr.hidden-xs,
+ th.hidden-xs,
+ td.hidden-xs {
+ display: none !important;
+ }
+}
+@media (min-width: 768px) and (max-width: 991px) {
+ .hidden-sm,
+ tr.hidden-sm,
+ th.hidden-sm,
+ td.hidden-sm {
+ display: none !important;
+ }
+}
+@media (min-width: 992px) and (max-width: 1199px) {
+ .hidden-md,
+ tr.hidden-md,
+ th.hidden-md,
+ td.hidden-md {
+ display: none !important;
+ }
+}
+@media (min-width: 1200px) {
+ .hidden-lg,
+ tr.hidden-lg,
+ th.hidden-lg,
+ td.hidden-lg {
+ display: none !important;
+ }
+}
+.visible-print,
+tr.visible-print,
+th.visible-print,
+td.visible-print {
+ display: none !important;
+}
+@media print {
+ .visible-print {
+ display: block !important;
+ }
+ table.visible-print {
+ display: table;
+ }
+ tr.visible-print {
+ display: table-row !important;
+ }
+ th.visible-print,
+ td.visible-print {
+ display: table-cell !important;
+ }
+}
+@media print {
+ .hidden-print,
+ tr.hidden-print,
+ th.hidden-print,
+ td.hidden-print {
+ display: none !important;
+ }
+}
+/*# sourceMappingURL=bootstrap.css.map */
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normalize.css v3.0.0 | MIT License | git.io/normalize */\n\n//\n// 1. Set default font family to sans-serif.\n// 2. Prevent iOS text size adjust after orientation change, without disabling\n// user zoom.\n//\n\nhtml {\n font-family: sans-serif; // 1\n -ms-text-size-adjust: 100%; // 2\n -webkit-text-size-adjust: 100%; // 2\n}\n\n//\n// Remove default margin.\n//\n\nbody {\n margin: 0;\n}\n\n// HTML5 display definitions\n// ==========================================================================\n\n//\n// Correct `block` display not defined in IE 8/9.\n//\n\narticle,\naside,\ndetails,\nfigcaption,\nfigure,\nfooter,\nheader,\nhgroup,\nmain,\nnav,\nsection,\nsummary {\n display: block;\n}\n\n//\n// 1. Correct `inline-block` display not defined in IE 8/9.\n// 2. Normalize vertical alignment of `progress` in Chrome, Firefox, and Opera.\n//\n\naudio,\ncanvas,\nprogress,\nvideo {\n display: inline-block; // 1\n vertical-align: baseline; // 2\n}\n\n//\n// Prevent modern browsers from displaying `audio` without controls.\n// Remove excess height in iOS 5 devices.\n//\n\naudio:not([controls]) {\n display: none;\n height: 0;\n}\n\n//\n// Address `[hidden]` styling not present in IE 8/9.\n// Hide the `template` element in IE, Safari, and Firefox < 22.\n//\n\n[hidden],\ntemplate {\n display: none;\n}\n\n// Links\n// ==========================================================================\n\n//\n// Remove the gray background color from active links in IE 10.\n//\n\na {\n background: transparent;\n}\n\n//\n// Improve readability when focused and also mouse hovered in all browsers.\n//\n\na:active,\na:hover {\n outline: 0;\n}\n\n// Text-level semantics\n// ==========================================================================\n\n//\n// Address styling not present in IE 8/9, Safari 5, and Chrome.\n//\n\nabbr[title] {\n border-bottom: 1px dotted;\n}\n\n//\n// Address style set to `bolder` in Firefox 4+, Safari 5, and Chrome.\n//\n\nb,\nstrong {\n font-weight: bold;\n}\n\n//\n// Address styling not present in Safari 5 and Chrome.\n//\n\ndfn {\n font-style: italic;\n}\n\n//\n// Address variable `h1` font-size and margin within `section` and `article`\n// contexts in Firefox 4+, Safari 5, and Chrome.\n//\n\nh1 {\n font-size: 2em;\n margin: 0.67em 0;\n}\n\n//\n// Address styling not present in IE 8/9.\n//\n\nmark {\n background: #ff0;\n color: #000;\n}\n\n//\n// Address inconsistent and variable font size in all browsers.\n//\n\nsmall {\n font-size: 80%;\n}\n\n//\n// Prevent `sub` and `sup` affecting `line-height` in all browsers.\n//\n\nsub,\nsup {\n font-size: 75%;\n line-height: 0;\n position: relative;\n vertical-align: baseline;\n}\n\nsup {\n top: -0.5em;\n}\n\nsub {\n bottom: -0.25em;\n}\n\n// Embedded content\n// ==========================================================================\n\n//\n// Remove border when inside `a` element in IE 8/9.\n//\n\nimg {\n border: 0;\n}\n\n//\n// Correct overflow displayed oddly in IE 9.\n//\n\nsvg:not(:root) {\n overflow: hidden;\n}\n\n// Grouping content\n// ==========================================================================\n\n//\n// Address margin not present in IE 8/9 and Safari 5.\n//\n\nfigure {\n margin: 1em 40px;\n}\n\n//\n// Address differences between Firefox and other browsers.\n//\n\nhr {\n -moz-box-sizing: content-box;\n box-sizing: content-box;\n height: 0;\n}\n\n//\n// Contain overflow in all browsers.\n//\n\npre {\n overflow: auto;\n}\n\n//\n// Address odd `em`-unit font size rendering in all browsers.\n//\n\ncode,\nkbd,\npre,\nsamp {\n font-family: monospace, monospace;\n font-size: 1em;\n}\n\n// Forms\n// ==========================================================================\n\n//\n// Known limitation: by default, Chrome and Safari on OS X allow very limited\n// styling of `select`, unless a `border` property is set.\n//\n\n//\n// 1. Correct color not being inherited.\n// Known issue: affects color of disabled elements.\n// 2. Correct font properties not being inherited.\n// 3. Address margins set differently in Firefox 4+, Safari 5, and Chrome.\n//\n\nbutton,\ninput,\noptgroup,\nselect,\ntextarea {\n color: inherit; // 1\n font: inherit; // 2\n margin: 0; // 3\n}\n\n//\n// Address `overflow` set to `hidden` in IE 8/9/10.\n//\n\nbutton {\n overflow: visible;\n}\n\n//\n// Address inconsistent `text-transform` inheritance for `button` and `select`.\n// All other form control elements do not inherit `text-transform` values.\n// Correct `button` style inheritance in Firefox, IE 8+, and Opera\n// Correct `select` style inheritance in Firefox.\n//\n\nbutton,\nselect {\n text-transform: none;\n}\n\n//\n// 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`\n// and `video` controls.\n// 2. Correct inability to style clickable `input` types in iOS.\n// 3. Improve usability and consistency of cursor style between image-type\n// `input` and others.\n//\n\nbutton,\nhtml input[type=\"button\"], // 1\ninput[type=\"reset\"],\ninput[type=\"submit\"] {\n -webkit-appearance: button; // 2\n cursor: pointer; // 3\n}\n\n//\n// Re-set default cursor for disabled elements.\n//\n\nbutton[disabled],\nhtml input[disabled] {\n cursor: default;\n}\n\n//\n// Remove inner padding and border in Firefox 4+.\n//\n\nbutton::-moz-focus-inner,\ninput::-moz-focus-inner {\n border: 0;\n padding: 0;\n}\n\n//\n// Address Firefox 4+ setting `line-height` on `input` using `!important` in\n// the UA stylesheet.\n//\n\ninput {\n line-height: normal;\n}\n\n//\n// It's recommended that you don't attempt to style these elements.\n// Firefox's implementation doesn't respect box-sizing, padding, or width.\n//\n// 1. Address box sizing set to `content-box` in IE 8/9/10.\n// 2. Remove excess padding in IE 8/9/10.\n//\n\ninput[type=\"checkbox\"],\ninput[type=\"radio\"] {\n box-sizing: border-box; // 1\n padding: 0; // 2\n}\n\n//\n// Fix the cursor style for Chrome's increment/decrement buttons. For certain\n// `font-size` values of the `input`, it causes the cursor style of the\n// decrement button to change from `default` to `text`.\n//\n\ninput[type=\"number\"]::-webkit-inner-spin-button,\ninput[type=\"number\"]::-webkit-outer-spin-button {\n height: auto;\n}\n\n//\n// 1. Address `appearance` set to `searchfield` in Safari 5 and Chrome.\n// 2. Address `box-sizing` set to `border-box` in Safari 5 and Chrome\n// (include `-moz` to future-proof).\n//\n\ninput[type=\"search\"] {\n -webkit-appearance: textfield; // 1\n -moz-box-sizing: content-box;\n -webkit-box-sizing: content-box; // 2\n box-sizing: content-box;\n}\n\n//\n// Remove inner padding and search cancel button in Safari and Chrome on OS X.\n// Safari (but not Chrome) clips the cancel button when the search input has\n// padding (and `textfield` appearance).\n//\n\ninput[type=\"search\"]::-webkit-search-cancel-button,\ninput[type=\"search\"]::-webkit-search-decoration {\n -webkit-appearance: none;\n}\n\n//\n// Define consistent border, margin, and padding.\n//\n\nfieldset {\n border: 1px solid #c0c0c0;\n margin: 0 2px;\n padding: 0.35em 0.625em 0.75em;\n}\n\n//\n// 1. Correct `color` not being inherited in IE 8/9.\n// 2. Remove padding so people aren't caught out if they zero out fieldsets.\n//\n\nlegend {\n border: 0; // 1\n padding: 0; // 2\n}\n\n//\n// Remove default vertical scrollbar in IE 8/9.\n//\n\ntextarea {\n overflow: auto;\n}\n\n//\n// Don't inherit the `font-weight` (applied by a rule above).\n// NOTE: the default cannot safely be changed in Chrome and Safari on OS X.\n//\n\noptgroup {\n font-weight: bold;\n}\n\n// Tables\n// ==========================================================================\n\n//\n// Remove most spacing between table cells.\n//\n\ntable {\n border-collapse: collapse;\n border-spacing: 0;\n}\n\ntd,\nth {\n padding: 0;\n}","//\n// Basic print styles\n// --------------------------------------------------\n// Source: https://github.com/h5bp/html5-boilerplate/blob/master/css/main.css\n\n@media print {\n\n * {\n text-shadow: none !important;\n color: #000 !important; // Black prints faster: h5bp.com/s\n background: transparent !important;\n box-shadow: none !important;\n }\n\n a,\n a:visited {\n text-decoration: underline;\n }\n\n a[href]:after {\n content: \" (\" attr(href) \")\";\n }\n\n abbr[title]:after {\n content: \" (\" attr(title) \")\";\n }\n\n // Don't show links for images, or javascript/internal links\n a[href^=\"javascript:\"]:after,\n a[href^=\"#\"]:after {\n content: \"\";\n }\n\n pre,\n blockquote {\n border: 1px solid #999;\n page-break-inside: avoid;\n }\n\n thead {\n display: table-header-group; // h5bp.com/t\n }\n\n tr,\n img {\n page-break-inside: avoid;\n }\n\n img {\n max-width: 100% !important;\n }\n\n p,\n h2,\n h3 {\n orphans: 3;\n widows: 3;\n }\n\n h2,\n h3 {\n page-break-after: avoid;\n }\n\n // Chrome (OSX) fix for https://github.com/twbs/bootstrap/issues/11245\n // Once fixed, we can just straight up remove this.\n select {\n background: #fff !important;\n }\n\n // Bootstrap components\n .navbar {\n display: none;\n }\n .table {\n td,\n th {\n background-color: #fff !important;\n }\n }\n .btn,\n .dropup > .btn {\n > .caret {\n border-top-color: #000 !important;\n }\n }\n .label {\n border: 1px solid #000;\n }\n\n .table {\n border-collapse: collapse !important;\n }\n .table-bordered {\n th,\n td {\n border: 1px solid #ddd !important;\n }\n }\n\n}\n","//\n// Scaffolding\n// --------------------------------------------------\n\n\n// Reset the box-sizing\n//\n// Heads up! This reset may cause conflicts with some third-party widgets.\n// For recommendations on resolving such conflicts, see\n// http://getbootstrap.com/getting-started/#third-box-sizing\n* {\n .box-sizing(border-box);\n}\n*:before,\n*:after {\n .box-sizing(border-box);\n}\n\n\n// Body reset\n\nhtml {\n font-size: 62.5%;\n -webkit-tap-highlight-color: rgba(0,0,0,0);\n}\n\nbody {\n font-family: @font-family-base;\n font-size: @font-size-base;\n line-height: @line-height-base;\n color: @text-color;\n background-color: @body-bg;\n}\n\n// Reset fonts for relevant elements\ninput,\nbutton,\nselect,\ntextarea {\n font-family: inherit;\n font-size: inherit;\n line-height: inherit;\n}\n\n\n// Links\n\na {\n color: @link-color;\n text-decoration: none;\n\n &:hover,\n &:focus {\n color: @link-hover-color;\n text-decoration: underline;\n }\n\n &:focus {\n .tab-focus();\n }\n}\n\n\n// Figures\n//\n// We reset this here because previously Normalize had no `figure` margins. This\n// ensures we don't break anyone's use of the element.\n\nfigure {\n margin: 0;\n}\n\n\n// Images\n\nimg {\n vertical-align: middle;\n}\n\n// Responsive images (ensure images don't scale beyond their parents)\n.img-responsive {\n .img-responsive();\n}\n\n// Rounded corners\n.img-rounded {\n border-radius: @border-radius-large;\n}\n\n// Image thumbnails\n//\n// Heads up! This is mixin-ed into thumbnails.less for `.thumbnail`.\n.img-thumbnail {\n padding: @thumbnail-padding;\n line-height: @line-height-base;\n background-color: @thumbnail-bg;\n border: 1px solid @thumbnail-border;\n border-radius: @thumbnail-border-radius;\n .transition(all .2s ease-in-out);\n\n // Keep them at most 100% wide\n .img-responsive(inline-block);\n}\n\n// Perfect circle\n.img-circle {\n border-radius: 50%; // set radius in percents\n}\n\n\n// Horizontal rules\n\nhr {\n margin-top: @line-height-computed;\n margin-bottom: @line-height-computed;\n border: 0;\n border-top: 1px solid @hr-border;\n}\n\n\n// Only display content to screen readers\n//\n// See: http://a11yproject.com/posts/how-to-hide-content/\n\n.sr-only {\n position: absolute;\n width: 1px;\n height: 1px;\n margin: -1px;\n padding: 0;\n overflow: hidden;\n clip: rect(0,0,0,0);\n border: 0;\n}\n","//\n// Mixins\n// --------------------------------------------------\n\n\n// Utilities\n// -------------------------\n\n// Clearfix\n// Source: http://nicolasgallagher.com/micro-clearfix-hack/\n//\n// For modern browsers\n// 1. The space content is one way to avoid an Opera bug when the\n// contenteditable attribute is included anywhere else in the document.\n// Otherwise it causes space to appear at the top and bottom of elements\n// that are clearfixed.\n// 2. The use of `table` rather than `block` is only necessary if using\n// `:before` to contain the top-margins of child elements.\n.clearfix() {\n &:before,\n &:after {\n content: \" \"; // 1\n display: table; // 2\n }\n &:after {\n clear: both;\n }\n}\n\n// WebKit-style focus\n.tab-focus() {\n // Default\n outline: thin dotted;\n // WebKit\n outline: 5px auto -webkit-focus-ring-color;\n outline-offset: -2px;\n}\n\n// Center-align a block level element\n.center-block() {\n display: block;\n margin-left: auto;\n margin-right: auto;\n}\n\n// Sizing shortcuts\n.size(@width; @height) {\n width: @width;\n height: @height;\n}\n.square(@size) {\n .size(@size; @size);\n}\n\n// Placeholder text\n.placeholder(@color: @input-color-placeholder) {\n &:-moz-placeholder { color: @color; } // Firefox 4-18\n &::-moz-placeholder { color: @color; // Firefox 19+\n opacity: 1; } // See https://github.com/twbs/bootstrap/pull/11526\n &:-ms-input-placeholder { color: @color; } // Internet Explorer 10+\n &::-webkit-input-placeholder { color: @color; } // Safari and Chrome\n}\n\n// Text overflow\n// Requires inline-block or block for proper styling\n.text-overflow() {\n overflow: hidden;\n text-overflow: ellipsis;\n white-space: nowrap;\n}\n\n// CSS image replacement\n//\n// Heads up! v3 launched with with only `.hide-text()`, but per our pattern for\n// mixins being reused as classes with the same name, this doesn't hold up. As\n// of v3.0.1 we have added `.text-hide()` and deprecated `.hide-text()`. Note\n// that we cannot chain the mixins together in Less, so they are repeated.\n//\n// Source: https://github.com/h5bp/html5-boilerplate/commit/aa0396eae757\n\n// Deprecated as of v3.0.1 (will be removed in v4)\n.hide-text() {\n font: ~\"0/0\" a;\n color: transparent;\n text-shadow: none;\n background-color: transparent;\n border: 0;\n}\n// New mixin to use as of v3.0.1\n.text-hide() {\n .hide-text();\n}\n\n\n\n// CSS3 PROPERTIES\n// --------------------------------------------------\n\n// Single side border-radius\n.border-top-radius(@radius) {\n border-top-right-radius: @radius;\n border-top-left-radius: @radius;\n}\n.border-right-radius(@radius) {\n border-bottom-right-radius: @radius;\n border-top-right-radius: @radius;\n}\n.border-bottom-radius(@radius) {\n border-bottom-right-radius: @radius;\n border-bottom-left-radius: @radius;\n}\n.border-left-radius(@radius) {\n border-bottom-left-radius: @radius;\n border-top-left-radius: @radius;\n}\n\n// Drop shadows\n//\n// Note: Deprecated `.box-shadow()` as of v3.1.0 since all of Bootstrap's\n// supported browsers that have box shadow capabilities now support the\n// standard `box-shadow` property.\n.box-shadow(@shadow) {\n -webkit-box-shadow: @shadow; // iOS <4.3 & Android <4.1\n box-shadow: @shadow;\n}\n\n// Transitions\n.transition(@transition) {\n -webkit-transition: @transition;\n transition: @transition;\n}\n.transition-property(@transition-property) {\n -webkit-transition-property: @transition-property;\n transition-property: @transition-property;\n}\n.transition-delay(@transition-delay) {\n -webkit-transition-delay: @transition-delay;\n transition-delay: @transition-delay;\n}\n.transition-duration(@transition-duration) {\n -webkit-transition-duration: @transition-duration;\n transition-duration: @transition-duration;\n}\n.transition-transform(@transition) {\n -webkit-transition: -webkit-transform @transition;\n -moz-transition: -moz-transform @transition;\n -o-transition: -o-transform @transition;\n transition: transform @transition;\n}\n\n// Transformations\n.rotate(@degrees) {\n -webkit-transform: rotate(@degrees);\n -ms-transform: rotate(@degrees); // IE9 only\n transform: rotate(@degrees);\n}\n.scale(@ratio; @ratio-y...) {\n -webkit-transform: scale(@ratio, @ratio-y);\n -ms-transform: scale(@ratio, @ratio-y); // IE9 only\n transform: scale(@ratio, @ratio-y);\n}\n.translate(@x; @y) {\n -webkit-transform: translate(@x, @y);\n -ms-transform: translate(@x, @y); // IE9 only\n transform: translate(@x, @y);\n}\n.skew(@x; @y) {\n -webkit-transform: skew(@x, @y);\n -ms-transform: skewX(@x) skewY(@y); // See https://github.com/twbs/bootstrap/issues/4885; IE9+\n transform: skew(@x, @y);\n}\n.translate3d(@x; @y; @z) {\n -webkit-transform: translate3d(@x, @y, @z);\n transform: translate3d(@x, @y, @z);\n}\n\n.rotateX(@degrees) {\n -webkit-transform: rotateX(@degrees);\n -ms-transform: rotateX(@degrees); // IE9 only\n transform: rotateX(@degrees);\n}\n.rotateY(@degrees) {\n -webkit-transform: rotateY(@degrees);\n -ms-transform: rotateY(@degrees); // IE9 only\n transform: rotateY(@degrees);\n}\n.perspective(@perspective) {\n -webkit-perspective: @perspective;\n -moz-perspective: @perspective;\n perspective: @perspective;\n}\n.perspective-origin(@perspective) {\n -webkit-perspective-origin: @perspective;\n -moz-perspective-origin: @perspective;\n perspective-origin: @perspective;\n}\n.transform-origin(@origin) {\n -webkit-transform-origin: @origin;\n -moz-transform-origin: @origin;\n -ms-transform-origin: @origin; // IE9 only\n transform-origin: @origin;\n}\n\n// Animations\n.animation(@animation) {\n -webkit-animation: @animation;\n animation: @animation;\n}\n.animation-name(@name) {\n -webkit-animation-name: @name;\n animation-name: @name;\n}\n.animation-duration(@duration) {\n -webkit-animation-duration: @duration;\n animation-duration: @duration;\n}\n.animation-timing-function(@timing-function) {\n -webkit-animation-timing-function: @timing-function;\n animation-timing-function: @timing-function;\n}\n.animation-delay(@delay) {\n -webkit-animation-delay: @delay;\n animation-delay: @delay;\n}\n.animation-iteration-count(@iteration-count) {\n -webkit-animation-iteration-count: @iteration-count;\n animation-iteration-count: @iteration-count;\n}\n.animation-direction(@direction) {\n -webkit-animation-direction: @direction;\n animation-direction: @direction;\n}\n\n// Backface visibility\n// Prevent browsers from flickering when using CSS 3D transforms.\n// Default value is `visible`, but can be changed to `hidden`\n.backface-visibility(@visibility){\n -webkit-backface-visibility: @visibility;\n -moz-backface-visibility: @visibility;\n backface-visibility: @visibility;\n}\n\n// Box sizing\n.box-sizing(@boxmodel) {\n -webkit-box-sizing: @boxmodel;\n -moz-box-sizing: @boxmodel;\n box-sizing: @boxmodel;\n}\n\n// User select\n// For selecting text on the page\n.user-select(@select) {\n -webkit-user-select: @select;\n -moz-user-select: @select;\n -ms-user-select: @select; // IE10+\n -o-user-select: @select;\n user-select: @select;\n}\n\n// Resize anything\n.resizable(@direction) {\n resize: @direction; // Options: horizontal, vertical, both\n overflow: auto; // Safari fix\n}\n\n// CSS3 Content Columns\n.content-columns(@column-count; @column-gap: @grid-gutter-width) {\n -webkit-column-count: @column-count;\n -moz-column-count: @column-count;\n column-count: @column-count;\n -webkit-column-gap: @column-gap;\n -moz-column-gap: @column-gap;\n column-gap: @column-gap;\n}\n\n// Optional hyphenation\n.hyphens(@mode: auto) {\n word-wrap: break-word;\n -webkit-hyphens: @mode;\n -moz-hyphens: @mode;\n -ms-hyphens: @mode; // IE10+\n -o-hyphens: @mode;\n hyphens: @mode;\n}\n\n// Opacity\n.opacity(@opacity) {\n opacity: @opacity;\n // IE8 filter\n @opacity-ie: (@opacity * 100);\n filter: ~\"alpha(opacity=@{opacity-ie})\";\n}\n\n\n\n// GRADIENTS\n// --------------------------------------------------\n\n#gradient {\n\n // Horizontal gradient, from left to right\n //\n // Creates two color stops, start and end, by specifying a color and position for each color stop.\n // Color stops are not available in IE9 and below.\n .horizontal(@start-color: #555; @end-color: #333; @start-percent: 0%; @end-percent: 100%) {\n background-image: -webkit-linear-gradient(left, color-stop(@start-color @start-percent), color-stop(@end-color @end-percent)); // Safari 5.1-6, Chrome 10+\n background-image: linear-gradient(to right, @start-color @start-percent, @end-color @end-percent); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n background-repeat: repeat-x;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)\",argb(@start-color),argb(@end-color))); // IE9 and down\n }\n\n // Vertical gradient, from top to bottom\n //\n // Creates two color stops, start and end, by specifying a color and position for each color stop.\n // Color stops are not available in IE9 and below.\n .vertical(@start-color: #555; @end-color: #333; @start-percent: 0%; @end-percent: 100%) {\n background-image: -webkit-linear-gradient(top, @start-color @start-percent, @end-color @end-percent); // Safari 5.1-6, Chrome 10+\n background-image: linear-gradient(to bottom, @start-color @start-percent, @end-color @end-percent); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n background-repeat: repeat-x;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)\",argb(@start-color),argb(@end-color))); // IE9 and down\n }\n\n .directional(@start-color: #555; @end-color: #333; @deg: 45deg) {\n background-repeat: repeat-x;\n background-image: -webkit-linear-gradient(@deg, @start-color, @end-color); // Safari 5.1-6, Chrome 10+\n background-image: linear-gradient(@deg, @start-color, @end-color); // Standard, IE10, Firefox 16+, Opera 12.10+, Safari 7+, Chrome 26+\n }\n .horizontal-three-colors(@start-color: #00b3ee; @mid-color: #7a43b6; @color-stop: 50%; @end-color: #c3325f) {\n background-image: -webkit-linear-gradient(left, @start-color, @mid-color @color-stop, @end-color);\n background-image: linear-gradient(to right, @start-color, @mid-color @color-stop, @end-color);\n background-repeat: no-repeat;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)\",argb(@start-color),argb(@end-color))); // IE9 and down, gets no color-stop at all for proper fallback\n }\n .vertical-three-colors(@start-color: #00b3ee; @mid-color: #7a43b6; @color-stop: 50%; @end-color: #c3325f) {\n background-image: -webkit-linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-image: linear-gradient(@start-color, @mid-color @color-stop, @end-color);\n background-repeat: no-repeat;\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)\",argb(@start-color),argb(@end-color))); // IE9 and down, gets no color-stop at all for proper fallback\n }\n .radial(@inner-color: #555; @outer-color: #333) {\n background-image: -webkit-radial-gradient(circle, @inner-color, @outer-color);\n background-image: radial-gradient(circle, @inner-color, @outer-color);\n background-repeat: no-repeat;\n }\n .striped(@color: rgba(255,255,255,.15); @angle: 45deg) {\n background-image: -webkit-linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n background-image: linear-gradient(@angle, @color 25%, transparent 25%, transparent 50%, @color 50%, @color 75%, transparent 75%, transparent);\n }\n}\n\n// Reset filters for IE\n//\n// When you need to remove a gradient background, do not forget to use this to reset\n// the IE filter for IE9 and below.\n.reset-filter() {\n filter: e(%(\"progid:DXImageTransform.Microsoft.gradient(enabled = false)\"));\n}\n\n\n\n// Retina images\n//\n// Short retina mixin for setting background-image and -size\n\n.img-retina(@file-1x; @file-2x; @width-1x; @height-1x) {\n background-image: url(\"@{file-1x}\");\n\n @media\n only screen and (-webkit-min-device-pixel-ratio: 2),\n only screen and ( min--moz-device-pixel-ratio: 2),\n only screen and ( -o-min-device-pixel-ratio: 2/1),\n only screen and ( min-device-pixel-ratio: 2),\n only screen and ( min-resolution: 192dpi),\n only screen and ( min-resolution: 2dppx) {\n background-image: url(\"@{file-2x}\");\n background-size: @width-1x @height-1x;\n }\n}\n\n\n// Responsive image\n//\n// Keep images from scaling beyond the width of their parents.\n\n.img-responsive(@display: block) {\n display: @display;\n max-width: 100%; // Part 1: Set a maximum relative to the parent\n height: auto; // Part 2: Scale the height according to the width, otherwise you get stretching\n}\n\n\n// COMPONENT MIXINS\n// --------------------------------------------------\n\n// Horizontal dividers\n// -------------------------\n// Dividers (basically an hr) within dropdowns and nav lists\n.nav-divider(@color: #e5e5e5) {\n height: 1px;\n margin: ((@line-height-computed / 2) - 1) 0;\n overflow: hidden;\n background-color: @color;\n}\n\n// Panels\n// -------------------------\n.panel-variant(@border; @heading-text-color; @heading-bg-color; @heading-border) {\n border-color: @border;\n\n & > .panel-heading {\n color: @heading-text-color;\n background-color: @heading-bg-color;\n border-color: @heading-border;\n\n + .panel-collapse .panel-body {\n border-top-color: @border;\n }\n }\n & > .panel-footer {\n + .panel-collapse .panel-body {\n border-bottom-color: @border;\n }\n }\n}\n\n// Alerts\n// -------------------------\n.alert-variant(@background; @border; @text-color) {\n background-color: @background;\n border-color: @border;\n color: @text-color;\n\n hr {\n border-top-color: darken(@border, 5%);\n }\n .alert-link {\n color: darken(@text-color, 10%);\n }\n}\n\n// Tables\n// -------------------------\n.table-row-variant(@state; @background) {\n // Exact selectors below required to override `.table-striped` and prevent\n // inheritance to nested tables.\n .table > thead > tr,\n .table > tbody > tr,\n .table > tfoot > tr {\n > td.@{state},\n > th.@{state},\n &.@{state} > td,\n &.@{state} > th {\n background-color: @background;\n }\n }\n\n // Hover states for `.table-hover`\n // Note: this is not available for cells or rows within `thead` or `tfoot`.\n .table-hover > tbody > tr {\n > td.@{state}:hover,\n > th.@{state}:hover,\n &.@{state}:hover > td,\n &.@{state}:hover > th {\n background-color: darken(@background, 5%);\n }\n }\n}\n\n// List Groups\n// -------------------------\n.list-group-item-variant(@state; @background; @color) {\n .list-group-item-@{state} {\n color: @color;\n background-color: @background;\n\n a& {\n color: @color;\n\n .list-group-item-heading { color: inherit; }\n\n &:hover,\n &:focus {\n color: @color;\n background-color: darken(@background, 5%);\n }\n &.active,\n &.active:hover,\n &.active:focus {\n color: #fff;\n background-color: @color;\n border-color: @color;\n }\n }\n }\n}\n\n// Button variants\n// -------------------------\n// Easily pump out default styles, as well as :hover, :focus, :active,\n// and disabled options for all buttons\n.button-variant(@color; @background; @border) {\n color: @color;\n background-color: @background;\n border-color: @border;\n\n &:hover,\n &:focus,\n &:active,\n &.active,\n .open .dropdown-toggle& {\n color: @color;\n background-color: darken(@background, 8%);\n border-color: darken(@border, 12%);\n }\n &:active,\n &.active,\n .open .dropdown-toggle& {\n background-image: none;\n }\n &.disabled,\n &[disabled],\n fieldset[disabled] & {\n &,\n &:hover,\n &:focus,\n &:active,\n &.active {\n background-color: @background;\n border-color: @border;\n }\n }\n\n .badge {\n color: @background;\n background-color: @color;\n }\n}\n\n// Button sizes\n// -------------------------\n.button-size(@padding-vertical; @padding-horizontal; @font-size; @line-height; @border-radius) {\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n line-height: @line-height;\n border-radius: @border-radius;\n}\n\n// Pagination\n// -------------------------\n.pagination-size(@padding-vertical; @padding-horizontal; @font-size; @border-radius) {\n > li {\n > a,\n > span {\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n }\n &:first-child {\n > a,\n > span {\n .border-left-radius(@border-radius);\n }\n }\n &:last-child {\n > a,\n > span {\n .border-right-radius(@border-radius);\n }\n }\n }\n}\n\n// Labels\n// -------------------------\n.label-variant(@color) {\n background-color: @color;\n &[href] {\n &:hover,\n &:focus {\n background-color: darken(@color, 10%);\n }\n }\n}\n\n// Contextual backgrounds\n// -------------------------\n.bg-variant(@color) {\n background-color: @color;\n a&:hover {\n background-color: darken(@color, 10%);\n }\n}\n\n// Typography\n// -------------------------\n.text-emphasis-variant(@color) {\n color: @color;\n a&:hover {\n color: darken(@color, 10%);\n }\n}\n\n// Navbar vertical align\n// -------------------------\n// Vertically center elements in the navbar.\n// Example: an element has a height of 30px, so write out `.navbar-vertical-align(30px);` to calculate the appropriate top margin.\n.navbar-vertical-align(@element-height) {\n margin-top: ((@navbar-height - @element-height) / 2);\n margin-bottom: ((@navbar-height - @element-height) / 2);\n}\n\n// Progress bars\n// -------------------------\n.progress-bar-variant(@color) {\n background-color: @color;\n .progress-striped & {\n #gradient > .striped();\n }\n}\n\n// Responsive utilities\n// -------------------------\n// More easily include all the states for responsive-utilities.less.\n.responsive-visibility() {\n display: block !important;\n table& { display: table; }\n tr& { display: table-row !important; }\n th&,\n td& { display: table-cell !important; }\n}\n\n.responsive-invisibility() {\n &,\n tr&,\n th&,\n td& { display: none !important; }\n}\n\n\n// Grid System\n// -----------\n\n// Centered container element\n.container-fixed() {\n margin-right: auto;\n margin-left: auto;\n padding-left: (@grid-gutter-width / 2);\n padding-right: (@grid-gutter-width / 2);\n &:extend(.clearfix all);\n}\n\n// Creates a wrapper for a series of columns\n.make-row(@gutter: @grid-gutter-width) {\n margin-left: (@gutter / -2);\n margin-right: (@gutter / -2);\n &:extend(.clearfix all);\n}\n\n// Generate the extra small columns\n.make-xs-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n float: left;\n width: percentage((@columns / @grid-columns));\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n}\n.make-xs-column-offset(@columns) {\n @media (min-width: @screen-xs-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-xs-column-push(@columns) {\n @media (min-width: @screen-xs-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-xs-column-pull(@columns) {\n @media (min-width: @screen-xs-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n\n// Generate the small columns\n.make-sm-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-sm-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-offset(@columns) {\n @media (min-width: @screen-sm-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-push(@columns) {\n @media (min-width: @screen-sm-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-sm-column-pull(@columns) {\n @media (min-width: @screen-sm-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n\n// Generate the medium columns\n.make-md-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-md-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-offset(@columns) {\n @media (min-width: @screen-md-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-push(@columns) {\n @media (min-width: @screen-md-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-md-column-pull(@columns) {\n @media (min-width: @screen-md-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n\n// Generate the large columns\n.make-lg-column(@columns; @gutter: @grid-gutter-width) {\n position: relative;\n min-height: 1px;\n padding-left: (@gutter / 2);\n padding-right: (@gutter / 2);\n\n @media (min-width: @screen-lg-min) {\n float: left;\n width: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-offset(@columns) {\n @media (min-width: @screen-lg-min) {\n margin-left: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-push(@columns) {\n @media (min-width: @screen-lg-min) {\n left: percentage((@columns / @grid-columns));\n }\n}\n.make-lg-column-pull(@columns) {\n @media (min-width: @screen-lg-min) {\n right: percentage((@columns / @grid-columns));\n }\n}\n\n\n// Framework grid generation\n//\n// Used only by Bootstrap to generate the correct number of grid classes given\n// any value of `@grid-columns`.\n\n.make-grid-columns() {\n // Common styles for all sizes of grid columns, widths 1-12\n .col(@index) when (@index = 1) { // initial\n @item: ~\".col-xs-@{index}, .col-sm-@{index}, .col-md-@{index}, .col-lg-@{index}\";\n .col((@index + 1), @item);\n }\n .col(@index, @list) when (@index =< @grid-columns) { // general; \"=<\" isn't a typo\n @item: ~\".col-xs-@{index}, .col-sm-@{index}, .col-md-@{index}, .col-lg-@{index}\";\n .col((@index + 1), ~\"@{list}, @{item}\");\n }\n .col(@index, @list) when (@index > @grid-columns) { // terminal\n @{list} {\n position: relative;\n // Prevent columns from collapsing when empty\n min-height: 1px;\n // Inner gutter via padding\n padding-left: (@grid-gutter-width / 2);\n padding-right: (@grid-gutter-width / 2);\n }\n }\n .col(1); // kickstart it\n}\n\n.make-grid-columns-float(@class) {\n .col(@index) when (@index = 1) { // initial\n @item: ~\".col-@{class}-@{index}\";\n .col((@index + 1), @item);\n }\n .col(@index, @list) when (@index =< @grid-columns) { // general\n @item: ~\".col-@{class}-@{index}\";\n .col((@index + 1), ~\"@{list}, @{item}\");\n }\n .col(@index, @list) when (@index > @grid-columns) { // terminal\n @{list} {\n float: left;\n }\n }\n .col(1); // kickstart it\n}\n\n.calc-grid(@index, @class, @type) when (@type = width) and (@index > 0) {\n .col-@{class}-@{index} {\n width: percentage((@index / @grid-columns));\n }\n}\n.calc-grid(@index, @class, @type) when (@type = push) {\n .col-@{class}-push-@{index} {\n left: percentage((@index / @grid-columns));\n }\n}\n.calc-grid(@index, @class, @type) when (@type = pull) {\n .col-@{class}-pull-@{index} {\n right: percentage((@index / @grid-columns));\n }\n}\n.calc-grid(@index, @class, @type) when (@type = offset) {\n .col-@{class}-offset-@{index} {\n margin-left: percentage((@index / @grid-columns));\n }\n}\n\n// Basic looping in LESS\n.make-grid(@index, @class, @type) when (@index >= 0) {\n .calc-grid(@index, @class, @type);\n // next iteration\n .make-grid((@index - 1), @class, @type);\n}\n\n\n// Form validation states\n//\n// Used in forms.less to generate the form validation CSS for warnings, errors,\n// and successes.\n\n.form-control-validation(@text-color: #555; @border-color: #ccc; @background-color: #f5f5f5) {\n // Color the label and help text\n .help-block,\n .control-label,\n .radio,\n .checkbox,\n .radio-inline,\n .checkbox-inline {\n color: @text-color;\n }\n // Set the border and box shadow on specific inputs to match\n .form-control {\n border-color: @border-color;\n .box-shadow(inset 0 1px 1px rgba(0,0,0,.075)); // Redeclare so transitions work\n &:focus {\n border-color: darken(@border-color, 10%);\n @shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 6px lighten(@border-color, 20%);\n .box-shadow(@shadow);\n }\n }\n // Set validation states also for addons\n .input-group-addon {\n color: @text-color;\n border-color: @border-color;\n background-color: @background-color;\n }\n // Optional feedback icon\n .form-control-feedback {\n color: @text-color;\n }\n}\n\n// Form control focus state\n//\n// Generate a customized focus state and for any input with the specified color,\n// which defaults to the `@input-focus-border` variable.\n//\n// We highly encourage you to not customize the default value, but instead use\n// this to tweak colors on an as-needed basis. This aesthetic change is based on\n// WebKit's default styles, but applicable to a wider range of browsers. Its\n// usability and accessibility should be taken into account with any change.\n//\n// Example usage: change the default blue border and shadow to white for better\n// contrast against a dark gray background.\n\n.form-control-focus(@color: @input-border-focus) {\n @color-rgba: rgba(red(@color), green(@color), blue(@color), .6);\n &:focus {\n border-color: @color;\n outline: 0;\n .box-shadow(~\"inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px @{color-rgba}\");\n }\n}\n\n// Form control sizing\n//\n// Relative text size, padding, and border-radii changes for form controls. For\n// horizontal sizing, wrap controls in the predefined grid classes. `<select>`\n// element gets special love because it's special, and that's a fact!\n\n.input-size(@input-height; @padding-vertical; @padding-horizontal; @font-size; @line-height; @border-radius) {\n height: @input-height;\n padding: @padding-vertical @padding-horizontal;\n font-size: @font-size;\n line-height: @line-height;\n border-radius: @border-radius;\n\n select& {\n height: @input-height;\n line-height: @input-height;\n }\n\n textarea&,\n select[multiple]& {\n height: auto;\n }\n}\n","//\n// Variables\n// --------------------------------------------------\n\n\n//== Colors\n//\n//## Gray and brand colors for use across Bootstrap.\n\n@gray-darker: lighten(#000, 13.5%); // #222\n@gray-dark: lighten(#000, 20%); // #333\n@gray: lighten(#000, 33.5%); // #555\n@gray-light: lighten(#000, 60%); // #999\n@gray-lighter: lighten(#000, 93.5%); // #eee\n\n@brand-primary: #428bca;\n@brand-success: #5cb85c;\n@brand-info: #5bc0de;\n@brand-warning: #f0ad4e;\n@brand-danger: #d9534f;\n\n\n//== Scaffolding\n//\n// ## Settings for some of the most global styles.\n\n//** Background color for `<body>`.\n@body-bg: #fff;\n//** Global text color on `<body>`.\n@text-color: @gray-dark;\n\n//** Global textual link color.\n@link-color: @brand-primary;\n//** Link hover color set via `darken()` function.\n@link-hover-color: darken(@link-color, 15%);\n\n\n//== Typography\n//\n//## Font, line-height, and color for body text, headings, and more.\n\n@font-family-sans-serif: \"Helvetica Neue\", Helvetica, Arial, sans-serif;\n@font-family-serif: Georgia, \"Times New Roman\", Times, serif;\n//** Default monospace fonts for `<code>`, `<kbd>`, and `<pre>`.\n@font-family-monospace: Menlo, Monaco, Consolas, \"Courier New\", monospace;\n@font-family-base: @font-family-sans-serif;\n\n@font-size-base: 14px;\n@font-size-large: ceil((@font-size-base * 1.25)); // ~18px\n@font-size-small: ceil((@font-size-base * 0.85)); // ~12px\n\n@font-size-h1: floor((@font-size-base * 2.6)); // ~36px\n@font-size-h2: floor((@font-size-base * 2.15)); // ~30px\n@font-size-h3: ceil((@font-size-base * 1.7)); // ~24px\n@font-size-h4: ceil((@font-size-base * 1.25)); // ~18px\n@font-size-h5: @font-size-base;\n@font-size-h6: ceil((@font-size-base * 0.85)); // ~12px\n\n//** Unit-less `line-height` for use in components like buttons.\n@line-height-base: 1.428571429; // 20/14\n//** Computed \"line-height\" (`font-size` * `line-height`) for use with `margin`, `padding`, etc.\n@line-height-computed: floor((@font-size-base * @line-height-base)); // ~20px\n\n//** By default, this inherits from the `<body>`.\n@headings-font-family: inherit;\n@headings-font-weight: 500;\n@headings-line-height: 1.1;\n@headings-color: inherit;\n\n\n//-- Iconography\n//\n//## Specify custom locations of the include Glyphicons icon font. Useful for those including Bootstrap via Bower.\n\n@icon-font-path: \"../fonts/\";\n@icon-font-name: \"glyphicons-halflings-regular\";\n@icon-font-svg-id:\t\t\t\t\"glyphicons_halflingsregular\";\n\n//== Components\n//\n//## Define common padding and border radius sizes and more. Values based on 14px text and 1.428 line-height (~20px to start).\n\n@padding-base-vertical: 6px;\n@padding-base-horizontal: 12px;\n\n@padding-large-vertical: 10px;\n@padding-large-horizontal: 16px;\n\n@padding-small-vertical: 5px;\n@padding-small-horizontal: 10px;\n\n@padding-xs-vertical: 1px;\n@padding-xs-horizontal: 5px;\n\n@line-height-large: 1.33;\n@line-height-small: 1.5;\n\n@border-radius-base: 4px;\n@border-radius-large: 6px;\n@border-radius-small: 3px;\n\n//** Global color for active items (e.g., navs or dropdowns).\n@component-active-color: #fff;\n//** Global background color for active items (e.g., navs or dropdowns).\n@component-active-bg: @brand-primary;\n\n//** Width of the `border` for generating carets that indicator dropdowns.\n@caret-width-base: 4px;\n//** Carets increase slightly in size for larger components.\n@caret-width-large: 5px;\n\n\n//== Tables\n//\n//## Customizes the `.table` component with basic values, each used across all table variations.\n\n//** Padding for `<th>`s and `<td>`s.\n@table-cell-padding: 8px;\n//** Padding for cells in `.table-condensed`.\n@table-condensed-cell-padding: 5px;\n\n//** Default background color used for all tables.\n@table-bg: transparent;\n//** Background color used for `.table-striped`.\n@table-bg-accent: #f9f9f9;\n//** Background color used for `.table-hover`.\n@table-bg-hover: #f5f5f5;\n@table-bg-active: @table-bg-hover;\n\n//** Border color for table and cell borders.\n@table-border-color: #ddd;\n\n\n//== Buttons\n//\n//## For each of Bootstrap's buttons, define text, background and border color.\n\n@btn-font-weight: normal;\n\n@btn-default-color: #333;\n@btn-default-bg: #fff;\n@btn-default-border: #ccc;\n\n@btn-primary-color: #fff;\n@btn-primary-bg: @brand-primary;\n@btn-primary-border: darken(@btn-primary-bg, 5%);\n\n@btn-success-color: #fff;\n@btn-success-bg: @brand-success;\n@btn-success-border: darken(@btn-success-bg, 5%);\n\n@btn-info-color: #fff;\n@btn-info-bg: @brand-info;\n@btn-info-border: darken(@btn-info-bg, 5%);\n\n@btn-warning-color: #fff;\n@btn-warning-bg: @brand-warning;\n@btn-warning-border: darken(@btn-warning-bg, 5%);\n\n@btn-danger-color: #fff;\n@btn-danger-bg: @brand-danger;\n@btn-danger-border: darken(@btn-danger-bg, 5%);\n\n@btn-link-disabled-color: @gray-light;\n\n\n//== Forms\n//\n//##\n\n//** `<input>` background color\n@input-bg: #fff;\n//** `<input disabled>` background color\n@input-bg-disabled: @gray-lighter;\n\n//** Text color for `<input>`s\n@input-color: @gray;\n//** `<input>` border color\n@input-border: #ccc;\n//** `<input>` border radius\n@input-border-radius: @border-radius-base;\n//** Border color for inputs on focus\n@input-border-focus: #66afe9;\n\n//** Placeholder text color\n@input-color-placeholder: @gray-light;\n\n//** Default `.form-control` height\n@input-height-base: (@line-height-computed + (@padding-base-vertical * 2) + 2);\n//** Large `.form-control` height\n@input-height-large: (ceil(@font-size-large * @line-height-large) + (@padding-large-vertical * 2) + 2);\n//** Small `.form-control` height\n@input-height-small: (floor(@font-size-small * @line-height-small) + (@padding-small-vertical * 2) + 2);\n\n@legend-color: @gray-dark;\n@legend-border-color: #e5e5e5;\n\n//** Background color for textual input addons\n@input-group-addon-bg: @gray-lighter;\n//** Border color for textual input addons\n@input-group-addon-border-color: @input-border;\n\n\n//== Dropdowns\n//\n//## Dropdown menu container and contents.\n\n//** Background for the dropdown menu.\n@dropdown-bg: #fff;\n//** Dropdown menu `border-color`.\n@dropdown-border: rgba(0,0,0,.15);\n//** Dropdown menu `border-color` **for IE8**.\n@dropdown-fallback-border: #ccc;\n//** Divider color for between dropdown items.\n@dropdown-divider-bg: #e5e5e5;\n\n//** Dropdown link text color.\n@dropdown-link-color: @gray-dark;\n//** Hover color for dropdown links.\n@dropdown-link-hover-color: darken(@gray-dark, 5%);\n//** Hover background for dropdown links.\n@dropdown-link-hover-bg: #f5f5f5;\n\n//** Active dropdown menu item text color.\n@dropdown-link-active-color: @component-active-color;\n//** Active dropdown menu item background color.\n@dropdown-link-active-bg: @component-active-bg;\n\n//** Disabled dropdown menu item background color.\n@dropdown-link-disabled-color: @gray-light;\n\n//** Text color for headers within dropdown menus.\n@dropdown-header-color: @gray-light;\n\n// Note: Deprecated @dropdown-caret-color as of v3.1.0\n@dropdown-caret-color: #000;\n\n\n//-- Z-index master list\n//\n// Warning: Avoid customizing these values. They're used for a bird's eye view\n// of components dependent on the z-axis and are designed to all work together.\n//\n// Note: These variables are not generated into the Customizer.\n\n@zindex-navbar: 1000;\n@zindex-dropdown: 1000;\n@zindex-popover: 1010;\n@zindex-tooltip: 1030;\n@zindex-navbar-fixed: 1030;\n@zindex-modal-background: 1040;\n@zindex-modal: 1050;\n\n\n//== Media queries breakpoints\n//\n//## Define the breakpoints at which your layout will change, adapting to different screen sizes.\n\n// Extra small screen / phone\n// Note: Deprecated @screen-xs and @screen-phone as of v3.0.1\n@screen-xs: 480px;\n@screen-xs-min: @screen-xs;\n@screen-phone: @screen-xs-min;\n\n// Small screen / tablet\n// Note: Deprecated @screen-sm and @screen-tablet as of v3.0.1\n@screen-sm: 768px;\n@screen-sm-min: @screen-sm;\n@screen-tablet: @screen-sm-min;\n\n// Medium screen / desktop\n// Note: Deprecated @screen-md and @screen-desktop as of v3.0.1\n@screen-md: 992px;\n@screen-md-min: @screen-md;\n@screen-desktop: @screen-md-min;\n\n// Large screen / wide desktop\n// Note: Deprecated @screen-lg and @screen-lg-desktop as of v3.0.1\n@screen-lg: 1200px;\n@screen-lg-min: @screen-lg;\n@screen-lg-desktop: @screen-lg-min;\n\n// So media queries don't overlap when required, provide a maximum\n@screen-xs-max: (@screen-sm-min - 1);\n@screen-sm-max: (@screen-md-min - 1);\n@screen-md-max: (@screen-lg-min - 1);\n\n\n//== Grid system\n//\n//## Define your custom responsive grid.\n\n//** Number of columns in the grid.\n@grid-columns: 12;\n//** Padding between columns. Gets divided in half for the left and right.\n@grid-gutter-width: 30px;\n// Navbar collapse\n//** Point at which the navbar becomes uncollapsed.\n@grid-float-breakpoint: @screen-sm-min;\n//** Point at which the navbar begins collapsing.\n@grid-float-breakpoint-max: (@grid-float-breakpoint - 1);\n\n\n//== Navbar\n//\n//##\n\n// Basics of a navbar\n@navbar-height: 50px;\n@navbar-margin-bottom: @line-height-computed;\n@navbar-border-radius: @border-radius-base;\n@navbar-padding-horizontal: floor((@grid-gutter-width / 2));\n@navbar-padding-vertical: ((@navbar-height - @line-height-computed) / 2);\n@navbar-collapse-max-height: 340px;\n\n@navbar-default-color: #777;\n@navbar-default-bg: #f8f8f8;\n@navbar-default-border: darken(@navbar-default-bg, 6.5%);\n\n// Navbar links\n@navbar-default-link-color: #777;\n@navbar-default-link-hover-color: #333;\n@navbar-default-link-hover-bg: transparent;\n@navbar-default-link-active-color: #555;\n@navbar-default-link-active-bg: darken(@navbar-default-bg, 6.5%);\n@navbar-default-link-disabled-color: #ccc;\n@navbar-default-link-disabled-bg: transparent;\n\n// Navbar brand label\n@navbar-default-brand-color: @navbar-default-link-color;\n@navbar-default-brand-hover-color: darken(@navbar-default-brand-color, 10%);\n@navbar-default-brand-hover-bg: transparent;\n\n// Navbar toggle\n@navbar-default-toggle-hover-bg: #ddd;\n@navbar-default-toggle-icon-bar-bg: #888;\n@navbar-default-toggle-border-color: #ddd;\n\n\n// Inverted navbar\n// Reset inverted navbar basics\n@navbar-inverse-color: @gray-light;\n@navbar-inverse-bg: #222;\n@navbar-inverse-border: darken(@navbar-inverse-bg, 10%);\n\n// Inverted navbar links\n@navbar-inverse-link-color: @gray-light;\n@navbar-inverse-link-hover-color: #fff;\n@navbar-inverse-link-hover-bg: transparent;\n@navbar-inverse-link-active-color: @navbar-inverse-link-hover-color;\n@navbar-inverse-link-active-bg: darken(@navbar-inverse-bg, 10%);\n@navbar-inverse-link-disabled-color: #444;\n@navbar-inverse-link-disabled-bg: transparent;\n\n// Inverted navbar brand label\n@navbar-inverse-brand-color: @navbar-inverse-link-color;\n@navbar-inverse-brand-hover-color: #fff;\n@navbar-inverse-brand-hover-bg: transparent;\n\n// Inverted navbar toggle\n@navbar-inverse-toggle-hover-bg: #333;\n@navbar-inverse-toggle-icon-bar-bg: #fff;\n@navbar-inverse-toggle-border-color: #333;\n\n\n//== Navs\n//\n//##\n\n//=== Shared nav styles\n@nav-link-padding: 10px 15px;\n@nav-link-hover-bg: @gray-lighter;\n\n@nav-disabled-link-color: @gray-light;\n@nav-disabled-link-hover-color: @gray-light;\n\n@nav-open-link-hover-color: #fff;\n\n//== Tabs\n@nav-tabs-border-color: #ddd;\n\n@nav-tabs-link-hover-border-color: @gray-lighter;\n\n@nav-tabs-active-link-hover-bg: @body-bg;\n@nav-tabs-active-link-hover-color: @gray;\n@nav-tabs-active-link-hover-border-color: #ddd;\n\n@nav-tabs-justified-link-border-color: #ddd;\n@nav-tabs-justified-active-link-border-color: @body-bg;\n\n//== Pills\n@nav-pills-border-radius: @border-radius-base;\n@nav-pills-active-link-hover-bg: @component-active-bg;\n@nav-pills-active-link-hover-color: @component-active-color;\n\n\n//== Pagination\n//\n//##\n\n@pagination-color: @link-color;\n@pagination-bg: #fff;\n@pagination-border: #ddd;\n\n@pagination-hover-color: @link-hover-color;\n@pagination-hover-bg: @gray-lighter;\n@pagination-hover-border: #ddd;\n\n@pagination-active-color: #fff;\n@pagination-active-bg: @brand-primary;\n@pagination-active-border: @brand-primary;\n\n@pagination-disabled-color: @gray-light;\n@pagination-disabled-bg: #fff;\n@pagination-disabled-border: #ddd;\n\n\n//== Pager\n//\n//##\n\n@pager-bg: @pagination-bg;\n@pager-border: @pagination-border;\n@pager-border-radius: 15px;\n\n@pager-hover-bg: @pagination-hover-bg;\n\n@pager-active-bg: @pagination-active-bg;\n@pager-active-color: @pagination-active-color;\n\n@pager-disabled-color: @pagination-disabled-color;\n\n\n//== Jumbotron\n//\n//##\n\n@jumbotron-padding: 30px;\n@jumbotron-color: inherit;\n@jumbotron-bg: @gray-lighter;\n@jumbotron-heading-color: inherit;\n@jumbotron-font-size: ceil((@font-size-base * 1.5));\n\n\n//== Form states and alerts\n//\n//## Define colors for form feedback states and, by default, alerts.\n\n@state-success-text: #3c763d;\n@state-success-bg: #dff0d8;\n@state-success-border: darken(spin(@state-success-bg, -10), 5%);\n\n@state-info-text: #31708f;\n@state-info-bg: #d9edf7;\n@state-info-border: darken(spin(@state-info-bg, -10), 7%);\n\n@state-warning-text: #8a6d3b;\n@state-warning-bg: #fcf8e3;\n@state-warning-border: darken(spin(@state-warning-bg, -10), 5%);\n\n@state-danger-text: #a94442;\n@state-danger-bg: #f2dede;\n@state-danger-border: darken(spin(@state-danger-bg, -10), 5%);\n\n\n//== Tooltips\n//\n//##\n\n//** Tooltip max width\n@tooltip-max-width: 200px;\n//** Tooltip text color\n@tooltip-color: #fff;\n//** Tooltip background color\n@tooltip-bg: #000;\n@tooltip-opacity: .9;\n\n//** Tooltip arrow width\n@tooltip-arrow-width: 5px;\n//** Tooltip arrow color\n@tooltip-arrow-color: @tooltip-bg;\n\n\n//== Popovers\n//\n//##\n\n//** Popover body background color\n@popover-bg: #fff;\n//** Popover maximum width\n@popover-max-width: 276px;\n//** Popover border color\n@popover-border-color: rgba(0,0,0,.2);\n//** Popover fallback border color\n@popover-fallback-border-color: #ccc;\n\n//** Popover title background color\n@popover-title-bg: darken(@popover-bg, 3%);\n\n//** Popover arrow width\n@popover-arrow-width: 10px;\n//** Popover arrow color\n@popover-arrow-color: #fff;\n\n//** Popover outer arrow width\n@popover-arrow-outer-width: (@popover-arrow-width + 1);\n//** Popover outer arrow color\n@popover-arrow-outer-color: rgba(0,0,0,.25);\n//** Popover outer arrow fallback color\n@popover-arrow-outer-fallback-color: #999;\n\n\n//== Labels\n//\n//##\n\n//** Default label background color\n@label-default-bg: @gray-light;\n//** Primary label background color\n@label-primary-bg: @brand-primary;\n//** Success label background color\n@label-success-bg: @brand-success;\n//** Info label background color\n@label-info-bg: @brand-info;\n//** Warning label background color\n@label-warning-bg: @brand-warning;\n//** Danger label background color\n@label-danger-bg: @brand-danger;\n\n//** Default label text color\n@label-color: #fff;\n//** Default text color of a linked label\n@label-link-hover-color: #fff;\n\n\n//== Modals\n//\n//##\n\n//** Padding applied to the modal body\n@modal-inner-padding: 20px;\n\n//** Padding applied to the modal title\n@modal-title-padding: 15px;\n//** Modal title line-height\n@modal-title-line-height: @line-height-base;\n\n//** Background color of modal content area\n@modal-content-bg: #fff;\n//** Modal content border color\n@modal-content-border-color: rgba(0,0,0,.2);\n//** Modal content border color **for IE8**\n@modal-content-fallback-border-color: #999;\n\n//** Modal backdrop background color\n@modal-backdrop-bg: #000;\n//** Modal backdrop opacity\n@modal-backdrop-opacity: .5;\n//** Modal header border color\n@modal-header-border-color: #e5e5e5;\n//** Modal footer border color\n@modal-footer-border-color: @modal-header-border-color;\n\n@modal-lg: 900px;\n@modal-md: 600px;\n@modal-sm: 300px;\n\n\n//== Alerts\n//\n//## Define alert colors, border radius, and padding.\n\n@alert-padding: 15px;\n@alert-border-radius: @border-radius-base;\n@alert-link-font-weight: bold;\n\n@alert-success-bg: @state-success-bg;\n@alert-success-text: @state-success-text;\n@alert-success-border: @state-success-border;\n\n@alert-info-bg: @state-info-bg;\n@alert-info-text: @state-info-text;\n@alert-info-border: @state-info-border;\n\n@alert-warning-bg: @state-warning-bg;\n@alert-warning-text: @state-warning-text;\n@alert-warning-border: @state-warning-border;\n\n@alert-danger-bg: @state-danger-bg;\n@alert-danger-text: @state-danger-text;\n@alert-danger-border: @state-danger-border;\n\n\n//== Progress bars\n//\n//##\n\n//** Background color of the whole progress component\n@progress-bg: #f5f5f5;\n//** Progress bar text color\n@progress-bar-color: #fff;\n\n//** Default progress bar color\n@progress-bar-bg: @brand-primary;\n//** Success progress bar color\n@progress-bar-success-bg: @brand-success;\n//** Warning progress bar color\n@progress-bar-warning-bg: @brand-warning;\n//** Danger progress bar color\n@progress-bar-danger-bg: @brand-danger;\n//** Info progress bar color\n@progress-bar-info-bg: @brand-info;\n\n\n//== List group\n//\n//##\n\n//** Background color on `.list-group-item`\n@list-group-bg: #fff;\n//** `.list-group-item` border color\n@list-group-border: #ddd;\n//** List group border radius\n@list-group-border-radius: @border-radius-base;\n\n//** Background color of single list elements on hover\n@list-group-hover-bg: #f5f5f5;\n//** Text color of active list elements\n@list-group-active-color: @component-active-color;\n//** Background color of active list elements\n@list-group-active-bg: @component-active-bg;\n//** Border color of active list elements\n@list-group-active-border: @list-group-active-bg;\n@list-group-active-text-color: lighten(@list-group-active-bg, 40%);\n\n@list-group-link-color: #555;\n@list-group-link-heading-color: #333;\n\n\n//== Panels\n//\n//##\n\n@panel-bg: #fff;\n@panel-body-padding: 15px;\n@panel-border-radius: @border-radius-base;\n\n//** Border color for elements within panels\n@panel-inner-border: #ddd;\n@panel-footer-bg: #f5f5f5;\n\n@panel-default-text: @gray-dark;\n@panel-default-border: #ddd;\n@panel-default-heading-bg: #f5f5f5;\n\n@panel-primary-text: #fff;\n@panel-primary-border: @brand-primary;\n@panel-primary-heading-bg: @brand-primary;\n\n@panel-success-text: @state-success-text;\n@panel-success-border: @state-success-border;\n@panel-success-heading-bg: @state-success-bg;\n\n@panel-info-text: @state-info-text;\n@panel-info-border: @state-info-border;\n@panel-info-heading-bg: @state-info-bg;\n\n@panel-warning-text: @state-warning-text;\n@panel-warning-border: @state-warning-border;\n@panel-warning-heading-bg: @state-warning-bg;\n\n@panel-danger-text: @state-danger-text;\n@panel-danger-border: @state-danger-border;\n@panel-danger-heading-bg: @state-danger-bg;\n\n\n//== Thumbnails\n//\n//##\n\n//** Padding around the thumbnail image\n@thumbnail-padding: 4px;\n//** Thumbnail background color\n@thumbnail-bg: @body-bg;\n//** Thumbnail border color\n@thumbnail-border: #ddd;\n//** Thumbnail border radius\n@thumbnail-border-radius: @border-radius-base;\n\n//** Custom text color for thumbnail captions\n@thumbnail-caption-color: @text-color;\n//** Padding around the thumbnail caption\n@thumbnail-caption-padding: 9px;\n\n\n//== Wells\n//\n//##\n\n@well-bg: #f5f5f5;\n@well-border: darken(@well-bg, 7%);\n\n\n//== Badges\n//\n//##\n\n@badge-color: #fff;\n//** Linked badge text color on hover\n@badge-link-hover-color: #fff;\n@badge-bg: @gray-light;\n\n//** Badge text color in active nav link\n@badge-active-color: @link-color;\n//** Badge background color in active nav link\n@badge-active-bg: #fff;\n\n@badge-font-weight: bold;\n@badge-line-height: 1;\n@badge-border-radius: 10px;\n\n\n//== Breadcrumbs\n//\n//##\n\n@breadcrumb-padding-vertical: 8px;\n@breadcrumb-padding-horizontal: 15px;\n//** Breadcrumb background color\n@breadcrumb-bg: #f5f5f5;\n//** Breadcrumb text color\n@breadcrumb-color: #ccc;\n//** Text color of current page in the breadcrumb\n@breadcrumb-active-color: @gray-light;\n//** Textual separator for between breadcrumb elements\n@breadcrumb-separator: \"/\";\n\n\n//== Carousel\n//\n//##\n\n@carousel-text-shadow: 0 1px 2px rgba(0,0,0,.6);\n\n@carousel-control-color: #fff;\n@carousel-control-width: 15%;\n@carousel-control-opacity: .5;\n@carousel-control-font-size: 20px;\n\n@carousel-indicator-active-bg: #fff;\n@carousel-indicator-border-color: #fff;\n\n@carousel-caption-color: #fff;\n\n\n//== Close\n//\n//##\n\n@close-font-weight: bold;\n@close-color: #000;\n@close-text-shadow: 0 1px 0 #fff;\n\n\n//== Code\n//\n//##\n\n@code-color: #c7254e;\n@code-bg: #f9f2f4;\n\n@kbd-color: #fff;\n@kbd-bg: #333;\n\n@pre-bg: #f5f5f5;\n@pre-color: @gray-dark;\n@pre-border-color: #ccc;\n@pre-scrollable-max-height: 340px;\n\n\n//== Type\n//\n//##\n\n//** Text muted color\n@text-muted: @gray-light;\n//** Abbreviations and acronyms border color\n@abbr-border-color: @gray-light;\n//** Headings small color\n@headings-small-color: @gray-light;\n//** Blockquote small color\n@blockquote-small-color: @gray-light;\n//** Blockquote border color\n@blockquote-border-color: @gray-lighter;\n//** Page header border color\n@page-header-border-color: @gray-lighter;\n\n\n//== Miscellaneous\n//\n//##\n\n//** Horizontal line color.\n@hr-border: @gray-lighter;\n\n//** Horizontal offset for forms and lists.\n@component-offset-horizontal: 180px;\n\n\n//== Container sizes\n//\n//## Define the maximum width of `.container` for different screen sizes.\n\n// Small screen / tablet\n@container-tablet: ((720px + @grid-gutter-width));\n//** For `@screen-sm-min` and up.\n@container-sm: @container-tablet;\n\n// Medium screen / desktop\n@container-desktop: ((940px + @grid-gutter-width));\n//** For `@screen-md-min` and up.\n@container-md: @container-desktop;\n\n// Large screen / wide desktop\n@container-large-desktop: ((1140px + @grid-gutter-width));\n//** For `@screen-lg-min` and up.\n@container-lg: @container-large-desktop;\n","//\n// Typography\n// --------------------------------------------------\n\n\n// Headings\n// -------------------------\n\nh1, h2, h3, h4, h5, h6,\n.h1, .h2, .h3, .h4, .h5, .h6 {\n font-family: @headings-font-family;\n font-weight: @headings-font-weight;\n line-height: @headings-line-height;\n color: @headings-color;\n\n small,\n .small {\n font-weight: normal;\n line-height: 1;\n color: @headings-small-color;\n }\n}\n\nh1, .h1,\nh2, .h2,\nh3, .h3 {\n margin-top: @line-height-computed;\n margin-bottom: (@line-height-computed / 2);\n\n small,\n .small {\n font-size: 65%;\n }\n}\nh4, .h4,\nh5, .h5,\nh6, .h6 {\n margin-top: (@line-height-computed / 2);\n margin-bottom: (@line-height-computed / 2);\n\n small,\n .small {\n font-size: 75%;\n }\n}\n\nh1, .h1 { font-size: @font-size-h1; }\nh2, .h2 { font-size: @font-size-h2; }\nh3, .h3 { font-size: @font-size-h3; }\nh4, .h4 { font-size: @font-size-h4; }\nh5, .h5 { font-size: @font-size-h5; }\nh6, .h6 { font-size: @font-size-h6; }\n\n\n// Body text\n// -------------------------\n\np {\n margin: 0 0 (@line-height-computed / 2);\n}\n\n.lead {\n margin-bottom: @line-height-computed;\n font-size: floor((@font-size-base * 1.15));\n font-weight: 200;\n line-height: 1.4;\n\n @media (min-width: @screen-sm-min) {\n font-size: (@font-size-base * 1.5);\n }\n}\n\n\n// Emphasis & misc\n// -------------------------\n\n// Ex: 14px base font * 85% = about 12px\nsmall,\n.small { font-size: 85%; }\n\n// Undo browser default styling\ncite { font-style: normal; }\n\n// Alignment\n.text-left { text-align: left; }\n.text-right { text-align: right; }\n.text-center { text-align: center; }\n.text-justify { text-align: justify; }\n\n// Contextual colors\n.text-muted {\n color: @text-muted;\n}\n.text-primary {\n .text-emphasis-variant(@brand-primary);\n}\n.text-success {\n .text-emphasis-variant(@state-success-text);\n}\n.text-info {\n .text-emphasis-variant(@state-info-text);\n}\n.text-warning {\n .text-emphasis-variant(@state-warning-text);\n}\n.text-danger {\n .text-emphasis-variant(@state-danger-text);\n}\n\n// Contextual backgrounds\n// For now we'll leave these alongside the text classes until v4 when we can\n// safely shift things around (per SemVer rules).\n.bg-primary {\n // Given the contrast here, this is the only class to have its color inverted\n // automatically.\n color: #fff;\n .bg-variant(@brand-primary);\n}\n.bg-success {\n .bg-variant(@state-success-bg);\n}\n.bg-info {\n .bg-variant(@state-info-bg);\n}\n.bg-warning {\n .bg-variant(@state-warning-bg);\n}\n.bg-danger {\n .bg-variant(@state-danger-bg);\n}\n\n\n// Page header\n// -------------------------\n\n.page-header {\n padding-bottom: ((@line-height-computed / 2) - 1);\n margin: (@line-height-computed * 2) 0 @line-height-computed;\n border-bottom: 1px solid @page-header-border-color;\n}\n\n\n// Lists\n// --------------------------------------------------\n\n// Unordered and Ordered lists\nul,\nol {\n margin-top: 0;\n margin-bottom: (@line-height-computed / 2);\n ul,\n ol {\n margin-bottom: 0;\n }\n}\n\n// List options\n\n// Unstyled keeps list items block level, just removes default browser padding and list-style\n.list-unstyled {\n padding-left: 0;\n list-style: none;\n}\n\n// Inline turns list items into inline-block\n.list-inline {\n .list-unstyled();\n\n > li {\n display: inline-block;\n padding-left: 5px;\n padding-right: 5px;\n\n &:first-child {\n padding-left: 0;\n }\n }\n}\n\n// Description Lists\ndl {\n margin-top: 0; // Remove browser default\n margin-bottom: @line-height-computed;\n}\ndt,\ndd {\n line-height: @line-height-base;\n}\ndt {\n font-weight: bold;\n}\ndd {\n margin-left: 0; // Undo browser default\n}\n\n// Horizontal description lists\n//\n// Defaults to being stacked without any of the below styles applied, until the\n// grid breakpoint is reached (default of ~768px).\n\n@media (min-width: @grid-float-breakpoint) {\n .dl-horizontal {\n dt {\n float: left;\n width: (@component-offset-horizontal - 20);\n clear: left;\n text-align: right;\n .text-overflow();\n }\n dd {\n margin-left: @component-offset-horizontal;\n &:extend(.clearfix all); // Clear the floated `dt` if an empty `dd` is present\n }\n }\n}\n\n// MISC\n// ----\n\n// Abbreviations and acronyms\nabbr[title],\n// Add data-* attribute to help out our tooltip plugin, per https://github.com/twbs/bootstrap/issues/5257\nabbr[data-original-title] {\n cursor: help;\n border-bottom: 1px dotted @abbr-border-color;\n}\n.initialism {\n font-size: 90%;\n text-transform: uppercase;\n}\n\n// Blockquotes\nblockquote {\n padding: (@line-height-computed / 2) @line-height-computed;\n margin: 0 0 @line-height-computed;\n font-size: (@font-size-base * 1.25);\n border-left: 5px solid @blockquote-border-color;\n\n p,\n ul,\n ol {\n &:last-child {\n margin-bottom: 0;\n }\n }\n\n // Note: Deprecated small and .small as of v3.1.0\n // Context: https://github.com/twbs/bootstrap/issues/11660\n footer,\n small,\n .small {\n display: block;\n font-size: 80%; // back to default font-size\n line-height: @line-height-base;\n color: @blockquote-small-color;\n\n &:before {\n content: '\\2014 \\00A0'; // em dash, nbsp\n }\n }\n}\n\n// Opposite alignment of blockquote\n//\n// Heads up: `blockquote.pull-right` has been deprecated as of v3.1.0.\n.blockquote-reverse,\nblockquote.pull-right {\n padding-right: 15px;\n padding-left: 0;\n border-right: 5px solid @blockquote-border-color;\n border-left: 0;\n text-align: right;\n\n // Account for citation\n footer,\n small,\n .small {\n &:before { content: ''; }\n &:after {\n content: '\\00A0 \\2014'; // nbsp, em dash\n }\n }\n}\n\n// Quotes\nblockquote:before,\nblockquote:after {\n content: \"\";\n}\n\n// Addresses\naddress {\n margin-bottom: @line-height-computed;\n font-style: normal;\n line-height: @line-height-base;\n}\n","//\n// Code (inline and block)\n// --------------------------------------------------\n\n\n// Inline and block code styles\ncode,\nkbd,\npre,\nsamp {\n font-family: @font-family-monospace;\n}\n\n// Inline code\ncode {\n padding: 2px 4px;\n font-size: 90%;\n color: @code-color;\n background-color: @code-bg;\n white-space: nowrap;\n border-radius: @border-radius-base;\n}\n\n// User input typically entered via keyboard\nkbd {\n padding: 2px 4px;\n font-size: 90%;\n color: @kbd-color;\n background-color: @kbd-bg;\n border-radius: @border-radius-small;\n box-shadow: inset 0 -1px 0 rgba(0,0,0,.25);\n}\n\n// Blocks of code\npre {\n display: block;\n padding: ((@line-height-computed - 1) / 2);\n margin: 0 0 (@line-height-computed / 2);\n font-size: (@font-size-base - 1); // 14px to 13px\n line-height: @line-height-base;\n word-break: break-all;\n word-wrap: break-word;\n color: @pre-color;\n background-color: @pre-bg;\n border: 1px solid @pre-border-color;\n border-radius: @border-radius-base;\n\n // Account for some code outputs that place code tags in pre tags\n code {\n padding: 0;\n font-size: inherit;\n color: inherit;\n white-space: pre-wrap;\n background-color: transparent;\n border-radius: 0;\n }\n}\n\n// Enable scrollable blocks of code\n.pre-scrollable {\n max-height: @pre-scrollable-max-height;\n overflow-y: scroll;\n}\n","//\n// Grid system\n// --------------------------------------------------\n\n\n// Container widths\n//\n// Set the container width, and override it for fixed navbars in media queries.\n\n.container {\n .container-fixed();\n\n @media (min-width: @screen-sm-min) {\n width: @container-sm;\n }\n @media (min-width: @screen-md-min) {\n width: @container-md;\n }\n @media (min-width: @screen-lg-min) {\n width: @container-lg;\n }\n}\n\n\n// Fluid container\n//\n// Utilizes the mixin meant for fixed width containers, but without any defined\n// width for fluid, full width layouts.\n\n.container-fluid {\n .container-fixed();\n}\n\n\n// Row\n//\n// Rows contain and clear the floats of your columns.\n\n.row {\n .make-row();\n}\n\n\n// Columns\n//\n// Common styles for small and large grid columns\n\n.make-grid-columns();\n\n\n// Extra small grid\n//\n// Columns, offsets, pushes, and pulls for extra small devices like\n// smartphones.\n\n.make-grid-columns-float(xs);\n.make-grid(@grid-columns, xs, width);\n.make-grid(@grid-columns, xs, pull);\n.make-grid(@grid-columns, xs, push);\n.make-grid(@grid-columns, xs, offset);\n\n\n// Small grid\n//\n// Columns, offsets, pushes, and pulls for the small device range, from phones\n// to tablets.\n\n@media (min-width: @screen-sm-min) {\n .make-grid-columns-float(sm);\n .make-grid(@grid-columns, sm, width);\n .make-grid(@grid-columns, sm, pull);\n .make-grid(@grid-columns, sm, push);\n .make-grid(@grid-columns, sm, offset);\n}\n\n\n// Medium grid\n//\n// Columns, offsets, pushes, and pulls for the desktop device range.\n\n@media (min-width: @screen-md-min) {\n .make-grid-columns-float(md);\n .make-grid(@grid-columns, md, width);\n .make-grid(@grid-columns, md, pull);\n .make-grid(@grid-columns, md, push);\n .make-grid(@grid-columns, md, offset);\n}\n\n\n// Large grid\n//\n// Columns, offsets, pushes, and pulls for the large desktop device range.\n\n@media (min-width: @screen-lg-min) {\n .make-grid-columns-float(lg);\n .make-grid(@grid-columns, lg, width);\n .make-grid(@grid-columns, lg, pull);\n .make-grid(@grid-columns, lg, push);\n .make-grid(@grid-columns, lg, offset);\n}\n","//\n// Tables\n// --------------------------------------------------\n\n\ntable {\n max-width: 100%;\n background-color: @table-bg;\n}\nth {\n text-align: left;\n}\n\n\n// Baseline styles\n\n.table {\n width: 100%;\n margin-bottom: @line-height-computed;\n // Cells\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th,\n > td {\n padding: @table-cell-padding;\n line-height: @line-height-base;\n vertical-align: top;\n border-top: 1px solid @table-border-color;\n }\n }\n }\n // Bottom align for column headings\n > thead > tr > th {\n vertical-align: bottom;\n border-bottom: 2px solid @table-border-color;\n }\n // Remove top border from thead by default\n > caption + thead,\n > colgroup + thead,\n > thead:first-child {\n > tr:first-child {\n > th,\n > td {\n border-top: 0;\n }\n }\n }\n // Account for multiple tbody instances\n > tbody + tbody {\n border-top: 2px solid @table-border-color;\n }\n\n // Nesting\n .table {\n background-color: @body-bg;\n }\n}\n\n\n// Condensed table w/ half padding\n\n.table-condensed {\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th,\n > td {\n padding: @table-condensed-cell-padding;\n }\n }\n }\n}\n\n\n// Bordered version\n//\n// Add borders all around the table and between all the columns.\n\n.table-bordered {\n border: 1px solid @table-border-color;\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th,\n > td {\n border: 1px solid @table-border-color;\n }\n }\n }\n > thead > tr {\n > th,\n > td {\n border-bottom-width: 2px;\n }\n }\n}\n\n\n// Zebra-striping\n//\n// Default zebra-stripe styles (alternating gray and transparent backgrounds)\n\n.table-striped {\n > tbody > tr:nth-child(odd) {\n > td,\n > th {\n background-color: @table-bg-accent;\n }\n }\n}\n\n\n// Hover effect\n//\n// Placed here since it has to come after the potential zebra striping\n\n.table-hover {\n > tbody > tr:hover {\n > td,\n > th {\n background-color: @table-bg-hover;\n }\n }\n}\n\n\n// Table cell sizing\n//\n// Reset default table behavior\n\ntable col[class*=\"col-\"] {\n position: static; // Prevent border hiding in Firefox and IE9/10 (see https://github.com/twbs/bootstrap/issues/11623)\n float: none;\n display: table-column;\n}\ntable {\n td,\n th {\n &[class*=\"col-\"] {\n position: static; // Prevent border hiding in Firefox and IE9/10 (see https://github.com/twbs/bootstrap/issues/11623)\n float: none;\n display: table-cell;\n }\n }\n}\n\n\n// Table backgrounds\n//\n// Exact selectors below required to override `.table-striped` and prevent\n// inheritance to nested tables.\n\n// Generate the contextual variants\n.table-row-variant(active; @table-bg-active);\n.table-row-variant(success; @state-success-bg);\n.table-row-variant(info; @state-info-bg);\n.table-row-variant(warning; @state-warning-bg);\n.table-row-variant(danger; @state-danger-bg);\n\n\n// Responsive tables\n//\n// Wrap your tables in `.table-responsive` and we'll make them mobile friendly\n// by enabling horizontal scrolling. Only applies <768px. Everything above that\n// will display normally.\n\n@media (max-width: @screen-xs-max) {\n .table-responsive {\n width: 100%;\n margin-bottom: (@line-height-computed * 0.75);\n overflow-y: hidden;\n overflow-x: scroll;\n -ms-overflow-style: -ms-autohiding-scrollbar;\n border: 1px solid @table-border-color;\n -webkit-overflow-scrolling: touch;\n\n // Tighten up spacing\n > .table {\n margin-bottom: 0;\n\n // Ensure the content doesn't wrap\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th,\n > td {\n white-space: nowrap;\n }\n }\n }\n }\n\n // Special overrides for the bordered tables\n > .table-bordered {\n border: 0;\n\n // Nuke the appropriate borders so that the parent can handle them\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th:first-child,\n > td:first-child {\n border-left: 0;\n }\n > th:last-child,\n > td:last-child {\n border-right: 0;\n }\n }\n }\n\n // Only nuke the last row's bottom-border in `tbody` and `tfoot` since\n // chances are there will be only one `tr` in a `thead` and that would\n // remove the border altogether.\n > tbody,\n > tfoot {\n > tr:last-child {\n > th,\n > td {\n border-bottom: 0;\n }\n }\n }\n\n }\n }\n}\n","//\n// Forms\n// --------------------------------------------------\n\n\n// Normalize non-controls\n//\n// Restyle and baseline non-control form elements.\n\nfieldset {\n padding: 0;\n margin: 0;\n border: 0;\n // Chrome and Firefox set a `min-width: -webkit-min-content;` on fieldsets,\n // so we reset that to ensure it behaves more like a standard block element.\n // See https://github.com/twbs/bootstrap/issues/12359.\n min-width: 0;\n}\n\nlegend {\n display: block;\n width: 100%;\n padding: 0;\n margin-bottom: @line-height-computed;\n font-size: (@font-size-base * 1.5);\n line-height: inherit;\n color: @legend-color;\n border: 0;\n border-bottom: 1px solid @legend-border-color;\n}\n\nlabel {\n display: inline-block;\n margin-bottom: 5px;\n font-weight: bold;\n}\n\n\n// Normalize form controls\n//\n// While most of our form styles require extra classes, some basic normalization\n// is required to ensure optimum display with or without those classes to better\n// address browser inconsistencies.\n\n// Override content-box in Normalize (* isn't specific enough)\ninput[type=\"search\"] {\n .box-sizing(border-box);\n}\n\n// Position radios and checkboxes better\ninput[type=\"radio\"],\ninput[type=\"checkbox\"] {\n margin: 4px 0 0;\n margin-top: 1px \\9; /* IE8-9 */\n line-height: normal;\n}\n\n// Set the height of file controls to match text inputs\ninput[type=\"file\"] {\n display: block;\n}\n\n// Make range inputs behave like textual form controls\ninput[type=\"range\"] {\n display: block;\n width: 100%;\n}\n\n// Make multiple select elements height not fixed\nselect[multiple],\nselect[size] {\n height: auto;\n}\n\n// Focus for file, radio, and checkbox\ninput[type=\"file\"]:focus,\ninput[type=\"radio\"]:focus,\ninput[type=\"checkbox\"]:focus {\n .tab-focus();\n}\n\n// Adjust output element\noutput {\n display: block;\n padding-top: (@padding-base-vertical + 1);\n font-size: @font-size-base;\n line-height: @line-height-base;\n color: @input-color;\n}\n\n\n// Common form controls\n//\n// Shared size and type resets for form controls. Apply `.form-control` to any\n// of the following form controls:\n//\n// select\n// textarea\n// input[type=\"text\"]\n// input[type=\"password\"]\n// input[type=\"datetime\"]\n// input[type=\"datetime-local\"]\n// input[type=\"date\"]\n// input[type=\"month\"]\n// input[type=\"time\"]\n// input[type=\"week\"]\n// input[type=\"number\"]\n// input[type=\"email\"]\n// input[type=\"url\"]\n// input[type=\"search\"]\n// input[type=\"tel\"]\n// input[type=\"color\"]\n\n.form-control {\n display: block;\n width: 100%;\n height: @input-height-base; // Make inputs at least the height of their button counterpart (base line-height + padding + border)\n padding: @padding-base-vertical @padding-base-horizontal;\n font-size: @font-size-base;\n line-height: @line-height-base;\n color: @input-color;\n background-color: @input-bg;\n background-image: none; // Reset unusual Firefox-on-Android default style; see https://github.com/necolas/normalize.css/issues/214\n border: 1px solid @input-border;\n border-radius: @input-border-radius;\n .box-shadow(inset 0 1px 1px rgba(0,0,0,.075));\n .transition(~\"border-color ease-in-out .15s, box-shadow ease-in-out .15s\");\n\n // Customize the `:focus` state to imitate native WebKit styles.\n .form-control-focus();\n\n // Placeholder\n .placeholder();\n\n // Disabled and read-only inputs\n // Note: HTML5 says that controls under a fieldset > legend:first-child won't\n // be disabled if the fieldset is disabled. Due to implementation difficulty,\n // we don't honor that edge case; we style them as disabled anyway.\n &[disabled],\n &[readonly],\n fieldset[disabled] & {\n cursor: not-allowed;\n background-color: @input-bg-disabled;\n opacity: 1; // iOS fix for unreadable disabled content\n }\n\n // Reset height for `textarea`s\n textarea& {\n height: auto;\n }\n}\n\n// Special styles for iOS date input\n//\n// In Mobile Safari, date inputs require a pixel line-height that matches the\n// given height of the input.\ninput[type=\"date\"] {\n line-height: @input-height-base;\n}\n\n\n// Form groups\n//\n// Designed to help with the organization and spacing of vertical forms. For\n// horizontal forms, use the predefined grid classes.\n\n.form-group {\n margin-bottom: 15px;\n}\n\n\n// Checkboxes and radios\n//\n// Indent the labels to position radios/checkboxes as hanging controls.\n\n.radio,\n.checkbox {\n display: block;\n min-height: @line-height-computed; // clear the floating input if there is no label text\n margin-top: 10px;\n margin-bottom: 10px;\n padding-left: 20px;\n label {\n display: inline;\n font-weight: normal;\n cursor: pointer;\n }\n}\n.radio input[type=\"radio\"],\n.radio-inline input[type=\"radio\"],\n.checkbox input[type=\"checkbox\"],\n.checkbox-inline input[type=\"checkbox\"] {\n float: left;\n margin-left: -20px;\n}\n.radio + .radio,\n.checkbox + .checkbox {\n margin-top: -5px; // Move up sibling radios or checkboxes for tighter spacing\n}\n\n// Radios and checkboxes on same line\n.radio-inline,\n.checkbox-inline {\n display: inline-block;\n padding-left: 20px;\n margin-bottom: 0;\n vertical-align: middle;\n font-weight: normal;\n cursor: pointer;\n}\n.radio-inline + .radio-inline,\n.checkbox-inline + .checkbox-inline {\n margin-top: 0;\n margin-left: 10px; // space out consecutive inline controls\n}\n\n// Apply same disabled cursor tweak as for inputs\n//\n// Note: Neither radios nor checkboxes can be readonly.\ninput[type=\"radio\"],\ninput[type=\"checkbox\"],\n.radio,\n.radio-inline,\n.checkbox,\n.checkbox-inline {\n &[disabled],\n fieldset[disabled] & {\n cursor: not-allowed;\n }\n}\n\n\n// Form control sizing\n//\n// Build on `.form-control` with modifier classes to decrease or increase the\n// height and font-size of form controls.\n\n.input-sm {\n .input-size(@input-height-small; @padding-small-vertical; @padding-small-horizontal; @font-size-small; @line-height-small; @border-radius-small);\n}\n\n.input-lg {\n .input-size(@input-height-large; @padding-large-vertical; @padding-large-horizontal; @font-size-large; @line-height-large; @border-radius-large);\n}\n\n\n// Form control feedback states\n//\n// Apply contextual and semantic states to individual form controls.\n\n.has-feedback {\n // Enable absolute positioning\n position: relative;\n\n // Ensure icons don't overlap text\n .form-control {\n padding-right: (@input-height-base * 1.25);\n }\n\n // Feedback icon (requires .glyphicon classes)\n .form-control-feedback {\n position: absolute;\n top: (@line-height-computed + 5); // Height of the `label` and its margin\n right: 0;\n display: block;\n width: @input-height-base;\n height: @input-height-base;\n line-height: @input-height-base;\n text-align: center;\n }\n}\n\n// Feedback states\n.has-success {\n .form-control-validation(@state-success-text; @state-success-text; @state-success-bg);\n}\n.has-warning {\n .form-control-validation(@state-warning-text; @state-warning-text; @state-warning-bg);\n}\n.has-error {\n .form-control-validation(@state-danger-text; @state-danger-text; @state-danger-bg);\n}\n\n\n// Static form control text\n//\n// Apply class to a `p` element to make any string of text align with labels in\n// a horizontal form layout.\n\n.form-control-static {\n margin-bottom: 0; // Remove default margin from `p`\n}\n\n\n// Help text\n//\n// Apply to any element you wish to create light text for placement immediately\n// below a form control. Use for general help, formatting, or instructional text.\n\n.help-block {\n display: block; // account for any element using help-block\n margin-top: 5px;\n margin-bottom: 10px;\n color: lighten(@text-color, 25%); // lighten the text some for contrast\n}\n\n\n\n// Inline forms\n//\n// Make forms appear inline(-block) by adding the `.form-inline` class. Inline\n// forms begin stacked on extra small (mobile) devices and then go inline when\n// viewports reach <768px.\n//\n// Requires wrapping inputs and labels with `.form-group` for proper display of\n// default HTML form controls and our custom form controls (e.g., input groups).\n//\n// Heads up! This is mixin-ed into `.navbar-form` in navbars.less.\n\n.form-inline {\n\n // Kick in the inline\n @media (min-width: @screen-sm-min) {\n // Inline-block all the things for \"inline\"\n .form-group {\n display: inline-block;\n margin-bottom: 0;\n vertical-align: middle;\n }\n\n // In navbar-form, allow folks to *not* use `.form-group`\n .form-control {\n display: inline-block;\n width: auto; // Prevent labels from stacking above inputs in `.form-group`\n vertical-align: middle;\n }\n\n .control-label {\n margin-bottom: 0;\n vertical-align: middle;\n }\n\n // Remove default margin on radios/checkboxes that were used for stacking, and\n // then undo the floating of radios and checkboxes to match (which also avoids\n // a bug in WebKit: https://github.com/twbs/bootstrap/issues/1969).\n .radio,\n .checkbox {\n display: inline-block;\n margin-top: 0;\n margin-bottom: 0;\n padding-left: 0;\n vertical-align: middle;\n }\n .radio input[type=\"radio\"],\n .checkbox input[type=\"checkbox\"] {\n float: none;\n margin-left: 0;\n }\n\n // Validation states\n //\n // Reposition the icon because it's now within a grid column and columns have\n // `position: relative;` on them. Also accounts for the grid gutter padding.\n .has-feedback .form-control-feedback {\n top: 0;\n }\n }\n}\n\n\n// Horizontal forms\n//\n// Horizontal forms are built on grid classes and allow you to create forms with\n// labels on the left and inputs on the right.\n\n.form-horizontal {\n\n // Consistent vertical alignment of labels, radios, and checkboxes\n .control-label,\n .radio,\n .checkbox,\n .radio-inline,\n .checkbox-inline {\n margin-top: 0;\n margin-bottom: 0;\n padding-top: (@padding-base-vertical + 1); // Default padding plus a border\n }\n // Account for padding we're adding to ensure the alignment and of help text\n // and other content below items\n .radio,\n .checkbox {\n min-height: (@line-height-computed + (@padding-base-vertical + 1));\n }\n\n // Make form groups behave like rows\n .form-group {\n .make-row();\n }\n\n .form-control-static {\n padding-top: (@padding-base-vertical + 1);\n }\n\n // Only right align form labels here when the columns stop stacking\n @media (min-width: @screen-sm-min) {\n .control-label {\n text-align: right;\n }\n }\n\n // Validation states\n //\n // Reposition the icon because it's now within a grid column and columns have\n // `position: relative;` on them. Also accounts for the grid gutter padding.\n .has-feedback .form-control-feedback {\n top: 0;\n right: (@grid-gutter-width / 2);\n }\n}\n","//\n// Buttons\n// --------------------------------------------------\n\n\n// Base styles\n// --------------------------------------------------\n\n.btn {\n display: inline-block;\n margin-bottom: 0; // For input.btn\n font-weight: @btn-font-weight;\n text-align: center;\n vertical-align: middle;\n cursor: pointer;\n background-image: none; // Reset unusual Firefox-on-Android default style; see https://github.com/necolas/normalize.css/issues/214\n border: 1px solid transparent;\n white-space: nowrap;\n .button-size(@padding-base-vertical; @padding-base-horizontal; @font-size-base; @line-height-base; @border-radius-base);\n .user-select(none);\n\n &:focus {\n .tab-focus();\n }\n\n &:hover,\n &:focus {\n color: @btn-default-color;\n text-decoration: none;\n }\n\n &:active,\n &.active {\n outline: 0;\n background-image: none;\n .box-shadow(inset 0 3px 5px rgba(0,0,0,.125));\n }\n\n &.disabled,\n &[disabled],\n fieldset[disabled] & {\n cursor: not-allowed;\n pointer-events: none; // Future-proof disabling of clicks\n .opacity(.65);\n .box-shadow(none);\n }\n}\n\n\n// Alternate buttons\n// --------------------------------------------------\n\n.btn-default {\n .button-variant(@btn-default-color; @btn-default-bg; @btn-default-border);\n}\n.btn-primary {\n .button-variant(@btn-primary-color; @btn-primary-bg; @btn-primary-border);\n}\n// Success appears as green\n.btn-success {\n .button-variant(@btn-success-color; @btn-success-bg; @btn-success-border);\n}\n// Info appears as blue-green\n.btn-info {\n .button-variant(@btn-info-color; @btn-info-bg; @btn-info-border);\n}\n// Warning appears as orange\n.btn-warning {\n .button-variant(@btn-warning-color; @btn-warning-bg; @btn-warning-border);\n}\n// Danger and error appear as red\n.btn-danger {\n .button-variant(@btn-danger-color; @btn-danger-bg; @btn-danger-border);\n}\n\n\n// Link buttons\n// -------------------------\n\n// Make a button look and behave like a link\n.btn-link {\n color: @link-color;\n font-weight: normal;\n cursor: pointer;\n border-radius: 0;\n\n &,\n &:active,\n &[disabled],\n fieldset[disabled] & {\n background-color: transparent;\n .box-shadow(none);\n }\n &,\n &:hover,\n &:focus,\n &:active {\n border-color: transparent;\n }\n &:hover,\n &:focus {\n color: @link-hover-color;\n text-decoration: underline;\n background-color: transparent;\n }\n &[disabled],\n fieldset[disabled] & {\n &:hover,\n &:focus {\n color: @btn-link-disabled-color;\n text-decoration: none;\n }\n }\n}\n\n\n// Button Sizes\n// --------------------------------------------------\n\n.btn-lg {\n // line-height: ensure even-numbered height of button next to large input\n .button-size(@padding-large-vertical; @padding-large-horizontal; @font-size-large; @line-height-large; @border-radius-large);\n}\n.btn-sm {\n // line-height: ensure proper height of button next to small input\n .button-size(@padding-small-vertical; @padding-small-horizontal; @font-size-small; @line-height-small; @border-radius-small);\n}\n.btn-xs {\n .button-size(@padding-xs-vertical; @padding-xs-horizontal; @font-size-small; @line-height-small; @border-radius-small);\n}\n\n\n// Block button\n// --------------------------------------------------\n\n.btn-block {\n display: block;\n width: 100%;\n padding-left: 0;\n padding-right: 0;\n}\n\n// Vertically space out multiple block buttons\n.btn-block + .btn-block {\n margin-top: 5px;\n}\n\n// Specificity overrides\ninput[type=\"submit\"],\ninput[type=\"reset\"],\ninput[type=\"button\"] {\n &.btn-block {\n width: 100%;\n }\n}\n","//\n// Component animations\n// --------------------------------------------------\n\n// Heads up!\n//\n// We don't use the `.opacity()` mixin here since it causes a bug with text\n// fields in IE7-8. Source: https://github.com/twitter/bootstrap/pull/3552.\n\n.fade {\n opacity: 0;\n .transition(opacity .15s linear);\n &.in {\n opacity: 1;\n }\n}\n\n.collapse {\n display: none;\n &.in {\n display: block;\n }\n}\n.collapsing {\n position: relative;\n height: 0;\n overflow: hidden;\n .transition(height .35s ease);\n}\n","//\n// Glyphicons for Bootstrap\n//\n// Since icons are fonts, they can be placed anywhere text is placed and are\n// thus automatically sized to match the surrounding child. To use, create an\n// inline element with the appropriate classes, like so:\n//\n// <a href=\"#\"><span class=\"glyphicon glyphicon-star\"></span> Star</a>\n\n// Import the fonts\n@font-face {\n font-family: 'Glyphicons Halflings';\n src: ~\"url('@{icon-font-path}@{icon-font-name}.eot')\";\n src: ~\"url('@{icon-font-path}@{icon-font-name}.eot?#iefix') format('embedded-opentype')\",\n ~\"url('@{icon-font-path}@{icon-font-name}.woff') format('woff')\",\n ~\"url('@{icon-font-path}@{icon-font-name}.ttf') format('truetype')\",\n ~\"url('@{icon-font-path}@{icon-font-name}.svg#@{icon-font-svg-id}') format('svg')\";\n}\n\n// Catchall baseclass\n.glyphicon {\n position: relative;\n top: 1px;\n display: inline-block;\n font-family: 'Glyphicons Halflings';\n font-style: normal;\n font-weight: normal;\n line-height: 1;\n -webkit-font-smoothing: antialiased;\n -moz-osx-font-smoothing: grayscale;\n}\n\n// Individual icons\n.glyphicon-asterisk { &:before { content: \"\\2a\"; } }\n.glyphicon-plus { &:before { content: \"\\2b\"; } }\n.glyphicon-euro { &:before { content: \"\\20ac\"; } }\n.glyphicon-minus { &:before { content: \"\\2212\"; } }\n.glyphicon-cloud { &:before { content: \"\\2601\"; } }\n.glyphicon-envelope { &:before { content: \"\\2709\"; } }\n.glyphicon-pencil { &:before { content: \"\\270f\"; } }\n.glyphicon-glass { &:before { content: \"\\e001\"; } }\n.glyphicon-music { &:before { content: \"\\e002\"; } }\n.glyphicon-search { &:before { content: \"\\e003\"; } }\n.glyphicon-heart { &:before { content: \"\\e005\"; } }\n.glyphicon-star { &:before { content: \"\\e006\"; } }\n.glyphicon-star-empty { &:before { content: \"\\e007\"; } }\n.glyphicon-user { &:before { content: \"\\e008\"; } }\n.glyphicon-film { &:before { content: \"\\e009\"; } }\n.glyphicon-th-large { &:before { content: \"\\e010\"; } }\n.glyphicon-th { &:before { content: \"\\e011\"; } }\n.glyphicon-th-list { &:before { content: \"\\e012\"; } }\n.glyphicon-ok { &:before { content: \"\\e013\"; } }\n.glyphicon-remove { &:before { content: \"\\e014\"; } }\n.glyphicon-zoom-in { &:before { content: \"\\e015\"; } }\n.glyphicon-zoom-out { &:before { content: \"\\e016\"; } }\n.glyphicon-off { &:before { content: \"\\e017\"; } }\n.glyphicon-signal { &:before { content: \"\\e018\"; } }\n.glyphicon-cog { &:before { content: \"\\e019\"; } }\n.glyphicon-trash { &:before { content: \"\\e020\"; } }\n.glyphicon-home { &:before { content: \"\\e021\"; } }\n.glyphicon-file { &:before { content: \"\\e022\"; } }\n.glyphicon-time { &:before { content: \"\\e023\"; } }\n.glyphicon-road { &:before { content: \"\\e024\"; } }\n.glyphicon-download-alt { &:before { content: \"\\e025\"; } }\n.glyphicon-download { &:before { content: \"\\e026\"; } }\n.glyphicon-upload { &:before { content: \"\\e027\"; } }\n.glyphicon-inbox { &:before { content: \"\\e028\"; } }\n.glyphicon-play-circle { &:before { content: \"\\e029\"; } }\n.glyphicon-repeat { &:before { content: \"\\e030\"; } }\n.glyphicon-refresh { &:before { content: \"\\e031\"; } }\n.glyphicon-list-alt { &:before { content: \"\\e032\"; } }\n.glyphicon-lock { &:before { content: \"\\e033\"; } }\n.glyphicon-flag { &:before { content: \"\\e034\"; } }\n.glyphicon-headphones { &:before { content: \"\\e035\"; } }\n.glyphicon-volume-off { &:before { content: \"\\e036\"; } }\n.glyphicon-volume-down { &:before { content: \"\\e037\"; } }\n.glyphicon-volume-up { &:before { content: \"\\e038\"; } }\n.glyphicon-qrcode { &:before { content: \"\\e039\"; } }\n.glyphicon-barcode { &:before { content: \"\\e040\"; } }\n.glyphicon-tag { &:before { content: \"\\e041\"; } }\n.glyphicon-tags { &:before { content: \"\\e042\"; } }\n.glyphicon-book { &:before { content: \"\\e043\"; } }\n.glyphicon-bookmark { &:before { content: \"\\e044\"; } }\n.glyphicon-print { &:before { content: \"\\e045\"; } }\n.glyphicon-camera { &:before { content: \"\\e046\"; } }\n.glyphicon-font { &:before { content: \"\\e047\"; } }\n.glyphicon-bold { &:before { content: \"\\e048\"; } }\n.glyphicon-italic { &:before { content: \"\\e049\"; } }\n.glyphicon-text-height { &:before { content: \"\\e050\"; } }\n.glyphicon-text-width { &:before { content: \"\\e051\"; } }\n.glyphicon-align-left { &:before { content: \"\\e052\"; } }\n.glyphicon-align-center { &:before { content: \"\\e053\"; } }\n.glyphicon-align-right { &:before { content: \"\\e054\"; } }\n.glyphicon-align-justify { &:before { content: \"\\e055\"; } }\n.glyphicon-list { &:before { content: \"\\e056\"; } }\n.glyphicon-indent-left { &:before { content: \"\\e057\"; } }\n.glyphicon-indent-right { &:before { content: \"\\e058\"; } }\n.glyphicon-facetime-video { &:before { content: \"\\e059\"; } }\n.glyphicon-picture { &:before { content: \"\\e060\"; } }\n.glyphicon-map-marker { &:before { content: \"\\e062\"; } }\n.glyphicon-adjust { &:before { content: \"\\e063\"; } }\n.glyphicon-tint { &:before { content: \"\\e064\"; } }\n.glyphicon-edit { &:before { content: \"\\e065\"; } }\n.glyphicon-share { &:before { content: \"\\e066\"; } }\n.glyphicon-check { &:before { content: \"\\e067\"; } }\n.glyphicon-move { &:before { content: \"\\e068\"; } }\n.glyphicon-step-backward { &:before { content: \"\\e069\"; } }\n.glyphicon-fast-backward { &:before { content: \"\\e070\"; } }\n.glyphicon-backward { &:before { content: \"\\e071\"; } }\n.glyphicon-play { &:before { content: \"\\e072\"; } }\n.glyphicon-pause { &:before { content: \"\\e073\"; } }\n.glyphicon-stop { &:before { content: \"\\e074\"; } }\n.glyphicon-forward { &:before { content: \"\\e075\"; } }\n.glyphicon-fast-forward { &:before { content: \"\\e076\"; } }\n.glyphicon-step-forward { &:before { content: \"\\e077\"; } }\n.glyphicon-eject { &:before { content: \"\\e078\"; } }\n.glyphicon-chevron-left { &:before { content: \"\\e079\"; } }\n.glyphicon-chevron-right { &:before { content: \"\\e080\"; } }\n.glyphicon-plus-sign { &:before { content: \"\\e081\"; } }\n.glyphicon-minus-sign { &:before { content: \"\\e082\"; } }\n.glyphicon-remove-sign { &:before { content: \"\\e083\"; } }\n.glyphicon-ok-sign { &:before { content: \"\\e084\"; } }\n.glyphicon-question-sign { &:before { content: \"\\e085\"; } }\n.glyphicon-info-sign { &:before { content: \"\\e086\"; } }\n.glyphicon-screenshot { &:before { content: \"\\e087\"; } }\n.glyphicon-remove-circle { &:before { content: \"\\e088\"; } }\n.glyphicon-ok-circle { &:before { content: \"\\e089\"; } }\n.glyphicon-ban-circle { &:before { content: \"\\e090\"; } }\n.glyphicon-arrow-left { &:before { content: \"\\e091\"; } }\n.glyphicon-arrow-right { &:before { content: \"\\e092\"; } }\n.glyphicon-arrow-up { &:before { content: \"\\e093\"; } }\n.glyphicon-arrow-down { &:before { content: \"\\e094\"; } }\n.glyphicon-share-alt { &:before { content: \"\\e095\"; } }\n.glyphicon-resize-full { &:before { content: \"\\e096\"; } }\n.glyphicon-resize-small { &:before { content: \"\\e097\"; } }\n.glyphicon-exclamation-sign { &:before { content: \"\\e101\"; } }\n.glyphicon-gift { &:before { content: \"\\e102\"; } }\n.glyphicon-leaf { &:before { content: \"\\e103\"; } }\n.glyphicon-fire { &:before { content: \"\\e104\"; } }\n.glyphicon-eye-open { &:before { content: \"\\e105\"; } }\n.glyphicon-eye-close { &:before { content: \"\\e106\"; } }\n.glyphicon-warning-sign { &:before { content: \"\\e107\"; } }\n.glyphicon-plane { &:before { content: \"\\e108\"; } }\n.glyphicon-calendar { &:before { content: \"\\e109\"; } }\n.glyphicon-random { &:before { content: \"\\e110\"; } }\n.glyphicon-comment { &:before { content: \"\\e111\"; } }\n.glyphicon-magnet { &:before { content: \"\\e112\"; } }\n.glyphicon-chevron-up { &:before { content: \"\\e113\"; } }\n.glyphicon-chevron-down { &:before { content: \"\\e114\"; } }\n.glyphicon-retweet { &:before { content: \"\\e115\"; } }\n.glyphicon-shopping-cart { &:before { content: \"\\e116\"; } }\n.glyphicon-folder-close { &:before { content: \"\\e117\"; } }\n.glyphicon-folder-open { &:before { content: \"\\e118\"; } }\n.glyphicon-resize-vertical { &:before { content: \"\\e119\"; } }\n.glyphicon-resize-horizontal { &:before { content: \"\\e120\"; } }\n.glyphicon-hdd { &:before { content: \"\\e121\"; } }\n.glyphicon-bullhorn { &:before { content: \"\\e122\"; } }\n.glyphicon-bell { &:before { content: \"\\e123\"; } }\n.glyphicon-certificate { &:before { content: \"\\e124\"; } }\n.glyphicon-thumbs-up { &:before { content: \"\\e125\"; } }\n.glyphicon-thumbs-down { &:before { content: \"\\e126\"; } }\n.glyphicon-hand-right { &:before { content: \"\\e127\"; } }\n.glyphicon-hand-left { &:before { content: \"\\e128\"; } }\n.glyphicon-hand-up { &:before { content: \"\\e129\"; } }\n.glyphicon-hand-down { &:before { content: \"\\e130\"; } }\n.glyphicon-circle-arrow-right { &:before { content: \"\\e131\"; } }\n.glyphicon-circle-arrow-left { &:before { content: \"\\e132\"; } }\n.glyphicon-circle-arrow-up { &:before { content: \"\\e133\"; } }\n.glyphicon-circle-arrow-down { &:before { content: \"\\e134\"; } }\n.glyphicon-globe { &:before { content: \"\\e135\"; } }\n.glyphicon-wrench { &:before { content: \"\\e136\"; } }\n.glyphicon-tasks { &:before { content: \"\\e137\"; } }\n.glyphicon-filter { &:before { content: \"\\e138\"; } }\n.glyphicon-briefcase { &:before { content: \"\\e139\"; } }\n.glyphicon-fullscreen { &:before { content: \"\\e140\"; } }\n.glyphicon-dashboard { &:before { content: \"\\e141\"; } }\n.glyphicon-paperclip { &:before { content: \"\\e142\"; } }\n.glyphicon-heart-empty { &:before { content: \"\\e143\"; } }\n.glyphicon-link { &:before { content: \"\\e144\"; } }\n.glyphicon-phone { &:before { content: \"\\e145\"; } }\n.glyphicon-pushpin { &:before { content: \"\\e146\"; } }\n.glyphicon-usd { &:before { content: \"\\e148\"; } }\n.glyphicon-gbp { &:before { content: \"\\e149\"; } }\n.glyphicon-sort { &:before { content: \"\\e150\"; } }\n.glyphicon-sort-by-alphabet { &:before { content: \"\\e151\"; } }\n.glyphicon-sort-by-alphabet-alt { &:before { content: \"\\e152\"; } }\n.glyphicon-sort-by-order { &:before { content: \"\\e153\"; } }\n.glyphicon-sort-by-order-alt { &:before { content: \"\\e154\"; } }\n.glyphicon-sort-by-attributes { &:before { content: \"\\e155\"; } }\n.glyphicon-sort-by-attributes-alt { &:before { content: \"\\e156\"; } }\n.glyphicon-unchecked { &:before { content: \"\\e157\"; } }\n.glyphicon-expand { &:before { content: \"\\e158\"; } }\n.glyphicon-collapse-down { &:before { content: \"\\e159\"; } }\n.glyphicon-collapse-up { &:before { content: \"\\e160\"; } }\n.glyphicon-log-in { &:before { content: \"\\e161\"; } }\n.glyphicon-flash { &:before { content: \"\\e162\"; } }\n.glyphicon-log-out { &:before { content: \"\\e163\"; } }\n.glyphicon-new-window { &:before { content: \"\\e164\"; } }\n.glyphicon-record { &:before { content: \"\\e165\"; } }\n.glyphicon-save { &:before { content: \"\\e166\"; } }\n.glyphicon-open { &:before { content: \"\\e167\"; } }\n.glyphicon-saved { &:before { content: \"\\e168\"; } }\n.glyphicon-import { &:before { content: \"\\e169\"; } }\n.glyphicon-export { &:before { content: \"\\e170\"; } }\n.glyphicon-send { &:before { content: \"\\e171\"; } }\n.glyphicon-floppy-disk { &:before { content: \"\\e172\"; } }\n.glyphicon-floppy-saved { &:before { content: \"\\e173\"; } }\n.glyphicon-floppy-remove { &:before { content: \"\\e174\"; } }\n.glyphicon-floppy-save { &:before { content: \"\\e175\"; } }\n.glyphicon-floppy-open { &:before { content: \"\\e176\"; } }\n.glyphicon-credit-card { &:before { content: \"\\e177\"; } }\n.glyphicon-transfer { &:before { content: \"\\e178\"; } }\n.glyphicon-cutlery { &:before { content: \"\\e179\"; } }\n.glyphicon-header { &:before { content: \"\\e180\"; } }\n.glyphicon-compressed { &:before { content: \"\\e181\"; } }\n.glyphicon-earphone { &:before { content: \"\\e182\"; } }\n.glyphicon-phone-alt { &:before { content: \"\\e183\"; } }\n.glyphicon-tower { &:before { content: \"\\e184\"; } }\n.glyphicon-stats { &:before { content: \"\\e185\"; } }\n.glyphicon-sd-video { &:before { content: \"\\e186\"; } }\n.glyphicon-hd-video { &:before { content: \"\\e187\"; } }\n.glyphicon-subtitles { &:before { content: \"\\e188\"; } }\n.glyphicon-sound-stereo { &:before { content: \"\\e189\"; } }\n.glyphicon-sound-dolby { &:before { content: \"\\e190\"; } }\n.glyphicon-sound-5-1 { &:before { content: \"\\e191\"; } }\n.glyphicon-sound-6-1 { &:before { content: \"\\e192\"; } }\n.glyphicon-sound-7-1 { &:before { content: \"\\e193\"; } }\n.glyphicon-copyright-mark { &:before { content: \"\\e194\"; } }\n.glyphicon-registration-mark { &:before { content: \"\\e195\"; } }\n.glyphicon-cloud-download { &:before { content: \"\\e197\"; } }\n.glyphicon-cloud-upload { &:before { content: \"\\e198\"; } }\n.glyphicon-tree-conifer { &:before { content: \"\\e199\"; } }\n.glyphicon-tree-deciduous { &:before { content: \"\\e200\"; } }\n","//\n// Dropdown menus\n// --------------------------------------------------\n\n\n// Dropdown arrow/caret\n.caret {\n display: inline-block;\n width: 0;\n height: 0;\n margin-left: 2px;\n vertical-align: middle;\n border-top: @caret-width-base solid;\n border-right: @caret-width-base solid transparent;\n border-left: @caret-width-base solid transparent;\n}\n\n// The dropdown wrapper (div)\n.dropdown {\n position: relative;\n}\n\n// Prevent the focus on the dropdown toggle when closing dropdowns\n.dropdown-toggle:focus {\n outline: 0;\n}\n\n// The dropdown menu (ul)\n.dropdown-menu {\n position: absolute;\n top: 100%;\n left: 0;\n z-index: @zindex-dropdown;\n display: none; // none by default, but block on \"open\" of the menu\n float: left;\n min-width: 160px;\n padding: 5px 0;\n margin: 2px 0 0; // override default ul\n list-style: none;\n font-size: @font-size-base;\n background-color: @dropdown-bg;\n border: 1px solid @dropdown-fallback-border; // IE8 fallback\n border: 1px solid @dropdown-border;\n border-radius: @border-radius-base;\n .box-shadow(0 6px 12px rgba(0,0,0,.175));\n background-clip: padding-box;\n\n // Aligns the dropdown menu to right\n //\n // Deprecated as of 3.1.0 in favor of `.dropdown-menu-[dir]`\n &.pull-right {\n right: 0;\n left: auto;\n }\n\n // Dividers (basically an hr) within the dropdown\n .divider {\n .nav-divider(@dropdown-divider-bg);\n }\n\n // Links within the dropdown menu\n > li > a {\n display: block;\n padding: 3px 20px;\n clear: both;\n font-weight: normal;\n line-height: @line-height-base;\n color: @dropdown-link-color;\n white-space: nowrap; // prevent links from randomly breaking onto new lines\n }\n}\n\n// Hover/Focus state\n.dropdown-menu > li > a {\n &:hover,\n &:focus {\n text-decoration: none;\n color: @dropdown-link-hover-color;\n background-color: @dropdown-link-hover-bg;\n }\n}\n\n// Active state\n.dropdown-menu > .active > a {\n &,\n &:hover,\n &:focus {\n color: @dropdown-link-active-color;\n text-decoration: none;\n outline: 0;\n background-color: @dropdown-link-active-bg;\n }\n}\n\n// Disabled state\n//\n// Gray out text and ensure the hover/focus state remains gray\n\n.dropdown-menu > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @dropdown-link-disabled-color;\n }\n}\n// Nuke hover/focus effects\n.dropdown-menu > .disabled > a {\n &:hover,\n &:focus {\n text-decoration: none;\n background-color: transparent;\n background-image: none; // Remove CSS gradient\n .reset-filter();\n cursor: not-allowed;\n }\n}\n\n// Open state for the dropdown\n.open {\n // Show the menu\n > .dropdown-menu {\n display: block;\n }\n\n // Remove the outline when :focus is triggered\n > a {\n outline: 0;\n }\n}\n\n// Menu positioning\n//\n// Add extra class to `.dropdown-menu` to flip the alignment of the dropdown\n// menu with the parent.\n.dropdown-menu-right {\n left: auto; // Reset the default from `.dropdown-menu`\n right: 0;\n}\n// With v3, we enabled auto-flipping if you have a dropdown within a right\n// aligned nav component. To enable the undoing of that, we provide an override\n// to restore the default dropdown menu alignment.\n//\n// This is only for left-aligning a dropdown menu within a `.navbar-right` or\n// `.pull-right` nav component.\n.dropdown-menu-left {\n left: 0;\n right: auto;\n}\n\n// Dropdown section headers\n.dropdown-header {\n display: block;\n padding: 3px 20px;\n font-size: @font-size-small;\n line-height: @line-height-base;\n color: @dropdown-header-color;\n}\n\n// Backdrop to catch body clicks on mobile, etc.\n.dropdown-backdrop {\n position: fixed;\n left: 0;\n right: 0;\n bottom: 0;\n top: 0;\n z-index: (@zindex-dropdown - 10);\n}\n\n// Right aligned dropdowns\n.pull-right > .dropdown-menu {\n right: 0;\n left: auto;\n}\n\n// Allow for dropdowns to go bottom up (aka, dropup-menu)\n//\n// Just add .dropup after the standard .dropdown class and you're set, bro.\n// TODO: abstract this so that the navbar fixed styles are not placed here?\n\n.dropup,\n.navbar-fixed-bottom .dropdown {\n // Reverse the caret\n .caret {\n border-top: 0;\n border-bottom: @caret-width-base solid;\n content: \"\";\n }\n // Different positioning for bottom up menu\n .dropdown-menu {\n top: auto;\n bottom: 100%;\n margin-bottom: 1px;\n }\n}\n\n\n// Component alignment\n//\n// Reiterate per navbar.less and the modified component alignment there.\n\n@media (min-width: @grid-float-breakpoint) {\n .navbar-right {\n .dropdown-menu {\n .dropdown-menu-right();\n }\n // Necessary for overrides of the default right aligned menu.\n // Will remove come v4 in all likelihood.\n .dropdown-menu-left {\n .dropdown-menu-left();\n }\n }\n}\n\n","//\n// Button groups\n// --------------------------------------------------\n\n// Make the div behave like a button\n.btn-group,\n.btn-group-vertical {\n position: relative;\n display: inline-block;\n vertical-align: middle; // match .btn alignment given font-size hack above\n > .btn {\n position: relative;\n float: left;\n // Bring the \"active\" button to the front\n &:hover,\n &:focus,\n &:active,\n &.active {\n z-index: 2;\n }\n &:focus {\n // Remove focus outline when dropdown JS adds it after closing the menu\n outline: none;\n }\n }\n}\n\n// Prevent double borders when buttons are next to each other\n.btn-group {\n .btn + .btn,\n .btn + .btn-group,\n .btn-group + .btn,\n .btn-group + .btn-group {\n margin-left: -1px;\n }\n}\n\n// Optional: Group multiple button groups together for a toolbar\n.btn-toolbar {\n margin-left: -5px; // Offset the first child's margin\n &:extend(.clearfix all);\n\n .btn-group,\n .input-group {\n float: left;\n }\n > .btn,\n > .btn-group,\n > .input-group {\n margin-left: 5px;\n }\n}\n\n.btn-group > .btn:not(:first-child):not(:last-child):not(.dropdown-toggle) {\n border-radius: 0;\n}\n\n// Set corners individual because sometimes a single button can be in a .btn-group and we need :first-child and :last-child to both match\n.btn-group > .btn:first-child {\n margin-left: 0;\n &:not(:last-child):not(.dropdown-toggle) {\n .border-right-radius(0);\n }\n}\n// Need .dropdown-toggle since :last-child doesn't apply given a .dropdown-menu immediately after it\n.btn-group > .btn:last-child:not(:first-child),\n.btn-group > .dropdown-toggle:not(:first-child) {\n .border-left-radius(0);\n}\n\n// Custom edits for including btn-groups within btn-groups (useful for including dropdown buttons within a btn-group)\n.btn-group > .btn-group {\n float: left;\n}\n.btn-group > .btn-group:not(:first-child):not(:last-child) > .btn {\n border-radius: 0;\n}\n.btn-group > .btn-group:first-child {\n > .btn:last-child,\n > .dropdown-toggle {\n .border-right-radius(0);\n }\n}\n.btn-group > .btn-group:last-child > .btn:first-child {\n .border-left-radius(0);\n}\n\n// On active and open, don't show outline\n.btn-group .dropdown-toggle:active,\n.btn-group.open .dropdown-toggle {\n outline: 0;\n}\n\n\n// Sizing\n//\n// Remix the default button sizing classes into new ones for easier manipulation.\n\n.btn-group-xs > .btn { .btn-xs(); }\n.btn-group-sm > .btn { .btn-sm(); }\n.btn-group-lg > .btn { .btn-lg(); }\n\n\n// Split button dropdowns\n// ----------------------\n\n// Give the line between buttons some depth\n.btn-group > .btn + .dropdown-toggle {\n padding-left: 8px;\n padding-right: 8px;\n}\n.btn-group > .btn-lg + .dropdown-toggle {\n padding-left: 12px;\n padding-right: 12px;\n}\n\n// The clickable button for toggling the menu\n// Remove the gradient and set the same inset shadow as the :active state\n.btn-group.open .dropdown-toggle {\n .box-shadow(inset 0 3px 5px rgba(0,0,0,.125));\n\n // Show no shadow for `.btn-link` since it has no other button styles.\n &.btn-link {\n .box-shadow(none);\n }\n}\n\n\n// Reposition the caret\n.btn .caret {\n margin-left: 0;\n}\n// Carets in other button sizes\n.btn-lg .caret {\n border-width: @caret-width-large @caret-width-large 0;\n border-bottom-width: 0;\n}\n// Upside down carets for .dropup\n.dropup .btn-lg .caret {\n border-width: 0 @caret-width-large @caret-width-large;\n}\n\n\n// Vertical button groups\n// ----------------------\n\n.btn-group-vertical {\n > .btn,\n > .btn-group,\n > .btn-group > .btn {\n display: block;\n float: none;\n width: 100%;\n max-width: 100%;\n }\n\n // Clear floats so dropdown menus can be properly placed\n > .btn-group {\n &:extend(.clearfix all);\n > .btn {\n float: none;\n }\n }\n\n > .btn + .btn,\n > .btn + .btn-group,\n > .btn-group + .btn,\n > .btn-group + .btn-group {\n margin-top: -1px;\n margin-left: 0;\n }\n}\n\n.btn-group-vertical > .btn {\n &:not(:first-child):not(:last-child) {\n border-radius: 0;\n }\n &:first-child:not(:last-child) {\n border-top-right-radius: @border-radius-base;\n .border-bottom-radius(0);\n }\n &:last-child:not(:first-child) {\n border-bottom-left-radius: @border-radius-base;\n .border-top-radius(0);\n }\n}\n.btn-group-vertical > .btn-group:not(:first-child):not(:last-child) > .btn {\n border-radius: 0;\n}\n.btn-group-vertical > .btn-group:first-child:not(:last-child) {\n > .btn:last-child,\n > .dropdown-toggle {\n .border-bottom-radius(0);\n }\n}\n.btn-group-vertical > .btn-group:last-child:not(:first-child) > .btn:first-child {\n .border-top-radius(0);\n}\n\n\n\n// Justified button groups\n// ----------------------\n\n.btn-group-justified {\n display: table;\n width: 100%;\n table-layout: fixed;\n border-collapse: separate;\n > .btn,\n > .btn-group {\n float: none;\n display: table-cell;\n width: 1%;\n }\n > .btn-group .btn {\n width: 100%;\n }\n}\n\n\n// Checkbox and radio options\n[data-toggle=\"buttons\"] > .btn > input[type=\"radio\"],\n[data-toggle=\"buttons\"] > .btn > input[type=\"checkbox\"] {\n display: none;\n}\n","//\n// Input groups\n// --------------------------------------------------\n\n// Base styles\n// -------------------------\n.input-group {\n position: relative; // For dropdowns\n display: table;\n border-collapse: separate; // prevent input groups from inheriting border styles from table cells when placed within a table\n\n // Undo padding and float of grid classes\n &[class*=\"col-\"] {\n float: none;\n padding-left: 0;\n padding-right: 0;\n }\n\n .form-control {\n // IE9 fubars the placeholder attribute in text inputs and the arrows on\n // select elements in input groups. To fix it, we float the input. Details:\n // https://github.com/twbs/bootstrap/issues/11561#issuecomment-28936855\n float: left;\n\n width: 100%;\n margin-bottom: 0;\n }\n}\n\n// Sizing options\n//\n// Remix the default form control sizing classes into new ones for easier\n// manipulation.\n\n.input-group-lg > .form-control,\n.input-group-lg > .input-group-addon,\n.input-group-lg > .input-group-btn > .btn { .input-lg(); }\n.input-group-sm > .form-control,\n.input-group-sm > .input-group-addon,\n.input-group-sm > .input-group-btn > .btn { .input-sm(); }\n\n\n// Display as table-cell\n// -------------------------\n.input-group-addon,\n.input-group-btn,\n.input-group .form-control {\n display: table-cell;\n\n &:not(:first-child):not(:last-child) {\n border-radius: 0;\n }\n}\n// Addon and addon wrapper for buttons\n.input-group-addon,\n.input-group-btn {\n width: 1%;\n white-space: nowrap;\n vertical-align: middle; // Match the inputs\n}\n\n// Text input groups\n// -------------------------\n.input-group-addon {\n padding: @padding-base-vertical @padding-base-horizontal;\n font-size: @font-size-base;\n font-weight: normal;\n line-height: 1;\n color: @input-color;\n text-align: center;\n background-color: @input-group-addon-bg;\n border: 1px solid @input-group-addon-border-color;\n border-radius: @border-radius-base;\n\n // Sizing\n &.input-sm {\n padding: @padding-small-vertical @padding-small-horizontal;\n font-size: @font-size-small;\n border-radius: @border-radius-small;\n }\n &.input-lg {\n padding: @padding-large-vertical @padding-large-horizontal;\n font-size: @font-size-large;\n border-radius: @border-radius-large;\n }\n\n // Nuke default margins from checkboxes and radios to vertically center within.\n input[type=\"radio\"],\n input[type=\"checkbox\"] {\n margin-top: 0;\n }\n}\n\n// Reset rounded corners\n.input-group .form-control:first-child,\n.input-group-addon:first-child,\n.input-group-btn:first-child > .btn,\n.input-group-btn:first-child > .btn-group > .btn,\n.input-group-btn:first-child > .dropdown-toggle,\n.input-group-btn:last-child > .btn:not(:last-child):not(.dropdown-toggle),\n.input-group-btn:last-child > .btn-group:not(:last-child) > .btn {\n .border-right-radius(0);\n}\n.input-group-addon:first-child {\n border-right: 0;\n}\n.input-group .form-control:last-child,\n.input-group-addon:last-child,\n.input-group-btn:last-child > .btn,\n.input-group-btn:last-child > .btn-group > .btn,\n.input-group-btn:last-child > .dropdown-toggle,\n.input-group-btn:first-child > .btn:not(:first-child),\n.input-group-btn:first-child > .btn-group:not(:first-child) > .btn {\n .border-left-radius(0);\n}\n.input-group-addon:last-child {\n border-left: 0;\n}\n\n// Button input groups\n// -------------------------\n.input-group-btn {\n position: relative;\n // Jankily prevent input button groups from wrapping with `white-space` and\n // `font-size` in combination with `inline-block` on buttons.\n font-size: 0;\n white-space: nowrap;\n\n // Negative margin for spacing, position for bringing hovered/focused/actived\n // element above the siblings.\n > .btn {\n position: relative;\n + .btn {\n margin-left: -1px;\n }\n // Bring the \"active\" button to the front\n &:hover,\n &:focus,\n &:active {\n z-index: 2;\n }\n }\n\n // Negative margin to only have a 1px border between the two\n &:first-child {\n > .btn,\n > .btn-group {\n margin-right: -1px;\n }\n }\n &:last-child {\n > .btn,\n > .btn-group {\n margin-left: -1px;\n }\n }\n}\n","//\n// Navs\n// --------------------------------------------------\n\n\n// Base class\n// --------------------------------------------------\n\n.nav {\n margin-bottom: 0;\n padding-left: 0; // Override default ul/ol\n list-style: none;\n &:extend(.clearfix all);\n\n > li {\n position: relative;\n display: block;\n\n > a {\n position: relative;\n display: block;\n padding: @nav-link-padding;\n &:hover,\n &:focus {\n text-decoration: none;\n background-color: @nav-link-hover-bg;\n }\n }\n\n // Disabled state sets text to gray and nukes hover/tab effects\n &.disabled > a {\n color: @nav-disabled-link-color;\n\n &:hover,\n &:focus {\n color: @nav-disabled-link-hover-color;\n text-decoration: none;\n background-color: transparent;\n cursor: not-allowed;\n }\n }\n }\n\n // Open dropdowns\n .open > a {\n &,\n &:hover,\n &:focus {\n background-color: @nav-link-hover-bg;\n border-color: @link-color;\n }\n }\n\n // Nav dividers (deprecated with v3.0.1)\n //\n // This should have been removed in v3 with the dropping of `.nav-list`, but\n // we missed it. We don't currently support this anywhere, but in the interest\n // of maintaining backward compatibility in case you use it, it's deprecated.\n .nav-divider {\n .nav-divider();\n }\n\n // Prevent IE8 from misplacing imgs\n //\n // See https://github.com/h5bp/html5-boilerplate/issues/984#issuecomment-3985989\n > li > a > img {\n max-width: none;\n }\n}\n\n\n// Tabs\n// -------------------------\n\n// Give the tabs something to sit on\n.nav-tabs {\n border-bottom: 1px solid @nav-tabs-border-color;\n > li {\n float: left;\n // Make the list-items overlay the bottom border\n margin-bottom: -1px;\n\n // Actual tabs (as links)\n > a {\n margin-right: 2px;\n line-height: @line-height-base;\n border: 1px solid transparent;\n border-radius: @border-radius-base @border-radius-base 0 0;\n &:hover {\n border-color: @nav-tabs-link-hover-border-color @nav-tabs-link-hover-border-color @nav-tabs-border-color;\n }\n }\n\n // Active state, and its :hover to override normal :hover\n &.active > a {\n &,\n &:hover,\n &:focus {\n color: @nav-tabs-active-link-hover-color;\n background-color: @nav-tabs-active-link-hover-bg;\n border: 1px solid @nav-tabs-active-link-hover-border-color;\n border-bottom-color: transparent;\n cursor: default;\n }\n }\n }\n // pulling this in mainly for less shorthand\n &.nav-justified {\n .nav-justified();\n .nav-tabs-justified();\n }\n}\n\n\n// Pills\n// -------------------------\n.nav-pills {\n > li {\n float: left;\n\n // Links rendered as pills\n > a {\n border-radius: @nav-pills-border-radius;\n }\n + li {\n margin-left: 2px;\n }\n\n // Active state\n &.active > a {\n &,\n &:hover,\n &:focus {\n color: @nav-pills-active-link-hover-color;\n background-color: @nav-pills-active-link-hover-bg;\n }\n }\n }\n}\n\n\n// Stacked pills\n.nav-stacked {\n > li {\n float: none;\n + li {\n margin-top: 2px;\n margin-left: 0; // no need for this gap between nav items\n }\n }\n}\n\n\n// Nav variations\n// --------------------------------------------------\n\n// Justified nav links\n// -------------------------\n\n.nav-justified {\n width: 100%;\n\n > li {\n float: none;\n > a {\n text-align: center;\n margin-bottom: 5px;\n }\n }\n\n > .dropdown .dropdown-menu {\n top: auto;\n left: auto;\n }\n\n @media (min-width: @screen-sm-min) {\n > li {\n display: table-cell;\n width: 1%;\n > a {\n margin-bottom: 0;\n }\n }\n }\n}\n\n// Move borders to anchors instead of bottom of list\n//\n// Mixin for adding on top the shared `.nav-justified` styles for our tabs\n.nav-tabs-justified {\n border-bottom: 0;\n\n > li > a {\n // Override margin from .nav-tabs\n margin-right: 0;\n border-radius: @border-radius-base;\n }\n\n > .active > a,\n > .active > a:hover,\n > .active > a:focus {\n border: 1px solid @nav-tabs-justified-link-border-color;\n }\n\n @media (min-width: @screen-sm-min) {\n > li > a {\n border-bottom: 1px solid @nav-tabs-justified-link-border-color;\n border-radius: @border-radius-base @border-radius-base 0 0;\n }\n > .active > a,\n > .active > a:hover,\n > .active > a:focus {\n border-bottom-color: @nav-tabs-justified-active-link-border-color;\n }\n }\n}\n\n\n// Tabbable tabs\n// -------------------------\n\n// Hide tabbable panes to start, show them when `.active`\n.tab-content {\n > .tab-pane {\n display: none;\n }\n > .active {\n display: block;\n }\n}\n\n\n// Dropdowns\n// -------------------------\n\n// Specific dropdowns\n.nav-tabs .dropdown-menu {\n // make dropdown border overlap tab border\n margin-top: -1px;\n // Remove the top rounded corners here since there is a hard edge above the menu\n .border-top-radius(0);\n}\n","//\n// Navbars\n// --------------------------------------------------\n\n\n// Wrapper and base class\n//\n// Provide a static navbar from which we expand to create full-width, fixed, and\n// other navbar variations.\n\n.navbar {\n position: relative;\n min-height: @navbar-height; // Ensure a navbar always shows (e.g., without a .navbar-brand in collapsed mode)\n margin-bottom: @navbar-margin-bottom;\n border: 1px solid transparent;\n\n // Prevent floats from breaking the navbar\n &:extend(.clearfix all);\n\n @media (min-width: @grid-float-breakpoint) {\n border-radius: @navbar-border-radius;\n }\n}\n\n\n// Navbar heading\n//\n// Groups `.navbar-brand` and `.navbar-toggle` into a single component for easy\n// styling of responsive aspects.\n\n.navbar-header {\n &:extend(.clearfix all);\n\n @media (min-width: @grid-float-breakpoint) {\n float: left;\n }\n}\n\n\n// Navbar collapse (body)\n//\n// Group your navbar content into this for easy collapsing and expanding across\n// various device sizes. By default, this content is collapsed when <768px, but\n// will expand past that for a horizontal display.\n//\n// To start (on mobile devices) the navbar links, forms, and buttons are stacked\n// vertically and include a `max-height` to overflow in case you have too much\n// content for the user's viewport.\n\n.navbar-collapse {\n max-height: @navbar-collapse-max-height;\n overflow-x: visible;\n padding-right: @navbar-padding-horizontal;\n padding-left: @navbar-padding-horizontal;\n border-top: 1px solid transparent;\n box-shadow: inset 0 1px 0 rgba(255,255,255,.1);\n &:extend(.clearfix all);\n -webkit-overflow-scrolling: touch;\n\n &.in {\n overflow-y: auto;\n }\n\n @media (min-width: @grid-float-breakpoint) {\n width: auto;\n border-top: 0;\n box-shadow: none;\n\n &.collapse {\n display: block !important;\n height: auto !important;\n padding-bottom: 0; // Override default setting\n overflow: visible !important;\n }\n\n &.in {\n overflow-y: visible;\n }\n\n // Undo the collapse side padding for navbars with containers to ensure\n // alignment of right-aligned contents.\n .navbar-fixed-top &,\n .navbar-static-top &,\n .navbar-fixed-bottom & {\n padding-left: 0;\n padding-right: 0;\n }\n }\n}\n\n\n// Both navbar header and collapse\n//\n// When a container is present, change the behavior of the header and collapse.\n\n.container,\n.container-fluid {\n > .navbar-header,\n > .navbar-collapse {\n margin-right: -@navbar-padding-horizontal;\n margin-left: -@navbar-padding-horizontal;\n\n @media (min-width: @grid-float-breakpoint) {\n margin-right: 0;\n margin-left: 0;\n }\n }\n}\n\n\n//\n// Navbar alignment options\n//\n// Display the navbar across the entirety of the page or fixed it to the top or\n// bottom of the page.\n\n// Static top (unfixed, but 100% wide) navbar\n.navbar-static-top {\n z-index: @zindex-navbar;\n border-width: 0 0 1px;\n\n @media (min-width: @grid-float-breakpoint) {\n border-radius: 0;\n }\n}\n\n// Fix the top/bottom navbars when screen real estate supports it\n.navbar-fixed-top,\n.navbar-fixed-bottom {\n position: fixed;\n right: 0;\n left: 0;\n z-index: @zindex-navbar-fixed;\n\n // Undo the rounded corners\n @media (min-width: @grid-float-breakpoint) {\n border-radius: 0;\n }\n}\n.navbar-fixed-top {\n top: 0;\n border-width: 0 0 1px;\n}\n.navbar-fixed-bottom {\n bottom: 0;\n margin-bottom: 0; // override .navbar defaults\n border-width: 1px 0 0;\n}\n\n\n// Brand/project name\n\n.navbar-brand {\n float: left;\n padding: @navbar-padding-vertical @navbar-padding-horizontal;\n font-size: @font-size-large;\n line-height: @line-height-computed;\n height: @line-height-computed;\n\n &:hover,\n &:focus {\n text-decoration: none;\n }\n\n @media (min-width: @grid-float-breakpoint) {\n .navbar > .container &,\n .navbar > .container-fluid & {\n margin-left: -@navbar-padding-horizontal;\n }\n }\n}\n\n\n// Navbar toggle\n//\n// Custom button for toggling the `.navbar-collapse`, powered by the collapse\n// JavaScript plugin.\n\n.navbar-toggle {\n position: relative;\n float: right;\n margin-right: @navbar-padding-horizontal;\n padding: 9px 10px;\n .navbar-vertical-align(34px);\n background-color: transparent;\n background-image: none; // Reset unusual Firefox-on-Android default style; see https://github.com/necolas/normalize.css/issues/214\n border: 1px solid transparent;\n border-radius: @border-radius-base;\n\n // We remove the `outline` here, but later compensate by attaching `:hover`\n // styles to `:focus`.\n &:focus {\n outline: none;\n }\n\n // Bars\n .icon-bar {\n display: block;\n width: 22px;\n height: 2px;\n border-radius: 1px;\n }\n .icon-bar + .icon-bar {\n margin-top: 4px;\n }\n\n @media (min-width: @grid-float-breakpoint) {\n display: none;\n }\n}\n\n\n// Navbar nav links\n//\n// Builds on top of the `.nav` components with its own modifier class to make\n// the nav the full height of the horizontal nav (above 768px).\n\n.navbar-nav {\n margin: (@navbar-padding-vertical / 2) -@navbar-padding-horizontal;\n\n > li > a {\n padding-top: 10px;\n padding-bottom: 10px;\n line-height: @line-height-computed;\n }\n\n @media (max-width: @grid-float-breakpoint-max) {\n // Dropdowns get custom display when collapsed\n .open .dropdown-menu {\n position: static;\n float: none;\n width: auto;\n margin-top: 0;\n background-color: transparent;\n border: 0;\n box-shadow: none;\n > li > a,\n .dropdown-header {\n padding: 5px 15px 5px 25px;\n }\n > li > a {\n line-height: @line-height-computed;\n &:hover,\n &:focus {\n background-image: none;\n }\n }\n }\n }\n\n // Uncollapse the nav\n @media (min-width: @grid-float-breakpoint) {\n float: left;\n margin: 0;\n\n > li {\n float: left;\n > a {\n padding-top: @navbar-padding-vertical;\n padding-bottom: @navbar-padding-vertical;\n }\n }\n\n &.navbar-right:last-child {\n margin-right: -@navbar-padding-horizontal;\n }\n }\n}\n\n\n// Component alignment\n//\n// Repurpose the pull utilities as their own navbar utilities to avoid specificity\n// issues with parents and chaining. Only do this when the navbar is uncollapsed\n// though so that navbar contents properly stack and align in mobile.\n\n@media (min-width: @grid-float-breakpoint) {\n .navbar-left { .pull-left(); }\n .navbar-right { .pull-right(); }\n}\n\n\n// Navbar form\n//\n// Extension of the `.form-inline` with some extra flavor for optimum display in\n// our navbars.\n\n.navbar-form {\n margin-left: -@navbar-padding-horizontal;\n margin-right: -@navbar-padding-horizontal;\n padding: 10px @navbar-padding-horizontal;\n border-top: 1px solid transparent;\n border-bottom: 1px solid transparent;\n @shadow: inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.1);\n .box-shadow(@shadow);\n\n // Mixin behavior for optimum display\n .form-inline();\n\n .form-group {\n @media (max-width: @grid-float-breakpoint-max) {\n margin-bottom: 5px;\n }\n }\n\n // Vertically center in expanded, horizontal navbar\n .navbar-vertical-align(@input-height-base);\n\n // Undo 100% width for pull classes\n @media (min-width: @grid-float-breakpoint) {\n width: auto;\n border: 0;\n margin-left: 0;\n margin-right: 0;\n padding-top: 0;\n padding-bottom: 0;\n .box-shadow(none);\n\n // Outdent the form if last child to line up with content down the page\n &.navbar-right:last-child {\n margin-right: -@navbar-padding-horizontal;\n }\n }\n}\n\n\n// Dropdown menus\n\n// Menu position and menu carets\n.navbar-nav > li > .dropdown-menu {\n margin-top: 0;\n .border-top-radius(0);\n}\n// Menu position and menu caret support for dropups via extra dropup class\n.navbar-fixed-bottom .navbar-nav > li > .dropdown-menu {\n .border-bottom-radius(0);\n}\n\n\n// Buttons in navbars\n//\n// Vertically center a button within a navbar (when *not* in a form).\n\n.navbar-btn {\n .navbar-vertical-align(@input-height-base);\n\n &.btn-sm {\n .navbar-vertical-align(@input-height-small);\n }\n &.btn-xs {\n .navbar-vertical-align(22);\n }\n}\n\n\n// Text in navbars\n//\n// Add a class to make any element properly align itself vertically within the navbars.\n\n.navbar-text {\n .navbar-vertical-align(@line-height-computed);\n\n @media (min-width: @grid-float-breakpoint) {\n float: left;\n margin-left: @navbar-padding-horizontal;\n margin-right: @navbar-padding-horizontal;\n\n // Outdent the form if last child to line up with content down the page\n &.navbar-right:last-child {\n margin-right: 0;\n }\n }\n}\n\n// Alternate navbars\n// --------------------------------------------------\n\n// Default navbar\n.navbar-default {\n background-color: @navbar-default-bg;\n border-color: @navbar-default-border;\n\n .navbar-brand {\n color: @navbar-default-brand-color;\n &:hover,\n &:focus {\n color: @navbar-default-brand-hover-color;\n background-color: @navbar-default-brand-hover-bg;\n }\n }\n\n .navbar-text {\n color: @navbar-default-color;\n }\n\n .navbar-nav {\n > li > a {\n color: @navbar-default-link-color;\n\n &:hover,\n &:focus {\n color: @navbar-default-link-hover-color;\n background-color: @navbar-default-link-hover-bg;\n }\n }\n > .active > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-default-link-active-color;\n background-color: @navbar-default-link-active-bg;\n }\n }\n > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-default-link-disabled-color;\n background-color: @navbar-default-link-disabled-bg;\n }\n }\n }\n\n .navbar-toggle {\n border-color: @navbar-default-toggle-border-color;\n &:hover,\n &:focus {\n background-color: @navbar-default-toggle-hover-bg;\n }\n .icon-bar {\n background-color: @navbar-default-toggle-icon-bar-bg;\n }\n }\n\n .navbar-collapse,\n .navbar-form {\n border-color: @navbar-default-border;\n }\n\n // Dropdown menu items\n .navbar-nav {\n // Remove background color from open dropdown\n > .open > a {\n &,\n &:hover,\n &:focus {\n background-color: @navbar-default-link-active-bg;\n color: @navbar-default-link-active-color;\n }\n }\n\n @media (max-width: @grid-float-breakpoint-max) {\n // Dropdowns get custom display when collapsed\n .open .dropdown-menu {\n > li > a {\n color: @navbar-default-link-color;\n &:hover,\n &:focus {\n color: @navbar-default-link-hover-color;\n background-color: @navbar-default-link-hover-bg;\n }\n }\n > .active > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-default-link-active-color;\n background-color: @navbar-default-link-active-bg;\n }\n }\n > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-default-link-disabled-color;\n background-color: @navbar-default-link-disabled-bg;\n }\n }\n }\n }\n }\n\n\n // Links in navbars\n //\n // Add a class to ensure links outside the navbar nav are colored correctly.\n\n .navbar-link {\n color: @navbar-default-link-color;\n &:hover {\n color: @navbar-default-link-hover-color;\n }\n }\n\n}\n\n// Inverse navbar\n\n.navbar-inverse {\n background-color: @navbar-inverse-bg;\n border-color: @navbar-inverse-border;\n\n .navbar-brand {\n color: @navbar-inverse-brand-color;\n &:hover,\n &:focus {\n color: @navbar-inverse-brand-hover-color;\n background-color: @navbar-inverse-brand-hover-bg;\n }\n }\n\n .navbar-text {\n color: @navbar-inverse-color;\n }\n\n .navbar-nav {\n > li > a {\n color: @navbar-inverse-link-color;\n\n &:hover,\n &:focus {\n color: @navbar-inverse-link-hover-color;\n background-color: @navbar-inverse-link-hover-bg;\n }\n }\n > .active > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-inverse-link-active-color;\n background-color: @navbar-inverse-link-active-bg;\n }\n }\n > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-inverse-link-disabled-color;\n background-color: @navbar-inverse-link-disabled-bg;\n }\n }\n }\n\n // Darken the responsive nav toggle\n .navbar-toggle {\n border-color: @navbar-inverse-toggle-border-color;\n &:hover,\n &:focus {\n background-color: @navbar-inverse-toggle-hover-bg;\n }\n .icon-bar {\n background-color: @navbar-inverse-toggle-icon-bar-bg;\n }\n }\n\n .navbar-collapse,\n .navbar-form {\n border-color: darken(@navbar-inverse-bg, 7%);\n }\n\n // Dropdowns\n .navbar-nav {\n > .open > a {\n &,\n &:hover,\n &:focus {\n background-color: @navbar-inverse-link-active-bg;\n color: @navbar-inverse-link-active-color;\n }\n }\n\n @media (max-width: @grid-float-breakpoint-max) {\n // Dropdowns get custom display\n .open .dropdown-menu {\n > .dropdown-header {\n border-color: @navbar-inverse-border;\n }\n .divider {\n background-color: @navbar-inverse-border;\n }\n > li > a {\n color: @navbar-inverse-link-color;\n &:hover,\n &:focus {\n color: @navbar-inverse-link-hover-color;\n background-color: @navbar-inverse-link-hover-bg;\n }\n }\n > .active > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-inverse-link-active-color;\n background-color: @navbar-inverse-link-active-bg;\n }\n }\n > .disabled > a {\n &,\n &:hover,\n &:focus {\n color: @navbar-inverse-link-disabled-color;\n background-color: @navbar-inverse-link-disabled-bg;\n }\n }\n }\n }\n }\n\n .navbar-link {\n color: @navbar-inverse-link-color;\n &:hover {\n color: @navbar-inverse-link-hover-color;\n }\n }\n\n}\n","//\n// Utility classes\n// --------------------------------------------------\n\n\n// Floats\n// -------------------------\n\n.clearfix {\n .clearfix();\n}\n.center-block {\n .center-block();\n}\n.pull-right {\n float: right !important;\n}\n.pull-left {\n float: left !important;\n}\n\n\n// Toggling content\n// -------------------------\n\n// Note: Deprecated .hide in favor of .hidden or .sr-only (as appropriate) in v3.0.1\n.hide {\n display: none !important;\n}\n.show {\n display: block !important;\n}\n.invisible {\n visibility: hidden;\n}\n.text-hide {\n .text-hide();\n}\n\n\n// Hide from screenreaders and browsers\n//\n// Credit: HTML5 Boilerplate\n\n.hidden {\n display: none !important;\n visibility: hidden !important;\n}\n\n\n// For Affix plugin\n// -------------------------\n\n.affix {\n position: fixed;\n}\n","//\n// Breadcrumbs\n// --------------------------------------------------\n\n\n.breadcrumb {\n padding: @breadcrumb-padding-vertical @breadcrumb-padding-horizontal;\n margin-bottom: @line-height-computed;\n list-style: none;\n background-color: @breadcrumb-bg;\n border-radius: @border-radius-base;\n\n > li {\n display: inline-block;\n\n + li:before {\n content: \"@{breadcrumb-separator}\\00a0\"; // Unicode space added since inline-block means non-collapsing white-space\n padding: 0 5px;\n color: @breadcrumb-color;\n }\n }\n\n > .active {\n color: @breadcrumb-active-color;\n }\n}\n","//\n// Pagination (multiple pages)\n// --------------------------------------------------\n.pagination {\n display: inline-block;\n padding-left: 0;\n margin: @line-height-computed 0;\n border-radius: @border-radius-base;\n\n > li {\n display: inline; // Remove list-style and block-level defaults\n > a,\n > span {\n position: relative;\n float: left; // Collapse white-space\n padding: @padding-base-vertical @padding-base-horizontal;\n line-height: @line-height-base;\n text-decoration: none;\n color: @pagination-color;\n background-color: @pagination-bg;\n border: 1px solid @pagination-border;\n margin-left: -1px;\n }\n &:first-child {\n > a,\n > span {\n margin-left: 0;\n .border-left-radius(@border-radius-base);\n }\n }\n &:last-child {\n > a,\n > span {\n .border-right-radius(@border-radius-base);\n }\n }\n }\n\n > li > a,\n > li > span {\n &:hover,\n &:focus {\n color: @pagination-hover-color;\n background-color: @pagination-hover-bg;\n border-color: @pagination-hover-border;\n }\n }\n\n > .active > a,\n > .active > span {\n &,\n &:hover,\n &:focus {\n z-index: 2;\n color: @pagination-active-color;\n background-color: @pagination-active-bg;\n border-color: @pagination-active-border;\n cursor: default;\n }\n }\n\n > .disabled {\n > span,\n > span:hover,\n > span:focus,\n > a,\n > a:hover,\n > a:focus {\n color: @pagination-disabled-color;\n background-color: @pagination-disabled-bg;\n border-color: @pagination-disabled-border;\n cursor: not-allowed;\n }\n }\n}\n\n// Sizing\n// --------------------------------------------------\n\n// Large\n.pagination-lg {\n .pagination-size(@padding-large-vertical; @padding-large-horizontal; @font-size-large; @border-radius-large);\n}\n\n// Small\n.pagination-sm {\n .pagination-size(@padding-small-vertical; @padding-small-horizontal; @font-size-small; @border-radius-small);\n}\n","//\n// Pager pagination\n// --------------------------------------------------\n\n\n.pager {\n padding-left: 0;\n margin: @line-height-computed 0;\n list-style: none;\n text-align: center;\n &:extend(.clearfix all);\n li {\n display: inline;\n > a,\n > span {\n display: inline-block;\n padding: 5px 14px;\n background-color: @pager-bg;\n border: 1px solid @pager-border;\n border-radius: @pager-border-radius;\n }\n\n > a:hover,\n > a:focus {\n text-decoration: none;\n background-color: @pager-hover-bg;\n }\n }\n\n .next {\n > a,\n > span {\n float: right;\n }\n }\n\n .previous {\n > a,\n > span {\n float: left;\n }\n }\n\n .disabled {\n > a,\n > a:hover,\n > a:focus,\n > span {\n color: @pager-disabled-color;\n background-color: @pager-bg;\n cursor: not-allowed;\n }\n }\n\n}\n","//\n// Labels\n// --------------------------------------------------\n\n.label {\n display: inline;\n padding: .2em .6em .3em;\n font-size: 75%;\n font-weight: bold;\n line-height: 1;\n color: @label-color;\n text-align: center;\n white-space: nowrap;\n vertical-align: baseline;\n border-radius: .25em;\n\n // Add hover effects, but only for links\n &[href] {\n &:hover,\n &:focus {\n color: @label-link-hover-color;\n text-decoration: none;\n cursor: pointer;\n }\n }\n\n // Empty labels collapse automatically (not available in IE8)\n &:empty {\n display: none;\n }\n\n // Quick fix for labels in buttons\n .btn & {\n position: relative;\n top: -1px;\n }\n}\n\n// Colors\n// Contextual variations (linked labels get darker on :hover)\n\n.label-default {\n .label-variant(@label-default-bg);\n}\n\n.label-primary {\n .label-variant(@label-primary-bg);\n}\n\n.label-success {\n .label-variant(@label-success-bg);\n}\n\n.label-info {\n .label-variant(@label-info-bg);\n}\n\n.label-warning {\n .label-variant(@label-warning-bg);\n}\n\n.label-danger {\n .label-variant(@label-danger-bg);\n}\n","//\n// Badges\n// --------------------------------------------------\n\n\n// Base classes\n.badge {\n display: inline-block;\n min-width: 10px;\n padding: 3px 7px;\n font-size: @font-size-small;\n font-weight: @badge-font-weight;\n color: @badge-color;\n line-height: @badge-line-height;\n vertical-align: baseline;\n white-space: nowrap;\n text-align: center;\n background-color: @badge-bg;\n border-radius: @badge-border-radius;\n\n // Empty badges collapse automatically (not available in IE8)\n &:empty {\n display: none;\n }\n\n // Quick fix for badges in buttons\n .btn & {\n position: relative;\n top: -1px;\n }\n .btn-xs & {\n top: 0;\n padding: 1px 5px;\n }\n}\n\n// Hover state, but only for links\na.badge {\n &:hover,\n &:focus {\n color: @badge-link-hover-color;\n text-decoration: none;\n cursor: pointer;\n }\n}\n\n// Account for counters in navs\na.list-group-item.active > .badge,\n.nav-pills > .active > a > .badge {\n color: @badge-active-color;\n background-color: @badge-active-bg;\n}\n.nav-pills > li > a > .badge {\n margin-left: 3px;\n}\n","//\n// Jumbotron\n// --------------------------------------------------\n\n\n.jumbotron {\n padding: @jumbotron-padding;\n margin-bottom: @jumbotron-padding;\n color: @jumbotron-color;\n background-color: @jumbotron-bg;\n\n h1,\n .h1 {\n color: @jumbotron-heading-color;\n }\n p {\n margin-bottom: (@jumbotron-padding / 2);\n font-size: @jumbotron-font-size;\n font-weight: 200;\n }\n\n .container & {\n border-radius: @border-radius-large; // Only round corners at higher resolutions if contained in a container\n }\n\n .container {\n max-width: 100%;\n }\n\n @media screen and (min-width: @screen-sm-min) {\n padding-top: (@jumbotron-padding * 1.6);\n padding-bottom: (@jumbotron-padding * 1.6);\n\n .container & {\n padding-left: (@jumbotron-padding * 2);\n padding-right: (@jumbotron-padding * 2);\n }\n\n h1,\n .h1 {\n font-size: (@font-size-base * 4.5);\n }\n }\n}\n","//\n// Thumbnails\n// --------------------------------------------------\n\n\n// Mixin and adjust the regular image class\n.thumbnail {\n display: block;\n padding: @thumbnail-padding;\n margin-bottom: @line-height-computed;\n line-height: @line-height-base;\n background-color: @thumbnail-bg;\n border: 1px solid @thumbnail-border;\n border-radius: @thumbnail-border-radius;\n .transition(all .2s ease-in-out);\n\n > img,\n a > img {\n .img-responsive();\n margin-left: auto;\n margin-right: auto;\n }\n\n // Add a hover state for linked versions only\n a&:hover,\n a&:focus,\n a&.active {\n border-color: @link-color;\n }\n\n // Image captions\n .caption {\n padding: @thumbnail-caption-padding;\n color: @thumbnail-caption-color;\n }\n}\n","//\n// Alerts\n// --------------------------------------------------\n\n\n// Base styles\n// -------------------------\n\n.alert {\n padding: @alert-padding;\n margin-bottom: @line-height-computed;\n border: 1px solid transparent;\n border-radius: @alert-border-radius;\n\n // Headings for larger alerts\n h4 {\n margin-top: 0;\n // Specified for the h4 to prevent conflicts of changing @headings-color\n color: inherit;\n }\n // Provide class for links that match alerts\n .alert-link {\n font-weight: @alert-link-font-weight;\n }\n\n // Improve alignment and spacing of inner content\n > p,\n > ul {\n margin-bottom: 0;\n }\n > p + p {\n margin-top: 5px;\n }\n}\n\n// Dismissable alerts\n//\n// Expand the right padding and account for the close button's positioning.\n\n.alert-dismissable {\n padding-right: (@alert-padding + 20);\n\n // Adjust close link position\n .close {\n position: relative;\n top: -2px;\n right: -21px;\n color: inherit;\n }\n}\n\n// Alternate styles\n//\n// Generate contextual modifier classes for colorizing the alert.\n\n.alert-success {\n .alert-variant(@alert-success-bg; @alert-success-border; @alert-success-text);\n}\n.alert-info {\n .alert-variant(@alert-info-bg; @alert-info-border; @alert-info-text);\n}\n.alert-warning {\n .alert-variant(@alert-warning-bg; @alert-warning-border; @alert-warning-text);\n}\n.alert-danger {\n .alert-variant(@alert-danger-bg; @alert-danger-border; @alert-danger-text);\n}\n","//\n// Progress bars\n// --------------------------------------------------\n\n\n// Bar animations\n// -------------------------\n\n// WebKit\n@-webkit-keyframes progress-bar-stripes {\n from { background-position: 40px 0; }\n to { background-position: 0 0; }\n}\n\n// Spec and IE10+\n@keyframes progress-bar-stripes {\n from { background-position: 40px 0; }\n to { background-position: 0 0; }\n}\n\n\n\n// Bar itself\n// -------------------------\n\n// Outer container\n.progress {\n overflow: hidden;\n height: @line-height-computed;\n margin-bottom: @line-height-computed;\n background-color: @progress-bg;\n border-radius: @border-radius-base;\n .box-shadow(inset 0 1px 2px rgba(0,0,0,.1));\n}\n\n// Bar of progress\n.progress-bar {\n float: left;\n width: 0%;\n height: 100%;\n font-size: @font-size-small;\n line-height: @line-height-computed;\n color: @progress-bar-color;\n text-align: center;\n background-color: @progress-bar-bg;\n .box-shadow(inset 0 -1px 0 rgba(0,0,0,.15));\n .transition(width .6s ease);\n}\n\n// Striped bars\n.progress-striped .progress-bar {\n #gradient > .striped();\n background-size: 40px 40px;\n}\n\n// Call animation for the active one\n.progress.active .progress-bar {\n .animation(progress-bar-stripes 2s linear infinite);\n}\n\n\n\n// Variations\n// -------------------------\n\n.progress-bar-success {\n .progress-bar-variant(@progress-bar-success-bg);\n}\n\n.progress-bar-info {\n .progress-bar-variant(@progress-bar-info-bg);\n}\n\n.progress-bar-warning {\n .progress-bar-variant(@progress-bar-warning-bg);\n}\n\n.progress-bar-danger {\n .progress-bar-variant(@progress-bar-danger-bg);\n}\n","// Media objects\n// Source: http://stubbornella.org/content/?p=497\n// --------------------------------------------------\n\n\n// Common styles\n// -------------------------\n\n// Clear the floats\n.media,\n.media-body {\n overflow: hidden;\n zoom: 1;\n}\n\n// Proper spacing between instances of .media\n.media,\n.media .media {\n margin-top: 15px;\n}\n.media:first-child {\n margin-top: 0;\n}\n\n// For images and videos, set to block\n.media-object {\n display: block;\n}\n\n// Reset margins on headings for tighter default spacing\n.media-heading {\n margin: 0 0 5px;\n}\n\n\n// Media image alignment\n// -------------------------\n\n.media {\n > .pull-left {\n margin-right: 10px;\n }\n > .pull-right {\n margin-left: 10px;\n }\n}\n\n\n// Media list variation\n// -------------------------\n\n// Undo default ul/ol styles\n.media-list {\n padding-left: 0;\n list-style: none;\n}\n","//\n// List groups\n// --------------------------------------------------\n\n\n// Base class\n//\n// Easily usable on <ul>, <ol>, or <div>.\n\n.list-group {\n // No need to set list-style: none; since .list-group-item is block level\n margin-bottom: 20px;\n padding-left: 0; // reset padding because ul and ol\n}\n\n\n// Individual list items\n//\n// Use on `li`s or `div`s within the `.list-group` parent.\n\n.list-group-item {\n position: relative;\n display: block;\n padding: 10px 15px;\n // Place the border on the list items and negative margin up for better styling\n margin-bottom: -1px;\n background-color: @list-group-bg;\n border: 1px solid @list-group-border;\n\n // Round the first and last items\n &:first-child {\n .border-top-radius(@list-group-border-radius);\n }\n &:last-child {\n margin-bottom: 0;\n .border-bottom-radius(@list-group-border-radius);\n }\n\n // Align badges within list items\n > .badge {\n float: right;\n }\n > .badge + .badge {\n margin-right: 5px;\n }\n}\n\n\n// Linked list items\n//\n// Use anchor elements instead of `li`s or `div`s to create linked list items.\n// Includes an extra `.active` modifier class for showing selected items.\n\na.list-group-item {\n color: @list-group-link-color;\n\n .list-group-item-heading {\n color: @list-group-link-heading-color;\n }\n\n // Hover state\n &:hover,\n &:focus {\n text-decoration: none;\n background-color: @list-group-hover-bg;\n }\n\n // Active class on item itself, not parent\n &.active,\n &.active:hover,\n &.active:focus {\n z-index: 2; // Place active items above their siblings for proper border styling\n color: @list-group-active-color;\n background-color: @list-group-active-bg;\n border-color: @list-group-active-border;\n\n // Force color to inherit for custom content\n .list-group-item-heading {\n color: inherit;\n }\n .list-group-item-text {\n color: @list-group-active-text-color;\n }\n }\n}\n\n\n// Contextual variants\n//\n// Add modifier classes to change text and background color on individual items.\n// Organizationally, this must come after the `:hover` states.\n\n.list-group-item-variant(success; @state-success-bg; @state-success-text);\n.list-group-item-variant(info; @state-info-bg; @state-info-text);\n.list-group-item-variant(warning; @state-warning-bg; @state-warning-text);\n.list-group-item-variant(danger; @state-danger-bg; @state-danger-text);\n\n\n// Custom content options\n//\n// Extra classes for creating well-formatted content within `.list-group-item`s.\n\n.list-group-item-heading {\n margin-top: 0;\n margin-bottom: 5px;\n}\n.list-group-item-text {\n margin-bottom: 0;\n line-height: 1.3;\n}\n","//\n// Panels\n// --------------------------------------------------\n\n\n// Base class\n.panel {\n margin-bottom: @line-height-computed;\n background-color: @panel-bg;\n border: 1px solid transparent;\n border-radius: @panel-border-radius;\n .box-shadow(0 1px 1px rgba(0,0,0,.05));\n}\n\n// Panel contents\n.panel-body {\n padding: @panel-body-padding;\n &:extend(.clearfix all);\n}\n\n\n// List groups in panels\n//\n// By default, space out list group content from panel headings to account for\n// any kind of custom content between the two.\n\n.panel {\n > .list-group {\n margin-bottom: 0;\n .list-group-item {\n border-width: 1px 0;\n border-radius: 0;\n &:first-child {\n border-top: 0;\n }\n &:last-child {\n border-bottom: 0;\n }\n }\n // Add border top radius for first one\n &:first-child {\n .list-group-item:first-child {\n .border-top-radius((@panel-border-radius - 1));\n }\n }\n // Add border bottom radius for last one\n &:last-child {\n .list-group-item:last-child {\n .border-bottom-radius((@panel-border-radius - 1));\n }\n }\n }\n}\n// Collapse space between when there's no additional content.\n.panel-heading + .list-group {\n .list-group-item:first-child {\n border-top-width: 0;\n }\n}\n\n\n// Tables in panels\n//\n// Place a non-bordered `.table` within a panel (not within a `.panel-body`) and\n// watch it go full width.\n\n.panel {\n > .table,\n > .table-responsive > .table {\n margin-bottom: 0;\n }\n // Add border top radius for first one\n > .table:first-child,\n > .table-responsive:first-child > .table:first-child {\n > thead:first-child,\n > tbody:first-child {\n > tr:first-child {\n td:first-child,\n th:first-child {\n border-top-left-radius: (@panel-border-radius - 1);\n }\n td:last-child,\n th:last-child {\n border-top-right-radius: (@panel-border-radius - 1);\n }\n }\n }\n }\n // Add border bottom radius for last one\n > .table:last-child,\n > .table-responsive:last-child > .table:last-child {\n > tbody:last-child,\n > tfoot:last-child {\n > tr:last-child {\n td:first-child,\n th:first-child {\n border-bottom-left-radius: (@panel-border-radius - 1);\n }\n td:last-child,\n th:last-child {\n border-bottom-right-radius: (@panel-border-radius - 1);\n }\n }\n }\n }\n > .panel-body + .table,\n > .panel-body + .table-responsive {\n border-top: 1px solid @table-border-color;\n }\n > .table > tbody:first-child > tr:first-child th,\n > .table > tbody:first-child > tr:first-child td {\n border-top: 0;\n }\n > .table-bordered,\n > .table-responsive > .table-bordered {\n border: 0;\n > thead,\n > tbody,\n > tfoot {\n > tr {\n > th:first-child,\n > td:first-child {\n border-left: 0;\n }\n > th:last-child,\n > td:last-child {\n border-right: 0;\n }\n &:first-child > th,\n &:first-child > td {\n border-top: 0;\n }\n &:last-child > th,\n &:last-child > td {\n border-bottom: 0;\n }\n }\n }\n }\n > .table-responsive {\n border: 0;\n margin-bottom: 0;\n }\n}\n\n\n// Optional heading\n.panel-heading {\n padding: 10px 15px;\n border-bottom: 1px solid transparent;\n .border-top-radius((@panel-border-radius - 1));\n\n > .dropdown .dropdown-toggle {\n color: inherit;\n }\n}\n\n// Within heading, strip any `h*` tag of its default margins for spacing.\n.panel-title {\n margin-top: 0;\n margin-bottom: 0;\n font-size: ceil((@font-size-base * 1.125));\n color: inherit;\n\n > a {\n color: inherit;\n }\n}\n\n// Optional footer (stays gray in every modifier class)\n.panel-footer {\n padding: 10px 15px;\n background-color: @panel-footer-bg;\n border-top: 1px solid @panel-inner-border;\n .border-bottom-radius((@panel-border-radius - 1));\n}\n\n\n// Collapsable panels (aka, accordion)\n//\n// Wrap a series of panels in `.panel-group` to turn them into an accordion with\n// the help of our collapse JavaScript plugin.\n\n.panel-group {\n margin-bottom: @line-height-computed;\n\n // Tighten up margin so it's only between panels\n .panel {\n margin-bottom: 0;\n border-radius: @panel-border-radius;\n overflow: hidden; // crop contents when collapsed\n + .panel {\n margin-top: 5px;\n }\n }\n\n .panel-heading {\n border-bottom: 0;\n + .panel-collapse .panel-body {\n border-top: 1px solid @panel-inner-border;\n }\n }\n .panel-footer {\n border-top: 0;\n + .panel-collapse .panel-body {\n border-bottom: 1px solid @panel-inner-border;\n }\n }\n}\n\n\n// Contextual variations\n.panel-default {\n .panel-variant(@panel-default-border; @panel-default-text; @panel-default-heading-bg; @panel-default-border);\n}\n.panel-primary {\n .panel-variant(@panel-primary-border; @panel-primary-text; @panel-primary-heading-bg; @panel-primary-border);\n}\n.panel-success {\n .panel-variant(@panel-success-border; @panel-success-text; @panel-success-heading-bg; @panel-success-border);\n}\n.panel-info {\n .panel-variant(@panel-info-border; @panel-info-text; @panel-info-heading-bg; @panel-info-border);\n}\n.panel-warning {\n .panel-variant(@panel-warning-border; @panel-warning-text; @panel-warning-heading-bg; @panel-warning-border);\n}\n.panel-danger {\n .panel-variant(@panel-danger-border; @panel-danger-text; @panel-danger-heading-bg; @panel-danger-border);\n}\n","//\n// Wells\n// --------------------------------------------------\n\n\n// Base class\n.well {\n min-height: 20px;\n padding: 19px;\n margin-bottom: 20px;\n background-color: @well-bg;\n border: 1px solid @well-border;\n border-radius: @border-radius-base;\n .box-shadow(inset 0 1px 1px rgba(0,0,0,.05));\n blockquote {\n border-color: #ddd;\n border-color: rgba(0,0,0,.15);\n }\n}\n\n// Sizes\n.well-lg {\n padding: 24px;\n border-radius: @border-radius-large;\n}\n.well-sm {\n padding: 9px;\n border-radius: @border-radius-small;\n}\n","//\n// Close icons\n// --------------------------------------------------\n\n\n.close {\n float: right;\n font-size: (@font-size-base * 1.5);\n font-weight: @close-font-weight;\n line-height: 1;\n color: @close-color;\n text-shadow: @close-text-shadow;\n .opacity(.2);\n\n &:hover,\n &:focus {\n color: @close-color;\n text-decoration: none;\n cursor: pointer;\n .opacity(.5);\n }\n\n // Additional properties for button version\n // iOS requires the button element instead of an anchor tag.\n // If you want the anchor version, it requires `href=\"#\"`.\n button& {\n padding: 0;\n cursor: pointer;\n background: transparent;\n border: 0;\n -webkit-appearance: none;\n }\n}\n","//\n// Modals\n// --------------------------------------------------\n\n// .modal-open - body class for killing the scroll\n// .modal - container to scroll within\n// .modal-dialog - positioning shell for the actual modal\n// .modal-content - actual modal w/ bg and corners and shit\n\n// Kill the scroll on the body\n.modal-open {\n overflow: hidden;\n}\n\n// Container that the modal scrolls within\n.modal {\n display: none;\n overflow: auto;\n overflow-y: scroll;\n position: fixed;\n top: 0;\n right: 0;\n bottom: 0;\n left: 0;\n z-index: @zindex-modal;\n -webkit-overflow-scrolling: touch;\n\n // Prevent Chrome on Windows from adding a focus outline. For details, see\n // https://github.com/twbs/bootstrap/pull/10951.\n outline: 0;\n\n // When fading in the modal, animate it to slide down\n &.fade .modal-dialog {\n .translate(0, -25%);\n .transition-transform(~\"0.3s ease-out\");\n }\n &.in .modal-dialog { .translate(0, 0)}\n}\n\n// Shell div to position the modal with bottom padding\n.modal-dialog {\n position: relative;\n width: auto;\n margin: 10px;\n}\n\n// Actual modal\n.modal-content {\n position: relative;\n background-color: @modal-content-bg;\n border: 1px solid @modal-content-fallback-border-color; //old browsers fallback (ie8 etc)\n border: 1px solid @modal-content-border-color;\n border-radius: @border-radius-large;\n .box-shadow(0 3px 9px rgba(0,0,0,.5));\n background-clip: padding-box;\n // Remove focus outline from opened modal\n outline: none;\n}\n\n// Modal background\n.modal-backdrop {\n position: fixed;\n top: 0;\n right: 0;\n bottom: 0;\n left: 0;\n z-index: @zindex-modal-background;\n background-color: @modal-backdrop-bg;\n // Fade for backdrop\n &.fade { .opacity(0); }\n &.in { .opacity(@modal-backdrop-opacity); }\n}\n\n// Modal header\n// Top section of the modal w/ title and dismiss\n.modal-header {\n padding: @modal-title-padding;\n border-bottom: 1px solid @modal-header-border-color;\n min-height: (@modal-title-padding + @modal-title-line-height);\n}\n// Close icon\n.modal-header .close {\n margin-top: -2px;\n}\n\n// Title text within header\n.modal-title {\n margin: 0;\n line-height: @modal-title-line-height;\n}\n\n// Modal body\n// Where all modal content resides (sibling of .modal-header and .modal-footer)\n.modal-body {\n position: relative;\n padding: @modal-inner-padding;\n}\n\n// Footer (for actions)\n.modal-footer {\n margin-top: 15px;\n padding: (@modal-inner-padding - 1) @modal-inner-padding @modal-inner-padding;\n text-align: right; // right align buttons\n border-top: 1px solid @modal-footer-border-color;\n &:extend(.clearfix all); // clear it in case folks use .pull-* classes on buttons\n\n // Properly space out buttons\n .btn + .btn {\n margin-left: 5px;\n margin-bottom: 0; // account for input[type=\"submit\"] which gets the bottom margin like all other inputs\n }\n // but override that for button groups\n .btn-group .btn + .btn {\n margin-left: -1px;\n }\n // and override it for block buttons as well\n .btn-block + .btn-block {\n margin-left: 0;\n }\n}\n\n// Scale up the modal\n@media (min-width: @screen-sm-min) {\n\n // Automatically set modal's width for larger viewports\n .modal-dialog {\n width: @modal-md;\n margin: 30px auto;\n }\n .modal-content {\n .box-shadow(0 5px 15px rgba(0,0,0,.5));\n }\n\n // Modal sizes\n .modal-sm { width: @modal-sm; }\n .modal-lg { width: @modal-lg; }\n\n}\n","//\n// Tooltips\n// --------------------------------------------------\n\n\n// Base class\n.tooltip {\n position: absolute;\n z-index: @zindex-tooltip;\n display: block;\n visibility: visible;\n font-size: @font-size-small;\n line-height: 1.4;\n .opacity(0);\n\n &.in { .opacity(@tooltip-opacity); }\n &.top { margin-top: -3px; padding: @tooltip-arrow-width 0; }\n &.right { margin-left: 3px; padding: 0 @tooltip-arrow-width; }\n &.bottom { margin-top: 3px; padding: @tooltip-arrow-width 0; }\n &.left { margin-left: -3px; padding: 0 @tooltip-arrow-width; }\n}\n\n// Wrapper for the tooltip content\n.tooltip-inner {\n max-width: @tooltip-max-width;\n padding: 3px 8px;\n color: @tooltip-color;\n text-align: center;\n text-decoration: none;\n background-color: @tooltip-bg;\n border-radius: @border-radius-base;\n}\n\n// Arrows\n.tooltip-arrow {\n position: absolute;\n width: 0;\n height: 0;\n border-color: transparent;\n border-style: solid;\n}\n.tooltip {\n &.top .tooltip-arrow {\n bottom: 0;\n left: 50%;\n margin-left: -@tooltip-arrow-width;\n border-width: @tooltip-arrow-width @tooltip-arrow-width 0;\n border-top-color: @tooltip-arrow-color;\n }\n &.top-left .tooltip-arrow {\n bottom: 0;\n left: @tooltip-arrow-width;\n border-width: @tooltip-arrow-width @tooltip-arrow-width 0;\n border-top-color: @tooltip-arrow-color;\n }\n &.top-right .tooltip-arrow {\n bottom: 0;\n right: @tooltip-arrow-width;\n border-width: @tooltip-arrow-width @tooltip-arrow-width 0;\n border-top-color: @tooltip-arrow-color;\n }\n &.right .tooltip-arrow {\n top: 50%;\n left: 0;\n margin-top: -@tooltip-arrow-width;\n border-width: @tooltip-arrow-width @tooltip-arrow-width @tooltip-arrow-width 0;\n border-right-color: @tooltip-arrow-color;\n }\n &.left .tooltip-arrow {\n top: 50%;\n right: 0;\n margin-top: -@tooltip-arrow-width;\n border-width: @tooltip-arrow-width 0 @tooltip-arrow-width @tooltip-arrow-width;\n border-left-color: @tooltip-arrow-color;\n }\n &.bottom .tooltip-arrow {\n top: 0;\n left: 50%;\n margin-left: -@tooltip-arrow-width;\n border-width: 0 @tooltip-arrow-width @tooltip-arrow-width;\n border-bottom-color: @tooltip-arrow-color;\n }\n &.bottom-left .tooltip-arrow {\n top: 0;\n left: @tooltip-arrow-width;\n border-width: 0 @tooltip-arrow-width @tooltip-arrow-width;\n border-bottom-color: @tooltip-arrow-color;\n }\n &.bottom-right .tooltip-arrow {\n top: 0;\n right: @tooltip-arrow-width;\n border-width: 0 @tooltip-arrow-width @tooltip-arrow-width;\n border-bottom-color: @tooltip-arrow-color;\n }\n}\n","//\n// Popovers\n// --------------------------------------------------\n\n\n.popover {\n position: absolute;\n top: 0;\n left: 0;\n z-index: @zindex-popover;\n display: none;\n max-width: @popover-max-width;\n padding: 1px;\n text-align: left; // Reset given new insertion method\n background-color: @popover-bg;\n background-clip: padding-box;\n border: 1px solid @popover-fallback-border-color;\n border: 1px solid @popover-border-color;\n border-radius: @border-radius-large;\n .box-shadow(0 5px 10px rgba(0,0,0,.2));\n\n // Overrides for proper insertion\n white-space: normal;\n\n // Offset the popover to account for the popover arrow\n &.top { margin-top: -10px; }\n &.right { margin-left: 10px; }\n &.bottom { margin-top: 10px; }\n &.left { margin-left: -10px; }\n}\n\n.popover-title {\n margin: 0; // reset heading margin\n padding: 8px 14px;\n font-size: @font-size-base;\n font-weight: normal;\n line-height: 18px;\n background-color: @popover-title-bg;\n border-bottom: 1px solid darken(@popover-title-bg, 5%);\n border-radius: 5px 5px 0 0;\n}\n\n.popover-content {\n padding: 9px 14px;\n}\n\n// Arrows\n//\n// .arrow is outer, .arrow:after is inner\n\n.popover .arrow {\n &,\n &:after {\n position: absolute;\n display: block;\n width: 0;\n height: 0;\n border-color: transparent;\n border-style: solid;\n }\n}\n.popover .arrow {\n border-width: @popover-arrow-outer-width;\n}\n.popover .arrow:after {\n border-width: @popover-arrow-width;\n content: \"\";\n}\n\n.popover {\n &.top .arrow {\n left: 50%;\n margin-left: -@popover-arrow-outer-width;\n border-bottom-width: 0;\n border-top-color: @popover-arrow-outer-fallback-color; // IE8 fallback\n border-top-color: @popover-arrow-outer-color;\n bottom: -@popover-arrow-outer-width;\n &:after {\n content: \" \";\n bottom: 1px;\n margin-left: -@popover-arrow-width;\n border-bottom-width: 0;\n border-top-color: @popover-arrow-color;\n }\n }\n &.right .arrow {\n top: 50%;\n left: -@popover-arrow-outer-width;\n margin-top: -@popover-arrow-outer-width;\n border-left-width: 0;\n border-right-color: @popover-arrow-outer-fallback-color; // IE8 fallback\n border-right-color: @popover-arrow-outer-color;\n &:after {\n content: \" \";\n left: 1px;\n bottom: -@popover-arrow-width;\n border-left-width: 0;\n border-right-color: @popover-arrow-color;\n }\n }\n &.bottom .arrow {\n left: 50%;\n margin-left: -@popover-arrow-outer-width;\n border-top-width: 0;\n border-bottom-color: @popover-arrow-outer-fallback-color; // IE8 fallback\n border-bottom-color: @popover-arrow-outer-color;\n top: -@popover-arrow-outer-width;\n &:after {\n content: \" \";\n top: 1px;\n margin-left: -@popover-arrow-width;\n border-top-width: 0;\n border-bottom-color: @popover-arrow-color;\n }\n }\n\n &.left .arrow {\n top: 50%;\n right: -@popover-arrow-outer-width;\n margin-top: -@popover-arrow-outer-width;\n border-right-width: 0;\n border-left-color: @popover-arrow-outer-fallback-color; // IE8 fallback\n border-left-color: @popover-arrow-outer-color;\n &:after {\n content: \" \";\n right: 1px;\n border-right-width: 0;\n border-left-color: @popover-arrow-color;\n bottom: -@popover-arrow-width;\n }\n }\n\n}\n","//\n// Carousel\n// --------------------------------------------------\n\n\n// Wrapper for the slide container and indicators\n.carousel {\n position: relative;\n}\n\n.carousel-inner {\n position: relative;\n overflow: hidden;\n width: 100%;\n\n > .item {\n display: none;\n position: relative;\n .transition(.6s ease-in-out left);\n\n // Account for jankitude on images\n > img,\n > a > img {\n .img-responsive();\n line-height: 1;\n }\n }\n\n > .active,\n > .next,\n > .prev { display: block; }\n\n > .active {\n left: 0;\n }\n\n > .next,\n > .prev {\n position: absolute;\n top: 0;\n width: 100%;\n }\n\n > .next {\n left: 100%;\n }\n > .prev {\n left: -100%;\n }\n > .next.left,\n > .prev.right {\n left: 0;\n }\n\n > .active.left {\n left: -100%;\n }\n > .active.right {\n left: 100%;\n }\n\n}\n\n// Left/right controls for nav\n// ---------------------------\n\n.carousel-control {\n position: absolute;\n top: 0;\n left: 0;\n bottom: 0;\n width: @carousel-control-width;\n .opacity(@carousel-control-opacity);\n font-size: @carousel-control-font-size;\n color: @carousel-control-color;\n text-align: center;\n text-shadow: @carousel-text-shadow;\n // We can't have this transition here because WebKit cancels the carousel\n // animation if you trip this while in the middle of another animation.\n\n // Set gradients for backgrounds\n &.left {\n #gradient > .horizontal(@start-color: rgba(0,0,0,.5); @end-color: rgba(0,0,0,.0001));\n }\n &.right {\n left: auto;\n right: 0;\n #gradient > .horizontal(@start-color: rgba(0,0,0,.0001); @end-color: rgba(0,0,0,.5));\n }\n\n // Hover/focus state\n &:hover,\n &:focus {\n outline: none;\n color: @carousel-control-color;\n text-decoration: none;\n .opacity(.9);\n }\n\n // Toggles\n .icon-prev,\n .icon-next,\n .glyphicon-chevron-left,\n .glyphicon-chevron-right {\n position: absolute;\n top: 50%;\n z-index: 5;\n display: inline-block;\n }\n .icon-prev,\n .glyphicon-chevron-left {\n left: 50%;\n }\n .icon-next,\n .glyphicon-chevron-right {\n right: 50%;\n }\n .icon-prev,\n .icon-next {\n width: 20px;\n height: 20px;\n margin-top: -10px;\n margin-left: -10px;\n font-family: serif;\n }\n\n .icon-prev {\n &:before {\n content: '\\2039';// SINGLE LEFT-POINTING ANGLE QUOTATION MARK (U+2039)\n }\n }\n .icon-next {\n &:before {\n content: '\\203a';// SINGLE RIGHT-POINTING ANGLE QUOTATION MARK (U+203A)\n }\n }\n}\n\n// Optional indicator pips\n//\n// Add an unordered list with the following class and add a list item for each\n// slide your carousel holds.\n\n.carousel-indicators {\n position: absolute;\n bottom: 10px;\n left: 50%;\n z-index: 15;\n width: 60%;\n margin-left: -30%;\n padding-left: 0;\n list-style: none;\n text-align: center;\n\n li {\n display: inline-block;\n width: 10px;\n height: 10px;\n margin: 1px;\n text-indent: -999px;\n border: 1px solid @carousel-indicator-border-color;\n border-radius: 10px;\n cursor: pointer;\n\n // IE8-9 hack for event handling\n //\n // Internet Explorer 8-9 does not support clicks on elements without a set\n // `background-color`. We cannot use `filter` since that's not viewed as a\n // background color by the browser. Thus, a hack is needed.\n //\n // For IE8, we set solid black as it doesn't support `rgba()`. For IE9, we\n // set alpha transparency for the best results possible.\n background-color: #000 \\9; // IE8\n background-color: rgba(0,0,0,0); // IE9\n }\n .active {\n margin: 0;\n width: 12px;\n height: 12px;\n background-color: @carousel-indicator-active-bg;\n }\n}\n\n// Optional captions\n// -----------------------------\n// Hidden by default for smaller viewports\n.carousel-caption {\n position: absolute;\n left: 15%;\n right: 15%;\n bottom: 20px;\n z-index: 10;\n padding-top: 20px;\n padding-bottom: 20px;\n color: @carousel-caption-color;\n text-align: center;\n text-shadow: @carousel-text-shadow;\n & .btn {\n text-shadow: none; // No shadow for button elements in carousel-caption\n }\n}\n\n\n// Scale up controls for tablets and up\n@media screen and (min-width: @screen-sm-min) {\n\n // Scale up the controls a smidge\n .carousel-control {\n .glyphicons-chevron-left,\n .glyphicons-chevron-right,\n .icon-prev,\n .icon-next {\n width: 30px;\n height: 30px;\n margin-top: -15px;\n margin-left: -15px;\n font-size: 30px;\n }\n }\n\n // Show and left align the captions\n .carousel-caption {\n left: 20%;\n right: 20%;\n padding-bottom: 30px;\n }\n\n // Move up the indicators\n .carousel-indicators {\n bottom: 20px;\n }\n}\n","//\n// Responsive: Utility classes\n// --------------------------------------------------\n\n\n// IE10 in Windows (Phone) 8\n//\n// Support for responsive views via media queries is kind of borked in IE10, for\n// Surface/desktop in split view and for Windows Phone 8. This particular fix\n// must be accompanied by a snippet of JavaScript to sniff the user agent and\n// apply some conditional CSS to *only* the Surface/desktop Windows 8. Look at\n// our Getting Started page for more information on this bug.\n//\n// For more information, see the following:\n//\n// Issue: https://github.com/twbs/bootstrap/issues/10497\n// Docs: http://getbootstrap.com/getting-started/#browsers\n// Source: http://timkadlec.com/2012/10/ie10-snap-mode-and-responsive-design/\n\n@-ms-viewport {\n width: device-width;\n}\n\n\n// Visibility utilities\n.visible-xs {\n .responsive-invisibility();\n\n @media (max-width: @screen-xs-max) {\n .responsive-visibility();\n }\n}\n.visible-sm {\n .responsive-invisibility();\n\n @media (min-width: @screen-sm-min) and (max-width: @screen-sm-max) {\n .responsive-visibility();\n }\n}\n.visible-md {\n .responsive-invisibility();\n\n @media (min-width: @screen-md-min) and (max-width: @screen-md-max) {\n .responsive-visibility();\n }\n}\n.visible-lg {\n .responsive-invisibility();\n\n @media (min-width: @screen-lg-min) {\n .responsive-visibility();\n }\n}\n\n.hidden-xs {\n @media (max-width: @screen-xs-max) {\n .responsive-invisibility();\n }\n}\n.hidden-sm {\n @media (min-width: @screen-sm-min) and (max-width: @screen-sm-max) {\n .responsive-invisibility();\n }\n}\n.hidden-md {\n @media (min-width: @screen-md-min) and (max-width: @screen-md-max) {\n .responsive-invisibility();\n }\n}\n.hidden-lg {\n @media (min-width: @screen-lg-min) {\n .responsive-invisibility();\n }\n}\n\n\n// Print utilities\n//\n// Media queries are placed on the inside to be mixin-friendly.\n\n.visible-print {\n .responsive-invisibility();\n\n @media print {\n .responsive-visibility();\n }\n}\n\n.hidden-print {\n @media print {\n .responsive-invisibility();\n }\n}\n"]}
\ No newline at end of file
--- /dev/null
+/*!
+ * Bootstrap v3.1.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
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+ font-size: 13px;
+ line-height: 1.42857;
+ color: rgb(51, 51, 51);
+ word-break: break-all;
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+ background-color: rgb(245, 245, 245);
+ border: 1px solid rgb(204, 204, 204);
+ border-radius: 4px 4px 4px 4px;
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--- /dev/null
+/*!
+ * Font Awesome 4.1.0 by @davegandy - http://fontawesome.io - @fontawesome
+ * License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License)
+ */
+/* FONT PATH
+ * -------------------------- */
+@font-face {
+ font-family: 'FontAwesome';
+ src: url('../fonts/fontawesome-webfont.eot?v=4.1.0');
+ src: url('../fonts/fontawesome-webfont.eot?#iefix&v=4.1.0') format('embedded-opentype'), url('../fonts/fontawesome-webfont.woff?v=4.1.0') format('woff'), url('../fonts/fontawesome-webfont.ttf?v=4.1.0') format('truetype'), url('../fonts/fontawesome-webfont.svg?v=4.1.0#fontawesomeregular') format('svg');
+ font-weight: normal;
+ font-style: normal;
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+ font-family: FontAwesome;
+ font-style: normal;
+ font-weight: normal;
+ line-height: 1;
+ -webkit-font-smoothing: antialiased;
+ -moz-osx-font-smoothing: grayscale;
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+/* makes the font 33% larger relative to the icon container */
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+ left: -2.14285714em;
+ width: 2.14285714em;
+ top: 0.14285714em;
+ text-align: center;
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+ left: -1.85714286em;
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+ border: solid 0.08em #eeeeee;
+ border-radius: .1em;
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+ float: right;
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+ float: left;
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+ margin-right: .3em;
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+ margin-left: .3em;
+}
+.fa-spin {
+ -webkit-animation: spin 2s infinite linear;
+ -moz-animation: spin 2s infinite linear;
+ -o-animation: spin 2s infinite linear;
+ animation: spin 2s infinite linear;
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+@-moz-keyframes spin {
+ 0% {
+ -moz-transform: rotate(0deg);
+ }
+ 100% {
+ -moz-transform: rotate(359deg);
+ }
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+ 0% {
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+ 100% {
+ -webkit-transform: rotate(359deg);
+ }
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+@-o-keyframes spin {
+ 0% {
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+ }
+ 100% {
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+ -webkit-transform: rotate(359deg);
+ transform: rotate(359deg);
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+ filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=1);
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+ -moz-transform: rotate(90deg);
+ -ms-transform: rotate(90deg);
+ -o-transform: rotate(90deg);
+ transform: rotate(90deg);
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+.fa-rotate-180 {
+ filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=2);
+ -webkit-transform: rotate(180deg);
+ -moz-transform: rotate(180deg);
+ -ms-transform: rotate(180deg);
+ -o-transform: rotate(180deg);
+ transform: rotate(180deg);
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+ -webkit-transform: rotate(270deg);
+ -moz-transform: rotate(270deg);
+ -ms-transform: rotate(270deg);
+ -o-transform: rotate(270deg);
+ transform: rotate(270deg);
+}
+.fa-flip-horizontal {
+ filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=0, mirror=1);
+ -webkit-transform: scale(-1, 1);
+ -moz-transform: scale(-1, 1);
+ -ms-transform: scale(-1, 1);
+ -o-transform: scale(-1, 1);
+ transform: scale(-1, 1);
+}
+.fa-flip-vertical {
+ filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=2, mirror=1);
+ -webkit-transform: scale(1, -1);
+ -moz-transform: scale(1, -1);
+ -ms-transform: scale(1, -1);
+ -o-transform: scale(1, -1);
+ transform: scale(1, -1);
+}
+.fa-stack {
+ position: relative;
+ display: inline-block;
+ width: 2em;
+ height: 2em;
+ line-height: 2em;
+ vertical-align: middle;
+}
+.fa-stack-1x,
+.fa-stack-2x {
+ position: absolute;
+ left: 0;
+ width: 100%;
+ text-align: center;
+}
+.fa-stack-1x {
+ line-height: inherit;
+}
+.fa-stack-2x {
+ font-size: 2em;
+}
+.fa-inverse {
+ color: #ffffff;
+}
+/* Font Awesome uses the Unicode Private Use Area (PUA) to ensure screen
+ readers do not read off random characters that represent icons */
+.fa-glass:before {
+ content: "\f000";
+}
+.fa-music:before {
+ content: "\f001";
+}
+.fa-search:before {
+ content: "\f002";
+}
+.fa-envelope-o:before {
+ content: "\f003";
+}
+.fa-heart:before {
+ content: "\f004";
+}
+.fa-star:before {
+ content: "\f005";
+}
+.fa-star-o:before {
+ content: "\f006";
+}
+.fa-user:before {
+ content: "\f007";
+}
+.fa-film:before {
+ content: "\f008";
+}
+.fa-th-large:before {
+ content: "\f009";
+}
+.fa-th:before {
+ content: "\f00a";
+}
+.fa-th-list:before {
+ content: "\f00b";
+}
+.fa-check:before {
+ content: "\f00c";
+}
+.fa-times:before {
+ content: "\f00d";
+}
+.fa-search-plus:before {
+ content: "\f00e";
+}
+.fa-search-minus:before {
+ content: "\f010";
+}
+.fa-power-off:before {
+ content: "\f011";
+}
+.fa-signal:before {
+ content: "\f012";
+}
+.fa-gear:before,
+.fa-cog:before {
+ content: "\f013";
+}
+.fa-trash-o:before {
+ content: "\f014";
+}
+.fa-home:before {
+ content: "\f015";
+}
+.fa-file-o:before {
+ content: "\f016";
+}
+.fa-clock-o:before {
+ content: "\f017";
+}
+.fa-road:before {
+ content: "\f018";
+}
+.fa-download:before {
+ content: "\f019";
+}
+.fa-arrow-circle-o-down:before {
+ content: "\f01a";
+}
+.fa-arrow-circle-o-up:before {
+ content: "\f01b";
+}
+.fa-inbox:before {
+ content: "\f01c";
+}
+.fa-play-circle-o:before {
+ content: "\f01d";
+}
+.fa-rotate-right:before,
+.fa-repeat:before {
+ content: "\f01e";
+}
+.fa-refresh:before {
+ content: "\f021";
+}
+.fa-list-alt:before {
+ content: "\f022";
+}
+.fa-lock:before {
+ content: "\f023";
+}
+.fa-flag:before {
+ content: "\f024";
+}
+.fa-headphones:before {
+ content: "\f025";
+}
+.fa-volume-off:before {
+ content: "\f026";
+}
+.fa-volume-down:before {
+ content: "\f027";
+}
+.fa-volume-up:before {
+ content: "\f028";
+}
+.fa-qrcode:before {
+ content: "\f029";
+}
+.fa-barcode:before {
+ content: "\f02a";
+}
+.fa-tag:before {
+ content: "\f02b";
+}
+.fa-tags:before {
+ content: "\f02c";
+}
+.fa-book:before {
+ content: "\f02d";
+}
+.fa-bookmark:before {
+ content: "\f02e";
+}
+.fa-print:before {
+ content: "\f02f";
+}
+.fa-camera:before {
+ content: "\f030";
+}
+.fa-font:before {
+ content: "\f031";
+}
+.fa-bold:before {
+ content: "\f032";
+}
+.fa-italic:before {
+ content: "\f033";
+}
+.fa-text-height:before {
+ content: "\f034";
+}
+.fa-text-width:before {
+ content: "\f035";
+}
+.fa-align-left:before {
+ content: "\f036";
+}
+.fa-align-center:before {
+ content: "\f037";
+}
+.fa-align-right:before {
+ content: "\f038";
+}
+.fa-align-justify:before {
+ content: "\f039";
+}
+.fa-list:before {
+ content: "\f03a";
+}
+.fa-dedent:before,
+.fa-outdent:before {
+ content: "\f03b";
+}
+.fa-indent:before {
+ content: "\f03c";
+}
+.fa-video-camera:before {
+ content: "\f03d";
+}
+.fa-photo:before,
+.fa-image:before,
+.fa-picture-o:before {
+ content: "\f03e";
+}
+.fa-pencil:before {
+ content: "\f040";
+}
+.fa-map-marker:before {
+ content: "\f041";
+}
+.fa-adjust:before {
+ content: "\f042";
+}
+.fa-tint:before {
+ content: "\f043";
+}
+.fa-edit:before,
+.fa-pencil-square-o:before {
+ content: "\f044";
+}
+.fa-share-square-o:before {
+ content: "\f045";
+}
+.fa-check-square-o:before {
+ content: "\f046";
+}
+.fa-arrows:before {
+ content: "\f047";
+}
+.fa-step-backward:before {
+ content: "\f048";
+}
+.fa-fast-backward:before {
+ content: "\f049";
+}
+.fa-backward:before {
+ content: "\f04a";
+}
+.fa-play:before {
+ content: "\f04b";
+}
+.fa-pause:before {
+ content: "\f04c";
+}
+.fa-stop:before {
+ content: "\f04d";
+}
+.fa-forward:before {
+ content: "\f04e";
+}
+.fa-fast-forward:before {
+ content: "\f050";
+}
+.fa-step-forward:before {
+ content: "\f051";
+}
+.fa-eject:before {
+ content: "\f052";
+}
+.fa-chevron-left:before {
+ content: "\f053";
+}
+.fa-chevron-right:before {
+ content: "\f054";
+}
+.fa-plus-circle:before {
+ content: "\f055";
+}
+.fa-minus-circle:before {
+ content: "\f056";
+}
+.fa-times-circle:before {
+ content: "\f057";
+}
+.fa-check-circle:before {
+ content: "\f058";
+}
+.fa-question-circle:before {
+ content: "\f059";
+}
+.fa-info-circle:before {
+ content: "\f05a";
+}
+.fa-crosshairs:before {
+ content: "\f05b";
+}
+.fa-times-circle-o:before {
+ content: "\f05c";
+}
+.fa-check-circle-o:before {
+ content: "\f05d";
+}
+.fa-ban:before {
+ content: "\f05e";
+}
+.fa-arrow-left:before {
+ content: "\f060";
+}
+.fa-arrow-right:before {
+ content: "\f061";
+}
+.fa-arrow-up:before {
+ content: "\f062";
+}
+.fa-arrow-down:before {
+ content: "\f063";
+}
+.fa-mail-forward:before,
+.fa-share:before {
+ content: "\f064";
+}
+.fa-expand:before {
+ content: "\f065";
+}
+.fa-compress:before {
+ content: "\f066";
+}
+.fa-plus:before {
+ content: "\f067";
+}
+.fa-minus:before {
+ content: "\f068";
+}
+.fa-asterisk:before {
+ content: "\f069";
+}
+.fa-exclamation-circle:before {
+ content: "\f06a";
+}
+.fa-gift:before {
+ content: "\f06b";
+}
+.fa-leaf:before {
+ content: "\f06c";
+}
+.fa-fire:before {
+ content: "\f06d";
+}
+.fa-eye:before {
+ content: "\f06e";
+}
+.fa-eye-slash:before {
+ content: "\f070";
+}
+.fa-warning:before,
+.fa-exclamation-triangle:before {
+ content: "\f071";
+}
+.fa-plane:before {
+ content: "\f072";
+}
+.fa-calendar:before {
+ content: "\f073";
+}
+.fa-random:before {
+ content: "\f074";
+}
+.fa-comment:before {
+ content: "\f075";
+}
+.fa-magnet:before {
+ content: "\f076";
+}
+.fa-chevron-up:before {
+ content: "\f077";
+}
+.fa-chevron-down:before {
+ content: "\f078";
+}
+.fa-retweet:before {
+ content: "\f079";
+}
+.fa-shopping-cart:before {
+ content: "\f07a";
+}
+.fa-folder:before {
+ content: "\f07b";
+}
+.fa-folder-open:before {
+ content: "\f07c";
+}
+.fa-arrows-v:before {
+ content: "\f07d";
+}
+.fa-arrows-h:before {
+ content: "\f07e";
+}
+.fa-bar-chart-o:before {
+ content: "\f080";
+}
+.fa-twitter-square:before {
+ content: "\f081";
+}
+.fa-facebook-square:before {
+ content: "\f082";
+}
+.fa-camera-retro:before {
+ content: "\f083";
+}
+.fa-key:before {
+ content: "\f084";
+}
+.fa-gears:before,
+.fa-cogs:before {
+ content: "\f085";
+}
+.fa-comments:before {
+ content: "\f086";
+}
+.fa-thumbs-o-up:before {
+ content: "\f087";
+}
+.fa-thumbs-o-down:before {
+ content: "\f088";
+}
+.fa-star-half:before {
+ content: "\f089";
+}
+.fa-heart-o:before {
+ content: "\f08a";
+}
+.fa-sign-out:before {
+ content: "\f08b";
+}
+.fa-linkedin-square:before {
+ content: "\f08c";
+}
+.fa-thumb-tack:before {
+ content: "\f08d";
+}
+.fa-external-link:before {
+ content: "\f08e";
+}
+.fa-sign-in:before {
+ content: "\f090";
+}
+.fa-trophy:before {
+ content: "\f091";
+}
+.fa-github-square:before {
+ content: "\f092";
+}
+.fa-upload:before {
+ content: "\f093";
+}
+.fa-lemon-o:before {
+ content: "\f094";
+}
+.fa-phone:before {
+ content: "\f095";
+}
+.fa-square-o:before {
+ content: "\f096";
+}
+.fa-bookmark-o:before {
+ content: "\f097";
+}
+.fa-phone-square:before {
+ content: "\f098";
+}
+.fa-twitter:before {
+ content: "\f099";
+}
+.fa-facebook:before {
+ content: "\f09a";
+}
+.fa-github:before {
+ content: "\f09b";
+}
+.fa-unlock:before {
+ content: "\f09c";
+}
+.fa-credit-card:before {
+ content: "\f09d";
+}
+.fa-rss:before {
+ content: "\f09e";
+}
+.fa-hdd-o:before {
+ content: "\f0a0";
+}
+.fa-bullhorn:before {
+ content: "\f0a1";
+}
+.fa-bell:before {
+ content: "\f0f3";
+}
+.fa-certificate:before {
+ content: "\f0a3";
+}
+.fa-hand-o-right:before {
+ content: "\f0a4";
+}
+.fa-hand-o-left:before {
+ content: "\f0a5";
+}
+.fa-hand-o-up:before {
+ content: "\f0a6";
+}
+.fa-hand-o-down:before {
+ content: "\f0a7";
+}
+.fa-arrow-circle-left:before {
+ content: "\f0a8";
+}
+.fa-arrow-circle-right:before {
+ content: "\f0a9";
+}
+.fa-arrow-circle-up:before {
+ content: "\f0aa";
+}
+.fa-arrow-circle-down:before {
+ content: "\f0ab";
+}
+.fa-globe:before {
+ content: "\f0ac";
+}
+.fa-wrench:before {
+ content: "\f0ad";
+}
+.fa-tasks:before {
+ content: "\f0ae";
+}
+.fa-filter:before {
+ content: "\f0b0";
+}
+.fa-briefcase:before {
+ content: "\f0b1";
+}
+.fa-arrows-alt:before {
+ content: "\f0b2";
+}
+.fa-group:before,
+.fa-users:before {
+ content: "\f0c0";
+}
+.fa-chain:before,
+.fa-link:before {
+ content: "\f0c1";
+}
+.fa-cloud:before {
+ content: "\f0c2";
+}
+.fa-flask:before {
+ content: "\f0c3";
+}
+.fa-cut:before,
+.fa-scissors:before {
+ content: "\f0c4";
+}
+.fa-copy:before,
+.fa-files-o:before {
+ content: "\f0c5";
+}
+.fa-paperclip:before {
+ content: "\f0c6";
+}
+.fa-save:before,
+.fa-floppy-o:before {
+ content: "\f0c7";
+}
+.fa-square:before {
+ content: "\f0c8";
+}
+.fa-navicon:before,
+.fa-reorder:before,
+.fa-bars:before {
+ content: "\f0c9";
+}
+.fa-list-ul:before {
+ content: "\f0ca";
+}
+.fa-list-ol:before {
+ content: "\f0cb";
+}
+.fa-strikethrough:before {
+ content: "\f0cc";
+}
+.fa-underline:before {
+ content: "\f0cd";
+}
+.fa-table:before {
+ content: "\f0ce";
+}
+.fa-magic:before {
+ content: "\f0d0";
+}
+.fa-truck:before {
+ content: "\f0d1";
+}
+.fa-pinterest:before {
+ content: "\f0d2";
+}
+.fa-pinterest-square:before {
+ content: "\f0d3";
+}
+.fa-google-plus-square:before {
+ content: "\f0d4";
+}
+.fa-google-plus:before {
+ content: "\f0d5";
+}
+.fa-money:before {
+ content: "\f0d6";
+}
+.fa-caret-down:before {
+ content: "\f0d7";
+}
+.fa-caret-up:before {
+ content: "\f0d8";
+}
+.fa-caret-left:before {
+ content: "\f0d9";
+}
+.fa-caret-right:before {
+ content: "\f0da";
+}
+.fa-columns:before {
+ content: "\f0db";
+}
+.fa-unsorted:before,
+.fa-sort:before {
+ content: "\f0dc";
+}
+.fa-sort-down:before,
+.fa-sort-desc:before {
+ content: "\f0dd";
+}
+.fa-sort-up:before,
+.fa-sort-asc:before {
+ content: "\f0de";
+}
+.fa-envelope:before {
+ content: "\f0e0";
+}
+.fa-linkedin:before {
+ content: "\f0e1";
+}
+.fa-rotate-left:before,
+.fa-undo:before {
+ content: "\f0e2";
+}
+.fa-legal:before,
+.fa-gavel:before {
+ content: "\f0e3";
+}
+.fa-dashboard:before,
+.fa-tachometer:before {
+ content: "\f0e4";
+}
+.fa-comment-o:before {
+ content: "\f0e5";
+}
+.fa-comments-o:before {
+ content: "\f0e6";
+}
+.fa-flash:before,
+.fa-bolt:before {
+ content: "\f0e7";
+}
+.fa-sitemap:before {
+ content: "\f0e8";
+}
+.fa-umbrella:before {
+ content: "\f0e9";
+}
+.fa-paste:before,
+.fa-clipboard:before {
+ content: "\f0ea";
+}
+.fa-lightbulb-o:before {
+ content: "\f0eb";
+}
+.fa-exchange:before {
+ content: "\f0ec";
+}
+.fa-cloud-download:before {
+ content: "\f0ed";
+}
+.fa-cloud-upload:before {
+ content: "\f0ee";
+}
+.fa-user-md:before {
+ content: "\f0f0";
+}
+.fa-stethoscope:before {
+ content: "\f0f1";
+}
+.fa-suitcase:before {
+ content: "\f0f2";
+}
+.fa-bell-o:before {
+ content: "\f0a2";
+}
+.fa-coffee:before {
+ content: "\f0f4";
+}
+.fa-cutlery:before {
+ content: "\f0f5";
+}
+.fa-file-text-o:before {
+ content: "\f0f6";
+}
+.fa-building-o:before {
+ content: "\f0f7";
+}
+.fa-hospital-o:before {
+ content: "\f0f8";
+}
+.fa-ambulance:before {
+ content: "\f0f9";
+}
+.fa-medkit:before {
+ content: "\f0fa";
+}
+.fa-fighter-jet:before {
+ content: "\f0fb";
+}
+.fa-beer:before {
+ content: "\f0fc";
+}
+.fa-h-square:before {
+ content: "\f0fd";
+}
+.fa-plus-square:before {
+ content: "\f0fe";
+}
+.fa-angle-double-left:before {
+ content: "\f100";
+}
+.fa-angle-double-right:before {
+ content: "\f101";
+}
+.fa-angle-double-up:before {
+ content: "\f102";
+}
+.fa-angle-double-down:before {
+ content: "\f103";
+}
+.fa-angle-left:before {
+ content: "\f104";
+}
+.fa-angle-right:before {
+ content: "\f105";
+}
+.fa-angle-up:before {
+ content: "\f106";
+}
+.fa-angle-down:before {
+ content: "\f107";
+}
+.fa-desktop:before {
+ content: "\f108";
+}
+.fa-laptop:before {
+ content: "\f109";
+}
+.fa-tablet:before {
+ content: "\f10a";
+}
+.fa-mobile-phone:before,
+.fa-mobile:before {
+ content: "\f10b";
+}
+.fa-circle-o:before {
+ content: "\f10c";
+}
+.fa-quote-left:before {
+ content: "\f10d";
+}
+.fa-quote-right:before {
+ content: "\f10e";
+}
+.fa-spinner:before {
+ content: "\f110";
+}
+.fa-circle:before {
+ content: "\f111";
+}
+.fa-mail-reply:before,
+.fa-reply:before {
+ content: "\f112";
+}
+.fa-github-alt:before {
+ content: "\f113";
+}
+.fa-folder-o:before {
+ content: "\f114";
+}
+.fa-folder-open-o:before {
+ content: "\f115";
+}
+.fa-smile-o:before {
+ content: "\f118";
+}
+.fa-frown-o:before {
+ content: "\f119";
+}
+.fa-meh-o:before {
+ content: "\f11a";
+}
+.fa-gamepad:before {
+ content: "\f11b";
+}
+.fa-keyboard-o:before {
+ content: "\f11c";
+}
+.fa-flag-o:before {
+ content: "\f11d";
+}
+.fa-flag-checkered:before {
+ content: "\f11e";
+}
+.fa-terminal:before {
+ content: "\f120";
+}
+.fa-code:before {
+ content: "\f121";
+}
+.fa-mail-reply-all:before,
+.fa-reply-all:before {
+ content: "\f122";
+}
+.fa-star-half-empty:before,
+.fa-star-half-full:before,
+.fa-star-half-o:before {
+ content: "\f123";
+}
+.fa-location-arrow:before {
+ content: "\f124";
+}
+.fa-crop:before {
+ content: "\f125";
+}
+.fa-code-fork:before {
+ content: "\f126";
+}
+.fa-unlink:before,
+.fa-chain-broken:before {
+ content: "\f127";
+}
+.fa-question:before {
+ content: "\f128";
+}
+.fa-info:before {
+ content: "\f129";
+}
+.fa-exclamation:before {
+ content: "\f12a";
+}
+.fa-superscript:before {
+ content: "\f12b";
+}
+.fa-subscript:before {
+ content: "\f12c";
+}
+.fa-eraser:before {
+ content: "\f12d";
+}
+.fa-puzzle-piece:before {
+ content: "\f12e";
+}
+.fa-microphone:before {
+ content: "\f130";
+}
+.fa-microphone-slash:before {
+ content: "\f131";
+}
+.fa-shield:before {
+ content: "\f132";
+}
+.fa-calendar-o:before {
+ content: "\f133";
+}
+.fa-fire-extinguisher:before {
+ content: "\f134";
+}
+.fa-rocket:before {
+ content: "\f135";
+}
+.fa-maxcdn:before {
+ content: "\f136";
+}
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+ content: "\f137";
+}
+.fa-chevron-circle-right:before {
+ content: "\f138";
+}
+.fa-chevron-circle-up:before {
+ content: "\f139";
+}
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+ content: "\f13a";
+}
+.fa-html5:before {
+ content: "\f13b";
+}
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+ content: "\f13c";
+}
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+ content: "\f13d";
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+.fa-unlock-alt:before {
+ content: "\f13e";
+}
+.fa-bullseye:before {
+ content: "\f140";
+}
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+ content: "\f141";
+}
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+ content: "\f142";
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+ content: "\f143";
+}
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+ content: "\f144";
+}
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+ content: "\f145";
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+.fa-minus-square:before {
+ content: "\f146";
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+ content: "\f147";
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+.fa-level-up:before {
+ content: "\f148";
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+ content: "\f149";
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+ content: "\f14a";
+}
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+ content: "\f14b";
+}
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+ content: "\f14c";
+}
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+ content: "\f14d";
+}
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+ content: "\f14e";
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+ content: "\f150";
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+ content: "\f151";
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+ content: "\f152";
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+ content: "\f153";
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+ content: "\f154";
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+ content: "\f155";
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+ content: "\f156";
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+ content: "\f157";
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+ content: "\f158";
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+.fa-won:before,
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+ content: "\f159";
+}
+.fa-bitcoin:before,
+.fa-btc:before {
+ content: "\f15a";
+}
+.fa-file:before {
+ content: "\f15b";
+}
+.fa-file-text:before {
+ content: "\f15c";
+}
+.fa-sort-alpha-asc:before {
+ content: "\f15d";
+}
+.fa-sort-alpha-desc:before {
+ content: "\f15e";
+}
+.fa-sort-amount-asc:before {
+ content: "\f160";
+}
+.fa-sort-amount-desc:before {
+ content: "\f161";
+}
+.fa-sort-numeric-asc:before {
+ content: "\f162";
+}
+.fa-sort-numeric-desc:before {
+ content: "\f163";
+}
+.fa-thumbs-up:before {
+ content: "\f164";
+}
+.fa-thumbs-down:before {
+ content: "\f165";
+}
+.fa-youtube-square:before {
+ content: "\f166";
+}
+.fa-youtube:before {
+ content: "\f167";
+}
+.fa-xing:before {
+ content: "\f168";
+}
+.fa-xing-square:before {
+ content: "\f169";
+}
+.fa-youtube-play:before {
+ content: "\f16a";
+}
+.fa-dropbox:before {
+ content: "\f16b";
+}
+.fa-stack-overflow:before {
+ content: "\f16c";
+}
+.fa-instagram:before {
+ content: "\f16d";
+}
+.fa-flickr:before {
+ content: "\f16e";
+}
+.fa-adn:before {
+ content: "\f170";
+}
+.fa-bitbucket:before {
+ content: "\f171";
+}
+.fa-bitbucket-square:before {
+ content: "\f172";
+}
+.fa-tumblr:before {
+ content: "\f173";
+}
+.fa-tumblr-square:before {
+ content: "\f174";
+}
+.fa-long-arrow-down:before {
+ content: "\f175";
+}
+.fa-long-arrow-up:before {
+ content: "\f176";
+}
+.fa-long-arrow-left:before {
+ content: "\f177";
+}
+.fa-long-arrow-right:before {
+ content: "\f178";
+}
+.fa-apple:before {
+ content: "\f179";
+}
+.fa-windows:before {
+ content: "\f17a";
+}
+.fa-android:before {
+ content: "\f17b";
+}
+.fa-linux:before {
+ content: "\f17c";
+}
+.fa-dribbble:before {
+ content: "\f17d";
+}
+.fa-skype:before {
+ content: "\f17e";
+}
+.fa-foursquare:before {
+ content: "\f180";
+}
+.fa-trello:before {
+ content: "\f181";
+}
+.fa-female:before {
+ content: "\f182";
+}
+.fa-male:before {
+ content: "\f183";
+}
+.fa-gittip:before {
+ content: "\f184";
+}
+.fa-sun-o:before {
+ content: "\f185";
+}
+.fa-moon-o:before {
+ content: "\f186";
+}
+.fa-archive:before {
+ content: "\f187";
+}
+.fa-bug:before {
+ content: "\f188";
+}
+.fa-vk:before {
+ content: "\f189";
+}
+.fa-weibo:before {
+ content: "\f18a";
+}
+.fa-renren:before {
+ content: "\f18b";
+}
+.fa-pagelines:before {
+ content: "\f18c";
+}
+.fa-stack-exchange:before {
+ content: "\f18d";
+}
+.fa-arrow-circle-o-right:before {
+ content: "\f18e";
+}
+.fa-arrow-circle-o-left:before {
+ content: "\f190";
+}
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+.fa-caret-square-o-left:before {
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+}
+.fa-dot-circle-o:before {
+ content: "\f192";
+}
+.fa-wheelchair:before {
+ content: "\f193";
+}
+.fa-vimeo-square:before {
+ content: "\f194";
+}
+.fa-turkish-lira:before,
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+ content: "\f195";
+}
+.fa-plus-square-o:before {
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+}
+.fa-space-shuttle:before {
+ content: "\f197";
+}
+.fa-slack:before {
+ content: "\f198";
+}
+.fa-envelope-square:before {
+ content: "\f199";
+}
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+ content: "\f19a";
+}
+.fa-openid:before {
+ content: "\f19b";
+}
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+ content: "\f19c";
+}
+.fa-mortar-board:before,
+.fa-graduation-cap:before {
+ content: "\f19d";
+}
+.fa-yahoo:before {
+ content: "\f19e";
+}
+.fa-google:before {
+ content: "\f1a0";
+}
+.fa-reddit:before {
+ content: "\f1a1";
+}
+.fa-reddit-square:before {
+ content: "\f1a2";
+}
+.fa-stumbleupon-circle:before {
+ content: "\f1a3";
+}
+.fa-stumbleupon:before {
+ content: "\f1a4";
+}
+.fa-delicious:before {
+ content: "\f1a5";
+}
+.fa-digg:before {
+ content: "\f1a6";
+}
+.fa-pied-piper-square:before,
+.fa-pied-piper:before {
+ content: "\f1a7";
+}
+.fa-pied-piper-alt:before {
+ content: "\f1a8";
+}
+.fa-drupal:before {
+ content: "\f1a9";
+}
+.fa-joomla:before {
+ content: "\f1aa";
+}
+.fa-language:before {
+ content: "\f1ab";
+}
+.fa-fax:before {
+ content: "\f1ac";
+}
+.fa-building:before {
+ content: "\f1ad";
+}
+.fa-child:before {
+ content: "\f1ae";
+}
+.fa-paw:before {
+ content: "\f1b0";
+}
+.fa-spoon:before {
+ content: "\f1b1";
+}
+.fa-cube:before {
+ content: "\f1b2";
+}
+.fa-cubes:before {
+ content: "\f1b3";
+}
+.fa-behance:before {
+ content: "\f1b4";
+}
+.fa-behance-square:before {
+ content: "\f1b5";
+}
+.fa-steam:before {
+ content: "\f1b6";
+}
+.fa-steam-square:before {
+ content: "\f1b7";
+}
+.fa-recycle:before {
+ content: "\f1b8";
+}
+.fa-automobile:before,
+.fa-car:before {
+ content: "\f1b9";
+}
+.fa-cab:before,
+.fa-taxi:before {
+ content: "\f1ba";
+}
+.fa-tree:before {
+ content: "\f1bb";
+}
+.fa-spotify:before {
+ content: "\f1bc";
+}
+.fa-deviantart:before {
+ content: "\f1bd";
+}
+.fa-soundcloud:before {
+ content: "\f1be";
+}
+.fa-database:before {
+ content: "\f1c0";
+}
+.fa-file-pdf-o:before {
+ content: "\f1c1";
+}
+.fa-file-word-o:before {
+ content: "\f1c2";
+}
+.fa-file-excel-o:before {
+ content: "\f1c3";
+}
+.fa-file-powerpoint-o:before {
+ content: "\f1c4";
+}
+.fa-file-photo-o:before,
+.fa-file-picture-o:before,
+.fa-file-image-o:before {
+ content: "\f1c5";
+}
+.fa-file-zip-o:before,
+.fa-file-archive-o:before {
+ content: "\f1c6";
+}
+.fa-file-sound-o:before,
+.fa-file-audio-o:before {
+ content: "\f1c7";
+}
+.fa-file-movie-o:before,
+.fa-file-video-o:before {
+ content: "\f1c8";
+}
+.fa-file-code-o:before {
+ content: "\f1c9";
+}
+.fa-vine:before {
+ content: "\f1ca";
+}
+.fa-codepen:before {
+ content: "\f1cb";
+}
+.fa-jsfiddle:before {
+ content: "\f1cc";
+}
+.fa-life-bouy:before,
+.fa-life-saver:before,
+.fa-support:before,
+.fa-life-ring:before {
+ content: "\f1cd";
+}
+.fa-circle-o-notch:before {
+ content: "\f1ce";
+}
+.fa-ra:before,
+.fa-rebel:before {
+ content: "\f1d0";
+}
+.fa-ge:before,
+.fa-empire:before {
+ content: "\f1d1";
+}
+.fa-git-square:before {
+ content: "\f1d2";
+}
+.fa-git:before {
+ content: "\f1d3";
+}
+.fa-hacker-news:before {
+ content: "\f1d4";
+}
+.fa-tencent-weibo:before {
+ content: "\f1d5";
+}
+.fa-qq:before {
+ content: "\f1d6";
+}
+.fa-wechat:before,
+.fa-weixin:before {
+ content: "\f1d7";
+}
+.fa-send:before,
+.fa-paper-plane:before {
+ content: "\f1d8";
+}
+.fa-send-o:before,
+.fa-paper-plane-o:before {
+ content: "\f1d9";
+}
+.fa-history:before {
+ content: "\f1da";
+}
+.fa-circle-thin:before {
+ content: "\f1db";
+}
+.fa-header:before {
+ content: "\f1dc";
+}
+.fa-paragraph:before {
+ content: "\f1dd";
+}
+.fa-sliders:before {
+ content: "\f1de";
+}
+.fa-share-alt:before {
+ content: "\f1e0";
+}
+.fa-share-alt-square:before {
+ content: "\f1e1";
+}
+.fa-bomb:before {
+ content: "\f1e2";
+}
--- /dev/null
+// NAV LIST
+// --------
+
+.nav-list {
+ padding-left: 15px;
+ padding-right: 15px;
+ margin-bottom: 0;
+}
+.nav-list > li > a,
+.nav-list .nav-header {
+ margin-left: -15px;
+ margin-right: -15px;
+ text-shadow: 0 1px 0 rgba(255,255,255,.5);
+}
+.nav-list > li > a {
+ padding: 3px 15px;
+}
+.nav-list > .active > a,
+.nav-list > .active > a:hover,
+.nav-list > .active > a:focus {
+ color: white;
+ text-shadow: 0 -1px 0 rgba(0,0,0,.2);
+ background-color: rgb(66, 139, 202);
+}
+
+.spaced-out li {
+ padding-bottom: 1em;
+}
+
+.inside-list ul {
+ list-style-position: inside;
+ padding-left: 0;
+}
\ No newline at end of file
--- /dev/null
+{
+ "name":"GATK / exome PE fastq to snp",
+ "components":{
+ "extract-reference":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
+ "script":"file-select",
+ "script_parameters":{
+ "names":[
+ "human_g1k_v37.fasta.gz",
+ "human_g1k_v37.fasta.fai.gz",
+ "human_g1k_v37.dict.gz"
+ ],
+ "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
+ },
+ "output_name":false
+ },
+ "bwa-index":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
+ "script":"bwa-index",
+ "script_parameters":{
+ "input":{
+ "output_of":"extract-reference"
+ },
+ "bwa_tbz":{
+ "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+ "required":true
+ }
+ },
+ "output_name":false
+ },
+ "bwa-aln":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
+ "script":"bwa-aln",
+ "script_parameters":{
+ "input":{
+ "dataclass":"Collection",
+ "required":"true"
+ },
+ "reference_index":{
+ "output_of":"bwa-index"
+ },
+ "samtools_tgz":{
+ "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
+ "required":true
+ },
+ "bwa_tbz":{
+ "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+ "required":true
+ }
+ },
+ "runtime_constraints":{
+ "max_tasks_per_node":1
+ },
+ "output_name":false
+ },
+ "picard-gatk2-prep":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
+ "script":"picard-gatk2-prep",
+ "script_parameters":{
+ "input":{
+ "output_of":"bwa-aln"
+ },
+ "reference":{
+ "output_of":"extract-reference"
+ },
+ "picard_zip":{
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
+ }
+ },
+ "runtime_constraints":{
+ "max_tasks_per_node":1
+ },
+ "output_name":false
+ },
+ "GATK2-realign":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
+ "script":"GATK2-realign",
+ "script_parameters":{
+ "input":{
+ "output_of":"picard-gatk2-prep"
+ },
+ "gatk_bundle":{
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
+ },
+ "picard_zip":{
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
+ },
+ "gatk_tbz":{
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
+ },
+ "regions":{
+ "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
+ },
+ "region_padding":{
+ "value":10
+ }
+ },
+ "runtime_constraints":{
+ "max_tasks_per_node":2
+ },
+ "output_name":false
+ },
+ "GATK2-bqsr":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
+ "script":"GATK2-bqsr",
+ "script_parameters":{
+ "input":{
+ "output_of":"GATK2-realign"
+ },
+ "gatk_bundle":{
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
+ },
+ "picard_zip":{
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
+ },
+ "gatk_tbz":{
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
+ }
+ },
+ "output_name":false
+ },
+ "GATK2-merge-call":{
+ "repository":"arvados",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
+ "script":"GATK2-merge-call",
+ "script_parameters":{
+ "input":{
+ "output_of":"GATK2-bqsr"
+ },
+ "gatk_bundle":{
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
+ },
+ "picard_zip":{
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
+ },
+ "gatk_tbz":{
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
+ },
+ "regions":{
+ "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
+ },
+ "region_padding":{
+ "value":10
+ },
+ "GATK2_UnifiedGenotyper_args":{
+ "default":[
+ "-stand_call_conf",
+ "30.0",
+ "-stand_emit_conf",
+ "30.0",
+ "-dcov",
+ "200"
+ ]
+ }
+ },
+ "output_name":"Variant calls from UnifiedGenotyper"
+ }
+ }
+}
--- /dev/null
+{
+ "name":"Real Time Genomics / PE fastq to snp",
+ "components":{
+ "extract_reference":{
+ "script":"file-select",
+ "script_parameters":{
+ "names":[
+ "human_g1k_v37.fasta.gz"
+ ],
+ "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
+ },
+ "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2"
+ },
+ "reformat_reference":{
+ "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
+ "script":"rtg-fasta2sdf",
+ "script_parameters":{
+ "input":{
+ "output_of":"extract_reference"
+ },
+ "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
+ "rtg_license":{
+ "optional":false
+ }
+ }
+ },
+ "reformat_reads":{
+ "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
+ "script":"rtg-fastq2sdf",
+ "script_parameters":{
+ "input":{
+ "optional":false
+ },
+ "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
+ "rtg_license":{
+ "optional":false
+ }
+ }
+ },
+ "map_reads":{
+ "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
+ "script":"rtg-map",
+ "script_parameters":{
+ "input":{
+ "output_of":"reformat_reads"
+ },
+ "reference":{
+ "output_of":"reformat_reference"
+ },
+ "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
+ "rtg_license":{
+ "optional":false
+ }
+ },
+ "runtime_constraints":{
+ "max_tasks_per_node":1
+ }
+ },
+ "report_snp":{
+ "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
+ "script":"rtg-snp",
+ "script_parameters":{
+ "input":{
+ "output_of":"map_reads"
+ },
+ "reference":{
+ "output_of":"reformat_reference"
+ },
+ "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
+ "rtg_license":{
+ "optional":false
+ }
+ }
+ }
+ }
+}
--- /dev/null
+#!/usr/bin/env ruby
+
+abort 'Error: Ruby >= 1.9.3 required.' if RUBY_VERSION < '1.9.3'
+
+require 'arvados'
+
+arv = Arvados.new(api_version: 'v1')
+arv.node.list[:items].each do |node|
+ if node[:crunch_worker_state] != 'down'
+ ping_age = (Time.now - Time.parse(node[:last_ping_at])).to_i rescue -1
+ puts "#{node[:uuid]} #{node[:crunch_worker_state]} #{ping_age}"
+ end
+end
--- /dev/null
+<?xml version="1.0" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd" >
+<svg xmlns="http://www.w3.org/2000/svg">
+<metadata></metadata>
+<defs>
+<font id="fontawesomeregular" horiz-adv-x="1536" >
+<font-face units-per-em="1792" ascent="1536" descent="-256" />
+<missing-glyph horiz-adv-x="448" />
+<glyph unicode=" " horiz-adv-x="448" />
+<glyph unicode="	" horiz-adv-x="448" />
+<glyph unicode=" " horiz-adv-x="448" />
+<glyph unicode="¨" horiz-adv-x="1792" />
+<glyph unicode="©" horiz-adv-x="1792" />
+<glyph unicode="®" horiz-adv-x="1792" />
+<glyph unicode="´" horiz-adv-x="1792" />
+<glyph unicode="Æ" horiz-adv-x="1792" />
+<glyph unicode="Ø" horiz-adv-x="1792" />
+<glyph unicode=" " horiz-adv-x="768" />
+<glyph unicode=" " horiz-adv-x="1537" />
+<glyph unicode=" " horiz-adv-x="768" />
+<glyph unicode=" " horiz-adv-x="1537" />
+<glyph unicode=" " horiz-adv-x="512" />
+<glyph unicode=" " horiz-adv-x="384" />
+<glyph unicode=" " horiz-adv-x="256" />
+<glyph unicode=" " horiz-adv-x="256" />
+<glyph unicode=" " horiz-adv-x="192" />
+<glyph unicode=" " horiz-adv-x="307" />
+<glyph unicode=" " horiz-adv-x="85" />
+<glyph unicode=" " horiz-adv-x="307" />
+<glyph unicode=" " horiz-adv-x="384" />
+<glyph unicode="™" horiz-adv-x="1792" />
+<glyph unicode="∞" horiz-adv-x="1792" />
+<glyph unicode="≠" horiz-adv-x="1792" />
+<glyph unicode="◼" horiz-adv-x="500" d="M0 0z" />
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+</font>
+</defs></svg>
\ No newline at end of file
--- /dev/null
+#! /usr/bin/env python
+
+# gen_api_method_docs.py
+#
+# Generate docs for Arvados methods.
+#
+# This script will retrieve the discovery document at
+# https://localhost:9900/discovery/v1/apis/arvados/v1/rest
+# and will generate Textile documentation files in the current
+# directory.
+
+import argparse
+import pprint
+import re
+import requests
+import os
+import sys #debugging
+
+p = argparse.ArgumentParser(description='Generate Arvados API method documentation.')
+
+p.add_argument('--host',
+ type=str,
+ default='localhost',
+ help="The hostname or IP address of the API server")
+
+p.add_argument('--port',
+ type=int,
+ default=9900,
+ help="The port of the API server")
+
+p.add_argument('--output-dir',
+ type=str,
+ default='.',
+ help="Directory in which to write output files.")
+
+args = p.parse_args()
+
+api_url = 'https://{host}:{port}/discovery/v1/apis/arvados/v1/rest'.format(**vars(args))
+
+r = requests.get(api_url, verify=False)
+if r.status_code != 200:
+ raise Exception('Bad status code %d: %s' % (r.status_code, r.text))
+
+if 'application/json' not in r.headers.get('content-type', ''):
+ raise Exception('Unexpected content type: %s: %s' %
+ (r.headers.get('content-type', ''), r.text))
+
+api = r.json()
+
+resource_num = 0
+for resource in sorted(api[u'resources']):
+ resource_num = resource_num + 1
+ out_fname = os.path.join(args.output_dir, resource + '.textile')
+ if os.path.exists(out_fname):
+ backup_name = out_fname + '.old'
+ try:
+ os.rename(out_fname, backup_name)
+ except OSError as e:
+ print "WARNING: could not back up {1} as {2}: {3}".format(
+ out_fname, backup_name, e)
+ outf = open(out_fname, 'w')
+ outf.write(
+"""---
+navsection: api
+navmenu: API Methods
+title: "{resource}"
+navorder: {resource_num}
+---
+
+h1. {resource}
+
+Required arguments are displayed in %{{background:#ccffcc}}green%.
+
+""".format(resource_num=resource_num, resource=resource))
+
+ methods = api['resources'][resource]['methods']
+ for method in sorted(methods.keys()):
+ methodinfo = methods[method]
+ outf.write(
+"""
+h2. {method}
+
+{description}
+
+Arguments:
+
+table(table table-bordered table-condensed).
+|_. Argument |_. Type |_. Description |_. Location |_. Example |
+""".format(
+ method=method, description=methodinfo['description']))
+
+ required = []
+ notrequired = []
+ for param, paraminfo in methodinfo['parameters'].iteritems():
+ paraminfo.setdefault(u'description', '')
+ paraminfo.setdefault(u'location', '')
+ limit = ''
+ if paraminfo.get('minimum', '') or paraminfo.get('maximum', ''):
+ limit = "range {0}-{1}".format(
+ paraminfo.get('minimum', ''),
+ paraminfo.get('maximum', 'unlimited'))
+ if paraminfo.get('default', ''):
+ if limit:
+ limit = limit + '; '
+ limit = limit + 'default %d' % paraminfo['default']
+ if limit:
+ paraminfo['type'] = '{0} ({1})'.format(
+ paraminfo['type'], limit)
+
+ row = "|{param}|{type}|{description}|{location}||\n".format(
+ param=param, **paraminfo)
+ if paraminfo.get('required', False):
+ required.append(row)
+ else:
+ notrequired.append(row)
+
+ for row in sorted(required):
+ outf.write("{background:#ccffcc}." + row)
+ for row in sorted(notrequired):
+ outf.write(row)
+
+ # pprint.pprint(methodinfo)
+
+ outf.close()
+ print "wrote ", out_fname
+
+
--- /dev/null
+#! /usr/bin/env python
+
+# gen_api_schema_docs.py
+#
+# Generate Textile documentation pages for Arvados schema resources.
+
+import requests
+import re
+import os
+
+r = requests.get('https://localhost:9900/arvados/v1/schema',
+ verify=False)
+if r.status_code != 200:
+ raise Exception('Bad status code %d: %s' % (r.status_code, r.text))
+
+if 'application/json' not in r.headers.get('content-type', ''):
+ raise Exception('Unexpected content type: %s: %s' %
+ (r.headers.get('content-type', ''), r.text))
+
+schema = r.json()
+navorder = 0
+for resource in sorted(schema.keys()):
+ navorder = navorder + 1
+ properties = schema[resource]
+ res_api_endpoint = re.sub(r'([a-z])([A-Z])', r'\1_\2', resource).lower()
+ outfile = "{}.textile".format(resource)
+ if os.path.exists(outfile):
+ outfile = "{}_new.textile".format(resource)
+ print outfile, "..."
+ with open(outfile, "w") as f:
+ f.write("""---
+layout: default
+navsection: api
+navmenu: Schema
+title: {resource}
+---
+
+h1. {resource}
+
+A **{resource}** represents...
+
+h2. Methods
+
+ See "REST methods for working with Arvados resources":{{{{site.baseurl}}}}/api/methods.html
+
+API endpoint base: @https://{{{{ site.arvados_api_host }}}}/arvados/v1/{res_api_endpoint}@
+
+h2. Creation
+
+h3. Prerequisites
+
+Prerequisites for creating a {resource}.
+
+h3. Side effects
+
+Side effects of creating a {resource}.
+
+h2. Resources
+
+Each {resource} has, in addition to the usual "attributes of Arvados resources":resources.html:
+
+table(table table-bordered table-condensed).
+|_. Attribute|_. Type|_. Description|_. Example|
+""".format(
+ resource=resource,
+ navorder=navorder,
+ res_api_endpoint=res_api_endpoint))
+
+ for prop in properties:
+ if prop not in ['id', 'uuid', 'href', 'kind', 'etag', 'self_link',
+ 'owner_uuid', 'created_at',
+ 'modified_by_client_uuid',
+ 'modified_by_user_uuid',
+ 'modified_at']:
+ f.write('|{name}|{type}|||\n'.format(**prop))
+
--- /dev/null
+---
+layout: default
+no_nav_left: true
+navsection: top
+title: Arvados | Documentation
+...
+
+<div class="jumbotron">
+ <div class="container">
+ <div class="row">
+ <div class="col-sm-6">
+ <h1>ARVADOS</h1>
+ <p>manuals, guides, and references</p>
+ </div>
+ <div class="col-sm-6">
+ <img src="images/dax-reading-book.png" style="max-height: 10em" alt="Dax reading a book" />
+ </div>
+ </div>
+ </div>
+</div>
+
+<div class="container-fluid">
+ <div class="row">
+ <div class="col-sm-5">
+ <p>This site contains documentation for the <a href="https://arvados.org/">Arvados platform</a>. The documentation is being developed as part of the open source project. It is a work in progress that has just gotten started. You can get involved by <a href="https://arvados.org/projects/arvados/wiki/Documentation">joining the documentation effort</a>.
+ </div>
+ <div class="col-sm-7" style="border-left: solid; border-width: 1px">
+ <p>
+ <a href="{{ site.baseurl }}/user/index.html">User Guide</a> — How to manage data and do analysis with Arvados.
+ </p>
+ <p>
+ <a href="{{ site.baseurl }}/sdk/index.html">SDK Reference</a> — Details about the accessing Arvados from various programming languages.
+ </p>
+ <p>
+ <a href="{{ site.baseurl }}/api/index.html">API Reference</a> — Details about the the Arvados REST API.
+ </p>
+ <p>
+ <a href="{{ site.baseurl }}/admin/index.html">Admin Guide</a> — How to administer an Arvados system.
+ </p>
+ <p>
+ <a href="{{ site.baseurl }}/install/index.html">Install Guide</a> — How to install Arvados on a cloud platform.
+ </p>
+ </div>
+ </div>
+</div>
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install client libraries
+
+...
+
+The "SDK Reference":{{site.baseurl}}/sdk/index.html page has installation instructions for each of the SDKs.
+
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Add an Arvados repository
+
+...
+
+Next, we're going to use the Arvados CLI tools on the <strong>shell server</strong> to create a few Arvados objects. These objects set up a hosted clone of the arvados repository on this cluster.
+
+This will be readable by the "All users" group, and therefore by every active user. This makes it possible for users to run the bundled Crunch scripts by specifying @"script_version":"master","repository":"arvados"@ rather than pulling the Arvados source tree into their own repositories.
+
+<notextile>
+<pre><code>~$ <span class="userinput">prefix=`arv --format=uuid user current | cut -d- -f1`</span>
+~$ <span class="userinput">echo "Site prefix is '$prefix'"</span>
+~$ <span class="userinput">all_users_group_uuid="$prefix-j7d0g-fffffffffffffff"</span>
+~$ <span class="userinput">repo_uuid=`arv --format=uuid repository create --repository '{"name":"arvados"}'`</span>
+~$ <span class="userinput">echo "Arvados repository uuid is '$repo_uuid'"</span>
+~$ <span class="userinput">read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"</span>
+<span class="userinput">{
+ "tail_uuid":"$all_users_group_uuid",
+ "head_uuid":"$repo_uuid",
+ "link_class":"permission",
+ "name":"can_read"
+}
+EOF</span>
+</code></pre></notextile>
+
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Installation overview
+...
+
+Arvados can be installed in multiple ways. Arvados does not depend on any particular cloud operating stack. Arvados runs on one or more GNU/Linux system(s). Arvados is being developed on Debian and Ubuntu GNU/Linux.
+
+h2. Quick installation
+
+Make sure curl and docker are installed on your system. Then, as a user in the docker group, execute
+
+<notextile>
+<pre><code>~$ <span class="userinput">\curl -sSL http://get.arvados.org | bash</span>
+</code></pre></notextile>
+
+This command will download the latest copy of the Arvados docker images. It also gets the arvdock command and saves it in the current working directory. It then uses arvdock to spin up Arvados. Depending on the speed of your internet connection, it can take a while to download the Arvados docker images.
+
+This installation method assumes your web browser and the Arvados docker containers run on the same host.
+
+If you prefer, you can also download the installation script and inspect it before running it. The @http://get.arvados.org@ url redirects to <a href="https://raw.githubusercontent.com/curoverse/arvados-dev/master/install/easy-docker-install.sh">https://raw.githubusercontent.com/curoverse/arvados-dev/master/install/easy-docker-install.sh</a>, which is the installation script.
+
+h2. Installation from source
+
+It is also possible to build the Arvados docker images from source. The instructions are available "here":install-docker.html.
+
+For production use or evaluation at scale a "Manual Installation":install-manual-overview.html is more appropriate. This installation method assumes you have a number of (virtual) machines at your disposal to install the different Arvados components onto.
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install the API server
+...
+
+This installation guide assumes you are on a 64 bit Debian or Ubuntu system.
+
+h2. Install prerequisites
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo apt-get install \
+ bison build-essential gettext libcurl3 libcurl3-gnutls \
+ libcurl4-openssl-dev libpcre3-dev libpq-dev libreadline-dev \
+ libssl-dev libxslt1.1 postgresql sudo wget zlib1g-dev
+</span></code></pre></notextile>
+
+Also make sure you have "Ruby and bundler":install-manual-prerequisites-ruby.html installed.
+
+h2. Download the source tree
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
+</code></pre></notextile>
+
+See also: "Downloading the source code":https://arvados.org/projects/arvados/wiki/Download on the Arvados wiki.
+
+The API server is in @services/api@ in the source tree.
+
+h2. Install gem dependencies
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd arvados/services/api</span>
+~/arvados/services/api$ <span class="userinput">bundle install</span>
+</code></pre></notextile>
+
+h2. Choose your environment
+
+The API server can be run in @development@ or in @production@ mode. Unless this installation is going to be used for development on the Arvados API server itself, you should run it in @production@ mode.
+
+Copy the example environment file for your environment. For example, if you choose @production@:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">cp -i config/environments/production.rb.example config/environments/production.rb</span>
+</code></pre></notextile>
+
+h2. Configure the API server
+
+First, copy the example configuration file:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">cp -i config/application.yml.example config/application.yml</span>
+</code></pre></notextile>
+
+The API server reads the @config/application.yml@ file, as well as the @config/application.defaults.yml@ file. Values in @config/application.yml@ take precedence over the defaults that are defined in @config/application.defaults.yml@. The @config/application.yml.example@ file is not read by the API server and is provided for installation convenience, only.
+
+Consult @config/application.default.yml@ for a full list of configuration options. Always put your local configuration in @config/application.yml@, never edit @config/application.default.yml@.
+
+h3(#uuid_prefix). uuid_prefix
+
+It is recommended to explicitly define your @uuid_prefix@ in @config/application.yml@, by setting the 'uuid_prefix' field in the section for your environment.
+
+h3(#git_repositories_dir). git_repositories_dir
+
+This field defaults to @/var/lib/arvados/git@. You can override the value by defining it in @config/application.yml@.
+
+Make sure a clone of the arvados repository exists in @git_repositories_dir@.
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">sudo mkdir -p /var/lib/arvados/git</span>
+~/arvados/services/api$ <span class="userinput">sudo git clone --bare ../../.git /var/lib/arvados/git/arvados.git</span>
+</code></pre></notextile>
+
+h3. secret_token
+
+Generate a new secret token for signing cookies:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">rake secret</span>
+zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
+</code></pre></notextile>
+
+Then put that value in the @secret_token@ field.
+
+h3. blob_signing_key
+
+If you want access control on your "Keepstore":install-keepstore.html server(s), you should set @blob_signing_key@ to the same value as the permission key you provide to your Keepstore daemon(s).
+
+h3. workbench_address
+
+Fill in the url of your workbench application in @workbench_address@, for example
+
+ https://workbench.@prefix_uuid@.your.domain
+
+h3. other options
+
+Consult @application.default.yml@ for a full list of configuration options. Always put your local configuration in @application.yml@ instead of editing @application.default.yml@.
+
+h2. Set up the database
+
+Generate a new database password. Nobody ever needs to memorize it or type it, so we'll make a strong one:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">ruby -e 'puts rand(2**128).to_s(36)'</span>
+6gqa1vu492idd7yca9tfandj3
+</code></pre></notextile>
+
+Create a new database user with permission to create its own databases.
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">sudo -u postgres createuser --createdb --encrypted --pwprompt arvados</span>
+[sudo] password for <b>you</b>: <span class="userinput">yourpassword</span>
+Enter password for new role: <span class="userinput">paste-password-you-generated</span>
+Enter it again: <span class="userinput">paste-password-again</span>
+Shall the new role be a superuser? (y/n) <span class="userinput">n</span>
+Shall the new role be allowed to create more new roles? (y/n) <span class="userinput">n</span>
+</code></pre></notextile>
+
+Configure API server to connect to your database by creating and updating @config/database.yml@. Replace the @xxxxxxxx@ database password placeholders with the new password you generated above.
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">cp -i config/database.yml.sample config/database.yml</span>
+~/arvados/services/api$ <span class="userinput">edit config/database.yml</span>
+</code></pre></notextile>
+
+Create and initialize the database. If you are planning a production system, choose the @production@ rails environment, otherwise use @development@.
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">RAILS_ENV=production bundle exec rake db:setup</span>
+</code></pre></notextile>
+
+Alternatively, if the database user you intend to use for the API server is not allowed to create new databases, you can create the database first and then populate it with rake. Be sure to adjust the database name if you are using the @development@ environment. This sequence of commands is functionally equivalent to the rake db:setup command above.
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">su postgres createdb arvados_production -E UTF8 -O arvados</span>
+~/arvados/services/api$ <span class="userinput">RAILS_ENV=production bundle exec rake db:structure:load</span>
+~/arvados/services/api$ <span class="userinput">RAILS_ENV=production bundle exec rake db:seed</span>
+</code></pre></notextile>
+
+<div class="alert alert-block alert-info">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <h4>Note!</h4>
+You can safely ignore the following error message you may see when loading the database structure:
+<notextile>
+<pre><code>ERROR: must be owner of extension plpgsql</code></pre></notextile>
+</div>
+
+h2(#omniauth). Set up omniauth
+
+First copy the omniauth configuration file:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">cp -i config/initializers/omniauth.rb.example config/initializers/omniauth.rb
+</code></pre></notextile>
+
+Edit @config/initializers/omniauth.rb@ to configure the SSO server for authentication. @APP_ID@ and @APP_SECRET@ correspond to the @app_id@ and @app_secret@ set in "Create arvados-server client for Single Sign On (SSO)":install-sso.html#client and @CUSTOM_PROVIDER_URL@ is the address of your SSO server.
+
+<notextile>
+<pre><code>APP_ID = 'arvados-server'
+APP_SECRET = 'xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx'
+CUSTOM_PROVIDER_URL = 'https://sso.example.com/'
+</code></pre>
+</notextile>
+
+h2. Start the API server
+
+h3. Development environment
+
+If you plan to run in development mode, you can now run the development server this way:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">bundle exec rails server --port=3030
+</code></pre></notextile>
+
+h3. Production environment
+
+We recommend "Passenger":https://www.phusionpassenger.com/ to run the API server in production.
+
+Point it to the services/api directory in the source tree.
+
+To enable streaming so users can monitor crunch jobs in real time, make sure to add the following to your Passenger configuration:
+
+<notextile>
+<pre><code><span class="userinput">PassengerBufferResponse off</span>
+</code></pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install the Crunch dispatcher
+
+...
+
+
+
+The dispatcher normally runs on the same host/VM as the API server.
+
+h4. Perl SDK dependencies
+
+Install the Perl SDK on the controller.
+
+* See "Perl SDK":{{site.baseurl}}/sdk/perl/index.html page for details.
+
+h4. Python SDK dependencies
+
+Install the Python SDK and CLI tools on controller and all compute nodes.
+
+* See "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html page for details.
+
+h4. Likely crunch job dependencies
+
+On compute nodes:
+
+* @pip install --upgrade pyvcf@
+
+h4. Crunch user account
+
+On compute nodes and controller:
+
+* @adduser crunch@
+
+The crunch user should have the same UID, GID, and home directory on all compute nodes and on the controller.
+
+h4. Repositories
+
+Crunch scripts must be in Git repositories in the directory configured as @git_repositories_dir@/*.git (see the "API server installation":install-api-server.html#git_repositories_dir).
+
+Once you have a repository with commits -- and you have read access to the repository -- you should be able to create a new job:
+
+<pre>
+read -rd $'\000' newjob <<EOF; arv job create --job "$newjob"
+{"script_parameters":{"input":"f815ec01d5d2f11cb12874ab2ed50daa"},
+ "script_version":"master",
+ "script":"hash",
+ "repository":"arvados"}
+EOF
+</pre>
+
+Without getting this error:
+
+<pre>
+ArgumentError: Specified script_version does not resolve to a commit
+</pre>
+
+h4. Running jobs
+
+* @services/api/script/crunch-dispatch.rb@ must be running.
+* @crunch-dispatch.rb@ needs @services/crunch/crunch-job@ in its @PATH@.
+* @crunch-job@ needs @sdk/perl/lib@ and @warehouse-apps/libwarehouse-perl/lib@ in its @PERLLIB@
+* @crunch-job@ needs @ARVADOS_API_HOST@ (and, if necessary in a development environment, @ARVADOS_API_HOST_INSECURE@)
+
+Example @/var/service/arvados_crunch_dispatch/run@ script:
+
+<pre>
+#!/bin/sh
+set -e
+
+rvmexec=""
+## uncomment this line if you use rvm:
+#rvmexec="/usr/local/rvm/bin/rvm-exec 2.1.1"
+
+export PATH="$PATH":/path/to/arvados/services/crunch
+export ARVADOS_API_HOST={{ site.arvados_api_host }}
+export CRUNCH_DISPATCH_LOCKFILE=/var/lock/crunch-dispatch
+
+fuser -TERM -k $CRUNCH_DISPATCH_LOCKFILE || true
+
+## Only if your SSL cert is unverifiable:
+# export ARVADOS_API_HOST_INSECURE=yes
+
+cd /path/to/arvados/services/api
+export RAILS_ENV=production
+exec $rvmexec bundle exec ./script/crunch-dispatch.rb 2>&1
+</pre>
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Installing with Docker
+...
+
+h2. Purpose
+
+This installation method is appropriate for local testing, evaluation, and development. For production use, this method is not recommended.
+
+h2. Prerequisites
+
+# A GNU/Linux (virtual) machine
+# A working Docker installation (see "Installing Docker":https://docs.docker.com/installation/)
+
+h2. Download the source tree
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
+</code></pre></notextile>
+
+See also: "Downloading the source code":https://arvados.org/projects/arvados/wiki/Download on the Arvados wiki.
+
+h2. Building the Arvados Docker containers
+
+First of all, a suitable @config.yml@ file is needed. The easiest way to generate one based on the provided @config.yml.example@ file is to run the @build.sh@ script. If no @config.yml@ file exists, it will will prompt for a few inputs, write the @config.yml@ file, and then proceed to build all the Docker containers. If @config.yml@ exists, invoking @build.sh@ will simply build all Docker containers or update those that need to be updated.
+
+Run @build.sh@ without arguments to generate @config.yml@ and build all Docker containers (this will take a while!):
+
+<notextile>
+<pre><code>
+~$ <span class="userinput">./build.sh</span>
+Generating config.yml.
+Arvados needs to know the email address of the administrative user,
+so that when that user logs in they are automatically made an admin.
+This should be an email address associated with a Google account.
+
+Enter your Google ID email address here:
+
+...
+
+Step 7 : ADD generated/setup.sh /usr/local/bin/setup.sh
+ ---> d7c0e7fdf7ab
+Removing intermediate container f3d81180795d
+Step 8 : CMD ["/usr/bin/supervisord", "-n"]
+ ---> Running in 84c64cb9f0d5
+ ---> d6cbb5002604
+Removing intermediate container 84c64cb9f0d5
+Successfully built d6cbb5002604
+date >shell-image
+</code></pre></notextile>
+
+If all goes well, you should now have a number of docker images built:
+
+<notextile>
+<pre><code>~$ <span class="userinput">docker.io images</span>
+REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE
+arvados/shell latest d6cbb5002604 10 minutes ago 1.613 GB
+arvados/sso latest 377f1fa0108e 11 minutes ago 1.807 GB
+arvados/keep latest ade0e0d2dd00 12 minutes ago 210.8 MB
+arvados/workbench latest b0e4fb6da385 12 minutes ago 2.218 GB
+arvados/doc latest 4b64daec9454 12 minutes ago 1.524 GB
+arvados/compute latest 7f1f5f7faf54 13 minutes ago 1.862 GB
+arvados/slurm latest f5bfd1008e6b 17 minutes ago 1.573 GB
+arvados/api latest 6b93c5f5fc42 17 minutes ago 2.274 GB
+arvados/passenger latest add2d11fdf24 18 minutes ago 1.738 GB
+arvados/base latest 81eaadd0c6f5 22 minutes ago 1.463 GB
+arvados/debian 7.6 f339ce275c01 6 days ago 116.8 MB
+arvados/debian latest f339ce275c01 6 days ago 116.8 MB
+arvados/debian wheezy f339ce275c01 6 days ago 116.8 MB
+crosbymichael/skydock latest e985023521f6 3 months ago 510.7 MB
+crosbymichael/skydns next 79c99a4608ed 3 months ago 525 MB
+crosbymichael/skydns latest 1923ce648d4c 5 months ago 137.5 MB
+</code></pre></notextile>
+
+h2. Updating the Arvados Docker containers
+
+@build.sh@ takes a few optional arguments:
+
+<notextile>
+<pre><code>
+~$ <span class="userinput"> ./build.sh --help</span>
+
+usage: ./build.sh [options]
+
+Calling ./build.sh without arguments will build all Arvados docker images
+
+./build.sh options:
+ -h, --help Print this help text
+ clean Clear all build information
+ realclean clean and remove all Arvados Docker images except arvados/debian
+ deepclean realclean and remove arvados/debian, crosbymichael/skydns and
+ crosbymichael/skydns Docker images
+</code></pre></notextile>
+
+If there has been an update to the Arvados Docker building code, it is safest to rebuild the Arvados Docker images from scratch. All build information can be cleared with the 'clean' option to build.sh:
+
+<notextile>
+<pre><code>~$ <span class="userinput">./build.sh clean</span></code></pre>
+</notextile>
+
+You can also use 'realclean', which does what 'clean' does and in addition removes all Arvados Docker containers and images from your system, with the exception of the arvados/debian image.
+
+<notextile>
+<pre><code>~$ <span class="userinput">./build.sh realclean</span></code></pre>
+</notextile>
+
+Finally, the 'deepclean' option does what 'realclean' does, and also removes the arvados/debian, crosbymichael/skydns and crosbymichael/skydock images.
+
+<notextile>
+<pre><code>~$ <span class="userinput">./build.sh deepclean</span></code></pre>
+</notextile>
+
+h2. Running the Arvados Docker containers
+
+The @arvdock@ command can be used to start and stop the docker containers. It has a number of options:
+
+<notextile>
+<pre><code>
+~$ <span class="userinput">./arvdock -h</span>
+
+usage: ./arvdock (start|stop|restart|test) [options]
+
+./arvdock start/stop/restart options:
+ -d[port], --doc[=port] Documentation server (default port 9898)
+ -w[port], --workbench[=port] Workbench server (default port 9899)
+ -s[port], --sso[=port] SSO server (default port 9901)
+ -a[port], --api[=port] API server (default port 9900)
+ -c, --compute Compute nodes (starts 2)
+ -v, --vm Shell server
+ -n, --nameserver Nameserver
+ -k, --keep Keep servers
+ --ssh Enable SSH access to server containers
+ -h, --help Display this help and exit
+
+ If no options are given, the action is applied to all servers.
+
+./arvdock test [testname] [testname] ...
+ By default, all tests are run.
+</code>
+</pre>
+</notextile>
+
+The @--ssh@ option can be useful to debug issues with the Docker containers; it allows you to ssh into the running containers as the @root@ user, provided you have access to the private key that matches the public key specified in @config.yml@'s PUBLIC_KEY_PATH variable.
+
+Start the docker containers:
+
+<notextile>
+<pre><code>
+~$ <span class="userinput">./arvdock start</span>
+sso_server
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 9901:443 --name sso_server arvados/sso
+api_server
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 9900:443 --name api_server --link sso_server:sso arvados/api
+keep_server_0
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 25107:25107 --name keep_server_0 -v /tmp/tmp.aCSx8Pq6Wb:/dev/keep-0 --link api_server:api arvados/keep
+keep_server_1
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 25108:25107 --name keep_server_1 -v /tmp/tmp.m4OQ9WB73G:/dev/keep-0 --link api_server:api arvados/keep
+doc_server
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 9898:80 --name doc_server arvados/doc
+
+*****************************************************************
+You can access the Arvados documentation at http://localhost:9898
+*****************************************************************
+
+workbench_server
+Starting container:
+ /usr/bin/docker.io run -d -i -t -p 9899:80 --name workbench_server --link api_server:api arvados/workbench
+
+*****************************************************************
+You can access the Arvados workbench at http://localhost:9899
+*****************************************************************
+</code></pre></notextile>
+
+h2. Accessing workbench
+
+Point your browser to the Dockerized workbench:
+
+<notextile>
+<pre><code><span class="userinput">https://localhost:9899</span>
+</code></pre>
+</notextile>
+
+Now use the google account you specified as @API_AUTO_ADMIN_USER@ in @config.yml@ to log in.
+
+You will be prompted by your browser that you are accessing a site with an untrusted SSL certificate. This is normal; by default the Arvados Docker installation uses self-signed SSL certificates for the SSO and API servers, respectively. If you use a local SSO server in a Docker container, you will be prompted *twice*. The default is to use the Curoverse SSO server.
+
+
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install Keepproxy server
+...
+
+This installation guide assumes you are on a 64 bit Debian or Ubuntu system.
+
+The Keepproxy server is a gateway into your Keep storage. Unlike the Keepstore servers, which are only accessible on the local LAN, Keepproxy is designed to provide secure access into Keep from anywhere on the internet.
+
+By convention, we use the following hostname for the Keepproxy:
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Hostname_|
+|keep.@uuid_prefix@.your.domain|
+</div>
+
+This hostname should resolve from anywhere on the internet.
+
+h2. Install Keepproxy
+
+First add the Arvados apt repository, and then install the Keepproxy package.
+
+<notextile>
+<pre><code>~$ <span class="userinput">echo "deb http://apt.arvados.org/ wheezy main" | sudo tee /etc/apt/sources.list.d/apt.arvados.org.list</span>
+~$ <span class="userinput">sudo /usr/bin/apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7</span>
+~$ <span class="userinput">sudo /usr/bin/apt-get update</span>
+~$ <span class="userinput">sudo /usr/bin/apt-get install keepproxy</span>
+</code></pre>
+</notextile>
+
+Verify that Keepproxy is functional:
+
+<notextile>
+<pre><code>~$ <span class="userinput">keepproxy -h</span>
+Usage of default:
+ -default-replicas=2: Default number of replicas to write if not specified by the client.
+ -listen=":25107": Interface on which to listen for requests, in the format ipaddr:port. e.g. -listen=10.0.1.24:8000. Use -listen=:port to listen on all network interfaces.
+ -no-get=false: If set, disable GET operations
+ -no-put=false: If set, disable PUT operations
+ -pid="": Path to write pid file
+</code></pre>
+</notextile>
+
+It's recommended to run Keepproxy under "runit":https://packages.debian.org/search?keywords=runit or something similar.
+
+h3. Create an API token for the Keepproxy server
+
+The Keepproxy server needs a token to talk to the API server.
+
+On the <strong>API server</strong>, use the following command to create the token:
+
+<notextile>
+<pre><code>~/arvados/services/api/script$ <span class="userinput">RAILS_ENV=production ./get_anonymous_user_token.rb</span>
+hoShoomoo2bai3Ju1xahg6aeng1siquuaZ1yae2gi2Uhaeng2r
+</code></pre></notextile>
+
+The value for the @api_token@ field should be added to Keepproxy's environment as ARVADOS_API_TOKEN. Make sure to also set ARVADOS_API_HOST to @uuid_prefix@.your.domain.
+
+h3. Set up a reverse proxy with SSL support
+
+Because the Keepproxy is intended for access from anywhere on the internet, it is recommended to use SSL for transport encryption.
+
+This is best achieved by putting a reverse proxy with SSL support in front of Keepproxy. Keepproxy itself runs on port 25107 by default; your reverse proxy can run on port 443 and pass requests to Keepproxy on port 25107.
+
+h3. Tell the API server about the Keepproxy server
+
+The API server needs to be informed about the presence of your Keepproxy server. Please execute the following commands on your <strong>shell server</strong>.
+
+<notextile>
+<pre><code>~$ <span class="userinput">prefix=`arv --format=uuid user current | cut -d- -f1`</span>
+~$ <span class="userinput">echo "Site prefix is '$prefix'"</span>
+~$ <span class="userinput">read -rd $'\000' keepservice <<EOF; arv keep_service create --keep-service "$keepservice"</span>
+<span class="userinput">{
+ "service_host":"keep.$prefix.your.domain",
+ "service_port":443,
+ "service_ssl_flag":true,
+ "service_type":"proxy"
+}
+EOF</span>
+</code></pre></notextile>
+
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install Keepstore servers
+...
+
+This installation guide assumes you are on a 64 bit Debian or Ubuntu system.
+
+We are going to install two Keepstore servers. By convention, we use the following hostname pattern:
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Hostname_|
+|keep0.@uuid_prefix@.your.domain|
+|keep1.@uuid_prefix@.your.domain|
+</div>
+
+Because the Keepstore servers are not directly accessible from the internet, these hostnames only need to resolve on the local network.
+
+h2. Install Keepstore
+
+First add the Arvados apt repository, and then install the Keepstore package.
+
+<notextile>
+<pre><code>~$ <span class="userinput">echo "deb http://apt.arvados.org/ wheezy main" | sudo tee /etc/apt/sources.list.d/apt.arvados.org.list</span>
+~$ <span class="userinput">sudo /usr/bin/apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7</span>
+~$ <span class="userinput">sudo /usr/bin/apt-get update</span>
+~$ <span class="userinput">sudo /usr/bin/apt-get install keepstore</span>
+</code></pre>
+</notextile>
+
+Verify that Keepstore is functional:
+
+<notextile>
+<pre><code>~$ <span class="userinput">keepstore -h</span>
+2014/10/29 14:23:38 Keep started: pid 6848
+Usage of keepstore:
+ -data-manager-token-file="": File with the API token used by the Data Manager. All DELETE requests or GET /index requests must carry this token.
+ -enforce-permissions=false: Enforce permission signatures on requests.
+ -listen=":25107": Interface on which to listen for requests, in the format ipaddr:port. e.g. -listen=10.0.1.24:8000. Use -listen=:port to listen on all network interfaces.
+ -never-delete=false: If set, nothing will be deleted. HTTP 405 will be returned for valid DELETE requests.
+ -permission-key-file="": File containing the secret key for generating and verifying permission signatures.
+ -permission-ttl=1209600: Expiration time (in seconds) for newly generated permission signatures.
+ -pid="": Path to write pid file
+ -serialize=false: If set, all read and write operations on local Keep volumes will be serialized.
+ -volumes="": Comma-separated list of directories to use for Keep volumes, e.g. -volumes=/var/keep1,/var/keep2. If empty or not supplied, Keep will scan mounted filesystems for volumes with a /keep top-level directory.
+</code></pre>
+</notextile>
+
+If you want access control on your Keepstore server(s), you should provide a permission key. The @-permission-key-file@ argument should contain the path to a file that contains a single line with a long random alphanumeric string. It should be the same as the @blob_signing_key@ that can be set in the "API server":install-api-server.html config/application.yml file.
+
+Prepare one or more volumes for Keepstore to use. Simply create a /keep directory on all the partitions you would like Keepstore to use, and then start Keepstore. For example, using 2 tmpfs volumes:
+
+<notextile>
+<pre><code>~$ <span class="userinput">keepstore</span>
+2014/10/29 11:41:37 Keep started: pid 20736
+2014/10/29 11:41:37 adding Keep volume: /tmp/tmp.vwSCtUCyeH/keep
+2014/10/29 11:41:37 adding Keep volume: /tmp/tmp.Lsn4w8N3Xv/keep
+2014/10/29 11:41:37 Running without a PermissionSecret. Block locators returned by this server will not be signed, and will be rejected by a server that enforces permissions.
+2014/10/29 11:41:37 To fix this, run Keep with --permission-key-file=<path> to define the location of a file containing the permission key.
+
+</code></pre>
+</notextile>
+
+It's recommended to run Keepstore under "runit":https://packages.debian.org/search?keywords=runit or something similar.
+
+Repeat this section for each Keepstore server you are setting up.
+
+h3. Tell the API server about the Keepstore servers
+
+The API server needs to be informed about the presence of your Keepstore servers. For each of the Keepstore servers you have created, please execute the following commands on your <strong>shell server</strong>.
+
+Make sure to update the @service_host@ value to match each of your Keepstore servers.
+
+<notextile>
+<pre><code>~$ <span class="userinput">prefix=`arv --format=uuid user current | cut -d- -f1`</span>
+~$ <span class="userinput">echo "Site prefix is '$prefix'"</span>
+~$ <span class="userinput">read -rd $'\000' keepservice <<EOF; arv keep_service create --keep-service "$keepservice"</span>
+<span class="userinput">{
+ "service_host":"keep0.$prefix.your.domain",
+ "service_port":25107,
+ "service_ssl_flag":false,
+ "service_type":"disk"
+}
+EOF</span>
+</code></pre></notextile>
+
+
+
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Overview
+...
+
+{% include 'alert_stub' %}
+
+The manual installation guide will walk you through setting up a basic Arvados cluster on a number of (virtual) GNU/Linux systems. This installation method is intended for evaluation or production use at scale.
+
+<div class="alert alert-block alert-info">
+ <button type="button" class="close" data-dismiss="alert">×</button>
+ <h4>Note</h4>
+ <p>If you are looking to evaluate Arvados on one machine, we recommend the "Docker installation method":install-docker.html instead.</p>
+</div>
+
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install Ruby and bundler
+...
+
+We recommend Ruby >= 2.1.
+
+h2(#rvm). Option 1: Install with rvm
+
+<notextile>
+<pre><code>~$ <span class="userinput">\curl -sSL https://get.rvm.io | bash -s stable --ruby=2.1</span>
+~$ <span class="userinput">gem install bundler
+</span></code></pre></notextile>
+
+h2(#fromsource). Option 2: Install from source
+
+<notextile>
+<pre><code><span class="userinput">mkdir -p ~/src
+cd ~/src
+wget http://cache.ruby-lang.org/pub/ruby/2.1/ruby-2.1.3.tar.gz
+tar xzf ruby-2.1.3.tar.gz
+cd ruby-2.1.3
+./configure
+make
+sudo make install
+
+sudo gem install bundler</span>
+</code></pre></notextile>
+
+
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Prerequisites
+...
+
+h2. Hardware (or virtual machines)
+
+This guide assumes you have seven systems available in the same network subnet:
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Function_|_Number of nodes_|
+|Arvados REST API, Websockets, Workbench and Crunch dispatcher|1|
+|Arvados SSO server|1|
+|Arvados Keepproxy server|1|
+|Arvados Keepstore servers|2|
+|Arvados shell server|1|
+|Arvados compute node|1|
+</div>
+
+The number of Keepstore, shell and compute nodes listed above is a minimum. In a real production installation, you will likely run many more of each of those types of nodes. In such a scenario, you would probably also want to dedicate a node to the Workbench server and Crunch dispatcher, respectively. For performance reasons, you may want to run the database server on a separate node as well.
+
+h2. A unique identifier
+
+Each Arvados installation should have a globally unique identifier, which is a unique 5-character alphanumeric string. Here is a snippet of ruby that generates such a string based on the hostname of your computer:
+
+<pre>
+Digest::MD5.hexdigest(`hostname`).to_i(16).to_s(36)[0..4]
+</pre>
+
+You may also use a different method to pick the unique identifier. The unique identifier will be part of the hostname of the services in your Arvados cluster. The rest of this documentation will refer to it as your @uuid_prefix@.
+
+
+h2. SSL certificates
+
+There are four public-facing services that will require an SSL certificate. If you do not have official SSL certificates, you can use self-signed certificates. By convention, we use the following hostname pattern:
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Function_|_Hostname_|
+|Arvados REST API|@uuid_prefix@.your.domain|
+|Arvados Websockets endpoint|ws.@uuid_prefix@.your.domain|
+|Arvados Keepproxy server|keep.@uuid_prefix@.your.domain|
+|Arvados Workbench|workbench.@uuid_prefix@.your.domain|
+</div>
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install a shell server
+...
+
+This installation guide assumes you are on a 64 bit Debian or Ubuntu system.
+
+There is nothing inherently special about an Arvados shell server. It is just a GNU/Linux machine with the Arvados SDKs installed. For optimal performance, the Arvados shell server should be on the same LAN as the Arvados cluster, but that is not required.
+
+h2. Install API tokens
+
+Please follow the "API token guide":{{site.baseurl}}/user/reference/api-tokens.html to get API tokens for your user and install them on your shell server. We will use those tokens to test the SDKs as we install them.
+
+h2. Install the SDKs
+
+Install the "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html and the "Command line SDK":{{site.baseurl}}/sdk/cli/install.html
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install Single Sign On (SSO) server
+...
+
+h2(#dependencies). Install dependencies
+
+Make sure you have "Ruby and Bundler":install-manual-prerequisites-ruby.html installed.
+
+h2(#install). Install SSO server
+
+h3. Get SSO server code and create database
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone https://github.com/curoverse/sso-devise-omniauth-provider.git</span>
+~$ <span class="userinput">cd sso-devise-omniauth-provider</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">bundle install</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rake db:create</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rake db:migrate</span>
+</code></pre>
+</notextile>
+
+h3. Configure Rails secret
+
+Create a secret:
+
+<notextile>
+<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">cp -i config/initializers/secret_token.rb.example config/initializers/secret_token.rb</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">rake secret</span>
+zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
+</code></pre>
+</notextile>
+
+Edit @config/initializers/secret_token.rb@ to set @config.secret_token@ to the string produced by @rake secret@.
+
+h3. Configure upstream authentication provider
+
+<notextile>
+<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">cp -i config/environments/production.rb.example config/environments/production.rb</span>
+</code></pre>
+</notextile>
+
+Edit @config/environments/production.rb@ to set @config.google_oauth2_client_id@ and @config.google_oauth2_client_secret@. See "Omniauth Google OAuth2 gem documentation":https://github.com/zquestz/omniauth-google-oauth2 and "Using OAuth 2.0 to Access Google APIs":https://developers.google.com/accounts/docs/OAuth2 for information about using the "Google Developers Console":https://console.developers.google.com to get a Google client id and client secret.
+
+h3(#client). Create arvados-server client
+
+Use @rails console@ to create a @Client@ record that will be used by the Arvados API server. The values of @app_id@ and @app_secret@ correspond to the @APP_ID@ and @APP_SECRET@ that must be set in in "Setting up Omniauth in the API server.":install-api-server.html#omniauth
+
+<notextile>
+<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">rake secret</span>
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rails console</span>
+irb(main):001:0> <span class="userinput">c = Client.new</span>
+irb(main):002:0> <span class="userinput">c.name = "joshid"</span>
+irb(main):003:0> <span class="userinput">c.app_id = "arvados-server"</span>
+irb(main):004:0> <span class="userinput">c.app_secret = "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"</span>
+irb(main):005:0> <span class="userinput">c.save!</span>
+irb(main):006:0> <span class="userinput">quit</span>
+</code></pre>
+</notextile>
+
+h2. Start the SSO server
+
+h3. Run a simple standalone server
+
+You can use the Webrick server that is bundled with Ruby to quickly verify that your installation is functioning:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">RAILS_ENV=production bundle exec rails server</span>
+</code></pre>
+</notextile>
+
+h3. Production environment
+
+As a Ruby on Rails application, the SSO server should be compatible with any Ruby application server that supports Rack applications. We recommend "Passenger":https://www.phusionpassenger.com/ to run the SSO server in production.
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install Workbench
+...
+
+This installation guide assumes you are on a 64 bit Debian or Ubuntu system.
+
+h2. Install prerequisites
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo apt-get install \
+ bison build-essential gettext libcurl3 libcurl3-gnutls \
+ libcurl4-openssl-dev libpcre3-dev libpq-dev libreadline-dev \
+ libssl-dev libxslt1.1 sudo wget zlib1g-dev graphviz
+</span></code></pre></notextile>
+
+Also make sure you have "Ruby and bundler":install-manual-prerequisites-ruby.html installed.
+
+Workbench doesn't need its own database, so it does not need to have PostgreSQL installed.
+
+h2. Download the source tree
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
+</code></pre></notextile>
+
+See also: "Downloading the source code":https://arvados.org/projects/arvados/wiki/Download on the Arvados wiki.
+
+The Workbench application is in @apps/workbench@ in the source tree.
+
+h2. Install gem dependencies
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd arvados/apps/workbench</span>
+~/arvados/apps/workbench$ <span class="userinput">bundle install</span>
+</code></pre>
+</notextile>
+
+Alternatively, if you don't have sudo/root privileges on the host, install the gems in your own directory instead of installing them system-wide:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd arvados/apps/workbench</span>
+~/arvados/apps/workbench$ <span class="userinput">bundle install --path=vendor/bundle</span>
+</code></pre></notextile>
+
+The @bundle install@ command might produce a warning about the themes_for_rails gem. This is OK:
+
+<notextile>
+<pre><code>themes_for_rails at /home/<b>you</b>/.rvm/gems/ruby-2.1.1/bundler/gems/themes_for_rails-1fd2d7897d75 did not have a valid gemspec.
+This prevents bundler from installing bins or native extensions, but that may not affect its functionality.
+The validation message from Rubygems was:
+ duplicate dependency on rails (= 3.0.11, development), (>= 3.0.0) use:
+ add_runtime_dependency 'rails', '= 3.0.11', '>= 3.0.0'
+Using themes_for_rails (0.5.1) from https://github.com/holtkampw/themes_for_rails (at 1fd2d78)
+</code></pre></notextile>
+
+h2. Choose your environment
+
+The Workbench application can be run in @development@ or in @production@ mode. Unless this installation is going to be used for development on the Workbench applicatoin itself, you should run it in @production@ mode.
+
+Copy the example environment file for your environment. For example, if you choose @production@:
+
+<notextile>
+<pre><code>~/arvados/apps/workbench$ <span class="userinput">cp -i config/environments/production.rb.example config/environments/production.rb</span>
+</code></pre></notextile>
+
+h2. Configure the Workbench application
+
+First, copy the example configuration file:
+
+<notextile>
+<pre><code>~/arvados/apps/workbench$ <span class="userinput">cp -i config/application.yml.example config/application.yml</span>
+</code></pre></notextile>
+
+The Workbench application reads the @config/application.yml@ file, as well as the @config/application.defaults.yml@ file. Values in @config/application.yml@ take precedence over the defaults that are defined in @config/application.defaults.yml@. The @config/application.yml.example@ file is not read by the Workbench application and is provided for installation convenience, only.
+
+Consult @config/application.default.yml@ for a full list of configuration options. Always put your local configuration in @config/application.yml@, never edit @config/application.default.yml@.
+
+h3. secret_token
+
+This application needs a secret token. Generate a new secret:
+
+<notextile>
+<pre><code>~/arvados/apps/workbench$ <span class="userinput">rake secret</span>
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+</code></pre>
+</notextile>
+
+Then put that value in the @secret_token@ field.
+
+h3. arvados_login_base and arvados_v1_base
+
+Point @arvados_login_base@ and @arvados_v1_base@ at your "API server":install-api-server.html. For example like this:
+
+<notextile>
+<pre><code>arvados_login_base: https://prefix_uuid.your.domain/login
+arvados_v1_base: https://prefix_uuid.your.domain/arvados/v1
+</code></pre>
+</notextile>
+
+h3. site_name
+
+@site_name@ can be set to any arbitrary string. It is used to identify this Workbench to people visiting it.
+
+h3. arvados_insecure_https
+
+If the SSL certificate you use for your API server isn't an official certificate signed by a CA, make sure @arvados_insecure_https@ is @true@.
+
+h3. other options
+
+Consult @application.default.yml@ for a full list of configuration options. Always put your local configuration in @application.yml@ instead of editing @application.default.yml@.
+
+Copy @config/piwik.yml.example@ to @config/piwik.yml@ and edit to suit.
+
+h2. Start the Workbench application
+
+h3. Development environment
+
+If you plan to run in development mode, you can now run the development server this way:
+
+<notextile>
+<pre><code>~/arvados/apps/workbench$ <span class="userinput">bundle exec rails server --port=3031</span>
+</code></pre></notextile>
+
+h3. Production environment
+
+We recommend "Passenger":https://www.phusionpassenger.com/ to run the API server in production.
+
+Point it to the apps/workbench directory in the source tree.
+
+h2. Trusted client setting
+
+Log in to Workbench once to ensure that the Arvados API server has a record of the Workbench client. (It's OK if Workbench says your account hasn't been activated yet. We'll deal with that next.)
+
+In the <strong>API server</strong> project root, start the rails console. Locate the ApiClient record for your Workbench installation (typically, while you're setting this up, the @last@ one in the database is the one you want), then set the @is_trusted@ flag for the appropriate client record:
+
+<notextile><pre><code>~/arvados/services/api$ <span class="userinput">RAILS_ENV=production bundle exec rails console</span>
+irb(main):001:0> <span class="userinput">wb = ApiClient.all.last; [wb.url_prefix, wb.created_at]</span>
+=> ["https://workbench.example.com/", Sat, 19 Apr 2014 03:35:12 UTC +00:00]
+irb(main):002:0> <span class="userinput">include CurrentApiClient</span>
+=> true
+irb(main):003:0> <span class="userinput">act_as_system_user do wb.update_attributes!(is_trusted: true) end</span>
+=> true
+</code></pre>
+</notextile>
+
+h2(#admin-user). Add an admin user
+
+Next, we're going to use the rails console on the <strong>API server</strong> to activate our own account and give yourself admin privileges:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">RAILS_ENV=production bundle exec rails console</span>
+irb(main):001:0> <span class="userinput">Thread.current[:user] = User.all.select(&:identity_url).last</span>
+irb(main):002:0> <span class="userinput">Thread.current[:user].is_admin = true</span>
+irb(main):003:0> <span class="userinput">Thread.current[:user].update_attributes is_admin: true, is_active: true</span>
+irb(main):004:0> <span class="userinput">User.where(is_admin: true).collect &:email</span>
+=> ["root", "<b>your_address@example.com</b>"]
+</code></pre></notextile>
+
+At this point, you should have a working Workbench login with administrator privileges. Revisit your Workbench URL in a browser and reload the page to access it.
--- /dev/null
+/*!
+ * Bootstrap v3.1.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+if (typeof jQuery === 'undefined') { throw new Error('Bootstrap requires jQuery') }
+
+/* ========================================================================
+ * Bootstrap: transition.js v3.1.0
+ * http://getbootstrap.com/javascript/#transitions
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // CSS TRANSITION SUPPORT (Shoutout: http://www.modernizr.com/)
+ // ============================================================
+
+ function transitionEnd() {
+ var el = document.createElement('bootstrap')
+
+ var transEndEventNames = {
+ 'WebkitTransition' : 'webkitTransitionEnd',
+ 'MozTransition' : 'transitionend',
+ 'OTransition' : 'oTransitionEnd otransitionend',
+ 'transition' : 'transitionend'
+ }
+
+ for (var name in transEndEventNames) {
+ if (el.style[name] !== undefined) {
+ return { end: transEndEventNames[name] }
+ }
+ }
+
+ return false // explicit for ie8 ( ._.)
+ }
+
+ // http://blog.alexmaccaw.com/css-transitions
+ $.fn.emulateTransitionEnd = function (duration) {
+ var called = false, $el = this
+ $(this).one($.support.transition.end, function () { called = true })
+ var callback = function () { if (!called) $($el).trigger($.support.transition.end) }
+ setTimeout(callback, duration)
+ return this
+ }
+
+ $(function () {
+ $.support.transition = transitionEnd()
+ })
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: alert.js v3.1.0
+ * http://getbootstrap.com/javascript/#alerts
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // ALERT CLASS DEFINITION
+ // ======================
+
+ var dismiss = '[data-dismiss="alert"]'
+ var Alert = function (el) {
+ $(el).on('click', dismiss, this.close)
+ }
+
+ Alert.prototype.close = function (e) {
+ var $this = $(this)
+ var selector = $this.attr('data-target')
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7
+ }
+
+ var $parent = $(selector)
+
+ if (e) e.preventDefault()
+
+ if (!$parent.length) {
+ $parent = $this.hasClass('alert') ? $this : $this.parent()
+ }
+
+ $parent.trigger(e = $.Event('close.bs.alert'))
+
+ if (e.isDefaultPrevented()) return
+
+ $parent.removeClass('in')
+
+ function removeElement() {
+ $parent.trigger('closed.bs.alert').remove()
+ }
+
+ $.support.transition && $parent.hasClass('fade') ?
+ $parent
+ .one($.support.transition.end, removeElement)
+ .emulateTransitionEnd(150) :
+ removeElement()
+ }
+
+
+ // ALERT PLUGIN DEFINITION
+ // =======================
+
+ var old = $.fn.alert
+
+ $.fn.alert = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.alert')
+
+ if (!data) $this.data('bs.alert', (data = new Alert(this)))
+ if (typeof option == 'string') data[option].call($this)
+ })
+ }
+
+ $.fn.alert.Constructor = Alert
+
+
+ // ALERT NO CONFLICT
+ // =================
+
+ $.fn.alert.noConflict = function () {
+ $.fn.alert = old
+ return this
+ }
+
+
+ // ALERT DATA-API
+ // ==============
+
+ $(document).on('click.bs.alert.data-api', dismiss, Alert.prototype.close)
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: button.js v3.1.0
+ * http://getbootstrap.com/javascript/#buttons
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // BUTTON PUBLIC CLASS DEFINITION
+ // ==============================
+
+ var Button = function (element, options) {
+ this.$element = $(element)
+ this.options = $.extend({}, Button.DEFAULTS, options)
+ this.isLoading = false
+ }
+
+ Button.DEFAULTS = {
+ loadingText: 'loading...'
+ }
+
+ Button.prototype.setState = function (state) {
+ var d = 'disabled'
+ var $el = this.$element
+ var val = $el.is('input') ? 'val' : 'html'
+ var data = $el.data()
+
+ state = state + 'Text'
+
+ if (!data.resetText) $el.data('resetText', $el[val]())
+
+ $el[val](data[state] || this.options[state])
+
+ // push to event loop to allow forms to submit
+ setTimeout($.proxy(function () {
+ if (state == 'loadingText') {
+ this.isLoading = true
+ $el.addClass(d).attr(d, d)
+ } else if (this.isLoading) {
+ this.isLoading = false
+ $el.removeClass(d).removeAttr(d)
+ }
+ }, this), 0)
+ }
+
+ Button.prototype.toggle = function () {
+ var changed = true
+ var $parent = this.$element.closest('[data-toggle="buttons"]')
+
+ if ($parent.length) {
+ var $input = this.$element.find('input')
+ if ($input.prop('type') == 'radio') {
+ if ($input.prop('checked') && this.$element.hasClass('active')) changed = false
+ else $parent.find('.active').removeClass('active')
+ }
+ if (changed) $input.prop('checked', !this.$element.hasClass('active')).trigger('change')
+ }
+
+ if (changed) this.$element.toggleClass('active')
+ }
+
+
+ // BUTTON PLUGIN DEFINITION
+ // ========================
+
+ var old = $.fn.button
+
+ $.fn.button = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.button')
+ var options = typeof option == 'object' && option
+
+ if (!data) $this.data('bs.button', (data = new Button(this, options)))
+
+ if (option == 'toggle') data.toggle()
+ else if (option) data.setState(option)
+ })
+ }
+
+ $.fn.button.Constructor = Button
+
+
+ // BUTTON NO CONFLICT
+ // ==================
+
+ $.fn.button.noConflict = function () {
+ $.fn.button = old
+ return this
+ }
+
+
+ // BUTTON DATA-API
+ // ===============
+
+ $(document).on('click.bs.button.data-api', '[data-toggle^=button]', function (e) {
+ var $btn = $(e.target)
+ if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn')
+ $btn.button('toggle')
+ e.preventDefault()
+ })
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: carousel.js v3.1.0
+ * http://getbootstrap.com/javascript/#carousel
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // CAROUSEL CLASS DEFINITION
+ // =========================
+
+ var Carousel = function (element, options) {
+ this.$element = $(element)
+ this.$indicators = this.$element.find('.carousel-indicators')
+ this.options = options
+ this.paused =
+ this.sliding =
+ this.interval =
+ this.$active =
+ this.$items = null
+
+ this.options.pause == 'hover' && this.$element
+ .on('mouseenter', $.proxy(this.pause, this))
+ .on('mouseleave', $.proxy(this.cycle, this))
+ }
+
+ Carousel.DEFAULTS = {
+ interval: 5000,
+ pause: 'hover',
+ wrap: true
+ }
+
+ Carousel.prototype.cycle = function (e) {
+ e || (this.paused = false)
+
+ this.interval && clearInterval(this.interval)
+
+ this.options.interval
+ && !this.paused
+ && (this.interval = setInterval($.proxy(this.next, this), this.options.interval))
+
+ return this
+ }
+
+ Carousel.prototype.getActiveIndex = function () {
+ this.$active = this.$element.find('.item.active')
+ this.$items = this.$active.parent().children()
+
+ return this.$items.index(this.$active)
+ }
+
+ Carousel.prototype.to = function (pos) {
+ var that = this
+ var activeIndex = this.getActiveIndex()
+
+ if (pos > (this.$items.length - 1) || pos < 0) return
+
+ if (this.sliding) return this.$element.one('slid.bs.carousel', function () { that.to(pos) })
+ if (activeIndex == pos) return this.pause().cycle()
+
+ return this.slide(pos > activeIndex ? 'next' : 'prev', $(this.$items[pos]))
+ }
+
+ Carousel.prototype.pause = function (e) {
+ e || (this.paused = true)
+
+ if (this.$element.find('.next, .prev').length && $.support.transition) {
+ this.$element.trigger($.support.transition.end)
+ this.cycle(true)
+ }
+
+ this.interval = clearInterval(this.interval)
+
+ return this
+ }
+
+ Carousel.prototype.next = function () {
+ if (this.sliding) return
+ return this.slide('next')
+ }
+
+ Carousel.prototype.prev = function () {
+ if (this.sliding) return
+ return this.slide('prev')
+ }
+
+ Carousel.prototype.slide = function (type, next) {
+ var $active = this.$element.find('.item.active')
+ var $next = next || $active[type]()
+ var isCycling = this.interval
+ var direction = type == 'next' ? 'left' : 'right'
+ var fallback = type == 'next' ? 'first' : 'last'
+ var that = this
+
+ if (!$next.length) {
+ if (!this.options.wrap) return
+ $next = this.$element.find('.item')[fallback]()
+ }
+
+ if ($next.hasClass('active')) return this.sliding = false
+
+ var e = $.Event('slide.bs.carousel', { relatedTarget: $next[0], direction: direction })
+ this.$element.trigger(e)
+ if (e.isDefaultPrevented()) return
+
+ this.sliding = true
+
+ isCycling && this.pause()
+
+ if (this.$indicators.length) {
+ this.$indicators.find('.active').removeClass('active')
+ this.$element.one('slid.bs.carousel', function () {
+ var $nextIndicator = $(that.$indicators.children()[that.getActiveIndex()])
+ $nextIndicator && $nextIndicator.addClass('active')
+ })
+ }
+
+ if ($.support.transition && this.$element.hasClass('slide')) {
+ $next.addClass(type)
+ $next[0].offsetWidth // force reflow
+ $active.addClass(direction)
+ $next.addClass(direction)
+ $active
+ .one($.support.transition.end, function () {
+ $next.removeClass([type, direction].join(' ')).addClass('active')
+ $active.removeClass(['active', direction].join(' '))
+ that.sliding = false
+ setTimeout(function () { that.$element.trigger('slid.bs.carousel') }, 0)
+ })
+ .emulateTransitionEnd($active.css('transition-duration').slice(0, -1) * 1000)
+ } else {
+ $active.removeClass('active')
+ $next.addClass('active')
+ this.sliding = false
+ this.$element.trigger('slid.bs.carousel')
+ }
+
+ isCycling && this.cycle()
+
+ return this
+ }
+
+
+ // CAROUSEL PLUGIN DEFINITION
+ // ==========================
+
+ var old = $.fn.carousel
+
+ $.fn.carousel = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.carousel')
+ var options = $.extend({}, Carousel.DEFAULTS, $this.data(), typeof option == 'object' && option)
+ var action = typeof option == 'string' ? option : options.slide
+
+ if (!data) $this.data('bs.carousel', (data = new Carousel(this, options)))
+ if (typeof option == 'number') data.to(option)
+ else if (action) data[action]()
+ else if (options.interval) data.pause().cycle()
+ })
+ }
+
+ $.fn.carousel.Constructor = Carousel
+
+
+ // CAROUSEL NO CONFLICT
+ // ====================
+
+ $.fn.carousel.noConflict = function () {
+ $.fn.carousel = old
+ return this
+ }
+
+
+ // CAROUSEL DATA-API
+ // =================
+
+ $(document).on('click.bs.carousel.data-api', '[data-slide], [data-slide-to]', function (e) {
+ var $this = $(this), href
+ var $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
+ var options = $.extend({}, $target.data(), $this.data())
+ var slideIndex = $this.attr('data-slide-to')
+ if (slideIndex) options.interval = false
+
+ $target.carousel(options)
+
+ if (slideIndex = $this.attr('data-slide-to')) {
+ $target.data('bs.carousel').to(slideIndex)
+ }
+
+ e.preventDefault()
+ })
+
+ $(window).on('load', function () {
+ $('[data-ride="carousel"]').each(function () {
+ var $carousel = $(this)
+ $carousel.carousel($carousel.data())
+ })
+ })
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: collapse.js v3.1.0
+ * http://getbootstrap.com/javascript/#collapse
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // COLLAPSE PUBLIC CLASS DEFINITION
+ // ================================
+
+ var Collapse = function (element, options) {
+ this.$element = $(element)
+ this.options = $.extend({}, Collapse.DEFAULTS, options)
+ this.transitioning = null
+
+ if (this.options.parent) this.$parent = $(this.options.parent)
+ if (this.options.toggle) this.toggle()
+ }
+
+ Collapse.DEFAULTS = {
+ toggle: true
+ }
+
+ Collapse.prototype.dimension = function () {
+ var hasWidth = this.$element.hasClass('width')
+ return hasWidth ? 'width' : 'height'
+ }
+
+ Collapse.prototype.show = function () {
+ if (this.transitioning || this.$element.hasClass('in')) return
+
+ var startEvent = $.Event('show.bs.collapse')
+ this.$element.trigger(startEvent)
+ if (startEvent.isDefaultPrevented()) return
+
+ var actives = this.$parent && this.$parent.find('> .panel > .in')
+
+ if (actives && actives.length) {
+ var hasData = actives.data('bs.collapse')
+ if (hasData && hasData.transitioning) return
+ actives.collapse('hide')
+ hasData || actives.data('bs.collapse', null)
+ }
+
+ var dimension = this.dimension()
+
+ this.$element
+ .removeClass('collapse')
+ .addClass('collapsing')
+ [dimension](0)
+
+ this.transitioning = 1
+
+ var complete = function () {
+ this.$element
+ .removeClass('collapsing')
+ .addClass('collapse in')
+ [dimension]('auto')
+ this.transitioning = 0
+ this.$element.trigger('shown.bs.collapse')
+ }
+
+ if (!$.support.transition) return complete.call(this)
+
+ var scrollSize = $.camelCase(['scroll', dimension].join('-'))
+
+ this.$element
+ .one($.support.transition.end, $.proxy(complete, this))
+ .emulateTransitionEnd(350)
+ [dimension](this.$element[0][scrollSize])
+ }
+
+ Collapse.prototype.hide = function () {
+ if (this.transitioning || !this.$element.hasClass('in')) return
+
+ var startEvent = $.Event('hide.bs.collapse')
+ this.$element.trigger(startEvent)
+ if (startEvent.isDefaultPrevented()) return
+
+ var dimension = this.dimension()
+
+ this.$element
+ [dimension](this.$element[dimension]())
+ [0].offsetHeight
+
+ this.$element
+ .addClass('collapsing')
+ .removeClass('collapse')
+ .removeClass('in')
+
+ this.transitioning = 1
+
+ var complete = function () {
+ this.transitioning = 0
+ this.$element
+ .trigger('hidden.bs.collapse')
+ .removeClass('collapsing')
+ .addClass('collapse')
+ }
+
+ if (!$.support.transition) return complete.call(this)
+
+ this.$element
+ [dimension](0)
+ .one($.support.transition.end, $.proxy(complete, this))
+ .emulateTransitionEnd(350)
+ }
+
+ Collapse.prototype.toggle = function () {
+ this[this.$element.hasClass('in') ? 'hide' : 'show']()
+ }
+
+
+ // COLLAPSE PLUGIN DEFINITION
+ // ==========================
+
+ var old = $.fn.collapse
+
+ $.fn.collapse = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.collapse')
+ var options = $.extend({}, Collapse.DEFAULTS, $this.data(), typeof option == 'object' && option)
+
+ if (!data && options.toggle && option == 'show') option = !option
+ if (!data) $this.data('bs.collapse', (data = new Collapse(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.collapse.Constructor = Collapse
+
+
+ // COLLAPSE NO CONFLICT
+ // ====================
+
+ $.fn.collapse.noConflict = function () {
+ $.fn.collapse = old
+ return this
+ }
+
+
+ // COLLAPSE DATA-API
+ // =================
+
+ $(document).on('click.bs.collapse.data-api', '[data-toggle=collapse]', function (e) {
+ var $this = $(this), href
+ var target = $this.attr('data-target')
+ || e.preventDefault()
+ || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7
+ var $target = $(target)
+ var data = $target.data('bs.collapse')
+ var option = data ? 'toggle' : $this.data()
+ var parent = $this.attr('data-parent')
+ var $parent = parent && $(parent)
+
+ if (!data || !data.transitioning) {
+ if ($parent) $parent.find('[data-toggle=collapse][data-parent="' + parent + '"]').not($this).addClass('collapsed')
+ $this[$target.hasClass('in') ? 'addClass' : 'removeClass']('collapsed')
+ }
+
+ $target.collapse(option)
+ })
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: dropdown.js v3.1.0
+ * http://getbootstrap.com/javascript/#dropdowns
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // DROPDOWN CLASS DEFINITION
+ // =========================
+
+ var backdrop = '.dropdown-backdrop'
+ var toggle = '[data-toggle=dropdown]'
+ var Dropdown = function (element) {
+ $(element).on('click.bs.dropdown', this.toggle)
+ }
+
+ Dropdown.prototype.toggle = function (e) {
+ var $this = $(this)
+
+ if ($this.is('.disabled, :disabled')) return
+
+ var $parent = getParent($this)
+ var isActive = $parent.hasClass('open')
+
+ clearMenus()
+
+ if (!isActive) {
+ if ('ontouchstart' in document.documentElement && !$parent.closest('.navbar-nav').length) {
+ // if mobile we use a backdrop because click events don't delegate
+ $('<div class="dropdown-backdrop"/>').insertAfter($(this)).on('click', clearMenus)
+ }
+
+ var relatedTarget = { relatedTarget: this }
+ $parent.trigger(e = $.Event('show.bs.dropdown', relatedTarget))
+
+ if (e.isDefaultPrevented()) return
+
+ $parent
+ .toggleClass('open')
+ .trigger('shown.bs.dropdown', relatedTarget)
+
+ $this.focus()
+ }
+
+ return false
+ }
+
+ Dropdown.prototype.keydown = function (e) {
+ if (!/(38|40|27)/.test(e.keyCode)) return
+
+ var $this = $(this)
+
+ e.preventDefault()
+ e.stopPropagation()
+
+ if ($this.is('.disabled, :disabled')) return
+
+ var $parent = getParent($this)
+ var isActive = $parent.hasClass('open')
+
+ if (!isActive || (isActive && e.keyCode == 27)) {
+ if (e.which == 27) $parent.find(toggle).focus()
+ return $this.click()
+ }
+
+ var desc = ' li:not(.divider):visible a'
+ var $items = $parent.find('[role=menu]' + desc + ', [role=listbox]' + desc)
+
+ if (!$items.length) return
+
+ var index = $items.index($items.filter(':focus'))
+
+ if (e.keyCode == 38 && index > 0) index-- // up
+ if (e.keyCode == 40 && index < $items.length - 1) index++ // down
+ if (!~index) index = 0
+
+ $items.eq(index).focus()
+ }
+
+ function clearMenus(e) {
+ $(backdrop).remove()
+ $(toggle).each(function () {
+ var $parent = getParent($(this))
+ var relatedTarget = { relatedTarget: this }
+ if (!$parent.hasClass('open')) return
+ $parent.trigger(e = $.Event('hide.bs.dropdown', relatedTarget))
+ if (e.isDefaultPrevented()) return
+ $parent.removeClass('open').trigger('hidden.bs.dropdown', relatedTarget)
+ })
+ }
+
+ function getParent($this) {
+ var selector = $this.attr('data-target')
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && /#[A-Za-z]/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
+ }
+
+ var $parent = selector && $(selector)
+
+ return $parent && $parent.length ? $parent : $this.parent()
+ }
+
+
+ // DROPDOWN PLUGIN DEFINITION
+ // ==========================
+
+ var old = $.fn.dropdown
+
+ $.fn.dropdown = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.dropdown')
+
+ if (!data) $this.data('bs.dropdown', (data = new Dropdown(this)))
+ if (typeof option == 'string') data[option].call($this)
+ })
+ }
+
+ $.fn.dropdown.Constructor = Dropdown
+
+
+ // DROPDOWN NO CONFLICT
+ // ====================
+
+ $.fn.dropdown.noConflict = function () {
+ $.fn.dropdown = old
+ return this
+ }
+
+
+ // APPLY TO STANDARD DROPDOWN ELEMENTS
+ // ===================================
+
+ $(document)
+ .on('click.bs.dropdown.data-api', clearMenus)
+ .on('click.bs.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() })
+ .on('click.bs.dropdown.data-api', toggle, Dropdown.prototype.toggle)
+ .on('keydown.bs.dropdown.data-api', toggle + ', [role=menu], [role=listbox]', Dropdown.prototype.keydown)
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: modal.js v3.1.0
+ * http://getbootstrap.com/javascript/#modals
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // MODAL CLASS DEFINITION
+ // ======================
+
+ var Modal = function (element, options) {
+ this.options = options
+ this.$element = $(element)
+ this.$backdrop =
+ this.isShown = null
+
+ if (this.options.remote) {
+ this.$element
+ .find('.modal-content')
+ .load(this.options.remote, $.proxy(function () {
+ this.$element.trigger('loaded.bs.modal')
+ }, this))
+ }
+ }
+
+ Modal.DEFAULTS = {
+ backdrop: true,
+ keyboard: true,
+ show: true
+ }
+
+ Modal.prototype.toggle = function (_relatedTarget) {
+ return this[!this.isShown ? 'show' : 'hide'](_relatedTarget)
+ }
+
+ Modal.prototype.show = function (_relatedTarget) {
+ var that = this
+ var e = $.Event('show.bs.modal', { relatedTarget: _relatedTarget })
+
+ this.$element.trigger(e)
+
+ if (this.isShown || e.isDefaultPrevented()) return
+
+ this.isShown = true
+
+ this.escape()
+
+ this.$element.on('click.dismiss.bs.modal', '[data-dismiss="modal"]', $.proxy(this.hide, this))
+
+ this.backdrop(function () {
+ var transition = $.support.transition && that.$element.hasClass('fade')
+
+ if (!that.$element.parent().length) {
+ that.$element.appendTo(document.body) // don't move modals dom position
+ }
+
+ that.$element
+ .show()
+ .scrollTop(0)
+
+ if (transition) {
+ that.$element[0].offsetWidth // force reflow
+ }
+
+ that.$element
+ .addClass('in')
+ .attr('aria-hidden', false)
+
+ that.enforceFocus()
+
+ var e = $.Event('shown.bs.modal', { relatedTarget: _relatedTarget })
+
+ transition ?
+ that.$element.find('.modal-dialog') // wait for modal to slide in
+ .one($.support.transition.end, function () {
+ that.$element.focus().trigger(e)
+ })
+ .emulateTransitionEnd(300) :
+ that.$element.focus().trigger(e)
+ })
+ }
+
+ Modal.prototype.hide = function (e) {
+ if (e) e.preventDefault()
+
+ e = $.Event('hide.bs.modal')
+
+ this.$element.trigger(e)
+
+ if (!this.isShown || e.isDefaultPrevented()) return
+
+ this.isShown = false
+
+ this.escape()
+
+ $(document).off('focusin.bs.modal')
+
+ this.$element
+ .removeClass('in')
+ .attr('aria-hidden', true)
+ .off('click.dismiss.bs.modal')
+
+ $.support.transition && this.$element.hasClass('fade') ?
+ this.$element
+ .one($.support.transition.end, $.proxy(this.hideModal, this))
+ .emulateTransitionEnd(300) :
+ this.hideModal()
+ }
+
+ Modal.prototype.enforceFocus = function () {
+ $(document)
+ .off('focusin.bs.modal') // guard against infinite focus loop
+ .on('focusin.bs.modal', $.proxy(function (e) {
+ if (this.$element[0] !== e.target && !this.$element.has(e.target).length) {
+ this.$element.focus()
+ }
+ }, this))
+ }
+
+ Modal.prototype.escape = function () {
+ if (this.isShown && this.options.keyboard) {
+ this.$element.on('keyup.dismiss.bs.modal', $.proxy(function (e) {
+ e.which == 27 && this.hide()
+ }, this))
+ } else if (!this.isShown) {
+ this.$element.off('keyup.dismiss.bs.modal')
+ }
+ }
+
+ Modal.prototype.hideModal = function () {
+ var that = this
+ this.$element.hide()
+ this.backdrop(function () {
+ that.removeBackdrop()
+ that.$element.trigger('hidden.bs.modal')
+ })
+ }
+
+ Modal.prototype.removeBackdrop = function () {
+ this.$backdrop && this.$backdrop.remove()
+ this.$backdrop = null
+ }
+
+ Modal.prototype.backdrop = function (callback) {
+ var animate = this.$element.hasClass('fade') ? 'fade' : ''
+
+ if (this.isShown && this.options.backdrop) {
+ var doAnimate = $.support.transition && animate
+
+ this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />')
+ .appendTo(document.body)
+
+ this.$element.on('click.dismiss.bs.modal', $.proxy(function (e) {
+ if (e.target !== e.currentTarget) return
+ this.options.backdrop == 'static'
+ ? this.$element[0].focus.call(this.$element[0])
+ : this.hide.call(this)
+ }, this))
+
+ if (doAnimate) this.$backdrop[0].offsetWidth // force reflow
+
+ this.$backdrop.addClass('in')
+
+ if (!callback) return
+
+ doAnimate ?
+ this.$backdrop
+ .one($.support.transition.end, callback)
+ .emulateTransitionEnd(150) :
+ callback()
+
+ } else if (!this.isShown && this.$backdrop) {
+ this.$backdrop.removeClass('in')
+
+ $.support.transition && this.$element.hasClass('fade') ?
+ this.$backdrop
+ .one($.support.transition.end, callback)
+ .emulateTransitionEnd(150) :
+ callback()
+
+ } else if (callback) {
+ callback()
+ }
+ }
+
+
+ // MODAL PLUGIN DEFINITION
+ // =======================
+
+ var old = $.fn.modal
+
+ $.fn.modal = function (option, _relatedTarget) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.modal')
+ var options = $.extend({}, Modal.DEFAULTS, $this.data(), typeof option == 'object' && option)
+
+ if (!data) $this.data('bs.modal', (data = new Modal(this, options)))
+ if (typeof option == 'string') data[option](_relatedTarget)
+ else if (options.show) data.show(_relatedTarget)
+ })
+ }
+
+ $.fn.modal.Constructor = Modal
+
+
+ // MODAL NO CONFLICT
+ // =================
+
+ $.fn.modal.noConflict = function () {
+ $.fn.modal = old
+ return this
+ }
+
+
+ // MODAL DATA-API
+ // ==============
+
+ $(document).on('click.bs.modal.data-api', '[data-toggle="modal"]', function (e) {
+ var $this = $(this)
+ var href = $this.attr('href')
+ var $target = $($this.attr('data-target') || (href && href.replace(/.*(?=#[^\s]+$)/, ''))) //strip for ie7
+ var option = $target.data('bs.modal') ? 'toggle' : $.extend({ remote: !/#/.test(href) && href }, $target.data(), $this.data())
+
+ if ($this.is('a')) e.preventDefault()
+
+ $target
+ .modal(option, this)
+ .one('hide', function () {
+ $this.is(':visible') && $this.focus()
+ })
+ })
+
+ $(document)
+ .on('show.bs.modal', '.modal', function () { $(document.body).addClass('modal-open') })
+ .on('hidden.bs.modal', '.modal', function () { $(document.body).removeClass('modal-open') })
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: tooltip.js v3.1.0
+ * http://getbootstrap.com/javascript/#tooltip
+ * Inspired by the original jQuery.tipsy by Jason Frame
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // TOOLTIP PUBLIC CLASS DEFINITION
+ // ===============================
+
+ var Tooltip = function (element, options) {
+ this.type =
+ this.options =
+ this.enabled =
+ this.timeout =
+ this.hoverState =
+ this.$element = null
+
+ this.init('tooltip', element, options)
+ }
+
+ Tooltip.DEFAULTS = {
+ animation: true,
+ placement: 'top',
+ selector: false,
+ template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',
+ trigger: 'hover focus',
+ title: '',
+ delay: 0,
+ html: false,
+ container: false
+ }
+
+ Tooltip.prototype.init = function (type, element, options) {
+ this.enabled = true
+ this.type = type
+ this.$element = $(element)
+ this.options = this.getOptions(options)
+
+ var triggers = this.options.trigger.split(' ')
+
+ for (var i = triggers.length; i--;) {
+ var trigger = triggers[i]
+
+ if (trigger == 'click') {
+ this.$element.on('click.' + this.type, this.options.selector, $.proxy(this.toggle, this))
+ } else if (trigger != 'manual') {
+ var eventIn = trigger == 'hover' ? 'mouseenter' : 'focusin'
+ var eventOut = trigger == 'hover' ? 'mouseleave' : 'focusout'
+
+ this.$element.on(eventIn + '.' + this.type, this.options.selector, $.proxy(this.enter, this))
+ this.$element.on(eventOut + '.' + this.type, this.options.selector, $.proxy(this.leave, this))
+ }
+ }
+
+ this.options.selector ?
+ (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) :
+ this.fixTitle()
+ }
+
+ Tooltip.prototype.getDefaults = function () {
+ return Tooltip.DEFAULTS
+ }
+
+ Tooltip.prototype.getOptions = function (options) {
+ options = $.extend({}, this.getDefaults(), this.$element.data(), options)
+
+ if (options.delay && typeof options.delay == 'number') {
+ options.delay = {
+ show: options.delay,
+ hide: options.delay
+ }
+ }
+
+ return options
+ }
+
+ Tooltip.prototype.getDelegateOptions = function () {
+ var options = {}
+ var defaults = this.getDefaults()
+
+ this._options && $.each(this._options, function (key, value) {
+ if (defaults[key] != value) options[key] = value
+ })
+
+ return options
+ }
+
+ Tooltip.prototype.enter = function (obj) {
+ var self = obj instanceof this.constructor ?
+ obj : $(obj.currentTarget)[this.type](this.getDelegateOptions()).data('bs.' + this.type)
+
+ clearTimeout(self.timeout)
+
+ self.hoverState = 'in'
+
+ if (!self.options.delay || !self.options.delay.show) return self.show()
+
+ self.timeout = setTimeout(function () {
+ if (self.hoverState == 'in') self.show()
+ }, self.options.delay.show)
+ }
+
+ Tooltip.prototype.leave = function (obj) {
+ var self = obj instanceof this.constructor ?
+ obj : $(obj.currentTarget)[this.type](this.getDelegateOptions()).data('bs.' + this.type)
+
+ clearTimeout(self.timeout)
+
+ self.hoverState = 'out'
+
+ if (!self.options.delay || !self.options.delay.hide) return self.hide()
+
+ self.timeout = setTimeout(function () {
+ if (self.hoverState == 'out') self.hide()
+ }, self.options.delay.hide)
+ }
+
+ Tooltip.prototype.show = function () {
+ var e = $.Event('show.bs.' + this.type)
+
+ if (this.hasContent() && this.enabled) {
+ this.$element.trigger(e)
+
+ if (e.isDefaultPrevented()) return
+ var that = this;
+
+ var $tip = this.tip()
+
+ this.setContent()
+
+ if (this.options.animation) $tip.addClass('fade')
+
+ var placement = typeof this.options.placement == 'function' ?
+ this.options.placement.call(this, $tip[0], this.$element[0]) :
+ this.options.placement
+
+ var autoToken = /\s?auto?\s?/i
+ var autoPlace = autoToken.test(placement)
+ if (autoPlace) placement = placement.replace(autoToken, '') || 'top'
+
+ $tip
+ .detach()
+ .css({ top: 0, left: 0, display: 'block' })
+ .addClass(placement)
+
+ this.options.container ? $tip.appendTo(this.options.container) : $tip.insertAfter(this.$element)
+
+ var pos = this.getPosition()
+ var actualWidth = $tip[0].offsetWidth
+ var actualHeight = $tip[0].offsetHeight
+
+ if (autoPlace) {
+ var $parent = this.$element.parent()
+
+ var orgPlacement = placement
+ var docScroll = document.documentElement.scrollTop || document.body.scrollTop
+ var parentWidth = this.options.container == 'body' ? window.innerWidth : $parent.outerWidth()
+ var parentHeight = this.options.container == 'body' ? window.innerHeight : $parent.outerHeight()
+ var parentLeft = this.options.container == 'body' ? 0 : $parent.offset().left
+
+ placement = placement == 'bottom' && pos.top + pos.height + actualHeight - docScroll > parentHeight ? 'top' :
+ placement == 'top' && pos.top - docScroll - actualHeight < 0 ? 'bottom' :
+ placement == 'right' && pos.right + actualWidth > parentWidth ? 'left' :
+ placement == 'left' && pos.left - actualWidth < parentLeft ? 'right' :
+ placement
+
+ $tip
+ .removeClass(orgPlacement)
+ .addClass(placement)
+ }
+
+ var calculatedOffset = this.getCalculatedOffset(placement, pos, actualWidth, actualHeight)
+
+ this.applyPlacement(calculatedOffset, placement)
+ this.hoverState = null
+
+ var complete = function() {
+ that.$element.trigger('shown.bs.' + that.type)
+ }
+
+ $.support.transition && this.$tip.hasClass('fade') ?
+ $tip
+ .one($.support.transition.end, complete)
+ .emulateTransitionEnd(150) :
+ complete()
+ }
+ }
+
+ Tooltip.prototype.applyPlacement = function (offset, placement) {
+ var replace
+ var $tip = this.tip()
+ var width = $tip[0].offsetWidth
+ var height = $tip[0].offsetHeight
+
+ // manually read margins because getBoundingClientRect includes difference
+ var marginTop = parseInt($tip.css('margin-top'), 10)
+ var marginLeft = parseInt($tip.css('margin-left'), 10)
+
+ // we must check for NaN for ie 8/9
+ if (isNaN(marginTop)) marginTop = 0
+ if (isNaN(marginLeft)) marginLeft = 0
+
+ offset.top = offset.top + marginTop
+ offset.left = offset.left + marginLeft
+
+ // $.fn.offset doesn't round pixel values
+ // so we use setOffset directly with our own function B-0
+ $.offset.setOffset($tip[0], $.extend({
+ using: function (props) {
+ $tip.css({
+ top: Math.round(props.top),
+ left: Math.round(props.left)
+ })
+ }
+ }, offset), 0)
+
+ $tip.addClass('in')
+
+ // check to see if placing tip in new offset caused the tip to resize itself
+ var actualWidth = $tip[0].offsetWidth
+ var actualHeight = $tip[0].offsetHeight
+
+ if (placement == 'top' && actualHeight != height) {
+ replace = true
+ offset.top = offset.top + height - actualHeight
+ }
+
+ if (/bottom|top/.test(placement)) {
+ var delta = 0
+
+ if (offset.left < 0) {
+ delta = offset.left * -2
+ offset.left = 0
+
+ $tip.offset(offset)
+
+ actualWidth = $tip[0].offsetWidth
+ actualHeight = $tip[0].offsetHeight
+ }
+
+ this.replaceArrow(delta - width + actualWidth, actualWidth, 'left')
+ } else {
+ this.replaceArrow(actualHeight - height, actualHeight, 'top')
+ }
+
+ if (replace) $tip.offset(offset)
+ }
+
+ Tooltip.prototype.replaceArrow = function (delta, dimension, position) {
+ this.arrow().css(position, delta ? (50 * (1 - delta / dimension) + '%') : '')
+ }
+
+ Tooltip.prototype.setContent = function () {
+ var $tip = this.tip()
+ var title = this.getTitle()
+
+ $tip.find('.tooltip-inner')[this.options.html ? 'html' : 'text'](title)
+ $tip.removeClass('fade in top bottom left right')
+ }
+
+ Tooltip.prototype.hide = function () {
+ var that = this
+ var $tip = this.tip()
+ var e = $.Event('hide.bs.' + this.type)
+
+ function complete() {
+ if (that.hoverState != 'in') $tip.detach()
+ that.$element.trigger('hidden.bs.' + that.type)
+ }
+
+ this.$element.trigger(e)
+
+ if (e.isDefaultPrevented()) return
+
+ $tip.removeClass('in')
+
+ $.support.transition && this.$tip.hasClass('fade') ?
+ $tip
+ .one($.support.transition.end, complete)
+ .emulateTransitionEnd(150) :
+ complete()
+
+ this.hoverState = null
+
+ return this
+ }
+
+ Tooltip.prototype.fixTitle = function () {
+ var $e = this.$element
+ if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') {
+ $e.attr('data-original-title', $e.attr('title') || '').attr('title', '')
+ }
+ }
+
+ Tooltip.prototype.hasContent = function () {
+ return this.getTitle()
+ }
+
+ Tooltip.prototype.getPosition = function () {
+ var el = this.$element[0]
+ return $.extend({}, (typeof el.getBoundingClientRect == 'function') ? el.getBoundingClientRect() : {
+ width: el.offsetWidth,
+ height: el.offsetHeight
+ }, this.$element.offset())
+ }
+
+ Tooltip.prototype.getCalculatedOffset = function (placement, pos, actualWidth, actualHeight) {
+ return placement == 'bottom' ? { top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2 } :
+ placement == 'top' ? { top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2 } :
+ placement == 'left' ? { top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth } :
+ /* placement == 'right' */ { top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width }
+ }
+
+ Tooltip.prototype.getTitle = function () {
+ var title
+ var $e = this.$element
+ var o = this.options
+
+ title = $e.attr('data-original-title')
+ || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title)
+
+ return title
+ }
+
+ Tooltip.prototype.tip = function () {
+ return this.$tip = this.$tip || $(this.options.template)
+ }
+
+ Tooltip.prototype.arrow = function () {
+ return this.$arrow = this.$arrow || this.tip().find('.tooltip-arrow')
+ }
+
+ Tooltip.prototype.validate = function () {
+ if (!this.$element[0].parentNode) {
+ this.hide()
+ this.$element = null
+ this.options = null
+ }
+ }
+
+ Tooltip.prototype.enable = function () {
+ this.enabled = true
+ }
+
+ Tooltip.prototype.disable = function () {
+ this.enabled = false
+ }
+
+ Tooltip.prototype.toggleEnabled = function () {
+ this.enabled = !this.enabled
+ }
+
+ Tooltip.prototype.toggle = function (e) {
+ var self = e ? $(e.currentTarget)[this.type](this.getDelegateOptions()).data('bs.' + this.type) : this
+ self.tip().hasClass('in') ? self.leave(self) : self.enter(self)
+ }
+
+ Tooltip.prototype.destroy = function () {
+ clearTimeout(this.timeout)
+ this.hide().$element.off('.' + this.type).removeData('bs.' + this.type)
+ }
+
+
+ // TOOLTIP PLUGIN DEFINITION
+ // =========================
+
+ var old = $.fn.tooltip
+
+ $.fn.tooltip = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.tooltip')
+ var options = typeof option == 'object' && option
+
+ if (!data && option == 'destroy') return
+ if (!data) $this.data('bs.tooltip', (data = new Tooltip(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.tooltip.Constructor = Tooltip
+
+
+ // TOOLTIP NO CONFLICT
+ // ===================
+
+ $.fn.tooltip.noConflict = function () {
+ $.fn.tooltip = old
+ return this
+ }
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: popover.js v3.1.0
+ * http://getbootstrap.com/javascript/#popovers
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // POPOVER PUBLIC CLASS DEFINITION
+ // ===============================
+
+ var Popover = function (element, options) {
+ this.init('popover', element, options)
+ }
+
+ if (!$.fn.tooltip) throw new Error('Popover requires tooltip.js')
+
+ Popover.DEFAULTS = $.extend({}, $.fn.tooltip.Constructor.DEFAULTS, {
+ placement: 'right',
+ trigger: 'click',
+ content: '',
+ template: '<div class="popover"><div class="arrow"></div><h3 class="popover-title"></h3><div class="popover-content"></div></div>'
+ })
+
+
+ // NOTE: POPOVER EXTENDS tooltip.js
+ // ================================
+
+ Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype)
+
+ Popover.prototype.constructor = Popover
+
+ Popover.prototype.getDefaults = function () {
+ return Popover.DEFAULTS
+ }
+
+ Popover.prototype.setContent = function () {
+ var $tip = this.tip()
+ var title = this.getTitle()
+ var content = this.getContent()
+
+ $tip.find('.popover-title')[this.options.html ? 'html' : 'text'](title)
+ $tip.find('.popover-content')[ // we use append for html objects to maintain js events
+ this.options.html ? (typeof content == 'string' ? 'html' : 'append') : 'text'
+ ](content)
+
+ $tip.removeClass('fade top bottom left right in')
+
+ // IE8 doesn't accept hiding via the `:empty` pseudo selector, we have to do
+ // this manually by checking the contents.
+ if (!$tip.find('.popover-title').html()) $tip.find('.popover-title').hide()
+ }
+
+ Popover.prototype.hasContent = function () {
+ return this.getTitle() || this.getContent()
+ }
+
+ Popover.prototype.getContent = function () {
+ var $e = this.$element
+ var o = this.options
+
+ return $e.attr('data-content')
+ || (typeof o.content == 'function' ?
+ o.content.call($e[0]) :
+ o.content)
+ }
+
+ Popover.prototype.arrow = function () {
+ return this.$arrow = this.$arrow || this.tip().find('.arrow')
+ }
+
+ Popover.prototype.tip = function () {
+ if (!this.$tip) this.$tip = $(this.options.template)
+ return this.$tip
+ }
+
+
+ // POPOVER PLUGIN DEFINITION
+ // =========================
+
+ var old = $.fn.popover
+
+ $.fn.popover = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.popover')
+ var options = typeof option == 'object' && option
+
+ if (!data && option == 'destroy') return
+ if (!data) $this.data('bs.popover', (data = new Popover(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.popover.Constructor = Popover
+
+
+ // POPOVER NO CONFLICT
+ // ===================
+
+ $.fn.popover.noConflict = function () {
+ $.fn.popover = old
+ return this
+ }
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: scrollspy.js v3.1.0
+ * http://getbootstrap.com/javascript/#scrollspy
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // SCROLLSPY CLASS DEFINITION
+ // ==========================
+
+ function ScrollSpy(element, options) {
+ var href
+ var process = $.proxy(this.process, this)
+
+ this.$element = $(element).is('body') ? $(window) : $(element)
+ this.$body = $('body')
+ this.$scrollElement = this.$element.on('scroll.bs.scroll-spy.data-api', process)
+ this.options = $.extend({}, ScrollSpy.DEFAULTS, options)
+ this.selector = (this.options.target
+ || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
+ || '') + ' .nav li > a'
+ this.offsets = $([])
+ this.targets = $([])
+ this.activeTarget = null
+
+ this.refresh()
+ this.process()
+ }
+
+ ScrollSpy.DEFAULTS = {
+ offset: 10
+ }
+
+ ScrollSpy.prototype.refresh = function () {
+ var offsetMethod = this.$element[0] == window ? 'offset' : 'position'
+
+ this.offsets = $([])
+ this.targets = $([])
+
+ var self = this
+ var $targets = this.$body
+ .find(this.selector)
+ .map(function () {
+ var $el = $(this)
+ var href = $el.data('target') || $el.attr('href')
+ var $href = /^#./.test(href) && $(href)
+
+ return ($href
+ && $href.length
+ && $href.is(':visible')
+ && [[ $href[offsetMethod]().top + (!$.isWindow(self.$scrollElement.get(0)) && self.$scrollElement.scrollTop()), href ]]) || null
+ })
+ .sort(function (a, b) { return a[0] - b[0] })
+ .each(function () {
+ self.offsets.push(this[0])
+ self.targets.push(this[1])
+ })
+ }
+
+ ScrollSpy.prototype.process = function () {
+ var scrollTop = this.$scrollElement.scrollTop() + this.options.offset
+ var scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight
+ var maxScroll = scrollHeight - this.$scrollElement.height()
+ var offsets = this.offsets
+ var targets = this.targets
+ var activeTarget = this.activeTarget
+ var i
+
+ if (scrollTop >= maxScroll) {
+ return activeTarget != (i = targets.last()[0]) && this.activate(i)
+ }
+
+ if (activeTarget && scrollTop <= offsets[0]) {
+ return activeTarget != (i = targets[0]) && this.activate(i)
+ }
+
+ for (i = offsets.length; i--;) {
+ activeTarget != targets[i]
+ && scrollTop >= offsets[i]
+ && (!offsets[i + 1] || scrollTop <= offsets[i + 1])
+ && this.activate( targets[i] )
+ }
+ }
+
+ ScrollSpy.prototype.activate = function (target) {
+ this.activeTarget = target
+
+ $(this.selector)
+ .parentsUntil(this.options.target, '.active')
+ .removeClass('active')
+
+ var selector = this.selector +
+ '[data-target="' + target + '"],' +
+ this.selector + '[href="' + target + '"]'
+
+ var active = $(selector)
+ .parents('li')
+ .addClass('active')
+
+ if (active.parent('.dropdown-menu').length) {
+ active = active
+ .closest('li.dropdown')
+ .addClass('active')
+ }
+
+ active.trigger('activate.bs.scrollspy')
+ }
+
+
+ // SCROLLSPY PLUGIN DEFINITION
+ // ===========================
+
+ var old = $.fn.scrollspy
+
+ $.fn.scrollspy = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.scrollspy')
+ var options = typeof option == 'object' && option
+
+ if (!data) $this.data('bs.scrollspy', (data = new ScrollSpy(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.scrollspy.Constructor = ScrollSpy
+
+
+ // SCROLLSPY NO CONFLICT
+ // =====================
+
+ $.fn.scrollspy.noConflict = function () {
+ $.fn.scrollspy = old
+ return this
+ }
+
+
+ // SCROLLSPY DATA-API
+ // ==================
+
+ $(window).on('load', function () {
+ $('[data-spy="scroll"]').each(function () {
+ var $spy = $(this)
+ $spy.scrollspy($spy.data())
+ })
+ })
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: tab.js v3.1.0
+ * http://getbootstrap.com/javascript/#tabs
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // TAB CLASS DEFINITION
+ // ====================
+
+ var Tab = function (element) {
+ this.element = $(element)
+ }
+
+ Tab.prototype.show = function () {
+ var $this = this.element
+ var $ul = $this.closest('ul:not(.dropdown-menu)')
+ var selector = $this.data('target')
+
+ if (!selector) {
+ selector = $this.attr('href')
+ selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
+ }
+
+ if ($this.parent('li').hasClass('active')) return
+
+ var previous = $ul.find('.active:last a')[0]
+ var e = $.Event('show.bs.tab', {
+ relatedTarget: previous
+ })
+
+ $this.trigger(e)
+
+ if (e.isDefaultPrevented()) return
+
+ var $target = $(selector)
+
+ this.activate($this.parent('li'), $ul)
+ this.activate($target, $target.parent(), function () {
+ $this.trigger({
+ type: 'shown.bs.tab',
+ relatedTarget: previous
+ })
+ })
+ }
+
+ Tab.prototype.activate = function (element, container, callback) {
+ var $active = container.find('> .active')
+ var transition = callback
+ && $.support.transition
+ && $active.hasClass('fade')
+
+ function next() {
+ $active
+ .removeClass('active')
+ .find('> .dropdown-menu > .active')
+ .removeClass('active')
+
+ element.addClass('active')
+
+ if (transition) {
+ element[0].offsetWidth // reflow for transition
+ element.addClass('in')
+ } else {
+ element.removeClass('fade')
+ }
+
+ if (element.parent('.dropdown-menu')) {
+ element.closest('li.dropdown').addClass('active')
+ }
+
+ callback && callback()
+ }
+
+ transition ?
+ $active
+ .one($.support.transition.end, next)
+ .emulateTransitionEnd(150) :
+ next()
+
+ $active.removeClass('in')
+ }
+
+
+ // TAB PLUGIN DEFINITION
+ // =====================
+
+ var old = $.fn.tab
+
+ $.fn.tab = function ( option ) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.tab')
+
+ if (!data) $this.data('bs.tab', (data = new Tab(this)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.tab.Constructor = Tab
+
+
+ // TAB NO CONFLICT
+ // ===============
+
+ $.fn.tab.noConflict = function () {
+ $.fn.tab = old
+ return this
+ }
+
+
+ // TAB DATA-API
+ // ============
+
+ $(document).on('click.bs.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) {
+ e.preventDefault()
+ $(this).tab('show')
+ })
+
+}(jQuery);
+
+/* ========================================================================
+ * Bootstrap: affix.js v3.1.0
+ * http://getbootstrap.com/javascript/#affix
+ * ========================================================================
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ * ======================================================================== */
+
+
++function ($) {
+ 'use strict';
+
+ // AFFIX CLASS DEFINITION
+ // ======================
+
+ var Affix = function (element, options) {
+ this.options = $.extend({}, Affix.DEFAULTS, options)
+ this.$window = $(window)
+ .on('scroll.bs.affix.data-api', $.proxy(this.checkPosition, this))
+ .on('click.bs.affix.data-api', $.proxy(this.checkPositionWithEventLoop, this))
+
+ this.$element = $(element)
+ this.affixed =
+ this.unpin =
+ this.pinnedOffset = null
+
+ this.checkPosition()
+ }
+
+ Affix.RESET = 'affix affix-top affix-bottom'
+
+ Affix.DEFAULTS = {
+ offset: 0
+ }
+
+ Affix.prototype.getPinnedOffset = function () {
+ if (this.pinnedOffset) return this.pinnedOffset
+ this.$element.removeClass(Affix.RESET).addClass('affix')
+ var scrollTop = this.$window.scrollTop()
+ var position = this.$element.offset()
+ return (this.pinnedOffset = position.top - scrollTop)
+ }
+
+ Affix.prototype.checkPositionWithEventLoop = function () {
+ setTimeout($.proxy(this.checkPosition, this), 1)
+ }
+
+ Affix.prototype.checkPosition = function () {
+ if (!this.$element.is(':visible')) return
+
+ var scrollHeight = $(document).height()
+ var scrollTop = this.$window.scrollTop()
+ var position = this.$element.offset()
+ var offset = this.options.offset
+ var offsetTop = offset.top
+ var offsetBottom = offset.bottom
+
+ if (this.affixed == 'top') position.top += scrollTop
+
+ if (typeof offset != 'object') offsetBottom = offsetTop = offset
+ if (typeof offsetTop == 'function') offsetTop = offset.top(this.$element)
+ if (typeof offsetBottom == 'function') offsetBottom = offset.bottom(this.$element)
+
+ var affix = this.unpin != null && (scrollTop + this.unpin <= position.top) ? false :
+ offsetBottom != null && (position.top + this.$element.height() >= scrollHeight - offsetBottom) ? 'bottom' :
+ offsetTop != null && (scrollTop <= offsetTop) ? 'top' : false
+
+ if (this.affixed === affix) return
+ if (this.unpin) this.$element.css('top', '')
+
+ var affixType = 'affix' + (affix ? '-' + affix : '')
+ var e = $.Event(affixType + '.bs.affix')
+
+ this.$element.trigger(e)
+
+ if (e.isDefaultPrevented()) return
+
+ this.affixed = affix
+ this.unpin = affix == 'bottom' ? this.getPinnedOffset() : null
+
+ this.$element
+ .removeClass(Affix.RESET)
+ .addClass(affixType)
+ .trigger($.Event(affixType.replace('affix', 'affixed')))
+
+ if (affix == 'bottom') {
+ this.$element.offset({ top: scrollHeight - offsetBottom - this.$element.height() })
+ }
+ }
+
+
+ // AFFIX PLUGIN DEFINITION
+ // =======================
+
+ var old = $.fn.affix
+
+ $.fn.affix = function (option) {
+ return this.each(function () {
+ var $this = $(this)
+ var data = $this.data('bs.affix')
+ var options = typeof option == 'object' && option
+
+ if (!data) $this.data('bs.affix', (data = new Affix(this, options)))
+ if (typeof option == 'string') data[option]()
+ })
+ }
+
+ $.fn.affix.Constructor = Affix
+
+
+ // AFFIX NO CONFLICT
+ // =================
+
+ $.fn.affix.noConflict = function () {
+ $.fn.affix = old
+ return this
+ }
+
+
+ // AFFIX DATA-API
+ // ==============
+
+ $(window).on('load', function () {
+ $('[data-spy="affix"]').each(function () {
+ var $spy = $(this)
+ var data = $spy.data()
+
+ data.offset = data.offset || {}
+
+ if (data.offsetBottom) data.offset.bottom = data.offsetBottom
+ if (data.offsetTop) data.offset.top = data.offsetTop
+
+ $spy.affix(data)
+ })
+ })
+
+}(jQuery);
--- /dev/null
+/*!
+ * Bootstrap v3.1.0 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+if("undefined"==typeof jQuery)throw new Error("Bootstrap requires jQuery");+function(a){"use strict";function b(){var a=document.createElement("bootstrap"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(var c in b)if(void 0!==a.style[c])return{end:b[c]};return!1}a.fn.emulateTransitionEnd=function(b){var c=!1,d=this;a(this).one(a.support.transition.end,function(){c=!0});var e=function(){c||a(d).trigger(a.support.transition.end)};return setTimeout(e,b),this},a(function(){a.support.transition=b()})}(jQuery),+function(a){"use strict";var b='[data-dismiss="alert"]',c=function(c){a(c).on("click",b,this.close)};c.prototype.close=function(b){function c(){f.trigger("closed.bs.alert").remove()}var d=a(this),e=d.attr("data-target");e||(e=d.attr("href"),e=e&&e.replace(/.*(?=#[^\s]*$)/,""));var 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\ No newline at end of file
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: CLI
+title: "Overview"
+
+...
+
+The @arv@ CLI tool provides a set of wrappers to make API calls. Additionally, it provides access to a number of subcommands.
+
+h3. Wrappers for API calls
+
+See the "arv reference":{{site.baseurl}}/sdk/cli/reference.html page.
+
+h3. Subcommands
+
+See the "arv subcommands":{{site.baseurl}}/sdk/cli/subcommands.html page.
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: CLI
+title: "Installation"
+
+...
+
+To use the @arv@ command, you can either install the @arvados-cli@ gem via RubyGems or build and install the package from source.
+
+h4. Prerequisites: Ruby >= 2.1.0 and curl libraries
+
+Make sure you have "Ruby and bundler":{{site.baseurl}}/install/install-manual-prerequisites-ruby.html installed.
+
+Install curl libraries with your system's package manager. For example, on Debian or Ubuntu:
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo apt-get install libcurl3 libcurl3-gnutls libcurl4-openssl-dev</code>
+</pre>
+</notextile>
+
+h4. Option 1: install with RubyGems
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo gem install arvados-cli</code>
+</pre>
+</notextile>
+
+h4. Option 2: build and install from source
+
+<notextile>
+<pre>
+$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">cd arvados/sdk/cli</code>
+$ <code class="userinput">gem build arvados-cli.gemspec</code>
+$ <code class="userinput">sudo gem install arvados-cli-*.gem</code>
+</pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: CLI
+title: "arv reference"
+...
+
+_In order to use the @arv@ command, make sure that you have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html_
+
+h3. Usage
+
+@arv [global_options] resource_type resource_method [method_parameters]@
+
+h4. Global options
+
+- @--format=json@ := Output response as JSON. This is the default format.
+
+- @--format=yaml@ := Output response as YAML
+
+- @--format=uuid@ := Output only the UUIDs of object(s) in the API response, one per line.
+
+
+h3. Resource types and methods
+
+Get list of resource types
+@arv --resources@
+
+Get list of resource methods for the "user" resource type
+@arv user --help@
+
+
+h3. Basic examples
+
+Get record for current user
+@arv user current@
+
+Get entire record for some specific user
+@arv user get --uuid 6dnxa-tpzed-iimd25zhzh84gbk@
+
+Update user record
+@arv user update --uuid 6dnxa-tpzed-iimd25zhzh84gbk --first-name "Bob"@
+
+Get list of groups
+@arv group list@
+
+Delete a group
+@arv group delete --uuid 6dnxa-j7d0g-iw7i6n43d37jtog@
+
+
+h3. Common commands
+
+Most @arv@ resources accept the following commands:
+
+* @get@
+* @list@
+* @create@
+* @update@
+* @delete@
+
+
+h4. @list@
+
+Arguments accepted by the @list@ subcommand include:
+
+<pre>
+ --limit, -l <i>: Maximum number of resources to return.
+ --offset, -o <i>: Number of users to skip before first returned record.
+ --filters, -f <s>: Conditions for filtering users.
+ --order, -r <s>: Order in which to return matching users.
+ --select, -s <s>: Select which fields to return
+ --distinct, -d: Return each distinct object
+</pre>
+
+The @--filters@ option takes a string describing a JSON list of filters on which the returned resources should be returned. Each filter is a three-element list of _[field, operator, value]_, where the _operator_ may be one of @=@, @<@, @<=@, @>@, @>=@, @!=@, @like@, or @ilike@.
+
+Example:
+
+@arv collection list --filters '[["name", "=", "PGP VAR inputs"], ["created_at", ">=", "2014-10-01"]]'@
+
+will return a list of all collections visible to the current user which are named "PGP VAR inputs" and were created on or after October 1, 2014.
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: CLI
+title: "arv subcommands"
+
+...
+
+_In order to use the @arv@ command, make sure that you have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html_
+
+h3(#arv-create). arv create
+
+@arv create@ can be used to create Arvados objects from the command line. Arv create opens up the editor of your choice (set the EDITOR environment variable) and allows you to type or paste a json or yaml description. When saved the object will be created on the API server, if it passes validation.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv create --help</code>
+Options:
+ --project-uuid, -p <s>: Project uuid in which to create the object
+ --help, -h: Show this message
+</pre>
+</notextile>
+
+h3(#arv-edit). arv edit
+
+@arv edit@ can be used to edit Arvados objects from the command line. Arv edit opens up the editor of your choice (set the EDITOR environment variable) with the json or yaml description of the object. Saving the file will update the Arvados object on the API server, if it passes validation.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv edit --help</code>
+Arvados command line client
+Usage: arv edit [uuid] [fields...]
+
+Fetch the specified Arvados object, select the specified fields,
+open an interactive text editor on a text representation (json or
+yaml, use --format) and then update the object. Will use 'nano'
+by default, customize with the EDITOR or VISUAL environment variable.
+</pre>
+</notextile>
+
+h3(#arv-copy). arv copy
+
+@arv copy@ can be used to copy a pipeline instance, template or collection from one Arvados instance to another. It takes care of copying the object and all its dependencies.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv copy --help</code>
+usage: arv-copy [-h] [-v] [--progress] [--no-progress] [-f] --src
+ SOURCE_ARVADOS --dst DESTINATION_ARVADOS [--recursive]
+ [--no-recursive] [--dst-git-repo DST_GIT_REPO]
+ [--project-uuid PROJECT_UUID] [--retries RETRIES]
+ object_uuid
+
+Copy a pipeline instance, template or collection from one Arvados instance to
+another.
+
+positional arguments:
+ object_uuid The UUID of the object to be copied.
+
+optional arguments:
+ -h, --help show this help message and exit
+ -v, --verbose Verbose output.
+ --progress Report progress on copying collections. (default)
+ --no-progress Do not report progress on copying collections.
+ -f, --force Perform copy even if the object appears to exist at
+ the remote destination.
+ --src SOURCE_ARVADOS The name of the source Arvados instance (required).
+ May be either a pathname to a config file, or the
+ basename of a file in
+ $HOME/.config/arvados/instance_name.conf.
+ --dst DESTINATION_ARVADOS
+ The name of the destination Arvados instance
+ (required). May be either a pathname to a config file,
+ or the basename of a file in
+ $HOME/.config/arvados/instance_name.conf.
+ --recursive Recursively copy any dependencies for this object.
+ (default)
+ --no-recursive Do not copy any dependencies. NOTE: if this option is
+ given, the copied object will need to be updated
+ manually in order to be functional.
+ --dst-git-repo DST_GIT_REPO
+ The name of the destination git repository. Required
+ when copying a pipeline recursively.
+ --project-uuid PROJECT_UUID
+ The UUID of the project at the destination to which
+ the pipeline should be copied.
+ --retries RETRIES Maximum number of times to retry server requests that
+ encounter temporary failures (e.g., server down).
+ Default 3.
+</pre>
+</notextile>
+
+h3(#arv-tag). arv tag
+
+@arv tag@ is used to tag Arvados objects.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv tag --help</code>
+
+Usage:
+arv tag add tag1 [tag2 ...] --object object_uuid1 [object_uuid2...]
+arv tag remove tag1 [tag2 ...] --object object_uuid1 [object_uuid2...]
+arv tag remove --all
+
+ --dry-run, -n: Don't actually do anything
+ --verbose, -v: Print some things on stderr
+ --uuid, -u: Return the UUIDs of the objects in the response, one per
+ line (default)
+ --json, -j: Return the entire response received from the API server, as
+ a JSON object
+ --human, -h: Return the response received from the API server, as a JSON
+ object with whitespace added for human consumption
+ --pretty, -p: Synonym of --human
+ --yaml, -y: Return the response received from the API server, in YAML
+ format
+ --help, -e: Show this message
+</pre>
+</notextile>
+
+
+h3(#arv-ws). arv ws
+
+@arv ws@ provides access to the websockets event stream.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv ws --help</code>
+usage: arv-ws [-h] [-u UUID] [-f FILTERS]
+ [--poll-interval POLL_INTERVAL | --no-poll]
+ [-p PIPELINE | -j JOB]
+
+optional arguments:
+ -h, --help show this help message and exit
+ -u UUID, --uuid UUID Filter events on object_uuid
+ -f FILTERS, --filters FILTERS
+ Arvados query filter to apply to log events (JSON
+ encoded)
+ --poll-interval POLL_INTERVAL
+ If websockets is not available, specify the polling
+ interval, default is every 15 seconds
+ --no-poll Do not poll if websockets are not available, just fail
+ -p PIPELINE, --pipeline PIPELINE
+ Supply pipeline uuid, print log output from pipeline
+ and its jobs
+ -j JOB, --job JOB Supply job uuid, print log output from jobs
+</pre>
+</notextile>
+
+h3(#arv-keep). arv keep
+
+@arv keep@ provides access to the Keep storage service.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv keep --help</code>
+Usage: arv keep [method] [--parameters]
+Use 'arv keep [method] --help' to get more information about specific methods.
+
+Available methods: ls, get, put, less, check, docker
+</pre>
+</notextile>
+
+h3(#arv-keep-ls). arv keep ls
+
+<notextile>
+<pre>
+$ <code class="userinput">arv keep ls --help</code>
+usage: arv-ls [-h] [--retries RETRIES] [-s] locator
+
+List contents of a manifest
+
+positional arguments:
+ locator Collection UUID or locator
+
+optional arguments:
+ -h, --help show this help message and exit
+ --retries RETRIES Maximum number of times to retry server requests that
+ encounter temporary failures (e.g., server down). Default
+ 3.
+ -s List file sizes, in KiB.
+</pre>
+</notextile>
+
+h3(#arv-keep-get). arv keep get
+
+<notextile>
+<pre>
+$ <code class="userinput">arv keep get --help</code>
+usage: arv-get [-h] [--retries RETRIES]
+ [--progress | --no-progress | --batch-progress]
+ [--hash HASH | --md5sum] [-n] [-r] [-f | --skip-existing]
+ locator [destination]
+
+Copy data from Keep to a local file or pipe.
+
+positional arguments:
+ locator Collection locator, optionally with a file path or
+ prefix.
+ destination Local file or directory where the data is to be written.
+ Default: /dev/stdout.
+
+optional arguments:
+ -h, --help show this help message and exit
+ --retries RETRIES Maximum number of times to retry server requests that
+ encounter temporary failures (e.g., server down). Default
+ 3.
+ --progress Display human-readable progress on stderr (bytes and, if
+ possible, percentage of total data size). This is the
+ default behavior when it is not expected to interfere
+ with the output: specifically, stderr is a tty _and_
+ either stdout is not a tty, or output is being written to
+ named files rather than stdout.
+ --no-progress Do not display human-readable progress on stderr.
+ --batch-progress Display machine-readable progress on stderr (bytes and,
+ if known, total data size).
+ --hash HASH Display the hash of each file as it is read from Keep,
+ using the given hash algorithm. Supported algorithms
+ include md5, sha1, sha224, sha256, sha384, and sha512.
+ --md5sum Display the MD5 hash of each file as it is read from
+ Keep.
+ -n Do not write any data -- just read from Keep, and report
+ md5sums if requested.
+ -r Retrieve all files in the specified collection/prefix.
+ This is the default behavior if the "locator" argument
+ ends with a forward slash.
+ -f Overwrite existing files while writing. The default
+ behavior is to refuse to write *anything* if any of the
+ output files already exist. As a special case, -f is not
+ needed to write to /dev/stdout.
+ --skip-existing Skip files that already exist. The default behavior is to
+ refuse to write *anything* if any files exist that would
+ have to be overwritten. This option causes even devices,
+ sockets, and fifos to be skipped.
+</pre>
+</notextile>
+
+h3(#arv-keep-put). arv keep put
+
+<notextile>
+<pre>
+$ <code class="userinput">arv keep put --help</code>
+usage: arv-put [-h] [--max-manifest-depth N | --normalize]
+ [--as-stream | --stream | --as-manifest | --in-manifest | --manifest | --as-raw | --raw]
+ [--use-filename FILENAME] [--filename FILENAME]
+ [--portable-data-hash] [--project-uuid UUID] [--name NAME]
+ [--progress | --no-progress | --batch-progress]
+ [--resume | --no-resume] [--retries RETRIES]
+ [path [path ...]]
+
+Copy data from the local filesystem to Keep.
+
+positional arguments:
+ path Local file or directory. Default: read from standard
+ input.
+
+optional arguments:
+ -h, --help show this help message and exit
+ --max-manifest-depth N
+ Maximum depth of directory tree to represent in the
+ manifest structure. A directory structure deeper than
+ this will be represented as a single stream in the
+ manifest. If N=0, the manifest will contain a single
+ stream. Default: -1 (unlimited), i.e., exactly one
+ manifest stream per filesystem directory that contains
+ files.
+ --normalize Normalize the manifest by re-ordering files and
+ streams after writing data.
+ --as-stream Synonym for --stream.
+ --stream Store the file content and display the resulting
+ manifest on stdout. Do not write the manifest to Keep
+ or save a Collection object in Arvados.
+ --as-manifest Synonym for --manifest.
+ --in-manifest Synonym for --manifest.
+ --manifest Store the file data and resulting manifest in Keep,
+ save a Collection object in Arvados, and display the
+ manifest locator (Collection uuid) on stdout. This is
+ the default behavior.
+ --as-raw Synonym for --raw.
+ --raw Store the file content and display the data block
+ locators on stdout, separated by commas, with a
+ trailing newline. Do not store a manifest.
+ --use-filename FILENAME
+ Synonym for --filename.
+ --filename FILENAME Use the given filename in the manifest, instead of the
+ name of the local file. This is useful when "-" or
+ "/dev/stdin" is given as an input file. It can be used
+ only if there is exactly one path given and it is not
+ a directory. Implies --manifest.
+ --portable-data-hash Print the portable data hash instead of the Arvados
+ UUID for the collection created by the upload.
+ --project-uuid UUID Store the collection in the specified project, instead
+ of your Home project.
+ --name NAME Save the collection with the specified name.
+ --progress Display human-readable progress on stderr (bytes and,
+ if possible, percentage of total data size). This is
+ the default behavior when stderr is a tty.
+ --no-progress Do not display human-readable progress on stderr, even
+ if stderr is a tty.
+ --batch-progress Display machine-readable progress on stderr (bytes
+ and, if known, total data size).
+ --resume Continue interrupted uploads from cached state
+ (default).
+ --no-resume Do not continue interrupted uploads from cached state.
+ --retries RETRIES Maximum number of times to retry server requests that
+ encounter temporary failures (e.g., server down).
+ Default 3.
+</pre>
+</notextile>
+
+
+h3(#arv-pipeline-run). arv pipeline run
+
+@arv pipeline run@ can be used to start a pipeline run from the command line.
+
+The User Guide has a page with a bit more information on "using arv pipeline run":{{site.baseurl}}/user/topics/running-pipeline-command-line.html.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv pipeline run --help</code>
+Options:
+ --dry-run, -n: Do not start any new jobs or wait for existing jobs to
+ finish. Just find out whether jobs are finished,
+ queued, or running for each component.
+ --status-text <s>: Store plain text status in given file. (Default:
+ /dev/stdout)
+ --status-json <s>: Store json-formatted pipeline in given file. (Default:
+ /dev/null)
+ --no-wait: Do not wait for jobs to finish. Just look up status,
+ submit new jobs if needed, and exit.
+ --no-reuse: Do not reuse existing jobs to satisfy pipeline
+ components. Submit a new job for every component.
+ --debug, -d: Print extra debugging information on stderr.
+ --debug-level <i>: Set debug verbosity level.
+ --template <s>: UUID of pipeline template, or path to local pipeline
+ template file.
+ --instance <s>: UUID of pipeline instance.
+ --submit: Submit the pipeline instance to the server, and exit.
+ Let the Crunch dispatch service satisfy the components
+ by finding/running jobs.
+ --run-pipeline-here: Manage the pipeline instance in-process. Submit jobs
+ to Crunch as needed. Do not exit until the pipeline
+ finishes (or fails).
+ --run-jobs-here: Run jobs in the local terminal session instead of
+ submitting them to Crunch. Implies
+ --run-pipeline-here. Note: this results in a
+ significantly different job execution environment, and
+ some Crunch features are not supported. It can be
+ necessary to modify a pipeline in order to make it run
+ this way.
+ --run-here: Synonym for --run-jobs-here.
+ --description <s>: Description for the pipeline instance.
+ --version, -v: Print version and exit
+ --help, -h: Show this message
+</pre>
+</notextile>
+
+h3(#arv-run). arv run
+
+The @arv-run@ command creates Arvados pipelines at the command line that fan out to multiple concurrent tasks across Arvados compute nodes.
+
+The User Guide has a page on "using arv-run":{{site.baseurl}}/user/topics/arv-run.html.
+
+<notextile>
+<pre>
+$ <code class="userinput">arv run --help</code>
+usage: arv-run [-h] [--retries RETRIES] [--dry-run] [--local]
+ [--docker-image DOCKER_IMAGE] [--ignore-rcode] [--no-reuse]
+ [--no-wait] [--project-uuid PROJECT_UUID] [--git-dir GIT_DIR]
+ [--repository REPOSITORY] [--script-version SCRIPT_VERSION]
+ ...
+
+positional arguments:
+ args
+
+optional arguments:
+ -h, --help show this help message and exit
+ --retries RETRIES Maximum number of times to retry server requests that
+ encounter temporary failures (e.g., server down).
+ Default 3.
+ --dry-run Print out the pipeline that would be submitted and
+ exit
+ --local Run locally using arv-run-pipeline-instance
+ --docker-image DOCKER_IMAGE
+ Docker image to use, default arvados/jobs
+ --ignore-rcode Commands that return non-zero return codes should not
+ be considered failed.
+ --no-reuse Do not reuse past jobs.
+ --no-wait Do not wait and display logs after submitting command,
+ just exit.
+ --project-uuid PROJECT_UUID
+ Parent project of the pipeline
+ --git-dir GIT_DIR Git repository passed to arv-crunch-job when using
+ --local
+ --repository REPOSITORY
+ repository field of component, default 'arvados'
+ --script-version SCRIPT_VERSION
+ script_version field of component, default 'master'
+</pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Go
+title: "Go SDK"
+
+...
+
+The Go ("Golang":http://golang.org) SDK provides a generic set of wrappers so you can make API calls easily.
+
+h3. Installation
+
+You don't need to install anything. Just import the client like this. The go tools will fetch the relevant code and dependencies for you.
+
+<notextile>{% code 'example_sdk_go_imports' as go %}</notextile>
+
+If you need pre-release client code, you can use the latest version from the repo by following "these instructions.":https://arvados.org/projects/arvados/wiki/Go#Using-Go-with-Arvados
+
+h3. Example
+
+You can save this source as a .go file and run it:
+
+<notextile>{% code 'example_sdk_go' as go %}</notextile>
+
+A few more usage examples can be found in the "services/keepproxy":https://arvados.org/projects/arvados/repository/revisions/master/show/services/keepproxy and "sdk/go/keepclient":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/go/keepclient directories in the arvados source tree.
--- /dev/null
+---
+layout: default
+navsection: sdk
+title: "Arvados SDK Reference"
+...
+
+This section documents how to access the Arvados API and Keep using various programming languages.
+
+* "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html
+* "Perl SDK":{{site.baseurl}}/sdk/perl/index.html
+* "Ruby SDK":{{site.baseurl}}/sdk/ruby/index.html
+* "Java SDK":{{site.baseurl}}/sdk/java/index.html
+* "Go SDK":{{site.baseurl}}/sdk/go/index.html
+* "Command line SDK":{{site.baseurl}}/sdk/cli/index.html ("arv")
+
+SDKs not yet implemented:
+
+* Rails SDK: Workbench uses an ActiveRecord-like interface to Arvados. This hasn't yet been extracted from Workbench and packaged as a gem.
+* R: We plan to support this, but it has not been implemented yet.
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Java
+title: "Java SDK"
+
+...
+
+The Java SDK provides a generic set of wrappers so you can make API calls in java.
+
+h3. Introdution
+
+* The Java SDK requires Java 6 or later
+
+* The Java SDK is implemented as a maven project. Hence, you would need a working
+maven environment to be able to build the source code. If you do not have maven setup,
+you may find the "Maven in 5 Minutes":http://maven.apache.org/guides/getting-started/maven-in-five-minutes.html link useful.
+
+* In this document $ARVADOS_HOME is used to refer to the directory where
+arvados code is cloned in your system. For ex: $ARVADOS_HOME = $HOME/arvados
+
+
+h3. Setting up the environment
+
+* The SDK requires a running Arvados API server. The following information
+ about the API server needs to be passed to the SDK using environment
+ variables or during the construction of the Arvados instance.
+
+<notextile>
+<pre>
+ARVADOS_API_TOKEN: API client token to be used to authorize with API server.
+
+ARVADOS_API_HOST: Host name of the API server.
+
+ARVADOS_API_HOST_INSECURE: Set this to true if you are using self-signed
+ certificates and would like to bypass certificate validations.
+</pre>
+</notextile>
+
+* Please see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for full details.
+
+
+h3. Building the Arvados SDK
+
+<notextile>
+<pre>
+$ <code class="userinput">cd $ARVADOS_HOME/sdk/java</code>
+
+$ <code class="userinput">mvn -Dmaven.test.skip=true clean package</code>
+ This will generate arvados sdk jar file in the target directory
+</pre>
+</notextile>
+
+
+h3. Implementing your code to use SDK
+
+* The following two sample programs serve as sample implementations using the SDK.
+<code class="userinput">$ARVADOS_HOME/sdk/java/ArvadosSDKJavaExample.java</code> is a simple program
+ that makes a few calls to API server.
+<code class="userinput">$ARVADOS_HOME/sdk/java/ArvadosSDKJavaExampleWithPrompt.java</code> can be
+ used to make calls to API server interactively.
+
+Please use these implementations to see how you would want use the SDK from your java program.
+
+Also, refer to <code class="userinput">$ARVADOS_HOME/arvados/sdk/java/src/test/java/org/arvados/sdk/java/ArvadosTest.java</code>
+for more sample API invocation examples.
+
+Below are the steps to compile and run these java program.
+
+* These programs create an instance of Arvados SDK class and use it to
+make various <code class="userinput">call</code> requests.
+
+* To compile the examples
+<notextile>
+<pre>
+$ <code class="userinput">javac -cp $ARVADOS_HOME/sdk/java/target/arvados-sdk-1.0-jar-with-dependencies.jar \
+ArvadosSDKJavaExample*.java</code>
+This results in the generation of the ArvadosSDKJavaExample*.class files
+in the same directory as the java files
+</pre>
+</notextile>
+
+* To run the samples
+<notextile>
+<pre>
+$ <code class="userinput">java -cp .:$ARVADOS_HOME/sdk/java/target/arvados-sdk-1.0-jar-with-dependencies.jar \
+ArvadosSDKJavaExample</code>
+$ <code class="userinput">java -cp .:$ARVADOS_HOME/sdk/java/target/arvados-sdk-1.0-jar-with-dependencies.jar \
+ArvadosSDKJavaExampleWithPrompt</code>
+</pre>
+</notextile>
+
+
+h3. Viewing and Managing SDK logging
+
+* SDK uses log4j logging
+
+* The default location of the log file is
+ <code class="userinput">$ARVADOS_HOME/sdk/java/log/arvados_sdk_java.log</code>
+
+* Update <code class="userinput">log4j.properties</code> file to change name and location of the log file.
+
+<notextile>
+<pre>
+$ <code class="userinput">nano $ARVADOS_HOME/sdk/java/src/main/resources/log4j.properties</code>
+and modify the <code class="userinput">log4j.appender.fileAppender.File</code> property as needed.
+
+Rebuild the SDK:
+$ <code class="userinput">mvn -Dmaven.test.skip=true clean package</code>
+</pre>
+</notextile>
+
+
+h3. Using the SDK in eclipse
+
+* To develop in eclipse, you can use the provided <code class="userinput">eclipse project</code>
+
+* Install "m2eclipse":https://www.eclipse.org/m2e/ plugin in your eclipse
+
+* Set <code class="userinput">M2_REPO</code> classpath variable in eclipse to point to your local repository.
+The local repository is usually located in your home directory at <code class="userinput">$HOME/.m2/repository</code>.
+
+<notextile>
+<pre>
+In Eclipse IDE:
+Window -> Preferences -> Java -> Build Path -> Classpath Variables
+ Click on the "New..." button and add a new
+ M2_REPO variable and set it to your local Maven repository
+</pre>
+</notextile>
+
+
+* Open the SDK project in eclipse
+<notextile>
+<pre>
+In Eclipse IDE:
+File -> Import -> Existing Projects into Workspace -> Next -> Browse
+ and select $ARVADOS_HOME/sdk/java
+</pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Perl
+title: "Perl SDK"
+
+...
+
+The Perl SDK provides a generic set of wrappers so you can make API calls easily.
+
+It should be treated as alpha/experimental. Currently, limitations include:
+* Verbose syntax.
+* No native Keep client.
+* No CPAN package.
+
+h3. Installation
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo apt-get install libjson-perl libio-socket-ssl-perl libwww-perl libipc-system-simple-perl</code>
+$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">cd arvados/sdk/perl</code>
+$ <code class="userinput">perl Makefile.PL</code>
+$ <code class="userinput">sudo make install</code>
+</pre>
+</notextile>
+
+h4. Test installation
+
+If the SDK is installed, @perl -MArvados -e ''@ should produce no errors.
+
+If your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ environment variables are set up correctly (see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for details), the following test script should work:
+
+<notextile>
+<pre>$ <code class="userinput">perl <<'EOF'
+use Arvados;
+my $arv = Arvados->new('apiVersion' => 'v1');
+my $me = $arv->{'users'}->{'current'}->execute;
+print ("arvados.v1.users.current.full_name = '", $me->{'full_name'}, "'\n");
+EOF</code>
+arvados.v1.users.current.full_name = 'Your Name'
+</pre>
+</notextile>
+
+h3. Examples
+
+Set up an API client user agent:
+
+<notextile>
+<pre><code class="userinput">my $arv = Arvados->new('apiVersion' => 'v1');
+</code></pre>
+</notextile>
+
+Get the User object for the current user:
+
+<notextile>
+<pre><code class="userinput">my $current_user = $arv->{'users'}->{'current'}->execute;
+</code></pre>
+</notextile>
+
+Get the UUID of an object that was retrieved using the SDK:
+
+<notextile>
+<pre><code class="userinput">my $current_user_uuid = $current_user->{'uuid'}
+</code></pre>
+</notextile>
+
+Retrieve an object by ID:
+
+<notextile>
+<pre><code class="userinput">my $some_user = $arv->{'users'}->{'get'}->execute('uuid' => $current_user_uuid);
+</code></pre>
+</notextile>
+
+Create an object:
+
+<notextile>
+<pre><code class="userinput">my $test_link = $arv->{'links'}->{'create'}->execute('link' => { 'link_class' => 'test', 'name' => 'test' });
+</code></pre>
+</notextile>
+
+Update an object:
+
+<notextile>
+<pre><code class="userinput">my $test_link = $arv->{'links'}->{'update'}->execute(
+ 'uuid' => $test_link->{'uuid'},
+ 'link' => { 'properties' => { 'foo' => 'bar' } });
+</code></pre>
+</notextile>
+
+Get a list of objects:
+
+<notextile>
+<pre><code class="userinput">my $repos = $arv->{'repositories'}->{'list'}->execute;
+print ("UUID of first repo returned is ", $repos->{'items'}->[0], "\n");
+</code></pre>
+</notextile>
+
+The SDK retrieves the list of API methods from the server at run time. Therefore, the set of available methods is determined by the server version rather than the SDK version.
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Python
+title: "Crunch utility libraries"
+
+...
+
+Several utility libraries are included with Arvados. They are intended to make it quicker and easier to write your own crunch scripts.
+
+* "Python SDK extras":#pythonsdk
+* "Toolkit wrappers":#toolkit_wrappers
+
+h2(#pythonsdk). Python SDK extras
+
+The Python SDK adds some convenience features that are particularly useful in crunch scripts, in addition to the standard set of API calls.
+
+In a crunch job, the environment variables @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ will be set up so the job has the privileges of the user who submitted the job.
+
+<pre>
+import arvados
+
+my_user = arvados.api().users().current().execute()
+my_uuid = my_user['uuid']
+</pre>
+
+h3. Get the current job and task parameters
+
+@arvados.current_job()@ and @arvados.current_task()@ are convenient ways to retrieve the current Job and Task, using the @JOB_UUID@ and @TASK_UUID@ environment variables provided to each crunch task process.
+
+<pre>
+this_job = arvados.current_job()
+this_task = arvados.current_task()
+this_job_input = this_job['script_parameters']['input']
+this_task_input = this_task['parameters']['input']
+</pre>
+
+h3(#one_task_per_input). Queue a task for each input file
+
+A common pattern for a crunch job is to run one task to scan the input, and one task per input file to do the work.
+
+The @one_task_per_input_file()@ function implements this pattern. Pseudocode:
+
+<pre>
+if this is the job's first (default) task:
+ for each file in the 'input' collection:
+ queue a new task, with parameters['input'] = file
+ exit
+else:
+ return
+</pre>
+
+Usage:
+
+<pre>
+import arvados
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True)
+
+# Now do the work on a single file
+my_input = this_task['parameters']['input']
+</pre>
+
+h3. Set the current task's output and success flag
+
+Each task in a crunch job must make an API call to record its output and set its @success@ attribute to True. The object returned by @current_task()@ has a @set_output()@ method to make the process more succinct.
+
+<pre>
+arvados.current_task().set_output(my_output_locator)
+</pre>
+
+h3. arvados_ipc.py
+
+Manage child processes and FIFOs (pipes).
+
+
+This module makes it easier to check the exit status of every child process you start, and close the unused end of each FIFO at the appropriate time.
+
+<pre>
+from arvados_ipc import *
+
+children = {}
+pipes = {}
+
+pipe_setup(pipes, 'hellopipe')
+if 0 == named_fork(children, 'child_a'):
+ pipe_closeallbut(pipes, ('hellopipe', 'w'))
+ os.write(pipes['hellopipe', 'w'], "Hello, parent.")
+ os._exit(0)
+
+pipe_closeallbut(pipes, ('hellopipe', 'r'))
+with os.fdopen(pipes['hellopipe', 'r'], 'rb') as f:
+ message = f.read()
+ sys.stderr.write("Child says: " + message + "\n")
+
+if not waitpid_and_check_children(children):
+ raise Exception("Child process exited non-zero.")
+</pre>
+
+The "crunch scripts" included with Arvados include some more examples of using the arvados_ipc module.
+
+h2(#toolkit_wrappers). Toolkit wrappers
+
+The following *arvados-∗.py* modules provide "extract, build, run" helpers to make it easy to incorporate common analysis tools in your crunch scripts.
+
+h3. arvados_bwa.py
+
+Build and run the "bwa":http://bio-bwa.sourceforge.net/bwa.shtml program.
+
+The module retrieves the bwa source code from Keep, using the job's @bwa_tbz@ parameter.
+
+<pre>
+import arvados_bwa
+arvados_bwa.run('aln', [ref_basename, '-'],
+ stdin=open(fastq_filename,'rb'),
+ stdout=open(aln_filename,'wb'))
+</pre>
+
+On qr1hi.arvadosapi.com, the source distribution @bwa-0.7.5a.tar.bz2@ is available in the collection @8b6e2c4916133e1d859c9e812861ce13+70@.
+
+<pre>
+{
+ "script_parameters":{
+ "bwa_tbz":"8b6e2c4916133e1d859c9e812861ce13+70",
+ ...
+ },
+ ...
+}
+</pre>
+
+h3. arvados_gatk2.py
+
+Extract and run the "Genome Analysis Toolkit":http://www.broadinstitute.org/gatk/ programs.
+
+The module retrieves the binary distribution tarball from Keep, using the job's @gatk_tbz@ parameter.
+
+<pre>
+arvados_gatk2.run(
+ args=[
+ '-nct', 8,
+ '-T', 'BaseRecalibrator',
+ '-R', ref_fasta_files[0],
+ '-I', input_bam_files[0],
+ '-o', recal_file,
+ ])
+</pre>
+
+On qr1hi.arvadosapi.com, the binary distribution @GenomeAnalysisTK-2.6-4.tar.bz2@ is available in the collection @5790482512cf6d5d6dfd50b7fd61e1d1+86@.
+
+The GATK data bundle is available in the collection @d237a90bae3870b3b033aea1e99de4a9+10820@.
+
+<pre>
+{
+ "script_parameters":{
+ "gatk_tbz":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820",
+ ...
+ },
+ ...
+}
+</pre>
+
+h3. arvados_samtools.py
+
+Build and run the "samtools":http://samtools.sourceforge.net/samtools.shtml program.
+
+
+The module retrieves the samtools source code from Keep, using the job's @samtools_tgz@ parameter.
+
+<pre>
+import arvados_samtools
+arvados_samtools.run('view', ['-S', '-b', '-'],
+ stdin=open(sam_filename,'rb'),
+ stdout=open(bam_filename,'wb'))
+</pre>
+
+On qr1hi.arvadosapi.com, the source distribution @samtools-0.1.19.tar.gz@ is available in the collection @c777e23cf13e5d5906abfdc08d84bfdb+74@.
+
+<pre>
+{
+ "script_parameters":{
+ "samtools_tgz":"c777e23cf13e5d5906abfdc08d84bfdb+74",
+ ...
+ },
+ ...
+}
+</pre>
+
+
+h3. arvados_picard.py
+
+Build and run the "picard":http://picard.sourceforge.net/command-line-overview.shtml program.
+
+
+The module retrieves the picard binary distribution from Keep, using the job's @picard_zip@ parameter.
+
+<pre>
+import arvados_picard
+arvados_picard.run(
+ 'FixMateInformation',
+ params={
+ 'i': input_bam_path,
+ 'o': '/dev/stdout',
+ 'quiet': 'true',
+ 'so': 'coordinate',
+ 'validation_stringency': 'LENIENT',
+ 'compression_level': 0
+ },
+ stdout=open('out.bam','wb'))
+</pre>
+
+On qr1hi.arvadosapi.com, the binary distribution @picard-tools-1.82.zip@ is available in the collection @687f74675c6a0e925dec619cc2bec25f+77@.
+
+<pre>
+{
+ "script_parameters":{
+ "picard_zip":"687f74675c6a0e925dec619cc2bec25f+77",
+ ...
+ },
+ ...
+}
+</pre>
+
+
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Python
+title: "PyDoc Reference"
+
+no_nav_left: true
+...
+
+notextile. <iframe src="arvados/" style="width:100%; height:100%; border:none" />
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Python
+title: "Python SDK"
+
+...
+
+The Python SDK provides a generic set of wrappers so you can make API calls easily. It performs some validation before connecting to the API server: for example, it refuses to do an API call if a required parameter is missing.
+
+The library also includes some conveniences for use in Crunch scripts; see "Crunch utility libraries":crunch-utility-libraries.html for details.
+
+h3. Installation
+
+If you are logged in to an Arvados VM, the Python SDK should be installed.
+
+To use the Python SDK elsewhere, you can either install the Python SDK via PyPI or build and install the package using the arvados source tree.
+
+{% include 'notebox_begin' %}
+The Python SDK requires Python 2.7
+{% include 'notebox_end' %}
+
+h4. Option 1: install with PyPI
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo apt-get install python-pip python-dev libattr1-dev libfuse-dev pkg-config python-yaml</code>
+$ <code class="userinput">sudo pip install arvados-python-client</code>
+</pre>
+</notextile>
+
+_If your version of @pip@ is 1.4 or newer, the @pip install@ command might give an error: "Could not find a version that satisfies the requirement arvados-python-client". If this happens, fix it by adding a @--pre@ flag:_
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo pip install --pre arvados-python-client</code>
+</pre>
+</notextile>
+
+h4. Option 2: install from distribution packages (Debian/Ubuntu only)
+
+First add @http://apt.arvados.org@ to your list of apt repositories:
+
+<notextile>
+<pre>
+$ <code class="userinput">echo "deb http://apt.arvados.org/ wheezy main" | sudo tee /etc/apt/sources.list.d/apt.arvados.org.list</code>
+</pre>
+</notextile>
+
+Then install the package:
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo apt-get update</code>
+$ <code class="userinput">sudo apt-get install python-arvados-python-client</code>
+</pre>
+</notextile>
+
+h4. Option 3: build and install from source
+
+<notextile>
+<pre>
+~$ <code class="userinput">sudo apt-get install python-dev libattr1-dev libfuse-dev pkg-config</code>
+~$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+~$ <code class="userinput">cd arvados/sdk/python</code>
+~/arvados/sdk/python$ <code class="userinput">sudo python setup.py install</code>
+</pre>
+</notextile>
+
+h4. Test installation
+
+If the SDK is installed and your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ environment variables are set up correctly (see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for details), @import arvados@ should produce no errors:
+
+<notextile>
+<pre>$ <code class="userinput">python</code>
+Python 2.7.4 (default, Sep 26 2013, 03:20:26)
+[GCC 4.7.3] on linux2
+Type "help", "copyright", "credits" or "license" for more information.
+>>> <code class="userinput">import arvados</code>
+>>> <code class="userinput">arvados.api('v1')</code>
+<apiclient.discovery.Resource object at 0x233bb50>
+</pre>
+</notextile>
+
+h3. Examples
+
+Get the User object for the current user:
+
+<notextile>
+<pre><code class="userinput">current_user = arvados.api('v1').users().current().execute()
+</code></pre>
+</notextile>
+
+Get the UUID of an object that was retrieved using the SDK:
+
+<notextile>
+<pre><code class="userinput">my_uuid = current_user['uuid']
+</code></pre>
+</notextile>
+
+Retrieve an object by ID:
+
+<notextile>
+<pre><code class="userinput">some_user = arvados.api('v1').users().get(uuid=my_uuid).execute()
+</code></pre>
+</notextile>
+
+Create an object:
+
+<notextile>
+<pre><code class="userinput">test_link = arvados.api('v1').links().create(
+ body={'link_class':'test','name':'test'}).execute()
+</code></pre>
+</notextile>
+
+Update an object:
+
+<notextile>
+<pre><code class="userinput">arvados.api('v1').links().update(
+ uuid=test_link['uuid'],
+ body={'properties':{'foo':'bar'}}).execute()
+</code></pre>
+</notextile>
+
+Get a list of objects:
+
+<notextile>
+<pre><code class="userinput">repos = arvados.api('v1').repositories().list().execute()
+len(repos['items'])</code>
+2
+<code class="userinput">repos['items'][0]['uuid']</code>
+u'qr1hi-s0uqq-kg8cawglrf74bmw'
+</code></pre>
+</notextile>
+
+h3. Notes
+
+The general form of an API call is:
+
+<notextile>
+<pre><code class="userinput">arvados.api(<i>api_version</i>).<i>plural_resource_type</i>().<i>api_method</i>(<i>parameter</i>=<i>value</i>, ...).execute()
+</code></pre>
+</notextile>
+
+Many API methods accept a parameter whose name is the same as the resource type. For example, @links.create@ accepts a parameter called @link@. This parameter should be given as @body@.
+
+<notextile>
+<pre><code class="userinput">arvados.api('v1').links().create(
+ uuid=test_link['uuid'],
+ body={'properties':{'foo':'bar'}}).execute()
+</code></pre>
+</notextile>
+
+One way to make API calls slightly less verbose is:
+
+<notextile>
+<pre><code class="userinput">arv = arvados.api('v1')
+j = arv.jobs().list().execute()
+</code></pre>
+</notextile>
+
+The SDK retrieves the list of API methods from the server at run time. Therefore, the set of available methods is determined by the server version rather than the SDK version.
+
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Ruby
+title: "Ruby SDK"
+
+...
+
+The Ruby SDK provides a generic set of wrappers so you can make API calls easily.
+
+h3. Installation
+
+If you are logged in to an Arvados VM, the Ruby SDK should be installed.
+
+To use it elsewhere, you can either install the @arvados@ gem via RubyGems or build and install the package using the arvados source tree.
+
+h4. Prerequisites: Ruby >= 2.0.0
+
+You can use "RVM":http://rvm.io/rvm/install to install and manage Ruby versions.
+
+h4. Option 1: install with RubyGems
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo gem install arvados</code>
+</pre>
+</notextile>
+
+h4. Option 2: build and install from source
+
+<notextile>
+<pre>
+$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">cd arvados/sdk/ruby</code>
+$ <code class="userinput">gem build arvados.gemspec</code>
+$ <code class="userinput">sudo gem install arvados-*.gem</code>
+</pre>
+</notextile>
+
+h4. Test installation
+
+If the SDK is installed, @ruby -r arvados -e 'puts "OK!"'@ should produce no errors.
+
+If your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ environment variables are set up correctly (see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for details), the following test script should work:
+
+<notextile>
+<pre>$ <code class="userinput">ruby -r arvados <<'EOF'
+arv = Arvados.new api_version: 'v1'
+my_full_name = arv.user.current[:full_name]
+puts "arvados.v1.users.current.full_name = '#{my_full_name}'"
+EOF</code>
+arvados.v1.users.current.full_name = 'Your Name'
+</pre>
+</notextile>
+
+h3. Examples
+
+Import the module (we skipped this step above by using "ruby -r arvados"):
+
+<notextile>
+<pre><code class="userinput">require 'arvados'
+</code></pre>
+</notextile>
+
+Set up an API client user agent:
+
+<notextile>
+<pre><code class="userinput">arv = Arvados.new(apiVersion: 'v1')
+</code></pre>
+</notextile>
+
+Get the User object for the current user:
+
+<notextile>
+<pre><code class="userinput">current_user = arv.user.current
+</code></pre>
+</notextile>
+
+Get the UUID of an object that was retrieved using the SDK:
+
+<notextile>
+<pre><code class="userinput">current_user_uuid = current_user[:uuid]
+</code></pre>
+</notextile>
+
+Retrieve an object by ID:
+
+<notextile>
+<pre><code class="userinput">some_user = arv.user.get(uuid: current_user_uuid)
+</code></pre>
+</notextile>
+
+Create an object:
+
+<notextile>
+<pre><code class="userinput">new_link = arv.link.create(link: {link_class: 'test', name: 'test'})
+</code></pre>
+</notextile>
+
+Update an object:
+
+<notextile>
+<pre><code class="userinput">updated_link = arv.link.update(uuid: new_link[:uuid],
+ link: {properties: {foo: 'bar'}})
+</code></pre>
+</notextile>
+
+Delete an object:
+
+<notextile>
+<pre><code class="userinput">arv.link.delete(uuid: new_link[:uuid])
+</code></pre>
+</notextile>
+
+Get a list of objects:
+
+<notextile>
+<pre><code class="userinput">repos = arv.repository.list
+first_repo = repos[:items][0]
+puts "UUID of first repo returned is #{first_repo[:uuid]}"</code>
+UUID of first repo returned is qr1hi-s0uqq-b1bnybpx3u5temz
+</pre>
+</notextile>
+
+The SDK retrieves the list of API methods from the server at run time. Therefore, the set of available methods is determined by the server version rather than the SDK version.
--- /dev/null
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--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "GNU Affero General Public License"
+...
+
+<p style="text-align: center;">Version 3, 19 November 2007</p>
+
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+produce the work, or an object code interpreter used to run it.</p>
+
+<p>The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities. However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work. For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.</p>
+
+<p>The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+Source.</p>
+
+<p>The Corresponding Source for a work in source code form is that
+same work.</p>
+
+<h4><a name="section2"></a>2. Basic Permissions.</h4>
+
+<p>All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met. This License explicitly affirms your unlimited
+permission to run the unmodified Program. The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work. This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.</p>
+
+<p>You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force. You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright. Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.</p>
+
+<p>Conveying under any other circumstances is permitted solely under
+the conditions stated below. Sublicensing is not allowed; section 10
+makes it unnecessary.</p>
+
+<h4><a name="section3"></a>3. Protecting Users' Legal Rights From Anti-Circumvention Law.</h4>
+
+<p>No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+measures.</p>
+
+<p>When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.</p>
+
+<h4><a name="section4"></a>4. Conveying Verbatim Copies.</h4>
+
+<p>You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.</p>
+
+<p>You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.</p>
+
+<h4><a name="section5"></a>5. Conveying Modified Source Versions.</h4>
+
+<p>You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:</p>
+
+<ul>
+
+<li>a) The work must carry prominent notices stating that you modified
+ it, and giving a relevant date.</li>
+
+<li>b) The work must carry prominent notices stating that it is
+ released under this License and any conditions added under section
+ 7. This requirement modifies the requirement in section 4 to
+ "keep intact all notices".</li>
+
+<li>c) You must license the entire work, as a whole, under this
+ License to anyone who comes into possession of a copy. This
+ License will therefore apply, along with any applicable section 7
+ additional terms, to the whole of the work, and all its parts,
+ regardless of how they are packaged. This License gives no
+ permission to license the work in any other way, but it does not
+ invalidate such permission if you have separately received it.</li>
+
+<li>d) If the work has interactive user interfaces, each must display
+ Appropriate Legal Notices; however, if the Program has interactive
+ interfaces that do not display Appropriate Legal Notices, your
+ work need not make them do so.</li>
+
+</ul>
+
+<p>A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work,
+and which are not combined with it such as to form a larger program,
+in or on a volume of a storage or distribution medium, is called an
+"aggregate" if the compilation and its resulting copyright are not
+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.</p>
+
+<h4><a name="section6"></a>6. Conveying Non-Source Forms.</h4>
+
+<p>You may convey a covered work in object code form under the terms
+of sections 4 and 5, provided that you also convey the
+machine-readable Corresponding Source under the terms of this License,
+in one of these ways:</p>
+
+<ul>
+
+<li>a) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by the
+ Corresponding Source fixed on a durable physical medium
+ customarily used for software interchange.</li>
+
+<li>b) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by a
+ written offer, valid for at least three years and valid for as
+ long as you offer spare parts or customer support for that product
+ model, to give anyone who possesses the object code either (1) a
+ copy of the Corresponding Source for all the software in the
+ product that is covered by this License, on a durable physical
+ medium customarily used for software interchange, for a price no
+ more than your reasonable cost of physically performing this
+ conveying of source, or (2) access to copy the
+ Corresponding Source from a network server at no charge.</li>
+
+<li>c) Convey individual copies of the object code with a copy of the
+ written offer to provide the Corresponding Source. This
+ alternative is allowed only occasionally and noncommercially, and
+ only if you received the object code with such an offer, in accord
+ with subsection 6b.</li>
+
+<li>d) Convey the object code by offering access from a designated
+ place (gratis or for a charge), and offer equivalent access to the
+ Corresponding Source in the same way through the same place at no
+ further charge. You need not require recipients to copy the
+ Corresponding Source along with the object code. If the place to
+ copy the object code is a network server, the Corresponding Source
+ may be on a different server (operated by you or a third party)
+ that supports equivalent copying facilities, provided you maintain
+ clear directions next to the object code saying where to find the
+ Corresponding Source. Regardless of what server hosts the
+ Corresponding Source, you remain obligated to ensure that it is
+ available for as long as needed to satisfy these requirements.</li>
+
+<li>e) Convey the object code using peer-to-peer transmission, provided
+ you inform other peers where the object code and Corresponding
+ Source of the work are being offered to the general public at no
+ charge under subsection 6d.</li>
+
+</ul>
+
+<p>A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.</p>
+
+<p>A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling. In determining whether a product is a consumer product,
+doubtful cases shall be resolved in favor of coverage. For a particular
+product received by a particular user, "normally used" refers to a
+typical or common use of that class of product, regardless of the status
+of the particular user or of the way in which the particular user
+actually uses, or expects or is expected to use, the product. A product
+is a consumer product regardless of whether the product has substantial
+commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.</p>
+
+<p>"Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from
+a modified version of its Corresponding Source. The information must
+suffice to ensure that the continued functioning of the modified object
+code is in no case prevented or interfered with solely because
+modification has been made.</p>
+
+<p>If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information. But this requirement does not apply
+if neither you nor any third party retains the ability to install
+modified object code on the User Product (for example, the work has
+been installed in ROM).</p>
+
+<p>The requirement to provide Installation Information does not include a
+requirement to continue to provide support service, warranty, or updates
+for a work that has been modified or installed by the recipient, or for
+the User Product in which it has been modified or installed. Access to a
+network may be denied when the modification itself materially and
+adversely affects the operation of the network or violates the rules and
+protocols for communication across the network.</p>
+
+<p>Corresponding Source conveyed, and Installation Information provided,
+in accord with this section must be in a format that is publicly
+documented (and with an implementation available to the public in
+source code form), and must require no special password or key for
+unpacking, reading or copying.</p>
+
+<h4><a name="section7"></a>7. Additional Terms.</h4>
+
+<p>"Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.</p>
+
+<p>When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
+additional permissions on material, added by you to a covered work,
+for which you have or can give appropriate copyright permission.</p>
+
+<p>Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:</p>
+
+<ul>
+
+<li>a) Disclaiming warranty or limiting liability differently from the
+ terms of sections 15 and 16 of this License; or</li>
+
+<li>b) Requiring preservation of specified reasonable legal notices or
+ author attributions in that material or in the Appropriate Legal
+ Notices displayed by works containing it; or</li>
+
+<li>c) Prohibiting misrepresentation of the origin of that material, or
+ requiring that modified versions of such material be marked in
+ reasonable ways as different from the original version; or</li>
+
+<li>d) Limiting the use for publicity purposes of names of licensors or
+ authors of the material; or</li>
+
+<li>e) Declining to grant rights under trademark law for use of some
+ trade names, trademarks, or service marks; or</li>
+
+<li>f) Requiring indemnification of licensors and authors of that
+ material by anyone who conveys the material (or modified versions of
+ it) with contractual assumptions of liability to the recipient, for
+ any liability that these contractual assumptions directly impose on
+ those licensors and authors.</li>
+
+</ul>
+
+<p>All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further restriction,
+you may remove that term. If a license document contains a further
+restriction but permits relicensing or conveying under this License, you
+may add to a covered work material governed by the terms of that license
+document, provided that the further restriction does not survive such
+relicensing or conveying.</p>
+
+<p>If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.</p>
+
+<p>Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.</p>
+
+<h4><a name="section8"></a>8. Termination.</h4>
+
+<p>You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).</p>
+
+<p>However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.</p>
+
+<p>Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.</p>
+
+<p>Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.</p>
+
+<h4><a name="section9"></a>9. Acceptance Not Required for Having Copies.</h4>
+
+<p>You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.</p>
+
+<h4><a name="section10"></a>10. Automatic Licensing of Downstream Recipients.</h4>
+
+<p>Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.</p>
+
+<p>An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.</p>
+
+<p>You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.</p>
+
+<h4><a name="section11"></a>11. Patents.</h4>
+
+<p>A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".</p>
+
+<p>A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.</p>
+
+<p>Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.</p>
+
+<p>In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.</p>
+
+<p>If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.</p>
+
+<p>If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.</p>
+
+<p>A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.</p>
+
+<p>Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.</p>
+
+<h4><a name="section12"></a>12. No Surrender of Others' Freedom.</h4>
+
+<p>If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.</p>
+
+<h4><a name="section13"></a>13. Remote Network Interaction; Use with the GNU General Public License.</h4>
+
+<p>Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
+Source of your version by providing access to the Corresponding Source
+from a network server at no charge, through some standard or customary
+means of facilitating copying of software. This Corresponding Source
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.</p>
+
+<p>Notwithstanding any other provision of this License, you have permission
+to link or combine any covered work with a work licensed under version 3
+of the GNU General Public License into a single combined work, and to
+convey the resulting work. The terms of this License will continue to
+apply to the part which is the covered work, but the work with which it is
+combined will remain governed by version 3 of the GNU General Public
+License.</p>
+
+<h4><a name="section14"></a>14. Revised Versions of this License.</h4>
+
+<p>The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may differ
+in detail to address new problems or concerns.</p>
+
+<p>Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero
+General Public License "or any later version" applies to it, you have
+the option of following the terms and conditions either of that
+numbered version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number
+of the GNU Affero General Public License, you may choose any version
+ever published by the Free Software Foundation.</p>
+
+<p>If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that
+proxy's public statement of acceptance of a version permanently
+authorizes you to choose that version for the Program.</p>
+
+<p>Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.</p>
+
+<h4><a name="section15"></a>15. Disclaimer of Warranty.</h4>
+
+<p>THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
+
+<h4><a name="section16"></a>16. Limitation of Liability.</h4>
+
+<p>IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.</p>
+
+<h4><a name="section17"></a>17. Interpretation of Sections 15 and 16.</h4>
+
+<p>If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.</p>
+
+<p>END OF TERMS AND CONDITIONS</p>
+
+<h3><a name="howto"></a>How to Apply These Terms to Your New Programs</h3>
+
+<p>If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.</p>
+
+<p>To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.</p>
+
+<pre> <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as
+ published by the Free Software Foundation, either version 3 of the
+ License, or (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+</pre>
+
+<p>Also add information on how to contact you by electronic and paper mail.</p>
+
+<p>If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.</p>
+
+<p>You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<<a href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/</a>>.</p>
+
+
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Creative Commons"
+...
+
+<div id="deed" class="green">
+ <div id="deed-head">
+
+ <div id="deed-license">
+ <h2>Attribution-ShareAlike 3.0 United States</h2>
+ </div>
+ </div>
+
+ <h3><em>License</em></h3>
+
+ <p>THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS
+ OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR
+ "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER
+ APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS
+ AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS
+ PROHIBITED.</p>
+
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+
+ </div>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Arvados Free Software Licenses"
+...
+
+Server-side components of Arvados contained in the apps/ and services/ directories, including the API Server, Workbench, Keep, and Crunch, are licenced under the "GNU Affero General Public License version 3":agpl-3.0.html.
+
+The Arvados client Software Development Kits contained in the sdk/ directory, example scripts in the crunch_scripts/ directory, and code samples in the Aravados documentation are licensed under the "Apache License, Version 2.0":LICENSE-2.0.html
+
+The Arvados Documentation located in the doc/ directory is licensed under the "Creative Commons Attribution-Share Alike 3.0 United States":by-sa-3.0.html
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Scripts provided by Arvados"
+...
+
+Several crunch scripts are included with Arvados in the "/crunch_scripts directory":https://arvados.org/projects/arvados/repository/revisions/master/show/crunch_scripts. They are intended to provide examples and starting points for writing your own scripts.
+
+h4. bwa-aln
+
+Run the bwa aligner on a set of paired-end fastq files, producing a BAM file for each pair. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-aln
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
+|samtools_tgz|Collection with the samtools source distribution.|@c777e23cf13e5d5906abfdc08d84bfdb+74@|
+|input|Collection with fastq reads (pairs of *_1.fastq.gz and *_2.fastq.gz).|@d0136bc494c21f79fc1b6a390561e6cb+2778@|
+</div>
+
+h4. bwa-index
+
+Generate an index of a fasta reference genome suitable for use by bwa-aln. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/bwa-index
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
+|input|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
+</div>
+
+h4. picard-gatk2-prep
+
+Using the FixMateInformation, SortSam, ReorderSam, AddOrReplaceReadGroups, and BuildBamIndex modules from picard, prepare a BAM file for use with the GATK2 tools. Additionally, run picard's CollectAlignmentSummaryMetrics module to produce a @*.casm.tsv@ statistics file for each BAM file. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/picard-gatk2-prep
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|input|Collection containing aligned bam files.||
+|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
+|reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
+</div>
+
+h4. GATK2-realign
+
+Run GATK's RealignerTargetCreator and IndelRealigner modules on a set of BAM files. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-realign
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|input|Collection containing aligned bam files.||
+|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
+|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
+|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
+|known_sites|List of files in the data bundle to use as GATK @-known@ arguments. Optional. |@["dbsnp_137.b37.vcf","Mills_and_1000G_gold_standard.indels.b37.vcf"]@ (this is the default value)|
+|regions|Collection with .bed files indicating sequencing target regions. Optional.||
+|region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
+</div>
+
+h4. GATK2-bqsr
+
+Run GATK's BaseQualityScoreRecalibration module on a set of BAM files. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-bqsr
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|input|Collection containing bam files.||
+|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
+|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
+</div>
+
+h4. GATK2-merge-call
+
+Merge a set of BAM files using picard, and run GATK's UnifiedGenotyper module on the merged set to produce a VCF file. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-merge-call
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|input|Collection containing bam files.||
+|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
+|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
+|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
+|regions|Collection with .bed files indicating sequencing target regions. Optional.||
+|region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
+</div>
+
+h4. file-select
+
+Pass through the named files from input to output collection, and ignore the rest. "View source.":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/file-select
+
+<div class="offset1">
+table(table table-bordered table-condensed).
+|_Parameter_|_Description_|_Example_|
+|names|List of filenames to include in the output.|@["human_g1k_v37.fasta.gz","human_g1k_v37.fasta.fai.gz"]@|
+</div>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Checking your environment"
+...
+
+First, log into an Arvados VM instance (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login) or install the Arvados "Command line SDK":{{site.baseurl}}/sdk/cli/install.html and "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html on your workstation.
+
+Check that you are able to access the Arvados API server using @arv user current@. If it is able to access the API server, it will print out information about your account:
+
+<notextile>
+<pre><code>$ <span class="userinput">arv user current</span>
+{
+ "href":"https://qr1hi.arvadosapi.com/arvados/v1/users/qr1hi-xioed-9z2p3pn12yqdaem",
+ "kind":"arvados#user",
+ "etag":"8u0xwb9f3otb2xx9hto4wyo03",
+ "uuid":"qr1hi-tpzed-92d3kxnimy3d4e8",
+ "owner_uuid":"qr1hi-tpqed-23iddeohxta2r59",
+ "created_at":"2013-12-02T17:05:47Z",
+ "modified_by_client_uuid":"qr1hi-xxfg8-owxa2oa2s33jyej",
+ "modified_by_user_uuid":"qr1hi-tpqed-23iddeohxta2r59",
+ "modified_at":"2013-12-02T17:07:08Z",
+ "updated_at":"2013-12-05T19:51:08Z",
+ "email":"you@example.com",
+ "full_name":"Example User",
+ "first_name":"Example",
+ "last_name":"User",
+ "identity_url":"https://www.google.com/accounts/o8/id?id=AItOawnhlZr-pQ_Ic2f2W22XaO02oL3avJ322k1",
+ "is_active": true,
+ "is_admin": false,
+ "prefs":{}
+}
+</code></pre>
+</notextile>
+
+However, if you receive the following message:
+
+bc. ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables
+
+follow the instructions for "getting an API token,":{{site.baseurl}}/user/reference/api-tokens.html and try @arv user current@ again.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: Arvados Community and Getting Help
+...
+
+h2. On the web
+
+The Arvados Free Sofware project page is located at "http://arvados.org":http://arvados.org . The "Arvados Wiki":https://arvados.org/projects/arvados/wiki is a collaborative site for documenting Arvados has an overview of the Arvados Platform and Components. The "Arvados blog":https://arvados.org/projects/arvados/blogs posts articles of interest about Arvados.
+
+h2. Mailing lists
+
+The "Arvados user mailing list":http://lists.arvados.org/mailman/listinfo/arvados is a forum for general discussion, questions, and news about Arvados development. The "Arvados developer mailing list":http://lists.arvados.org/mailman/listinfo/arvados-dev is a forum for more technical discussion, intended for developers and contributers to Arvados.
+
+h2. IRC
+
+The "#arvados":irc://irc.oftc.net:6667/#arvados IRC (Internet Relay Chat) channel at on the "Open and Free Technology Community (irc.oftc.net)":http://www.oftc.net/oftc/ is available for live discussion and support. You can use a traditional IRC client or "join OFTC over the web.":https://webchat.oftc.net/?channels=arvados
+
+h2. Bug tracking
+
+If you think you have found a bug, or would like to make a feature request, check the "Arvados issue tracker":https://arvados.org/projects/arvados/issues to see if has already been reported or "add a new issue.":https://arvados.org/projects/arvados/issues/new
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: Accessing an Arvados VM with SSH - Unix Environments
+...
+
+This document is for Unix environments (Linux, OS X, Cygwin). If you are using a Windows environment, please visit the "Accessing an Arvados VM with SSH - Windows Environments":ssh-access-windows.html page.
+
+{% include 'ssh_intro' %}
+
+h1(#gettingkey). Getting your SSH key
+
+h3(#unix). Generate a key using ssh-keygen
+
+Start by opening a terminal window. Check if you have an existing public key:
+
+notextile. <pre><code>$ <span class="userinput">ls ~/.ssh/id_rsa.pub</span></code></pre>
+
+If the file @id_rsa.pub@ exists, then you may use your existing key. Copy the contents of @~/.ssh/id_rsa.pub@ onto the clipboard (this is your public key). You can skip the rest of this section and proceed by "adding your key to the Arvados Workbench.":#workbench
+
+If there is no file @~/.ssh/id_rsa.pub@, you must generate a new key. Use @ssh-keygen@ to do this:
+
+<notextile>
+<pre><code>$ <span class="userinput">ssh-keygen -t rsa -C "you@example.com"</span>
+Generating public/private rsa key pair.
+Enter file in which to save the key (/home/example/.ssh/id_rsa):
+Enter passphrase (empty for no passphrase):
+Enter same passphrase again:
+</code></pre>
+</notextile>
+
+* @-t@ specifies the key type (must be "rsa")
+* @-C@ specifies a comment (to remember which account the key is associated with)
+
+We strongly recommend that you protect your key with a passphrase. This means that when the key is used, you will be required to enter the passphrase. However, unlike logging into remote system using a password, the passphrase is never sent over the network, it is only used to decrypt your private key.
+
+Display the contents of @~/.ssh/id_rsa.pub@ (this is your public key) using @cat@ and then copy it onto the clipboard:
+
+<notextile>
+<pre><code>$ <span class="userinput">cat ~/.ssh/id_rsa.pub</span>
+ssh-rsa AAAAB3NzaC1ycEDoNotUseExampleKeyDoNotUseExampleKeyDoNotUseExampleKeyDoNotUse9lmzkpBq983bQradKGT3LuKda9QOGe8MatI6wzSrJLSGhHm3hk6D8OWWUG4SneuCtKIk2bH0pgBj1G29+uzDIez90WzfCTZKbz4RcVQmPkowSSUAQDwb0ffwvRDhCgcJ1loT1wQAJzqJmljQ7xEYaCOIMqnfYE0lX7B3MSvCV6Ie2rWL33YecLp48LVtqiCOZU4XRyO8RSDFRFLVW+mjkLirwtDHZCRtORScaIEN0jw51p+T+9X5iA9QH/Mn+xlgk7fCgH+JtpBj808N/Qds2Gpff+Kb6ulUrVVfMK6L you@example.com
+</code></pre>
+</notextile>
+
+Now you can set up @ssh-agent@ (next) or proceed with "adding your key to the Arvados Workbench.":#workbench
+
+h3. Set up ssh-agent (recommended)
+
+If you find you are entering your passphrase frequently, you can use @ssh-agent@ to manage your credentials. Use @ssh-add -l@ to test if you already have ssh-agent running:
+
+notextile. <pre><code>$ <span class="userinput">ssh-add -l</span></code></pre>
+
+If you get the error "Could not open a connection to your authentication agent" you will need to run @ssh-agent@ with the following command:
+
+notextile. <pre><code>$ <span class="userinput">eval $(ssh-agent -s)</span></code></pre>
+
+@ssh-agent -s@ prints out values for environment variables SSH_AUTH_SOCK and SSH_AGENT_PID and then runs in the background. Using "eval" on the output as shown here causes those variables to be set in the current shell environment so that subsequent calls to SSH can discover how to access the agent process.
+
+After running @ssh-agent@, or if @ssh-add -l@ prints "The agent has no identities", add your key using the following command. The passphrase to decrypt the key is the same used to protect the key when it was created with @ssh-keygen@:
+
+<notextile>
+<pre><code>$ <span class="userinput">ssh-add</span>
+Enter passphrase for /home/example/.ssh/id_rsa:
+Identity added: /home/example/.ssh/id_rsa (/home/example/.ssh/id_rsa)
+</code></pre>
+</notextile>
+
+When everything is set up, @ssh-add -l@ should yield output that looks something like this:
+
+<notextile>
+<pre><code>$ <span class="userinput">ssh-add -l</span>
+2048 eb:fa:15:f2:44:26:95:58:37:37:f4:aa:ff:ee:c2:85 you@example.com (RSA)
+</code></pre>
+</notextile>
+
+{% include 'ssh_addkey' %}
+
+h3. Connecting to the virtual machine
+
+Use the following command to connect to the _shell_ VM instance as _you_. Replace *<code>you@shell</code>* at the end of the following command with your *login* and *hostname* from Workbench:
+
+notextile. <pre><code>$ <span class="userinput">ssh -o "ProxyCommand ssh -a -x -p2222 turnout@switchyard.{{ site.arvados_api_host }} <b>shell</b>" -A -x <b>you@shell</b></span></code></pre>
+
+This command does several things at once. You usually cannot log in directly to virtual machines over the public Internet. Instead, you log into a "switchyard" server and then tell the switchyard which virtual machine you want to connect to.
+
+* @-o "ProxyCommand ..."@ configures SSH to run the specified command to create a proxy and route your connection through it.
+* @-a@ tells SSH not to forward your ssh-agent credentials to the switchyard.
+* @-x@ tells SSH not to forward your X session to the switchyard.
+* @-p2222@ specifies that the switchyard is running on non-standard port 2222.
+* <code>turnout@switchyard.{{ site.arvados_api_host }}</code> specifies the user (@turnout@) and hostname (@switchyard.{{ site.arvados_api_host }}@) of the switchyard server that will proxy our connection to the VM.
+* *@shell@* is the name of the VM that we want to connect to. This is sent to the switchyard server as if it were an SSH command, and the switchyard server connects to the VM on our behalf.
+* After the ProxyCommand section, we repeat @-x@ to disable X session forwarding to the virtual machine.
+* @-A@ specifies that we want to forward access to @ssh-agent@ to the VM.
+* Finally, *<code>you@shell</code>* specifies your login name and repeats the hostname of the VM. The username can be found in the *logins* column in the VMs Workbench page, discussed in the previous section.
+
+You should now be able to log into the Arvados VM and "check your environment.":check-environment.html
+
+h3. Configuration (recommended)
+
+The command line above is cumbersome, but you can configure SSH to remember many of these settings. Add this text to the file @.ssh/config@ in your home directory (create a new file if @.ssh/config@ doesn't exist):
+
+<notextile>
+<pre><code class="userinput">Host *.arvados
+ ProxyCommand ssh -a -x -p2222 turnout@switchyard.{{ site.arvados_api_host }} $SSH_PROXY_FLAGS %h
+ User <b>you</b>
+ ForwardAgent yes
+ ForwardX11 no
+</code></pre>
+</notextile>
+
+This will recognize any host ending in ".arvados" and automatically apply the proxy, user and forwarding settings from the configuration file, allowing you to log in with a much simpler command:
+
+notextile. <pre><code>$ <span class="userinput">ssh <b>shell</b>.arvados</span></code></pre>
+
+You should now be able to log into the Arvados VM and "check your environment.":check-environment.html
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: Accessing an Arvados VM with SSH - Windows Environments
+...
+
+This document is for Windows environments. If you are using a Unix environment (Linux, OS X, Cygwin), please visit the "Accessing an Arvados VM with SSH - Unix Environments":ssh-access-unix.html page.
+
+{% include 'ssh_intro' %}
+
+h1(#gettingkey). Getting your SSH key
+
+(Note: if you are using the SSH client that comes with "Cygwin":http://cygwin.com, please use instructions found in the "Accessing an Arvados VM with SSH - Unix Environments":ssh-access-unix.html page.)
+
+We will be using PuTTY to connect to Arvados. "PuTTY":http://www.chiark.greenend.org.uk/~sgtatham/putty/ is a free (MIT-licensed) Win32 Telnet and SSH client. PuTTY includes all the tools a Windows user needs to create private keys and make SSH connections to your virtual machines in the Arvados Cloud.
+
+You can "download PuTTY from its Web site":http://www.chiark.greenend.org.uk/~sgtatham/putty/. Note that you should download the installer or .zip file with all of the PuTTY tools (PuTTYtel is not required).
+
+If you downloaded the zip file, extract it to the location you wish to install the PuTTY applications. This document assumes that you installed PuTTY in the default directory under @C:\Program Files\@ or @C:\Program Files (x86)\@ (if you are using a 64 bit operating system).
+
+h3. Step 1 - Adding PuTTY to the PATH
+
+# After downloading PuTTY and installing it, you should have a PuTTY folder in @C:\Program Files\@ or @C:\Program Files (x86)\@ (if you are using a 64 bit operating system).
+# Open the Control Panel.
+# Select _Advanced System Settings_, and choose _Environment Variables_.
+If you are using newer systems like Windows 7, you may use the following to open _Advanced System Settings_. Open Control Panel. Click on _System and Security_. Click on _System_. Click on _Advanced system settings_ and choose _Environment Variables..._
+# Under system variables, find and edit @PATH@.
+# If you installed PuTTY in @C:\Program Files\PuTTY\@, add the following to the end of PATH:
+<code>;C:\Program Files\PuTTY</code>
+If you installed PuTTY in @C:\Program Files (x86)\PuTTY\@, add the following to the end of PATH:
+<code>;C:\Program Files (x86)\PuTTY</code>
+# Click through the OKs to close all the dialogs you’ve opened.
+
+h3. Step 2 - Creating a Public Key
+
+# Start PuTTYgen from the Start Menu or the folder where it was installed.
+# At the bottom of the window, make sure the ‘Number of bits in a generated key’ field is set to 4096.
+# Click Generate and follow the instructions to generate a key.
+# Click the _Save public key_ button.
+# Click the _Save private key_ button (we recommend using a strong passphrase).
+# Select the text of the Public Key and copy it to the clipboard.
+
+h3. Step 3 - Set up Pageant
+
+Pageant is a PuTTY utility that manages your private keys so is not necessary to enter your private key passphrase every time you make a new SSH connection.
+
+# Start Pageant from the Start Menu or the folder where it was installed.
+# Pageant will now be running in the system tray. Click the Pageant icon to configure.
+# Choose _Add Key_ and add the private key which you created in the previous step.
+
+{% include 'ssh_addkey' %}
+
+h3. Initial configuration
+
+# Open PuTTY from the Start Menu.
+# On the Session screen set the Host Name (or IP address) to “shell”, which is the hostname listed in the _Virtual Machines_ page.
+# On the Session screen set the Port to “22”.
+# On the Connection %(rarr)→% Data screen set the Auto-login username to the username listed in the *logins* column on the Arvados Workbench _Settings %(rarr)→% Virtual machines_ page.
+# On the Connection %(rarr)→% Proxy screen set the Proxy Type to “Local”.
+# On the Connection %(rarr)→% Proxy screen in the “Telnet command, or local proxy command” box enter:
+<code>plink -P 2222 turnout@switchyard.{{ site.arvados_api_host }} %host</code>
+Make sure there is no newline at the end of the text entry.
+# Return to the Session screen. In the Saved Sessions box, enter a name for this configuration and click Save.
+
+_Note: We recommend you do not delete the “Default” Saved Session._
+
+h3. Connecting to the VM
+
+# Open PuTTY from the Start Menu.
+# Click on the Saved Session name you created in the previous section.
+# Click Load to load those saved session settings.
+# Click Open to open the SSH window at the command prompt. You will now be logged into your virtual machine.
+
+_Note_: If you see a hung PuTTY terminal window with no further action: open a new _Command Prompt_ window using the Windows -> Start menu and type <code>plink -P 2222 turnout@switchyard.{{ site.arvados_api_host }} shell</code> in it. Please make sure to replace *shell* with the hostname listed in the _Virtual Machines_ page. Hit enter and type _y_ when prompted to cache the session state. Go back and start PuTTY session using the start menu button.
+
+You should now be able to log into the Arvados VM and "check your environment.":check-environment.html
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: Accessing Arvados Workbench
+...
+
+If you are using the default Arvados instance for this guide, you can Access Arvados Workbench using this link:
+
+<a href="https://{{ site.arvados_workbench_host }}/" target="_blank">https://{{ site.arvados_workbench_host }}/</a>
+
+(If you are using a different Arvados instance than the default for this guide, replace *{{ site.arvados_workbench_host }}* with your private instance in all of the examples in this guide.)
+
+You may be asked to log in using a Google account. Arvados uses only your name and email address from Google services for identification, and will never access any personal information. If you are accessing Arvados for the first time, the Workbench may indicate your account status is *New / inactive*. If this is the case, contact the administrator of the Arvados instance to request activation of your account.
+
+Once your account is active, logging in to the Workbench will present you with the Dashboard. This gives a summary of your projects and recent activity in the Arvados instance. "You are now ready to run your first pipeline.":{{ site.baseurl }}/user/tutorials/tutorial-pipeline-workbench.html
+
+!{{ site.baseurl }}/images/workbench-dashboard.png!
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: Welcome to Arvados!
+...
+
+_If you are new to Arvados and want to get started quickly, go to "Accessing Arvados Workbench.":{{site.baseurl}}/user/getting_started/workbench.html_
+
+This guide provides an introduction to using Arvados to solve big data bioinformatics problems, including:
+
+* Robust storage of very large files, such as whole genome sequences, using the "Arvados Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html content-addressable cluster file system.
+* Running compute-intensive genomic analysis pipelines, such as alignment and variant calls using the "Arvados Crunch":{{site.baseurl}}/user/tutorials/intro-crunch.html cluster compute engine.
+* Storing and querying metadata about genome sequence files, such as human subjects and their phenotypic traits using the "Arvados Metadata Database.":{{site.baseurl}}/user/topics/tutorial-trait-search.html
+* Accessing, organizing, and sharing data, pipelines and results using the "Arvados Workbench":{{site.baseurl}}/user/getting_started/workbench.html web application.
+
+The examples in this guide use the Arvados instance located at <a href="https://{{ site.arvados_workbench_host }}/" target="_blank">https://{{ site.arvados_workbench_host }}</a>. If you are using a different Arvados instance replace @{{ site.arvados_workbench_host }}@ with your private instance in all of the examples in this guide.
+
+Curoverse maintains a public Arvados instance located at <a href="https://workbench.qr1hi.arvadosapi.com/" target="_blank">https://workbench.qr1hi.arvadosapi.com/</a>. You must have an account in order to use this service. If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com.
+
+h2. Typographic conventions
+
+This manual uses the following typographic conventions:
+
+<notextile>
+<ul>
+<li>Code blocks which are set aside from the text indicate user input to the system. Commands that should be entered into a Unix shell are indicated by the directory where you should enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black. For example, the following block indicates that you should type <code>ls foo.*</code> while in your home directory and the expected output will be "foo.input" and "foo.output".
+<pre><code>~$ <span class="userinput">ls foo.*</span>
+foo.input foo.output
+</code></pre>
+</li>
+
+<li>Code blocks inline with text emphasize specific <code>programs</code>, <code>files</code>, or <code>options</code> that are being discussed.</li>
+<li>Bold text emphasizes <b>specific items</b> to review on Arvados Workbench pages.</li>
+<li>A sequence of steps separated by right arrows (<span class="rarr">→</span>) indicate a path the user should follow through the Arvados Workbench. The steps indicate a menu, hyperlink, column name, field name, or other label on the page that guide the user where to look or click.
+</li>
+</ul>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Getting an API token"
+...
+
+The Arvados API token is a secret key that enables the @arv@ command line client to access Arvados with the proper permissions.
+
+Access the Arvados Workbench using this link: "https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/ (Replace @{{ site.arvados_api_host }}@ with the hostname of your local Arvados instance if necessary.)
+
+Open a shell on the system where you want to use the Arvados client. This may be your local workstation, or an Arvados virtual machine accessed with SSH (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login).
+
+Click on the link with your _email address_ in the upper right corner to access your account menu, then click on the menu item *Manage account* to go to the account management page. On the *Manage account* page, you will see the *Current Token* panel, which lists your current token and instructions to set up your environment.
+
+h2. Setting environment variables
+
+For your convenience, the *Manage account* page on Workbench provides the *Current Token* panel that includes a command you may copy and paste directly into the shell. It will look something as the following.
+
+bc. HISTIGNORE=$HISTIGNORE:'export ARVADOS_API_TOKEN=*'
+export ARVADOS_API_TOKEN=2jv9346o396exampledonotuseexampledonotuseexes7j1ld
+export ARVADOS_API_HOST={{ site.arvados_api_host }}
+unset ARVADOS_API_HOST_INSECURE
+
+* The @export@ command puts a local shell variable into the environment that will be inherited by child processes such as the @arv@ client.
+
+h2. settings.conf
+
+Arvados tools will also look for the authentication information in @~/.config/arvados/settings.conf@. If you have already put the variables into the environment following the instructions above, you can use these commands to create an Arvados configuration file:
+
+<notextile>
+<pre><code>$ <span class="userinput">echo "ARVADOS_API_HOST=$ARVADOS_API_HOST" > ~/.config/arvados/settings.conf</span>
+$ <span class="userinput">echo "ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN" >> ~/.config/arvados/settings.conf</span>
+</code></pre>
+</notextile>
+
+h2. .bashrc
+
+Alternately, you may add the declarations of @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ to the @~/.bashrc@ file on the system on which you intend to use the Arvados client. If you have already put the variables into the environment following the instructions above, you can use these commands to append the environment variables to your @~/.bashrc@:
+
+<notextile>
+<pre><code>$ <span class="userinput">echo "export ARVADOS_API_HOST=$ARVADOS_API_HOST" >> ~/.bashrc</span>
+$ <span class="userinput">echo "export ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN" >> ~/.bashrc</span>
+</code></pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Pipeline template reference"
+...
+
+Pipeline template options are described on the "pipeline template schema page.":{{site.baseurl}}/api/schema/PipelineTemplate.html
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Customizing Crunch environment using Docker"
+...
+
+This page describes how to customize the runtime environment (e.g. the programs, libraries, and other dependencies needed to run a job) that a crunch script will be run in using "Docker.":https://www.docker.com/ Docker is a tool for building and running containers that isolate applications from other applications running on the same node. For detailed information about Docker, see the "Docker User Guide.":https://docs.docker.com/userguide/
+
+This page will demonstrate how to:
+
+# Fetch the arvados/jobs Docker image
+# Manually install additional software into the container
+# Create a new custom image
+# Upload that image to Arvados for use by Crunch jobs
+# Share your image with others
+
+{% include 'tutorial_expectations' %}
+
+You also need ensure that "Docker is installed,":https://docs.docker.com/installation/ the Docker daemon is running, and you have permission to access Docker. You can test this by running @docker version@. If you receive a permission denied error, your user account may need to be added to the @docker@ group. If you have root access, you can add yourself to the @docker@ group using @$ sudo addgroup $USER docker@ then log out and log back in again; otherwise consult your local sysadmin.
+
+h2. Fetch a starting image
+
+The easiest way to begin is to start from the "arvados/jobs" image which already has the Arvados SDK installed along with other configuration required for use with Crunch.
+
+Download the latest "arvados/jobs" image from the Docker registry:
+
+<notextile>
+<pre><code>$ <span class="userinput">docker pull arvados/jobs</span>
+Pulling repository arvados/jobs
+3132168f2acb: Download complete
+a42b7f2c59b6: Download complete
+e5afdf26a7ae: Download complete
+5cae48636278: Download complete
+7a4f91b70558: Download complete
+a04a275c1fd6: Download complete
+c433ff206a22: Download complete
+b2e539b45f96: Download complete
+073b2581c6be: Download complete
+593915af19dc: Download complete
+32260b35005e: Download complete
+6e5b860c1cde: Download complete
+95f0bfb43d4d: Download complete
+c7fd77eedb96: Download complete
+0d7685aafd00: Download complete
+</code></pre>
+</notextile>
+
+h2. Install new packages
+
+Next, enter the container using @docker run@, providing the arvados/jobs image and the program you want to run (in this case the bash shell).
+
+<notextile>
+<pre><code>$ <span class="userinput">docker run --interactive --tty --user root arvados/jobs /bin/bash</span>
+root@a0e8299b59aa:/#
+</code></pre>
+</notextile>
+
+Next, update the package list using @apt-get update@.
+
+<notextile>
+<pre><code>root@a0e8299b59aa:/# <span class="userinput">apt-get update</span>
+Get:1 http://apt.arvados.org wheezy Release.gpg [490 B]
+Get:2 http://apt.arvados.org wheezy Release [1568 B]
+Get:3 http://apt.arvados.org wheezy/main amd64 Packages [34.6 kB]
+Get:4 http://ftp.us.debian.org wheezy Release.gpg [1655 B]
+Get:5 http://ftp.us.debian.org wheezy-updates Release.gpg [836 B]
+Get:6 http://ftp.us.debian.org wheezy Release [168 kB]
+Ign http://apt.arvados.org wheezy/main Translation-en
+Get:7 http://security.debian.org wheezy/updates Release.gpg [836 B]
+Get:8 http://security.debian.org wheezy/updates Release [102 kB]
+Get:9 http://ftp.us.debian.org wheezy-updates Release [124 kB]
+Get:10 http://ftp.us.debian.org wheezy/main amd64 Packages [5841 kB]
+Get:11 http://security.debian.org wheezy/updates/main amd64 Packages [218 kB]
+Get:12 http://security.debian.org wheezy/updates/main Translation-en [123 kB]
+Hit http://ftp.us.debian.org wheezy/main Translation-en
+Hit http://ftp.us.debian.org wheezy-updates/main amd64 Packages/DiffIndex
+Hit http://ftp.us.debian.org wheezy-updates/main Translation-en/DiffIndex
+Fetched 6617 kB in 5s (1209 kB/s)
+Reading package lists... Done
+</code></pre>
+</notextile>
+
+In this example, we will install the "R" statistical language Debian package "r-base-core". Use @apt-get install@:
+
+<notextile>
+<pre><code>root@a0e8299b59aa:/# <span class="userinput">apt-get install r-base-core</span>
+Reading package lists... Done
+Building dependency tree
+Reading state information... Done
+The following extra packages will be installed:
+ [...]
+libxv1 libxxf86dga1 libxxf86vm1 r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools
+ [...]
+Suggested packages:
+ [...]
+The following NEW packages will be installed:
+ [...]
+ libxv1 libxxf86dga1 libxxf86vm1 r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster
+ [...]
+0 upgraded, 107 newly installed, 0 to remove and 9 not upgraded.
+Need to get 88.2 MB of archives.
+After this operation, 219 MB of additional disk space will be used.
+Do you want to continue [Y/n]? y
+[...]
+Get:85 http://ftp.us.debian.org/debian/ wheezy/main r-base-core amd64 2.15.1-4 [20.6 MB]
+Get:86 http://ftp.us.debian.org/debian/ wheezy/main r-base-dev all 2.15.1-4 [3882 B]
+Get:87 http://ftp.us.debian.org/debian/ wheezy/main r-cran-boot all 1.3-5-1 [472 kB]
+[...]
+Fetched 88.2 MB in 2min 17s (642 kB/s)
+Extracting templates from packages: 100%
+Preconfiguring packages ...
+[...]
+Unpacking r-base-core (from .../r-base-core_2.15.1-4_amd64.deb) ...
+Selecting previously unselected package r-base-dev.
+Unpacking r-base-dev (from .../r-base-dev_2.15.1-4_all.deb) ...
+Selecting previously unselected package r-cran-boot.
+Unpacking r-cran-boot (from .../r-cran-boot_1.3-5-1_all.deb) ...
+[...]
+Setting up r-base-core (2.15.1-4) ...
+Setting R_PAPERSIZE_USER default to 'a4'
+
+Creating config file /etc/R/Renviron with new version
+Setting up r-base-dev (2.15.1-4) ...
+Setting up r-cran-boot (1.3-5-1) ...
+[...]
+</code></pre>
+</notextile>
+
+Now we can verify that "R" is installed:
+
+<notextile>
+<pre><code>root@a0e8299b59aa:/# <span class="userinput">R</span>
+
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-pc-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+>
+</code></pre>
+</notextile>
+
+Note that you are not limited to installing Debian packages. You may compile programs or libraries from source and install them, edit systemwide configuration files, use other package managers such as @pip@ or @gem@, and perform any other customization necessary to run your program.
+
+h2. Create a new image
+
+We're now ready to create a new Docker image. First, quit the container, then use @docker commit@ to create a new image from the stopped container. The container id can be found in the default hostname of the container displayed in the prompt, in this case @a0e8299b59aa@:
+
+<notextile>
+<pre><code>root@a0e8299b59aa:/# <span class="userinput">exit</span>
+$ <span class="userinput">docker commit a0e8299b59aa arvados/jobs-with-r</span>
+33ea6b87792364cb9989a149c36a31e5a9c8cf96694ba05f66545ad7b842522e
+$ <span class="userinput">docker images</span>
+REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE
+arvados/jobs-with-r latest 33ea6b877923 43 seconds ago 1.607 GB
+arvados/jobs latest 3132168f2acb 22 hours ago 1.314 GB
+</code></pre>
+</notextile>
+
+h2. Upload your image
+
+Finally, we are ready to upload the new Docker image to Arvados. Use @arv keep docker@ with the image repository name to upload the image. Without arguments, @arv keep docker@ will print out the list of Docker images in Arvados that are available to you.
+
+<notextile>
+<pre><code>$ <span class="userinput">arv keep docker arvados/jobs-with-r</span>
+1591M / 1591M 100.0%
+Collection saved as 'Docker image arvados/jobs-with-r:latest 33ea6b877923'
+qr1hi-4zz18-3fk2px2ji25nst2
+$ <span class="userinput">arv keep docker</span>
+REPOSITORY TAG IMAGE ID COLLECTION CREATED
+arvados/jobs-with-r latest 33ea6b877923 qr1hi-4zz18-3fk2px2ji25nst2 Thu Oct 16 13:58:53 2014
+</code></pre>
+</notextile>
+
+You are now able to specify the runtime environment for your program using the @docker_image@ field of the @runtime_constaints@ section of your pipeline components:
+
+<notextile>
+{% code 'example_docker' as javascript %}
+</notextile>
+
+* The @docker_image@ field can be one of: the Docker repository name (as shown above), the Docker image hash, the Arvados collection UUID, or the Arvados collection portable data hash.
+
+h2. Share Docker images
+
+Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others (or wish to share a pipeline template that uses your Docker image) you will need to use @arv keep docker@ with the @--project-uuid@ option to upload the image to a shared project.
+
+<notextile>
+<pre><code>$ <span class="userinput">arv keep docker --project-uuid zzzzz-j7d0g-u7zg1qdaowykd8d arvados/jobs-with-r</span>
+</code></pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Using arv-run"
+...
+
+The @arv-run@ command enables you create Arvados pipelines at the command line that fan out to multiple concurrent tasks across Arvados compute nodes.
+
+{% include 'tutorial_expectations' %}
+
+h1. Usage
+
+Using @arv-run@ you can write and test command lines interactively, then insert @arv-run@ at the beginning of the command line to run the command on Arvados. For example:
+
+<notextile>
+<pre>
+$ <span class="userinput">cd ~/keep/by_id/3229739b505d2b878b62aed09895a55a+142</span>
+$ <span class="userinput">ls *.fastq</span>
+HWI-ST1027_129_D0THKACXX.1_1.fastq HWI-ST1027_129_D0THKACXX.1_2.fastq
+$ <span class="userinput">grep -H -n ATTGGAGGAAAGATGAGTGAC HWI-ST1027_129_D0THKACXX.1_1.fastq</span>
+HWI-ST1027_129_D0THKACXX.1_1.fastq:14:TCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCCCAACCTA
+HWI-ST1027_129_D0THKACXX.1_1.fastq:18:AACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCT
+HWI-ST1027_129_D0THKACXX.1_1.fastq:30:ATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCTGTGATACG
+$ <span class="userinput">arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC HWI-ST1027_129_D0THKACXX.1_1.fastq</span>
+Running pipeline qr1hi-d1hrv-mg3bju0u7r6w241
+[...]
+ 0 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq
+ 0 stderr /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq:14:TCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCCCAACCTA
+ 0 stderr /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq:18:AACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCT
+ 0 stderr /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq:30:ATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCTGTGATACG
+ 0 stderr run-command: completed with exit code 0 (success)
+[...]
+</pre>
+</notextile>
+
+A key feature of @arv-run@ is the ability to introspect the command line to determine which arguments are file inputs, and transform those paths so they are usable inside the Arvados container. In the above example, @HWI-ST1027_129_D0THKACXX.1_2.fastq@ is transformed into @/keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq@. @arv-run@ also works together with @arv-mount@ to identify that the file is already part of an Arvados collection. In this case, it will use the existing collection without any upload step. If you specify a file that is only available on the local filesystem, @arv-run@ will upload a new collection.
+
+If you find that @arv-run@ is incorrectly rewriting one of your command line arguments, place a backslash @\@ at the beginning of the affected argument to quote it (suppress rewriting).
+
+h2. Parallel tasks
+
+@arv-run@ will parallelize over files listed on the command line after @--@.
+
+<notextile>
+<pre>
+HWI-ST1027_129_D0THKACXX.1_1.fastq HWI-ST1027_129_D0THKACXX.1_2.fastq
+$ <span class="userinput">arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC -- *.fastq</span>
+Running pipeline qr1hi-d1hrv-mg3bju0u7r6w241
+[...]
+ 0 stderr run-command: parallelizing on input0 with items [u'/keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq', u'/keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq']
+[...]
+ 1 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq
+ 2 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq
+[...]
+ 1 stderr /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq:14:TCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCCCAACCTA
+ 1 stderr /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq:18:AACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCT
+ 1 stderr /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq:30:ATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCTGTGATACG
+ 1 stderr run-command: completed with exit code 0 (success)
+ 2 stderr /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq:34:CTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAG
+ 2 stderr run-command: completed with exit code 0 (success)
+</pre>
+</notextile>
+
+You may specify @--batch-size N@ (or the short form @-bN@) after the @--@ but before listing any files to specify how many files to provide put on the command line for each task. See "Putting it all together" below for an example.
+
+h2. Redirection
+
+You may use standard input (@<@) and standard output (@>@) redirection. This will create a separate task for each file listed in standard input. You are only permitted to supply a single file name for stdout @>@ redirection. If there are multiple tasks with their output sent to the same file, the output will be collated at the end of the pipeline.
+
+(Note: because the syntax is designed to mimic standard shell syntax, it is necessary to quote the metacharacters @<@, @>@ and @|@ as either @\<@, @\>@ and @\|@ or @'<'@, @'>'@ and @'|'@.)
+
+<notextile>
+<pre>
+$ <span class="userinput">arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC \< *.fastq \> output.txt</span>
+[...]
+ 1 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq > output.txt
+ 2 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq > output.txt
+ 2 stderr run-command: completed with exit code 0 (success)
+ 2 stderr run-command: the following output files will be saved to keep:
+ 2 stderr run-command: 121 ./output.txt
+ 2 stderr run-command: start writing output to keep
+ 1 stderr run-command: completed with exit code 0 (success)
+ 1 stderr run-command: the following output files will be saved to keep:
+ 1 stderr run-command: 363 ./output.txt
+ 1 stderr run-command: start writing output to keep
+ 2 stderr upload wrote 121 total 121
+ 1 stderr upload wrote 363 total 363
+[..]
+</pre>
+</notextile>
+
+You may use "run-command":run-command.html parameter substitution in the output file name to generate different filenames for each task:
+
+<notextile>
+<pre>
+$ <span class="userinput">arv-run grep -H -n ATTGGAGGAAAGATGAGTGAC \< *.fastq \> '$(task.uuid).txt'</span>
+[...]
+ 1 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq > qr1hi-ot0gb-hmmxf2zubfpmhfk.txt
+ 2 stderr run-command: grep -H -n ATTGGAGGAAAGATGAGTGAC < /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq > qr1hi-ot0gb-iu2xgy4hkx4mmri.txt
+ 1 stderr run-command: completed with exit code 0 (success)
+ 1 stderr run-command: the following output files will be saved to keep:
+ 1 stderr run-command: 363 ./qr1hi-ot0gb-hmmxf2zubfpmhfk.txt
+ 1 stderr run-command: start writing output to keep
+ 1 stderr upload wrote 363 total 363
+ 2 stderr run-command: completed with exit code 0 (success)
+ 2 stderr run-command: the following output files will be saved to keep:
+ 2 stderr run-command: 121 ./qr1hi-ot0gb-iu2xgy4hkx4mmri.txt
+ 2 stderr run-command: start writing output to keep
+ 2 stderr upload wrote 121 total 121
+[...]
+</pre>
+</notextile>
+
+h2. Pipes
+
+Multiple commands may be connected by pipes and execute in the same container:
+
+<notextile>
+<pre>
+$ <span class="userinput">arv-run cat -- *.fastq \| grep -H -n ATTGGAGGAAAGATGAGTGAC \> output.txt</span>
+[...]
+ 1 stderr run-command: cat /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq | grep -H -n ATTGGAGGAAAGATGAGTGAC > output.txt
+ 2 stderr run-command: cat /keep/3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_2.fastq | grep -H -n ATTGGAGGAAAGATGAGTGAC > output.txt
+[...]
+</pre>
+</notextile>
+
+If you need to capture intermediate results of a pipe, use the @tee@ command.
+
+h2. Running a shell script
+
+<notextile>
+<pre>
+$ <span class="userinput">echo 'echo hello world' > hello.sh</span>
+$ <span class="userinput">arv-run /bin/sh hello.sh</span>
+Upload local files: "hello.sh"
+Uploaded to qr1hi-4zz18-23u3hxugbm71qmn
+Running pipeline qr1hi-d1hrv-slcnhq5czo764b1
+[...]
+ 0 stderr run-command: /bin/sh /keep/5d3a4131b7d8f233f2a917d8a5c3c2b2+52/hello.sh
+ 0 stderr hello world
+ 0 stderr run-command: completed with exit code 0 (success)
+[...]
+</pre>
+</notextile>
+
+h2. Additional options
+
+* @--docker-image IMG@ : By default, commands run inside a Docker container created from the latest "arvados/jobs" Docker image. Use this option to specify a different image to use. Note: the Docker image must be uploaded to Arvados using @arv keep docker@.
+* @--dry-run@ : Print out the final Arvados pipeline generated by @arv-run@ without submitting it.
+* @--local@ : By default, the pipeline will be submitted to your configured Arvados instance. Use this option to run the command locally using @arv-run-pipeline-instance --run-jobs-here@.
+* @--ignore-rcode@ : Some commands use non-zero exit codes to indicate nonfatal conditions (e.g. @grep@ returns 1 when no match is found). Set this to indicate that commands that return non-zero return codes should not be considered failed.
+* @--no-wait@ : Do not wait and display logs after submitting command, just exit.
+
+h2. Putting it all together: bwa mem
+
+<notextile>
+<pre>
+$ <span class="userinput">cd ~/keep/by_id/d0136bc494c21f79fc1b6a390561e6cb+2778</span>
+$ <span class="userinput">arv-run --docker-image arvados/jobs-java-bwa-samtools bwa mem ../3514b8e5da0e8d109946bc809b20a78a+5698/human_g1k_v37.fasta -- --batch-size 2 *.fastq.gz \> '$(task.uuid).sam'</span>
+ 0 stderr run-command: parallelizing on input0 with items [[u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_1.fastq.gz', u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_2.fastq.gz'], [u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.2_1.fastq.gz', u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.2_2.fastq.gz']]
+[...]
+ 1 stderr run-command: bwa mem /keep/3514b8e5da0e8d109946bc809b20a78a+5698/human_g1k_v37.fasta /keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_1.fastq.gz /keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_2.fastq.gz > qr1hi-ot0gb-a4bzzyqqz4ubair.sam
+ 2 stderr run-command: bwa mem /keep/3514b8e5da0e8d109946bc809b20a78a+5698/human_g1k_v37.fasta /keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.2_1.fastq.gz /keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.2_2.fastq.gz > qr1hi-ot0gb-14j9ncw0ymkxq0v.sam
+</pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "How Keep works"
+...
+
+The Arvados distributed file system is called *Keep*. Keep is a content-addressable file system. This means that files are managed using special unique identifiers derived from the _contents_ of the file (specifically, the MD5 hash), rather than human-assigned file names. This has a number of advantages:
+* Files can be stored and replicated across a cluster of servers without requiring a central name server.
+* Both the server and client systematically validate data integrity because the checksum is built into the identifier.
+* Data duplication is minimized—two files with the same contents will have in the same identifier, and will not be stored twice.
+* It avoids data race conditions, since an identifier always points to the same data.
+
+In Keep, information is stored in *data blocks*. Data blocks are normally between 1 byte and 64 megabytes in size. If a file exceeds the maximum size of a single data block, the file will be split across multiple data blocks until the entire file can be stored. These data blocks may be stored and replicated across multiple disks, servers, or clusters. Each data block has its own identifier for the contents of that specific data block.
+
+In order to reassemble the file, Keep stores a *collection* data block which lists in sequence the data blocks that make up the original file. A collection data block may store the information for multiple files, including a directory structure.
+
+In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@, which we added to Keep in "how to upload data":{{ site.baseurl }}/user/tutorials/tutorial-keep.html. First let us examine the contents of this collection using @arv keep get@:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210</span>
+. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
+</code></pre>
+</notextile>
+
+The command @arv keep get@ fetches the contents of the collection @c1bad4b39ca5a924e481008009d94e32+210@. In this example, this collection includes a single file @var-GS000016015-ASM.tsv.bz2@ which is 227212247 bytes long, and is stored using four sequential data blocks, @204e43b8a1185621ca55a94839582e6f+67108864@, @b9677abbac956bd3e86b1deb28dfac03+67108864@, @fc15aff2a762b13f521baf042140acec+67108864@, and @323d2a3ce20370c4ca1d3462a344f8fd+25885655@.
+
+Let's use @arv keep get@ to download the first data block:
+
+notextile. <pre><code>~$ <span class="userinput">cd /scratch/<b>you</b></span>
+/scratch/<b>you</b>$ <span class="userinput">arv keep get 204e43b8a1185621ca55a94839582e6f+67108864 > block1</span></code></pre>
+
+{% include 'notebox_begin' %}
+
+When you run this command, you may get this API warning:
+
+notextile. <pre><code>WARNING:root:API lookup failed for collection 204e43b8a1185621ca55a94839582e6f+67108864 (<class 'apiclient.errors.HttpError'>: <HttpError 404 when requesting https://qr1hi.arvadosapi.com/arvados/v1/collections/204e43b8a1185621ca55a94839582e6f%2B67108864?alt=json returned "Not Found">)</code></pre>
+
+This happens because @arv keep get@ tries to find a collection with this identifier. When that fails, it emits this warning, then looks for a datablock instead, which succeeds.
+
+{% include 'notebox_end' %}
+
+Let's look at the size and compute the MD5 hash of @block1@:
+
+<notextile>
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">ls -l block1</span>
+-rw-r--r-- 1 you group 67108864 Dec 9 20:14 block1
+/scratch/<b>you</b>$ <span class="userinput">md5sum block1</span>
+204e43b8a1185621ca55a94839582e6f block1
+</code></pre>
+</notextile>
+
+Notice that the block identifer <code>204e43b8a1185621ca55a94839582e6f+67108864</code> consists of:
+* the MD5 hash of @block1@, @204e43b8a1185621ca55a94839582e6f@, plus
+* the size of @block1@, @67108864@.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "run-command reference"
+...
+
+The @run-command@ crunch script enables you run command line programs.
+
+h1. Using run-command
+
+The basic @run-command@ process evaluates its inputs and builds a command line, executes the command, and saves the contents of the output directory back to Keep. For large datasets, @run-command@ can schedule concurrent tasks to execute the wrapped program over a range of inputs (see @task.foreach@ below.)
+
+@run-command@ is controlled through the @script_parameters@ section of a pipeline component. @script_parameters@ is a JSON object consisting of key-value pairs. There are three categories of keys that are meaningful to run-command:
+* The @command@ section defining the template to build the command line of task
+* Special processing directives such as @task.foreach@ @task.cwd@ @task.vwd@ @task.stdin@ @task.stdout@
+* User-defined parameters (everything else)
+
+In the following examples, you can use "dry run mode" to determine the command line that @run-command@ will use without actually running the command. For example:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME/arvados/crunch_scripts</span>
+~$ <span class="userinput">./run-command --dry-run --script-parameters '{
+ "command": ["echo", "hello world"]
+}'</span>
+run-command: echo hello world
+</code></pre>
+</notextile>
+
+h2. Command template
+
+The value of the "command" key is a list. The first parameter of the list is the actual program to invoke, followed by the command arguments. The simplest @run-command@ invocation simply runs a program with static parameters. In this example, run "echo" with the first argument "hello world":
+
+<pre>
+{
+ "command": ["echo", "hello world"]
+}
+</pre>
+
+Running this job will print "hello world" to the job log.
+
+By default, the command will start with the current working directory set to the output directory. Anything written to the output directory will be saved to Keep when the command is finished. You can change the default working directory using @task.cwd@ and get the path to the output directory using @$(task.outdir)@ as explained below.
+
+Items in the "command" list may include lists and objects in addition to strings. Lists are flattened to produce the final command line. JSON objects are evaluated as list item functions (see below). For example, the following evaluates to @["echo", "hello", "world"]@:
+
+<pre>
+{
+ "command": ["echo", ["hello", "world"]]
+}
+</pre>
+
+Finally, if "command" is a list of lists, it specifies a Unix pipeline where the standard output of the previous command is piped into the standard input of the next command. The following example describes the Unix pipeline @cat foo | grep bar@:
+
+<pre>
+{
+ "command": [["cat", "foo"], ["grep", "bar"]]
+}
+</pre>
+
+h2. Parameter substitution
+
+The "command" list can include parameter substitutions. Substitutions are enclosed in "$(...)" and may contain the name of a user-defined parameter. In the following example, the value of "a" is "hello world"; so when "command" is evaluated, it will substitute "hello world" for "$(a)":
+
+<pre>
+{
+ "a": "c1bad4b39ca5a924e481008009d94e32+210/var-GS000016015-ASM.tsv.bz2",
+ "command": ["echo", "$(file $(a))"]
+}
+</pre>
+
+table(table table-bordered table-condensed).
+|_. Function|_. Action|
+|$(file ...) | Takes a reference to a file within an Arvados collection and evaluates to a file path on the local file system where that file can be accessed by your command. Will raise an error if the file is not accessible.|
+|$(dir ...) | Takes a reference to an Arvados collection or directory within an Arvados collection and evaluates to a directory path on the local file system where that directory can be accessed by your command. The path may include a file name, in which case it will evaluate to the parent directory of the file. Uses Python's os.path.dirname(), so "/foo/bar" will evaluate to "/foo" but "/foo/bar/" will evaluate to "/foo/bar". Will raise an error if the directory is not accessible. |
+|$(basename ...) | Strip leading directory and trailing file extension from the path provided. For example, $(basename /foo/bar.baz.txt) will evaluate to "bar.baz".|
+|$(glob ...) | Take a Unix shell path pattern (supports @*@ @?@ and @[]@) and search the local filesystem, returning the first match found. Use together with $(dir ...) to get a local filesystem path for Arvados collections. For example: $(glob $(dir $(mycollection)/*.bam)) will find the first .bam file in the collection specified by the user parameter "mycollection". If there is more than one match, which one is returned is undefined. Will raise an error if no matches are found.|
+
+h2. List context
+
+Where specified by the documentation, parameters may be evaluated in a "list context". That means the value will evaluate to a list instead of a string. Parameter values can be a static list, a path to a file, a path to a directory, or a JSON object describing a list context function.
+
+If the value is a string, it is interpreted as a path. If the path specifies a regular file, that file will be opened as a text file and produce a list with one item for each line in the file (end-of-line characters will be stripped). If the path specifies a directory, produce a list containing all of the entries in the directory. Note that parameter expansion is not performed on list items produced this way.
+
+If the value is a static list, it will evaluate each item and return the expanded list. Each item may be a string (evaluated for parameter substitution), a list (recursively evaluated), or a JSON object (indicating a list function, described below).
+
+If the value is a JSON object, it is evaluated as a list function described below.
+
+h2. List functions
+
+When @run-command@ is evaluating a list (such as "command"), in addition to string parameter substitution, you can use list item functions. In the following functions, you specify the name of a user parameter to act on (@"$(a)"@ in the first example); the value of that user parameter will be evaluated in a list context (as described above) to get the list value. Alternately, you can provide list value directly in line. As an example, the following two fragments yield the same result:
+
+<pre>
+{
+ "a": ["alice", "bob"],
+ "command": ["echo", {"foreach": "$(a)",
+ "var": "a_var",
+ "command": ["--something", "$(a_var)"]}]
+}
+</pre>
+
+<pre>
+{
+ "command": ["echo", {"foreach": ["alice", "bob"],
+ "var": "a_var",
+ "command": ["--something", "$(a_var)"]}]
+}
+</pre>
+
+Note: when you provide the list inline with "foreach" or "index", you must include the "var" parameter to specify the substitution variable name to use when evaluating the command fragment.
+
+You can also nest functions. This filters @["alice", "bob", "betty"]@ on the regular expression @"b.*"@ to get the list @["bob", "betty"]@, assigns @a_var@ to each value of the list, then expands @"command"@ to get @["--something", "bob", "--something", "betty"]@.
+
+<pre>
+{
+ "command": ["echo", {"foreach": {"filter": ["alice", "bob", "betty"],
+ "regex": "b.*"},
+ "var": "a_var",
+ "command": ["--something", "$(a_var)"]}]
+}
+</pre>
+
+h3. foreach
+
+The @foreach@ list item function (not to be confused with the @task.foreach@ directive) expands a command template for each item in the specified user parameter (the value of the user parameter is evaluated in a list context, as described above). The following example will evaluate "command" to @["echo", "--something", "alice", "--something", "bob"]@:
+
+<pre>
+{
+ "a": ["alice", "bob"],
+ "command": ["echo", {"foreach": "$(a)",
+ "var": "a_var",
+ "command": ["--something", "$(a_var)"]}]
+}
+</pre>
+
+h3. index
+
+This function extracts a single item from a list. The value of @index@ is zero-based (i.e. the first item is at index 0, the second item index 1, etc). The following example will evaluate "command" to @["echo", "--something", "bob"]@:
+
+<pre>
+{
+ "a": ["alice", "bob"],
+ "command": ["echo", {"list": "$(a)",
+ "var": "a_var",
+ "index": 1,
+ "command": ["--something", "$(a_var)"]}]
+}
+</pre>
+
+h3. filter
+
+Filter the list so that it only includes items that match a regular expression. The following example will evaluate to @["echo", "bob"]@
+
+<pre>
+{
+ "a": ["alice", "bob"],
+ "command": ["echo", {"filter": "$(a)",
+ "regex": "b.*"}]
+}
+</pre>
+
+h3. group
+
+Generate a list of lists, where items are grouped on common subexpression match. Items which don't match the regular expression are excluded. In the following example, the subexpression is @(a?)@, resulting in two groups, strings that contain the letter 'a' and strings that do not. The following example evaluates to @["echo", "--group", "alice", "carol", "dave", "--group", "bob", "betty"]@:
+
+<pre>
+{
+ "a": ["alice", "bob", "betty", "carol", "dave"],
+ "b": {"group": "$(a)",
+ "regex": "[^a]*(a?).*"},
+ "command": ["echo", {"foreach": "$(b)",
+ "var": "b_var",
+ "command": ["--group", "$(b_var)"]}]
+}
+</pre>
+
+h3. extract
+
+Generate a list of lists, where items are split by subexpression match. Items which don't match the regular expression are excluded. The following example evaluates to @["echo", "--something", "c", "a", "rol", "--something", "d", "a", "ve"]@:
+
+<pre>
+{
+ "a": ["alice", "bob", "carol", "dave"],
+ "b": {"extract": "$(a)",
+ "regex": "(.+)(a)(.*)"},
+ "command": ["echo", {"foreach": "$(b)",
+ "var": "b_var",
+ "command": ["--something", "$(b_var)"]}]
+}
+</pre>
+
+h3. batch
+
+Generate a list of lists, where items are split into a batch size. If the list does not divide evenly into batch sizes, the last batch will be short. The following example evaluates to @["echo", "--something", "alice", "bob", "--something", "carol", "dave"]@
+
+<pre>
+{
+ "a": ["alice", "bob", "carol", "dave"],
+ "command": ["echo", {"foreach":{"batch": "$(a)",
+ "size": 2},
+ "var": "a_var",
+ "command": ["--something", "$(a_var)"]}]
+}
+</pre>
+
+h2. Directives
+
+Directives alter the behavior of run-command. All directives are optional.
+
+h3. task.cwd
+
+This directive sets the initial current working directory in which your command will run. If @task.cwd@ is not specified, the default current working directory is @task.outdir@.
+
+h3. task.ignore_rcode
+
+By Unix convention a task which exits with a non-zero return code is considered failed. However, some programs (such as @grep@) return non-zero codes for conditions that should not be considered fatal errors. Set @"task.ignore_rcode": true@ to indicate the task should always be considered a success regardless of the return code.
+
+h3. task.stdin and task.stdout
+
+Provide standard input and standard output redirection.
+
+@task.stdin@ must evaluate to a path to a file to be bound to the standard input stream of the command. When command describes a Unix pipeline, this goes into the first command.
+
+@task.stdout@ specifies the desired file name in the output directory to save the content of standard output. When command describes a Unix pipeline, this captures the output of the last command.
+
+h3. task.vwd
+
+Background: because Keep collections are read-only, this does not play well with certain tools that expect to be able to write their outputs alongside their inputs (such as tools that generate indexes that are closely associated with the original file.) The run-command's solution to this is the "virtual working directory".
+
+@task.vwd@ specifies a Keep collection with the starting contents of the directory. @run-command@ will then populate @task.outdir@ with directories and symlinks to mirror the contents of the @task.vwd@ collection. Your command will then be able to both access its input files and write its output files in @task.outdir@. When the command completes, the output collection will merge the output of your command with the contents of the starting collection. Note that files in the starting collection remain read-only and cannot be altered or deleted.
+
+h3. task.foreach
+
+Using @task.foreach@, you can run your command concurrently over large datasets.
+
+@task.foreach@ takes the names of one or more user-defined parameters. The value of these parameters are evaluated in a list context. @run-command@ then generates tasks based on the Cartesian product (i.e. all combinations) of the input lists. The outputs of all tasks are merged to create the final output collection. Note that if two tasks output a file in the same directory with the same name, that file will be concatenated in the final output. In the following example, three tasks will be created for the "grep" command, based on the contents of user parameter "a":
+
+<pre>
+{
+ "command": ["echo", "$(a)"],
+ "task.foreach": "a",
+ "a": ["alice", "bob", "carol"]
+}
+</pre>
+
+This evaluates to the commands:
+<notextile>
+<pre>
+["echo", "alice"]
+["echo", "bob"]
+["echo", "carol"]
+</pre>
+</notextile>
+
+You can also specify multiple parameters:
+
+<pre>
+{
+ "a": ["alice", "bob"],
+ "b": ["carol", "dave"],
+ "task.foreach": ["a", "b"],
+ "command": ["echo", "$(a)", "$(b)"]
+}
+</pre>
+
+This evaluates to the commands:
+
+<pre>
+["echo", "alice", "carol"]
+["echo", "alice", "dave"]
+["echo", "bob", "carol"]
+["echo", "bob", "dave"]
+</pre>
+
+h1. Examples
+
+The following is a single task pipeline using @run-command@ to run the bwa alignment tool to align a single paired-end read fastq sample. The input to this pipeline is the reference genome and a collection consisting of two fastq files for the read pair.
+
+<notextile>{% code 'run_command_simple_example' as javascript %}</notextile>
+
+The following is a concurrent task pipeline using @run-command@ to run the bwa alignment tool to align a set of fastq reads over multiple samples. The input to this pipeline is the reference genome and a collection consisting subdirectories for each sample, with each subdirectory containing pairs of fastq files for each set of reads.
+
+<notextile>{% code 'run_command_foreach_example' as javascript %}</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Running a pipeline on the command line"
+...
+
+This tutorial demonstrates how to use the command line to run the same pipeline as described in "running a pipeline using Workbench.":{{site.baseurl}}/user/tutorials/tutorial-pipeline-workbench.html
+
+{% include 'tutorial_expectations' %}
+
+When you use the command line, you must use Arvados unique identifiers to refer to objects. The identifiers in this example correspond to the following Arvados objects:
+
+* <i class="fa fa-fw fa-gear"></i> "Tutorial align using bwa mem (qr1hi-p5p6p-itzkwxblfermlwv)":https://{{ site.arvados_workbench_host }}/pipeline_templates/qr1hi-p5p6p-itzkwxblfermlwv
+* <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":https://{{ site.arvados_workbench_host }}/collections/2463fa9efeb75e099685528b3b9071e0+438
+* <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":https://{{ site.arvados_workbench_host }}/collections/3229739b505d2b878b62aed09895a55a+142
+
+Use @arv pipeline run@ to run the pipeline, supplying the inputs to the bwa-mem component on the command line:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv pipeline run --run-pipeline-here --template qr1hi-p5p6p-itzkwxblfermlwv bwa-mem::reference_collection=2463fa9efeb75e099685528b3b9071e0+438 bwa-mem::sample=3229739b505d2b878b62aed09895a55a+142</span>
+
+2014-07-25 18:05:26 +0000 -- pipeline_instance qr1hi-d1hrv-d14trje19pna7f2
+bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 queued 2014-07-25T18:05:25Z
+
+2014-07-25 18:05:36 +0000 -- pipeline_instance qr1hi-d1hrv-d14trje19pna7f2
+bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 {:done=>0, :running=>1, :failed=>0, :todo=>0}
+
+2014-07-25 18:05:46 +0000 -- pipeline_instance qr1hi-d1hrv-d14trje19pna7f2
+bwa-mem qr1hi-8i9sb-67n1qvsronmd2z6 49bae1066f4ebce72e2587a3efa61c7d+88
+</code></pre>
+</notextile>
+
+This instantiates your pipeline and displays periodic status reports in your terminal window. The new pipeline instance will also show up on the Workbench Dashboard.
+
+@arv pipeline run@ submits a job for each pipeline component as soon as the component's inputs are known (i.e., any dependencies are satsified). It terminates when there is no work left to do: this means either all components are satisfied and all jobs have completed successfully, _or_ one or more jobs have failed and it is therefore unproductive to submit any further jobs.
+
+The Keep locators of the output of of the @bwa-mem@ components are available from the last status report shown above:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep ls -s 49bae1066f4ebce72e2587a3efa61c7d+88</span>
+ 29226 ./HWI-ST1027_129_D0THKACXX.1_1.sam
+</code></pre>
+</notextile>
+
+h2. Re-using existing jobs and outputs
+
+When satisfying a pipeline component that is not marked as nondeterministic in the pipeline template, @arv pipeline run@ checks for a previously submitted job that satisfies the component's requirements. If such a job is found, @arv pipeline run@ uses the existing job rather than submitting a new one. Usually this is a safe way to conserve time and compute resources. In some cases it's desirable to re-run jobs with identical specifications (e.g., to demonstrate that a job or entire pipeline thought to be repeatable is in fact repeatable). For such cases, job re-use features can be disabled entirely by passing the @--no-reuse@ flag to the @arv pipeline run@ command.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Using GATK with Arvados"
+...
+
+This tutorial demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
+
+{% include 'tutorial_expectations' %}
+
+h2. Installing GATK
+
+Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep put GenomeAnalysisTK-2.6-4.tar.bz2</span>
+c905c8d8443a9c44274d98b7c6cfaa32+94
+</code></pre>
+</notextile>
+
+Next, you need the GATK Resource Bundle[2]. This may already be available in Arvados. If not, you will need to download the files listed below and put them into Keep.
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep ls -s d237a90bae3870b3b033aea1e99de4a9+10820</span>
+ 50342 1000G_omni2.5.b37.vcf.gz
+ 1 1000G_omni2.5.b37.vcf.gz.md5
+ 464 1000G_omni2.5.b37.vcf.idx.gz
+ 1 1000G_omni2.5.b37.vcf.idx.gz.md5
+ 43981 1000G_phase1.indels.b37.vcf.gz
+ 1 1000G_phase1.indels.b37.vcf.gz.md5
+ 326 1000G_phase1.indels.b37.vcf.idx.gz
+ 1 1000G_phase1.indels.b37.vcf.idx.gz.md5
+ 537210 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.gz
+ 1 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.gz.md5
+ 3473 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz
+ 1 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz.md5
+ 19403 Mills_and_1000G_gold_standard.indels.b37.vcf.gz
+ 1 Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5
+ 536 Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz
+ 1 Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz.md5
+ 29291 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz
+ 1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz.md5
+ 565 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz
+ 1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz.md5
+ 37930 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz
+ 1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz.md5
+ 592 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz
+ 1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz.md5
+5898484 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam
+ 112 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz
+ 1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz.md5
+ 1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.md5
+ 3837 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz
+ 1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz.md5
+ 65 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz
+ 1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz.md5
+ 275757 dbsnp_137.b37.excluding_sites_after_129.vcf.gz
+ 1 dbsnp_137.b37.excluding_sites_after_129.vcf.gz.md5
+ 3735 dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz
+ 1 dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz.md5
+ 998153 dbsnp_137.b37.vcf.gz
+ 1 dbsnp_137.b37.vcf.gz.md5
+ 3890 dbsnp_137.b37.vcf.idx.gz
+ 1 dbsnp_137.b37.vcf.idx.gz.md5
+ 58418 hapmap_3.3.b37.vcf.gz
+ 1 hapmap_3.3.b37.vcf.gz.md5
+ 999 hapmap_3.3.b37.vcf.idx.gz
+ 1 hapmap_3.3.b37.vcf.idx.gz.md5
+ 3 human_g1k_v37.dict.gz
+ 1 human_g1k_v37.dict.gz.md5
+ 2 human_g1k_v37.fasta.fai.gz
+ 1 human_g1k_v37.fasta.fai.gz.md5
+ 849537 human_g1k_v37.fasta.gz
+ 1 human_g1k_v37.fasta.gz.md5
+ 1 human_g1k_v37.stats.gz
+ 1 human_g1k_v37.stats.gz.md5
+ 3 human_g1k_v37_decoy.dict.gz
+ 1 human_g1k_v37_decoy.dict.gz.md5
+ 2 human_g1k_v37_decoy.fasta.fai.gz
+ 1 human_g1k_v37_decoy.fasta.fai.gz.md5
+ 858592 human_g1k_v37_decoy.fasta.gz
+ 1 human_g1k_v37_decoy.fasta.gz.md5
+ 1 human_g1k_v37_decoy.stats.gz
+ 1 human_g1k_v37_decoy.stats.gz.md5
+</code></pre>
+</notextile>
+
+h2. Submit a GATK job
+
+The Arvados distribution includes an example crunch script ("crunch_scripts/GATK2-VariantFiltration":https://arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-VariantFiltration) that runs the GATK VariantFiltration tool with some default settings.
+
+<notextile>
+<pre><code>~$ <span class="userinput">src_version=76588bfc57f33ea1b36b82ca7187f465b73b4ca4</span>
+~$ <span class="userinput">vcf_input=5ee633fe2569d2a42dd81b07490d5d13+82</span>
+~$ <span class="userinput">gatk_binary=c905c8d8443a9c44274d98b7c6cfaa32+94</span>
+~$ <span class="userinput">gatk_bundle=d237a90bae3870b3b033aea1e99de4a9+10820</span>
+~$ <span class="userinput">cat >the_job <<EOF
+{
+ "script":"GATK2-VariantFiltration",
+ "repository":"arvados",
+ "script_version":"$src_version",
+ "script_parameters":
+ {
+ "input":"$vcf_input",
+ "gatk_binary_tarball":"$gatk_binary",
+ "gatk_bundle":"$gatk_bundle"
+ }
+}
+EOF</span>
+</code></pre>
+</notextile>
+
+* @"input"@ is collection containing the source VCF data. Here we are using an exome report from PGP participant hu34D5B9.
+* @"gatk_binary_tarball"@ is a Keep collection containing the GATK 2 binary distribution[1] tar file.
+* @"gatk_bundle"@ is a Keep collection containing the GATK resource bundle[2].
+
+Now start a job:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv job create --job "$(cat the_job)"</span>
+{
+ "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4",
+ "kind":"arvados#job",
+ "etag":"9j99n1feoxw3az448f8ises12",
+ "uuid":"qr1hi-8i9sb-n9k7qyp7bs5b9d4",
+ "owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "created_at":"2013-12-17T19:02:15Z",
+ "modified_by_client_uuid":"qr1hi-ozdt8-obw7foaks3qjyej",
+ "modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "modified_at":"2013-12-17T19:02:15Z",
+ "updated_at":"2013-12-17T19:02:15Z",
+ "submit_id":null,
+ "priority":null,
+ "script":"GATK2-VariantFiltration",
+ "script_parameters":{
+ "input":"5ee633fe2569d2a42dd81b07490d5d13+82",
+ "gatk_binary_tarball":"c905c8d8443a9c44274d98b7c6cfaa32+94",
+ "gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820"
+ },
+ "script_version":"76588bfc57f33ea1b36b82ca7187f465b73b4ca4",
+ "cancelled_at":null,
+ "cancelled_by_client_uuid":null,
+ "cancelled_by_user_uuid":null,
+ "started_at":null,
+ "finished_at":null,
+ "output":null,
+ "success":null,
+ "running":null,
+ "is_locked_by_uuid":null,
+ "log":null,
+ "runtime_constraints":{},
+ "tasks_summary":{},
+ "dependencies":[
+ "5ee633fe2569d2a42dd81b07490d5d13+82",
+ "c905c8d8443a9c44274d98b7c6cfaa32+94",
+ "d237a90bae3870b3b033aea1e99de4a9+10820"
+ ]
+}
+</code></pre>
+</notextile>
+
+Once the job completes, the output can be found in hu34D5B9-exome-filtered.vcf:
+
+<notextile><pre><code>~$ <span class="userinput">arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91</span>
+hu34D5B9-exome-filtered.vcf
+</code></pre>
+</notextile>
+
+h2. Notes
+
+fn1. "Download the GATK tools":http://www.broadinstitute.org/gatk/download
+
+fn2. "Information about the GATK resource bundle":http://gatkforums.broadinstitute.org/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it and "direct download link":ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.5/b37/ (if prompted, submit an empty password)
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Running a Crunch job on the command line"
+...
+
+This tutorial introduces how to run individual Crunch jobs using the @arv@ command line tool.
+
+{% include 'tutorial_expectations' %}
+
+You will create a job to run the "hash" Crunch script. The "hash" script computes the MD5 hash of each file in a collection.
+
+h2. Jobs
+
+Crunch pipelines consist of one or more jobs. A "job" is a single run of a specific version of a Crunch script with a specific input. You can also run jobs individually.
+
+A request to run a Crunch job are is described using a JSON object. For example:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cat >~/the_job <<EOF
+{
+ "script": "hash",
+ "repository": "arvados",
+ "script_version": "master",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ },
+ "no_reuse": "true"
+}
+EOF
+</code></pre>
+</notextile>
+
+* @cat@ is a standard Unix utility that writes a sequence of input to standard output.
+* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@.
+* @>~/the_job@ redirects standard output to a file called @~/the_job@.
+* @"repository"@ is the name of a Git repository to search for the script version. You can access a list of available git repositories on the Arvados Workbench under "*Code repositories*":https://{{site.arvados_workbench_host}}/repositories.
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit Git revision hash, a tag, or a branch. Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
+* @"script"@ specifies the name of the script to run. The script must be given relative to the @crunch_scripts/@ subdirectory of the Git repository.
+* @"script_parameters"@ are provided to the script. In this case, the input is the PGP data Collection that we "put in Keep earlier":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
+* Setting the @"no_reuse"@ flag tells Crunch not to reuse work from past jobs. This helps ensure that you can watch a new Job process for the rest of this tutorial, without reusing output from a past run that you made, or somebody else marked as public. (If you want to experiment, after the first run below finishes, feel free to edit this job to remove the @"no_reuse"@ line and resubmit it. See what happens!)
+
+Use @arv job create@ to actually submit the job. It should print out a JSON object which describes the newly created job:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv job create --job "$(cat ~/the_job)"</span>
+{
+ "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss",
+ "kind":"arvados#job",
+ "etag":"ax3cn7w9whq2hdh983yxvq09p",
+ "uuid":"qr1hi-8i9sb-1pm1t02dezhupss",
+ "owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "created_at":"2013-12-16T20:44:32Z",
+ "modified_by_client_uuid":"qr1hi-ozdt8-obw7foaks3qjyej",
+ "modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "modified_at":"2013-12-16T20:44:32Z",
+ "updated_at":"2013-12-16T20:44:33Z",
+ "submit_id":null,
+ "priority":null,
+ "script":"hash",
+ "script_parameters":{
+ "input":"c1bad4b39ca5a924e481008009d94e32+210"
+ },
+ "script_version":"d9cd657b733d578ac0d2167dd75967aa4f22e0ac",
+ "cancelled_at":null,
+ "cancelled_by_client_uuid":null,
+ "cancelled_by_user_uuid":null,
+ "started_at":null,
+ "finished_at":null,
+ "output":null,
+ "success":null,
+ "running":null,
+ "is_locked_by_uuid":null,
+ "log":null,
+ "runtime_constraints":{},
+ "tasks_summary":{},
+ "dependencies":[
+ "c1bad4b39ca5a924e481008009d94e32+210"
+ ]
+}
+</code></pre>
+</notextile>
+
+The job is now queued and will start running as soon as it reaches the front of the queue. Fields to pay attention to include:
+
+ * @"uuid"@ is the unique identifier for this specific job.
+ * @"script_version"@ is the actual revision of the script used. This is useful if the version was described using the "repository:branch" format.
+
+h2. Monitor job progress
+
+Go to "*Recent jobs*":https://{{site.arvados_workbench_host}}/jobs in Workbench. Your job should be near the top of the table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
+
+h2. Inspect the job output
+
+On the "Workbench Dashboard":https://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *file* column to view a file, or click on the download button <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
+
+On the command line, you can use @arv job get@ to access a JSON object describing the output:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv job get --uuid qr1hi-8i9sb-xxxxxxxxxxxxxxx</span>
+{
+ "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss",
+ "kind":"arvados#job",
+ "etag":"1bk98tdj0qipjy0rvrj03ta5r",
+ "uuid":"qr1hi-8i9sb-1pm1t02dezhupss",
+ "owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "created_at":"2013-12-16T20:44:32Z",
+ "modified_by_client_uuid":null,
+ "modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "modified_at":"2013-12-16T20:44:55Z",
+ "updated_at":"2013-12-16T20:44:55Z",
+ "submit_id":null,
+ "priority":null,
+ "script":"hash",
+ "script_parameters":{
+ "input":"c1bad4b39ca5a924e481008009d94e32+210"
+ },
+ "script_version":"d9cd657b733d578ac0d2167dd75967aa4f22e0ac",
+ "cancelled_at":null,
+ "cancelled_by_client_uuid":null,
+ "cancelled_by_user_uuid":null,
+ "started_at":"2013-12-16T20:44:36Z",
+ "finished_at":"2013-12-16T20:44:53Z",
+ "output":"dd755dbc8d49a67f4fe7dc843e4f10a6+54",
+ "success":true,
+ "running":false,
+ "is_locked_by_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
+ "log":"2afdc6c8b67372ffd22d8ce89d35411f+91",
+ "runtime_constraints":{},
+ "tasks_summary":{
+ "done":2,
+ "running":0,
+ "failed":0,
+ "todo":0
+ },
+ "dependencies":[
+ "c1bad4b39ca5a924e481008009d94e32+210"
+ ]
+}
+</code></pre>
+</notextile>
+
+* @"output"@ is the unique identifier for this specific job's output. This is a Keep collection. Because the output of Arvados jobs should be deterministic, the known expected output is <code>dd755dbc8d49a67f4fe7dc843e4f10a6+54</code>.
+
+Now you can list the files in the collection:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep ls dd755dbc8d49a67f4fe7dc843e4f10a6+54</span>
+./md5sum.txt
+</code></pre>
+</notextile>
+
+This collection consists of the @md5sum.txt@ file. Use @arv keep get@ to show the contents of the @md5sum.txt@ file:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep get dd755dbc8d49a67f4fe7dc843e4f10a6+54/md5sum.txt</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f ./var-GS000016015-ASM.tsv.bz2
+</code></pre>
+</notextile>
+
+This MD5 hash matches the MD5 hash which we "computed earlier":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
+
+h2. The job log
+
+When the job completes, you can access the job log. On the Workbench, visit "*Recent jobs*":https://{{site.arvados_workbench_host}}/jobs %(rarr)→% your job's UUID under the *uuid* column %(rarr)→% the collection link on the *log* row.
+
+On the command line, the Keep identifier listed in the @"log"@ field from @arv job get@ specifies a collection. You can list the files in the collection:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep ls xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx+91</span>
+./qr1hi-8i9sb-xxxxxxxxxxxxxxx.log.txt
+</code></pre>
+</notextile>
+
+The log collection consists of one log file named with the job's UUID. You can access it using @arv keep get@:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep get xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx+91/qr1hi-8i9sb-xxxxxxxxxxxxxxx.log.txt</span>
+2013-12-16_20:44:35 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 check slurm allocation
+2013-12-16_20:44:35 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 node compute13 - 8 slots
+2013-12-16_20:44:36 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 start
+2013-12-16_20:44:36 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 Install revision d9cd657b733d578ac0d2167dd75967aa4f22e0ac
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 Clean-work-dir exited 0
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 Install exited 0
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 script hash
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 script_version d9cd657b733d578ac0d2167dd75967aa4f22e0ac
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 script_parameters {"input":"c1bad4b39ca5a924e481008009d94e32+210"}
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 runtime_constraints {"max_tasks_per_node":0}
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 start level 0
+2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 0 done, 0 running, 1 todo
+2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 job_task qr1hi-ot0gb-23c1k3kwrf8da62
+2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 child 7681 started on compute13.1
+2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 0 done, 1 running, 0 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 child 7681 on compute13.1 exit 0 signal 0 success=true
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 success in 1 seconds
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 output
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 wait for last 0 children to finish
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 1 done, 0 running, 1 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 start level 1
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 1 done, 0 running, 1 todo
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 job_task qr1hi-ot0gb-iwr0o3unqothg28
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 child 7716 started on compute13.1
+2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 1 done, 1 running, 0 todo
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 child 7716 on compute13.1 exit 0 signal 0 success=true
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 success in 13 seconds
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 output dd755dbc8d49a67f4fe7dc843e4f10a6+54
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 wait for last 0 children to finish
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 status: 2 done, 0 running, 0 todo
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 release job allocation
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 Freeze not implemented
+2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 collate
+2013-12-16_20:44:53 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 output dd755dbc8d49a67f4fe7dc843e4f10a6+54+K@qr1hi
+2013-12-16_20:44:53 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 finish
+</code></pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Concurrent Crunch tasks"
+...
+
+In the previous tutorials, we used @arvados.job_setup.one_task_per_input_file()@ to automatically create concurrent jobs by creating a separate task per file. For some types of jobs, you may need to split the work up differently, for example creating tasks to process different segments of a single large file. In this this tutorial will demonstrate how to create Crunch tasks directly.
+
+Start by entering the @crunch_scripts@ directory of your Git repository:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $USER/crunch_scripts</span>
+</code></pre>
+</notextile>
+
+Next, using @nano@ or your favorite Unix text editor, create a new file called @concurrent-hash.py@ in the @crunch_scripts@ directory.
+
+notextile. <pre>~/$USER/crunch_scripts$ <code class="userinput">nano concurrent-hash.py</code></pre>
+
+Add the following code to compute the MD5 hash of each file in a collection:
+
+<notextile> {% code 'concurrent_hash_script_py' as python %} </notextile>
+
+Make the file executable:
+
+notextile. <pre><code>~/$USER/crunch_scripts$ <span class="userinput">chmod +x concurrent-hash.py</span></code></pre>
+
+Add the file to the Git staging area, commit, and push:
+
+<notextile>
+<pre><code>~/$USER/crunch_scripts$ <span class="userinput">git add concurrent-hash.py</span>
+~/$USER/crunch_scripts$ <span class="userinput">git commit -m"concurrent hash"</span>
+~/$USER/crunch_scripts$ <span class="userinput">git push origin master</span>
+</code></pre>
+</notextile>
+
+You should now be able to run your new script using Crunch, with "script" referring to our new "concurrent-hash.py" script. We will use a different input from our previous examples. We will use @887cd41e9c613463eab2f0d885c6dd96+83@ which consists of three files, "alice.txt", "bob.txt" and "carol.txt" (the example collection used previously in "fetching data from Arvados using Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html#dir).
+
+<notextile>
+<pre><code>~/$USER/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
+{
+ "script": "concurrent-hash.py",
+ "repository": "$USER",
+ "script_version": "master",
+ "script_parameters":
+ {
+ "input": "887cd41e9c613463eab2f0d885c6dd96+83"
+ }
+}
+EOF</span>
+~/$USER/crunch_scripts$ <span class="userinput">arv job create --job "$(cat ~/the_job)"</span>
+{
+ ...
+ "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
+ ...
+}
+~/$USER/crunch_scripts$ <span class="userinput">arv job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx</span>
+{
+ ...
+ "output":"e2ccd204bca37c77c0ba59fc470cd0f7+162",
+ ...
+}
+</code></pre>
+</notextile>
+
+(Your shell should automatically fill in @$USER@ with your login name. The job JSON that gets saved should have @"repository"@ pointed at your personal Git repository.)
+
+Because the job ran in concurrent, each instance of concurrent-hash creates a separate @md5sum.txt@ as output. Arvados automatically collates theses files into a single collection, which is the output of the job:
+
+<notextile>
+<pre><code>~/$USER/crunch_scripts$ <span class="userinput">arv keep ls e2ccd204bca37c77c0ba59fc470cd0f7+162</span>
+./md5sum.txt
+~/$USER/crunch_scripts$ <span class="userinput">arv keep get e2ccd204bca37c77c0ba59fc470cd0f7+162/md5sum.txt</span>
+0f1d6bcf55c34bed7f92a805d2d89bbf alice.txt
+504938460ef369cd275e4ef58994cffe bob.txt
+8f3b36aff310e06f3c5b9e95678ff77a carol.txt
+</code></pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Querying the Metadata Database"
+...
+
+This tutorial introduces the Arvados Metadata Database. The Metadata Database stores information about files in Keep. This example will use the Python SDK to find public WGS (Whole Genome Sequencing) data for people who have reported a certain medical condition.
+
+{% include 'tutorial_expectations' %}
+
+In the tutorial examples, three angle brackets (>>>) will be used to denote code to enter at the interactive Python prompt.
+
+Start by running Python.
+
+<notextile>
+<pre><code>~$ <span class="userinput">python</span>
+Python 2.7.3 (default, Jan 2 2013, 13:56:14)
+[GCC 4.7.2] on linux2
+Type "help", "copyright", "credits" or "license" for more information.
+>>>
+</code></pre>
+</notextile>
+
+If everything is set up correctly, you will be able to import the arvados SDK.
+
+notextile. <pre><code>>>> <span class="userinput">import arvados</span></pre></code>
+
+This tutorial will also use the regular expression (re) python module:
+
+<notextile>
+<pre><code>>>> <span class="userinput">import re</span>
+</code></pre>
+</notextile>
+
+h2. Finding traits
+
+notextile. <pre><code>>>> <span class="userinput">all_traits = arvados.api().traits().list(limit=1000).execute()</span></code></pre>
+
+* @arvados.api()@ gets an object that provides access to the Arvados API server
+* @.traits()@ gets an object that provides access to the "traits" resource on the Arvados API server
+* @.list(limit=1000)@ constructs a query to list all elements of the "traits" resource, with a limit of 1000 entries returned
+* @.execute()@ executes the query and returns the result, which we assign to "all_traits"
+
+notextile. <pre><code>>>> <span class="userinput">cancer_traits = filter(lambda t: re.search('cancer', t['name']), all_traits['items'])</span></code></pre>
+
+* @lambda t: re.search('cancer', t['name'])@ is an inline function that takes a parameter @t@ and uses a simple regular expression to test if @t['name']@ contains the substring 'cancer'
+* @all_traits['items']@ is the input sequence of traits
+* @filter@ tests each element @t@ and constructs a new sequence consisting only of the elements that pass the filter
+* @cancer_traits@ gets the result of @filter@
+
+<notextile>
+<pre><code>>>> <span class="userinput">for t in cancer_traits: print(t['uuid'], t['name'])</span>
+...
+qr1hi-q1cn2-8q57g2diohwnzm0 Cervical cancer
+qr1hi-q1cn2-vqp4243janpjbyj Breast cancer
+qr1hi-q1cn2-v6usijujcpwqrn1 Non-melanoma skin cancer
+...
+</code></pre>
+</notextile>
+
+In this tutorial wil will use "Non-melanoma skin cancer" trait with uuid @qr1hi-q1cn2-v6usijujcpwqrn1@.
+
+notextile. <pre><code>>>> <span class="userinput">non_melanoma_cancer = 'qr1hi-q1cn2-v6usijujcpwqrn1'</code></pre>
+
+h2. Finding humans with the selected trait
+
+We query the "links" resource to find humans that report the selected trait. Links are directional connections between Arvados data items, for example, from a human to their reported traits.
+
+<notextile>
+<pre><code>>>> <span class="userinput">trait_filter = [
+ ['link_class', '=', 'human_trait'],
+ ['tail_uuid', 'is_a', 'arvados#human'],
+ ['head_uuid', '=', non_melanoma_cancer],
+ ]
+</code></pre>
+</notextile>
+
+* @['link_class', '=', 'human_trait']@ filters on links that connect phenotype traits to individuals in the database.
+* @['tail_uuid', 'is_a', 'arvados#human']@ filters that the "tail" must be a "human" database object.
+* @['head_uuid', '=', non_melanoma_cancer]@ filters that the "head" of the link must connect to the "trait" database object non_melanoma_cancer .
+
+The query will return links that match all three conditions.
+
+<notextile>
+<pre><code>>>> <span class="userinput">trait_links = arvados.api().links().list(limit=1000, filters=trait_filter).execute()</span>
+</code></pre>
+</notextile>
+
+* @arvados.api()@ gets an object that provides access to the Arvados API server
+* @.links()@ gets an object that provides access to the "links" resource on the Arvados API server
+* @.list(limit=1000, filters=trait_filter)@ constructs a query to elements of the "links" resource that match the criteria discussed above, with a limit of 1000 entries returned
+* @.execute()@ executes the query and returns the result, which we assign to "trait_links"
+
+<notextile>
+<pre><code>>>> <span class="userinput">human_uuids = map(lambda l: l['tail_uuid'], trait_links['items'])</span>
+>>> <span class="userinput">human_uuids</span>
+[u'1h9kt-7a9it-c0uqa4kcdh29wdf', u'1h9kt-7a9it-x4tru6mn40hc6ah',
+u'1h9kt-7a9it-yqb8m5s9cpy88i8', u'1h9kt-7a9it-46sm75w200ngwny',
+u'1h9kt-7a9it-gx85a4tdkpzsg3w', u'1h9kt-7a9it-8cvlaa8909lgeo9',
+u'1h9kt-7a9it-as37qum2pq8vizb', u'1h9kt-7a9it-14fph66z2baqxb9',
+u'1h9kt-7a9it-e9zc7i4crmw3v69', u'1h9kt-7a9it-np7f35hlijlxdmt',
+u'1h9kt-7a9it-j9hqyjwbvo9cojn', u'1h9kt-7a9it-lqxdtm1gynmsv13',
+u'1h9kt-7a9it-zkhhxjfg2o22ywq', u'1h9kt-7a9it-nsjoxqd33lzldw9',
+u'1h9kt-7a9it-ytect4smzcgd4kg', u'1h9kt-7a9it-y6tl353b3jc4tos',
+u'1h9kt-7a9it-98f8qave4f8vbs5', u'1h9kt-7a9it-gd72sh15q0p4wq3',
+u'1h9kt-7a9it-zlx25dscak94q9h', u'1h9kt-7a9it-8gronw4rbgmim01',
+u'1h9kt-7a9it-wclfkjcb23tr5es', u'1h9kt-7a9it-rvp2qe7szfz4dy6',
+u'1h9kt-7a9it-50iffhmpzsktwjm', u'1h9kt-7a9it-ul412id5y31a5o8',
+u'1h9kt-7a9it-732kwkfzylmt4ik', u'1h9kt-7a9it-v9zqxegpblsbtai',
+u'1h9kt-7a9it-kmaraqduit1v5wd', u'1h9kt-7a9it-t1nwtlo1hru5vvq',
+u'1h9kt-7a9it-q3w6j9od4ibpoyl', u'1h9kt-7a9it-qz8vzkuuz97ezwv',
+u'1h9kt-7a9it-t1v8sjz6dm9jmjf', u'1h9kt-7a9it-qe8wrbyvuqs5jew']
+</code></pre>
+</notextile>
+
+* @lambda l: l['tail_uuid']@ is an inline function that returns the 'tail_uuid' attribute of 'l'
+* @trait_links['items']@ is the input set from the query
+* @map@ converts each item in a sequence into a different item using the embedded function, in this case to produce a sequence of uuids which refer to humans that have the specified trait.
+
+h2. Find Personal Genome Project identifiers from Arvados UUIDs
+
+<notextile>
+<pre><code>>>> <span class="userinput">human_filters = [
+ ["link_class", "=", "identifier"],
+ ["head_uuid", "in", human_uuids]
+ ]</span>
+>>> <span class="userinput">pgpid_links = arvados.api('v1').links().list(limit=1000, filters=human_filters).execute()</span>
+>>> <span class="userinput">map(lambda l: l['name'], pgpid_links['items'])</span>
+[u'hu01024B', u'hu11603C', u'hu15402B', u'hu174334', u'hu1BD549', u'hu237A50',
+ u'hu34A921', u'hu397733', u'hu414115', u'hu43860C', u'hu474789', u'hu553620',
+ u'hu56B3B6', u'hu5917F3', u'hu599905', u'hu5E55F5', u'hu602487', u'hu633787',
+ u'hu68F245', u'hu6C3F34', u'hu7260DD', u'hu7A2F1D', u'hu94040B', u'hu9E356F',
+ u'huAB8707', u'huB1FD55', u'huB4883B', u'huD09050', u'huD09534', u'huD3A569',
+ u'huDF04CC', u'huE2E371']
+</code></pre>
+</notextile>
+
+These PGP IDs let us find public profiles, for example:
+
+* "https://my.pgp-hms.org/profile/huE2E371":https://my.pgp-hms.org/profile/huE2E371
+* "https://my.pgp-hms.org/profile/huDF04CC":https://my.pgp-hms.org/profile/huDF04CC
+* ...
+
+h2. Find genomic data from specific humans
+
+Now we want to find collections in Keep that were provided by these humans. We search the "links" resource for "provenance" links that point to entries in the list of humans with the non-melanoma skin cancer trait:
+
+<notextile>
+<pre><code>>>> <span class="userinput">provenance_links = arvados.api().links().list(limit=1000, filters=[
+ ["link_class", "=", "provenance"],
+ ["name", "=", "provided"],
+ ["tail_uuid", "in", human_uuids]
+ ]).execute()
+collection_uuids = map(lambda l: l['head_uuid'], provenance_links['items'])
+
+# build map of human uuid -> PGP ID
+pgpid = {}
+for pgpid_link in pgpid_links['items']:
+ pgpid[pgpid_link['head_uuid']] = pgpid_link['name']
+
+# build map of collection uuid -> PGP ID
+for p_link in provenance_links['items']:
+ pgpid[p_link['head_uuid']] = pgpid[p_link['tail_uuid']]
+
+# get details (e.g., list of files) of each collection
+collections = arvados.api('v1').collections().list(filters=[
+ ["uuid", "in", collection_uuids]
+ ]).execute()
+
+# print PGP public profile links with file locators
+for c in collections['items']:
+ for f in c['files']:
+ print "https://my.pgp-hms.org/profile/%s %s %s%s" % (pgpid[c['uuid']], c['uuid'], ('' if f[0] == '.' else f[0]+'/'), f[1])
+</span>
+https://my.pgp-hms.org/profile/hu43860C a58dca7609fa84c8c38a7e926a97b2fc var-GS00253-DNA_A01_200_37-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/huB1FD55 ea30eb9e46eedf7f05ed6e348c2baf5d var-GS000010320-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/huDF04CC 4ab0df8f22f595d1747a22c476c05873 var-GS000010427-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/hu7A2F1D 756d0ada29b376140f64e7abfe6aa0e7 var-GS000014566-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/hu553620 7ed4e425bb1c7cc18387cbd9388181df var-GS000015272-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/huD09534 542112e210daff30dd3cfea4801a9f2f var-GS000016374-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/hu599905 33a9f3842b01ea3fdf27cc582f5ea2af var-GS000016015-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/hu43860C a58dca7609fa84c8c38a7e926a97b2fc+302 var-GS00253-DNA_A01_200_37-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/huB1FD55 ea30eb9e46eedf7f05ed6e348c2baf5d+291 var-GS000010320-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/huDF04CC 4ab0df8f22f595d1747a22c476c05873+242 var-GS000010427-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/hu7A2F1D 756d0ada29b376140f64e7abfe6aa0e7+242 var-GS000014566-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/hu553620 7ed4e425bb1c7cc18387cbd9388181df+242 var-GS000015272-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/huD09534 542112e210daff30dd3cfea4801a9f2f+242 var-GS000016374-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/hu599905 33a9f3842b01ea3fdf27cc582f5ea2af+242 var-GS000016015-ASM.tsv.bz2
+https://my.pgp-hms.org/profile/hu599905 d6e2e57cd60ba5979006d0b03e45e726+81 Witch_results.zip
+https://my.pgp-hms.org/profile/hu553620 ea4f2d325592a1272f989d141a917fdd+85 Devenwood_results.zip
+https://my.pgp-hms.org/profile/hu7A2F1D 4580f6620bb15b25b18373766e14e4a7+85 Innkeeper_results.zip
+https://my.pgp-hms.org/profile/huD09534 fee37be9440b912eb90f5e779f272416+82 Hallet_results.zip
+</code></pre>
+</notextile>
+
+h3. Search for a variant
+
+Now we will use crunch to issue a 'grep' job to look for variant rs1126809 in each of the "var-" files (these contain variant calls from WGS data).
+
+<notextile>
+<pre><code>>>> <span class="userinput">job = {}
+for c in collections['items']:
+ if [] != filter(lambda f: re.search('^var-.*\.tsv\.bz2', f[1]), c['files']):
+ job[c['uuid']] = arvados.api('v1').jobs().create(body={
+ 'script': 'grep',
+ 'script_parameters': {'input': c['uuid'], 'pattern': "rs1126809\\b"},
+ 'script_version': 'e7aeb42'
+ }).execute()
+ print "%s %s" % (pgpid[c['uuid']], job[c['uuid']]['uuid'])
+</span>
+hu43860C qr1hi-8i9sb-wbf3uthbhkcy8ji
+huB1FD55 qr1hi-8i9sb-scklkiy8dc27dab
+huDF04CC qr1hi-8i9sb-pg0w4rfrwfd9srg
+hu7A2F1D qr1hi-8i9sb-n7u0u0rj8b47168
+hu553620 qr1hi-8i9sb-k7gst7vyhg20pt1
+huD09534 qr1hi-8i9sb-4w65pm48123fte5
+hu599905 qr1hi-8i9sb-wmwa5b5r3eghnev
+hu43860C qr1hi-8i9sb-j1mngmakdh8iv9o
+huB1FD55 qr1hi-8i9sb-4j6ehiatcolaoxb
+huDF04CC qr1hi-8i9sb-n6lcmcr3lowqr5u
+hu7A2F1D qr1hi-8i9sb-0hwsdtojfcxjo40
+hu553620 qr1hi-8i9sb-cvvqzqea7jhwb0i
+huD09534 qr1hi-8i9sb-d0y0qtzuwzbrjj0
+hu599905 qr1hi-8i9sb-i9ec9g8d7rt70xg
+</code></pre>
+</notextile>
+
+
+Monitor job progress by refreshing the Jobs page in Workbench, or by using the API:
+
+<notextile>
+<pre><code>>>> <span class="userinput">map(lambda j: arvados.api('v1').jobs().get(uuid=j['uuid']).execute()['success'], job.values())
+[None, True, None, None, None, None, None, None, None, None, None, None, None, None]
+</code></pre>
+</notextile>
+
+Unfinished jobs will appear as None, failed jobs as False, and completed jobs as True.
+
+After the jobs have completed, check output file sizes.
+
+<notextile>
+<pre><code>>>> <span class="userinput">for collection_uuid in job:
+ job_uuid = job[collection_uuid]['uuid']
+ job_output = arvados.api('v1').jobs().get(uuid=job_uuid).execute()['output']
+ output_files = arvados.api('v1').collections().get(uuid=job_output).execute()['files']
+ # Test the output size. If greater than zero, that means 'grep' found the variant
+ if output_files[0][2] > 0:
+ print("%s has variant rs1126809" % (pgpid[collection_uuid]))
+ else:
+ print("%s does not have variant rs1126809" % (pgpid[collection_uuid]))
+</span>
+hu553620 does not have variant rs1126809
+hu43860C does not have variant rs1126809
+hu599905 has variant rs1126809
+huD09534 has variant rs1126809
+hu553620 does not have variant rs1126809
+huB1FD55 does not have variant rs1126809
+huDF04CC has variant rs1126809
+hu7A2F1D has variant rs1126809
+hu7A2F1D has variant rs1126809
+hu599905 has variant rs1126809
+huDF04CC has variant rs1126809
+huB1FD55 does not have variant rs1126809
+huD09534 has variant rs1126809
+hu43860C does not have variant rs1126809
+</code></pre>
+</notextile>
+
+Thus, of the 14 WGS results available for PGP participants reporting non-melanoma skin cancer, 8 include the rs1126809 variant.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: Introduction to Crunch
+...
+
+The Arvados "Crunch" framework is designed to support processing very large data batches (gigabytes to terabytes) efficiently, and provides the following benefits:
+* Increase concurrency by running tasks asynchronously, using many CPUs and network interfaces at once (especially beneficial for CPU-bound and I/O-bound tasks respectively).
+* Track inputs, outputs, and settings so you can verify that the inputs, settings, and sequence of programs you used to arrive at an output is really what you think it was.
+* Ensure that your programs and workflows are repeatable with different versions of your code, OS updates, etc.
+* Interrupt and resume long-running jobs consisting of many short tasks.
+* Maintain timing statistics automatically, so they're there when you want them.
+
+h2. Prerequisites
+
+To get the most value out of this section, you should be comfortable with the following:
+
+# Using a secure shell client such as SSH or PuTTY to log on to a remote server
+# Using the Unix command line shell, Bash
+# Viewing and editing files using a unix text editor such as vi, Emacs, or nano
+# Programming in Python
+# Revision control using Git
+
+We also recommend you read the "Arvados Platform Overview":https://arvados.org/projects/arvados/wiki#Platform-Overview for an introduction and background information about Arvados.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Writing a pipeline template"
+...
+
+This tutorial demonstrates how to construct a two stage pipeline template that uses the "bwa mem":http://bio-bwa.sourceforge.net/ tool to produce a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file, then uses the "Picard SortSam tool":http://picard.sourceforge.net/command-line-overview.shtml#SortSam to produce a BAM (Binary Alignment/Map) file.
+
+{% include 'tutorial_expectations' %}
+
+Use the following command to create an empty template using @arv create pipeline_template@:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv create pipeline_template</span></code></pre>
+</notextile>
+
+This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@). Now, update the contents of the editor with the following content:
+
+<notextile>{% code 'tutorial_bwa_sortsam_pipeline' as javascript %}</notextile>
+
+* @"name"@ is a human-readable name for the pipeline.
+* @"components"@ is a set of scripts or commands that make up the pipeline. Each component is given an identifier (@"bwa-mem"@ and @"SortSam"@) in this example).
+** Each entry in components @"components"@ is an Arvados job submission. For more information about individual jobs, see the "job object reference":{{site.baseurl}}/api/schema/Job.html and "job create method.":{{site.baseurl}}/api/methods/jobs.html#create
+* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados. These parameters are described in more detail in "Writing a script":tutorial-firstscript.html
+* @"runtime_constraints"@ describes runtime resource requirements for the component.
+** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job. The Docker image @"arvados/jobs-java-bwa-samtools"@ supplied here has the Arvados SDK, Java runtime environment, bwa, and samtools installed.
+* @"script_parameters"@ describes the component parameters.
+** @"command"@ is the actual command line to invoke the @bwa@ and then @SortSam@. The notation @$()@ denotes macro substitution commands evaluated by the run-command tool wrapper.
+** @"stdout"@ indicates that the output of this command should be captured to a file.
+** @$(node.cores)@ evaluates to the number of cores available on the compute node at time the command is run.
+** @$(tmpdir)@ evaluates to the local path for temporary directory the command should use for scratch data.
+** @$(reference_collection)@ evaluates to the script_parameter @"reference_collection"@
+** @$(dir $(...))@ constructs a local path to a directory representing the supplied Arvados collection.
+** @$(file $(...))@ constructs a local path to a given file within the supplied Arvados collection.
+** @$(glob $(...))@ searches the specified path based on a file glob pattern and evalutes to the first result.
+** @$(basename $(...))@ evaluates to the supplied path with leading path portion and trailing filename extensions stripped
+** @"output_of"@ indicates that the @output@ of the @bwa-mem@ component should be used as the @"input"@ of @SortSam@. Arvados uses these dependencies between components to automatically determine the correct order to run them.
+
+When using @run-command@, the tool should write its output to the current working directory. The output will be automatically uploaded to Keep when the job completes.
+
+See the "run-command reference":{{site.baseurl}}/user/topics/run-command.html for more information about using @run-command@.
+
+h2. Running your pipeline
+
+Your new pipeline template should appear at the top of the Workbench "pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page. You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
+
+Test data is available in the "Arvados Tutorial":https://{{ site.arvados_workbench_host }}/projects/qr1hi-j7d0g-u7zg1qdaowykd8d project:
+
+* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial chromosome 19 reference (2463fa9efeb75e099685528b3b9071e0+438)":https://{{ site.arvados_workbench_host }}/collections/2463fa9efeb75e099685528b3b9071e0+438 for the "reference_collection" parameter
+* Choose <i class="fa fa-fw fa-archive"></i> "Tutorial sample exome (3229739b505d2b878b62aed09895a55a+142)":https://{{ site.arvados_workbench_host }}/collections/3229739b505d2b878b62aed09895a55a+142 for the "sample" parameter
+
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
--- /dev/null
+---
+layout: default
+navsection: userguide
+navmenu: Tutorials
+title: "Writing a Crunch script"
+...
+
+This tutorial demonstrates how to write a script using Arvados Python SDK. The Arvados SDK supports access to advanced features not available using the @run-command@ wrapper, such as scheduling concurrent tasks across nodes.
+
+{% include 'tutorial_expectations' %}
+
+This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples.
+
+Start by creating a directory called @$USER@ . Next, create a subdirectory called @crunch_scripts@ and change to that directory:
+
+<notextile>
+<pre><code>~$ <span class="userinput">mkdir -p tutorial/crunch_scripts</span>
+~$ <span class="userinput">cd tutorial/crunch_scripts</span></code></pre>
+</notextile>
+
+Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
+
+notextile. <pre>~/tutorial/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
+
+Add the following code to compute the MD5 hash of each file in a collection:
+
+<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
+
+Make the file executable:
+
+notextile. <pre><code>~/tutorial/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
+
+Next, create a submission job record. This describes a specific invocation of your script:
+
+<notextile>
+<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
+{
+ "repository":"",
+ "script":"hash.py",
+ "script_version":"$HOME/tutorial",
+ "script_parameters":{
+ "input":"c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+EOF</span>
+</code></pre>
+</notextile>
+
+You can now run your script on your local workstation or VM using @arv-crunch-job@:
+
+<notextile>
+<pre><code>~/tutorial/crunch_scripts</span>$ <span class="userinput">arv-crunch-job --job "$(cat ~/the_job)"</span>
+2014-08-06_15:16:22 qr1hi-8i9sb-qyrat80ef927lam 14473 check slurm allocation
+2014-08-06_15:16:22 qr1hi-8i9sb-qyrat80ef927lam 14473 node localhost - 1 slots
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 start
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 script hash.py
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 script_version $HOME/tutorial
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 script_parameters {"input":"c1bad4b39ca5a924e481008009d94e32+210"}
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 runtime_constraints {"max_tasks_per_node":0}
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 start level 0
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 0 done, 0 running, 1 todo
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 0 job_task qr1hi-ot0gb-lptn85mwkrn9pqo
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 0 child 14478 started on localhost.1
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 0 done, 1 running, 0 todo
+2014-08-06_15:16:24 qr1hi-8i9sb-qyrat80ef927lam 14473 0 stderr crunchstat: Running [stdbuf --output=0 --error=0 /home/$USER/tutorial/crunch_scripts/hash.py]
+2014-08-06_15:16:24 qr1hi-8i9sb-qyrat80ef927lam 14473 0 child 14478 on localhost.1 exit 0 signal 0 success=true
+2014-08-06_15:16:24 qr1hi-8i9sb-qyrat80ef927lam 14473 0 success in 1 seconds
+2014-08-06_15:16:24 qr1hi-8i9sb-qyrat80ef927lam 14473 0 output
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 wait for last 0 children to finish
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 1 done, 0 running, 1 todo
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 start level 1
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 1 done, 0 running, 1 todo
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 1 job_task qr1hi-ot0gb-e3obm0lv6k6p56a
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 1 child 14504 started on localhost.1
+2014-08-06_15:16:25 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 1 done, 1 running, 0 todo
+2014-08-06_15:16:26 qr1hi-8i9sb-qyrat80ef927lam 14473 1 stderr crunchstat: Running [stdbuf --output=0 --error=0 /home/$USER/tutorial/crunch_scripts/hash.py]
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 child 14504 on localhost.1 exit 0 signal 0 success=true
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 success in 10 seconds
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 1 output 8c20281b9840f624a486e4f1a78a1da8+105+A234be74ceb5ea31db6e11b6be26f3eb76d288ad0@54987018
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 wait for last 0 children to finish
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 status: 2 done, 0 running, 0 todo
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 release job allocation
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 Freeze not implemented
+2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473 collate
+2014-08-06_15:16:36 qr1hi-8i9sb-qyrat80ef927lam 14473 output uuid qr1hi-4zz18-n91qrqfp3zivexo
+2014-08-06_15:16:36 qr1hi-8i9sb-qyrat80ef927lam 14473 output hash c1b44b6dc41ef334cf1136033ca950e6+54
+2014-08-06_15:16:37 qr1hi-8i9sb-qyrat80ef927lam 14473 finish
+2014-08-06_15:16:38 qr1hi-8i9sb-qyrat80ef927lam 14473 log manifest is 7fe8cf1d45d438a3ca3ac4a184b7aff4+83
+</code></pre>
+</notextile>
+
+Although the job runs locally, the output of the job has been saved to Keep, the Arvados file store. The "output uuid" line (fourth from the bottom) provides the UUID of the Arvados collection where the script's output has been saved. Copy the output identifier and use @arv-ls@ to list the contents of your output collection, and @arv-get@ to download it to the current directory:
+
+<notextile>
+<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">arv-ls qr1hi-4zz18-n91qrqfp3zivexo</span>
+./md5sum.txt
+~/tutorial/crunch_scripts$ <span class="userinput">arv-get qr1hi-4zz18-n91qrqfp3zivexo/ .</span>
+0 MiB / 0 MiB 100.0%
+~/tutorial/crunch_scripts$ <span class="userinput">cat md5sum.txt</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f c1bad4b39ca5a924e481008009d94e32+210/var-GS000016015-ASM.tsv.bz2
+</code></pre>
+</notextile>
+
+Running locally is convenient for development and debugging, as it permits a fast iterative development cycle. Your job run is also recorded by Arvados, and will appear in the *Recent jobs and pipelines* panel on the "Workbench Dashboard":https://{{site.arvados_workbench_host}}. This provides limited provenance, by recording the input parameters, the execution log, and the output. However, running locally does not allow you to scale out to multiple nodes, and does not store the complete system snapshot required to achieve reproducibility; to do that you need to "submit a job to the Arvados cluster":{{site.baseurl}}/user/tutorials/tutorial-submit-job.html.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Downloading data"
+...
+
+This tutorial describes how to list and download Arvados data collections using the command line tools @arv-ls@ and @arv-get@. It is also possible to download files from a collection from the Workbench page for the collection, covered in "running a pipeline using Workbench":{{site.baseurl}}/user/tutorials/tutorial-pipeline-workbench.html
+
+{% include 'tutorial_expectations' %}
+
+You can view the contents of a collection using @arv-ls@:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv-ls c1bad4b39ca5a924e481008009d94e32+210</span>
+var-GS000016015-ASM.tsv.bz2
+</code></pre>
+
+<pre><code>~$ <span class="userinput">arv-ls 887cd41e9c613463eab2f0d885c6dd96+83</span>
+alice.txt
+bob.txt
+carol.txt
+</code></pre>
+</notextile>
+
+Use @-s@ to print file sizes rounded up to the nearest kilobyte:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv-ls -s c1bad4b39ca5a924e481008009d94e32+210</span>
+221887 var-GS000016015-ASM.tsv.bz2
+</code></pre>
+</notextile>
+
+Use @arv-get@ to download the contents of a collection and place it in the directory specified in the second argument (in this example, @.@ for the current directory):
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv-get c1bad4b39ca5a924e481008009d94e32+210/ .</span>
+~$ <span class="userinput">ls var-GS000016015-ASM.tsv.bz2</span>
+var-GS000016015-ASM.tsv.bz2
+</code></pre>
+</notextile>
+
+You can also download individual files:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv-get 887cd41e9c613463eab2f0d885c6dd96+83/alice.txt .</span>
+</code></pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Mounting Keep as a filesystem"
+...
+
+This tutoral describes how to access Arvados collections using traditional filesystem tools by mounting Keep as a read-only file system using @arv-mount@.
+
+{% include 'tutorial_expectations' %}
+
+h2. Arv-mount
+
+@arv-mount@ provides several features:
+
+* You can browse, open and read Keep entries as if they are regular files.
+* It is easy for existing tools to access files in Keep.
+* Data is downloaded on demand. It is not necessary to download an entire file or collection to start processing.
+
+The default mode permits browsing any collection in Arvados as a subdirectory under the mount directory. To avoid having to fetch a potentially large list of all collections, collection directories only come into existence when explicitly accessed by their Keep locator. For instance, a collection may be found by its content hash in the @keep/by_id@ directory.
+
+<notextile>
+<pre><code>~$ <span class="userinput">mkdir -p keep</span>
+~$ <span class="userinput">arv-mount keep</span>
+~$ <span class="userinput">cd keep/by_id/c1bad4b39ca5a924e481008009d94e32+210</span>
+~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">ls</span>
+var-GS000016015-ASM.tsv.bz2
+~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">md5sum var-GS000016015-ASM.tsv.bz2</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">cd ../..</span>
+~$ <span class="userinput">fusermount -u keep</span>
+</code></pre>
+</notextile>
+
+The last line unmounts Keep. Subdirectories will no longer be accessible.
+
+Within each directory on Keep, there is a @.arvados#collection@ file that does not show up with @ls@. Its contents include, for instance, the @portable_data_hash@, which is the same as the Keep locator.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Uploading data"
+...
+
+This tutorial describes how to to upload new Arvados data collections using the command line tool @arv keep put@.
+
+notextile. <div class="spaced-out">
+
+{% include 'tutorial_expectations' %}
+
+h3. Upload
+
+To upload a file to Keep using @arv keep put@:
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep put var-GS000016015-ASM.tsv.bz2</span>
+216M / 216M 100.0%
+Collection saved as ...
+qr1hi-4zz18-xxxxxxxxxxxxxxx
+</code></pre>
+</notextile>
+
+The output value @qr1hi-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
+
+The file used in this example is a freely available TSV file containing variant annotations from "Personal Genome Project (PGP)":http://www.pgp-hms.org participant "hu599905.":https://my.pgp-hms.org/profile/hu599905), downloadable "here":https://warehouse.pgp-hms.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2.
+
+<notextile><a name="dir"></a></notextile>It is also possible to upload an entire directory with @arv keep put@:
+
+<notextile>
+<pre><code>~$ <span class="userinput">mkdir tmp</span>
+~$ <span class="userinput">echo "hello alice" > tmp/alice.txt</span>
+~$ <span class="userinput">echo "hello bob" > tmp/bob.txt</span>
+~$ <span class="userinput">echo "hello carol" > tmp/carol.txt</span>
+~$ <span class="userinput">arv keep put tmp</span>
+0M / 0M 100.0%
+Collection saved as ...
+qr1hi-4zz18-yyyyyyyyyyyyyyy
+</code></pre>
+</notextile>
+
+In both examples, the @arv keep put@ command created a collection. The first collection contains the single uploaded file. The second collection contains the entire uploaded directory.
+
+@arv keep put@ accepts quite a few optional command line arguments, which are described "on the arv subcommands":{{site.baseurl}}/sdk/cli/subcommands.html#arv-keep-put page.
+
+h3. Locate your collection in Workbench
+
+Visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu, select your *Home* project. Your newly uploaded collection should appear near the top of the *Data collections* tab. The collection locator printed by @arv keep put@ will appear under the *name* column.
+
+To move the collection to a different project, check the box at the left of the collection row. Pull down the *Selection...*<span class="caret"></span> menu near the top of the page tab, and select *Move selected*. This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
+
+!{{ site.baseurl }}/images/workbench-move-selected.png!
+
+Click on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection's listing on a project page to go to the Workbench page for your collection. On this page, you can see the collection's contents, download individual files, and set sharing options.
+
+notextile. </div>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Running a pipeline using Workbench"
+...
+
+A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from a sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This tutorial will introduce the following Arvados features:
+
+<div class="inside-list">
+* How to create a new pipeline from an existing template.
+* How to browse and select input data for the pipeline and submit the pipeline to run on the Arvados cluster.
+* How to access your pipeline results.
+</div>
+
+notextile. <div class="spaced-out">
+
+# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
+# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> button. This will open a dialog box titled *Choose a pipeline to run*.
+# Click to open the *All projects <span class="caret"></span>* menu. Under the *Projects shared with me* header, select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.
+# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will create a new pipeline in your *Home* project and will open it. You can now supply the inputs for the pipeline.
+# The first input parameter to the pipeline is *Reference genoma (fasta)*. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath that header. This will open a dialog box titled *Choose a dataset for Reference genome (fasta)*.
+# Once again, open the *All projects <span class="caret"></span>* menu and select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*. Select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
+# Repeat the previous two steps to set the *Input genome (fastq)* parameter to *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.
+# Click on the <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
+# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a <span class="label label-success">complete</span> label under the *job* column when the pipeline completes successfully.
+# Click on the *Output* link to see the results of the job. This will load a new page listing the output files from this pipeline. You'll see the output SAM file from the alignment tool under the *Files* tab.
+# Click on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.
+
+notextile. </div>
--- /dev/null
+---
+layout: default
+navsection: userguide
+navmenu: Tutorials
+title: "Running on an Arvados cluster"
+...
+
+This tutorial demonstrates how to create a pipeline to run your crunch script on an Arvados cluster. Cluster jobs can scale out to multiple nodes, and use @git@ and @docker@ to store the complete system snapshot required to achieve reproducibilty.
+
+{% include 'tutorial_expectations' %}
+
+This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples.
+
+h2. Setting up Git
+
+All Crunch scripts are managed through the Git revision control system. Before you start using Git, you should do some basic configuration (you only need to do this the first time):
+
+<notextile>
+<pre><code>~$ <span class="userinput">git config --global user.name "Your Name"</span>
+~$ <span class="userinput">git config --global user.email $USER@example.com</span></code></pre>
+</notextile>
+
+On the Arvados Workbench, navigate to "Code repositories":https://{{site.arvados_workbench_host}}/repositories. You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:$USER.git</code></notextile>.
+
+Next, on the Arvados virtual machine, clone your Git repository:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone git@git.{{ site.arvados_api_host }}:$USER.git</span>
+Cloning into '$USER'...</code></pre>
+</notextile>
+
+This will create a Git repository in the directory called @$USER@ in your home directory. Say yes when prompted to continue with connection.
+Ignore any warning that you are cloning an empty repository.
+
+{% include 'notebox_begin' %}
+For more information about using Git, try
+
+notextile. <pre><code>$ <span class="userinput">man gittutorial</span></code></pre>
+
+or *"search Google for Git tutorials":http://google.com/#q=git+tutorial*.
+{% include 'notebox_end' %}
+
+h2. Creating a Crunch script
+
+Start by entering the @$USER@ directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd $USER</span>
+~/$USER$ <span class="userinput">mkdir crunch_scripts</span>
+~/$USER$ <span class="userinput">cd crunch_scripts</span></code></pre>
+</notextile>
+
+Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
+
+notextile. <pre>~/$USER/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
+
+Add the following code to compute the MD5 hash of each file in a collection (if you already completed "Writing a Crunch script":tutorial-firstscript.html you can just copy the @hash.py@ file you created previously.)
+
+<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
+
+Make the file executable:
+
+notextile. <pre><code>~/$USER/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
+
+Next, add the file to the staging area. This tells @git@ that the file should be included on the next commit.
+
+notextile. <pre><code>~/$USER/crunch_scripts$ <span class="userinput">git add hash.py</span></code></pre>
+
+Next, commit your changes. All staged changes are recorded into the local git repository:
+
+<notextile>
+<pre><code>~/$USER/crunch_scripts$ <span class="userinput">git commit -m"my first script"</span>
+[master (root-commit) 27fd88b] my first script
+ 1 file changed, 45 insertions(+)
+ create mode 100755 crunch_scripts/hash.py</code></pre>
+</notextile>
+
+Finally, upload your changes to the Arvados server:
+
+<notextile>
+<pre><code>~/$USER/crunch_scripts$ <span class="userinput">git push origin master</span>
+Counting objects: 4, done.
+Compressing objects: 100% (2/2), done.
+Writing objects: 100% (4/4), 682 bytes, done.
+Total 4 (delta 0), reused 0 (delta 0)
+To git@git.qr1hi.arvadosapi.com:$USER.git
+ * [new branch] master -> master</code></pre>
+</notextile>
+
+h2. Create a pipeline template
+
+Next, create a new template using @arv create pipeline_template@:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv create pipeline_template</span></code></pre>
+</notextile>
+
+In the editor, enter the following template:
+
+<notextile> {% code 'tutorial_submit_job' as javascript %} </notextile>
+
+* @"repository"@ is the name of a git repository to search for the script version. You can access a list of available git repositories on the Arvados Workbench under "Code repositories":https://{{site.arvados_workbench_host}}/repositories.
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit Git revision hash, a tag, or a branch (in which case it will use the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
+* @"script"@ specifies the filename of the script to run. Crunch expects to find this in the @crunch_scripts/@ subdirectory of the Git repository.
+* @"runtime_constraints"@ describes the runtime environment required to run the job. These are described in the "job record schema":{{site.baseurl}}/api/schema/Job.html
+
+h2. Running your pipeline
+
+Your new pipeline template should appear at the top of the Workbench "pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page. You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html
+
+For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html
--- /dev/null
+require 'zenweb'
+require 'liquid'
+
+module ZenwebLiquid
+ VERSION = '0.0.1'
+end
+
+module Zenweb
+
+ class Page
+
+ def render_liquid page, content
+ liquid self.body, content, page, binding
+ end
+
+ ##
+ # Render a page's liquid and return the intermediate result
+ def liquid template, content, page, binding = TOPLEVEL_BINDING
+ Liquid::Template.file_system = Liquid::LocalFileSystem.new(File.join(File.dirname(Rake.application().rakefile), "_includes"))
+ unless defined? @liquid_template
+ @liquid_template = Liquid::Template.parse(template)
+ end
+
+ vars = {}
+ vars["content"] = content
+
+ vars["site"] = site.config.h.clone
+ pages = {}
+ site.pages.each do |f, p|
+ pages[f] = p.config.h.clone
+ pages[f]["url"] = p.url
+ end
+ vars["site"]["pages"] = pages
+
+ vars["page"] = page.config.h.clone
+ vars["page"]["url"] = page.url
+
+ @liquid_template.render(vars)
+ end
+ end
+
+ class LiquidCode < Liquid::Include
+ Syntax = /(#{Liquid::QuotedFragment}+)(\s+(?:as)\s+(#{Liquid::QuotedFragment}+))?/o
+
+ def initialize(tag_name, markup, tokens)
+ Liquid::Tag.instance_method(:initialize).bind(self).call(tag_name, markup, tokens)
+
+ if markup =~ Syntax
+ @template_name = $1
+ @language = $3
+ @attributes = {}
+ else
+ raise SyntaxError.new("Error in tag 'code' - Valid syntax: include '[code_file]' as '[language]'")
+ end
+ end
+
+ def render(context)
+ require 'coderay'
+
+ partial = load_cached_partial(context)
+ html = ''
+
+ context.stack do
+ html = CodeRay.scan(partial.root.nodelist.join, @language).div
+ end
+
+ html
+ end
+
+ Liquid::Template.register_tag('code', LiquidCode)
+ end
+end
--- /dev/null
+require 'zenweb'
+
+module ZenwebTextile
+ VERSION = '0.0.1'
+end
+
+module Zenweb
+ class Page
+
+ ##
+ # Render a page's textile and return the resulting html
+ def render_textile page, content
+ require 'RedCloth'
+ RedCloth.new(content ? content : self.body).to_html
+ end
+ end
+end
--- /dev/null
+*-image
+build/
--- /dev/null
+Deploying Arvados in Docker Containers
+======================================
+
+This file explains how to build and deploy Arvados servers in Docker
+containers, so that they can be run easily in different environments
+(a dedicated server, a developer's laptop, a virtual machine,
+etc).
+
+This is a work in progress; instructions will almost certainly be
+incomplete and possibly out of date.
+
+Prerequisites
+-------------
+
+* Docker
+
+ Docker is a Linux container management system based on LXC. It is a
+ very young system but is being developed rapidly.
+ [Installation packages](http://www.docker.io/gettingstarted/)
+ are available for several platforms.
+
+ If a prebuilt docker package is not available for your platform, the
+ short instructions for installing it are:
+
+ 1. Create a `docker` group and add yourself to it.
+
+ <pre>
+ $ sudo addgroup docker
+ $ sudo adduser `whoami` docker
+ </pre>
+
+ Log out and back in.
+
+ 2. Add a `cgroup` filesystem and mount it:
+
+ <pre>
+ $ mkdir -p /cgroup
+ $ grep cgroup /etc/fstab
+ none /cgroup cgroup defaults 0 0
+ $ sudo mount /cgroup
+ </pre>
+
+ 3. [Download and run a docker binary from docker.io.](http://docs.docker.io/en/latest/installation/binaries/)
+
+* Ruby (version 1.9.3 or greater)
+
+* sudo privileges to run `debootstrap`
+
+Building
+--------
+
+Type `./build.sh` to configure and build the following Docker images:
+
+ * arvados/api - the Arvados API server
+ * arvados/doc - Arvados documentation
+ * arvados/warehouse - Keep, the Arvados content-addressable filesystem
+ * arvados/workbench - the Arvados console
+ * arvados/sso - the Arvados single-signon authentication server
+
+`build.sh` will generate reasonable defaults for all configuration
+settings. If you want more control over the way Arvados is
+configured, first copy `config.yml.example` to `config.yml` and edit
+it with appropriate configuration settings, and then run `./build.sh`.
+
+Running
+-------
+
+The `arvdock` script in this directory is used to start, stop and
+restart Arvados servers on your machine. The simplest and easiest way
+to use it is `./arvdock start` to start the full complement of Arvados
+servers, and `./arvdock stop` and `./arvdock restart` to stop and
+restart all servers, respectively.
+
+Developers who are working on individual servers can start, stop or
+restart just those containers, e.g.:
+
+* `./arvdock start --api --sso` to start just the API and SSO services.
+* `./arvdock stop --keep` to stop just the Keep services.
+* `./arvdock restart --workbench=8000` restarts just the Workbench service on port 8000.
+
+For a full set of arguments, use `./arvdock --help`.
--- /dev/null
+# Arvados API server Docker container.
+
+FROM arvados/passenger
+MAINTAINER Tim Pierce <twp@curoverse.com>
+
+# Install postgres and apache.
+RUN apt-get update -qq
+RUN apt-get install -qqy \
+ procps postgresql postgresql-server-dev-9.1 apache2 slurm-llnl munge \
+ supervisor sudo libwww-perl libio-socket-ssl-perl libcrypt-ssleay-perl \
+ libjson-perl cron openssh-server
+
+ADD munge.key /etc/munge/
+RUN chown munge:munge /etc/munge/munge.key && chmod 600 /etc/munge/munge.key
+ADD generated/slurm.conf /etc/slurm-llnl/
+
+RUN /usr/local/rvm/bin/rvm-exec default gem install arvados-cli arvados
+# /for crunch-dispatch
+
+RUN /bin/mkdir -p /usr/src/arvados/services
+ADD generated/api.tar.gz /usr/src/arvados/services/
+
+# Install generated config files
+ADD generated/database.yml /usr/src/arvados/services/api/config/database.yml
+ADD generated/omniauth.rb /usr/src/arvados/services/api/config/initializers/omniauth.rb
+RUN /bin/cp /usr/src/arvados/services/api/config/environments/production.rb.example /usr/src/arvados/services/api/config/environments/production.rb
+ADD generated/application.yml /usr/src/arvados/services/api/config/application.yml
+ADD generated/apache2_vhost /etc/apache2/sites-available/arvados
+
+# Configure Rails databases.
+ENV RAILS_ENV production
+ADD generated/config_databases.sh /tmp/config_databases.sh
+ADD generated/superuser_token /tmp/superuser_token
+RUN /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/services/api/Gemfile && \
+ sh /tmp/config_databases.sh && \
+ rm /tmp/config_databases.sh && \
+ /etc/init.d/postgresql start && \
+ cd /usr/src/arvados/services/api && \
+ /usr/local/rvm/bin/rvm-exec default bundle exec rake db:structure:load && \
+ /usr/local/rvm/bin/rvm-exec default bundle exec rake db:seed && \
+ /usr/local/rvm/bin/rvm-exec default bundle exec rake assets:precompile && \
+ /usr/local/rvm/bin/rvm-exec default ./script/create_superuser_token.rb $(cat /tmp/superuser_token) && \
+ chown www-data:www-data config.ru && \
+ chown www-data:www-data log -R && \
+ mkdir -p tmp && \
+ chown www-data:www-data tmp -R
+
+# Configure Apache and Passenger.
+RUN a2dissite default && \
+ a2ensite arvados && \
+ a2enmod rewrite && \
+ a2enmod ssl && \
+ /bin/mkdir /var/run/apache2
+
+# Install a token for root
+RUN mkdir -p /root/.config/arvados; echo "ARVADOS_API_HOST=api" >> /root/.config/arvados/settings.conf && echo "ARVADOS_API_HOST_INSECURE=yes" >> /root/.config/arvados/settings.conf && echo "ARVADOS_API_TOKEN=$(cat /tmp/superuser_token)" >> /root/.config/arvados/settings.conf && chmod 600 /root/.config/arvados/settings.conf
+
+# Set up directory for job commit repo
+RUN mkdir -p /var/lib/arvados
+# Add crunch user
+RUN addgroup --gid 4005 crunch && mkdir /home/crunch && useradd --uid 4005 --gid 4005 crunch && chown crunch:crunch /home/crunch
+
+# Create keep and compute node objects
+ADD keep_server_0.json /root/
+ADD keep_server_1.json /root/
+
+# Set up update-gitolite.rb
+RUN mkdir /usr/local/arvados/config -p
+ADD generated/arvados-clients.yml /usr/local/arvados/config/
+ADD update-gitolite.rb /usr/local/arvados/
+
+# Supervisor.
+ADD supervisor.conf /etc/supervisor/conf.d/arvados.conf
+ADD generated/setup.sh /usr/local/bin/setup.sh
+ADD generated/setup-gitolite.sh /usr/local/bin/setup-gitolite.sh
+ADD crunch-dispatch-run.sh /usr/local/bin/crunch-dispatch-run.sh
+ADD apache2_foreground.sh /etc/apache2/foreground.sh
+
+# Start the supervisor.
+CMD ["/usr/bin/supervisord", "-n"]
--- /dev/null
+#! /bin/bash
+
+read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
+trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
+
+source /etc/apache2/envvars
+/usr/sbin/apache2 -D FOREGROUND
--- /dev/null
+# VirtualHost definition for the Arvados API server
+
+<VirtualHost *:80>
+ ServerName @@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@
+ ServerAdmin sysadmin@curoverse.com
+
+ RedirectPermanent / https://@@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@/
+
+ LogLevel warn
+ ErrorLog ${APACHE_LOG_DIR}/error.log
+ CustomLog ${APACHE_LOG_DIR}/access.log combined
+
+</VirtualHost>
+
+<VirtualHost *:443>
+ ServerName @@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@
+ ServerAdmin sysadmin@curoverse.com
+
+ RailsEnv production
+ RackBaseURI /
+ RailsAppSpawnerIdleTime 1200
+
+ # Enable streaming
+ PassengerBufferResponse off
+
+ # Index file and Document Root (where the public files are located)
+ DirectoryIndex index.html
+ DocumentRoot /usr/src/arvados/services/api/public
+
+ LogLevel warn
+ ErrorLog ${APACHE_LOG_DIR}/ssl_error.log
+ CustomLog ${APACHE_LOG_DIR}/ssl_access.log combined
+
+ <Directory /usr/src/arvados/services/api/public>
+ Options Indexes FollowSymLinks MultiViews IncludesNoExec
+ AllowOverride None
+ Order allow,deny
+ allow from all
+ </Directory>
+
+ <IfModule mod_ssl.c>
+ SSLEngine on
+ # SSLCertificateChainFile /etc/ssl/certs/startcom.sub.class1.server.ca.pem
+ # SSLCACertificateFile /etc/ssl/certs/startcom.ca.pem
+ # SSLCertificateFile /etc/ssl/certs/qr1hi.arvadosapi.com.crt.pem
+ # SSLCertificateKeyFile /etc/ssl/private/qr1hi.arvadosapi.com.key.pem
+ SSLCertificateFile /etc/ssl/certs/ssl-cert-snakeoil.pem
+ SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key
+ SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown
+ </IfModule>
+
+</VirtualHost>
--- /dev/null
+# Copy this file to application.yml and edit to suit.
+#
+# Consult application.default.yml for the full list of configuration
+# settings.
+#
+# The order of precedence is:
+# 1. config/environments/{RAILS_ENV}.rb (deprecated)
+# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
+# 3. Section in application.yml called "common"
+# 4. Section in application.default.yml corresponding to RAILS_ENV
+# 5. Section in application.default.yml called "common"
+
+development:
+ # The blob_signing_key is a string of alphanumeric characters used
+ # to sign permission hints for Keep locators. It must be identical
+ # to the permission key given to Keep. If you run both apiserver
+ # and Keep in development, change this to a hardcoded string and
+ # make sure both systems use the same value.
+ blob_signing_key: ~
+
+production:
+ # At minimum, you need a nice long randomly generated secret_token here.
+ # Use a long string of alphanumeric characters (at least 36).
+ secret_token: @@API_SECRET@@
+
+ # blob_signing_key is required and must be identical to the
+ # permission secret provisioned to Keep.
+ # Use a long string of alphanumeric characters (at least 36).
+ blob_signing_key: @@KEEP_SIGNING_SECRET@@
+
+ uuid_prefix: @@API_HOSTNAME@@
+
+ # The e-mail address of the user you would like to become marked as an admin
+ # user on their first login.
+ # In the default configuration, authentication happens through the Arvados SSO
+ # server, which uses openid against Google's servers, so in that case this
+ # should be an address associated with a Google account.
+ auto_admin_user: @@API_AUTO_ADMIN_USER@@
+
+ # compute_node_domain: example.org
+ # compute_node_nameservers:
+ # - 127.0.0.1
+ # - 192.168.1.1
+ #
+ # The version below is suitable for AWS.
+ # Uncomment and change <%# to <%= to use it.
+ # compute_node_nameservers: <%#
+ # require 'net/http'
+ # ['local', 'public'].collect do |iface|
+ # Net::HTTP.get(URI("http://169.254.169.254/latest/meta-data/#{iface}-ipv4")).match(/^[\d\.]+$/)[0]
+ # end << '172.16.0.23'
+ # %>
+ permit_create_collection_with_unsigned_manifest: true
+ git_repositories_dir: /home/git/repositories
+ crunch_job_wrapper: :slurm_immediate
+ action_mailer.raise_delivery_errors: false
+ action_mailer.perform_deliveries: false
+
+ workbench_address: @@API_WORKBENCH_ADDRESS@@
+
+ auto_setup_new_users: true
+
+ auto_admin_first_user: true
+
+test:
+ uuid_prefix: zzzzz
+ secret_token: <%= rand(2**512).to_s(36) %>
+
+common:
+ #git_repositories_dir: /var/cache/git
+ #git_internal_dir: /var/cache/arvados/internal.git
+
--- /dev/null
+# apt.arvados.org
+deb http://apt.arvados.org/ wheezy main
--- /dev/null
+production:
+ gitolite_url: 'git@api:gitolite-admin.git'
+ gitolite_tmp: 'gitolite-tmp'
+ arvados_api_host: 'api'
+ arvados_api_token: '@@API_SUPERUSER_SECRET@@'
+ arvados_api_host_insecure: true
--- /dev/null
+#! /bin/sh
+
+# Configure postgresql in a docker instance.
+
+/bin/su postgres -c '/usr/lib/postgresql/9.1/bin/postgres --single -D /var/lib/postgresql/9.1/main -c config_file=/etc/postgresql/9.1/main/postgresql.conf' <<EOF
+alter role postgres with encrypted password '@@POSTGRES_ROOT_PW@@';
+
+create user @@ARVADOS_DEV_USER@@ with encrypted password '@@ARVADOS_DEV_PW@@';
+create database @@ARVADOS_DEV_DB@@ with owner @@ARVADOS_DEV_USER@@;
+
+create user @@ARVADOS_TEST_USER@@ with createdb encrypted password '@@ARVADOS_TEST_PW@@';
+
+create user @@ARVADOS_PROD_USER@@ with encrypted password '@@ARVADOS_PROD_PW@@';
+create database @@ARVADOS_PROD_DB@@ with owner @@ARVADOS_PROD_USER@@;
+EOF
--- /dev/null
+#!/bin/bash
+set -e
+export PATH="$PATH":/usr/src/arvados/services/crunch
+export PERLLIB=/usr/src/arvados/sdk/perl/lib
+export ARVADOS_API_HOST=api
+export ARVADOS_API_HOST_INSECURE=yes
+export CRUNCH_DISPATCH_LOCKFILE=/var/lock/crunch-dispatch
+
+if [[ ! -e $CRUNCH_DISPATCH_LOCKFILE ]]; then
+ touch $CRUNCH_DISPATCH_LOCKFILE
+fi
+
+export CRUNCH_JOB_BIN=/usr/src/arvados/services/crunch/crunch-job
+export HOME=`pwd`
+fuser -TERM -k $CRUNCH_DISPATCH_LOCKFILE || true
+
+# Give the compute nodes some time to start up
+sleep 5
+
+cd /usr/src/arvados/services/api
+export RAILS_ENV=production
+/usr/local/rvm/bin/rvm-exec default bundle install
+exec /usr/local/rvm/bin/rvm-exec default bundle exec ./script/crunch-dispatch.rb 2>&1
+
--- /dev/null
+development:
+ adapter: postgresql
+ encoding: utf8
+ database: @@ARVADOS_DEV_DB@@
+ username: @@ARVADOS_DEV_USER@@
+ password: @@ARVADOS_DEV_PW@@
+ host: localhost
+
+test:
+ adapter: postgresql
+ encoding: utf8
+ template: template0
+ database: @@ARVADOS_TEST_DB@@
+ username: @@ARVADOS_TEST_USER@@
+ password: @@ARVADOS_TEST_PW@@
+ host: localhost
+
+production:
+ adapter: postgresql
+ encoding: utf8
+ database: @@ARVADOS_PROD_DB@@
+ username: @@ARVADOS_PROD_USER@@
+ password: @@ARVADOS_PROD_PW@@
+ host: localhost
+
--- /dev/null
+{
+ "service_host": "keep_server_0.keep.dev.arvados",
+ "service_port": 25107,
+ "service_ssl_flag": "false",
+ "service_type": "disk"
+}
--- /dev/null
+{
+ "service_host": "keep_server_1.keep.dev.arvados",
+ "service_port": 25107,
+ "service_ssl_flag": "false",
+ "service_type": "disk"
+}
+
--- /dev/null
+# Change this omniauth configuration to point to your registered provider
+# Since this is a registered application, add the app id and secret here
+APP_ID = '@@SSO_CLIENT_APP_ID@@'
+APP_SECRET = '@@SSO_CLIENT_SECRET@@'
+
+# Update your custom Omniauth provider URL here
+if '@@OMNIAUTH_URL@@' != ''
+ CUSTOM_PROVIDER_URL = '@@OMNIAUTH_URL@@'
+else
+ CUSTOM_PROVIDER_URL = 'https://' + ENV['SSO_PORT_443_TCP_ADDR'].to_s
+end
+
+# This is a development sandbox, we use self-signed certificates
+OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE
+
+Rails.application.config.middleware.use OmniAuth::Builder do
+ provider :josh_id, APP_ID, APP_SECRET, CUSTOM_PROVIDER_URL
+end
--- /dev/null
+#!/bin/bash
+
+ssh-keygen -q -N '' -t rsa -f /root/.ssh/id_rsa
+
+useradd git
+mkdir /home/git
+
+# Set up gitolite repository
+cp ~root/.ssh/id_rsa.pub ~git/root-authorized_keys.pub
+chown git:git /home/git -R
+su - git -c "mkdir -p ~/bin"
+
+su - git -c "git clone git://github.com/sitaramc/gitolite"
+su - git -c "gitolite/install -ln ~/bin"
+su - git -c "PATH=/home/git/bin:$PATH gitolite setup -pk ~git/root-authorized_keys.pub"
+
+# Make sure the repositories are created in such a way that they are readable
+# by the api server
+sed -i 's/0077/0022/g' /home/git/.gitolite.rc
+
+# And make sure that the existing repos are equally readable, or the API server commit model will freak out...
+chmod 755 /home/git/repositories
+chmod +rx /home/git/repositories/*git -R
+
+# Now set up the gitolite repo(s) we use
+mkdir -p /usr/local/arvados/gitolite-tmp/
+# Make ssh store the host key
+ssh -o "StrictHostKeyChecking no" git@api info
+# Now check out the tree
+git clone git@api:gitolite-admin.git /usr/local/arvados/gitolite-tmp/gitolite-admin/
+cd /usr/local/arvados/gitolite-tmp/gitolite-admin
+mkdir keydir/arvados
+mkdir conf/admin
+mkdir conf/auto
+echo "
+
+@arvados_git_user = arvados_git_user
+
+repo @all
+ RW+ = @arvados_git_user
+
+" > conf/admin/arvados.conf
+echo '
+include "auto/*.conf"
+include "admin/*.conf"
+' >> conf/gitolite.conf
+
+#su - git -c "ssh-keygen -t rsa"
+cp /root/.ssh/id_rsa.pub keydir/arvados/arvados_git_user.pub
+# Replace the 'root' key with the user key, just in case
+cp /root/.ssh/authorized_keys keydir/root-authorized_keys.pub
+# But also make sure we have the root key installed so it can access all keys
+git add keydir/root-authorized_keys.pub
+git add keydir/arvados/arvados_git_user.pub
+git add conf/admin/arvados.conf
+git add keydir/arvados/
+git add conf/gitolite.conf
+git commit -a -m 'git server setup'
+git push
+
+# Prepopulate the arvados.git repo with our source. Silly, but until we can check out from remote trees,
+# we need this to make the tutorials work.
+su - git -c "git clone --bare git://github.com/curoverse/arvados.git /home/git/repositories/arvados.git"
+
+echo "ARVADOS_API_HOST_INSECURE=yes" > /etc/cron.d/gitolite-update
+echo "*/2 * * * * root /bin/bash -c 'source /etc/profile.d/rvm.sh && /usr/local/arvados/update-gitolite.rb production'" >> /etc/cron.d/gitolite-update
+
+# Create/update the repos now
+. /etc/profile.d/rvm.sh
+export ARVADOS_API_HOST=api
+export ARVADOS_API_HOST_INSECURE=yes
+export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
+/usr/local/arvados/update-gitolite.rb production
+
+echo "PATH=/usr/bin:/bin:/sbin" > /etc/cron.d/arvados-repo-update
+echo "*/5 * * * * git cd ~git/repositories/arvados.git; git fetch https://github.com/curoverse/arvados.git master:master" >> /etc/cron.d/arvados-repo-update
+
--- /dev/null
+#!/bin/bash
+
+set -x
+
+. /etc/profile.d/rvm.sh
+
+export ARVADOS_API_HOST=api
+export ARVADOS_API_HOST_INSECURE=yes
+export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
+
+# Arvados repository object
+all_users_group_uuid="$prefix-j7d0g-fffffffffffffff"
+repo_uuid=`arv --format=uuid repository create --repository '{"name":"arvados","fetch_url":"git@api:arvados.git","push_url":"git@api:arvados.git"}'`
+echo "Arvados repository uuid is $repo_uuid"
+
+read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
+{
+ "tail_uuid":"$all_users_group_uuid",
+ "head_uuid":"$repo_uuid",
+ "link_class":"permission",
+ "name":"can_read"
+}
+EOF
+
+# Make sure the necessary keep_service objects exist
+arv keep_service list > /tmp/keep_service.list
+
+grep -q keep_server_0 /tmp/keep_service.list
+if [[ "$?" != "0" ]]; then
+ arv keep_service create --keep-service "$(cat /root/keep_server_0.json)"
+fi
+
+grep -q keep_server_1 /tmp/keep_service.list
+if [[ "$?" != "0" ]]; then
+ arv keep_service create --keep-service "$(cat /root/keep_server_1.json)"
+fi
+
+# User repository object
+user_uuid=`arv --format=uuid user current`
+repo_uuid=`arv --format=uuid repository create --repository '{"name":"@@ARVADOS_USER_NAME@@","fetch_url":"git@api:@@ARVADOS_USER_NAME@@.git","push_url":"git@api:@@ARVADOS_USER_NAME@@.git"}'`
+echo "User repository uuid is $repo_uuid"
+
+read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
+{
+ "tail_uuid":"$user_uuid",
+ "head_uuid":"$repo_uuid",
+ "link_class":"permission",
+ "name":"can_write"
+}
+EOF
+
+# Shell machine object
+arv virtual_machine create --virtual-machine '{"hostname":"shell"}'
--- /dev/null
+
+ControlMachine=api
+#SlurmUser=slurmd
+SlurmctldPort=6817
+SlurmdPort=6818
+AuthType=auth/munge
+#JobCredentialPrivateKey=/etc/slurm-llnl/slurm-key.pem
+#JobCredentialPublicCertificate=/etc/slurm-llnl/slurm-cert.pem
+StateSaveLocation=/tmp
+SlurmdSpoolDir=/tmp/slurmd
+SwitchType=switch/none
+MpiDefault=none
+SlurmctldPidFile=/var/run/slurmctld.pid
+SlurmdPidFile=/var/run/slurmd.pid
+ProctrackType=proctrack/pgid
+CacheGroups=0
+ReturnToService=2
+TaskPlugin=task/affinity
+#
+# TIMERS
+SlurmctldTimeout=300
+SlurmdTimeout=300
+InactiveLimit=0
+MinJobAge=300
+KillWait=30
+Waittime=0
+#
+# SCHEDULING
+SchedulerType=sched/backfill
+#SchedulerType=sched/builtin
+SchedulerPort=7321
+#SchedulerRootFilter=
+#SelectType=select/linear
+SelectType=select/cons_res
+SelectTypeParameters=CR_CPU_Memory
+FastSchedule=1
+#
+# LOGGING
+SlurmctldDebug=3
+#SlurmctldLogFile=
+SlurmdDebug=3
+#SlurmdLogFile=
+JobCompType=jobcomp/none
+#JobCompLoc=
+JobAcctGatherType=jobacct_gather/none
+#JobAcctLogfile=
+#JobAcctFrequency=
+#
+# COMPUTE NODES
+NodeName=DEFAULT
+# CPUs=8 State=UNKNOWN RealMemory=6967 Weight=6967
+PartitionName=DEFAULT MaxTime=INFINITE State=UP
+PartitionName=compute Default=YES Shared=yes
+#PartitionName=sysadmin Hidden=YES Shared=yes
+
+NodeName=compute[0-1]
+#NodeName=compute0 RealMemory=6967 Weight=6967
+
+PartitionName=compute Nodes=compute[0-1]
+PartitionName=crypto Nodes=compute[0-1]
--- /dev/null
+@@API_SUPERUSER_SECRET@@
--- /dev/null
+[program:ssh]
+user=root
+command=/etc/init.d/ssh start
+startsecs=0
+
+[program:postgres]
+user=postgres
+command=/usr/lib/postgresql/9.1/bin/postgres -D /var/lib/postgresql/9.1/main -c config_file=/etc/postgresql/9.1/main/postgresql.conf
+autorestart=true
+
+[program:apache2]
+command=/etc/apache2/foreground.sh
+stopsignal=6
+autorestart=true
+
+[program:munge]
+user=root
+command=/etc/init.d/munge start
+startsecs=0
+
+[program:slurm]
+user=root
+command=/etc/init.d/slurm-llnl start
+startsecs=0
+
+[program:cron]
+user=root
+command=/etc/init.d/cron start
+startsecs=0
+
+[program:setup]
+user=root
+command=/usr/local/bin/setup.sh
+startsecs=0
+
+[program:setup-gitolite]
+user=root
+command=/usr/local/bin/setup-gitolite.sh
+startsecs=0
+
+[program:crunch-dispatch]
+user=root
+command=/usr/local/bin/crunch-dispatch-run.sh
+autorestart=true
--- /dev/null
+#!/usr/bin/env ruby
+
+require 'rubygems'
+require 'pp'
+require 'arvados'
+require 'active_support/all'
+require 'yaml'
+
+# This script does the actual gitolite config management on disk.
+#
+# Ward Vandewege <ward@curoverse.com>
+
+# Default is development
+production = ARGV[0] == "production"
+
+ENV["RAILS_ENV"] = "development"
+ENV["RAILS_ENV"] = "production" if production
+
+DEBUG = 1
+
+# load and merge in the environment-specific application config info
+# if present, overriding base config parameters as specified
+path = File.dirname(__FILE__) + '/config/arvados-clients.yml'
+if File.exists?(path) then
+ cp_config = YAML.load_file(path)[ENV['RAILS_ENV']]
+else
+ puts "Please create a\n " + File.dirname(__FILE__) + "/config/arvados-clients.yml\n file"
+ exit 1
+end
+
+gitolite_url = cp_config['gitolite_url']
+gitolite_tmp = cp_config['gitolite_tmp']
+
+gitolite_admin = File.join(File.expand_path(File.dirname(__FILE__)) + '/' + gitolite_tmp + '/gitolite-admin')
+
+ENV['ARVADOS_API_HOST'] = cp_config['arvados_api_host']
+ENV['ARVADOS_API_TOKEN'] = cp_config['arvados_api_token']
+if cp_config['arvados_api_host_insecure']
+ ENV['ARVADOS_API_HOST_INSECURE'] = 'true'
+else
+ ENV.delete('ARVADOS_API_HOST_INSECURE')
+end
+
+keys = ''
+
+seen = Hash.new
+
+def ensure_repo(name,permissions,user_keys,gitolite_admin)
+ tmp = ''
+ # Just in case...
+ name.gsub!(/[^a-z0-9]/i,'')
+
+ keys = Hash.new()
+
+ user_keys.each do |uuid,p|
+ p.each do |k|
+ next if k[:public_key].nil?
+ keys[uuid] = Array.new() if not keys.key?(uuid)
+
+ key = k[:public_key]
+ # Handle putty-style ssh public keys
+ key.sub!(/^(Comment: "r[^\n]*\n)(.*)$/m,'ssh-rsa \2 \1')
+ key.sub!(/^(Comment: "d[^\n]*\n)(.*)$/m,'ssh-dss \2 \1')
+ key.gsub!(/\n/,'')
+ key.strip
+
+ keys[uuid].push(key)
+ end
+ end
+
+ cf = gitolite_admin + '/conf/auto/' + name + '.conf'
+
+ conf = "\nrepo #{name}\n"
+
+ commit = false
+
+ seen = {}
+ permissions.sort.each do |uuid,v|
+ conf += "\t#{v[:gitolite_permissions]}\t= #{uuid.to_s}\n"
+
+ count = 0
+ keys.include?(uuid) and keys[uuid].each do |v|
+ kf = gitolite_admin + '/keydir/arvados/' + uuid.to_s + "@#{count}.pub"
+ seen[kf] = true
+ if !File.exists?(kf) or IO::read(kf) != v then
+ commit = true
+ f = File.new(kf + ".tmp",'w')
+ f.write(v)
+ f.close()
+ # File.rename will overwrite the destination file if it exists
+ File.rename(kf + ".tmp",kf);
+ end
+ count += 1
+ end
+ end
+
+ if !File.exists?(cf) or IO::read(cf) != conf then
+ commit = true
+ f = File.new(cf + ".tmp",'w')
+ f.write(conf)
+ f.close()
+ # this is about as atomic as we can make the replacement of the file...
+ File.unlink(cf) if File.exists?(cf)
+ File.rename(cf + ".tmp",cf);
+ end
+
+ return commit,seen
+end
+
+begin
+
+ pwd = Dir.pwd
+ # Get our local gitolite-admin repo up to snuff
+ if not File.exists?(File.dirname(__FILE__) + '/' + gitolite_tmp) then
+ Dir.mkdir(File.join(File.dirname(__FILE__) + '/' + gitolite_tmp), 0700)
+ end
+ if not File.exists?(gitolite_admin) then
+ Dir.chdir(File.join(File.dirname(__FILE__) + '/' + gitolite_tmp))
+ `git clone #{gitolite_url}`
+ else
+ Dir.chdir(gitolite_admin)
+ `git pull`
+ end
+ Dir.chdir(pwd)
+
+ arv = Arvados.new( { :suppress_ssl_warnings => false } )
+
+ permissions = arv.repository.get_all_permissions
+
+ repos = permissions[:repositories]
+ user_keys = permissions[:user_keys]
+
+ @commit = false
+
+ @seen = {}
+
+ repos.each do |r|
+ next if r[:name].nil?
+ (@c,@s) = ensure_repo(r[:name],r[:user_permissions],user_keys,gitolite_admin)
+ @seen.merge!(@s)
+ @commit = true if @c
+ end
+
+ # Clean up public key files that should not be present
+ Dir.glob(gitolite_admin + '/keydir/arvados/*.pub') do |key_file|
+ next if key_file =~ /arvados_git_user.pub$/
+ next if @seen.has_key?(key_file)
+ puts "Extra file #{key_file}"
+ @commit = true
+ Dir.chdir(gitolite_admin)
+ key_file.gsub!(/^#{gitolite_admin}\//,'')
+ `git rm #{key_file}`
+ end
+
+ if @commit then
+ message = "#{Time.now().to_s}: update from API"
+ Dir.chdir(gitolite_admin)
+ `git add --all`
+ `git commit -m '#{message}'`
+ `git push`
+ end
+
+rescue Exception => bang
+ puts "Error: " + bang.to_s
+ puts bang.backtrace.join("\n")
+ exit 1
+end
+
--- /dev/null
+#!/bin/bash
+
+DOCKER=`which docker.io`
+
+if [[ "$DOCKER" == "" ]]; then
+ DOCKER=`which docker`
+fi
+
+COMPUTE_COUNTER=0
+
+function usage {
+ echo >&2
+ echo >&2 "usage: $0 (start|stop|restart|test) [options]"
+ echo >&2
+ echo >&2 "$0 start/stop/restart options:"
+ echo >&2 " -d[port], --doc[=port] Documentation server (default port 9898)"
+ echo >&2 " -w[port], --workbench[=port] Workbench server (default port 9899)"
+ echo >&2 " -s[port], --sso[=port] SSO server (default port 9901)"
+ echo >&2 " -a[port], --api[=port] API server (default port 9900)"
+ echo >&2 " -c, --compute Compute nodes (starts 2)"
+ echo >&2 " -v, --vm Shell server"
+ echo >&2 " -n, --nameserver Nameserver"
+ echo >&2 " -k, --keep Keep servers"
+ echo >&2 " -h, --help Display this help and exit"
+ echo >&2
+ echo >&2 " If no options are given, the action is applied to all servers."
+ echo >&2
+ echo >&2 "$0 test [testname] [testname] ..."
+ echo >&2 " By default, all tests are run."
+}
+
+function ip_address {
+ local container=$1
+ echo `$DOCKER inspect $container |grep IPAddress |cut -f4 -d\"`
+}
+
+function start_container {
+ local args="-d -i -t"
+ if [[ "$1" != '' ]]; then
+ local port="$1"
+ args="$args -p $port"
+ fi
+ if [[ "$2" != '' ]]; then
+ local name="$2"
+ if [[ "$name" == "api_server" ]]; then
+ args="$args --dns=172.17.42.1 --dns-search=compute.dev.arvados --hostname api -P --name $name"
+ elif [[ "$name" == "compute" ]]; then
+ name=$name$COMPUTE_COUNTER
+ # We need --privileged because we run docker-inside-docker on the compute nodes
+ args="$args --dns=172.17.42.1 --dns-search=compute.dev.arvados --hostname compute$COMPUTE_COUNTER -P --privileged --name $name"
+ let COMPUTE_COUNTER=$(($COMPUTE_COUNTER + 1))
+ else
+ args="$args --dns=172.17.42.1 --dns-search=dev.arvados --hostname ${name#_server} --name $name"
+ fi
+ fi
+ if [[ "$3" != '' ]]; then
+ local volume="$3"
+ args="$args -v $volume"
+ fi
+ if [[ "$4" != '' ]]; then
+ local link="$4"
+ args="$args --link $link"
+ fi
+ local image=$5
+
+ `$DOCKER ps |grep -P "$name[^/]" -q`
+ if [[ "$?" == "0" ]]; then
+ echo "You have a running container with name $name -- skipping."
+ return
+ fi
+
+ # Remove any existing container by this name.
+ $DOCKER rm "$name" 2>/dev/null
+
+ echo "Starting container:"
+ #echo " $DOCKER run --dns=127.0.0.1 $args $image"
+ echo " $DOCKER run $args $image"
+ container=`$DOCKER run $args $image`
+ if [ "$?" != "0" -o "$container" = "" ]; then
+ echo "Unable to start container"
+ exit 1
+ else
+ echo "Started container: $container"
+ fi
+
+ if [[ "$name" == "doc_server" ]]; then
+ echo
+ echo "*****************************************************************"
+ echo "You can access the Arvados documentation at http://localhost:${port%:*}"
+ echo "*****************************************************************"
+ echo
+ fi
+
+ if [[ "$name" == "workbench_server" ]]; then
+ echo
+ echo "*****************************************************************"
+ echo "You can access the Arvados workbench at http://localhost:${port%:*}"
+ echo "*****************************************************************"
+ echo
+ fi
+
+
+}
+
+declare -a keep_volumes
+
+# Initialize the global `keep_volumes' array. If any keep volumes
+# already appear to exist (mounted volumes with a top-level "keep"
+# directory), use them; create temporary volumes if necessary.
+#
+function make_keep_volumes () {
+ # Mount a keep volume if we don't already have one
+ for mountpoint in $(cut -d ' ' -f 2 /proc/mounts); do
+ if [[ -d "$mountpoint/keep" && "$mountpoint" != "/" ]]; then
+ keep_volumes+=($mountpoint)
+ fi
+ done
+
+ # Create any keep volumes that do not yet exist.
+ while [ ${#keep_volumes[*]} -lt 2 ]
+ do
+ new_keep=$(mktemp -d)
+ echo >&2 "mounting 2G tmpfs keep volume in $new_keep"
+ sudo mount -t tmpfs -o size=2G tmpfs $new_keep
+ mkdir $new_keep/keep
+ keep_volumes+=($new_keep)
+ done
+}
+
+function do_start {
+ local start_doc=false
+ local start_sso=false
+ local start_api=false
+ local start_compute=false
+ local start_workbench=false
+ local start_vm=false
+ local start_nameserver=false
+ local start_keep=false
+
+ # NOTE: This requires GNU getopt (part of the util-linux package on Debian-based distros).
+ local TEMP=`getopt -o d::s::a::cw::nkvh \
+ --long doc::,sso::,api::,compute,workbench::,nameserver,keep,vm,help \
+ -n "$0" -- "$@"`
+
+ if [ $? != 0 ] ; then echo "Use -h for help"; exit 1 ; fi
+
+ # Note the quotes around `$TEMP': they are essential!
+ eval set -- "$TEMP"
+
+ while [ $# -ge 1 ]
+ do
+ case $1 in
+ -d | --doc)
+ case "$2" in
+ "") start_doc=9898; shift 2 ;;
+ *) start_doc=$2; shift 2 ;;
+ esac
+ ;;
+ -s | --sso)
+ case "$2" in
+ "") start_sso=9901; shift 2 ;;
+ *) start_sso=$2; shift 2 ;;
+ esac
+ ;;
+ -a | --api)
+ case "$2" in
+ "") start_api=9900; shift 2 ;;
+ *) start_api=$2; shift 2 ;;
+ esac
+ ;;
+ -c | --compute)
+ start_compute=2
+ shift
+ ;;
+ -w | --workbench)
+ case "$2" in
+ "") start_workbench=9899; shift 2 ;;
+ *) start_workbench=$2; shift 2 ;;
+ esac
+ ;;
+ -v | --vm)
+ start_vm=true
+ shift
+ ;;
+ -n | --nameserver)
+ start_nameserver=true
+ shift
+ ;;
+ -k | --keep)
+ start_keep=true
+ shift
+ ;;
+ --)
+ shift
+ break
+ ;;
+ *)
+ usage
+ exit 1
+ ;;
+ esac
+ done
+
+ # If no options were selected, then start all servers.
+ if [[ $start_doc == false &&
+ $start_sso == false &&
+ $start_api == false &&
+ $start_compute == false &&
+ $start_workbench == false &&
+ $start_vm == false &&
+ $start_nameserver == false &&
+ $start_keep == false ]]
+ then
+ start_doc=9898
+ #the sso server is currently not used by default so don't start it unless explicitly requested
+ #start_sso=9901
+ start_api=9900
+ start_compute=2
+ start_workbench=9899
+ start_vm=true
+ start_nameserver=true
+ start_keep=true
+ fi
+
+ if [[ $start_sso != false ]]
+ then
+ start_container "$start_sso:443" "sso_server" '' '' "arvados/sso"
+ fi
+
+ if [[ $start_api != false ]]
+ then
+ if [[ $start_sso != false ]]; then
+ start_container "$start_api:443" "api_server" '' "sso_server:sso" "arvados/api"
+ else
+ start_container "$start_api:443" "api_server" '' '' "arvados/api"
+ fi
+ fi
+
+ if [[ $start_nameserver != false ]]
+ then
+ # We rely on skydock and skydns for dns discovery between the slurm controller and compute nodes,
+ # so make sure they are running
+ $DOCKER ps | grep skydns >/dev/null
+ if [[ "$?" != "0" ]]; then
+ echo "Starting crosbymichael/skydns container..."
+ $DOCKER rm "skydns" 2>/dev/null
+ $DOCKER run -d -p 172.17.42.1:53:53/udp --name skydns crosbymichael/skydns -nameserver 8.8.8.8:53 -domain arvados
+ fi
+ $DOCKER ps | grep skydock >/dev/null
+ if [[ "$?" != "0" ]]; then
+ echo "Starting crosbymichael/skydock container..."
+ $DOCKER rm "skydock" 2>/dev/null
+ $DOCKER run -d -v /var/run/docker.sock:/docker.sock --name skydock crosbymichael/skydock -ttl 30 -environment dev -s /docker.sock -domain arvados -name skydns
+ fi
+ fi
+
+ if [[ $start_compute != false ]]
+ then
+ for i in `seq 0 $(($start_compute - 1))`; do
+ start_container "" "compute" '' "api_server:api" "arvados/compute"
+ done
+ fi
+
+ if [[ $start_keep != false ]]
+ then
+ # create `keep_volumes' array with a list of keep mount points
+ # remove any stale metadata from those volumes before starting them
+ make_keep_volumes
+ for v in ${keep_volumes[*]}
+ do
+ [ -f $v/keep/.metadata.yml ] && sudo rm $v/keep/.metadata.yml
+ done
+ start_container "25107:25107" "keep_server_0" \
+ "${keep_volumes[0]}:/keep-data" \
+ "api_server:api" \
+ "arvados/keep"
+ start_container "25108:25107" "keep_server_1" \
+ "${keep_volumes[1]}:/keep-data" \
+ "api_server:api" \
+ "arvados/keep"
+ fi
+
+ if [[ $start_doc != false ]]
+ then
+ start_container "$start_doc:80" "doc_server" '' '' "arvados/doc"
+ fi
+
+ if [[ $start_vm != false ]]
+ then
+ start_container "" "shell" '' "api_server:api" "arvados/shell"
+ fi
+
+ if [[ $start_workbench != false ]]
+ then
+ start_container "$start_workbench:80" "workbench_server" '' "api_server:api" "arvados/workbench"
+ fi
+
+ if [[ $start_api != false ]]
+ then
+ if [[ -f "api/generated/superuser_token" ]]
+ then
+ if [ -d $HOME/.config/arvados ] || mkdir -p $HOME/.config/arvados
+ then
+ cat >$HOME/.config/arvados/settings.conf <<EOF
+ARVADOS_API_HOST=$(ip_address "api_server")
+ARVADOS_API_HOST_INSECURE=yes
+ARVADOS_API_TOKEN=$(cat api/generated/superuser_token)
+EOF
+ fi
+ fi
+ fi
+}
+
+function do_stop {
+ local stop_doc=""
+ local stop_sso=""
+ local stop_api=""
+ local stop_compute=""
+ local stop_workbench=""
+ local stop_nameserver=""
+ local stop_vm=""
+ local stop_keep=""
+
+ # NOTE: This requires GNU getopt (part of the util-linux package on Debian-based distros).
+ local TEMP=`getopt -o dsacwnkvh \
+ --long doc,sso,api,compute,workbench,nameserver,keep,vm,help \
+ -n "$0" -- "$@"`
+
+ if [ $? != 0 ] ; then echo "Use -h for help"; exit 1 ; fi
+
+ # Note the quotes around `$TEMP': they are essential!
+ eval set -- "$TEMP"
+
+ while [ $# -ge 1 ]
+ do
+ case $1 in
+ -d | --doc)
+ stop_doc=doc_server ; shift ;;
+ -s | --sso)
+ stop_sso=sso_server ; shift ;;
+ -a | --api)
+ stop_api=api_server ; shift ;;
+ -c | --compute)
+ stop_compute=`$DOCKER ps |grep -P "compute\d+" |grep -v api_server |cut -f1 -d ' '` ; shift ;;
+ -w | --workbench)
+ stop_workbench=workbench_server ; shift ;;
+ -n | --nameserver )
+ stop_nameserver="skydock skydns" ; shift ;;
+ -v | --vm )
+ stop_vm="shell" ; shift ;;
+ -k | --keep )
+ stop_keep="keep_server_0 keep_server_1" ; shift ;;
+ --)
+ shift
+ break
+ ;;
+ *)
+ usage
+ exit 1
+ ;;
+ esac
+ done
+
+ # If no options were selected, then stop all servers.
+ if [[ $stop_doc == "" &&
+ $stop_sso == "" &&
+ $stop_api == "" &&
+ $stop_compute == "" &&
+ $stop_workbench == "" &&
+ $stop_vm == "" &&
+ $stop_nameserver == "" &&
+ $stop_keep == "" ]]
+ then
+ stop_doc=doc_server
+ stop_sso=sso_server
+ stop_api=api_server
+ stop_compute=`$DOCKER ps |grep -P "compute\d+" |grep -v api_server |cut -f1 -d ' '`
+ stop_workbench=workbench_server
+ stop_vm=shell
+ stop_nameserver="skydock skydns"
+ stop_keep="keep_server_0 keep_server_1"
+ fi
+
+ $DOCKER stop $stop_doc $stop_sso $stop_api $stop_compute $stop_workbench $stop_nameserver $stop_keep $stop_vm \
+ 2>/dev/null
+}
+
+function do_test {
+ local alltests
+ if [ $# -lt 1 ]
+ then
+ alltests="python-sdk api"
+ else
+ alltests="$@"
+ fi
+
+ for testname in $alltests
+ do
+ echo "testing $testname..."
+ case $testname in
+ python-sdk)
+ do_start --api --keep --sso
+ export ARVADOS_API_HOST=$(ip_address "api_server")
+ export ARVADOS_API_HOST_INSECURE=yes
+ export ARVADOS_API_TOKEN=$(cat api/generated/superuser_token)
+ python -m unittest discover ../sdk/python
+ ;;
+ api)
+ $DOCKER run -t -i arvados/api \
+ /usr/src/arvados/services/api/script/rake_test.sh
+ ;;
+ *)
+ echo >&2 "unknown test $testname"
+ ;;
+ esac
+ done
+}
+
+if [ $# -lt 1 ]
+then
+ usage
+ exit 1
+fi
+
+case $1 in
+ start)
+ shift
+ do_start $@
+ ;;
+ stop)
+ shift
+ do_stop $@
+ ;;
+ restart)
+ shift
+ do_stop $@
+ do_start $@
+ ;;
+ test)
+ shift
+ do_test $@
+ ;;
+ *)
+ usage
+ exit 1
+ ;;
+esac
--- /dev/null
+# Arvados base image (wheezy+rvm+Arvados source) in Docker
+
+# Based on Debian Wheezy
+FROM arvados/debian:wheezy
+MAINTAINER Tim Pierce <twp@curoverse.com>
+
+ENV DEBIAN_FRONTEND noninteractive
+
+# Install prerequisite packages for Arvados
+# * git, curl, rvm
+# * Arvados source code in /usr/src/arvados, for preseeding gem installation
+
+ADD apt.arvados.org.list /etc/apt/sources.list.d/
+RUN apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7
+RUN apt-get update -qq
+
+RUN apt-get install -qqy apt-utils git curl \
+ libcurl3 libcurl3-gnutls libcurl4-openssl-dev locales \
+ postgresql-server-dev-9.1 python-arvados-python-client
+
+RUN gpg --keyserver pool.sks-keyservers.net --recv-keys D39DC0E3 && \
+ /bin/sed -ri 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
+ /usr/sbin/locale-gen && \
+ curl -L https://get.rvm.io | bash -s stable && \
+ /usr/local/rvm/bin/rvm install 2.1 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.1 && \
+ /bin/mkdir -p /usr/src/arvados
+
+ADD generated/arvados.tar.gz /usr/src/arvados/
+
+# Update gem. This (hopefully) fixes
+# https://github.com/rubygems/rubygems.org/issues/613.
+RUN /usr/local/rvm/bin/rvm-exec default gem update --system && \
+ /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+ /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/apps/workbench/Gemfile && \
+ /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/services/api/Gemfile && \
+ /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/doc/Gemfile
--- /dev/null
+# apt.arvados.org
+deb http://apt.arvados.org/ wheezy main
--- /dev/null
+# Install Arvados SDK into bcbio-nextgen Docker image.
+#
+# To build bcbio-nextgen:
+#
+# $ git clone https://github.com/chapmanb/bcbio-nextgen.git
+# $ cd bcbio-nextgen
+# $ docker build
+# $ docker tag <image> bcbio-nextgen
+#
+
+FROM bcbio-nextgen
+MAINTAINER Peter Amstutz <peter.amstutz@curoverse.com>
+
+USER root
+
+# Install Ruby 2.1.0
+RUN apt-get remove --quiet --assume-yes ruby && \
+ curl -L https://get.rvm.io | bash -s stable && \
+ /usr/local/rvm/bin/rvm install 2.1.0 && \
+ /bin/mkdir -p /usr/src/arvados
+
+ADD generated/arvados.tar.gz /usr/src/arvados/
+ENV GEM_HOME /usr/local/rvm/gems/ruby-2.1.0
+ENV GEM_PATH /usr/local/rvm/gems/ruby-2.1.0:/usr/local/rvm/gems/ruby-2.1.0@global
+ENV PATH /usr/local/rvm/gems/ruby-2.1.0/bin:/usr/local/rvm/gems/ruby-2.1.0@global/bin:/usr/local/rvm/rubies/ruby-2.1.0/bin:/usr/local/rvm/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+
+# Install dependencies and set up system.
+# The FUSE packages help ensure that we can install the Python SDK (arv-mount).
+RUN /usr/bin/apt-get update && \
+ /usr/bin/apt-get install --quiet --assume-yes python-dev python-llfuse python-pip \
+ libio-socket-ssl-perl libjson-perl liburi-perl libwww-perl \
+ fuse libattr1-dev libfuse-dev && \
+ /usr/sbin/adduser --disabled-password \
+ --gecos 'Crunch execution user' crunch && \
+ /usr/bin/install --directory --owner=crunch --group=crunch --mode=0700 /keep /tmp/crunch-src /tmp/crunch-job && \
+ /bin/ln -s /usr/src/arvados /usr/local/src/arvados
+
+# Install Arvados packages.
+RUN gem update --system && \
+ find /usr/src/arvados/sdk -name '*.gem' -print0 | \
+ xargs -0rn 1 gem install && \
+ cd /usr/src/arvados/services/fuse && \
+ python setup.py install && \
+ cd /usr/src/arvados/sdk/python && \
+ python setup.py install
+
+USER crunch
--- /dev/null
+#! /bin/bash
+
+# make sure a Ruby version greater than or equal to 1.9.3 is installed before proceeding
+if ! ruby -e 'exit RUBY_VERSION >= "1.9.3"' 2>/dev/null
+then
+ echo "Building the Arvados docker containers requires at least Ruby 1.9.3."
+ echo "Please install ruby 1.9.3 or higher before executing this script."
+ exit 1
+fi
+
+function usage {
+ echo >&2
+ echo >&2 "usage: $0 [options]"
+ echo >&2
+ echo >&2 "Calling $0 without arguments will build all Arvados docker images"
+ echo >&2
+ echo >&2 "$0 options:"
+ echo >&2 " -h, --help Print this help text"
+ echo >&2 " clean Clear all build information"
+ echo >&2 " realclean clean and remove all Arvados Docker images except arvados/debian"
+ echo >&2 " deepclean realclean and remove arvados/debian, crosbymichael/skydns and "
+ echo >&2 " crosbymichael/skydns Docker images"
+ echo >&2
+}
+
+if [ "$1" = '-h' ] || [ "$1" = '--help' ]; then
+ usage
+ exit 1
+fi
+
+build_tools/build.rb
+
+if [[ "$?" == "0" ]]; then
+ DOCKER=`which docker.io`
+
+ if [[ "$DOCKER" == "" ]]; then
+ DOCKER=`which docker`
+ fi
+
+ DOCKER=$DOCKER /usr/bin/make -f build_tools/Makefile $*
+fi
--- /dev/null
+# This is the 'shell hack'. Call make with DUMP=1 to see the effect.
+ifdef DUMP
+OLD_SHELL := $(SHELL)
+SHELL = $(warning [$@])$(OLD_SHELL) -x
+endif
+
+all: skydns-image skydock-image api-image compute-image doc-image workbench-image keep-image sso-image shell-image
+
+IMAGE_FILES := $(shell ls *-image 2>/dev/null |grep -v -E 'debian-arvados-image|skydns-image|skydock-image')
+GENERATED_DIRS := $(shell ls */generated 2>/dev/null)
+
+# `make clean' removes the files generated in the build directory
+# but does not remove any docker images generated in previous builds
+clean:
+ @echo "make clean"
+ -@rm -rf build
+ +@[ "$(IMAGE_FILES)" = "" ] || rm -f $(IMAGE_FILES) 2>/dev/null
+ +@[ "$(GENERATED_DIRS)" = "" ] || rm -rf */generated 2>/dev/null
+
+DEBIAN_IMAGE := $(shell $(DOCKER) images -q arvados/debian |head -n1)
+
+REALCLEAN_CONTAINERS := $(shell $(DOCKER) ps -a |grep -e arvados -e api_server -e keep_server -e doc_server -e workbench_server |cut -f 1 -d' ')
+REALCLEAN_IMAGES := $(shell $(DOCKER) images -q arvados/* |grep -v $(DEBIAN_IMAGE) 2>/dev/null)
+DEEPCLEAN_IMAGES := $(shell $(DOCKER) images -q arvados/*)
+SKYDNS_CONTAINERS := $(shell $(DOCKER) ps -a |grep -e crosbymichael/skydns -e crosbymichael/skydock |cut -f 1 -d' ')
+SKYDNS_IMAGES := $(shell $(DOCKER) images -q crosbymichael/skyd*)
+
+# `make realclean' will also remove the Arvados docker images (but not the
+# arvados/debian image) and force subsequent makes to build the entire chain
+# from the ground up
+realclean: clean
+ @echo "make realclean"
+ +@[ "`$(DOCKER) ps -q`" = '' ] || $(DOCKER) stop `$(DOCKER) ps -q`
+ +@[ "$(REALCLEAN_CONTAINERS)" = '' ] || $(DOCKER) rm $(REALCLEAN_CONTAINERS)
+ +@[ "$(REALCLEAN_IMAGES)" = '' ] || $(DOCKER) rmi $(REALCLEAN_IMAGES)
+
+# `make deepclean' will remove all Arvados docker images and the skydns/skydock
+# images and force subsequent makes to build the entire chain from the ground up
+deepclean: clean
+ @echo "make deepclean"
+ -@rm -f debian-arvados-image 2>/dev/null
+ -@rm -f skydns-image skydock-image 2>/dev/null
+ +@[ "`$(DOCKER) ps -q`" = '' ] || $(DOCKER) stop `$(DOCKER) ps -q`
+ +@[ "$(REALCLEAN_CONTAINERS)" = '' ] || $(DOCKER) rm $(REALCLEAN_CONTAINERS)
+ +@[ "$(DEEPCLEAN_IMAGES)" = '' ] || $(DOCKER) rmi $(DEEPCLEAN_IMAGES)
+ +@[ "$(SKYDNS_CONTAINERS)" = '' ] || $(DOCKER) rm $(SKYDNS_CONTAINERS)
+ +@[ "$(SKYDNS_IMAGES)" = '' ] || $(DOCKER) rmi $(SKYDNS_IMAGES)
+
+# ============================================================
+# Dependencies for */generated files which are prerequisites
+# for building docker images.
+
+CONFIG_RB = build_tools/config.rb
+
+BUILD = build/.buildstamp
+
+BASE_DEPS = base/Dockerfile config.yml $(BASE_GENERATED)
+
+SLURM_DEPS = slurm/Dockerfile config.yml $(SLURM_GENERATED)
+
+JOBS_DEPS = jobs/Dockerfile
+
+JAVA_BWA_SAMTOOLS_DEPS = java-bwa-samtools/Dockerfile
+
+API_DEPS = api/* config.yml $(API_GENERATED)
+
+SHELL_DEPS = shell/* config.yml $(SHELL_GENERATED)
+
+COMPUTE_DEPS = compute/* config.yml $(COMPUTE_GENERATED)
+
+DOC_DEPS = doc/Dockerfile doc/apache2_vhost
+
+WORKBENCH_DEPS = workbench/Dockerfile \
+ config.yml \
+ $(WORKBENCH_GENERATED)
+
+KEEP_DEPS = keep/Dockerfile config.yml $(KEEP_GENERATED)
+
+SSO_DEPS = config.yml $(SSO_GENERATED)
+
+BCBIO_NEXTGEN_DEPS = bcbio-nextgen/Dockerfile
+
+BASE_GENERATED = base/generated/arvados.tar.gz
+
+COMPUTE_GENERATED_IN = compute/*.in
+COMPUTE_GENERATED = compute/generated/*
+
+KEEP_GENERATED_IN = keep/*.in
+KEEP_GENERATED = keep/generated/*
+
+API_GENERATED_IN = api/*.in
+API_GENERATED = api/generated/*
+
+SHELL_GENERATED_IN = shell/*.in
+SHELL_GENERATED = shell/generated/*
+
+SLURM_GENERATED_IN = slurm/*.in
+SLURM_GENERATED = slurm/generated/*
+
+WORKBENCH_GENERATED_IN = workbench/*.in
+WORKBENCH_GENERATED = workbench/generated/*
+
+SSO_GENERATED_IN = sso/*.in
+SSO_GENERATED = sso/generated/*
+
+KEEP_DEPS += keep/generated/bin/keepproxy
+KEEP_DEPS += keep/generated/bin/keepstore
+keep/generated/bin/%: $(wildcard build/services/%/*.go)
+ mkdir -p keep/generated/src/git.curoverse.com
+ ln -sfn ../../../../.. keep/generated/src/git.curoverse.com/arvados.git
+ GOPATH=$(shell pwd)/keep/generated go get $(@:keep/generated/bin/%=git.curoverse.com/arvados.git/services/%)
+
+$(BUILD):
+ mkdir -p build
+ rsync -rlp --exclude=docker/ --exclude='**/log/*' --exclude='**/tmp/*' \
+ --chmod=Da+rx,Fa+rX ../ build/
+ find build/ -name \*.gem -delete
+ cd build/services/fuse/ && python setup.py build
+ cd build/sdk/python/ && python setup.py build
+ cd build/sdk/cli && gem build arvados-cli.gemspec
+ cd build/sdk/ruby && gem build arvados.gemspec
+ touch build/.buildstamp
+
+$(SLURM_GENERATED): $(BUILD)
+ $(CONFIG_RB) slurm
+ mkdir -p slurm/generated
+
+$(BASE_GENERATED): $(BUILD)
+ $(CONFIG_RB) base
+ mkdir -p base/generated
+ tar -czf base/generated/arvados.tar.gz -C build .
+
+$(API_GENERATED): $(API_GENERATED_IN)
+ $(CONFIG_RB) api
+
+$(SHELL_GENERATED): $(SHELL_GENERATED_IN)
+ $(CONFIG_RB) shell
+
+$(WORKBENCH_GENERATED): $(WORKBENCH_GENERATED_IN)
+ $(CONFIG_RB) workbench
+
+$(COMPUTE_GENERATED): $(COMPUTE_GENERATED_IN)
+ $(CONFIG_RB) compute
+
+$(SSO_GENERATED): $(SSO_GENERATED_IN)
+ $(CONFIG_RB) sso
+
+$(KEEP_GENERATED): $(KEEP_GENERATED_IN)
+ $(CONFIG_RB) keep
+
+DOCKER_BUILD = $(DOCKER) build --rm=true
+
+# ============================================================
+# The main Arvados servers: api, doc, workbench, compute
+
+api-image: passenger-image $(BUILD) $(API_DEPS)
+ @echo "Building api-image"
+ mkdir -p api/generated
+ tar -czf api/generated/api.tar.gz -C build/services api
+ $(DOCKER_BUILD) -t arvados/api api
+ date >api-image
+
+shell-image: base-image $(BUILD) $(SHELL_DEPS)
+ @echo "Building shell-image"
+ mkdir -p shell/generated
+ $(DOCKER_BUILD) -t arvados/shell shell
+ date >shell-image
+
+compute-image: slurm-image $(BUILD) $(COMPUTE_DEPS)
+ @echo "Building compute-image"
+ $(DOCKER_BUILD) -t arvados/compute compute
+ date >compute-image
+
+doc-image: base-image $(BUILD) $(DOC_DEPS)
+ @echo "Building doc-image"
+ mkdir -p doc/generated
+ tar -czf doc/generated/doc.tar.gz -C build doc
+ $(DOCKER_BUILD) -t arvados/doc doc
+ date >doc-image
+
+keep-image: debian-arvados-image $(BUILD) $(KEEP_DEPS)
+ @echo "Building keep-image"
+ $(DOCKER_BUILD) -t arvados/keep keep
+ date >keep-image
+
+jobs-image: base-image $(BUILD) $(JOBS_DEPS)
+ $(DOCKER_BUILD) -t arvados/jobs jobs
+ date >jobs-image
+
+java-bwa-samtools-image: jobs-image $(BUILD) $(JAVA_BWA_SAMTOOLS_DEPS)
+ $(DOCKER_BUILD) -t arvados/jobs-java-bwa-samtools java-bwa-samtools
+ date >java-bwa-samtools-image
+
+bcbio-nextgen-image: $(BUILD) $(BASE_GENERATED) $(BCBIO_NEXTGEN_DEPS)
+ rm -rf bcbio-nextgen/generated
+ cp -r base/generated bcbio-nextgen
+ $(DOCKER_BUILD) -t arvados/bcbio-nextgen bcbio-nextgen
+ date >bcbio-nextgen-image
+
+workbench-image: passenger-image $(BUILD) $(WORKBENCH_DEPS)
+ @echo "Building workbench-image"
+ mkdir -p workbench/generated
+ tar -czf workbench/generated/workbench.tar.gz -C build/apps workbench
+ $(DOCKER_BUILD) -t arvados/workbench workbench
+ date >workbench-image
+
+sso-image: passenger-image $(SSO_DEPS)
+ @echo "Building sso-image"
+ $(DOCKER_BUILD) -t arvados/sso sso
+ date >sso-image
+
+# ============================================================
+# The arvados/base image is the base Debian image plus packages
+# that are dependencies for every Arvados service.
+
+passenger-image: base-image
+ @echo "Building passenger-image"
+ $(DOCKER_BUILD) -t arvados/passenger passenger
+ date >passenger-image
+
+slurm-image: base-image $(SLURM_DEPS)
+ @echo "Building slurm-image"
+ $(DOCKER_BUILD) -t arvados/slurm slurm
+ date >slurm-image
+
+base-image: debian-arvados-image $(BASE_DEPS)
+ @echo "Building base-image"
+ $(DOCKER_BUILD) -t arvados/base base
+ date >base-image
+
+debian-arvados-image:
+ @echo "Building debian-arvados-image"
+ ./mkimage-debootstrap.sh arvados/debian wheezy ftp://ftp.us.debian.org/debian/
+ date >debian-arvados-image
+
+skydns-image:
+ @echo "Downloading skydns-image"
+ $(DOCKER) pull crosbymichael/skydns
+ date >skydns-image
+
+skydock-image:
+ @echo "Downloading skydock-image"
+ $(DOCKER) pull crosbymichael/skydock
+ date >skydock-image
--- /dev/null
+#! /usr/bin/env ruby
+
+require 'optparse'
+require 'tempfile'
+require 'yaml'
+
+def main options
+ if not ip_forwarding_enabled?
+ warn "NOTE: IP forwarding must be enabled in the kernel."
+ warn "Turning IP forwarding on now."
+ sudo %w(/sbin/sysctl net.ipv4.ip_forward=1)
+ end
+
+ # Check that:
+ # * Docker is installed and can be found in the user's path
+ # * Docker can be run as a non-root user
+ # - TODO: put the user in the docker group if necessary
+ # - TODO: mount cgroup automatically
+ # - TODO: start the docker service if not started
+
+ docker_path = %x(which docker.io).chomp
+
+ if docker_path.empty?
+ docker_path = %x(which docker).chomp
+ end
+
+ if docker_path.empty?
+ warn "Docker not found."
+ warn ""
+ warn "Please make sure that Docker has been installed and"
+ warn "can be found in your PATH."
+ warn ""
+ warn "Installation instructions for a variety of platforms can be found at"
+ warn "http://docs.docker.io/en/latest/installation/"
+ exit 1
+ elsif not docker_ok? docker_path
+ warn "WARNING: docker could not be run."
+ warn "Please make sure that:"
+ warn " * You have permission to read and write /var/run/docker.sock"
+ warn " * a 'cgroup' volume is mounted on your machine"
+ warn " * the docker daemon is running"
+ exit 2
+ end
+
+ # Check that debootstrap is installed.
+ if not debootstrap_ok?
+ warn "Installing debootstrap."
+ sudo '/usr/bin/apt-get', 'install', 'debootstrap'
+ end
+
+ # Generate a config.yml if it does not exist or is empty
+ if not File.size? 'config.yml'
+ print "Generating config.yml.\n"
+ print "Arvados needs to know the email address of the administrative user,\n"
+ print "so that when that user logs in they are automatically made an admin.\n"
+ print "This should be an email address associated with a Google account.\n"
+ print "\n"
+ admin_email_address = ""
+ until is_valid_email? admin_email_address
+ print "Enter your Google ID email address here: "
+ admin_email_address = gets.strip
+ if not is_valid_email? admin_email_address
+ print "That doesn't look like a valid email address. Please try again.\n"
+ end
+ end
+
+ print "Arvados needs to know the shell login name for the administrative user.\n"
+ print "This will also be used as the name for your git repository.\n"
+ print "\n"
+ user_name = ""
+ until is_valid_user_name? user_name
+ print "Enter a shell login name here: "
+ user_name = gets.strip
+ if not is_valid_user_name? user_name
+ print "That doesn't look like a valid shell login name. Please try again.\n"
+ end
+ end
+
+ File.open 'config.yml', 'w' do |config_out|
+ config_out.write "# If a _PW or _SECRET variable is set to an empty string, a password\n"
+ config_out.write "# will be chosen randomly at build time. This is the\n"
+ config_out.write "# recommended setting.\n\n"
+ config = YAML.load_file 'config.yml.example'
+ config['API_AUTO_ADMIN_USER'] = admin_email_address
+ config['ARVADOS_USER_NAME'] = user_name
+ config['API_HOSTNAME'] = generate_api_hostname
+ config['API_WORKBENCH_ADDRESS'] = 'false'
+ config.each_key do |var|
+ config_out.write "#{var}: #{config[var]}\n"
+ end
+ end
+ end
+
+ # If all prerequisites are met, go ahead and build.
+ if ip_forwarding_enabled? and
+ docker_ok? docker_path and
+ debootstrap_ok? and
+ File.exists? 'config.yml'
+ exit 0
+ else
+ exit 6
+ end
+end
+
+# sudo
+# Execute the arg list 'cmd' under sudo.
+# cmd can be passed either as a series of arguments or as a
+# single argument consisting of a list, e.g.:
+# sudo 'apt-get', 'update'
+# sudo(['/usr/bin/gpasswd', '-a', ENV['USER'], 'docker'])
+# sudo %w(/usr/bin/apt-get install lxc-docker)
+#
+def sudo(*cmd)
+ # user can pass a single list in as an argument
+ # to allow usage like: sudo %w(apt-get install foo)
+ warn "You may need to enter your password here."
+ if cmd.length == 1 and cmd[0].class == Array
+ cmd = cmd[0]
+ end
+ system '/usr/bin/sudo', *cmd
+end
+
+# is_valid_email?
+# Returns true if its arg looks like a valid email address.
+# This is a very very loose sanity check.
+#
+def is_valid_email? str
+ str.match /^\S+@\S+\.\S+$/
+end
+
+# is_valid_user_name?
+# Returns true if its arg looks like a valid unix username.
+# This is a very very loose sanity check.
+#
+def is_valid_user_name? str
+ # borrowed from Debian's adduser (version 3.110)
+ str.match /^[_.A-Za-z0-9][-\@_.A-Za-z0-9]*\$?$/
+end
+
+# generate_api_hostname
+# Generates a 5-character randomly chosen API hostname.
+#
+def generate_api_hostname
+ rand(2**256).to_s(36)[0...5]
+end
+
+# ip_forwarding_enabled?
+# Returns 'true' if IP forwarding is enabled in the kernel
+#
+def ip_forwarding_enabled?
+ %x(/sbin/sysctl -n net.ipv4.ip_forward) == "1\n"
+end
+
+# debootstrap_ok?
+# Returns 'true' if debootstrap is installed and working.
+#
+def debootstrap_ok?
+ return system '/usr/sbin/debootstrap --version > /dev/null 2>&1'
+end
+
+# docker_ok?
+# Returns 'true' if docker can be run as the current user.
+#
+def docker_ok?(docker_path)
+ return system "#{docker_path} images > /dev/null 2>&1"
+end
+
+# install_docker
+# Determines which Docker package is suitable for this Linux distro
+# and installs it, resolving any dependencies.
+# NOTE: not in use yet.
+
+def install_docker
+ linux_distro = %x(lsb_release --id).split.last
+ linux_release = %x(lsb_release --release).split.last
+ linux_version = linux_distro + " " + linux_release
+ kernel_release = `uname -r`
+
+ case linux_distro
+ when 'Ubuntu'
+ if not linux_release.match '^1[234]\.'
+ warn "Arvados requires at least Ubuntu 12.04 (Precise Pangolin)."
+ warn "Your system is Ubuntu #{linux_release}."
+ exit 3
+ end
+ if linux_release.match '^12' and kernel_release.start_with? '3.2'
+ # Ubuntu Precise ships with a 3.2 kernel and must be upgraded.
+ warn "Your kernel #{kernel_release} must be upgraded to run Docker."
+ warn "To do this:"
+ warn " sudo apt-get update"
+ warn " sudo apt-get install linux-image-generic-lts-raring linux-headers-generic-lts-raring"
+ warn " sudo reboot"
+ exit 4
+ else
+ # install AUFS
+ sudo 'apt-get', 'update'
+ sudo 'apt-get', 'install', "linux-image-extra-#{kernel_release}"
+ end
+
+ # add Docker repository
+ sudo %w(/usr/bin/apt-key adv
+ --keyserver keyserver.ubuntu.com
+ --recv-keys 36A1D7869245C8950F966E92D8576A8BA88D21E9)
+ source_file = Tempfile.new('arv')
+ source_file.write("deb http://get.docker.io/ubuntu docker main\n")
+ source_file.close
+ sudo '/bin/mv', source_file.path, '/etc/apt/sources.list.d/docker.list'
+ sudo %w(/usr/bin/apt-get update)
+ sudo %w(/usr/bin/apt-get install lxc-docker)
+
+ # Set up for non-root access
+ sudo %w(/usr/sbin/groupadd docker)
+ sudo '/usr/bin/gpasswd', '-a', ENV['USER'], 'docker'
+ sudo %w(/usr/sbin/service docker restart)
+ when 'Debian'
+ else
+ warn "Must be running a Debian or Ubuntu release in order to run Docker."
+ exit 5
+ end
+end
+
+
+if __FILE__ == $PROGRAM_NAME
+ options = { :makefile => File.join(File.dirname(__FILE__), 'Makefile') }
+ OptionParser.new do |opts|
+ opts.on('-m', '--makefile MAKEFILE-PATH',
+ 'Path to the Makefile used to build Arvados Docker images') do |mk|
+ options[:makefile] = mk
+ end
+ end
+ main options
+end
--- /dev/null
+#! /usr/bin/env ruby
+
+require 'yaml'
+require 'fileutils'
+require 'digest'
+
+abort 'Error: Ruby >= 1.9.3 required.' if RUBY_VERSION < '1.9.3'
+
+# Initialize config settings from config.yml
+config = YAML.load_file('config.yml')
+
+# ============================================================
+# Add dynamically chosen config settings. These settings should
+# be suitable for any installation.
+
+# Any _PW/_SECRET config settings represent passwords/secrets. If they
+# are blank, choose a password. Make sure the generated password
+# doesn't change if config.yml doesn't change. Otherwise, keys won't
+# match any more if (say) keep's files get regenerated but apiserver's
+# don't.
+config.sort.map do |var,val|
+ if (var.end_with?('_PW') || var.end_with?('_SECRET')) && (config[var].nil? || config[var].empty?)
+ config[var] = Digest::SHA1.hexdigest(`hostname` + var + config.to_yaml)
+ end
+end
+
+# ============================================================
+# For each *.in file in the docker directories, substitute any
+# @@variables@@ found in the file with the appropriate config
+# variable. Support up to 10 levels of nesting.
+#
+# TODO(twp): add the *.in files directory to the source tree, and
+# when expanding them, add them to the "generated" directory with
+# the same tree structure as in the original source. Then all
+# the files can be added to the docker container with a single ADD.
+
+if ARGV[0] and ARGV[0].length > 0
+ globdir = ARGV[0]
+else
+ globdir = '*'
+end
+
+FileUtils.rm_r Dir.glob(globdir + '/generated/*')
+
+File.umask(022)
+Dir.glob(globdir + '/*.in') do |template_file|
+ generated_dir = File.join(File.dirname(template_file), 'generated')
+ Dir.mkdir(generated_dir) unless Dir.exists? generated_dir
+ output_path = File.join(generated_dir, File.basename(template_file, '.in'))
+ output_mode = (File.stat(template_file).mode & 0100) ? 0755 : 0644
+ File.open(output_path, "w", output_mode) do |output|
+ File.open(template_file) do |input|
+ input.each_line do |line|
+
+ # This count is used to short-circuit potential
+ # infinite loops of variable substitution.
+ @count = 0
+ while @count < 10
+ @out = line.gsub!(/@@(.*?)@@/) do |var|
+ if config.key?(Regexp.last_match[1])
+ config[Regexp.last_match[1]]
+ else
+ var.gsub!(/@@/, '@_NOT_FOUND_@')
+ end
+ end
+ break if @out.nil?
+ @count += 1
+ end
+
+ output.write(line)
+ end
+ end
+ end
+end
--- /dev/null
+# Arvados compute node Docker container.
+
+FROM arvados/slurm
+MAINTAINER Ward Vandewege <ward@curoverse.com>
+
+RUN apt-get update -qq
+RUN apt-get install -qqy supervisor python-pip python-pyvcf python-gflags python-google-api-python-client python-virtualenv libattr1-dev libfuse-dev python-dev python-llfuse fuse crunchstat python-arvados-fuse cron dnsmasq
+
+ADD fuse.conf /etc/fuse.conf
+RUN chmod 644 /etc/fuse.conf
+
+RUN /usr/local/rvm/bin/rvm-exec default gem install arvados-cli arvados
+
+# Install Docker from the Arvados package repository (cf. arvados/base)
+RUN apt-get install -qqy iptables ca-certificates lxc apt-transport-https docker.io
+
+RUN addgroup --gid 4005 crunch && mkdir /home/crunch && useradd --uid 4005 --gid 4005 crunch && usermod crunch -G fuse,docker && chown crunch:crunch /home/crunch
+
+# Supervisor.
+ADD supervisor.conf /etc/supervisor/conf.d/arvados.conf
+ADD generated/setup.sh /usr/local/bin/setup.sh
+ADD wrapdocker /usr/local/bin/wrapdocker.sh
+
+VOLUME /var/lib/docker
+# Start the supervisor.
+CMD ["/usr/bin/supervisord", "-n"]
--- /dev/null
+# Set the maximum number of FUSE mounts allowed to non-root users.
+# The default is 1000.
+#
+#mount_max = 1000
+
+# Allow non-root users to specify the 'allow_other' or 'allow_root'
+# mount options.
+#
+user_allow_other
+
--- /dev/null
+#!/bin/bash
+
+. /etc/profile.d/rvm.sh
+
+export ARVADOS_API_HOST=api
+export ARVADOS_API_HOST_INSECURE=yes
+export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
+
+arv node create --node {} > /tmp/node.json
+
+UUID=`grep \"uuid\" /tmp//node.json |cut -f4 -d\"`
+PING_SECRET=`grep \"ping_secret\" /tmp//node.json |cut -f4 -d\"`
+
+echo "*/5 * * * * root /usr/bin/curl -k -d ping_secret=$PING_SECRET https://api/arvados/v1/nodes/$UUID/ping" > /etc/cron.d/node_ping
+
+# Send a ping now
+/usr/bin/curl -k -d ping_secret=$PING_SECRET https://api/arvados/v1/nodes/$UUID/ping?ping_secret=$PING_SECRET
+
+# Just make sure /dev/fuse permissions are correct (the device appears after fuse is loaded)
+chmod 1660 /dev/fuse && chgrp fuse /dev/fuse
--- /dev/null
+[program:munge]
+user=root
+command=/etc/init.d/munge start
+startsecs=0
+
+[program:slurm]
+user=root
+command=/etc/init.d/slurm-llnl start
+startsecs=0
+
+[program:cron]
+user=root
+command=/etc/init.d/cron start
+startsecs=0
+
+[program:setup]
+user=root
+command=/usr/local/bin/setup.sh
+startsecs=0
+
+[program:docker]
+user=root
+command=/usr/local/bin/wrapdocker.sh
+
+[program:dnsmasq]
+user=root
+command=/etc/init.d/dnsmasq start
+startsecs=0
+
--- /dev/null
+#!/bin/bash
+
+# Borrowed from https://github.com/jpetazzo/dind under Apache2
+# and slightly modified.
+
+# First, make sure that cgroups are mounted correctly.
+CGROUP=/sys/fs/cgroup
+: {LOG:=stdio}
+
+[ -d $CGROUP ] ||
+ mkdir $CGROUP
+
+mountpoint -q $CGROUP ||
+ mount -n -t tmpfs -o uid=0,gid=0,mode=0755 cgroup $CGROUP || {
+ echo "Could not make a tmpfs mount. Did you use -privileged?"
+ exit 1
+ }
+
+if [ -d /sys/kernel/security ] && ! mountpoint -q /sys/kernel/security
+then
+ mount -t securityfs none /sys/kernel/security || {
+ echo "Could not mount /sys/kernel/security."
+ echo "AppArmor detection and -privileged mode might break."
+ }
+fi
+
+# Mount the cgroup hierarchies exactly as they are in the parent system.
+for SUBSYS in $(cut -d: -f2 /proc/1/cgroup)
+do
+ [ -d $CGROUP/$SUBSYS ] || mkdir $CGROUP/$SUBSYS
+ mountpoint -q $CGROUP/$SUBSYS ||
+ mount -n -t cgroup -o $SUBSYS cgroup $CGROUP/$SUBSYS
+
+ # The two following sections address a bug which manifests itself
+ # by a cryptic "lxc-start: no ns_cgroup option specified" when
+ # trying to start containers withina container.
+ # The bug seems to appear when the cgroup hierarchies are not
+ # mounted on the exact same directories in the host, and in the
+ # container.
+
+ # Named, control-less cgroups are mounted with "-o name=foo"
+ # (and appear as such under /proc/<pid>/cgroup) but are usually
+ # mounted on a directory named "foo" (without the "name=" prefix).
+ # Systemd and OpenRC (and possibly others) both create such a
+ # cgroup. To avoid the aforementioned bug, we symlink "foo" to
+ # "name=foo". This shouldn't have any adverse effect.
+ echo $SUBSYS | grep -q ^name= && {
+ NAME=$(echo $SUBSYS | sed s/^name=//)
+ ln -s $SUBSYS $CGROUP/$NAME
+ }
+
+ # Likewise, on at least one system, it has been reported that
+ # systemd would mount the CPU and CPU accounting controllers
+ # (respectively "cpu" and "cpuacct") with "-o cpuacct,cpu"
+ # but on a directory called "cpu,cpuacct" (note the inversion
+ # in the order of the groups). This tries to work around it.
+ [ $SUBSYS = cpuacct,cpu ] && ln -s $SUBSYS $CGROUP/cpu,cpuacct
+done
+
+# Note: as I write those lines, the LXC userland tools cannot setup
+# a "sub-container" properly if the "devices" cgroup is not in its
+# own hierarchy. Let's detect this and issue a warning.
+grep -q :devices: /proc/1/cgroup ||
+ echo "WARNING: the 'devices' cgroup should be in its own hierarchy."
+grep -qw devices /proc/1/cgroup ||
+ echo "WARNING: it looks like the 'devices' cgroup is not mounted."
+
+# Now, close extraneous file descriptors.
+pushd /proc/self/fd >/dev/null
+for FD in *
+do
+ case "$FD" in
+ # Keep stdin/stdout/stderr
+ [012])
+ ;;
+ # Nuke everything else
+ *)
+ eval exec "$FD>&-"
+ ;;
+ esac
+done
+popd >/dev/null
+
+
+# If a pidfile is still around (for example after a container restart),
+# delete it so that docker can start.
+rm -rf /var/run/docker.pid
+
+exec docker -d
+
--- /dev/null
+# Configuration for the Rails databases (database names,
+# usernames and passwords).
+
+# Username for your Arvados user. This will be used as your shell login name
+# as well as the name for your git repository.
+ARVADOS_USER_NAME:
+
+# ARVADOS_DOMAIN: the Internet domain of this installation.
+# ARVADOS_DNS_SERVER: the authoritative nameserver for ARVADOS_DOMAIN.
+ARVADOS_DOMAIN: # e.g. arvados.internal
+ARVADOS_DNS_SERVER: # e.g. 192.168.0.1
+
+# ==============================
+# API server settings
+# ==============================
+
+# The API server hostname. Must be a 5-character
+# string unique within this installation. This string
+# will also be used as config.uuid_prefix.
+API_HOSTNAME: # e.g. qr1hi
+
+# The e-mail address of the user you would like to become marked as an admin
+# user on their first login.
+# In the default configuration, authentication happens through the Arvados SSO
+# server, which uses openid against Google's servers, so in that case this
+# should be an address associated with a Google account.
+API_AUTO_ADMIN_USER:
+
+# The location of the Workbench application where users should be
+# redirected if they point their browsers at the API server, e.g.,
+# https://localhost:9899
+API_WORKBENCH_ADDRESS:
+
+# If a _PW variable is set to an empty string, a password
+# will be chosen randomly at build time. This is the
+# recommended setting.
+ARVADOS_DEV_DB: arvados_development
+ARVADOS_DEV_USER: arvados_dev
+ARVADOS_DEV_PW:
+ARVADOS_TEST_DB: arvados_test
+ARVADOS_TEST_USER: arvados_test
+ARVADOS_TEST_PW:
+ARVADOS_PROD_DB: arvados_production
+ARVADOS_PROD_USER: arvados_prod
+ARVADOS_PROD_PW:
+
+# If a _SECRET variable is set to an empty string, a password
+# will be chosen randomly at build time. This is the
+# recommended setting.
+
+# The signing key shared by Keep at the API server to verify
+# blob permission signatures.
+KEEP_SIGNING_SECRET:
+
+# The value for the Rails config.secret_token setting.
+API_SECRET:
+
+# A "superuser" token with which servers can authenticate to
+# the API server, before an administrative user has been created.
+# Leave this blank to generate a secret randomly at build time (recommended).
+API_SUPERUSER_SECRET:
+
+# More than anything this should be auto-generated, but
+# we don't presently have a good place to store it. So just
+# change it and don't be dumb.
+POSTGRES_ROOT_PW: dummy_pw
+
+# The URL of the SSO server that you want your API server to use. If
+# blank, use the sso docker container.
+OMNIAUTH_URL:
+
+# ==============================
+# Workbench settings
+# ==============================
+WORKBENCH_RAILS_MODE: production
+WORKBENCH_DATA_IMPORT_DIR: /data/arvados-workbench-upload/data
+WORKBENCH_DATA_EXPORT_DIR: /data/arvados-workbench-download/data
+WORKBENCH_VCF_PIPELINE_UUID:
+WORKBENCH_SITE_NAME: Arvados Workbench
+WORKBENCH_INSECURE_HTTPS: true
+WORKBENCH_ACTIVATION_CONTACT_LINK: mailto:arvados@curoverse.com
+WORKBENCH_ARVADOS_LOGIN_BASE: https://@@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@/login
+WORKBENCH_ARVADOS_V1_BASE: https://@@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@/arvados/v1
+WORKBENCH_SECRET:
+
+# ==============================
+# SSO settings
+# ==============================
+SSO_HOSTNAME: sso
+SSO_SECRET:
+SSO_CLIENT_NAME: devsandbox
+# ==============================
+# Default to using auth.curoverse.com as SSO server
+# To use your a local Docker SSO server, set OMNIAUTH_URL and SSO_CLIENT_SECRET
+# to the empty string
+# ==============================
+OMNIAUTH_URL: https://auth.curoverse.com
+SSO_CLIENT_APP_ID: local_docker_installation
+SSO_CLIENT_SECRET: yohbai4eecohshoo1Yoot7tea9zoca9Eiz3Tajahweo9eePaeshaegh9meiye2ph
--- /dev/null
+# Arvados Documentation Docker container.
+
+FROM arvados/base
+maintainer Ward Vandewege <ward@curoverse.com>
+
+# Install packages
+RUN /bin/mkdir -p /usr/src/arvados && \
+ apt-get update -qq && \
+ apt-get install -qqy curl procps apache2-mpm-worker
+
+ADD generated/doc.tar.gz /usr/src/arvados/
+
+# Build static site
+RUN /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/doc/Gemfile && \
+ /bin/sed -ri 's/^baseurl: .*$/baseurl: /' /usr/src/arvados/doc/_config.yml && \
+ cd /usr/src/arvados/doc && \
+ LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" /usr/local/rvm/bin/rvm-exec default bundle exec rake
+
+# Configure Apache
+ADD apache2_vhost /etc/apache2/sites-available/doc
+RUN \
+ a2dissite default && \
+ a2ensite doc
+
+ADD apache2_foreground.sh /etc/apache2/foreground.sh
+
+# Start Apache
+CMD ["/etc/apache2/foreground.sh"]
--- /dev/null
+#! /bin/bash
+
+read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
+trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
+
+source /etc/apache2/envvars
+/usr/sbin/apache2 -D FOREGROUND
--- /dev/null
+
+ServerName doc.arvados.org
+
+<VirtualHost *:80>
+ ServerAdmin sysadmin@curoverse.com
+
+ ServerName doc.arvados.org
+
+ DocumentRoot /usr/src/arvados/doc/.site/
+
+</VirtualHost>
+
--- /dev/null
+#! /bin/sh
+
+# Install prerequisites.
+sudo apt-get install curl libcurl3 libcurl3-gnutls libcurl4-openssl-dev python-pip
+
+# Install RVM.
+curl -sSL https://get.rvm.io | bash -s stable
+source ~/.rvm/scripts/rvm
+rvm install 2.1.0
+
+# Install arvados-cli.
+gem install arvados-cli
+sudo pip install --upgrade httplib2
--- /dev/null
+FROM arvados/jobs
+MAINTAINER Peter Amstutz <peter.amstutz@curoverse.com>
+
+USER root
+
+RUN apt-get update -qq
+RUN apt-get install -qqy openjdk-7-jre-headless && \
+ cd /tmp && \
+ curl --location http://cache.arvados.org/sourceforge.net/project/bio-bwa/bwa-0.7.9a.tar.bz2 -o bwa-0.7.9a.tar.bz2 && \
+ tar xjf bwa-0.7.9a.tar.bz2 && \
+ cd bwa-0.7.9a && \
+ make && \
+ (find . -executable -type f -print0 | xargs -0 -I {} mv {} /usr/local/bin) && \
+ rm -r /tmp/bwa-0.7.9a* && \
+ cd /tmp && \
+ curl --location http://cache.arvados.org/sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 -o samtools-0.1.19.tar.bz2 && \
+ tar xjf samtools-0.1.19.tar.bz2 && \
+ cd samtools-0.1.19 && \
+ make && \
+ (find . -executable -type f -print0 | xargs -0 -I {} mv {} /usr/local/bin) && \
+ rm -r /tmp/samtools-0.1.19*
+
+USER crunch
--- /dev/null
+FROM arvados/base
+MAINTAINER Brett Smith <brett@curoverse.com>
+
+# Install dependencies and set up system.
+# The FUSE packages help ensure that we can install the Python SDK (arv-mount).
+RUN /usr/bin/apt-get install -q -y \
+ python-dev python-llfuse python-pip python-virtualenv \
+ libio-socket-ssl-perl libjson-perl liburi-perl libwww-perl dtrx \
+ fuse libattr1-dev libfuse-dev && \
+ /usr/sbin/adduser --disabled-password \
+ --gecos 'Crunch execution user' crunch && \
+ /usr/bin/install --directory --owner=crunch --group=crunch --mode=0700 /keep /tmp/crunch-src /tmp/crunch-job && \
+ /bin/ln -s /usr/src/arvados /usr/local/src/arvados
+
+# Install Arvados packages.
+RUN (find /usr/src/arvados/sdk -name '*.gem' -print0 | \
+ xargs -0rn 1 /usr/local/rvm/bin/rvm-exec default gem install) && \
+ apt-get -qqy install python-arvados-fuse
+
+USER crunch
--- /dev/null
+# Based on Debian Wheezy
+FROM arvados/debian:wheezy
+MAINTAINER Ward Vandewege <ward@curoverse.com>
+
+ADD generated/bin/keepstore /usr/local/bin/
+ADD generated/bin/keepproxy /usr/local/bin/
+ADD generated/run-keep /usr/local/bin/
+
+ADD generated/keep_signing_secret /etc/
+
+# Start keep
+CMD ["/usr/local/bin/run-keep"]
--- /dev/null
+@@KEEP_SIGNING_SECRET@@
\ No newline at end of file
--- /dev/null
+#!/bin/sh
+
+pkf="/etc/keep_signing_secret"
+if [ -s "$pkf" ]
+then
+ permission_args="-permission-key-file=$pkf -enforce-permissions"
+else
+ permission_args=""
+fi
+
+exec keepstore $permission_args -listen=":25107" -volumes="/keep-data"
--- /dev/null
+#!/bin/bash
+set -e
+
+variant='minbase'
+include='iproute,iputils-ping'
+arch='amd64' # intentionally undocumented for now
+skipDetection=
+strictDebootstrap=
+justTar=
+
+usage() {
+ echo >&2
+
+ echo >&2 "usage: $0 [options] repo suite [mirror]"
+
+ echo >&2
+ echo >&2 'options: (not recommended)'
+ echo >&2 " -p set an http_proxy for debootstrap"
+ echo >&2 " -v $variant # change default debootstrap variant"
+ echo >&2 " -i $include # change default package includes"
+ echo >&2 " -d # strict debootstrap (do not apply any docker-specific tweaks)"
+ echo >&2 " -s # skip version detection and tagging (ie, precise also tagged as 12.04)"
+ echo >&2 " # note that this will also skip adding universe and/or security/updates to sources.list"
+ echo >&2 " -t # just create a tarball, especially for dockerbrew (uses repo as tarball name)"
+
+ echo >&2
+ echo >&2 " ie: $0 username/debian squeeze"
+ echo >&2 " $0 username/debian squeeze http://ftp.uk.debian.org/debian/"
+
+ echo >&2
+ echo >&2 " ie: $0 username/ubuntu precise"
+ echo >&2 " $0 username/ubuntu precise http://mirrors.melbourne.co.uk/ubuntu/"
+
+ echo >&2
+ echo >&2 " ie: $0 -t precise.tar.bz2 precise"
+ echo >&2 " $0 -t wheezy.tgz wheezy"
+ echo >&2 " $0 -t wheezy-uk.tar.xz wheezy http://ftp.uk.debian.org/debian/"
+
+ echo >&2
+}
+
+# these should match the names found at http://www.debian.org/releases/
+debianStable=wheezy
+debianUnstable=sid
+# this should match the name found at http://releases.ubuntu.com/
+ubuntuLatestLTS=precise
+
+while getopts v:i:a:p:dst name; do
+ case "$name" in
+ p)
+ http_proxy="$OPTARG"
+ ;;
+ v)
+ variant="$OPTARG"
+ ;;
+ i)
+ include="$OPTARG"
+ ;;
+ a)
+ arch="$OPTARG"
+ ;;
+ d)
+ strictDebootstrap=1
+ ;;
+ s)
+ skipDetection=1
+ ;;
+ t)
+ justTar=1
+ ;;
+ ?)
+ usage
+ exit 0
+ ;;
+ esac
+done
+shift $(($OPTIND - 1))
+
+repo="$1"
+suite="$2"
+mirror="${3:-}" # stick to the default debootstrap mirror if one is not provided
+
+if [ ! "$repo" ] || [ ! "$suite" ]; then
+ usage
+ exit 1
+fi
+
+# some rudimentary detection for whether we need to "sudo" our docker calls
+set +e
+docker=`which docker.io`
+if [[ "$docker" == "" ]]; then
+ docker=`which docker`
+fi
+set -e
+
+if $docker version > /dev/null 2>&1; then
+ docker="$docker"
+elif sudo $docker version > /dev/null 2>&1; then
+ docker="sudo $docker"
+elif command -v $docker > /dev/null 2>&1; then
+ docker="$docker"
+else
+ echo >&2 "warning: either docker isn't installed, or your current user cannot run it;"
+ echo >&2 " this script is not likely to work as expected"
+ sleep 3
+ docker='docker' # give us a command-not-found later
+fi
+
+# make sure we have an absolute path to our final tarball so we can still reference it properly after we change directory
+if [ "$justTar" ]; then
+ if [ ! -d "$(dirname "$repo")" ]; then
+ echo >&2 "error: $(dirname "$repo") does not exist"
+ exit 1
+ fi
+ repo="$(cd "$(dirname "$repo")" && pwd -P)/$(basename "$repo")"
+fi
+
+# will be filled in later, if [ -z "$skipDetection" ]
+lsbDist=''
+
+target="/tmp/docker-rootfs-debootstrap-$suite-$$-$RANDOM"
+
+cd "$(dirname "$(readlink -f "$BASH_SOURCE")")"
+returnTo="$(pwd -P)"
+
+set -x
+
+# bootstrap
+mkdir -p "$target"
+sudo http_proxy=$http_proxy debootstrap --verbose --variant="$variant" --include="$include" --arch="$arch" "$suite" "$target" "$mirror"
+
+cd "$target"
+
+if [ -z "$strictDebootstrap" ]; then
+ # prevent init scripts from running during install/update
+ # policy-rc.d (for most scripts)
+ echo $'#!/bin/sh\nexit 101' | sudo tee usr/sbin/policy-rc.d > /dev/null
+ sudo chmod +x usr/sbin/policy-rc.d
+ # initctl (for some pesky upstart scripts)
+ sudo chroot . dpkg-divert --local --rename --add /sbin/initctl
+ sudo ln -sf /bin/true sbin/initctl
+ # see https://github.com/dotcloud/docker/issues/446#issuecomment-16953173
+
+ # shrink the image, since apt makes us fat (wheezy: ~157.5MB vs ~120MB)
+ sudo chroot . apt-get clean
+
+ # while we're at it, apt is unnecessarily slow inside containers
+ # this forces dpkg not to call sync() after package extraction and speeds up install
+ # the benefit is huge on spinning disks, and the penalty is nonexistent on SSD or decent server virtualization
+ echo 'force-unsafe-io' | sudo tee etc/dpkg/dpkg.cfg.d/02apt-speedup > /dev/null
+ # we want to effectively run "apt-get clean" after every install to keep images small
+ echo 'DPkg::Post-Invoke {"/bin/rm -f /var/cache/apt/archives/*.deb || true";};' | sudo tee etc/apt/apt.conf.d/no-cache > /dev/null
+
+ # helpful undo lines for each the above tweaks (for lack of a better home to keep track of them):
+ # rm /usr/sbin/policy-rc.d
+ # rm /sbin/initctl; dpkg-divert --rename --remove /sbin/initctl
+ # rm /etc/dpkg/dpkg.cfg.d/02apt-speedup
+ # rm /etc/apt/apt.conf.d/no-cache
+
+ if [ -z "$skipDetection" ]; then
+ # see also rudimentary platform detection in hack/install.sh
+ lsbDist=''
+ if [ -r etc/lsb-release ]; then
+ lsbDist="$(. etc/lsb-release && echo "$DISTRIB_ID")"
+ fi
+ if [ -z "$lsbDist" ] && [ -r etc/debian_version ]; then
+ lsbDist='Debian'
+ fi
+
+ case "$lsbDist" in
+ Debian)
+ # add the updates and security repositories
+ if [ "$suite" != "$debianUnstable" -a "$suite" != 'unstable' ]; then
+ # ${suite}-updates only applies to non-unstable
+ sudo sed -i "p; s/ $suite main$/ ${suite}-updates main/" etc/apt/sources.list
+
+ # same for security updates
+ echo "deb http://security.debian.org/ $suite/updates main" | sudo tee -a etc/apt/sources.list > /dev/null
+ fi
+ ;;
+ Ubuntu)
+ # add the universe, updates, and security repositories
+ sudo sed -i "
+ s/ $suite main$/ $suite main universe/; p;
+ s/ $suite main/ ${suite}-updates main/; p;
+ s/ $suite-updates main/ ${suite}-security main/
+ " etc/apt/sources.list
+ ;;
+ esac
+ fi
+fi
+
+if [ "$justTar" ]; then
+ # create the tarball file so it has the right permissions (ie, not root)
+ touch "$repo"
+
+ # fill the tarball
+ sudo tar --numeric-owner -caf "$repo" .
+else
+ # create the image (and tag $repo:$suite)
+ sudo tar --numeric-owner -c . | $docker import - $repo:$suite
+
+ # test the image
+ $docker run -i -t $repo:$suite echo success
+
+ if [ -z "$skipDetection" ]; then
+ case "$lsbDist" in
+ Debian)
+ if [ "$suite" = "$debianStable" -o "$suite" = 'stable' ] && [ -r etc/debian_version ]; then
+ # tag latest
+ $docker tag $repo:$suite $repo:latest
+
+ if [ -r etc/debian_version ]; then
+ # tag the specific debian release version (which is only reasonable to tag on debian stable)
+ ver=$(cat etc/debian_version)
+ $docker tag $repo:$suite $repo:$ver
+ fi
+ fi
+ ;;
+ Ubuntu)
+ if [ "$suite" = "$ubuntuLatestLTS" ]; then
+ # tag latest
+ $docker tag $repo:$suite $repo:latest
+ fi
+ if [ -r etc/lsb-release ]; then
+ lsbRelease="$(. etc/lsb-release && echo "$DISTRIB_RELEASE")"
+ if [ "$lsbRelease" ]; then
+ # tag specific Ubuntu version number, if available (12.04, etc.)
+ $docker tag $repo:$suite $repo:$lsbRelease
+ fi
+ fi
+ ;;
+ esac
+ fi
+fi
+
+# cleanup
+cd "$returnTo"
+sudo rm -rf "$target"
--- /dev/null
+# Arvados passenger image
+
+FROM arvados/base
+MAINTAINER Ward Vandewege <ward@curoverse.com>
+
+# Install packages and build the passenger apache module
+
+RUN apt-get update -qq
+RUN apt-get install -qqy \
+ apt-utils git curl procps apache2-mpm-worker \
+ libcurl4-openssl-dev apache2-threaded-dev \
+ libapr1-dev libaprutil1-dev
+
+RUN cd /usr/src/arvados/services/api && \
+ /usr/local/rvm/bin/rvm-exec default bundle exec passenger-install-apache2-module --auto --languages ruby
+
+RUN cd /usr/src/arvados/services/api && \
+ /usr/local/rvm/bin/rvm-exec default bundle exec passenger-install-apache2-module --snippet > /etc/apache2/conf.d/passenger
+
--- /dev/null
+# PostgreSQL Docker container for Arvados.
+
+FROM arvados/debian:wheezy
+MAINTAINER Tim Pierce <twp@curoverse.com>
+
+# TODO(twp): parameterize variables via autoconf or similar.
+ENV POSTGRES_ROOT_PW dummy_pw
+
+ENV ARVADOS_DEV_DB arvados_development
+ENV ARVADOS_DEV_USER arvados
+ENV ARVADOS_DEV_PW dummy_pw
+
+ENV ARVADOS_TEST_DB arvados_test
+ENV ARVADOS_TEST_USER arvados
+ENV ARVADOS_TEST_PW dummy_pw
+
+ENV ARVADOS_PROD_DB arvados_production
+ENV ARVADOS_PROD_USER arvados
+ENV ARVADOS_PROD_PW dummy_pw
+
+# Install postgres and apache
+RUN apt-get -q -y install procps postgresql postgresql-server-dev-9.1
+
+# Configure databases and users.
+ADD postgresql.conf /etc/postgresql/9.1/main/
+ADD pg_hba.conf /etc/postgresql/9.1/main/
+
+ADD postgresql_config.sh /tmp/postgresql_config.sh
+RUN /tmp/postgresql_config.sh
+RUN rm /tmp/postgresql_config.sh
+
+# Accept database connections on port 5432 from outside the container.
+EXPOSE 5432
+
+CMD ["/bin/su", "postgres", "-c", "/usr/lib/postgresql/9.1/bin/postgres -D /var/lib/postgresql/9.1/main -c config_file=/etc/postgresql/9.1/main/postgresql.conf"]
--- /dev/null
+# For full documentation see
+# http://www.postgresql.org/docs/9.1/static/auth-pg-hba-conf.html
+
+# Database administrative login by Unix domain socket
+local all postgres peer
+
+# TYPE DATABASE USER ADDRESS METHOD
+host all all 0.0.0.0/0 md5
+
+# "local" is for Unix domain socket connections only
+local all all peer
+# IPv4 local connections:
+host all all 127.0.0.1/32 md5
+# IPv6 local connections:
+host all all ::1/128 md5
--- /dev/null
+# For full documentation on run-time settings see
+# http://www.postgresql.org/docs/9.2/static/runtime-config.html
+
+listen_addresses = '*'
+data_directory = '/var/lib/postgresql/9.1/main' # use data in another directory
+hba_file = '/etc/postgresql/9.1/main/pg_hba.conf' # host-based authentication file
+ident_file = '/etc/postgresql/9.1/main/pg_ident.conf' # ident configuration file
+external_pid_file = '/var/run/postgresql/9.1-main.pid' # write an extra PID file
+port = 5432 # (change requires restart)
+max_connections = 100 # (change requires restart)
+unix_socket_directory = '/var/run/postgresql' # (change requires restart)
+ssl = true # (change requires restart)
+shared_buffers = 24MB # min 128kB
+log_line_prefix = '%t ' # special values:
+datestyle = 'iso, mdy'
+lc_messages = 'C' # locale for system error message
+lc_monetary = 'C' # locale for monetary formatting
+lc_numeric = 'C' # locale for number formatting
+lc_time = 'C' # locale for time formatting
+default_text_search_config = 'pg_catalog.english'
--- /dev/null
+# Slurm node Docker container.
+
+FROM arvados/base
+MAINTAINER Ward Vandewege <ward@curoverse.com>
+
+RUN apt-get update -qq
+RUN apt-get install -qqy \
+ python-pip python-pyvcf python-gflags python-google-api-python-client \
+ python-virtualenv libattr1-dev libfuse-dev python-dev python-llfuse fuse \
+ crunchstat python-arvados-fuse cron vim supervisor openssh-server
+
+ADD fuse.conf /etc/fuse.conf
+RUN chmod 644 /etc/fuse.conf
+
+ADD generated/superuser_token /tmp/superuser_token
+
+RUN /usr/local/rvm/bin/rvm-exec default gem install arvados-cli arvados
+
+# Supervisor.
+ADD supervisor.conf /etc/supervisor/conf.d/arvados.conf
+ADD generated/setup.sh /usr/local/bin/setup.sh
+
+# Start the supervisor.
+CMD ["/usr/bin/supervisord", "-n"]
--- /dev/null
+# Set the maximum number of FUSE mounts allowed to non-root users.
+# The default is 1000.
+#
+#mount_max = 1000
+
+# Allow non-root users to specify the 'allow_other' or 'allow_root'
+# mount options.
+#
+user_allow_other
+
--- /dev/null
+#!/bin/bash
+
+USER_NAME="@@ARVADOS_USER_NAME@@"
+
+useradd $USER_NAME -s /bin/bash
+mkdir /home/$USER_NAME/.ssh -p
+
+# Install our token
+mkdir -p /home/$USER_NAME/.config/arvados;
+echo "ARVADOS_API_HOST=api" >> /home/$USER_NAME/.config/arvados/settings.conf
+echo "ARVADOS_API_HOST_INSECURE=yes" >> /home/$USER_NAME/.config/arvados/settings.conf
+echo "ARVADOS_API_TOKEN=$(cat /tmp/superuser_token)" >> /home/$USER_NAME/.config/arvados/settings.conf
+chmod 600 /home/$USER_NAME/.config/arvados/settings.conf
+
+chown $USER_NAME:$USER_NAME /home/$USER_NAME -R
+
+rm -f /tmp/superuser_token
+
+
--- /dev/null
+@@API_SUPERUSER_SECRET@@
--- /dev/null
+[program:ssh]
+user=root
+command=/etc/init.d/ssh start
+startsecs=0
+
+[program:cron]
+user=root
+command=/etc/init.d/cron start
+startsecs=0
+
+[program:setup]
+user=root
+command=/usr/local/bin/setup.sh
+startsecs=0
+
--- /dev/null
+# Slurm node Docker container.
+
+FROM arvados/base
+MAINTAINER Ward Vandewege <ward@curoverse.com>
+
+RUN apt-get update -qq
+RUN apt-get install -qqy slurm-llnl munge
+
+ADD munge.key /etc/munge/
+RUN chown munge:munge /etc/munge/munge.key && chmod 600 /etc/munge/munge.key
+ADD generated/slurm.conf /etc/slurm-llnl/
+
--- /dev/null
+
+ControlMachine=api
+#SlurmUser=slurmd
+SlurmctldPort=6817
+SlurmdPort=6818
+AuthType=auth/munge
+#JobCredentialPrivateKey=/etc/slurm-llnl/slurm-key.pem
+#JobCredentialPublicCertificate=/etc/slurm-llnl/slurm-cert.pem
+StateSaveLocation=/tmp
+SlurmdSpoolDir=/tmp/slurmd
+SwitchType=switch/none
+MpiDefault=none
+SlurmctldPidFile=/var/run/slurmctld.pid
+SlurmdPidFile=/var/run/slurmd.pid
+ProctrackType=proctrack/pgid
+CacheGroups=0
+ReturnToService=2
+TaskPlugin=task/affinity
+#
+# TIMERS
+SlurmctldTimeout=300
+SlurmdTimeout=300
+InactiveLimit=0
+MinJobAge=300
+KillWait=30
+Waittime=0
+#
+# SCHEDULING
+SchedulerType=sched/backfill
+#SchedulerType=sched/builtin
+SchedulerPort=7321
+#SchedulerRootFilter=
+#SelectType=select/linear
+SelectType=select/cons_res
+SelectTypeParameters=CR_CPU_Memory
+FastSchedule=1
+#
+# LOGGING
+SlurmctldDebug=3
+#SlurmctldLogFile=
+SlurmdDebug=3
+#SlurmdLogFile=
+JobCompType=jobcomp/none
+#JobCompLoc=
+JobAcctGatherType=jobacct_gather/none
+#JobAcctLogfile=
+#JobAcctFrequency=
+#
+# COMPUTE NODES
+NodeName=DEFAULT
+# CPUs=8 State=UNKNOWN RealMemory=6967 Weight=6967
+PartitionName=DEFAULT MaxTime=INFINITE State=UP
+PartitionName=compute Default=YES Shared=yes
+#PartitionName=sysadmin Hidden=YES Shared=yes
+
+NodeName=compute[0-1]
+#NodeName=compute0 RealMemory=6967 Weight=6967
+
+PartitionName=compute Nodes=compute[0-1]
+PartitionName=crypto Nodes=compute[0-1]
--- /dev/null
+[program:munge]
+user=root
+command=/etc/init.d/munge start
+
+[program:slurm]
+user=root
+command=/etc/init.d/slurm-llnl start
--- /dev/null
+# Arvados API server Docker container.
+
+FROM arvados/passenger
+MAINTAINER Ward Vandewege <ward@curoverse.com>
+
+RUN git clone git://github.com/curoverse/sso-devise-omniauth-provider.git /usr/src/sso-provider && \
+ /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/sso-provider/Gemfile
+
+# Install generated config files
+ADD generated/secret_token.rb /usr/src/sso-provider/config/initializers/secret_token.rb
+ADD generated/seeds.rb /usr/src/sso-provider/db/seeds.rb
+ADD generated/apache2_vhost /etc/apache2/sites-available/sso-provider
+ADD generated/apache2_vhost /etc/apache2/sites-available/sso-provider
+
+# Configure Apache and Passenger.
+RUN a2dissite default && \
+ a2ensite sso-provider && \
+ a2enmod rewrite && \
+ a2enmod ssl && \
+ cd /usr/src/sso-provider && \
+ RAILS_ENV=production /usr/local/rvm/bin/rvm-exec default bundle exec rake db:setup && \
+ /usr/local/rvm/bin/rvm-exec default bundle exec rake assets:precompile && \
+ chown www-data:www-data tmp_omniauth log config.ru -R && \
+ chown www-data:www-data db db/production.sqlite3 && \
+ /bin/mkdir /var/run/apache2
+
+ADD apache2_foreground.sh /etc/apache2/foreground.sh
+
+# Start the supervisor.
+CMD ["/etc/apache2/foreground.sh"]
--- /dev/null
+#! /bin/bash
+
+read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
+trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
+
+source /etc/apache2/envvars
+/usr/sbin/apache2 -D FOREGROUND
--- /dev/null
+# VirtualHost definition for the Arvados API server
+
+<VirtualHost *:80>
+ ServerName @@SSO_HOSTNAME@@.@@ARVADOS_DOMAIN@@
+ ServerAdmin sysadmin@curoverse.com
+
+ RedirectPermanent / https://@@SSO_HOSTNAME@@.@@ARVADOS_DOMAIN@@/
+
+ LogLevel warn
+ ErrorLog ${APACHE_LOG_DIR}/error.log
+ CustomLog ${APACHE_LOG_DIR}/access.log combined
+
+</VirtualHost>
+
+<VirtualHost *:443>
+ ServerName @@SSO_HOSTNAME@@.@@ARVADOS_DOMAIN@@
+ ServerAdmin sysadmin@curoverse.com
+
+ RailsEnv production
+ RackBaseURI /
+ RailsAppSpawnerIdleTime 1200
+
+ # Enable streaming
+ PassengerBufferResponse off
+
+ # Index file and Document Root (where the public files are located)
+ DirectoryIndex index.html
+ DocumentRoot /usr/src/sso-provider/public
+
+ LogLevel warn
+ ErrorLog ${APACHE_LOG_DIR}/ssl_error.log
+ CustomLog ${APACHE_LOG_DIR}/ssl_access.log combined
+
+ <Directory /usr/src/sso-provider/public>
+ Options Indexes FollowSymLinks MultiViews IncludesNoExec
+ AllowOverride None
+ Order allow,deny
+ allow from all
+ </Directory>
+
+ <IfModule mod_ssl.c>
+ SSLEngine on
+ # SSLCertificateChainFile /etc/ssl/certs/startcom.sub.class1.server.ca.pem
+ # SSLCACertificateFile /etc/ssl/certs/startcom.ca.pem
+ # SSLCertificateFile /etc/ssl/certs/qr1hi.arvadosapi.com.crt.pem
+ # SSLCertificateKeyFile /etc/ssl/private/qr1hi.arvadosapi.com.key.pem
+ SSLCertificateFile /etc/ssl/certs/ssl-cert-snakeoil.pem
+ SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key
+ SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown
+ </IfModule>
+
+</VirtualHost>
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# Your secret key for verifying the integrity of signed cookies.
+# If you change this key, all old signed cookies will become invalid!
+# Make sure the secret is at least 30 characters and all random,
+# no regular words or you'll be exposed to dictionary attacks.
+CfiOauthProvider::Application.config.secret_token = '@@SSO_SECRET@@'
--- /dev/null
+
+Client.delete_all
+
+c = Client.new()
+c.name = "@@SSO_CLIENT_NAME@@"
+c.app_id = "@@SSO_CLIENT_APP_ID@@"
+c.app_secret = "@@SSO_CLIENT_SECRET@@"
+c.save!
+
--- /dev/null
+apache2_vhost
+production.rb
+secret_token.rb
--- /dev/null
+# Arvados Workbench Docker container.
+
+FROM arvados/passenger
+MAINTAINER Ward Vandewege <ward@curoverse.com>
+
+# We need graphviz for the provenance graphs
+RUN apt-get update -qq
+RUN apt-get install -qqy graphviz
+
+# Update Arvados source
+RUN /bin/mkdir -p /usr/src/arvados/apps
+ADD generated/workbench.tar.gz /usr/src/arvados/apps/
+ADD generated/workbench_rails_env /etc/
+RUN /bin/cp /usr/src/arvados/apps/workbench/config/environments/$(cat /etc/workbench_rails_env).rb.example /usr/src/arvados/apps/workbench/config/environments/$(cat /etc/workbench_rails_env).rb
+ADD generated/application.yml /usr/src/arvados/apps/workbench/config/application.yml
+
+RUN RAILS_ENV=$(cat /etc/workbench_rails_env) && \
+ /usr/local/rvm/bin/rvm-exec default bundle install --gemfile=/usr/src/arvados/apps/workbench/Gemfile && \
+ touch /usr/src/arvados/apps/workbench/log/$RAILS_ENV.log && \
+ chmod 666 /usr/src/arvados/apps/workbench/log/$RAILS_ENV.log && \
+ touch /usr/src/arvados/apps/workbench/db/$RAILS_ENV.sqlite3 && \
+ cd /usr/src/arvados/apps/workbench && \
+ /usr/local/rvm/bin/rvm-exec default bundle exec rake assets:precompile && \
+ chown -R www-data:www-data /usr/src/arvados/apps/workbench
+
+# Configure Apache
+ADD generated/apache2_vhost /etc/apache2/sites-available/workbench
+RUN \
+ a2dissite default && \
+ a2ensite workbench && \
+ a2enmod rewrite
+
+ADD apache2_foreground.sh /etc/apache2/foreground.sh
+
+# Start Apache
+CMD ["/etc/apache2/foreground.sh"]
+
--- /dev/null
+#! /bin/bash
+
+read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
+trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
+
+# Override the default API server address if necessary.
+if [[ "$API_PORT_443_TCP_ADDR" != "" ]]; then
+ sed -i "s/localhost:9900/$API_PORT_443_TCP_ADDR/" /usr/src/arvados/apps/workbench/config/application.yml
+fi
+
+source /etc/apache2/envvars
+/usr/sbin/apache2 -D FOREGROUND
--- /dev/null
+<VirtualHost *:80>
+
+ ServerName workbench.@@API_HOSTNAME@@.@@ARVADOS_DOMAIN@@
+ ServerAdmin sysadmin@curoverse.com
+
+ RailsEnv @@WORKBENCH_RAILS_MODE@@
+ RackBaseURI /
+ RailsAppSpawnerIdleTime 1200
+
+ # Index file and Document Root (where the public files are located)
+ DirectoryIndex index.html
+ DocumentRoot /usr/src/arvados/apps/workbench/public
+
+ LogLevel warn
+ ErrorLog ${APACHE_LOG_DIR}/error.log
+ CustomLog ${APACHE_LOG_DIR}/access.log combined
+
+ <Directory /usr/src/arvados/apps/workbench>
+ Options Indexes FollowSymLinks MultiViews IncludesNoExec
+ AllowOverride None
+ Order allow,deny
+ allow from all
+ </Directory>
+
+</VirtualHost>
+
--- /dev/null
+# Copy this file to application.yml and edit to suit.
+#
+# Consult application.default.yml for the full list of configuration
+# settings.
+#
+# The order of precedence is:
+# 1. config/environments/{RAILS_ENV}.rb (deprecated)
+# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
+# 3. Section in application.yml called "common"
+# 4. Section in application.default.yml corresponding to RAILS_ENV
+# 5. Section in application.default.yml called "common"
+
+common:
+ # At minimum, you need a nice long randomly generated secret_token here.
+ secret_token: @@WORKBENCH_SECRET@@
+
+ # You probably also want to point to your API server.
+ arvados_login_base: 'https://localhost:9900/login'
+ arvados_v1_base: 'https://localhost:9900/arvados/v1'
+ arvados_insecure_https: @@WORKBENCH_INSECURE_HTTPS@@
+
+ data_import_dir: @@WORKBENCH_DATA_IMPORT_DIR@@
+ data_export_dir: @@WORKBENCH_DATA_EXPORT_DIR@@
+
+ site_name: @@WORKBENCH_SITE_NAME@@
+ activation_contact_link: @@WORKBENCH_ACTIVATION_CONTACT_LINK@@
+
--- /dev/null
+ArvadosWorkbench::Application.configure do
+ # Settings specified here will take precedence over those in config/application.rb
+
+ # Code is not reloaded between requests
+ config.cache_classes = true
+
+ # Full error reports are disabled and caching is turned on
+ config.consider_all_requests_local = false
+ config.action_controller.perform_caching = true
+
+ # Disable Rails's static asset server (Apache or nginx will already do this)
+ config.serve_static_assets = false
+
+ # Compress JavaScripts and CSS
+ config.assets.compress = true
+
+ # Don't fallback to assets pipeline if a precompiled asset is missed
+ config.assets.compile = false
+
+ # Generate digests for assets URLs
+ config.assets.digest = true
+
+ # Defaults to nil and saved in location specified by config.assets.prefix
+ # config.assets.manifest = YOUR_PATH
+
+ # Specifies the header that your server uses for sending files
+ # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
+ # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
+
+ # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
+ # config.force_ssl = true
+
+ # See everything in the log (default is :info)
+ # config.log_level = :debug
+
+ # Prepend all log lines with the following tags
+ # config.log_tags = [ :subdomain, :uuid ]
+
+ # Use a different logger for distributed setups
+ # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
+
+ # Use a different cache store in production
+ # config.cache_store = :mem_cache_store
+
+ # Enable serving of images, stylesheets, and JavaScripts from an asset server
+ # config.action_controller.asset_host = "http://assets.example.com"
+
+ # Precompile additional assets (application.js, application.css, and all non-JS/CSS are already added)
+ # config.assets.precompile += %w( search.js )
+
+ # Disable delivery errors, bad email addresses will be ignored
+ # config.action_mailer.raise_delivery_errors = false
+
+ # Enable threaded mode
+ # config.threadsafe!
+
+ # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
+ # the I18n.default_locale when a translation can not be found)
+ config.i18n.fallbacks = true
+
+ # Send deprecation notices to registered listeners
+ config.active_support.deprecation = :notify
+
+ # Log the query plan for queries taking more than this (works
+ # with SQLite, MySQL, and PostgreSQL)
+ # config.active_record.auto_explain_threshold_in_seconds = 0.5
+
+ # Log timing data for API transactions
+ config.profiling_enabled = false
+
+ config.arvados_login_base = 'https://' + ENV['API_PORT_443_TCP_ADDR'].to_s + '/login'
+ config.arvados_v1_base = 'https://' + ENV['API_PORT_443_TCP_ADDR'].to_s + '/arvados/v1'
+ config.arvados_insecure_https = @@WORKBENCH_INSECURE_HTTPS@@ # true = do not check server certificate
+
+ config.data_import_dir = '@@WORKBENCH_DATA_IMPORT_DIR@@'
+ config.data_export_dir = '@@WORKBENCH_DATA_EXPORT_DIR@@'
+
+ # Authentication stub: hard code pre-approved API tokens.
+ # config.accept_api_token = { rand(2**256).to_s(36) => true }
+ config.accept_api_token = {}
+
+ config.vcf_pipeline_uuid = '@@WORKBENCH_VCF_PIPELINE_UUID@@'
+
+ config.site_name = '@@WORKBENCH_SITE_NAME@@'
+ config.activation_contact_link = '@@WORKBENCH_ACTIVATION_CONTACT_LINK@@'
+ config.arvados_docsite = 'http://doc.arvados.org'
+
+ config.arvados_theme = 'default'
+
+ config.show_user_agreement_inline = false
+end
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# Your secret key for verifying the integrity of signed cookies.
+# If you change this key, all old signed cookies will become invalid!
+# Make sure the secret is at least 30 characters and all random,
+# no regular words or you'll be exposed to dictionary attacks.
+ArvadosWorkbench::Application.config.secret_token = '@@WORKBENCH_SECRET@@'
--- /dev/null
+@@WORKBENCH_RAILS_MODE@@
\ No newline at end of file
--- /dev/null
+arvados-cli*gem
+tmp
+Gemfile.lock
--- /dev/null
+source 'https://rubygems.org'
+gemspec
+gem 'minitest', '>= 5.0.0'
+gem 'rake'
--- /dev/null
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+ t.libs << 'test'
+end
+
+desc 'Run tests'
+task default: :test
--- /dev/null
+if not File.exists?('/usr/bin/git') then
+ STDERR.puts "\nGit binary not found, aborting. Please install git and run gem build from a checked out copy of the git repository.\n\n"
+ exit
+end
+
+git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H .`.chomp.split(":")
+git_timestamp = Time.at(git_timestamp.to_i).utc
+
+Gem::Specification.new do |s|
+ s.name = 'arvados-cli'
+ s.version = "0.1.#{git_timestamp.strftime('%Y%m%d%H%M%S')}"
+ s.date = git_timestamp.strftime("%Y-%m-%d")
+ s.summary = "Arvados CLI tools"
+ s.description = "Arvados command line tools, git commit #{git_hash}"
+ s.authors = ["Arvados Authors"]
+ s.email = 'gem-dev@curoverse.com'
+ #s.bindir = '.'
+ s.licenses = ['Apache License, Version 2.0']
+ s.files = ["bin/arv","bin/arv-run-pipeline-instance","bin/arv-crunch-job","bin/arv-tag","bin/crunch-job"]
+ s.executables << "arv"
+ s.executables << "arv-run-pipeline-instance"
+ s.executables << "arv-crunch-job"
+ s.executables << "arv-tag"
+ s.required_ruby_version = '>= 2.1.0'
+ s.add_runtime_dependency 'arvados', '~> 0.1', '>= 0.1.0'
+ s.add_runtime_dependency 'google-api-client', '~> 0.6.3', '>= 0.6.3'
+ s.add_runtime_dependency 'activesupport', '~> 3.2', '>= 3.2.13'
+ s.add_runtime_dependency 'json', '~> 1.7', '>= 1.7.7'
+ s.add_runtime_dependency 'trollop', '~> 2.0'
+ s.add_runtime_dependency 'andand', '~> 1.3', '>= 1.3.3'
+ s.add_runtime_dependency 'oj', '~> 2.0', '>= 2.0.3'
+ s.add_runtime_dependency 'curb', '~> 0.8'
+ s.add_runtime_dependency('jwt', '>= 0.1.5', '< 1.0.0')
+ s.homepage =
+ 'https://arvados.org'
+end
--- /dev/null
+#!/usr/bin/env ruby
+
+# Arvados cli client
+#
+# Ward Vandewege <ward@curoverse.com>
+
+require 'fileutils'
+
+if RUBY_VERSION < '1.9.3' then
+ abort <<-EOS
+#{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher.
+ EOS
+end
+
+begin
+ require 'curb'
+ require 'rubygems'
+ require 'google/api_client'
+ require 'json'
+ require 'pp'
+ require 'trollop'
+ require 'andand'
+ require 'oj'
+ require 'active_support/inflector'
+ require 'yaml'
+ require 'tempfile'
+ require 'net/http'
+rescue LoadError
+ abort <<-EOS
+
+Please install all required gems:
+
+ gem install activesupport andand curb google-api-client json oj trollop yaml
+
+ EOS
+end
+
+# Search for 'ENTRY POINT' to see where things get going
+
+ActiveSupport::Inflector.inflections do |inflect|
+ inflect.irregular 'specimen', 'specimens'
+ inflect.irregular 'human', 'humans'
+end
+
+module Kernel
+ def suppress_warnings
+ original_verbosity = $VERBOSE
+ $VERBOSE = nil
+ result = yield
+ $VERBOSE = original_verbosity
+ return result
+ end
+end
+
+class Google::APIClient
+ def discovery_document(api, version)
+ api = api.to_s
+ discovery_uri = self.discovery_uri(api, version)
+ discovery_uri_hash = Digest::MD5.hexdigest(discovery_uri)
+ return @discovery_documents[discovery_uri_hash] ||=
+ begin
+ # fetch new API discovery doc if stale
+ cached_doc = File.expand_path "~/.cache/arvados/discovery-#{discovery_uri_hash}.json" rescue nil
+
+ if cached_doc.nil? or not File.exist?(cached_doc) or (Time.now - File.mtime(cached_doc)) > 86400
+ response = self.execute!(:http_method => :get,
+ :uri => discovery_uri,
+ :authenticated => false)
+
+ begin
+ FileUtils.makedirs(File.dirname cached_doc)
+ File.open(cached_doc, 'w') do |f|
+ f.puts response.body
+ end
+ rescue
+ return JSON.load response.body
+ end
+ end
+
+ File.open(cached_doc) { |f| JSON.load f }
+ end
+ end
+end
+
+class ArvadosClient < Google::APIClient
+ def execute(*args)
+ if args.last.is_a? Hash
+ args.last[:headers] ||= {}
+ args.last[:headers]['Accept'] ||= 'application/json'
+ end
+ super(*args)
+ end
+end
+
+def init_config
+ # read authentication data from arvados configuration file if present
+ lineno = 0
+ config_file = File.expand_path('~/.config/arvados/settings.conf') rescue nil
+ if not config_file.nil? and File.exist? config_file then
+ File.open(config_file, 'r').each do |line|
+ lineno = lineno + 1
+ # skip comments
+ if line.match('^\s*#') then
+ next
+ end
+ var, val = line.chomp.split('=', 2)
+ # allow environment settings to override config files.
+ if var and val
+ ENV[var] ||= val
+ else
+ warn "#{config_file}: #{lineno}: could not parse `#{line}'"
+ end
+ end
+ end
+end
+
+
+subcommands = %w(copy create edit keep pipeline run tag ws)
+
+def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
+ case subcommand
+ when 'create'
+ arv_create client, arvados, global_opts, remaining_opts
+ when 'edit'
+ arv_edit client, arvados, global_opts, remaining_opts
+ when 'copy', 'tag', 'ws', 'run'
+ exec `which arv-#{subcommand}`.strip, *remaining_opts
+ when 'keep'
+ @sub = remaining_opts.shift
+ if ['get', 'put', 'ls', 'normalize'].index @sub then
+ # Native Arvados
+ exec `which arv-#{@sub}`.strip, *remaining_opts
+ elsif ['less', 'check'].index @sub then
+ # wh* shims
+ exec `which wh#{@sub}`.strip, *remaining_opts
+ elsif @sub == 'docker'
+ exec `which arv-keepdocker`.strip, *remaining_opts
+ else
+ puts "Usage: arv keep [method] [--parameters]\n"
+ puts "Use 'arv keep [method] --help' to get more information about specific methods.\n\n"
+ puts "Available methods: ls, get, put, less, check, docker"
+ end
+ abort
+ when 'pipeline'
+ sub = remaining_opts.shift
+ if sub == 'run'
+ exec `which arv-run-pipeline-instance`.strip, *remaining_opts
+ else
+ puts "Usage: arv pipeline [method] [--parameters]\n"
+ puts "Use 'arv pipeline [method] --help' to get more information about specific methods.\n\n"
+ puts "Available methods: run"
+ end
+ abort
+ end
+end
+
+def command_exists?(command)
+ File.executable?(command) || ENV['PATH'].split(':').any? {|folder| File.executable?(File.join(folder, command))}
+end
+
+def run_editor path
+ pid = Process::fork
+ if pid.nil?
+ editor = nil
+ [ENV["VISUAL"], ENV["EDITOR"], "nano", "vi"].each do |e|
+ editor ||= e if e and command_exists? e
+ end
+ if editor.nil?
+ abort "Could not find any editor to use, please set $VISUAL or $EDITOR to your desired editor."
+ end
+ exec editor, path
+ else
+ Process.wait pid
+ end
+
+ if $?.exitstatus != 0
+ raise "Editor exited with status #{$?.exitstatus}"
+ end
+end
+
+def edit_and_commit_object initial_obj, tmp_stem, global_opts, &block
+
+ content = case global_opts[:format]
+ when 'json'
+ Oj.dump(initial_obj, :indent => 1)
+ when 'yaml'
+ initial_obj.to_yaml
+ else
+ abort "Unrecognized format #{global_opts[:format]}"
+ end
+
+ tmp_file = Tempfile.new([tmp_stem, ".#{global_opts[:format]}"])
+ tmp_file.write(content)
+ tmp_file.close
+
+ begin
+ error_text = ''
+ while true
+ begin
+ run_editor tmp_file.path
+
+ tmp_file.open
+ newcontent = tmp_file.read()
+ tmp_file.close
+
+ # Strip lines starting with '#'
+ newcontent = newcontent.lines.select {|l| !l.start_with? '#'}.join
+
+ # Load the new object
+ newobj = case global_opts[:format]
+ when 'json'
+ Oj.load(newcontent)
+ when 'yaml'
+ YAML.load(newcontent)
+ end
+
+ yield newobj
+
+ break
+ rescue => e
+ can_retry = true
+ if e.is_a? Psych::SyntaxError
+ this_error = "YAML error parsing your input: #{e}"
+ elsif e.is_a? JSON::ParserError or e.is_a? Oj::ParseError
+ this_error = "JSON error parsing your input: #{e}"
+ elsif e.is_a? ArvadosAPIError
+ this_error = "API responded with error #{e}"
+ else
+ this_error = "#{e.class}: #{e}"
+ can_retry = false
+ end
+ puts this_error
+
+ tmp_file.open
+ newcontent = tmp_file.read()
+ tmp_file.close
+
+ if newcontent == error_text or not can_retry
+ FileUtils::cp tmp_file.path, tmp_file.path + ".saved"
+ puts "File is unchanged, edit aborted." if can_retry
+ abort "Saved contents to " + tmp_file.path + ".saved"
+ else
+ tmp_file.open
+ tmp_file.truncate 0
+ error_text = this_error.to_s.lines.map {|l| '# ' + l}.join + "\n"
+ error_text += "# Please fix the error and try again.\n"
+ error_text += newcontent.lines.select {|l| !l.start_with? '#'}.join
+ tmp_file.write error_text
+ tmp_file.close
+ end
+ end
+ end
+ ensure
+ tmp_file.close(true)
+ end
+
+ nil
+end
+
+class ArvadosAPIError < RuntimeError
+end
+
+def check_response result
+ begin
+ results = JSON.parse result.body
+ rescue JSON::ParserError, Oj::ParseError => e
+ raise "Failed to parse server response:\n" + e.to_s
+ end
+
+ if result.response.status != 200
+ raise ArvadosAPIError.new("#{result.response.status}: #{
+ ((results['errors'] && results['errors'].join('\n')) ||
+ Net::HTTPResponse::CODE_TO_OBJ[status.to_s].to_s.sub(/^Net::HTTP/, '').titleize)}")
+ end
+
+ results
+end
+
+def arv_edit client, arvados, global_opts, remaining_opts
+ uuid = remaining_opts.shift
+ if uuid.nil? or uuid == "-h" or uuid == "--help"
+ puts head_banner
+ puts "Usage: arv edit [uuid] [fields...]\n\n"
+ puts "Fetch the specified Arvados object, select the specified fields, \n"
+ puts "open an interactive text editor on a text representation (json or\n"
+ puts "yaml, use --format) and then update the object. Will use 'nano'\n"
+ puts "by default, customize with the EDITOR or VISUAL environment variable.\n"
+ exit 255
+ end
+
+ if not $stdout.tty?
+ puts "Not connected to a TTY, cannot run interactive editor."
+ exit 1
+ end
+
+ # determine controller
+
+ m = /([a-z0-9]{5})-([a-z0-9]{5})-([a-z0-9]{15})/.match uuid
+ if !m
+ if /^[a-f0-9]{32}/.match uuid
+ abort "Arvados collections are not editable."
+ else
+ abort "'#{uuid}' does not appear to be an Arvados uuid"
+ end
+ end
+
+ rsc = nil
+ arvados.discovery_document["resources"].each do |k,v|
+ klass = k.singularize.camelize
+ dig = Digest::MD5.hexdigest(klass).to_i(16).to_s(36)[-5..-1]
+ if dig == m[2]
+ rsc = k
+ end
+ end
+
+ if rsc.nil?
+ abort "Could not determine resource type #{m[2]}"
+ end
+
+ begin
+ result = client.execute(:api_method => eval('arvados.' + rsc + '.get'),
+ :parameters => {"uuid" => uuid},
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ oldobj = check_response result
+ rescue => e
+ abort "Server error: #{e}"
+ end
+
+ if remaining_opts.length > 0
+ oldobj.select! { |k, v| remaining_opts.include? k }
+ end
+
+ edit_and_commit_object oldobj, uuid, global_opts do |newobj|
+ newobj.select! {|k| newobj[k] != oldobj[k]}
+ if !newobj.empty?
+ result = client.execute(:api_method => eval('arvados.' + rsc + '.update'),
+ :parameters => {"uuid" => uuid},
+ :body_object => { rsc.singularize => newobj },
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ results = check_response result
+ puts "Updated object #{results['uuid']}"
+ else
+ puts "Object is unchanged, did not update."
+ end
+ end
+
+ exit 0
+end
+
+def arv_create client, arvados, global_opts, remaining_opts
+ types = resource_types(arvados.discovery_document)
+ create_opts = Trollop::options do
+ opt :project_uuid, "Project uuid in which to create the object", :type => :string
+ stop_on resource_types(arvados.discovery_document)
+ end
+
+ object_type = remaining_opts.shift
+ if object_type.nil?
+ abort "Missing resource type, must be one of #{types.join ', '}"
+ end
+
+ rsc = arvados.discovery_document["resources"].keys.select { |k| object_type == k.singularize }
+ if rsc.empty?
+ abort "Could not determine resource type #{object_type}"
+ end
+ rsc = rsc.first
+
+ discovered_params = arvados.discovery_document["resources"][rsc]["methods"]["create"]["parameters"]
+ method_opts = Trollop::options do
+ banner head_banner
+ banner "Usage: arv create [--project-uuid] #{object_type} [create parameters]"
+ banner ""
+ banner "This method supports the following parameters:"
+ banner ""
+ discovered_params.each do |k,v|
+ opts = Hash.new()
+ opts[:type] = v["type"].to_sym if v.include?("type")
+ if [:datetime, :text, :object, :array].index opts[:type]
+ opts[:type] = :string # else trollop bork
+ end
+ opts[:default] = v["default"] if v.include?("default")
+ opts[:default] = v["default"].to_i if opts[:type] == :integer
+ opts[:default] = to_boolean(v["default"]) if opts[:type] == :boolean
+ opts[:required] = true if v.include?("required") and v["required"]
+ description = ''
+ description = ' ' + v["description"] if v.include?("description")
+ opt k.to_sym, description, opts
+ end
+ end
+
+ initial_obj = {}
+ if create_opts[:project_uuid]
+ initial_obj["owner_uuid"] = create_opts[:project_uuid]
+ end
+
+ edit_and_commit_object initial_obj, "", global_opts do |newobj|
+ result = client.execute(:api_method => eval('arvados.' + rsc + '.create'),
+ :parameters => method_opts,
+ :body_object => {object_type => newobj},
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ results = check_response result
+ puts "Created object #{results['uuid']}"
+ end
+
+ exit 0
+end
+
+def to_boolean(s)
+ !!(s =~ /^(true|t|yes|y|1)$/i)
+end
+
+def head_banner
+ "Arvados command line client\n"
+end
+
+def help_methods(discovery_document, resource, method=nil)
+ banner = head_banner
+ banner += "Usage: arv #{resource} [method] [--parameters]\n"
+ banner += "Use 'arv #{resource} [method] --help' to get more information about specific methods.\n\n"
+ banner += "The #{resource} resource supports the following methods:"
+ banner += "\n\n"
+ discovery_document["resources"][resource.pluralize]["methods"].
+ each do |k,v|
+ description = ''
+ if v.include? "description"
+ # add only the first line of the discovery doc description
+ description = ' ' + v["description"].split("\n").first.chomp
+ end
+ banner += " #{sprintf("%20s",k)}#{description}\n"
+ end
+ banner += "\n"
+ STDERR.puts banner
+
+ if not method.nil? and method != '--help' and method != '-h' then
+ abort "Unknown method #{method.inspect} " +
+ "for resource #{resource.inspect}"
+ end
+ exit 255
+end
+
+def help_resources(option_parser, discovery_document, resource)
+ option_parser.educate
+ exit 255
+end
+
+def resource_types discovery_document
+ resource_types = Array.new()
+ discovery_document["resources"].each do |k,v|
+ resource_types << k.singularize
+ end
+ resource_types
+end
+
+def parse_arguments(discovery_document, subcommands)
+ resources_and_subcommands = resource_types(discovery_document) + subcommands
+
+ option_parser = Trollop::Parser.new do
+ version __FILE__
+ banner head_banner
+ banner "Usage: arv [--flags] subcommand|resource [method] [--parameters]"
+ banner ""
+ banner "Available flags:"
+
+ opt :dry_run, "Don't actually do anything", :short => "-n"
+ opt :verbose, "Print some things on stderr"
+ opt :format,
+ "Set the output format. Must be one of json (default), yaml or uuid.",
+ :type => :string,
+ :default => 'json'
+ opt :short, "Return only UUIDs (equivalent to --format=uuid)"
+
+ banner ""
+ banner "Use 'arv subcommand|resource --help' to get more information about a particular command or resource."
+ banner ""
+ banner "Available subcommands: #{subcommands.join(', ')}"
+ banner ""
+
+ banner "Available resources: #{discovery_document['resources'].keys.map { |k| k.singularize }.join(', ')}"
+
+ banner ""
+ banner "Additional options:"
+
+ conflicts :short, :format
+ stop_on resources_and_subcommands
+ end
+
+ global_opts = Trollop::with_standard_exception_handling option_parser do
+ o = option_parser.parse ARGV
+ end
+
+ unless %w(json yaml uuid).include?(global_opts[:format])
+ $stderr.puts "#{$0}: --format must be one of json, yaml or uuid."
+ $stderr.puts "Use #{$0} --help for more information."
+ abort
+ end
+
+ if global_opts[:short]
+ global_opts[:format] = 'uuid'
+ end
+
+ resource = ARGV.shift
+
+ if not subcommands.include? resource
+ if not resources_and_subcommands.include?(resource)
+ puts "Resource or subcommand '#{resource}' is not recognized.\n\n" if !resource.nil?
+ help_resources(option_parser, discovery_document, resource)
+ end
+
+ method = ARGV.shift
+ if not (discovery_document["resources"][resource.pluralize]["methods"].
+ include?(method))
+ help_methods(discovery_document, resource, method)
+ end
+
+ discovered_params = discovery_document\
+ ["resources"][resource.pluralize]\
+ ["methods"][method]["parameters"]
+ method_opts = Trollop::options do
+ banner head_banner
+ banner "Usage: arv #{resource} #{method} [--parameters]"
+ banner ""
+ banner "This method supports the following parameters:"
+ banner ""
+ discovered_params.each do |k,v|
+ opts = Hash.new()
+ opts[:type] = v["type"].to_sym if v.include?("type")
+ if [:datetime, :text, :object, :array].index opts[:type]
+ opts[:type] = :string # else trollop bork
+ end
+ opts[:default] = v["default"] if v.include?("default")
+ opts[:default] = v["default"].to_i if opts[:type] == :integer
+ opts[:default] = to_boolean(v["default"]) if opts[:type] == :boolean
+ opts[:required] = true if v.include?("required") and v["required"]
+ description = ''
+ description = ' ' + v["description"] if v.include?("description")
+ opt k.to_sym, description, opts
+ end
+
+ body_object = discovery_document["resources"][resource.pluralize]["methods"][method]["request"]
+ if body_object and discovered_params[resource].nil?
+ is_required = true
+ if body_object["required"] == false
+ is_required = false
+ end
+ opt resource.to_sym, "#{resource} (request body)", {
+ required: is_required,
+ type: :string
+ }
+ end
+ end
+
+ discovered_params.each do |k,v|
+ k = k.to_sym
+ if ['object', 'array'].index(v["type"]) and method_opts.has_key? k
+ if method_opts[k].andand.match /^\//
+ method_opts[k] = File.open method_opts[k], 'rb' do |f| f.read end
+ end
+ end
+ end
+ end
+
+ return resource, method, method_opts, global_opts, ARGV
+end
+
+#
+# ENTRY POINT
+#
+
+init_config
+
+ENV['ARVADOS_API_VERSION'] ||= 'v1'
+
+if not ENV.include?('ARVADOS_API_HOST') or not ENV.include?('ARVADOS_API_TOKEN') then
+ abort <<-EOS
+ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables.
+ EOS
+end
+
+# do this if you're testing with a dev server and you don't care about SSL certificate checks:
+if ENV['ARVADOS_API_HOST_INSECURE']
+ suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
+end
+
+begin
+ client = ArvadosClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0')
+ arvados = client.discovered_api('arvados', ENV['ARVADOS_API_VERSION'])
+rescue Exception => e
+ puts "Failed to connect to Arvados API server: #{e}"
+ exit 1
+end
+
+# Parse arguments here
+resource_schema, method, method_opts, global_opts, remaining_opts = parse_arguments(arvados.discovery_document, subcommands)
+
+check_subcommands client, arvados, resource_schema, global_opts, remaining_opts
+
+controller = resource_schema.pluralize
+
+api_method = 'arvados.' + controller + '.' + method
+
+if global_opts[:dry_run]
+ if global_opts[:verbose]
+ $stderr.puts "#{api_method} #{method_opts.inspect}"
+ end
+ exit
+end
+
+request_parameters = {_profile:true}.merge(method_opts)
+resource_body = request_parameters.delete(resource_schema.to_sym)
+if resource_body
+ request_body = {
+ resource_schema => resource_body
+ }
+else
+ request_body = nil
+end
+
+case api_method
+when
+ 'arvados.jobs.log_tail_follow'
+
+ # Special case for methods that respond with data streams rather
+ # than JSON (TODO: use the discovery document instead of a static
+ # list of methods)
+ uri_s = eval(api_method).generate_uri(request_parameters)
+ Curl::Easy.perform(uri_s) do |curl|
+ curl.headers['Accept'] = 'text/plain'
+ curl.headers['Authorization'] = "OAuth2 #{ENV['ARVADOS_API_TOKEN']}"
+ if ENV['ARVADOS_API_HOST_INSECURE']
+ curl.ssl_verify_peer = false
+ curl.ssl_verify_host = false
+ end
+ if global_opts[:verbose]
+ curl.on_header { |data| $stderr.write data }
+ end
+ curl.on_body { |data| $stdout.write data }
+ end
+ exit 0
+else
+ result = client.execute(:api_method => eval(api_method),
+ :parameters => request_parameters,
+ :body_object => request_body,
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+end
+
+begin
+ results = JSON.parse result.body
+rescue JSON::ParserError => e
+ abort "Failed to parse server response:\n" + e.to_s
+end
+
+if results["errors"] then
+ abort "Error: #{results["errors"][0]}"
+end
+
+case global_opts[:format]
+when 'json'
+ puts Oj.dump(results, :indent => 1)
+when 'yaml'
+ puts results.to_yaml
+else
+ if results["items"] and results["kind"].match /list$/i
+ results['items'].each do |i| puts i['uuid'] end
+ elsif results['uuid'].nil?
+ abort("Response did not include a uuid:\n" +
+ Oj.dump(results, :indent => 1) +
+ "\n")
+ else
+ puts results['uuid']
+ end
+end
--- /dev/null
+../../python/bin/arv-copy
\ No newline at end of file
--- /dev/null
+#!/usr/bin/env ruby
+exec File.join(File.dirname(File.realpath(__FILE__)), 'crunch-job'), *ARGV
--- /dev/null
+../../python/bin/arv-get
\ No newline at end of file
--- /dev/null
+../../python/bin/arv-keepdocker
\ No newline at end of file
--- /dev/null
+../../python/bin/arv-ls
\ No newline at end of file
--- /dev/null
+../../../services/fuse/bin/arv-mount
\ No newline at end of file
--- /dev/null
+../../python/bin/arv-normalize
\ No newline at end of file
--- /dev/null
+../../python/bin/arv-put
\ No newline at end of file
--- /dev/null
+#!/usr/bin/env ruby
+
+# == Synopsis
+#
+# arv-run-pipeline-instance --template pipeline-template-uuid [options] [--] [parameters]
+# arv-run-pipeline-instance --instance pipeline-instance-uuid [options]
+#
+# Satisfy a pipeline template by finding or submitting a mapreduce job
+# for each pipeline component.
+#
+# == Options
+#
+# [--template uuid] Use the specified pipeline template.
+#
+# [--template path] Load the pipeline template from the specified
+# local file.
+#
+# [--instance uuid] Use the specified pipeline instance.
+#
+# [-n, --dry-run] Do not start any new jobs or wait for existing jobs
+# to finish. Just find out whether jobs are finished,
+# queued, or running for each component
+#
+# [--submit] Do not try to satisfy any components. Just
+# create an instance, print its UUID to
+# stdout, and exit.
+#
+# [--no-wait] Make only as much progress as possible without entering
+# a sleep/poll loop.
+#
+# [--no-reuse] Do not reuse existing jobs to satisfy pipeline
+# components. Submit a new job for every component.
+#
+# [--debug] Print extra debugging information on stderr.
+#
+# [--debug-level N] Increase amount of debugging information. Default
+# 1, possible range 0..3.
+#
+# [--status-text path] Print plain text status report to a file or
+# fifo. Default: /dev/stdout
+#
+# [--status-json path] Print JSON status report to a file or
+# fifo. Default: /dev/null
+#
+# [--description] Description for the pipeline instance.
+#
+# == Parameters
+#
+# [param_name=param_value]
+#
+# [param_name param_value] Set (or override) the default value for
+# every parameter with the given name.
+#
+# [component_name::param_name=param_value]
+# [component_name::param_name param_value]
+# [--component_name::param_name=param_value]
+# [--component_name::param_name param_value] Set the value of a
+# parameter for a single
+# component.
+#
+class WhRunPipelineInstance
+end
+
+if RUBY_VERSION < '1.9.3' then
+ abort <<-EOS
+#{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher.
+ EOS
+end
+
+$arvados_api_version = ENV['ARVADOS_API_VERSION'] || 'v1'
+$arvados_api_host = ENV['ARVADOS_API_HOST'] or
+ abort "#{$0}: fatal: ARVADOS_API_HOST environment variable not set."
+$arvados_api_token = ENV['ARVADOS_API_TOKEN'] or
+ abort "#{$0}: fatal: ARVADOS_API_TOKEN environment variable not set."
+
+begin
+ require 'arvados'
+ require 'rubygems'
+ require 'json'
+ require 'pp'
+ require 'trollop'
+ require 'google/api_client'
+rescue LoadError => l
+ puts $:
+ abort <<-EOS
+#{$0}: fatal: #{l.message}
+Some runtime dependencies may be missing.
+Try: gem install arvados pp google-api-client json trollop
+ EOS
+end
+
+def debuglog(message, verbosity=1)
+ $stderr.puts "#{File.split($0).last} #{$$}: #{message}" if $debuglevel >= verbosity
+end
+
+module Kernel
+ def suppress_warnings
+ original_verbosity = $VERBOSE
+ $VERBOSE = nil
+ result = yield
+ $VERBOSE = original_verbosity
+ return result
+ end
+end
+
+if $arvados_api_host.match /local/
+ # You probably don't care about SSL certificate checks if you're
+ # testing with a dev server.
+ suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
+end
+
+
+# Parse command line options (the kind that control the behavior of
+# this program, that is, not the pipeline component parameters).
+
+p = Trollop::Parser.new do
+ version __FILE__
+ opt(:dry_run,
+ "Do not start any new jobs or wait for existing jobs to finish. Just find out whether jobs are finished, queued, or running for each component.",
+ :type => :boolean,
+ :short => :n)
+ opt(:status_text,
+ "Store plain text status in given file.",
+ :short => :none,
+ :type => :string,
+ :default => '/dev/stdout')
+ opt(:status_json,
+ "Store json-formatted pipeline in given file.",
+ :short => :none,
+ :type => :string,
+ :default => '/dev/null')
+ opt(:no_wait,
+ "Do not wait for jobs to finish. Just look up status, submit new jobs if needed, and exit.",
+ :short => :none,
+ :type => :boolean)
+ opt(:no_reuse,
+ "Do not reuse existing jobs to satisfy pipeline components. Submit a new job for every component.",
+ :short => :none,
+ :type => :boolean)
+ opt(:debug,
+ "Print extra debugging information on stderr.",
+ :type => :boolean)
+ opt(:debug_level,
+ "Set debug verbosity level.",
+ :short => :none,
+ :type => :integer)
+ opt(:template,
+ "UUID of pipeline template, or path to local pipeline template file.",
+ :short => :none,
+ :type => :string)
+ opt(:instance,
+ "UUID of pipeline instance.",
+ :short => :none,
+ :type => :string)
+ opt(:submit,
+ "Submit the pipeline instance to the server, and exit. Let the Crunch dispatch service satisfy the components by finding/running jobs.",
+ :short => :none,
+ :type => :boolean)
+ opt(:run_pipeline_here,
+ "Manage the pipeline instance in-process. Submit jobs to Crunch as needed. Do not exit until the pipeline finishes (or fails).",
+ :short => :none,
+ :type => :boolean)
+ opt(:run_jobs_here,
+ "Run jobs in the local terminal session instead of submitting them to Crunch. Implies --run-pipeline-here. Note: this results in a significantly different job execution environment, and some Crunch features are not supported. It can be necessary to modify a pipeline in order to make it run this way.",
+ :short => :none,
+ :type => :boolean)
+ opt(:run_here,
+ "Synonym for --run-jobs-here.",
+ :short => :none,
+ :type => :boolean)
+ opt(:description,
+ "Description for the pipeline instance.",
+ :short => :none,
+ :type => :string)
+ stop_on [:'--']
+end
+$options = Trollop::with_standard_exception_handling p do
+ p.parse ARGV
+end
+$debuglevel = $options[:debug_level] || ($options[:debug] && 1) || 0
+
+$options[:run_jobs_here] ||= $options[:run_here] # old flag name
+$options[:run_pipeline_here] ||= $options[:run_jobs_here] # B requires A
+
+if $options[:instance]
+ if $options[:template] or $options[:submit]
+ abort "#{$0}: syntax error: --instance cannot be combined with --template or --submit."
+ end
+elsif not $options[:template]
+ puts "error: you must supply a --template or --instance."
+ p.educate
+ abort
+end
+
+if $options[:run_pipeline_here] == $options[:submit]
+ abort "#{$0}: error: you must supply --run-pipeline-here, --run-jobs-here, or --submit."
+end
+
+# Suppress SSL certificate checks if ARVADOS_API_HOST_INSECURE
+
+module Kernel
+ def suppress_warnings
+ original_verbosity = $VERBOSE
+ $VERBOSE = nil
+ result = yield
+ $VERBOSE = original_verbosity
+ return result
+ end
+end
+
+if ENV['ARVADOS_API_HOST_INSECURE']
+ suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
+end
+
+# Set up the API client.
+
+$arv = Arvados.new api_version: 'v1'
+$client = $arv.client
+$arvados = $arv.arvados_api
+
+class PipelineInstance
+ def self.find(uuid)
+ result = $client.execute(:api_method => $arvados.pipeline_instances.get,
+ :parameters => {
+ :uuid => uuid
+ },
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ j = JSON.parse result.body, :symbolize_names => true
+ unless j.is_a? Hash and j[:uuid]
+ debuglog "Failed to get pipeline_instance: #{j[:errors] rescue nil}", 0
+ nil
+ else
+ debuglog "Retrieved pipeline_instance #{j[:uuid]}"
+ self.new(j)
+ end
+ end
+ def self.create(attributes)
+ result = $client.execute(:api_method => $arvados.pipeline_instances.create,
+ :body_object => {
+ :pipeline_instance => attributes
+ },
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ j = JSON.parse result.body, :symbolize_names => true
+ unless j.is_a? Hash and j[:uuid]
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nFailed to create pipeline_instance: #{j[:errors] rescue nil} #{j.inspect}"
+ end
+ debuglog "Created pipeline instance: #{j[:uuid]}"
+ self.new(j)
+ end
+ def save
+ result = $client.execute(:api_method => $arvados.pipeline_instances.update,
+ :parameters => {
+ :uuid => @pi[:uuid]
+ },
+ :body_object => {
+ :pipeline_instance => @attributes_to_update
+ },
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ j = JSON.parse result.body, :symbolize_names => true
+ unless j.is_a? Hash and j[:uuid]
+ debuglog "Failed to save pipeline_instance: #{j[:errors] rescue nil}", 0
+ nil
+ else
+ @attributes_to_update = {}
+ @pi = j
+ end
+ end
+ def []=(x,y)
+ @attributes_to_update[x] = y
+ @pi[x] = y
+ end
+ def [](x)
+ @pi[x]
+ end
+
+ def log_stderr(msg)
+ $arv.log.create log: {
+ event_type: 'stderr',
+ object_uuid: self[:uuid],
+ owner_uuid: self[:owner_uuid],
+ properties: {"text" => msg},
+ }
+ end
+
+ protected
+ def initialize(j)
+ @attributes_to_update = {}
+ @pi = j
+ end
+end
+
+class JobCache
+ def self.get(uuid)
+ @cache ||= {}
+ result = $client.execute(:api_method => $arvados.jobs.get,
+ :parameters => {
+ :uuid => uuid
+ },
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ @cache[uuid] = JSON.parse result.body, :symbolize_names => true
+ end
+ def self.where(conditions)
+ result = $client.execute(:api_method => $arvados.jobs.list,
+ :parameters => {
+ :limit => 10000,
+ :where => conditions.to_json
+ },
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ list = JSON.parse result.body, :symbolize_names => true
+ if list and list[:items].is_a? Array
+ list[:items]
+ else
+ []
+ end
+ end
+ def self.create(pipeline, component, job, create_params)
+ @cache ||= {}
+
+ body = {job: no_nil_values(job)}.merge(no_nil_values(create_params))
+
+ result = $client.execute(:api_method => $arvados.jobs.create,
+ :body_object => body,
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ j = JSON.parse result.body, :symbolize_names => true
+ if j.is_a? Hash and j[:uuid]
+ @cache[j[:uuid]] = j
+ else
+ debuglog "create job: #{j[:errors] rescue nil} with attributes #{body}", 0
+
+ msg = ""
+ j[:errors].each do |err|
+ msg += "Error creating job for component #{component}: #{err}\n"
+ end
+ msg += "Job submission was: #{body.to_json}"
+
+ pipeline.log_stderr(msg)
+ nil
+ end
+ end
+
+ protected
+
+ def self.no_nil_values(hash)
+ hash.reject { |key, value| value.nil? }
+ end
+end
+
+class WhRunPipelineInstance
+ attr_reader :instance
+
+ def initialize(_options)
+ @options = _options
+ end
+
+ def fetch_template(template)
+ if template.match /[^-0-9a-z]/
+ # Doesn't look like a uuid -- use it as a filename.
+ @template = JSON.parse File.read(template), :symbolize_names => true
+ else
+ result = $client.execute(:api_method => $arvados.pipeline_templates.get,
+ :parameters => {
+ :uuid => template
+ },
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
+ @template = JSON.parse result.body, :symbolize_names => true
+ if !@template[:uuid]
+ abort "#{$0}: fatal: failed to retrieve pipeline template #{template} #{@template[:errors].inspect rescue nil}"
+ end
+ end
+ self
+ end
+
+ def fetch_instance(instance_uuid)
+ @instance = PipelineInstance.find(instance_uuid)
+ @template = @instance
+ self
+ end
+
+ def apply_parameters(params_args)
+ params_args.shift if params_args[0] == '--'
+ params = {}
+ while !params_args.empty?
+ if (re = params_args[0].match /^(--)?([^-].*?)=(.+)/)
+ params[re[2]] = re[3]
+ params_args.shift
+ elsif params_args.size > 1
+ param = params_args.shift.sub /^--/, ''
+ params[param] = params_args.shift
+ else
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: I do not know what to do with arg \"#{params_args[0]}\""
+ end
+ end
+
+ if not @template[:components].is_a?(Hash)
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Template missing \"components\" hash"
+ end
+ @components = @template[:components].dup
+
+ bad_components = @components.each_pair.select do |cname, cspec|
+ not cspec.is_a?(Hash)
+ end
+ if bad_components.any?
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Components not specified with hashes: #{bad_components.map(&:first).join(', ')}"
+ end
+
+ bad_components = @components.each_pair.select do |cname, cspec|
+ not cspec[:script_parameters].is_a?(Hash)
+ end
+ if bad_components.any?
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nSyntax error: Components missing \"script_parameters\" hashes: #{bad_components.map(&:first).join(', ')}"
+ end
+
+ errors = []
+ @components.each do |componentname, component|
+ component[:script_parameters].each do |parametername, parameter|
+ parameter = { :value => parameter } unless parameter.is_a? Hash
+ value =
+ (params["#{componentname}::#{parametername}"] ||
+ parameter[:value] ||
+ (parameter[:output_of].nil? &&
+ (params[parametername.to_s] ||
+ parameter[:default])) ||
+ nil)
+ if value.nil? and
+ ![false,'false',0,'0'].index parameter[:required]
+ if parameter[:output_of]
+ if not @components[parameter[:output_of].intern]
+ errors << [componentname, parametername, "output_of refers to nonexistent component '#{parameter[:output_of]}'"]
+ end
+ next
+ end
+ errors << [componentname, parametername, "required parameter is missing"]
+ end
+ debuglog "parameter #{componentname}::#{parametername} == #{value}"
+
+ component[:script_parameters][parametername] =
+ parameter.dup.merge(value: value)
+ end
+ end
+ if !errors.empty?
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nErrors:\n#{errors.collect { |c,p,e| "#{c}::#{p} - #{e}\n" }.join ""}"
+ end
+ debuglog "options=" + @options.pretty_inspect
+ self
+ end
+
+ def setup_instance
+ if @instance
+ @instance[:properties][:run_options] ||= {}
+ if @options[:no_reuse]
+ # override properties of existing instance
+ @instance[:properties][:run_options][:enable_job_reuse] = false
+ else
+ # Default to "enable reuse" if not specified. (This code path
+ # can go away when old clients go away.)
+ if @instance[:properties][:run_options][:enable_job_reuse].nil?
+ @instance[:properties][:run_options][:enable_job_reuse] = true
+ end
+ end
+ else
+ description = $options[:description]
+ description = ("Created at #{Time.now.localtime}" + (@template[:name].andand.size.andand>0 ? " using the pipeline template *#{@template[:name]}*" : "")) if !description
+ @instance = PipelineInstance.
+ create(components: @components,
+ properties: {
+ run_options: {
+ enable_job_reuse: !@options[:no_reuse]
+ }
+ },
+ pipeline_template_uuid: @template[:uuid],
+ description: description,
+ state: ($options[:submit] ? 'RunningOnServer' : 'RunningOnClient'))
+ end
+ self
+ end
+
+ def run
+ moretodo = true
+ interrupted = false
+
+ if @instance[:started_at].nil?
+ @instance[:started_at] = Time.now
+ end
+
+ job_creation_failed = 0
+ while moretodo
+ moretodo = false
+ @components.each do |cname, c|
+ job = nil
+ owner_uuid = @instance[:owner_uuid]
+ # Is the job satisfying this component already known to be
+ # finished? (Already meaning "before we query API server about
+ # the job's current state")
+ c_already_finished = (c[:job] &&
+ c[:job][:uuid] &&
+ ["Complete", "Failed", "Cancelled"].include?(c[:job][:state]))
+ if !c[:job] and
+ c[:script_parameters].select { |pname, p| p.is_a? Hash and p[:output_of]}.empty?
+ # No job yet associated with this component and is component inputs
+ # are fully specified (any output_of script_parameters are resolved
+ # to real value)
+ my_submit_id = "instance #{@instance[:uuid]} rand #{rand(2**64).to_s(36)}"
+ job = JobCache.create(@instance, cname, {
+ :script => c[:script],
+ :script_parameters => Hash[c[:script_parameters].map do |key, spec|
+ [key, spec[:value]]
+ end],
+ :script_version => c[:script_version],
+ :repository => c[:repository],
+ :nondeterministic => c[:nondeterministic],
+ :runtime_constraints => c[:runtime_constraints],
+ :owner_uuid => owner_uuid,
+ :is_locked_by_uuid => (@options[:run_jobs_here] ? owner_uuid : nil),
+ :submit_id => my_submit_id,
+ :state => (if @options[:run_jobs_here] then "Running" else "Queued" end)
+ }, {
+ # This is the right place to put these attributes when
+ # dealing with new API servers.
+ :minimum_script_version => c[:minimum_script_version],
+ :exclude_script_versions => c[:exclude_minimum_script_versions],
+ :find_or_create => (@instance[:properties][:run_options].andand[:enable_job_reuse] &&
+ !c[:nondeterministic]),
+ :filters => c[:filters]
+ })
+ if job
+ debuglog "component #{cname} new job #{job[:uuid]}"
+ c[:job] = job
+ c[:run_in_process] = (@options[:run_jobs_here] and
+ job[:submit_id] == my_submit_id)
+ else
+ debuglog "component #{cname} new job failed", 0
+ job_creation_failed += 1
+ end
+ end
+
+ if c[:job] and c[:run_in_process] and not ["Complete", "Failed", "Cancelled"].include? c[:job][:state]
+ report_status
+ begin
+ require 'open3'
+ Open3.popen3("arv-crunch-job", "--force-unlock",
+ "--job", c[:job][:uuid]) do |stdin, stdout, stderr, wait_thr|
+ debuglog "arv-crunch-job pid #{wait_thr.pid} started", 0
+ stdin.close
+ while true
+ rready, wready, = IO.select([stdout, stderr], [])
+ break if !rready[0]
+ begin
+ buf = rready[0].read_nonblock(2**20)
+ rescue EOFError
+ break
+ end
+ (rready[0] == stdout ? $stdout : $stderr).write(buf)
+ end
+ stdout.close
+ stderr.close
+ debuglog "arv-crunch-job pid #{wait_thr.pid} exit #{wait_thr.value.to_i}", 0
+ end
+ if not $arv.job.get(uuid: c[:job][:uuid])[:finished_at]
+ raise Exception.new("arv-crunch-job did not set finished_at.")
+ end
+ rescue Exception => e
+ debuglog "Interrupted (#{e}). Failing job.", 0
+ $arv.job.update(uuid: c[:job][:uuid],
+ job: {
+ state: "Failed"
+ })
+ end
+ end
+
+ if c[:job] and c[:job][:uuid]
+ if ["Running", "Queued"].include?(c[:job][:state])
+ # Job is running (or may be soon) so update copy of job record
+ c[:job] = JobCache.get(c[:job][:uuid])
+ end
+
+ if c[:job][:state] == "Complete"
+ # Populate script_parameters of other components waiting for
+ # this job
+ @components.each do |c2name, c2|
+ c2[:script_parameters].each do |pname, p|
+ if p.is_a? Hash and p[:output_of] == cname.to_s
+ debuglog "parameter #{c2name}::#{pname} == #{c[:job][:output]}"
+ c2[:script_parameters][pname] = {value: c[:job][:output]}
+ moretodo = true
+ end
+ end
+ end
+ unless c_already_finished
+ # This is my first time discovering that the job
+ # succeeded. (At the top of this loop, I was still
+ # waiting for it to finish.)
+
+ if @instance[:name].andand.length.andand > 0
+ pipeline_name = @instance[:name]
+ elsif @template.andand[:name].andand.length.andand > 0
+ pipeline_name = @template[:name]
+ else
+ pipeline_name = @instance[:uuid]
+ end
+ if c[:output_name] != false
+ # Create a collection located in the same project as the pipeline with the contents of the output.
+ portable_data_hash = c[:job][:output]
+ collections = $arv.collection.list(limit: 1,
+ filters: [['portable_data_hash', '=', portable_data_hash]],
+ select: ["portable_data_hash", "manifest_text"]
+ )[:items]
+ if collections.any?
+ name = c[:output_name] || "Output #{portable_data_hash[0..7]} of #{cname} of #{pipeline_name}"
+
+ # check if there is a name collision.
+ name_collisions = $arv.collection.list(filters: [["owner_uuid", "=", owner_uuid],
+ ["name", "=", name]])[:items]
+
+ newcollection_actual = nil
+ if name_collisions.any? and name_collisions.first[:portable_data_hash] == portable_data_hash
+ # There is already a collection with the same name and the
+ # same contents, so just point to that.
+ newcollection_actual = name_collisions.first
+ end
+
+ if newcollection_actual.nil?
+ # Did not find a collection with the same name (or the
+ # collection has a different portable data hash) so create
+ # a new collection with ensure_unique_name: true.
+ newcollection = {
+ owner_uuid: owner_uuid,
+ name: name,
+ portable_data_hash: collections.first[:portable_data_hash],
+ manifest_text: collections.first[:manifest_text]
+ }
+ debuglog "Creating collection #{newcollection}", 0
+ newcollection_actual = $arv.collection.create collection: newcollection, ensure_unique_name: true
+ end
+
+ c[:output_uuid] = newcollection_actual[:uuid]
+ else
+ debuglog "Could not find a collection with portable data hash #{portable_data_hash}", 0
+ end
+ end
+ end
+ elsif ["Queued", "Running"].include? c[:job][:state]
+ # Job is running or queued to run, so indicate that pipeline
+ # should continue to run
+ moretodo = true
+ elsif c[:job][:state] == "Cancelled"
+ debuglog "component #{cname} job #{c[:job][:uuid]} cancelled."
+ moretodo = false
+ elsif c[:job][:state] == "Failed"
+ moretodo = false
+ end
+ end
+ end
+ @instance[:components] = @components
+ report_status
+
+ if @options[:no_wait]
+ moretodo = false
+ end
+
+ # If job creation fails, just give up on this pipeline instance.
+ if job_creation_failed > 0
+ moretodo = false
+ end
+
+ if moretodo
+ begin
+ sleep 10
+ rescue Interrupt
+ debuglog "interrupt", 0
+ interrupted = true
+ break
+ end
+ end
+ end
+
+ c_in_state = @components.values.group_by { |c|
+ c[:job] and c[:job][:state]
+ }
+ succeeded = c_in_state["Complete"].andand.count || 0
+ failed = (c_in_state["Failed"].andand.count || 0) + (c_in_state["Cancelled"].andand.count || 0)
+ ended = succeeded + failed
+
+ success = (succeeded == @components.length)
+
+ # A job create call failed. Just give up.
+ if job_creation_failed > 0
+ debuglog "job creation failed - giving up on this pipeline instance", 0
+ success = false
+ failed += 1
+ end
+
+ if interrupted
+ if success
+ @instance[:state] = 'Complete'
+ else
+ @instance[:state] = 'Paused'
+ end
+ else
+ if ended == @components.length or failed > 0
+ @instance[:state] = success ? 'Complete' : 'Failed'
+ end
+ end
+
+ if @instance[:finished_at].nil? and ['Complete', 'Failed'].include? @instance[:state]
+ @instance[:finished_at] = Time.now
+ end
+
+ debuglog "pipeline instance state is #{@instance[:state]}"
+
+ # set components_summary
+ components_summary = {"todo" => @components.length - ended, "done" => succeeded, "failed" => failed}
+ @instance[:components_summary] = components_summary
+
+ @instance.save
+ end
+
+ def cleanup
+ if @instance and @instance[:state] == 'RunningOnClient'
+ @instance[:state] = 'Paused'
+ @instance.save
+ end
+ end
+
+ def uuid
+ @instance[:uuid]
+ end
+
+ protected
+
+ def report_status
+ @instance.save
+
+ if @options[:status_json] != '/dev/null'
+ File.open(@options[:status_json], 'w') do |f|
+ f.puts @components.pretty_inspect
+ end
+ end
+
+ if @options[:status_text] != '/dev/null'
+ File.open(@options[:status_text], 'w') do |f|
+ f.puts ""
+ f.puts "#{Time.now} -- pipeline_instance #{@instance[:uuid]}"
+ namewidth = @components.collect { |cname, c| cname.size }.max
+ @components.each do |cname, c|
+ jstatus = if !c[:job]
+ "-"
+ else case c[:job][:state]
+ when "Running"
+ "#{c[:job][:tasks_summary].inspect}"
+ when "Complete"
+ c[:job][:output]
+ when "Cancelled"
+ "cancelled #{c[:job][:cancelled_at]}"
+ when "Failed"
+ "failed #{c[:job][:finished_at]}"
+ when "Queued"
+ "queued #{c[:job][:created_at]}"
+ end
+ end
+ f.puts "#{cname.to_s.ljust namewidth} #{c[:job] ? c[:job][:uuid] : '-'.ljust(27)} #{jstatus}"
+ end
+ end
+ end
+ end
+
+ def abort(msg)
+ if @instance
+ if ["New", "Ready", "RunningOnClient",
+ "RunningOnServer"].include?(@instance[:state])
+ @instance[:state] = "Failed"
+ @instance[:finished_at] = Time.now
+ @instance.save
+ end
+ @instance.log_stderr(msg)
+ end
+ Kernel::abort(msg)
+ end
+end
+
+runner = WhRunPipelineInstance.new($options)
+begin
+ if $options[:template]
+ runner.fetch_template($options[:template])
+ else
+ runner.fetch_instance($options[:instance])
+ end
+ runner.apply_parameters(p.leftovers)
+ runner.setup_instance
+ if $options[:submit]
+ runner.instance.save
+ puts runner.instance[:uuid]
+ else
+ runner.run
+ end
+rescue Exception => e
+ runner.cleanup
+ raise e
+end
--- /dev/null
+#! /usr/bin/env ruby
+
+# arv tag usage:
+# arv tag add tag1 [tag2 ...] --object obj_uuid1 [--object obj_uuid2 ...]
+# arv tag remove tag1 [tag2 ...] --object obj_uuid1 [--object obj_uuid2 ...]
+# arv tag remove tag1 [tag2 ...] --all
+
+def usage_string
+ return "\nUsage:\n" +
+ "arv tag add tag1 [tag2 ...] --object object_uuid1 [object_uuid2...]\n" +
+ "arv tag remove tag1 [tag2 ...] --object object_uuid1 [object_uuid2...]\n" +
+ "arv tag remove --all\n"
+end
+
+def usage
+ abort usage_string
+end
+
+def api_call(method, parameters:{}, request_body:{})
+ request_body[:api_token] = ENV['ARVADOS_API_TOKEN']
+ result = $client.execute(:api_method => method,
+ :parameters => parameters,
+ :body_object => request_body,
+ :authenticated => false)
+
+ begin
+ results = JSON.parse result.body
+ rescue JSON::ParserError => e
+ abort "Failed to parse server response:\n" + e.to_s
+ end
+
+ if results["errors"]
+ abort "Error: #{results["errors"][0]}"
+ end
+
+ return results
+end
+
+def tag_add(tag, obj_uuid)
+ return api_call($arvados.links.create,
+ request_body: {
+ :link => {
+ :name => tag,
+ :link_class => :tag,
+ :head_uuid => obj_uuid,
+ }
+ })
+end
+
+def tag_remove(tag, obj_uuids=nil)
+ # If we got a list of objects to untag, look up the uuids for the
+ # links that need to be deleted.
+ link_uuids = []
+ if obj_uuids
+ obj_uuids.each do |uuid|
+ link = api_call($arvados.links.list,
+ request_body: {
+ :where => {
+ :link_class => :tag,
+ :name => tag,
+ :head_uuid => uuid,
+ }
+ })
+ if link['items_available'] > 0
+ link_uuids.push link['items'][0]['uuid']
+ end
+ end
+ else
+ all_tag_links = api_call($arvados.links.list,
+ request_body: {
+ :where => {
+ :link_class => :tag,
+ :name => tag,
+ }
+ })
+ link_uuids = all_tag_links['items'].map { |obj| obj['uuid'] }
+ end
+
+ results = []
+ if link_uuids
+ link_uuids.each do |uuid|
+ results.push api_call($arvados.links.delete, parameters:{ :uuid => uuid })
+ end
+ else
+ $stderr.puts "no tags found to remove"
+ end
+
+ return results
+end
+
+if RUBY_VERSION < '1.9.3' then
+ abort <<-EOS
+#{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher.
+EOS
+end
+
+$arvados_api_version = ENV['ARVADOS_API_VERSION'] || 'v1'
+$arvados_api_host = ENV['ARVADOS_API_HOST'] or
+ abort "#{$0}: fatal: ARVADOS_API_HOST environment variable not set."
+$arvados_api_token = ENV['ARVADOS_API_TOKEN'] or
+ abort "#{$0}: fatal: ARVADOS_API_TOKEN environment variable not set."
+$arvados_api_host_insecure = ENV['ARVADOS_API_HOST_INSECURE'] == 'yes'
+
+begin
+ require 'rubygems'
+ require 'google/api_client'
+ require 'json'
+ require 'pp'
+ require 'oj'
+ require 'trollop'
+rescue LoadError
+ abort <<-EOS
+#{$0}: fatal: some runtime dependencies are missing.
+Try: gem install pp google-api-client json trollop
+ EOS
+end
+
+def debuglog(message, verbosity=1)
+ $stderr.puts "#{File.split($0).last} #{$$}: #{message}" if $debuglevel >= verbosity
+end
+
+module Kernel
+ def suppress_warnings
+ original_verbosity = $VERBOSE
+ $VERBOSE = nil
+ result = yield
+ $VERBOSE = original_verbosity
+ return result
+ end
+end
+
+if $arvados_api_host_insecure or $arvados_api_host.match /local/
+ # You probably don't care about SSL certificate checks if you're
+ # testing with a dev server.
+ suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
+end
+
+class Google::APIClient
+ def discovery_document(api, version)
+ api = api.to_s
+ return @discovery_documents["#{api}:#{version}"] ||=
+ begin
+ response = self.execute!(
+ :http_method => :get,
+ :uri => self.discovery_uri(api, version),
+ :authenticated => false
+ )
+ response.body.class == String ? JSON.parse(response.body) : response.body
+ end
+ end
+end
+
+global_opts = Trollop::options do
+ banner usage_string
+ banner ""
+ opt :dry_run, "Don't actually do anything", :short => "-n"
+ opt :verbose, "Print some things on stderr", :short => "-v"
+ opt :uuid, "Return the UUIDs of the objects in the response, one per line (default)", :short => nil
+ opt :json, "Return the entire response received from the API server, as a JSON object", :short => "-j"
+ opt :human, "Return the response received from the API server, as a JSON object with whitespace added for human consumption", :short => "-h"
+ opt :pretty, "Synonym of --human", :short => nil
+ opt :yaml, "Return the response received from the API server, in YAML format", :short => "-y"
+ stop_on ['add', 'remove']
+end
+
+p = Trollop::Parser.new do
+ opt(:all,
+ "Remove this tag from all objects under your ownership. Only valid with `tag remove'.",
+ :short => :none)
+ opt(:object,
+ "The UUID of an object to which this tag operation should be applied.",
+ :type => :string,
+ :multi => true,
+ :short => :o)
+end
+
+$options = Trollop::with_standard_exception_handling p do
+ p.parse ARGV
+end
+
+if $options[:all] and ARGV[0] != 'remove'
+ usage
+end
+
+# Set up the API client.
+
+$client ||= Google::APIClient.
+ new(:host => $arvados_api_host,
+ :application_name => File.split($0).last,
+ :application_version => $application_version.to_s)
+$arvados = $client.discovered_api('arvados', $arvados_api_version)
+
+results = []
+cmd = ARGV.shift
+
+if ARGV.empty?
+ usage
+end
+
+case cmd
+when 'add'
+ ARGV.each do |tag|
+ $options[:object].each do |obj|
+ results.push(tag_add(tag, obj))
+ end
+ end
+when 'remove'
+ ARGV.each do |tag|
+ if $options[:all] then
+ results.concat tag_remove(tag)
+ else
+ results.concat tag_remove(tag, $options[:object])
+ end
+ end
+else
+ usage
+end
+
+if global_opts[:human] or global_opts[:pretty] then
+ puts Oj.dump(results, :indent => 1)
+elsif global_opts[:yaml] then
+ puts results.to_yaml
+elsif global_opts[:json] then
+ puts Oj.dump(results)
+else
+ results.each do |r|
+ if r['uuid'].nil?
+ abort("Response did not include a uuid:\n" +
+ Oj.dump(r, :indent => 1) +
+ "\n")
+ else
+ puts r['uuid']
+ end
+ end
+end
--- /dev/null
+../../python/bin/arv-ws
\ No newline at end of file
--- /dev/null
+#!/usr/bin/perl
+# -*- mode: perl; perl-indent-level: 2; indent-tabs-mode: nil; -*-
+
+=head1 NAME
+
+crunch-job: Execute job steps, save snapshots as requested, collate output.
+
+=head1 SYNOPSIS
+
+Obtain job details from Arvados, run tasks on compute nodes (typically
+invoked by scheduler on controller):
+
+ crunch-job --job x-y-z --git-dir /path/to/repo/.git
+
+Obtain job details from command line, run tasks on local machine
+(typically invoked by application or developer on VM):
+
+ crunch-job --job '{"script_version":"/path/to/working/tree","script":"scriptname",...}'
+
+ crunch-job --job '{"repository":"https://github.com/curoverse/arvados.git","script_version":"master","script":"scriptname",...}'
+
+=head1 OPTIONS
+
+=over
+
+=item --force-unlock
+
+If the job is already locked, steal the lock and run it anyway.
+
+=item --git-dir
+
+Path to a .git directory (or a git URL) where the commit given in the
+job's C<script_version> attribute is to be found. If this is I<not>
+given, the job's C<repository> attribute will be used.
+
+=item --job-api-token
+
+Arvados API authorization token to use during the course of the job.
+
+=item --no-clear-tmp
+
+Do not clear per-job/task temporary directories during initial job
+setup. This can speed up development and debugging when running jobs
+locally.
+
+=item --job
+
+UUID of the job to run, or a JSON-encoded job resource without a
+UUID. If the latter is given, a new job object will be created.
+
+=back
+
+=head1 RUNNING JOBS LOCALLY
+
+crunch-job's log messages appear on stderr along with the job tasks'
+stderr streams. The log is saved in Keep at each checkpoint and when
+the job finishes.
+
+If the job succeeds, the job's output locator is printed on stdout.
+
+While the job is running, the following signals are accepted:
+
+=over
+
+=item control-C, SIGINT, SIGQUIT
+
+Save a checkpoint, terminate any job tasks that are running, and stop.
+
+=item SIGALRM
+
+Save a checkpoint and continue.
+
+=item SIGHUP
+
+Refresh node allocation (i.e., check whether any nodes have been added
+or unallocated) and attributes of the Job record that should affect
+behavior (e.g., cancel job if cancelled_at becomes non-nil).
+
+=back
+
+=cut
+
+
+use strict;
+use POSIX ':sys_wait_h';
+use POSIX qw(strftime);
+use Fcntl qw(F_GETFL F_SETFL O_NONBLOCK);
+use Arvados;
+use Cwd qw(realpath);
+use Data::Dumper;
+use Digest::MD5 qw(md5_hex);
+use Getopt::Long;
+use IPC::Open2;
+use IO::Select;
+use File::Temp;
+use Fcntl ':flock';
+use File::Path qw( make_path remove_tree );
+
+use constant EX_TEMPFAIL => 75;
+
+$ENV{"TMPDIR"} ||= "/tmp";
+unless (defined $ENV{"CRUNCH_TMP"}) {
+ $ENV{"CRUNCH_TMP"} = $ENV{"TMPDIR"} . "/crunch-job";
+ if ($ENV{"USER"} ne "crunch" && $< != 0) {
+ # use a tmp dir unique for my uid
+ $ENV{"CRUNCH_TMP"} .= "-$<";
+ }
+}
+
+# Create the tmp directory if it does not exist
+if ( ! -d $ENV{"CRUNCH_TMP"} ) {
+ make_path $ENV{"CRUNCH_TMP"} or die "Failed to create temporary working directory: " . $ENV{"CRUNCH_TMP"};
+}
+
+$ENV{"JOB_WORK"} = $ENV{"CRUNCH_TMP"} . "/work";
+$ENV{"CRUNCH_INSTALL"} = "$ENV{CRUNCH_TMP}/opt";
+$ENV{"CRUNCH_WORK"} = $ENV{"JOB_WORK"}; # deprecated
+mkdir ($ENV{"JOB_WORK"});
+
+my $force_unlock;
+my $git_dir;
+my $jobspec;
+my $job_api_token;
+my $no_clear_tmp;
+my $resume_stash;
+GetOptions('force-unlock' => \$force_unlock,
+ 'git-dir=s' => \$git_dir,
+ 'job=s' => \$jobspec,
+ 'job-api-token=s' => \$job_api_token,
+ 'no-clear-tmp' => \$no_clear_tmp,
+ 'resume-stash=s' => \$resume_stash,
+ );
+
+if (defined $job_api_token) {
+ $ENV{ARVADOS_API_TOKEN} = $job_api_token;
+}
+
+my $have_slurm = exists $ENV{SLURM_JOBID} && exists $ENV{SLURM_NODELIST};
+my $local_job = 0;
+
+
+$SIG{'USR1'} = sub
+{
+ $main::ENV{CRUNCH_DEBUG} = 1;
+};
+$SIG{'USR2'} = sub
+{
+ $main::ENV{CRUNCH_DEBUG} = 0;
+};
+
+
+
+my $arv = Arvados->new('apiVersion' => 'v1');
+
+my $Job;
+my $job_id;
+my $dbh;
+my $sth;
+my @jobstep;
+
+my $User = api_call("users/current");
+
+if ($jobspec =~ /^[-a-z\d]+$/)
+{
+ # $jobspec is an Arvados UUID, not a JSON job specification
+ $Job = api_call("jobs/get", uuid => $jobspec);
+ if (!$force_unlock) {
+ # Claim this job, and make sure nobody else does
+ eval { api_call("jobs/lock", uuid => $Job->{uuid}); };
+ if ($@) {
+ Log(undef, "Error while locking job, exiting ".EX_TEMPFAIL);
+ exit EX_TEMPFAIL;
+ };
+ }
+}
+else
+{
+ $Job = JSON::decode_json($jobspec);
+
+ if (!$resume_stash)
+ {
+ map { croak ("No $_ specified") unless $Job->{$_} }
+ qw(script script_version script_parameters);
+ }
+
+ $Job->{'is_locked_by_uuid'} = $User->{'uuid'};
+ $Job->{'started_at'} = gmtime;
+ $Job->{'state'} = 'Running';
+
+ $Job = api_call("jobs/create", job => $Job);
+}
+$job_id = $Job->{'uuid'};
+
+my $keep_logfile = $job_id . '.log.txt';
+log_writer_start($keep_logfile);
+
+$Job->{'runtime_constraints'} ||= {};
+$Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0;
+my $max_ncpus = $Job->{'runtime_constraints'}->{'max_tasks_per_node'};
+
+my $gem_versions = `gem list --quiet arvados-cli 2>/dev/null`;
+if ($? == 0) {
+ $gem_versions =~ s/^arvados-cli \(/ with arvados-cli Gem version(s) /;
+ chomp($gem_versions);
+ chop($gem_versions); # Closing parentheses
+} else {
+ $gem_versions = "";
+}
+Log(undef,
+ "running from " . ((-e $0) ? realpath($0) : "stdin") . $gem_versions);
+
+Log (undef, "check slurm allocation");
+my @slot;
+my @node;
+# Should use $ENV{SLURM_TASKS_PER_NODE} instead of sinfo? (eg. "4(x3),2,4(x2)")
+my @sinfo;
+if (!$have_slurm)
+{
+ my $localcpus = 0 + `grep -cw ^processor /proc/cpuinfo` || 1;
+ push @sinfo, "$localcpus localhost";
+}
+if (exists $ENV{SLURM_NODELIST})
+{
+ push @sinfo, `sinfo -h --format='%c %N' --nodes=\Q$ENV{SLURM_NODELIST}\E`;
+}
+foreach (@sinfo)
+{
+ my ($ncpus, $slurm_nodelist) = split;
+ $ncpus = $max_ncpus if $max_ncpus && $ncpus > $max_ncpus;
+
+ my @nodelist;
+ while ($slurm_nodelist =~ s/^([^\[,]+?(\[.*?\])?)(,|$)//)
+ {
+ my $nodelist = $1;
+ if ($nodelist =~ /\[((\d+)(-(\d+))?(,(\d+)(-(\d+))?)*)\]/)
+ {
+ my $ranges = $1;
+ foreach (split (",", $ranges))
+ {
+ my ($a, $b);
+ if (/(\d+)-(\d+)/)
+ {
+ $a = $1;
+ $b = $2;
+ }
+ else
+ {
+ $a = $_;
+ $b = $_;
+ }
+ push @nodelist, map {
+ my $n = $nodelist;
+ $n =~ s/\[[-,\d]+\]/$_/;
+ $n;
+ } ($a..$b);
+ }
+ }
+ else
+ {
+ push @nodelist, $nodelist;
+ }
+ }
+ foreach my $nodename (@nodelist)
+ {
+ Log (undef, "node $nodename - $ncpus slots");
+ my $node = { name => $nodename,
+ ncpus => $ncpus,
+ losing_streak => 0,
+ hold_until => 0 };
+ foreach my $cpu (1..$ncpus)
+ {
+ push @slot, { node => $node,
+ cpu => $cpu };
+ }
+ }
+ push @node, @nodelist;
+}
+
+
+
+# Ensure that we get one jobstep running on each allocated node before
+# we start overloading nodes with concurrent steps
+
+@slot = sort { $a->{cpu} <=> $b->{cpu} } @slot;
+
+
+$Job->update_attributes(
+ 'tasks_summary' => { 'failed' => 0,
+ 'todo' => 1,
+ 'running' => 0,
+ 'done' => 0 });
+
+Log (undef, "start");
+$SIG{'INT'} = sub { $main::please_freeze = 1; };
+$SIG{'QUIT'} = sub { $main::please_freeze = 1; };
+$SIG{'TERM'} = \&croak;
+$SIG{'TSTP'} = sub { $main::please_freeze = 1; };
+$SIG{'ALRM'} = sub { $main::please_info = 1; };
+$SIG{'CONT'} = sub { $main::please_continue = 1; };
+$SIG{'HUP'} = sub { $main::please_refresh = 1; };
+
+$main::please_freeze = 0;
+$main::please_info = 0;
+$main::please_continue = 0;
+$main::please_refresh = 0;
+my $jobsteps_must_output_keys = 0; # becomes 1 when any task outputs a key
+
+grep { $ENV{$1} = $2 if /^(NOCACHE.*?)=(.*)/ } split ("\n", $$Job{knobs});
+$ENV{"CRUNCH_JOB_UUID"} = $job_id;
+$ENV{"JOB_UUID"} = $job_id;
+
+
+my @jobstep_todo = ();
+my @jobstep_done = ();
+my @jobstep_tomerge = ();
+my $jobstep_tomerge_level = 0;
+my $squeue_checked;
+my $squeue_kill_checked;
+my $latest_refresh = scalar time;
+
+
+
+if (defined $Job->{thawedfromkey})
+{
+ thaw ($Job->{thawedfromkey});
+}
+else
+{
+ my $first_task = api_call("job_tasks/create", job_task => {
+ 'job_uuid' => $Job->{'uuid'},
+ 'sequence' => 0,
+ 'qsequence' => 0,
+ 'parameters' => {},
+ });
+ push @jobstep, { 'level' => 0,
+ 'failures' => 0,
+ 'arvados_task' => $first_task,
+ };
+ push @jobstep_todo, 0;
+}
+
+
+if (!$have_slurm)
+{
+ must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
+}
+
+my $build_script = handle_readall(\*DATA);
+my $nodelist = join(",", @node);
+my $git_tar_count = 0;
+
+if (!defined $no_clear_tmp) {
+ # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src*
+ Log (undef, "Clean work dirs");
+
+ my $cleanpid = fork();
+ if ($cleanpid == 0)
+ {
+ srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
+ ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then for i in $JOB_WORK/*keep $CRUNCH_TMP/task/*.keep; do /bin/fusermount -z -u $i; done; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_INSTALL $CRUNCH_TMP/task $CRUNCH_TMP/src*']);
+ exit (1);
+ }
+ while (1)
+ {
+ last if $cleanpid == waitpid (-1, WNOHANG);
+ freeze_if_want_freeze ($cleanpid);
+ select (undef, undef, undef, 0.1);
+ }
+ Log (undef, "Cleanup command exited ".exit_status_s($?));
+}
+
+# If this job requires a Docker image, install that.
+my $docker_bin = "/usr/bin/docker.io";
+my ($docker_locator, $docker_stream, $docker_hash);
+if ($docker_locator = $Job->{docker_image_locator}) {
+ ($docker_stream, $docker_hash) = find_docker_image($docker_locator);
+ if (!$docker_hash)
+ {
+ croak("No Docker image hash found from locator $docker_locator");
+ }
+ $docker_stream =~ s/^\.//;
+ my $docker_install_script = qq{
+if ! $docker_bin images -q --no-trunc | grep -qxF \Q$docker_hash\E; then
+ arv-get \Q$docker_locator$docker_stream/$docker_hash.tar\E | $docker_bin load
+fi
+};
+ my $docker_pid = fork();
+ if ($docker_pid == 0)
+ {
+ srun (["srun", "--nodelist=" . join(',', @node)],
+ ["/bin/sh", "-ec", $docker_install_script]);
+ exit ($?);
+ }
+ while (1)
+ {
+ last if $docker_pid == waitpid (-1, WNOHANG);
+ freeze_if_want_freeze ($docker_pid);
+ select (undef, undef, undef, 0.1);
+ }
+ if ($? != 0)
+ {
+ croak("Installing Docker image from $docker_locator exited "
+ .exit_status_s($?));
+ }
+
+ if ($Job->{arvados_sdk_version}) {
+ # The job also specifies an Arvados SDK version. Add the SDKs to the
+ # tar file for the build script to install.
+ Log(undef, sprintf("Packing Arvados SDK version %s for installation",
+ $Job->{arvados_sdk_version}));
+ add_git_archive("git", "--git-dir=$git_dir", "archive",
+ "--prefix=.arvados.sdk/",
+ $Job->{arvados_sdk_version}, "sdk");
+ }
+}
+
+if (!defined $git_dir && $Job->{'script_version'} =~ m{^/}) {
+ # If script_version looks like an absolute path, *and* the --git-dir
+ # argument was not given -- which implies we were not invoked by
+ # crunch-dispatch -- we will use the given path as a working
+ # directory instead of resolving script_version to a git commit (or
+ # doing anything else with git).
+ $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{'script_version'};
+ $ENV{"CRUNCH_SRC"} = $Job->{'script_version'};
+}
+else {
+ # Resolve the given script_version to a git commit sha1. Also, if
+ # the repository is remote, clone it into our local filesystem: this
+ # ensures "git archive" will work, and is necessary to reliably
+ # resolve a symbolic script_version like "master^".
+ $ENV{"CRUNCH_SRC"} = "$ENV{CRUNCH_TMP}/src";
+
+ Log (undef, "Looking for version ".$Job->{script_version}." from repository ".$Job->{repository});
+
+ $ENV{"CRUNCH_SRC_COMMIT"} = $Job->{script_version};
+
+ # If we're running under crunch-dispatch, it will have already
+ # pulled the appropriate source tree into its own repository, and
+ # given us that repo's path as $git_dir.
+ #
+ # If we're running a "local" job, we might have to fetch content
+ # from a remote repository.
+ #
+ # (Currently crunch-dispatch gives a local path with --git-dir, but
+ # we might as well accept URLs there too in case it changes its
+ # mind.)
+ my $repo = $git_dir || $Job->{'repository'};
+
+ # Repository can be remote or local. If remote, we'll need to fetch it
+ # to a local dir before doing `git log` et al.
+ my $repo_location;
+
+ if ($repo =~ m{://|^[^/]*:}) {
+ # $repo is a git url we can clone, like git:// or https:// or
+ # file:/// or [user@]host:repo.git. Note "user/name@host:foo" is
+ # not recognized here because distinguishing that from a local
+ # path is too fragile. If you really need something strange here,
+ # use the ssh:// form.
+ $repo_location = 'remote';
+ } elsif ($repo =~ m{^\.*/}) {
+ # $repo is a local path to a git index. We'll also resolve ../foo
+ # to ../foo/.git if the latter is a directory. To help
+ # disambiguate local paths from named hosted repositories, this
+ # form must be given as ./ or ../ if it's a relative path.
+ if (-d "$repo/.git") {
+ $repo = "$repo/.git";
+ }
+ $repo_location = 'local';
+ } else {
+ # $repo is none of the above. It must be the name of a hosted
+ # repository.
+ my $arv_repo_list = api_call("repositories/list",
+ 'filters' => [['name','=',$repo]]);
+ my @repos_found = @{$arv_repo_list->{'items'}};
+ my $n_found = $arv_repo_list->{'serverResponse'}->{'items_available'};
+ if ($n_found > 0) {
+ Log(undef, "Repository '$repo' -> "
+ . join(", ", map { $_->{'uuid'} } @repos_found));
+ }
+ if ($n_found != 1) {
+ croak("Error: Found $n_found repositories with name '$repo'.");
+ }
+ $repo = $repos_found[0]->{'fetch_url'};
+ $repo_location = 'remote';
+ }
+ Log(undef, "Using $repo_location repository '$repo'");
+ $ENV{"CRUNCH_SRC_URL"} = $repo;
+
+ # Resolve given script_version (we'll call that $treeish here) to a
+ # commit sha1 ($commit).
+ my $treeish = $Job->{'script_version'};
+ my $commit;
+ if ($repo_location eq 'remote') {
+ # We minimize excess object-fetching by re-using the same bare
+ # repository in CRUNCH_TMP/.git for multiple crunch-jobs -- we
+ # just keep adding remotes to it as needed.
+ my $local_repo = $ENV{'CRUNCH_TMP'}."/.git";
+ my $gitcmd = "git --git-dir=\Q$local_repo\E";
+
+ # Set up our local repo for caching remote objects, making
+ # archives, etc.
+ if (!-d $local_repo) {
+ make_path($local_repo) or croak("Error: could not create $local_repo");
+ }
+ # This works (exits 0 and doesn't delete fetched objects) even
+ # if $local_repo is already initialized:
+ `$gitcmd init --bare`;
+ if ($?) {
+ croak("Error: $gitcmd init --bare exited ".exit_status_s($?));
+ }
+
+ # If $treeish looks like a hash (or abbrev hash) we look it up in
+ # our local cache first, since that's cheaper. (We don't want to
+ # do that with tags/branches though -- those change over time, so
+ # they should always be resolved by the remote repo.)
+ if ($treeish =~ /^[0-9a-f]{7,40}$/s) {
+ # Hide stderr because it's normal for this to fail:
+ my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E 2>/dev/null`;
+ if ($? == 0 &&
+ # Careful not to resolve a branch named abcdeff to commit 1234567:
+ $sha1 =~ /^$treeish/ &&
+ $sha1 =~ /^([0-9a-f]{40})$/s) {
+ $commit = $1;
+ Log(undef, "Commit $commit already present in $local_repo");
+ }
+ }
+
+ if (!defined $commit) {
+ # If $treeish isn't just a hash or abbrev hash, or isn't here
+ # yet, we need to fetch the remote to resolve it correctly.
+
+ # First, remove all local heads. This prevents a name that does
+ # not exist on the remote from resolving to (or colliding with)
+ # a previously fetched branch or tag (possibly from a different
+ # remote).
+ remove_tree("$local_repo/refs/heads", {keep_root => 1});
+
+ Log(undef, "Fetching objects from $repo to $local_repo");
+ `$gitcmd fetch --no-progress --tags ''\Q$repo\E \Q+refs/heads/*:refs/heads/*\E`;
+ if ($?) {
+ croak("Error: `$gitcmd fetch` exited ".exit_status_s($?));
+ }
+ }
+
+ # Now that the data is all here, we will use our local repo for
+ # the rest of our git activities.
+ $repo = $local_repo;
+ }
+
+ my $gitcmd = "git --git-dir=\Q$repo\E";
+ my $sha1 = `$gitcmd rev-list -n1 ''\Q$treeish\E`;
+ unless ($? == 0 && $sha1 =~ /^([0-9a-f]{40})$/) {
+ croak("`$gitcmd rev-list` exited "
+ .exit_status_s($?)
+ .", '$treeish' not found. Giving up.");
+ }
+ $commit = $1;
+ Log(undef, "Version $treeish is commit $commit");
+
+ if ($commit ne $Job->{'script_version'}) {
+ # Record the real commit id in the database, frozentokey, logs,
+ # etc. -- instead of an abbreviation or a branch name which can
+ # become ambiguous or point to a different commit in the future.
+ if (!$Job->update_attributes('script_version' => $commit)) {
+ croak("Error: failed to update job's script_version attribute");
+ }
+ }
+
+ $ENV{"CRUNCH_SRC_COMMIT"} = $commit;
+ add_git_archive("$gitcmd archive ''\Q$commit\E");
+}
+
+my $git_archive = combined_git_archive();
+if (!defined $git_archive) {
+ Log(undef, "Skip install phase (no git archive)");
+ if ($have_slurm) {
+ Log(undef, "Warning: This probably means workers have no source tree!");
+ }
+}
+else {
+ Log(undef, "Run install script on all workers");
+
+ my @srunargs = ("srun",
+ "--nodelist=$nodelist",
+ "-D", $ENV{'TMPDIR'}, "--job-name=$job_id");
+ my @execargs = ("sh", "-c",
+ "mkdir -p $ENV{CRUNCH_INSTALL} && cd $ENV{CRUNCH_TMP} && perl -");
+
+ my $installpid = fork();
+ if ($installpid == 0)
+ {
+ srun (\@srunargs, \@execargs, {}, $build_script . $git_archive);
+ exit (1);
+ }
+ while (1)
+ {
+ last if $installpid == waitpid (-1, WNOHANG);
+ freeze_if_want_freeze ($installpid);
+ select (undef, undef, undef, 0.1);
+ }
+ my $install_exited = $?;
+ Log (undef, "Install script exited ".exit_status_s($install_exited));
+ foreach my $tar_filename (map { tar_filename_n($_); } (1..$git_tar_count)) {
+ unlink($tar_filename);
+ }
+ exit (1) if $install_exited != 0;
+}
+
+foreach (qw (script script_version script_parameters runtime_constraints))
+{
+ Log (undef,
+ "$_ " .
+ (ref($Job->{$_}) ? JSON::encode_json($Job->{$_}) : $Job->{$_}));
+}
+foreach (split (/\n/, $Job->{knobs}))
+{
+ Log (undef, "knob " . $_);
+}
+
+
+
+$main::success = undef;
+
+
+
+ONELEVEL:
+
+my $thisround_succeeded = 0;
+my $thisround_failed = 0;
+my $thisround_failed_multiple = 0;
+
+@jobstep_todo = sort { $jobstep[$a]->{level} <=> $jobstep[$b]->{level}
+ or $a <=> $b } @jobstep_todo;
+my $level = $jobstep[$jobstep_todo[0]]->{level};
+Log (undef, "start level $level");
+
+
+
+my %proc;
+my @freeslot = (0..$#slot);
+my @holdslot;
+my %reader;
+my $progress_is_dirty = 1;
+my $progress_stats_updated = 0;
+
+update_progress_stats();
+
+
+
+THISROUND:
+for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
+{
+ my $id = $jobstep_todo[$todo_ptr];
+ my $Jobstep = $jobstep[$id];
+ if ($Jobstep->{level} != $level)
+ {
+ next;
+ }
+
+ pipe $reader{$id}, "writer" or croak ($!);
+ my $flags = fcntl ($reader{$id}, F_GETFL, 0) or croak ($!);
+ fcntl ($reader{$id}, F_SETFL, $flags | O_NONBLOCK) or croak ($!);
+
+ my $childslot = $freeslot[0];
+ my $childnode = $slot[$childslot]->{node};
+ my $childslotname = join (".",
+ $slot[$childslot]->{node}->{name},
+ $slot[$childslot]->{cpu});
+ my $childpid = fork();
+ if ($childpid == 0)
+ {
+ $SIG{'INT'} = 'DEFAULT';
+ $SIG{'QUIT'} = 'DEFAULT';
+ $SIG{'TERM'} = 'DEFAULT';
+
+ foreach (values (%reader))
+ {
+ close($_);
+ }
+ fcntl ("writer", F_SETFL, 0) or croak ($!); # no close-on-exec
+ open(STDOUT,">&writer");
+ open(STDERR,">&writer");
+
+ undef $dbh;
+ undef $sth;
+
+ delete $ENV{"GNUPGHOME"};
+ $ENV{"TASK_UUID"} = $Jobstep->{'arvados_task'}->{'uuid'};
+ $ENV{"TASK_QSEQUENCE"} = $id;
+ $ENV{"TASK_SEQUENCE"} = $level;
+ $ENV{"JOB_SCRIPT"} = $Job->{script};
+ while (my ($param, $value) = each %{$Job->{script_parameters}}) {
+ $param =~ tr/a-z/A-Z/;
+ $ENV{"JOB_PARAMETER_$param"} = $value;
+ }
+ $ENV{"TASK_SLOT_NODE"} = $slot[$childslot]->{node}->{name};
+ $ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
+ $ENV{"TASK_WORK"} = $ENV{"CRUNCH_TMP"}."/task/$childslotname";
+ $ENV{"HOME"} = $ENV{"TASK_WORK"};
+ $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}.".keep";
+ $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
+ $ENV{"CRUNCH_NODE_SLOTS"} = $slot[$childslot]->{node}->{ncpus};
+ $ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"};
+
+ $ENV{"GZIP"} = "-n";
+
+ my @srunargs = (
+ "srun",
+ "--nodelist=".$childnode->{name},
+ qw(-n1 -c1 -N1 -D), $ENV{'TMPDIR'},
+ "--job-name=$job_id.$id.$$",
+ );
+ my $command =
+ "if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
+ ."mkdir -p $ENV{CRUNCH_TMP} $ENV{JOB_WORK} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "
+ ."&& cd $ENV{CRUNCH_TMP} ";
+ $command .= "&& exec arv-mount --by-id --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
+ if ($docker_hash)
+ {
+ my $cidfile = "$ENV{CRUNCH_TMP}/$ENV{TASK_UUID}.cid";
+ $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$cidfile -poll=10000 ";
+ $command .= "$docker_bin run --rm=true --attach=stdout --attach=stderr --attach=stdin -i --user=crunch --cidfile=$cidfile --sig-proxy ";
+
+ # Dynamically configure the container to use the host system as its
+ # DNS server. Get the host's global addresses from the ip command,
+ # and turn them into docker --dns options using gawk.
+ $command .=
+ q{$(ip -o address show scope global |
+ gawk 'match($4, /^([0-9\.:]+)\//, x){print "--dns", x[1]}') };
+
+ # The source tree and $destdir directory (which we have
+ # installed on the worker host) are available in the container,
+ # under the same path.
+ $command .= "--volume=\Q$ENV{CRUNCH_SRC}:$ENV{CRUNCH_SRC}:ro\E ";
+ $command .= "--volume=\Q$ENV{CRUNCH_INSTALL}:$ENV{CRUNCH_INSTALL}:ro\E ";
+
+ # Currently, we make arv-mount's mount point appear at /keep
+ # inside the container (instead of using the same path as the
+ # host like we do with CRUNCH_SRC and CRUNCH_INSTALL). However,
+ # crunch scripts and utilities must not rely on this. They must
+ # use $TASK_KEEPMOUNT.
+ $command .= "--volume=\Q$ENV{TASK_KEEPMOUNT}:/keep:ro\E ";
+ $ENV{TASK_KEEPMOUNT} = "/keep";
+
+ # TASK_WORK is almost exactly like a docker data volume: it
+ # starts out empty, is writable, and persists until no
+ # containers use it any more. We don't use --volumes-from to
+ # share it with other containers: it is only accessible to this
+ # task, and it goes away when this task stops.
+ #
+ # However, a docker data volume is writable only by root unless
+ # the mount point already happens to exist in the container with
+ # different permissions. Therefore, we [1] assume /tmp already
+ # exists in the image and is writable by the crunch user; [2]
+ # avoid putting TASK_WORK inside CRUNCH_TMP (which won't be
+ # writable if they are created by docker while setting up the
+ # other --volumes); and [3] create $TASK_WORK inside the
+ # container using $build_script.
+ $command .= "--volume=/tmp ";
+ $ENV{"TASK_WORK"} = "/tmp/crunch-job-task-work/$childslotname";
+ $ENV{"HOME"} = $ENV{"TASK_WORK"};
+ $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
+
+ # TODO: Share a single JOB_WORK volume across all task
+ # containers on a given worker node, and delete it when the job
+ # ends (and, in case that doesn't work, when the next job
+ # starts).
+ #
+ # For now, use the same approach as TASK_WORK above.
+ $ENV{"JOB_WORK"} = "/tmp/crunch-job-work";
+
+ while (my ($env_key, $env_val) = each %ENV)
+ {
+ if ($env_key =~ /^(ARVADOS|CRUNCH|JOB|TASK)_/) {
+ $command .= "--env=\Q$env_key=$env_val\E ";
+ }
+ }
+ $command .= "--env=\QHOME=$ENV{HOME}\E ";
+ $command .= "\Q$docker_hash\E ";
+ $command .= "stdbuf --output=0 --error=0 ";
+ $command .= "perl - $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+ } else {
+ # Non-docker run
+ $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 ";
+ $command .= "stdbuf --output=0 --error=0 ";
+ $command .= "perl - $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+ }
+
+ my @execargs = ('bash', '-c', $command);
+ srun (\@srunargs, \@execargs, undef, $build_script);
+ # exec() failed, we assume nothing happened.
+ die "srun() failed on build script\n";
+ }
+ close("writer");
+ if (!defined $childpid)
+ {
+ close $reader{$id};
+ delete $reader{$id};
+ next;
+ }
+ shift @freeslot;
+ $proc{$childpid} = { jobstep => $id,
+ time => time,
+ slot => $childslot,
+ jobstepname => "$job_id.$id.$childpid",
+ };
+ croak ("assert failed: \$slot[$childslot]->{'pid'} exists") if exists $slot[$childslot]->{pid};
+ $slot[$childslot]->{pid} = $childpid;
+
+ Log ($id, "job_task ".$Jobstep->{'arvados_task'}->{'uuid'});
+ Log ($id, "child $childpid started on $childslotname");
+ $Jobstep->{starttime} = time;
+ $Jobstep->{node} = $childnode->{name};
+ $Jobstep->{slotindex} = $childslot;
+ delete $Jobstep->{stderr};
+ delete $Jobstep->{finishtime};
+
+ $Jobstep->{'arvados_task'}->{started_at} = strftime "%Y-%m-%dT%H:%M:%SZ", gmtime($Jobstep->{starttime});
+ $Jobstep->{'arvados_task'}->save;
+
+ splice @jobstep_todo, $todo_ptr, 1;
+ --$todo_ptr;
+
+ $progress_is_dirty = 1;
+
+ while (!@freeslot
+ ||
+ (@slot > @freeslot && $todo_ptr+1 > $#jobstep_todo))
+ {
+ last THISROUND if $main::please_freeze;
+ if ($main::please_info)
+ {
+ $main::please_info = 0;
+ freeze();
+ create_output_collection();
+ save_meta(1);
+ update_progress_stats();
+ }
+ my $gotsome
+ = readfrompipes ()
+ + reapchildren ();
+ if (!$gotsome)
+ {
+ check_refresh_wanted();
+ check_squeue();
+ update_progress_stats();
+ select (undef, undef, undef, 0.1);
+ }
+ elsif (time - $progress_stats_updated >= 30)
+ {
+ update_progress_stats();
+ }
+ if (($thisround_failed_multiple >= 8 && $thisround_succeeded == 0) ||
+ ($thisround_failed_multiple >= 16 && $thisround_failed_multiple > $thisround_succeeded))
+ {
+ my $message = "Repeated failure rate too high ($thisround_failed_multiple/"
+ .($thisround_failed+$thisround_succeeded)
+ .") -- giving up on this round";
+ Log (undef, $message);
+ last THISROUND;
+ }
+
+ # move slots from freeslot to holdslot (or back to freeslot) if necessary
+ for (my $i=$#freeslot; $i>=0; $i--) {
+ if ($slot[$freeslot[$i]]->{node}->{hold_until} > scalar time) {
+ push @holdslot, (splice @freeslot, $i, 1);
+ }
+ }
+ for (my $i=$#holdslot; $i>=0; $i--) {
+ if ($slot[$holdslot[$i]]->{node}->{hold_until} <= scalar time) {
+ push @freeslot, (splice @holdslot, $i, 1);
+ }
+ }
+
+ # give up if no nodes are succeeding
+ if (!grep { $_->{node}->{losing_streak} == 0 &&
+ $_->{node}->{hold_count} < 4 } @slot) {
+ my $message = "Every node has failed -- giving up on this round";
+ Log (undef, $message);
+ last THISROUND;
+ }
+ }
+}
+
+
+push @freeslot, splice @holdslot;
+map { $slot[$freeslot[$_]]->{node}->{losing_streak} = 0 } (0..$#freeslot);
+
+
+Log (undef, "wait for last ".(scalar keys %proc)." children to finish");
+while (%proc)
+{
+ if ($main::please_continue) {
+ $main::please_continue = 0;
+ goto THISROUND;
+ }
+ $main::please_info = 0, freeze(), create_output_collection(), save_meta(1) if $main::please_info;
+ readfrompipes ();
+ if (!reapchildren())
+ {
+ check_refresh_wanted();
+ check_squeue();
+ update_progress_stats();
+ select (undef, undef, undef, 0.1);
+ killem (keys %proc) if $main::please_freeze;
+ }
+}
+
+update_progress_stats();
+freeze_if_want_freeze();
+
+
+if (!defined $main::success)
+{
+ if (@jobstep_todo &&
+ $thisround_succeeded == 0 &&
+ ($thisround_failed == 0 || $thisround_failed > 4))
+ {
+ my $message = "stop because $thisround_failed tasks failed and none succeeded";
+ Log (undef, $message);
+ $main::success = 0;
+ }
+ if (!@jobstep_todo)
+ {
+ $main::success = 1;
+ }
+}
+
+goto ONELEVEL if !defined $main::success;
+
+
+release_allocation();
+freeze();
+my $collated_output = &create_output_collection();
+
+if (!$collated_output) {
+ Log (undef, "Failed to write output collection");
+}
+else {
+ Log(undef, "output hash " . $collated_output);
+ $Job->update_attributes('output' => $collated_output);
+}
+
+Log (undef, "finish");
+
+save_meta();
+
+my $final_state;
+if ($collated_output && $main::success) {
+ $final_state = 'Complete';
+} else {
+ $final_state = 'Failed';
+}
+$Job->update_attributes('state' => $final_state);
+
+exit (($final_state eq 'Complete') ? 0 : 1);
+
+
+
+sub update_progress_stats
+{
+ $progress_stats_updated = time;
+ return if !$progress_is_dirty;
+ my ($todo, $done, $running) = (scalar @jobstep_todo,
+ scalar @jobstep_done,
+ scalar @slot - scalar @freeslot - scalar @holdslot);
+ $Job->{'tasks_summary'} ||= {};
+ $Job->{'tasks_summary'}->{'todo'} = $todo;
+ $Job->{'tasks_summary'}->{'done'} = $done;
+ $Job->{'tasks_summary'}->{'running'} = $running;
+ $Job->update_attributes('tasks_summary' => $Job->{'tasks_summary'});
+ Log (undef, "status: $done done, $running running, $todo todo");
+ $progress_is_dirty = 0;
+}
+
+
+
+sub reapchildren
+{
+ my $pid = waitpid (-1, WNOHANG);
+ return 0 if $pid <= 0;
+
+ my $whatslot = ($slot[$proc{$pid}->{slot}]->{node}->{name}
+ . "."
+ . $slot[$proc{$pid}->{slot}]->{cpu});
+ my $jobstepid = $proc{$pid}->{jobstep};
+ my $elapsed = time - $proc{$pid}->{time};
+ my $Jobstep = $jobstep[$jobstepid];
+
+ my $childstatus = $?;
+ my $exitvalue = $childstatus >> 8;
+ my $exitinfo = "exit ".exit_status_s($childstatus);
+ $Jobstep->{'arvados_task'}->reload;
+ my $task_success = $Jobstep->{'arvados_task'}->{success};
+
+ Log ($jobstepid, "child $pid on $whatslot $exitinfo success=$task_success");
+
+ if (!defined $task_success) {
+ # task did not indicate one way or the other --> fail
+ $Jobstep->{'arvados_task'}->{success} = 0;
+ $Jobstep->{'arvados_task'}->save;
+ $task_success = 0;
+ }
+
+ if (!$task_success)
+ {
+ my $temporary_fail;
+ $temporary_fail ||= $Jobstep->{node_fail};
+ $temporary_fail ||= ($exitvalue == 111);
+
+ ++$thisround_failed;
+ ++$thisround_failed_multiple if $Jobstep->{'failures'} >= 1;
+
+ # Check for signs of a failed or misconfigured node
+ if (++$slot[$proc{$pid}->{slot}]->{node}->{losing_streak} >=
+ 2+$slot[$proc{$pid}->{slot}]->{node}->{ncpus}) {
+ # Don't count this against jobstep failure thresholds if this
+ # node is already suspected faulty and srun exited quickly
+ if ($slot[$proc{$pid}->{slot}]->{node}->{hold_until} &&
+ $elapsed < 5) {
+ Log ($jobstepid, "blaming failure on suspect node " .
+ $slot[$proc{$pid}->{slot}]->{node}->{name});
+ $temporary_fail ||= 1;
+ }
+ ban_node_by_slot($proc{$pid}->{slot});
+ }
+
+ Log ($jobstepid, sprintf('failure (#%d, %s) after %d seconds',
+ ++$Jobstep->{'failures'},
+ $temporary_fail ? 'temporary ' : 'permanent',
+ $elapsed));
+
+ if (!$temporary_fail || $Jobstep->{'failures'} >= 3) {
+ # Give up on this task, and the whole job
+ $main::success = 0;
+ $main::please_freeze = 1;
+ }
+ # Put this task back on the todo queue
+ push @jobstep_todo, $jobstepid;
+ $Job->{'tasks_summary'}->{'failed'}++;
+ }
+ else
+ {
+ ++$thisround_succeeded;
+ $slot[$proc{$pid}->{slot}]->{node}->{losing_streak} = 0;
+ $slot[$proc{$pid}->{slot}]->{node}->{hold_until} = 0;
+ push @jobstep_done, $jobstepid;
+ Log ($jobstepid, "success in $elapsed seconds");
+ }
+ $Jobstep->{exitcode} = $childstatus;
+ $Jobstep->{finishtime} = time;
+ $Jobstep->{'arvados_task'}->{finished_at} = strftime "%Y-%m-%dT%H:%M:%SZ", gmtime($Jobstep->{finishtime});
+ $Jobstep->{'arvados_task'}->save;
+ process_stderr ($jobstepid, $task_success);
+ Log ($jobstepid, "output " . $Jobstep->{'arvados_task'}->{output});
+
+ close $reader{$jobstepid};
+ delete $reader{$jobstepid};
+ delete $slot[$proc{$pid}->{slot}]->{pid};
+ push @freeslot, $proc{$pid}->{slot};
+ delete $proc{$pid};
+
+ if ($task_success) {
+ # Load new tasks
+ my $newtask_list = [];
+ my $newtask_results;
+ do {
+ $newtask_results = api_call(
+ "job_tasks/list",
+ 'where' => {
+ 'created_by_job_task_uuid' => $Jobstep->{'arvados_task'}->{uuid}
+ },
+ 'order' => 'qsequence',
+ 'offset' => scalar(@$newtask_list),
+ );
+ push(@$newtask_list, @{$newtask_results->{items}});
+ } while (@{$newtask_results->{items}});
+ foreach my $arvados_task (@$newtask_list) {
+ my $jobstep = {
+ 'level' => $arvados_task->{'sequence'},
+ 'failures' => 0,
+ 'arvados_task' => $arvados_task
+ };
+ push @jobstep, $jobstep;
+ push @jobstep_todo, $#jobstep;
+ }
+ }
+
+ $progress_is_dirty = 1;
+ 1;
+}
+
+sub check_refresh_wanted
+{
+ my @stat = stat $ENV{"CRUNCH_REFRESH_TRIGGER"};
+ if (@stat && $stat[9] > $latest_refresh) {
+ $latest_refresh = scalar time;
+ my $Job2 = api_call("jobs/get", uuid => $jobspec);
+ for my $attr ('cancelled_at',
+ 'cancelled_by_user_uuid',
+ 'cancelled_by_client_uuid',
+ 'state') {
+ $Job->{$attr} = $Job2->{$attr};
+ }
+ if ($Job->{'state'} ne "Running") {
+ if ($Job->{'state'} eq "Cancelled") {
+ Log (undef, "Job cancelled at " . $Job->{'cancelled_at'} . " by user " . $Job->{'cancelled_by_user_uuid'});
+ } else {
+ Log (undef, "Job state unexpectedly changed to " . $Job->{'state'});
+ }
+ $main::success = 0;
+ $main::please_freeze = 1;
+ }
+ }
+}
+
+sub check_squeue
+{
+ # return if the kill list was checked <4 seconds ago
+ if (defined $squeue_kill_checked && $squeue_kill_checked > time - 4)
+ {
+ return;
+ }
+ $squeue_kill_checked = time;
+
+ # use killem() on procs whose killtime is reached
+ for (keys %proc)
+ {
+ if (exists $proc{$_}->{killtime}
+ && $proc{$_}->{killtime} <= time)
+ {
+ killem ($_);
+ }
+ }
+
+ # return if the squeue was checked <60 seconds ago
+ if (defined $squeue_checked && $squeue_checked > time - 60)
+ {
+ return;
+ }
+ $squeue_checked = time;
+
+ if (!$have_slurm)
+ {
+ # here is an opportunity to check for mysterious problems with local procs
+ return;
+ }
+
+ # get a list of steps still running
+ my @squeue = `squeue -s -h -o '%i %j' && echo ok`;
+ chop @squeue;
+ if ($squeue[-1] ne "ok")
+ {
+ return;
+ }
+ pop @squeue;
+
+ # which of my jobsteps are running, according to squeue?
+ my %ok;
+ foreach (@squeue)
+ {
+ if (/^(\d+)\.(\d+) (\S+)/)
+ {
+ if ($1 eq $ENV{SLURM_JOBID})
+ {
+ $ok{$3} = 1;
+ }
+ }
+ }
+
+ # which of my active child procs (>60s old) were not mentioned by squeue?
+ foreach (keys %proc)
+ {
+ if ($proc{$_}->{time} < time - 60
+ && !exists $ok{$proc{$_}->{jobstepname}}
+ && !exists $proc{$_}->{killtime})
+ {
+ # kill this proc if it hasn't exited in 30 seconds
+ $proc{$_}->{killtime} = time + 30;
+ }
+ }
+}
+
+
+sub release_allocation
+{
+ if ($have_slurm)
+ {
+ Log (undef, "release job allocation");
+ system "scancel $ENV{SLURM_JOBID}";
+ }
+}
+
+
+sub readfrompipes
+{
+ my $gotsome = 0;
+ foreach my $job (keys %reader)
+ {
+ my $buf;
+ while (0 < sysread ($reader{$job}, $buf, 8192))
+ {
+ print STDERR $buf if $ENV{CRUNCH_DEBUG};
+ $jobstep[$job]->{stderr} .= $buf;
+ preprocess_stderr ($job);
+ if (length ($jobstep[$job]->{stderr}) > 16384)
+ {
+ substr ($jobstep[$job]->{stderr}, 0, 8192) = "";
+ }
+ $gotsome = 1;
+ }
+ }
+ return $gotsome;
+}
+
+
+sub preprocess_stderr
+{
+ my $job = shift;
+
+ while ($jobstep[$job]->{stderr} =~ /^(.*?)\n/) {
+ my $line = $1;
+ substr $jobstep[$job]->{stderr}, 0, 1+length($line), "";
+ Log ($job, "stderr $line");
+ if ($line =~ /srun: error: (SLURM job $ENV{SLURM_JOB_ID} has expired|Unable to confirm allocation for job $ENV{SLURM_JOB_ID})/) {
+ # whoa.
+ $main::please_freeze = 1;
+ }
+ elsif ($line =~ /srun: error: (Node failure on|Unable to create job step) /) {
+ $jobstep[$job]->{node_fail} = 1;
+ ban_node_by_slot($jobstep[$job]->{slotindex});
+ }
+ }
+}
+
+
+sub process_stderr
+{
+ my $job = shift;
+ my $task_success = shift;
+ preprocess_stderr ($job);
+
+ map {
+ Log ($job, "stderr $_");
+ } split ("\n", $jobstep[$job]->{stderr});
+}
+
+sub fetch_block
+{
+ my $hash = shift;
+ my ($keep, $child_out, $output_block);
+
+ my $cmd = "arv-get \Q$hash\E";
+ open($keep, '-|', $cmd) or die "fetch_block: $cmd: $!";
+ $output_block = '';
+ while (1) {
+ my $buf;
+ my $bytes = sysread($keep, $buf, 1024 * 1024);
+ if (!defined $bytes) {
+ die "reading from arv-get: $!";
+ } elsif ($bytes == 0) {
+ # sysread returns 0 at the end of the pipe.
+ last;
+ } else {
+ # some bytes were read into buf.
+ $output_block .= $buf;
+ }
+ }
+ close $keep;
+ return $output_block;
+}
+
+# create_output_collections generates a new collection containing the
+# output of each successfully completed task, and returns the
+# portable_data_hash for the new collection.
+#
+sub create_output_collection
+{
+ Log (undef, "collate");
+
+ my ($child_out, $child_in);
+ my $pid = open2($child_out, $child_in, 'python', '-c',
+ 'import arvados; ' .
+ 'import sys; ' .
+ 'print arvados.api()' .
+ '.collections()' .
+ '.create(body={"manifest_text":sys.stdin.read()})' .
+ '.execute()["portable_data_hash"]'
+ );
+
+ for (@jobstep)
+ {
+ next if (!exists $_->{'arvados_task'}->{'output'} ||
+ !$_->{'arvados_task'}->{'success'});
+ my $output = $_->{'arvados_task'}->{output};
+ if ($output !~ /^[0-9a-f]{32}(\+\S+)*$/)
+ {
+ print $child_in $output;
+ }
+ elsif (defined (my $outblock = fetch_block ($output)))
+ {
+ print $child_in $outblock;
+ }
+ else
+ {
+ Log (undef, "XXX fetch_block($output) failed XXX");
+ $main::success = 0;
+ }
+ }
+ $child_in->close;
+
+ my $joboutput;
+ my $s = IO::Select->new($child_out);
+ if ($s->can_read(120)) {
+ sysread($child_out, $joboutput, 64 * 1024 * 1024);
+ chomp($joboutput);
+ # TODO: Ensure exit status == 0.
+ } else {
+ Log (undef, "timed out while creating output collection");
+ }
+ # TODO: kill $pid instead of waiting, now that we've decided to
+ # ignore further output.
+ waitpid($pid, 0);
+
+ return $joboutput;
+}
+
+
+sub killem
+{
+ foreach (@_)
+ {
+ my $sig = 2; # SIGINT first
+ if (exists $proc{$_}->{"sent_$sig"} &&
+ time - $proc{$_}->{"sent_$sig"} > 4)
+ {
+ $sig = 15; # SIGTERM if SIGINT doesn't work
+ }
+ if (exists $proc{$_}->{"sent_$sig"} &&
+ time - $proc{$_}->{"sent_$sig"} > 4)
+ {
+ $sig = 9; # SIGKILL if SIGTERM doesn't work
+ }
+ if (!exists $proc{$_}->{"sent_$sig"})
+ {
+ Log ($proc{$_}->{jobstep}, "sending 2x signal $sig to pid $_");
+ kill $sig, $_;
+ select (undef, undef, undef, 0.1);
+ if ($sig == 2)
+ {
+ kill $sig, $_; # srun wants two SIGINT to really interrupt
+ }
+ $proc{$_}->{"sent_$sig"} = time;
+ $proc{$_}->{"killedafter"} = time - $proc{$_}->{"time"};
+ }
+ }
+}
+
+
+sub fhbits
+{
+ my($bits);
+ for (@_) {
+ vec($bits,fileno($_),1) = 1;
+ }
+ $bits;
+}
+
+
+# Send log output to Keep via arv-put.
+#
+# $log_pipe_in and $log_pipe_out are the input and output filehandles to the arv-put pipe.
+# $log_pipe_pid is the pid of the arv-put subprocess.
+#
+# The only functions that should access these variables directly are:
+#
+# log_writer_start($logfilename)
+# Starts an arv-put pipe, reading data on stdin and writing it to
+# a $logfilename file in an output collection.
+#
+# log_writer_send($txt)
+# Writes $txt to the output log collection.
+#
+# log_writer_finish()
+# Closes the arv-put pipe and returns the output that it produces.
+#
+# log_writer_is_active()
+# Returns a true value if there is currently a live arv-put
+# process, false otherwise.
+#
+my ($log_pipe_in, $log_pipe_out, $log_pipe_pid);
+
+sub log_writer_start($)
+{
+ my $logfilename = shift;
+ $log_pipe_pid = open2($log_pipe_out, $log_pipe_in,
+ 'arv-put', '--portable-data-hash',
+ '--retries', '3',
+ '--filename', $logfilename,
+ '-');
+}
+
+sub log_writer_send($)
+{
+ my $txt = shift;
+ print $log_pipe_in $txt;
+}
+
+sub log_writer_finish()
+{
+ return unless $log_pipe_pid;
+
+ close($log_pipe_in);
+ my $arv_put_output;
+
+ my $s = IO::Select->new($log_pipe_out);
+ if ($s->can_read(120)) {
+ sysread($log_pipe_out, $arv_put_output, 1024);
+ chomp($arv_put_output);
+ } else {
+ Log (undef, "timed out reading from 'arv-put'");
+ }
+
+ waitpid($log_pipe_pid, 0);
+ $log_pipe_pid = $log_pipe_in = $log_pipe_out = undef;
+ if ($?) {
+ Log("log_writer_finish: arv-put exited ".exit_status_s($?))
+ }
+
+ return $arv_put_output;
+}
+
+sub log_writer_is_active() {
+ return $log_pipe_pid;
+}
+
+sub Log # ($jobstep_id, $logmessage)
+{
+ if ($_[1] =~ /\n/) {
+ for my $line (split (/\n/, $_[1])) {
+ Log ($_[0], $line);
+ }
+ return;
+ }
+ my $fh = select STDERR; $|=1; select $fh;
+ my $message = sprintf ("%s %d %s %s", $job_id, $$, @_);
+ $message =~ s{([^ -\176])}{"\\" . sprintf ("%03o", ord($1))}ge;
+ $message .= "\n";
+ my $datetime;
+ if (log_writer_is_active() || -t STDERR) {
+ my @gmtime = gmtime;
+ $datetime = sprintf ("%04d-%02d-%02d_%02d:%02d:%02d",
+ $gmtime[5]+1900, $gmtime[4]+1, @gmtime[3,2,1,0]);
+ }
+ print STDERR ((-t STDERR) ? ($datetime." ".$message) : $message);
+
+ if (log_writer_is_active()) {
+ log_writer_send($datetime . " " . $message);
+ }
+}
+
+
+sub croak
+{
+ my ($package, $file, $line) = caller;
+ my $message = "@_ at $file line $line\n";
+ Log (undef, $message);
+ freeze() if @jobstep_todo;
+ create_output_collection() if @jobstep_todo;
+ cleanup();
+ save_meta();
+ die;
+}
+
+
+sub cleanup
+{
+ return unless $Job;
+ if ($Job->{'state'} eq 'Cancelled') {
+ $Job->update_attributes('finished_at' => scalar gmtime);
+ } else {
+ $Job->update_attributes('state' => 'Failed');
+ }
+}
+
+
+sub save_meta
+{
+ my $justcheckpoint = shift; # false if this will be the last meta saved
+ return if $justcheckpoint; # checkpointing is not relevant post-Warehouse.pm
+ return unless log_writer_is_active();
+
+ my $loglocator = log_writer_finish();
+ Log (undef, "log manifest is $loglocator");
+ $Job->{'log'} = $loglocator;
+ $Job->update_attributes('log', $loglocator);
+}
+
+
+sub freeze_if_want_freeze
+{
+ if ($main::please_freeze)
+ {
+ release_allocation();
+ if (@_)
+ {
+ # kill some srun procs before freeze+stop
+ map { $proc{$_} = {} } @_;
+ while (%proc)
+ {
+ killem (keys %proc);
+ select (undef, undef, undef, 0.1);
+ my $died;
+ while (($died = waitpid (-1, WNOHANG)) > 0)
+ {
+ delete $proc{$died};
+ }
+ }
+ }
+ freeze();
+ create_output_collection();
+ cleanup();
+ save_meta();
+ exit 1;
+ }
+}
+
+
+sub freeze
+{
+ Log (undef, "Freeze not implemented");
+ return;
+}
+
+
+sub thaw
+{
+ croak ("Thaw not implemented");
+}
+
+
+sub freezequote
+{
+ my $s = shift;
+ $s =~ s/\\/\\\\/g;
+ $s =~ s/\n/\\n/g;
+ return $s;
+}
+
+
+sub freezeunquote
+{
+ my $s = shift;
+ $s =~ s{\\(.)}{$1 eq "n" ? "\n" : $1}ge;
+ return $s;
+}
+
+
+sub srun
+{
+ my $srunargs = shift;
+ my $execargs = shift;
+ my $opts = shift || {};
+ my $stdin = shift;
+ my $args = $have_slurm ? [@$srunargs, @$execargs] : $execargs;
+
+ $Data::Dumper::Terse = 1;
+ $Data::Dumper::Indent = 0;
+ my $show_cmd = Dumper($args);
+ $show_cmd =~ s/(TOKEN\\*=)[^\s\']+/${1}[...]/g;
+ $show_cmd =~ s/\n/ /g;
+ warn "starting: $show_cmd\n";
+
+ if (defined $stdin) {
+ my $child = open STDIN, "-|";
+ defined $child or die "no fork: $!";
+ if ($child == 0) {
+ print $stdin or die $!;
+ close STDOUT or die $!;
+ exit 0;
+ }
+ }
+
+ return system (@$args) if $opts->{fork};
+
+ exec @$args;
+ warn "ENV size is ".length(join(" ",%ENV));
+ die "exec failed: $!: @$args";
+}
+
+
+sub ban_node_by_slot {
+ # Don't start any new jobsteps on this node for 60 seconds
+ my $slotid = shift;
+ $slot[$slotid]->{node}->{hold_until} = 60 + scalar time;
+ $slot[$slotid]->{node}->{hold_count}++;
+ Log (undef, "backing off node " . $slot[$slotid]->{node}->{name} . " for 60 seconds");
+}
+
+sub must_lock_now
+{
+ my ($lockfile, $error_message) = @_;
+ open L, ">", $lockfile or croak("$lockfile: $!");
+ if (!flock L, LOCK_EX|LOCK_NB) {
+ croak("Can't lock $lockfile: $error_message\n");
+ }
+}
+
+sub find_docker_image {
+ # Given a Keep locator, check to see if it contains a Docker image.
+ # If so, return its stream name and Docker hash.
+ # If not, return undef for both values.
+ my $locator = shift;
+ my ($streamname, $filename);
+ my $image = api_call("collections/get", uuid => $locator);
+ if ($image) {
+ foreach my $line (split(/\n/, $image->{manifest_text})) {
+ my @tokens = split(/\s+/, $line);
+ next if (!@tokens);
+ $streamname = shift(@tokens);
+ foreach my $filedata (grep(/^\d+:\d+:/, @tokens)) {
+ if (defined($filename)) {
+ return (undef, undef); # More than one file in the Collection.
+ } else {
+ $filename = (split(/:/, $filedata, 3))[2];
+ }
+ }
+ }
+ }
+ if (defined($filename) and ($filename =~ /^([0-9A-Fa-f]{64})\.tar$/)) {
+ return ($streamname, $1);
+ } else {
+ return (undef, undef);
+ }
+}
+
+sub retry_count {
+ # Calculate the number of times an operation should be retried,
+ # assuming exponential backoff, and that we're willing to retry as
+ # long as tasks have been running. Enforce a minimum of 3 retries.
+ my ($starttime, $endtime, $timediff, $retries);
+ if (@jobstep) {
+ $starttime = $jobstep[0]->{starttime};
+ $endtime = $jobstep[-1]->{finishtime};
+ }
+ if (!defined($starttime)) {
+ $timediff = 0;
+ } elsif (!defined($endtime)) {
+ $timediff = time - $starttime;
+ } else {
+ $timediff = ($endtime - $starttime) - (time - $endtime);
+ }
+ if ($timediff > 0) {
+ $retries = int(log($timediff) / log(2));
+ } else {
+ $retries = 1; # Use the minimum.
+ }
+ return ($retries > 3) ? $retries : 3;
+}
+
+sub retry_op {
+ # Pass in two function references.
+ # This method will be called with the remaining arguments.
+ # If it dies, retry it with exponential backoff until it succeeds,
+ # or until the current retry_count is exhausted. After each failure
+ # that can be retried, the second function will be called with
+ # the current try count (0-based), next try time, and error message.
+ my $operation = shift;
+ my $retry_callback = shift;
+ my $retries = retry_count();
+ foreach my $try_count (0..$retries) {
+ my $next_try = time + (2 ** $try_count);
+ my $result = eval { $operation->(@_); };
+ if (!$@) {
+ return $result;
+ } elsif ($try_count < $retries) {
+ $retry_callback->($try_count, $next_try, $@);
+ my $sleep_time = $next_try - time;
+ sleep($sleep_time) if ($sleep_time > 0);
+ }
+ }
+ # Ensure the error message ends in a newline, so Perl doesn't add
+ # retry_op's line number to it.
+ chomp($@);
+ die($@ . "\n");
+}
+
+sub api_call {
+ # Pass in a /-separated API method name, and arguments for it.
+ # This function will call that method, retrying as needed until
+ # the current retry_count is exhausted, with a log on the first failure.
+ my $method_name = shift;
+ my $log_api_retry = sub {
+ my ($try_count, $next_try_at, $errmsg) = @_;
+ $errmsg =~ s/\s*\bat \Q$0\E line \d+\.?\s*//;
+ $errmsg =~ s/\s/ /g;
+ $errmsg =~ s/\s+$//;
+ my $retry_msg;
+ if ($next_try_at < time) {
+ $retry_msg = "Retrying.";
+ } else {
+ my $next_try_fmt = strftime "%Y-%m-%dT%H:%M:%SZ", gmtime($next_try_at);
+ $retry_msg = "Retrying at $next_try_fmt.";
+ }
+ Log(undef, "API method $method_name failed: $errmsg. $retry_msg");
+ };
+ my $method = $arv;
+ foreach my $key (split(/\//, $method_name)) {
+ $method = $method->{$key};
+ }
+ return retry_op(sub { $method->execute(@_); }, $log_api_retry, @_);
+}
+
+sub exit_status_s {
+ # Given a $?, return a human-readable exit code string like "0" or
+ # "1" or "0 with signal 1" or "1 with signal 11".
+ my $exitcode = shift;
+ my $s = $exitcode >> 8;
+ if ($exitcode & 0x7f) {
+ $s .= " with signal " . ($exitcode & 0x7f);
+ }
+ if ($exitcode & 0x80) {
+ $s .= " with core dump";
+ }
+ return $s;
+}
+
+sub handle_readall {
+ # Pass in a glob reference to a file handle.
+ # Read all its contents and return them as a string.
+ my $fh_glob_ref = shift;
+ local $/ = undef;
+ return <$fh_glob_ref>;
+}
+
+sub tar_filename_n {
+ my $n = shift;
+ return sprintf("%s/git.%s.%d.tar", $ENV{CRUNCH_TMP}, $job_id, $n);
+}
+
+sub add_git_archive {
+ # Pass in a git archive command as a string or list, a la system().
+ # This method will save its output to be included in the archive sent to the
+ # build script.
+ my $git_input;
+ $git_tar_count++;
+ if (!open(GIT_ARCHIVE, ">", tar_filename_n($git_tar_count))) {
+ croak("Failed to save git archive: $!");
+ }
+ my $git_pid = open2(">&GIT_ARCHIVE", $git_input, @_);
+ close($git_input);
+ waitpid($git_pid, 0);
+ close(GIT_ARCHIVE);
+ if ($?) {
+ croak("Failed to save git archive: git exited " . exit_status_s($?));
+ }
+}
+
+sub combined_git_archive {
+ # Combine all saved tar archives into a single archive, then return its
+ # contents in a string. Return undef if no archives have been saved.
+ if ($git_tar_count < 1) {
+ return undef;
+ }
+ my $base_tar_name = tar_filename_n(1);
+ foreach my $tar_to_append (map { tar_filename_n($_); } (2..$git_tar_count)) {
+ my $tar_exit = system("tar", "-Af", $base_tar_name, $tar_to_append);
+ if ($tar_exit != 0) {
+ croak("Error preparing build archive: tar -A exited " .
+ exit_status_s($tar_exit));
+ }
+ }
+ if (!open(GIT_TAR, "<", $base_tar_name)) {
+ croak("Could not open build archive: $!");
+ }
+ my $tar_contents = handle_readall(\*GIT_TAR);
+ close(GIT_TAR);
+ return $tar_contents;
+}
+
+__DATA__
+#!/usr/bin/perl
+#
+# This is crunch-job's internal dispatch script. crunch-job running on the API
+# server invokes this script on individual compute nodes, or localhost if we're
+# running a job locally. It gets called in two modes:
+#
+# * No arguments: Installation mode. Read a tar archive from the DATA
+# file handle; it includes the Crunch script's source code, and
+# maybe SDKs as well. Those should be installed in the proper
+# locations. This runs outside of any Docker container, so don't try to
+# introspect Crunch's runtime environment.
+#
+# * With arguments: Crunch script run mode. This script should set up the
+# environment, then run the command specified in the arguments. This runs
+# inside any Docker container.
+
+use Fcntl ':flock';
+use File::Path qw( make_path remove_tree );
+use POSIX qw(getcwd);
+
+# Map SDK subdirectories to the path environments they belong to.
+my %SDK_ENVVARS = ("perl/lib" => "PERLLIB", "ruby/lib" => "RUBYLIB");
+
+my $destdir = $ENV{"CRUNCH_SRC"};
+my $commit = $ENV{"CRUNCH_SRC_COMMIT"};
+my $repo = $ENV{"CRUNCH_SRC_URL"};
+my $install_dir = $ENV{"CRUNCH_INSTALL"} || (getcwd() . "/opt");
+my $job_work = $ENV{"JOB_WORK"};
+my $task_work = $ENV{"TASK_WORK"};
+
+for my $dir ($destdir, $job_work, $task_work) {
+ if ($dir) {
+ make_path $dir;
+ -e $dir or die "Failed to create temporary directory ($dir): $!";
+ }
+}
+
+if ($task_work) {
+ remove_tree($task_work, {keep_root => 1});
+}
+
+open(STDOUT_ORIG, ">&", STDOUT);
+open(STDERR_ORIG, ">&", STDERR);
+open(STDOUT, ">>", "$destdir.log");
+open(STDERR, ">&", STDOUT);
+
+### Crunch script run mode
+if (@ARGV) {
+ # We want to do routine logging during task 0 only. This gives the user
+ # the information they need, but avoids repeating the information for every
+ # task.
+ my $Log;
+ if ($ENV{TASK_SEQUENCE} eq "0") {
+ $Log = sub {
+ my $msg = shift;
+ printf STDERR_ORIG "[Crunch] $msg\n", @_;
+ };
+ } else {
+ $Log = sub { };
+ }
+
+ my $python_src = "$install_dir/python";
+ my $venv_dir = "$job_work/.arvados.venv";
+ my $venv_built = -e "$venv_dir/bin/activate";
+ if ((!$venv_built) and (-d $python_src) and can_run("virtualenv")) {
+ shell_or_die("virtualenv", "--quiet", "--system-site-packages",
+ "--python=python2.7", $venv_dir);
+ shell_or_die("$venv_dir/bin/pip", "--quiet", "install", $python_src);
+ $venv_built = 1;
+ $Log->("Built Python SDK virtualenv");
+ }
+
+ my $pkgs;
+ if ($venv_built) {
+ $Log->("Running in Python SDK virtualenv");
+ $pkgs = `(\Q$venv_dir/bin/pip\E freeze 2>/dev/null | grep arvados) || dpkg-query --show '*arvados*'`;
+ my $orig_argv = join(" ", map { quotemeta($_); } @ARGV);
+ @ARGV = ("/bin/sh", "-ec",
+ ". \Q$venv_dir/bin/activate\E; exec $orig_argv");
+ } elsif (-d $python_src) {
+ $Log->("Warning: virtualenv not found inside Docker container default " +
+ "\$PATH. Can't install Python SDK.");
+ } else {
+ $pkgs = `(pip freeze 2>/dev/null | grep arvados) || dpkg-query --show '*arvados*'`;
+ }
+
+ if ($pkgs) {
+ $Log->("Using Arvados SDK:");
+ foreach my $line (split /\n/, $pkgs) {
+ $Log->($line);
+ }
+ } else {
+ $Log->("Arvados SDK packages not found");
+ }
+
+ while (my ($sdk_dir, $sdk_envkey) = each(%SDK_ENVVARS)) {
+ my $sdk_path = "$install_dir/$sdk_dir";
+ if (-d $sdk_path) {
+ if ($ENV{$sdk_envkey}) {
+ $ENV{$sdk_envkey} = "$sdk_path:" . $ENV{$sdk_envkey};
+ } else {
+ $ENV{$sdk_envkey} = $sdk_path;
+ }
+ $Log->("Arvados SDK added to %s", $sdk_envkey);
+ }
+ }
+
+ close(STDOUT);
+ close(STDERR);
+ open(STDOUT, ">&", STDOUT_ORIG);
+ open(STDERR, ">&", STDERR_ORIG);
+ exec(@ARGV);
+ die "Cannot exec `@ARGV`: $!";
+}
+
+### Installation mode
+open L, ">", "$destdir.lock" or die "$destdir.lock: $!";
+flock L, LOCK_EX;
+if (readlink ("$destdir.commit") eq $commit && -d $destdir) {
+ # This version already installed -> nothing to do.
+ exit(0);
+}
+
+unlink "$destdir.commit";
+mkdir $destdir;
+open TARX, "|-", "tar", "-xC", $destdir;
+{
+ local $/ = undef;
+ print TARX <DATA>;
+}
+if(!close(TARX)) {
+ die "'tar -xC $destdir' exited $?: $!";
+}
+
+mkdir $install_dir;
+
+my $sdk_root = "$destdir/.arvados.sdk/sdk";
+if (-d $sdk_root) {
+ foreach my $sdk_lang (("python",
+ map { (split /\//, $_, 2)[0]; } keys(%SDK_ENVVARS))) {
+ if (-d "$sdk_root/$sdk_lang") {
+ if (!rename("$sdk_root/$sdk_lang", "$install_dir/$sdk_lang")) {
+ die "Failed to install $sdk_lang SDK: $!";
+ }
+ }
+ }
+}
+
+my $python_dir = "$install_dir/python";
+if ((-d $python_dir) and can_run("python2.7") and
+ (system("python2.7", "$python_dir/setup.py", "--quiet", "egg_info") != 0)) {
+ # egg_info failed, probably when it asked git for a build tag.
+ # Specify no build tag.
+ open(my $pysdk_cfg, ">>", "$python_dir/setup.cfg");
+ print $pysdk_cfg "\n[egg_info]\ntag_build =\n";
+ close($pysdk_cfg);
+}
+
+if (-e "$destdir/crunch_scripts/install") {
+ shell_or_die ("$destdir/crunch_scripts/install", $install_dir);
+} elsif (!-e "./install.sh" && -e "./tests/autotests.sh") {
+ # Old version
+ shell_or_die ("./tests/autotests.sh", $install_dir);
+} elsif (-e "./install.sh") {
+ shell_or_die ("./install.sh", $install_dir);
+}
+
+if ($commit) {
+ unlink "$destdir.commit.new";
+ symlink ($commit, "$destdir.commit.new") or die "$destdir.commit.new: $!";
+ rename ("$destdir.commit.new", "$destdir.commit") or die "$destdir.commit: $!";
+}
+
+close L;
+
+sub can_run {
+ my $command_name = shift;
+ open(my $which, "-|", "which", $command_name);
+ while (<$which>) { }
+ close($which);
+ return ($? == 0);
+}
+
+sub shell_or_die
+{
+ if ($ENV{"DEBUG"}) {
+ print STDERR "@_\n";
+ }
+ if (system (@_) != 0) {
+ my $err = $!;
+ my $exitstatus = sprintf("exit %d signal %d", $? >> 8, $? & 0x7f);
+ open STDERR, ">&STDERR_ORIG";
+ system ("cat $destdir.log >&2");
+ die "@_ failed ($err): $exitstatus";
+ }
+}
+
+__DATA__
--- /dev/null
+require 'minitest/autorun'
+require 'digest/md5'
+require 'active_support/core_ext'
+
+class TestCollectionCreate < Minitest::Test
+ def setup
+ end
+
+ def test_small_collection
+ skip "Waiting unitl #4534 is implemented"
+
+ uuid = Digest::MD5.hexdigest(foo_manifest) + '+' + foo_manifest.size.to_s
+ out, err = capture_subprocess_io do
+ assert_arv('--format', 'uuid', 'collection', 'create', '--collection', {
+ uuid: uuid,
+ manifest_text: foo_manifest
+ }.to_json)
+ end
+ assert /^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/.match(out)
+ assert_equal '', err
+ $stderr.puts err
+ end
+
+ protected
+ def assert_arv(*args)
+ expect = case args.first
+ when true, false
+ args.shift
+ else
+ true
+ end
+ assert_equal(expect,
+ system(['./bin/arv', 'arv'], *args),
+ "`arv #{args.join ' '}` " +
+ "should exit #{if expect then 0 else 'non-zero' end}")
+ end
+
+ def foo_manifest
+ ". #{Digest::MD5.hexdigest('foo')}+3 0:3:foo\n"
+ end
+end
--- /dev/null
+require 'minitest/autorun'
+require 'digest/md5'
+
+class TestArvGet < Minitest::Test
+ def setup
+ begin
+ Dir.mkdir './tmp'
+ rescue Errno::EEXIST
+ end
+ @@foo_manifest_locator ||= `echo -n foo | ./bin/arv-put --filename foo --no-progress -`.strip
+ @@baz_locator ||= `echo -n baz | ./bin/arv-put --as-raw --no-progress -`.strip
+ @@multilevel_manifest_locator ||= `echo ./foo/bar #{@@baz_locator} 0:3:baz | ./bin/arv-put --as-raw --no-progress -`.strip
+ end
+
+ def test_no_args
+ out, err = capture_subprocess_io do
+ assert_arv_get false
+ end
+ assert_equal '', out
+ assert_match /^usage:/, err
+ end
+
+ def test_help
+ out, err = capture_subprocess_io do
+ assert_arv_get '-h'
+ end
+ $stderr.write err
+ assert_equal '', err
+ assert_match /^usage:/, out
+ end
+
+ def test_file_to_dev_stdout
+ skip "Waiting unitl #4534 is implemented"
+
+ test_file_to_stdout('/dev/stdout')
+ end
+
+ def test_file_to_stdout(specify_stdout_as='-')
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert_arv_get @@foo_manifest_locator + '/foo', specify_stdout_as
+ end
+ assert_equal '', err
+ assert_equal 'foo', out
+ end
+
+ def test_file_to_file
+ skip "Waiting unitl #4534 is implemented"
+
+ remove_tmp_foo
+ out, err = capture_subprocess_io do
+ assert_arv_get @@foo_manifest_locator + '/foo', 'tmp/foo'
+ end
+ assert_equal '', err
+ assert_equal '', out
+ assert_equal 'foo', IO.read('tmp/foo')
+ end
+
+ def test_file_to_file_no_overwrite_file
+ skip "Waiting unitl #4534 is implemented"
+ File.open './tmp/foo', 'wb' do |f|
+ f.write 'baz'
+ end
+ out, err = capture_subprocess_io do
+ assert_arv_get false, @@foo_manifest_locator + '/foo', 'tmp/foo'
+ end
+ assert_match /Error:/, err
+ assert_equal '', out
+ assert_equal 'baz', IO.read('tmp/foo')
+ end
+
+ def test_file_to_file_no_overwrite_file_in_dir
+ skip "Waiting unitl #4534 is implemented"
+ File.open './tmp/foo', 'wb' do |f|
+ f.write 'baz'
+ end
+ out, err = capture_subprocess_io do
+ assert_arv_get false, @@foo_manifest_locator + '/', 'tmp/'
+ end
+ assert_match /Error:/, err
+ assert_equal '', out
+ assert_equal 'baz', IO.read('tmp/foo')
+ end
+
+ def test_file_to_file_force_overwrite
+ skip "Waiting unitl #4534 is implemented"
+
+ File.open './tmp/foo', 'wb' do |f|
+ f.write 'baz'
+ end
+ assert_equal 'baz', IO.read('tmp/foo')
+ out, err = capture_subprocess_io do
+ assert_arv_get '-f', @@foo_manifest_locator + '/', 'tmp/'
+ end
+ assert_match '', err
+ assert_equal '', out
+ assert_equal 'foo', IO.read('tmp/foo')
+ end
+
+ def test_file_to_file_skip_existing
+ skip "Waiting unitl #4534 is implemented"
+
+ File.open './tmp/foo', 'wb' do |f|
+ f.write 'baz'
+ end
+ assert_equal 'baz', IO.read('tmp/foo')
+ out, err = capture_subprocess_io do
+ assert_arv_get '--skip-existing', @@foo_manifest_locator + '/', 'tmp/'
+ end
+ assert_match '', err
+ assert_equal '', out
+ assert_equal 'baz', IO.read('tmp/foo')
+ end
+
+ def test_file_to_dir
+ skip "Waiting unitl #4534 is implemented"
+
+ remove_tmp_foo
+ out, err = capture_subprocess_io do
+ assert_arv_get @@foo_manifest_locator + '/foo', 'tmp/'
+ end
+ assert_equal '', err
+ assert_equal '', out
+ assert_equal 'foo', IO.read('tmp/foo')
+ end
+
+ def test_dir_to_file
+ out, err = capture_subprocess_io do
+ assert_arv_get false, @@foo_manifest_locator + '/', 'tmp/foo'
+ end
+ assert_equal '', out
+ assert_match /^usage:/, err
+ end
+
+ def test_dir_to_empty_string
+ out, err = capture_subprocess_io do
+ assert_arv_get false, @@foo_manifest_locator + '/', ''
+ end
+ assert_equal '', out
+ assert_match /^usage:/, err
+ end
+
+ def test_nonexistent_block
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert_arv_get false, 'f1554a91e925d6213ce7c3103c5110c6'
+ end
+ assert_equal '', out
+ assert_match /Error:/, err
+ end
+
+ def test_nonexistent_manifest
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert_arv_get false, 'f1554a91e925d6213ce7c3103c5110c6/', 'tmp/'
+ end
+ assert_equal '', out
+ assert_match /Error:/, err
+ end
+
+ def test_manifest_root_to_dir
+ skip "Waiting unitl #4534 is implemented"
+
+ remove_tmp_foo
+ out, err = capture_subprocess_io do
+ assert_arv_get '-r', @@foo_manifest_locator + '/', 'tmp/'
+ end
+ assert_equal '', err
+ assert_equal '', out
+ assert_equal 'foo', IO.read('tmp/foo')
+ end
+
+ def test_manifest_root_to_dir_noslash
+ skip "Waiting unitl #4534 is implemented"
+
+ remove_tmp_foo
+ out, err = capture_subprocess_io do
+ assert_arv_get '-r', @@foo_manifest_locator + '/', 'tmp'
+ end
+ assert_equal '', err
+ assert_equal '', out
+ assert_equal 'foo', IO.read('tmp/foo')
+ end
+
+ def test_display_md5sum
+ skip "Waiting unitl #4534 is implemented"
+
+ remove_tmp_foo
+ out, err = capture_subprocess_io do
+ assert_arv_get '-r', '--md5sum', @@foo_manifest_locator + '/', 'tmp/'
+ end
+ assert_equal "#{Digest::MD5.hexdigest('foo')} ./foo\n", err
+ assert_equal '', out
+ assert_equal 'foo', IO.read('tmp/foo')
+ end
+
+ def test_md5sum_nowrite
+ skip "Waiting unitl #4534 is implemented"
+
+ remove_tmp_foo
+ out, err = capture_subprocess_io do
+ assert_arv_get '-n', '--md5sum', @@foo_manifest_locator + '/', 'tmp/'
+ end
+ assert_equal "#{Digest::MD5.hexdigest('foo')} ./foo\n", err
+ assert_equal '', out
+ assert_equal false, File.exists?('tmp/foo')
+ end
+
+ def test_sha1_nowrite
+ skip "Waiting unitl #4534 is implemented"
+
+ remove_tmp_foo
+ out, err = capture_subprocess_io do
+ assert_arv_get '-n', '-r', '--hash', 'sha1', @@foo_manifest_locator+'/', 'tmp/'
+ end
+ assert_equal "#{Digest::SHA1.hexdigest('foo')} ./foo\n", err
+ assert_equal '', out
+ assert_equal false, File.exists?('tmp/foo')
+ end
+
+ def test_block_to_file
+ skip "Waiting unitl #4534 is implemented"
+
+ remove_tmp_foo
+ out, err = capture_subprocess_io do
+ assert_arv_get @@foo_manifest_locator, 'tmp/foo'
+ end
+ assert_equal '', err
+ assert_equal '', out
+
+ digest = Digest::MD5.hexdigest('foo')
+ !(IO.read('tmp/foo')).gsub!( /^(. #{digest}+3)(.*)( 0:3:foo)$/).nil?
+ end
+
+ def test_create_directory_tree
+ skip "Waiting unitl #4534 is implemented"
+
+ `rm -rf ./tmp/arv-get-test/`
+ Dir.mkdir './tmp/arv-get-test'
+ out, err = capture_subprocess_io do
+ assert_arv_get @@multilevel_manifest_locator + '/', 'tmp/arv-get-test/'
+ end
+ assert_equal '', err
+ assert_equal '', out
+ assert_equal 'baz', IO.read('tmp/arv-get-test/foo/bar/baz')
+ end
+
+ def test_create_partial_directory_tree
+ skip "Waiting unitl #4534 is implemented"
+
+ `rm -rf ./tmp/arv-get-test/`
+ Dir.mkdir './tmp/arv-get-test'
+ out, err = capture_subprocess_io do
+ assert_arv_get(@@multilevel_manifest_locator + '/foo/',
+ 'tmp/arv-get-test/')
+ end
+ assert_equal '', err
+ assert_equal '', out
+ assert_equal 'baz', IO.read('tmp/arv-get-test/bar/baz')
+ end
+
+ protected
+ def assert_arv_get(*args)
+ expect = case args.first
+ when true, false
+ args.shift
+ else
+ true
+ end
+ assert_equal(expect,
+ system(['./bin/arv-get', 'arv-get'], *args),
+ "`arv-get #{args.join ' '}` " +
+ "should exit #{if expect then 0 else 'non-zero' end}")
+ end
+
+ def remove_tmp_foo
+ begin
+ File.unlink('tmp/foo')
+ rescue Errno::ENOENT
+ end
+ end
+end
--- /dev/null
+require 'minitest/autorun'
+require 'digest/md5'
+
+class TestArvPut < Minitest::Test
+ def setup
+ begin Dir.mkdir './tmp' rescue Errno::EEXIST end
+ begin Dir.mkdir './tmp/empty_dir' rescue Errno::EEXIST end
+ File.open './tmp/empty_file', 'wb' do
+ end
+ File.open './tmp/foo', 'wb' do |f|
+ f.write 'foo'
+ end
+ end
+
+ def test_help
+ out, err = capture_subprocess_io do
+ assert arv_put('-h'), 'arv-put -h exits zero'
+ end
+ $stderr.write err
+ assert_empty err
+ assert_match /^usage:/, out
+ end
+
+ def test_raw_stdin
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ r,w = IO.pipe
+ wpid = fork do
+ r.close
+ w << 'foo'
+ end
+ w.close
+ assert arv_put('--raw', {in: r})
+ r.close
+ Process.waitpid wpid
+ end
+ $stderr.write err
+ assert_match '', err
+ assert_equal "acbd18db4cc2f85cedef654fccc4a4d8+3\n", out
+ end
+
+ def test_raw_file
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert arv_put('--raw', './tmp/foo')
+ end
+ $stderr.write err
+ assert_match '', err
+ assert_equal "acbd18db4cc2f85cedef654fccc4a4d8+3\n", out
+ end
+
+ def test_raw_empty_file
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert arv_put('--raw', './tmp/empty_file')
+ end
+ $stderr.write err
+ assert_match '', err
+ assert_equal "d41d8cd98f00b204e9800998ecf8427e+0\n", out
+ end
+
+ def test_filename_arg_with_directory
+ out, err = capture_subprocess_io do
+ assert_equal(false, arv_put('--filename', 'foo', './tmp/empty_dir/.'),
+ 'arv-put --filename refuses directory')
+ end
+ assert_match /^usage:.*error:/m, err
+ assert_empty out
+ end
+
+ def test_filename_arg_with_multiple_files
+ out, err = capture_subprocess_io do
+ assert_equal(false, arv_put('--filename', 'foo',
+ './tmp/empty_file',
+ './tmp/empty_file'),
+ 'arv-put --filename refuses directory')
+ end
+ assert_match /^usage:.*error:/m, err
+ assert_empty out
+ end
+
+ def test_filename_arg_with_empty_file
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert arv_put('--filename', 'foo', './tmp/empty_file')
+ end
+ $stderr.write err
+ assert_match '', err
+ assert match_collection_uuid(out)
+ end
+
+ def test_as_stream
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert arv_put('--as-stream', './tmp/foo')
+ end
+ $stderr.write err
+ assert_match '', err
+ assert_equal foo_manifest, out
+ end
+
+ def test_progress
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert arv_put('--manifest', '--progress', './tmp/foo')
+ end
+ assert_match /%/, err
+ assert match_collection_uuid(out)
+ end
+
+ def test_batch_progress
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ assert arv_put('--manifest', '--batch-progress', './tmp/foo')
+ end
+ assert_match /: 0 written 3 total/, err
+ assert_match /: 3 written 3 total/, err
+ assert match_collection_uuid(out)
+ end
+
+ def test_progress_and_batch_progress
+ out, err = capture_subprocess_io do
+ assert_equal(false,
+ arv_put('--progress', '--batch-progress', './tmp/foo'),
+ 'arv-put --progress --batch-progress is contradictory')
+ end
+ assert_match /^usage:.*error:/m, err
+ assert_empty out
+ end
+
+ def test_read_from_implicit_stdin
+ skip "Waiting unitl #4534 is implemented"
+
+ test_read_from_stdin(specify_stdin_as='--manifest')
+ end
+
+ def test_read_from_dev_stdin
+ skip "Waiting unitl #4534 is implemented"
+
+ test_read_from_stdin(specify_stdin_as='/dev/stdin')
+ end
+
+ def test_read_from_stdin(specify_stdin_as='-')
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ r,w = IO.pipe
+ wpid = fork do
+ r.close
+ w << 'foo'
+ end
+ w.close
+ assert arv_put('--filename', 'foo', specify_stdin_as,
+ { in: r })
+ r.close
+ Process.waitpid wpid
+ end
+ $stderr.write err
+ assert_match '', err
+ assert match_collection_uuid(out)
+ end
+
+ def test_read_from_implicit_stdin_implicit_manifest
+ skip "Waiting unitl #4534 is implemented"
+
+ test_read_from_stdin_implicit_manifest(specify_stdin_as=nil,
+ expect_filename='stdin')
+ end
+
+ def test_read_from_dev_stdin_implicit_manifest
+ skip "Waiting unitl #4534 is implemented"
+
+ test_read_from_stdin_implicit_manifest(specify_stdin_as='/dev/stdin')
+ end
+
+ def test_read_from_stdin_implicit_manifest(specify_stdin_as='-',
+ expect_filename=nil)
+ skip "Waiting unitl #4534 is implemented"
+
+ expect_filename = expect_filename || specify_stdin_as.split('/').last
+ out, err = capture_subprocess_io do
+ r,w = IO.pipe
+ wpid = fork do
+ r.close
+ w << 'foo'
+ end
+ w.close
+ args = []
+ args.push specify_stdin_as if specify_stdin_as
+ assert arv_put(*args, { in: r })
+ r.close
+ Process.waitpid wpid
+ end
+ $stderr.write err
+ assert_match '', err
+ assert match_collection_uuid(out)
+ end
+
+ protected
+ def arv_put(*args)
+ system ['./bin/arv-put', 'arv-put'], *args
+ end
+
+ def foo_manifest(filename='foo')
+ ". #{Digest::MD5.hexdigest('foo')}+3 0:3:#{filename}\n"
+ end
+
+ def foo_manifest_locator(filename='foo')
+ Digest::MD5.hexdigest(foo_manifest(filename)) +
+ "+#{foo_manifest(filename).length}"
+ end
+
+ def match_collection_uuid(uuid)
+ /^([0-9a-z]{5}-4zz18-[0-9a-z]{15})?$/.match(uuid)
+ end
+end
--- /dev/null
+require 'minitest/autorun'
+
+class TestRunPipelineInstance < Minitest::Test
+ def setup
+ end
+
+ def test_run_pipeline_instance_get_help
+ skip "Waiting unitl #4534 is implemented"
+
+ out, err = capture_subprocess_io do
+ system ('arv-run-pipeline-instance -h')
+ end
+ assert_equal '', err
+ end
+
+ def test_run_pipeline_instance_with_no_such_option
+ out, err = capture_subprocess_io do
+ system ('arv-run-pipeline-instance --junk')
+ end
+ refute_equal '', err
+ end
+
+ def test_run_pipeline_instance_for_bogus_template_uuid
+ out, err = capture_subprocess_io do
+ # fails with error SSL_connect error because HOST_INSECURE is not being used
+ # system ('arv-run-pipeline-instance --template bogus-abcde-fghijklmnopqrs input=c1bad4b39ca5a924e481008009d94e32+210')
+
+ # fails with error: fatal: cannot load such file -- arvados
+ # system ('./bin/arv-run-pipeline-instance --template bogus-abcde-fghijklmnopqrs input=c1bad4b39ca5a924e481008009d94e32+210')
+ end
+ #refute_equal '', err
+ assert_equal '', err
+ end
+
+end
--- /dev/null
+require 'minitest/autorun'
+require 'digest/md5'
+require 'json'
+
+def assert_failure *args
+ assert_equal false, *args
+end
+
+class TestArvTag < Minitest::Test
+
+ def test_no_args
+ skip "Waiting unitl #4534 is implemented"
+
+ # arv-tag exits with failure if run with no args
+ out, err = capture_subprocess_io do
+ assert_equal false, arv_tag
+ end
+ assert_empty out
+ assert_match /^usage:/i, err
+ end
+
+ # Test adding and removing a single tag on a single object.
+ def test_single_tag_single_obj
+ skip "TBD"
+
+ # Add a single tag.
+ tag_uuid, err = capture_subprocess_io do
+ assert arv_tag '--short', 'add', 'test_tag1', '--object', 'uuid1'
+ end
+ assert_empty err
+
+ out, err = capture_subprocess_io do
+ assert arv 'link', 'show', '--uuid', tag_uuid.rstrip
+ end
+
+ assert_empty err
+ link = JSON.parse out
+ assert_tag link, 'test_tag1', 'uuid1'
+
+ # Remove the tag.
+ out, err = capture_subprocess_io do
+ assert arv_tag 'remove', 'test_tag1', '--object', 'uuid1'
+ end
+
+ assert_empty err
+ links = JSON.parse out
+ assert_equal 1, links.length
+ assert_tag links[0], 'test_tag1', 'uuid1'
+
+ # Verify that the link no longer exists.
+ out, err = capture_subprocess_io do
+ assert_equal false, arv('link', 'show', '--uuid', links[0]['uuid'])
+ end
+
+ assert_equal "Error: Path not found\n", err
+ end
+
+ # Test adding and removing a single tag with multiple objects.
+ def test_single_tag_multi_objects
+ skip "TBD"
+
+ out, err = capture_subprocess_io do
+ assert arv_tag('add', 'test_tag1',
+ '--object', 'uuid1',
+ '--object', 'uuid2',
+ '--object', 'uuid3')
+ end
+ assert_empty err
+
+ out, err = capture_subprocess_io do
+ assert arv 'link', 'list', '--where', '{"link_class":"tag","name":"test_tag1"}'
+ end
+
+ assert_empty err
+ json_out = JSON.parse out
+ links = json_out['items'].sort { |a,b| a['head_uuid'] <=> b['head_uuid'] }
+ assert_equal 3, links.length
+ assert_tag links[0], 'test_tag1', 'uuid1'
+ assert_tag links[1], 'test_tag1', 'uuid2'
+ assert_tag links[2], 'test_tag1', 'uuid3'
+
+ out, err = capture_subprocess_io do
+ assert arv_tag('remove', 'test_tag1',
+ '--object', 'uuid1',
+ '--object', 'uuid2',
+ '--object', 'uuid3')
+ end
+ assert_empty err
+
+ out, err = capture_subprocess_io do
+ assert arv 'link', 'list', '--where', '{"link_class":"tag","name":"test_tag1"}'
+ end
+
+ assert_empty err
+ assert_empty out
+ end
+
+ protected
+ def arv_tag(*args)
+ system ['./bin/arv-tag', 'arv-tag'], *args
+ end
+
+ def arv(*args)
+ system ['./bin/arv', 'arv'], *args
+ end
+
+ def assert_tag(link, name, head_uuid)
+ assert_equal 'tag', link['link_class']
+ assert_equal name, link['name']
+ assert_equal head_uuid, link['head_uuid']
+ end
+end
--- /dev/null
+require 'minitest/autorun'
+
+class TestArvWs < Minitest::Test
+ def setup
+ end
+
+ def test_arv_ws_get_help
+ out, err = capture_subprocess_io do
+ system ('arv-ws -h')
+ end
+ assert_equal '', err
+ end
+
+ def test_arv_ws_such_option
+ out, err = capture_subprocess_io do
+ system ('arv-ws --junk')
+ end
+ refute_equal '', err
+ end
+
+end
--- /dev/null
+/* Simple Arvados Go SDK for communicating with API server. */
+
+package arvadosclient
+
+import (
+ "bytes"
+ "crypto/tls"
+ "encoding/json"
+ "errors"
+ "fmt"
+ "io"
+ "net/http"
+ "net/url"
+ "os"
+ "strings"
+)
+
+// Errors
+var MissingArvadosApiHost = errors.New("Missing required environment variable ARVADOS_API_HOST")
+var MissingArvadosApiToken = errors.New("Missing required environment variable ARVADOS_API_TOKEN")
+
+type ArvadosApiError struct {
+ error
+ HttpStatusCode int
+ HttpStatus string
+}
+
+func (e ArvadosApiError) Error() string { return e.error.Error() }
+
+// Helper type so we don't have to write out 'map[string]interface{}' every time.
+type Dict map[string]interface{}
+
+// Information about how to contact the Arvados server
+type ArvadosClient struct {
+ // Arvados API server, form "host:port"
+ ApiServer string
+
+ // Arvados API token for authentication
+ ApiToken string
+
+ // Whether to require a valid SSL certificate or not
+ ApiInsecure bool
+
+ // Client object shared by client requests. Supports HTTP KeepAlive.
+ Client *http.Client
+
+ // If true, sets the X-External-Client header to indicate
+ // the client is outside the cluster.
+ External bool
+}
+
+// Create a new KeepClient, initialized with standard Arvados environment
+// variables ARVADOS_API_HOST, ARVADOS_API_TOKEN, and (optionally)
+// ARVADOS_API_HOST_INSECURE.
+func MakeArvadosClient() (kc ArvadosClient, err error) {
+ insecure := (os.Getenv("ARVADOS_API_HOST_INSECURE") == "true")
+ external := (os.Getenv("ARVADOS_EXTERNAL_CLIENT") == "true")
+
+ kc = ArvadosClient{
+ ApiServer: os.Getenv("ARVADOS_API_HOST"),
+ ApiToken: os.Getenv("ARVADOS_API_TOKEN"),
+ ApiInsecure: insecure,
+ Client: &http.Client{Transport: &http.Transport{
+ TLSClientConfig: &tls.Config{InsecureSkipVerify: insecure}}},
+ External: external}
+
+ if os.Getenv("ARVADOS_API_HOST") == "" {
+ return kc, MissingArvadosApiHost
+ }
+ if os.Getenv("ARVADOS_API_TOKEN") == "" {
+ return kc, MissingArvadosApiToken
+ }
+
+ return kc, err
+}
+
+// Low-level access to a resource.
+//
+// method - HTTP method, one of GET, HEAD, PUT, POST or DELETE
+// resource - the arvados resource to act on
+// uuid - the uuid of the specific item to access (may be empty)
+// action - sub-action to take on the resource or uuid (may be empty)
+// parameters - method parameters
+//
+// return
+// reader - the body reader, or nil if there was an error
+// err - error accessing the resource, or nil if no error
+func (this ArvadosClient) CallRaw(method string, resource string, uuid string, action string, parameters Dict) (reader io.ReadCloser, err error) {
+ var req *http.Request
+
+ u := url.URL{
+ Scheme: "https",
+ Host: this.ApiServer}
+
+ u.Path = "/arvados/v1"
+
+ if resource != "" {
+ u.Path = u.Path + "/" + resource
+ }
+ if uuid != "" {
+ u.Path = u.Path + "/" + uuid
+ }
+ if action != "" {
+ u.Path = u.Path + "/" + action
+ }
+
+ if parameters == nil {
+ parameters = make(Dict)
+ }
+
+ parameters["format"] = "json"
+
+ vals := make(url.Values)
+ for k, v := range parameters {
+ m, err := json.Marshal(v)
+ if err == nil {
+ vals.Set(k, string(m))
+ }
+ }
+
+ if method == "GET" || method == "HEAD" {
+ u.RawQuery = vals.Encode()
+ if req, err = http.NewRequest(method, u.String(), nil); err != nil {
+ return nil, err
+ }
+ } else {
+ if req, err = http.NewRequest(method, u.String(), bytes.NewBufferString(vals.Encode())); err != nil {
+ return nil, err
+ }
+ req.Header.Add("Content-Type", "application/x-www-form-urlencoded")
+ }
+
+ // Add api token header
+ req.Header.Add("Authorization", fmt.Sprintf("OAuth2 %s", this.ApiToken))
+ if this.External {
+ req.Header.Add("X-External-Client", "1")
+ }
+
+ // Make the request
+ var resp *http.Response
+ if resp, err = this.Client.Do(req); err != nil {
+ return nil, err
+ }
+
+ if resp.StatusCode == http.StatusOK {
+ return resp.Body, nil
+ }
+
+ defer resp.Body.Close()
+ errorText := fmt.Sprintf("API response: %s", resp.Status)
+
+ // If the response body has {"errors":["reason1","reason2"]}
+ // then return those reasons.
+ var errInfo = Dict{}
+ if err := json.NewDecoder(resp.Body).Decode(&errInfo); err == nil {
+ if errorList, ok := errInfo["errors"]; ok {
+ var errorStrings []string
+ if errArray, ok := errorList.([]interface{}); ok {
+ for _, errItem := range errArray {
+ // We expect an array of strings here.
+ // Non-strings will be passed along
+ // JSON-encoded.
+ if s, ok := errItem.(string); ok {
+ errorStrings = append(errorStrings, s)
+ } else if j, err := json.Marshal(errItem); err == nil {
+ errorStrings = append(errorStrings, string(j))
+ }
+ }
+ errorText = strings.Join(errorStrings, "; ")
+ }
+ }
+ }
+ return nil, ArvadosApiError{errors.New(errorText), resp.StatusCode, resp.Status}
+}
+
+// Access to a resource.
+//
+// method - HTTP method, one of GET, HEAD, PUT, POST or DELETE
+// resource - the arvados resource to act on
+// uuid - the uuid of the specific item to access (may be empty)
+// action - sub-action to take on the resource or uuid (may be empty)
+// parameters - method parameters
+// output - a map or annotated struct which is a legal target for encoding/json/Decoder
+// return
+// err - error accessing the resource, or nil if no error
+func (this ArvadosClient) Call(method string, resource string, uuid string, action string, parameters Dict, output interface{}) (err error) {
+ var reader io.ReadCloser
+ reader, err = this.CallRaw(method, resource, uuid, action, parameters)
+ if reader != nil {
+ defer reader.Close()
+ }
+ if err != nil {
+ return err
+ }
+
+ if output != nil {
+ dec := json.NewDecoder(reader)
+ if err = dec.Decode(output); err != nil {
+ return err
+ }
+ }
+ return nil
+}
+
+// Create a new instance of a resource.
+//
+// resource - the arvados resource on which to create an item
+// parameters - method parameters
+// output - a map or annotated struct which is a legal target for encoding/json/Decoder
+// return
+// err - error accessing the resource, or nil if no error
+func (this ArvadosClient) Create(resource string, parameters Dict, output interface{}) (err error) {
+ return this.Call("POST", resource, "", "", parameters, output)
+}
+
+// Delete an instance of a resource.
+//
+// resource - the arvados resource on which to delete an item
+// uuid - the item to delete
+// parameters - method parameters
+// output - a map or annotated struct which is a legal target for encoding/json/Decoder
+// return
+// err - error accessing the resource, or nil if no error
+func (this ArvadosClient) Delete(resource string, uuid string, parameters Dict, output interface{}) (err error) {
+ return this.Call("DELETE", resource, uuid, "", parameters, output)
+}
+
+// Update fields of an instance of a resource.
+//
+// resource - the arvados resource on which to update the item
+// uuid - the item to update
+// parameters - method parameters
+// output - a map or annotated struct which is a legal target for encoding/json/Decoder
+// return
+// err - error accessing the resource, or nil if no error
+func (this ArvadosClient) Update(resource string, uuid string, parameters Dict, output interface{}) (err error) {
+ return this.Call("PUT", resource, uuid, "", parameters, output)
+}
+
+// List the instances of a resource
+//
+// resource - the arvados resource on which to list
+// parameters - method parameters
+// output - a map or annotated struct which is a legal target for encoding/json/Decoder
+// return
+// err - error accessing the resource, or nil if no error
+func (this ArvadosClient) List(resource string, parameters Dict, output interface{}) (err error) {
+ return this.Call("GET", resource, "", "", parameters, output)
+}
--- /dev/null
+package arvadosclient
+
+import (
+ "fmt"
+ . "gopkg.in/check.v1"
+ "net/http"
+ "os"
+ "os/exec"
+ "testing"
+)
+
+// Gocheck boilerplate
+func Test(t *testing.T) {
+ TestingT(t)
+}
+
+var _ = Suite(&ServerRequiredSuite{})
+
+// Tests that require the Keep server running
+type ServerRequiredSuite struct{}
+
+func pythonDir() string {
+ cwd, _ := os.Getwd()
+ return fmt.Sprintf("%s/../../python/tests", cwd)
+}
+
+func (s *ServerRequiredSuite) SetUpSuite(c *C) {
+ os.Chdir(pythonDir())
+ if err := exec.Command("python", "run_test_server.py", "start").Run(); err != nil {
+ panic("'python run_test_server.py start' returned error")
+ }
+ if err := exec.Command("python", "run_test_server.py", "start_keep").Run(); err != nil {
+ panic("'python run_test_server.py start_keep' returned error")
+ }
+}
+
+func (s *ServerRequiredSuite) TestMakeArvadosClient(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "localhost:3000")
+ os.Setenv("ARVADOS_API_TOKEN", "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "")
+
+ kc, err := MakeArvadosClient()
+ c.Check(kc.ApiServer, Equals, "localhost:3000")
+ c.Check(kc.ApiToken, Equals, "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ c.Check(kc.ApiInsecure, Equals, false)
+
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "true")
+
+ kc, err = MakeArvadosClient()
+ c.Check(kc.ApiServer, Equals, "localhost:3000")
+ c.Check(kc.ApiToken, Equals, "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ c.Check(kc.ApiInsecure, Equals, true)
+ c.Check(kc.Client.Transport.(*http.Transport).TLSClientConfig.InsecureSkipVerify, Equals, true)
+
+ c.Assert(err, Equals, nil)
+}
+
+func (s *ServerRequiredSuite) TestCreatePipelineTemplate(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "localhost:3000")
+ os.Setenv("ARVADOS_API_TOKEN", "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "true")
+
+ arv, err := MakeArvadosClient()
+
+ getback := make(Dict)
+ err = arv.Create("pipeline_templates",
+ Dict{"pipeline_template": Dict{
+ "name": "tmp",
+ "components": Dict{
+ "c1": map[string]string{"script": "script1"},
+ "c2": map[string]string{"script": "script2"}}}},
+ &getback)
+ c.Assert(err, Equals, nil)
+ c.Assert(getback["name"], Equals, "tmp")
+ c.Assert(getback["components"].(map[string]interface{})["c2"].(map[string]interface{})["script"], Equals, "script2")
+
+ uuid := getback["uuid"].(string)
+ getback = make(Dict)
+ err = arv.Update("pipeline_templates", uuid,
+ Dict{
+ "pipeline_template": Dict{"name": "tmp2"}},
+ &getback)
+ c.Assert(err, Equals, nil)
+ c.Assert(getback["name"], Equals, "tmp2")
+
+ c.Assert(getback["uuid"].(string), Equals, uuid)
+ getback = make(Dict)
+ err = arv.Delete("pipeline_templates", uuid, nil, &getback)
+ c.Assert(err, Equals, nil)
+ c.Assert(getback["name"], Equals, "tmp2")
+}
+
+func (s *ServerRequiredSuite) TestErrorResponse(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "localhost:3000")
+ os.Setenv("ARVADOS_API_TOKEN", "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "true")
+
+ arv, _ := MakeArvadosClient()
+
+ getback := make(Dict)
+
+ {
+ err := arv.Create("logs",
+ Dict{"log": Dict{"bogus_attr": "foo"}},
+ &getback)
+ c.Assert(err, ErrorMatches, ".*unknown attribute: bogus_attr.*")
+ c.Assert(err, FitsTypeOf, ArvadosApiError{})
+ c.Assert(err.(ArvadosApiError).HttpStatusCode, Equals, 422)
+ }
+
+ {
+ err := arv.Create("bogus",
+ Dict{"bogus": Dict{}},
+ &getback)
+ c.Assert(err, ErrorMatches, "Path not found")
+ c.Assert(err, FitsTypeOf, ArvadosApiError{})
+ c.Assert(err.(ArvadosApiError).HttpStatusCode, Equals, 404)
+ }
+}
--- /dev/null
+// Lightweight implementation of io.ReadCloser that checks the contents read
+// from the underlying io.Reader a against checksum hash. To avoid reading the
+// entire contents into a buffer up front, the hash is updated with each read,
+// and the actual checksum is not checked until the underlying reader returns
+// EOF.
+package keepclient
+
+import (
+ "errors"
+ "fmt"
+ "hash"
+ "io"
+)
+
+var BadChecksum = errors.New("Reader failed checksum")
+
+type HashCheckingReader struct {
+ // The underlying data source
+ io.Reader
+
+ // The hashing function to use
+ hash.Hash
+
+ // The hash value to check against. Must be a hex-encoded lowercase string.
+ Check string
+}
+
+// Read from the underlying reader, update the hashing function, and pass the
+// results through. Will return BadChecksum on the last read instead of EOF if
+// the checksum doesn't match.
+func (this HashCheckingReader) Read(p []byte) (n int, err error) {
+ n, err = this.Reader.Read(p)
+ if n > 0 {
+ this.Hash.Write(p[:n])
+ }
+ if err == io.EOF {
+ sum := this.Hash.Sum(make([]byte, 0, this.Hash.Size()))
+ if fmt.Sprintf("%x", sum) != this.Check {
+ err = BadChecksum
+ }
+ }
+ return n, err
+}
+
+// Write entire contents of this.Reader to 'dest'. Returns BadChecksum if the
+// data written to 'dest' doesn't match the hash code of this.Check.
+func (this HashCheckingReader) WriteTo(dest io.Writer) (written int64, err error) {
+ if writeto, ok := this.Reader.(io.WriterTo); ok {
+ written, err = writeto.WriteTo(io.MultiWriter(dest, this.Hash))
+ } else {
+ written, err = io.Copy(io.MultiWriter(dest, this.Hash), this.Reader)
+ }
+
+ sum := this.Hash.Sum(make([]byte, 0, this.Hash.Size()))
+
+ if fmt.Sprintf("%x", sum) != this.Check {
+ err = BadChecksum
+ }
+
+ return written, err
+}
+
+// Close() the underlying Reader if it is castable to io.ReadCloser. This will
+// drain the underlying reader of any remaining data and check the checksum.
+func (this HashCheckingReader) Close() (err error) {
+ _, err = io.Copy(this.Hash, this.Reader)
+
+ if closer, ok := this.Reader.(io.ReadCloser); ok {
+ err = closer.Close()
+ }
+
+ sum := this.Hash.Sum(make([]byte, 0, this.Hash.Size()))
+ if fmt.Sprintf("%x", sum) != this.Check {
+ err = BadChecksum
+ }
+
+ return err
+}
--- /dev/null
+package keepclient
+
+import (
+ "bytes"
+ "crypto/md5"
+ "fmt"
+ . "gopkg.in/check.v1"
+ "io"
+ "io/ioutil"
+)
+
+type HashcheckSuiteSuite struct{}
+
+// Gocheck boilerplate
+var _ = Suite(&HashcheckSuiteSuite{})
+
+func (h *HashcheckSuiteSuite) TestRead(c *C) {
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+
+ {
+ r, w := io.Pipe()
+ hcr := HashCheckingReader{r, md5.New(), hash}
+ go func() {
+ w.Write([]byte("foo"))
+ w.Close()
+ }()
+ p, err := ioutil.ReadAll(hcr)
+ c.Check(len(p), Equals, 3)
+ c.Check(err, Equals, nil)
+ }
+
+ {
+ r, w := io.Pipe()
+ hcr := HashCheckingReader{r, md5.New(), hash}
+ go func() {
+ w.Write([]byte("bar"))
+ w.Close()
+ }()
+ p, err := ioutil.ReadAll(hcr)
+ c.Check(len(p), Equals, 3)
+ c.Check(err, Equals, BadChecksum)
+ }
+}
+
+func (h *HashcheckSuiteSuite) TestWriteTo(c *C) {
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+
+ {
+ bb := bytes.NewBufferString("foo")
+ hcr := HashCheckingReader{bb, md5.New(), hash}
+ r, w := io.Pipe()
+ done := make(chan bool)
+ go func() {
+ p, err := ioutil.ReadAll(r)
+ c.Check(len(p), Equals, 3)
+ c.Check(err, Equals, nil)
+ done <- true
+ }()
+
+ n, err := hcr.WriteTo(w)
+ w.Close()
+ c.Check(n, Equals, int64(3))
+ c.Check(err, Equals, nil)
+ <-done
+ }
+
+ {
+ bb := bytes.NewBufferString("bar")
+ hcr := HashCheckingReader{bb, md5.New(), hash}
+ r, w := io.Pipe()
+ done := make(chan bool)
+ go func() {
+ p, err := ioutil.ReadAll(r)
+ c.Check(len(p), Equals, 3)
+ c.Check(err, Equals, nil)
+ done <- true
+ }()
+
+ n, err := hcr.WriteTo(w)
+ w.Close()
+ c.Check(n, Equals, int64(3))
+ c.Check(err, Equals, BadChecksum)
+ <-done
+ }
+}
--- /dev/null
+/* Provides low-level Get/Put primitives for accessing Arvados Keep blocks. */
+package keepclient
+
+import (
+ "crypto/md5"
+ "errors"
+ "fmt"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/streamer"
+ "io"
+ "io/ioutil"
+ "log"
+ "net/http"
+ "regexp"
+ "strings"
+ "sync"
+ "sync/atomic"
+ "time"
+ "unsafe"
+)
+
+// A Keep "block" is 64MB.
+const BLOCKSIZE = 64 * 1024 * 1024
+
+var BlockNotFound = errors.New("Block not found")
+var InsufficientReplicasError = errors.New("Could not write sufficient replicas")
+var OversizeBlockError = errors.New("Block too big")
+var MissingArvadosApiHost = errors.New("Missing required environment variable ARVADOS_API_HOST")
+var MissingArvadosApiToken = errors.New("Missing required environment variable ARVADOS_API_TOKEN")
+
+const X_Keep_Desired_Replicas = "X-Keep-Desired-Replicas"
+const X_Keep_Replicas_Stored = "X-Keep-Replicas-Stored"
+
+// Information about Arvados and Keep servers.
+type KeepClient struct {
+ Arvados *arvadosclient.ArvadosClient
+ Want_replicas int
+ Using_proxy bool
+ service_roots *map[string]string
+ lock sync.Mutex
+ Client *http.Client
+}
+
+// Create a new KeepClient. This will contact the API server to discover Keep
+// servers.
+func MakeKeepClient(arv *arvadosclient.ArvadosClient) (kc KeepClient, err error) {
+ kc = KeepClient{
+ Arvados: arv,
+ Want_replicas: 2,
+ Using_proxy: false,
+ Client: &http.Client{},
+ }
+ err = (&kc).DiscoverKeepServers()
+
+ return kc, err
+}
+
+// Put a block given the block hash, a reader with the block data, and the
+// expected length of that data. The desired number of replicas is given in
+// KeepClient.Want_replicas. Returns the number of replicas that were written
+// and if there was an error. Note this will return InsufficientReplias
+// whenever 0 <= replicas < this.Wants_replicas.
+func (this KeepClient) PutHR(hash string, r io.Reader, expectedLength int64) (locator string, replicas int, err error) {
+
+ // Buffer for reads from 'r'
+ var bufsize int
+ if expectedLength > 0 {
+ if expectedLength > BLOCKSIZE {
+ return "", 0, OversizeBlockError
+ }
+ bufsize = int(expectedLength)
+ } else {
+ bufsize = BLOCKSIZE
+ }
+
+ t := streamer.AsyncStreamFromReader(bufsize, HashCheckingReader{r, md5.New(), hash})
+ defer t.Close()
+
+ return this.putReplicas(hash, t, expectedLength)
+}
+
+// Put a block given the block hash and a byte buffer. The desired number of
+// replicas is given in KeepClient.Want_replicas. Returns the number of
+// replicas that were written and if there was an error. Note this will return
+// InsufficientReplias whenever 0 <= replicas < this.Wants_replicas.
+func (this KeepClient) PutHB(hash string, buf []byte) (locator string, replicas int, err error) {
+ t := streamer.AsyncStreamFromSlice(buf)
+ defer t.Close()
+
+ return this.putReplicas(hash, t, int64(len(buf)))
+}
+
+// Put a block given a buffer. The hash will be computed. The desired number
+// of replicas is given in KeepClient.Want_replicas. Returns the number of
+// replicas that were written and if there was an error. Note this will return
+// InsufficientReplias whenever 0 <= replicas < this.Wants_replicas.
+func (this KeepClient) PutB(buffer []byte) (locator string, replicas int, err error) {
+ hash := fmt.Sprintf("%x", md5.Sum(buffer))
+ return this.PutHB(hash, buffer)
+}
+
+// Put a block, given a Reader. This will read the entire reader into a buffer
+// to compute the hash. The desired number of replicas is given in
+// KeepClient.Want_replicas. Returns the number of replicas that were written
+// and if there was an error. Note this will return InsufficientReplias
+// whenever 0 <= replicas < this.Wants_replicas. Also nhote that if the block
+// hash and data size are available, PutHR() is more efficient.
+func (this KeepClient) PutR(r io.Reader) (locator string, replicas int, err error) {
+ if buffer, err := ioutil.ReadAll(r); err != nil {
+ return "", 0, err
+ } else {
+ return this.PutB(buffer)
+ }
+}
+
+// Get a block given a hash. Return a reader, the expected data length, the
+// URL the block was fetched from, and if there was an error. If the block
+// checksum does not match, the final Read() on the reader returned by this
+// method will return a BadChecksum error instead of EOF.
+func (this KeepClient) Get(hash string) (reader io.ReadCloser,
+ contentLength int64, url string, err error) {
+ return this.AuthorizedGet(hash, "", "")
+}
+
+// Get a block given a hash, with additional authorization provided by
+// signature and timestamp. Return a reader, the expected data length, the URL
+// the block was fetched from, and if there was an error. If the block
+// checksum does not match, the final Read() on the reader returned by this
+// method will return a BadChecksum error instead of EOF.
+func (this KeepClient) AuthorizedGet(hash string,
+ signature string,
+ timestamp string) (reader io.ReadCloser,
+ contentLength int64, url string, err error) {
+
+ // Take the hash of locator and timestamp in order to identify this
+ // specific transaction in log statements.
+ requestId := fmt.Sprintf("%x", md5.Sum([]byte(hash+time.Now().String())))[0:8]
+
+ // Calculate the ordering for asking servers
+ sv := NewRootSorter(this.ServiceRoots(), hash).GetSortedRoots()
+
+ for _, host := range sv {
+ var req *http.Request
+ var err error
+ var url string
+ if signature != "" {
+ url = fmt.Sprintf("%s/%s+A%s@%s", host, hash,
+ signature, timestamp)
+ } else {
+ url = fmt.Sprintf("%s/%s", host, hash)
+ }
+ if req, err = http.NewRequest("GET", url, nil); err != nil {
+ continue
+ }
+
+ req.Header.Add("Authorization", fmt.Sprintf("OAuth2 %s", this.Arvados.ApiToken))
+
+ log.Printf("[%v] Begin download %s", requestId, url)
+
+ var resp *http.Response
+ if resp, err = this.Client.Do(req); err != nil || resp.StatusCode != http.StatusOK {
+ respbody, _ := ioutil.ReadAll(&io.LimitedReader{resp.Body, 4096})
+ response := strings.TrimSpace(string(respbody))
+ log.Printf("[%v] Download %v status code: %v error: \"%v\" response: \"%v\"",
+ requestId, url, resp.StatusCode, err, response)
+ continue
+ }
+
+ if resp.StatusCode == http.StatusOK {
+ log.Printf("[%v] Download %v status code: %v", requestId, url, resp.StatusCode)
+ return HashCheckingReader{resp.Body, md5.New(), hash}, resp.ContentLength, url, nil
+ }
+ }
+
+ return nil, 0, "", BlockNotFound
+}
+
+// Determine if a block with the given hash is available and readable, but does
+// not return the block contents.
+func (this KeepClient) Ask(hash string) (contentLength int64, url string, err error) {
+ return this.AuthorizedAsk(hash, "", "")
+}
+
+// Determine if a block with the given hash is available and readable with the
+// given signature and timestamp, but does not return the block contents.
+func (this KeepClient) AuthorizedAsk(hash string, signature string,
+ timestamp string) (contentLength int64, url string, err error) {
+ // Calculate the ordering for asking servers
+ sv := NewRootSorter(this.ServiceRoots(), hash).GetSortedRoots()
+
+ for _, host := range sv {
+ var req *http.Request
+ var err error
+ if signature != "" {
+ url = fmt.Sprintf("%s/%s+A%s@%s", host, hash,
+ signature, timestamp)
+ } else {
+ url = fmt.Sprintf("%s/%s", host, hash)
+ }
+
+ if req, err = http.NewRequest("HEAD", url, nil); err != nil {
+ continue
+ }
+
+ req.Header.Add("Authorization", fmt.Sprintf("OAuth2 %s", this.Arvados.ApiToken))
+
+ var resp *http.Response
+ if resp, err = this.Client.Do(req); err != nil {
+ continue
+ }
+
+ if resp.StatusCode == http.StatusOK {
+ return resp.ContentLength, url, nil
+ }
+ }
+
+ return 0, "", BlockNotFound
+
+}
+
+// Atomically read the service_roots field.
+func (this *KeepClient) ServiceRoots() map[string]string {
+ r := (*map[string]string)(atomic.LoadPointer((*unsafe.Pointer)(unsafe.Pointer(&this.service_roots))))
+ return *r
+}
+
+// Atomically update the service_roots field. Enables you to update
+// service_roots without disrupting any GET or PUT operations that might
+// already be in progress.
+func (this *KeepClient) SetServiceRoots(new_roots map[string]string) {
+ roots := make(map[string]string)
+ for uuid, root := range new_roots {
+ roots[uuid] = root
+ }
+ atomic.StorePointer((*unsafe.Pointer)(unsafe.Pointer(&this.service_roots)),
+ unsafe.Pointer(&roots))
+}
+
+type Locator struct {
+ Hash string
+ Size int
+ Signature string
+ Timestamp string
+}
+
+func MakeLocator2(hash string, hints string) (locator Locator) {
+ locator.Hash = hash
+ if hints != "" {
+ signature_pat, _ := regexp.Compile("^A([[:xdigit:]]+)@([[:xdigit:]]{8})$")
+ for _, hint := range strings.Split(hints, "+") {
+ if hint != "" {
+ if match, _ := regexp.MatchString("^[[:digit:]]+$", hint); match {
+ fmt.Sscanf(hint, "%d", &locator.Size)
+ } else if m := signature_pat.FindStringSubmatch(hint); m != nil {
+ locator.Signature = m[1]
+ locator.Timestamp = m[2]
+ } else if match, _ := regexp.MatchString("^[:upper:]", hint); match {
+ // Any unknown hint that starts with an uppercase letter is
+ // presumed to be valid and ignored, to permit forward compatibility.
+ } else {
+ // Unknown format; not a valid locator.
+ return Locator{"", 0, "", ""}
+ }
+ }
+ }
+ }
+ return locator
+}
+
+func MakeLocator(path string) Locator {
+ pathpattern, err := regexp.Compile("^([0-9a-f]{32})([+].*)?$")
+ if err != nil {
+ log.Print("Don't like regexp", err)
+ }
+
+ sm := pathpattern.FindStringSubmatch(path)
+ if sm == nil {
+ log.Print("Failed match ", path)
+ return Locator{"", 0, "", ""}
+ }
+
+ return MakeLocator2(sm[1], sm[2])
+}
--- /dev/null
+package keepclient
+
+import (
+ "crypto/md5"
+ "flag"
+ "fmt"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/streamer"
+ . "gopkg.in/check.v1"
+ "io"
+ "io/ioutil"
+ "log"
+ "net"
+ "net/http"
+ "os"
+ "os/exec"
+ "testing"
+)
+
+// Gocheck boilerplate
+func Test(t *testing.T) {
+ TestingT(t)
+}
+
+// Gocheck boilerplate
+var _ = Suite(&ServerRequiredSuite{})
+var _ = Suite(&StandaloneSuite{})
+
+var no_server = flag.Bool("no-server", false, "Skip 'ServerRequireSuite'")
+
+// Tests that require the Keep server running
+type ServerRequiredSuite struct{}
+
+// Standalone tests
+type StandaloneSuite struct{}
+
+func pythonDir() string {
+ cwd, _ := os.Getwd()
+ return fmt.Sprintf("%s/../../python/tests", cwd)
+}
+
+func (s *ServerRequiredSuite) SetUpSuite(c *C) {
+ if *no_server {
+ c.Skip("Skipping tests that require server")
+ return
+ }
+ os.Chdir(pythonDir())
+ {
+ cmd := exec.Command("python", "run_test_server.py", "start")
+ stderr, err := cmd.StderrPipe()
+ if err != nil {
+ log.Fatalf("Setting up stderr pipe: %s", err)
+ }
+ go io.Copy(os.Stderr, stderr)
+ if err := cmd.Run(); err != nil {
+ panic(fmt.Sprintf("'python run_test_server.py start' returned error %s", err))
+ }
+ }
+ {
+ cmd := exec.Command("python", "run_test_server.py", "start_keep")
+ stderr, err := cmd.StderrPipe()
+ if err != nil {
+ log.Fatalf("Setting up stderr pipe: %s", err)
+ }
+ go io.Copy(os.Stderr, stderr)
+ if err := cmd.Run(); err != nil {
+ panic(fmt.Sprintf("'python run_test_server.py start_keep' returned error %s", err))
+ }
+ }
+}
+
+func (s *ServerRequiredSuite) TearDownSuite(c *C) {
+ os.Chdir(pythonDir())
+ exec.Command("python", "run_test_server.py", "stop_keep").Run()
+ exec.Command("python", "run_test_server.py", "stop").Run()
+}
+
+func (s *ServerRequiredSuite) TestMakeKeepClient(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "localhost:3000")
+ os.Setenv("ARVADOS_API_TOKEN", "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "true")
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ c.Assert(err, Equals, nil)
+
+ kc, err := MakeKeepClient(&arv)
+
+ c.Assert(err, Equals, nil)
+ c.Check(len(kc.ServiceRoots()), Equals, 2)
+ for _, root := range kc.ServiceRoots() {
+ c.Check(root, Matches, "http://localhost:2510[\\d]")
+ }
+}
+
+type StubPutHandler struct {
+ c *C
+ expectPath string
+ expectApiToken string
+ expectBody string
+ handled chan string
+}
+
+func (this StubPutHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ this.c.Check(req.URL.Path, Equals, "/"+this.expectPath)
+ this.c.Check(req.Header.Get("Authorization"), Equals, fmt.Sprintf("OAuth2 %s", this.expectApiToken))
+ body, err := ioutil.ReadAll(req.Body)
+ this.c.Check(err, Equals, nil)
+ this.c.Check(body, DeepEquals, []byte(this.expectBody))
+ resp.WriteHeader(200)
+ this.handled <- fmt.Sprintf("http://%s", req.Host)
+}
+
+func RunFakeKeepServer(st http.Handler) (ks KeepServer) {
+ var err error
+ ks.listener, err = net.ListenTCP("tcp", &net.TCPAddr{Port: 0})
+ if err != nil {
+ panic(fmt.Sprintf("Could not listen on any port"))
+ }
+ ks.url = fmt.Sprintf("http://%s", ks.listener.Addr().String())
+ go http.Serve(ks.listener, st)
+ return
+}
+
+func UploadToStubHelper(c *C, st http.Handler, f func(KeepClient, string,
+ io.ReadCloser, io.WriteCloser, chan uploadStatus)) {
+
+ ks := RunFakeKeepServer(st)
+ defer ks.listener.Close()
+
+ arv, _ := arvadosclient.MakeArvadosClient()
+ arv.ApiToken = "abc123"
+
+ kc, _ := MakeKeepClient(&arv)
+
+ reader, writer := io.Pipe()
+ upload_status := make(chan uploadStatus)
+
+ f(kc, ks.url, reader, writer, upload_status)
+}
+
+func (s *StandaloneSuite) TestUploadToStubKeepServer(c *C) {
+ log.Printf("TestUploadToStubKeepServer")
+
+ st := StubPutHandler{
+ c,
+ "acbd18db4cc2f85cedef654fccc4a4d8",
+ "abc123",
+ "foo",
+ make(chan string)}
+
+ UploadToStubHelper(c, st,
+ func(kc KeepClient, url string, reader io.ReadCloser,
+ writer io.WriteCloser, upload_status chan uploadStatus) {
+
+ go kc.uploadToKeepServer(url, st.expectPath, reader, upload_status, int64(len("foo")), "TestUploadToStubKeepServer")
+
+ writer.Write([]byte("foo"))
+ writer.Close()
+
+ <-st.handled
+ status := <-upload_status
+ c.Check(status, DeepEquals, uploadStatus{nil, fmt.Sprintf("%s/%s", url, st.expectPath), 200, 1, ""})
+ })
+
+ log.Printf("TestUploadToStubKeepServer done")
+}
+
+func (s *StandaloneSuite) TestUploadToStubKeepServerBufferReader(c *C) {
+ log.Printf("TestUploadToStubKeepServerBufferReader")
+
+ st := StubPutHandler{
+ c,
+ "acbd18db4cc2f85cedef654fccc4a4d8",
+ "abc123",
+ "foo",
+ make(chan string)}
+
+ UploadToStubHelper(c, st,
+ func(kc KeepClient, url string, reader io.ReadCloser,
+ writer io.WriteCloser, upload_status chan uploadStatus) {
+
+ tr := streamer.AsyncStreamFromReader(512, reader)
+ defer tr.Close()
+
+ br1 := tr.MakeStreamReader()
+
+ go kc.uploadToKeepServer(url, st.expectPath, br1, upload_status, 3, "TestUploadToStubKeepServerBufferReader")
+
+ writer.Write([]byte("foo"))
+ writer.Close()
+
+ <-st.handled
+
+ status := <-upload_status
+ c.Check(status, DeepEquals, uploadStatus{nil, fmt.Sprintf("%s/%s", url, st.expectPath), 200, 1, ""})
+ })
+
+ log.Printf("TestUploadToStubKeepServerBufferReader done")
+}
+
+type FailHandler struct {
+ handled chan string
+}
+
+func (this FailHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ resp.WriteHeader(500)
+ this.handled <- fmt.Sprintf("http://%s", req.Host)
+}
+
+func (s *StandaloneSuite) TestFailedUploadToStubKeepServer(c *C) {
+ log.Printf("TestFailedUploadToStubKeepServer")
+
+ st := FailHandler{
+ make(chan string)}
+
+ hash := "acbd18db4cc2f85cedef654fccc4a4d8"
+
+ UploadToStubHelper(c, st,
+ func(kc KeepClient, url string, reader io.ReadCloser,
+ writer io.WriteCloser, upload_status chan uploadStatus) {
+
+ go kc.uploadToKeepServer(url, hash, reader, upload_status, 3, "TestFailedUploadToStubKeepServer")
+
+ writer.Write([]byte("foo"))
+ writer.Close()
+
+ <-st.handled
+
+ status := <-upload_status
+ c.Check(status.url, Equals, fmt.Sprintf("%s/%s", url, hash))
+ c.Check(status.statusCode, Equals, 500)
+ })
+ log.Printf("TestFailedUploadToStubKeepServer done")
+}
+
+type KeepServer struct {
+ listener net.Listener
+ url string
+}
+
+func RunSomeFakeKeepServers(st http.Handler, n int) (ks []KeepServer) {
+ ks = make([]KeepServer, n)
+
+ for i := 0; i < n; i += 1 {
+ ks[i] = RunFakeKeepServer(st)
+ }
+
+ return ks
+}
+
+func (s *StandaloneSuite) TestPutB(c *C) {
+ log.Printf("TestPutB")
+
+ hash := Md5String("foo")
+
+ st := StubPutHandler{
+ c,
+ hash,
+ "abc123",
+ "foo",
+ make(chan string, 5)}
+
+ arv, _ := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+
+ kc.Want_replicas = 2
+ arv.ApiToken = "abc123"
+ service_roots := make(map[string]string)
+
+ ks := RunSomeFakeKeepServers(st, 5)
+
+ for i, k := range ks {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i)] = k.url
+ defer k.listener.Close()
+ }
+
+ kc.SetServiceRoots(service_roots)
+
+ kc.PutB([]byte("foo"))
+
+ shuff := NewRootSorter(
+ kc.ServiceRoots(), Md5String("foo")).GetSortedRoots()
+
+ s1 := <-st.handled
+ s2 := <-st.handled
+ c.Check((s1 == shuff[0] && s2 == shuff[1]) ||
+ (s1 == shuff[1] && s2 == shuff[0]),
+ Equals,
+ true)
+
+ log.Printf("TestPutB done")
+}
+
+func (s *StandaloneSuite) TestPutHR(c *C) {
+ log.Printf("TestPutHR")
+
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+
+ st := StubPutHandler{
+ c,
+ hash,
+ "abc123",
+ "foo",
+ make(chan string, 5)}
+
+ arv, _ := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+
+ kc.Want_replicas = 2
+ arv.ApiToken = "abc123"
+ service_roots := make(map[string]string)
+
+ ks := RunSomeFakeKeepServers(st, 5)
+
+ for i, k := range ks {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i)] = k.url
+ defer k.listener.Close()
+ }
+
+ kc.SetServiceRoots(service_roots)
+
+ reader, writer := io.Pipe()
+
+ go func() {
+ writer.Write([]byte("foo"))
+ writer.Close()
+ }()
+
+ kc.PutHR(hash, reader, 3)
+
+ shuff := NewRootSorter(kc.ServiceRoots(), hash).GetSortedRoots()
+ log.Print(shuff)
+
+ s1 := <-st.handled
+ s2 := <-st.handled
+
+ c.Check((s1 == shuff[0] && s2 == shuff[1]) ||
+ (s1 == shuff[1] && s2 == shuff[0]),
+ Equals,
+ true)
+
+ log.Printf("TestPutHR done")
+}
+
+func (s *StandaloneSuite) TestPutWithFail(c *C) {
+ log.Printf("TestPutWithFail")
+
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+
+ st := StubPutHandler{
+ c,
+ hash,
+ "abc123",
+ "foo",
+ make(chan string, 4)}
+
+ fh := FailHandler{
+ make(chan string, 1)}
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+
+ kc.Want_replicas = 2
+ arv.ApiToken = "abc123"
+ service_roots := make(map[string]string)
+
+ ks1 := RunSomeFakeKeepServers(st, 4)
+ ks2 := RunSomeFakeKeepServers(fh, 1)
+
+ for i, k := range ks1 {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i)] = k.url
+ defer k.listener.Close()
+ }
+ for i, k := range ks2 {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i+len(ks1))] = k.url
+ defer k.listener.Close()
+ }
+
+ kc.SetServiceRoots(service_roots)
+
+ shuff := NewRootSorter(
+ kc.ServiceRoots(), Md5String("foo")).GetSortedRoots()
+
+ phash, replicas, err := kc.PutB([]byte("foo"))
+
+ <-fh.handled
+
+ c.Check(err, Equals, nil)
+ c.Check(phash, Equals, "")
+ c.Check(replicas, Equals, 2)
+
+ s1 := <-st.handled
+ s2 := <-st.handled
+
+ c.Check((s1 == shuff[1] && s2 == shuff[2]) ||
+ (s1 == shuff[2] && s2 == shuff[1]),
+ Equals,
+ true)
+}
+
+func (s *StandaloneSuite) TestPutWithTooManyFail(c *C) {
+ log.Printf("TestPutWithTooManyFail")
+
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+
+ st := StubPutHandler{
+ c,
+ hash,
+ "abc123",
+ "foo",
+ make(chan string, 1)}
+
+ fh := FailHandler{
+ make(chan string, 4)}
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+
+ kc.Want_replicas = 2
+ arv.ApiToken = "abc123"
+ service_roots := make(map[string]string)
+
+ ks1 := RunSomeFakeKeepServers(st, 1)
+ ks2 := RunSomeFakeKeepServers(fh, 4)
+
+ for i, k := range ks1 {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i)] = k.url
+ defer k.listener.Close()
+ }
+ for i, k := range ks2 {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i+len(ks1))] = k.url
+ defer k.listener.Close()
+ }
+
+ kc.SetServiceRoots(service_roots)
+
+ _, replicas, err := kc.PutB([]byte("foo"))
+
+ c.Check(err, Equals, InsufficientReplicasError)
+ c.Check(replicas, Equals, 1)
+ c.Check(<-st.handled, Equals, ks1[0].url)
+
+ log.Printf("TestPutWithTooManyFail done")
+}
+
+type StubGetHandler struct {
+ c *C
+ expectPath string
+ expectApiToken string
+ returnBody []byte
+}
+
+func (this StubGetHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ this.c.Check(req.URL.Path, Equals, "/"+this.expectPath)
+ this.c.Check(req.Header.Get("Authorization"), Equals, fmt.Sprintf("OAuth2 %s", this.expectApiToken))
+ resp.Header().Set("Content-Length", fmt.Sprintf("%d", len(this.returnBody)))
+ resp.Write(this.returnBody)
+}
+
+func (s *StandaloneSuite) TestGet(c *C) {
+ log.Printf("TestGet")
+
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+
+ st := StubGetHandler{
+ c,
+ hash,
+ "abc123",
+ []byte("foo")}
+
+ ks := RunFakeKeepServer(st)
+ defer ks.listener.Close()
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+ arv.ApiToken = "abc123"
+ kc.SetServiceRoots(map[string]string{"x": ks.url})
+
+ r, n, url2, err := kc.Get(hash)
+ defer r.Close()
+ c.Check(err, Equals, nil)
+ c.Check(n, Equals, int64(3))
+ c.Check(url2, Equals, fmt.Sprintf("%s/%s", ks.url, hash))
+
+ content, err2 := ioutil.ReadAll(r)
+ c.Check(err2, Equals, nil)
+ c.Check(content, DeepEquals, []byte("foo"))
+
+ log.Printf("TestGet done")
+}
+
+func (s *StandaloneSuite) TestGetFail(c *C) {
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+
+ st := FailHandler{make(chan string, 1)}
+
+ ks := RunFakeKeepServer(st)
+ defer ks.listener.Close()
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+ arv.ApiToken = "abc123"
+ kc.SetServiceRoots(map[string]string{"x": ks.url})
+
+ r, n, url2, err := kc.Get(hash)
+ c.Check(err, Equals, BlockNotFound)
+ c.Check(n, Equals, int64(0))
+ c.Check(url2, Equals, "")
+ c.Check(r, Equals, nil)
+}
+
+type BarHandler struct {
+ handled chan string
+}
+
+func (this BarHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ resp.Write([]byte("bar"))
+ this.handled <- fmt.Sprintf("http://%s", req.Host)
+}
+
+func (s *StandaloneSuite) TestChecksum(c *C) {
+ foohash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+ barhash := fmt.Sprintf("%x", md5.Sum([]byte("bar")))
+
+ st := BarHandler{make(chan string, 1)}
+
+ ks := RunFakeKeepServer(st)
+ defer ks.listener.Close()
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+ arv.ApiToken = "abc123"
+ kc.SetServiceRoots(map[string]string{"x": ks.url})
+
+ r, n, _, err := kc.Get(barhash)
+ _, err = ioutil.ReadAll(r)
+ c.Check(n, Equals, int64(3))
+ c.Check(err, Equals, nil)
+
+ <-st.handled
+
+ r, n, _, err = kc.Get(foohash)
+ _, err = ioutil.ReadAll(r)
+ c.Check(n, Equals, int64(3))
+ c.Check(err, Equals, BadChecksum)
+
+ <-st.handled
+}
+
+func (s *StandaloneSuite) TestGetWithFailures(c *C) {
+ content := []byte("waz")
+ hash := fmt.Sprintf("%x", md5.Sum(content))
+
+ fh := FailHandler{
+ make(chan string, 4)}
+
+ st := StubGetHandler{
+ c,
+ hash,
+ "abc123",
+ content}
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+ arv.ApiToken = "abc123"
+ service_roots := make(map[string]string)
+
+ ks1 := RunSomeFakeKeepServers(st, 1)
+ ks2 := RunSomeFakeKeepServers(fh, 4)
+
+ for i, k := range ks1 {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i)] = k.url
+ defer k.listener.Close()
+ }
+ for i, k := range ks2 {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i+len(ks1))] = k.url
+ defer k.listener.Close()
+ }
+
+ kc.SetServiceRoots(service_roots)
+
+ // This test works only if one of the failing services is
+ // attempted before the succeeding service. Otherwise,
+ // <-fh.handled below will just hang! (Probe order depends on
+ // the choice of block content "waz" and the UUIDs of the fake
+ // servers, so we just tried different strings until we found
+ // an example that passes this Assert.)
+ c.Assert(NewRootSorter(service_roots, hash).GetSortedRoots()[0], Not(Equals), ks1[0].url)
+
+ r, n, url2, err := kc.Get(hash)
+
+ <-fh.handled
+ c.Check(err, Equals, nil)
+ c.Check(n, Equals, int64(3))
+ c.Check(url2, Equals, fmt.Sprintf("%s/%s", ks1[0].url, hash))
+
+ read_content, err2 := ioutil.ReadAll(r)
+ c.Check(err2, Equals, nil)
+ c.Check(read_content, DeepEquals, content)
+}
+
+func (s *ServerRequiredSuite) TestPutGetHead(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "localhost:3000")
+ os.Setenv("ARVADOS_API_TOKEN", "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "true")
+ content := []byte("TestPutGetHead")
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, err := MakeKeepClient(&arv)
+ c.Assert(err, Equals, nil)
+
+ hash := fmt.Sprintf("%x", md5.Sum(content))
+
+ {
+ n, _, err := kc.Ask(hash)
+ c.Check(err, Equals, BlockNotFound)
+ c.Check(n, Equals, int64(0))
+ }
+ {
+ hash2, replicas, err := kc.PutB(content)
+ c.Check(hash2, Equals, fmt.Sprintf("%s+%d", hash, len(content)))
+ c.Check(replicas, Equals, 2)
+ c.Check(err, Equals, nil)
+ }
+ {
+ r, n, url2, err := kc.Get(hash)
+ c.Check(err, Equals, nil)
+ c.Check(n, Equals, int64(len(content)))
+ c.Check(url2, Equals, fmt.Sprintf("http://localhost:25108/%s", hash))
+
+ read_content, err2 := ioutil.ReadAll(r)
+ c.Check(err2, Equals, nil)
+ c.Check(read_content, DeepEquals, content)
+ }
+ {
+ n, url2, err := kc.Ask(hash)
+ c.Check(err, Equals, nil)
+ c.Check(n, Equals, int64(len(content)))
+ c.Check(url2, Equals, fmt.Sprintf("http://localhost:25108/%s", hash))
+ }
+}
+
+type StubProxyHandler struct {
+ handled chan string
+}
+
+func (this StubProxyHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ resp.Header().Set("X-Keep-Replicas-Stored", "2")
+ this.handled <- fmt.Sprintf("http://%s", req.Host)
+}
+
+func (s *StandaloneSuite) TestPutProxy(c *C) {
+ log.Printf("TestPutProxy")
+
+ st := StubProxyHandler{make(chan string, 1)}
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+
+ kc.Want_replicas = 2
+ kc.Using_proxy = true
+ arv.ApiToken = "abc123"
+ service_roots := make(map[string]string)
+
+ ks1 := RunSomeFakeKeepServers(st, 1)
+
+ for i, k := range ks1 {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i)] = k.url
+ defer k.listener.Close()
+ }
+
+ kc.SetServiceRoots(service_roots)
+
+ _, replicas, err := kc.PutB([]byte("foo"))
+ <-st.handled
+
+ c.Check(err, Equals, nil)
+ c.Check(replicas, Equals, 2)
+
+ log.Printf("TestPutProxy done")
+}
+
+func (s *StandaloneSuite) TestPutProxyInsufficientReplicas(c *C) {
+ log.Printf("TestPutProxy")
+
+ st := StubProxyHandler{make(chan string, 1)}
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ kc, _ := MakeKeepClient(&arv)
+
+ kc.Want_replicas = 3
+ kc.Using_proxy = true
+ arv.ApiToken = "abc123"
+ service_roots := make(map[string]string)
+
+ ks1 := RunSomeFakeKeepServers(st, 1)
+
+ for i, k := range ks1 {
+ service_roots[fmt.Sprintf("zzzzz-bi6l4-fakefakefake%03d", i)] = k.url
+ defer k.listener.Close()
+ }
+ kc.SetServiceRoots(service_roots)
+
+ _, replicas, err := kc.PutB([]byte("foo"))
+ <-st.handled
+
+ c.Check(err, Equals, InsufficientReplicasError)
+ c.Check(replicas, Equals, 2)
+
+ log.Printf("TestPutProxy done")
+}
+
+func (s *StandaloneSuite) TestMakeLocator(c *C) {
+ l := MakeLocator("91f372a266fe2bf2823cb8ec7fda31ce+3+Aabcde@12345678")
+
+ c.Check(l.Hash, Equals, "91f372a266fe2bf2823cb8ec7fda31ce")
+ c.Check(l.Size, Equals, 3)
+ c.Check(l.Signature, Equals, "abcde")
+ c.Check(l.Timestamp, Equals, "12345678")
+}
--- /dev/null
+package keepclient
+
+import (
+ "sort"
+)
+
+type RootSorter struct {
+ root []string
+ weight []string
+ order []int
+}
+
+func NewRootSorter(serviceRoots map[string]string, hash string) (*RootSorter) {
+ rs := new(RootSorter)
+ rs.root = make([]string, len(serviceRoots))
+ rs.weight = make([]string, len(serviceRoots))
+ rs.order = make([]int, len(serviceRoots))
+ i := 0
+ for uuid, root := range serviceRoots {
+ rs.root[i] = root
+ rs.weight[i] = rs.getWeight(hash, uuid)
+ rs.order[i] = i
+ i++
+ }
+ sort.Sort(rs)
+ return rs
+}
+
+func (rs RootSorter) getWeight(hash string, uuid string) (string) {
+ if len(uuid) == 27 {
+ return Md5String(hash + uuid[12:])
+ } else {
+ // Only useful for testing, a set of one service root, etc.
+ return Md5String(hash + uuid)
+ }
+}
+
+func (rs RootSorter) GetSortedRoots() ([]string) {
+ sorted := make([]string, len(rs.order))
+ for i := range rs.order {
+ sorted[i] = rs.root[rs.order[i]]
+ }
+ return sorted
+}
+
+// Less is really More here: the heaviest root will be at the front of the list.
+func (rs RootSorter) Less(i, j int) bool {
+ return rs.weight[rs.order[j]] < rs.weight[rs.order[i]]
+}
+
+func (rs RootSorter) Len() int {
+ return len(rs.order)
+}
+
+func (rs RootSorter) Swap(i, j int) {
+ sort.IntSlice(rs.order).Swap(i, j)
+}
--- /dev/null
+package keepclient
+
+import (
+ "fmt"
+ . "gopkg.in/check.v1"
+ "strconv"
+ "strings"
+)
+
+type RootSorterSuite struct{}
+var _ = Suite(&RootSorterSuite{})
+
+func FakeSvcRoot(i uint64) (string) {
+ return fmt.Sprintf("https://%x.svc/", i)
+}
+
+func FakeSvcUuid(i uint64) (string) {
+ return fmt.Sprintf("zzzzz-bi6l4-%015x", i)
+}
+
+func FakeServiceRoots(n uint64) (map[string]string) {
+ sr := map[string]string{}
+ for i := uint64(0); i < n; i ++ {
+ sr[FakeSvcUuid(i)] = FakeSvcRoot(i)
+ }
+ return sr
+}
+
+func (*RootSorterSuite) EmptyRoots(c *C) {
+ rs := NewRootSorter(map[string]string{}, Md5String("foo"))
+ c.Check(rs.GetSortedRoots(), Equals, []string{})
+}
+
+func (*RootSorterSuite) JustOneRoot(c *C) {
+ rs := NewRootSorter(FakeServiceRoots(1), Md5String("foo"))
+ c.Check(rs.GetSortedRoots(), Equals, []string{FakeSvcRoot(0)})
+}
+
+func (*RootSorterSuite) ReferenceSet(c *C) {
+ fakeroots := FakeServiceRoots(16)
+ // These reference probe orders are explained further in
+ // ../../python/tests/test_keep_client.py:
+ expected_orders := []string{
+ "3eab2d5fc9681074",
+ "097dba52e648f1c3",
+ "c5b4e023f8a7d691",
+ "9d81c02e76a3bf54",
+ }
+ for h, expected_order := range expected_orders {
+ hash := Md5String(fmt.Sprintf("%064x", h))
+ roots := NewRootSorter(fakeroots, hash).GetSortedRoots()
+ for i, svc_id_s := range strings.Split(expected_order, "") {
+ svc_id, err := strconv.ParseUint(svc_id_s, 16, 64)
+ c.Assert(err, Equals, nil)
+ c.Check(roots[i], Equals, FakeSvcRoot(svc_id))
+ }
+ }
+}
--- /dev/null
+/* Internal methods to support keepclient.go */
+package keepclient
+
+import (
+ "crypto/md5"
+ "errors"
+ "fmt"
+ "git.curoverse.com/arvados.git/sdk/go/streamer"
+ "io"
+ "io/ioutil"
+ "log"
+ "net"
+ "net/http"
+ "os"
+ "strings"
+ "time"
+)
+
+type keepDisk struct {
+ Uuid string `json:"uuid"`
+ Hostname string `json:"service_host"`
+ Port int `json:"service_port"`
+ SSL bool `json:"service_ssl_flag"`
+ SvcType string `json:"service_type"`
+}
+
+func Md5String(s string) string {
+ return fmt.Sprintf("%x", md5.Sum([]byte(s)))
+}
+
+// Set timeouts apply when connecting to keepproxy services (assumed to be over
+// the Internet).
+func (this *KeepClient) setClientSettingsProxy() {
+ if this.Client.Timeout == 0 {
+ // Maximum time to wait for a complete response
+ this.Client.Timeout = 300 * time.Second
+
+ // TCP and TLS connection settings
+ this.Client.Transport = &http.Transport{
+ Dial: (&net.Dialer{
+ // The maximum time to wait to set up
+ // the initial TCP connection.
+ Timeout: 30 * time.Second,
+
+ // The TCP keep alive heartbeat
+ // interval.
+ KeepAlive: 120 * time.Second,
+ }).Dial,
+
+ TLSHandshakeTimeout: 10 * time.Second,
+ }
+ }
+
+}
+
+// Set timeouts apply when connecting to keepstore services directly (assumed
+// to be on the local network).
+func (this *KeepClient) setClientSettingsStore() {
+ if this.Client.Timeout == 0 {
+ // Maximum time to wait for a complete response
+ this.Client.Timeout = 20 * time.Second
+
+ // TCP and TLS connection timeouts
+ this.Client.Transport = &http.Transport{
+ Dial: (&net.Dialer{
+ // The maximum time to wait to set up
+ // the initial TCP connection.
+ Timeout: 2 * time.Second,
+
+ // The TCP keep alive heartbeat
+ // interval.
+ KeepAlive: 180 * time.Second,
+ }).Dial,
+
+ TLSHandshakeTimeout: 4 * time.Second,
+ }
+ }
+}
+
+func (this *KeepClient) DiscoverKeepServers() error {
+ if prx := os.Getenv("ARVADOS_KEEP_PROXY"); prx != "" {
+ sr := map[string]string{"proxy": prx}
+ this.SetServiceRoots(sr)
+ this.Using_proxy = true
+ this.setClientSettingsProxy()
+ return nil
+ }
+
+ type svcList struct {
+ Items []keepDisk `json:"items"`
+ }
+ var m svcList
+
+ err := this.Arvados.Call("GET", "keep_services", "", "accessible", nil, &m)
+
+ if err != nil {
+ if err := this.Arvados.List("keep_disks", nil, &m); err != nil {
+ return err
+ }
+ }
+
+ listed := make(map[string]bool)
+ service_roots := make(map[string]string)
+
+ for _, element := range m.Items {
+ n := ""
+
+ if element.SSL {
+ n = "s"
+ }
+
+ // Construct server URL
+ url := fmt.Sprintf("http%s://%s:%d", n, element.Hostname, element.Port)
+
+ // Skip duplicates
+ if !listed[url] {
+ listed[url] = true
+ service_roots[element.Uuid] = url
+ }
+ if element.SvcType == "proxy" {
+ this.Using_proxy = true
+ }
+ }
+
+ if this.Using_proxy {
+ this.setClientSettingsProxy()
+ } else {
+ this.setClientSettingsStore()
+ }
+
+ this.SetServiceRoots(service_roots)
+
+ return nil
+}
+
+type uploadStatus struct {
+ err error
+ url string
+ statusCode int
+ replicas_stored int
+ response string
+}
+
+func (this KeepClient) uploadToKeepServer(host string, hash string, body io.ReadCloser,
+ upload_status chan<- uploadStatus, expectedLength int64, requestId string) {
+
+ var req *http.Request
+ var err error
+ var url = fmt.Sprintf("%s/%s", host, hash)
+ if req, err = http.NewRequest("PUT", url, nil); err != nil {
+ log.Printf("[%v] Error creating request PUT %v error: %v", requestId, url, err.Error())
+ upload_status <- uploadStatus{err, url, 0, 0, ""}
+ body.Close()
+ return
+ }
+
+ req.ContentLength = expectedLength
+ if expectedLength > 0 {
+ // http.Client.Do will close the body ReadCloser when it is
+ // done with it.
+ req.Body = body
+ } else {
+ // "For client requests, a value of 0 means unknown if Body is
+ // not nil." In this case we do want the body to be empty, so
+ // don't set req.Body. However, we still need to close the
+ // body ReadCloser.
+ body.Close()
+ }
+
+ req.Header.Add("Authorization", fmt.Sprintf("OAuth2 %s", this.Arvados.ApiToken))
+ req.Header.Add("Content-Type", "application/octet-stream")
+
+ if this.Using_proxy {
+ req.Header.Add(X_Keep_Desired_Replicas, fmt.Sprint(this.Want_replicas))
+ }
+
+ var resp *http.Response
+ if resp, err = this.Client.Do(req); err != nil {
+ log.Printf("[%v] Upload failed %v error: %v", requestId, url, err.Error())
+ upload_status <- uploadStatus{err, url, 0, 0, ""}
+ return
+ }
+
+ rep := 1
+ if xr := resp.Header.Get(X_Keep_Replicas_Stored); xr != "" {
+ fmt.Sscanf(xr, "%d", &rep)
+ }
+
+ defer resp.Body.Close()
+ defer io.Copy(ioutil.Discard, resp.Body)
+
+ respbody, err2 := ioutil.ReadAll(&io.LimitedReader{resp.Body, 4096})
+ response := strings.TrimSpace(string(respbody))
+ if err2 != nil && err2 != io.EOF {
+ log.Printf("[%v] Upload %v error: %v response: %v", requestId, url, err2.Error(), response)
+ upload_status <- uploadStatus{err2, url, resp.StatusCode, rep, response}
+ } else if resp.StatusCode == http.StatusOK {
+ log.Printf("[%v] Upload %v success", requestId, url)
+ upload_status <- uploadStatus{nil, url, resp.StatusCode, rep, response}
+ } else {
+ log.Printf("[%v] Upload %v error: %v response: %v", requestId, url, resp.StatusCode, response)
+ upload_status <- uploadStatus{errors.New(resp.Status), url, resp.StatusCode, rep, response}
+ }
+}
+
+func (this KeepClient) putReplicas(
+ hash string,
+ tr *streamer.AsyncStream,
+ expectedLength int64) (locator string, replicas int, err error) {
+
+ // Take the hash of locator and timestamp in order to identify this
+ // specific transaction in log statements.
+ requestId := fmt.Sprintf("%x", md5.Sum([]byte(locator+time.Now().String())))[0:8]
+
+ // Calculate the ordering for uploading to servers
+ sv := NewRootSorter(this.ServiceRoots(), hash).GetSortedRoots()
+
+ // The next server to try contacting
+ next_server := 0
+
+ // The number of active writers
+ active := 0
+
+ // Used to communicate status from the upload goroutines
+ upload_status := make(chan uploadStatus)
+ defer close(upload_status)
+
+ // Desired number of replicas
+ remaining_replicas := this.Want_replicas
+
+ for remaining_replicas > 0 {
+ for active < remaining_replicas {
+ // Start some upload requests
+ if next_server < len(sv) {
+ log.Printf("[%v] Begin upload %s to %s", requestId, hash, sv[next_server])
+ go this.uploadToKeepServer(sv[next_server], hash, tr.MakeStreamReader(), upload_status, expectedLength, requestId)
+ next_server += 1
+ active += 1
+ } else {
+ if active == 0 {
+ return locator, (this.Want_replicas - remaining_replicas), InsufficientReplicasError
+ } else {
+ break
+ }
+ }
+ }
+ log.Printf("[%v] Replicas remaining to write: %v active uploads: %v",
+ requestId, remaining_replicas, active)
+
+ // Now wait for something to happen.
+ status := <-upload_status
+ active -= 1
+
+ if status.statusCode == 200 {
+ // good news!
+ remaining_replicas -= status.replicas_stored
+ locator = status.response
+ }
+ }
+
+ return locator, this.Want_replicas, nil
+}
--- /dev/null
+/* AsyncStream pulls data in from a io.Reader source (such as a file or network
+socket) and fans out to any number of StreamReader sinks.
+
+Unlike io.TeeReader() or io.MultiWriter(), new StreamReaders can be created at
+any point in the lifetime of the AsyncStream, and each StreamReader will read
+the contents of the buffer up to the "frontier" of the buffer, at which point
+the StreamReader blocks until new data is read from the source.
+
+This is useful for minimizing readthrough latency as sinks can read and act on
+data from the source without waiting for the source to be completely buffered.
+It is also useful as a cache in situations where re-reading the original source
+potentially is costly, since the buffer retains a copy of the source data.
+
+Usage:
+
+Begin reading into a buffer with maximum size 'buffersize' from 'source':
+ stream := AsyncStreamFromReader(buffersize, source)
+
+To create a new reader (this can be called multiple times, each reader starts
+at the beginning of the buffer):
+ reader := tr.MakeStreamReader()
+
+Make sure to close the reader when you're done with it.
+ reader.Close()
+
+When you're done with the stream:
+ stream.Close()
+
+Alternately, if you already have a filled buffer and just want to read out from it:
+ stream := AsyncStreamFromSlice(buf)
+
+ r := tr.MakeStreamReader()
+
+*/
+
+package streamer
+
+import (
+ "io"
+)
+
+type AsyncStream struct {
+ buffer []byte
+ requests chan sliceRequest
+ add_reader chan bool
+ subtract_reader chan bool
+ wait_zero_readers chan bool
+}
+
+// Reads from the buffer managed by the Transfer()
+type StreamReader struct {
+ offset int
+ stream *AsyncStream
+ responses chan sliceResult
+}
+
+func AsyncStreamFromReader(buffersize int, source io.Reader) *AsyncStream {
+ t := &AsyncStream{make([]byte, buffersize), make(chan sliceRequest), make(chan bool), make(chan bool), make(chan bool)}
+
+ go t.transfer(source)
+ go t.readersMonitor()
+
+ return t
+}
+
+func AsyncStreamFromSlice(buf []byte) *AsyncStream {
+ t := &AsyncStream{buf, make(chan sliceRequest), make(chan bool), make(chan bool), make(chan bool)}
+
+ go t.transfer(nil)
+ go t.readersMonitor()
+
+ return t
+}
+
+func (this *AsyncStream) MakeStreamReader() *StreamReader {
+ this.add_reader <- true
+ return &StreamReader{0, this, make(chan sliceResult)}
+}
+
+// Reads from the buffer managed by the Transfer()
+func (this *StreamReader) Read(p []byte) (n int, err error) {
+ this.stream.requests <- sliceRequest{this.offset, len(p), this.responses}
+ rr, valid := <-this.responses
+ if valid {
+ this.offset += len(rr.slice)
+ return copy(p, rr.slice), rr.err
+ } else {
+ return 0, io.ErrUnexpectedEOF
+ }
+}
+
+func (this *StreamReader) WriteTo(dest io.Writer) (written int64, err error) {
+ // Record starting offset in order to correctly report the number of bytes sent
+ starting_offset := this.offset
+ for {
+ this.stream.requests <- sliceRequest{this.offset, 32 * 1024, this.responses}
+ rr, valid := <-this.responses
+ if valid {
+ this.offset += len(rr.slice)
+ if rr.err != nil {
+ if rr.err == io.EOF {
+ // EOF is not an error.
+ return int64(this.offset - starting_offset), nil
+ } else {
+ return int64(this.offset - starting_offset), rr.err
+ }
+ } else {
+ dest.Write(rr.slice)
+ }
+ } else {
+ return int64(this.offset), io.ErrUnexpectedEOF
+ }
+ }
+}
+
+// Close the responses channel
+func (this *StreamReader) Close() error {
+ this.stream.subtract_reader <- true
+ close(this.responses)
+ this.stream = nil
+ return nil
+}
+
+func (this *AsyncStream) Close() {
+ this.wait_zero_readers <- true
+ close(this.requests)
+ close(this.add_reader)
+ close(this.subtract_reader)
+ close(this.wait_zero_readers)
+}
--- /dev/null
+package streamer
+
+import (
+ . "gopkg.in/check.v1"
+ "io"
+ "testing"
+ "time"
+)
+
+// Gocheck boilerplate
+func Test(t *testing.T) { TestingT(t) }
+
+var _ = Suite(&StandaloneSuite{})
+
+// Standalone tests
+type StandaloneSuite struct{}
+
+func (s *StandaloneSuite) TestReadIntoBuffer(c *C) {
+ ReadIntoBufferHelper(c, 225)
+ ReadIntoBufferHelper(c, 224)
+}
+
+func HelperWrite128andCheck(c *C, buffer []byte, writer io.Writer, slices chan nextSlice) {
+ out := make([]byte, 128)
+ for i := 0; i < 128; i += 1 {
+ out[i] = byte(i)
+ }
+ writer.Write(out)
+ s1 := <-slices
+ c.Check(len(s1.slice), Equals, 128)
+ c.Check(s1.reader_error, Equals, nil)
+ for i := 0; i < 128; i += 1 {
+ c.Check(s1.slice[i], Equals, byte(i))
+ }
+ for i := 0; i < len(buffer); i += 1 {
+ if i < 128 {
+ c.Check(buffer[i], Equals, byte(i))
+ } else {
+ c.Check(buffer[i], Equals, byte(0))
+ }
+ }
+}
+
+func HelperWrite96andCheck(c *C, buffer []byte, writer io.Writer, slices chan nextSlice) {
+ out := make([]byte, 96)
+ for i := 0; i < 96; i += 1 {
+ out[i] = byte(i / 2)
+ }
+ writer.Write(out)
+ s1 := <-slices
+ c.Check(len(s1.slice), Equals, 96)
+ c.Check(s1.reader_error, Equals, nil)
+ for i := 0; i < 96; i += 1 {
+ c.Check(s1.slice[i], Equals, byte(i/2))
+ }
+ for i := 0; i < len(buffer); i += 1 {
+ if i < 128 {
+ c.Check(buffer[i], Equals, byte(i))
+ } else if i < (128 + 96) {
+ c.Check(buffer[i], Equals, byte((i-128)/2))
+ } else {
+ c.Check(buffer[i], Equals, byte(0))
+ }
+ }
+}
+
+func ReadIntoBufferHelper(c *C, bufsize int) {
+ buffer := make([]byte, bufsize)
+
+ reader, writer := io.Pipe()
+ slices := make(chan nextSlice)
+
+ go readIntoBuffer(buffer, reader, slices)
+
+ HelperWrite128andCheck(c, buffer, writer, slices)
+ HelperWrite96andCheck(c, buffer, writer, slices)
+
+ writer.Close()
+ s1 := <-slices
+ c.Check(len(s1.slice), Equals, 0)
+ c.Check(s1.reader_error, Equals, io.EOF)
+}
+
+func (s *StandaloneSuite) TestReadIntoShortBuffer(c *C) {
+ buffer := make([]byte, 223)
+ reader, writer := io.Pipe()
+ slices := make(chan nextSlice)
+
+ go readIntoBuffer(buffer, reader, slices)
+
+ HelperWrite128andCheck(c, buffer, writer, slices)
+
+ out := make([]byte, 96)
+ for i := 0; i < 96; i += 1 {
+ out[i] = byte(i / 2)
+ }
+
+ // Write will deadlock because it can't write all the data, so
+ // spin it off to a goroutine
+ go writer.Write(out)
+ s1 := <-slices
+
+ c.Check(len(s1.slice), Equals, 95)
+ c.Check(s1.reader_error, Equals, nil)
+ for i := 0; i < 95; i += 1 {
+ c.Check(s1.slice[i], Equals, byte(i/2))
+ }
+ for i := 0; i < len(buffer); i += 1 {
+ if i < 128 {
+ c.Check(buffer[i], Equals, byte(i))
+ } else if i < (128 + 95) {
+ c.Check(buffer[i], Equals, byte((i-128)/2))
+ } else {
+ c.Check(buffer[i], Equals, byte(0))
+ }
+ }
+
+ writer.Close()
+ s1 = <-slices
+ c.Check(len(s1.slice), Equals, 0)
+ c.Check(s1.reader_error, Equals, io.ErrShortBuffer)
+}
+
+func (s *StandaloneSuite) TestTransfer(c *C) {
+ reader, writer := io.Pipe()
+
+ tr := AsyncStreamFromReader(512, reader)
+
+ br1 := tr.MakeStreamReader()
+ out := make([]byte, 128)
+
+ {
+ // Write some data, and read into a buffer shorter than
+ // available data
+ for i := 0; i < 128; i += 1 {
+ out[i] = byte(i)
+ }
+
+ writer.Write(out[:100])
+
+ in := make([]byte, 64)
+ n, err := br1.Read(in)
+
+ c.Check(n, Equals, 64)
+ c.Check(err, Equals, nil)
+
+ for i := 0; i < 64; i += 1 {
+ c.Check(in[i], Equals, out[i])
+ }
+ }
+
+ {
+ // Write some more data, and read into buffer longer than
+ // available data
+ in := make([]byte, 64)
+ n, err := br1.Read(in)
+ c.Check(n, Equals, 36)
+ c.Check(err, Equals, nil)
+
+ for i := 0; i < 36; i += 1 {
+ c.Check(in[i], Equals, out[64+i])
+ }
+
+ }
+
+ {
+ // Test read before write
+ type Rd struct {
+ n int
+ err error
+ }
+ rd := make(chan Rd)
+ in := make([]byte, 64)
+
+ go func() {
+ n, err := br1.Read(in)
+ rd <- Rd{n, err}
+ }()
+
+ time.Sleep(100 * time.Millisecond)
+ writer.Write(out[100:])
+
+ got := <-rd
+
+ c.Check(got.n, Equals, 28)
+ c.Check(got.err, Equals, nil)
+
+ for i := 0; i < 28; i += 1 {
+ c.Check(in[i], Equals, out[100+i])
+ }
+ }
+
+ br2 := tr.MakeStreamReader()
+ {
+ // Test 'catch up' reader
+ in := make([]byte, 256)
+ n, err := br2.Read(in)
+
+ c.Check(n, Equals, 128)
+ c.Check(err, Equals, nil)
+
+ for i := 0; i < 128; i += 1 {
+ c.Check(in[i], Equals, out[i])
+ }
+ }
+
+ {
+ // Test closing the reader
+ writer.Close()
+
+ in := make([]byte, 256)
+ n1, err1 := br1.Read(in)
+ n2, err2 := br2.Read(in)
+ c.Check(n1, Equals, 0)
+ c.Check(err1, Equals, io.EOF)
+ c.Check(n2, Equals, 0)
+ c.Check(err2, Equals, io.EOF)
+ }
+
+ {
+ // Test 'catch up' reader after closing
+ br3 := tr.MakeStreamReader()
+ in := make([]byte, 256)
+ n, err := br3.Read(in)
+
+ c.Check(n, Equals, 128)
+ c.Check(err, Equals, nil)
+
+ for i := 0; i < 128; i += 1 {
+ c.Check(in[i], Equals, out[i])
+ }
+
+ n, err = br3.Read(in)
+
+ c.Check(n, Equals, 0)
+ c.Check(err, Equals, io.EOF)
+ }
+}
+
+func (s *StandaloneSuite) TestTransferShortBuffer(c *C) {
+ reader, writer := io.Pipe()
+
+ tr := AsyncStreamFromReader(100, reader)
+ defer tr.Close()
+
+ sr := tr.MakeStreamReader()
+ defer sr.Close()
+
+ out := make([]byte, 101)
+ go writer.Write(out)
+
+ n, err := sr.Read(out)
+ c.Check(n, Equals, 100)
+
+ n, err = sr.Read(out)
+ c.Check(n, Equals, 0)
+ c.Check(err, Equals, io.ErrShortBuffer)
+}
+
+func (s *StandaloneSuite) TestTransferFromBuffer(c *C) {
+ // Buffer for reads from 'r'
+ buffer := make([]byte, 100)
+ for i := 0; i < 100; i += 1 {
+ buffer[i] = byte(i)
+ }
+
+ tr := AsyncStreamFromSlice(buffer)
+
+ br1 := tr.MakeStreamReader()
+
+ in := make([]byte, 64)
+ {
+ n, err := br1.Read(in)
+
+ c.Check(n, Equals, 64)
+ c.Check(err, Equals, nil)
+
+ for i := 0; i < 64; i += 1 {
+ c.Check(in[i], Equals, buffer[i])
+ }
+ }
+ {
+ n, err := br1.Read(in)
+
+ c.Check(n, Equals, 36)
+ c.Check(err, Equals, nil)
+
+ for i := 0; i < 36; i += 1 {
+ c.Check(in[i], Equals, buffer[64+i])
+ }
+ }
+ {
+ n, err := br1.Read(in)
+
+ c.Check(n, Equals, 0)
+ c.Check(err, Equals, io.EOF)
+ }
+}
+
+func (s *StandaloneSuite) TestTransferIoCopy(c *C) {
+ // Buffer for reads from 'r'
+ buffer := make([]byte, 100)
+ for i := 0; i < 100; i += 1 {
+ buffer[i] = byte(i)
+ }
+
+ tr := AsyncStreamFromSlice(buffer)
+ defer tr.Close()
+
+ br1 := tr.MakeStreamReader()
+ defer br1.Close()
+
+ reader, writer := io.Pipe()
+
+ go func() {
+ p := make([]byte, 100)
+ n, err := reader.Read(p)
+ c.Check(n, Equals, 100)
+ c.Check(err, Equals, nil)
+ c.Check(p, DeepEquals, buffer)
+ }()
+
+ io.Copy(writer, br1)
+}
+
+func (s *StandaloneSuite) TestManyReaders(c *C) {
+ reader, writer := io.Pipe()
+
+ tr := AsyncStreamFromReader(512, reader)
+ defer tr.Close()
+
+ sr := tr.MakeStreamReader()
+ go func() {
+ time.Sleep(100 * time.Millisecond)
+ sr.Close()
+ }()
+
+ for i := 0; i < 200; i += 1 {
+ go func() {
+ br1 := tr.MakeStreamReader()
+ defer br1.Close()
+
+ p := make([]byte, 3)
+ n, err := br1.Read(p)
+ c.Check(n, Equals, 3)
+ c.Check(p[0:3], DeepEquals, []byte("foo"))
+
+ n, err = br1.Read(p)
+ c.Check(n, Equals, 3)
+ c.Check(p[0:3], DeepEquals, []byte("bar"))
+
+ n, err = br1.Read(p)
+ c.Check(n, Equals, 3)
+ c.Check(p[0:3], DeepEquals, []byte("baz"))
+
+ n, err = br1.Read(p)
+ c.Check(n, Equals, 0)
+ c.Check(err, Equals, io.EOF)
+ }()
+ }
+
+ writer.Write([]byte("foo"))
+ writer.Write([]byte("bar"))
+ writer.Write([]byte("baz"))
+ writer.Close()
+}
--- /dev/null
+/* Internal implementation of AsyncStream.
+Outline of operation:
+
+The kernel is the transfer() goroutine. It manages concurrent reads and
+appends to the "body" slice. "body" is a slice of "source_buffer" that
+represents the segment of the buffer that is already filled in and available
+for reading.
+
+To fill in the buffer, transfer() starts the readIntoBuffer() goroutine to read
+from the io.Reader source directly into source_buffer. Each read goes into a
+slice of buffer which spans the section immediately following the end of the
+current "body". Each time a Read completes, a slice representing the the
+section just filled in (or any read errors/EOF) is sent over the "slices"
+channel back to the transfer() function.
+
+Meanwhile, the transfer() function selects() on two channels, the "requests"
+channel and the "slices" channel.
+
+When a message is recieved on the "slices" channel, this means the a new
+section of the buffer has data, or an error is signaled. Since the data has
+been read directly into the source_buffer, it is able to simply increases the
+size of the body slice to encompass the newly filled in section. Then any
+pending reads are serviced with handleReadRequest (described below).
+
+When a message is recieved on the "requests" channel, it means a StreamReader
+wants access to a slice of the buffer. This is passed to handleReadRequest().
+
+The handleReadRequest() function takes a sliceRequest consisting of a buffer
+offset, maximum size, and channel to send the response. If there was an error
+reported from the source reader, it is returned. If the offset is less than
+the size of the body, the request can proceed, and it sends a body slice
+spanning the segment from offset to min(offset+maxsize, end of the body). If
+source reader status is EOF (done filling the buffer) and the read request
+offset is beyond end of the body, it responds with EOF. Otherwise, the read
+request is for a slice beyond the current size of "body" but we expect the body
+to expand as more data is added, so the request gets added to a wait list.
+
+The transfer() runs until the requests channel is closed by AsyncStream.Close()
+
+To track readers, streamer uses the readersMonitor() goroutine. This goroutine
+chooses which channels to receive from based on the number of outstanding
+readers. When a new reader is created, it sends a message on the add_reader
+channel. If the number of readers is already at MAX_READERS, this blocks the
+sender until an existing reader is closed. When a reader is closed, it sends a
+message on the subtract_reader channel. Finally, when AsyncStream.Close() is
+called, it sends a message on the wait_zero_readers channel, which will block
+the sender unless there are zero readers and it is safe to shut down the
+AsyncStream.
+*/
+
+package streamer
+
+import (
+ "io"
+)
+
+const MAX_READERS = 100
+
+// A slice passed from readIntoBuffer() to transfer()
+type nextSlice struct {
+ slice []byte
+ reader_error error
+}
+
+// A read request to the Transfer() function
+type sliceRequest struct {
+ offset int
+ maxsize int
+ result chan<- sliceResult
+}
+
+// A read result from the Transfer() function
+type sliceResult struct {
+ slice []byte
+ err error
+}
+
+// Supports writing into a buffer
+type bufferWriter struct {
+ buf []byte
+ ptr int
+}
+
+// Copy p into this.buf, increment pointer and return number of bytes read.
+func (this *bufferWriter) Write(p []byte) (n int, err error) {
+ n = copy(this.buf[this.ptr:], p)
+ this.ptr += n
+ return n, nil
+}
+
+// Read repeatedly from the reader and write sequentially into the specified
+// buffer, and report each read to channel 'c'. Completes when Reader 'r'
+// reports on the error channel and closes channel 'c'.
+func readIntoBuffer(buffer []byte, r io.Reader, slices chan<- nextSlice) {
+ defer close(slices)
+
+ if writeto, ok := r.(io.WriterTo); ok {
+ n, err := writeto.WriteTo(&bufferWriter{buffer, 0})
+ if err != nil {
+ slices <- nextSlice{nil, err}
+ } else {
+ slices <- nextSlice{buffer[:n], nil}
+ slices <- nextSlice{nil, io.EOF}
+ }
+ return
+ } else {
+ // Initially entire buffer is available
+ ptr := buffer[:]
+ for {
+ var n int
+ var err error
+ if len(ptr) > 0 {
+ const readblock = 64 * 1024
+ // Read 64KiB into the next part of the buffer
+ if len(ptr) > readblock {
+ n, err = r.Read(ptr[:readblock])
+ } else {
+ n, err = r.Read(ptr)
+ }
+ } else {
+ // Ran out of buffer space, try reading one more byte
+ var b [1]byte
+ n, err = r.Read(b[:])
+
+ if n > 0 {
+ // Reader has more data but we have nowhere to
+ // put it, so we're stuffed
+ slices <- nextSlice{nil, io.ErrShortBuffer}
+ } else {
+ // Return some other error (hopefully EOF)
+ slices <- nextSlice{nil, err}
+ }
+ return
+ }
+
+ // End on error (includes EOF)
+ if err != nil {
+ slices <- nextSlice{nil, err}
+ return
+ }
+
+ if n > 0 {
+ // Make a slice with the contents of the read
+ slices <- nextSlice{ptr[:n], nil}
+
+ // Adjust the scratch space slice
+ ptr = ptr[n:]
+ }
+ }
+ }
+}
+
+// Handle a read request. Returns true if a response was sent, and false if
+// the request should be queued.
+func handleReadRequest(req sliceRequest, body []byte, reader_status error) bool {
+ if (reader_status != nil) && (reader_status != io.EOF) {
+ req.result <- sliceResult{nil, reader_status}
+ return true
+ } else if req.offset < len(body) {
+ var end int
+ if req.offset+req.maxsize < len(body) {
+ end = req.offset + req.maxsize
+ } else {
+ end = len(body)
+ }
+ req.result <- sliceResult{body[req.offset:end], nil}
+ return true
+ } else if (reader_status == io.EOF) && (req.offset >= len(body)) {
+ req.result <- sliceResult{nil, io.EOF}
+ return true
+ } else {
+ return false
+ }
+}
+
+// Mediates between reads and appends.
+// If 'source_reader' is not nil, reads data from 'source_reader' and stores it
+// in the provided buffer. Otherwise, use the contents of 'buffer' as is.
+// Accepts read requests on the buffer on the 'requests' channel. Completes
+// when 'requests' channel is closed.
+func (this *AsyncStream) transfer(source_reader io.Reader) {
+ source_buffer := this.buffer
+ requests := this.requests
+
+ // currently buffered data
+ var body []byte
+
+ // for receiving slices from readIntoBuffer
+ var slices chan nextSlice = nil
+
+ // indicates the status of the underlying reader
+ var reader_status error = nil
+
+ if source_reader != nil {
+ // 'body' is the buffer slice representing the body content read so far
+ body = source_buffer[:0]
+
+ // used to communicate slices of the buffer as they are
+ // readIntoBuffer will close 'slices' when it is done with it
+ slices = make(chan nextSlice)
+
+ // Spin it off
+ go readIntoBuffer(source_buffer, source_reader, slices)
+ } else {
+ // use the whole buffer
+ body = source_buffer[:]
+
+ // buffer is complete
+ reader_status = io.EOF
+ }
+
+ pending_requests := make([]sliceRequest, 0)
+
+ for {
+ select {
+ case req, valid := <-requests:
+ // Handle a buffer read request
+ if valid {
+ if !handleReadRequest(req, body, reader_status) {
+ pending_requests = append(pending_requests, req)
+ }
+ } else {
+ // closed 'requests' channel indicates we're done
+ return
+ }
+
+ case bk, valid := <-slices:
+ // Got a new slice from the reader
+ if valid {
+ reader_status = bk.reader_error
+
+ if bk.slice != nil {
+ // adjust body bounds now that another slice has been read
+ body = source_buffer[0 : len(body)+len(bk.slice)]
+ }
+
+ // handle pending reads
+ n := 0
+ for n < len(pending_requests) {
+ if handleReadRequest(pending_requests[n], body, reader_status) {
+ // move the element from the back of the slice to
+ // position 'n', then shorten the slice by one element
+ pending_requests[n] = pending_requests[len(pending_requests)-1]
+ pending_requests = pending_requests[0 : len(pending_requests)-1]
+ } else {
+
+ // Request wasn't handled, so keep it in the request slice
+ n += 1
+ }
+ }
+ } else {
+ if reader_status == io.EOF {
+ // no more reads expected, so this is ok
+ } else {
+ // slices channel closed without signaling EOF
+ reader_status = io.ErrUnexpectedEOF
+ }
+ slices = nil
+ }
+ }
+ }
+}
+
+func (this *AsyncStream) readersMonitor() {
+ var readers int = 0
+
+ for {
+ if readers == 0 {
+ select {
+ case _, ok := <-this.wait_zero_readers:
+ if ok {
+ // nothing, just implicitly unblock the sender
+ } else {
+ return
+ }
+ case _, ok := <-this.add_reader:
+ if ok {
+ readers += 1
+ } else {
+ return
+ }
+ }
+ } else if readers > 0 && readers < MAX_READERS {
+ select {
+ case _, ok := <-this.add_reader:
+ if ok {
+ readers += 1
+ } else {
+ return
+ }
+
+ case _, ok := <-this.subtract_reader:
+ if ok {
+ readers -= 1
+ } else {
+ return
+ }
+ }
+ } else if readers == MAX_READERS {
+ _, ok := <-this.subtract_reader
+ if ok {
+ readers -= 1
+ } else {
+ return
+ }
+ }
+ }
+}
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry including="**/*.java" kind="src" output="target/test-classes" path="src/test/java"/>
+ <classpathentry including="**/*.java" kind="src" path="src/main/java"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="var" path="M2_REPO/com/google/apis/google-api-services-discovery/v1-rev42-1.18.0-rc/google-api-services-discovery-v1-rev42-1.18.0-rc.jar"/>
+ <classpathentry kind="var" path="M2_REPO/com/google/api-client/google-api-client/1.18.0-rc/google-api-client-1.18.0-rc.jar"/>
+ <classpathentry kind="var" path="M2_REPO/com/google/http-client/google-http-client/1.18.0-rc/google-http-client-1.18.0-rc.jar"/>
+ <classpathentry kind="var" path="M2_REPO/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar"/>
+ <classpathentry kind="var" path="M2_REPO/org/apache/httpcomponents/httpclient/4.0.1/httpclient-4.0.1.jar"/>
+ <classpathentry kind="var" path="M2_REPO/org/apache/httpcomponents/httpcore/4.0.1/httpcore-4.0.1.jar"/>
+ <classpathentry kind="var" path="M2_REPO/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar"/>
+ <classpathentry kind="var" path="M2_REPO/commons-codec/commons-codec/1.3/commons-codec-1.3.jar"/>
+ <classpathentry kind="var" path="M2_REPO/com/google/http-client/google-http-client-jackson2/1.18.0-rc/google-http-client-jackson2-1.18.0-rc.jar"/>
+ <classpathentry kind="var" path="M2_REPO/com/fasterxml/jackson/core/jackson-core/2.1.3/jackson-core-2.1.3.jar"/>
+ <classpathentry kind="var" path="M2_REPO/com/google/guava/guava/r05/guava-r05.jar"/>
+ <classpathentry kind="var" path="M2_REPO/log4j/log4j/1.2.16/log4j-1.2.16.jar"/>
+ <classpathentry kind="var" path="M2_REPO/com/googlecode/json-simple/json-simple/1.1.1/json-simple-1.1.1.jar"/>
+ <classpathentry kind="var" path="M2_REPO/junit/junit/4.8.1/junit-4.8.1.jar"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>java</name>
+ <comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
+ <projects/>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>
\ No newline at end of file
--- /dev/null
+#Mon Apr 28 10:33:40 EDT 2014
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
--- /dev/null
+/**
+ * This Sample test program is useful in getting started with working with Arvados Java SDK.
+ * @author radhika
+ *
+ */
+
+import org.arvados.sdk.java.Arvados;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+public class ArvadosSDKJavaExample {
+ /** Make sure the following environment variables are set before using Arvados:
+ * ARVADOS_API_TOKEN, ARVADOS_API_HOST and ARVADOS_API_HOST_INSECURE
+ * Set ARVADOS_API_HOST_INSECURE to true if you are using self-singed
+ * certificates in development and want to bypass certificate validations.
+ *
+ * If you are not using env variables, you can pass them to Arvados constructor.
+ *
+ * Please refer to http://doc.arvados.org/api/index.html for a complete list
+ * of the available API methods.
+ */
+ public static void main(String[] args) throws Exception {
+ String apiName = "arvados";
+ String apiVersion = "v1";
+
+ Arvados arv = new Arvados(apiName, apiVersion);
+
+ // Make a users list call. Here list on users is the method being invoked.
+ // Expect a Map containing the list of users as the response.
+ System.out.println("Making an arvados users.list api call");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("users", "list", params);
+ System.out.println("Arvados users.list:\n");
+ printResponse(response);
+
+ // get uuid of the first user from the response
+ List items = (List)response.get("items");
+
+ Map firstUser = (Map)items.get(0);
+ String userUuid = (String)firstUser.get("uuid");
+
+ // Make a users get call on the uuid obtained above
+ System.out.println("\n\n\nMaking a users.get call for " + userUuid);
+ params = new HashMap<String, Object>();
+ params.put("uuid", userUuid);
+ response = arv.call("users", "get", params);
+ System.out.println("Arvados users.get:\n");
+ printResponse(response);
+
+ // Make a pipeline_templates list call
+ System.out.println("\n\n\nMaking a pipeline_templates.list call.");
+
+ params = new HashMap<String, Object>();
+ response = arv.call("pipeline_templates", "list", params);
+
+ System.out.println("Arvados pipelinetempates.list:\n");
+ printResponse(response);
+ }
+
+ private static void printResponse(Map response){
+ Set<Entry<String,Object>> entrySet = (Set<Entry<String,Object>>)response.entrySet();
+ for (Map.Entry<String, Object> entry : entrySet) {
+ if ("items".equals(entry.getKey())) {
+ List items = (List)entry.getValue();
+ for (Object item : items) {
+ System.out.println(" " + item);
+ }
+ } else {
+ System.out.println(entry.getKey() + " = " + entry.getValue());
+ }
+ }
+ }
+}
\ No newline at end of file
--- /dev/null
+/**
+ * This Sample test program is useful in getting started with using Arvados Java SDK.
+ * This program creates an Arvados instance using the configured environment variables.
+ * It then provides a prompt to input method name and input parameters.
+ * The program them invokes the API server to execute the specified method.
+ *
+ * @author radhika
+ */
+
+import org.arvados.sdk.java.Arvados;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+
+public class ArvadosSDKJavaExampleWithPrompt {
+ /**
+ * Make sure the following environment variables are set before using Arvados:
+ * ARVADOS_API_TOKEN, ARVADOS_API_HOST and ARVADOS_API_HOST_INSECURE Set
+ * ARVADOS_API_HOST_INSECURE to true if you are using self-singed certificates
+ * in development and want to bypass certificate validations.
+ *
+ * Please refer to http://doc.arvados.org/api/index.html for a complete list
+ * of the available API methods.
+ */
+ public static void main(String[] args) throws Exception {
+ String apiName = "arvados";
+ String apiVersion = "v1";
+
+ System.out.print("Welcome to Arvados Java SDK.");
+ System.out.println("\nYou can use this example to call API methods interactively.");
+ System.out.println("\nPlease refer to http://doc.arvados.org/api/index.html for api documentation");
+ System.out.println("\nTo make the calls, enter input data at the prompt.");
+ System.out.println("When entering parameters, you may enter a simple string or a well-formed json.");
+ System.out.println("For example to get a user you may enter: user, zzzzz-12345-67890");
+ System.out.println("Or to filter links, you may enter: filters, [[ \"name\", \"=\", \"can_manage\"]]");
+
+ System.out.println("\nEnter ^C when you want to quit");
+
+ // use configured env variables for API TOKEN, HOST and HOST_INSECURE
+ Arvados arv = new Arvados(apiName, apiVersion);
+
+ while (true) {
+ try {
+ // prompt for resource
+ System.out.println("\n\nEnter Resource name (for example users)");
+ System.out.println("\nAvailable resources are: " + arv.getAvailableResourses());
+ System.out.print("\n>>> ");
+
+ // read resource name
+ BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
+ String resourceName = in.readLine().trim();
+ if ("".equals(resourceName)) {
+ throw (new Exception("No resource name entered"));
+ }
+ // read method name
+ System.out.println("\nEnter method name (for example get)");
+ System.out.println("\nAvailable methods are: " + arv.getAvailableMethodsForResourse(resourceName));
+ System.out.print("\n>>> ");
+ String methodName = in.readLine().trim();
+ if ("".equals(methodName)) {
+ throw (new Exception("No method name entered"));
+ }
+
+ // read method parameters
+ System.out.println("\nEnter parameter name, value (for example uuid, uuid-value)");
+ System.out.println("\nAvailable parameters are: " +
+ arv.getAvailableParametersForMethod(resourceName, methodName));
+
+ System.out.print("\n>>> ");
+ Map paramsMap = new HashMap();
+ String param = "";
+ try {
+ do {
+ param = in.readLine();
+ if (param.isEmpty())
+ break;
+ int index = param.indexOf(","); // first comma
+ String paramName = param.substring(0, index);
+ String paramValue = param.substring(index+1);
+ paramsMap.put(paramName.trim(), paramValue.trim());
+
+ System.out.println("\nEnter parameter name, value (for example uuid, uuid-value)");
+ System.out.print("\n>>> ");
+ } while (!param.isEmpty());
+ } catch (Exception e) {
+ System.out.println (e.getMessage());
+ System.out.println ("\nSet up a new call");
+ continue;
+ }
+
+ // Make a "call" for the given resource name and method name
+ try {
+ System.out.println ("Making a call for " + resourceName + " " + methodName);
+ Map response = arv.call(resourceName, methodName, paramsMap);
+
+ Set<Entry<String,Object>> entrySet = (Set<Entry<String,Object>>)response.entrySet();
+ for (Map.Entry<String, Object> entry : entrySet) {
+ if ("items".equals(entry.getKey())) {
+ List items = (List)entry.getValue();
+ for (Object item : items) {
+ System.out.println(" " + item);
+ }
+ } else {
+ System.out.println(entry.getKey() + " = " + entry.getValue());
+ }
+ }
+ } catch (Exception e){
+ System.out.println (e.getMessage());
+ System.out.println ("\nSet up a new call");
+ }
+ } catch (Exception e) {
+ System.out.println (e.getMessage());
+ System.out.println ("\nSet up a new call");
+ }
+ }
+ }
+}
--- /dev/null
+Welcome to Arvados Java SDK.
+
+Please refer to http://doc.arvados.org/sdk/java/index.html to get started
+ with Arvados Java SDK.
--- /dev/null
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.arvados.sdk.java</groupId>
+ <artifactId>java</artifactId>
+ <packaging>jar</packaging>
+ <version>1.0-SNAPSHOT</version>
+ <name>java</name>
+ <url>http://maven.apache.org</url>
+
+ <dependencies>
+ <dependency>
+ <groupId>com.google.apis</groupId>
+ <artifactId>google-api-services-discovery</artifactId>
+ <version>v1-rev42-1.18.0-rc</version>
+ </dependency>
+ <dependency>
+ <groupId>com.google.api-client</groupId>
+ <artifactId>google-api-client</artifactId>
+ <version>1.18.0-rc</version>
+ </dependency>
+ <dependency>
+ <groupId>com.google.http-client</groupId>
+ <artifactId>google-http-client-jackson2</artifactId>
+ <version>1.18.0-rc</version>
+ </dependency>
+ <dependency>
+ <groupId>com.google.guava</groupId>
+ <artifactId>guava</artifactId>
+ <version>r05</version>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>1.2.16</version>
+ </dependency>
+ <dependency>
+ <groupId>com.googlecode.json-simple</groupId>
+ <artifactId>json-simple</artifactId>
+ <version>1.1.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.1</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <finalName>arvados-sdk-1.0</finalName>
+
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>3.1</version>
+ <configuration>
+ <source>1.6</source>
+ <target>1.6</target>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <executions>
+ <execution>
+ <goals>
+ <goal>attached</goal>
+ </goals>
+ <phase>package</phase>
+ <configuration>
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ <archive>
+ <manifest>
+ <mainClass>org.arvados.sdk.Arvados</mainClass>
+ </manifest>
+ <manifestEntries>
+ <!--<Premain-Class>Your.agent.class</Premain-Class> <Agent-Class>Your.agent.class</Agent-Class> -->
+ <Can-Redefine-Classes>true</Can-Redefine-Classes>
+ <Can-Retransform-Classes>true</Can-Retransform-Classes>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ <targetPath>${basedir}/target/classes</targetPath>
+ <includes>
+ <include>log4j.properties</include>
+ </includes>
+ <filtering>true</filtering>
+ </resource>
+ <resource>
+ <directory>src/test/resources</directory>
+ <filtering>true</filtering>
+ </resource>
+ </resources>
+ </build>
+</project>
--- /dev/null
+package org.arvados.sdk.java;
+
+import com.google.api.client.http.javanet.*;
+import com.google.api.client.http.ByteArrayContent;
+import com.google.api.client.http.GenericUrl;
+import com.google.api.client.http.HttpContent;
+import com.google.api.client.http.HttpRequest;
+import com.google.api.client.http.HttpRequestFactory;
+import com.google.api.client.http.HttpTransport;
+import com.google.api.client.http.UriTemplate;
+import com.google.api.client.json.JsonFactory;
+import com.google.api.client.json.jackson2.JacksonFactory;
+import com.google.api.client.util.Maps;
+import com.google.api.services.discovery.Discovery;
+import com.google.api.services.discovery.model.JsonSchema;
+import com.google.api.services.discovery.model.RestDescription;
+import com.google.api.services.discovery.model.RestMethod;
+import com.google.api.services.discovery.model.RestMethod.Request;
+import com.google.api.services.discovery.model.RestResource;
+
+import java.math.BigDecimal;
+import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+
+/**
+ * This class provides a java SDK interface to Arvados API server.
+ *
+ * Please refer to http://doc.arvados.org/api/ to learn about the
+ * various resources and methods exposed by the API server.
+ *
+ * @author radhika
+ */
+public class Arvados {
+ // HttpTransport and JsonFactory are thread-safe. So, use global instances.
+ private HttpTransport httpTransport;
+ private final JsonFactory jsonFactory = JacksonFactory.getDefaultInstance();
+
+ private String arvadosApiToken;
+ private String arvadosApiHost;
+ private boolean arvadosApiHostInsecure;
+
+ private String arvadosRootUrl;
+
+ private static final Logger logger = Logger.getLogger(Arvados.class);
+
+ // Get it once and reuse on the call requests
+ RestDescription restDescription = null;
+ String apiName = null;
+ String apiVersion = null;
+
+ public Arvados (String apiName, String apiVersion) throws Exception {
+ this (apiName, apiVersion, null, null, null);
+ }
+
+ public Arvados (String apiName, String apiVersion, String token,
+ String host, String hostInsecure) throws Exception {
+ this.apiName = apiName;
+ this.apiVersion = apiVersion;
+
+ // Read needed environmental variables if they are not passed
+ if (token != null) {
+ arvadosApiToken = token;
+ } else {
+ arvadosApiToken = System.getenv().get("ARVADOS_API_TOKEN");
+ if (arvadosApiToken == null) {
+ throw new Exception("Missing environment variable: ARVADOS_API_TOKEN");
+ }
+ }
+
+ if (host != null) {
+ arvadosApiHost = host;
+ } else {
+ arvadosApiHost = System.getenv().get("ARVADOS_API_HOST");
+ if (arvadosApiHost == null) {
+ throw new Exception("Missing environment variable: ARVADOS_API_HOST");
+ }
+ }
+ arvadosRootUrl = "https://" + arvadosApiHost;
+ arvadosRootUrl += (arvadosApiHost.endsWith("/")) ? "" : "/";
+
+ if (hostInsecure != null) {
+ arvadosApiHostInsecure = Boolean.valueOf(hostInsecure);
+ } else {
+ arvadosApiHostInsecure =
+ "true".equals(System.getenv().get("ARVADOS_API_HOST_INSECURE")) ? true : false;
+ }
+
+ // Create HTTP_TRANSPORT object
+ NetHttpTransport.Builder builder = new NetHttpTransport.Builder();
+ if (arvadosApiHostInsecure) {
+ builder.doNotValidateCertificate();
+ }
+ httpTransport = builder.build();
+
+ // initialize rest description
+ restDescription = loadArvadosApi();
+ }
+
+ /**
+ * Make a call to API server with the provide call information.
+ * @param resourceName
+ * @param methodName
+ * @param paramsMap
+ * @return Map
+ * @throws Exception
+ */
+ public Map call(String resourceName, String methodName,
+ Map<String, Object> paramsMap) throws Exception {
+ RestMethod method = getMatchingMethod(resourceName, methodName);
+
+ HashMap<String, Object> parameters = loadParameters(paramsMap, method);
+
+ GenericUrl url = new GenericUrl(UriTemplate.expand(
+ arvadosRootUrl + restDescription.getBasePath() + method.getPath(),
+ parameters, true));
+
+ try {
+ // construct the request
+ HttpRequestFactory requestFactory;
+ requestFactory = httpTransport.createRequestFactory();
+
+ // possibly required content
+ HttpContent content = null;
+
+ if (!method.getHttpMethod().equals("GET") &&
+ !method.getHttpMethod().equals("DELETE")) {
+ String objectName = resourceName.substring(0, resourceName.length()-1);
+ Object requestBody = paramsMap.get(objectName);
+ if (requestBody == null) {
+ error("POST method requires content object " + objectName);
+ }
+
+ content = new ByteArrayContent("application/json",((String)requestBody).getBytes());
+ }
+
+ HttpRequest request =
+ requestFactory.buildRequest(method.getHttpMethod(), url, content);
+
+ // make the request
+ List<String> authHeader = new ArrayList<String>();
+ authHeader.add("OAuth2 " + arvadosApiToken);
+ request.getHeaders().put("Authorization", authHeader);
+ String response = request.execute().parseAsString();
+
+ Map responseMap = jsonFactory.createJsonParser(response).parse(HashMap.class);
+
+ logger.debug(responseMap);
+
+ return responseMap;
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * Get all supported resources by the API
+ * @return Set
+ */
+ public Set<String> getAvailableResourses() {
+ return (restDescription.getResources().keySet());
+ }
+
+ /**
+ * Get all supported method names for the given resource
+ * @param resourceName
+ * @return Set
+ * @throws Exception
+ */
+ public Set<String> getAvailableMethodsForResourse(String resourceName)
+ throws Exception {
+ Map<String, RestMethod> methodMap = getMatchingMethodMap (resourceName);
+ return (methodMap.keySet());
+ }
+
+ /**
+ * Get the parameters for the method in the resource sought.
+ * @param resourceName
+ * @param methodName
+ * @return Set
+ * @throws Exception
+ */
+ public Map<String,List<String>> getAvailableParametersForMethod(String resourceName, String methodName)
+ throws Exception {
+ RestMethod method = getMatchingMethod(resourceName, methodName);
+ Map<String, List<String>> parameters = new HashMap<String, List<String>>();
+ List<String> requiredParameters = new ArrayList<String>();
+ List<String> optionalParameters = new ArrayList<String>();
+ parameters.put ("required", requiredParameters);
+ parameters.put("optional", optionalParameters);
+
+ try {
+ // get any request parameters
+ Request request = method.getRequest();
+ if (request != null) {
+ Object required = request.get("required");
+ Object requestProperties = request.get("properties");
+ if (requestProperties != null) {
+ if (requestProperties instanceof Map) {
+ Map properties = (Map)requestProperties;
+ Set<String> propertyKeys = properties.keySet();
+ for (String property : propertyKeys) {
+ if (Boolean.TRUE.equals(required)) {
+ requiredParameters.add(property);
+ } else {
+ optionalParameters.add(property);
+ }
+ }
+ }
+ }
+ }
+
+ // get other listed parameters
+ Map<String,JsonSchema> methodParameters = method.getParameters();
+ for (Map.Entry<String, JsonSchema> entry : methodParameters.entrySet()) {
+ if (Boolean.TRUE.equals(entry.getValue().getRequired())) {
+ requiredParameters.add(entry.getKey());
+ } else {
+ optionalParameters.add(entry.getKey());
+ }
+ }
+ } catch (Exception e){
+ logger.error(e);
+ }
+
+ return parameters;
+ }
+
+ private HashMap<String, Object> loadParameters(Map<String, Object> paramsMap,
+ RestMethod method) throws Exception {
+ HashMap<String, Object> parameters = Maps.newHashMap();
+
+ // required parameters
+ if (method.getParameterOrder() != null) {
+ for (String parameterName : method.getParameterOrder()) {
+ JsonSchema parameter = method.getParameters().get(parameterName);
+ if (Boolean.TRUE.equals(parameter.getRequired())) {
+ Object parameterValue = paramsMap.get(parameterName);
+ if (parameterValue == null) {
+ error("missing required parameter: " + parameter);
+ } else {
+ putParameter(null, parameters, parameterName, parameter, parameterValue);
+ }
+ }
+ }
+ }
+
+ for (Map.Entry<String, Object> entry : paramsMap.entrySet()) {
+ String parameterName = entry.getKey();
+ Object parameterValue = entry.getValue();
+
+ if (parameterName.equals("contentType")) {
+ if (method.getHttpMethod().equals("GET") || method.getHttpMethod().equals("DELETE")) {
+ error("HTTP content type cannot be specified for this method: " + parameterName);
+ }
+ } else {
+ JsonSchema parameter = null;
+ if (restDescription.getParameters() != null) {
+ parameter = restDescription.getParameters().get(parameterName);
+ }
+ if (parameter == null && method.getParameters() != null) {
+ parameter = method.getParameters().get(parameterName);
+ }
+ putParameter(parameterName, parameters, parameterName, parameter, parameterValue);
+ }
+ }
+
+ return parameters;
+ }
+
+ private RestMethod getMatchingMethod(String resourceName, String methodName)
+ throws Exception {
+ Map<String, RestMethod> methodMap = getMatchingMethodMap(resourceName);
+
+ if (methodName == null) {
+ error("missing method name");
+ }
+
+ RestMethod method =
+ methodMap == null ? null : methodMap.get(methodName);
+ if (method == null) {
+ error("method not found: ");
+ }
+
+ return method;
+ }
+
+ private Map<String, RestMethod> getMatchingMethodMap(String resourceName)
+ throws Exception {
+ if (resourceName == null) {
+ error("missing resource name");
+ }
+
+ Map<String, RestMethod> methodMap = null;
+ Map<String, RestResource> resources = restDescription.getResources();
+ RestResource resource = resources.get(resourceName);
+ if (resource == null) {
+ error("resource not found");
+ }
+ methodMap = resource.getMethods();
+ return methodMap;
+ }
+
+ /**
+ * Not thread-safe. So, create for each request.
+ * @param apiName
+ * @param apiVersion
+ * @return
+ * @throws Exception
+ */
+ private RestDescription loadArvadosApi()
+ throws Exception {
+ try {
+ Discovery discovery;
+
+ Discovery.Builder discoveryBuilder =
+ new Discovery.Builder(httpTransport, jsonFactory, null);
+
+ discoveryBuilder.setRootUrl(arvadosRootUrl);
+ discoveryBuilder.setApplicationName(apiName);
+
+ discovery = discoveryBuilder.build();
+
+ return discovery.apis().getRest(apiName, apiVersion).execute();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * Convert the input parameter into its equivalent json string.
+ * Add this json string value to the parameters map to be sent to server.
+ * @param argName
+ * @param parameters
+ * @param parameterName
+ * @param parameter
+ * @param parameterValue
+ * @throws Exception
+ */
+ private void putParameter(String argName, Map<String, Object> parameters,
+ String parameterName, JsonSchema parameter, Object parameterValue)
+ throws Exception {
+ Object value = parameterValue;
+ if (parameter != null) {
+ if ("boolean".equals(parameter.getType())) {
+ value = Boolean.valueOf(parameterValue.toString());
+ } else if ("number".equals(parameter.getType())) {
+ value = new BigDecimal(parameterValue.toString());
+ } else if ("integer".equals(parameter.getType())) {
+ value = new BigInteger(parameterValue.toString());
+ } else if ("float".equals(parameter.getType())) {
+ value = new BigDecimal(parameterValue.toString());
+ } else if ("Java.util.Calendar".equals(parameter.getType())) {
+ value = new BigDecimal(parameterValue.toString());
+ } else if (("array".equals(parameter.getType())) ||
+ ("Array".equals(parameter.getType()))) {
+ if (parameterValue.getClass().isArray()){
+ value = getJsonValueFromArrayType(parameterValue);
+ } else if (List.class.isAssignableFrom(parameterValue.getClass())) {
+ value = getJsonValueFromListType(parameterValue);
+ }
+ } else if (("Hash".equals(parameter.getType())) ||
+ ("hash".equals(parameter.getType()))) {
+ value = getJsonValueFromMapType(parameterValue);
+ } else {
+ if (parameterValue.getClass().isArray()){
+ value = getJsonValueFromArrayType(parameterValue);
+ } else if (List.class.isAssignableFrom(parameterValue.getClass())) {
+ value = getJsonValueFromListType(parameterValue);
+ } else if (Map.class.isAssignableFrom(parameterValue.getClass())) {
+ value = getJsonValueFromMapType(parameterValue);
+ }
+ }
+ }
+
+ parameters.put(parameterName, value);
+ }
+
+ /**
+ * Convert the given input array into json string before sending to server.
+ * @param parameterValue
+ * @return
+ */
+ private String getJsonValueFromArrayType (Object parameterValue) {
+ String arrayStr = Arrays.deepToString((Object[])parameterValue);
+
+ // we can expect either an array of array objects or an array of objects
+ if (arrayStr.startsWith("[[") && arrayStr.endsWith("]]")) {
+ Object[][] array = new Object[1][];
+ arrayStr = arrayStr.substring(2, arrayStr.length()-2);
+ String jsonStr = getJsonStringForArrayStr(arrayStr);
+ String value = "[" + jsonStr + "]";
+ return value;
+ } else {
+ arrayStr = arrayStr.substring(1, arrayStr.length()-1);
+ return (getJsonStringForArrayStr(arrayStr));
+ }
+ }
+
+ private String getJsonStringForArrayStr(String arrayStr) {
+ Object[] array = arrayStr.split(",");
+ Object[] trimmedArray = new Object[array.length];
+ for (int i=0; i<array.length; i++){
+ trimmedArray[i] = array[i].toString().trim();
+ }
+ String value = JSONArray.toJSONString(Arrays.asList(trimmedArray));
+ return value;
+ }
+
+ /**
+ * Convert the given input List into json string before sending to server.
+ * @param parameterValue
+ * @return
+ */
+ private String getJsonValueFromListType (Object parameterValue) {
+ List paramList = (List)parameterValue;
+ Object[] array = new Object[paramList.size()];
+ Arrays.deepToString(paramList.toArray(array));
+ return (getJsonValueFromArrayType(array));
+ }
+
+ /**
+ * Convert the given input map into json string before sending to server.
+ * @param parameterValue
+ * @return
+ */
+ private String getJsonValueFromMapType (Object parameterValue) {
+ JSONObject json = new JSONObject((Map)parameterValue);
+ return json.toString();
+ }
+
+ private static void error(String detail) throws Exception {
+ String errorDetail = "ERROR: " + detail;
+
+ logger.debug(errorDetail);
+ throw new Exception(errorDetail);
+ }
+
+ public static void main(String[] args){
+ System.out.println("Welcome to Arvados Java SDK.");
+ System.out.println("Please refer to http://doc.arvados.org/sdk/java/index.html to get started with the the SDK.");
+ }
+
+}
--- /dev/null
+package org.arvados.sdk.java;
+
+import com.google.api.client.util.Lists;
+import com.google.api.client.util.Sets;
+
+import java.util.ArrayList;
+import java.util.SortedSet;
+
+public class MethodDetails implements Comparable<MethodDetails> {
+ String name;
+ ArrayList<String> requiredParameters = Lists.newArrayList();
+ SortedSet<String> optionalParameters = Sets.newTreeSet();
+ boolean hasContent;
+
+ @Override
+ public int compareTo(MethodDetails o) {
+ if (o == this) {
+ return 0;
+ }
+ return name.compareTo(o.name);
+ }
+}
\ No newline at end of file
--- /dev/null
+# To change log location, change log4j.appender.fileAppender.File
+
+log4j.rootLogger=DEBUG, fileAppender
+
+log4j.appender.fileAppender=org.apache.log4j.RollingFileAppender
+log4j.appender.fileAppender.File=${basedir}/log/arvados_sdk_java.log
+log4j.appender.fileAppender.Append=true
+log4j.appender.file.MaxFileSize=10MB
+log4j.appender.file.MaxBackupIndex=10
+log4j.appender.fileAppender.layout=org.apache.log4j.PatternLayout
+log4j.appender.fileAppender.layout.ConversionPattern=[%d] %-5p %c %L %x - %m%n
--- /dev/null
+package org.arvados.sdk.java;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.math.BigDecimal;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+/**
+ * Unit test for Arvados.
+ */
+public class ArvadosTest {
+
+ /**
+ * Test users.list api
+ * @throws Exception
+ */
+ @Test
+ public void testCallUsersList() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("users", "list", params);
+ assertEquals("Expected kind to be users.list", "arvados#userList", response.get("kind"));
+
+ List items = (List)response.get("items");
+ assertNotNull("expected users list items", items);
+ assertTrue("expected at least one item in users list", items.size()>0);
+
+ Map firstUser = (Map)items.get(0);
+ assertNotNull ("Expcted at least one user", firstUser);
+
+ assertEquals("Expected kind to be user", "arvados#user", firstUser.get("kind"));
+ assertNotNull("Expected uuid for first user", firstUser.get("uuid"));
+ }
+
+ /**
+ * Test users.get <uuid> api
+ * @throws Exception
+ */
+ @Test
+ public void testCallUsersGet() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ // call user.system and get uuid of this user
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("users", "list", params);
+
+ assertNotNull("expected users list", response);
+ List items = (List)response.get("items");
+ assertNotNull("expected users list items", items);
+
+ Map firstUser = (Map)items.get(0);
+ String userUuid = (String)firstUser.get("uuid");
+
+ // invoke users.get with the system user uuid
+ params = new HashMap<String, Object>();
+ params.put("uuid", userUuid);
+
+ response = arv.call("users", "get", params);
+
+ assertNotNull("Expected uuid for first user", response.get("uuid"));
+ assertEquals("Expected system user uuid", userUuid, response.get("uuid"));
+ }
+
+ /**
+ * Test users.create api
+ * @throws Exception
+ */
+ @Test
+ public void testCreateUser() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+ params.put("user", "{}");
+ Map response = arv.call("users", "create", params);
+
+ assertEquals("Expected kind to be user", "arvados#user", response.get("kind"));
+
+ Object uuid = response.get("uuid");
+ assertNotNull("Expected uuid for first user", uuid);
+
+ // delete the object
+ params = new HashMap<String, Object>();
+ params.put("uuid", uuid);
+ response = arv.call("users", "delete", params);
+
+ // invoke users.get with the system user uuid
+ params = new HashMap<String, Object>();
+ params.put("uuid", uuid);
+
+ Exception caught = null;
+ try {
+ arv.call("users", "get", params);
+ } catch (Exception e) {
+ caught = e;
+ }
+
+ assertNotNull ("expected exception", caught);
+ assertTrue ("Expected 404", caught.getMessage().contains("Path not found"));
+ }
+
+ @Test
+ public void testCreateUserWithMissingRequiredParam() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Exception caught = null;
+ try {
+ arv.call("users", "create", params);
+ } catch (Exception e) {
+ caught = e;
+ }
+
+ assertNotNull ("expected exception", caught);
+ assertTrue ("Expected POST method requires content object user",
+ caught.getMessage().contains("ERROR: POST method requires content object user"));
+ }
+
+ /**
+ * Test users.create api
+ * @throws Exception
+ */
+ @Test
+ public void testCreateAndUpdateUser() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+ params.put("user", "{}");
+ Map response = arv.call("users", "create", params);
+
+ assertEquals("Expected kind to be user", "arvados#user", response.get("kind"));
+
+ Object uuid = response.get("uuid");
+ assertNotNull("Expected uuid for first user", uuid);
+
+ // update this user
+ params = new HashMap<String, Object>();
+ params.put("user", "{}");
+ params.put("uuid", uuid);
+ response = arv.call("users", "update", params);
+
+ assertEquals("Expected kind to be user", "arvados#user", response.get("kind"));
+
+ uuid = response.get("uuid");
+ assertNotNull("Expected uuid for first user", uuid);
+
+ // delete the object
+ params = new HashMap<String, Object>();
+ params.put("uuid", uuid);
+ response = arv.call("users", "delete", params);
+ }
+
+ /**
+ * Test unsupported api version api
+ * @throws Exception
+ */
+ @Test
+ public void testUnsupportedApiName() throws Exception {
+ Exception caught = null;
+ try {
+ Arvados arv = new Arvados("not_arvados", "v1");
+ } catch (Exception e) {
+ caught = e;
+ }
+
+ assertNotNull ("expected exception", caught);
+ assertTrue ("Expected 404 when unsupported api is used", caught.getMessage().contains("404 Not Found"));
+ }
+
+ /**
+ * Test unsupported api version api
+ * @throws Exception
+ */
+ @Test
+ public void testUnsupportedVersion() throws Exception {
+ Exception caught = null;
+ try {
+ Arvados arv = new Arvados("arvados", "v2");
+ } catch (Exception e) {
+ caught = e;
+ }
+
+ assertNotNull ("expected exception", caught);
+ assertTrue ("Expected 404 when unsupported version is used", caught.getMessage().contains("404 Not Found"));
+ }
+
+ /**
+ * Test unsupported api version api
+ * @throws Exception
+ */
+ @Test
+ public void testCallForNoSuchResrouce() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Exception caught = null;
+ try {
+ arv.call("abcd", "list", null);
+ } catch (Exception e) {
+ caught = e;
+ }
+
+ assertNotNull ("expected exception", caught);
+ assertTrue ("Expected ERROR: 404 not found", caught.getMessage().contains("ERROR: resource not found"));
+ }
+
+ /**
+ * Test unsupported api version api
+ * @throws Exception
+ */
+ @Test
+ public void testCallForNoSuchResrouceMethod() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Exception caught = null;
+ try {
+ arv.call("users", "abcd", null);
+ } catch (Exception e) {
+ caught = e;
+ }
+
+ assertNotNull ("expected exception", caught);
+ assertTrue ("Expected ERROR: 404 not found", caught.getMessage().contains("ERROR: method not found"));
+ }
+
+ /**
+ * Test pipeline_tempates.create api
+ * @throws Exception
+ */
+ @Test
+ public void testCreateAndGetPipelineTemplate() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ File file = new File(getClass().getResource( "/first_pipeline.json" ).toURI());
+ byte[] data = new byte[(int)file.length()];
+ try {
+ FileInputStream is = new FileInputStream(file);
+ is.read(data);
+ is.close();
+ }catch(Exception e) {
+ e.printStackTrace();
+ }
+
+ Map<String, Object> params = new HashMap<String, Object>();
+ params.put("pipeline_template", new String(data));
+ Map response = arv.call("pipeline_templates", "create", params);
+
+ assertEquals("Expected kind to be user", "arvados#pipelineTemplate", response.get("kind"));
+ String uuid = (String)response.get("uuid");
+ assertNotNull("Expected uuid for pipeline template", uuid);
+
+ // get the pipeline
+ params = new HashMap<String, Object>();
+ params.put("uuid", uuid);
+ response = arv.call("pipeline_templates", "get", params);
+
+ assertEquals("Expected kind to be user", "arvados#pipelineTemplate", response.get("kind"));
+ assertEquals("Expected uuid for pipeline template", uuid, response.get("uuid"));
+
+ // delete the object
+ params = new HashMap<String, Object>();
+ params.put("uuid", uuid);
+ response = arv.call("pipeline_templates", "delete", params);
+ }
+
+ /**
+ * Test users.list api
+ * @throws Exception
+ */
+ @Test
+ public void testArvadosWithTokenPassed() throws Exception {
+ String token = System.getenv().get("ARVADOS_API_TOKEN");
+ String host = System.getenv().get("ARVADOS_API_HOST");
+ String hostInsecure = System.getenv().get("ARVADOS_API_HOST_INSECURE");
+
+ Arvados arv = new Arvados("arvados", "v1", token, host, hostInsecure);
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("users", "list", params);
+ assertEquals("Expected kind to be users.list", "arvados#userList", response.get("kind"));
+ }
+
+ /**
+ * Test users.list api
+ * @throws Exception
+ */
+ @Test
+ public void testCallUsersListWithLimit() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("users", "list", params);
+ assertEquals("Expected users.list in response", "arvados#userList", response.get("kind"));
+
+ List items = (List)response.get("items");
+ assertNotNull("expected users list items", items);
+ assertTrue("expected at least one item in users list", items.size()>0);
+
+ int numUsersListItems = items.size();
+
+ // make the request again with limit
+ params = new HashMap<String, Object>();
+ params.put("limit", numUsersListItems-1);
+
+ response = arv.call("users", "list", params);
+
+ assertEquals("Expected kind to be users.list", "arvados#userList", response.get("kind"));
+
+ items = (List)response.get("items");
+ assertNotNull("expected users list items", items);
+ assertTrue("expected at least one item in users list", items.size()>0);
+
+ int numUsersListItems2 = items.size();
+ assertEquals ("Got more users than requested", numUsersListItems-1, numUsersListItems2);
+ }
+
+ @Test
+ public void testGetLinksWithFilters() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("links", "list", params);
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+
+ String[][] filters = new String[1][];
+ String[] condition = new String[3];
+ condition[0] = "name";
+ condition[1] = "=";
+ condition[2] = "can_manage";
+ filters[0] = condition;
+ params.put("filters", filters);
+
+ response = arv.call("links", "list", params);
+
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+ assertFalse("Expected no can_manage in response", response.toString().contains("\"name\":\"can_manage\""));
+ }
+
+ @Test
+ public void testGetLinksWithFiltersAsList() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("links", "list", params);
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+
+ List<List> filters = new ArrayList<List>();
+ List<String> condition = new ArrayList<String>();
+ condition.add("name");
+ condition.add("is_a");
+ condition.add("can_manage");
+ filters.add(condition);
+ params.put("filters", filters);
+
+ response = arv.call("links", "list", params);
+
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+ assertFalse("Expected no can_manage in response", response.toString().contains("\"name\":\"can_manage\""));
+ }
+
+ @Test
+ public void testGetLinksWithTimestampFilters() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map response = arv.call("links", "list", params);
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+
+ // get links created "tomorrow". Expect none in response
+ Calendar calendar = new GregorianCalendar();
+ calendar.setTime(new Date());
+ calendar.add(Calendar.DAY_OF_MONTH, 1);
+
+ Object[][] filters = new Object[1][];
+ Object[] condition = new Object[3];
+ condition[0] = "created_at";
+ condition[1] = ">";
+ condition[2] = calendar.get(Calendar.YEAR) + "-" + (calendar.get(Calendar.MONTH)+1) + "-" + calendar.get(Calendar.DAY_OF_MONTH);
+ filters[0] = condition;
+ params.put("filters", filters);
+
+ response = arv.call("links", "list", params);
+
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+ int items_avail = ((BigDecimal)response.get("items_available")).intValue();
+ assertEquals("Expected zero links", items_avail, 0);
+ }
+
+ @Test
+ public void testGetLinksWithWhereClause() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+
+ Map<String, Object> params = new HashMap<String, Object>();
+
+ Map<String, String> where = new HashMap<String, String>();
+ where.put("where", "updated_at > '2014-05-01'");
+
+ params.put("where", where);
+
+ Map response = arv.call("links", "list", params);
+
+ assertEquals("Expected links.list in response", "arvados#linkList", response.get("kind"));
+ }
+
+ @Test
+ public void testGetAvailableResources() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+ Set<String> resources = arv.getAvailableResourses();
+ assertNotNull("Expected resources", resources);
+ assertTrue("Excected users in resrouces", resources.contains("users"));
+ }
+
+ @Test
+ public void testGetAvailableMethodsResources() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+ Set<String> methods = arv.getAvailableMethodsForResourse("users");
+ assertNotNull("Expected resources", methods);
+ assertTrue("Excected create method for users", methods.contains("create"));
+ }
+
+ @Test
+ public void testGetAvailableParametersForUsersGetMethod() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+ Map<String,List<String>> parameters = arv.getAvailableParametersForMethod("users", "get");
+ assertNotNull("Expected parameters", parameters);
+ assertTrue("Excected uuid parameter for get method for users", parameters.get("required").contains("uuid"));
+ }
+
+ @Test
+ public void testGetAvailableParametersForUsersCreateMethod() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+ Map<String,List<String>> parameters = arv.getAvailableParametersForMethod("users", "create");
+ assertNotNull("Expected parameters", parameters);
+ assertTrue("Excected user parameter for get method for users", parameters.get("required").contains("user"));
+ }
+
+ @Test
+ public void testGetAvailableParametersForUsersListMethod() throws Exception {
+ Arvados arv = new Arvados("arvados", "v1");
+ Map<String,List<String>> parameters = arv.getAvailableParametersForMethod("users", "list");
+ assertNotNull("Expected parameters", parameters);
+ assertTrue("Excected no required parameter for list method for users", parameters.get("required").size() == 0);
+ assertTrue("Excected some optional parameters for list method for users", parameters.get("optional").contains("filters"));
+ }
+
+}
\ No newline at end of file
--- /dev/null
+{
+ "name":"first pipeline",
+ "components":{
+ "do_hash":{
+ "script":"hash.py",
+ "script_parameters":{
+ "input":{
+ "required": true,
+ "dataclass": "Collection"
+ }
+ },
+ "script_version":"master",
+ "output_is_persistent":true
+ }
+ }
+}
--- /dev/null
+#! /usr/bin/perl
+
+use strict;
+
+use ExtUtils::MakeMaker;
+
+WriteMakefile(
+ NAME => 'Arvados',
+ VERSION_FROM => 'lib/Arvados.pm'
+);
--- /dev/null
+=head1 NAME
+
+Arvados -- client library for Arvados services
+
+=head1 SYNOPSIS
+
+ use Arvados;
+ $arv = Arvados->new(apiHost => 'arvados.local');
+
+ my $instances = $arv->{'pipeline_instances'}->{'list'}->execute();
+ print "UUID is ", $instances->{'items'}->[0]->{'uuid'}, "\n";
+
+ $uuid = 'eiv0u-arx5y-2c5ovx43zw90gvh';
+ $instance = $arv->{'pipeline_instances'}->{'get'}->execute('uuid' => $uuid);
+ print "ETag is ", $instance->{'etag'}, "\n";
+
+ $instance->{'active'} = 1;
+ $instance->{'name'} = '';
+ $instance->save();
+ print "ETag is ", $instance->{'etag'}, "\n";
+
+=head1 METHODS
+
+=head2 new()
+
+ my $whc = Arvados->new( %OPTIONS );
+
+Set up a client and retrieve the schema from the server.
+
+=head3 Options
+
+=over
+
+=item apiHost
+
+Hostname of API discovery service. Default: C<ARVADOS_API_HOST>
+environment variable, or C<arvados>
+
+=item apiProtocolScheme
+
+Protocol scheme. Default: C<ARVADOS_API_PROTOCOL_SCHEME> environment
+variable, or C<https>
+
+=item authToken
+
+Authorization token. Default: C<ARVADOS_API_TOKEN> environment variable
+
+=item apiService
+
+Default C<arvados>
+
+=item apiVersion
+
+Default C<v1>
+
+=back
+
+=cut
+
+package Arvados;
+
+use Net::SSL (); # From Crypt-SSLeay
+BEGIN {
+ $Net::HTTPS::SSL_SOCKET_CLASS = "Net::SSL"; # Force use of Net::SSL
+}
+
+use JSON;
+use Carp;
+use Arvados::ResourceAccessor;
+use Arvados::ResourceMethod;
+use Arvados::ResourceProxy;
+use Arvados::ResourceProxyList;
+use Arvados::Request;
+use Data::Dumper;
+
+$Arvados::VERSION = 0.1;
+
+sub new
+{
+ my $class = shift;
+ my %self = @_;
+ my $self = \%self;
+ bless ($self, $class);
+ return $self->build(@_);
+}
+
+sub build
+{
+ my $self = shift;
+
+ $config = load_config_file("$ENV{HOME}/.config/arvados/settings.conf");
+
+ $self->{'authToken'} ||=
+ $ENV{ARVADOS_API_TOKEN} || $config->{ARVADOS_API_TOKEN};
+
+ $self->{'apiHost'} ||=
+ $ENV{ARVADOS_API_HOST} || $config->{ARVADOS_API_HOST};
+
+ $self->{'noVerifyHostname'} ||=
+ $ENV{ARVADOS_API_HOST_INSECURE};
+
+ $self->{'apiProtocolScheme'} ||=
+ $ENV{ARVADOS_API_PROTOCOL_SCHEME} ||
+ $config->{ARVADOS_API_PROTOCOL_SCHEME};
+
+ $self->{'ua'} = new Arvados::Request;
+
+ my $host = $self->{'apiHost'} || 'arvados';
+ my $service = $self->{'apiService'} || 'arvados';
+ my $version = $self->{'apiVersion'} || 'v1';
+ my $scheme = $self->{'apiProtocolScheme'} || 'https';
+ my $uri = "$scheme://$host/discovery/v1/apis/$service/$version/rest";
+ my $r = $self->new_request;
+ $r->set_uri($uri);
+ $r->set_method("GET");
+ $r->process_request();
+ my $data, $headers;
+ my ($status_number, $status_phrase) = $r->get_status();
+ $data = $r->get_body() if $status_number == 200;
+ $headers = $r->get_headers();
+ if ($data) {
+ my $doc = $self->{'discoveryDocument'} = JSON::decode_json($data);
+ print STDERR Dumper $doc if $ENV{'DEBUG_ARVADOS_API_DISCOVERY'};
+ my $k, $v;
+ while (($k, $v) = each %{$doc->{'resources'}}) {
+ $self->{$k} = Arvados::ResourceAccessor->new($self, $k);
+ }
+ } else {
+ croak "No discovery doc at $uri - $status_number $status_phrase";
+ }
+ $self;
+}
+
+sub new_request
+{
+ my $self = shift;
+ local $ENV{'PERL_LWP_SSL_VERIFY_HOSTNAME'};
+ if ($self->{'noVerifyHostname'} || ($host =~ /\.local$/)) {
+ $ENV{'PERL_LWP_SSL_VERIFY_HOSTNAME'} = 0;
+ }
+ Arvados::Request->new();
+}
+
+sub load_config_file ($)
+{
+ my $config_file = shift;
+ my %config;
+
+ if (open (CONF, $config_file)) {
+ while (<CONF>) {
+ next if /^\s*#/ || /^\s*$/; # skip comments and blank lines
+ chomp;
+ my ($key, $val) = split /\s*=\s*/, $_, 2;
+ $config{$key} = $val;
+ }
+ }
+ close CONF;
+ return \%config;
+}
+
+1;
--- /dev/null
+package Arvados::Request;
+use Data::Dumper;
+use LWP::UserAgent;
+use URI::Escape;
+use Encode;
+use strict;
+@Arvados::HTTP::ISA = qw(LWP::UserAgent);
+
+sub new
+{
+ my $class = shift;
+ my $self = {};
+ bless ($self, $class);
+ return $self->_init(@_);
+}
+
+sub _init
+{
+ my $self = shift;
+ $self->{'ua'} = new LWP::UserAgent(@_);
+ $self->{'ua'}->agent ("libarvados-perl/".$Arvados::VERSION);
+ $self;
+}
+
+sub set_uri
+{
+ my $self = shift;
+ $self->{'uri'} = shift;
+}
+
+sub process_request
+{
+ my $self = shift;
+ my %req;
+ my %content;
+ my $method = $self->{'method'};
+ if ($method eq 'GET' || $method eq 'HEAD') {
+ $content{'_method'} = $method;
+ $method = 'POST';
+ }
+ $req{$method} = $self->{'uri'};
+ $self->{'req'} = new HTTP::Request (%req);
+ $self->{'req'}->header('Authorization' => ('OAuth2 ' . $self->{'authToken'})) if $self->{'authToken'};
+ $self->{'req'}->header('Accept' => 'application/json');
+ my ($p, $v);
+ while (($p, $v) = each %{$self->{'queryParams'}}) {
+ $content{$p} = (ref($v) eq "") ? $v : JSON::encode_json($v);
+ }
+ my $content;
+ while (($p, $v) = each %content) {
+ $content .= '&' unless $content eq '';
+ $content .= uri_escape($p);
+ $content .= '=';
+ $content .= uri_escape($v);
+ }
+ $self->{'req'}->content_type("application/x-www-form-urlencoded; charset='utf8'");
+ $self->{'req'}->content(Encode::encode('utf8', $content));
+ $self->{'res'} = $self->{'ua'}->request ($self->{'req'});
+}
+
+sub get_status
+{
+ my $self = shift;
+ return ($self->{'res'}->code(),
+ $self->{'res'}->message());
+}
+
+sub get_body
+{
+ my $self = shift;
+ return $self->{'res'}->content;
+}
+
+sub set_method
+{
+ my $self = shift;
+ $self->{'method'} = shift;
+}
+
+sub set_query_params
+{
+ my $self = shift;
+ $self->{'queryParams'} = shift;
+}
+
+sub set_auth_token
+{
+ my $self = shift;
+ $self->{'authToken'} = shift;
+}
+
+sub get_headers
+{
+ ""
+}
+
+1;
--- /dev/null
+package Arvados::ResourceAccessor;
+use Carp;
+use Data::Dumper;
+
+sub new
+{
+ my $class = shift;
+ my $self = {};
+ bless ($self, $class);
+
+ $self->{'api'} = shift;
+ $self->{'resourcesName'} = shift;
+ $self->{'methods'} = $self->{'api'}->{'discoveryDocument'}->{'resources'}->{$self->{'resourcesName'}}->{'methods'};
+ my $method_name, $method;
+ while (($method_name, $method) = each %{$self->{'methods'}}) {
+ $self->{$method_name} = Arvados::ResourceMethod->new($self, $method);
+ }
+ $self;
+}
+
+1;
--- /dev/null
+package Arvados::ResourceMethod;
+use Carp;
+use Data::Dumper;
+
+sub new
+{
+ my $class = shift;
+ my $self = {};
+ bless ($self, $class);
+ return $self->_init(@_);
+}
+
+sub _init
+{
+ my $self = shift;
+ $self->{'resourceAccessor'} = shift;
+ $self->{'method'} = shift;
+ return $self;
+}
+
+sub execute
+{
+ my $self = shift;
+ my $method = $self->{'method'};
+
+ my $path = $method->{'path'};
+
+ my %body_params;
+ my %given_params = @_;
+ my %extra_params = %given_params;
+ my %method_params = %{$method->{'parameters'}};
+ if ($method->{'request'}->{'properties'}) {
+ while (my ($prop_name, $prop_value) =
+ each %{$method->{'request'}->{'properties'}}) {
+ if (ref($prop_value) eq 'HASH' && $prop_value->{'$ref'}) {
+ $method_params{$prop_name} = { 'type' => 'object' };
+ }
+ }
+ }
+ while (my ($param_name, $param) = each %method_params) {
+ delete $extra_params{$param_name};
+ if ($param->{'required'} && !exists $given_params{$param_name}) {
+ croak("Required parameter not supplied: $param_name");
+ }
+ elsif ($param->{'location'} eq 'path') {
+ $path =~ s/{\Q$param_name\E}/$given_params{$param_name}/eg;
+ }
+ elsif (!exists $given_params{$param_name}) {
+ ;
+ }
+ elsif ($param->{'type'} eq 'object') {
+ my %param_value;
+ my ($p, $v);
+ if (exists $param->{'properties'}) {
+ while (my ($property_name, $property) =
+ each %{$param->{'properties'}}) {
+ # if the discovery doc specifies object structure,
+ # convert to true/false depending on supplied type
+ if (!exists $given_params{$param_name}->{$property_name}) {
+ ;
+ }
+ elsif (!defined $given_params{$param_name}->{$property_name}) {
+ $param_value{$property_name} = JSON::null;
+ }
+ elsif ($property->{'type'} eq 'boolean') {
+ $param_value{$property_name} = $given_params{$param_name}->{$property_name} ? JSON::true : JSON::false;
+ }
+ else {
+ $param_value{$property_name} = $given_params{$param_name}->{$property_name};
+ }
+ }
+ }
+ else {
+ while (my ($property_name, $property) =
+ each %{$given_params{$param_name}}) {
+ if (ref $property eq '' || $property eq undef) {
+ $param_value{$property_name} = $property;
+ }
+ elsif (ref $property eq 'HASH') {
+ $param_value{$property_name} = {};
+ while (my ($k, $v) = each %$property) {
+ $param_value{$property_name}->{$k} = $v;
+ }
+ }
+ }
+ }
+ $body_params{$param_name} = \%param_value;
+ } elsif ($param->{'type'} eq 'boolean') {
+ $body_params{$param_name} = $given_params{$param_name} ? JSON::true : JSON::false;
+ } else {
+ $body_params{$param_name} = $given_params{$param_name};
+ }
+ }
+ if (%extra_params) {
+ croak("Unsupported parameter(s) passed to API call /$path: \"" . join('", "', keys %extra_params) . '"');
+ }
+ my $r = $self->{'resourceAccessor'}->{'api'}->new_request;
+ my $base_uri = $self->{'resourceAccessor'}->{'api'}->{'discoveryDocument'}->{'baseUrl'};
+ $base_uri =~ s:/$::;
+ $r->set_uri($base_uri . "/" . $path);
+ $r->set_method($method->{'httpMethod'});
+ $r->set_auth_token($self->{'resourceAccessor'}->{'api'}->{'authToken'});
+ $r->set_query_params(\%body_params) if %body_params;
+ $r->process_request();
+ my $data, $headers;
+ my ($status_number, $status_phrase) = $r->get_status();
+ if ($status_number != 200) {
+ croak("API call /$path failed: $status_number $status_phrase\n". $r->get_body());
+ }
+ $data = $r->get_body();
+ $headers = $r->get_headers();
+ my $result = JSON::decode_json($data);
+ if ($method->{'response'}->{'$ref'} =~ /List$/) {
+ Arvados::ResourceProxyList->new($result, $self->{'resourceAccessor'});
+ } else {
+ Arvados::ResourceProxy->new($result, $self->{'resourceAccessor'});
+ }
+}
+
+1;
--- /dev/null
+package Arvados::ResourceProxy;
+
+sub new
+{
+ my $class = shift;
+ my $self = shift;
+ $self->{'resourceAccessor'} = shift;
+ bless ($self, $class);
+ $self;
+}
+
+sub save
+{
+ my $self = shift;
+ $response = $self->{'resourceAccessor'}->{'update'}->execute('uuid' => $self->{'uuid'}, $self->resource_parameter_name() => $self);
+ foreach my $param (keys %$self) {
+ if (exists $response->{$param}) {
+ $self->{$param} = $response->{$param};
+ }
+ }
+ $self;
+}
+
+sub update_attributes
+{
+ my $self = shift;
+ my %updates = @_;
+ $response = $self->{'resourceAccessor'}->{'update'}->execute('uuid' => $self->{'uuid'}, $self->resource_parameter_name() => \%updates);
+ foreach my $param (keys %updates) {
+ if (exists $response->{$param}) {
+ $self->{$param} = $response->{$param};
+ }
+ }
+ $self;
+}
+
+sub reload
+{
+ my $self = shift;
+ $response = $self->{'resourceAccessor'}->{'get'}->execute('uuid' => $self->{'uuid'});
+ foreach my $param (keys %$self) {
+ if (exists $response->{$param}) {
+ $self->{$param} = $response->{$param};
+ }
+ }
+ $self;
+}
+
+sub resource_parameter_name
+{
+ my $self = shift;
+ my $pname = $self->{'resourceAccessor'}->{'resourcesName'};
+ $pname =~ s/s$//; # XXX not a very good singularize()
+ $pname;
+}
+
+1;
--- /dev/null
+package Arvados::ResourceProxyList;
+
+sub new
+{
+ my $class = shift;
+ my $self = {};
+ bless ($self, $class);
+ $self->_init(@_);
+}
+
+sub _init
+{
+ my $self = shift;
+ $self->{'serverResponse'} = shift;
+ $self->{'resourceAccessor'} = shift;
+ $self->{'items'} = [ map { Arvados::ResourceProxy->new($_, $self->{'resourceAccessor'}) } @{$self->{'serverResponse'}->{'items'}} ];
+ $self;
+}
+
+1;
--- /dev/null
+*.pyc
+/build/
+/dist/
+*.egg
+*.egg-info
+/tests/tmp
+.eggs
--- /dev/null
+include README.rst
--- /dev/null
+=====================
+Arvados Python Client
+=====================
+
+Overview
+--------
+
+This package provides the ``arvados`` module, an API client for
+Arvados_. It also includes higher-level functions to help you write
+Crunch scripts, and command-line tools to store and retrieve data in
+the Keep storage server.
+
+.. _Arvados: https://arvados.org/
+
+Installation
+------------
+
+Installing under your user account
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This method lets you install the package without root access.
+However, other users on the same system won't be able to use it.
+
+1. Run ``pip install --user arvados-python-client``.
+
+2. In your shell configuration, make sure you add ``$HOME/.local/bin``
+ to your PATH environment variable. For example, you could add the
+ command ``PATH=$PATH:$HOME/.local/bin`` to your ``.bashrc`` file.
+
+3. Reload your shell configuration. For example, bash users could run
+ ``source ~/.bashrc``.
+
+Installing on Debian systems
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+1. Add this Arvados repository to your sources list::
+
+ deb http://apt.arvados.org/ wheezy main
+
+2. Update your package list.
+
+3. Install the ``python-arvados-python-client`` package.
+
+Configuration
+-------------
+
+This client software needs two pieces of information to connect to
+Arvados: the DNS name of the API server, and an API authorization
+token. You can set these in environment variables, or the file
+``$HOME/.config/arvados/settings.conf``. `The Arvados user
+documentation
+<http://doc.arvados.org/user/reference/api-tokens.html>`_ describes
+how to find this information in the Arvados Workbench, and install it
+on your system.
+
+Testing and Development
+-----------------------
+
+This package is one part of the Arvados source package, and it has
+integration tests to check interoperability with other Arvados
+components. Our `hacking guide
+<https://arvados.org/projects/arvados/wiki/Hacking_Python_SDK>`_
+describes how to set up a development environment and run tests.
--- /dev/null
+import gflags
+import httplib
+import httplib2
+import logging
+import os
+import pprint
+import sys
+import types
+import subprocess
+import json
+import UserDict
+import re
+import hashlib
+import string
+import bz2
+import zlib
+import fcntl
+import time
+import threading
+
+from api import *
+from collection import *
+from keep import *
+from stream import *
+import errors
+import util
+
+# Set up Arvados logging based on the user's configuration.
+# All Arvados code should log under the arvados hierarchy.
+log_handler = logging.StreamHandler()
+log_handler.setFormatter(logging.Formatter(
+ '%(asctime)s %(name)s[%(process)d] %(levelname)s: %(message)s',
+ '%Y-%m-%d %H:%M:%S'))
+logger = logging.getLogger('arvados')
+logger.addHandler(log_handler)
+logger.setLevel(logging.DEBUG if config.get('ARVADOS_DEBUG')
+ else logging.WARNING)
+
+def task_set_output(self,s):
+ api('v1').job_tasks().update(uuid=self['uuid'],
+ body={
+ 'output':s,
+ 'success':True,
+ 'progress':1.0
+ }).execute()
+
+_current_task = None
+def current_task():
+ global _current_task
+ if _current_task:
+ return _current_task
+ t = api('v1').job_tasks().get(uuid=os.environ['TASK_UUID']).execute()
+ t = UserDict.UserDict(t)
+ t.set_output = types.MethodType(task_set_output, t)
+ t.tmpdir = os.environ['TASK_WORK']
+ _current_task = t
+ return t
+
+_current_job = None
+def current_job():
+ global _current_job
+ if _current_job:
+ return _current_job
+ t = api('v1').jobs().get(uuid=os.environ['JOB_UUID']).execute()
+ t = UserDict.UserDict(t)
+ t.tmpdir = os.environ['JOB_WORK']
+ _current_job = t
+ return t
+
+def getjobparam(*args):
+ return current_job()['script_parameters'].get(*args)
+
+def get_job_param_mount(*args):
+ return os.path.join(os.environ['TASK_KEEPMOUNT'], current_job()['script_parameters'].get(*args))
+
+def get_task_param_mount(*args):
+ return os.path.join(os.environ['TASK_KEEPMOUNT'], current_task()['parameters'].get(*args))
+
+class JobTask(object):
+ def __init__(self, parameters=dict(), runtime_constraints=dict()):
+ print "init jobtask %s %s" % (parameters, runtime_constraints)
+
+class job_setup:
+ @staticmethod
+ def one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=False):
+ if if_sequence != current_task()['sequence']:
+ return
+ job_input = current_job()['script_parameters']['input']
+ cr = CollectionReader(job_input)
+ cr.normalize()
+ for s in cr.all_streams():
+ for f in s.all_files():
+ if input_as_path:
+ task_input = os.path.join(job_input, s.name(), f.name())
+ else:
+ task_input = f.as_manifest()
+ new_task_attrs = {
+ 'job_uuid': current_job()['uuid'],
+ 'created_by_job_task_uuid': current_task()['uuid'],
+ 'sequence': if_sequence + 1,
+ 'parameters': {
+ 'input':task_input
+ }
+ }
+ api('v1').job_tasks().create(body=new_task_attrs).execute()
+ if and_end_task:
+ api('v1').job_tasks().update(uuid=current_task()['uuid'],
+ body={'success':True}
+ ).execute()
+ exit(0)
+
+ @staticmethod
+ def one_task_per_input_stream(if_sequence=0, and_end_task=True):
+ if if_sequence != current_task()['sequence']:
+ return
+ job_input = current_job()['script_parameters']['input']
+ cr = CollectionReader(job_input)
+ for s in cr.all_streams():
+ task_input = s.tokens()
+ new_task_attrs = {
+ 'job_uuid': current_job()['uuid'],
+ 'created_by_job_task_uuid': current_task()['uuid'],
+ 'sequence': if_sequence + 1,
+ 'parameters': {
+ 'input':task_input
+ }
+ }
+ api('v1').job_tasks().create(body=new_task_attrs).execute()
+ if and_end_task:
+ api('v1').job_tasks().update(uuid=current_task()['uuid'],
+ body={'success':True}
+ ).execute()
+ exit(0)
+
+
--- /dev/null
+import httplib2
+import json
+import logging
+import os
+import re
+import types
+
+import apiclient
+from apiclient import discovery as apiclient_discovery
+from apiclient import errors as apiclient_errors
+import config
+import errors
+import util
+
+_logger = logging.getLogger('arvados.api')
+conncache = {}
+
+class CredentialsFromToken(object):
+ def __init__(self, api_token):
+ self.api_token = api_token
+
+ @staticmethod
+ def http_request(self, uri, **kwargs):
+ from httplib import BadStatusLine
+ if 'headers' not in kwargs:
+ kwargs['headers'] = {}
+
+ if config.get("ARVADOS_EXTERNAL_CLIENT", "") == "true":
+ kwargs['headers']['X-External-Client'] = '1'
+
+ kwargs['headers']['Authorization'] = 'OAuth2 %s' % self.arvados_api_token
+ try:
+ return self.orig_http_request(uri, **kwargs)
+ except BadStatusLine:
+ # This is how httplib tells us that it tried to reuse an
+ # existing connection but it was already closed by the
+ # server. In that case, yes, we would like to retry.
+ # Unfortunately, we are not absolutely certain that the
+ # previous call did not succeed, so this is slightly
+ # risky.
+ return self.orig_http_request(uri, **kwargs)
+ def authorize(self, http):
+ http.arvados_api_token = self.api_token
+ http.orig_http_request = http.request
+ http.request = types.MethodType(self.http_request, http)
+ return http
+
+# Monkey patch discovery._cast() so objects and arrays get serialized
+# with json.dumps() instead of str().
+_cast_orig = apiclient_discovery._cast
+def _cast_objects_too(value, schema_type):
+ global _cast_orig
+ if (type(value) != type('') and
+ (schema_type == 'object' or schema_type == 'array')):
+ return json.dumps(value)
+ else:
+ return _cast_orig(value, schema_type)
+apiclient_discovery._cast = _cast_objects_too
+
+# Convert apiclient's HttpErrors into our own API error subclass for better
+# error reporting.
+# Reassigning apiclient_errors.HttpError is not sufficient because most of the
+# apiclient submodules import the class into their own namespace.
+def _new_http_error(cls, *args, **kwargs):
+ return super(apiclient_errors.HttpError, cls).__new__(
+ errors.ApiError, *args, **kwargs)
+apiclient_errors.HttpError.__new__ = staticmethod(_new_http_error)
+
+def http_cache(data_type):
+ path = os.environ['HOME'] + '/.cache/arvados/' + data_type
+ try:
+ util.mkdir_dash_p(path)
+ except OSError:
+ path = None
+ return path
+
+def api(version=None, cache=True, host=None, token=None, insecure=False, **kwargs):
+ """Return an apiclient Resources object for an Arvados instance.
+
+ Arguments:
+ * version: A string naming the version of the Arvados API to use (for
+ example, 'v1').
+ * cache: If True (default), return an existing Resources object if
+ one already exists with the same endpoint and credentials. If
+ False, create a new one, and do not keep it in the cache (i.e.,
+ do not return it from subsequent api(cache=True) calls with
+ matching endpoint and credentials).
+ * host: The Arvados API server host (and optional :port) to connect to.
+ * token: The authentication token to send with each API call.
+ * insecure: If True, ignore SSL certificate validation errors.
+
+ Additional keyword arguments will be passed directly to
+ `apiclient_discovery.build` if a new Resource object is created.
+ If the `discoveryServiceUrl` or `http` keyword arguments are
+ missing, this function will set default values for them, based on
+ the current Arvados configuration settings.
+
+ """
+
+ if not version:
+ version = 'v1'
+ _logger.info("Using default API version. " +
+ "Call arvados.api('%s') instead." %
+ version)
+ if 'discoveryServiceUrl' in kwargs:
+ if host:
+ raise ValueError("both discoveryServiceUrl and host provided")
+ # Here we can't use a token from environment, config file,
+ # etc. Those probably have nothing to do with the host
+ # provided by the caller.
+ if not token:
+ raise ValueError("discoveryServiceUrl provided, but token missing")
+ elif host and token:
+ pass
+ elif not host and not token:
+ # Load from user configuration or environment
+ for x in ['ARVADOS_API_HOST', 'ARVADOS_API_TOKEN']:
+ if x not in config.settings():
+ raise ValueError("%s is not set. Aborting." % x)
+ host = config.get('ARVADOS_API_HOST')
+ token = config.get('ARVADOS_API_TOKEN')
+ insecure = config.flag_is_true('ARVADOS_API_HOST_INSECURE')
+ else:
+ # Caller provided one but not the other
+ if not host:
+ raise ValueError("token argument provided, but host missing.")
+ else:
+ raise ValueError("host argument provided, but token missing.")
+
+ if host:
+ # Caller wants us to build the discoveryServiceUrl
+ kwargs['discoveryServiceUrl'] = (
+ 'https://%s/discovery/v1/apis/{api}/{apiVersion}/rest' % (host,))
+
+ if cache:
+ connprofile = (version, host, token, insecure)
+ svc = conncache.get(connprofile)
+ if svc:
+ return svc
+
+ if 'http' not in kwargs:
+ http_kwargs = {}
+ # Prefer system's CA certificates (if available) over httplib2's.
+ certs_path = '/etc/ssl/certs/ca-certificates.crt'
+ if os.path.exists(certs_path):
+ http_kwargs['ca_certs'] = certs_path
+ if cache:
+ http_kwargs['cache'] = http_cache('discovery')
+ if insecure:
+ http_kwargs['disable_ssl_certificate_validation'] = True
+ kwargs['http'] = httplib2.Http(**http_kwargs)
+
+ credentials = CredentialsFromToken(api_token=token)
+ kwargs['http'] = credentials.authorize(kwargs['http'])
+
+ svc = apiclient_discovery.build('arvados', version, **kwargs)
+ svc.api_token = token
+ kwargs['http'].cache = None
+ if cache:
+ conncache[connprofile] = svc
+ return svc
--- /dev/null
+import functools
+
+class ArvadosFileBase(object):
+ def __init__(self, name, mode):
+ self.name = name
+ self.mode = mode
+ self.closed = False
+
+ @staticmethod
+ def _before_close(orig_func):
+ @functools.wraps(orig_func)
+ def wrapper(self, *args, **kwargs):
+ if self.closed:
+ raise ValueError("I/O operation on closed stream file")
+ return orig_func(self, *args, **kwargs)
+ return wrapper
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ try:
+ self.close()
+ except Exception:
+ if exc_type is None:
+ raise
+
+ def close(self):
+ self.closed = True
--- /dev/null
+import functools
+import logging
+import os
+import re
+
+from collections import deque
+from stat import *
+
+from .arvfile import ArvadosFileBase
+from keep import *
+from .stream import StreamReader, split
+import config
+import errors
+import util
+
+_logger = logging.getLogger('arvados.collection')
+
+def normalize_stream(s, stream):
+ stream_tokens = [s]
+ sortedfiles = list(stream.keys())
+ sortedfiles.sort()
+
+ blocks = {}
+ streamoffset = 0L
+ for f in sortedfiles:
+ for b in stream[f]:
+ if b[arvados.LOCATOR] not in blocks:
+ stream_tokens.append(b[arvados.LOCATOR])
+ blocks[b[arvados.LOCATOR]] = streamoffset
+ streamoffset += b[arvados.BLOCKSIZE]
+
+ if len(stream_tokens) == 1:
+ stream_tokens.append(config.EMPTY_BLOCK_LOCATOR)
+
+ for f in sortedfiles:
+ current_span = None
+ fout = f.replace(' ', '\\040')
+ for segment in stream[f]:
+ segmentoffset = blocks[segment[arvados.LOCATOR]] + segment[arvados.OFFSET]
+ if current_span is None:
+ current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]]
+ else:
+ if segmentoffset == current_span[1]:
+ current_span[1] += segment[arvados.SEGMENTSIZE]
+ else:
+ stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout))
+ current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]]
+
+ if current_span is not None:
+ stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout))
+
+ if not stream[f]:
+ stream_tokens.append("0:0:{0}".format(fout))
+
+ return stream_tokens
+
+
+class CollectionBase(object):
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ pass
+
+ def _my_keep(self):
+ if self._keep_client is None:
+ self._keep_client = KeepClient(api_client=self._api_client,
+ num_retries=self.num_retries)
+ return self._keep_client
+
+ def stripped_manifest(self):
+ """
+ Return the manifest for the current collection with all
+ non-portable hints (i.e., permission signatures and other
+ hints other than size hints) removed from the locators.
+ """
+ raw = self.manifest_text()
+ clean = []
+ for line in raw.split("\n"):
+ fields = line.split()
+ if fields:
+ clean_fields = fields[:1] + [
+ (re.sub(r'\+[^\d][^\+]*', '', x)
+ if re.match(util.keep_locator_pattern, x)
+ else x)
+ for x in fields[1:]]
+ clean += [' '.join(clean_fields), "\n"]
+ return ''.join(clean)
+
+
+class CollectionReader(CollectionBase):
+ def __init__(self, manifest_locator_or_text, api_client=None,
+ keep_client=None, num_retries=0):
+ """Instantiate a CollectionReader.
+
+ This class parses Collection manifests to provide a simple interface
+ to read its underlying files.
+
+ Arguments:
+ * manifest_locator_or_text: One of a Collection UUID, portable data
+ hash, or full manifest text.
+ * api_client: The API client to use to look up Collections. If not
+ provided, CollectionReader will build one from available Arvados
+ configuration.
+ * keep_client: The KeepClient to use to download Collection data.
+ If not provided, CollectionReader will build one from available
+ Arvados configuration.
+ * num_retries: The default number of times to retry failed
+ service requests. Default 0. You may change this value
+ after instantiation, but note those changes may not
+ propagate to related objects like the Keep client.
+ """
+ self._api_client = api_client
+ self._keep_client = keep_client
+ self.num_retries = num_retries
+ if re.match(util.keep_locator_pattern, manifest_locator_or_text):
+ self._manifest_locator = manifest_locator_or_text
+ self._manifest_text = None
+ elif re.match(util.collection_uuid_pattern, manifest_locator_or_text):
+ self._manifest_locator = manifest_locator_or_text
+ self._manifest_text = None
+ elif re.match(util.manifest_pattern, manifest_locator_or_text):
+ self._manifest_text = manifest_locator_or_text
+ self._manifest_locator = None
+ else:
+ raise errors.ArgumentError(
+ "Argument to CollectionReader must be a manifest or a collection UUID")
+ self._api_response = None
+ self._streams = None
+
+ def _populate_from_api_server(self):
+ # As in KeepClient itself, we must wait until the last
+ # possible moment to instantiate an API client, in order to
+ # avoid tripping up clients that don't have access to an API
+ # server. If we do build one, make sure our Keep client uses
+ # it. If instantiation fails, we'll fall back to the except
+ # clause, just like any other Collection lookup
+ # failure. Return an exception, or None if successful.
+ try:
+ if self._api_client is None:
+ self._api_client = arvados.api('v1')
+ self._keep_client = None # Make a new one with the new api.
+ self._api_response = self._api_client.collections().get(
+ uuid=self._manifest_locator).execute(
+ num_retries=self.num_retries)
+ self._manifest_text = self._api_response['manifest_text']
+ return None
+ except Exception as e:
+ return e
+
+ def _populate_from_keep(self):
+ # Retrieve a manifest directly from Keep. This has a chance of
+ # working if [a] the locator includes a permission signature
+ # or [b] the Keep services are operating in world-readable
+ # mode. Return an exception, or None if successful.
+ try:
+ self._manifest_text = self._my_keep().get(
+ self._manifest_locator, num_retries=self.num_retries)
+ except Exception as e:
+ return e
+
+ def _populate(self):
+ error_via_api = None
+ error_via_keep = None
+ should_try_keep = ((self._manifest_text is None) and
+ util.keep_locator_pattern.match(
+ self._manifest_locator))
+ if ((self._manifest_text is None) and
+ util.signed_locator_pattern.match(self._manifest_locator)):
+ error_via_keep = self._populate_from_keep()
+ if self._manifest_text is None:
+ error_via_api = self._populate_from_api_server()
+ if error_via_api is not None and not should_try_keep:
+ raise error_via_api
+ if ((self._manifest_text is None) and
+ not error_via_keep and
+ should_try_keep):
+ # Looks like a keep locator, and we didn't already try keep above
+ error_via_keep = self._populate_from_keep()
+ if self._manifest_text is None:
+ # Nothing worked!
+ raise arvados.errors.NotFoundError(
+ ("Failed to retrieve collection '{}' " +
+ "from either API server ({}) or Keep ({})."
+ ).format(
+ self._manifest_locator,
+ error_via_api,
+ error_via_keep))
+ self._streams = [sline.split()
+ for sline in self._manifest_text.split("\n")
+ if sline]
+
+ def _populate_first(orig_func):
+ # Decorator for methods that read actual Collection data.
+ @functools.wraps(orig_func)
+ def wrapper(self, *args, **kwargs):
+ if self._streams is None:
+ self._populate()
+ return orig_func(self, *args, **kwargs)
+ return wrapper
+
+ @_populate_first
+ def api_response(self):
+ """api_response() -> dict or None
+
+ Returns information about this Collection fetched from the API server.
+ If the Collection exists in Keep but not the API server, currently
+ returns None. Future versions may provide a synthetic response.
+ """
+ return self._api_response
+
+ @_populate_first
+ def normalize(self):
+ # Rearrange streams
+ streams = {}
+ for s in self.all_streams():
+ for f in s.all_files():
+ streamname, filename = split(s.name() + "/" + f.name())
+ if streamname not in streams:
+ streams[streamname] = {}
+ if filename not in streams[streamname]:
+ streams[streamname][filename] = []
+ for r in f.segments:
+ streams[streamname][filename].extend(s.locators_and_ranges(r[0], r[1]))
+
+ self._streams = [normalize_stream(s, streams[s])
+ for s in sorted(streams)]
+
+ # Regenerate the manifest text based on the normalized streams
+ self._manifest_text = ''.join(
+ [StreamReader(stream, keep=self._my_keep()).manifest_text()
+ for stream in self._streams])
+
+ @_populate_first
+ def open(self, streampath, filename=None):
+ """open(streampath[, filename]) -> file-like object
+
+ Pass in the path of a file to read from the Collection, either as a
+ single string or as two separate stream name and file name arguments.
+ This method returns a file-like object to read that file.
+ """
+ if filename is None:
+ streampath, filename = split(streampath)
+ keep_client = self._my_keep()
+ for stream_s in self._streams:
+ stream = StreamReader(stream_s, keep_client,
+ num_retries=self.num_retries)
+ if stream.name() == streampath:
+ break
+ else:
+ raise ValueError("stream '{}' not found in Collection".
+ format(streampath))
+ try:
+ return stream.files()[filename]
+ except KeyError:
+ raise ValueError("file '{}' not found in Collection stream '{}'".
+ format(filename, streampath))
+
+ @_populate_first
+ def all_streams(self):
+ return [StreamReader(s, self._my_keep(), num_retries=self.num_retries)
+ for s in self._streams]
+
+ def all_files(self):
+ for s in self.all_streams():
+ for f in s.all_files():
+ yield f
+
+ @_populate_first
+ def manifest_text(self, strip=False, normalize=False):
+ if normalize:
+ cr = CollectionReader(self.manifest_text())
+ cr.normalize()
+ return cr.manifest_text(strip=strip, normalize=False)
+ elif strip:
+ return self.stripped_manifest()
+ else:
+ return self._manifest_text
+
+
+class _WriterFile(ArvadosFileBase):
+ def __init__(self, coll_writer, name):
+ super(_WriterFile, self).__init__(name, 'wb')
+ self.dest = coll_writer
+
+ def close(self):
+ super(_WriterFile, self).close()
+ self.dest.finish_current_file()
+
+ @ArvadosFileBase._before_close
+ def write(self, data):
+ self.dest.write(data)
+
+ @ArvadosFileBase._before_close
+ def writelines(self, seq):
+ for data in seq:
+ self.write(data)
+
+ @ArvadosFileBase._before_close
+ def flush(self):
+ self.dest.flush_data()
+
+
+class CollectionWriter(CollectionBase):
+ KEEP_BLOCK_SIZE = 2**26
+
+ def __init__(self, api_client=None, num_retries=0):
+ """Instantiate a CollectionWriter.
+
+ CollectionWriter lets you build a new Arvados Collection from scratch.
+ Write files to it. The CollectionWriter will upload data to Keep as
+ appropriate, and provide you with the Collection manifest text when
+ you're finished.
+
+ Arguments:
+ * api_client: The API client to use to look up Collections. If not
+ provided, CollectionReader will build one from available Arvados
+ configuration.
+ * num_retries: The default number of times to retry failed
+ service requests. Default 0. You may change this value
+ after instantiation, but note those changes may not
+ propagate to related objects like the Keep client.
+ """
+ self._api_client = api_client
+ self.num_retries = num_retries
+ self._keep_client = None
+ self._data_buffer = []
+ self._data_buffer_len = 0
+ self._current_stream_files = []
+ self._current_stream_length = 0
+ self._current_stream_locators = []
+ self._current_stream_name = '.'
+ self._current_file_name = None
+ self._current_file_pos = 0
+ self._finished_streams = []
+ self._close_file = None
+ self._queued_file = None
+ self._queued_dirents = deque()
+ self._queued_trees = deque()
+ self._last_open = None
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ if exc_type is None:
+ self.finish()
+
+ def do_queued_work(self):
+ # The work queue consists of three pieces:
+ # * _queued_file: The file object we're currently writing to the
+ # Collection.
+ # * _queued_dirents: Entries under the current directory
+ # (_queued_trees[0]) that we want to write or recurse through.
+ # This may contain files from subdirectories if
+ # max_manifest_depth == 0 for this directory.
+ # * _queued_trees: Directories that should be written as separate
+ # streams to the Collection.
+ # This function handles the smallest piece of work currently queued
+ # (current file, then current directory, then next directory) until
+ # no work remains. The _work_THING methods each do a unit of work on
+ # THING. _queue_THING methods add a THING to the work queue.
+ while True:
+ if self._queued_file:
+ self._work_file()
+ elif self._queued_dirents:
+ self._work_dirents()
+ elif self._queued_trees:
+ self._work_trees()
+ else:
+ break
+
+ def _work_file(self):
+ while True:
+ buf = self._queued_file.read(self.KEEP_BLOCK_SIZE)
+ if not buf:
+ break
+ self.write(buf)
+ self.finish_current_file()
+ if self._close_file:
+ self._queued_file.close()
+ self._close_file = None
+ self._queued_file = None
+
+ def _work_dirents(self):
+ path, stream_name, max_manifest_depth = self._queued_trees[0]
+ if stream_name != self.current_stream_name():
+ self.start_new_stream(stream_name)
+ while self._queued_dirents:
+ dirent = self._queued_dirents.popleft()
+ target = os.path.join(path, dirent)
+ if os.path.isdir(target):
+ self._queue_tree(target,
+ os.path.join(stream_name, dirent),
+ max_manifest_depth - 1)
+ else:
+ self._queue_file(target, dirent)
+ break
+ if not self._queued_dirents:
+ self._queued_trees.popleft()
+
+ def _work_trees(self):
+ path, stream_name, max_manifest_depth = self._queued_trees[0]
+ d = util.listdir_recursive(
+ path, max_depth = (None if max_manifest_depth == 0 else 0))
+ if d:
+ self._queue_dirents(stream_name, d)
+ else:
+ self._queued_trees.popleft()
+
+ def _queue_file(self, source, filename=None):
+ assert (self._queued_file is None), "tried to queue more than one file"
+ if not hasattr(source, 'read'):
+ source = open(source, 'rb')
+ self._close_file = True
+ else:
+ self._close_file = False
+ if filename is None:
+ filename = os.path.basename(source.name)
+ self.start_new_file(filename)
+ self._queued_file = source
+
+ def _queue_dirents(self, stream_name, dirents):
+ assert (not self._queued_dirents), "tried to queue more than one tree"
+ self._queued_dirents = deque(sorted(dirents))
+
+ def _queue_tree(self, path, stream_name, max_manifest_depth):
+ self._queued_trees.append((path, stream_name, max_manifest_depth))
+
+ def write_file(self, source, filename=None):
+ self._queue_file(source, filename)
+ self.do_queued_work()
+
+ def write_directory_tree(self,
+ path, stream_name='.', max_manifest_depth=-1):
+ self._queue_tree(path, stream_name, max_manifest_depth)
+ self.do_queued_work()
+
+ def write(self, newdata):
+ if hasattr(newdata, '__iter__'):
+ for s in newdata:
+ self.write(s)
+ return
+ self._data_buffer.append(newdata)
+ self._data_buffer_len += len(newdata)
+ self._current_stream_length += len(newdata)
+ while self._data_buffer_len >= self.KEEP_BLOCK_SIZE:
+ self.flush_data()
+
+ def open(self, streampath, filename=None):
+ """open(streampath[, filename]) -> file-like object
+
+ Pass in the path of a file to write to the Collection, either as a
+ single string or as two separate stream name and file name arguments.
+ This method returns a file-like object you can write to add it to the
+ Collection.
+
+ You may only have one file object from the Collection open at a time,
+ so be sure to close the object when you're done. Using the object in
+ a with statement makes that easy::
+
+ with cwriter.open('./doc/page1.txt') as outfile:
+ outfile.write(page1_data)
+ with cwriter.open('./doc/page2.txt') as outfile:
+ outfile.write(page2_data)
+ """
+ if filename is None:
+ streampath, filename = split(streampath)
+ if self._last_open and not self._last_open.closed:
+ raise errors.AssertionError(
+ "can't open '{}' when '{}' is still open".format(
+ filename, self._last_open.name))
+ if streampath != self.current_stream_name():
+ self.start_new_stream(streampath)
+ self.set_current_file_name(filename)
+ self._last_open = _WriterFile(self, filename)
+ return self._last_open
+
+ def flush_data(self):
+ data_buffer = ''.join(self._data_buffer)
+ if data_buffer:
+ self._current_stream_locators.append(
+ self._my_keep().put(data_buffer[0:self.KEEP_BLOCK_SIZE]))
+ self._data_buffer = [data_buffer[self.KEEP_BLOCK_SIZE:]]
+ self._data_buffer_len = len(self._data_buffer[0])
+
+ def start_new_file(self, newfilename=None):
+ self.finish_current_file()
+ self.set_current_file_name(newfilename)
+
+ def set_current_file_name(self, newfilename):
+ if re.search(r'[\t\n]', newfilename):
+ raise errors.AssertionError(
+ "Manifest filenames cannot contain whitespace: %s" %
+ newfilename)
+ elif re.search(r'\x00', newfilename):
+ raise errors.AssertionError(
+ "Manifest filenames cannot contain NUL characters: %s" %
+ newfilename)
+ self._current_file_name = newfilename
+
+ def current_file_name(self):
+ return self._current_file_name
+
+ def finish_current_file(self):
+ if self._current_file_name is None:
+ if self._current_file_pos == self._current_stream_length:
+ return
+ raise errors.AssertionError(
+ "Cannot finish an unnamed file " +
+ "(%d bytes at offset %d in '%s' stream)" %
+ (self._current_stream_length - self._current_file_pos,
+ self._current_file_pos,
+ self._current_stream_name))
+ self._current_stream_files.append([
+ self._current_file_pos,
+ self._current_stream_length - self._current_file_pos,
+ self._current_file_name])
+ self._current_file_pos = self._current_stream_length
+ self._current_file_name = None
+
+ def start_new_stream(self, newstreamname='.'):
+ self.finish_current_stream()
+ self.set_current_stream_name(newstreamname)
+
+ def set_current_stream_name(self, newstreamname):
+ if re.search(r'[\t\n]', newstreamname):
+ raise errors.AssertionError(
+ "Manifest stream names cannot contain whitespace")
+ self._current_stream_name = '.' if newstreamname=='' else newstreamname
+
+ def current_stream_name(self):
+ return self._current_stream_name
+
+ def finish_current_stream(self):
+ self.finish_current_file()
+ self.flush_data()
+ if not self._current_stream_files:
+ pass
+ elif self._current_stream_name is None:
+ raise errors.AssertionError(
+ "Cannot finish an unnamed stream (%d bytes in %d files)" %
+ (self._current_stream_length, len(self._current_stream_files)))
+ else:
+ if not self._current_stream_locators:
+ self._current_stream_locators.append(config.EMPTY_BLOCK_LOCATOR)
+ self._finished_streams.append([self._current_stream_name,
+ self._current_stream_locators,
+ self._current_stream_files])
+ self._current_stream_files = []
+ self._current_stream_length = 0
+ self._current_stream_locators = []
+ self._current_stream_name = None
+ self._current_file_pos = 0
+ self._current_file_name = None
+
+ def finish(self):
+ # Store the manifest in Keep and return its locator.
+ return self._my_keep().put(self.manifest_text())
+
+ def portable_data_hash(self):
+ stripped = self.stripped_manifest()
+ return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
+
+ def manifest_text(self):
+ self.finish_current_stream()
+ manifest = ''
+
+ for stream in self._finished_streams:
+ if not re.search(r'^\.(/.*)?$', stream[0]):
+ manifest += './'
+ manifest += stream[0].replace(' ', '\\040')
+ manifest += ' ' + ' '.join(stream[1])
+ manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2])
+ manifest += "\n"
+
+ return manifest
+
+ def data_locators(self):
+ ret = []
+ for name, locators, files in self._finished_streams:
+ ret += locators
+ return ret
+
+
+class ResumableCollectionWriter(CollectionWriter):
+ STATE_PROPS = ['_current_stream_files', '_current_stream_length',
+ '_current_stream_locators', '_current_stream_name',
+ '_current_file_name', '_current_file_pos', '_close_file',
+ '_data_buffer', '_dependencies', '_finished_streams',
+ '_queued_dirents', '_queued_trees']
+
+ def __init__(self, api_client=None, num_retries=0):
+ self._dependencies = {}
+ super(ResumableCollectionWriter, self).__init__(
+ api_client, num_retries=num_retries)
+
+ @classmethod
+ def from_state(cls, state, *init_args, **init_kwargs):
+ # Try to build a new writer from scratch with the given state.
+ # If the state is not suitable to resume (because files have changed,
+ # been deleted, aren't predictable, etc.), raise a
+ # StaleWriterStateError. Otherwise, return the initialized writer.
+ # The caller is responsible for calling writer.do_queued_work()
+ # appropriately after it's returned.
+ writer = cls(*init_args, **init_kwargs)
+ for attr_name in cls.STATE_PROPS:
+ attr_value = state[attr_name]
+ attr_class = getattr(writer, attr_name).__class__
+ # Coerce the value into the same type as the initial value, if
+ # needed.
+ if attr_class not in (type(None), attr_value.__class__):
+ attr_value = attr_class(attr_value)
+ setattr(writer, attr_name, attr_value)
+ # Check dependencies before we try to resume anything.
+ if any(KeepLocator(ls).permission_expired()
+ for ls in writer._current_stream_locators):
+ raise errors.StaleWriterStateError(
+ "locators include expired permission hint")
+ writer.check_dependencies()
+ if state['_current_file'] is not None:
+ path, pos = state['_current_file']
+ try:
+ writer._queued_file = open(path, 'rb')
+ writer._queued_file.seek(pos)
+ except IOError as error:
+ raise errors.StaleWriterStateError(
+ "failed to reopen active file {}: {}".format(path, error))
+ return writer
+
+ def check_dependencies(self):
+ for path, orig_stat in self._dependencies.items():
+ if not S_ISREG(orig_stat[ST_MODE]):
+ raise errors.StaleWriterStateError("{} not file".format(path))
+ try:
+ now_stat = tuple(os.stat(path))
+ except OSError as error:
+ raise errors.StaleWriterStateError(
+ "failed to stat {}: {}".format(path, error))
+ if ((not S_ISREG(now_stat[ST_MODE])) or
+ (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or
+ (orig_stat[ST_SIZE] != now_stat[ST_SIZE])):
+ raise errors.StaleWriterStateError("{} changed".format(path))
+
+ def dump_state(self, copy_func=lambda x: x):
+ state = {attr: copy_func(getattr(self, attr))
+ for attr in self.STATE_PROPS}
+ if self._queued_file is None:
+ state['_current_file'] = None
+ else:
+ state['_current_file'] = (os.path.realpath(self._queued_file.name),
+ self._queued_file.tell())
+ return state
+
+ def _queue_file(self, source, filename=None):
+ try:
+ src_path = os.path.realpath(source)
+ except Exception:
+ raise errors.AssertionError("{} not a file path".format(source))
+ try:
+ path_stat = os.stat(src_path)
+ except OSError as stat_error:
+ path_stat = None
+ super(ResumableCollectionWriter, self)._queue_file(source, filename)
+ fd_stat = os.fstat(self._queued_file.fileno())
+ if not S_ISREG(fd_stat.st_mode):
+ # We won't be able to resume from this cache anyway, so don't
+ # worry about further checks.
+ self._dependencies[source] = tuple(fd_stat)
+ elif path_stat is None:
+ raise errors.AssertionError(
+ "could not stat {}: {}".format(source, stat_error))
+ elif path_stat.st_ino != fd_stat.st_ino:
+ raise errors.AssertionError(
+ "{} changed between open and stat calls".format(source))
+ else:
+ self._dependencies[src_path] = tuple(fd_stat)
+
+ def write(self, data):
+ if self._queued_file is None:
+ raise errors.AssertionError(
+ "resumable writer can't accept unsourced data")
+ return super(ResumableCollectionWriter, self).write(data)
--- /dev/null
+#!/usr/bin/env python
+
+import argparse
+import errno
+import os
+
+def _pos_int(s):
+ num = int(s)
+ if num < 0:
+ raise ValueError("can't accept negative value: %s" % (num,))
+ return num
+
+retry_opt = argparse.ArgumentParser(add_help=False)
+retry_opt.add_argument('--retries', type=_pos_int, default=3, help="""
+Maximum number of times to retry server requests that encounter temporary
+failures (e.g., server down). Default 3.""")
+
+def _ignore_error(error):
+ return None
+
+def _raise_error(error):
+ raise error
+
+def make_home_conf_dir(path, mode=None, errors='ignore'):
+ # Make the directory path under the user's home directory, making parent
+ # directories as needed.
+ # If the directory is newly created, and a mode is specified, chmod it
+ # with those permissions.
+ # If there's an error, return None if errors is 'ignore', else raise an
+ # exception.
+ error_handler = _ignore_error if (errors == 'ignore') else _raise_error
+ tilde_path = os.path.join('~', path)
+ abs_path = os.path.expanduser(tilde_path)
+ if abs_path == tilde_path:
+ return error_handler(ValueError("no home directory available"))
+ try:
+ os.makedirs(abs_path)
+ except OSError as error:
+ if error.errno != errno.EEXIST:
+ return error_handler(error)
+ else:
+ if mode is not None:
+ os.chmod(abs_path, mode)
+ return abs_path
--- /dev/null
+#! /usr/bin/env python
+
+# arv-copy [--recursive] [--no-recursive] object-uuid src dst
+#
+# Copies an object from Arvados instance src to instance dst.
+#
+# By default, arv-copy recursively copies any dependent objects
+# necessary to make the object functional in the new instance
+# (e.g. for a pipeline instance, arv-copy copies the pipeline
+# template, input collection, docker images, git repositories). If
+# --no-recursive is given, arv-copy copies only the single record
+# identified by object-uuid.
+#
+# The user must have files $HOME/.config/arvados/{src}.conf and
+# $HOME/.config/arvados/{dst}.conf with valid login credentials for
+# instances src and dst. If either of these files is not found,
+# arv-copy will issue an error.
+
+import argparse
+import getpass
+import os
+import re
+import shutil
+import sys
+import logging
+import tempfile
+
+import arvados
+import arvados.config
+import arvados.keep
+import arvados.util
+import arvados.commands._util as arv_cmd
+import arvados.commands.keepdocker
+
+logger = logging.getLogger('arvados.arv-copy')
+
+# local_repo_dir records which git repositories from the Arvados source
+# instance have been checked out locally during this run, and to which
+# directories.
+# e.g. if repository 'twp' from src_arv has been cloned into
+# /tmp/gitfHkV9lu44A then local_repo_dir['twp'] = '/tmp/gitfHkV9lu44A'
+#
+local_repo_dir = {}
+
+# List of collections that have been copied in this session, and their
+# destination collection UUIDs.
+collections_copied = {}
+
+def main():
+ copy_opts = argparse.ArgumentParser(add_help=False)
+
+ copy_opts.add_argument(
+ '-v', '--verbose', dest='verbose', action='store_true',
+ help='Verbose output.')
+ copy_opts.add_argument(
+ '--progress', dest='progress', action='store_true',
+ help='Report progress on copying collections. (default)')
+ copy_opts.add_argument(
+ '--no-progress', dest='progress', action='store_false',
+ help='Do not report progress on copying collections.')
+ copy_opts.add_argument(
+ '-f', '--force', dest='force', action='store_true',
+ help='Perform copy even if the object appears to exist at the remote destination.')
+ copy_opts.add_argument(
+ '--src', dest='source_arvados', required=True,
+ help='The name of the source Arvados instance (required). May be either a pathname to a config file, or the basename of a file in $HOME/.config/arvados/instance_name.conf.')
+ copy_opts.add_argument(
+ '--dst', dest='destination_arvados', required=True,
+ help='The name of the destination Arvados instance (required). May be either a pathname to a config file, or the basename of a file in $HOME/.config/arvados/instance_name.conf.')
+ copy_opts.add_argument(
+ '--recursive', dest='recursive', action='store_true',
+ help='Recursively copy any dependencies for this object. (default)')
+ copy_opts.add_argument(
+ '--no-recursive', dest='recursive', action='store_false',
+ help='Do not copy any dependencies. NOTE: if this option is given, the copied object will need to be updated manually in order to be functional.')
+ copy_opts.add_argument(
+ '--dst-git-repo', dest='dst_git_repo',
+ help='The name of the destination git repository. Required when copying a pipeline recursively.')
+ copy_opts.add_argument(
+ '--project-uuid', dest='project_uuid',
+ help='The UUID of the project at the destination to which the pipeline should be copied.')
+ copy_opts.add_argument(
+ 'object_uuid',
+ help='The UUID of the object to be copied.')
+ copy_opts.set_defaults(progress=True)
+ copy_opts.set_defaults(recursive=True)
+
+ parser = argparse.ArgumentParser(
+ description='Copy a pipeline instance, template or collection from one Arvados instance to another.',
+ parents=[copy_opts, arv_cmd.retry_opt])
+ args = parser.parse_args()
+
+ if args.verbose:
+ logger.setLevel(logging.DEBUG)
+ else:
+ logger.setLevel(logging.INFO)
+
+ # Create API clients for the source and destination instances
+ src_arv = api_for_instance(args.source_arvados)
+ dst_arv = api_for_instance(args.destination_arvados)
+
+ # Identify the kind of object we have been given, and begin copying.
+ t = uuid_type(src_arv, args.object_uuid)
+ if t == 'Collection':
+ result = copy_collection(args.object_uuid,
+ src_arv, dst_arv,
+ args)
+ elif t == 'PipelineInstance':
+ result = copy_pipeline_instance(args.object_uuid,
+ src_arv, dst_arv,
+ args)
+ elif t == 'PipelineTemplate':
+ result = copy_pipeline_template(args.object_uuid,
+ src_arv, dst_arv, args)
+ else:
+ abort("cannot copy object {} of type {}".format(args.object_uuid, t))
+
+ # Clean up any outstanding temp git repositories.
+ for d in local_repo_dir.values():
+ shutil.rmtree(d, ignore_errors=True)
+
+ # If no exception was thrown and the response does not have an
+ # error_token field, presume success
+ if 'error_token' in result or 'uuid' not in result:
+ logger.error("API server returned an error result: {}".format(result))
+ exit(1)
+
+ logger.info("")
+ logger.info("Success: created copy with uuid {}".format(result['uuid']))
+ exit(0)
+
+# api_for_instance(instance_name)
+#
+# Creates an API client for the Arvados instance identified by
+# instance_name.
+#
+# If instance_name contains a slash, it is presumed to be a path
+# (either local or absolute) to a file with Arvados configuration
+# settings.
+#
+# Otherwise, it is presumed to be the name of a file in
+# $HOME/.config/arvados/instance_name.conf
+#
+def api_for_instance(instance_name):
+ if '/' in instance_name:
+ config_file = instance_name
+ else:
+ config_file = os.path.join(os.environ['HOME'], '.config', 'arvados', "{}.conf".format(instance_name))
+
+ try:
+ cfg = arvados.config.load(config_file)
+ except (IOError, OSError) as e:
+ abort(("Could not open config file {}: {}\n" +
+ "You must make sure that your configuration tokens\n" +
+ "for Arvados instance {} are in {} and that this\n" +
+ "file is readable.").format(
+ config_file, e, instance_name, config_file))
+
+ if 'ARVADOS_API_HOST' in cfg and 'ARVADOS_API_TOKEN' in cfg:
+ api_is_insecure = (
+ cfg.get('ARVADOS_API_HOST_INSECURE', '').lower() in set(
+ ['1', 't', 'true', 'y', 'yes']))
+ client = arvados.api('v1',
+ host=cfg['ARVADOS_API_HOST'],
+ token=cfg['ARVADOS_API_TOKEN'],
+ insecure=api_is_insecure,
+ cache=False)
+ else:
+ abort('need ARVADOS_API_HOST and ARVADOS_API_TOKEN for {}'.format(instance_name))
+ return client
+
+# copy_pipeline_instance(pi_uuid, src, dst, args)
+#
+# Copies a pipeline instance identified by pi_uuid from src to dst.
+#
+# If the args.recursive option is set:
+# 1. Copies all input collections
+# * For each component in the pipeline, include all collections
+# listed as job dependencies for that component)
+# 2. Copy docker images
+# 3. Copy git repositories
+# 4. Copy the pipeline template
+#
+# The only changes made to the copied pipeline instance are:
+# 1. The original pipeline instance UUID is preserved in
+# the 'properties' hash as 'copied_from_pipeline_instance_uuid'.
+# 2. The pipeline_template_uuid is changed to the new template uuid.
+# 3. The owner_uuid of the instance is changed to the user who
+# copied it.
+#
+def copy_pipeline_instance(pi_uuid, src, dst, args):
+ # Fetch the pipeline instance record.
+ pi = src.pipeline_instances().get(uuid=pi_uuid).execute()
+
+ if args.recursive:
+ if not args.dst_git_repo:
+ abort('--dst-git-repo is required when copying a pipeline recursively.')
+ # Copy the pipeline template and save the copied template.
+ if pi.get('pipeline_template_uuid', None):
+ pt = copy_pipeline_template(pi['pipeline_template_uuid'],
+ src, dst, args)
+
+ # Copy input collections, docker images and git repos.
+ pi = copy_collections(pi, src, dst, args)
+ copy_git_repos(pi, src, dst, args.dst_git_repo)
+ copy_docker_images(pi, src, dst, args)
+
+ # Update the fields of the pipeline instance with the copied
+ # pipeline template.
+ if pi.get('pipeline_template_uuid', None):
+ pi['pipeline_template_uuid'] = pt['uuid']
+
+ else:
+ # not recursive
+ logger.info("Copying only pipeline instance %s.", pi_uuid)
+ logger.info("You are responsible for making sure all pipeline dependencies have been updated.")
+
+ # Update the pipeline instance properties, and create the new
+ # instance at dst.
+ pi['properties']['copied_from_pipeline_instance_uuid'] = pi_uuid
+ pi['description'] = "Pipeline copied from {}\n\n{}".format(
+ pi_uuid,
+ pi['description'] if pi.get('description', None) else '')
+ if args.project_uuid:
+ pi['owner_uuid'] = args.project_uuid
+ else:
+ del pi['owner_uuid']
+ del pi['uuid']
+
+ new_pi = dst.pipeline_instances().create(body=pi, ensure_unique_name=True).execute()
+ return new_pi
+
+# copy_pipeline_template(pt_uuid, src, dst, args)
+#
+# Copies a pipeline template identified by pt_uuid from src to dst.
+#
+# If args.recursive is True, also copy any collections, docker
+# images and git repositories that this template references.
+#
+# The owner_uuid of the new template is changed to that of the user
+# who copied the template.
+#
+# Returns the copied pipeline template object.
+#
+def copy_pipeline_template(pt_uuid, src, dst, args):
+ # fetch the pipeline template from the source instance
+ pt = src.pipeline_templates().get(uuid=pt_uuid).execute()
+
+ if args.recursive:
+ if not args.dst_git_repo:
+ abort('--dst-git-repo is required when copying a pipeline recursively.')
+ # Copy input collections, docker images and git repos.
+ pt = copy_collections(pt, src, dst, args)
+ copy_git_repos(pt, src, dst, args.dst_git_repo)
+ copy_docker_images(pt, src, dst, args)
+
+ pt['description'] = "Pipeline template copied from {}\n\n{}".format(
+ pt_uuid,
+ pt['description'] if pt.get('description', None) else '')
+ pt['name'] = "{} copied from {}".format(pt.get('name', ''), pt_uuid)
+ del pt['uuid']
+ del pt['owner_uuid']
+
+ return dst.pipeline_templates().create(body=pt, ensure_unique_name=True).execute()
+
+# copy_collections(obj, src, dst, args)
+#
+# Recursively copies all collections referenced by 'obj' from src
+# to dst. obj may be a dict or a list, in which case we run
+# copy_collections on every value it contains. If it is a string,
+# search it for any substring that matches a collection hash or uuid
+# (this will find hidden references to collections like
+# "input0": "$(file 3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq)")
+#
+# Returns a copy of obj with any old collection uuids replaced by
+# the new ones.
+#
+def copy_collections(obj, src, dst, args):
+
+ def copy_collection_fn(collection_match):
+ """Helper function for regex substitution: copies a single collection,
+ identified by the collection_match MatchObject, to the
+ destination. Returns the destination collection uuid (or the
+ portable data hash if that's what src_id is).
+
+ """
+ src_id = collection_match.group(0)
+ if src_id not in collections_copied:
+ dst_col = copy_collection(src_id, src, dst, args)
+ if src_id in [dst_col['uuid'], dst_col['portable_data_hash']]:
+ collections_copied[src_id] = src_id
+ else:
+ collections_copied[src_id] = dst_col['uuid']
+ return collections_copied[src_id]
+
+ if isinstance(obj, basestring):
+ # Copy any collections identified in this string to dst, replacing
+ # them with the dst uuids as necessary.
+ obj = arvados.util.portable_data_hash_pattern.sub(copy_collection_fn, obj)
+ obj = arvados.util.collection_uuid_pattern.sub(copy_collection_fn, obj)
+ return obj
+ elif type(obj) == dict:
+ return {v: copy_collections(obj[v], src, dst, args) for v in obj}
+ elif type(obj) == list:
+ return [copy_collections(v, src, dst, args) for v in obj]
+ return obj
+
+# copy_git_repos(p, src, dst, dst_repo)
+#
+# Copies all git repositories referenced by pipeline instance or
+# template 'p' from src to dst.
+#
+# For each component c in the pipeline:
+# * Copy git repositories named in c['repository'] and c['job']['repository'] if present
+# * Rename script versions:
+# * c['script_version']
+# * c['job']['script_version']
+# * c['job']['supplied_script_version']
+# to the commit hashes they resolve to, since any symbolic
+# names (tags, branches) are not preserved in the destination repo.
+#
+# The pipeline object is updated in place with the new repository
+# names. The return value is undefined.
+#
+def copy_git_repos(p, src, dst, dst_repo):
+ copied = set()
+ for c in p['components']:
+ component = p['components'][c]
+ if 'repository' in component:
+ repo = component['repository']
+ script_version = component.get('script_version', None)
+ if repo not in copied:
+ copy_git_repo(repo, src, dst, dst_repo, script_version)
+ copied.add(repo)
+ component['repository'] = dst_repo
+ if script_version:
+ repo_dir = local_repo_dir[repo]
+ component['script_version'] = git_rev_parse(script_version, repo_dir)
+ if 'job' in component:
+ j = component['job']
+ if 'repository' in j:
+ repo = j['repository']
+ script_version = j.get('script_version', None)
+ if repo not in copied:
+ copy_git_repo(repo, src, dst, dst_repo, script_version)
+ copied.add(repo)
+ j['repository'] = dst_repo
+ repo_dir = local_repo_dir[repo]
+ if script_version:
+ j['script_version'] = git_rev_parse(script_version, repo_dir)
+ if 'supplied_script_version' in j:
+ j['supplied_script_version'] = git_rev_parse(j['supplied_script_version'], repo_dir)
+
+def total_collection_size(manifest_text):
+ """Return the total number of bytes in this collection (excluding
+ duplicate blocks)."""
+
+ total_bytes = 0
+ locators_seen = {}
+ for line in manifest_text.splitlines():
+ words = line.split()
+ for word in words[1:]:
+ try:
+ loc = arvados.KeepLocator(word)
+ except ValueError:
+ continue # this word isn't a locator, skip it
+ if loc.md5sum not in locators_seen:
+ locators_seen[loc.md5sum] = True
+ total_bytes += loc.size
+
+ return total_bytes
+
+# copy_collection(obj_uuid, src, dst, args)
+#
+# Copies the collection identified by obj_uuid from src to dst.
+# Returns the collection object created at dst.
+#
+# If args.progress is True, produce a human-friendly progress
+# report.
+#
+# If a collection with the desired portable_data_hash already
+# exists at dst, and args.force is False, copy_collection returns
+# the existing collection without copying any blocks. Otherwise
+# (if no collection exists or if args.force is True)
+# copy_collection copies all of the collection data blocks from src
+# to dst.
+#
+# For this application, it is critical to preserve the
+# collection's manifest hash, which is not guaranteed with the
+# arvados.CollectionReader and arvados.CollectionWriter classes.
+# Copying each block in the collection manually, followed by
+# the manifest block, ensures that the collection's manifest
+# hash will not change.
+#
+def copy_collection(obj_uuid, src, dst, args):
+ c = src.collections().get(uuid=obj_uuid).execute()
+
+ # If a collection with this hash already exists at the
+ # destination, and 'force' is not true, just return that
+ # collection.
+ if not args.force:
+ if 'portable_data_hash' in c:
+ colhash = c['portable_data_hash']
+ else:
+ colhash = c['uuid']
+ dstcol = dst.collections().list(
+ filters=[['portable_data_hash', '=', colhash]]
+ ).execute()
+ if dstcol['items_available'] > 0:
+ logger.debug("Skipping collection %s (already at dst)", obj_uuid)
+ return dstcol['items'][0]
+
+ # Fetch the collection's manifest.
+ manifest = c['manifest_text']
+ logger.debug("Copying collection %s with manifest: <%s>", obj_uuid, manifest)
+
+ # Copy each block from src_keep to dst_keep.
+ # Use the newly signed locators returned from dst_keep to build
+ # a new manifest as we go.
+ src_keep = arvados.keep.KeepClient(api_client=src, num_retries=args.retries)
+ dst_keep = arvados.keep.KeepClient(api_client=dst, num_retries=args.retries)
+ dst_manifest = ""
+ dst_locators = {}
+ bytes_written = 0
+ bytes_expected = total_collection_size(manifest)
+ if args.progress:
+ progress_writer = ProgressWriter(human_progress)
+ else:
+ progress_writer = None
+
+ for line in manifest.splitlines(True):
+ words = line.split()
+ dst_manifest_line = words[0]
+ for word in words[1:]:
+ try:
+ loc = arvados.KeepLocator(word)
+ blockhash = loc.md5sum
+ # copy this block if we haven't seen it before
+ # (otherwise, just reuse the existing dst_locator)
+ if blockhash not in dst_locators:
+ logger.debug("Copying block %s (%s bytes)", blockhash, loc.size)
+ if progress_writer:
+ progress_writer.report(obj_uuid, bytes_written, bytes_expected)
+ data = src_keep.get(word)
+ dst_locator = dst_keep.put(data)
+ dst_locators[blockhash] = dst_locator
+ bytes_written += loc.size
+ dst_manifest_line += ' ' + dst_locators[blockhash]
+ except ValueError:
+ # If 'word' can't be parsed as a locator,
+ # presume it's a filename.
+ dst_manifest_line += ' ' + word
+ dst_manifest += dst_manifest_line
+ if line.endswith("\n"):
+ dst_manifest += "\n"
+
+ if progress_writer:
+ progress_writer.report(obj_uuid, bytes_written, bytes_expected)
+ progress_writer.finish()
+
+ # Copy the manifest and save the collection.
+ logger.debug('saving %s with manifest: <%s>', obj_uuid, dst_manifest)
+ dst_keep.put(dst_manifest)
+
+ if 'uuid' in c:
+ del c['uuid']
+ if 'owner_uuid' in c:
+ del c['owner_uuid']
+ c['manifest_text'] = dst_manifest
+ return dst.collections().create(body=c, ensure_unique_name=True).execute()
+
+# copy_git_repo(src_git_repo, src, dst, dst_git_repo, script_version)
+#
+# Copies commits from git repository 'src_git_repo' on Arvados
+# instance 'src' to 'dst_git_repo' on 'dst'. Both src_git_repo
+# and dst_git_repo are repository names, not UUIDs (i.e. "arvados"
+# or "jsmith")
+#
+# All commits will be copied to a destination branch named for the
+# source repository URL.
+#
+# Because users cannot create their own repositories, the
+# destination repository must already exist.
+#
+# The user running this command must be authenticated
+# to both repositories.
+#
+def copy_git_repo(src_git_repo, src, dst, dst_git_repo, script_version):
+ # Identify the fetch and push URLs for the git repositories.
+ r = src.repositories().list(
+ filters=[['name', '=', src_git_repo]]).execute()
+ if r['items_available'] != 1:
+ raise Exception('cannot identify source repo {}; {} repos found'
+ .format(src_git_repo, r['items_available']))
+ src_git_url = r['items'][0]['fetch_url']
+ logger.debug('src_git_url: {}'.format(src_git_url))
+
+ r = dst.repositories().list(
+ filters=[['name', '=', dst_git_repo]]).execute()
+ if r['items_available'] != 1:
+ raise Exception('cannot identify destination repo {}; {} repos found'
+ .format(dst_git_repo, r['items_available']))
+ dst_git_push_url = r['items'][0]['push_url']
+ logger.debug('dst_git_push_url: {}'.format(dst_git_push_url))
+
+ # script_version is the "script_version" parameter from the source
+ # component or job. It is used here to tie the destination branch
+ # to the commit that was used on the source. If no script_version
+ # was supplied in the component or job, it is a mistake in the pipeline,
+ # but for the purposes of copying the repository, default to "master".
+ #
+ if not script_version:
+ script_version = "master"
+
+ dst_branch = re.sub(r'\W+', '_', "{}_{}".format(src_git_url, script_version))
+
+ # Copy git commits from src repo to dst repo (but only if
+ # we have not already copied this repo in this session).
+ #
+ if src_git_repo in local_repo_dir:
+ logger.debug('already copied src repo %s, skipping', src_git_repo)
+ else:
+ tmprepo = tempfile.mkdtemp()
+ local_repo_dir[src_git_repo] = tmprepo
+ arvados.util.run_command(
+ ["git", "clone", "--bare", src_git_url, tmprepo],
+ cwd=os.path.dirname(tmprepo))
+ arvados.util.run_command(
+ ["git", "branch", dst_branch, script_version],
+ cwd=tmprepo)
+ arvados.util.run_command(["git", "remote", "add", "dst", dst_git_push_url], cwd=tmprepo)
+ arvados.util.run_command(["git", "push", "dst", dst_branch], cwd=tmprepo)
+
+
+def copy_docker_images(pipeline, src, dst, args):
+ """Copy any docker images named in the pipeline components'
+ runtime_constraints field from src to dst."""
+
+ logger.debug('copy_docker_images: {}'.format(pipeline['uuid']))
+ for c_name, c_info in pipeline['components'].iteritems():
+ if ('runtime_constraints' in c_info and
+ 'docker_image' in c_info['runtime_constraints']):
+ copy_docker_image(
+ c_info['runtime_constraints']['docker_image'],
+ c_info['runtime_constraints'].get('docker_image_tag', 'latest'),
+ src, dst, args)
+
+
+def copy_docker_image(docker_image, docker_image_tag, src, dst, args):
+ """Copy the docker image identified by docker_image and
+ docker_image_tag from src to dst. Create appropriate
+ docker_image_repo+tag and docker_image_hash links at dst.
+
+ """
+
+ logger.debug('copying docker image {}:{}'.format(docker_image, docker_image_tag))
+
+ # Find the link identifying this docker image.
+ docker_image_list = arvados.commands.keepdocker.list_images_in_arv(
+ src, args.retries, docker_image, docker_image_tag)
+ image_uuid, image_info = docker_image_list[0]
+ logger.debug('copying collection {} {}'.format(image_uuid, image_info))
+
+ # Copy the collection it refers to.
+ dst_image_col = copy_collection(image_uuid, src, dst, args)
+
+ # Create docker_image_repo+tag and docker_image_hash links
+ # at the destination.
+ lk = dst.links().create(
+ body={
+ 'head_uuid': dst_image_col['uuid'],
+ 'link_class': 'docker_image_repo+tag',
+ 'name': "{}:{}".format(docker_image, docker_image_tag),
+ }
+ ).execute(num_retries=args.retries)
+ logger.debug('created dst link {}'.format(lk))
+
+ lk = dst.links().create(
+ body={
+ 'head_uuid': dst_image_col['uuid'],
+ 'link_class': 'docker_image_hash',
+ 'name': dst_image_col['portable_data_hash'],
+ }
+ ).execute(num_retries=args.retries)
+ logger.debug('created dst link {}'.format(lk))
+
+
+# git_rev_parse(rev, repo)
+#
+# Returns the 40-character commit hash corresponding to 'rev' in
+# git repository 'repo' (which must be the path of a local git
+# repository)
+#
+def git_rev_parse(rev, repo):
+ gitout, giterr = arvados.util.run_command(
+ ['git', 'rev-parse', rev], cwd=repo)
+ return gitout.strip()
+
+# uuid_type(api, object_uuid)
+#
+# Returns the name of the class that object_uuid belongs to, based on
+# the second field of the uuid. This function consults the api's
+# schema to identify the object class.
+#
+# It returns a string such as 'Collection', 'PipelineInstance', etc.
+#
+# Special case: if handed a Keep locator hash, return 'Collection'.
+#
+def uuid_type(api, object_uuid):
+ if re.match(r'^[a-f0-9]{32}\+[0-9]+(\+[A-Za-z0-9+-]+)?$', object_uuid):
+ return 'Collection'
+ p = object_uuid.split('-')
+ if len(p) == 3:
+ type_prefix = p[1]
+ for k in api._schema.schemas:
+ obj_class = api._schema.schemas[k].get('uuidPrefix', None)
+ if type_prefix == obj_class:
+ return k
+ return None
+
+def abort(msg, code=1):
+ logger.info("arv-copy: %s", msg)
+ exit(code)
+
+
+# Code for reporting on the progress of a collection upload.
+# Stolen from arvados.commands.put.ArvPutCollectionWriter
+# TODO(twp): figure out how to refactor into a shared library
+# (may involve refactoring some arvados.commands.arv_copy.copy_collection
+# code)
+
+def machine_progress(obj_uuid, bytes_written, bytes_expected):
+ return "{} {}: {} {} written {} total\n".format(
+ sys.argv[0],
+ os.getpid(),
+ obj_uuid,
+ bytes_written,
+ -1 if (bytes_expected is None) else bytes_expected)
+
+def human_progress(obj_uuid, bytes_written, bytes_expected):
+ if bytes_expected:
+ return "\r{}: {}M / {}M {:.1%} ".format(
+ obj_uuid,
+ bytes_written >> 20, bytes_expected >> 20,
+ float(bytes_written) / bytes_expected)
+ else:
+ return "\r{}: {} ".format(obj_uuid, bytes_written)
+
+class ProgressWriter(object):
+ _progress_func = None
+ outfile = sys.stderr
+
+ def __init__(self, progress_func):
+ self._progress_func = progress_func
+
+ def report(self, obj_uuid, bytes_written, bytes_expected):
+ if self._progress_func is not None:
+ self.outfile.write(
+ self._progress_func(obj_uuid, bytes_written, bytes_expected))
+
+ def finish(self):
+ self.outfile.write("\n")
+
+if __name__ == '__main__':
+ main()
--- /dev/null
+#!/usr/bin/env python
+
+import argparse
+import datetime
+import errno
+import json
+import os
+import subprocess
+import sys
+import tarfile
+import tempfile
+import _strptime
+
+from collections import namedtuple
+from stat import *
+
+import arvados
+import arvados.commands._util as arv_cmd
+import arvados.commands.put as arv_put
+
+STAT_CACHE_ERRORS = (IOError, OSError, ValueError)
+
+DockerImage = namedtuple('DockerImage',
+ ['repo', 'tag', 'hash', 'created', 'vsize'])
+
+keepdocker_parser = argparse.ArgumentParser(add_help=False)
+keepdocker_parser.add_argument(
+ '-f', '--force', action='store_true', default=False,
+ help="Re-upload the image even if it already exists on the server")
+
+_group = keepdocker_parser.add_mutually_exclusive_group()
+_group.add_argument(
+ '--pull', action='store_true', default=False,
+ help="Try to pull the latest image from Docker registry")
+_group.add_argument(
+ '--no-pull', action='store_false', dest='pull',
+ help="Use locally installed image only, don't pull image from Docker registry (default)")
+
+keepdocker_parser.add_argument(
+ 'image', nargs='?',
+ help="Docker image to upload, as a repository name or hash")
+keepdocker_parser.add_argument(
+ 'tag', nargs='?', default='latest',
+ help="Tag of the Docker image to upload (default 'latest')")
+
+# Combine keepdocker options listed above with run_opts options of arv-put.
+# The options inherited from arv-put include --name, --project-uuid,
+# --progress/--no-progress/--batch-progress and --resume/--no-resume.
+arg_parser = argparse.ArgumentParser(
+ description="Upload or list Docker images in Arvados",
+ parents=[keepdocker_parser, arv_put.run_opts, arv_cmd.retry_opt])
+
+class DockerError(Exception):
+ pass
+
+
+def popen_docker(cmd, *args, **kwargs):
+ manage_stdin = ('stdin' not in kwargs)
+ kwargs.setdefault('stdin', subprocess.PIPE)
+ kwargs.setdefault('stdout', sys.stderr)
+ try:
+ docker_proc = subprocess.Popen(['docker.io'] + cmd, *args, **kwargs)
+ except OSError: # No docker.io in $PATH
+ docker_proc = subprocess.Popen(['docker'] + cmd, *args, **kwargs)
+ if manage_stdin:
+ docker_proc.stdin.close()
+ return docker_proc
+
+def check_docker(proc, description):
+ proc.wait()
+ if proc.returncode != 0:
+ raise DockerError("docker {} returned status code {}".
+ format(description, proc.returncode))
+
+def docker_images():
+ # Yield a DockerImage tuple for each installed image.
+ list_proc = popen_docker(['images', '--no-trunc'], stdout=subprocess.PIPE)
+ list_output = iter(list_proc.stdout)
+ next(list_output) # Ignore the header line
+ for line in list_output:
+ words = line.split()
+ size_index = len(words) - 2
+ repo, tag, imageid = words[:3]
+ ctime = ' '.join(words[3:size_index])
+ vsize = ' '.join(words[size_index:])
+ yield DockerImage(repo, tag, imageid, ctime, vsize)
+ list_proc.stdout.close()
+ check_docker(list_proc, "images")
+
+def find_image_hashes(image_search, image_tag=None):
+ # Given one argument, search for Docker images with matching hashes,
+ # and return their full hashes in a set.
+ # Given two arguments, also search for a Docker image with the
+ # same repository and tag. If one is found, return its hash in a
+ # set; otherwise, fall back to the one-argument hash search.
+ # Returns None if no match is found, or a hash search is ambiguous.
+ hash_search = image_search.lower()
+ hash_matches = set()
+ for image in docker_images():
+ if (image.repo == image_search) and (image.tag == image_tag):
+ return set([image.hash])
+ elif image.hash.startswith(hash_search):
+ hash_matches.add(image.hash)
+ return hash_matches
+
+def find_one_image_hash(image_search, image_tag=None):
+ hashes = find_image_hashes(image_search, image_tag)
+ hash_count = len(hashes)
+ if hash_count == 1:
+ return hashes.pop()
+ elif hash_count == 0:
+ raise DockerError("no matching image found")
+ else:
+ raise DockerError("{} images match {}".format(hash_count, image_search))
+
+def stat_cache_name(image_file):
+ return getattr(image_file, 'name', image_file) + '.stat'
+
+def pull_image(image_name, image_tag):
+ check_docker(popen_docker(['pull', '{}:{}'.format(image_name, image_tag)]),
+ "pull")
+
+def save_image(image_hash, image_file):
+ # Save the specified Docker image to image_file, then try to save its
+ # stats so we can try to resume after interruption.
+ check_docker(popen_docker(['save', image_hash], stdout=image_file),
+ "save")
+ image_file.flush()
+ try:
+ with open(stat_cache_name(image_file), 'w') as statfile:
+ json.dump(tuple(os.fstat(image_file.fileno())), statfile)
+ except STAT_CACHE_ERRORS:
+ pass # We won't resume from this cache. No big deal.
+
+def prep_image_file(filename):
+ # Return a file object ready to save a Docker image,
+ # and a boolean indicating whether or not we need to actually save the
+ # image (False if a cached save is available).
+ cache_dir = arv_cmd.make_home_conf_dir(
+ os.path.join('.cache', 'arvados', 'docker'), 0o700)
+ if cache_dir is None:
+ image_file = tempfile.NamedTemporaryFile(suffix='.tar')
+ need_save = True
+ else:
+ file_path = os.path.join(cache_dir, filename)
+ try:
+ with open(stat_cache_name(file_path)) as statfile:
+ prev_stat = json.load(statfile)
+ now_stat = os.stat(file_path)
+ need_save = any(prev_stat[field] != now_stat[field]
+ for field in [ST_MTIME, ST_SIZE])
+ except STAT_CACHE_ERRORS + (AttributeError, IndexError):
+ need_save = True # We couldn't compare against old stats
+ image_file = open(file_path, 'w+b' if need_save else 'rb')
+ return image_file, need_save
+
+def make_link(api_client, num_retries, link_class, link_name, **link_attrs):
+ link_attrs.update({'link_class': link_class, 'name': link_name})
+ return api_client.links().create(body=link_attrs).execute(
+ num_retries=num_retries)
+
+def ptimestamp(t):
+ s = t.split(".")
+ if len(s) == 2:
+ t = s[0] + s[1][-1:]
+ return datetime.datetime.strptime(t, "%Y-%m-%dT%H:%M:%SZ")
+
+def list_images_in_arv(api_client, num_retries, image_name=None, image_tag=None):
+ """List all Docker images known to the api_client with image_name and
+ image_tag. If no image_name is given, defaults to listing all
+ Docker images.
+
+ Returns a list of tuples representing matching Docker images,
+ sorted in preference order (i.e. the first collection in the list
+ is the one that the API server would use). Each tuple is a
+ (collection_uuid, collection_info) pair, where collection_info is
+ a dict with fields "dockerhash", "repo", "tag", and "timestamp".
+
+ """
+ docker_image_filters = [['link_class', 'in', ['docker_image_hash', 'docker_image_repo+tag']]]
+ if image_name:
+ image_link_name = "{}:{}".format(image_name, image_tag or 'latest')
+ docker_image_filters.append(['name', '=', image_link_name])
+
+ existing_links = api_client.links().list(
+ filters=docker_image_filters
+ ).execute(num_retries=num_retries)['items']
+ images = {}
+ for link in existing_links:
+ collection_uuid = link["head_uuid"]
+ if collection_uuid not in images:
+ images[collection_uuid]= {"dockerhash": "<none>",
+ "repo":"<none>",
+ "tag":"<none>",
+ "timestamp": ptimestamp("1970-01-01T00:00:01Z")}
+
+ if link["link_class"] == "docker_image_hash":
+ images[collection_uuid]["dockerhash"] = link["name"]
+
+ if link["link_class"] == "docker_image_repo+tag":
+ r = link["name"].split(":")
+ images[collection_uuid]["repo"] = r[0]
+ if len(r) > 1:
+ images[collection_uuid]["tag"] = r[1]
+
+ if "image_timestamp" in link["properties"]:
+ images[collection_uuid]["timestamp"] = ptimestamp(link["properties"]["image_timestamp"])
+ else:
+ images[collection_uuid]["timestamp"] = ptimestamp(link["created_at"])
+
+ return sorted(images.items(), lambda a, b: cmp(b[1]["timestamp"], a[1]["timestamp"]))
+
+
+def main(arguments=None):
+ args = arg_parser.parse_args(arguments)
+ api = arvados.api('v1')
+
+ if args.image is None or args.image == 'images':
+ fmt = "{:30} {:10} {:12} {:29} {:20}"
+ print fmt.format("REPOSITORY", "TAG", "IMAGE ID", "COLLECTION", "CREATED")
+ for i, j in list_images_in_arv(api, args.retries):
+ print(fmt.format(j["repo"], j["tag"], j["dockerhash"][0:12], i, j["timestamp"].strftime("%c")))
+ sys.exit(0)
+
+ # Pull the image if requested, unless the image is specified as a hash
+ # that we already have.
+ if args.pull and not find_image_hashes(args.image):
+ pull_image(args.image, args.tag)
+
+ try:
+ image_hash = find_one_image_hash(args.image, args.tag)
+ except DockerError as error:
+ print >>sys.stderr, "arv-keepdocker:", error.message
+ sys.exit(1)
+
+ image_repo_tag = '{}:{}'.format(args.image, args.tag) if not image_hash.startswith(args.image.lower()) else None
+
+ if args.name is None:
+ if image_repo_tag:
+ collection_name = 'Docker image {} {}'.format(image_repo_tag, image_hash[0:12])
+ else:
+ collection_name = 'Docker image {}'.format(image_hash[0:12])
+ else:
+ collection_name = args.name
+
+ if not args.force:
+ # Check if this image is already in Arvados.
+
+ # Project where everything should be owned
+ if args.project_uuid:
+ parent_project_uuid = args.project_uuid
+ else:
+ parent_project_uuid = api.users().current().execute(
+ num_retries=args.retries)['uuid']
+
+ # Find image hash tags
+ existing_links = api.links().list(
+ filters=[['link_class', '=', 'docker_image_hash'],
+ ['name', '=', image_hash]]
+ ).execute(num_retries=args.retries)['items']
+ if existing_links:
+ # get readable collections
+ collections = api.collections().list(
+ filters=[['uuid', 'in', [link['head_uuid'] for link in existing_links]]],
+ select=["uuid", "owner_uuid", "name", "manifest_text"]
+ ).execute(num_retries=args.retries)['items']
+
+ if collections:
+ # check for repo+tag links on these collections
+ existing_repo_tag = (api.links().list(
+ filters=[['link_class', '=', 'docker_image_repo+tag'],
+ ['name', '=', image_repo_tag],
+ ['head_uuid', 'in', collections]]
+ ).execute(num_retries=args.retries)['items']) if image_repo_tag else []
+
+ # Filter on elements owned by the parent project
+ owned_col = [c for c in collections if c['owner_uuid'] == parent_project_uuid]
+ owned_img = [c for c in existing_links if c['owner_uuid'] == parent_project_uuid]
+ owned_rep = [c for c in existing_repo_tag if c['owner_uuid'] == parent_project_uuid]
+
+ if owned_col:
+ # already have a collection owned by this project
+ coll_uuid = owned_col[0]['uuid']
+ else:
+ # create new collection owned by the project
+ coll_uuid = api.collections().create(
+ body={"manifest_text": collections[0]['manifest_text'],
+ "name": collection_name,
+ "owner_uuid": parent_project_uuid},
+ ensure_unique_name=True
+ ).execute(num_retries=args.retries)['uuid']
+
+ link_base = {'owner_uuid': parent_project_uuid,
+ 'head_uuid': coll_uuid }
+
+ if not owned_img:
+ # create image link owned by the project
+ make_link(api, args.retries,
+ 'docker_image_hash', image_hash, **link_base)
+
+ if not owned_rep and image_repo_tag:
+ # create repo+tag link owned by the project
+ make_link(api, args.retries, 'docker_image_repo+tag',
+ image_repo_tag, **link_base)
+
+ print(coll_uuid)
+
+ sys.exit(0)
+
+ # Open a file for the saved image, and write it if needed.
+ outfile_name = '{}.tar'.format(image_hash)
+ image_file, need_save = prep_image_file(outfile_name)
+ if need_save:
+ save_image(image_hash, image_file)
+
+ # Call arv-put with switches we inherited from it
+ # (a.k.a., switches that aren't our own).
+ put_args = keepdocker_parser.parse_known_args(arguments)[1]
+
+ if args.name is None:
+ put_args += ['--name', collection_name]
+
+ coll_uuid = arv_put.main(
+ put_args + ['--filename', outfile_name, image_file.name]).strip()
+
+ # Read the image metadata and make Arvados links from it.
+ image_file.seek(0)
+ image_tar = tarfile.open(fileobj=image_file)
+ json_file = image_tar.extractfile(image_tar.getmember(image_hash + '/json'))
+ image_metadata = json.load(json_file)
+ json_file.close()
+ image_tar.close()
+ link_base = {'head_uuid': coll_uuid, 'properties': {}}
+ if 'created' in image_metadata:
+ link_base['properties']['image_timestamp'] = image_metadata['created']
+ if args.project_uuid is not None:
+ link_base['owner_uuid'] = args.project_uuid
+
+ make_link(api, args.retries, 'docker_image_hash', image_hash, **link_base)
+ if image_repo_tag:
+ make_link(api, args.retries,
+ 'docker_image_repo+tag', image_repo_tag, **link_base)
+
+ # Clean up.
+ image_file.close()
+ for filename in [stat_cache_name(image_file), image_file.name]:
+ try:
+ os.unlink(filename)
+ except OSError as error:
+ if error.errno != errno.ENOENT:
+ raise
+
+if __name__ == '__main__':
+ main()
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+
+import arvados
+import arvados.commands._util as arv_cmd
+
+def parse_args(args):
+ parser = argparse.ArgumentParser(
+ description='List contents of a manifest',
+ parents=[arv_cmd.retry_opt])
+
+ parser.add_argument('locator', type=str,
+ help="""Collection UUID or locator""")
+ parser.add_argument('-s', action='store_true',
+ help="""List file sizes, in KiB.""")
+
+ return parser.parse_args(args)
+
+def size_formatter(coll_file):
+ return "{:>10}".format((coll_file.size() + 1023) / 1024)
+
+def name_formatter(coll_file):
+ return "{}/{}".format(coll_file.stream_name(), coll_file.name)
+
+def main(args, stdout, stderr, api_client=None):
+ args = parse_args(args)
+
+ if api_client is None:
+ api_client = arvados.api('v1')
+
+ try:
+ cr = arvados.CollectionReader(args.locator, api_client=api_client,
+ num_retries=args.retries)
+ cr.normalize()
+ except (arvados.errors.ArgumentError,
+ arvados.errors.NotFoundError) as error:
+ print("arv-ls: error fetching collection: {}".format(error),
+ file=stderr)
+ return 1
+
+ formatters = []
+ if args.s:
+ formatters.append(size_formatter)
+ formatters.append(name_formatter)
+
+ for f in cr.all_files():
+ print(*(info_func(f) for info_func in formatters), file=stdout)
+
+ return 0
--- /dev/null
+#!/usr/bin/env python
+
+# TODO:
+# --md5sum - display md5 of each file as read from disk
+
+import argparse
+import arvados
+import base64
+import datetime
+import errno
+import fcntl
+import hashlib
+import json
+import os
+import pwd
+import signal
+import socket
+import sys
+import tempfile
+from apiclient import errors as apiclient_errors
+
+import arvados.commands._util as arv_cmd
+
+CAUGHT_SIGNALS = [signal.SIGINT, signal.SIGQUIT, signal.SIGTERM]
+api_client = None
+
+upload_opts = argparse.ArgumentParser(add_help=False)
+
+upload_opts.add_argument('paths', metavar='path', type=str, nargs='*',
+ help="""
+Local file or directory. Default: read from standard input.
+""")
+
+_group = upload_opts.add_mutually_exclusive_group()
+
+_group.add_argument('--max-manifest-depth', type=int, metavar='N',
+ default=-1, help="""
+Maximum depth of directory tree to represent in the manifest
+structure. A directory structure deeper than this will be represented
+as a single stream in the manifest. If N=0, the manifest will contain
+a single stream. Default: -1 (unlimited), i.e., exactly one manifest
+stream per filesystem directory that contains files.
+""")
+
+_group.add_argument('--normalize', action='store_true',
+ help="""
+Normalize the manifest by re-ordering files and streams after writing
+data.
+""")
+
+_group = upload_opts.add_mutually_exclusive_group()
+
+_group.add_argument('--as-stream', action='store_true', dest='stream',
+ help="""
+Synonym for --stream.
+""")
+
+_group.add_argument('--stream', action='store_true',
+ help="""
+Store the file content and display the resulting manifest on
+stdout. Do not write the manifest to Keep or save a Collection object
+in Arvados.
+""")
+
+_group.add_argument('--as-manifest', action='store_true', dest='manifest',
+ help="""
+Synonym for --manifest.
+""")
+
+_group.add_argument('--in-manifest', action='store_true', dest='manifest',
+ help="""
+Synonym for --manifest.
+""")
+
+_group.add_argument('--manifest', action='store_true',
+ help="""
+Store the file data and resulting manifest in Keep, save a Collection
+object in Arvados, and display the manifest locator (Collection uuid)
+on stdout. This is the default behavior.
+""")
+
+_group.add_argument('--as-raw', action='store_true', dest='raw',
+ help="""
+Synonym for --raw.
+""")
+
+_group.add_argument('--raw', action='store_true',
+ help="""
+Store the file content and display the data block locators on stdout,
+separated by commas, with a trailing newline. Do not store a
+manifest.
+""")
+
+upload_opts.add_argument('--use-filename', type=str, default=None,
+ dest='filename', help="""
+Synonym for --filename.
+""")
+
+upload_opts.add_argument('--filename', type=str, default=None,
+ help="""
+Use the given filename in the manifest, instead of the name of the
+local file. This is useful when "-" or "/dev/stdin" is given as an
+input file. It can be used only if there is exactly one path given and
+it is not a directory. Implies --manifest.
+""")
+
+upload_opts.add_argument('--portable-data-hash', action='store_true',
+ help="""
+Print the portable data hash instead of the Arvados UUID for the collection
+created by the upload.
+""")
+
+run_opts = argparse.ArgumentParser(add_help=False)
+
+run_opts.add_argument('--project-uuid', metavar='UUID', help="""
+Store the collection in the specified project, instead of your Home
+project.
+""")
+
+run_opts.add_argument('--name', help="""
+Save the collection with the specified name.
+""")
+
+_group = run_opts.add_mutually_exclusive_group()
+_group.add_argument('--progress', action='store_true',
+ help="""
+Display human-readable progress on stderr (bytes and, if possible,
+percentage of total data size). This is the default behavior when
+stderr is a tty.
+""")
+
+_group.add_argument('--no-progress', action='store_true',
+ help="""
+Do not display human-readable progress on stderr, even if stderr is a
+tty.
+""")
+
+_group.add_argument('--batch-progress', action='store_true',
+ help="""
+Display machine-readable progress on stderr (bytes and, if known,
+total data size).
+""")
+
+_group = run_opts.add_mutually_exclusive_group()
+_group.add_argument('--resume', action='store_true', default=True,
+ help="""
+Continue interrupted uploads from cached state (default).
+""")
+_group.add_argument('--no-resume', action='store_false', dest='resume',
+ help="""
+Do not continue interrupted uploads from cached state.
+""")
+
+arg_parser = argparse.ArgumentParser(
+ description='Copy data from the local filesystem to Keep.',
+ parents=[upload_opts, run_opts, arv_cmd.retry_opt])
+
+def parse_arguments(arguments):
+ args = arg_parser.parse_args(arguments)
+
+ if len(args.paths) == 0:
+ args.paths += ['/dev/stdin']
+
+ if len(args.paths) != 1 or os.path.isdir(args.paths[0]):
+ if args.filename:
+ arg_parser.error("""
+ --filename argument cannot be used when storing a directory or
+ multiple files.
+ """)
+
+ # Turn on --progress by default if stderr is a tty.
+ if (not (args.batch_progress or args.no_progress)
+ and os.isatty(sys.stderr.fileno())):
+ args.progress = True
+
+ if args.paths == ['-']:
+ args.paths = ['/dev/stdin']
+ if not args.filename:
+ args.filename = '-'
+
+ return args
+
+class ResumeCacheConflict(Exception):
+ pass
+
+
+class ResumeCache(object):
+ CACHE_DIR = '.cache/arvados/arv-put'
+
+ def __init__(self, file_spec):
+ self.cache_file = open(file_spec, 'a+')
+ self._lock_file(self.cache_file)
+ self.filename = self.cache_file.name
+
+ @classmethod
+ def make_path(cls, args):
+ md5 = hashlib.md5()
+ md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost'))
+ realpaths = sorted(os.path.realpath(path) for path in args.paths)
+ md5.update('\0'.join(realpaths))
+ if any(os.path.isdir(path) for path in realpaths):
+ md5.update(str(max(args.max_manifest_depth, -1)))
+ elif args.filename:
+ md5.update(args.filename)
+ return os.path.join(
+ arv_cmd.make_home_conf_dir(cls.CACHE_DIR, 0o700, 'raise'),
+ md5.hexdigest())
+
+ def _lock_file(self, fileobj):
+ try:
+ fcntl.flock(fileobj, fcntl.LOCK_EX | fcntl.LOCK_NB)
+ except IOError:
+ raise ResumeCacheConflict("{} locked".format(fileobj.name))
+
+ def load(self):
+ self.cache_file.seek(0)
+ return json.load(self.cache_file)
+
+ def save(self, data):
+ try:
+ new_cache_fd, new_cache_name = tempfile.mkstemp(
+ dir=os.path.dirname(self.filename))
+ self._lock_file(new_cache_fd)
+ new_cache = os.fdopen(new_cache_fd, 'r+')
+ json.dump(data, new_cache)
+ os.rename(new_cache_name, self.filename)
+ except (IOError, OSError, ResumeCacheConflict) as error:
+ try:
+ os.unlink(new_cache_name)
+ except NameError: # mkstemp failed.
+ pass
+ else:
+ self.cache_file.close()
+ self.cache_file = new_cache
+
+ def close(self):
+ self.cache_file.close()
+
+ def destroy(self):
+ try:
+ os.unlink(self.filename)
+ except OSError as error:
+ if error.errno != errno.ENOENT: # That's what we wanted anyway.
+ raise
+ self.close()
+
+ def restart(self):
+ self.destroy()
+ self.__init__(self.filename)
+
+
+class ArvPutCollectionWriter(arvados.ResumableCollectionWriter):
+ STATE_PROPS = (arvados.ResumableCollectionWriter.STATE_PROPS +
+ ['bytes_written', '_seen_inputs'])
+
+ def __init__(self, cache=None, reporter=None, bytes_expected=None,
+ api_client=None, num_retries=0):
+ self.bytes_written = 0
+ self._seen_inputs = []
+ self.cache = cache
+ self.reporter = reporter
+ self.bytes_expected = bytes_expected
+ super(ArvPutCollectionWriter, self).__init__(
+ api_client, num_retries=num_retries)
+
+ @classmethod
+ def from_cache(cls, cache, reporter=None, bytes_expected=None,
+ num_retries=0):
+ try:
+ state = cache.load()
+ state['_data_buffer'] = [base64.decodestring(state['_data_buffer'])]
+ writer = cls.from_state(state, cache, reporter, bytes_expected,
+ num_retries=num_retries)
+ except (TypeError, ValueError,
+ arvados.errors.StaleWriterStateError) as error:
+ return cls(cache, reporter, bytes_expected, num_retries=num_retries)
+ else:
+ return writer
+
+ def cache_state(self):
+ if self.cache is None:
+ return
+ state = self.dump_state()
+ # Transform attributes for serialization.
+ for attr, value in state.items():
+ if attr == '_data_buffer':
+ state[attr] = base64.encodestring(''.join(value))
+ elif hasattr(value, 'popleft'):
+ state[attr] = list(value)
+ self.cache.save(state)
+
+ def report_progress(self):
+ if self.reporter is not None:
+ self.reporter(self.bytes_written, self.bytes_expected)
+
+ def flush_data(self):
+ start_buffer_len = self._data_buffer_len
+ start_block_count = self.bytes_written / self.KEEP_BLOCK_SIZE
+ super(ArvPutCollectionWriter, self).flush_data()
+ if self._data_buffer_len < start_buffer_len: # We actually PUT data.
+ self.bytes_written += (start_buffer_len - self._data_buffer_len)
+ self.report_progress()
+ if (self.bytes_written / self.KEEP_BLOCK_SIZE) > start_block_count:
+ self.cache_state()
+
+ def _record_new_input(self, input_type, source_name, dest_name):
+ # The key needs to be a list because that's what we'll get back
+ # from JSON deserialization.
+ key = [input_type, source_name, dest_name]
+ if key in self._seen_inputs:
+ return False
+ self._seen_inputs.append(key)
+ return True
+
+ def write_file(self, source, filename=None):
+ if self._record_new_input('file', source, filename):
+ super(ArvPutCollectionWriter, self).write_file(source, filename)
+
+ def write_directory_tree(self,
+ path, stream_name='.', max_manifest_depth=-1):
+ if self._record_new_input('directory', path, stream_name):
+ super(ArvPutCollectionWriter, self).write_directory_tree(
+ path, stream_name, max_manifest_depth)
+
+
+def expected_bytes_for(pathlist):
+ # Walk the given directory trees and stat files, adding up file sizes,
+ # so we can display progress as percent
+ bytesum = 0
+ for path in pathlist:
+ if os.path.isdir(path):
+ for filename in arvados.util.listdir_recursive(path):
+ bytesum += os.path.getsize(os.path.join(path, filename))
+ elif not os.path.isfile(path):
+ return None
+ else:
+ bytesum += os.path.getsize(path)
+ return bytesum
+
+_machine_format = "{} {}: {{}} written {{}} total\n".format(sys.argv[0],
+ os.getpid())
+def machine_progress(bytes_written, bytes_expected):
+ return _machine_format.format(
+ bytes_written, -1 if (bytes_expected is None) else bytes_expected)
+
+def human_progress(bytes_written, bytes_expected):
+ if bytes_expected:
+ return "\r{}M / {}M {:.1%} ".format(
+ bytes_written >> 20, bytes_expected >> 20,
+ float(bytes_written) / bytes_expected)
+ else:
+ return "\r{} ".format(bytes_written)
+
+def progress_writer(progress_func, outfile=sys.stderr):
+ def write_progress(bytes_written, bytes_expected):
+ outfile.write(progress_func(bytes_written, bytes_expected))
+ return write_progress
+
+def exit_signal_handler(sigcode, frame):
+ sys.exit(-sigcode)
+
+def desired_project_uuid(api_client, project_uuid, num_retries):
+ if not project_uuid:
+ query = api_client.users().current()
+ elif arvados.util.user_uuid_pattern.match(project_uuid):
+ query = api_client.users().get(uuid=project_uuid)
+ elif arvados.util.group_uuid_pattern.match(project_uuid):
+ query = api_client.groups().get(uuid=project_uuid)
+ else:
+ raise ValueError("Not a valid project UUID: {}".format(project_uuid))
+ return query.execute(num_retries=num_retries)['uuid']
+
+def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
+ global api_client
+
+ args = parse_arguments(arguments)
+ status = 0
+ if api_client is None:
+ api_client = arvados.api('v1')
+
+ # Determine the name to use
+ if args.name:
+ if args.stream or args.raw:
+ print >>stderr, "Cannot use --name with --stream or --raw"
+ sys.exit(1)
+ collection_name = args.name
+ else:
+ collection_name = "Saved at {} by {}@{}".format(
+ datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC"),
+ pwd.getpwuid(os.getuid()).pw_name,
+ socket.gethostname())
+
+ if args.project_uuid and (args.stream or args.raw):
+ print >>stderr, "Cannot use --project-uuid with --stream or --raw"
+ sys.exit(1)
+
+ # Determine the parent project
+ try:
+ project_uuid = desired_project_uuid(api_client, args.project_uuid,
+ args.retries)
+ except (apiclient_errors.Error, ValueError) as error:
+ print >>stderr, error
+ sys.exit(1)
+
+ if args.progress:
+ reporter = progress_writer(human_progress)
+ elif args.batch_progress:
+ reporter = progress_writer(machine_progress)
+ else:
+ reporter = None
+ bytes_expected = expected_bytes_for(args.paths)
+
+ resume_cache = None
+ if args.resume:
+ try:
+ resume_cache = ResumeCache(ResumeCache.make_path(args))
+ except (IOError, OSError, ValueError):
+ pass # Couldn't open cache directory/file. Continue without it.
+ except ResumeCacheConflict:
+ print >>stderr, "\n".join([
+ "arv-put: Another process is already uploading this data.",
+ " Use --no-resume if this is really what you want."])
+ sys.exit(1)
+
+ if resume_cache is None:
+ writer = ArvPutCollectionWriter(resume_cache, reporter, bytes_expected,
+ num_retries=args.retries)
+ else:
+ writer = ArvPutCollectionWriter.from_cache(
+ resume_cache, reporter, bytes_expected, num_retries=args.retries)
+
+ # Install our signal handler for each code in CAUGHT_SIGNALS, and save
+ # the originals.
+ orig_signal_handlers = {sigcode: signal.signal(sigcode, exit_signal_handler)
+ for sigcode in CAUGHT_SIGNALS}
+
+ if writer.bytes_written > 0: # We're resuming a previous upload.
+ print >>stderr, "\n".join([
+ "arv-put: Resuming previous upload from last checkpoint.",
+ " Use the --no-resume option to start over."])
+
+ writer.report_progress()
+ writer.do_queued_work() # Do work resumed from cache.
+ for path in args.paths: # Copy file data to Keep.
+ if os.path.isdir(path):
+ writer.write_directory_tree(
+ path, max_manifest_depth=args.max_manifest_depth)
+ else:
+ writer.start_new_stream()
+ writer.write_file(path, args.filename or os.path.basename(path))
+ writer.finish_current_stream()
+
+ if args.progress: # Print newline to split stderr from stdout for humans.
+ print >>stderr
+
+ if args.stream:
+ output = writer.manifest_text()
+ if args.normalize:
+ output = CollectionReader(output).manifest_text(normalize=True)
+ elif args.raw:
+ output = ','.join(writer.data_locators())
+ else:
+ try:
+ manifest_text = writer.manifest_text()
+ if args.normalize:
+ manifest_text = CollectionReader(manifest_text).manifest_text(normalize=True)
+ # Register the resulting collection in Arvados.
+ collection = api_client.collections().create(
+ body={
+ 'owner_uuid': project_uuid,
+ 'name': collection_name,
+ 'manifest_text': manifest_text
+ },
+ ensure_unique_name=True
+ ).execute(num_retries=args.retries)
+
+ print >>stderr, "Collection saved as '%s'" % collection['name']
+
+ if args.portable_data_hash and 'portable_data_hash' in collection and collection['portable_data_hash']:
+ output = collection['portable_data_hash']
+ else:
+ output = collection['uuid']
+
+ except apiclient_errors.Error as error:
+ print >>stderr, (
+ "arv-put: Error creating Collection on project: {}.".format(
+ error))
+ status = 1
+
+ # Print the locator (uuid) of the new collection.
+ stdout.write(output)
+ if not output.endswith('\n'):
+ stdout.write('\n')
+
+ for sigcode, orig_handler in orig_signal_handlers.items():
+ signal.signal(sigcode, orig_handler)
+
+ if status != 0:
+ sys.exit(status)
+
+ if resume_cache is not None:
+ resume_cache.destroy()
+
+ return output
+
+if __name__ == '__main__':
+ main()
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import arvados.commands.ws as ws
+import argparse
+import json
+import re
+import os
+import stat
+import put
+import time
+import subprocess
+import logging
+import arvados.commands._util as arv_cmd
+
+logger = logging.getLogger('arvados.arv-run')
+
+arvrun_parser = argparse.ArgumentParser(parents=[arv_cmd.retry_opt])
+arvrun_parser.add_argument('--dry-run', action="store_true", help="Print out the pipeline that would be submitted and exit")
+arvrun_parser.add_argument('--local', action="store_true", help="Run locally using arv-run-pipeline-instance")
+arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs", help="Docker image to use, default arvados/jobs")
+arvrun_parser.add_argument('--ignore-rcode', action="store_true", help="Commands that return non-zero return codes should not be considered failed.")
+arvrun_parser.add_argument('--no-reuse', action="store_true", help="Do not reuse past jobs.")
+arvrun_parser.add_argument('--no-wait', action="store_true", help="Do not wait and display logs after submitting command, just exit.")
+arvrun_parser.add_argument('--project-uuid', type=str, help="Parent project of the pipeline")
+arvrun_parser.add_argument('--git-dir', type=str, default="", help="Git repository passed to arv-crunch-job when using --local")
+arvrun_parser.add_argument('--repository', type=str, default="arvados", help="repository field of component, default 'arvados'")
+arvrun_parser.add_argument('--script-version', type=str, default="master", help="script_version field of component, default 'master'")
+arvrun_parser.add_argument('args', nargs=argparse.REMAINDER)
+
+class ArvFile(object):
+ def __init__(self, prefix, fn):
+ self.prefix = prefix
+ self.fn = fn
+
+class UploadFile(ArvFile):
+ pass
+
+# Determine if a file is in a collection, and return a tuple consisting of the
+# portable data hash and the path relative to the root of the collection.
+# Return None if the path isn't with an arv-mount collection or there was is error.
+def is_in_collection(root, branch):
+ try:
+ if root == "/":
+ return (None, None)
+ fn = os.path.join(root, ".arvados#collection")
+ if os.path.exists(fn):
+ with file(fn, 'r') as f:
+ c = json.load(f)
+ return (c["portable_data_hash"], branch)
+ else:
+ sp = os.path.split(root)
+ return is_in_collection(sp[0], os.path.join(sp[1], branch))
+ except IOError, OSError:
+ return (None, None)
+
+# Determine the project to place the output of this command by searching upward
+# for arv-mount psuedofile indicating the project. If the cwd isn't within
+# an arv-mount project or there is an error, return current_user.
+def determine_project(root, current_user):
+ try:
+ if root == "/":
+ return current_user
+ fn = os.path.join(root, ".arvados#project")
+ if os.path.exists(fn):
+ with file(fn, 'r') as f:
+ c = json.load(f)
+ if 'writable_by' in c and current_user in c['writable_by']:
+ return c["uuid"]
+ else:
+ return current_user
+ else:
+ sp = os.path.split(root)
+ return determine_project(sp[0], current_user)
+ except IOError, OSError:
+ return current_user
+
+# Determine if string corresponds to a file, and if that file is part of a
+# arv-mounted collection or only local to the machine. Returns one of
+# ArvFile() (file already exists in a collection), UploadFile() (file needs to
+# be uploaded to a collection), or simply returns prefix+fn (which yields the
+# original parameter string).
+def statfile(prefix, fn):
+ absfn = os.path.abspath(fn)
+ if os.path.exists(absfn):
+ st = os.stat(absfn)
+ if stat.S_ISREG(st.st_mode):
+ sp = os.path.split(absfn)
+ (pdh, branch) = is_in_collection(sp[0], sp[1])
+ if pdh:
+ return ArvFile(prefix, "$(file %s/%s)" % (pdh, branch))
+ else:
+ # trim leading '/' for path prefix test later
+ return UploadFile(prefix, absfn[1:])
+ if stat.S_ISDIR(st.st_mode):
+ sp = os.path.split(absfn)
+ (pdh, branch) = is_in_collection(sp[0], sp[1])
+ if pdh:
+ return ArvFile(prefix, "$(dir %s/%s/)" % (pdh, branch))
+
+ return prefix+fn
+
+def main(arguments=None):
+ args = arvrun_parser.parse_args(arguments)
+
+ if len(args.args) == 0:
+ arvrun_parser.print_help()
+ return
+
+ starting_args = args.args
+
+ reading_into = 2
+
+ # Parse the command arguments into 'slots'.
+ # All words following '>' are output arguments and are collected into slots[0].
+ # All words following '<' are input arguments and are collected into slots[1].
+ # slots[2..] store the parameters of each command in the pipeline.
+ #
+ # e.g. arv-run foo arg1 arg2 '|' bar arg3 arg4 '<' input1 input2 input3 '>' output.txt
+ # will be parsed into:
+ # [['output.txt'],
+ # ['input1', 'input2', 'input3'],
+ # ['foo', 'arg1', 'arg2'],
+ # ['bar', 'arg3', 'arg4']]
+ slots = [[], [], []]
+ for c in args.args:
+ if c.startswith('>'):
+ reading_into = 0
+ if len(c) > 1:
+ slots[reading_into].append(c[1:])
+ elif c.startswith('<'):
+ reading_into = 1
+ if len(c) > 1:
+ slots[reading_into].append(c[1:])
+ elif c == '|':
+ reading_into = len(slots)
+ slots.append([])
+ else:
+ slots[reading_into].append(c)
+
+ if slots[0] and len(slots[0]) > 1:
+ logger.error("Can only specify a single stdout file (run-command substitutions are permitted)")
+ return
+
+ if not args.dry_run:
+ api = arvados.api('v1')
+ if args.project_uuid:
+ project = args.project_uuid
+ else:
+ project = determine_project(os.getcwd(), api.users().current().execute()["uuid"])
+
+ # Identify input files. Look at each parameter and test to see if there is
+ # a file by that name. This uses 'patterns' to look for within
+ # command line arguments, such as --foo=file.txt or -lfile.txt
+ patterns = [re.compile("([^=]+=)(.*)"),
+ re.compile("(-[A-Za-z])(.+)")]
+ for j, command in enumerate(slots[1:]):
+ for i, a in enumerate(command):
+ if j > 0 and i == 0:
+ # j == 0 is stdin, j > 0 is commands
+ # always skip program executable (i == 0) in commands
+ pass
+ elif a.startswith('\\'):
+ # if it starts with a \ then don't do any interpretation
+ command[i] = a[1:]
+ else:
+ # See if it looks like a file
+ command[i] = statfile('', a)
+
+ # If a file named command[i] was found, it would now be an
+ # ArvFile or UploadFile. If command[i] is a basestring, that
+ # means it doesn't correspond exactly to a file, so do some
+ # pattern matching.
+ if isinstance(command[i], basestring):
+ for p in patterns:
+ m = p.match(a)
+ if m:
+ command[i] = statfile(m.group(1), m.group(2))
+ break
+
+ n = True
+ pathprefix = "/"
+ files = [c for command in slots[1:] for c in command if isinstance(c, UploadFile)]
+ if len(files) > 0:
+ # Find the smallest path prefix that includes all the files that need to be uploaded.
+ # This starts at the root and iteratively removes common parent directory prefixes
+ # until all file pathes no longer have a common parent.
+ while n:
+ pathstep = None
+ for c in files:
+ if pathstep is None:
+ sp = c.fn.split('/')
+ if len(sp) < 2:
+ # no parent directories left
+ n = False
+ break
+ # path step takes next directory
+ pathstep = sp[0] + "/"
+ else:
+ # check if pathstep is common prefix for all files
+ if not c.fn.startswith(pathstep):
+ n = False
+ break
+ if n:
+ # pathstep is common parent directory for all files, so remove the prefix
+ # from each path
+ pathprefix += pathstep
+ for c in files:
+ c.fn = c.fn[len(pathstep):]
+
+ orgdir = os.getcwd()
+ os.chdir(pathprefix)
+
+ print("Upload local files: \"%s\"" % '" "'.join([c.fn for c in files]))
+
+ if args.dry_run:
+ print("$(input) is %s" % pathprefix.rstrip('/'))
+ pdh = "$(input)"
+ else:
+ files = sorted(files, key=lambda x: x.fn)
+ collection = arvados.CollectionWriter(api, num_retries=args.retries)
+ stream = None
+ for f in files:
+ sp = os.path.split(f.fn)
+ if sp[0] != stream:
+ stream = sp[0]
+ collection.start_new_stream(stream)
+ collection.write_file(f.fn, sp[1])
+ item = api.collections().create(body={"owner_uuid": project, "manifest_text": collection.manifest_text()}).execute()
+ pdh = item["portable_data_hash"]
+ print "Uploaded to %s" % item["uuid"]
+
+ for c in files:
+ c.fn = "$(file %s/%s)" % (pdh, c.fn)
+
+ os.chdir(orgdir)
+
+ for i in xrange(1, len(slots)):
+ slots[i] = [("%s%s" % (c.prefix, c.fn)) if isinstance(c, ArvFile) else c for c in slots[i]]
+
+ component = {
+ "script": "run-command",
+ "script_version": args.script_version,
+ "repository": args.repository,
+ "script_parameters": {
+ },
+ "runtime_constraints": {
+ "docker_image": args.docker_image
+ }
+ }
+
+ task_foreach = []
+ group_parser = argparse.ArgumentParser()
+ group_parser.add_argument('-b', '--batch-size', type=int)
+ group_parser.add_argument('args', nargs=argparse.REMAINDER)
+
+ for s in xrange(2, len(slots)):
+ for i in xrange(0, len(slots[s])):
+ if slots[s][i] == '--':
+ inp = "input%i" % (s-2)
+ groupargs = group_parser.parse_args(slots[2][i+1:])
+ if groupargs.batch_size:
+ component["script_parameters"][inp] = {"value": {"batch":groupargs.args, "size":groupargs.batch_size}}
+ slots[s] = slots[s][0:i] + [{"foreach": inp, "command": "$(%s)" % inp}]
+ else:
+ component["script_parameters"][inp] = groupargs.args
+ slots[s] = slots[s][0:i] + ["$(%s)" % inp]
+ task_foreach.append(inp)
+ break
+ if slots[s][i] == '\--':
+ slots[s][i] = '--'
+
+ if slots[0]:
+ component["script_parameters"]["task.stdout"] = slots[0][0]
+ if slots[1]:
+ task_foreach.append("stdin")
+ component["script_parameters"]["stdin"] = slots[1]
+ component["script_parameters"]["task.stdin"] = "$(stdin)"
+
+ if task_foreach:
+ component["script_parameters"]["task.foreach"] = task_foreach
+
+ component["script_parameters"]["command"] = slots[2:]
+ if args.ignore_rcode:
+ component["script_parameters"]["task.ignore_rcode"] = args.ignore_rcode
+
+ pipeline = {
+ "name": "arv-run " + " | ".join([s[0] for s in slots[2:]]),
+ "description": "@" + " ".join(starting_args) + "@",
+ "components": {
+ "command": component
+ },
+ "state": "RunningOnClient" if args.local else "RunningOnServer"
+ }
+
+ if args.dry_run:
+ print(json.dumps(pipeline, indent=4))
+ else:
+ pipeline["owner_uuid"] = project
+ pi = api.pipeline_instances().create(body=pipeline, ensure_unique_name=True).execute()
+ print "Running pipeline %s" % pi["uuid"]
+
+ if args.local:
+ subprocess.call(["arv-run-pipeline-instance", "--instance", pi["uuid"], "--run-jobs-here"] + (["--no-reuse"] if args.no_reuse else []))
+ elif not args.no_wait:
+ ws.main(["--pipeline", pi["uuid"]])
+
+ pi = api.pipeline_instances().get(uuid=pi["uuid"]).execute()
+ print "Pipeline is %s" % pi["state"]
+ if "output_uuid" in pi["components"]["command"]:
+ print "Output is %s" % pi["components"]["command"]["output_uuid"]
+ else:
+ print "No output"
+
+if __name__ == '__main__':
+ main()
--- /dev/null
+#!/usr/bin/env python
+
+import sys
+import logging
+import argparse
+import arvados
+import json
+from arvados.events import subscribe
+import signal
+
+def main(arguments=None):
+ logger = logging.getLogger('arvados.arv-ws')
+
+ parser = argparse.ArgumentParser()
+ parser.add_argument('-u', '--uuid', type=str, default="", help="Filter events on object_uuid")
+ parser.add_argument('-f', '--filters', type=str, default="", help="Arvados query filter to apply to log events (JSON encoded)")
+
+ group = parser.add_mutually_exclusive_group()
+ group.add_argument('--poll-interval', default=15, type=int, help="If websockets is not available, specify the polling interval, default is every 15 seconds")
+ group.add_argument('--no-poll', action='store_false', dest='poll_interval', help="Do not poll if websockets are not available, just fail")
+
+ group = parser.add_mutually_exclusive_group()
+ group.add_argument('-p', '--pipeline', type=str, default="", help="Supply pipeline uuid, print log output from pipeline and its jobs")
+ group.add_argument('-j', '--job', type=str, default="", help="Supply job uuid, print log output from jobs")
+
+ args = parser.parse_args(arguments)
+
+ global filters
+ global known_component_jobs
+ global ws
+
+ filters = []
+ known_component_jobs = set()
+ ws = None
+
+ def update_subscribed_components(components):
+ global known_component_jobs
+ global filters
+ pipeline_jobs = set()
+ for c in components:
+ if "job" in components[c]:
+ pipeline_jobs.add(components[c]["job"]["uuid"])
+ if known_component_jobs != pipeline_jobs:
+ ws.unsubscribe(filters)
+ filters = [['object_uuid', 'in', [args.pipeline] + list(pipeline_jobs)]]
+ ws.subscribe([['object_uuid', 'in', [args.pipeline] + list(pipeline_jobs)]])
+ known_component_jobs = pipeline_jobs
+
+ api = arvados.api('v1', cache=False)
+
+ if args.uuid:
+ filters += [ ['object_uuid', '=', args.uuid] ]
+
+ if args.filters:
+ filters += json.loads(args.filters)
+
+ if args.job:
+ filters += [ ['object_uuid', '=', args.job] ]
+
+ if args.pipeline:
+ filters += [ ['object_uuid', '=', args.pipeline] ]
+
+ def on_message(ev):
+ global filters
+ global ws
+
+ logger.debug(ev)
+ if 'event_type' in ev and (args.pipeline or args.job):
+ if ev['event_type'] in ('stderr', 'stdout'):
+ sys.stdout.write(ev["properties"]["text"])
+ elif ev["event_type"] in ("create", "update"):
+ if ev["object_kind"] == "arvados#pipelineInstance":
+ update_subscribed_components(ev["properties"]["new_attributes"]["components"])
+
+ if ev["object_kind"] == "arvados#pipelineInstance" and args.pipeline:
+ if ev["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Paused"):
+ ws.close()
+
+ if ev["object_kind"] == "arvados#job" and args.job:
+ if ev["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled"):
+ ws.close()
+ elif 'status' in ev and ev['status'] == 200:
+ pass
+ else:
+ print json.dumps(ev)
+
+ try:
+ ws = subscribe(arvados.api('v1', cache=False), filters, on_message, poll_fallback=args.poll_interval)
+ if ws:
+ if args.pipeline:
+ c = api.pipeline_instances().get(uuid=args.pipeline).execute()
+ update_subscribed_components(c["components"])
+ if c["state"] in ("Complete", "Failed", "Paused"):
+ ws.close()
+ ws.run_forever()
+ except KeyboardInterrupt:
+ pass
+ except Exception as e:
+ logger.error(e)
+ finally:
+ if ws:
+ ws.close()
--- /dev/null
+# config.py - configuration settings and global variables for Arvados clients
+#
+# Arvados configuration settings are taken from $HOME/.config/arvados.
+# Environment variables override settings in the config file.
+
+import os
+import re
+
+_settings = None
+if os.environ.get('HOME') is not None:
+ default_config_file = os.environ['HOME'] + '/.config/arvados/settings.conf'
+else:
+ default_config_file = ''
+
+EMPTY_BLOCK_LOCATOR = 'd41d8cd98f00b204e9800998ecf8427e+0'
+
+def initialize(config_file=default_config_file):
+ global _settings
+ _settings = {}
+
+ # load the specified config file if available
+ try:
+ _settings = load(config_file)
+ except IOError:
+ pass
+
+ # override any settings with environment vars
+ for var in os.environ:
+ if var.startswith('ARVADOS_'):
+ _settings[var] = os.environ[var]
+
+def load(config_file):
+ cfg = {}
+ with open(config_file, "r") as f:
+ for config_line in f:
+ if re.match('^\s*$', config_line):
+ continue
+ if re.match('^\s*#', config_line):
+ continue
+ var, val = config_line.rstrip().split('=', 2)
+ cfg[var] = val
+ return cfg
+
+def flag_is_true(key):
+ return get(key, '').lower() in set(['1', 't', 'true', 'y', 'yes'])
+
+def get(key, default_val=None):
+ return settings().get(key, default_val)
+
+def settings():
+ if _settings is None:
+ initialize()
+ return _settings
--- /dev/null
+# errors.py - Arvados-specific exceptions.
+
+import json
+from apiclient import errors as apiclient_errors
+
+class ApiError(apiclient_errors.HttpError):
+ def _get_reason(self):
+ try:
+ return '; '.join(json.loads(self.content)['errors'])
+ except (KeyError, TypeError, ValueError):
+ return super(ApiError, self)._get_reason()
+
+
+class ArgumentError(Exception):
+ pass
+class SyntaxError(Exception):
+ pass
+class AssertionError(Exception):
+ pass
+class CommandFailedError(Exception):
+ pass
+class KeepReadError(Exception):
+ pass
+class KeepWriteError(Exception):
+ pass
+class NotFoundError(KeepReadError):
+ pass
+class NotImplementedError(Exception):
+ pass
+class NoKeepServersError(Exception):
+ pass
+class StaleWriterStateError(Exception):
+ pass
--- /dev/null
+from ws4py.client.threadedclient import WebSocketClient
+import threading
+import json
+import os
+import time
+import ssl
+import re
+import config
+import logging
+import arvados
+
+_logger = logging.getLogger('arvados.events')
+
+class EventClient(WebSocketClient):
+ def __init__(self, url, filters, on_event):
+ ssl_options = None
+ if re.match(r'(?i)^(true|1|yes)$',
+ config.get('ARVADOS_API_HOST_INSECURE', 'no')):
+ ssl_options={'cert_reqs': ssl.CERT_NONE}
+ else:
+ ssl_options={'cert_reqs': ssl.CERT_REQUIRED}
+ super(EventClient, self).__init__(url, ssl_options=ssl_options)
+ self.filters = filters
+ self.on_event = on_event
+
+ def opened(self):
+ self.subscribe(self.filters)
+
+ def received_message(self, m):
+ self.on_event(json.loads(str(m)))
+
+ def close_connection(self):
+ try:
+ self.sock.shutdown(socket.SHUT_RDWR)
+ self.sock.close()
+ except:
+ pass
+
+ def subscribe(self, filters, last_log_id=None):
+ m = {"method": "subscribe", "filters": filters}
+ if last_log_id is not None:
+ m["last_log_id"] = last_log_id
+ self.send(json.dumps(m))
+
+ def unsubscribe(self, filters):
+ self.send(json.dumps({"method": "unsubscribe", "filters": filters}))
+
+class PollClient(threading.Thread):
+ def __init__(self, api, filters, on_event, poll_time):
+ super(PollClient, self).__init__()
+ self.api = api
+ if filters:
+ self.filters = [filters]
+ else:
+ self.filters = [[]]
+ self.on_event = on_event
+ self.poll_time = poll_time
+ self.stop = threading.Event()
+
+ def run(self):
+ self.id = 0
+ for f in self.filters:
+ items = self.api.logs().list(limit=1, order="id desc", filters=f).execute()['items']
+ if items:
+ if items[0]['id'] > self.id:
+ self.id = items[0]['id']
+
+ self.on_event({'status': 200})
+
+ while not self.stop.isSet():
+ max_id = self.id
+ for f in self.filters:
+ items = self.api.logs().list(order="id asc", filters=f+[["id", ">", str(self.id)]]).execute()['items']
+ for i in items:
+ if i['id'] > max_id:
+ max_id = i['id']
+ self.on_event(i)
+ self.id = max_id
+ self.stop.wait(self.poll_time)
+
+ def run_forever(self):
+ self.stop.wait()
+
+ def close(self):
+ self.stop.set()
+ try:
+ self.join()
+ except RuntimeError:
+ # "join() raises a RuntimeError if an attempt is made to join the
+ # current thread as that would cause a deadlock. It is also an
+ # error to join() a thread before it has been started and attempts
+ # to do so raises the same exception."
+ pass
+
+ def subscribe(self, filters):
+ self.on_event({'status': 200})
+ self.filters.append(filters)
+
+ def unsubscribe(self, filters):
+ del self.filters[self.filters.index(filters)]
+
+
+def subscribe(api, filters, on_event, poll_fallback=15):
+ '''
+ api: Must be a newly created from arvados.api(cache=False), not shared with the caller, as it may be used by a background thread.
+ filters: Initial subscription filters.
+ on_event: The callback when a message is received
+ poll_fallback: If websockets are not available, fall back to polling every N seconds. If poll_fallback=False, this will return None if websockets are not available.
+ '''
+ ws = None
+ if 'websocketUrl' in api._rootDesc:
+ try:
+ url = "{}?api_token={}".format(api._rootDesc['websocketUrl'], api.api_token)
+ ws = EventClient(url, filters, on_event)
+ ws.connect()
+ return ws
+ except Exception as e:
+ _logger.warn("Got exception %s trying to connect to websockets at %s" % (e, api._rootDesc['websocketUrl']))
+ if ws:
+ ws.close_connection()
+ if poll_fallback:
+ _logger.warn("Websockets not available, falling back to log table polling")
+ p = PollClient(api, filters, on_event, poll_fallback)
+ p.start()
+ return p
+ else:
+ _logger.error("Websockets not available")
+ return None
--- /dev/null
+import gflags
+import logging
+import os
+import pprint
+import sys
+import types
+import subprocess
+import json
+import UserDict
+import re
+import hashlib
+import string
+import bz2
+import zlib
+import fcntl
+import time
+import threading
+import timer
+import datetime
+import ssl
+import socket
+import requests
+
+import arvados
+import arvados.config as config
+import arvados.errors
+import arvados.retry as retry
+import arvados.util
+
+_logger = logging.getLogger('arvados.keep')
+global_client_object = None
+
+class KeepLocator(object):
+ EPOCH_DATETIME = datetime.datetime.utcfromtimestamp(0)
+ HINT_RE = re.compile(r'^[A-Z][A-Za-z0-9@_-]+$')
+
+ def __init__(self, locator_str):
+ self.hints = []
+ self._perm_sig = None
+ self._perm_expiry = None
+ pieces = iter(locator_str.split('+'))
+ self.md5sum = next(pieces)
+ try:
+ self.size = int(next(pieces))
+ except StopIteration:
+ self.size = None
+ for hint in pieces:
+ if self.HINT_RE.match(hint) is None:
+ raise ValueError("unrecognized hint data {}".format(hint))
+ elif hint.startswith('A'):
+ self.parse_permission_hint(hint)
+ else:
+ self.hints.append(hint)
+
+ def __str__(self):
+ return '+'.join(
+ str(s) for s in [self.md5sum, self.size,
+ self.permission_hint()] + self.hints
+ if s is not None)
+
+ def _make_hex_prop(name, length):
+ # Build and return a new property with the given name that
+ # must be a hex string of the given length.
+ data_name = '_{}'.format(name)
+ def getter(self):
+ return getattr(self, data_name)
+ def setter(self, hex_str):
+ if not arvados.util.is_hex(hex_str, length):
+ raise ValueError("{} must be a {}-digit hex string: {}".
+ format(name, length, hex_str))
+ setattr(self, data_name, hex_str)
+ return property(getter, setter)
+
+ md5sum = _make_hex_prop('md5sum', 32)
+ perm_sig = _make_hex_prop('perm_sig', 40)
+
+ @property
+ def perm_expiry(self):
+ return self._perm_expiry
+
+ @perm_expiry.setter
+ def perm_expiry(self, value):
+ if not arvados.util.is_hex(value, 1, 8):
+ raise ValueError(
+ "permission timestamp must be a hex Unix timestamp: {}".
+ format(value))
+ self._perm_expiry = datetime.datetime.utcfromtimestamp(int(value, 16))
+
+ def permission_hint(self):
+ data = [self.perm_sig, self.perm_expiry]
+ if None in data:
+ return None
+ data[1] = int((data[1] - self.EPOCH_DATETIME).total_seconds())
+ return "A{}@{:08x}".format(*data)
+
+ def parse_permission_hint(self, s):
+ try:
+ self.perm_sig, self.perm_expiry = s[1:].split('@', 1)
+ except IndexError:
+ raise ValueError("bad permission hint {}".format(s))
+
+ def permission_expired(self, as_of_dt=None):
+ if self.perm_expiry is None:
+ return False
+ elif as_of_dt is None:
+ as_of_dt = datetime.datetime.now()
+ return self.perm_expiry <= as_of_dt
+
+
+class Keep(object):
+ """Simple interface to a global KeepClient object.
+
+ THIS CLASS IS DEPRECATED. Please instantiate your own KeepClient with your
+ own API client. The global KeepClient will build an API client from the
+ current Arvados configuration, which may not match the one you built.
+ """
+ _last_key = None
+
+ @classmethod
+ def global_client_object(cls):
+ global global_client_object
+ # Previously, KeepClient would change its behavior at runtime based
+ # on these configuration settings. We simulate that behavior here
+ # by checking the values and returning a new KeepClient if any of
+ # them have changed.
+ key = (config.get('ARVADOS_API_HOST'),
+ config.get('ARVADOS_API_TOKEN'),
+ config.flag_is_true('ARVADOS_API_HOST_INSECURE'),
+ config.get('ARVADOS_KEEP_PROXY'),
+ config.get('ARVADOS_EXTERNAL_CLIENT') == 'true',
+ os.environ.get('KEEP_LOCAL_STORE'))
+ if (global_client_object is None) or (cls._last_key != key):
+ global_client_object = KeepClient()
+ cls._last_key = key
+ return global_client_object
+
+ @staticmethod
+ def get(locator, **kwargs):
+ return Keep.global_client_object().get(locator, **kwargs)
+
+ @staticmethod
+ def put(data, **kwargs):
+ return Keep.global_client_object().put(data, **kwargs)
+
+class KeepBlockCache(object):
+ # Default RAM cache is 256MiB
+ def __init__(self, cache_max=(256 * 1024 * 1024)):
+ self.cache_max = cache_max
+ self._cache = []
+ self._cache_lock = threading.Lock()
+
+ class CacheSlot(object):
+ def __init__(self, locator):
+ self.locator = locator
+ self.ready = threading.Event()
+ self.content = None
+
+ def get(self):
+ self.ready.wait()
+ return self.content
+
+ def set(self, value):
+ self.content = value
+ self.ready.set()
+
+ def size(self):
+ if self.content is None:
+ return 0
+ else:
+ return len(self.content)
+
+ def cap_cache(self):
+ '''Cap the cache size to self.cache_max'''
+ self._cache_lock.acquire()
+ try:
+ # Select all slots except those where ready.is_set() and content is
+ # None (that means there was an error reading the block).
+ self._cache = [c for c in self._cache if not (c.ready.is_set() and c.content is None)]
+ sm = sum([slot.size() for slot in self._cache])
+ while len(self._cache) > 0 and sm > self.cache_max:
+ for i in xrange(len(self._cache)-1, -1, -1):
+ if self._cache[i].ready.is_set():
+ del self._cache[i]
+ break
+ sm = sum([slot.size() for slot in self._cache])
+ finally:
+ self._cache_lock.release()
+
+ def reserve_cache(self, locator):
+ '''Reserve a cache slot for the specified locator,
+ or return the existing slot.'''
+ self._cache_lock.acquire()
+ try:
+ # Test if the locator is already in the cache
+ for i in xrange(0, len(self._cache)):
+ if self._cache[i].locator == locator:
+ n = self._cache[i]
+ if i != 0:
+ # move it to the front
+ del self._cache[i]
+ self._cache.insert(0, n)
+ return n, False
+
+ # Add a new cache slot for the locator
+ n = KeepBlockCache.CacheSlot(locator)
+ self._cache.insert(0, n)
+ return n, True
+ finally:
+ self._cache_lock.release()
+
+class KeepClient(object):
+
+ # Default Keep server connection timeout: 2 seconds
+ # Default Keep server read timeout: 300 seconds
+ # Default Keep proxy connection timeout: 20 seconds
+ # Default Keep proxy read timeout: 300 seconds
+ DEFAULT_TIMEOUT = (2, 300)
+ DEFAULT_PROXY_TIMEOUT = (20, 300)
+
+ class ThreadLimiter(object):
+ """
+ Limit the number of threads running at a given time to
+ {desired successes} minus {successes reported}. When successes
+ reported == desired, wake up the remaining threads and tell
+ them to quit.
+
+ Should be used in a "with" block.
+ """
+ def __init__(self, todo):
+ self._todo = todo
+ self._done = 0
+ self._response = None
+ self._todo_lock = threading.Semaphore(todo)
+ self._done_lock = threading.Lock()
+
+ def __enter__(self):
+ self._todo_lock.acquire()
+ return self
+
+ def __exit__(self, type, value, traceback):
+ self._todo_lock.release()
+
+ def shall_i_proceed(self):
+ """
+ Return true if the current thread should do stuff. Return
+ false if the current thread should just stop.
+ """
+ with self._done_lock:
+ return (self._done < self._todo)
+
+ def save_response(self, response_body, replicas_stored):
+ """
+ Records a response body (a locator, possibly signed) returned by
+ the Keep server. It is not necessary to save more than
+ one response, since we presume that any locator returned
+ in response to a successful request is valid.
+ """
+ with self._done_lock:
+ self._done += replicas_stored
+ self._response = response_body
+
+ def response(self):
+ """
+ Returns the body from the response to a PUT request.
+ """
+ with self._done_lock:
+ return self._response
+
+ def done(self):
+ """
+ Return how many successes were reported.
+ """
+ with self._done_lock:
+ return self._done
+
+
+ class KeepService(object):
+ # Make requests to a single Keep service, and track results.
+ HTTP_ERRORS = (requests.exceptions.RequestException,
+ socket.error, ssl.SSLError)
+
+ def __init__(self, root, **headers):
+ self.root = root
+ self.last_result = None
+ self.success_flag = None
+ self.get_headers = {'Accept': 'application/octet-stream'}
+ self.get_headers.update(headers)
+ self.put_headers = headers
+
+ def usable(self):
+ return self.success_flag is not False
+
+ def finished(self):
+ return self.success_flag is not None
+
+ def last_status(self):
+ try:
+ return self.last_result.status_code
+ except AttributeError:
+ return None
+
+ def get(self, locator, timeout=None):
+ # locator is a KeepLocator object.
+ url = self.root + str(locator)
+ _logger.debug("Request: GET %s", url)
+ try:
+ with timer.Timer() as t:
+ result = requests.get(url.encode('utf-8'),
+ headers=self.get_headers,
+ timeout=timeout)
+ except self.HTTP_ERRORS as e:
+ _logger.debug("Request fail: GET %s => %s: %s",
+ url, type(e), str(e))
+ self.last_result = e
+ else:
+ self.last_result = result
+ self.success_flag = retry.check_http_response_success(result)
+ content = result.content
+ _logger.info("%s response: %s bytes in %s msec (%.3f MiB/sec)",
+ self.last_status(), len(content), t.msecs,
+ (len(content)/(1024.0*1024))/t.secs)
+ if self.success_flag:
+ resp_md5 = hashlib.md5(content).hexdigest()
+ if resp_md5 == locator.md5sum:
+ return content
+ _logger.warning("Checksum fail: md5(%s) = %s",
+ url, resp_md5)
+ return None
+
+ def put(self, hash_s, body, timeout=None):
+ url = self.root + hash_s
+ _logger.debug("Request: PUT %s", url)
+ try:
+ result = requests.put(url.encode('utf-8'),
+ data=body,
+ headers=self.put_headers,
+ timeout=timeout)
+ except self.HTTP_ERRORS as e:
+ _logger.debug("Request fail: PUT %s => %s: %s",
+ url, type(e), str(e))
+ self.last_result = e
+ else:
+ self.last_result = result
+ self.success_flag = retry.check_http_response_success(result)
+ return self.success_flag
+
+
+ class KeepWriterThread(threading.Thread):
+ """
+ Write a blob of data to the given Keep server. On success, call
+ save_response() of the given ThreadLimiter to save the returned
+ locator.
+ """
+ def __init__(self, keep_service, **kwargs):
+ super(KeepClient.KeepWriterThread, self).__init__()
+ self.service = keep_service
+ self.args = kwargs
+ self._success = False
+
+ def success(self):
+ return self._success
+
+ def run(self):
+ with self.args['thread_limiter'] as limiter:
+ if not limiter.shall_i_proceed():
+ # My turn arrived, but the job has been done without
+ # me.
+ return
+ self.run_with_limiter(limiter)
+
+ def run_with_limiter(self, limiter):
+ if self.service.finished():
+ return
+ _logger.debug("KeepWriterThread %s proceeding %s %s",
+ str(threading.current_thread()),
+ self.args['data_hash'],
+ self.args['service_root'])
+ self._success = bool(self.service.put(
+ self.args['data_hash'],
+ self.args['data'],
+ timeout=self.args.get('timeout', None)))
+ status = self.service.last_status()
+ if self._success:
+ result = self.service.last_result
+ _logger.debug("KeepWriterThread %s succeeded %s %s",
+ str(threading.current_thread()),
+ self.args['data_hash'],
+ self.args['service_root'])
+ # Tick the 'done' counter for the number of replica
+ # reported stored by the server, for the case that
+ # we're talking to a proxy or other backend that
+ # stores to multiple copies for us.
+ try:
+ replicas_stored = int(result.headers['x-keep-replicas-stored'])
+ except (KeyError, ValueError):
+ replicas_stored = 1
+ limiter.save_response(result.text.strip(), replicas_stored)
+ elif status is not None:
+ _logger.debug("Request fail: PUT %s => %s %s",
+ self.args['data_hash'], status,
+ self.service.last_result.text)
+
+
+ def __init__(self, api_client=None, proxy=None,
+ timeout=DEFAULT_TIMEOUT, proxy_timeout=DEFAULT_PROXY_TIMEOUT,
+ api_token=None, local_store=None, block_cache=None,
+ num_retries=0):
+ """Initialize a new KeepClient.
+
+ Arguments:
+ * api_client: The API client to use to find Keep services. If not
+ provided, KeepClient will build one from available Arvados
+ configuration.
+ * proxy: If specified, this KeepClient will send requests to this
+ Keep proxy. Otherwise, KeepClient will fall back to the setting
+ of the ARVADOS_KEEP_PROXY configuration setting. If you want to
+ ensure KeepClient does not use a proxy, pass in an empty string.
+ * timeout: The timeout (in seconds) for HTTP requests to Keep
+ non-proxy servers. A tuple of two floats is interpreted as
+ (connection_timeout, read_timeout): see
+ http://docs.python-requests.org/en/latest/user/advanced/#timeouts.
+ Default: (2, 300).
+ * proxy_timeout: The timeout (in seconds) for HTTP requests to
+ Keep proxies. A tuple of two floats is interpreted as
+ (connection_timeout, read_timeout). Default: (20, 300).
+ * api_token: If you're not using an API client, but only talking
+ directly to a Keep proxy, this parameter specifies an API token
+ to authenticate Keep requests. It is an error to specify both
+ api_client and api_token. If you specify neither, KeepClient
+ will use one available from the Arvados configuration.
+ * local_store: If specified, this KeepClient will bypass Keep
+ services, and save data to the named directory. If unspecified,
+ KeepClient will fall back to the setting of the $KEEP_LOCAL_STORE
+ environment variable. If you want to ensure KeepClient does not
+ use local storage, pass in an empty string. This is primarily
+ intended to mock a server for testing.
+ * num_retries: The default number of times to retry failed requests.
+ This will be used as the default num_retries value when get() and
+ put() are called. Default 0.
+ """
+ self.lock = threading.Lock()
+ if proxy is None:
+ proxy = config.get('ARVADOS_KEEP_PROXY')
+ if api_token is None:
+ if api_client is None:
+ api_token = config.get('ARVADOS_API_TOKEN')
+ else:
+ api_token = api_client.api_token
+ elif api_client is not None:
+ raise ValueError(
+ "can't build KeepClient with both API client and token")
+ if local_store is None:
+ local_store = os.environ.get('KEEP_LOCAL_STORE')
+
+ self.block_cache = block_cache if block_cache else KeepBlockCache()
+ self.timeout = timeout
+ self.proxy_timeout = proxy_timeout
+
+ if local_store:
+ self.local_store = local_store
+ self.get = self.local_store_get
+ self.put = self.local_store_put
+ else:
+ self.num_retries = num_retries
+ if proxy:
+ if not proxy.endswith('/'):
+ proxy += '/'
+ self.api_token = api_token
+ self._keep_services = [{
+ 'uuid': 'proxy',
+ '_service_root': proxy,
+ }]
+ self.using_proxy = True
+ self._static_services_list = True
+ else:
+ # It's important to avoid instantiating an API client
+ # unless we actually need one, for testing's sake.
+ if api_client is None:
+ api_client = arvados.api('v1')
+ self.api_client = api_client
+ self.api_token = api_client.api_token
+ self._keep_services = None
+ self.using_proxy = None
+ self._static_services_list = False
+
+ def current_timeout(self):
+ """Return the appropriate timeout to use for this client: the proxy
+ timeout setting if the backend service is currently a proxy,
+ the regular timeout setting otherwise.
+ """
+ # TODO(twp): the timeout should be a property of a
+ # KeepService, not a KeepClient. See #4488.
+ return self.proxy_timeout if self.using_proxy else self.timeout
+
+ def build_services_list(self, force_rebuild=False):
+ if (self._static_services_list or
+ (self._keep_services and not force_rebuild)):
+ return
+ with self.lock:
+ try:
+ keep_services = self.api_client.keep_services().accessible()
+ except Exception: # API server predates Keep services.
+ keep_services = self.api_client.keep_disks().list()
+
+ self._keep_services = keep_services.execute().get('items')
+ if not self._keep_services:
+ raise arvados.errors.NoKeepServersError()
+
+ self.using_proxy = any(ks.get('service_type') == 'proxy'
+ for ks in self._keep_services)
+
+ # Precompute the base URI for each service.
+ for r in self._keep_services:
+ r['_service_root'] = "{}://[{}]:{:d}/".format(
+ 'https' if r['service_ssl_flag'] else 'http',
+ r['service_host'],
+ r['service_port'])
+ _logger.debug(str(self._keep_services))
+
+ def _service_weight(self, data_hash, service_uuid):
+ """Compute the weight of a Keep service endpoint for a data
+ block with a known hash.
+
+ The weight is md5(h + u) where u is the last 15 characters of
+ the service endpoint's UUID.
+ """
+ return hashlib.md5(data_hash + service_uuid[-15:]).hexdigest()
+
+ def weighted_service_roots(self, data_hash, force_rebuild=False):
+ """Return an array of Keep service endpoints, in the order in
+ which they should be probed when reading or writing data with
+ the given hash.
+ """
+ self.build_services_list(force_rebuild)
+
+ # Sort the available services by weight (heaviest first) for
+ # this data_hash, and return their service_roots (base URIs)
+ # in that order.
+ sorted_roots = [
+ svc['_service_root'] for svc in sorted(
+ self._keep_services,
+ reverse=True,
+ key=lambda svc: self._service_weight(data_hash, svc['uuid']))]
+ _logger.debug(data_hash + ': ' + str(sorted_roots))
+ return sorted_roots
+
+ def map_new_services(self, roots_map, md5_s, force_rebuild, **headers):
+ # roots_map is a dictionary, mapping Keep service root strings
+ # to KeepService objects. Poll for Keep services, and add any
+ # new ones to roots_map. Return the current list of local
+ # root strings.
+ headers.setdefault('Authorization', "OAuth2 %s" % (self.api_token,))
+ local_roots = self.weighted_service_roots(md5_s, force_rebuild)
+ for root in local_roots:
+ if root not in roots_map:
+ roots_map[root] = self.KeepService(root, **headers)
+ return local_roots
+
+ @staticmethod
+ def _check_loop_result(result):
+ # KeepClient RetryLoops should save results as a 2-tuple: the
+ # actual result of the request, and the number of servers available
+ # to receive the request this round.
+ # This method returns True if there's a real result, False if
+ # there are no more servers available, otherwise None.
+ if isinstance(result, Exception):
+ return None
+ result, tried_server_count = result
+ if (result is not None) and (result is not False):
+ return True
+ elif tried_server_count < 1:
+ _logger.info("No more Keep services to try; giving up")
+ return False
+ else:
+ return None
+
+ @retry.retry_method
+ def get(self, loc_s, num_retries=None):
+ """Get data from Keep.
+
+ This method fetches one or more blocks of data from Keep. It
+ sends a request each Keep service registered with the API
+ server (or the proxy provided when this client was
+ instantiated), then each service named in location hints, in
+ sequence. As soon as one service provides the data, it's
+ returned.
+
+ Arguments:
+ * loc_s: A string of one or more comma-separated locators to fetch.
+ This method returns the concatenation of these blocks.
+ * num_retries: The number of times to retry GET requests to
+ *each* Keep server if it returns temporary failures, with
+ exponential backoff. Note that, in each loop, the method may try
+ to fetch data from every available Keep service, along with any
+ that are named in location hints in the locator. The default value
+ is set when the KeepClient is initialized.
+ """
+ if ',' in loc_s:
+ return ''.join(self.get(x) for x in loc_s.split(','))
+ locator = KeepLocator(loc_s)
+ expect_hash = locator.md5sum
+
+ slot, first = self.block_cache.reserve_cache(expect_hash)
+ if not first:
+ v = slot.get()
+ return v
+
+ # See #3147 for a discussion of the loop implementation. Highlights:
+ # * Refresh the list of Keep services after each failure, in case
+ # it's being updated.
+ # * Retry until we succeed, we're out of retries, or every available
+ # service has returned permanent failure.
+ hint_roots = ['http://keep.{}.arvadosapi.com/'.format(hint[2:])
+ for hint in locator.hints if hint.startswith('K@')]
+ # Map root URLs their KeepService objects.
+ roots_map = {root: self.KeepService(root) for root in hint_roots}
+ blob = None
+ loop = retry.RetryLoop(num_retries, self._check_loop_result,
+ backoff_start=2)
+ for tries_left in loop:
+ try:
+ local_roots = self.map_new_services(
+ roots_map, expect_hash,
+ force_rebuild=(tries_left < num_retries))
+ except Exception as error:
+ loop.save_result(error)
+ continue
+
+ # Query KeepService objects that haven't returned
+ # permanent failure, in our specified shuffle order.
+ services_to_try = [roots_map[root]
+ for root in (local_roots + hint_roots)
+ if roots_map[root].usable()]
+ for keep_service in services_to_try:
+ blob = keep_service.get(locator, timeout=self.current_timeout())
+ if blob is not None:
+ break
+ loop.save_result((blob, len(services_to_try)))
+
+ # Always cache the result, then return it if we succeeded.
+ slot.set(blob)
+ self.block_cache.cap_cache()
+ if loop.success():
+ return blob
+
+ # No servers fulfilled the request. Count how many responded
+ # "not found;" if the ratio is high enough (currently 75%), report
+ # Not Found; otherwise a generic error.
+ # Q: Including 403 is necessary for the Keep tests to continue
+ # passing, but maybe they should expect KeepReadError instead?
+ not_founds = sum(1 for ks in roots_map.values()
+ if ks.last_status() in set([403, 404, 410]))
+ if roots_map and ((float(not_founds) / len(roots_map)) >= .75):
+ raise arvados.errors.NotFoundError(loc_s)
+ else:
+ raise arvados.errors.KeepReadError(loc_s)
+
+ @retry.retry_method
+ def put(self, data, copies=2, num_retries=None):
+ """Save data in Keep.
+
+ This method will get a list of Keep services from the API server, and
+ send the data to each one simultaneously in a new thread. Once the
+ uploads are finished, if enough copies are saved, this method returns
+ the most recent HTTP response body. If requests fail to upload
+ enough copies, this method raises KeepWriteError.
+
+ Arguments:
+ * data: The string of data to upload.
+ * copies: The number of copies that the user requires be saved.
+ Default 2.
+ * num_retries: The number of times to retry PUT requests to
+ *each* Keep server if it returns temporary failures, with
+ exponential backoff. The default value is set when the
+ KeepClient is initialized.
+ """
+ data_hash = hashlib.md5(data).hexdigest()
+ if copies < 1:
+ return data_hash
+
+ headers = {}
+ if self.using_proxy:
+ # Tell the proxy how many copies we want it to store
+ headers['X-Keep-Desired-Replication'] = str(copies)
+ roots_map = {}
+ thread_limiter = KeepClient.ThreadLimiter(copies)
+ loop = retry.RetryLoop(num_retries, self._check_loop_result,
+ backoff_start=2)
+ for tries_left in loop:
+ try:
+ local_roots = self.map_new_services(
+ roots_map, data_hash,
+ force_rebuild=(tries_left < num_retries), **headers)
+ except Exception as error:
+ loop.save_result(error)
+ continue
+
+ threads = []
+ for service_root, ks in roots_map.iteritems():
+ if ks.finished():
+ continue
+ t = KeepClient.KeepWriterThread(
+ ks,
+ data=data,
+ data_hash=data_hash,
+ service_root=service_root,
+ thread_limiter=thread_limiter,
+ timeout=self.current_timeout())
+ t.start()
+ threads.append(t)
+ for t in threads:
+ t.join()
+ loop.save_result((thread_limiter.done() >= copies, len(threads)))
+
+ if loop.success():
+ return thread_limiter.response()
+ raise arvados.errors.KeepWriteError(
+ "Write fail for %s: wanted %d but wrote %d" %
+ (data_hash, copies, thread_limiter.done()))
+
+ # Local storage methods need no-op num_retries arguments to keep
+ # integration tests happy. With better isolation they could
+ # probably be removed again.
+ def local_store_put(self, data, num_retries=0):
+ md5 = hashlib.md5(data).hexdigest()
+ locator = '%s+%d' % (md5, len(data))
+ with open(os.path.join(self.local_store, md5 + '.tmp'), 'w') as f:
+ f.write(data)
+ os.rename(os.path.join(self.local_store, md5 + '.tmp'),
+ os.path.join(self.local_store, md5))
+ return locator
+
+ def local_store_get(self, loc_s, num_retries=0):
+ try:
+ locator = KeepLocator(loc_s)
+ except ValueError:
+ raise arvados.errors.NotFoundError(
+ "Invalid data locator: '%s'" % loc_s)
+ if locator.md5sum == config.EMPTY_BLOCK_LOCATOR.split('+')[0]:
+ return ''
+ with open(os.path.join(self.local_store, locator.md5sum), 'r') as f:
+ return f.read()
--- /dev/null
+#!/usr/bin/env python
+
+import functools
+import inspect
+import time
+
+from collections import deque
+
+import arvados.errors
+
+_HTTP_SUCCESSES = set(xrange(200, 300))
+_HTTP_CAN_RETRY = set([408, 409, 422, 423, 500, 502, 503, 504])
+
+class RetryLoop(object):
+ """Coordinate limited retries of code.
+
+ RetryLoop coordinates a loop that runs until it records a
+ successful result or tries too many times, whichever comes first.
+ Typical use looks like:
+
+ loop = RetryLoop(num_retries=2)
+ for tries_left in loop:
+ try:
+ result = do_something()
+ except TemporaryError as error:
+ log("error: {} ({} tries left)".format(error, tries_left))
+ else:
+ loop.save_result(result)
+ if loop.success():
+ return loop.last_result()
+ """
+ def __init__(self, num_retries, success_check=lambda r: True,
+ backoff_start=0, backoff_growth=2, save_results=1):
+ """Construct a new RetryLoop.
+
+ Arguments:
+ * num_retries: The maximum number of times to retry the loop if it
+ doesn't succeed. This means the loop could run at most 1+N times.
+ * success_check: This is a function that will be called each
+ time the loop saves a result. The function should return
+ True if the result indicates loop success, False if it
+ represents a permanent failure state, and None if the loop
+ should continue. If no function is provided, the loop will
+ end as soon as it records any result.
+ * backoff_start: The number of seconds that must pass before the
+ loop's second iteration. Default 0, which disables all waiting.
+ * backoff_growth: The wait time multiplier after each iteration.
+ Default 2 (i.e., double the wait time each time).
+ * save_results: Specify a number to save the last N results
+ that the loop recorded. These records are available through
+ the results attribute, oldest first. Default 1.
+ """
+ self.tries_left = num_retries + 1
+ self.check_result = success_check
+ self.backoff_wait = backoff_start
+ self.backoff_growth = backoff_growth
+ self.next_start_time = 0
+ self.results = deque(maxlen=save_results)
+ self._running = None
+ self._success = None
+
+ def __iter__(self):
+ return self
+
+ def running(self):
+ return self._running and (self._success is None)
+
+ def next(self):
+ if self._running is None:
+ self._running = True
+ if (self.tries_left < 1) or not self.running():
+ self._running = False
+ raise StopIteration
+ else:
+ wait_time = max(0, self.next_start_time - time.time())
+ time.sleep(wait_time)
+ self.backoff_wait *= self.backoff_growth
+ self.next_start_time = time.time() + self.backoff_wait
+ self.tries_left -= 1
+ return self.tries_left
+
+ def save_result(self, result):
+ """Record a loop result.
+
+ Save the given result, and end the loop if it indicates
+ success or permanent failure. See __init__'s documentation
+ about success_check to learn how to make that indication.
+ """
+ if not self.running():
+ raise arvados.errors.AssertionError(
+ "recorded a loop result after the loop finished")
+ self.results.append(result)
+ self._success = self.check_result(result)
+
+ def success(self):
+ """Return the loop's end state.
+
+ Returns True if the loop obtained a successful result, False if it
+ encountered permanent failure, or else None.
+ """
+ return self._success
+
+ def last_result(self):
+ """Return the most recent result the loop recorded."""
+ try:
+ return self.results[-1]
+ except IndexError:
+ raise arvados.errors.AssertionError(
+ "queried loop results before any were recorded")
+
+
+def check_http_response_success(result):
+ """Convert a 'requests' response to a loop control flag.
+
+ Pass this method a requests.Response object. It returns True if
+ the response indicates success, None if it indicates temporary
+ failure, and False otherwise. You can use this as the
+ success_check for a RetryLoop.
+
+ Implementation details:
+ * Any 2xx result returns True.
+ * A select few status codes, or any malformed responses, return None.
+ 422 Unprocessable Entity is in this category. This may not meet the
+ letter of the HTTP specification, but the Arvados API server will
+ use it for various server-side problems like database connection
+ errors.
+ * Everything else returns False. Note that this includes 1xx and
+ 3xx status codes. They don't indicate success, and you can't
+ retry those requests verbatim.
+ """
+ try:
+ status = result.status_code
+ except Exception:
+ return None
+ if status in _HTTP_SUCCESSES:
+ return True
+ elif status in _HTTP_CAN_RETRY:
+ return None
+ elif 100 <= status < 600:
+ return False
+ else:
+ return None # Get well soon, server.
+
+def retry_method(orig_func):
+ """Provide a default value for a method's num_retries argument.
+
+ This is a decorator for instance and class methods that accept a
+ num_retries argument, with a None default. When the method is called
+ without a value for num_retries, it will be set from the underlying
+ instance or class' num_retries attribute.
+ """
+ @functools.wraps(orig_func)
+ def num_retries_setter(self, *args, **kwargs):
+ arg_vals = inspect.getcallargs(orig_func, self, *args, **kwargs)
+ if arg_vals['num_retries'] is None:
+ kwargs['num_retries'] = self.num_retries
+ return orig_func(self, *args, **kwargs)
+ return num_retries_setter
--- /dev/null
+import bz2
+import collections
+import hashlib
+import os
+import re
+import zlib
+
+from .arvfile import ArvadosFileBase
+from arvados.retry import retry_method
+from keep import *
+import config
+import errors
+
+LOCATOR = 0
+BLOCKSIZE = 1
+OFFSET = 2
+SEGMENTSIZE = 3
+
+def locators_and_ranges(data_locators, range_start, range_size, debug=False):
+ '''
+ Get blocks that are covered by the range
+ data_locators: list of [locator, block_size, block_start], assumes that blocks are in order and contigous
+ range_start: start of range
+ range_size: size of range
+ returns list of [block locator, blocksize, segment offset, segment size] that satisfies the range
+ '''
+ if range_size == 0:
+ return []
+ resp = []
+ range_start = long(range_start)
+ range_size = long(range_size)
+ range_end = range_start + range_size
+ block_start = 0L
+
+ # range_start/block_start is the inclusive lower bound
+ # range_end/block_end is the exclusive upper bound
+
+ hi = len(data_locators)
+ lo = 0
+ i = int((hi + lo) / 2)
+ block_size = data_locators[i][BLOCKSIZE]
+ block_start = data_locators[i][OFFSET]
+ block_end = block_start + block_size
+ if debug: print '---'
+
+ # perform a binary search for the first block
+ # assumes that all of the blocks are contigious, so range_start is guaranteed
+ # to either fall into the range of a block or be outside the block range entirely
+ while not (range_start >= block_start and range_start < block_end):
+ if lo == i:
+ # must be out of range, fail
+ return []
+ if range_start > block_start:
+ lo = i
+ else:
+ hi = i
+ i = int((hi + lo) / 2)
+ if debug: print lo, i, hi
+ block_size = data_locators[i][BLOCKSIZE]
+ block_start = data_locators[i][OFFSET]
+ block_end = block_start + block_size
+
+ while i < len(data_locators):
+ locator, block_size, block_start = data_locators[i]
+ block_end = block_start + block_size
+ if debug:
+ print locator, "range_start", range_start, "block_start", block_start, "range_end", range_end, "block_end", block_end
+ if range_end <= block_start:
+ # range ends before this block starts, so don't look at any more locators
+ break
+
+ #if range_start >= block_end:
+ # range starts after this block ends, so go to next block
+ # we should always start at the first block due to the binary above, so this test is redundant
+ #next
+
+ if range_start >= block_start and range_end <= block_end:
+ # range starts and ends in this block
+ resp.append([locator, block_size, range_start - block_start, range_size])
+ elif range_start >= block_start and range_end > block_end:
+ # range starts in this block
+ resp.append([locator, block_size, range_start - block_start, block_end - range_start])
+ elif range_start < block_start and range_end > block_end:
+ # range starts in a previous block and extends to further blocks
+ resp.append([locator, block_size, 0L, block_size])
+ elif range_start < block_start and range_end <= block_end:
+ # range starts in a previous block and ends in this block
+ resp.append([locator, block_size, 0L, range_end - block_start])
+ block_start = block_end
+ i += 1
+ return resp
+
+def split(path):
+ """split(path) -> streamname, filename
+
+ Separate the stream name and file name in a /-separated stream path.
+ If no stream name is available, assume '.'.
+ """
+ try:
+ stream_name, file_name = path.rsplit('/', 1)
+ except ValueError: # No / in string
+ stream_name, file_name = '.', path
+ return stream_name, file_name
+
+class StreamFileReader(ArvadosFileBase):
+ class _NameAttribute(str):
+ # The Python file API provides a plain .name attribute.
+ # Older SDK provided a name() method.
+ # This class provides both, for maximum compatibility.
+ def __call__(self):
+ return self
+
+
+ def __init__(self, stream, segments, name):
+ super(StreamFileReader, self).__init__(self._NameAttribute(name), 'rb')
+ self._stream = stream
+ self.segments = segments
+ self._filepos = 0L
+ self.num_retries = stream.num_retries
+ self._readline_cache = (None, None)
+
+ def __iter__(self):
+ while True:
+ data = self.readline()
+ if not data:
+ break
+ yield data
+
+ def decompressed_name(self):
+ return re.sub('\.(bz2|gz)$', '', self.name)
+
+ def stream_name(self):
+ return self._stream.name()
+
+ @ArvadosFileBase._before_close
+ def seek(self, pos, whence=os.SEEK_CUR):
+ if whence == os.SEEK_CUR:
+ pos += self._filepos
+ elif whence == os.SEEK_END:
+ pos += self.size()
+ self._filepos = min(max(pos, 0L), self.size())
+
+ def tell(self):
+ return self._filepos
+
+ def size(self):
+ n = self.segments[-1]
+ return n[OFFSET] + n[BLOCKSIZE]
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def read(self, size, num_retries=None):
+ """Read up to 'size' bytes from the stream, starting at the current file position"""
+ if size == 0:
+ return ''
+
+ data = ''
+ available_chunks = locators_and_ranges(self.segments, self._filepos, size)
+ if available_chunks:
+ locator, blocksize, segmentoffset, segmentsize = available_chunks[0]
+ data = self._stream.readfrom(locator+segmentoffset, segmentsize,
+ num_retries=num_retries)
+
+ self._filepos += len(data)
+ return data
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def readfrom(self, start, size, num_retries=None):
+ """Read up to 'size' bytes from the stream, starting at 'start'"""
+ if size == 0:
+ return ''
+
+ data = []
+ for locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self.segments, start, size):
+ data.append(self._stream.readfrom(locator+segmentoffset, segmentsize,
+ num_retries=num_retries))
+ return ''.join(data)
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def readall(self, size=2**20, num_retries=None):
+ while True:
+ data = self.read(size, num_retries=num_retries)
+ if data == '':
+ break
+ yield data
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def readline(self, size=float('inf'), num_retries=None):
+ cache_pos, cache_data = self._readline_cache
+ if self.tell() == cache_pos:
+ data = [cache_data]
+ else:
+ data = ['']
+ data_size = len(data[-1])
+ while (data_size < size) and ('\n' not in data[-1]):
+ next_read = self.read(2 ** 20, num_retries=num_retries)
+ if not next_read:
+ break
+ data.append(next_read)
+ data_size += len(next_read)
+ data = ''.join(data)
+ try:
+ nextline_index = data.index('\n') + 1
+ except ValueError:
+ nextline_index = len(data)
+ nextline_index = min(nextline_index, size)
+ self._readline_cache = (self.tell(), data[nextline_index:])
+ return data[:nextline_index]
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def decompress(self, decompress, size, num_retries=None):
+ for segment in self.readall(size, num_retries):
+ data = decompress(segment)
+ if data:
+ yield data
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def readall_decompressed(self, size=2**20, num_retries=None):
+ self.seek(0)
+ if self.name.endswith('.bz2'):
+ dc = bz2.BZ2Decompressor()
+ return self.decompress(dc.decompress, size,
+ num_retries=num_retries)
+ elif self.name.endswith('.gz'):
+ dc = zlib.decompressobj(16+zlib.MAX_WBITS)
+ return self.decompress(lambda segment: dc.decompress(dc.unconsumed_tail + segment),
+ size, num_retries=num_retries)
+ else:
+ return self.readall(size, num_retries=num_retries)
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def readlines(self, sizehint=float('inf'), num_retries=None):
+ data = []
+ data_size = 0
+ for s in self.readall(num_retries=num_retries):
+ data.append(s)
+ data_size += len(s)
+ if data_size >= sizehint:
+ break
+ return ''.join(data).splitlines(True)
+
+ def as_manifest(self):
+ manifest_text = ['.']
+ manifest_text.extend([d[LOCATOR] for d in self._stream._data_locators])
+ manifest_text.extend(["{}:{}:{}".format(seg[LOCATOR], seg[BLOCKSIZE], self.name().replace(' ', '\\040')) for seg in self.segments])
+ return arvados.CollectionReader(' '.join(manifest_text) + '\n').manifest_text(normalize=True)
+
+
+class StreamReader(object):
+ def __init__(self, tokens, keep=None, debug=False, _empty=False,
+ num_retries=0):
+ self._stream_name = None
+ self._data_locators = []
+ self._files = collections.OrderedDict()
+ self._keep = keep
+ self.num_retries = num_retries
+
+ streamoffset = 0L
+
+ # parse stream
+ for tok in tokens:
+ if debug: print 'tok', tok
+ if self._stream_name is None:
+ self._stream_name = tok.replace('\\040', ' ')
+ continue
+
+ s = re.match(r'^[0-9a-f]{32}\+(\d+)(\+\S+)*$', tok)
+ if s:
+ blocksize = long(s.group(1))
+ self._data_locators.append([tok, blocksize, streamoffset])
+ streamoffset += blocksize
+ continue
+
+ s = re.search(r'^(\d+):(\d+):(\S+)', tok)
+ if s:
+ pos = long(s.group(1))
+ size = long(s.group(2))
+ name = s.group(3).replace('\\040', ' ')
+ if name not in self._files:
+ self._files[name] = StreamFileReader(self, [[pos, size, 0]], name)
+ else:
+ n = self._files[name]
+ n.segments.append([pos, size, n.size()])
+ continue
+
+ raise errors.SyntaxError("Invalid manifest format")
+
+ def name(self):
+ return self._stream_name
+
+ def files(self):
+ return self._files
+
+ def all_files(self):
+ return self._files.values()
+
+ def size(self):
+ n = self._data_locators[-1]
+ return n[OFFSET] + n[BLOCKSIZE]
+
+ def locators_and_ranges(self, range_start, range_size):
+ return locators_and_ranges(self._data_locators, range_start, range_size)
+
+ @retry_method
+ def readfrom(self, start, size, num_retries=None):
+ """Read up to 'size' bytes from the stream, starting at 'start'"""
+ if size == 0:
+ return ''
+ if self._keep is None:
+ self._keep = KeepClient(num_retries=self.num_retries)
+ data = []
+ for locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self._data_locators, start, size):
+ data.append(self._keep.get(locator, num_retries=num_retries)[segmentoffset:segmentoffset+segmentsize])
+ return ''.join(data)
+
+ def manifest_text(self, strip=False):
+ manifest_text = [self.name().replace(' ', '\\040')]
+ if strip:
+ for d in self._data_locators:
+ m = re.match(r'^[0-9a-f]{32}\+\d+', d[LOCATOR])
+ manifest_text.append(m.group(0))
+ else:
+ manifest_text.extend([d[LOCATOR] for d in self._data_locators])
+ manifest_text.extend([' '.join(["{}:{}:{}".format(seg[LOCATOR], seg[BLOCKSIZE], f.name().replace(' ', '\\040'))
+ for seg in f.segments])
+ for f in self._files.values()])
+ return ' '.join(manifest_text) + '\n'
--- /dev/null
+import time
+
+class Timer(object):
+ def __init__(self, verbose=False):
+ self.verbose = verbose
+
+ def __enter__(self):
+ self.start = time.time()
+ return self
+
+ def __exit__(self, *args):
+ self.end = time.time()
+ self.secs = self.end - self.start
+ self.msecs = self.secs * 1000 # millisecs
+ if self.verbose:
+ print 'elapsed time: %f ms' % self.msecs
--- /dev/null
+import fcntl
+import hashlib
+import os
+import re
+import subprocess
+import errno
+import sys
+from arvados.collection import *
+
+HEX_RE = re.compile(r'^[0-9a-fA-F]+$')
+
+keep_locator_pattern = re.compile(r'[0-9a-f]{32}\+\d+(\+\S+)*')
+signed_locator_pattern = re.compile(r'[0-9a-f]{32}\+\d+(\+\S+)*\+A\S+(\+\S+)*')
+portable_data_hash_pattern = re.compile(r'[0-9a-f]{32}\+\d+')
+uuid_pattern = re.compile(r'[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}')
+collection_uuid_pattern = re.compile(r'[a-z0-9]{5}-4zz18-[a-z0-9]{15}')
+group_uuid_pattern = re.compile(r'[a-z0-9]{5}-j7d0g-[a-z0-9]{15}')
+user_uuid_pattern = re.compile(r'[a-z0-9]{5}-tpzed-[a-z0-9]{15}')
+link_uuid_pattern = re.compile(r'[a-z0-9]{5}-o0j2j-[a-z0-9]{15}')
+manifest_pattern = re.compile(r'((\S+)( +[a-f0-9]{32}(\+\d+)(\+\S+)*)+( +\d+:\d+:\S+)+$)+', flags=re.MULTILINE)
+
+def clear_tmpdir(path=None):
+ """
+ Ensure the given directory (or TASK_TMPDIR if none given)
+ exists and is empty.
+ """
+ if path is None:
+ path = arvados.current_task().tmpdir
+ if os.path.exists(path):
+ p = subprocess.Popen(['rm', '-rf', path])
+ stdout, stderr = p.communicate(None)
+ if p.returncode != 0:
+ raise Exception('rm -rf %s: %s' % (path, stderr))
+ os.mkdir(path)
+
+def run_command(execargs, **kwargs):
+ kwargs.setdefault('stdin', subprocess.PIPE)
+ kwargs.setdefault('stdout', subprocess.PIPE)
+ kwargs.setdefault('stderr', sys.stderr)
+ kwargs.setdefault('close_fds', True)
+ kwargs.setdefault('shell', False)
+ p = subprocess.Popen(execargs, **kwargs)
+ stdoutdata, stderrdata = p.communicate(None)
+ if p.returncode != 0:
+ raise errors.CommandFailedError(
+ "run_command %s exit %d:\n%s" %
+ (execargs, p.returncode, stderrdata))
+ return stdoutdata, stderrdata
+
+def git_checkout(url, version, path):
+ if not re.search('^/', path):
+ path = os.path.join(arvados.current_job().tmpdir, path)
+ if not os.path.exists(path):
+ run_command(["git", "clone", url, path],
+ cwd=os.path.dirname(path))
+ run_command(["git", "checkout", version],
+ cwd=path)
+ return path
+
+def tar_extractor(path, decompress_flag):
+ return subprocess.Popen(["tar",
+ "-C", path,
+ ("-x%sf" % decompress_flag),
+ "-"],
+ stdout=None,
+ stdin=subprocess.PIPE, stderr=sys.stderr,
+ shell=False, close_fds=True)
+
+def tarball_extract(tarball, path):
+ """Retrieve a tarball from Keep and extract it to a local
+ directory. Return the absolute path where the tarball was
+ extracted. If the top level of the tarball contained just one
+ file or directory, return the absolute path of that single
+ item.
+
+ tarball -- collection locator
+ path -- where to extract the tarball: absolute, or relative to job tmp
+ """
+ if not re.search('^/', path):
+ path = os.path.join(arvados.current_job().tmpdir, path)
+ lockfile = open(path + '.lock', 'w')
+ fcntl.flock(lockfile, fcntl.LOCK_EX)
+ try:
+ os.stat(path)
+ except OSError:
+ os.mkdir(path)
+ already_have_it = False
+ try:
+ if os.readlink(os.path.join(path, '.locator')) == tarball:
+ already_have_it = True
+ except OSError:
+ pass
+ if not already_have_it:
+
+ # emulate "rm -f" (i.e., if the file does not exist, we win)
+ try:
+ os.unlink(os.path.join(path, '.locator'))
+ except OSError:
+ if os.path.exists(os.path.join(path, '.locator')):
+ os.unlink(os.path.join(path, '.locator'))
+
+ for f in CollectionReader(tarball).all_files():
+ if re.search('\.(tbz|tar.bz2)$', f.name()):
+ p = tar_extractor(path, 'j')
+ elif re.search('\.(tgz|tar.gz)$', f.name()):
+ p = tar_extractor(path, 'z')
+ elif re.search('\.tar$', f.name()):
+ p = tar_extractor(path, '')
+ else:
+ raise errors.AssertionError(
+ "tarball_extract cannot handle filename %s" % f.name())
+ while True:
+ buf = f.read(2**20)
+ if len(buf) == 0:
+ break
+ p.stdin.write(buf)
+ p.stdin.close()
+ p.wait()
+ if p.returncode != 0:
+ lockfile.close()
+ raise errors.CommandFailedError(
+ "tar exited %d" % p.returncode)
+ os.symlink(tarball, os.path.join(path, '.locator'))
+ tld_extracts = filter(lambda f: f != '.locator', os.listdir(path))
+ lockfile.close()
+ if len(tld_extracts) == 1:
+ return os.path.join(path, tld_extracts[0])
+ return path
+
+def zipball_extract(zipball, path):
+ """Retrieve a zip archive from Keep and extract it to a local
+ directory. Return the absolute path where the archive was
+ extracted. If the top level of the archive contained just one
+ file or directory, return the absolute path of that single
+ item.
+
+ zipball -- collection locator
+ path -- where to extract the archive: absolute, or relative to job tmp
+ """
+ if not re.search('^/', path):
+ path = os.path.join(arvados.current_job().tmpdir, path)
+ lockfile = open(path + '.lock', 'w')
+ fcntl.flock(lockfile, fcntl.LOCK_EX)
+ try:
+ os.stat(path)
+ except OSError:
+ os.mkdir(path)
+ already_have_it = False
+ try:
+ if os.readlink(os.path.join(path, '.locator')) == zipball:
+ already_have_it = True
+ except OSError:
+ pass
+ if not already_have_it:
+
+ # emulate "rm -f" (i.e., if the file does not exist, we win)
+ try:
+ os.unlink(os.path.join(path, '.locator'))
+ except OSError:
+ if os.path.exists(os.path.join(path, '.locator')):
+ os.unlink(os.path.join(path, '.locator'))
+
+ for f in CollectionReader(zipball).all_files():
+ if not re.search('\.zip$', f.name()):
+ raise errors.NotImplementedError(
+ "zipball_extract cannot handle filename %s" % f.name())
+ zip_filename = os.path.join(path, os.path.basename(f.name()))
+ zip_file = open(zip_filename, 'wb')
+ while True:
+ buf = f.read(2**20)
+ if len(buf) == 0:
+ break
+ zip_file.write(buf)
+ zip_file.close()
+
+ p = subprocess.Popen(["unzip",
+ "-q", "-o",
+ "-d", path,
+ zip_filename],
+ stdout=None,
+ stdin=None, stderr=sys.stderr,
+ shell=False, close_fds=True)
+ p.wait()
+ if p.returncode != 0:
+ lockfile.close()
+ raise errors.CommandFailedError(
+ "unzip exited %d" % p.returncode)
+ os.unlink(zip_filename)
+ os.symlink(zipball, os.path.join(path, '.locator'))
+ tld_extracts = filter(lambda f: f != '.locator', os.listdir(path))
+ lockfile.close()
+ if len(tld_extracts) == 1:
+ return os.path.join(path, tld_extracts[0])
+ return path
+
+def collection_extract(collection, path, files=[], decompress=True):
+ """Retrieve a collection from Keep and extract it to a local
+ directory. Return the absolute path where the collection was
+ extracted.
+
+ collection -- collection locator
+ path -- where to extract: absolute, or relative to job tmp
+ """
+ matches = re.search(r'^([0-9a-f]+)(\+[\w@]+)*$', collection)
+ if matches:
+ collection_hash = matches.group(1)
+ else:
+ collection_hash = hashlib.md5(collection).hexdigest()
+ if not re.search('^/', path):
+ path = os.path.join(arvados.current_job().tmpdir, path)
+ lockfile = open(path + '.lock', 'w')
+ fcntl.flock(lockfile, fcntl.LOCK_EX)
+ try:
+ os.stat(path)
+ except OSError:
+ os.mkdir(path)
+ already_have_it = False
+ try:
+ if os.readlink(os.path.join(path, '.locator')) == collection_hash:
+ already_have_it = True
+ except OSError:
+ pass
+
+ # emulate "rm -f" (i.e., if the file does not exist, we win)
+ try:
+ os.unlink(os.path.join(path, '.locator'))
+ except OSError:
+ if os.path.exists(os.path.join(path, '.locator')):
+ os.unlink(os.path.join(path, '.locator'))
+
+ files_got = []
+ for s in CollectionReader(collection).all_streams():
+ stream_name = s.name()
+ for f in s.all_files():
+ if (files == [] or
+ ((f.name() not in files_got) and
+ (f.name() in files or
+ (decompress and f.decompressed_name() in files)))):
+ outname = f.decompressed_name() if decompress else f.name()
+ files_got += [outname]
+ if os.path.exists(os.path.join(path, stream_name, outname)):
+ continue
+ mkdir_dash_p(os.path.dirname(os.path.join(path, stream_name, outname)))
+ outfile = open(os.path.join(path, stream_name, outname), 'wb')
+ for buf in (f.readall_decompressed() if decompress
+ else f.readall()):
+ outfile.write(buf)
+ outfile.close()
+ if len(files_got) < len(files):
+ raise errors.AssertionError(
+ "Wanted files %s but only got %s from %s" %
+ (files, files_got,
+ [z.name() for z in CollectionReader(collection).all_files()]))
+ os.symlink(collection_hash, os.path.join(path, '.locator'))
+
+ lockfile.close()
+ return path
+
+def mkdir_dash_p(path):
+ if not os.path.isdir(path):
+ try:
+ os.makedirs(path)
+ except OSError as e:
+ if e.errno == errno.EEXIST and os.path.isdir(path):
+ # It is not an error if someone else creates the
+ # directory between our exists() and makedirs() calls.
+ pass
+ else:
+ raise
+
+def stream_extract(stream, path, files=[], decompress=True):
+ """Retrieve a stream from Keep and extract it to a local
+ directory. Return the absolute path where the stream was
+ extracted.
+
+ stream -- StreamReader object
+ path -- where to extract: absolute, or relative to job tmp
+ """
+ if not re.search('^/', path):
+ path = os.path.join(arvados.current_job().tmpdir, path)
+ lockfile = open(path + '.lock', 'w')
+ fcntl.flock(lockfile, fcntl.LOCK_EX)
+ try:
+ os.stat(path)
+ except OSError:
+ os.mkdir(path)
+
+ files_got = []
+ for f in stream.all_files():
+ if (files == [] or
+ ((f.name() not in files_got) and
+ (f.name() in files or
+ (decompress and f.decompressed_name() in files)))):
+ outname = f.decompressed_name() if decompress else f.name()
+ files_got += [outname]
+ if os.path.exists(os.path.join(path, outname)):
+ os.unlink(os.path.join(path, outname))
+ mkdir_dash_p(os.path.dirname(os.path.join(path, outname)))
+ outfile = open(os.path.join(path, outname), 'wb')
+ for buf in (f.readall_decompressed() if decompress
+ else f.readall()):
+ outfile.write(buf)
+ outfile.close()
+ if len(files_got) < len(files):
+ raise errors.AssertionError(
+ "Wanted files %s but only got %s from %s" %
+ (files, files_got, [z.name() for z in stream.all_files()]))
+ lockfile.close()
+ return path
+
+def listdir_recursive(dirname, base=None, max_depth=None):
+ """listdir_recursive(dirname, base, max_depth)
+
+ Return a list of file and directory names found under dirname.
+
+ If base is not None, prepend "{base}/" to each returned name.
+
+ If max_depth is None, descend into directories and return only the
+ names of files found in the directory tree.
+
+ If max_depth is a non-negative integer, stop descending into
+ directories at the given depth, and at that point return directory
+ names instead.
+
+ If max_depth==0 (and base is None) this is equivalent to
+ sorted(os.listdir(dirname)).
+ """
+ allfiles = []
+ for ent in sorted(os.listdir(dirname)):
+ ent_path = os.path.join(dirname, ent)
+ ent_base = os.path.join(base, ent) if base else ent
+ if os.path.isdir(ent_path) and max_depth != 0:
+ allfiles += listdir_recursive(
+ ent_path, base=ent_base,
+ max_depth=(max_depth-1 if max_depth else None))
+ else:
+ allfiles += [ent_base]
+ return allfiles
+
+def is_hex(s, *length_args):
+ """is_hex(s[, length[, max_length]]) -> boolean
+
+ Return True if s is a string of hexadecimal digits.
+ If one length argument is given, the string must contain exactly
+ that number of digits.
+ If two length arguments are given, the string must contain a number of
+ digits between those two lengths, inclusive.
+ Return False otherwise.
+ """
+ num_length_args = len(length_args)
+ if num_length_args > 2:
+ raise errors.ArgumentError("is_hex accepts up to 3 arguments ({} given)"
+ .format(1 + num_length_args))
+ elif num_length_args == 2:
+ good_len = (length_args[0] <= len(s) <= length_args[1])
+ elif num_length_args == 1:
+ good_len = (len(s) == length_args[0])
+ else:
+ good_len = True
+ return bool(good_len and HEX_RE.match(s))
+
+def list_all(fn, num_retries=0, **kwargs):
+ items = []
+ offset = 0
+ items_available = sys.maxint
+ while len(items) < items_available:
+ c = fn(offset=offset, **kwargs).execute(num_retries=num_retries)
+ items += c['items']
+ items_available = c['items_available']
+ offset = c['offset'] + len(c['items'])
+ return items
--- /dev/null
+#!/usr/bin/env python
+
+from arvados.commands.arv_copy import main
+main()
--- /dev/null
+#!/usr/bin/env python
+
+import argparse
+import hashlib
+import os
+import re
+import string
+import sys
+import logging
+
+import arvados
+import arvados.commands._util as arv_cmd
+
+logger = logging.getLogger('arvados.arv-get')
+
+def abort(msg, code=1):
+ print >>sys.stderr, "arv-get:", msg
+ exit(code)
+
+parser = argparse.ArgumentParser(
+ description='Copy data from Keep to a local file or pipe.',
+ parents=[arv_cmd.retry_opt])
+parser.add_argument('locator', type=str,
+ help="""
+Collection locator, optionally with a file path or prefix.
+""")
+parser.add_argument('destination', type=str, nargs='?', default='/dev/stdout',
+ help="""
+Local file or directory where the data is to be written. Default:
+/dev/stdout.
+""")
+group = parser.add_mutually_exclusive_group()
+group.add_argument('--progress', action='store_true',
+ help="""
+Display human-readable progress on stderr (bytes and, if possible,
+percentage of total data size). This is the default behavior when it
+is not expected to interfere with the output: specifically, stderr is
+a tty _and_ either stdout is not a tty, or output is being written to
+named files rather than stdout.
+""")
+group.add_argument('--no-progress', action='store_true',
+ help="""
+Do not display human-readable progress on stderr.
+""")
+group.add_argument('--batch-progress', action='store_true',
+ help="""
+Display machine-readable progress on stderr (bytes and, if known,
+total data size).
+""")
+group = parser.add_mutually_exclusive_group()
+group.add_argument('--hash',
+ help="""
+Display the hash of each file as it is read from Keep, using the given
+hash algorithm. Supported algorithms include md5, sha1, sha224,
+sha256, sha384, and sha512.
+""")
+group.add_argument('--md5sum', action='store_const',
+ dest='hash', const='md5',
+ help="""
+Display the MD5 hash of each file as it is read from Keep.
+""")
+parser.add_argument('-n', action='store_true',
+ help="""
+Do not write any data -- just read from Keep, and report md5sums if
+requested.
+""")
+parser.add_argument('-r', action='store_true',
+ help="""
+Retrieve all files in the specified collection/prefix. This is the
+default behavior if the "locator" argument ends with a forward slash.
+""")
+group = parser.add_mutually_exclusive_group()
+group.add_argument('-f', action='store_true',
+ help="""
+Overwrite existing files while writing. The default behavior is to
+refuse to write *anything* if any of the output files already
+exist. As a special case, -f is not needed to write to /dev/stdout.
+""")
+group.add_argument('--skip-existing', action='store_true',
+ help="""
+Skip files that already exist. The default behavior is to refuse to
+write *anything* if any files exist that would have to be
+overwritten. This option causes even devices, sockets, and fifos to be
+skipped.
+""")
+
+args = parser.parse_args()
+
+if args.locator[-1] == os.sep:
+ args.r = True
+if (args.r and
+ not args.n and
+ not (args.destination and
+ os.path.isdir(args.destination))):
+ parser.error('Destination is not a directory.')
+if not args.r and (os.path.isdir(args.destination) or
+ args.destination[-1] == os.path.sep):
+ args.destination = os.path.join(args.destination,
+ os.path.basename(args.locator))
+ logger.debug("Appended source file name to destination directory: %s",
+ args.destination)
+
+if args.destination == '-':
+ args.destination = '/dev/stdout'
+if args.destination == '/dev/stdout':
+ # Normally you have to use -f to write to a file (or device) that
+ # already exists, but "-" and "/dev/stdout" are common enough to
+ # merit a special exception.
+ args.f = True
+else:
+ args.destination = args.destination.rstrip(os.sep)
+
+# Turn on --progress by default if stderr is a tty and output is
+# either going to a named file, or going (via stdout) to something
+# that isn't a tty.
+if (not (args.batch_progress or args.no_progress)
+ and sys.stderr.isatty()
+ and (args.destination != '/dev/stdout'
+ or not sys.stdout.isatty())):
+ args.progress = True
+
+
+r = re.search(r'^(.*?)(/.*)?$', args.locator)
+collection = r.group(1)
+get_prefix = r.group(2)
+if args.r and not get_prefix:
+ get_prefix = os.sep
+api_client = arvados.api('v1')
+reader = arvados.CollectionReader(collection, num_retries=args.retries)
+
+if not get_prefix:
+ if not args.n:
+ open_flags = os.O_CREAT | os.O_WRONLY
+ if not args.f:
+ open_flags |= os.O_EXCL
+ try:
+ out_fd = os.open(args.destination, open_flags)
+ with os.fdopen(out_fd, 'wb') as out_file:
+ out_file.write(reader.manifest_text())
+ except (IOError, OSError) as error:
+ abort("can't write to '{}': {}".format(args.destination, error))
+ except (arvados.errors.ApiError, arvados.errors.KeepReadError) as error:
+ abort("failed to download '{}': {}".format(collection, error))
+ sys.exit(0)
+
+reader.normalize()
+
+# Scan the collection. Make an array of (stream, file, local
+# destination filename) tuples, and add up total size to extract.
+todo = []
+todo_bytes = 0
+try:
+ for s in reader.all_streams():
+ for f in s.all_files():
+ if get_prefix and get_prefix[-1] == os.sep:
+ if 0 != string.find(os.path.join(s.name(), f.name()),
+ '.' + get_prefix):
+ continue
+ dest_path = os.path.join(
+ args.destination,
+ os.path.join(s.name(), f.name())[len(get_prefix)+1:])
+ if (not (args.n or args.f or args.skip_existing) and
+ os.path.exists(dest_path)):
+ abort('Local file %s already exists.' % (dest_path,))
+ else:
+ if os.path.join(s.name(), f.name()) != '.' + get_prefix:
+ continue
+ dest_path = args.destination
+ todo += [(s, f, dest_path)]
+ todo_bytes += f.size()
+except arvados.errors.NotFoundError as e:
+ abort(e)
+
+# Read data, and (if not -n) write to local file(s) or pipe.
+
+out_bytes = 0
+for s,f,outfilename in todo:
+ outfile = None
+ digestor = None
+ if not args.n:
+ if args.skip_existing and os.path.exists(outfilename):
+ logger.debug('Local file %s exists. Skipping.', outfilename)
+ continue
+ elif not args.f and (os.path.isfile(outfilename) or
+ os.path.isdir(outfilename)):
+ # Good thing we looked again: apparently this file wasn't
+ # here yet when we checked earlier.
+ abort('Local file %s already exists.' % (outfilename,))
+ if args.r:
+ arvados.util.mkdir_dash_p(os.path.dirname(outfilename))
+ try:
+ outfile = open(outfilename, 'wb')
+ except Exception as error:
+ abort('Open(%s) failed: %s' % (outfilename, error))
+ if args.hash:
+ digestor = hashlib.new(args.hash)
+ try:
+ for data in f.readall():
+ if outfile:
+ outfile.write(data)
+ if digestor:
+ digestor.update(data)
+ out_bytes += len(data)
+ if args.progress:
+ sys.stderr.write('\r%d MiB / %d MiB %.1f%%' %
+ (out_bytes >> 20,
+ todo_bytes >> 20,
+ (100
+ if todo_bytes==0
+ else 100.0*out_bytes/todo_bytes)))
+ elif args.batch_progress:
+ sys.stderr.write('%s %d read %d total\n' %
+ (sys.argv[0], os.getpid(),
+ out_bytes, todo_bytes))
+ if digestor:
+ sys.stderr.write("%s %s/%s\n"
+ % (digestor.hexdigest(), s.name(), f.name()))
+ except KeyboardInterrupt:
+ if outfile and outfilename != '/dev/stdout':
+ os.unlink(outfilename)
+ break
+
+if args.progress:
+ sys.stderr.write('\n')
--- /dev/null
+#!/usr/bin/env python
+
+from arvados.commands.keepdocker import main
+main()
--- /dev/null
+#!/usr/bin/env python
+
+import sys
+
+from arvados.commands.ls import main
+
+sys.exit(main(sys.argv[1:], sys.stdout, sys.stderr))
--- /dev/null
+#!/usr/bin/env python
+
+import argparse
+import hashlib
+import os
+import re
+import string
+import sys
+
+parser = argparse.ArgumentParser(
+ description='Read manifest on standard input and put normalized manifest on standard output.')
+
+parser.add_argument('--extract', type=str, help="The file to extract from the input manifest")
+parser.add_argument('--strip', action='store_true', help="Strip authorization tokens")
+
+args = parser.parse_args()
+
+import arvados
+
+r = sys.stdin.read()
+
+cr = arvados.CollectionReader(r)
+cr.normalize()
+
+if args.extract:
+ i = args.extract.rfind('/')
+ if i == -1:
+ stream = '.'
+ fn = args.extract
+ else:
+ stream = args.extract[:i]
+ fn = args.extract[(i+1):]
+ for s in cr.all_streams():
+ if s.name() == stream:
+ if fn in s.files():
+ sys.stdout.write(s.files()[fn].as_manifest())
+else:
+ sys.stdout.write(cr.manifest_text(args.strip))
--- /dev/null
+#!/usr/bin/env python
+
+from arvados.commands.put import main
+main()
--- /dev/null
+#!/usr/bin/env python
+
+from arvados.commands.run import main
+main()
--- /dev/null
+#!/usr/bin/env python
+
+from arvados.commands.ws import main
+main()
--- /dev/null
+#!/usr/bin/env python
+
+import os
+import subprocess
+import time
+
+from setuptools import setup, find_packages
+from setuptools.command.egg_info import egg_info
+
+SETUP_DIR = os.path.dirname(__file__)
+README = os.path.join(SETUP_DIR, 'README.rst')
+
+class TagBuildWithCommit(egg_info):
+ """Tag the build with the sha1 and date of the last git commit.
+
+ If a build tag has already been set (e.g., "egg_info -b", building
+ from source package), leave it alone.
+ """
+ def tags(self):
+ if self.tag_build is None:
+ git_tags = subprocess.check_output(
+ ['git', 'log', '--first-parent', '--max-count=1',
+ '--format=format:%ct %h', SETUP_DIR]).split()
+ assert len(git_tags) == 2
+ git_tags[0] = time.strftime(
+ '%Y%m%d%H%M%S', time.gmtime(int(git_tags[0])))
+ self.tag_build = '.{}+{}'.format(*git_tags)
+ return egg_info.tags(self)
+
+
+setup(name='arvados-python-client',
+ version='0.1',
+ description='Arvados client library',
+ long_description=open(README).read(),
+ author='Arvados',
+ author_email='info@arvados.org',
+ url="https://arvados.org",
+ download_url="https://github.com/curoverse/arvados.git",
+ license='Apache 2.0',
+ packages=find_packages(),
+ scripts=[
+ 'bin/arv-copy',
+ 'bin/arv-get',
+ 'bin/arv-keepdocker',
+ 'bin/arv-ls',
+ 'bin/arv-normalize',
+ 'bin/arv-put',
+ 'bin/arv-run',
+ 'bin/arv-ws'
+ ],
+ install_requires=[
+ 'python-gflags',
+ 'google-api-python-client',
+ 'httplib2',
+ 'requests>=2.4',
+ 'urllib3',
+ 'ws4py'
+ ],
+ test_suite='tests',
+ tests_require=['mock>=1.0', 'PyYAML'],
+ zip_safe=False,
+ cmdclass={'egg_info': TagBuildWithCommit},
+ )
--- /dev/null
+#!/usr/bin/env python
+
+import errno
+import hashlib
+import httplib
+import httplib2
+import io
+import mock
+import os
+import requests
+import shutil
+import tempfile
+import unittest
+
+# Use this hostname when you want to make sure the traffic will be
+# instantly refused. 100::/64 is a dedicated black hole.
+TEST_HOST = '100::'
+
+skip_sleep = mock.patch('time.sleep', lambda n: None) # clown'll eat me
+
+# fake_httplib2_response and mock_responses
+# mock calls to httplib2.Http.request()
+def fake_httplib2_response(code, **headers):
+ headers.update(status=str(code),
+ reason=httplib.responses.get(code, "Unknown Response"))
+ return httplib2.Response(headers)
+
+def mock_responses(body, *codes, **headers):
+ return mock.patch('httplib2.Http.request', side_effect=(
+ (fake_httplib2_response(code, **headers), body) for code in codes))
+
+# fake_requests_response, mock_get_responses and mock_put_responses
+# mock calls to requests.get() and requests.put()
+def fake_requests_response(code, body, **headers):
+ r = requests.Response()
+ r.status_code = code
+ r.reason = httplib.responses.get(code, "Unknown Response")
+ r.headers = headers
+ r.raw = io.BytesIO(body)
+ return r
+
+def mock_get_responses(body, *codes, **headers):
+ return mock.patch('requests.get', side_effect=(
+ fake_requests_response(code, body, **headers) for code in codes))
+
+def mock_put_responses(body, *codes, **headers):
+ return mock.patch('requests.put', side_effect=(
+ fake_requests_response(code, body, **headers) for code in codes))
+
+def mock_requestslib_responses(method, body, *codes, **headers):
+ return mock.patch(method, side_effect=(
+ fake_requests_response(code, body, **headers) for code in codes))
+
+class MockStreamReader(object):
+ def __init__(self, name='.', *data):
+ self._name = name
+ self._data = ''.join(data)
+ self._data_locators = ['{}+{}'.format(hashlib.md5(d).hexdigest(),
+ len(d)) for d in data]
+ self.num_retries = 0
+
+ def name(self):
+ return self._name
+
+ def readfrom(self, start, size, num_retries=None):
+ return self._data[start:start + size]
+
+
+class ArvadosBaseTestCase(unittest.TestCase):
+ # This class provides common utility functions for our tests.
+
+ def setUp(self):
+ self._tempdirs = []
+
+ def tearDown(self):
+ for workdir in self._tempdirs:
+ shutil.rmtree(workdir, ignore_errors=True)
+
+ def make_tmpdir(self):
+ self._tempdirs.append(tempfile.mkdtemp())
+ return self._tempdirs[-1]
+
+ def data_file(self, filename):
+ try:
+ basedir = os.path.dirname(__file__)
+ except NameError:
+ basedir = '.'
+ return open(os.path.join(basedir, 'data', filename))
+
+ def build_directory_tree(self, tree):
+ tree_root = self.make_tmpdir()
+ for leaf in tree:
+ path = os.path.join(tree_root, leaf)
+ try:
+ os.makedirs(os.path.dirname(path))
+ except OSError as error:
+ if error.errno != errno.EEXIST:
+ raise
+ with open(path, 'w') as tmpfile:
+ tmpfile.write(leaf)
+ return tree_root
+
+ def make_test_file(self, text="test"):
+ testfile = tempfile.NamedTemporaryFile()
+ testfile.write(text)
+ testfile.flush()
+ return testfile
--- /dev/null
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647497211:3555843:CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz 651053054:128:CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz.md5 651053182:19868212:Mills_and_1000G_gold_standard.indels.b37.vcf.gz 670921394:118:Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5 670921512:547962:Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz 671469474:122:Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz.md5 671469596:29993649:NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz 701463245:128:NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz.md5 701463373:578447:NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz 702041820:132:NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz.md5 702041952:38839441:NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz 740881393:122:NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz.md5 740881515:605289:NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz 741486804:126:NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz.md5 741486930:6040047539:NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam 6781534469:113749:NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz 6781648218:124:NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz.md5 6781648342:117:NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.md5 6781648459:3928395:NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz 6785576854:120:NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz.md5 6785576974:66113:NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz 6785643087:124:NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz.md5 6785643211:282374229:dbsnp_137.b37.excluding_sites_after_129.vcf.gz 7068017440:117:dbsnp_137.b37.excluding_sites_after_129.vcf.gz.md5 7068017557:3824375:dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz 7071841932:121:dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz.md5 7071842053:1022107667:dbsnp_137.b37.vcf.gz 8093949720:91:dbsnp_137.b37.vcf.gz.md5 8093949811:3982568:dbsnp_137.b37.vcf.idx.gz 8097932379:95:dbsnp_137.b37.vcf.idx.gz.md5 8097932474:59819710:hapmap_3.3.b37.vcf.gz 8157752184:92:hapmap_3.3.b37.vcf.gz.md5 8157752276:1022297:hapmap_3.3.b37.vcf.idx.gz 8158774573:96:hapmap_3.3.b37.vcf.idx.gz.md5 8158774669:2597:human_g1k_v37.dict.gz 8158777266:92:human_g1k_v37.dict.gz.md5 8158777358:1044:human_g1k_v37.fasta.fai.gz 8158778402:97:human_g1k_v37.fasta.fai.gz.md5 8158778499:869925027:human_g1k_v37.fasta.gz 9028703526:93:human_g1k_v37.fasta.gz.md5 9028703619:85:human_g1k_v37.stats.gz 9028703704:93:human_g1k_v37.stats.gz.md5 9028703797:2689:human_g1k_v37_decoy.dict.gz 9028706486:98:human_g1k_v37_decoy.dict.gz.md5 9028706584:1095:human_g1k_v37_decoy.fasta.fai.gz 9028707679:103:human_g1k_v37_decoy.fasta.fai.gz.md5 9028707782:879197576:human_g1k_v37_decoy.fasta.gz 9907905358:99:human_g1k_v37_decoy.fasta.gz.md5 9907905457:91:human_g1k_v37_decoy.stats.gz 9907905548:99:human_g1k_v37_decoy.stats.gz.md5
--- /dev/null
+./PG0002577-DNA-jlake-germline ec9ae2be7620af8b6efd96809e5e75e0+1917833 0:6148:.DS_Store 6148:4096:._.DS_Store 10244:1904161:PG0002577-DNA.pdf 1914405:76:PersonalGenome_Mac.command 1914481:704:PersonalGenome_Windows.bat 1915185:2648:md5sum.txt
+./PG0002577-DNA-jlake-germline/Assembly 42a43977e2303a4337129331577d122a+10244 0:6148:.DS_Store 6148:4096:._.DS_Store
+./PG0002577-DNA-jlake-germline/Assembly/conf 95747f01cc916acc1f385ea2d018841a+165976 0:61440:dirs.tar 61440:11245:project.conf 72685:61440:project.dirs.tar 134125:31851:run.conf.xml
+./PG0002577-DNA-jlake-germline/Assembly/genome 6762e2e508fc8eb451f7ec0ea0faee33+10244 0:6148:.DS_Store 6148:4096:._.DS_Store
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+./PG0002578-DNA-jlake-tumor/Genotyping 74a29b8642eafbee843c51f46fb526c0+67108864 c659bb8049be3ac13768227a5ac78228+67108864 388f348c50d59fc16bfb566f088e85aa+4019621 0:138237349:FinalReport_HumanOmni2.5-8v1_PG0002578.txt
+./PG0002578-DNA-jlake-tumor/IGV 1ae944d18638508fece1b0a8bfcf8c9e+15934904 0:2898:.igv_session.xml 2898:2898:.mac_igv_session.xml 5796:2526:GID_session.xml 8322:171972:batik-codec.jar 180294:202:igv.bat 180496:43:igv.command 180539:15725768:igv.jar 15906307:42:igv.sh 15906349:1150:illumina.ico 15907499:26167:license_LGPL-2.1.txt 15933666:1238:readme.txt
+./PG0002578-DNA-jlake-tumor/Variations c16493faff63b09072395f9131e38152+67108864 f8f61d884faf2a66f162af422c2749ee+67108864 75b165151b45b7aee32b4690f0644b38+67108864 a33a13617e75d300715e46c57162fc33+67108864 ca46c7a4c725d0efe0568dce26bc5213+67108864 18f8e870d93a271f8a894fc4c4351e60+67108864 adb2c4f3e1e99be24e3ab19cf5db7631+67108864 fefc2d2bfafc240776c7b06ddc8d475b+67108864 adf6ee298b575c59143eda731f83c1cf+67108864 78cf4992604945f97209402eabb2eb7d+67108864 8bf9394ad0435a51e2b2e57a841300c1+67108864 a6f8c5582335c30d06d111ecd79d85bf+67108864 7765bf35e97576b071639d17d9bdd090+67108864 8b9b746b76b18e32ba8047176e9f74d2+67108864 56590e49063b1f814005d9c02000ddfd+67108864 10a639f273764b31451b5e8d95a8e98d+67108864 1b1c8235e66633bb95d2a2a2bede6f3f+67108864 4cc650efa04c38fd0502287a92786737+67108864 4433bac63122a8f9058334633904e988+67108864 3b470c2e8bc8d0ed981ea14353f08eaa+67108864 13de261edeba63d0c330f85bf3544656+67108864 7aee17fb67ed1a622f2bed2b3a50ff78+67108864 8c7ecacdbd99ec2cb3cbd276984bb361+67108864 4bee2d90998217971ef72b2f94054966+12779495 0:1432964600:PG0002578-DNA.genome.block.anno.vcf.gz 1432964600:3650551:PG0002578-DNA.genome.block.anno.vcf.gz.tbi 1436615151:118084986:PG0002578-DNA.snps.vcf.gz 1554700137:1583230:PG0002578-DNA.snps.vcf.gz.tbi
--- /dev/null
+#!/usr/bin/env python
+
+import argparse
+import os
+import shutil
+import signal
+import subprocess
+import sys
+import tempfile
+import time
+import unittest
+import yaml
+
+MY_DIRNAME = os.path.dirname(os.path.realpath(__file__))
+if __name__ == '__main__' and os.path.exists(
+ os.path.join(MY_DIRNAME, '..', 'arvados', '__init__.py')):
+ # We're being launched to support another test suite.
+ # Add the Python SDK source to the library path.
+ sys.path.insert(1, os.path.dirname(MY_DIRNAME))
+
+import arvados.api
+import arvados.config
+
+SERVICES_SRC_DIR = os.path.join(MY_DIRNAME, '../../../services')
+SERVER_PID_PATH = 'tmp/pids/webrick-test.pid'
+WEBSOCKETS_SERVER_PID_PATH = 'tmp/pids/passenger-test.pid'
+if 'GOPATH' in os.environ:
+ gopaths = os.environ['GOPATH'].split(':')
+ gobins = [os.path.join(path, 'bin') for path in gopaths]
+ os.environ['PATH'] = ':'.join(gobins) + ':' + os.environ['PATH']
+
+if os.path.isdir('tests'):
+ TEST_TMPDIR = 'tests/tmp'
+else:
+ TEST_TMPDIR = 'tmp'
+
+def find_server_pid(PID_PATH, wait=10):
+ now = time.time()
+ timeout = now + wait
+ good_pid = False
+ while (not good_pid) and (now <= timeout):
+ time.sleep(0.2)
+ try:
+ with open(PID_PATH, 'r') as f:
+ server_pid = int(f.read())
+ good_pid = (os.kill(server_pid, 0) is None)
+ except IOError:
+ good_pid = False
+ except OSError:
+ good_pid = False
+ now = time.time()
+
+ if not good_pid:
+ return None
+
+ return server_pid
+
+def kill_server_pid(PID_PATH, wait=10):
+ try:
+ now = time.time()
+ timeout = now + wait
+ with open(PID_PATH, 'r') as f:
+ server_pid = int(f.read())
+ while now <= timeout:
+ os.kill(server_pid, signal.SIGTERM)
+ os.getpgid(server_pid) # throw OSError if no such pid
+ now = time.time()
+ time.sleep(0.1)
+ except IOError:
+ good_pid = False
+ except OSError:
+ good_pid = False
+
+def run(websockets=False, reuse_server=False):
+ cwd = os.getcwd()
+ os.chdir(os.path.join(SERVICES_SRC_DIR, 'api'))
+
+ if websockets:
+ pid_file = WEBSOCKETS_SERVER_PID_PATH
+ else:
+ pid_file = SERVER_PID_PATH
+
+ test_pid = find_server_pid(pid_file, 0)
+
+ if test_pid is None or not reuse_server:
+ # do not try to run both server variants at once
+ stop()
+
+ # delete cached discovery document
+ shutil.rmtree(arvados.http_cache('discovery'))
+
+ # Setup database
+ os.environ["RAILS_ENV"] = "test"
+ subprocess.call(['bundle', 'exec', 'rake', 'tmp:cache:clear'])
+ subprocess.call(['bundle', 'exec', 'rake', 'db:test:load'])
+ subprocess.call(['bundle', 'exec', 'rake', 'db:fixtures:load'])
+
+ subprocess.call(['bundle', 'exec', 'rails', 'server', '-d',
+ '--pid',
+ os.path.join(os.getcwd(), SERVER_PID_PATH),
+ '-p3000'])
+ os.environ["ARVADOS_API_HOST"] = "127.0.0.1:3000"
+
+ if websockets:
+ os.environ["ARVADOS_WEBSOCKETS"] = "ws-only"
+ subprocess.call(['bundle', 'exec',
+ 'passenger', 'start', '-d', '-p3333',
+ '--pid-file',
+ os.path.join(os.getcwd(), WEBSOCKETS_SERVER_PID_PATH)
+ ])
+
+ pid = find_server_pid(SERVER_PID_PATH)
+
+ os.environ["ARVADOS_API_HOST_INSECURE"] = "true"
+ os.environ["ARVADOS_API_TOKEN"] = ""
+ os.chdir(cwd)
+
+def stop():
+ cwd = os.getcwd()
+ os.chdir(os.path.join(SERVICES_SRC_DIR, 'api'))
+
+ kill_server_pid(WEBSOCKETS_SERVER_PID_PATH, 0)
+ kill_server_pid(SERVER_PID_PATH, 0)
+
+ try:
+ os.unlink('self-signed.pem')
+ except:
+ pass
+
+ try:
+ os.unlink('self-signed.key')
+ except:
+ pass
+
+ os.chdir(cwd)
+
+def _start_keep(n, keep_args):
+ keep0 = tempfile.mkdtemp()
+ keep_cmd = ["keepstore",
+ "-volumes={}".format(keep0),
+ "-listen=:{}".format(25107+n),
+ "-pid={}".format("{}/keep{}.pid".format(TEST_TMPDIR, n))]
+
+ for arg, val in keep_args.iteritems():
+ keep_cmd.append("{}={}".format(arg, val))
+
+ kp0 = subprocess.Popen(keep_cmd)
+ with open("{}/keep{}.pid".format(TEST_TMPDIR, n), 'w') as f:
+ f.write(str(kp0.pid))
+
+ with open("{}/keep{}.volume".format(TEST_TMPDIR, n), 'w') as f:
+ f.write(keep0)
+
+def run_keep(blob_signing_key=None, enforce_permissions=False):
+ stop_keep()
+
+ if not os.path.exists(TEST_TMPDIR):
+ os.mkdir(TEST_TMPDIR)
+
+ keep_args = {}
+ if blob_signing_key:
+ with open(os.path.join(TEST_TMPDIR, "keep.blob_signing_key"), "w") as f:
+ keep_args['--permission-key-file'] = f.name
+ f.write(blob_signing_key)
+ if enforce_permissions:
+ keep_args['--enforce-permissions'] = 'true'
+
+ _start_keep(0, keep_args)
+ _start_keep(1, keep_args)
+
+ os.environ["ARVADOS_API_HOST"] = "127.0.0.1:3000"
+ os.environ["ARVADOS_API_HOST_INSECURE"] = "true"
+
+ authorize_with("admin")
+ api = arvados.api('v1', cache=False)
+ for d in api.keep_services().list().execute()['items']:
+ api.keep_services().delete(uuid=d['uuid']).execute()
+ for d in api.keep_disks().list().execute()['items']:
+ api.keep_disks().delete(uuid=d['uuid']).execute()
+
+ s1 = api.keep_services().create(body={"keep_service": {
+ "uuid": "zzzzz-bi6l4-5bo5n1iekkjyz6b",
+ "service_host": "localhost",
+ "service_port": 25107,
+ "service_type": "disk"
+ }}).execute()
+ s2 = api.keep_services().create(body={"keep_service": {
+ "uuid": "zzzzz-bi6l4-2nz60e0ksj7vr3s",
+ "service_host": "localhost",
+ "service_port": 25108,
+ "service_type": "disk"
+ }}).execute()
+ api.keep_disks().create(body={"keep_disk": {"keep_service_uuid": s1["uuid"] } }).execute()
+ api.keep_disks().create(body={"keep_disk": {"keep_service_uuid": s2["uuid"] } }).execute()
+
+def _stop_keep(n):
+ kill_server_pid("{}/keep{}.pid".format(TEST_TMPDIR, n), 0)
+ if os.path.exists("{}/keep{}.volume".format(TEST_TMPDIR, n)):
+ with open("{}/keep{}.volume".format(TEST_TMPDIR, n), 'r') as r:
+ shutil.rmtree(r.read(), True)
+ os.unlink("{}/keep{}.volume".format(TEST_TMPDIR, n))
+ if os.path.exists(os.path.join(TEST_TMPDIR, "keep.blob_signing_key")):
+ os.remove(os.path.join(TEST_TMPDIR, "keep.blob_signing_key"))
+
+def stop_keep():
+ _stop_keep(0)
+ _stop_keep(1)
+
+def run_keep_proxy(auth):
+ stop_keep_proxy()
+
+ if not os.path.exists(TEST_TMPDIR):
+ os.mkdir(TEST_TMPDIR)
+
+ os.environ["ARVADOS_API_HOST"] = "127.0.0.1:3000"
+ os.environ["ARVADOS_API_HOST_INSECURE"] = "true"
+ os.environ["ARVADOS_API_TOKEN"] = fixture("api_client_authorizations")[auth]["api_token"]
+
+ kp0 = subprocess.Popen(["keepproxy",
+ "-pid={}/keepproxy.pid".format(TEST_TMPDIR),
+ "-listen=:{}".format(25101)])
+
+ authorize_with("admin")
+ api = arvados.api('v1', cache=False)
+ api.keep_services().create(body={"keep_service": {"service_host": "localhost", "service_port": 25101, "service_type": "proxy"} }).execute()
+
+ os.environ["ARVADOS_KEEP_PROXY"] = "http://localhost:25101"
+
+def stop_keep_proxy():
+ kill_server_pid(os.path.join(TEST_TMPDIR, "keepproxy.pid"), 0)
+
+def fixture(fix):
+ '''load a fixture yaml file'''
+ with open(os.path.join(SERVICES_SRC_DIR, 'api', "test", "fixtures",
+ fix + ".yml")) as f:
+ yaml_file = f.read()
+ try:
+ trim_index = yaml_file.index("# Test Helper trims the rest of the file")
+ yaml_file = yaml_file[0:trim_index]
+ except ValueError:
+ pass
+ return yaml.load(yaml_file)
+
+def authorize_with(token):
+ '''token is the symbolic name of the token from the api_client_authorizations fixture'''
+ arvados.config.settings()["ARVADOS_API_TOKEN"] = fixture("api_client_authorizations")[token]["api_token"]
+ arvados.config.settings()["ARVADOS_API_HOST"] = os.environ.get("ARVADOS_API_HOST")
+ arvados.config.settings()["ARVADOS_API_HOST_INSECURE"] = "true"
+
+class TestCaseWithServers(unittest.TestCase):
+ """TestCase to start and stop supporting Arvados servers.
+
+ Define any of MAIN_SERVER, KEEP_SERVER, and/or KEEP_PROXY_SERVER
+ class variables as a dictionary of keyword arguments. If you do,
+ setUpClass will start the corresponding servers by passing these
+ keyword arguments to the run, run_keep, and/or run_keep_server
+ functions, respectively. It will also set Arvados environment
+ variables to point to these servers appropriately. If you don't
+ run a Keep or Keep proxy server, setUpClass will set up a
+ temporary directory for Keep local storage, and set it as
+ KEEP_LOCAL_STORE.
+
+ tearDownClass will stop any servers started, and restore the
+ original environment.
+ """
+ MAIN_SERVER = None
+ KEEP_SERVER = None
+ KEEP_PROXY_SERVER = None
+
+ @staticmethod
+ def _restore_dict(src, dest):
+ for key in dest.keys():
+ if key not in src:
+ del dest[key]
+ dest.update(src)
+
+ @classmethod
+ def setUpClass(cls):
+ cls._orig_environ = os.environ.copy()
+ cls._orig_config = arvados.config.settings().copy()
+ cls._cleanup_funcs = []
+ for server_kwargs, start_func, stop_func in (
+ (cls.MAIN_SERVER, run, stop),
+ (cls.KEEP_SERVER, run_keep, stop_keep),
+ (cls.KEEP_PROXY_SERVER, run_keep_proxy, stop_keep_proxy)):
+ if server_kwargs is not None:
+ start_func(**server_kwargs)
+ cls._cleanup_funcs.append(stop_func)
+ os.environ.pop('ARVADOS_EXTERNAL_CLIENT', None)
+ if cls.KEEP_PROXY_SERVER is None:
+ os.environ.pop('ARVADOS_KEEP_PROXY', None)
+ if (cls.KEEP_SERVER is None) and (cls.KEEP_PROXY_SERVER is None):
+ cls.local_store = tempfile.mkdtemp()
+ os.environ['KEEP_LOCAL_STORE'] = cls.local_store
+ cls._cleanup_funcs.append(
+ lambda: shutil.rmtree(cls.local_store, ignore_errors=True))
+ else:
+ os.environ.pop('KEEP_LOCAL_STORE', None)
+ arvados.config.initialize()
+
+ @classmethod
+ def tearDownClass(cls):
+ for clean_func in cls._cleanup_funcs:
+ clean_func()
+ cls._restore_dict(cls._orig_environ, os.environ)
+ cls._restore_dict(cls._orig_config, arvados.config.settings())
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+ parser.add_argument('action', type=str, help='''one of "start", "stop", "start_keep", "stop_keep"''')
+ parser.add_argument('--websockets', action='store_true', default=False)
+ parser.add_argument('--reuse', action='store_true', default=False)
+ parser.add_argument('--auth', type=str, help='Print authorization info for given api_client_authorizations fixture')
+ args = parser.parse_args()
+
+ if args.action == 'start':
+ run(websockets=args.websockets, reuse_server=args.reuse)
+ if args.auth is not None:
+ authorize_with(args.auth)
+ print("export ARVADOS_API_HOST={}".format(arvados.config.settings()["ARVADOS_API_HOST"]))
+ print("export ARVADOS_API_TOKEN={}".format(arvados.config.settings()["ARVADOS_API_TOKEN"]))
+ print("export ARVADOS_API_HOST_INSECURE={}".format(arvados.config.settings()["ARVADOS_API_HOST_INSECURE"]))
+ elif args.action == 'stop':
+ stop()
+ elif args.action == 'start_keep':
+ run_keep()
+ elif args.action == 'stop_keep':
+ stop_keep()
+ elif args.action == 'start_keep_proxy':
+ run_keep_proxy("admin")
+ elif args.action == 'stop_keep_proxy':
+ stop_keep_proxy()
+ else:
+ print('Unrecognized action "{}", actions are "start", "stop", "start_keep", "stop_keep"'.format(args.action))
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import httplib2
+import json
+import mimetypes
+import os
+import run_test_server
+import unittest
+from apiclient import errors as apiclient_errors
+from apiclient import http as apiclient_http
+
+from arvados_testutil import fake_httplib2_response
+
+if not mimetypes.inited:
+ mimetypes.init()
+
+class ArvadosApiClientTest(unittest.TestCase):
+ ERROR_HEADERS = {'Content-Type': mimetypes.types_map['.json']}
+
+ @classmethod
+ def api_error_response(cls, code, *errors):
+ return (fake_httplib2_response(code, **cls.ERROR_HEADERS),
+ json.dumps({'errors': errors,
+ 'error_token': '1234567890+12345678'}))
+
+ @classmethod
+ def setUpClass(cls):
+ # The apiclient library has support for mocking requests for
+ # testing, but it doesn't extend to the discovery document
+ # itself. For now, bring up an API server that will serve
+ # a discovery document.
+ # FIXME: Figure out a better way to stub this out.
+ run_test_server.run()
+ mock_responses = {
+ 'arvados.humans.delete': (
+ fake_httplib2_response(500, **cls.ERROR_HEADERS),
+ ""),
+ 'arvados.humans.get': cls.api_error_response(
+ 422, "Bad UUID format", "Bad output format"),
+ 'arvados.humans.list': (None, json.dumps(
+ {'items_available': 0, 'items': []})),
+ }
+ req_builder = apiclient_http.RequestMockBuilder(mock_responses)
+ cls.api = arvados.api('v1', cache=False,
+ host=os.environ['ARVADOS_API_HOST'],
+ token='discovery-doc-only-no-token-needed',
+ insecure=True,
+ requestBuilder=req_builder)
+
+ @classmethod
+ def tearDownClass(cls):
+ run_test_server.stop()
+
+ def test_basic_list(self):
+ answer = self.api.humans().list(
+ filters=[['uuid', 'is', None]]).execute()
+ self.assertEqual(answer['items_available'], len(answer['items']))
+
+ def test_exceptions_include_errors(self):
+ with self.assertRaises(apiclient_errors.HttpError) as err_ctx:
+ self.api.humans().get(uuid='xyz-xyz-abcdef').execute()
+ err_s = str(err_ctx.exception)
+ for msg in ["Bad UUID format", "Bad output format"]:
+ self.assertIn(msg, err_s)
+
+ def test_exceptions_without_errors_have_basic_info(self):
+ with self.assertRaises(apiclient_errors.HttpError) as err_ctx:
+ self.api.humans().delete(uuid='xyz-xyz-abcdef').execute()
+ self.assertIn("500", str(err_ctx.exception))
+
+
+if __name__ == '__main__':
+ unittest.main()
--- /dev/null
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import hashlib
+import io
+import random
+
+import mock
+
+import arvados.errors as arv_error
+import arvados.commands.ls as arv_ls
+import run_test_server
+
+class ArvLsTestCase(run_test_server.TestCaseWithServers):
+ FAKE_UUID = 'zzzzz-4zz18-12345abcde12345'
+
+ def newline_join(self, seq):
+ return '\n'.join(seq) + '\n'
+
+ def random_blocks(self, *sizes):
+ return ' '.join('{:032x}+{:d}'.format(
+ random.randint(0, (16 ** 32) - 1), size
+ ) for size in sizes)
+
+ def mock_api_for_manifest(self, manifest_lines, uuid=FAKE_UUID):
+ manifest_text = self.newline_join(manifest_lines)
+ pdh = '{}+{}'.format(hashlib.md5(manifest_text).hexdigest(),
+ len(manifest_text))
+ coll_info = {'uuid': uuid,
+ 'portable_data_hash': pdh,
+ 'manifest_text': manifest_text}
+ api_client = mock.MagicMock(name='mock_api_client')
+ api_client.collections().get().execute.return_value = coll_info
+ return coll_info, api_client
+
+ def run_ls(self, args, api_client):
+ self.stdout = io.BytesIO()
+ self.stderr = io.BytesIO()
+ return arv_ls.main(args, self.stdout, self.stderr, api_client)
+
+ def test_plain_listing(self):
+ collection, api_client = self.mock_api_for_manifest(
+ ['. {} 0:3:one.txt 3:4:two.txt'.format(self.random_blocks(5, 2)),
+ './dir {} 1:5:sub.txt'.format(self.random_blocks(8))])
+ self.assertEqual(0, self.run_ls([collection['uuid']], api_client))
+ self.assertEqual(
+ self.newline_join(['./one.txt', './two.txt', './dir/sub.txt']),
+ self.stdout.getvalue())
+ self.assertEqual('', self.stderr.getvalue())
+
+ def test_size_listing(self):
+ collection, api_client = self.mock_api_for_manifest(
+ ['. {} 0:0:0.txt 0:1000:1.txt 1000:2000:2.txt'.format(
+ self.random_blocks(3000))])
+ self.assertEqual(0, self.run_ls(['-s', collection['uuid']], api_client))
+ self.stdout.seek(0, 0)
+ for expected in range(3):
+ actual_size, actual_name = self.stdout.readline().split()
+ # But she seems much bigger to me...
+ self.assertEqual(str(expected), actual_size)
+ self.assertEqual('./{}.txt'.format(expected), actual_name)
+ self.assertEqual('', self.stdout.read(-1))
+ self.assertEqual('', self.stderr.getvalue())
+
+ def test_nonnormalized_manifest(self):
+ collection, api_client = self.mock_api_for_manifest(
+ ['. {} 0:1010:non.txt'.format(self.random_blocks(1010)),
+ '. {} 0:2020:non.txt'.format(self.random_blocks(2020))])
+ self.assertEqual(0, self.run_ls(['-s', collection['uuid']], api_client))
+ self.stdout.seek(0, 0)
+ self.assertEqual(['3', './non.txt'], self.stdout.readline().split())
+ self.assertEqual('', self.stdout.read(-1))
+ self.assertEqual('', self.stderr.getvalue())
+
+ def test_locator_failure(self):
+ api_client = mock.MagicMock(name='mock_api_client')
+ api_client.collections().get().execute.side_effect = (
+ arv_error.NotFoundError)
+ self.assertNotEqual(0, self.run_ls([self.FAKE_UUID], api_client))
+ self.assertNotEqual('', self.stderr.getvalue())
--- /dev/null
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import apiclient
+import os
+import pwd
+import re
+import shutil
+import subprocess
+import sys
+import tempfile
+import time
+import unittest
+import yaml
+
+from cStringIO import StringIO
+
+import arvados
+import arvados.commands.put as arv_put
+
+from arvados_testutil import ArvadosBaseTestCase
+import run_test_server
+
+class ArvadosPutResumeCacheTest(ArvadosBaseTestCase):
+ CACHE_ARGSET = [
+ [],
+ ['/dev/null'],
+ ['/dev/null', '--filename', 'empty'],
+ ['/tmp'],
+ ['/tmp', '--max-manifest-depth', '0'],
+ ['/tmp', '--max-manifest-depth', '1']
+ ]
+
+ def tearDown(self):
+ super(ArvadosPutResumeCacheTest, self).tearDown()
+ try:
+ self.last_cache.destroy()
+ except AttributeError:
+ pass
+
+ def cache_path_from_arglist(self, arglist):
+ return arv_put.ResumeCache.make_path(arv_put.parse_arguments(arglist))
+
+ def test_cache_names_stable(self):
+ for argset in self.CACHE_ARGSET:
+ self.assertEquals(self.cache_path_from_arglist(argset),
+ self.cache_path_from_arglist(argset),
+ "cache name changed for {}".format(argset))
+
+ def test_cache_names_unique(self):
+ results = []
+ for argset in self.CACHE_ARGSET:
+ path = self.cache_path_from_arglist(argset)
+ self.assertNotIn(path, results)
+ results.append(path)
+
+ def test_cache_names_simple(self):
+ # The goal here is to make sure the filename doesn't use characters
+ # reserved by the filesystem. Feel free to adjust this regexp as
+ # long as it still does that.
+ bad_chars = re.compile(r'[^-\.\w]')
+ for argset in self.CACHE_ARGSET:
+ path = self.cache_path_from_arglist(argset)
+ self.assertFalse(bad_chars.search(os.path.basename(path)),
+ "path too exotic: {}".format(path))
+
+ def test_cache_names_ignore_argument_order(self):
+ self.assertEquals(
+ self.cache_path_from_arglist(['a', 'b', 'c']),
+ self.cache_path_from_arglist(['c', 'a', 'b']))
+ self.assertEquals(
+ self.cache_path_from_arglist(['-', '--filename', 'stdin']),
+ self.cache_path_from_arglist(['--filename', 'stdin', '-']))
+
+ def test_cache_names_differ_for_similar_paths(self):
+ # This test needs names at / that don't exist on the real filesystem.
+ self.assertNotEqual(
+ self.cache_path_from_arglist(['/_arvputtest1', '/_arvputtest2']),
+ self.cache_path_from_arglist(['/_arvputtest1/_arvputtest2']))
+
+ def test_cache_names_ignore_irrelevant_arguments(self):
+ # Workaround: parse_arguments bails on --filename with a directory.
+ path1 = self.cache_path_from_arglist(['/tmp'])
+ args = arv_put.parse_arguments(['/tmp'])
+ args.filename = 'tmp'
+ path2 = arv_put.ResumeCache.make_path(args)
+ self.assertEquals(path1, path2,
+ "cache path considered --filename for directory")
+ self.assertEquals(
+ self.cache_path_from_arglist(['-']),
+ self.cache_path_from_arglist(['-', '--max-manifest-depth', '1']),
+ "cache path considered --max-manifest-depth for file")
+
+ def test_cache_names_treat_negative_manifest_depths_identically(self):
+ base_args = ['/tmp', '--max-manifest-depth']
+ self.assertEquals(
+ self.cache_path_from_arglist(base_args + ['-1']),
+ self.cache_path_from_arglist(base_args + ['-2']))
+
+ def test_cache_names_treat_stdin_consistently(self):
+ self.assertEquals(
+ self.cache_path_from_arglist(['-', '--filename', 'test']),
+ self.cache_path_from_arglist(['/dev/stdin', '--filename', 'test']))
+
+ def test_cache_names_identical_for_synonymous_names(self):
+ self.assertEquals(
+ self.cache_path_from_arglist(['.']),
+ self.cache_path_from_arglist([os.path.realpath('.')]))
+ testdir = self.make_tmpdir()
+ looplink = os.path.join(testdir, 'loop')
+ os.symlink(testdir, looplink)
+ self.assertEquals(
+ self.cache_path_from_arglist([testdir]),
+ self.cache_path_from_arglist([looplink]))
+
+ def test_cache_names_different_by_api_host(self):
+ config = arvados.config.settings()
+ orig_host = config.get('ARVADOS_API_HOST')
+ try:
+ name1 = self.cache_path_from_arglist(['.'])
+ config['ARVADOS_API_HOST'] = 'x' + (orig_host or 'localhost')
+ self.assertNotEqual(name1, self.cache_path_from_arglist(['.']))
+ finally:
+ if orig_host is None:
+ del config['ARVADOS_API_HOST']
+ else:
+ config['ARVADOS_API_HOST'] = orig_host
+
+ def test_basic_cache_storage(self):
+ thing = ['test', 'list']
+ with tempfile.NamedTemporaryFile() as cachefile:
+ self.last_cache = arv_put.ResumeCache(cachefile.name)
+ self.last_cache.save(thing)
+ self.assertEquals(thing, self.last_cache.load())
+
+ def test_empty_cache(self):
+ with tempfile.NamedTemporaryFile() as cachefile:
+ cache = arv_put.ResumeCache(cachefile.name)
+ self.assertRaises(ValueError, cache.load)
+
+ def test_cache_persistent(self):
+ thing = ['test', 'list']
+ path = os.path.join(self.make_tmpdir(), 'cache')
+ cache = arv_put.ResumeCache(path)
+ cache.save(thing)
+ cache.close()
+ self.last_cache = arv_put.ResumeCache(path)
+ self.assertEquals(thing, self.last_cache.load())
+
+ def test_multiple_cache_writes(self):
+ thing = ['short', 'list']
+ with tempfile.NamedTemporaryFile() as cachefile:
+ self.last_cache = arv_put.ResumeCache(cachefile.name)
+ # Start writing an object longer than the one we test, to make
+ # sure the cache file gets truncated.
+ self.last_cache.save(['long', 'long', 'list'])
+ self.last_cache.save(thing)
+ self.assertEquals(thing, self.last_cache.load())
+
+ def test_cache_is_locked(self):
+ with tempfile.NamedTemporaryFile() as cachefile:
+ cache = arv_put.ResumeCache(cachefile.name)
+ self.assertRaises(arv_put.ResumeCacheConflict,
+ arv_put.ResumeCache, cachefile.name)
+
+ def test_cache_stays_locked(self):
+ with tempfile.NamedTemporaryFile() as cachefile:
+ self.last_cache = arv_put.ResumeCache(cachefile.name)
+ path = cachefile.name
+ self.last_cache.save('test')
+ self.assertRaises(arv_put.ResumeCacheConflict,
+ arv_put.ResumeCache, path)
+
+ def test_destroy_cache(self):
+ cachefile = tempfile.NamedTemporaryFile(delete=False)
+ try:
+ cache = arv_put.ResumeCache(cachefile.name)
+ cache.save('test')
+ cache.destroy()
+ try:
+ arv_put.ResumeCache(cachefile.name)
+ except arv_put.ResumeCacheConflict:
+ self.fail("could not load cache after destroying it")
+ self.assertRaises(ValueError, cache.load)
+ finally:
+ if os.path.exists(cachefile.name):
+ os.unlink(cachefile.name)
+
+ def test_restart_cache(self):
+ path = os.path.join(self.make_tmpdir(), 'cache')
+ cache = arv_put.ResumeCache(path)
+ cache.save('test')
+ cache.restart()
+ self.assertRaises(ValueError, cache.load)
+ self.assertRaises(arv_put.ResumeCacheConflict,
+ arv_put.ResumeCache, path)
+
+
+class ArvadosPutCollectionWriterTest(run_test_server.TestCaseWithServers,
+ ArvadosBaseTestCase):
+ def setUp(self):
+ super(ArvadosPutCollectionWriterTest, self).setUp()
+ run_test_server.authorize_with('active')
+ with tempfile.NamedTemporaryFile(delete=False) as cachefile:
+ self.cache = arv_put.ResumeCache(cachefile.name)
+ self.cache_filename = cachefile.name
+
+ def tearDown(self):
+ super(ArvadosPutCollectionWriterTest, self).tearDown()
+ if os.path.exists(self.cache_filename):
+ self.cache.destroy()
+ self.cache.close()
+
+ def test_writer_caches(self):
+ cwriter = arv_put.ArvPutCollectionWriter(self.cache)
+ cwriter.write_file('/dev/null')
+ cwriter.cache_state()
+ self.assertTrue(self.cache.load())
+ self.assertEquals(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:null\n", cwriter.manifest_text())
+
+ def test_writer_works_without_cache(self):
+ cwriter = arv_put.ArvPutCollectionWriter()
+ cwriter.write_file('/dev/null')
+ self.assertEquals(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:null\n", cwriter.manifest_text())
+
+ def test_writer_resumes_from_cache(self):
+ cwriter = arv_put.ArvPutCollectionWriter(self.cache)
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name, 'test')
+ cwriter.cache_state()
+ new_writer = arv_put.ArvPutCollectionWriter.from_cache(
+ self.cache)
+ self.assertEquals(
+ ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:test\n",
+ new_writer.manifest_text())
+
+ def test_new_writer_from_stale_cache(self):
+ cwriter = arv_put.ArvPutCollectionWriter(self.cache)
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name, 'test')
+ new_writer = arv_put.ArvPutCollectionWriter.from_cache(self.cache)
+ new_writer.write_file('/dev/null')
+ self.assertEquals(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:null\n", new_writer.manifest_text())
+
+ def test_new_writer_from_empty_cache(self):
+ cwriter = arv_put.ArvPutCollectionWriter.from_cache(self.cache)
+ cwriter.write_file('/dev/null')
+ self.assertEquals(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:null\n", cwriter.manifest_text())
+
+ def test_writer_resumable_after_arbitrary_bytes(self):
+ cwriter = arv_put.ArvPutCollectionWriter(self.cache)
+ # These bytes are intentionally not valid UTF-8.
+ with self.make_test_file('\x00\x07\xe2') as testfile:
+ cwriter.write_file(testfile.name, 'test')
+ cwriter.cache_state()
+ new_writer = arv_put.ArvPutCollectionWriter.from_cache(
+ self.cache)
+ self.assertEquals(cwriter.manifest_text(), new_writer.manifest_text())
+
+ def make_progress_tester(self):
+ progression = []
+ def record_func(written, expected):
+ progression.append((written, expected))
+ return progression, record_func
+
+ def test_progress_reporting(self):
+ for expect_count in (None, 8):
+ progression, reporter = self.make_progress_tester()
+ cwriter = arv_put.ArvPutCollectionWriter(
+ reporter=reporter, bytes_expected=expect_count)
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name, 'test')
+ cwriter.finish_current_stream()
+ self.assertIn((4, expect_count), progression)
+
+ def test_resume_progress(self):
+ cwriter = arv_put.ArvPutCollectionWriter(self.cache, bytes_expected=4)
+ with self.make_test_file() as testfile:
+ # Set up a writer with some flushed bytes.
+ cwriter.write_file(testfile.name, 'test')
+ cwriter.finish_current_stream()
+ cwriter.cache_state()
+ new_writer = arv_put.ArvPutCollectionWriter.from_cache(self.cache)
+ self.assertEqual(new_writer.bytes_written, 4)
+
+
+class ArvadosExpectedBytesTest(ArvadosBaseTestCase):
+ TEST_SIZE = os.path.getsize(__file__)
+
+ def test_expected_bytes_for_file(self):
+ self.assertEquals(self.TEST_SIZE,
+ arv_put.expected_bytes_for([__file__]))
+
+ def test_expected_bytes_for_tree(self):
+ tree = self.make_tmpdir()
+ shutil.copyfile(__file__, os.path.join(tree, 'one'))
+ shutil.copyfile(__file__, os.path.join(tree, 'two'))
+ self.assertEquals(self.TEST_SIZE * 2,
+ arv_put.expected_bytes_for([tree]))
+ self.assertEquals(self.TEST_SIZE * 3,
+ arv_put.expected_bytes_for([tree, __file__]))
+
+ def test_expected_bytes_for_device(self):
+ self.assertIsNone(arv_put.expected_bytes_for(['/dev/null']))
+ self.assertIsNone(arv_put.expected_bytes_for([__file__, '/dev/null']))
+
+
+class ArvadosPutReportTest(ArvadosBaseTestCase):
+ def test_machine_progress(self):
+ for count, total in [(0, 1), (0, None), (1, None), (235, 9283)]:
+ expect = ": {} written {} total\n".format(
+ count, -1 if (total is None) else total)
+ self.assertTrue(
+ arv_put.machine_progress(count, total).endswith(expect))
+
+ def test_known_human_progress(self):
+ for count, total in [(0, 1), (2, 4), (45, 60)]:
+ expect = '{:.1%}'.format(float(count) / total)
+ actual = arv_put.human_progress(count, total)
+ self.assertTrue(actual.startswith('\r'))
+ self.assertIn(expect, actual)
+
+ def test_unknown_human_progress(self):
+ for count in [1, 20, 300, 4000, 50000]:
+ self.assertTrue(re.search(r'\b{}\b'.format(count),
+ arv_put.human_progress(count, None)))
+
+
+class ArvadosPutTest(run_test_server.TestCaseWithServers, ArvadosBaseTestCase):
+ MAIN_SERVER = {}
+ Z_UUID = 'zzzzz-zzzzz-zzzzzzzzzzzzzzz'
+
+ def call_main_with_args(self, args):
+ self.main_stdout = StringIO()
+ self.main_stderr = StringIO()
+ return arv_put.main(args, self.main_stdout, self.main_stderr)
+
+ def call_main_on_test_file(self):
+ with self.make_test_file() as testfile:
+ path = testfile.name
+ self.call_main_with_args(['--stream', '--no-progress', path])
+ self.assertTrue(
+ os.path.exists(os.path.join(os.environ['KEEP_LOCAL_STORE'],
+ '098f6bcd4621d373cade4e832627b4f6')),
+ "did not find file stream in Keep store")
+
+ def setUp(self):
+ super(ArvadosPutTest, self).setUp()
+ run_test_server.authorize_with('active')
+ arv_put.api_client = None
+
+ def tearDown(self):
+ for outbuf in ['main_stdout', 'main_stderr']:
+ if hasattr(self, outbuf):
+ getattr(self, outbuf).close()
+ delattr(self, outbuf)
+ super(ArvadosPutTest, self).tearDown()
+
+ def test_simple_file_put(self):
+ self.call_main_on_test_file()
+
+ def test_put_with_unwriteable_cache_dir(self):
+ orig_cachedir = arv_put.ResumeCache.CACHE_DIR
+ cachedir = self.make_tmpdir()
+ os.chmod(cachedir, 0o0)
+ arv_put.ResumeCache.CACHE_DIR = cachedir
+ try:
+ self.call_main_on_test_file()
+ finally:
+ arv_put.ResumeCache.CACHE_DIR = orig_cachedir
+ os.chmod(cachedir, 0o700)
+
+ def test_put_with_unwritable_cache_subdir(self):
+ orig_cachedir = arv_put.ResumeCache.CACHE_DIR
+ cachedir = self.make_tmpdir()
+ os.chmod(cachedir, 0o0)
+ arv_put.ResumeCache.CACHE_DIR = os.path.join(cachedir, 'cachedir')
+ try:
+ self.call_main_on_test_file()
+ finally:
+ arv_put.ResumeCache.CACHE_DIR = orig_cachedir
+ os.chmod(cachedir, 0o700)
+
+ def test_error_name_without_collection(self):
+ self.assertRaises(SystemExit, self.call_main_with_args,
+ ['--name', 'test without Collection',
+ '--stream', '/dev/null'])
+
+ def test_error_when_project_not_found(self):
+ self.assertRaises(SystemExit,
+ self.call_main_with_args,
+ ['--project-uuid', self.Z_UUID])
+
+ def test_error_bad_project_uuid(self):
+ self.assertRaises(SystemExit,
+ self.call_main_with_args,
+ ['--project-uuid', self.Z_UUID, '--stream'])
+
+class ArvPutIntegrationTest(run_test_server.TestCaseWithServers,
+ ArvadosBaseTestCase):
+ def _getKeepServerConfig():
+ for config_file in ['application.yml', 'application.default.yml']:
+ with open(os.path.join(run_test_server.SERVICES_SRC_DIR,
+ "api", "config", config_file)) as f:
+ rails_config = yaml.load(f.read())
+ for config_section in ['test', 'common']:
+ try:
+ key = rails_config[config_section]["blob_signing_key"]
+ except (KeyError, TypeError):
+ pass
+ else:
+ return {'blob_signing_key': key,
+ 'enforce_permissions': True}
+ return {'blog_signing_key': None, 'enforce_permissions': False}
+
+ MAIN_SERVER = {}
+ KEEP_SERVER = _getKeepServerConfig()
+ PROJECT_UUID = run_test_server.fixture('groups')['aproject']['uuid']
+
+ @classmethod
+ def setUpClass(cls):
+ super(ArvPutIntegrationTest, cls).setUpClass()
+ cls.ENVIRON = os.environ.copy()
+ cls.ENVIRON['PYTHONPATH'] = ':'.join(sys.path)
+
+ def setUp(self):
+ super(ArvPutIntegrationTest, self).setUp()
+ arv_put.api_client = None
+
+ def authorize_with(self, token_name):
+ run_test_server.authorize_with(token_name)
+ for v in ["ARVADOS_API_HOST",
+ "ARVADOS_API_HOST_INSECURE",
+ "ARVADOS_API_TOKEN"]:
+ self.ENVIRON[v] = arvados.config.settings()[v]
+ arv_put.api_client = arvados.api('v1', cache=False)
+
+ def current_user(self):
+ return arv_put.api_client.users().current().execute()
+
+ def test_check_real_project_found(self):
+ self.authorize_with('active')
+ self.assertTrue(arv_put.desired_project_uuid(arv_put.api_client, self.PROJECT_UUID, 0),
+ "did not correctly find test fixture project")
+
+ def test_check_error_finding_nonexistent_uuid(self):
+ BAD_UUID = 'zzzzz-zzzzz-zzzzzzzzzzzzzzz'
+ self.authorize_with('active')
+ try:
+ result = arv_put.desired_project_uuid(arv_put.api_client, BAD_UUID,
+ 0)
+ except ValueError as error:
+ self.assertIn(BAD_UUID, error.message)
+ else:
+ self.assertFalse(result, "incorrectly found nonexistent project")
+
+ def test_check_error_finding_nonexistent_project(self):
+ BAD_UUID = 'zzzzz-tpzed-zzzzzzzzzzzzzzz'
+ self.authorize_with('active')
+ with self.assertRaises(apiclient.errors.HttpError):
+ result = arv_put.desired_project_uuid(arv_put.api_client, BAD_UUID,
+ 0)
+
+ def test_short_put_from_stdin(self):
+ # Have to run this as an integration test since arv-put can't
+ # read from the tests' stdin.
+ # arv-put usually can't stat(os.path.realpath('/dev/stdin')) in this
+ # case, because the /proc entry is already gone by the time it tries.
+ pipe = subprocess.Popen(
+ [sys.executable, arv_put.__file__, '--stream'],
+ stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT, env=self.ENVIRON)
+ pipe.stdin.write('stdin test\n')
+ pipe.stdin.close()
+ deadline = time.time() + 5
+ while (pipe.poll() is None) and (time.time() < deadline):
+ time.sleep(.1)
+ returncode = pipe.poll()
+ if returncode is None:
+ pipe.terminate()
+ self.fail("arv-put did not PUT from stdin within 5 seconds")
+ elif returncode != 0:
+ sys.stdout.write(pipe.stdout.read())
+ self.fail("arv-put returned exit code {}".format(returncode))
+ self.assertIn('4a9c8b735dce4b5fa3acf221a0b13628+11', pipe.stdout.read())
+
+ def test_ArvPutSignedManifest(self):
+ # ArvPutSignedManifest runs "arv-put foo" and then attempts to get
+ # the newly created manifest from the API server, testing to confirm
+ # that the block locators in the returned manifest are signed.
+ self.authorize_with('active')
+
+ # Before doing anything, demonstrate that the collection
+ # we're about to create is not present in our test fixture.
+ manifest_uuid = "00b4e9f40ac4dd432ef89749f1c01e74+47"
+ with self.assertRaises(apiclient.errors.HttpError):
+ notfound = arv_put.api_client.collections().get(
+ uuid=manifest_uuid).execute()
+
+ datadir = self.make_tmpdir()
+ with open(os.path.join(datadir, "foo"), "w") as f:
+ f.write("The quick brown fox jumped over the lazy dog")
+ p = subprocess.Popen([sys.executable, arv_put.__file__, datadir],
+ stdout=subprocess.PIPE, env=self.ENVIRON)
+ (arvout, arverr) = p.communicate()
+ self.assertEqual(arverr, None)
+ self.assertEqual(p.returncode, 0)
+
+ # The manifest text stored in the API server under the same
+ # manifest UUID must use signed locators.
+ c = arv_put.api_client.collections().get(uuid=manifest_uuid).execute()
+ self.assertRegexpMatches(
+ c['manifest_text'],
+ r'^\. 08a008a01d498c404b0c30852b39d3b8\+44\+A[0-9a-f]+@[0-9a-f]+ 0:44:foo\n')
+
+ os.remove(os.path.join(datadir, "foo"))
+ os.rmdir(datadir)
+
+ def run_and_find_collection(self, text, extra_args=[]):
+ self.authorize_with('active')
+ pipe = subprocess.Popen(
+ [sys.executable, arv_put.__file__] + extra_args,
+ stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE, env=self.ENVIRON)
+ stdout, stderr = pipe.communicate(text)
+ collection_list = arvados.api('v1', cache=False).collections().list(
+ filters=[['portable_data_hash', '=', stdout.strip()]]).execute().get('items', [])
+ self.assertEqual(1, len(collection_list))
+ return collection_list[0]
+
+ def test_put_collection_with_unnamed_project_link(self):
+ link = self.run_and_find_collection("Test unnamed collection",
+ ['--portable-data-hash', '--project-uuid', self.PROJECT_UUID])
+ username = pwd.getpwuid(os.getuid()).pw_name
+ self.assertRegexpMatches(
+ link['name'],
+ r'^Saved at .* by {}@'.format(re.escape(username)))
+
+ def test_put_collection_with_name_and_no_project(self):
+ link_name = 'Test Collection Link in home project'
+ collection = self.run_and_find_collection("Test named collection in home project",
+ ['--portable-data-hash', '--name', link_name])
+ self.assertEqual(link_name, collection['name'])
+ my_user_uuid = self.current_user()['uuid']
+ self.assertEqual(my_user_uuid, collection['owner_uuid'])
+
+ def test_put_collection_with_named_project_link(self):
+ link_name = 'Test auto Collection Link'
+ collection = self.run_and_find_collection("Test named collection",
+ ['--portable-data-hash',
+ '--name', link_name,
+ '--project-uuid', self.PROJECT_UUID])
+ self.assertEqual(link_name, collection['name'])
+
+
+if __name__ == '__main__':
+ unittest.main()
--- /dev/null
+# usage example:
+#
+# ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover
+
+import arvados
+import copy
+import hashlib
+import mock
+import os
+import pprint
+import re
+import tempfile
+import unittest
+
+import run_test_server
+import arvados_testutil as tutil
+
+class TestResumableWriter(arvados.ResumableCollectionWriter):
+ KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K.
+
+ def current_state(self):
+ return self.dump_state(copy.deepcopy)
+
+
+class ArvadosCollectionsTest(run_test_server.TestCaseWithServers,
+ tutil.ArvadosBaseTestCase):
+ MAIN_SERVER = {}
+
+ @classmethod
+ def setUpClass(cls):
+ super(ArvadosCollectionsTest, cls).setUpClass()
+ run_test_server.authorize_with('active')
+ cls.api_client = arvados.api('v1')
+ cls.keep_client = arvados.KeepClient(api_client=cls.api_client,
+ local_store=cls.local_store)
+
+ def write_foo_bar_baz(self):
+ cw = arvados.CollectionWriter(self.api_client)
+ self.assertEqual(cw.current_stream_name(), '.',
+ 'current_stream_name() should be "." now')
+ cw.set_current_file_name('foo.txt')
+ cw.write('foo')
+ self.assertEqual(cw.current_file_name(), 'foo.txt',
+ 'current_file_name() should be foo.txt now')
+ cw.start_new_file('bar.txt')
+ cw.write('bar')
+ cw.start_new_stream('baz')
+ cw.write('baz')
+ cw.set_current_file_name('baz.txt')
+ self.assertEqual(cw.manifest_text(),
+ ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" +
+ "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n",
+ "wrong manifest: got {}".format(cw.manifest_text()))
+ cw.finish()
+ return cw.portable_data_hash()
+
+ def test_keep_local_store(self):
+ self.assertEqual(self.keep_client.put('foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
+ self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), 'foo', 'wrong data from Keep.get')
+
+ def test_local_collection_writer(self):
+ self.assertEqual(self.write_foo_bar_baz(),
+ '23ca013983d6239e98931cc779e68426+114',
+ 'wrong locator hash: ' + self.write_foo_bar_baz())
+
+ def test_local_collection_reader(self):
+ foobarbaz = self.write_foo_bar_baz()
+ cr = arvados.CollectionReader(
+ foobarbaz + '+Xzizzle', self.api_client)
+ got = []
+ for s in cr.all_streams():
+ for f in s.all_files():
+ got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]]
+ expected = [[3, '.', 'foo.txt', 'foo'],
+ [3, '.', 'bar.txt', 'bar'],
+ [3, './baz', 'baz.txt', 'baz']]
+ self.assertEqual(got,
+ expected)
+ stream0 = cr.all_streams()[0]
+ self.assertEqual(stream0.readfrom(0, 0),
+ '',
+ 'reading zero bytes should have returned empty string')
+ self.assertEqual(stream0.readfrom(0, 2**26),
+ 'foobar',
+ 'reading entire stream failed')
+ self.assertEqual(stream0.readfrom(2**26, 0),
+ '',
+ 'reading zero bytes should have returned empty string')
+
+ def _test_subset(self, collection, expected):
+ cr = arvados.CollectionReader(collection, self.api_client)
+ for s in cr.all_streams():
+ for ex in expected:
+ if ex[0] == s:
+ f = s.files()[ex[2]]
+ got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))]
+ self.assertEqual(got,
+ ex,
+ 'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex))
+
+ def test_collection_manifest_subset(self):
+ foobarbaz = self.write_foo_bar_baz()
+ self._test_subset(foobarbaz,
+ [[3, '.', 'bar.txt', 'bar'],
+ [3, '.', 'foo.txt', 'foo'],
+ [3, './baz', 'baz.txt', 'baz']])
+ self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" %
+ (self.keep_client.put("foo"),
+ self.keep_client.put("bar"))),
+ [[3, '.', 'bar.txt', 'bar'],
+ [3, '.', 'foo.txt', 'foo']])
+ self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" %
+ (self.keep_client.put("foo"),
+ self.keep_client.put("bar"))),
+ [[2, '.', 'fo.txt', 'fo'],
+ [4, '.', 'obar.txt', 'obar']])
+ self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" %
+ (self.keep_client.put("foo"),
+ self.keep_client.put("bar"))),
+ [[2, '.', 'ar.txt', 'ar'],
+ [2, '.', 'fo.txt', 'fo'],
+ [2, '.', 'ob.txt', 'ob'],
+ [0, '.', 'zero.txt', '']])
+
+ def test_collection_empty_file(self):
+ cw = arvados.CollectionWriter(self.api_client)
+ cw.start_new_file('zero.txt')
+ cw.write('')
+
+ self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n")
+ self.check_manifest_file_sizes(cw.manifest_text(), [0])
+ cw = arvados.CollectionWriter(self.api_client)
+ cw.start_new_file('zero.txt')
+ cw.write('')
+ cw.start_new_file('one.txt')
+ cw.write('1')
+ cw.start_new_stream('foo')
+ cw.start_new_file('zero.txt')
+ cw.write('')
+ self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0])
+
+ def test_no_implicit_normalize(self):
+ cw = arvados.CollectionWriter(self.api_client)
+ cw.start_new_file('b')
+ cw.write('b')
+ cw.start_new_file('a')
+ cw.write('')
+ self.check_manifest_file_sizes(cw.manifest_text(), [1,0])
+ self.check_manifest_file_sizes(
+ arvados.CollectionReader(
+ cw.manifest_text()).manifest_text(normalize=True),
+ [0,1])
+
+ def check_manifest_file_sizes(self, manifest_text, expect_sizes):
+ cr = arvados.CollectionReader(manifest_text, self.api_client)
+ got_sizes = []
+ for f in cr.all_files():
+ got_sizes += [f.size()]
+ self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes))
+
+ def test_normalized_collection(self):
+ m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
+. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
+"""
+ self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True),
+ """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
+""")
+
+ m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
+"""
+ self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(normalize=True), m2)
+
+ m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
+. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
+"""
+ self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(normalize=True),
+ """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
+""")
+
+ m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
+"""
+ self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(normalize=True),
+ """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+""")
+
+ m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar
+"""
+ self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(normalize=True),
+ """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+""")
+
+ with self.data_file('1000G_ref_manifest') as f6:
+ m6 = f6.read()
+ self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(normalize=True), m6)
+
+ with self.data_file('jlake_manifest') as f7:
+ m7 = f7.read()
+ self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(normalize=True), m7)
+
+ m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt
+"""
+ self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8)
+
+ def test_locators_and_ranges(self):
+ blocks2 = [['a', 10, 0],
+ ['b', 10, 10],
+ ['c', 10, 20],
+ ['d', 10, 30],
+ ['e', 10, 40],
+ ['f', 10, 50]]
+
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 2, 2), [['a', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [['b', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [['c', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [['d', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [['e', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [['f', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), [])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 0, 2), [['a', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [['b', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [['c', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [['d', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [['e', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [['f', 10, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), [])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), [])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 9, 2), [['a', 10, 9, 1], ['b', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [['b', 10, 9, 1], ['c', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [['c', 10, 9, 1], ['d', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [['d', 10, 9, 1], ['e', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [['e', 10, 9, 1], ['f', 10, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [['f', 10, 9, 1]])
+
+
+ blocks3 = [['a', 10, 0],
+ ['b', 10, 10],
+ ['c', 10, 20],
+ ['d', 10, 30],
+ ['e', 10, 40],
+ ['f', 10, 50],
+ ['g', 10, 60]]
+
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 2, 2), [['a', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [['b', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [['c', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [['d', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [['e', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [['f', 10, 2, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [['g', 10, 2, 2]])
+
+
+ blocks = [['a', 10, 0],
+ ['b', 15, 10],
+ ['c', 5, 25]]
+ self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), [])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [['a', 10, 0, 5]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [['a', 10, 3, 5]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [['a', 10, 0, 10]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [['a', 10, 0, 10],
+ ['b', 15, 0, 1]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [['a', 10, 1, 9],
+ ['b', 15, 0, 2]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [['a', 10, 0, 10],
+ ['b', 15, 0, 15]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [['a', 10, 0, 10],
+ ['b', 15, 0, 15],
+ ['c', 5, 0, 5]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [['a', 10, 1, 9],
+ ['b', 15, 0, 15],
+ ['c', 5, 0, 5]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [['a', 10, 0, 10],
+ ['b', 15, 0, 15],
+ ['c', 5, 0, 5]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [['b', 15, 5, 5]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [['a', 10, 8, 2],
+ ['b', 15, 0, 15]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [['a', 10, 8, 2],
+ ['b', 15, 0, 15],
+ ['c', 5, 0, 3]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [['c', 5, 1, 2]])
+
+ self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [['a', 10, 9, 1],
+ ['b', 15, 0, 14]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [['b', 15, 0, 15]])
+ self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [['b', 15, 1, 14],
+ ['c', 5, 0, 1]])
+
+ class MockKeep(object):
+ def __init__(self, content, num_retries=0):
+ self.content = content
+
+ def get(self, locator, num_retries=0):
+ return self.content[locator]
+
+ def test_stream_reader(self):
+ keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij',
+ 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy',
+ 'cccccccccccccccccccccccccccccccc+5': 'z0123'}
+ mk = self.MockKeep(keepblocks)
+
+ sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk)
+
+ content = 'abcdefghijklmnopqrstuvwxyz0123456789'
+
+ self.assertEqual(sr.readfrom(0, 30), content[0:30])
+ self.assertEqual(sr.readfrom(2, 30), content[2:30])
+
+ self.assertEqual(sr.readfrom(2, 8), content[2:10])
+ self.assertEqual(sr.readfrom(0, 10), content[0:10])
+
+ self.assertEqual(sr.readfrom(0, 5), content[0:5])
+ self.assertEqual(sr.readfrom(5, 5), content[5:10])
+ self.assertEqual(sr.readfrom(10, 5), content[10:15])
+ self.assertEqual(sr.readfrom(15, 5), content[15:20])
+ self.assertEqual(sr.readfrom(20, 5), content[20:25])
+ self.assertEqual(sr.readfrom(25, 5), content[25:30])
+ self.assertEqual(sr.readfrom(30, 5), '')
+
+ def test_extract_file(self):
+ m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt
+. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt
+"""
+
+ m2 = arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True)
+
+ self.assertEqual(m2,
+ ". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt 43:41:md6sum.txt 84:43:md7sum.txt 6:37:md8sum.txt 84:43:md8sum.txt 83:1:md9sum.txt 0:43:md9sum.txt 84:36:md9sum.txt\n")
+ files = arvados.CollectionReader(
+ m2, self.api_client).all_streams()[0].files()
+
+ self.assertEqual(files['md5sum.txt'].as_manifest(),
+ ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n")
+ self.assertEqual(files['md6sum.txt'].as_manifest(),
+ ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n")
+ self.assertEqual(files['md7sum.txt'].as_manifest(),
+ ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n")
+ self.assertEqual(files['md9sum.txt'].as_manifest(),
+ ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n")
+
+ def test_write_directory_tree(self):
+ cwriter = arvados.CollectionWriter(self.api_client)
+ cwriter.write_directory_tree(self.build_directory_tree(
+ ['basefile', 'subdir/subfile']))
+ self.assertEqual(cwriter.manifest_text(),
+ """. c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
+./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
+
+ def test_write_named_directory_tree(self):
+ cwriter = arvados.CollectionWriter(self.api_client)
+ cwriter.write_directory_tree(self.build_directory_tree(
+ ['basefile', 'subdir/subfile']), 'root')
+ self.assertEqual(
+ cwriter.manifest_text(),
+ """./root c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile
+./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""")
+
+ def test_write_directory_tree_in_one_stream(self):
+ cwriter = arvados.CollectionWriter(self.api_client)
+ cwriter.write_directory_tree(self.build_directory_tree(
+ ['basefile', 'subdir/subfile']), max_manifest_depth=0)
+ self.assertEqual(cwriter.manifest_text(),
+ """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile 8:14:subdir/subfile\n""")
+
+ def test_write_directory_tree_with_limited_recursion(self):
+ cwriter = arvados.CollectionWriter(self.api_client)
+ cwriter.write_directory_tree(
+ self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
+ max_manifest_depth=1)
+ self.assertEqual(cwriter.manifest_text(),
+ """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1
+./d1 50170217e5b04312024aa5cd42934494+13 0:8:d2/f3 8:5:f2\n""")
+
+ def test_write_directory_tree_with_zero_recursion(self):
+ cwriter = arvados.CollectionWriter(self.api_client)
+ content = 'd1/d2/f3d1/f2f1'
+ blockhash = hashlib.md5(content).hexdigest() + '+' + str(len(content))
+ cwriter.write_directory_tree(
+ self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']),
+ max_manifest_depth=0)
+ self.assertEqual(
+ cwriter.manifest_text(),
+ ". {} 0:8:d1/d2/f3 8:5:d1/f2 13:2:f1\n".format(blockhash))
+
+ def test_write_one_file(self):
+ cwriter = arvados.CollectionWriter(self.api_client)
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name)
+ self.assertEqual(
+ cwriter.manifest_text(),
+ ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:{}\n".format(
+ os.path.basename(testfile.name)))
+
+ def test_write_named_file(self):
+ cwriter = arvados.CollectionWriter(self.api_client)
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name, 'foo')
+ self.assertEqual(cwriter.manifest_text(),
+ ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:foo\n")
+
+ def test_write_multiple_files(self):
+ cwriter = arvados.CollectionWriter(self.api_client)
+ for letter in 'ABC':
+ with self.make_test_file(letter) as testfile:
+ cwriter.write_file(testfile.name, letter)
+ self.assertEqual(
+ cwriter.manifest_text(),
+ ". 902fbdd2b1df0c4f70b4a5d23525e932+3 0:1:A 1:1:B 2:1:C\n")
+
+ def test_basic_resume(self):
+ cwriter = TestResumableWriter()
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name, 'test')
+ resumed = TestResumableWriter.from_state(cwriter.current_state())
+ self.assertEquals(cwriter.manifest_text(), resumed.manifest_text(),
+ "resumed CollectionWriter had different manifest")
+
+ def test_resume_fails_when_missing_dependency(self):
+ cwriter = TestResumableWriter()
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name, 'test')
+ self.assertRaises(arvados.errors.StaleWriterStateError,
+ TestResumableWriter.from_state,
+ cwriter.current_state())
+
+ def test_resume_fails_when_dependency_mtime_changed(self):
+ cwriter = TestResumableWriter()
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name, 'test')
+ os.utime(testfile.name, (0, 0))
+ self.assertRaises(arvados.errors.StaleWriterStateError,
+ TestResumableWriter.from_state,
+ cwriter.current_state())
+
+ def test_resume_fails_when_dependency_is_nonfile(self):
+ cwriter = TestResumableWriter()
+ cwriter.write_file('/dev/null', 'empty')
+ self.assertRaises(arvados.errors.StaleWriterStateError,
+ TestResumableWriter.from_state,
+ cwriter.current_state())
+
+ def test_resume_fails_when_dependency_size_changed(self):
+ cwriter = TestResumableWriter()
+ with self.make_test_file() as testfile:
+ cwriter.write_file(testfile.name, 'test')
+ orig_mtime = os.fstat(testfile.fileno()).st_mtime
+ testfile.write('extra')
+ testfile.flush()
+ os.utime(testfile.name, (orig_mtime, orig_mtime))
+ self.assertRaises(arvados.errors.StaleWriterStateError,
+ TestResumableWriter.from_state,
+ cwriter.current_state())
+
+ def test_resume_fails_with_expired_locator(self):
+ cwriter = TestResumableWriter()
+ state = cwriter.current_state()
+ # Add an expired locator to the state.
+ state['_current_stream_locators'].append(''.join([
+ 'a' * 32, '+1+A', 'b' * 40, '@', '10000000']))
+ self.assertRaises(arvados.errors.StaleWriterStateError,
+ TestResumableWriter.from_state, state)
+
+ def test_arbitrary_objects_not_resumable(self):
+ cwriter = TestResumableWriter()
+ with open('/dev/null') as badfile:
+ self.assertRaises(arvados.errors.AssertionError,
+ cwriter.write_file, badfile)
+
+ def test_arbitrary_writes_not_resumable(self):
+ cwriter = TestResumableWriter()
+ self.assertRaises(arvados.errors.AssertionError,
+ cwriter.write, "badtext")
+
+ def test_read_arbitrary_data_with_collection_reader(self):
+ # arv-get relies on this to do "arv-get {keep-locator} -".
+ self.write_foo_bar_baz()
+ self.assertEqual(
+ 'foobar',
+ arvados.CollectionReader(
+ '3858f62230ac3c915f300c664312c63f+6'
+ ).manifest_text())
+
+
+class CollectionTestMixin(object):
+ PROXY_RESPONSE = {
+ 'items_available': 1,
+ 'items': [{
+ 'uuid': 'zzzzz-bi6l4-mockproxy012345',
+ 'owner_uuid': 'zzzzz-tpzed-mockowner012345',
+ 'service_host': tutil.TEST_HOST,
+ 'service_port': 65535,
+ 'service_ssl_flag': True,
+ 'service_type': 'proxy',
+ }]}
+ API_COLLECTIONS = run_test_server.fixture('collections')
+ DEFAULT_COLLECTION = API_COLLECTIONS['foo_file']
+ DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash']
+ DEFAULT_MANIFEST = DEFAULT_COLLECTION['manifest_text']
+ DEFAULT_UUID = DEFAULT_COLLECTION['uuid']
+ ALT_COLLECTION = API_COLLECTIONS['bar_file']
+ ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash']
+ ALT_MANIFEST = ALT_COLLECTION['manifest_text']
+
+ def _mock_api_call(self, mock_method, code, body):
+ mock_method = mock_method().execute
+ if code == 200:
+ mock_method.return_value = body
+ else:
+ mock_method.side_effect = arvados.errors.ApiError(
+ tutil.fake_httplib2_response(code), "{}")
+
+ def mock_keep_services(self, api_mock, code, body):
+ self._mock_api_call(api_mock.keep_services().accessible, code, body)
+
+ def api_client_mock(self, code=200):
+ client = mock.MagicMock(name='api_client')
+ self.mock_keep_services(client, code, self.PROXY_RESPONSE)
+ return client
+
+
+@tutil.skip_sleep
+class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin):
+ def mock_get_collection(self, api_mock, code, body):
+ body = self.API_COLLECTIONS.get(body)
+ self._mock_api_call(api_mock.collections().get, code, body)
+
+ def api_client_mock(self, code=200):
+ client = super(CollectionReaderTestCase, self).api_client_mock(code)
+ self.mock_get_collection(client, code, 'foo_file')
+ return client
+
+ def test_init_no_default_retries(self):
+ client = self.api_client_mock(200)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
+ reader.manifest_text()
+ client.collections().get().execute.assert_called_with(num_retries=0)
+
+ def test_uuid_init_success(self):
+ client = self.api_client_mock(200)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
+ num_retries=3)
+ self.assertEqual(self.DEFAULT_COLLECTION['manifest_text'],
+ reader.manifest_text())
+ client.collections().get().execute.assert_called_with(num_retries=3)
+
+ def test_uuid_init_failure_raises_api_error(self):
+ client = self.api_client_mock(500)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
+ with self.assertRaises(arvados.errors.ApiError):
+ reader.manifest_text()
+
+ def test_locator_init(self):
+ client = self.api_client_mock(200)
+ # Ensure Keep will not return anything if asked.
+ with tutil.mock_get_responses(None, 404):
+ reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
+ api_client=client)
+ self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
+
+ def test_locator_init_fallback_to_keep(self):
+ # crunch-job needs this to read manifests that have only ever
+ # been written to Keep.
+ client = self.api_client_mock(200)
+ self.mock_get_collection(client, 404, None)
+ with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
+ reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
+ api_client=client)
+ self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text())
+
+ def test_uuid_init_no_fallback_to_keep(self):
+ # Do not look up a collection UUID in Keep.
+ client = self.api_client_mock(404)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID,
+ api_client=client)
+ with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
+ with self.assertRaises(arvados.errors.ApiError):
+ reader.manifest_text()
+
+ def test_try_keep_first_if_permission_hint(self):
+ # To verify that CollectionReader tries Keep first here, we
+ # mock API server to return the wrong data.
+ client = self.api_client_mock(200)
+ with tutil.mock_get_responses(self.ALT_MANIFEST, 200):
+ self.assertEqual(
+ self.ALT_MANIFEST,
+ arvados.CollectionReader(
+ self.ALT_DATA_HASH + '+Affffffffffffffffffffffffffffffffffffffff@fedcba98',
+ api_client=client).manifest_text())
+
+ def test_init_num_retries_propagated(self):
+ # More of an integration test...
+ client = self.api_client_mock(200)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client,
+ num_retries=3)
+ with tutil.mock_get_responses('foo', 500, 500, 200):
+ self.assertEqual('foo',
+ ''.join(f.read(9) for f in reader.all_files()))
+
+ def test_read_nonnormalized_manifest_with_collection_reader(self):
+ # client should be able to use CollectionReader on a manifest without normalizing it
+ client = self.api_client_mock(500)
+ nonnormal = ". acbd18db4cc2f85cedef654fccc4a4d8+3+Aabadbadbee@abeebdee 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n"
+ reader = arvados.CollectionReader(
+ nonnormal,
+ api_client=client, num_retries=0)
+ # Ensure stripped_manifest() doesn't mangle our manifest in
+ # any way other than stripping hints.
+ self.assertEqual(
+ re.sub('\+[^\d\s\+]+', '', nonnormal),
+ reader.stripped_manifest())
+ # Ensure stripped_manifest() didn't mutate our reader.
+ self.assertEqual(nonnormal, reader.manifest_text())
+ # Ensure the files appear in the order given in the manifest.
+ self.assertEqual(
+ [[6, '.', 'foo.txt'],
+ [0, '.', 'bar.txt']],
+ [[f.size(), f.stream_name(), f.name()]
+ for f in reader.all_streams()[0].all_files()])
+
+ def test_read_empty_collection(self):
+ client = self.api_client_mock(200)
+ self.mock_get_collection(client, 200, 'empty')
+ reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0',
+ api_client=client)
+ self.assertEqual('', reader.manifest_text())
+
+ def test_api_response(self):
+ client = self.api_client_mock()
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
+ self.assertEqual(self.DEFAULT_COLLECTION, reader.api_response())
+
+ def test_api_response_with_collection_from_keep(self):
+ client = self.api_client_mock()
+ self.mock_get_collection(client, 404, 'foo')
+ with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200):
+ reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH,
+ api_client=client)
+ api_response = reader.api_response()
+ self.assertIsNone(api_response)
+
+ def check_open_file(self, coll_file, stream_name, file_name, file_size):
+ self.assertFalse(coll_file.closed, "returned file is not open")
+ self.assertEqual(stream_name, coll_file.stream_name())
+ self.assertEqual(file_name, coll_file.name())
+ self.assertEqual(file_size, coll_file.size())
+
+ def test_open_collection_file_one_argument(self):
+ client = self.api_client_mock(200)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
+ cfile = reader.open('./foo')
+ self.check_open_file(cfile, '.', 'foo', 3)
+
+ def test_open_collection_file_two_arguments(self):
+ client = self.api_client_mock(200)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
+ cfile = reader.open('.', 'foo')
+ self.check_open_file(cfile, '.', 'foo', 3)
+
+ def test_open_deep_file(self):
+ coll_name = 'collection_with_files_in_subdir'
+ client = self.api_client_mock(200)
+ self.mock_get_collection(client, 200, coll_name)
+ reader = arvados.CollectionReader(
+ self.API_COLLECTIONS[coll_name]['uuid'], api_client=client)
+ cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt')
+ self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt',
+ 32)
+
+ def test_open_nonexistent_stream(self):
+ client = self.api_client_mock(200)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
+ self.assertRaises(ValueError, reader.open, './nonexistent', 'foo')
+
+ def test_open_nonexistent_file(self):
+ client = self.api_client_mock(200)
+ reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client)
+ self.assertRaises(ValueError, reader.open, '.', 'nonexistent')
+
+
+@tutil.skip_sleep
+class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin):
+ def mock_keep(self, body, *codes, **headers):
+ headers.setdefault('x-keep-replicas-stored', 2)
+ return tutil.mock_put_responses(body, *codes, **headers)
+
+ def foo_writer(self, **kwargs):
+ api_client = self.api_client_mock()
+ writer = arvados.CollectionWriter(api_client, **kwargs)
+ writer.start_new_file('foo')
+ writer.write('foo')
+ return writer
+
+ def test_write_whole_collection(self):
+ writer = self.foo_writer()
+ with self.mock_keep(self.DEFAULT_DATA_HASH, 200, 200):
+ self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
+
+ def test_write_no_default(self):
+ writer = self.foo_writer()
+ with self.mock_keep(None, 500):
+ with self.assertRaises(arvados.errors.KeepWriteError):
+ writer.finish()
+
+ def test_write_whole_collection_through_retries(self):
+ writer = self.foo_writer(num_retries=2)
+ with self.mock_keep(self.DEFAULT_DATA_HASH,
+ 500, 500, 200, 500, 500, 200):
+ self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish())
+
+ def test_flush_data_retries(self):
+ writer = self.foo_writer(num_retries=2)
+ foo_hash = self.DEFAULT_MANIFEST.split()[1]
+ with self.mock_keep(foo_hash, 500, 200):
+ writer.flush_data()
+ self.assertEqual(self.DEFAULT_MANIFEST, writer.manifest_text())
+
+ def test_one_open(self):
+ client = self.api_client_mock()
+ writer = arvados.CollectionWriter(client)
+ with writer.open('out') as out_file:
+ self.assertEqual('.', writer.current_stream_name())
+ self.assertEqual('out', writer.current_file_name())
+ out_file.write('test data')
+ data_loc = hashlib.md5('test data').hexdigest() + '+9'
+ self.assertTrue(out_file.closed, "writer file not closed after context")
+ self.assertRaises(ValueError, out_file.write, 'extra text')
+ with self.mock_keep(data_loc, 200) as keep_mock:
+ self.assertEqual(". {} 0:9:out\n".format(data_loc),
+ writer.manifest_text())
+
+ def test_open_writelines(self):
+ client = self.api_client_mock()
+ writer = arvados.CollectionWriter(client)
+ with writer.open('six') as out_file:
+ out_file.writelines(['12', '34', '56'])
+ data_loc = hashlib.md5('123456').hexdigest() + '+6'
+ with self.mock_keep(data_loc, 200) as keep_mock:
+ self.assertEqual(". {} 0:6:six\n".format(data_loc),
+ writer.manifest_text())
+
+ def test_open_flush(self):
+ client = self.api_client_mock()
+ writer = arvados.CollectionWriter(client)
+ with writer.open('flush_test') as out_file:
+ out_file.write('flush1')
+ data_loc1 = hashlib.md5('flush1').hexdigest() + '+6'
+ with self.mock_keep(data_loc1, 200) as keep_mock:
+ out_file.flush()
+ out_file.write('flush2')
+ data_loc2 = hashlib.md5('flush2').hexdigest() + '+6'
+ with self.mock_keep(data_loc2, 200) as keep_mock:
+ self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1,
+ data_loc2),
+ writer.manifest_text())
+
+ def test_two_opens_same_stream(self):
+ client = self.api_client_mock()
+ writer = arvados.CollectionWriter(client)
+ with writer.open('.', '1') as out_file:
+ out_file.write('1st')
+ with writer.open('.', '2') as out_file:
+ out_file.write('2nd')
+ data_loc = hashlib.md5('1st2nd').hexdigest() + '+6'
+ with self.mock_keep(data_loc, 200) as keep_mock:
+ self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc),
+ writer.manifest_text())
+
+ def test_two_opens_two_streams(self):
+ client = self.api_client_mock()
+ writer = arvados.CollectionWriter(client)
+ with writer.open('file') as out_file:
+ out_file.write('file')
+ data_loc1 = hashlib.md5('file').hexdigest() + '+4'
+ with self.mock_keep(data_loc1, 200) as keep_mock:
+ with writer.open('./dir', 'indir') as out_file:
+ out_file.write('indir')
+ data_loc2 = hashlib.md5('indir').hexdigest() + '+5'
+ with self.mock_keep(data_loc2, 200) as keep_mock:
+ expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format(
+ data_loc1, data_loc2)
+ self.assertEqual(expected, writer.manifest_text())
+
+ def test_dup_open_fails(self):
+ client = self.api_client_mock()
+ writer = arvados.CollectionWriter(client)
+ file1 = writer.open('one')
+ self.assertRaises(arvados.errors.AssertionError, writer.open, 'two')
+
+
+if __name__ == '__main__':
+ unittest.main()
--- /dev/null
+import hashlib
+import mock
+import os
+import re
+import socket
+import unittest
+import urlparse
+
+import arvados
+import arvados.retry
+import arvados_testutil as tutil
+import run_test_server
+
+class KeepTestCase(run_test_server.TestCaseWithServers):
+ MAIN_SERVER = {}
+ KEEP_SERVER = {}
+
+ @classmethod
+ def setUpClass(cls):
+ super(KeepTestCase, cls).setUpClass()
+ run_test_server.authorize_with("admin")
+ cls.api_client = arvados.api('v1')
+ cls.keep_client = arvados.KeepClient(api_client=cls.api_client,
+ proxy='', local_store='')
+
+ def test_KeepBasicRWTest(self):
+ foo_locator = self.keep_client.put('foo')
+ self.assertRegexpMatches(
+ foo_locator,
+ '^acbd18db4cc2f85cedef654fccc4a4d8\+3',
+ 'wrong md5 hash from Keep.put("foo"): ' + foo_locator)
+ self.assertEqual(self.keep_client.get(foo_locator),
+ 'foo',
+ 'wrong content from Keep.get(md5("foo"))')
+
+ def test_KeepBinaryRWTest(self):
+ blob_str = '\xff\xfe\xf7\x00\x01\x02'
+ blob_locator = self.keep_client.put(blob_str)
+ self.assertRegexpMatches(
+ blob_locator,
+ '^7fc7c53b45e53926ba52821140fef396\+6',
+ ('wrong locator from Keep.put(<binarydata>):' + blob_locator))
+ self.assertEqual(self.keep_client.get(blob_locator),
+ blob_str,
+ 'wrong content from Keep.get(md5(<binarydata>))')
+
+ def test_KeepLongBinaryRWTest(self):
+ blob_str = '\xff\xfe\xfd\xfc\x00\x01\x02\x03'
+ for i in range(0,23):
+ blob_str = blob_str + blob_str
+ blob_locator = self.keep_client.put(blob_str)
+ self.assertRegexpMatches(
+ blob_locator,
+ '^84d90fc0d8175dd5dcfab04b999bc956\+67108864',
+ ('wrong locator from Keep.put(<binarydata>): ' + blob_locator))
+ self.assertEqual(self.keep_client.get(blob_locator),
+ blob_str,
+ 'wrong content from Keep.get(md5(<binarydata>))')
+
+ def test_KeepSingleCopyRWTest(self):
+ blob_str = '\xff\xfe\xfd\xfc\x00\x01\x02\x03'
+ blob_locator = self.keep_client.put(blob_str, copies=1)
+ self.assertRegexpMatches(
+ blob_locator,
+ '^c902006bc98a3eb4a3663b65ab4a6fab\+8',
+ ('wrong locator from Keep.put(<binarydata>): ' + blob_locator))
+ self.assertEqual(self.keep_client.get(blob_locator),
+ blob_str,
+ 'wrong content from Keep.get(md5(<binarydata>))')
+
+ def test_KeepEmptyCollectionTest(self):
+ blob_locator = self.keep_client.put('', copies=1)
+ self.assertRegexpMatches(
+ blob_locator,
+ '^d41d8cd98f00b204e9800998ecf8427e\+0',
+ ('wrong locator from Keep.put(""): ' + blob_locator))
+
+
+class KeepPermissionTestCase(run_test_server.TestCaseWithServers):
+ MAIN_SERVER = {}
+ KEEP_SERVER = {'blob_signing_key': 'abcdefghijk0123456789',
+ 'enforce_permissions': True}
+
+ def test_KeepBasicRWTest(self):
+ run_test_server.authorize_with('active')
+ keep_client = arvados.KeepClient()
+ foo_locator = keep_client.put('foo')
+ self.assertRegexpMatches(
+ foo_locator,
+ r'^acbd18db4cc2f85cedef654fccc4a4d8\+3\+A[a-f0-9]+@[a-f0-9]+$',
+ 'invalid locator from Keep.put("foo"): ' + foo_locator)
+ self.assertEqual(keep_client.get(foo_locator),
+ 'foo',
+ 'wrong content from Keep.get(md5("foo"))')
+
+ # GET with an unsigned locator => NotFound
+ bar_locator = keep_client.put('bar')
+ unsigned_bar_locator = "37b51d194a7513e45b56f6524f2d51f2+3"
+ self.assertRegexpMatches(
+ bar_locator,
+ r'^37b51d194a7513e45b56f6524f2d51f2\+3\+A[a-f0-9]+@[a-f0-9]+$',
+ 'invalid locator from Keep.put("bar"): ' + bar_locator)
+ self.assertRaises(arvados.errors.NotFoundError,
+ keep_client.get,
+ unsigned_bar_locator)
+
+ # GET from a different user => NotFound
+ run_test_server.authorize_with('spectator')
+ self.assertRaises(arvados.errors.NotFoundError,
+ arvados.Keep.get,
+ bar_locator)
+
+ # Unauthenticated GET for a signed locator => NotFound
+ # Unauthenticated GET for an unsigned locator => NotFound
+ keep_client.api_token = ''
+ self.assertRaises(arvados.errors.NotFoundError,
+ keep_client.get,
+ bar_locator)
+ self.assertRaises(arvados.errors.NotFoundError,
+ keep_client.get,
+ unsigned_bar_locator)
+
+
+# KeepOptionalPermission: starts Keep with --permission-key-file
+# but not --enforce-permissions (i.e. generate signatures on PUT
+# requests, but do not require them for GET requests)
+#
+# All of these requests should succeed when permissions are optional:
+# * authenticated request, signed locator
+# * authenticated request, unsigned locator
+# * unauthenticated request, signed locator
+# * unauthenticated request, unsigned locator
+class KeepOptionalPermission(run_test_server.TestCaseWithServers):
+ MAIN_SERVER = {}
+ KEEP_SERVER = {'blob_signing_key': 'abcdefghijk0123456789',
+ 'enforce_permissions': False}
+
+ @classmethod
+ def setUpClass(cls):
+ super(KeepOptionalPermission, cls).setUpClass()
+ run_test_server.authorize_with("admin")
+ cls.api_client = arvados.api('v1')
+
+ def setUp(self):
+ super(KeepOptionalPermission, self).setUp()
+ self.keep_client = arvados.KeepClient(api_client=self.api_client,
+ proxy='', local_store='')
+
+ def _put_foo_and_check(self):
+ signed_locator = self.keep_client.put('foo')
+ self.assertRegexpMatches(
+ signed_locator,
+ r'^acbd18db4cc2f85cedef654fccc4a4d8\+3\+A[a-f0-9]+@[a-f0-9]+$',
+ 'invalid locator from Keep.put("foo"): ' + signed_locator)
+ return signed_locator
+
+ def test_KeepAuthenticatedSignedTest(self):
+ signed_locator = self._put_foo_and_check()
+ self.assertEqual(self.keep_client.get(signed_locator),
+ 'foo',
+ 'wrong content from Keep.get(md5("foo"))')
+
+ def test_KeepAuthenticatedUnsignedTest(self):
+ signed_locator = self._put_foo_and_check()
+ self.assertEqual(self.keep_client.get("acbd18db4cc2f85cedef654fccc4a4d8"),
+ 'foo',
+ 'wrong content from Keep.get(md5("foo"))')
+
+ def test_KeepUnauthenticatedSignedTest(self):
+ # Check that signed GET requests work even when permissions
+ # enforcement is off.
+ signed_locator = self._put_foo_and_check()
+ self.keep_client.api_token = ''
+ self.assertEqual(self.keep_client.get(signed_locator),
+ 'foo',
+ 'wrong content from Keep.get(md5("foo"))')
+
+ def test_KeepUnauthenticatedUnsignedTest(self):
+ # Since --enforce-permissions is not in effect, GET requests
+ # need not be authenticated.
+ signed_locator = self._put_foo_and_check()
+ self.keep_client.api_token = ''
+ self.assertEqual(self.keep_client.get("acbd18db4cc2f85cedef654fccc4a4d8"),
+ 'foo',
+ 'wrong content from Keep.get(md5("foo"))')
+
+
+class KeepProxyTestCase(run_test_server.TestCaseWithServers):
+ MAIN_SERVER = {}
+ KEEP_SERVER = {}
+ KEEP_PROXY_SERVER = {'auth': 'admin'}
+
+ @classmethod
+ def setUpClass(cls):
+ super(KeepProxyTestCase, cls).setUpClass()
+ cls.api_client = arvados.api('v1')
+
+ def tearDown(self):
+ arvados.config.settings().pop('ARVADOS_EXTERNAL_CLIENT', None)
+ super(KeepProxyTestCase, self).tearDown()
+
+ def test_KeepProxyTest1(self):
+ # Will use ARVADOS_KEEP_PROXY environment variable that is set by
+ # setUpClass().
+ keep_client = arvados.KeepClient(api_client=self.api_client,
+ local_store='')
+ baz_locator = keep_client.put('baz')
+ self.assertRegexpMatches(
+ baz_locator,
+ '^73feffa4b7f6bb68e44cf984c85f6e88\+3',
+ 'wrong md5 hash from Keep.put("baz"): ' + baz_locator)
+ self.assertEqual(keep_client.get(baz_locator),
+ 'baz',
+ 'wrong content from Keep.get(md5("baz"))')
+ self.assertTrue(keep_client.using_proxy)
+
+ def test_KeepProxyTest2(self):
+ # Don't instantiate the proxy directly, but set the X-External-Client
+ # header. The API server should direct us to the proxy.
+ arvados.config.settings()['ARVADOS_EXTERNAL_CLIENT'] = 'true'
+ keep_client = arvados.KeepClient(api_client=self.api_client,
+ proxy='', local_store='')
+ baz_locator = keep_client.put('baz2')
+ self.assertRegexpMatches(
+ baz_locator,
+ '^91f372a266fe2bf2823cb8ec7fda31ce\+4',
+ 'wrong md5 hash from Keep.put("baz2"): ' + baz_locator)
+ self.assertEqual(keep_client.get(baz_locator),
+ 'baz2',
+ 'wrong content from Keep.get(md5("baz2"))')
+ self.assertTrue(keep_client.using_proxy)
+
+
+class KeepClientServiceTestCase(unittest.TestCase):
+ def mock_keep_services(self, *services):
+ api_client = mock.MagicMock(name='api_client')
+ api_client.keep_services().accessible().execute.return_value = {
+ 'items_available': len(services),
+ 'items': [{
+ 'uuid': 'zzzzz-bi6l4-{:015x}'.format(index),
+ 'owner_uuid': 'zzzzz-tpzed-000000000000000',
+ 'service_host': host,
+ 'service_port': port,
+ 'service_ssl_flag': ssl,
+ 'service_type': servtype,
+ } for index, (host, port, ssl, servtype)
+ in enumerate(services)],
+ }
+ return api_client
+
+ def mock_n_keep_disks(self, service_count):
+ return self.mock_keep_services(
+ *[("keep0x{:x}".format(index), 80, False, 'disk')
+ for index in range(service_count)])
+
+ def get_service_roots(self, *services):
+ api_client = self.mock_keep_services(*services)
+ keep_client = arvados.KeepClient(api_client=api_client)
+ services = keep_client.weighted_service_roots('000000')
+ return [urlparse.urlparse(url) for url in sorted(services)]
+
+ def test_ssl_flag_respected_in_roots(self):
+ services = self.get_service_roots(('keep', 10, False, 'disk'),
+ ('keep', 20, True, 'disk'))
+ self.assertEqual(10, services[0].port)
+ self.assertEqual('http', services[0].scheme)
+ self.assertEqual(20, services[1].port)
+ self.assertEqual('https', services[1].scheme)
+
+ def test_correct_ports_with_ipv6_addresses(self):
+ service = self.get_service_roots(('100::1', 10, True, 'proxy'))[0]
+ self.assertEqual('100::1', service.hostname)
+ self.assertEqual(10, service.port)
+
+ # test_get_timeout and test_put_timeout test that
+ # KeepClient.get and KeepClient.put use the appropriate timeouts
+ # when connected directly to a Keep server (i.e. non-proxy timeout)
+
+ def test_get_timeout(self):
+ api_client = self.mock_keep_services(('keep', 10, False, 'disk'))
+ keep_client = arvados.KeepClient(api_client=api_client)
+ force_timeout = [socket.timeout("timed out")]
+ with mock.patch('requests.get', side_effect=force_timeout) as mock_request:
+ with self.assertRaises(arvados.errors.KeepReadError):
+ keep_client.get('ffffffffffffffffffffffffffffffff')
+ self.assertTrue(mock_request.called)
+ self.assertEqual(
+ arvados.KeepClient.DEFAULT_TIMEOUT,
+ mock_request.call_args[1]['timeout'])
+
+ def test_put_timeout(self):
+ api_client = self.mock_keep_services(('keep', 10, False, 'disk'))
+ keep_client = arvados.KeepClient(api_client=api_client)
+ force_timeout = [socket.timeout("timed out")]
+ with mock.patch('requests.put', side_effect=force_timeout) as mock_request:
+ with self.assertRaises(arvados.errors.KeepWriteError):
+ keep_client.put('foo')
+ self.assertTrue(mock_request.called)
+ self.assertEqual(
+ arvados.KeepClient.DEFAULT_TIMEOUT,
+ mock_request.call_args[1]['timeout'])
+
+ def test_proxy_get_timeout(self):
+ # Force a timeout, verifying that the requests.get or
+ # requests.put method was called with the proxy_timeout
+ # setting rather than the default timeout.
+ api_client = self.mock_keep_services(('keep', 10, False, 'proxy'))
+ keep_client = arvados.KeepClient(api_client=api_client)
+ force_timeout = [socket.timeout("timed out")]
+ with mock.patch('requests.get', side_effect=force_timeout) as mock_request:
+ with self.assertRaises(arvados.errors.KeepReadError):
+ keep_client.get('ffffffffffffffffffffffffffffffff')
+ self.assertTrue(mock_request.called)
+ self.assertEqual(
+ arvados.KeepClient.DEFAULT_PROXY_TIMEOUT,
+ mock_request.call_args[1]['timeout'])
+
+ def test_proxy_put_timeout(self):
+ # Force a timeout, verifying that the requests.get or
+ # requests.put method was called with the proxy_timeout
+ # setting rather than the default timeout.
+ api_client = self.mock_keep_services(('keep', 10, False, 'proxy'))
+ keep_client = arvados.KeepClient(api_client=api_client)
+ force_timeout = [socket.timeout("timed out")]
+ with mock.patch('requests.put', side_effect=force_timeout) as mock_request:
+ with self.assertRaises(arvados.errors.KeepWriteError):
+ keep_client.put('foo')
+ self.assertTrue(mock_request.called)
+ self.assertEqual(
+ arvados.KeepClient.DEFAULT_PROXY_TIMEOUT,
+ mock_request.call_args[1]['timeout'])
+
+ def test_probe_order_reference_set(self):
+ # expected_order[i] is the probe order for
+ # hash=md5(sprintf("%064x",i)) where there are 16 services
+ # with uuid sprintf("anything-%015x",j) with j in 0..15. E.g.,
+ # the first probe for the block consisting of 64 "0"
+ # characters is the service whose uuid is
+ # "zzzzz-bi6l4-000000000000003", so expected_order[0][0]=='3'.
+ expected_order = [
+ list('3eab2d5fc9681074'),
+ list('097dba52e648f1c3'),
+ list('c5b4e023f8a7d691'),
+ list('9d81c02e76a3bf54'),
+ ]
+ hashes = [
+ hashlib.md5("{:064x}".format(x)).hexdigest()
+ for x in range(len(expected_order))]
+ api_client = self.mock_n_keep_disks(16)
+ keep_client = arvados.KeepClient(api_client=api_client)
+ for i, hash in enumerate(hashes):
+ roots = keep_client.weighted_service_roots(hash)
+ got_order = [
+ re.search(r'//\[?keep0x([0-9a-f]+)', root).group(1)
+ for root in roots]
+ self.assertEqual(expected_order[i], got_order)
+
+ def test_probe_waste_adding_one_server(self):
+ hashes = [
+ hashlib.md5("{:064x}".format(x)).hexdigest() for x in range(100)]
+ initial_services = 12
+ api_client = self.mock_n_keep_disks(initial_services)
+ keep_client = arvados.KeepClient(api_client=api_client)
+ probes_before = [
+ keep_client.weighted_service_roots(hash) for hash in hashes]
+ for added_services in range(1, 12):
+ api_client = self.mock_n_keep_disks(initial_services+added_services)
+ keep_client = arvados.KeepClient(api_client=api_client)
+ total_penalty = 0
+ for hash_index in range(len(hashes)):
+ probe_after = keep_client.weighted_service_roots(
+ hashes[hash_index])
+ penalty = probe_after.index(probes_before[hash_index][0])
+ self.assertLessEqual(penalty, added_services)
+ total_penalty += penalty
+ # Average penalty per block should not exceed
+ # N(added)/N(orig) by more than 20%, and should get closer
+ # to the ideal as we add data points.
+ expect_penalty = (
+ added_services *
+ len(hashes) / initial_services)
+ max_penalty = (
+ expect_penalty *
+ (120 - added_services)/100)
+ min_penalty = (
+ expect_penalty * 8/10)
+ self.assertTrue(
+ min_penalty <= total_penalty <= max_penalty,
+ "With {}+{} services, {} blocks, penalty {} but expected {}..{}".format(
+ initial_services,
+ added_services,
+ len(hashes),
+ total_penalty,
+ min_penalty,
+ max_penalty))
+
+
+class KeepClientRetryTestMixin(object):
+ # Testing with a local Keep store won't exercise the retry behavior.
+ # Instead, our strategy is:
+ # * Create a client with one proxy specified (pointed at a black
+ # hole), so there's no need to instantiate an API client, and
+ # all HTTP requests come from one place.
+ # * Mock httplib's request method to provide simulated responses.
+ # This lets us test the retry logic extensively without relying on any
+ # supporting servers, and prevents side effects in case something hiccups.
+ # To use this mixin, define DEFAULT_EXPECT, DEFAULT_EXCEPTION, and
+ # run_method().
+ #
+ # Test classes must define TEST_PATCHER to a method that mocks
+ # out appropriate methods in the client.
+
+ PROXY_ADDR = 'http://[%s]:65535/' % (tutil.TEST_HOST,)
+ TEST_DATA = 'testdata'
+ TEST_LOCATOR = 'ef654c40ab4f1747fc699915d4f70902+8'
+
+ def setUp(self):
+ self.client_kwargs = {'proxy': self.PROXY_ADDR, 'local_store': ''}
+
+ def new_client(self, **caller_kwargs):
+ kwargs = self.client_kwargs.copy()
+ kwargs.update(caller_kwargs)
+ return arvados.KeepClient(**kwargs)
+
+ def run_method(self, *args, **kwargs):
+ raise NotImplementedError("test subclasses must define run_method")
+
+ def check_success(self, expected=None, *args, **kwargs):
+ if expected is None:
+ expected = self.DEFAULT_EXPECT
+ self.assertEqual(expected, self.run_method(*args, **kwargs))
+
+ def check_exception(self, error_class=None, *args, **kwargs):
+ if error_class is None:
+ error_class = self.DEFAULT_EXCEPTION
+ self.assertRaises(error_class, self.run_method, *args, **kwargs)
+
+ def test_immediate_success(self):
+ with self.TEST_PATCHER(self.DEFAULT_EXPECT, 200):
+ self.check_success()
+
+ def test_retry_then_success(self):
+ with self.TEST_PATCHER(self.DEFAULT_EXPECT, 500, 200):
+ self.check_success(num_retries=3)
+
+ def test_no_default_retry(self):
+ with self.TEST_PATCHER(self.DEFAULT_EXPECT, 500, 200):
+ self.check_exception()
+
+ def test_no_retry_after_permanent_error(self):
+ with self.TEST_PATCHER(self.DEFAULT_EXPECT, 403, 200):
+ self.check_exception(num_retries=3)
+
+ def test_error_after_retries_exhausted(self):
+ with self.TEST_PATCHER(self.DEFAULT_EXPECT, 500, 500, 200):
+ self.check_exception(num_retries=1)
+
+ def test_num_retries_instance_fallback(self):
+ self.client_kwargs['num_retries'] = 3
+ with self.TEST_PATCHER(self.DEFAULT_EXPECT, 500, 200):
+ self.check_success()
+
+
+@tutil.skip_sleep
+class KeepClientRetryGetTestCase(KeepClientRetryTestMixin, unittest.TestCase):
+ DEFAULT_EXPECT = KeepClientRetryTestMixin.TEST_DATA
+ DEFAULT_EXCEPTION = arvados.errors.KeepReadError
+ HINTED_LOCATOR = KeepClientRetryTestMixin.TEST_LOCATOR + '+K@xyzzy'
+ TEST_PATCHER = staticmethod(tutil.mock_get_responses)
+
+ def run_method(self, locator=KeepClientRetryTestMixin.TEST_LOCATOR,
+ *args, **kwargs):
+ return self.new_client().get(locator, *args, **kwargs)
+
+ def test_specific_exception_when_not_found(self):
+ with tutil.mock_get_responses(self.DEFAULT_EXPECT, 404, 200):
+ self.check_exception(arvados.errors.NotFoundError, num_retries=3)
+
+ def test_general_exception_with_mixed_errors(self):
+ # get should raise a NotFoundError if no server returns the block,
+ # and a high threshold of servers report that it's not found.
+ # This test rigs up 50/50 disagreement between two servers, and
+ # checks that it does not become a NotFoundError.
+ client = self.new_client()
+ with tutil.mock_get_responses(self.DEFAULT_EXPECT, 404, 500):
+ with self.assertRaises(arvados.errors.KeepReadError) as exc_check:
+ client.get(self.HINTED_LOCATOR)
+ self.assertNotIsInstance(
+ exc_check.exception, arvados.errors.NotFoundError,
+ "mixed errors raised NotFoundError")
+
+ def test_hint_server_can_succeed_without_retries(self):
+ with tutil.mock_get_responses(self.DEFAULT_EXPECT, 404, 200, 500):
+ self.check_success(locator=self.HINTED_LOCATOR)
+
+ def test_try_next_server_after_timeout(self):
+ side_effects = [
+ socket.timeout("timed out"),
+ tutil.fake_requests_response(200, self.DEFAULT_EXPECT)]
+ with mock.patch('requests.get',
+ side_effect=iter(side_effects)):
+ self.check_success(locator=self.HINTED_LOCATOR)
+
+ def test_retry_data_with_wrong_checksum(self):
+ side_effects = (tutil.fake_requests_response(200, s)
+ for s in ['baddata', self.TEST_DATA])
+ with mock.patch('requests.get', side_effect=side_effects):
+ self.check_success(locator=self.HINTED_LOCATOR)
+
+
+@tutil.skip_sleep
+class KeepClientRetryPutTestCase(KeepClientRetryTestMixin, unittest.TestCase):
+ DEFAULT_EXPECT = KeepClientRetryTestMixin.TEST_LOCATOR
+ DEFAULT_EXCEPTION = arvados.errors.KeepWriteError
+ TEST_PATCHER = staticmethod(tutil.mock_put_responses)
+
+ def run_method(self, data=KeepClientRetryTestMixin.TEST_DATA,
+ copies=1, *args, **kwargs):
+ return self.new_client().put(data, copies, *args, **kwargs)
+
+ def test_do_not_send_multiple_copies_to_same_server(self):
+ with tutil.mock_put_responses(self.DEFAULT_EXPECT, 200):
+ self.check_exception(copies=2, num_retries=3)
--- /dev/null
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import datetime
+import itertools
+import random
+import unittest
+
+from arvados.keep import KeepLocator
+
+class ArvadosKeepLocatorTest(unittest.TestCase):
+ DEFAULT_TEST_COUNT = 10
+
+ def numstrs(fmtstr, base, exponent):
+ def genstrs(self, count=None):
+ return (fmtstr.format(random.randint(0, base ** exponent))
+ for c in xrange(count or self.DEFAULT_TEST_COUNT))
+ return genstrs
+
+ checksums = numstrs('{:032x}', 16, 32)
+ sizes = numstrs('{:d}', 2, 26)
+ signatures = numstrs('{:040x}', 16, 40)
+ timestamps = numstrs('{:08x}', 16, 8)
+
+ def base_locators(self, count=DEFAULT_TEST_COUNT):
+ return ('+'.join(pair) for pair in
+ itertools.izip(self.checksums(count), self.sizes(count)))
+
+ def perm_hints(self, count=DEFAULT_TEST_COUNT):
+ for sig, ts in itertools.izip(self.signatures(count),
+ self.timestamps(count)):
+ yield 'A{}@{}'.format(sig, ts)
+
+ def test_good_locators_returned(self):
+ for hint_gens in [(), (self.sizes(),),
+ (self.sizes(), self.perm_hints())]:
+ for loc_data in itertools.izip(self.checksums(), *hint_gens):
+ locator = '+'.join(loc_data)
+ self.assertEquals(locator, str(KeepLocator(locator)))
+
+ def test_nonchecksum_rejected(self):
+ for badstr in ['', 'badbadbad', '8f9e68d957b504a29ba76c526c3145dj',
+ '+8f9e68d957b504a29ba76c526c3145d9',
+ '3+8f9e68d957b504a29ba76c526c3145d9']:
+ self.assertRaises(ValueError, KeepLocator, badstr)
+
+ def test_unknown_hints_accepted(self):
+ base = next(self.base_locators(1))
+ for weirdhint in ['Zfoo', 'Ybar234', 'Xa@b_c-372', 'W99']:
+ locator = '+'.join([base, weirdhint])
+ self.assertEquals(locator, str(KeepLocator(locator)))
+
+ def test_bad_hints_rejected(self):
+ base = next(self.base_locators(1))
+ for badhint in ['', 'A', 'lowercase', '+32']:
+ self.assertRaises(ValueError, KeepLocator,
+ '+'.join([base, badhint]))
+
+ def test_multiple_locator_hints_accepted(self):
+ base = next(self.base_locators(1))
+ for loc_hints in itertools.permutations(['Kab1cd', 'Kef2gh', 'Kij3kl']):
+ locator = '+'.join((base,) + loc_hints)
+ self.assertEquals(locator, str(KeepLocator(locator)))
+
+ def test_expiry_passed(self):
+ base = next(self.base_locators(1))
+ signature = next(self.signatures(1))
+ dt1980 = datetime.datetime(1980, 1, 1)
+ dt2000 = datetime.datetime(2000, 2, 2)
+ dt2080 = datetime.datetime(2080, 3, 3)
+ locator = KeepLocator(base)
+ self.assertFalse(locator.permission_expired())
+ self.assertFalse(locator.permission_expired(dt1980))
+ self.assertFalse(locator.permission_expired(dt2080))
+ # Timestamped to 1987-01-05 18:48:32.
+ locator = KeepLocator('{}+A{}@20000000'.format(base, signature))
+ self.assertTrue(locator.permission_expired())
+ self.assertTrue(locator.permission_expired(dt2000))
+ self.assertFalse(locator.permission_expired(dt1980))
+
+
+if __name__ == '__main__':
+ unittest.main()
--- /dev/null
+# usage example:
+#
+# ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover
+
+import unittest
+import arvados
+import apiclient
+import run_test_server
+
+class PipelineTemplateTest(unittest.TestCase):
+ def setUp(self):
+ run_test_server.run()
+
+ def runTest(self):
+ run_test_server.authorize_with("admin")
+ pt_uuid = arvados.api('v1', cache=False).pipeline_templates().create(
+ body={'name':__file__}
+ ).execute()['uuid']
+ self.assertEqual(len(pt_uuid), 27,
+ 'Unexpected format of pipeline template UUID ("%s")'
+ % pt_uuid)
+ components = {
+ 'x': 'x',
+ '-x-': [1,2,{'foo':'bar'}],
+ 'Boggis': {'Bunce': '[\'Bean\']'},
+ 'SpassBox': True,
+ 'spass_box': False,
+ 'spass-box': [True, 'Maybe', False]
+ }
+ update_response = arvados.api('v1', cache=False).pipeline_templates().update(
+ uuid=pt_uuid,
+ body={'components':components}
+ ).execute()
+ self.assertEqual('uuid' in update_response, True,
+ 'update() response did not include a uuid')
+ self.assertEqual(update_response['uuid'], pt_uuid,
+ 'update() response has a different uuid (%s, not %s)'
+ % (update_response['uuid'], pt_uuid))
+ self.assertEqual(update_response['name'], __file__,
+ 'update() response has a different name (%s, not %s)'
+ % (update_response['name'], __file__))
+ get_response = arvados.api('v1', cache=False).pipeline_templates().get(
+ uuid=pt_uuid
+ ).execute()
+ self.assertEqual(get_response['components'], components,
+ 'components got munged by server (%s -> %s)'
+ % (components, update_response['components']))
+ delete_response = arvados.api('v1', cache=False).pipeline_templates().delete(
+ uuid=pt_uuid
+ ).execute()
+ self.assertEqual(delete_response['uuid'], pt_uuid,
+ 'delete() response has wrong uuid (%s, not %s)'
+ % (delete_response['uuid'], pt_uuid))
+ with self.assertRaises(apiclient.errors.HttpError):
+ geterror_response = arvados.api('v1', cache=False).pipeline_templates().get(
+ uuid=pt_uuid
+ ).execute()
+
+ def tearDown(self):
+ run_test_server.stop()
--- /dev/null
+#!/usr/bin/env python
+
+import itertools
+import unittest
+
+import arvados.errors as arv_error
+import arvados.retry as arv_retry
+import mock
+
+from arvados_testutil import fake_requests_response
+
+class RetryLoopTestMixin(object):
+ @staticmethod
+ def loop_success(result):
+ # During the tests, we use integers that look like HTTP status
+ # codes as loop results. Then we define simplified HTTP
+ # heuristics here to decide whether the result is success (True),
+ # permanent failure (False), or temporary failure (None).
+ if result < 400:
+ return True
+ elif result < 500:
+ return False
+ else:
+ return None
+
+ def run_loop(self, num_retries, *results, **kwargs):
+ responses = itertools.chain(results, itertools.repeat(None))
+ retrier = arv_retry.RetryLoop(num_retries, self.loop_success,
+ **kwargs)
+ for tries_left, response in itertools.izip(retrier, responses):
+ retrier.save_result(response)
+ return retrier
+
+ def check_result(self, retrier, expect_success, last_code):
+ self.assertIs(retrier.success(), expect_success,
+ "loop success flag is incorrect")
+ self.assertEqual(last_code, retrier.last_result())
+
+
+class RetryLoopTestCase(unittest.TestCase, RetryLoopTestMixin):
+ def test_zero_retries_and_success(self):
+ retrier = self.run_loop(0, 200)
+ self.check_result(retrier, True, 200)
+
+ def test_zero_retries_and_tempfail(self):
+ retrier = self.run_loop(0, 500, 501)
+ self.check_result(retrier, None, 500)
+
+ def test_zero_retries_and_permfail(self):
+ retrier = self.run_loop(0, 400, 201)
+ self.check_result(retrier, False, 400)
+
+ def test_one_retry_with_immediate_success(self):
+ retrier = self.run_loop(1, 200, 201)
+ self.check_result(retrier, True, 200)
+
+ def test_one_retry_with_delayed_success(self):
+ retrier = self.run_loop(1, 500, 201)
+ self.check_result(retrier, True, 201)
+
+ def test_one_retry_with_no_success(self):
+ retrier = self.run_loop(1, 500, 501, 502)
+ self.check_result(retrier, None, 501)
+
+ def test_one_retry_but_permfail(self):
+ retrier = self.run_loop(1, 400, 201)
+ self.check_result(retrier, False, 400)
+
+ def test_two_retries_with_immediate_success(self):
+ retrier = self.run_loop(2, 200, 201, 202)
+ self.check_result(retrier, True, 200)
+
+ def test_two_retries_with_success_after_one(self):
+ retrier = self.run_loop(2, 500, 201, 502)
+ self.check_result(retrier, True, 201)
+
+ def test_two_retries_with_success_after_two(self):
+ retrier = self.run_loop(2, 500, 501, 202, 503)
+ self.check_result(retrier, True, 202)
+
+ def test_two_retries_with_no_success(self):
+ retrier = self.run_loop(2, 500, 501, 502, 503)
+ self.check_result(retrier, None, 502)
+
+ def test_two_retries_with_permfail(self):
+ retrier = self.run_loop(2, 500, 401, 202)
+ self.check_result(retrier, False, 401)
+
+ def test_save_result_before_start_is_error(self):
+ retrier = arv_retry.RetryLoop(0)
+ self.assertRaises(arv_error.AssertionError, retrier.save_result, 1)
+
+ def test_save_result_after_end_is_error(self):
+ retrier = arv_retry.RetryLoop(0)
+ for count in retrier:
+ pass
+ self.assertRaises(arv_error.AssertionError, retrier.save_result, 1)
+
+
+@mock.patch('time.time', side_effect=itertools.count())
+@mock.patch('time.sleep')
+class RetryLoopBackoffTestCase(unittest.TestCase, RetryLoopTestMixin):
+ def run_loop(self, num_retries, *results, **kwargs):
+ kwargs.setdefault('backoff_start', 8)
+ return super(RetryLoopBackoffTestCase, self).run_loop(
+ num_retries, *results, **kwargs)
+
+ def check_backoff(self, sleep_mock, sleep_count, multiplier=1):
+ # Figure out how much time we actually spent sleeping.
+ sleep_times = [arglist[0][0] for arglist in sleep_mock.call_args_list
+ if arglist[0][0] > 0]
+ self.assertEqual(sleep_count, len(sleep_times),
+ "loop did not back off correctly")
+ last_wait = 0
+ for this_wait in sleep_times:
+ self.assertGreater(this_wait, last_wait * multiplier,
+ "loop did not grow backoff times correctly")
+ last_wait = this_wait
+
+ def test_no_backoff_with_no_retries(self, sleep_mock, time_mock):
+ self.run_loop(0, 500, 201)
+ self.check_backoff(sleep_mock, 0)
+
+ def test_no_backoff_after_success(self, sleep_mock, time_mock):
+ self.run_loop(1, 200, 501)
+ self.check_backoff(sleep_mock, 0)
+
+ def test_no_backoff_after_permfail(self, sleep_mock, time_mock):
+ self.run_loop(1, 400, 201)
+ self.check_backoff(sleep_mock, 0)
+
+ def test_backoff_before_success(self, sleep_mock, time_mock):
+ self.run_loop(5, 500, 501, 502, 203, 504)
+ self.check_backoff(sleep_mock, 3)
+
+ def test_backoff_before_permfail(self, sleep_mock, time_mock):
+ self.run_loop(5, 500, 501, 502, 403, 504)
+ self.check_backoff(sleep_mock, 3)
+
+ def test_backoff_all_tempfail(self, sleep_mock, time_mock):
+ self.run_loop(3, 500, 501, 502, 503, 504)
+ self.check_backoff(sleep_mock, 3)
+
+ def test_backoff_multiplier(self, sleep_mock, time_mock):
+ self.run_loop(5, 500, 501, 502, 503, 504, 505,
+ backoff_start=5, backoff_growth=10)
+ self.check_backoff(sleep_mock, 5, 9)
+
+
+class CheckHTTPResponseSuccessTestCase(unittest.TestCase):
+ def results_map(self, *codes):
+ for code in codes:
+ response = fake_requests_response(code, None)
+ yield code, arv_retry.check_http_response_success(response)
+
+ def check(assert_name):
+ def check_method(self, expected, *codes):
+ assert_func = getattr(self, assert_name)
+ for code, actual in self.results_map(*codes):
+ assert_func(expected, actual,
+ "{} status flagged {}".format(code, actual))
+ if assert_name != 'assertIs':
+ self.assertTrue(
+ actual is True or actual is False or actual is None,
+ "{} status returned {}".format(code, actual))
+ return check_method
+
+ check_is = check('assertIs')
+ check_is_not = check('assertIsNot')
+
+ def test_obvious_successes(self):
+ self.check_is(True, *range(200, 207))
+
+ def test_obvious_stops(self):
+ self.check_is(False, 424, 426, 428, 431,
+ *range(400, 408) + range(410, 420))
+
+ def test_obvious_retries(self):
+ self.check_is(None, 500, 502, 503, 504)
+
+ def test_4xx_retries(self):
+ self.check_is(None, 408, 409, 422, 423)
+
+ def test_5xx_failures(self):
+ self.check_is(False, 501, *range(505, 512))
+
+ def test_1xx_not_retried(self):
+ self.check_is_not(None, 100, 101)
+
+ def test_redirects_not_retried(self):
+ self.check_is_not(None, *range(300, 309))
+
+ def test_wacky_code_retries(self):
+ self.check_is(None, 0, 99, 600, -200)
+
+
+class RetryMethodTestCase(unittest.TestCase):
+ class Tester(object):
+ def __init__(self):
+ self.num_retries = 1
+
+ @arv_retry.retry_method
+ def check(self, a, num_retries=None, z=0):
+ return (a, num_retries, z)
+
+
+ def test_positional_arg_passed(self):
+ self.assertEqual((3, 2, 0), self.Tester().check(3, 2))
+
+ def test_keyword_arg_passed(self):
+ self.assertEqual((4, 3, 0), self.Tester().check(num_retries=3, a=4))
+
+ def test_not_specified(self):
+ self.assertEqual((0, 1, 0), self.Tester().check(0))
+
+ def test_not_specified_with_other_kwargs(self):
+ self.assertEqual((1, 1, 1), self.Tester().check(1, z=1))
+
+ def test_bad_call(self):
+ with self.assertRaises(TypeError):
+ self.Tester().check(num_retries=2)
+
+
+if __name__ == '__main__':
+ unittest.main()
--- /dev/null
+import mock
+import os
+import unittest
+
+import arvados
+import arvados.collection
+
+class TestSDK(unittest.TestCase):
+
+ @mock.patch('arvados.api')
+ @mock.patch('arvados.current_task')
+ @mock.patch('arvados.current_job')
+ def test_one_task_per_input_file_normalize(self, mock_job, mock_task, mock_api):
+ # This manifest will be reduced from three lines to one when it is
+ # normalized.
+ nonnormalized_manifest = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
+. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
+"""
+ dummy_hash = 'ffffffffffffffffffffffffffffffff+0'
+
+ mock_job.return_value = {
+ 'uuid': 'none',
+ 'script_parameters': {
+ 'input': dummy_hash
+ }
+ }
+ mock_task.return_value = {
+ 'uuid': 'none',
+ 'sequence': 0,
+ }
+ # mock the API client to return a collection with a nonnormalized manifest.
+ mock_api('v1').collections().get().execute.return_value = {
+ 'uuid': 'zzzzz-4zz18-mockcollection0',
+ 'portable_data_hash': dummy_hash,
+ 'manifest_text': nonnormalized_manifest,
+ }
+
+ # Because one_task_per_input_file normalizes this collection,
+ # it should now create only one job task and not three.
+ arvados.job_setup.one_task_per_input_file(and_end_task=False)
+ mock_api('v1').job_tasks().create().execute.assert_called_once_with()
+
--- /dev/null
+#!/usr/bin/env python
+
+import bz2
+import gzip
+import io
+import mock
+import os
+import unittest
+
+import arvados
+from arvados import StreamReader, StreamFileReader
+
+import arvados_testutil as tutil
+import run_test_server
+
+class StreamFileReaderTestCase(unittest.TestCase):
+ def make_count_reader(self):
+ stream = tutil.MockStreamReader('.', '01234', '34567', '67890')
+ return StreamFileReader(stream, [[1, 3, 0], [6, 3, 3], [11, 3, 6]],
+ 'count.txt')
+
+ def test_read_returns_first_block(self):
+ # read() calls will be aligned on block boundaries - see #3663.
+ sfile = self.make_count_reader()
+ self.assertEqual('123', sfile.read(10))
+
+ def test_small_read(self):
+ sfile = self.make_count_reader()
+ self.assertEqual('12', sfile.read(2))
+
+ def test_successive_reads(self):
+ sfile = self.make_count_reader()
+ for expect in ['123', '456', '789', '']:
+ self.assertEqual(expect, sfile.read(10))
+
+ def test_readfrom_spans_blocks(self):
+ sfile = self.make_count_reader()
+ self.assertEqual('6789', sfile.readfrom(5, 12))
+
+ def test_small_readfrom_spanning_blocks(self):
+ sfile = self.make_count_reader()
+ self.assertEqual('2345', sfile.readfrom(1, 4))
+
+ def test_readall(self):
+ sfile = self.make_count_reader()
+ self.assertEqual('123456789', ''.join(sfile.readall()))
+
+ def test_one_arg_seek(self):
+ self.test_relative_seek([])
+
+ def test_absolute_seek(self, args=[os.SEEK_SET]):
+ sfile = self.make_count_reader()
+ sfile.seek(6, *args)
+ self.assertEqual('78', sfile.read(2))
+ sfile.seek(4, *args)
+ self.assertEqual('56', sfile.read(2))
+
+ def test_relative_seek(self, args=[os.SEEK_CUR]):
+ sfile = self.make_count_reader()
+ self.assertEqual('12', sfile.read(2))
+ sfile.seek(2, *args)
+ self.assertEqual('56', sfile.read(2))
+
+ def test_end_seek(self):
+ sfile = self.make_count_reader()
+ sfile.seek(-6, os.SEEK_END)
+ self.assertEqual('45', sfile.read(2))
+
+ def test_seek_min_zero(self):
+ sfile = self.make_count_reader()
+ sfile.seek(-2, os.SEEK_SET)
+ self.assertEqual(0, sfile.tell())
+
+ def test_seek_max_size(self):
+ sfile = self.make_count_reader()
+ sfile.seek(2, os.SEEK_END)
+ self.assertEqual(9, sfile.tell())
+
+ def test_size(self):
+ self.assertEqual(9, self.make_count_reader().size())
+
+ def test_tell_after_block_read(self):
+ sfile = self.make_count_reader()
+ sfile.read(5)
+ self.assertEqual(3, sfile.tell())
+
+ def test_tell_after_small_read(self):
+ sfile = self.make_count_reader()
+ sfile.read(1)
+ self.assertEqual(1, sfile.tell())
+
+ def test_no_read_after_close(self):
+ sfile = self.make_count_reader()
+ sfile.close()
+ self.assertRaises(ValueError, sfile.read, 2)
+
+ def test_context(self):
+ with self.make_count_reader() as sfile:
+ self.assertFalse(sfile.closed, "reader is closed inside context")
+ self.assertEqual('12', sfile.read(2))
+ self.assertTrue(sfile.closed, "reader is open after context")
+
+ def make_newlines_reader(self):
+ stream = tutil.MockStreamReader('.', 'one\ntwo\n\nth', 'ree\nfour\n\n')
+ return StreamFileReader(stream, [[0, 11, 0], [11, 10, 11]], 'count.txt')
+
+ def check_lines(self, actual):
+ self.assertEqual(['one\n', 'two\n', '\n', 'three\n', 'four\n', '\n'],
+ actual)
+
+ def test_readline(self):
+ reader = self.make_newlines_reader()
+ actual = []
+ while True:
+ data = reader.readline()
+ if not data:
+ break
+ actual.append(data)
+ self.check_lines(actual)
+
+ def test_readlines(self):
+ self.check_lines(self.make_newlines_reader().readlines())
+
+ def test_iteration(self):
+ self.check_lines(list(iter(self.make_newlines_reader())))
+
+ def test_readline_size(self):
+ reader = self.make_newlines_reader()
+ self.assertEqual('on', reader.readline(2))
+ self.assertEqual('e\n', reader.readline(4))
+ self.assertEqual('two\n', reader.readline(6))
+ self.assertEqual('\n', reader.readline(8))
+ self.assertEqual('thre', reader.readline(4))
+
+ def test_readlines_sizehint(self):
+ result = self.make_newlines_reader().readlines(8)
+ self.assertEqual(['one\n', 'two\n'], result[:2])
+ self.assertNotIn('three\n', result)
+
+ def test_name_attribute(self):
+ # Test both .name and .name() (for backward compatibility)
+ stream = tutil.MockStreamReader()
+ sfile = StreamFileReader(stream, [[0, 0, 0]], 'nametest')
+ self.assertEqual('nametest', sfile.name)
+ self.assertEqual('nametest', sfile.name())
+
+ def check_decompression(self, compress_ext, compress_func):
+ test_text = 'decompression\ntest\n'
+ test_data = compress_func(test_text)
+ stream = tutil.MockStreamReader('.', test_data)
+ reader = StreamFileReader(stream, [[0, len(test_data), 0]],
+ 'test.' + compress_ext)
+ self.assertEqual(test_text, ''.join(reader.readall_decompressed()))
+
+ @staticmethod
+ def gzip_compress(data):
+ compressed_data = io.BytesIO()
+ with gzip.GzipFile(fileobj=compressed_data, mode='wb') as gzip_file:
+ gzip_file.write(data)
+ return compressed_data.getvalue()
+
+ def test_no_decompression(self):
+ self.check_decompression('log', lambda s: s)
+
+ def test_gzip_decompression(self):
+ self.check_decompression('gz', self.gzip_compress)
+
+ def test_bz2_decompression(self):
+ self.check_decompression('bz2', bz2.compress)
+
+
+class StreamRetryTestMixin(object):
+ # Define reader_for(coll_name, **kwargs)
+ # and read_for_test(reader, size, **kwargs).
+ API_COLLECTIONS = run_test_server.fixture('collections')
+
+ def keep_client(self):
+ return arvados.KeepClient(proxy='http://[%s]:1' % (tutil.TEST_HOST,),
+ local_store='')
+
+ def manifest_for(self, coll_name):
+ return self.API_COLLECTIONS[coll_name]['manifest_text']
+
+ @tutil.skip_sleep
+ def test_success_without_retries(self):
+ reader = self.reader_for('bar_file')
+ with tutil.mock_get_responses('bar', 200):
+ self.assertEqual('bar', self.read_for_test(reader, 3))
+
+ @tutil.skip_sleep
+ def test_read_no_default_retry(self):
+ reader = self.reader_for('user_agreement')
+ with tutil.mock_get_responses('', 500):
+ with self.assertRaises(arvados.errors.KeepReadError):
+ self.read_for_test(reader, 10)
+
+ @tutil.skip_sleep
+ def test_read_with_instance_retries(self):
+ reader = self.reader_for('foo_file', num_retries=3)
+ with tutil.mock_get_responses('foo', 500, 200):
+ self.assertEqual('foo', self.read_for_test(reader, 3))
+
+ @tutil.skip_sleep
+ def test_read_with_method_retries(self):
+ reader = self.reader_for('foo_file')
+ with tutil.mock_get_responses('foo', 500, 200):
+ self.assertEqual('foo',
+ self.read_for_test(reader, 3, num_retries=3))
+
+ @tutil.skip_sleep
+ def test_read_instance_retries_exhausted(self):
+ reader = self.reader_for('bar_file', num_retries=3)
+ with tutil.mock_get_responses('bar', 500, 500, 500, 500, 200):
+ with self.assertRaises(arvados.errors.KeepReadError):
+ self.read_for_test(reader, 3)
+
+ @tutil.skip_sleep
+ def test_read_method_retries_exhausted(self):
+ reader = self.reader_for('bar_file')
+ with tutil.mock_get_responses('bar', 500, 500, 500, 500, 200):
+ with self.assertRaises(arvados.errors.KeepReadError):
+ self.read_for_test(reader, 3, num_retries=3)
+
+ @tutil.skip_sleep
+ def test_method_retries_take_precedence(self):
+ reader = self.reader_for('user_agreement', num_retries=10)
+ with tutil.mock_get_responses('', 500, 500, 500, 200):
+ with self.assertRaises(arvados.errors.KeepReadError):
+ self.read_for_test(reader, 10, num_retries=1)
+
+
+class StreamReaderTestCase(unittest.TestCase, StreamRetryTestMixin):
+ def reader_for(self, coll_name, **kwargs):
+ return StreamReader(self.manifest_for(coll_name).split(),
+ self.keep_client(), **kwargs)
+
+ def read_for_test(self, reader, byte_count, **kwargs):
+ return reader.readfrom(0, byte_count, **kwargs)
+
+ def test_manifest_text_without_keep_client(self):
+ mtext = self.manifest_for('multilevel_collection_1')
+ for line in mtext.rstrip('\n').split('\n'):
+ reader = StreamReader(line.split())
+ self.assertEqual(line + '\n', reader.manifest_text())
+
+
+class StreamFileReadTestCase(unittest.TestCase, StreamRetryTestMixin):
+ def reader_for(self, coll_name, **kwargs):
+ return StreamReader(self.manifest_for(coll_name).split(),
+ self.keep_client(), **kwargs).all_files()[0]
+
+ def read_for_test(self, reader, byte_count, **kwargs):
+ return reader.read(byte_count, **kwargs)
+
+
+class StreamFileReadFromTestCase(StreamFileReadTestCase):
+ def read_for_test(self, reader, byte_count, **kwargs):
+ return reader.readfrom(0, byte_count, **kwargs)
+
+
+class StreamFileReadAllTestCase(StreamFileReadTestCase):
+ def read_for_test(self, reader, byte_count, **kwargs):
+ return ''.join(reader.readall(**kwargs))
+
+
+class StreamFileReadAllDecompressedTestCase(StreamFileReadTestCase):
+ def read_for_test(self, reader, byte_count, **kwargs):
+ return ''.join(reader.readall_decompressed(**kwargs))
+
+
+class StreamFileReadlinesTestCase(StreamFileReadTestCase):
+ def read_for_test(self, reader, byte_count, **kwargs):
+ return ''.join(reader.readlines(**kwargs))
+
+
+if __name__ == '__main__':
+ unittest.main()
--- /dev/null
+import unittest
+import os
+import arvados.util
+
+class MkdirDashPTest(unittest.TestCase):
+ def setUp(self):
+ try:
+ os.path.mkdir('./tmp')
+ except:
+ pass
+ def tearDown(self):
+ try:
+ os.unlink('./tmp/bar')
+ os.rmdir('./tmp/foo')
+ os.rmdir('./tmp')
+ except:
+ pass
+ def runTest(self):
+ arvados.util.mkdir_dash_p('./tmp/foo')
+ with open('./tmp/bar', 'wb') as f:
+ f.write('bar')
+ self.assertRaises(OSError, arvados.util.mkdir_dash_p, './tmp/bar')
--- /dev/null
+import run_test_server
+import unittest
+import arvados
+import arvados.events
+import threading
+
+class EventTestBase(object):
+ def on_event(self, ev):
+ if self.state == 1:
+ self.assertEqual(200, ev['status'])
+ self.state = 2
+ self.subscribed.set()
+ elif self.state == 2:
+ self.assertEqual(self.h[u'uuid'], ev[u'object_uuid'])
+ self.state = 3
+ self.done.set()
+ elif self.state == 3:
+ self.fail()
+
+ def runTest(self):
+ self.ws = None
+ self.state = 1
+ self.subscribed = threading.Event()
+ self.done = threading.Event()
+
+ run_test_server.authorize_with("admin")
+ api = arvados.api('v1', cache=False)
+ self.ws = arvados.events.subscribe(arvados.api('v1', cache=False), [['object_uuid', 'is_a', 'arvados#human']], self.on_event, poll_fallback=2)
+ self.assertIsInstance(self.ws, self.WS_TYPE)
+ self.subscribed.wait(10)
+ self.h = api.humans().create(body={}).execute()
+ self.done.wait(10)
+ self.assertEqual(3, self.state)
+
+class WebsocketTest(run_test_server.TestCaseWithServers, EventTestBase):
+ MAIN_SERVER = {'websockets': True}
+ WS_TYPE = arvados.events.EventClient
+
+ def tearDown(self):
+ if self.ws:
+ self.ws.close()
+ super(WebsocketTest, self).tearDown()
+
+
+class PollClientTest(run_test_server.TestCaseWithServers, EventTestBase):
+ MAIN_SERVER = {}
+ WS_TYPE = arvados.events.PollClient
+
+ def tearDown(self):
+ if self.ws:
+ self.ws.close()
+ super(PollClientTest, self).tearDown()
--- /dev/null
+Gemfile.lock
+arvados*gem
--- /dev/null
+source 'https://rubygems.org'
+gemspec
+gem 'rake'
+gem 'minitest', '>= 5.0.0'
--- /dev/null
+
+This directory contains contains the Ruby SDK.
+
+## Installation instructions
+
+You can build the gem with the following command:
+
+ gem build arvados.gemspec
+
+and install it like this:
+
+ gem install ./arvados-0.1.0.gem
+
+## Code example
+
+#!/usr/bin/env ruby
+
+ENV['ARVADOS_API_HOST'] = 'arvados.local'
+ENV['ARVADOS_API_TOKEN'] = 'qwertyuiopasdfghjklzxcvbnm1234567890abcdefghijklmn'
+
+require 'arvados'
+arv = Arvados.new( { :suppress_ssl_warnings => false } )
+
+pt_list = arv.pipeline_template.list(where:{})
+puts pt_list[:items].first.inspect
+
+pt = arv.pipeline_template.get(uuid:"9zb4a-p5p6p-fkkbrl98u3pk87m")
+puts pt.inspect
--- /dev/null
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+ t.libs << 'test'
+end
+
+desc 'Run tests'
+task default: :test
--- /dev/null
+if not File.exists?('/usr/bin/git') then
+ STDERR.puts "\nGit binary not found, aborting. Please install git and run gem build from a checked out copy of the git repository.\n\n"
+ exit
+end
+
+git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H .`.chomp.split(":")
+git_timestamp = Time.at(git_timestamp.to_i).utc
+
+Gem::Specification.new do |s|
+ s.name = 'arvados'
+ s.version = "0.1.#{git_timestamp.strftime('%Y%m%d%H%M%S')}"
+ s.date = git_timestamp.strftime("%Y-%m-%d")
+ s.summary = "Arvados client library"
+ s.description = "Arvados client library, git commit #{git_hash}"
+ s.authors = ["Arvados Authors"]
+ s.email = 'gem-dev@curoverse.com'
+ s.licenses = ['Apache License, Version 2.0']
+ s.files = ["lib/arvados.rb", "lib/arvados/keep.rb"]
+ s.required_ruby_version = '>= 2.1.0'
+ s.add_dependency('google-api-client', '~> 0.6.3', '>= 0.6.3')
+ s.add_dependency('activesupport', '>= 3.2.13')
+ s.add_dependency('json', '~> 1.7', '>= 1.7.7')
+ s.add_dependency('andand', '~> 1.3', '>= 1.3.3')
+ s.add_runtime_dependency('jwt', '>= 0.1.5', '< 1.0.0')
+ s.homepage =
+ 'https://arvados.org'
+end
--- /dev/null
+require 'rubygems'
+require 'google/api_client'
+require 'active_support/inflector'
+require 'json'
+require 'fileutils'
+require 'andand'
+
+ActiveSupport::Inflector.inflections do |inflect|
+ inflect.irregular 'specimen', 'specimens'
+ inflect.irregular 'human', 'humans'
+end
+
+module Kernel
+ def suppress_warnings
+ original_verbosity = $VERBOSE
+ $VERBOSE = nil
+ result = yield
+ $VERBOSE = original_verbosity
+ return result
+ end
+end
+
+class Arvados
+
+ class TransactionFailedError < StandardError
+ end
+
+ @@config = nil
+ @@debuglevel = 0
+ class << self
+ attr_accessor :debuglevel
+ end
+
+ def initialize(opts={})
+ @application_version ||= 0.0
+ @application_name ||= File.split($0).last
+
+ @arvados_api_version = opts[:api_version] || 'v1'
+
+ @arvados_api_host = opts[:api_host] ||
+ config['ARVADOS_API_HOST'] or
+ raise "#{$0}: no :api_host or ENV[ARVADOS_API_HOST] provided."
+ @arvados_api_token = opts[:api_token] ||
+ config['ARVADOS_API_TOKEN'] or
+ raise "#{$0}: no :api_token or ENV[ARVADOS_API_TOKEN] provided."
+
+ if (opts[:suppress_ssl_warnings] or
+ %w(1 true yes).index(config['ARVADOS_API_HOST_INSECURE'].
+ andand.downcase))
+ suppress_warnings do
+ OpenSSL::SSL.const_set 'VERIFY_PEER', OpenSSL::SSL::VERIFY_NONE
+ end
+ end
+
+ # Define a class and an Arvados instance method for each Arvados
+ # resource. After this, self.job will return Arvados::Job;
+ # self.job.new() and self.job.find() will do what you want.
+ _arvados = self
+ namespace_class = Arvados.const_set "A#{self.object_id}", Class.new
+ self.arvados_api.schemas.each do |classname, schema|
+ next if classname.match /List$/
+ klass = Class.new(Arvados::Model) do
+ def self.arvados
+ @arvados
+ end
+ def self.api_models_sym
+ @api_models_sym
+ end
+ def self.api_model_sym
+ @api_model_sym
+ end
+ end
+
+ # Define the resource methods (create, get, update, delete, ...)
+ self.
+ arvados_api.
+ send(classname.underscore.split('/').last.pluralize.to_sym).
+ discovered_methods.
+ each do |method|
+ class << klass; self; end.class_eval do
+ define_method method.name do |*params|
+ self.api_exec method, *params
+ end
+ end
+ end
+
+ # Give the new class access to the API
+ klass.instance_eval do
+ @arvados = _arvados
+ # TODO: Pull these from the discovery document instead.
+ @api_models_sym = classname.underscore.split('/').last.pluralize.to_sym
+ @api_model_sym = classname.underscore.split('/').last.to_sym
+ end
+
+ # Create the new class in namespace_class so it doesn't
+ # interfere with classes created by other Arvados objects. The
+ # result looks like Arvados::A26949680::Job.
+ namespace_class.const_set classname, klass
+
+ self.class.class_eval do
+ define_method classname.underscore do
+ klass
+ end
+ end
+ end
+ end
+
+ class Google::APIClient
+ def discovery_document(api, version)
+ api = api.to_s
+ discovery_uri = self.discovery_uri(api, version)
+ discovery_uri_hash = Digest::MD5.hexdigest(discovery_uri)
+ return @discovery_documents[discovery_uri_hash] ||=
+ begin
+ # fetch new API discovery doc if stale
+ cached_doc = File.expand_path "~/.cache/arvados/discovery-#{discovery_uri_hash}.json" rescue nil
+ if cached_doc.nil? or not File.exist?(cached_doc) or (Time.now - File.mtime(cached_doc)) > 86400
+ response = self.execute!(:http_method => :get,
+ :uri => discovery_uri,
+ :authenticated => false)
+ begin
+ FileUtils.makedirs(File.dirname cached_doc)
+ File.open(cached_doc, 'w') do |f|
+ f.puts response.body
+ end
+ rescue
+ return JSON.load response.body
+ end
+ end
+
+ File.open(cached_doc) { |f| JSON.load f }
+ end
+ end
+ end
+
+ def client
+ @client ||= Google::APIClient.
+ new(:host => @arvados_api_host,
+ :application_name => @application_name,
+ :application_version => @application_version.to_s)
+ end
+
+ def arvados_api
+ @arvados_api ||= self.client.discovered_api('arvados', @arvados_api_version)
+ end
+
+ def self.debuglog(message, verbosity=1)
+ $stderr.puts "#{File.split($0).last} #{$$}: #{message}" if @@debuglevel >= verbosity
+ end
+
+ def debuglog *args
+ self.class.debuglog *args
+ end
+
+ def config(config_file_path="~/.config/arvados/settings.conf")
+ return @@config if @@config
+
+ # Initialize config settings with environment variables.
+ config = {}
+ config['ARVADOS_API_HOST'] = ENV['ARVADOS_API_HOST']
+ config['ARVADOS_API_TOKEN'] = ENV['ARVADOS_API_TOKEN']
+ config['ARVADOS_API_HOST_INSECURE'] = ENV['ARVADOS_API_HOST_INSECURE']
+
+ if config['ARVADOS_API_HOST'] and config['ARVADOS_API_TOKEN']
+ # Environment variables take precedence over the config file, so
+ # there is no point reading the config file. If the environment
+ # specifies a _HOST without asking for _INSECURE, we certainly
+ # shouldn't give the config file a chance to create a
+ # system-wide _INSECURE state for this user.
+ #
+ # Note: If we start using additional configuration settings from
+ # this file in the future, we might have to read the file anyway
+ # instead of returning here.
+ return (@@config = config)
+ end
+
+ begin
+ expanded_path = File.expand_path config_file_path
+ if File.exist? expanded_path
+ # Load settings from the config file.
+ lineno = 0
+ File.open(expanded_path).each do |line|
+ lineno = lineno + 1
+ # skip comments and blank lines
+ next if line.match('^\s*#') or not line.match('\S')
+ var, val = line.chomp.split('=', 2)
+ var.strip!
+ val.strip!
+ # allow environment settings to override config files.
+ if !var.empty? and val
+ config[var] ||= val
+ else
+ debuglog "#{expanded_path}: #{lineno}: could not parse `#{line}'", 0
+ end
+ end
+ end
+ rescue StandardError => e
+ debuglog "Ignoring error reading #{config_file_path}: #{e}", 0
+ end
+
+ @@config = config
+ end
+
+ class Model
+ def self.arvados_api
+ arvados.arvados_api
+ end
+ def self.client
+ arvados.client
+ end
+ def self.debuglog(*args)
+ arvados.class.debuglog *args
+ end
+ def debuglog(*args)
+ self.class.arvados.class.debuglog *args
+ end
+ def self.api_exec(method, parameters={})
+ api_method = arvados_api.send(api_models_sym).send(method.name.to_sym)
+ parameters.each do |k,v|
+ parameters[k] = v.to_json if v.is_a? Array or v.is_a? Hash
+ end
+ # Look for objects expected by request.properties.(key).$ref and
+ # move them from parameters (query string) to request body.
+ body = nil
+ method.discovery_document['request'].
+ andand['properties'].
+ andand.each do |k,v|
+ if v.is_a? Hash and v['$ref']
+ body ||= {}
+ body[k] = parameters.delete k.to_sym
+ end
+ end
+ result = client.
+ execute(:api_method => api_method,
+ :authenticated => false,
+ :parameters => parameters,
+ :body_object => body,
+ :headers => {
+ authorization: 'OAuth2 '+arvados.config['ARVADOS_API_TOKEN']
+ })
+ resp = JSON.parse result.body, :symbolize_names => true
+ if resp[:errors]
+ raise Arvados::TransactionFailedError.new(resp[:errors])
+ elsif resp[:uuid] and resp[:etag]
+ self.new(resp)
+ elsif resp[:items].is_a? Array
+ resp.merge(items: resp[:items].collect do |i|
+ self.new(i)
+ end)
+ else
+ resp
+ end
+ end
+
+ def []=(x,y)
+ @attributes_to_update[x] = y
+ @attributes[x] = y
+ end
+ def [](x)
+ if @attributes[x].is_a? Hash or @attributes[x].is_a? Array
+ # We won't be notified via []= if these change, so we'll just
+ # assume they are going to get changed, and submit them if
+ # save() is called.
+ @attributes_to_update[x] = @attributes[x]
+ end
+ @attributes[x]
+ end
+ def save
+ @attributes_to_update.keys.each do |k|
+ @attributes_to_update[k] = @attributes[k]
+ end
+ j = self.class.api_exec :update, {
+ :uuid => @attributes[:uuid],
+ self.class.api_model_sym => @attributes_to_update.to_json
+ }
+ unless j.respond_to? :[] and j[:uuid]
+ debuglog "Failed to save #{self.to_s}: #{j[:errors] rescue nil}", 0
+ nil
+ else
+ @attributes_to_update = {}
+ @attributes = j
+ end
+ end
+
+ protected
+
+ def initialize(j)
+ @attributes_to_update = {}
+ @attributes = j
+ end
+ end
+end
--- /dev/null
+module Keep
+ class Locator
+ # A Locator is used to parse and manipulate Keep locator strings.
+ #
+ # Locators obey the following syntax:
+ #
+ # locator ::= address hint*
+ # address ::= digest size-hint
+ # digest ::= <32 hexadecimal digits>
+ # size-hint ::= "+" [0-9]+
+ # hint ::= "+" hint-type hint-content
+ # hint-type ::= [A-Z]
+ # hint-content ::= [A-Za-z0-9@_-]+
+ #
+ # Individual hints may have their own required format:
+ #
+ # sign-hint ::= "+A" <40 lowercase hex digits> "@" sign-timestamp
+ # sign-timestamp ::= <8 lowercase hex digits>
+ attr_reader :hash, :hints, :size
+
+ def initialize(hasharg, sizearg, hintarg)
+ @hash = hasharg
+ @size = sizearg
+ @hints = hintarg
+ end
+
+ # Locator.parse returns a Locator object parsed from the string tok.
+ # Returns nil if tok could not be parsed as a valid locator.
+ def self.parse(tok)
+ begin
+ Locator.parse!(tok)
+ rescue ArgumentError => e
+ nil
+ end
+ end
+
+ # Locator.parse! returns a Locator object parsed from the string tok,
+ # raising an ArgumentError if tok cannot be parsed.
+ def self.parse!(tok)
+ if tok.nil? or tok.empty?
+ raise ArgumentError.new "locator is nil or empty"
+ end
+
+ m = /^([[:xdigit:]]{32})(\+([[:digit:]]+))?(\+([[:upper:]][[:alnum:]+@_-]*))?$/.match(tok.strip)
+ unless m
+ raise ArgumentError.new "not a valid locator #{tok}"
+ end
+
+ tokhash, _, toksize, _, trailer = m[1..5]
+ tokhints = []
+ if trailer
+ trailer.split('+').each do |hint|
+ if hint =~ /^[[:upper:]][[:alnum:]@_-]+$/
+ tokhints.push(hint)
+ else
+ raise ArgumentError.new "unknown hint #{hint}"
+ end
+ end
+ end
+
+ Locator.new(tokhash, toksize, tokhints)
+ end
+
+ # Returns the signature hint supplied with this locator,
+ # or nil if the locator was not signed.
+ def signature
+ @hints.grep(/^A/).first
+ end
+
+ # Returns an unsigned Locator.
+ def without_signature
+ Locator.new(@hash, @size, @hints.reject { |o| o.start_with?("A") })
+ end
+
+ def strip_hints
+ Locator.new(@hash, @size, [])
+ end
+
+ def strip_hints!
+ @hints = []
+ self
+ end
+
+ def to_s
+ if @size
+ [ @hash, @size, *@hints ].join('+')
+ else
+ [ @hash, *@hints ].join('+')
+ end
+ end
+ end
+
+ class Manifest
+ # Class to parse a manifest text and provide common views of that data.
+ def initialize(manifest_text)
+ @text = manifest_text
+ @files = nil
+ end
+
+ def each_line
+ return to_enum(__method__) unless block_given?
+ @text.each_line do |line|
+ tokens = line.split
+ next if tokens.empty?
+ stream_name = unescape(tokens.shift)
+ blocks = []
+ while loc = Locator.parse(tokens.first)
+ blocks << loc
+ tokens.shift
+ end
+ yield [stream_name, blocks, tokens.map { |s| unescape(s) }]
+ end
+ end
+
+ def unescape(s)
+ # Parse backslash escapes in a Keep manifest stream or file name.
+ s.gsub(/\\(\\|[0-7]{3})/) do |_|
+ case $1
+ when '\\'
+ '\\'
+ else
+ $1.to_i(8).chr
+ end
+ end
+ end
+
+ def each_file_spec(speclist)
+ return to_enum(__method__, speclist) unless block_given?
+ speclist.each do |filespec|
+ start_pos, filesize, filename = filespec.split(':', 3)
+ yield [start_pos.to_i, filesize.to_i, filename]
+ end
+ end
+
+ def files
+ if @files.nil?
+ file_sizes = Hash.new(0)
+ each_line do |streamname, blocklist, filelist|
+ each_file_spec(filelist) do |_, filesize, filename|
+ file_sizes[[streamname, filename]] += filesize
+ end
+ end
+ @files = file_sizes.each_pair.map do |(streamname, filename), size|
+ [streamname, filename, size]
+ end
+ end
+ @files
+ end
+
+ def files_count(stop_after=nil)
+ # Return the number of files represented in this manifest.
+ # If stop_after is provided, files_count will read the manifest
+ # incrementally, and return immediately when it counts that number of
+ # files. This can help you avoid parsing the entire manifest if you
+ # just want to check if a small number of files are specified.
+ if stop_after.nil? or not @files.nil?
+ return files.size
+ end
+ seen_files = {}
+ each_line do |streamname, blocklist, filelist|
+ each_file_spec(filelist) do |_, _, filename|
+ seen_files[[streamname, filename]] = true
+ return stop_after if (seen_files.size >= stop_after)
+ end
+ end
+ seen_files.size
+ end
+
+ def exact_file_count?(want_count)
+ files_count(want_count + 1) == want_count
+ end
+
+ def minimum_file_count?(want_count)
+ files_count(want_count) >= want_count
+ end
+
+ def has_file?(want_stream, want_file=nil)
+ if want_file.nil?
+ want_stream, want_file = File.split(want_stream)
+ end
+ each_line do |stream_name, _, filelist|
+ if (stream_name == want_stream) and
+ each_file_spec(filelist).any? { |_, _, name| name == want_file }
+ return true
+ end
+ end
+ false
+ end
+ end
+end
--- /dev/null
+require 'minitest/autorun'
+require 'arvados'
+require 'digest/md5'
+
+class TestBigRequest < Minitest::Test
+ def boring_manifest nblocks
+ x = '.'
+ (0..nblocks).each do |z|
+ x += ' d41d8cd98f00b204e9800998ecf8427e+0'
+ end
+ x += " 0:0:foo.txt\n"
+ x
+ end
+
+ def test_create_manifest nblocks=1
+ skip "Test needs an API server to run against"
+ manifest_text = boring_manifest nblocks
+ uuid = Digest::MD5.hexdigest(manifest_text) + '+' + manifest_text.size.to_s
+ c = Arvados.new.collection.create(collection: {
+ uuid: uuid,
+ manifest_text: manifest_text,
+ })
+ assert_equal uuid, c[:portable_data_hash]
+ end
+
+ def test_create_big_manifest
+ # This ensures that manifest_text is passed in the request body:
+ # it's too large to fit in the query string.
+ test_create_manifest 9999
+ end
+end
--- /dev/null
+require "minitest/autorun"
+require "arvados/keep"
+
+def random_block(size=nil)
+ sprintf("%032x+%d", rand(16 ** 32), size || rand(64 * 1024 * 1024))
+end
+
+class ManifestTest < Minitest::Test
+ SIMPLEST_MANIFEST = ". #{random_block(9)} 0:9:simple.txt\n"
+ MULTIBLOCK_FILE_MANIFEST =
+ [". #{random_block(8)} 0:4:repfile 4:4:uniqfile",
+ "./s1 #{random_block(6)} 0:3:repfile 3:3:uniqfile",
+ ". #{random_block(8)} 0:7:uniqfile2 7:1:repfile\n"].join("\n")
+ MULTILEVEL_MANIFEST =
+ [". #{random_block(9)} 0:3:file1 3:3:file2 6:3:file3\n",
+ "./dir1 #{random_block(9)} 0:3:file1 3:3:file2 6:3:file3\n",
+ "./dir1/subdir #{random_block(9)} 0:3:file1 3:3:file2 6:3:file3\n",
+ "./dir2 #{random_block(9)} 0:3:file1 3:3:file2 6:3:file3\n"].join("")
+
+ def check_stream(stream, exp_name, exp_blocks, exp_files)
+ assert_equal(exp_name, stream.first)
+ assert_equal(exp_blocks, stream[1].map(&:to_s))
+ assert_equal(exp_files, stream.last)
+ end
+
+ def test_simple_each_line_array
+ manifest = Keep::Manifest.new(SIMPLEST_MANIFEST)
+ stream_name, block_s, file = SIMPLEST_MANIFEST.strip.split
+ stream_a = manifest.each_line.to_a
+ assert_equal(1, stream_a.size, "wrong number of streams")
+ check_stream(stream_a.first, stream_name, [block_s], [file])
+ end
+
+ def test_simple_each_line_block
+ manifest = Keep::Manifest.new(SIMPLEST_MANIFEST)
+ result = []
+ manifest.each_line do |stream, blocks, files|
+ result << files
+ end
+ assert_equal([[SIMPLEST_MANIFEST.split.last]], result,
+ "wrong result from each_line block")
+ end
+
+ def test_multilevel_each_line
+ manifest = Keep::Manifest.new(MULTILEVEL_MANIFEST)
+ seen = []
+ manifest.each_line do |stream, blocks, files|
+ refute(seen.include?(stream),
+ "each_line already yielded stream #{stream}")
+ seen << stream
+ assert_equal(3, files.size, "wrong file count for stream #{stream}")
+ end
+ assert_equal(4, seen.size, "wrong number of streams")
+ end
+
+ def test_empty_each_line
+ assert_empty(Keep::Manifest.new("").each_line.to_a)
+ end
+
+ def test_empty_line_within_manifest
+ block_s = random_block
+ manifest = Keep::Manifest.
+ new([". #{block_s} 0:1:file1 1:2:file2\n",
+ "\n",
+ ". #{block_s} 3:3:file3 6:4:file4\n"].join(""))
+ streams = manifest.each_line.to_a
+ assert_equal(2, streams.size)
+ check_stream(streams[0], ".", [block_s], ["0:1:file1", "1:2:file2"])
+ check_stream(streams[1], ".", [block_s], ["3:3:file3", "6:4:file4"])
+ end
+
+ def test_backslash_escape_parsing
+ m_text = "./dir\\040name #{random_block} 0:0:file\\\\name\\011\\here.txt\n"
+ manifest = Keep::Manifest.new(m_text)
+ streams = manifest.each_line.to_a
+ assert_equal(1, streams.size, "wrong number of streams with whitespace")
+ assert_equal("./dir name", streams.first.first,
+ "wrong stream name with whitespace")
+ assert_equal(["0:0:file\\name\t\\here.txt"], streams.first.last,
+ "wrong filename(s) with whitespace")
+ end
+
+ def test_simple_files
+ manifest = Keep::Manifest.new(SIMPLEST_MANIFEST)
+ assert_equal([[".", "simple.txt", 9]], manifest.files)
+ end
+
+ def test_multilevel_files
+ manifest = Keep::Manifest.new(MULTILEVEL_MANIFEST)
+ seen = Hash.new { |this, key| this[key] = [] }
+ manifest.files.each do |stream, basename, size|
+ refute(seen[stream].include?(basename),
+ "each_file repeated #{stream}/#{basename}")
+ seen[stream] << basename
+ assert_equal(3, size, "wrong size for #{stream}/#{basename}")
+ end
+ seen.each_pair do |stream, basenames|
+ assert_equal(%w(file1 file2 file3), basenames.sort,
+ "wrong file list for #{stream}")
+ end
+ end
+
+ def test_files_with_colons_in_names
+ manifest = Keep::Manifest.new(". #{random_block(9)} 0:9:file:test.txt\n")
+ assert_equal([[".", "file:test.txt", 9]], manifest.files)
+ end
+
+ def test_files_spanning_multiple_blocks
+ manifest = Keep::Manifest.new(MULTIBLOCK_FILE_MANIFEST)
+ assert_equal([[".", "repfile", 5],
+ [".", "uniqfile", 4],
+ [".", "uniqfile2", 7],
+ ["./s1", "repfile", 3],
+ ["./s1", "uniqfile", 3]],
+ manifest.files.sort)
+ end
+
+ def test_minimum_file_count_simple
+ manifest = Keep::Manifest.new(SIMPLEST_MANIFEST)
+ assert(manifest.minimum_file_count?(1), "real minimum file count false")
+ refute(manifest.minimum_file_count?(2), "fake minimum file count true")
+ end
+
+ def test_minimum_file_count_multiblock
+ manifest = Keep::Manifest.new(MULTIBLOCK_FILE_MANIFEST)
+ assert(manifest.minimum_file_count?(2), "low minimum file count false")
+ assert(manifest.minimum_file_count?(5), "real minimum file count false")
+ refute(manifest.minimum_file_count?(6), "fake minimum file count true")
+ end
+
+ def test_exact_file_count_simple
+ manifest = Keep::Manifest.new(SIMPLEST_MANIFEST)
+ assert(manifest.exact_file_count?(1), "exact file count false")
+ refute(manifest.exact_file_count?(0), "-1 file count true")
+ refute(manifest.exact_file_count?(2), "+1 file count true")
+ end
+
+ def test_exact_file_count_multiblock
+ manifest = Keep::Manifest.new(MULTIBLOCK_FILE_MANIFEST)
+ assert(manifest.exact_file_count?(5), "exact file count false")
+ refute(manifest.exact_file_count?(4), "-1 file count true")
+ refute(manifest.exact_file_count?(6), "+1 file count true")
+ end
+
+ def test_has_file
+ manifest = Keep::Manifest.new(MULTIBLOCK_FILE_MANIFEST)
+ assert(manifest.has_file?("./repfile"), "one-arg repfile not found")
+ assert(manifest.has_file?(".", "repfile"), "two-arg repfile not found")
+ assert(manifest.has_file?("./s1/repfile"), "one-arg s1/repfile not found")
+ assert(manifest.has_file?("./s1", "repfile"), "two-arg s1/repfile not found")
+ refute(manifest.has_file?("./s1/uniqfile2"), "one-arg missing file found")
+ refute(manifest.has_file?("./s1", "uniqfile2"), "two-arg missing file found")
+ refute(manifest.has_file?("./s2/repfile"), "one-arg missing stream found")
+ refute(manifest.has_file?("./s2", "repfile"), "two-arg missing stream found")
+ end
+end
--- /dev/null
+# Ignore the default SQLite database.
+/db/*.sqlite3
+
+# Ignore all logfiles and tempfiles.
+/log/*.log
+/tmp
+
+# Sensitive files and local configuration
+/config/database.yml
+/config/initializers/omniauth.rb
+/config/application.yml
+
+# asset cache
+/public/assets/
+
+/config/environments/development.rb
+/config/environments/production.rb
+/config/environments/test.rb
+
+# Capistrano files are coming from another repo
+/Capfile*
+/config/deploy*
+
+# SimpleCov reports
+/coverage
+
+# Dev/test SSL certificates
+/self-signed.key
+/self-signed.pem
--- /dev/null
+source 'https://rubygems.org'
+
+gem 'rails', '~> 3.2.0'
+
+# Bundle edge Rails instead:
+# gem 'rails', :git => 'git://github.com/rails/rails.git'
+
+group :test, :development do
+ gem 'factory_girl_rails'
+ gem 'database_cleaner'
+ # Note: "require: false" here tells bunder not to automatically
+ # 'require' the packages during application startup. Installation is
+ # still mandatory.
+ gem 'simplecov', '~> 0.7.1', require: false
+ gem 'simplecov-rcov', require: false
+end
+
+# This might not be needed in :test and :development, but we load it
+# anyway to make sure it always gets in Gemfile.lock and to help
+# reveal install problems sooner rather than later.
+gem 'pg'
+
+# Start using multi_json once we are on Rails 3.2;
+# Rails 3.1 has a dependency on multi_json < 1.3.0 but we need version 1.3.4 to
+# fix bug https://github.com/collectiveidea/json_spec/issues/27
+gem 'multi_json'
+gem 'oj'
+
+# Gems used only for assets and not required
+# in production environments by default.
+group :assets do
+ gem 'sass-rails', '>= 3.2.0'
+ gem 'coffee-rails', '~> 3.2.0'
+
+ # See https://github.com/sstephenson/execjs#readme for more supported runtimes
+ gem 'therubyracer'
+
+ gem 'uglifier', '>= 1.0.3'
+end
+
+gem 'jquery-rails'
+
+# To use ActiveModel has_secure_password
+# gem 'bcrypt-ruby', '~> 3.0.0'
+
+# Use unicorn as the web server
+# gem 'unicorn'
+
+# Deploy with Capistrano
+# gem 'capistrano'
+
+# To use debugger
+# gem 'ruby-debug'
+
+gem 'rvm-capistrano', :group => :test
+
+gem 'acts_as_api'
+
+gem 'passenger', :group => :production
+
+gem 'omniauth', '1.1.1'
+gem 'omniauth-oauth2', '1.1.1'
+
+gem 'andand'
+
+gem 'test_after_commit', :group => :test
+
+gem 'google-api-client', '~> 0.6.3'
+gem 'trollop'
+gem 'faye-websocket'
+
+gem 'themes_for_rails'
+
+gem 'arvados', '>= 0.1.20140919104705'
+gem 'arvados-cli', '>= 0.1.20141202211726'
+
+# pg_power lets us use partial indexes in schema.rb in Rails 3
+gem 'pg_power'
+
+gem 'puma'
+gem 'sshkey'
--- /dev/null
+GEM
+ remote: https://rubygems.org/
+ specs:
+ actionmailer (3.2.17)
+ actionpack (= 3.2.17)
+ mail (~> 2.5.4)
+ actionpack (3.2.17)
+ activemodel (= 3.2.17)
+ activesupport (= 3.2.17)
+ builder (~> 3.0.0)
+ erubis (~> 2.7.0)
+ journey (~> 1.0.4)
+ rack (~> 1.4.5)
+ rack-cache (~> 1.2)
+ rack-test (~> 0.6.1)
+ sprockets (~> 2.2.1)
+ activemodel (3.2.17)
+ activesupport (= 3.2.17)
+ builder (~> 3.0.0)
+ activerecord (3.2.17)
+ activemodel (= 3.2.17)
+ activesupport (= 3.2.17)
+ arel (~> 3.0.2)
+ tzinfo (~> 0.3.29)
+ activeresource (3.2.17)
+ activemodel (= 3.2.17)
+ activesupport (= 3.2.17)
+ activesupport (3.2.17)
+ i18n (~> 0.6, >= 0.6.4)
+ multi_json (~> 1.0)
+ acts_as_api (0.4.2)
+ activemodel (>= 3.0.0)
+ activesupport (>= 3.0.0)
+ rack (>= 1.1.0)
+ addressable (2.3.6)
+ andand (1.3.3)
+ arel (3.0.3)
+ arvados (0.1.20141114230720)
+ activesupport (>= 3.2.13)
+ andand (~> 1.3, >= 1.3.3)
+ google-api-client (~> 0.6.3, >= 0.6.3)
+ json (~> 1.7, >= 1.7.7)
+ jwt (>= 0.1.5, < 1.0.0)
+ arvados-cli (0.1.20141209151444)
+ activesupport (~> 3.2, >= 3.2.13)
+ andand (~> 1.3, >= 1.3.3)
+ arvados (~> 0.1, >= 0.1.0)
+ curb (~> 0.8)
+ google-api-client (~> 0.6.3, >= 0.6.3)
+ json (~> 1.7, >= 1.7.7)
+ jwt (>= 0.1.5, < 1.0.0)
+ oj (~> 2.0, >= 2.0.3)
+ trollop (~> 2.0)
+ autoparse (0.3.3)
+ addressable (>= 2.3.1)
+ extlib (>= 0.9.15)
+ multi_json (>= 1.0.0)
+ builder (3.0.4)
+ capistrano (2.15.5)
+ highline
+ net-scp (>= 1.0.0)
+ net-sftp (>= 2.0.0)
+ net-ssh (>= 2.0.14)
+ net-ssh-gateway (>= 1.1.0)
+ coffee-rails (3.2.1)
+ coffee-script (>= 2.2.0)
+ railties (~> 3.2.0.beta)
+ coffee-script (2.2.0)
+ coffee-script-source
+ execjs
+ coffee-script-source (1.7.0)
+ curb (0.8.6)
+ daemon_controller (1.2.0)
+ database_cleaner (1.2.0)
+ erubis (2.7.0)
+ eventmachine (1.0.3)
+ execjs (2.0.2)
+ extlib (0.9.16)
+ factory_girl (4.4.0)
+ activesupport (>= 3.0.0)
+ factory_girl_rails (4.4.1)
+ factory_girl (~> 4.4.0)
+ railties (>= 3.0.0)
+ faraday (0.8.9)
+ multipart-post (~> 1.2.0)
+ faye-websocket (0.7.2)
+ eventmachine (>= 0.12.0)
+ websocket-driver (>= 0.3.1)
+ google-api-client (0.6.4)
+ addressable (>= 2.3.2)
+ autoparse (>= 0.3.3)
+ extlib (>= 0.9.15)
+ faraday (~> 0.8.4)
+ jwt (>= 0.1.5)
+ launchy (>= 2.1.1)
+ multi_json (>= 1.0.0)
+ signet (~> 0.4.5)
+ uuidtools (>= 2.1.0)
+ hashie (1.2.0)
+ highline (1.6.21)
+ hike (1.2.3)
+ httpauth (0.2.1)
+ i18n (0.6.11)
+ journey (1.0.4)
+ jquery-rails (3.1.0)
+ railties (>= 3.0, < 5.0)
+ thor (>= 0.14, < 2.0)
+ json (1.8.1)
+ jwt (0.1.13)
+ multi_json (>= 1.5)
+ launchy (2.4.3)
+ addressable (~> 2.3)
+ libv8 (3.16.14.3)
+ mail (2.5.4)
+ mime-types (~> 1.16)
+ treetop (~> 1.4.8)
+ mime-types (1.25.1)
+ multi_json (1.10.1)
+ multipart-post (1.2.0)
+ net-scp (1.2.0)
+ net-ssh (>= 2.6.5)
+ net-sftp (2.1.2)
+ net-ssh (>= 2.6.5)
+ net-ssh (2.8.0)
+ net-ssh-gateway (1.2.0)
+ net-ssh (>= 2.6.5)
+ oauth2 (0.8.1)
+ faraday (~> 0.8)
+ httpauth (~> 0.1)
+ jwt (~> 0.1.4)
+ multi_json (~> 1.0)
+ rack (~> 1.2)
+ oj (2.11.1)
+ omniauth (1.1.1)
+ hashie (~> 1.2)
+ rack
+ omniauth-oauth2 (1.1.1)
+ oauth2 (~> 0.8.0)
+ omniauth (~> 1.0)
+ passenger (4.0.41)
+ daemon_controller (>= 1.2.0)
+ rack
+ rake (>= 0.8.1)
+ pg (0.17.1)
+ pg_power (1.6.4)
+ pg
+ rails (~> 3.1)
+ polyglot (0.3.4)
+ puma (2.8.2)
+ rack (>= 1.1, < 2.0)
+ rack (1.4.5)
+ rack-cache (1.2)
+ rack (>= 0.4)
+ rack-ssl (1.3.4)
+ rack
+ rack-test (0.6.2)
+ rack (>= 1.0)
+ rails (3.2.17)
+ actionmailer (= 3.2.17)
+ actionpack (= 3.2.17)
+ activerecord (= 3.2.17)
+ activeresource (= 3.2.17)
+ activesupport (= 3.2.17)
+ bundler (~> 1.0)
+ railties (= 3.2.17)
+ railties (3.2.17)
+ actionpack (= 3.2.17)
+ activesupport (= 3.2.17)
+ rack-ssl (~> 1.3.2)
+ rake (>= 0.8.7)
+ rdoc (~> 3.4)
+ thor (>= 0.14.6, < 2.0)
+ rake (10.2.2)
+ rdoc (3.12.2)
+ json (~> 1.4)
+ ref (1.0.5)
+ rvm-capistrano (1.5.1)
+ capistrano (~> 2.15.4)
+ sass (3.3.4)
+ sass-rails (3.2.6)
+ railties (~> 3.2.0)
+ sass (>= 3.1.10)
+ tilt (~> 1.3)
+ signet (0.4.5)
+ addressable (>= 2.2.3)
+ faraday (~> 0.8.1)
+ jwt (>= 0.1.5)
+ multi_json (>= 1.0.0)
+ simplecov (0.7.1)
+ multi_json (~> 1.0)
+ simplecov-html (~> 0.7.1)
+ simplecov-html (0.7.1)
+ simplecov-rcov (0.2.3)
+ simplecov (>= 0.4.1)
+ sprockets (2.2.2)
+ hike (~> 1.2)
+ multi_json (~> 1.0)
+ rack (~> 1.0)
+ tilt (~> 1.1, != 1.3.0)
+ sshkey (1.6.1)
+ test_after_commit (0.2.3)
+ themes_for_rails (0.5.1)
+ rails (>= 3.0.0)
+ therubyracer (0.12.1)
+ libv8 (~> 3.16.14.0)
+ ref
+ thor (0.19.1)
+ tilt (1.4.1)
+ treetop (1.4.15)
+ polyglot
+ polyglot (>= 0.3.1)
+ trollop (2.0)
+ tzinfo (0.3.39)
+ uglifier (2.5.0)
+ execjs (>= 0.3.0)
+ json (>= 1.8.0)
+ uuidtools (2.1.5)
+ websocket-driver (0.3.2)
+
+PLATFORMS
+ ruby
+
+DEPENDENCIES
+ acts_as_api
+ andand
+ arvados (>= 0.1.20140919104705)
+ arvados-cli (>= 0.1.20141202211726)
+ coffee-rails (~> 3.2.0)
+ database_cleaner
+ factory_girl_rails
+ faye-websocket
+ google-api-client (~> 0.6.3)
+ jquery-rails
+ multi_json
+ oj
+ omniauth (= 1.1.1)
+ omniauth-oauth2 (= 1.1.1)
+ passenger
+ pg
+ pg_power
+ puma
+ rails (~> 3.2.0)
+ rvm-capistrano
+ sass-rails (>= 3.2.0)
+ simplecov (~> 0.7.1)
+ simplecov-rcov
+ sshkey
+ test_after_commit
+ themes_for_rails
+ therubyracer
+ trollop
+ uglifier (>= 1.0.3)
--- /dev/null
+== Welcome to Rails
+
+Rails is a web-application framework that includes everything needed to create
+database-backed web applications according to the Model-View-Control pattern.
+
+This pattern splits the view (also called the presentation) into "dumb"
+templates that are primarily responsible for inserting pre-built data in between
+HTML tags. The model contains the "smart" domain objects (such as Account,
+Product, Person, Post) that holds all the business logic and knows how to
+persist themselves to a database. The controller handles the incoming requests
+(such as Save New Account, Update Product, Show Post) by manipulating the model
+and directing data to the view.
+
+In Rails, the model is handled by what's called an object-relational mapping
+layer entitled Active Record. This layer allows you to present the data from
+database rows as objects and embellish these data objects with business logic
+methods. You can read more about Active Record in
+link:files/vendor/rails/activerecord/README.html.
+
+The controller and view are handled by the Action Pack, which handles both
+layers by its two parts: Action View and Action Controller. These two layers
+are bundled in a single package due to their heavy interdependence. This is
+unlike the relationship between the Active Record and Action Pack that is much
+more separate. Each of these packages can be used independently outside of
+Rails. You can read more about Action Pack in
+link:files/vendor/rails/actionpack/README.html.
+
+
+== Getting Started
+
+1. At the command prompt, create a new Rails application:
+ <tt>rails new myapp</tt> (where <tt>myapp</tt> is the application name)
+
+2. Change directory to <tt>myapp</tt> and start the web server:
+ <tt>cd myapp; rails server</tt> (run with --help for options)
+
+3. Go to http://localhost:3000/ and you'll see:
+ "Welcome aboard: You're riding Ruby on Rails!"
+
+4. Follow the guidelines to start developing your application. You can find
+the following resources handy:
+
+* The Getting Started Guide: http://guides.rubyonrails.org/getting_started.html
+* Ruby on Rails Tutorial Book: http://www.railstutorial.org/
+
+
+== Debugging Rails
+
+Sometimes your application goes wrong. Fortunately there are a lot of tools that
+will help you debug it and get it back on the rails.
+
+First area to check is the application log files. Have "tail -f" commands
+running on the server.log and development.log. Rails will automatically display
+debugging and runtime information to these files. Debugging info will also be
+shown in the browser on requests from 127.0.0.1.
+
+You can also log your own messages directly into the log file from your code
+using the Ruby logger class from inside your controllers. Example:
+
+ class WeblogController < ActionController::Base
+ def destroy
+ @weblog = Weblog.find(params[:id])
+ @weblog.destroy
+ logger.info("#{Time.now} Destroyed Weblog ID ##{@weblog.id}!")
+ end
+ end
+
+The result will be a message in your log file along the lines of:
+
+ Mon Oct 08 14:22:29 +1000 2007 Destroyed Weblog ID #1!
+
+More information on how to use the logger is at http://www.ruby-doc.org/core/
+
+Also, Ruby documentation can be found at http://www.ruby-lang.org/. There are
+several books available online as well:
+
+* Programming Ruby: http://www.ruby-doc.org/docs/ProgrammingRuby/ (Pickaxe)
+* Learn to Program: http://pine.fm/LearnToProgram/ (a beginners guide)
+
+These two books will bring you up to speed on the Ruby language and also on
+programming in general.
+
+
+== Debugger
+
+Debugger support is available through the debugger command when you start your
+Mongrel or WEBrick server with --debugger. This means that you can break out of
+execution at any point in the code, investigate and change the model, and then,
+resume execution! You need to install ruby-debug to run the server in debugging
+mode. With gems, use <tt>sudo gem install ruby-debug</tt>. Example:
+
+ class WeblogController < ActionController::Base
+ def index
+ @posts = Post.all
+ debugger
+ end
+ end
+
+So the controller will accept the action, run the first line, then present you
+with a IRB prompt in the server window. Here you can do things like:
+
+ >> @posts.inspect
+ => "[#<Post:0x14a6be8
+ @attributes={"title"=>nil, "body"=>nil, "id"=>"1"}>,
+ #<Post:0x14a6620
+ @attributes={"title"=>"Rails", "body"=>"Only ten..", "id"=>"2"}>]"
+ >> @posts.first.title = "hello from a debugger"
+ => "hello from a debugger"
+
+...and even better, you can examine how your runtime objects actually work:
+
+ >> f = @posts.first
+ => #<Post:0x13630c4 @attributes={"title"=>nil, "body"=>nil, "id"=>"1"}>
+ >> f.
+ Display all 152 possibilities? (y or n)
+
+Finally, when you're ready to resume execution, you can enter "cont".
+
+
+== Console
+
+The console is a Ruby shell, which allows you to interact with your
+application's domain model. Here you'll have all parts of the application
+configured, just like it is when the application is running. You can inspect
+domain models, change values, and save to the database. Starting the script
+without arguments will launch it in the development environment.
+
+To start the console, run <tt>rails console</tt> from the application
+directory.
+
+Options:
+
+* Passing the <tt>-s, --sandbox</tt> argument will rollback any modifications
+ made to the database.
+* Passing an environment name as an argument will load the corresponding
+ environment. Example: <tt>rails console production</tt>.
+
+To reload your controllers and models after launching the console run
+<tt>reload!</tt>
+
+More information about irb can be found at:
+link:http://www.rubycentral.org/pickaxe/irb.html
+
+
+== dbconsole
+
+You can go to the command line of your database directly through <tt>rails
+dbconsole</tt>. You would be connected to the database with the credentials
+defined in database.yml. Starting the script without arguments will connect you
+to the development database. Passing an argument will connect you to a different
+database, like <tt>rails dbconsole production</tt>. Currently works for MySQL,
+PostgreSQL and SQLite 3.
+
+== Description of Contents
+
+The default directory structure of a generated Ruby on Rails application:
+
+ |-- app
+ | |-- assets
+ | |-- images
+ | |-- javascripts
+ | `-- stylesheets
+ | |-- controllers
+ | |-- helpers
+ | |-- mailers
+ | |-- models
+ | `-- views
+ | `-- layouts
+ |-- config
+ | |-- environments
+ | |-- initializers
+ | `-- locales
+ |-- db
+ |-- doc
+ |-- lib
+ | `-- tasks
+ |-- log
+ |-- public
+ |-- script
+ |-- test
+ | |-- fixtures
+ | |-- functional
+ | |-- integration
+ | |-- performance
+ | `-- unit
+ |-- tmp
+ | |-- cache
+ | |-- pids
+ | |-- sessions
+ | `-- sockets
+ `-- vendor
+ |-- assets
+ `-- stylesheets
+ `-- plugins
+
+app
+ Holds all the code that's specific to this particular application.
+
+app/assets
+ Contains subdirectories for images, stylesheets, and JavaScript files.
+
+app/controllers
+ Holds controllers that should be named like weblogs_controller.rb for
+ automated URL mapping. All controllers should descend from
+ ApplicationController which itself descends from ActionController::Base.
+
+app/models
+ Holds models that should be named like post.rb. Models descend from
+ ActiveRecord::Base by default.
+
+app/views
+ Holds the template files for the view that should be named like
+ weblogs/index.html.erb for the WeblogsController#index action. All views use
+ eRuby syntax by default.
+
+app/views/layouts
+ Holds the template files for layouts to be used with views. This models the
+ common header/footer method of wrapping views. In your views, define a layout
+ using the <tt>layout :default</tt> and create a file named default.html.erb.
+ Inside default.html.erb, call <% yield %> to render the view using this
+ layout.
+
+app/helpers
+ Holds view helpers that should be named like weblogs_helper.rb. These are
+ generated for you automatically when using generators for controllers.
+ Helpers can be used to wrap functionality for your views into methods.
+
+config
+ Configuration files for the Rails environment, the routing map, the database,
+ and other dependencies.
+
+db
+ Contains the database schema in schema.rb. db/migrate contains all the
+ sequence of Migrations for your schema.
+
+doc
+ This directory is where your application documentation will be stored when
+ generated using <tt>rake doc:app</tt>
+
+lib
+ Application specific libraries. Basically, any kind of custom code that
+ doesn't belong under controllers, models, or helpers. This directory is in
+ the load path.
+
+public
+ The directory available for the web server. Also contains the dispatchers and the
+ default HTML files. This should be set as the DOCUMENT_ROOT of your web
+ server.
+
+script
+ Helper scripts for automation and generation.
+
+test
+ Unit and functional tests along with fixtures. When using the rails generate
+ command, template test files will be generated for you and placed in this
+ directory.
+
+vendor
+ External libraries that the application depends on. Also includes the plugins
+ subdirectory. If the app has frozen rails, those gems also go here, under
+ vendor/rails/. This directory is in the load path.
--- /dev/null
+#!/usr/bin/env rake
+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
+
+require File.expand_path('../config/application', __FILE__)
+
+begin
+ ok = PgPower
+rescue
+ abort "Hm, pg_power is missing. Make sure you use 'bundle exec rake ...'"
+end
+
+Server::Application.load_tasks
--- /dev/null
+// Place all the styles related to the ApiClientAuthorizations controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the ApiClients controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+/*
+ * This is a manifest file that'll automatically include all the stylesheets available in this directory
+ * and any sub-directories. You're free to add application-wide styles to this file and they'll appear at
+ * the top of the compiled file, but it's generally better to create a new file per style scope.
+ *= require_self
+ *= require_tree .
+*/
+
+.contain-align-left {
+ text-align: left;
+}
+
+body {
+ margin: 0;
+}
+body > div {
+ margin: 2px;
+}
+div#footer {
+ font-family: Verdana,Arial,sans-serif;
+ font-size: 12px;
+ margin-top: 24px;
+ border-top: 1px solid #ccc;
+}
+div#footer, div#footer a {
+ color: #777;
+}
+div#header {
+ margin: 0;
+ padding: .5em 1em;
+ background: #000;
+ font-weight: bold;
+ font-size: 18px;
+ font-family: Verdana,Arial,sans-serif;
+ vertical-align: middle;
+ color: #ddd;
+}
+div#header > div {
+ display: inline-block;
+ font-size: 12px;
+ line-height: 18px;
+}
+div#header > .apptitle {
+ font-size: 18px;
+}
+div#header a.logout {
+ color: #fff;
+ font-weight: normal;
+}
+div#header button {
+ font-size: 12px;
+}
+div#header span.beta {
+ opacity: 0.5;
+}
+div#header span.beta > span {
+ border-top: 1px solid #fff;
+ border-bottom: 1px solid #fff;
+ font-size: 0.8em;
+}
+img.curoverse-logo {
+ width: 221px;
+ height: 44px;
+}
+#intropage {
+ font-family: Verdana,Arial,sans-serif;
+}
+#errorpage {
+ font-family: Verdana,Arial,sans-serif;
+}
+
+div.full-page-tab-set > ul > li {
+ font-size: 14px;
+}
+.titlebanner p {
+ font-size: 16px;
+}
+p {
+ font-size: 12px;
+}
+.small-text {
+ font-size: 12px;
+}
+.autoui-icon-float-left {
+ float: left;
+ margin-right: .3em;
+}
+.autoui-pad {
+ padding: 0 1em;
+}
+table.datatablesme {
+ border: 0;
+ border-collapse: collapse;
+ width: 100%;
+}
+.loadinggif {
+ background: #fff url(/images/ajax-loader-16-fff-aad.gif) no-repeat;
+}
+.clientprogressgif {
+ /* warning: depends on 24px outer container. */
+ position: absolute;
+ left: 4px;
+ top: 4px;
+ width: 16px;
+ height: 16px;
+}
+.counttable {
+ width: 100%;
+ display: table;
+ border-collapse: collapse;
+ margin-bottom: 0.5em;
+}
+.counttable > div {
+ display: table-row;
+}
+.counttable > div > div {
+ display: table-cell;
+ text-align: center;
+ background: #ccf;
+ padding: 0 2px;
+ font-size: 0.8em;
+}
+.counttable > div > div.counter {
+ font-size: 2em;
+ padding: 4px 2px 0 2px;
+}
+table.admin_table {
+ border-collapse: collapse;
+}
+table.admin_table tbody tr {
+ height: 2.5em;
+}
+table.admin_table th,table.admin_table td {
+ text-align: left;
+ border: 1px solid #bbb;
+ padding: 3px;
+}
+table.admin_table tbody tr:hover {
+ background: #ff8;
+}
+table.admin_table tbody tr:hover td {
+ background: transparent;
+}
+
+div.helptopics {
+ position: fixed;
+}
+div.helptopics ul {
+ padding: 0;
+ margin-left: 1em;
+ list-style-type: none;
+}
+div.helptopics ul li {
+ margin: 0 0 1em 0;
+}
+div.helpcontent li {
+ margin-bottom: .5em;
+}
+
+div.preview {
+ color: red;
+ font-weight: bold;
+ text-align: center;
+}
+
+.sudo-warning {
+ padding: 4px 10px;
+ background: #ffdd00;
+ color: red;
+ -webkit-border-radius: 3px;
+ -moz-border-radius: 3px;
+ border-radius: 3px
+}
+
+div#header a.sudo-logout {
+ color: #000;
+ font-weight: bold;
+}
+
--- /dev/null
+// Place all the styles related to the AuthorizedKeys controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Collections controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the commit_ancestors controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the commits controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Groups controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Humans controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the JobTasks controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Jobs controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the KeepDisks controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the links controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Logs controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+/*
+ Place all the styles related to the matching controller here.
+ They will automatically be included in application.css.
+*/
+.node-status {
+ /* unknown status - might be bad */
+ background: #ff8888;
+}
+.node-status-running .node-status {
+ background: #88ff88;
+}
+.node-status-missing .node-status {
+ background: #ff8888;
+}
+.node-status-terminated .node-status {
+ background: #ffffff;
+}
+
+.node-slurm-state {
+ /* unknown status - might be bad */
+ background: #ff8888;
+}
+.node-status-missing .node-slurm-state {
+ background: #ffffff;
+}
+.node-status-terminated .node-slurm-state {
+ background: #ffffff;
+}
+.node-status-running .node-slurm-state-alloc {
+ background: #88ff88;
+}
+.node-status-running .node-slurm-state-idle {
+ background: #ffbbbb;
+}
+.node-status-running .node-slurm-state-down {
+ background: #ff8888;
+}
--- /dev/null
+// Place all the styles related to the Nodes controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the PipelineInstances controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the PipelineTemplates controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Repositories controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+body {
+ background-color: #fff;
+ color: #333;
+ font-family: verdana, arial, helvetica, sans-serif;
+ font-size: 13px;
+ line-height: 18px;
+}
+
+p, ol, ul, td {
+ font-family: verdana, arial, helvetica, sans-serif;
+ font-size: 13px;
+ line-height: 18px;
+}
+
+pre {
+ background-color: #eee;
+ padding: 10px;
+ font-size: 11px;
+}
+
+a {
+ color: #000;
+ &:visited {
+ color: #666;
+ }
+ &:hover {
+ color: #fff;
+ background-color: #000;
+ }
+}
+
+div {
+ &.field, &.actions {
+ margin-bottom: 10px;
+ }
+}
+
+#notice {
+ color: green;
+}
+
+.field_with_errors {
+ padding: 2px;
+ background-color: red;
+ display: table;
+}
+
+#error_explanation {
+ width: 450px;
+ border: 2px solid red;
+ padding: 7px;
+ padding-bottom: 0;
+ margin-bottom: 20px;
+ background-color: #f0f0f0;
+ h2 {
+ text-align: left;
+ font-weight: bold;
+ padding: 5px 5px 5px 15px;
+ font-size: 12px;
+ margin: -7px;
+ margin-bottom: 0px;
+ background-color: #c00;
+ color: #fff;
+ }
+ ul li {
+ font-size: 12px;
+ list-style: square;
+ }
+}
--- /dev/null
+// Place all the styles related to the Specimens controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the Traits controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+// Place all the styles related to the VirtualMachines controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/
--- /dev/null
+module ApiTemplateOverride
+ def allowed_to_render?(fieldset, field, model, options)
+ return false if !super
+ if options[:select]
+ options[:select].include? field.to_s
+ else
+ true
+ end
+ end
+end
+
+class ActsAsApi::ApiTemplate
+ prepend ApiTemplateOverride
+end
+
+require 'load_param'
+require 'record_filters'
+
+class ApplicationController < ActionController::Base
+ include CurrentApiClient
+ include ThemesForRails::ActionController
+ include LoadParam
+ include RecordFilters
+
+ respond_to :json
+ protect_from_forgery
+
+ ERROR_ACTIONS = [:render_error, :render_not_found]
+
+ before_filter :set_cors_headers
+ before_filter :respond_with_json_by_default
+ before_filter :remote_ip
+ before_filter :load_read_auths
+ before_filter :require_auth_scope, except: ERROR_ACTIONS
+
+ before_filter :catch_redirect_hint
+ before_filter(:find_object_by_uuid,
+ except: [:index, :create] + ERROR_ACTIONS)
+ before_filter :load_required_parameters
+ before_filter :load_limit_offset_order_params, only: [:index, :contents]
+ before_filter :load_where_param, only: [:index, :contents]
+ before_filter :load_filters_param, only: [:index, :contents]
+ before_filter :find_objects_for_index, :only => :index
+ before_filter :reload_object_before_update, :only => :update
+ before_filter(:render_404_if_no_object,
+ except: [:index, :create] + ERROR_ACTIONS)
+
+ theme :select_theme
+
+ attr_accessor :resource_attrs
+
+ begin
+ rescue_from(Exception,
+ ArvadosModel::PermissionDeniedError,
+ :with => :render_error)
+ rescue_from(ActiveRecord::RecordNotFound,
+ ActionController::RoutingError,
+ ActionController::UnknownController,
+ AbstractController::ActionNotFound,
+ :with => :render_not_found)
+ end
+
+ def default_url_options
+ if Rails.configuration.host
+ {:host => Rails.configuration.host}
+ else
+ {}
+ end
+ end
+
+ def index
+ @objects.uniq!(&:id) if @select.nil? or @select.include? "id"
+ if params[:eager] and params[:eager] != '0' and params[:eager] != 0 and params[:eager] != ''
+ @objects.each(&:eager_load_associations)
+ end
+ render_list
+ end
+
+ def show
+ render json: @object.as_api_response(nil, select: @select)
+ end
+
+ def create
+ @object = model_class.new resource_attrs
+
+ if @object.respond_to? :name and params[:ensure_unique_name]
+ # Record the original name. See below.
+ name_stem = @object.name
+ counter = 1
+ end
+
+ begin
+ @object.save!
+ rescue ActiveRecord::RecordNotUnique => rn
+ raise unless params[:ensure_unique_name]
+
+ # Dig into the error to determine if it is specifically calling out a
+ # (owner_uuid, name) uniqueness violation. In this specific case, and
+ # the client requested a unique name with ensure_unique_name==true,
+ # update the name field and try to save again. Loop as necessary to
+ # discover a unique name. It is necessary to handle name choosing at
+ # this level (as opposed to the client) to ensure that record creation
+ # never fails due to a race condition.
+ raise unless rn.original_exception.is_a? PG::UniqueViolation
+
+ # Unfortunately ActiveRecord doesn't abstract out any of the
+ # necessary information to figure out if this the error is actually
+ # the specific case where we want to apply the ensure_unique_name
+ # behavior, so the following code is specialized to Postgres.
+ err = rn.original_exception
+ detail = err.result.error_field(PG::Result::PG_DIAG_MESSAGE_DETAIL)
+ raise unless /^Key \(owner_uuid, name\)=\([a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}, .*?\) already exists\./.match detail
+
+ # OK, this exception really is just a unique name constraint
+ # violation, and we've been asked to ensure_unique_name.
+ counter += 1
+ @object.uuid = nil
+ @object.name = "#{name_stem} (#{counter})"
+ redo
+ end while false
+ show
+ end
+
+ def update
+ attrs_to_update = resource_attrs.reject { |k,v|
+ [:kind, :etag, :href].index k
+ }
+ @object.update_attributes! attrs_to_update
+ show
+ end
+
+ def destroy
+ @object.destroy
+ show
+ end
+
+ def catch_redirect_hint
+ if !current_user
+ if params.has_key?('redirect_to') then
+ session[:redirect_to] = params[:redirect_to]
+ end
+ end
+ end
+
+ def render_404_if_no_object
+ render_not_found "Object not found" if !@object
+ end
+
+ def render_error(e)
+ logger.error e.inspect
+ if e.respond_to? :backtrace and e.backtrace
+ logger.error e.backtrace.collect { |x| x + "\n" }.join('')
+ end
+ if (@object.respond_to? :errors and
+ @object.errors.andand.full_messages.andand.any?)
+ errors = @object.errors.full_messages
+ logger.error errors.inspect
+ else
+ errors = [e.inspect]
+ end
+ status = e.respond_to?(:http_status) ? e.http_status : 422
+ send_error(*errors, status: status)
+ end
+
+ def render_not_found(e=ActionController::RoutingError.new("Path not found"))
+ logger.error e.inspect
+ send_error("Path not found", status: 404)
+ end
+
+ protected
+
+ def send_error(*args)
+ if args.last.is_a? Hash
+ err = args.pop
+ else
+ err = {}
+ end
+ err[:errors] ||= args
+ err[:error_token] = [Time.now.utc.to_i, "%08x" % rand(16 ** 8)].join("+")
+ status = err.delete(:status) || 422
+ logger.error "Error #{err[:error_token]}: #{status}"
+ render json: err, status: status
+ end
+
+ def find_objects_for_index
+ @objects ||= model_class.readable_by(*@read_users)
+ apply_where_limit_order_params
+ end
+
+ def apply_filters model_class=nil
+ model_class ||= self.model_class
+ ft = record_filters @filters, model_class
+ if ft[:cond_out].any?
+ @objects = @objects.where('(' + ft[:cond_out].join(') AND (') + ')',
+ *ft[:param_out])
+ end
+ end
+
+ def apply_where_limit_order_params *args
+ apply_filters *args
+
+ ar_table_name = @objects.table_name
+ if @where.is_a? Hash and @where.any?
+ conditions = ['1=1']
+ @where.each do |attr,value|
+ if attr.to_s == 'any'
+ if value.is_a?(Array) and
+ value.length == 2 and
+ value[0] == 'contains' then
+ ilikes = []
+ model_class.searchable_columns('ilike').each do |column|
+ # Including owner_uuid in an "any column" search will
+ # probably just return a lot of false positives.
+ next if column == 'owner_uuid'
+ ilikes << "#{ar_table_name}.#{column} ilike ?"
+ conditions << "%#{value[1]}%"
+ end
+ if ilikes.any?
+ conditions[0] << ' and (' + ilikes.join(' or ') + ')'
+ end
+ end
+ elsif attr.to_s.match(/^[a-z][_a-z0-9]+$/) and
+ model_class.columns.collect(&:name).index(attr.to_s)
+ if value.nil?
+ conditions[0] << " and #{ar_table_name}.#{attr} is ?"
+ conditions << nil
+ elsif value.is_a? Array
+ if value[0] == 'contains' and value.length == 2
+ conditions[0] << " and #{ar_table_name}.#{attr} like ?"
+ conditions << "%#{value[1]}%"
+ else
+ conditions[0] << " and #{ar_table_name}.#{attr} in (?)"
+ conditions << value
+ end
+ elsif value.is_a? String or value.is_a? Fixnum or value == true or value == false
+ conditions[0] << " and #{ar_table_name}.#{attr}=?"
+ conditions << value
+ elsif value.is_a? Hash
+ # Not quite the same thing as "equal?" but better than nothing?
+ value.each do |k,v|
+ if v.is_a? String
+ conditions[0] << " and #{ar_table_name}.#{attr} ilike ?"
+ conditions << "%#{k}%#{v}%"
+ end
+ end
+ end
+ end
+ end
+ if conditions.length > 1
+ conditions[0].sub!(/^1=1 and /, '')
+ @objects = @objects.
+ where(*conditions)
+ end
+ end
+
+ if @select
+ unless action_name.in? %w(create update destroy)
+ # Map attribute names in @select to real column names, resolve
+ # those to fully-qualified SQL column names, and pass the
+ # resulting string to the select method.
+ api_column_map = model_class.attributes_required_columns
+ columns_list = @select.
+ flat_map { |attr| api_column_map[attr] }.
+ uniq.
+ map { |s| "#{table_name}.#{ActiveRecord::Base.connection.quote_column_name s}" }
+ @objects = @objects.select(columns_list.join(", "))
+ end
+
+ # This information helps clients understand what they're seeing
+ # (Workbench always expects it), but they can't select it explicitly
+ # because it's not an SQL column. Always add it.
+ # (This is harmless, given that clients can deduce what they're
+ # looking at by the returned UUID anyway.)
+ @select |= ["kind"]
+ end
+ @objects = @objects.order(@orders.join ", ") if @orders.any?
+ @objects = @objects.limit(@limit)
+ @objects = @objects.offset(@offset)
+ @objects = @objects.uniq(@distinct) if not @distinct.nil?
+ end
+
+ def resource_attrs
+ return @attrs if @attrs
+ @attrs = params[resource_name]
+ if @attrs.is_a? String
+ @attrs = Oj.load @attrs, symbol_keys: true
+ end
+ unless @attrs.is_a? Hash
+ message = "No #{resource_name}"
+ if resource_name.index('_')
+ message << " (or #{resource_name.camelcase(:lower)})"
+ end
+ message << " hash provided with request"
+ raise ArgumentError.new(message)
+ end
+ %w(created_at modified_by_client_uuid modified_by_user_uuid modified_at).each do |x|
+ @attrs.delete x.to_sym
+ end
+ @attrs = @attrs.symbolize_keys if @attrs.is_a? HashWithIndifferentAccess
+ @attrs
+ end
+
+ # Authentication
+ def load_read_auths
+ @read_auths = []
+ if current_api_client_authorization
+ @read_auths << current_api_client_authorization
+ end
+ # Load reader tokens if this is a read request.
+ # If there are too many reader tokens, assume the request is malicious
+ # and ignore it.
+ if request.get? and params[:reader_tokens] and
+ params[:reader_tokens].size < 100
+ @read_auths += ApiClientAuthorization
+ .includes(:user)
+ .where('api_token IN (?) AND
+ (expires_at IS NULL OR expires_at > CURRENT_TIMESTAMP)',
+ params[:reader_tokens])
+ .all
+ end
+ @read_auths.select! { |auth| auth.scopes_allow_request? request }
+ @read_users = @read_auths.map { |auth| auth.user }.uniq
+ end
+
+ def require_login
+ if not current_user
+ respond_to do |format|
+ format.json { send_error("Not logged in", status: 401) }
+ format.html { redirect_to '/auth/joshid' }
+ end
+ false
+ end
+ end
+
+ def admin_required
+ unless current_user and current_user.is_admin
+ send_error("Forbidden", status: 403)
+ end
+ end
+
+ def require_auth_scope
+ if @read_auths.empty?
+ if require_login != false
+ send_error("Forbidden", status: 403)
+ end
+ false
+ end
+ end
+
+ def set_cors_headers
+ response.headers['Access-Control-Allow-Origin'] = '*'
+ response.headers['Access-Control-Allow-Methods'] = 'GET, HEAD, PUT, POST, DELETE'
+ response.headers['Access-Control-Allow-Headers'] = 'Authorization'
+ response.headers['Access-Control-Max-Age'] = '86486400'
+ end
+
+ def respond_with_json_by_default
+ html_index = request.accepts.index(Mime::HTML)
+ if html_index.nil? or request.accepts[0...html_index].include?(Mime::JSON)
+ request.format = :json
+ end
+ end
+
+ def model_class
+ controller_name.classify.constantize
+ end
+
+ def resource_name # params[] key used by client
+ controller_name.singularize
+ end
+
+ def table_name
+ controller_name
+ end
+
+ def find_object_by_uuid
+ if params[:id] and params[:id].match /\D/
+ params[:uuid] = params.delete :id
+ end
+ @where = { uuid: params[:uuid] }
+ @offset = 0
+ @limit = 1
+ @orders = []
+ @filters = []
+ @objects = nil
+ find_objects_for_index
+ @object = @objects.first
+ end
+
+ def reload_object_before_update
+ # This is necessary to prevent an ActiveRecord::ReadOnlyRecord
+ # error when updating an object which was retrieved using a join.
+ if @object.andand.readonly?
+ @object = model_class.find_by_uuid(@objects.first.uuid)
+ end
+ end
+
+ def load_json_value(hash, key, must_be_class=nil)
+ if hash[key].is_a? String
+ hash[key] = Oj.load(hash[key], symbol_keys: false)
+ if must_be_class and !hash[key].is_a? must_be_class
+ raise TypeError.new("parameter #{key.to_s} must be a #{must_be_class.to_s}")
+ end
+ end
+ end
+
+ def self.accept_attribute_as_json(attr, must_be_class=nil)
+ before_filter lambda { accept_attribute_as_json attr, must_be_class }
+ end
+ accept_attribute_as_json :properties, Hash
+ accept_attribute_as_json :info, Hash
+ def accept_attribute_as_json(attr, must_be_class)
+ if params[resource_name] and resource_attrs.is_a? Hash
+ if resource_attrs[attr].is_a? Hash
+ # Convert symbol keys to strings (in hashes provided by
+ # resource_attrs)
+ resource_attrs[attr] = resource_attrs[attr].
+ with_indifferent_access.to_hash
+ else
+ load_json_value(resource_attrs, attr, must_be_class)
+ end
+ end
+ end
+
+ def self.accept_param_as_json(key, must_be_class=nil)
+ prepend_before_filter lambda { load_json_value(params, key, must_be_class) }
+ end
+ accept_param_as_json :reader_tokens, Array
+
+ def render_list
+ @object_list = {
+ :kind => "arvados##{(@response_resource_name || resource_name).camelize(:lower)}List",
+ :etag => "",
+ :self_link => "",
+ :offset => @offset,
+ :limit => @limit,
+ :items => @objects.as_api_response(nil, {select: @select})
+ }
+ if @objects.respond_to? :except
+ @object_list[:items_available] = @objects.
+ except(:limit).except(:offset).
+ count(:id, distinct: true)
+ end
+ render json: @object_list
+ end
+
+ def remote_ip
+ # Caveat: this is highly dependent on the proxy setup. YMMV.
+ if request.headers.has_key?('HTTP_X_REAL_IP') then
+ # We're behind a reverse proxy
+ @remote_ip = request.headers['HTTP_X_REAL_IP']
+ else
+ # Hopefully, we are not!
+ @remote_ip = request.env['REMOTE_ADDR']
+ end
+ end
+
+ def load_required_parameters
+ (self.class.send "_#{params[:action]}_requires_parameters" rescue {}).
+ each do |key, info|
+ if info[:required] and not params.include?(key)
+ raise ArgumentError.new("#{key} parameter is required")
+ elsif info[:type] == 'boolean'
+ # Make sure params[key] is either true or false -- not a
+ # string, not nil, etc.
+ if not params.include?(key)
+ params[key] = info[:default]
+ elsif [false, 'false', '0', 0].include? params[key]
+ params[key] = false
+ elsif [true, 'true', '1', 1].include? params[key]
+ params[key] = true
+ else
+ raise TypeError.new("#{key} parameter must be a boolean, true or false")
+ end
+ end
+ end
+ true
+ end
+
+ def self._create_requires_parameters
+ {
+ ensure_unique_name: {
+ type: "boolean",
+ description: "Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.",
+ location: "query",
+ required: false,
+ default: false
+ }
+ }
+ end
+
+ def self._index_requires_parameters
+ {
+ filters: { type: 'array', required: false },
+ where: { type: 'object', required: false },
+ order: { type: 'array', required: false },
+ select: { type: 'array', required: false },
+ distinct: { type: 'boolean', required: false },
+ limit: { type: 'integer', required: false, default: DEFAULT_LIMIT },
+ offset: { type: 'integer', required: false, default: 0 },
+ }
+ end
+
+ def client_accepts_plain_text_stream
+ (request.headers['Accept'].split(' ') &
+ ['text/plain', '*/*']).count > 0
+ end
+
+ def render *opts
+ if opts.first
+ response = opts.first[:json]
+ if response.is_a?(Hash) &&
+ params[:_profile] &&
+ Thread.current[:request_starttime]
+ response[:_profile] = {
+ request_time: Time.now - Thread.current[:request_starttime]
+ }
+ end
+ end
+ super *opts
+ end
+
+ def select_theme
+ return Rails.configuration.arvados_theme
+ end
+end
--- /dev/null
+class Arvados::V1::ApiClientAuthorizationsController < ApplicationController
+ accept_attribute_as_json :scopes, Array
+ before_filter :current_api_client_is_trusted
+ before_filter :admin_required, :only => :create_system_auth
+ skip_before_filter :render_404_if_no_object, :only => :create_system_auth
+
+ def self._create_system_auth_requires_parameters
+ {
+ api_client_id: {type: 'integer', required: false},
+ scopes: {type: 'array', required: false}
+ }
+ end
+ def create_system_auth
+ @object = ApiClientAuthorization.
+ new(user_id: system_user.id,
+ api_client_id: params[:api_client_id] || current_api_client.andand.id,
+ created_by_ip_address: remote_ip,
+ scopes: Oj.load(params[:scopes] || '["all"]'))
+ @object.save!
+ show
+ end
+
+ def create
+ # Note: the user could specify a owner_uuid for a different user, which on
+ # the surface appears to be a security hole. However, the record will be
+ # rejected before being saved to the database by the ApiClientAuthorization
+ # model which enforces that user_id == current user or the user is an
+ # admin.
+
+ if resource_attrs[:owner_uuid]
+ # The model has an owner_id attribute instead of owner_uuid, but
+ # we can't expect the client to know the local numeric ID. We
+ # translate UUID to numeric ID here.
+ resource_attrs[:user_id] =
+ User.where(uuid: resource_attrs.delete(:owner_uuid)).first.andand.id
+ elsif not resource_attrs[:user_id]
+ resource_attrs[:user_id] = current_user.id
+ end
+ resource_attrs[:api_client_id] = Thread.current[:api_client].id
+ super
+ end
+
+ protected
+
+ def default_orders
+ ["#{table_name}.created_at desc"]
+ end
+
+ def find_objects_for_index
+ # Here we are deliberately less helpful about searching for client
+ # authorizations. We look up tokens belonging to the current user
+ # and filter by exact matches on api_token and scopes.
+ wanted_scopes = []
+ if @filters
+ wanted_scopes.concat(@filters.map { |attr, operator, operand|
+ ((attr == 'scopes') and (operator == '=')) ? operand : nil
+ })
+ @filters.select! { |attr, operator, operand|
+ (attr == 'uuid') and (operator == '=')
+ }
+ end
+ if @where
+ wanted_scopes << @where['scopes']
+ @where.select! { |attr, val| attr == 'uuid' }
+ end
+ @objects = model_class.
+ includes(:user, :api_client).
+ where('user_id=?', current_user.id)
+ super
+ wanted_scopes.compact.each do |scope_list|
+ sorted_scopes = scope_list.sort
+ @objects = @objects.select { |auth| auth.scopes.sort == sorted_scopes }
+ end
+ end
+
+ def find_object_by_uuid
+ # Again, to make things easier for the client and our own routing,
+ # here we look for the api_token key in a "uuid" (POST) or "id"
+ # (GET) parameter.
+ @object = model_class.where('api_token=?', params[:uuid] || params[:id]).first
+ end
+
+ def current_api_client_is_trusted
+ unless Thread.current[:api_client].andand.is_trusted
+ send_error('Forbidden: this API client cannot manipulate other clients\' access tokens.',
+ status: 403)
+ end
+ end
+end
--- /dev/null
+class Arvados::V1::ApiClientsController < ApplicationController
+ before_filter :admin_required
+end
--- /dev/null
+class Arvados::V1::AuthorizedKeysController < ApplicationController
+end
--- /dev/null
+require "arvados/keep"
+
+class Arvados::V1::CollectionsController < ApplicationController
+ def create
+ if resource_attrs[:uuid] and (loc = Keep::Locator.parse(resource_attrs[:uuid]))
+ resource_attrs[:portable_data_hash] = loc.to_s
+ resource_attrs.delete :uuid
+ end
+ super
+ end
+
+ def find_object_by_uuid
+ if loc = Keep::Locator.parse(params[:id])
+ loc.strip_hints!
+ if c = Collection.readable_by(*@read_users).where({ portable_data_hash: loc.to_s }).limit(1).first
+ @object = {
+ uuid: c.portable_data_hash,
+ portable_data_hash: c.portable_data_hash,
+ manifest_text: c.signed_manifest_text,
+ }
+ end
+ else
+ super
+ end
+ true
+ end
+
+ def show
+ if @object.is_a? Collection
+ super
+ else
+ render json: @object
+ end
+ end
+
+ def index
+ super
+ end
+
+ def find_collections(visited, sp, &b)
+ case sp
+ when ArvadosModel
+ sp.class.columns.each do |c|
+ find_collections(visited, sp[c.name.to_sym], &b) if c.name != "log"
+ end
+ when Hash
+ sp.each do |k, v|
+ find_collections(visited, v, &b)
+ end
+ when Array
+ sp.each do |v|
+ find_collections(visited, v, &b)
+ end
+ when String
+ if m = /[a-f0-9]{32}\+\d+/.match(sp)
+ yield m[0], nil
+ elsif m = Collection.uuid_regex.match(sp)
+ yield nil, m[0]
+ end
+ end
+ end
+
+ def search_edges(visited, uuid, direction)
+ if uuid.nil? or uuid.empty? or visited[uuid]
+ return
+ end
+
+ if loc = Keep::Locator.parse(uuid)
+ loc.strip_hints!
+ return if visited[loc.to_s]
+ end
+
+ logger.debug "visiting #{uuid}"
+
+ if loc
+ # uuid is a portable_data_hash
+ collections = Collection.readable_by(*@read_users).where(portable_data_hash: loc.to_s)
+ c = collections.limit(2).all
+ if c.size == 1
+ visited[loc.to_s] = c[0]
+ elsif c.size > 1
+ name = collections.limit(1).where("name <> ''").first
+ if name
+ visited[loc.to_s] = {
+ portable_data_hash: c[0].portable_data_hash,
+ name: "#{name.name} + #{collections.count-1} more"
+ }
+ else
+ visited[loc.to_s] = {
+ portable_data_hash: c[0].portable_data_hash,
+ name: loc.to_s
+ }
+ end
+ end
+
+ if direction == :search_up
+ # Search upstream for jobs where this locator is the output of some job
+ Job.readable_by(*@read_users).where(output: loc.to_s).each do |job|
+ search_edges(visited, job.uuid, :search_up)
+ end
+
+ Job.readable_by(*@read_users).where(log: loc.to_s).each do |job|
+ search_edges(visited, job.uuid, :search_up)
+ end
+ elsif direction == :search_down
+ if loc.to_s == "d41d8cd98f00b204e9800998ecf8427e+0"
+ # Special case, don't follow the empty collection.
+ return
+ end
+
+ # Search downstream for jobs where this locator is in script_parameters
+ Job.readable_by(*@read_users).where(["jobs.script_parameters like ?", "%#{loc.to_s}%"]).each do |job|
+ search_edges(visited, job.uuid, :search_down)
+ end
+
+ Job.readable_by(*@read_users).where(["jobs.docker_image_locator = ?", "#{loc.to_s}"]).each do |job|
+ search_edges(visited, job.uuid, :search_down)
+ end
+ end
+ else
+ # uuid is a regular Arvados UUID
+ rsc = ArvadosModel::resource_class_for_uuid uuid
+ if rsc == Job
+ Job.readable_by(*@read_users).where(uuid: uuid).each do |job|
+ visited[uuid] = job.as_api_response
+ if direction == :search_up
+ # Follow upstream collections referenced in the script parameters
+ find_collections(visited, job) do |hash, uuid|
+ search_edges(visited, hash, :search_up) if hash
+ search_edges(visited, uuid, :search_up) if uuid
+ end
+ elsif direction == :search_down
+ # Follow downstream job output
+ search_edges(visited, job.output, direction)
+ end
+ end
+ elsif rsc == Collection
+ if c = Collection.readable_by(*@read_users).where(uuid: uuid).limit(1).first
+ search_edges(visited, c.portable_data_hash, direction)
+ visited[c.portable_data_hash] = c.as_api_response
+ end
+ elsif rsc != nil
+ rsc.where(uuid: uuid).each do |r|
+ visited[uuid] = r.as_api_response
+ end
+ end
+ end
+
+ if direction == :search_up
+ # Search for provenance links pointing to the current uuid
+ Link.readable_by(*@read_users).
+ where(head_uuid: uuid, link_class: "provenance").
+ each do |link|
+ visited[link.uuid] = link.as_api_response
+ search_edges(visited, link.tail_uuid, direction)
+ end
+ elsif direction == :search_down
+ # Search for provenance links emanating from the current uuid
+ Link.readable_by(current_user).
+ where(tail_uuid: uuid, link_class: "provenance").
+ each do |link|
+ visited[link.uuid] = link.as_api_response
+ search_edges(visited, link.head_uuid, direction)
+ end
+ end
+ end
+
+ def provenance
+ visited = {}
+ search_edges(visited, @object[:portable_data_hash], :search_up)
+ search_edges(visited, @object[:uuid], :search_up)
+ render json: visited
+ end
+
+ def used_by
+ visited = {}
+ search_edges(visited, @object[:uuid], :search_down)
+ search_edges(visited, @object[:portable_data_hash], :search_down)
+ render json: visited
+ end
+
+ protected
+
+ def load_limit_offset_order_params *args
+ if action_name == 'index'
+ # Omit manifest_text from index results unless expressly selected.
+ @select ||= model_class.api_accessible_attributes(:user).
+ map { |attr_spec| attr_spec.first.to_s } - ["manifest_text"]
+ end
+ super
+ end
+end
--- /dev/null
+class Arvados::V1::GroupsController < ApplicationController
+
+ def self._contents_requires_parameters
+ _index_requires_parameters.
+ merge({
+ uuid: {
+ type: 'string', required: false, default: nil
+ },
+ # include_linked returns name links, which are obsolete, so
+ # remove it when clients have been migrated.
+ include_linked: {
+ type: 'boolean', required: false, default: false
+ },
+ })
+ end
+
+ def render_404_if_no_object
+ if params[:action] == 'contents'
+ if !params[:uuid]
+ # OK!
+ @object = nil
+ true
+ elsif @object
+ # Project group
+ true
+ elsif (@object = User.where(uuid: params[:uuid]).first)
+ # "Home" pseudo-project
+ true
+ else
+ super
+ end
+ else
+ super
+ end
+ end
+
+ def contents
+ # Set @objects:
+ # include_linked returns name links, which are obsolete, so
+ # remove it when clients have been migrated.
+ load_searchable_objects(owner_uuid: @object.andand.uuid,
+ include_linked: params[:include_linked])
+ sql = 'link_class=? and head_uuid in (?)'
+ sql_params = ['name', @objects.collect(&:uuid)]
+ if @object
+ sql += ' and tail_uuid=?'
+ sql_params << @object.uuid
+ end
+ @links = Link.where sql, *sql_params
+ @object_list = {
+ :kind => "arvados#objectList",
+ :etag => "",
+ :self_link => "",
+ :links => @links.as_api_response(nil),
+ :offset => @offset,
+ :limit => @limit,
+ :items_available => @items_available,
+ :items => @objects.as_api_response(nil)
+ }
+ render json: @object_list
+ end
+
+ protected
+
+ def load_searchable_objects opts
+ all_objects = []
+ @items_available = 0
+
+ # Trick apply_where_limit_order_params into applying suitable
+ # per-table values. *_all are the real ones we'll apply to the
+ # aggregate set.
+ limit_all = @limit
+ offset_all = @offset
+ # save the orders from the current request as determined by load_param,
+ # but otherwise discard them because we're going to be getting objects
+ # from many models
+ request_orders = @orders.clone
+ @orders = []
+
+ [Group,
+ Job, PipelineInstance, PipelineTemplate,
+ Collection,
+ Human, Specimen, Trait].each do |klass|
+ @objects = klass.readable_by(*@read_users)
+ if klass == Group
+ @objects = @objects.where(group_class: 'project')
+ end
+ if opts[:owner_uuid]
+ conds = []
+ cond_params = []
+ conds << "#{klass.table_name}.owner_uuid = ?"
+ cond_params << opts[:owner_uuid]
+ if conds.any?
+ cond_sql = '(' + conds.join(') OR (') + ')'
+ @objects = @objects.where(cond_sql, *cond_params)
+ end
+ end
+
+ # If the currently requested orders specifically match the table_name for the current klass, apply the order
+ request_order = request_orders && request_orders.find{ |r| r =~ /^#{klass.table_name}\./i }
+ if request_order
+ @objects = @objects.order(request_order)
+ else
+ # default to created_at desc, ignoring any currently requested ordering because it doesn't apply to this klass
+ @objects = @objects.order("#{klass.table_name}.created_at desc")
+ end
+
+ @limit = limit_all - all_objects.count
+ apply_where_limit_order_params klass
+ klass_items_available = @objects.
+ except(:limit).except(:offset).
+ count(:id, distinct: true)
+ @items_available += klass_items_available
+ @offset = [@offset - klass_items_available, 0].max
+
+ all_objects += @objects.to_a
+ end
+
+ @objects = all_objects
+ @limit = limit_all
+ @offset = offset_all
+ end
+
+end
--- /dev/null
+class Arvados::V1::HumansController < ApplicationController
+end
--- /dev/null
+class Arvados::V1::JobTasksController < ApplicationController
+ accept_attribute_as_json :parameters, Hash
+end
--- /dev/null
+class Arvados::V1::JobsController < ApplicationController
+ accept_attribute_as_json :script_parameters, Hash
+ accept_attribute_as_json :runtime_constraints, Hash
+ accept_attribute_as_json :tasks_summary, Hash
+ skip_before_filter :find_object_by_uuid, :only => [:queue, :queue_size]
+ skip_before_filter :render_404_if_no_object, :only => [:queue, :queue_size]
+
+ def create
+ [:repository, :script, :script_version, :script_parameters].each do |r|
+ if !resource_attrs[r]
+ return send_error("#{r} attribute must be specified",
+ status: :unprocessable_entity)
+ end
+ end
+
+ # We used to ask for the minimum_, exclude_, and no_reuse params
+ # in the job resource. Now we advertise them as flags that alter
+ # the behavior of the create action.
+ [:minimum_script_version, :exclude_script_versions].each do |attr|
+ if resource_attrs.has_key? attr
+ params[attr] = resource_attrs.delete attr
+ end
+ end
+ if resource_attrs.has_key? :no_reuse
+ params[:find_or_create] = !resource_attrs.delete(:no_reuse)
+ end
+
+ if params[:find_or_create]
+ return if false.equal?(load_filters_param)
+ if @filters.empty? # Translate older creation parameters into filters.
+ @filters =
+ [["repository", "=", resource_attrs[:repository]],
+ ["script", "=", resource_attrs[:script]],
+ ["script_version", "in git",
+ params[:minimum_script_version] || resource_attrs[:script_version]],
+ ["script_version", "not in git", params[:exclude_script_versions]],
+ ].reject { |filter| filter.last.nil? or filter.last.empty? }
+ if image_search = resource_attrs[:runtime_constraints].andand["docker_image"]
+ if image_tag = resource_attrs[:runtime_constraints]["docker_image_tag"]
+ image_search += ":#{image_tag}"
+ end
+ @filters.append(["docker_image_locator", "in docker", image_search])
+ else
+ @filters.append(["docker_image_locator", "=", nil])
+ end
+ if sdk_version = resource_attrs[:runtime_constraints].andand["arvados_sdk_version"]
+ @filters.append(["arvados_sdk_version", "in git", sdk_version])
+ end
+ begin
+ load_job_specific_filters
+ rescue ArgumentError => error
+ return send_error(error.message)
+ end
+ end
+
+ # Check specified filters for some reasonableness.
+ filter_names = @filters.map { |f| f.first }.uniq
+ ["repository", "script"].each do |req_filter|
+ if not filter_names.include?(req_filter)
+ return send_error("#{req_filter} filter required")
+ end
+ end
+
+ # Search for a reusable Job, and return it if found.
+ @objects = Job.readable_by(current_user)
+ apply_filters
+ @object = nil
+ incomplete_job = nil
+ @objects.each do |j|
+ if j.nondeterministic != true and
+ ["Queued", "Running", "Complete"].include?(j.state) and
+ j.script_parameters == resource_attrs[:script_parameters]
+ if j.state != "Complete" && j.owner_uuid == current_user.uuid
+ # We'll use this if we don't find a job that has completed
+ incomplete_job ||= j
+ else
+ if Collection.readable_by(current_user).find_by_portable_data_hash(j.output)
+ # Record the first job in the list
+ if !@object
+ @object = j
+ end
+ # Ensure that all candidate jobs actually did produce the same output
+ if @object.output != j.output
+ @object = nil
+ break
+ end
+ end
+ end
+ end
+ @object ||= incomplete_job
+ if @object
+ return show
+ end
+ end
+ end
+
+ super
+ end
+
+ def cancel
+ reload_object_before_update
+ @object.update_attributes! state: Job::Cancelled
+ show
+ end
+
+ def lock
+ @object.lock current_user.uuid
+ show
+ end
+
+ class LogStreamer
+ Q_UPDATE_INTERVAL = 12
+ def initialize(job, opts={})
+ @job = job
+ @opts = opts
+ end
+ def each
+ if @job.finished_at
+ yield "#{@job.uuid} finished at #{@job.finished_at}\n"
+ return
+ end
+ while not @job.started_at
+ # send a summary (job queue + available nodes) to the client
+ # every few seconds while waiting for the job to start
+ last_ack_at ||= Time.now - Q_UPDATE_INTERVAL - 1
+ if Time.now - last_ack_at >= Q_UPDATE_INTERVAL
+ nodes_in_state = {idle: 0, alloc: 0}
+ ActiveRecord::Base.uncached do
+ Node.where('hostname is not ?', nil).collect do |n|
+ if n.info[:slurm_state]
+ nodes_in_state[n.info[:slurm_state]] ||= 0
+ nodes_in_state[n.info[:slurm_state]] += 1
+ end
+ end
+ end
+ job_queue = Job.queue
+ n_queued_before_me = 0
+ job_queue.each do |j|
+ break if j.uuid == @job.uuid
+ n_queued_before_me += 1
+ end
+ yield "#{Time.now}" \
+ " job #{@job.uuid}" \
+ " queue_position #{n_queued_before_me}" \
+ " queue_size #{job_queue.size}" \
+ " nodes_idle #{nodes_in_state[:idle]}" \
+ " nodes_alloc #{nodes_in_state[:alloc]}\n"
+ last_ack_at = Time.now
+ end
+ sleep 3
+ ActiveRecord::Base.uncached do
+ @job.reload
+ end
+ end
+ end
+ end
+
+ def queue
+ params[:order] ||= ['priority desc', 'created_at']
+ load_limit_offset_order_params
+ load_where_param
+ @where.merge!({state: Job::Queued})
+ return if false.equal?(load_filters_param)
+ find_objects_for_index
+ index
+ end
+
+ def queue_size
+ # Users may not be allowed to see all the jobs in the queue, so provide a
+ # method to get just the queue size in order to get a gist of how busy the
+ # cluster is.
+ render :json => {:queue_size => Job.queue.size}
+ end
+
+ def self._create_requires_parameters
+ (super rescue {}).
+ merge({
+ find_or_create: {
+ type: 'boolean', required: false, default: false
+ },
+ filters: {
+ type: 'array', required: false
+ },
+ minimum_script_version: {
+ type: 'string', required: false
+ },
+ exclude_script_versions: {
+ type: 'array', required: false
+ },
+ })
+ end
+
+ def self._queue_requires_parameters
+ self._index_requires_parameters
+ end
+
+ protected
+
+ def load_job_specific_filters
+ # Convert Job-specific @filters entries into general SQL filters.
+ script_info = {"repository" => nil, "script" => nil}
+ git_filters = Hash.new do |hash, key|
+ hash[key] = {"max_version" => "HEAD", "exclude_versions" => []}
+ end
+ @filters.select! do |(attr, operator, operand)|
+ if (script_info.has_key? attr) and (operator == "=")
+ if script_info[attr].nil?
+ script_info[attr] = operand
+ elsif script_info[attr] != operand
+ raise ArgumentError.new("incompatible #{attr} filters")
+ end
+ end
+ case operator
+ when "in git"
+ git_filters[attr]["min_version"] = operand
+ false
+ when "not in git"
+ git_filters[attr]["exclude_versions"] += Array.wrap(operand)
+ false
+ when "in docker", "not in docker"
+ image_hashes = Array.wrap(operand).flat_map do |search_term|
+ image_search, image_tag = search_term.split(':', 2)
+ Collection.
+ find_all_for_docker_image(image_search, image_tag, @read_users).
+ map(&:portable_data_hash)
+ end
+ @filters << [attr, operator.sub(/ docker$/, ""), image_hashes]
+ false
+ else
+ true
+ end
+ end
+
+ # Build a real script_version filter from any "not? in git" filters.
+ git_filters.each_pair do |attr, filter|
+ case attr
+ when "script_version"
+ script_info.each_pair do |key, value|
+ if value.nil?
+ raise ArgumentError.new("script_version filter needs #{key} filter")
+ end
+ end
+ filter["repository"] = script_info["repository"]
+ begin
+ filter["max_version"] = resource_attrs[:script_version]
+ rescue
+ # Using HEAD, set earlier by the hash default, is fine.
+ end
+ when "arvados_sdk_version"
+ filter["repository"] = "arvados"
+ else
+ raise ArgumentError.new("unknown attribute for git filter: #{attr}")
+ end
+ version_range = Commit.find_commit_range(current_user,
+ filter["repository"],
+ filter["min_version"],
+ filter["max_version"],
+ filter["exclude_versions"])
+ if version_range.nil?
+ raise ArgumentError.
+ new("error searching #{filter['repository']} from " +
+ "'#{filter['min_version']}' to '#{filter['max_version']}', " +
+ "excluding #{filter['exclude_versions']}")
+ end
+ @filters.append([attr, "in", version_range])
+ end
+ end
+
+ def load_filters_param
+ begin
+ super
+ load_job_specific_filters
+ rescue ArgumentError => error
+ send_error(error.message)
+ false
+ end
+ end
+end
--- /dev/null
+class Arvados::V1::KeepDisksController < ApplicationController
+ skip_before_filter :require_auth_scope, :only => :ping
+
+ def self._ping_requires_parameters
+ {
+ uuid: {required: false},
+ ping_secret: {required: true},
+ node_uuid: {required: false},
+ filesystem_uuid: {required: false},
+ service_host: {required: false},
+ service_port: {required: true},
+ service_ssl_flag: {required: true}
+ }
+ end
+
+ def ping
+ params[:service_host] ||= request.env['REMOTE_ADDR']
+ act_as_system_user do
+ if not @object.ping params
+ return render_not_found "object not found"
+ end
+ # Render the :superuser view (i.e., include the ping_secret) even
+ # if !current_user.is_admin. This is safe because @object.ping's
+ # success implies the ping_secret was already known by the client.
+ render json: @object.as_api_response(:superuser)
+ end
+ end
+
+ def find_objects_for_index
+ # all users can list all keep disks
+ @objects = model_class.where('1=1')
+ super
+ end
+
+ def find_object_by_uuid
+ @object = KeepDisk.where(uuid: (params[:id] || params[:uuid])).first
+ if !@object && current_user.andand.is_admin
+ # Create a new KeepDisk and ping it.
+ @object = KeepDisk.new(filesystem_uuid: params[:filesystem_uuid])
+ @object.save!
+
+ # In the first ping from this new filesystem_uuid, we can't
+ # expect the keep node to know the ping_secret so we made sure
+ # we got an admin token. Here we add ping_secret to params so
+ # KeepNode.ping() understands this update is properly
+ # authenticated.
+ params[:ping_secret] = @object.ping_secret
+ end
+ end
+end
--- /dev/null
+class Arvados::V1::KeepServicesController < ApplicationController
+
+ skip_before_filter :find_object_by_uuid, only: :accessible
+ skip_before_filter :render_404_if_no_object, only: :accessible
+
+ def find_objects_for_index
+ # all users can list all keep services
+ @objects = model_class.where('1=1')
+ super
+ end
+
+ def accessible
+ if request.headers['X-External-Client'] == '1'
+ @objects = model_class.where('service_type=?', 'proxy')
+ else
+ @objects = model_class.where('service_type=?', 'disk')
+ end
+ render_list
+ end
+
+end
--- /dev/null
+class Arvados::V1::LinksController < ApplicationController
+
+ def check_uuid_kind uuid, kind
+ if kind and ArvadosModel::resource_class_for_uuid(uuid).andand.kind != kind
+ send_error("'#{kind}' does not match uuid '#{uuid}', expected '#{ArvadosModel::resource_class_for_uuid(uuid).andand.kind}'",
+ status: 422)
+ nil
+ else
+ true
+ end
+ end
+
+ def create
+ return if ! check_uuid_kind resource_attrs[:head_uuid], resource_attrs[:head_kind]
+ return if ! check_uuid_kind resource_attrs[:tail_uuid], resource_attrs[:tail_kind]
+
+ resource_attrs.delete :head_kind
+ resource_attrs.delete :tail_kind
+ super
+ end
+
+ def get_permissions
+ if current_user.can?(manage: @object)
+ # find all links and return them
+ @objects = Link.where(link_class: "permission",
+ head_uuid: params[:uuid])
+ @offset = 0
+ @limit = @objects.count
+ render_list
+ else
+ render :json => { errors: ['Forbidden'] }.to_json, status: 403
+ end
+ end
+
+ protected
+
+ def find_object_by_uuid
+ if action_name == 'get_permissions'
+ # get_permissions accepts a UUID for any kind of object.
+ @object = ArvadosModel::resource_class_for_uuid(params[:uuid])
+ .readable_by(*@read_users)
+ .where(uuid: params[:uuid])
+ .first
+ else
+ super
+ if @object.nil?
+ # Normally group permission links are not readable_by users.
+ # Make an exception for users with permission to manage the group.
+ # FIXME: Solve this more generally - see the controller tests.
+ link = Link.find_by_uuid(params[:uuid])
+ if (not link.nil?) and
+ (link.link_class == "permission") and
+ (@read_users.any? { |u| u.can?(manage: link.head_uuid) })
+ @object = link
+ end
+ end
+ end
+ end
+
+ # Overrides ApplicationController load_where_param
+ def load_where_param
+ super
+
+ # head_kind and tail_kind columns are now virtual,
+ # equivilent functionality is now provided by
+ # 'is_a', so fix up any old-style 'where' clauses.
+ if @where
+ @filters ||= []
+ if @where[:head_kind]
+ @filters << ['head_uuid', 'is_a', @where[:head_kind]]
+ @where.delete :head_kind
+ end
+ if @where[:tail_kind]
+ @filters << ['tail_uuid', 'is_a', @where[:tail_kind]]
+ @where.delete :tail_kind
+ end
+ end
+ end
+
+ # Overrides ApplicationController load_filters_param
+ def load_filters_param
+ super
+
+ # head_kind and tail_kind columns are now virtual,
+ # equivilent functionality is now provided by
+ # 'is_a', so fix up any old-style 'filter' clauses.
+ @filters = @filters.map do |k|
+ if k[0] == 'head_kind' and k[1] == '='
+ ['head_uuid', 'is_a', k[2]]
+ elsif k[0] == 'tail_kind' and k[1] == '='
+ ['tail_uuid', 'is_a', k[2]]
+ else
+ k
+ end
+ end
+ end
+
+end
--- /dev/null
+class Arvados::V1::LogsController < ApplicationController
+ # Overrides ApplicationController load_where_param
+ def load_where_param
+ super
+
+ # object_kind and column is now virtual,
+ # equivilent functionality is now provided by
+ # 'is_a', so fix up any old-style 'where' clauses.
+ if @where
+ @filters ||= []
+ if @where[:object_kind]
+ @filters << ['object_uuid', 'is_a', @where[:object_kind]]
+ @where.delete :object_kind
+ end
+ end
+ end
+
+ # Overrides ApplicationController load_filters_param
+ def load_filters_param
+ super
+
+ # object_kind and column is now virtual,
+ # equivilent functionality is now provided by
+ # 'is_a', so fix up any old-style 'filter' clauses.
+ @filters = @filters.map do |k|
+ if k[0] == 'object_kind' and k[1] == '='
+ ['object_uuid', 'is_a', k[2]]
+ else
+ k
+ end
+ end
+ end
+
+end
--- /dev/null
+class Arvados::V1::NodesController < ApplicationController
+ skip_before_filter :require_auth_scope, :only => :ping
+ skip_before_filter :find_object_by_uuid, :only => :ping
+ skip_before_filter :render_404_if_no_object, :only => :ping
+
+ def update
+ if resource_attrs[:job_uuid]
+ @object.job_readable = readable_job_uuids(resource_attrs[:job_uuid]).any?
+ end
+ super
+ end
+
+ def self._ping_requires_parameters
+ { ping_secret: {required: true} }
+ end
+
+ def ping
+ act_as_system_user do
+ @object = Node.where(uuid: (params[:id] || params[:uuid])).first
+ if !@object
+ return render_not_found
+ end
+ ping_data = {
+ ip: params[:local_ipv4] || request.env['REMOTE_ADDR'],
+ ec2_instance_id: params[:instance_id]
+ }
+ [:ping_secret, :total_cpu_cores, :total_ram_mb, :total_scratch_mb]
+ .each do |key|
+ ping_data[key] = params[key] if params[key]
+ end
+ @object.ping(ping_data)
+ if @object.info['ping_secret'] == params[:ping_secret]
+ render json: @object.as_api_response(:superuser)
+ else
+ raise "Invalid ping_secret after ping"
+ end
+ end
+ end
+
+ def find_objects_for_index
+ if !current_user.andand.is_admin && current_user.andand.is_active
+ # active non-admin users can list nodes that are (or were
+ # recently) working
+ @objects = model_class.where('last_ping_at >= ?', Time.now - 1.hours)
+ end
+ super
+ job_uuids = @objects.map { |n| n[:job_uuid] }.compact
+ assoc_jobs = readable_job_uuids(job_uuids)
+ @objects.each do |node|
+ node.job_readable = assoc_jobs.include?(node[:job_uuid])
+ end
+ end
+
+ protected
+
+ def readable_job_uuids(*uuids)
+ Job.readable_by(*@read_users).select(:uuid).where(uuid: uuids).map(&:uuid)
+ end
+end
--- /dev/null
+class Arvados::V1::PipelineInstancesController < ApplicationController
+ accept_attribute_as_json :components, Hash
+ accept_attribute_as_json :properties, Hash
+ accept_attribute_as_json :components_summary, Hash
+end
--- /dev/null
+class Arvados::V1::PipelineTemplatesController < ApplicationController
+ accept_attribute_as_json :components, Hash
+end
--- /dev/null
+class Arvados::V1::RepositoriesController < ApplicationController
+ skip_before_filter :find_object_by_uuid, :only => :get_all_permissions
+ skip_before_filter :render_404_if_no_object, :only => :get_all_permissions
+ before_filter :admin_required, :only => :get_all_permissions
+ def get_all_permissions
+ @users = {}
+ User.includes(:authorized_keys).all.each do |u|
+ @users[u.uuid] = u
+ end
+ admins = @users.select { |k,v| v.is_admin }
+ @user_aks = {}
+ @repo_info = {}
+ @repos = Repository.includes(:permissions).all
+ @repos.each do |repo|
+ gitolite_permissions = ''
+ perms = []
+ repo.permissions.each do |perm|
+ if ArvadosModel::resource_class_for_uuid(perm.tail_uuid) == Group
+ @users.each do |user_uuid, user|
+ user.group_permissions.each do |group_uuid, perm_mask|
+ if perm_mask[:manage]
+ perms << {name: 'can_manage', user_uuid: user_uuid}
+ elsif perm_mask[:write]
+ perms << {name: 'can_write', user_uuid: user_uuid}
+ elsif perm_mask[:read]
+ perms << {name: 'can_read', user_uuid: user_uuid}
+ end
+ end
+ end
+ else
+ perms << {name: perm.name, user_uuid: perm.tail_uuid}
+ end
+ end
+ # Owner of the repository, and all admins, can RW
+ ([repo.owner_uuid] + admins.keys).each do |user_uuid|
+ perms << {name: 'can_write', user_uuid: user_uuid}
+ end
+ perms.each do |perm|
+ user_uuid = perm[:user_uuid]
+ @user_aks[user_uuid] = @users[user_uuid].andand.authorized_keys.andand.
+ collect do |ak|
+ {
+ public_key: ak.public_key,
+ authorized_key_uuid: ak.uuid
+ }
+ end || []
+ if @user_aks[user_uuid].any?
+ @repo_info[repo.uuid] ||= {
+ uuid: repo.uuid,
+ name: repo.name,
+ push_url: repo.push_url,
+ fetch_url: repo.fetch_url,
+ user_permissions: {}
+ }
+ ri = (@repo_info[repo.uuid][:user_permissions][user_uuid] ||= {})
+ ri[perm[:name]] = true
+ end
+ end
+ end
+ @repo_info.values.each do |repo_users|
+ repo_users[:user_permissions].each do |user_uuid,perms|
+ if perms['can_manage']
+ perms[:gitolite_permissions] = 'RW'
+ perms['can_write'] = true
+ perms['can_read'] = true
+ elsif perms['can_write']
+ perms[:gitolite_permissions] = 'RW'
+ perms['can_read'] = true
+ elsif perms['can_read']
+ perms[:gitolite_permissions] = 'R'
+ end
+ end
+ end
+ render json: {
+ kind: 'arvados#RepositoryPermissionSnapshot',
+ repositories: @repo_info.values,
+ user_keys: @user_aks
+ }
+ end
+end
--- /dev/null
+class Arvados::V1::SchemaController < ApplicationController
+ skip_before_filter :find_objects_for_index
+ skip_before_filter :find_object_by_uuid
+ skip_before_filter :render_404_if_no_object
+ skip_before_filter :require_auth_scope
+
+ def index
+ expires_in 24.hours, public: true
+ discovery = Rails.cache.fetch 'arvados_v1_rest_discovery' do
+ Rails.application.eager_load!
+ discovery = {
+ kind: "discovery#restDescription",
+ discoveryVersion: "v1",
+ id: "arvados:v1",
+ name: "arvados",
+ version: "v1",
+ revision: "20131114",
+ source_version: (Rails.application.config.source_version ? Rails.application.config.source_version : "No version information available") + (Rails.application.config.local_modified ? Rails.application.config.local_modified.to_s : ''),
+ generatedAt: Time.now.iso8601,
+ title: "Arvados API",
+ description: "The API to interact with Arvados.",
+ documentationLink: "http://doc.arvados.org/api/index.html",
+ protocol: "rest",
+ baseUrl: root_url + "arvados/v1/",
+ basePath: "/arvados/v1/",
+ rootUrl: root_url,
+ servicePath: "arvados/v1/",
+ batchPath: "batch",
+ defaultTrashLifetime: Rails.application.config.default_trash_lifetime,
+ parameters: {
+ alt: {
+ type: "string",
+ description: "Data format for the response.",
+ default: "json",
+ enum: [
+ "json"
+ ],
+ enumDescriptions: [
+ "Responses with Content-Type of application/json"
+ ],
+ location: "query"
+ },
+ fields: {
+ type: "string",
+ description: "Selector specifying which fields to include in a partial response.",
+ location: "query"
+ },
+ key: {
+ type: "string",
+ description: "API key. Your API key identifies your project and provides you with API access, quota, and reports. Required unless you provide an OAuth 2.0 token.",
+ location: "query"
+ },
+ oauth_token: {
+ type: "string",
+ description: "OAuth 2.0 token for the current user.",
+ location: "query"
+ }
+ },
+ auth: {
+ oauth2: {
+ scopes: {
+ "https://api.curoverse.com/auth/arvados" => {
+ description: "View and manage objects"
+ },
+ "https://api.curoverse.com/auth/arvados.readonly" => {
+ description: "View objects"
+ }
+ }
+ }
+ },
+ schemas: {},
+ resources: {}
+ }
+
+ if Rails.application.config.websocket_address
+ discovery[:websocketUrl] = Rails.application.config.websocket_address
+ elsif ENV['ARVADOS_WEBSOCKETS']
+ discovery[:websocketUrl] = (root_url.sub /^http/, 'ws') + "websocket"
+ end
+
+ ActiveRecord::Base.descendants.reject(&:abstract_class?).each do |k|
+ begin
+ ctl_class = "Arvados::V1::#{k.to_s.pluralize}Controller".constantize
+ rescue
+ # No controller -> no discovery.
+ next
+ end
+ object_properties = {}
+ k.columns.
+ select { |col| col.name != 'id' }.
+ collect do |col|
+ if k.serialized_attributes.has_key? col.name
+ object_properties[col.name] = {
+ type: k.serialized_attributes[col.name].object_class.to_s
+ }
+ else
+ object_properties[col.name] = {
+ type: col.type
+ }
+ end
+ end
+ discovery[:schemas][k.to_s + 'List'] = {
+ id: k.to_s + 'List',
+ description: k.to_s + ' list',
+ type: "object",
+ properties: {
+ kind: {
+ type: "string",
+ description: "Object type. Always arvados##{k.to_s.camelcase(:lower)}List.",
+ default: "arvados##{k.to_s.camelcase(:lower)}List"
+ },
+ etag: {
+ type: "string",
+ description: "List version."
+ },
+ items: {
+ type: "array",
+ description: "The list of #{k.to_s.pluralize}.",
+ items: {
+ "$ref" => k.to_s
+ }
+ },
+ next_link: {
+ type: "string",
+ description: "A link to the next page of #{k.to_s.pluralize}."
+ },
+ next_page_token: {
+ type: "string",
+ description: "The page token for the next page of #{k.to_s.pluralize}."
+ },
+ selfLink: {
+ type: "string",
+ description: "A link back to this list."
+ }
+ }
+ }
+ discovery[:schemas][k.to_s] = {
+ id: k.to_s,
+ description: k.to_s,
+ type: "object",
+ uuidPrefix: (k.respond_to?(:uuid_prefix) ? k.uuid_prefix : nil),
+ properties: {
+ uuid: {
+ type: "string",
+ description: "Object ID."
+ },
+ etag: {
+ type: "string",
+ description: "Object version."
+ }
+ }.merge(object_properties)
+ }
+ discovery[:resources][k.to_s.underscore.pluralize] = {
+ methods: {
+ get: {
+ id: "arvados.#{k.to_s.underscore.pluralize}.get",
+ path: "#{k.to_s.underscore.pluralize}/{uuid}",
+ httpMethod: "GET",
+ description: "Gets a #{k.to_s}'s metadata by UUID.",
+ parameters: {
+ uuid: {
+ type: "string",
+ description: "The UUID of the #{k.to_s} in question.",
+ required: true,
+ location: "path"
+ }
+ },
+ parameterOrder: [
+ "uuid"
+ ],
+ response: {
+ "$ref" => k.to_s
+ },
+ scopes: [
+ "https://api.curoverse.com/auth/arvados",
+ "https://api.curoverse.com/auth/arvados.readonly"
+ ]
+ },
+ list: {
+ id: "arvados.#{k.to_s.underscore.pluralize}.list",
+ path: k.to_s.underscore.pluralize,
+ httpMethod: "GET",
+ description:
+ %|List #{k.to_s.pluralize}.
+
+ The <code>list</code> method returns a
+ <a href="/api/resources.html">resource list</a> of
+ matching #{k.to_s.pluralize}. For example:
+
+ <pre>
+ {
+ "kind":"arvados##{k.to_s.camelcase(:lower)}List",
+ "etag":"",
+ "self_link":"",
+ "next_page_token":"",
+ "next_link":"",
+ "items":[
+ ...
+ ],
+ "items_available":745,
+ "_profile":{
+ "request_time":0.157236317
+ }
+ </pre>|,
+ parameters: {
+ limit: {
+ type: "integer",
+ description: "Maximum number of #{k.to_s.underscore.pluralize} to return.",
+ default: "100",
+ format: "int32",
+ minimum: "0",
+ location: "query",
+ },
+ offset: {
+ type: "integer",
+ description: "Number of #{k.to_s.underscore.pluralize} to skip before first returned record.",
+ default: "0",
+ format: "int32",
+ minimum: "0",
+ location: "query",
+ },
+ filters: {
+ type: "array",
+ description: "Conditions for filtering #{k.to_s.underscore.pluralize}.",
+ location: "query"
+ },
+ where: {
+ type: "object",
+ description: "Conditions for filtering #{k.to_s.underscore.pluralize}. (Deprecated. Use filters instead.)",
+ location: "query"
+ },
+ order: {
+ type: "string",
+ description: "Order in which to return matching #{k.to_s.underscore.pluralize}.",
+ location: "query"
+ },
+ select: {
+ type: "array",
+ description: "Select which fields to return",
+ location: "query"
+ },
+ distinct: {
+ type: "boolean",
+ description: "Return each distinct object",
+ location: "query"
+ }
+ },
+ response: {
+ "$ref" => "#{k.to_s}List"
+ },
+ scopes: [
+ "https://api.curoverse.com/auth/arvados",
+ "https://api.curoverse.com/auth/arvados.readonly"
+ ]
+ },
+ create: {
+ id: "arvados.#{k.to_s.underscore.pluralize}.create",
+ path: "#{k.to_s.underscore.pluralize}",
+ httpMethod: "POST",
+ description: "Create a new #{k.to_s}.",
+ parameters: {},
+ request: {
+ required: true,
+ properties: {
+ k.to_s.underscore => {
+ "$ref" => k.to_s
+ }
+ }
+ },
+ response: {
+ "$ref" => k.to_s
+ },
+ scopes: [
+ "https://api.curoverse.com/auth/arvados"
+ ]
+ },
+ update: {
+ id: "arvados.#{k.to_s.underscore.pluralize}.update",
+ path: "#{k.to_s.underscore.pluralize}/{uuid}",
+ httpMethod: "PUT",
+ description: "Update attributes of an existing #{k.to_s}.",
+ parameters: {
+ uuid: {
+ type: "string",
+ description: "The UUID of the #{k.to_s} in question.",
+ required: true,
+ location: "path"
+ }
+ },
+ request: {
+ required: true,
+ properties: {
+ k.to_s.underscore => {
+ "$ref" => k.to_s
+ }
+ }
+ },
+ response: {
+ "$ref" => k.to_s
+ },
+ scopes: [
+ "https://api.curoverse.com/auth/arvados"
+ ]
+ },
+ delete: {
+ id: "arvados.#{k.to_s.underscore.pluralize}.delete",
+ path: "#{k.to_s.underscore.pluralize}/{uuid}",
+ httpMethod: "DELETE",
+ description: "Delete an existing #{k.to_s}.",
+ parameters: {
+ uuid: {
+ type: "string",
+ description: "The UUID of the #{k.to_s} in question.",
+ required: true,
+ location: "path"
+ }
+ },
+ response: {
+ "$ref" => k.to_s
+ },
+ scopes: [
+ "https://api.curoverse.com/auth/arvados"
+ ]
+ }
+ }
+ }
+ # Check for Rails routes that don't match the usual actions
+ # listed above
+ d_methods = discovery[:resources][k.to_s.underscore.pluralize][:methods]
+ Rails.application.routes.routes.each do |route|
+ action = route.defaults[:action]
+ httpMethod = ['GET', 'POST', 'PUT', 'DELETE'].map { |method|
+ method if route.verb.match(method)
+ }.compact.first
+ if httpMethod and
+ route.defaults[:controller] == 'arvados/v1/' + k.to_s.underscore.pluralize and
+ ctl_class.action_methods.include? action
+ if !d_methods[action.to_sym]
+ method = {
+ id: "arvados.#{k.to_s.underscore.pluralize}.#{action}",
+ path: route.path.spec.to_s.sub('/arvados/v1/','').sub('(.:format)','').sub(/:(uu)?id/,'{uuid}'),
+ httpMethod: httpMethod,
+ description: "#{action} #{k.to_s.underscore.pluralize}",
+ parameters: {},
+ response: {
+ "$ref" => (action == 'index' ? "#{k.to_s}List" : k.to_s)
+ },
+ scopes: [
+ "https://api.curoverse.com/auth/arvados"
+ ]
+ }
+ route.segment_keys.each do |key|
+ if key != :format
+ key = :uuid if key == :id
+ method[:parameters][key] = {
+ type: "string",
+ description: "",
+ required: true,
+ location: "path"
+ }
+ end
+ end
+ else
+ # We already built a generic method description, but we
+ # might find some more required parameters through
+ # introspection.
+ method = d_methods[action.to_sym]
+ end
+ if ctl_class.respond_to? "_#{action}_requires_parameters".to_sym
+ ctl_class.send("_#{action}_requires_parameters".to_sym).each do |k, v|
+ if v.is_a? Hash
+ method[:parameters][k] = v
+ else
+ method[:parameters][k] = {}
+ end
+ if !method[:parameters][k][:default].nil?
+ # The JAVA SDK is sensitive to all values being strings
+ method[:parameters][k][:default] = method[:parameters][k][:default].to_s
+ end
+ method[:parameters][k][:type] ||= 'string'
+ method[:parameters][k][:description] ||= ''
+ method[:parameters][k][:location] = (route.segment_keys.include?(k) ? 'path' : 'query')
+ if method[:parameters][k][:required].nil?
+ method[:parameters][k][:required] = v != false
+ end
+ end
+ end
+ d_methods[action.to_sym] = method
+ end
+ end
+ end
+ discovery
+ end
+ render json: discovery
+ end
+end
--- /dev/null
+class Arvados::V1::SpecimensController < ApplicationController
+end
--- /dev/null
+class Arvados::V1::TraitsController < ApplicationController
+end
--- /dev/null
+class Arvados::V1::UserAgreementsController < ApplicationController
+ before_filter :admin_required, except: [:index, :sign, :signatures]
+ skip_before_filter :find_object_by_uuid, only: [:sign, :signatures]
+ skip_before_filter :render_404_if_no_object, only: [:sign, :signatures]
+
+ def model_class
+ Link
+ end
+
+ def table_name
+ 'links'
+ end
+
+ def index
+ if not current_user.is_invited
+ # New users cannot see user agreements until/unless invited to
+ # use this installation.
+ @objects = []
+ else
+ current_user_uuid = current_user.uuid
+ act_as_system_user do
+ uuids = Link.where("owner_uuid = ? and link_class = ? and name = ? and tail_uuid = ? and head_uuid like ?",
+ system_user_uuid,
+ 'signature',
+ 'require',
+ system_user_uuid,
+ Collection.uuid_like_pattern).
+ collect &:head_uuid
+ @objects = Collection.where('uuid in (?)', uuids)
+ end
+ end
+ @response_resource_name = 'collection'
+ super
+ end
+
+ def signatures
+ current_user_uuid = (current_user.andand.is_admin && params[:uuid]) ||
+ current_user.uuid
+ act_as_system_user do
+ @objects = Link.where("owner_uuid = ? and link_class = ? and name = ? and tail_uuid = ? and head_uuid like ?",
+ system_user_uuid,
+ 'signature',
+ 'click',
+ current_user_uuid,
+ Collection.uuid_like_pattern)
+ end
+ @response_resource_name = 'link'
+ render_list
+ end
+
+ def sign
+ current_user_uuid = current_user.uuid
+ act_as_system_user do
+ @object = Link.create(link_class: 'signature',
+ name: 'click',
+ tail_uuid: current_user_uuid,
+ head_uuid: params[:uuid])
+ end
+ show
+ end
+
+ def create
+ usage_error
+ end
+
+ def new
+ usage_error
+ end
+
+ def update
+ usage_error
+ end
+
+ def destroy
+ usage_error
+ end
+
+ protected
+ def usage_error
+ raise ArgumentError.new \
+ "Manage user agreements via Collections and Links instead."
+ end
+
+end
--- /dev/null
+class Arvados::V1::UsersController < ApplicationController
+ accept_attribute_as_json :prefs, Hash
+
+ skip_before_filter :find_object_by_uuid, only:
+ [:activate, :current, :system, :setup]
+ skip_before_filter :render_404_if_no_object, only:
+ [:activate, :current, :system, :setup]
+ before_filter :admin_required, only: [:setup, :unsetup]
+
+ def current
+ @object = current_user
+ show
+ end
+ def system
+ @object = system_user
+ show
+ end
+
+ def activate
+ if current_user.andand.is_admin && params[:uuid]
+ @object = User.find params[:uuid]
+ else
+ @object = current_user
+ end
+ if not @object.is_active
+ if not (current_user.is_admin or @object.is_invited)
+ logger.warn "User #{@object.uuid} called users.activate " +
+ "but is not invited"
+ raise ArgumentError.new "Cannot activate without being invited."
+ end
+ act_as_system_user do
+ required_uuids = Link.where("owner_uuid = ? and link_class = ? and name = ? and tail_uuid = ? and head_uuid like ?",
+ system_user_uuid,
+ 'signature',
+ 'require',
+ system_user_uuid,
+ Collection.uuid_like_pattern).
+ collect(&:head_uuid)
+ signed_uuids = Link.where(owner_uuid: system_user_uuid,
+ link_class: 'signature',
+ name: 'click',
+ tail_uuid: @object.uuid,
+ head_uuid: required_uuids).
+ collect(&:head_uuid)
+ todo_uuids = required_uuids - signed_uuids
+ if todo_uuids.empty?
+ @object.update_attributes is_active: true
+ logger.info "User #{@object.uuid} activated"
+ else
+ logger.warn "User #{@object.uuid} called users.activate " +
+ "before signing agreements #{todo_uuids.inspect}"
+ raise ArvadosModel::PermissionDeniedError.new \
+ "Cannot activate without user agreements #{todo_uuids.inspect}."
+ end
+ end
+ end
+ show
+ end
+
+ # create user object and all the needed links
+ def setup
+ @object = nil
+ if params[:uuid]
+ @object = User.find_by_uuid params[:uuid]
+ if !@object
+ return render_404_if_no_object
+ end
+ object_found = true
+ else
+ if !params[:user]
+ raise ArgumentError.new "Required uuid or user"
+ else
+ if params[:user]['uuid']
+ @object = User.find_by_uuid params[:user]['uuid']
+ if @object
+ object_found = true
+ end
+ end
+
+ if !@object
+ if !params[:user]['email']
+ raise ArgumentError.new "Require user email"
+ end
+
+ if !params[:openid_prefix]
+ raise ArgumentError.new "Required openid_prefix parameter is missing."
+ end
+
+ @object = model_class.create! resource_attrs
+ end
+ end
+ end
+
+ if object_found
+ @response = @object.setup_repo_vm_links params[:repo_name],
+ params[:vm_uuid], params[:openid_prefix]
+ else
+ @response = User.setup @object, params[:openid_prefix],
+ params[:repo_name], params[:vm_uuid]
+ end
+
+ # setup succeeded. send email to user
+ if params[:send_notification_email] == true || params[:send_notification_email] == 'true'
+ UserNotifier.account_is_setup(@object).deliver
+ end
+
+ render json: { kind: "arvados#HashList", items: @response.as_api_response(nil) }
+ end
+
+ # delete user agreements, vm, repository, login links; set state to inactive
+ def unsetup
+ reload_object_before_update
+ @object.unsetup
+ show
+ end
+
+ protected
+
+ def self._setup_requires_parameters
+ {
+ user: {
+ type: 'object', required: false
+ },
+ openid_prefix: {
+ type: 'string', required: false
+ },
+ repo_name: {
+ type: 'string', required: false
+ },
+ vm_uuid: {
+ type: 'string', required: false
+ },
+ send_notification_email: {
+ type: 'boolean', required: false, default: false
+ },
+ }
+ end
+
+ def apply_filters
+ return super if @read_users.any? &:is_admin
+ if params[:uuid] != current_user.andand.uuid
+ # Non-admin index/show returns very basic information about readable users.
+ safe_attrs = ["uuid", "is_active", "email", "first_name", "last_name"]
+ if @select
+ @select = @select & safe_attrs
+ else
+ @select = safe_attrs
+ end
+ @filters += [['is_active', '=', true]]
+ end
+ super
+ end
+end
--- /dev/null
+class Arvados::V1::VirtualMachinesController < ApplicationController
+ skip_before_filter :find_object_by_uuid, :only => :get_all_logins
+ skip_before_filter :render_404_if_no_object, :only => :get_all_logins
+ before_filter(:admin_required,
+ :only => [:logins, :get_all_logins])
+
+ def logins
+ get_all_logins
+ end
+
+ def get_all_logins
+ @users = {}
+ User.includes(:authorized_keys).all.each do |u|
+ @users[u.uuid] = u
+ end
+ @response = []
+ @vms = VirtualMachine.includes(:login_permissions)
+ if @object
+ @vms = @vms.where('uuid=?', @object.uuid)
+ else
+ @vms = @vms.all
+ end
+ @vms.each do |vm|
+ vm.login_permissions.each do |perm|
+ user_uuid = perm.tail_uuid
+ @users[user_uuid].andand.authorized_keys.andand.each do |ak|
+ username = perm.properties.andand['username']
+ if username
+ @response << {
+ username: username,
+ hostname: vm.hostname,
+ public_key: ak.public_key,
+ user_uuid: user_uuid,
+ virtual_machine_uuid: vm.uuid,
+ authorized_key_uuid: ak.uuid
+ }
+ end
+ end
+ end
+ end
+ render json: { kind: "arvados#HashList", items: @response }
+ end
+end
--- /dev/null
+class DatabaseController < ApplicationController
+ skip_before_filter :find_object_by_uuid
+ skip_before_filter :render_404_if_no_object
+ before_filter :admin_required
+ def reset
+ raise ArvadosModel::PermissionDeniedError unless Rails.env == 'test'
+
+ # Sanity check: If someone has actually logged in here, this might
+ # not really be a throwaway database. Client test suites should
+ # use @example.com email addresses when creating user records, so
+ # we can tell they're not valuable.
+ user_uuids = User.
+ where('email is null or email not like ?', '%@example.com').
+ collect &:uuid
+ fixture_uuids =
+ YAML::load_file(File.expand_path('../../../test/fixtures/users.yml',
+ __FILE__)).
+ values.collect { |u| u['uuid'] }
+ unexpected_uuids = user_uuids - fixture_uuids
+ if unexpected_uuids.any?
+ logger.error("Running in test environment, but non-fixture users exist: " +
+ "#{unexpected_uuids}")
+ raise ArvadosModel::PermissionDeniedError
+ end
+
+ require 'active_record/fixtures'
+
+ # What kinds of fixtures do we have?
+ fixturesets = Dir.glob(Rails.root.join('test', 'fixtures', '*.yml')).
+ collect { |yml| yml.match(/([^\/]*)\.yml$/)[1] }
+
+ table_names = '"' + ActiveRecord::Base.connection.tables.join('","') + '"'
+
+ attempts_left = 20
+ begin
+ ActiveRecord::Base.transaction do
+ # Avoid deadlock by locking all tables before doing anything
+ # drastic.
+ ActiveRecord::Base.connection.execute \
+ "LOCK TABLE #{table_names} IN ACCESS EXCLUSIVE MODE"
+
+ # Delete existing fixtures (and everything else) from fixture
+ # tables
+ fixturesets.each do |x|
+ x.classify.constantize.unscoped.delete_all
+ end
+
+ # create_fixtures() is a no-op for cached fixture sets, so
+ # uncache them all.
+ ActiveRecord::Fixtures.reset_cache
+ ActiveRecord::Fixtures.
+ create_fixtures(Rails.root.join('test', 'fixtures'), fixturesets)
+
+ # Dump cache of permissions etc.
+ Rails.cache.clear
+ ActiveRecord::Base.connection.clear_query_cache
+
+ # Reload database seeds
+ DatabaseSeeds.install
+ end
+ rescue ActiveRecord::StatementInvalid => e
+ if "#{e.inspect}" =~ /deadlock detected/i and (attempts_left -= 1) > 0
+ logger.info "Waiting for lock -- #{e.inspect}"
+ sleep 0.5
+ retry
+ end
+ raise
+ end
+
+ # Done.
+ render json: {success: true}
+ end
+end
--- /dev/null
+class StaticController < ApplicationController
+ respond_to :json, :html
+
+ skip_before_filter :find_object_by_uuid
+ skip_before_filter :render_404_if_no_object
+ skip_before_filter :require_auth_scope, only: [:home, :empty, :login_failure]
+
+ def home
+ respond_to do |f|
+ f.html do
+ if Rails.configuration.workbench_address
+ redirect_to Rails.configuration.workbench_address
+ else
+ render_not_found "Oops, this is an API endpoint. You probably want to point your browser to an Arvados Workbench site instead."
+ end
+ end
+ f.json do
+ render_not_found "Path not found."
+ end
+ end
+ end
+
+ def empty
+ render text: "-"
+ end
+
+end
--- /dev/null
+class UserSessionsController < ApplicationController
+ before_filter :require_auth_scope, :only => [ :destroy ]
+
+ skip_before_filter :set_cors_headers
+ skip_before_filter :find_object_by_uuid
+ skip_before_filter :render_404_if_no_object
+
+ respond_to :html
+
+ # omniauth callback method
+ def create
+ omniauth = env['omniauth.auth']
+
+ identity_url_ok = (omniauth['info']['identity_url'].length > 0) rescue false
+ unless identity_url_ok
+ # Whoa. This should never happen.
+ logger.error "UserSessionsController.create: omniauth object missing/invalid"
+ logger.error "omniauth.pretty_inspect():\n\n#{omniauth.pretty_inspect()}"
+
+ return redirect_to login_failure_url
+ end
+
+ user = User.find_by_identity_url(omniauth['info']['identity_url'])
+ if not user
+ # Check for permission to log in to an existing User record with
+ # a different identity_url
+ Link.where("link_class = ? and name = ? and tail_uuid = ? and head_uuid like ?",
+ 'permission',
+ 'can_login',
+ omniauth['info']['email'],
+ User.uuid_like_pattern).each do |link|
+ if prefix = link.properties['identity_url_prefix']
+ if prefix == omniauth['info']['identity_url'][0..prefix.size-1]
+ user = User.find_by_uuid(link.head_uuid)
+ break if user
+ end
+ end
+ end
+ end
+ if not user
+ # New user registration
+ user = User.new(:email => omniauth['info']['email'],
+ :first_name => omniauth['info']['first_name'],
+ :last_name => omniauth['info']['last_name'],
+ :identity_url => omniauth['info']['identity_url'],
+ :is_active => Rails.configuration.new_users_are_active,
+ :owner_uuid => system_user_uuid)
+ act_as_system_user do
+ user.save or raise Exception.new(user.errors.messages)
+ end
+ else
+ user.email = omniauth['info']['email']
+ user.first_name = omniauth['info']['first_name']
+ user.last_name = omniauth['info']['last_name']
+ if user.identity_url.nil?
+ # First login to a pre-activated account
+ user.identity_url = omniauth['info']['identity_url']
+ end
+ end
+
+ # For the benefit of functional and integration tests:
+ @user = user
+
+ # prevent ArvadosModel#before_create and _update from throwing
+ # "unauthorized":
+ Thread.current[:user] = user
+
+ user.save or raise Exception.new(user.errors.messages)
+
+ omniauth.delete('extra')
+
+ # Give the authenticated user a cookie for direct API access
+ session[:user_id] = user.id
+ session[:api_client_uuid] = nil
+ session[:api_client_trusted] = true # full permission to see user's secrets
+
+ @redirect_to = root_path
+ if params.has_key?(:return_to)
+ return send_api_token_to(params[:return_to], user)
+ end
+ redirect_to @redirect_to
+ end
+
+ # Omniauth failure callback
+ def failure
+ flash[:notice] = params[:message]
+ end
+
+ # logout - Clear our rack session BUT essentially redirect to the provider
+ # to clean up the Devise session from there too !
+ def logout
+ session[:user_id] = nil
+
+ flash[:notice] = 'You have logged off'
+ return_to = params[:return_to] || root_url
+ redirect_to "#{CUSTOM_PROVIDER_URL}/users/sign_out?redirect_uri=#{CGI.escape return_to}"
+ end
+
+ # login - Just bounce to /auth/joshid. The only purpose of this function is
+ # to save the return_to parameter (if it exists; see the application
+ # controller). /auth/joshid bypasses the application controller.
+ def login
+ auth_provider = if params[:auth_provider] then "auth_provider=#{CGI.escape(params[:auth_provider])}" else "" end
+
+ if current_user and params[:return_to]
+ # Already logged in; just need to send a token to the requesting
+ # API client.
+ #
+ # FIXME: if current_user has never authorized this app before,
+ # ask for confirmation here!
+
+ send_api_token_to(params[:return_to], current_user)
+ elsif params[:return_to]
+ redirect_to "/auth/joshid?return_to=#{CGI.escape(params[:return_to])}&#{auth_provider}"
+ else
+ redirect_to "/auth/joshid?#{auth_provider}"
+ end
+ end
+
+ def send_api_token_to(callback_url, user)
+ # Give the API client a token for making API calls on behalf of
+ # the authenticated user
+
+ # Stub: automatically register all new API clients
+ api_client_url_prefix = callback_url.match(%r{^.*?://[^/]+})[0] + '/'
+ act_as_system_user do
+ @api_client = ApiClient.find_or_create_by_url_prefix api_client_url_prefix
+ end
+
+ api_client_auth = ApiClientAuthorization.
+ new(user: user,
+ api_client: @api_client,
+ created_by_ip_address: remote_ip,
+ scopes: ["all"])
+ api_client_auth.save!
+
+ if callback_url.index('?')
+ callback_url += '&'
+ else
+ callback_url += '?'
+ end
+ callback_url += 'api_token=' + api_client_auth.api_token
+ redirect_to callback_url
+ end
+
+ def cross_origin_forbidden
+ send_error 'Forbidden', status: 403
+ end
+end
--- /dev/null
+module ApiClientAuthorizationsHelper
+end
--- /dev/null
+module ApiClientsHelper
+end
--- /dev/null
+module ApplicationHelper
+ include CurrentApiClient
+end
--- /dev/null
+module AuthorizedKeysHelper
+end
--- /dev/null
+module CollectionsHelper
+end
--- /dev/null
+module CommitAncestorsHelper
+end
--- /dev/null
+module CommitsHelper
+end
--- /dev/null
+module GroupsHelper
+end
--- /dev/null
+module HumansHelper
+end
--- /dev/null
+module JobTasksHelper
+end
--- /dev/null
+module JobsHelper
+end
--- /dev/null
+module KeepDisksHelper
+end
--- /dev/null
+module LinksHelper
+end
--- /dev/null
+module LogsHelper
+end
--- /dev/null
+module NodesHelper
+end
--- /dev/null
+module PipelineInstancesHelper
+end
--- /dev/null
+module PipelineTemplatesHelper
+end
--- /dev/null
+module RepositoriesHelper
+end
--- /dev/null
+module SpecimensHelper
+end
--- /dev/null
+module TraitsHelper
+end
--- /dev/null
+module VirtualMachinesHelper
+end
--- /dev/null
+class AdminNotifier < ActionMailer::Base
+ include AbstractController::Callbacks
+
+ default from: Rails.configuration.admin_notifier_email_from
+
+ def new_user(user)
+ @user = user
+ if not Rails.configuration.new_user_notification_recipients.empty? then
+ @recipients = Rails.configuration.new_user_notification_recipients
+ logger.info "Sending mail to #{@recipients} about new user #{@user.uuid} (#{@user.full_name} <#{@user.email}>)"
+
+ add_to_subject = ''
+ if Rails.configuration.auto_setup_new_users
+ add_to_subject = @user.is_invited ? ' and setup' : ', but not setup'
+ end
+
+ mail(to: @recipients,
+ subject: "#{Rails.configuration.email_subject_prefix}New user created#{add_to_subject} notification"
+ )
+ end
+ end
+
+ def new_inactive_user(user)
+ @user = user
+ if not Rails.configuration.new_inactive_user_notification_recipients.empty? then
+ @recipients = Rails.configuration.new_inactive_user_notification_recipients
+ logger.info "Sending mail to #{@recipients} about new user #{@user.uuid} (#{@user.full_name} <#{@user.email}>)"
+ mail(to: @recipients,
+ subject: "#{Rails.configuration.email_subject_prefix}New inactive user notification"
+ )
+ end
+ end
+
+end
--- /dev/null
+class ProfileNotifier < ActionMailer::Base
+ default from: Rails.configuration.admin_notifier_email_from
+
+ def profile_created(user, address)
+ @user = user
+ mail(to: address, subject: "Profile created by #{@user.email}")
+ end
+end
--- /dev/null
+class UserNotifier < ActionMailer::Base
+ include AbstractController::Callbacks
+
+ default from: Rails.configuration.user_notifier_email_from
+
+ def account_is_setup(user)
+ @user = user
+ mail(to: user.email, subject: 'Welcome to Curoverse')
+ end
+
+end
--- /dev/null
+# Perform api_token checking very early in the request process. We want to do
+# this in the Rack stack instead of in ApplicationController because
+# websockets needs access to authentication but doesn't use any of the rails
+# active dispatch infrastructure.
+class ArvadosApiToken
+
+ # Create a new ArvadosApiToken handler
+ # +app+ The next layer of the Rack stack.
+ def initialize(app = nil, options = nil)
+ @app = app if app.respond_to?(:call)
+ end
+
+ def call env
+ # First, clean up just in case we have a multithreaded server and thread
+ # local variables are still set from a prior request. Also useful for
+ # tests that call this code to set up the environment.
+ Thread.current[:api_client_ip_address] = nil
+ Thread.current[:api_client_authorization] = nil
+ Thread.current[:api_client_uuid] = nil
+ Thread.current[:api_client] = nil
+ Thread.current[:user] = nil
+
+ request = Rack::Request.new(env)
+ params = request.params
+ remote_ip = env["action_dispatch.remote_ip"]
+
+ Thread.current[:request_starttime] = Time.now
+ user = nil
+ api_client = nil
+ api_client_auth = nil
+ supplied_token =
+ params["api_token"] ||
+ params["oauth_token"] ||
+ env["HTTP_AUTHORIZATION"].andand.match(/OAuth2 ([a-z0-9]+)/).andand[1]
+ if supplied_token
+ api_client_auth = ApiClientAuthorization.
+ includes(:api_client, :user).
+ where('api_token=? and (expires_at is null or expires_at > CURRENT_TIMESTAMP)', supplied_token).
+ first
+ if api_client_auth.andand.user
+ user = api_client_auth.user
+ api_client = api_client_auth.api_client
+ else
+ # Token seems valid, but points to a non-existent (deleted?) user.
+ api_client_auth = nil
+ end
+ end
+ Thread.current[:api_client_ip_address] = remote_ip
+ Thread.current[:api_client_authorization] = api_client_auth
+ Thread.current[:api_client_uuid] = api_client.andand.uuid
+ Thread.current[:api_client] = api_client
+ Thread.current[:user] = user
+ if api_client_auth
+ api_client_auth.last_used_at = Time.now
+ api_client_auth.last_used_by_ip_address = remote_ip.to_s
+ api_client_auth.save validate: false
+ end
+
+ @app.call env if @app
+ end
+end
--- /dev/null
+require 'rack'
+require 'faye/websocket'
+require 'eventmachine'
+
+# A Rack middleware to handle inbound websocket connection requests and hand
+# them over to the faye websocket library.
+class RackSocket
+
+ DEFAULT_ENDPOINT = '/websocket'
+
+ # Stop EventMachine on signal, this should give it a chance to to unwind any
+ # open connections.
+ def die_gracefully_on_signal
+ Signal.trap("INT") { EM.stop }
+ Signal.trap("TERM") { EM.stop }
+ end
+
+ # Create a new RackSocket handler
+ # +app+ The next layer of the Rack stack.
+ #
+ # Accepts options:
+ # +:handler+ (Required) A class to handle new connections. #initialize will
+ # call handler.new to create the actual handler instance object. When a new
+ # websocket connection is established, #on_connect on the handler instance
+ # object will be called with the new connection.
+ #
+ # +:mount+ The HTTP request path that will be recognized for websocket
+ # connect requests, defaults to '/websocket'.
+ #
+ # +:websocket_only+ If true, the server will only handle websocket requests,
+ # and all other requests will result in an error. If false, unhandled
+ # non-websocket requests will be passed along on to 'app' in the usual Rack
+ # way.
+ def initialize(app = nil, options = nil)
+ @app = app if app.respond_to?(:call)
+ @options = [app, options].grep(Hash).first || {}
+ @endpoint = @options[:mount] || DEFAULT_ENDPOINT
+ @websocket_only = @options[:websocket_only] || false
+
+ # from https://gist.github.com/eatenbyagrue/1338545#file-eventmachine-rb
+ if defined?(PhusionPassenger)
+ PhusionPassenger.on_event(:starting_worker_process) do |forked|
+ # for passenger, we need to avoid orphaned threads
+ if forked && EM.reactor_running?
+ EM.stop
+ end
+ Thread.new {
+ EM.run
+ }
+ die_gracefully_on_signal
+ end
+ else
+ # faciliates debugging
+ Thread.abort_on_exception = true
+ # just spawn a thread and start it up
+ Thread.new {
+ EM.run
+ }
+ end
+
+ # Create actual handler instance object from handler class.
+ @handler = @options[:handler].new
+ end
+
+ # Handle websocket connection request, or pass on to the next middleware
+ # supplied in +app+ initialize (unless +:websocket_only+ option is true, in
+ # which case return an error response.)
+ # +env+ the Rack environment with information about the request.
+ def call env
+ request = Rack::Request.new(env)
+ if request.path_info == @endpoint and Faye::WebSocket.websocket?(env)
+ ws = Faye::WebSocket.new(env, nil, :ping => 30)
+
+ # Notify handler about new connection
+ @handler.on_connect ws
+
+ # Return async Rack response
+ ws.rack_response
+ elsif not @websocket_only
+ @app.call env
+ else
+ [406, {"Content-Type" => "text/plain"}, ["Only websocket connections are permitted on this port."]]
+ end
+ end
+
+end
--- /dev/null
+class ApiClient < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ has_many :api_client_authorizations
+
+ api_accessible :user, extend: :common do |t|
+ t.add :name
+ t.add :url_prefix
+ t.add :is_trusted
+ end
+end
--- /dev/null
+class ApiClientAuthorization < ArvadosModel
+ include KindAndEtag
+ include CommonApiTemplate
+
+ belongs_to :api_client
+ belongs_to :user
+ after_initialize :assign_random_api_token
+ serialize :scopes, Array
+
+ api_accessible :user, extend: :common do |t|
+ t.add :owner_uuid
+ t.add :user_id
+ t.add :api_client_id
+ t.add :api_token
+ t.add :created_by_ip_address
+ t.add :default_owner_uuid
+ t.add :expires_at
+ t.add :last_used_at
+ t.add :last_used_by_ip_address
+ t.add :scopes
+ end
+
+ UNLOGGED_CHANGES = ['last_used_at', 'last_used_by_ip_address', 'updated_at']
+
+ def assign_random_api_token
+ self.api_token ||= rand(2**256).to_s(36)
+ end
+
+ def owner_uuid
+ self.user.andand.uuid
+ end
+ def owner_uuid_was
+ self.user_id_changed? ? User.where(id: self.user_id_was).first.andand.uuid : self.user.andand.uuid
+ end
+ def owner_uuid_changed?
+ self.user_id_changed?
+ end
+
+ def uuid
+ self.api_token
+ end
+ def uuid=(x) end
+ def uuid_was
+ self.api_token_was
+ end
+ def uuid_changed?
+ self.api_token_changed?
+ end
+
+ def modified_by_client_uuid
+ nil
+ end
+ def modified_by_client_uuid=(x) end
+
+ def modified_by_user_uuid
+ nil
+ end
+ def modified_by_user_uuid=(x) end
+
+ def modified_at
+ nil
+ end
+ def modified_at=(x) end
+
+ def scopes_allow?(req_s)
+ scopes.each do |scope|
+ return true if (scope == 'all') or (scope == req_s) or
+ ((scope.end_with? '/') and (req_s.start_with? scope))
+ end
+ false
+ end
+
+ def scopes_allow_request?(request)
+ scopes_allow? [request.request_method, request.path].join(' ')
+ end
+
+ def logged_attributes
+ attrs = attributes.dup
+ attrs.delete('api_token')
+ attrs
+ end
+
+ protected
+
+ def permission_to_create
+ current_user.andand.is_admin or (current_user.andand.id == self.user_id)
+ end
+
+ def permission_to_update
+ (permission_to_create and
+ not self.user_id_changed? and
+ not self.owner_uuid_changed?)
+ end
+
+ def log_update
+ super unless (changed - UNLOGGED_CHANGES).empty?
+ end
+end
--- /dev/null
+require 'has_uuid'
+
+class ArvadosModel < ActiveRecord::Base
+ self.abstract_class = true
+
+ include CurrentApiClient # current_user, current_api_client, etc.
+
+ attr_protected :created_at
+ attr_protected :modified_by_user_uuid
+ attr_protected :modified_by_client_uuid
+ attr_protected :modified_at
+ after_initialize :log_start_state
+ before_save :ensure_permission_to_save
+ before_save :ensure_owner_uuid_is_permitted
+ before_save :ensure_ownership_path_leads_to_user
+ before_destroy :ensure_owner_uuid_is_permitted
+ before_destroy :ensure_permission_to_destroy
+ before_create :update_modified_by_fields
+ before_update :maybe_update_modified_by_fields
+ after_create :log_create
+ after_update :log_update
+ after_destroy :log_destroy
+ after_find :convert_serialized_symbols_to_strings
+ before_validation :normalize_collection_uuids
+ validate :ensure_serialized_attribute_type
+ validate :ensure_valid_uuids
+
+ # Note: This only returns permission links. It does not account for
+ # permissions obtained via user.is_admin or
+ # user.uuid==object.owner_uuid.
+ has_many :permissions, :foreign_key => :head_uuid, :class_name => 'Link', :primary_key => :uuid, :conditions => "link_class = 'permission'"
+
+ class PermissionDeniedError < StandardError
+ def http_status
+ 403
+ end
+ end
+
+ class AlreadyLockedError < StandardError
+ def http_status
+ 403
+ end
+ end
+
+ class UnauthorizedError < StandardError
+ def http_status
+ 401
+ end
+ end
+
+ def self.kind_class(kind)
+ kind.match(/^arvados\#(.+)$/)[1].classify.safe_constantize rescue nil
+ end
+
+ def href
+ "#{current_api_base}/#{self.class.to_s.pluralize.underscore}/#{self.uuid}"
+ end
+
+ def self.searchable_columns operator
+ textonly_operator = !operator.match(/[<=>]/)
+ self.columns.select do |col|
+ case col.type
+ when :string, :text
+ true
+ when :datetime, :integer, :boolean
+ !textonly_operator
+ else
+ false
+ end
+ end.map(&:name)
+ end
+
+ def self.attribute_column attr
+ self.columns.select { |col| col.name == attr.to_s }.first
+ end
+
+ def self.attributes_required_columns
+ # This method returns a hash. Each key is the name of an API attribute,
+ # and it's mapped to a list of database columns that must be fetched
+ # to generate that attribute.
+ # This implementation generates a simple map of attributes to
+ # matching column names. Subclasses can override this method
+ # to specify that method-backed API attributes need to fetch
+ # specific columns from the database.
+ all_columns = columns.map(&:name)
+ api_column_map = Hash.new { |hash, key| hash[key] = [] }
+ methods.grep(/^api_accessible_\w+$/).each do |method_name|
+ next if method_name == :api_accessible_attributes
+ send(method_name).each_pair do |api_attr_name, col_name|
+ col_name = col_name.to_s
+ if all_columns.include?(col_name)
+ api_column_map[api_attr_name.to_s] |= [col_name]
+ end
+ end
+ end
+ api_column_map
+ end
+
+ # If current user can manage the object, return an array of uuids of
+ # users and groups that have permission to write the object. The
+ # first two elements are always [self.owner_uuid, current user's
+ # uuid].
+ #
+ # If current user can write but not manage the object, return
+ # [self.owner_uuid, current user's uuid].
+ #
+ # If current user cannot write this object, just return
+ # [self.owner_uuid].
+ def writable_by
+ unless (owner_uuid == current_user.uuid or
+ current_user.is_admin or
+ (current_user.groups_i_can(:manage) & [uuid, owner_uuid]).any?)
+ if ((current_user.groups_i_can(:write) + [current_user.uuid]) &
+ [uuid, owner_uuid]).any?
+ return [owner_uuid, current_user.uuid]
+ else
+ return [owner_uuid]
+ end
+ end
+ [owner_uuid, current_user.uuid] + permissions.collect do |p|
+ if ['can_write', 'can_manage'].index p.name
+ p.tail_uuid
+ end
+ end.compact.uniq
+ end
+
+ # Return a query with read permissions restricted to the union of of the
+ # permissions of the members of users_list, i.e. if something is readable by
+ # any user in users_list, it will be readable in the query returned by this
+ # function.
+ def self.readable_by(*users_list)
+ # Get rid of troublesome nils
+ users_list.compact!
+
+ # Load optional keyword arguments, if they exist.
+ if users_list.last.is_a? Hash
+ kwargs = users_list.pop
+ else
+ kwargs = {}
+ end
+
+ # Check if any of the users are admin. If so, we're done.
+ if users_list.select { |u| u.is_admin }.any?
+ return self
+ end
+
+ # Collect the uuids for each user and any groups readable by each user.
+ user_uuids = users_list.map { |u| u.uuid }
+ uuid_list = user_uuids + users_list.flat_map { |u| u.groups_i_can(:read) }
+ sql_conds = []
+ sql_params = []
+ sql_table = kwargs.fetch(:table_name, table_name)
+ or_object_uuid = ''
+
+ # This row is owned by a member of users_list, or owned by a group
+ # readable by a member of users_list
+ # or
+ # This row uuid is the uuid of a member of users_list
+ # or
+ # A permission link exists ('write' and 'manage' implicitly include
+ # 'read') from a member of users_list, or a group readable by users_list,
+ # to this row, or to the owner of this row (see join() below).
+ sql_conds += ["#{sql_table}.uuid in (?)"]
+ sql_params += [user_uuids]
+
+ if uuid_list.any?
+ sql_conds += ["#{sql_table}.owner_uuid in (?)"]
+ sql_params += [uuid_list]
+
+ sanitized_uuid_list = uuid_list.
+ collect { |uuid| sanitize(uuid) }.join(', ')
+ permitted_uuids = "(SELECT head_uuid FROM links WHERE link_class='permission' AND tail_uuid IN (#{sanitized_uuid_list}))"
+ sql_conds += ["#{sql_table}.uuid IN #{permitted_uuids}"]
+ end
+
+ if sql_table == "links" and users_list.any?
+ # This row is a 'permission' or 'resources' link class
+ # The uuid for a member of users_list is referenced in either the head
+ # or tail of the link
+ sql_conds += ["(#{sql_table}.link_class in (#{sanitize 'permission'}, #{sanitize 'resources'}) AND (#{sql_table}.head_uuid IN (?) OR #{sql_table}.tail_uuid IN (?)))"]
+ sql_params += [user_uuids, user_uuids]
+ end
+
+ if sql_table == "logs" and users_list.any?
+ # Link head points to the object described by this row
+ sql_conds += ["#{sql_table}.object_uuid IN #{permitted_uuids}"]
+
+ # This object described by this row is owned by this user, or owned by a group readable by this user
+ sql_conds += ["#{sql_table}.object_owner_uuid in (?)"]
+ sql_params += [uuid_list]
+ end
+
+ # Link head points to this row, or to the owner of this row (the
+ # thing to be read)
+ #
+ # Link tail originates from this user, or a group that is readable
+ # by this user (the identity with authorization to read)
+ #
+ # Link class is 'permission' ('write' and 'manage' implicitly
+ # include 'read')
+ where(sql_conds.join(' OR '), *sql_params)
+ end
+
+ def logged_attributes
+ attributes
+ end
+
+ protected
+
+ def ensure_ownership_path_leads_to_user
+ if new_record? or owner_uuid_changed?
+ uuid_in_path = {owner_uuid => true, uuid => true}
+ x = owner_uuid
+ while (owner_class = ArvadosModel::resource_class_for_uuid(x)) != User
+ begin
+ if x == uuid
+ # Test for cycles with the new version, not the DB contents
+ x = owner_uuid
+ elsif !owner_class.respond_to? :find_by_uuid
+ raise ActiveRecord::RecordNotFound.new
+ else
+ x = owner_class.find_by_uuid(x).owner_uuid
+ end
+ rescue ActiveRecord::RecordNotFound => e
+ errors.add :owner_uuid, "is not owned by any user: #{e}"
+ return false
+ end
+ if uuid_in_path[x]
+ if x == owner_uuid
+ errors.add :owner_uuid, "would create an ownership cycle"
+ else
+ errors.add :owner_uuid, "has an ownership cycle"
+ end
+ return false
+ end
+ uuid_in_path[x] = true
+ end
+ end
+ true
+ end
+
+ def ensure_owner_uuid_is_permitted
+ raise PermissionDeniedError if !current_user
+
+ if new_record? and respond_to? :owner_uuid=
+ self.owner_uuid ||= current_user.uuid
+ end
+
+ if self.owner_uuid.nil?
+ errors.add :owner_uuid, "cannot be nil"
+ raise PermissionDeniedError
+ end
+
+ rsc_class = ArvadosModel::resource_class_for_uuid owner_uuid
+ unless rsc_class == User or rsc_class == Group
+ errors.add :owner_uuid, "must be set to User or Group"
+ raise PermissionDeniedError
+ end
+
+ # Verify "write" permission on old owner
+ # default fail unless one of:
+ # owner_uuid did not change
+ # previous owner_uuid is nil
+ # current user is the old owner
+ # current user is this object
+ # current user can_write old owner
+ unless !owner_uuid_changed? or
+ owner_uuid_was.nil? or
+ current_user.uuid == self.owner_uuid_was or
+ current_user.uuid == self.uuid or
+ current_user.can? write: self.owner_uuid_was
+ logger.warn "User #{current_user.uuid} tried to modify #{self.class.to_s} #{uuid} but does not have permission to write old owner_uuid #{owner_uuid_was}"
+ errors.add :owner_uuid, "cannot be changed without write permission on old owner"
+ raise PermissionDeniedError
+ end
+
+ # Verify "write" permission on new owner
+ # default fail unless one of:
+ # current_user is this object
+ # current user can_write new owner
+ unless current_user == self or current_user.can? write: owner_uuid
+ logger.warn "User #{current_user.uuid} tried to modify #{self.class.to_s} #{uuid} but does not have permission to write new owner_uuid #{owner_uuid}"
+ errors.add :owner_uuid, "cannot be changed without write permission on new owner"
+ raise PermissionDeniedError
+ end
+
+ true
+ end
+
+ def ensure_permission_to_save
+ unless (new_record? ? permission_to_create : permission_to_update)
+ raise PermissionDeniedError
+ end
+ end
+
+ def permission_to_create
+ current_user.andand.is_active
+ end
+
+ def permission_to_update
+ if !current_user
+ logger.warn "Anonymous user tried to update #{self.class.to_s} #{self.uuid_was}"
+ return false
+ end
+ if !current_user.is_active
+ logger.warn "Inactive user #{current_user.uuid} tried to update #{self.class.to_s} #{self.uuid_was}"
+ return false
+ end
+ return true if current_user.is_admin
+ if self.uuid_changed?
+ logger.warn "User #{current_user.uuid} tried to change uuid of #{self.class.to_s} #{self.uuid_was} to #{self.uuid}"
+ return false
+ end
+ return true
+ end
+
+ def ensure_permission_to_destroy
+ raise PermissionDeniedError unless permission_to_destroy
+ end
+
+ def permission_to_destroy
+ permission_to_update
+ end
+
+ def maybe_update_modified_by_fields
+ update_modified_by_fields if self.changed? or self.new_record?
+ true
+ end
+
+ def update_modified_by_fields
+ self.updated_at = Time.now
+ self.owner_uuid ||= current_default_owner if self.respond_to? :owner_uuid=
+ self.modified_at = Time.now
+ self.modified_by_user_uuid = current_user ? current_user.uuid : nil
+ self.modified_by_client_uuid = current_api_client ? current_api_client.uuid : nil
+ true
+ end
+
+ def self.has_symbols? x
+ if x.is_a? Hash
+ x.each do |k,v|
+ return true if has_symbols?(k) or has_symbols?(v)
+ end
+ false
+ elsif x.is_a? Array
+ x.each do |k|
+ return true if has_symbols?(k)
+ end
+ false
+ else
+ (x.class == Symbol)
+ end
+ end
+
+ def self.recursive_stringify x
+ if x.is_a? Hash
+ Hash[x.collect do |k,v|
+ [recursive_stringify(k), recursive_stringify(v)]
+ end]
+ elsif x.is_a? Array
+ x.collect do |k|
+ recursive_stringify k
+ end
+ elsif x.is_a? Symbol
+ x.to_s
+ else
+ x
+ end
+ end
+
+ def ensure_serialized_attribute_type
+ # Specifying a type in the "serialize" declaration causes rails to
+ # raise an exception if a different data type is retrieved from
+ # the database during load(). The validation preventing such
+ # crash-inducing records from being inserted in the database in
+ # the first place seems to have been left as an exercise to the
+ # developer.
+ self.class.serialized_attributes.each do |colname, attr|
+ if attr.object_class
+ if self.attributes[colname].class != attr.object_class
+ self.errors.add colname.to_sym, "must be a #{attr.object_class.to_s}, not a #{self.attributes[colname].class.to_s}"
+ elsif self.class.has_symbols? attributes[colname]
+ self.errors.add colname.to_sym, "must not contain symbols: #{attributes[colname].inspect}"
+ end
+ end
+ end
+ end
+
+ def convert_serialized_symbols_to_strings
+ # ensure_serialized_attribute_type should prevent symbols from
+ # getting into the database in the first place. If someone managed
+ # to get them into the database (perhaps using an older version)
+ # we'll convert symbols to strings when loading from the
+ # database. (Otherwise, loading and saving an object with existing
+ # symbols in a serialized field will crash.)
+ self.class.serialized_attributes.each do |colname, attr|
+ if self.class.has_symbols? attributes[colname]
+ attributes[colname] = self.class.recursive_stringify attributes[colname]
+ self.send(colname + '=',
+ self.class.recursive_stringify(attributes[colname]))
+ end
+ end
+ end
+
+ def foreign_key_attributes
+ attributes.keys.select { |a| a.match /_uuid$/ }
+ end
+
+ def skip_uuid_read_permission_check
+ %w(modified_by_client_uuid)
+ end
+
+ def skip_uuid_existence_check
+ []
+ end
+
+ def normalize_collection_uuids
+ foreign_key_attributes.each do |attr|
+ attr_value = send attr
+ if attr_value.is_a? String and
+ attr_value.match /^[0-9a-f]{32,}(\+[@\w]+)*$/
+ begin
+ send "#{attr}=", Collection.normalize_uuid(attr_value)
+ rescue
+ # TODO: abort instead of silently accepting unnormalizable value?
+ end
+ end
+ end
+ end
+
+ @@prefixes_hash = nil
+ def self.uuid_prefixes
+ unless @@prefixes_hash
+ @@prefixes_hash = {}
+ ActiveRecord::Base.descendants.reject(&:abstract_class?).each do |k|
+ if k.respond_to?(:uuid_prefix)
+ @@prefixes_hash[k.uuid_prefix] = k
+ end
+ end
+ end
+ @@prefixes_hash
+ end
+
+ def self.uuid_like_pattern
+ "_____-#{uuid_prefix}-_______________"
+ end
+
+ def self.uuid_regex
+ %r/[a-z0-9]{5}-#{uuid_prefix}-[a-z0-9]{15}/
+ end
+
+ def ensure_valid_uuids
+ specials = [system_user_uuid]
+
+ foreign_key_attributes.each do |attr|
+ if new_record? or send (attr + "_changed?")
+ next if skip_uuid_existence_check.include? attr
+ attr_value = send attr
+ next if specials.include? attr_value
+ if attr_value
+ if (r = ArvadosModel::resource_class_for_uuid attr_value)
+ unless skip_uuid_read_permission_check.include? attr
+ r = r.readable_by(current_user)
+ end
+ if r.where(uuid: attr_value).count == 0
+ errors.add(attr, "'#{attr_value}' not found")
+ end
+ end
+ end
+ end
+ end
+ end
+
+ class Email
+ def self.kind
+ "email"
+ end
+
+ def kind
+ self.class.kind
+ end
+
+ def self.readable_by (*u)
+ self
+ end
+
+ def self.where (u)
+ [{:uuid => u[:uuid]}]
+ end
+ end
+
+ def self.resource_class_for_uuid(uuid)
+ if uuid.is_a? ArvadosModel
+ return uuid.class
+ end
+ unless uuid.is_a? String
+ return nil
+ end
+ resource_class = nil
+
+ Rails.application.eager_load!
+ uuid.match HasUuid::UUID_REGEX do |re|
+ return uuid_prefixes[re[1]] if uuid_prefixes[re[1]]
+ end
+
+ if uuid.match /.+@.+/
+ return Email
+ end
+
+ nil
+ end
+
+ # ArvadosModel.find_by_uuid needs extra magic to allow it to return
+ # an object in any class.
+ def self.find_by_uuid uuid
+ if self == ArvadosModel
+ # If called directly as ArvadosModel.find_by_uuid rather than via subclass,
+ # delegate to the appropriate subclass based on the given uuid.
+ self.resource_class_for_uuid(uuid).find_by_uuid(uuid)
+ else
+ super
+ end
+ end
+
+ def log_start_state
+ @old_etag = etag
+ @old_attributes = logged_attributes
+ end
+
+ def log_change(event_type)
+ log = Log.new(event_type: event_type).fill_object(self)
+ yield log
+ log.save!
+ log_start_state
+ end
+
+ def log_create
+ log_change('create') do |log|
+ log.fill_properties('old', nil, nil)
+ log.update_to self
+ end
+ end
+
+ def log_update
+ log_change('update') do |log|
+ log.fill_properties('old', @old_etag, @old_attributes)
+ log.update_to self
+ end
+ end
+
+ def log_destroy
+ log_change('destroy') do |log|
+ log.fill_properties('old', @old_etag, @old_attributes)
+ log.update_to nil
+ end
+ end
+end
--- /dev/null
+class AuthorizedKey < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ before_create :permission_to_set_authorized_user_uuid
+ before_update :permission_to_set_authorized_user_uuid
+
+ belongs_to :authorized_user, :foreign_key => :authorized_user_uuid, :class_name => 'User', :primary_key => :uuid
+
+ validate :public_key_must_be_unique
+
+ api_accessible :user, extend: :common do |t|
+ t.add :name
+ t.add :key_type
+ t.add :authorized_user_uuid
+ t.add :public_key
+ t.add :expires_at
+ end
+
+ def permission_to_set_authorized_user_uuid
+ # Anonymous users cannot do anything here
+ return false if !current_user
+
+ # Administrators can attach a key to any user account
+ return true if current_user.is_admin
+
+ # All users can attach keys to their own accounts
+ return true if current_user.uuid == authorized_user_uuid
+
+ # Default = deny.
+ false
+ end
+
+ def public_key_must_be_unique
+ if self.public_key
+ #key = /^ssh-(rsa|dss) [A-Za-z0-9+\/=\+]+\b/.match(self.public_key)
+ valid_key = SSHKey.valid_ssh_public_key? self.public_key
+
+ if not valid_key
+ errors.add(:public_key, "does not appear to be a valid ssh-rsa or dsa public key")
+ else
+ # Valid if no other rows have this public key
+ if self.class.where('public_key like ?', "%#{self.public_key}%").any?
+ errors.add(:public_key, "already exists in the database, use a different key.")
+ return false
+ end
+ end
+ end
+ return true
+ end
+end
--- /dev/null
+class Blob
+
+ def initialize locator
+ @locator = locator
+ end
+
+ def empty?
+ !!@locator.match(/^d41d8cd98f00b204e9800998ecf8427e(\+.*)?$/)
+ end
+
+ # In order to get a Blob from Keep, you have to prove either
+ # [a] you have recently written it to Keep yourself, or
+ # [b] apiserver has recently decided that you should be able to read it
+ #
+ # To ensure that the requestor of a blob is authorized to read it,
+ # Keep requires clients to timestamp the blob locator with an expiry
+ # time, and to sign the timestamped locator with their API token.
+ #
+ # A signed blob locator has the form:
+ # locator_hash +A blob_signature @ timestamp
+ # where the timestamp is a Unix time expressed as a hexadecimal value,
+ # and the blob_signature is the signed locator_hash + API token + timestamp.
+ #
+ class InvalidSignatureError < StandardError
+ end
+
+ # Blob.sign_locator: return a signed and timestamped blob locator.
+ #
+ # The 'opts' argument should include:
+ # [required] :key - the Arvados server-side blobstore key
+ # [required] :api_token - user's API token
+ # [optional] :ttl - number of seconds before signature should expire
+ # [optional] :expire - unix timestamp when signature should expire
+ #
+ def self.sign_locator blob_locator, opts
+ # We only use the hash portion for signatures.
+ blob_hash = blob_locator.split('+').first
+
+ # Generate an expiry timestamp (seconds after epoch, base 16)
+ if opts[:expire]
+ if opts[:ttl]
+ raise "Cannot specify both :ttl and :expire options"
+ end
+ timestamp = opts[:expire]
+ else
+ timestamp = Time.now.to_i + (opts[:ttl] || 1209600)
+ end
+ timestamp_hex = timestamp.to_s(16)
+ # => "53163cb4"
+
+ # Generate a signature.
+ signature =
+ generate_signature opts[:key], blob_hash, opts[:api_token], timestamp_hex
+
+ blob_locator + '+A' + signature + '@' + timestamp_hex
+ end
+
+ # Blob.verify_signature
+ # Safely verify the signature on a blob locator.
+ # Return value: true if the locator has a valid signature, false otherwise
+ # Arguments: signed_blob_locator, opts
+ #
+ def self.verify_signature *args
+ begin
+ self.verify_signature! *args
+ true
+ rescue Blob::InvalidSignatureError
+ false
+ end
+ end
+
+ # Blob.verify_signature!
+ # Verify the signature on a blob locator.
+ # Return value: true if the locator has a valid signature
+ # Arguments: signed_blob_locator, opts
+ # Exceptions:
+ # Blob::InvalidSignatureError if the blob locator does not include a
+ # valid signature
+ #
+ def self.verify_signature! signed_blob_locator, opts
+ blob_hash = signed_blob_locator.split('+').first
+ given_signature, timestamp = signed_blob_locator.
+ split('+A').last.
+ split('+').first.
+ split('@')
+
+ if !timestamp
+ raise Blob::InvalidSignatureError.new 'No signature provided.'
+ end
+ if !timestamp.match /^[\da-f]+$/
+ raise Blob::InvalidSignatureError.new 'Timestamp is not a base16 number.'
+ end
+ if timestamp.to_i(16) < Time.now.to_i
+ raise Blob::InvalidSignatureError.new 'Signature expiry time has passed.'
+ end
+
+ my_signature =
+ generate_signature opts[:key], blob_hash, opts[:api_token], timestamp
+
+ if my_signature != given_signature
+ raise Blob::InvalidSignatureError.new 'Signature is invalid.'
+ end
+
+ true
+ end
+
+ def self.generate_signature key, blob_hash, api_token, timestamp
+ OpenSSL::HMAC.hexdigest('sha1', key,
+ [blob_hash,
+ api_token,
+ timestamp].join('@'))
+ end
+end
--- /dev/null
+require 'arvados/keep'
+
+class Collection < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+
+ before_validation :check_encoding
+ before_validation :check_signatures
+ before_validation :strip_manifest_text
+ before_validation :set_portable_data_hash
+ validate :ensure_hash_matches_manifest_text
+
+ # Query only undeleted collections by default.
+ default_scope where("expires_at IS NULL or expires_at > CURRENT_TIMESTAMP")
+
+ api_accessible :user, extend: :common do |t|
+ t.add :name
+ t.add :description
+ t.add :properties
+ t.add :portable_data_hash
+ t.add :signed_manifest_text, as: :manifest_text
+ end
+
+ def self.attributes_required_columns
+ # If we don't list this explicitly, the params[:select] code gets
+ # confused by the way we expose signed_manifest_text as
+ # manifest_text in the API response, and never let clients select
+ # the manifest_text column.
+ super.merge('manifest_text' => ['manifest_text'])
+ end
+
+ def check_signatures
+ return false if self.manifest_text.nil?
+
+ return true if current_user.andand.is_admin
+
+ # Provided the manifest_text hasn't changed materially since an
+ # earlier validation, it's safe to pass this validation on
+ # subsequent passes without checking any signatures. This is
+ # important because the signatures have probably been stripped off
+ # by the time we get to a second validation pass!
+ return true if @signatures_checked and @signatures_checked == compute_pdh
+
+ if self.manifest_text_changed?
+ # Check permissions on the collection manifest.
+ # If any signature cannot be verified, raise PermissionDeniedError
+ # which will return 403 Permission denied to the client.
+ api_token = current_api_client_authorization.andand.api_token
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token,
+ ttl: Rails.configuration.blob_signing_ttl,
+ }
+ self.manifest_text.lines.each do |entry|
+ entry.split[1..-1].each do |tok|
+ if /^[[:digit:]]+:[[:digit:]]+:/.match tok
+ # This is a filename token, not a blob locator. Note that we
+ # keep checking tokens after this, even though manifest
+ # format dictates that all subsequent tokens will also be
+ # filenames. Safety first!
+ elsif Blob.verify_signature tok, signing_opts
+ # OK.
+ elsif Keep::Locator.parse(tok).andand.signature
+ # Signature provided, but verify_signature did not like it.
+ logger.warn "Invalid signature on locator #{tok}"
+ raise ArvadosModel::PermissionDeniedError
+ elsif Rails.configuration.permit_create_collection_with_unsigned_manifest
+ # No signature provided, but we are running in insecure mode.
+ logger.debug "Missing signature on locator #{tok} ignored"
+ elsif Blob.new(tok).empty?
+ # No signature provided -- but no data to protect, either.
+ else
+ logger.warn "Missing signature on locator #{tok}"
+ raise ArvadosModel::PermissionDeniedError
+ end
+ end
+ end
+ end
+ @signatures_checked = compute_pdh
+ end
+
+ def strip_manifest_text
+ if self.manifest_text_changed?
+ # Remove any permission signatures from the manifest.
+ self.class.munge_manifest_locators!(self[:manifest_text]) do |loc|
+ loc.without_signature.to_s
+ end
+ end
+ true
+ end
+
+ def set_portable_data_hash
+ if (portable_data_hash.nil? or
+ portable_data_hash == "" or
+ (manifest_text_changed? and !portable_data_hash_changed?))
+ @need_pdh_validation = false
+ self.portable_data_hash = compute_pdh
+ elsif portable_data_hash_changed?
+ @need_pdh_validation = true
+ begin
+ loc = Keep::Locator.parse!(self.portable_data_hash)
+ loc.strip_hints!
+ if loc.size
+ self.portable_data_hash = loc.to_s
+ else
+ self.portable_data_hash = "#{loc.hash}+#{portable_manifest_text.bytesize}"
+ end
+ rescue ArgumentError => e
+ errors.add(:portable_data_hash, "#{e}")
+ return false
+ end
+ end
+ true
+ end
+
+ def ensure_hash_matches_manifest_text
+ return true unless manifest_text_changed? or portable_data_hash_changed?
+ # No need verify it if :set_portable_data_hash just computed it!
+ return true if not @need_pdh_validation
+ expect_pdh = compute_pdh
+ if expect_pdh != portable_data_hash
+ errors.add(:portable_data_hash,
+ "does not match computed hash #{expect_pdh}")
+ return false
+ end
+ end
+
+ def check_encoding
+ if manifest_text.encoding.name == 'UTF-8' and manifest_text.valid_encoding?
+ true
+ else
+ begin
+ # If Ruby thinks the encoding is something else, like 7-bit
+ # ASCII, but its stored bytes are equal to the (valid) UTF-8
+ # encoding of the same string, we declare it to be a UTF-8
+ # string.
+ utf8 = manifest_text
+ utf8.force_encoding Encoding::UTF_8
+ if utf8.valid_encoding? and utf8 == manifest_text.encode(Encoding::UTF_8)
+ manifest_text = utf8
+ return true
+ end
+ rescue
+ end
+ errors.add :manifest_text, "must use UTF-8 encoding"
+ false
+ end
+ end
+
+ def redundancy_status
+ if redundancy_confirmed_as.nil?
+ 'unconfirmed'
+ elsif redundancy_confirmed_as < redundancy
+ 'degraded'
+ else
+ if redundancy_confirmed_at.nil?
+ 'unconfirmed'
+ elsif Time.now - redundancy_confirmed_at < 7.days
+ 'OK'
+ else
+ 'stale'
+ end
+ end
+ end
+
+ def signed_manifest_text
+ if has_attribute? :manifest_text
+ token = current_api_client_authorization.andand.api_token
+ @signed_manifest_text = self.class.sign_manifest manifest_text, token
+ end
+ end
+
+ def self.sign_manifest manifest, token
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: token,
+ ttl: Rails.configuration.blob_signing_ttl,
+ }
+ m = manifest.dup
+ munge_manifest_locators!(m) do |loc|
+ Blob.sign_locator(loc.to_s, signing_opts)
+ end
+ return m
+ end
+
+ def self.munge_manifest_locators! manifest
+ # Given a manifest text and a block, yield each locator,
+ # and replace it with whatever the block returns.
+ manifest.andand.gsub!(/ [[:xdigit:]]{32}(\+[[:digit:]]+)?(\+\S+)/) do |word|
+ if loc = Keep::Locator.parse(word.strip)
+ " " + yield(loc)
+ else
+ " " + word
+ end
+ end
+ end
+
+ def self.normalize_uuid uuid
+ hash_part = nil
+ size_part = nil
+ uuid.split('+').each do |token|
+ if token.match /^[0-9a-f]{32,}$/
+ raise "uuid #{uuid} has multiple hash parts" if hash_part
+ hash_part = token
+ elsif token.match /^\d+$/
+ raise "uuid #{uuid} has multiple size parts" if size_part
+ size_part = token
+ end
+ end
+ raise "uuid #{uuid} has no hash part" if !hash_part
+ [hash_part, size_part].compact.join '+'
+ end
+
+ # Return array of Collection objects
+ def self.find_all_for_docker_image(search_term, search_tag=nil, readers=nil)
+ readers ||= [Thread.current[:user]]
+ base_search = Link.
+ readable_by(*readers).
+ readable_by(*readers, table_name: "collections").
+ joins("JOIN collections ON links.head_uuid = collections.uuid").
+ order("links.created_at DESC")
+
+ # If the search term is a Collection locator that contains one file
+ # that looks like a Docker image, return it.
+ if loc = Keep::Locator.parse(search_term)
+ loc.strip_hints!
+ coll_match = readable_by(*readers).where(portable_data_hash: loc.to_s).limit(1).first
+ if coll_match
+ # Check if the Collection contains exactly one file whose name
+ # looks like a saved Docker image.
+ manifest = Keep::Manifest.new(coll_match.manifest_text)
+ if manifest.exact_file_count?(1) and
+ (manifest.files[0][1] =~ /^[0-9A-Fa-f]{64}\.tar$/)
+ return [coll_match]
+ end
+ end
+ end
+
+ if search_tag.nil? and (n = search_term.index(":"))
+ search_tag = search_term[n+1..-1]
+ search_term = search_term[0..n-1]
+ end
+
+ # Find Collections with matching Docker image repository+tag pairs.
+ matches = base_search.
+ where(link_class: "docker_image_repo+tag",
+ name: "#{search_term}:#{search_tag || 'latest'}")
+
+ # If that didn't work, find Collections with matching Docker image hashes.
+ if matches.empty?
+ matches = base_search.
+ where("link_class = ? and links.name LIKE ?",
+ "docker_image_hash", "#{search_term}%")
+ end
+
+ # Generate an order key for each result. We want to order the results
+ # so that anything with an image timestamp is considered more recent than
+ # anything without; then we use the link's created_at as a tiebreaker.
+ uuid_timestamps = {}
+ matches.all.map do |link|
+ uuid_timestamps[link.head_uuid] = [(-link.properties["image_timestamp"].to_datetime.to_i rescue 0),
+ -link.created_at.to_i]
+ end
+ Collection.where('uuid in (?)', uuid_timestamps.keys).sort_by { |c| uuid_timestamps[c.uuid] }
+ end
+
+ def self.for_latest_docker_image(search_term, search_tag=nil, readers=nil)
+ find_all_for_docker_image(search_term, search_tag, readers).first
+ end
+
+ protected
+ def portable_manifest_text
+ portable_manifest = self[:manifest_text].dup
+ self.class.munge_manifest_locators!(portable_manifest) do |loc|
+ loc.hash + '+' + loc.size.to_s
+ end
+ portable_manifest
+ end
+
+ def compute_pdh
+ portable_manifest = portable_manifest_text
+ (Digest::MD5.hexdigest(portable_manifest) +
+ '+' +
+ portable_manifest.bytesize.to_s)
+ end
+end
--- /dev/null
+class Commit < ActiveRecord::Base
+ require 'shellwords'
+
+ def self.git_check_ref_format(e)
+ if !e or e.empty? or e[0] == '-' or e[0] == '$'
+ # definitely not valid
+ false
+ else
+ `git check-ref-format --allow-onelevel #{e.shellescape}`
+ $?.success?
+ end
+ end
+
+ def self.find_commit_range(current_user, repository, minimum, maximum, exclude)
+ if minimum and minimum.empty?
+ minimum = nil
+ end
+
+ if minimum and !git_check_ref_format(minimum)
+ logger.warn "find_commit_range called with invalid minimum revision: '#{minimum}'"
+ return nil
+ end
+
+ if maximum and !git_check_ref_format(maximum)
+ logger.warn "find_commit_range called with invalid maximum revision: '#{maximum}'"
+ return nil
+ end
+
+ if !maximum
+ maximum = "HEAD"
+ end
+
+ # Get list of actual repository directories under management
+ on_disk_repos = repositories
+
+ # Get list of repository objects readable by user
+ readable = Repository.readable_by(current_user)
+
+ # filter repository objects on requested repository name
+ if repository
+ readable = readable.where(name: repository)
+ end
+
+ commits = []
+ readable.each do |r|
+ if on_disk_repos[r.name]
+ ENV['GIT_DIR'] = on_disk_repos[r.name][:git_dir]
+
+ # We've filtered for invalid characters, so we can pass the contents of
+ # minimum and maximum safely on the command line
+
+ # Get the commit hash for the upper bound
+ max_hash = nil
+ IO.foreach("|git rev-list --max-count=1 #{maximum.shellescape} --") do |line|
+ max_hash = line.strip
+ end
+
+ # If not found or string is invalid, nothing else to do
+ next if !max_hash or !git_check_ref_format(max_hash)
+
+ resolved_exclude = nil
+ if exclude
+ resolved_exclude = []
+ exclude.each do |e|
+ if git_check_ref_format(e)
+ IO.foreach("|git rev-list --max-count=1 #{e.shellescape} --") do |line|
+ resolved_exclude.push(line.strip)
+ end
+ else
+ logger.warn "find_commit_range called with invalid exclude invalid characters: '#{exclude}'"
+ return nil
+ end
+ end
+ end
+
+ if minimum
+ # Get the commit hash for the lower bound
+ min_hash = nil
+ IO.foreach("|git rev-list --max-count=1 #{minimum.shellescape} --") do |line|
+ min_hash = line.strip
+ end
+
+ # If not found or string is invalid, nothing else to do
+ next if !min_hash or !git_check_ref_format(min_hash)
+
+ # Now find all commits between them
+ IO.foreach("|git rev-list #{min_hash.shellescape}..#{max_hash.shellescape} --") do |line|
+ hash = line.strip
+ commits.push(hash) if !resolved_exclude or !resolved_exclude.include? hash
+ end
+
+ commits.push(min_hash) if !resolved_exclude or !resolved_exclude.include? min_hash
+ else
+ commits.push(max_hash) if !resolved_exclude or !resolved_exclude.include? max_hash
+ end
+ else
+ logger.warn "Repository #{r.name} exists in table but not found on disk"
+ end
+ end
+
+ if !commits or commits.empty?
+ nil
+ else
+ commits
+ end
+ end
+
+ # Import all commits from configured git directory into the commits
+ # database.
+
+ def self.import_all
+ repositories.each do |repo_name, repo|
+ stat = { true => 0, false => 0 }
+ ENV['GIT_DIR'] = repo[:git_dir]
+ IO.foreach("|git rev-list --format=oneline --all") do |line|
+ sha1, message = line.strip.split " ", 2
+ imported = false
+ Commit.find_or_create_by_repository_name_and_sha1_and_message(repo_name, sha1, message[0..254]) do
+ imported = true
+ end
+ stat[!!imported] += 1
+ if (stat[true] + stat[false]) % 100 == 0
+ if $stdout.tty? or ARGV[0] == '-v'
+ puts "#{$0} #{$$}: repo #{repo_name} add #{stat[true]} skip #{stat[false]}"
+ end
+ end
+ end
+ if $stdout.tty? or ARGV[0] == '-v'
+ puts "#{$0} #{$$}: repo #{repo_name} add #{stat[true]} skip #{stat[false]}"
+ end
+ end
+ end
+
+ def self.refresh_repositories
+ @repositories = nil
+ end
+
+ protected
+
+ def self.repositories
+ return @repositories if @repositories
+
+ @repositories = {}
+ @gitdirbase = Rails.configuration.git_repositories_dir
+ Dir.foreach @gitdirbase do |repo|
+ next if repo.match /^\./
+ git_dir = File.join(@gitdirbase,
+ repo.match(/\.git$/) ? repo : File.join(repo, '.git'))
+ next if git_dir == Rails.configuration.git_internal_dir
+ repo_name = repo.sub(/\.git$/, '')
+ @repositories[repo_name] = {git_dir: git_dir}
+ end
+
+ @repositories
+ end
+end
--- /dev/null
+# Usage:
+#
+# x = CommitAncestor.find_or_create_by_descendant_and_ancestor(a, b)
+# "b is an ancestor of a" if x.is
+#
+
+class CommitAncestor < ActiveRecord::Base
+ before_create :ask_git_whether_is
+
+ class CommitNotFoundError < ArgumentError
+ end
+
+ protected
+
+ def ask_git_whether_is
+ @gitdirbase = Rails.configuration.git_repositories_dir
+ self.is = nil
+ Dir.foreach @gitdirbase do |repo|
+ next if repo.match /^\./
+ git_dir = repo.match(/\.git$/) ? repo : File.join(repo, '.git')
+ repo_name = repo.sub(/\.git$/, '')
+ ENV['GIT_DIR'] = File.join(@gitdirbase, git_dir)
+ IO.foreach("|git rev-list --format=oneline '#{self.descendant.gsub /[^0-9a-f]/,""}'") do |line|
+ self.is = false
+ sha1, message = line.strip.split(" ", 2)
+ if sha1 == self.ancestor
+ self.is = true
+ break
+ end
+ end
+ if !self.is.nil?
+ self.repository_name = repo_name
+ break
+ end
+ end
+ if self.is.nil?
+ raise CommitNotFoundError.new "Specified commit was not found"
+ end
+ end
+end
--- /dev/null
+class DatabaseSeeds
+ extend CurrentApiClient
+ def self.install
+ system_user
+ system_group
+ all_users_group
+ anonymous_group
+ anonymous_user
+ empty_collection
+ end
+end
--- /dev/null
+require 'can_be_an_owner'
+
+class Group < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ include CanBeAnOwner
+ after_create :invalidate_permissions_cache
+ after_update :maybe_invalidate_permissions_cache
+ before_create :assign_name
+
+ api_accessible :user, extend: :common do |t|
+ t.add :name
+ t.add :group_class
+ t.add :description
+ t.add :writable_by
+ end
+
+ def maybe_invalidate_permissions_cache
+ if uuid_changed? or owner_uuid_changed?
+ # This can change users' permissions on other groups as well as
+ # this one.
+ invalidate_permissions_cache
+ end
+ end
+
+ def invalidate_permissions_cache
+ # Ensure a new group can be accessed by the appropriate users
+ # immediately after being created.
+ User.invalidate_permissions_cache
+ end
+
+ def assign_name
+ if self.new_record? and (self.name.nil? or self.name.empty?)
+ self.name = self.uuid
+ end
+ true
+ end
+
+end
--- /dev/null
+class Human < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :properties, Hash
+
+ api_accessible :user, extend: :common do |t|
+ t.add :properties
+ end
+end
--- /dev/null
+class Job < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ attr_protected :arvados_sdk_version, :docker_image_locator
+ serialize :script_parameters, Hash
+ serialize :runtime_constraints, Hash
+ serialize :tasks_summary, Hash
+ before_create :ensure_unique_submit_id
+ after_commit :trigger_crunch_dispatch_if_cancelled, :on => :update
+ before_validation :set_priority
+ before_validation :update_state_from_old_state_attrs
+ validate :ensure_script_version_is_commit
+ validate :find_arvados_sdk_version
+ validate :find_docker_image_locator
+ validate :validate_status
+ validate :validate_state_change
+ validate :ensure_no_collection_uuids_in_script_params
+ before_save :update_timestamps_when_state_changes
+
+ has_many :commit_ancestors, :foreign_key => :descendant, :primary_key => :script_version
+ has_many(:nodes, foreign_key: :job_uuid, primary_key: :uuid)
+
+ class SubmitIdReused < StandardError
+ end
+
+ api_accessible :user, extend: :common do |t|
+ t.add :submit_id
+ t.add :priority
+ t.add :script
+ t.add :script_parameters
+ t.add :script_version
+ t.add :cancelled_at
+ t.add :cancelled_by_client_uuid
+ t.add :cancelled_by_user_uuid
+ t.add :started_at
+ t.add :finished_at
+ t.add :output
+ t.add :success
+ t.add :running
+ t.add :state
+ t.add :is_locked_by_uuid
+ t.add :log
+ t.add :runtime_constraints
+ t.add :tasks_summary
+ t.add :dependencies
+ t.add :nondeterministic
+ t.add :repository
+ t.add :supplied_script_version
+ t.add :arvados_sdk_version
+ t.add :docker_image_locator
+ t.add :queue_position
+ t.add :node_uuids
+ t.add :description
+ end
+
+ # Supported states for a job
+ States = [
+ (Queued = 'Queued'),
+ (Running = 'Running'),
+ (Cancelled = 'Cancelled'),
+ (Failed = 'Failed'),
+ (Complete = 'Complete'),
+ ]
+
+ def assert_finished
+ update_attributes(finished_at: finished_at || Time.now,
+ success: success.nil? ? false : success,
+ running: false)
+ end
+
+ def node_uuids
+ nodes.map(&:uuid)
+ end
+
+ def self.queue
+ self.where('state = ?', Queued).order('priority desc, created_at')
+ end
+
+ def queue_position
+ Job::queue.each_with_index do |job, index|
+ if job[:uuid] == self.uuid
+ return index
+ end
+ end
+ nil
+ end
+
+ def self.running
+ self.where('running = ?', true).
+ order('priority desc, created_at')
+ end
+
+ def lock locked_by_uuid
+ transaction do
+ self.reload
+ unless self.state == Queued and self.is_locked_by_uuid.nil?
+ raise AlreadyLockedError
+ end
+ self.state = Running
+ self.is_locked_by_uuid = locked_by_uuid
+ self.save!
+ end
+ end
+
+ protected
+
+ def foreign_key_attributes
+ super + %w(output log)
+ end
+
+ def skip_uuid_read_permission_check
+ super + %w(cancelled_by_client_uuid)
+ end
+
+ def skip_uuid_existence_check
+ super + %w(output log)
+ end
+
+ def set_priority
+ if self.priority.nil?
+ self.priority = 0
+ end
+ true
+ end
+
+ def ensure_script_version_is_commit
+ if self.state == Running
+ # Apparently client has already decided to go for it. This is
+ # needed to run a local job using a local working directory
+ # instead of a commit-ish.
+ return true
+ end
+ if new_record? or script_version_changed?
+ sha1 = Commit.find_commit_range(current_user, self.repository, nil, self.script_version, nil)[0] rescue nil
+ if sha1
+ self.supplied_script_version = self.script_version if self.supplied_script_version.nil? or self.supplied_script_version.empty?
+ self.script_version = sha1
+ else
+ self.errors.add :script_version, "#{self.script_version} does not resolve to a commit"
+ return false
+ end
+ end
+ end
+
+ def ensure_unique_submit_id
+ if !submit_id.nil?
+ if Job.where('submit_id=?',self.submit_id).first
+ raise SubmitIdReused.new
+ end
+ end
+ true
+ end
+
+ def resolve_runtime_constraint(key, attr_sym)
+ if ((runtime_constraints.is_a? Hash) and
+ (search = runtime_constraints[key]))
+ ok, result = yield search
+ else
+ ok, result = true, nil
+ end
+ if ok
+ send("#{attr_sym}=".to_sym, result)
+ else
+ errors.add(attr_sym, result)
+ end
+ ok
+ end
+
+ def find_arvados_sdk_version
+ resolve_runtime_constraint("arvados_sdk_version",
+ :arvados_sdk_version) do |git_search|
+ commits = Commit.find_commit_range(current_user, "arvados",
+ nil, git_search, nil)
+ if commits.nil? or commits.empty?
+ [false, "#{git_search} does not resolve to a commit"]
+ elsif not runtime_constraints["docker_image"]
+ [false, "cannot be specified without a Docker image constraint"]
+ else
+ [true, commits.first]
+ end
+ end
+ end
+
+ def find_docker_image_locator
+ resolve_runtime_constraint("docker_image",
+ :docker_image_locator) do |image_search|
+ image_tag = runtime_constraints['docker_image_tag']
+ if coll = Collection.for_latest_docker_image(image_search, image_tag)
+ [true, coll.portable_data_hash]
+ else
+ [false, "not found for #{image_search}"]
+ end
+ end
+ end
+
+ def dependencies
+ deps = {}
+ queue = self.script_parameters.values
+ while not queue.empty?
+ queue = queue.flatten.compact.collect do |v|
+ if v.is_a? Hash
+ v.values
+ elsif v.is_a? String
+ v.match(/^(([0-9a-f]{32})\b(\+[^,]+)?,?)*$/) do |locator|
+ deps[locator.to_s] = true
+ end
+ nil
+ end
+ end
+ end
+ deps.keys
+ end
+
+ def permission_to_update
+ if is_locked_by_uuid_was and !(current_user and
+ (current_user.uuid == is_locked_by_uuid_was or
+ current_user.uuid == system_user.uuid))
+ if script_changed? or
+ script_parameters_changed? or
+ script_version_changed? or
+ (!cancelled_at_was.nil? and
+ (cancelled_by_client_uuid_changed? or
+ cancelled_by_user_uuid_changed? or
+ cancelled_at_changed?)) or
+ started_at_changed? or
+ finished_at_changed? or
+ running_changed? or
+ success_changed? or
+ output_changed? or
+ log_changed? or
+ tasks_summary_changed? or
+ state_changed?
+ logger.warn "User #{current_user.uuid if current_user} tried to change protected job attributes on locked #{self.class.to_s} #{uuid_was}"
+ return false
+ end
+ end
+ if !is_locked_by_uuid_changed?
+ super
+ else
+ if !current_user
+ logger.warn "Anonymous user tried to change lock on #{self.class.to_s} #{uuid_was}"
+ false
+ elsif is_locked_by_uuid_was and is_locked_by_uuid_was != current_user.uuid
+ logger.warn "User #{current_user.uuid} tried to steal lock on #{self.class.to_s} #{uuid_was} from #{is_locked_by_uuid_was}"
+ false
+ elsif !is_locked_by_uuid.nil? and is_locked_by_uuid != current_user.uuid
+ logger.warn "User #{current_user.uuid} tried to lock #{self.class.to_s} #{uuid_was} with uuid #{is_locked_by_uuid}"
+ false
+ else
+ super
+ end
+ end
+ end
+
+ def update_modified_by_fields
+ if self.cancelled_at_changed?
+ # Ensure cancelled_at cannot be set to arbitrary non-now times,
+ # or changed once it is set.
+ if self.cancelled_at and not self.cancelled_at_was
+ self.cancelled_at = Time.now
+ self.cancelled_by_user_uuid = current_user.uuid
+ self.cancelled_by_client_uuid = current_api_client.andand.uuid
+ @need_crunch_dispatch_trigger = true
+ else
+ self.cancelled_at = self.cancelled_at_was
+ self.cancelled_by_user_uuid = self.cancelled_by_user_uuid_was
+ self.cancelled_by_client_uuid = self.cancelled_by_client_uuid_was
+ end
+ end
+ super
+ end
+
+ def trigger_crunch_dispatch_if_cancelled
+ if @need_crunch_dispatch_trigger
+ File.open(Rails.configuration.crunch_refresh_trigger, 'wb') do
+ # That's all, just create/touch a file for crunch-job to see.
+ end
+ end
+ end
+
+ def update_timestamps_when_state_changes
+ return if not (state_changed? or new_record?)
+
+ case state
+ when Running
+ self.started_at ||= Time.now
+ when Failed, Complete
+ self.finished_at ||= Time.now
+ when Cancelled
+ self.cancelled_at ||= Time.now
+ end
+
+ # TODO: Remove the following case block when old "success" and
+ # "running" attrs go away. Until then, this ensures we still
+ # expose correct success/running flags to older clients, even if
+ # some new clients are writing only the new state attribute.
+ case state
+ when Queued
+ self.running = false
+ self.success = nil
+ when Running
+ self.running = true
+ self.success = nil
+ when Cancelled, Failed
+ self.running = false
+ self.success = false
+ when Complete
+ self.running = false
+ self.success = true
+ end
+ self.running ||= false # Default to false instead of nil.
+
+ @need_crunch_dispatch_trigger = true
+
+ true
+ end
+
+ def update_state_from_old_state_attrs
+ # If a client has touched the legacy state attrs, update the
+ # "state" attr to agree with the updated values of the legacy
+ # attrs.
+ #
+ # TODO: Remove this method when old "success" and "running" attrs
+ # go away.
+ if cancelled_at_changed? or
+ success_changed? or
+ running_changed? or
+ state.nil?
+ if cancelled_at
+ self.state = Cancelled
+ elsif success == false
+ self.state = Failed
+ elsif success == true
+ self.state = Complete
+ elsif running == true
+ self.state = Running
+ else
+ self.state = Queued
+ end
+ end
+ true
+ end
+
+ def validate_status
+ if self.state.in?(States)
+ true
+ else
+ errors.add :state, "#{state.inspect} must be one of: #{States.inspect}"
+ false
+ end
+ end
+
+ def validate_state_change
+ ok = true
+ if self.state_changed?
+ ok = case self.state_was
+ when nil
+ # state isn't set yet
+ true
+ when Queued
+ # Permit going from queued to any state
+ true
+ when Running
+ # From running, may only transition to a finished state
+ [Complete, Failed, Cancelled].include? self.state
+ when Complete, Failed, Cancelled
+ # Once in a finished state, don't permit any more state changes
+ false
+ else
+ # Any other state transition is also invalid
+ false
+ end
+ if not ok
+ errors.add :state, "invalid change from #{self.state_was} to #{self.state}"
+ end
+ end
+ ok
+ end
+
+ def ensure_no_collection_uuids_in_script_params
+ # recursive_hash_search searches recursively through hashes and
+ # arrays in 'thing' for string fields matching regular expression
+ # 'pattern'. Returns true if pattern is found, false otherwise.
+ def recursive_hash_search thing, pattern
+ if thing.is_a? Hash
+ thing.each do |k, v|
+ return true if recursive_hash_search v, pattern
+ end
+ elsif thing.is_a? Array
+ thing.each do |k|
+ return true if recursive_hash_search k, pattern
+ end
+ elsif thing.is_a? String
+ return true if thing.match pattern
+ end
+ false
+ end
+
+ # Fail validation if any script_parameters field includes a string containing a
+ # collection uuid pattern.
+ if self.script_parameters_changed?
+ if recursive_hash_search(self.script_parameters, Collection.uuid_regex)
+ self.errors.add :script_parameters, "must use portable_data_hash instead of collection uuid"
+ return false
+ end
+ end
+ true
+ end
+end
--- /dev/null
+class JobTask < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :parameters, Hash
+ before_create :set_default_qsequence
+ after_update :delete_created_job_tasks_if_failed
+
+ api_accessible :user, extend: :common do |t|
+ t.add :job_uuid
+ t.add :created_by_job_task_uuid
+ t.add :sequence
+ t.add :qsequence
+ t.add :parameters
+ t.add :output
+ t.add :progress
+ t.add :success
+ t.add :started_at
+ t.add :finished_at
+ end
+
+ protected
+
+ def delete_created_job_tasks_if_failed
+ if self.success == false and self.success != self.success_was
+ JobTask.delete_all ['created_by_job_task_uuid = ?', self.uuid]
+ end
+ end
+
+ def set_default_qsequence
+ self.qsequence ||= self.class.connection.
+ select_value("SELECT nextval('job_tasks_qsequence_seq')")
+ end
+end
--- /dev/null
+class KeepDisk < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ before_validation :ensure_ping_secret
+
+ api_accessible :user, extend: :common do |t|
+ t.add :node_uuid
+ t.add :filesystem_uuid
+ t.add :bytes_total
+ t.add :bytes_free
+ t.add :is_readable
+ t.add :is_writable
+ t.add :last_read_at
+ t.add :last_write_at
+ t.add :last_ping_at
+ t.add :service_host
+ t.add :service_port
+ t.add :service_ssl_flag
+ t.add :keep_service_uuid
+ end
+ api_accessible :superuser, :extend => :user do |t|
+ t.add :ping_secret
+ end
+
+ def foreign_key_attributes
+ super.reject { |a| a == "filesystem_uuid" }
+ end
+
+ def ping(o)
+ raise "must have :service_host and :ping_secret" unless o[:service_host] and o[:ping_secret]
+
+ if o[:ping_secret] != self.ping_secret
+ logger.info "Ping: secret mismatch: received \"#{o[:ping_secret]}\" != \"#{self.ping_secret}\""
+ return nil
+ end
+
+ @bypass_arvados_authorization = true
+ self.update_attributes!(o.select { |k,v|
+ [:bytes_total,
+ :bytes_free,
+ :is_readable,
+ :is_writable,
+ :last_read_at,
+ :last_write_at
+ ].collect(&:to_s).index k
+ }.merge(last_ping_at: Time.now))
+ end
+
+ def service_host
+ KeepService.find_by_uuid(self.keep_service_uuid).andand.service_host
+ end
+
+ def service_port
+ KeepService.find_by_uuid(self.keep_service_uuid).andand.service_port
+ end
+
+ def service_ssl_flag
+ KeepService.find_by_uuid(self.keep_service_uuid).andand.service_ssl_flag
+ end
+
+ protected
+
+ def ensure_ping_secret
+ self.ping_secret ||= rand(2**256).to_s(36)
+ end
+
+ def permission_to_update
+ @bypass_arvados_authorization or super
+ end
+
+ def permission_to_create
+ current_user and current_user.is_admin
+ end
+end
--- /dev/null
+class KeepService < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+
+ api_accessible :user, extend: :common do |t|
+ t.add :service_host
+ t.add :service_port
+ t.add :service_ssl_flag
+ t.add :service_type
+ end
+ api_accessible :superuser, :extend => :user do |t|
+ end
+
+end
--- /dev/null
+class Link < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :properties, Hash
+ before_create :permission_to_attach_to_objects
+ before_update :permission_to_attach_to_objects
+ after_update :maybe_invalidate_permissions_cache
+ after_create :maybe_invalidate_permissions_cache
+ after_destroy :maybe_invalidate_permissions_cache
+ attr_accessor :head_kind, :tail_kind
+ validate :name_links_are_obsolete
+
+ api_accessible :user, extend: :common do |t|
+ t.add :tail_uuid
+ t.add :link_class
+ t.add :name
+ t.add :head_uuid
+ t.add :head_kind
+ t.add :tail_kind
+ t.add :properties
+ end
+
+ def properties
+ @properties ||= Hash.new
+ super
+ end
+
+ def head_kind
+ if k = ArvadosModel::resource_class_for_uuid(head_uuid)
+ k.kind
+ end
+ end
+
+ def tail_kind
+ if k = ArvadosModel::resource_class_for_uuid(tail_uuid)
+ k.kind
+ end
+ end
+
+ protected
+
+ def permission_to_attach_to_objects
+ # Anonymous users cannot write links
+ return false if !current_user
+
+ # All users can write links that don't affect permissions
+ return true if self.link_class != 'permission'
+
+ # Administrators can grant permissions
+ return true if current_user.is_admin
+
+ # All users can grant permissions on objects they own or can manage
+ head_obj = ArvadosModel.find_by_uuid(head_uuid)
+ return true if current_user.can?(manage: head_obj)
+
+ # Default = deny.
+ false
+ end
+
+ def maybe_invalidate_permissions_cache
+ if self.link_class == 'permission'
+ # Clearing the entire permissions cache can generate many
+ # unnecessary queries if many active users are not affected by
+ # this change. In such cases it would be better to search cached
+ # permissions for head_uuid and tail_uuid, and invalidate the
+ # cache for only those users. (This would require a browseable
+ # cache.)
+ User.invalidate_permissions_cache
+ end
+ end
+
+ def name_links_are_obsolete
+ if link_class == 'name'
+ errors.add('name', 'Name links are obsolete')
+ false
+ else
+ true
+ end
+ end
+
+ # A user is permitted to create, update or modify a permission link
+ # if and only if they have "manage" permission on the object
+ # indicated by the permission link's head_uuid.
+ #
+ # All other links are treated as regular ArvadosModel objects.
+ #
+ def ensure_owner_uuid_is_permitted
+ if link_class == 'permission'
+ ob = ArvadosModel.find_by_uuid(head_uuid)
+ raise PermissionDeniedError unless current_user.can?(manage: ob)
+ # All permission links should be owned by the system user.
+ self.owner_uuid = system_user_uuid
+ return true
+ else
+ super
+ end
+ end
+
+end
--- /dev/null
+class Log < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :properties, Hash
+ before_validation :set_default_event_at
+ attr_accessor :object, :object_kind
+ after_save :send_notify
+
+ api_accessible :user, extend: :common do |t|
+ t.add :id
+ t.add :object_uuid
+ t.add :object_owner_uuid
+ t.add :object_kind
+ t.add :event_at
+ t.add :event_type
+ t.add :summary
+ t.add :properties
+ end
+
+ def object_kind
+ if k = ArvadosModel::resource_class_for_uuid(object_uuid)
+ k.kind
+ end
+ end
+
+ def fill_object(thing)
+ self.object_uuid ||= thing.uuid
+ if respond_to? :object_owner_uuid=
+ # Skip this if the object_owner_uuid migration hasn't happened
+ # yet, i.e., we're in the process of migrating an old database.
+ self.object_owner_uuid = thing.owner_uuid
+ end
+ self.summary ||= "#{self.event_type} of #{thing.uuid}"
+ self
+ end
+
+ def fill_properties(age, etag_prop, attrs_prop)
+ self.properties.merge!({"#{age}_etag" => etag_prop,
+ "#{age}_attributes" => attrs_prop})
+ end
+
+ def update_to(thing)
+ fill_properties('new', thing.andand.etag, thing.andand.logged_attributes)
+ case event_type
+ when "create"
+ self.event_at = thing.created_at
+ when "update"
+ self.event_at = thing.modified_at
+ when "destroy"
+ self.event_at = Time.now
+ end
+ self
+ end
+
+ protected
+
+ def permission_to_create
+ true
+ end
+
+ def permission_to_update
+ current_user.andand.is_admin
+ end
+
+ alias_method :permission_to_delete, :permission_to_update
+
+ def set_default_event_at
+ self.event_at ||= Time.now
+ end
+
+ def log_start_state
+ # don't log start state on logs
+ end
+
+ def log_change(event_type)
+ # Don't log changes to logs.
+ end
+
+ def ensure_valid_uuids
+ # logs can have references to deleted objects
+ end
+
+ def send_notify
+ connection.execute "NOTIFY logs, '#{self.id}'"
+ end
+
+end
--- /dev/null
+class Node < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :info, Hash
+ serialize :properties, Hash
+ before_validation :ensure_ping_secret
+ after_update :dns_server_update
+
+ # Only a controller can figure out whether or not the current API tokens
+ # have access to the associated Job. They're expected to set
+ # job_readable=true if the Job UUID can be included in the API response.
+ belongs_to(:job, foreign_key: :job_uuid, primary_key: :uuid)
+ attr_accessor :job_readable
+
+ MAX_SLOTS = 64
+
+ @@dns_server_conf_dir = Rails.configuration.dns_server_conf_dir
+ @@dns_server_conf_template = Rails.configuration.dns_server_conf_template
+ @@dns_server_reload_command = Rails.configuration.dns_server_reload_command
+ @@uuid_prefix = Rails.configuration.uuid_prefix
+ @@domain = Rails.configuration.compute_node_domain rescue `hostname --domain`.strip
+ @@nameservers = Rails.configuration.compute_node_nameservers
+
+ api_accessible :user, :extend => :common do |t|
+ t.add :hostname
+ t.add :domain
+ t.add :ip_address
+ t.add :last_ping_at
+ t.add :slot_number
+ t.add :status
+ t.add :api_job_uuid, as: :job_uuid
+ t.add :crunch_worker_state
+ t.add :properties
+ end
+ api_accessible :superuser, :extend => :user do |t|
+ t.add :first_ping_at
+ t.add :info
+ t.add lambda { |x| @@nameservers }, :as => :nameservers
+ end
+
+ def domain
+ super || @@domain
+ end
+
+ def api_job_uuid
+ job_readable ? job_uuid : nil
+ end
+
+ def crunch_worker_state
+ return 'down' if slot_number.nil?
+ case self.info.andand['slurm_state']
+ when 'alloc', 'comp'
+ 'busy'
+ when 'idle'
+ 'idle'
+ else
+ 'down'
+ end
+ end
+
+ def status
+ if !self.last_ping_at
+ if Time.now - self.created_at > 5.minutes
+ 'startup-fail'
+ else
+ 'pending'
+ end
+ elsif Time.now - self.last_ping_at > 1.hours
+ 'missing'
+ else
+ 'running'
+ end
+ end
+
+ def ping(o)
+ raise "must have :ip and :ping_secret" unless o[:ip] and o[:ping_secret]
+
+ if o[:ping_secret] != self.info['ping_secret']
+ logger.info "Ping: secret mismatch: received \"#{o[:ping_secret]}\" != \"#{self.info['ping_secret']}\""
+ raise ArvadosModel::UnauthorizedError.new("Incorrect ping_secret")
+ end
+ self.last_ping_at = Time.now
+
+ @bypass_arvados_authorization = true
+
+ # Record IP address
+ if self.ip_address.nil?
+ logger.info "#{self.uuid} ip_address= #{o[:ip]}"
+ self.ip_address = o[:ip]
+ self.first_ping_at = Time.now
+ end
+
+ # Record instance ID if not already known
+ if o[:ec2_instance_id]
+ if !self.info['ec2_instance_id']
+ self.info['ec2_instance_id'] = o[:ec2_instance_id]
+ elsif self.info['ec2_instance_id'] != o[:ec2_instance_id]
+ logger.debug "Multiple nodes have credentials for #{self.uuid}"
+ raise "#{self.uuid} is already running at #{self.info['ec2_instance_id']} so rejecting ping from #{o[:ec2_instance_id]}"
+ end
+ end
+
+ # Assign hostname
+ if self.slot_number.nil?
+ try_slot = 0
+ begin
+ self.slot_number = try_slot
+ begin
+ self.save!
+ break
+ rescue ActiveRecord::RecordNotUnique
+ try_slot += 1
+ end
+ raise "No available node slots" if try_slot == MAX_SLOTS
+ end while true
+ self.hostname = self.class.hostname_for_slot(self.slot_number)
+ end
+
+ # Record other basic stats
+ ['total_cpu_cores', 'total_ram_mb', 'total_scratch_mb'].each do |key|
+ if value = (o[key] or o[key.to_sym])
+ self.properties[key] = value.to_i
+ else
+ self.properties.delete(key)
+ end
+ end
+
+ save!
+ end
+
+ protected
+
+ def ensure_ping_secret
+ self.info['ping_secret'] ||= rand(2**256).to_s(36)
+ end
+
+ def dns_server_update
+ if self.hostname_changed? or self.ip_address_changed?
+ if not self.ip_address.nil?
+ stale_conflicting_nodes = Node.where('id != ? and ip_address = ? and last_ping_at < ?',self.id,self.ip_address,10.minutes.ago)
+ if not stale_conflicting_nodes.empty?
+ # One or more stale compute node records have the same IP address as the new node.
+ # Clear the ip_address field on the stale nodes.
+ stale_conflicting_nodes.each do |stale_node|
+ stale_node.ip_address = nil
+ stale_node.save!
+ end
+ end
+ end
+ if self.hostname and self.ip_address
+ self.class.dns_server_update(self.hostname, self.ip_address)
+ end
+ end
+ end
+
+ def self.dns_server_update(hostname, ip_address)
+ return unless @@dns_server_conf_dir and @@dns_server_conf_template
+ ptr_domain = ip_address.
+ split('.').reverse.join('.').concat('.in-addr.arpa')
+ hostfile = File.join @@dns_server_conf_dir, "#{hostname}.conf"
+
+ begin
+ template = IO.read(@@dns_server_conf_template)
+ rescue => e
+ STDERR.puts "Unable to read dns_server_conf_template #{@@dns_server_conf_template}: #{e.message}"
+ return
+ end
+
+ populated = template % {hostname:hostname, uuid_prefix:@@uuid_prefix, ip_address:ip_address, ptr_domain:ptr_domain}
+
+ begin
+ File.open hostfile, 'w' do |f|
+ f.puts populated
+ end
+ rescue => e
+ STDERR.puts "Unable to write #{hostfile}: #{e.message}"
+ return
+ end
+ File.open(File.join(@@dns_server_conf_dir, 'restart.txt'), 'w') do |f|
+ # this will trigger a dns server restart
+ f.puts @@dns_server_reload_command
+ end
+ end
+
+ def self.hostname_for_slot(slot_number)
+ "compute#{slot_number}"
+ end
+
+ # At startup, make sure all DNS entries exist. Otherwise, slurmctld
+ # will refuse to start.
+ if @@dns_server_conf_dir and @@dns_server_conf_template
+ (0..MAX_SLOTS-1).each do |slot_number|
+ hostname = hostname_for_slot(slot_number)
+ hostfile = File.join @@dns_server_conf_dir, "#{hostname}.conf"
+ if !File.exists? hostfile
+ n = Node.where(:slot_number => slot_number).first
+ if n.nil? or n.ip_address.nil?
+ dns_server_update(hostname, '127.40.4.0')
+ else
+ dns_server_update(hostname, n.ip_address)
+ end
+ end
+ end
+ end
+
+ def permission_to_update
+ @bypass_arvados_authorization or super
+ end
+
+ def permission_to_create
+ current_user and current_user.is_admin
+ end
+end
--- /dev/null
+class PipelineInstance < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :components, Hash
+ serialize :properties, Hash
+ serialize :components_summary, Hash
+ belongs_to :pipeline_template, :foreign_key => :pipeline_template_uuid, :primary_key => :uuid
+
+ before_validation :bootstrap_components
+ before_validation :update_state
+ before_validation :verify_status
+ before_create :set_state_before_save
+ before_save :set_state_before_save
+
+ api_accessible :user, extend: :common do |t|
+ t.add :pipeline_template_uuid
+ t.add :pipeline_template, :if => :pipeline_template
+ t.add :name
+ t.add :components
+ t.add :dependencies
+ t.add :properties
+ t.add :state
+ t.add :components_summary
+ t.add :description
+ t.add :started_at
+ t.add :finished_at
+ end
+
+ # Supported states for a pipeline instance
+ States =
+ [
+ (New = 'New'),
+ (Ready = 'Ready'),
+ (RunningOnServer = 'RunningOnServer'),
+ (RunningOnClient = 'RunningOnClient'),
+ (Paused = 'Paused'),
+ (Failed = 'Failed'),
+ (Complete = 'Complete'),
+ ]
+
+ def dependencies
+ dependency_search(self.components).keys
+ end
+
+ # if all components have input, the pipeline is Ready
+ def components_look_ready?
+ if !self.components || self.components.empty?
+ return false
+ end
+
+ all_components_have_input = true
+ self.components.each do |name, component|
+ component['script_parameters'].andand.each do |parametername, parameter|
+ parameter = { 'value' => parameter } unless parameter.is_a? Hash
+ if parameter['value'].nil? and parameter['required']
+ if parameter['output_of']
+ next
+ end
+ all_components_have_input = false
+ break
+ end
+ end
+ end
+ return all_components_have_input
+ end
+
+ def progress_table
+ begin
+ # v0 pipeline format
+ nrow = -1
+ components['steps'].collect do |step|
+ nrow += 1
+ row = [nrow, step['name']]
+ if step['complete'] and step['complete'] != 0
+ if step['output_data_locator']
+ row << 1.0
+ else
+ row << 0.0
+ end
+ else
+ row << 0.0
+ if step['failed']
+ self.state = Failed
+ end
+ end
+ row << (step['warehousejob']['id'] rescue nil)
+ row << (step['warehousejob']['revision'] rescue nil)
+ row << step['output_data_locator']
+ row << (Time.parse(step['warehousejob']['finishtime']) rescue nil)
+ row
+ end
+ rescue
+ []
+ end
+ end
+
+ def progress_ratio
+ t = progress_table
+ return 0 if t.size < 1
+ t.collect { |r| r[2] }.inject(0.0) { |sum,a| sum += a } / t.size
+ end
+
+ def self.queue
+ self.where("state = 'RunningOnServer'")
+ end
+
+ protected
+ def bootstrap_components
+ if pipeline_template and (!components or components.empty?)
+ self.components = pipeline_template.components.deep_dup
+ end
+ end
+
+ def update_state
+ if components and progress_ratio == 1.0
+ self.state = Complete
+ end
+ end
+
+ def dependency_search(haystack)
+ if haystack.is_a? String
+ if (re = haystack.match /^([0-9a-f]{32}(\+[^,]+)*)+/)
+ {re[1] => true}
+ else
+ {}
+ end
+ elsif haystack.is_a? Array
+ deps = {}
+ haystack.each do |value|
+ deps.merge! dependency_search(value)
+ end
+ deps
+ elsif haystack.respond_to? :keys
+ deps = {}
+ haystack.each do |key, value|
+ deps.merge! dependency_search(value)
+ end
+ deps
+ else
+ {}
+ end
+ end
+
+ def verify_status
+ changed_attributes = self.changed
+
+ if new_record? or 'components'.in? changed_attributes
+ self.state ||= New
+ if (self.state == New) and self.components_look_ready?
+ self.state = Ready
+ end
+ end
+
+ if self.state.in?(States)
+ true
+ else
+ errors.add :state, "'#{state.inspect} must be one of: [#{States.join ', '}]"
+ false
+ end
+ end
+
+ def set_state_before_save
+ if self.components_look_ready? && (!self.state || self.state == New)
+ self.state = Ready
+ end
+ end
+
+end
--- /dev/null
+class PipelineTemplate < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :components, Hash
+
+ api_accessible :user, extend: :common do |t|
+ t.add :name
+ t.add :components
+ t.add :description
+ end
+end
--- /dev/null
+class Repository < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+
+ api_accessible :user, extend: :common do |t|
+ t.add :name
+ t.add :fetch_url
+ t.add :push_url
+ end
+
+ def push_url
+ super || self.name && "git@git.#{Rails.configuration.uuid_prefix}.arvadosapi.com:#{self.name}.git"
+ end
+
+ def fetch_url
+ super || push_url
+ end
+
+ protected
+
+ def permission_to_create
+ current_user and current_user.is_admin
+ end
+ def permission_to_update
+ current_user and current_user.is_admin
+ end
+end
--- /dev/null
+class Specimen < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :properties, Hash
+
+ api_accessible :user, extend: :common do |t|
+ t.add :material
+ t.add :properties
+ end
+
+ def properties
+ @properties ||= Hash.new
+ super
+ end
+end
--- /dev/null
+class Trait < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ serialize :properties, Hash
+
+ api_accessible :user, extend: :common do |t|
+ t.add :name
+ t.add :properties
+ end
+end
--- /dev/null
+require 'can_be_an_owner'
+
+class User < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+ include CanBeAnOwner
+
+ serialize :prefs, Hash
+ has_many :api_client_authorizations
+ before_update :prevent_privilege_escalation
+ before_update :prevent_inactive_admin
+ before_create :check_auto_admin
+ after_create :add_system_group_permission_link
+ after_create :auto_setup_new_user
+ after_create :send_admin_notifications
+ after_update :send_profile_created_notification
+
+
+ has_many :authorized_keys, :foreign_key => :authorized_user_uuid, :primary_key => :uuid
+
+ api_accessible :user, extend: :common do |t|
+ t.add :email
+ t.add :full_name
+ t.add :first_name
+ t.add :last_name
+ t.add :identity_url
+ t.add :is_active
+ t.add :is_admin
+ t.add :is_invited
+ t.add :prefs
+ t.add :writable_by
+ end
+
+ ALL_PERMISSIONS = {read: true, write: true, manage: true}
+
+ def full_name
+ "#{first_name} #{last_name}".strip
+ end
+
+ def is_invited
+ !!(self.is_active ||
+ Rails.configuration.new_users_are_active ||
+ self.groups_i_can(:read).select { |x| x.match /-f+$/ }.first)
+ end
+
+ def groups_i_can(verb)
+ my_groups = self.group_permissions.select { |uuid, mask| mask[verb] }.keys
+ if verb == :read
+ my_groups << anonymous_group_uuid
+ end
+ my_groups
+ end
+
+ def can?(actions)
+ return true if is_admin
+ actions.each do |action, target|
+ unless target.nil?
+ if target.respond_to? :uuid
+ target_uuid = target.uuid
+ else
+ target_uuid = target
+ target = ArvadosModel.find_by_uuid(target_uuid)
+ end
+ end
+ next if target_uuid == self.uuid
+ next if (group_permissions[target_uuid] and
+ group_permissions[target_uuid][action])
+ if target.respond_to? :owner_uuid
+ next if target.owner_uuid == self.uuid
+ next if (group_permissions[target.owner_uuid] and
+ group_permissions[target.owner_uuid][action])
+ end
+ sufficient_perms = case action
+ when :manage
+ ['can_manage']
+ when :write
+ ['can_manage', 'can_write']
+ when :read
+ ['can_manage', 'can_write', 'can_read']
+ else
+ # (Skip this kind of permission opportunity
+ # if action is an unknown permission type)
+ end
+ if sufficient_perms
+ # Check permission links with head_uuid pointing directly at
+ # the target object. If target is a Group, this is redundant
+ # and will fail except [a] if permission caching is broken or
+ # [b] during a race condition, where a permission link has
+ # *just* been added.
+ if Link.where(link_class: 'permission',
+ name: sufficient_perms,
+ tail_uuid: groups_i_can(action) + [self.uuid],
+ head_uuid: target_uuid).any?
+ next
+ end
+ end
+ return false
+ end
+ true
+ end
+
+ def self.invalidate_permissions_cache
+ Rails.cache.delete_matched(/^groups_for_user_/)
+ end
+
+ # Return a hash of {group_uuid: perm_hash} where perm_hash[:read]
+ # and perm_hash[:write] are true if this user can read and write
+ # objects owned by group_uuid.
+ #
+ # The permission graph is built by repeatedly enumerating all
+ # permission links reachable from self.uuid, and then calling
+ # search_permissions
+ def group_permissions
+ Rails.cache.fetch "groups_for_user_#{self.uuid}" do
+ permissions_from = {}
+ todo = {self.uuid => true}
+ done = {}
+ # Build the equivalence class of permissions starting with
+ # self.uuid. On each iteration of this loop, todo contains
+ # the next set of uuids in the permission equivalence class
+ # to evaluate.
+ while !todo.empty?
+ lookup_uuids = todo.keys
+ lookup_uuids.each do |uuid| done[uuid] = true end
+ todo = {}
+ newgroups = []
+ # include all groups owned by the current set of uuids.
+ Group.where('owner_uuid in (?)', lookup_uuids).each do |group|
+ newgroups << [group.owner_uuid, group.uuid, 'can_manage']
+ end
+ # add any permission links from the current lookup_uuids to a Group.
+ Link.where('link_class = ? and tail_uuid in (?) and ' \
+ '(head_uuid like ? or (name = ? and head_uuid like ?))',
+ 'permission',
+ lookup_uuids,
+ Group.uuid_like_pattern,
+ 'can_manage',
+ User.uuid_like_pattern).each do |link|
+ newgroups << [link.tail_uuid, link.head_uuid, link.name]
+ end
+ newgroups.each do |tail_uuid, head_uuid, perm_name|
+ unless done.has_key? head_uuid
+ todo[head_uuid] = true
+ end
+ link_permissions = {}
+ case perm_name
+ when 'can_read'
+ link_permissions = {read:true}
+ when 'can_write'
+ link_permissions = {read:true,write:true}
+ when 'can_manage'
+ link_permissions = ALL_PERMISSIONS
+ end
+ permissions_from[tail_uuid] ||= {}
+ permissions_from[tail_uuid][head_uuid] ||= {}
+ link_permissions.each do |k,v|
+ permissions_from[tail_uuid][head_uuid][k] ||= v
+ end
+ end
+ end
+ search_permissions(self.uuid, permissions_from)
+ end
+ end
+
+ def self.setup(user, openid_prefix, repo_name=nil, vm_uuid=nil)
+ return user.setup_repo_vm_links(repo_name, vm_uuid, openid_prefix)
+ end
+
+ # create links
+ def setup_repo_vm_links(repo_name, vm_uuid, openid_prefix)
+ oid_login_perm = create_oid_login_perm openid_prefix
+ repo_perm = create_user_repo_link repo_name
+ vm_login_perm = create_vm_login_permission_link vm_uuid, repo_name
+ group_perm = create_user_group_link
+
+ return [oid_login_perm, repo_perm, vm_login_perm, group_perm, self].compact
+ end
+
+ # delete user signatures, login, repo, and vm perms, and mark as inactive
+ def unsetup
+ # delete oid_login_perms for this user
+ Link.destroy_all(tail_uuid: self.email,
+ link_class: 'permission',
+ name: 'can_login')
+
+ # delete repo_perms for this user
+ Link.destroy_all(tail_uuid: self.uuid,
+ link_class: 'permission',
+ name: 'can_manage')
+
+ # delete vm_login_perms for this user
+ Link.destroy_all(tail_uuid: self.uuid,
+ link_class: 'permission',
+ name: 'can_login')
+
+ # delete "All users" group read permissions for this user
+ group = Group.where(name: 'All users').select do |g|
+ g[:uuid].match /-f+$/
+ end.first
+ Link.destroy_all(tail_uuid: self.uuid,
+ head_uuid: group[:uuid],
+ link_class: 'permission',
+ name: 'can_read')
+
+ # delete any signatures by this user
+ Link.destroy_all(link_class: 'signature',
+ tail_uuid: self.uuid)
+
+ # delete user preferences (including profile)
+ self.prefs = {}
+
+ # mark the user as inactive
+ self.is_active = false
+ self.save!
+ end
+
+ protected
+
+ def ensure_ownership_path_leads_to_user
+ true
+ end
+
+ def permission_to_update
+ # users must be able to update themselves (even if they are
+ # inactive) in order to create sessions
+ self == current_user or super
+ end
+
+ def permission_to_create
+ current_user.andand.is_admin or
+ (self == current_user and
+ self.is_active == Rails.configuration.new_users_are_active)
+ end
+
+ def check_auto_admin
+ return if self.uuid.end_with?('anonymouspublic')
+ if (User.where("email = ?",self.email).where(:is_admin => true).count == 0 and
+ Rails.configuration.auto_admin_user and self.email == Rails.configuration.auto_admin_user) or
+ (User.where("uuid not like '%-000000000000000'").where(:is_admin => true).count == 0 and
+ Rails.configuration.auto_admin_first_user)
+ self.is_admin = true
+ self.is_active = true
+ end
+ end
+
+ def prevent_privilege_escalation
+ if current_user.andand.is_admin
+ return true
+ end
+ if self.is_active_changed?
+ if self.is_active != self.is_active_was
+ logger.warn "User #{current_user.uuid} tried to change is_active from #{self.is_admin_was} to #{self.is_admin} for #{self.uuid}"
+ self.is_active = self.is_active_was
+ end
+ end
+ if self.is_admin_changed?
+ if self.is_admin != self.is_admin_was
+ logger.warn "User #{current_user.uuid} tried to change is_admin from #{self.is_admin_was} to #{self.is_admin} for #{self.uuid}"
+ self.is_admin = self.is_admin_was
+ end
+ end
+ true
+ end
+
+ def prevent_inactive_admin
+ if self.is_admin and not self.is_active
+ # There is no known use case for the strange set of permissions
+ # that would result from this change. It's safest to assume it's
+ # a mistake and disallow it outright.
+ raise "Admin users cannot be inactive"
+ end
+ true
+ end
+
+ def search_permissions(start, graph, merged={}, upstream_mask=nil, upstream_path={})
+ nextpaths = graph[start]
+ return merged if !nextpaths
+ return merged if upstream_path.has_key? start
+ upstream_path[start] = true
+ upstream_mask ||= ALL_PERMISSIONS
+ nextpaths.each do |head, mask|
+ merged[head] ||= {}
+ mask.each do |k,v|
+ merged[head][k] ||= v if upstream_mask[k]
+ end
+ search_permissions(head, graph, merged, upstream_mask.select { |k,v| v && merged[head][k] }, upstream_path)
+ end
+ upstream_path.delete start
+ merged
+ end
+
+ def create_oid_login_perm (openid_prefix)
+ login_perm_props = { "identity_url_prefix" => openid_prefix}
+
+ # Check oid_login_perm
+ oid_login_perms = Link.where(tail_uuid: self.email,
+ link_class: 'permission',
+ name: 'can_login').where("head_uuid = ?", self.uuid)
+
+ if !oid_login_perms.any?
+ # create openid login permission
+ oid_login_perm = Link.create(link_class: 'permission',
+ name: 'can_login',
+ tail_uuid: self.email,
+ head_uuid: self.uuid,
+ properties: login_perm_props
+ )
+ logger.info { "openid login permission: " + oid_login_perm[:uuid] }
+ else
+ oid_login_perm = oid_login_perms.first
+ end
+
+ return oid_login_perm
+ end
+
+ def create_user_repo_link(repo_name)
+ # repo_name is optional
+ if not repo_name
+ logger.warn ("Repository name not given for #{self.uuid}.")
+ return
+ end
+
+ # Check for an existing repository with the same name we're about to use.
+ repo = Repository.where(name: repo_name).first
+
+ if repo
+ logger.warn "Repository exists for #{repo_name}: #{repo[:uuid]}."
+
+ # Look for existing repository access for this repo
+ repo_perms = Link.where(tail_uuid: self.uuid,
+ head_uuid: repo[:uuid],
+ link_class: 'permission',
+ name: 'can_manage')
+ if repo_perms.any?
+ logger.warn "User already has repository access " +
+ repo_perms.collect { |p| p[:uuid] }.inspect
+ return repo_perms.first
+ end
+ end
+
+ # create repo, if does not already exist
+ repo ||= Repository.create(name: repo_name)
+ logger.info { "repo uuid: " + repo[:uuid] }
+
+ repo_perm = Link.create(tail_uuid: self.uuid,
+ head_uuid: repo[:uuid],
+ link_class: 'permission',
+ name: 'can_manage')
+ logger.info { "repo permission: " + repo_perm[:uuid] }
+ return repo_perm
+ end
+
+ # create login permission for the given vm_uuid, if it does not already exist
+ def create_vm_login_permission_link(vm_uuid, repo_name)
+ begin
+
+ # vm uuid is optional
+ if vm_uuid
+ vm = VirtualMachine.where(uuid: vm_uuid).first
+
+ if not vm
+ logger.warn "Could not find virtual machine for #{vm_uuid.inspect}"
+ raise "No vm found for #{vm_uuid}"
+ end
+ else
+ return
+ end
+
+ logger.info { "vm uuid: " + vm[:uuid] }
+
+ login_perms = Link.where(tail_uuid: self.uuid,
+ head_uuid: vm[:uuid],
+ link_class: 'permission',
+ name: 'can_login')
+
+ perm_exists = false
+ login_perms.each do |perm|
+ if perm.properties['username'] == repo_name
+ perm_exists = perm
+ break
+ end
+ end
+
+ if perm_exists
+ login_perm = perm_exists
+ else
+ login_perm = Link.create(tail_uuid: self.uuid,
+ head_uuid: vm[:uuid],
+ link_class: 'permission',
+ name: 'can_login',
+ properties: {'username' => repo_name})
+ logger.info { "login permission: " + login_perm[:uuid] }
+ end
+
+ return login_perm
+ end
+ end
+
+ # add the user to the 'All users' group
+ def create_user_group_link
+ return (Link.where(tail_uuid: self.uuid,
+ head_uuid: all_users_group[:uuid],
+ link_class: 'permission',
+ name: 'can_read').first or
+ Link.create(tail_uuid: self.uuid,
+ head_uuid: all_users_group[:uuid],
+ link_class: 'permission',
+ name: 'can_read'))
+ end
+
+ # Give the special "System group" permission to manage this user and
+ # all of this user's stuff.
+ #
+ def add_system_group_permission_link
+ act_as_system_user do
+ Link.create(link_class: 'permission',
+ name: 'can_manage',
+ tail_uuid: system_group_uuid,
+ head_uuid: self.uuid)
+ end
+ end
+
+ # Send admin notifications
+ def send_admin_notifications
+ AdminNotifier.new_user(self).deliver
+ if not self.is_active then
+ AdminNotifier.new_inactive_user(self).deliver
+ end
+ end
+
+ # Automatically setup new user during creation
+ def auto_setup_new_user
+ return true if !Rails.configuration.auto_setup_new_users
+ return true if !self.email
+ return true if self.uuid == system_user_uuid
+ return true if self.uuid == anonymous_user_uuid
+
+ if Rails.configuration.auto_setup_new_users_with_vm_uuid ||
+ Rails.configuration.auto_setup_new_users_with_repository
+ username = self.email.partition('@')[0] if self.email
+ return true if !username
+
+ blacklisted_usernames = Rails.configuration.auto_setup_name_blacklist
+ if blacklisted_usernames.include?(username)
+ return true
+ elsif !(/^[a-zA-Z][-._a-zA-Z0-9]{0,30}[a-zA-Z0-9]$/.match(username))
+ return true
+ else
+ return true if !(username = derive_unique_username username)
+ end
+ end
+
+ # setup user
+ setup_repo_vm_links(username,
+ Rails.configuration.auto_setup_new_users_with_vm_uuid,
+ Rails.configuration.default_openid_prefix)
+ end
+
+ # Find a username that starts with the given string and does not collide
+ # with any existing repository name or VM login name
+ def derive_unique_username username
+ while true
+ if Repository.where(name: username).empty?
+ login_collisions = Link.where(link_class: 'permission',
+ name: 'can_login').select do |perm|
+ perm.properties['username'] == username
+ end
+ return username if login_collisions.empty?
+ end
+ username = username + SecureRandom.random_number(10).to_s
+ end
+ end
+
+ # Send notification if the user saved profile for the first time
+ def send_profile_created_notification
+ if self.prefs_changed?
+ if self.prefs_was.andand.empty? || !self.prefs_was.andand['profile']
+ profile_notification_address = Rails.configuration.user_profile_notification_address
+ ProfileNotifier.profile_created(self, profile_notification_address).deliver if profile_notification_address
+ end
+ end
+ end
+
+end
--- /dev/null
+class UserAgreement < Collection
+ # This class exists so that Arvados::V1::SchemaController includes
+ # UserAgreementsController's methods in the discovery document.
+end
--- /dev/null
+class VirtualMachine < ArvadosModel
+ include HasUuid
+ include KindAndEtag
+ include CommonApiTemplate
+
+ has_many :login_permissions, :foreign_key => :head_uuid, :class_name => 'Link', :primary_key => :uuid, :conditions => "link_class = 'permission' and name = 'can_login'"
+
+ api_accessible :user, extend: :common do |t|
+ t.add :hostname
+ end
+
+ protected
+
+ def permission_to_create
+ current_user and current_user.is_admin
+ end
+ def permission_to_update
+ current_user and current_user.is_admin
+ end
+end
--- /dev/null
+
+A new user landed on the inactive user page:
+
+ <%= @user.full_name %> <<%= @user.email %>>
+
+<% if Rails.configuration.workbench_address -%>
+Please see workbench for more information:
+
+ <%= Rails.configuration.workbench_address %>
+
+<% end -%>
+Thanks,
+Your friendly Arvados robot.
--- /dev/null
+<%
+ add_to_message = ''
+ if Rails.configuration.auto_setup_new_users
+ add_to_message = @user.is_invited ? ' and setup' : ', but not setup'
+ end
+%>
+A new user has been created<%=add_to_message%>:
+
+ <%= @user.full_name %> <<%= @user.email %>>
+
+This user is <%= @user.is_active ? '' : 'NOT ' %>active.
+
+<% if Rails.configuration.workbench_address -%>
+Please see workbench for more information:
+
+ <%= Rails.configuration.workbench_address %>
+
+<% end -%>
+Thanks,
+Your friendly Arvados robot.
+
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+ <title>Server</title>
+ <%= stylesheet_link_tag "application" %>
+ <%= javascript_include_tag "application" %>
+ <%= csrf_meta_tags %>
+</head>
+<body>
+<div id="header">
+ <div class="apptitle">ARVADOS <span class="beta"><span>BETA</span></span></div>
+ <div style="float:right">
+ <% if current_user %>
+ <%= current_user.full_name %>
+ <% if current_user.is_admin %>
+ •
+ <a class="logout" href="/admin/users">Admin</a>
+ <% end %>
+ •
+ <a class="logout" href="/logout">Log out</a>
+ <% else %>
+ <a class="logout" href="/auth/joshid">Log in</a>
+ <% end %>
+
+ <% if current_user and session[:real_uid] and session[:switch_back_to] and User.find(session[:real_uid].to_i).verify_userswitch_cookie(session[:switch_back_to]) %>
+ •
+ <span class="sudo-warning">Logged in as <b><%= current_user.full_name %></b>. <%= link_to "Back to #{User.find(session[:real_uid]).full_name}", switch_to_user_path(session[:real_uid]), :method => :post, :class => 'sudo-logout' %></span>
+ <% end %>
+ </div>
+</div>
+
+
+<%= yield %>
+
+<div style="clear:both"></div>
+
+<% if current_user or session['invite_code'] %>
+<div id="footer">
+ <div style="float:right">Questions → <a href="mailto:arvados@curoverse.com">arvados@curoverse.com</a></div>
+ <div style="clear:both"></div>
+</div>
+<% end %>
+
+</body>
+</html>
--- /dev/null
+Profile created by user <%=@user.full_name%> <%=@user.email%>
+User's profile: <%=@user.prefs['profile']%>
--- /dev/null
+<% content_for :js do %>
+$(function(){
+ $('button.login').button().click(function(){window.location=$(this).attr('href')});
+});
+<% end %>
+<div id="intropage">
+ <img class="curoverse-logo" src="<%= asset_path('logo.png') %>" style="display:block; margin:2em auto"/>
+ <div style="width:30em; margin:2em auto 0 auto">
+ <h1>Welcome</h1>
+ <h4>Curoverse ARVADOS</h4>
+
+ <% if !current_user and session['invite_code'] %>
+
+ <p>Curoverse Arvados lets you manage and process human genomes and exomes. You can start using the private beta
+ now with your Google account.</p>
+ <p style="float:right;margin-top:1em">
+ <button class="login" href="/auth/joshid">Log in and get started</button>
+ </p>
+
+ <% else %>
+
+ <p>Curoverse ARVADOS is transforming how researchers and
+ clinical geneticists use whole genome sequences. </p>
+ <p>If you’re interested in learning more, we’d love to hear
+ from you —
+ contact <a href="mailto:arvados@curoverse.com">arvados@curoverse.com</a>.</p>
+
+ <% if !current_user %>
+ <p style="float:right;margin-top:1em">
+ <a href="/auth/joshid">Log in here.</a>
+ </p>
+ <% end %>
+
+ <% end %>
+
+ <div style="clear:both;height:8em"></div>
+ </div>
+</div>
--- /dev/null
+<% content_for :js do %>
+$(function(){
+ $('button.login').button().click(function(){window.location=$(this).attr('href')});
+});
+<% end %>
+
+
+<div id="intropage">
+ <img class="curoverse-logo" src="<%= asset_path('logo.png') %>" style="display:block; margin:2em auto"/>
+ <div style="width:30em; margin:2em auto 0 auto">
+
+ <h1>Error</h1>
+
+ <p>Sorry, something went wrong logging you in. Please try again.</p>
+
+ <p style="float:right;margin-top:1em">
+ <a href="/auth/joshid">Log in here.</a>
+ </p>
+
+ <div style="clear:both;height:8em"></div>
+ </div>
+</div>
--- /dev/null
+<% if not @user.full_name.empty? -%>
+<%= @user.full_name %>,
+<% else -%>
+Hi there,
+<% end -%>
+
+Your Arvados account has been set up. You can log in with your Google account
+associated with the e-mail address <%= @user.email %><% if Rails.configuration.workbench_address %> at:
+
+ <%= Rails.configuration.workbench_address %><% else %>.<% end %>
+
+Thanks,
+The Arvados team.
--- /dev/null
+<h1>Fail</h1>
+
+<%= notice %>
+
+<br/>
+<a href="/auth/joshid">Retry Login</a>
--- /dev/null
+# This file is used by Rack-based servers to start the application.
+
+require ::File.expand_path('../config/environment', __FILE__)
+run Server::Application
--- /dev/null
+# Do not use this file for site configuration. Create application.yml
+# instead (see application.yml.example).
+
+development:
+ force_ssl: false
+ cache_classes: false
+ whiny_nils: true
+ consider_all_requests_local: true
+ action_controller.perform_caching: false
+ action_mailer.raise_delivery_errors: false
+ action_mailer.perform_deliveries: false
+ active_support.deprecation: :log
+ action_dispatch.best_standards_support: :builtin
+ active_record.mass_assignment_sanitizer: :strict
+ active_record.auto_explain_threshold_in_seconds: 0.5
+ assets.compress: false
+ assets.debug: true
+ local_modified: "<%= '-modified' if `git status -s` != '' %>"
+
+production:
+ force_ssl: true
+ cache_classes: true
+ consider_all_requests_local: false
+ action_controller.perform_caching: true
+ serve_static_assets: false
+ assets.compress: true
+ assets.compile: false
+ assets.digest: true
+
+test:
+ force_ssl: false
+ cache_classes: true
+ serve_static_assets: true
+ static_cache_control: public, max-age=3600
+ whiny_nils: true
+ consider_all_requests_local: true
+ action_controller.perform_caching: false
+ action_dispatch.show_exceptions: false
+ action_controller.allow_forgery_protection: false
+ action_mailer.delivery_method: :test
+ active_support.deprecation: :stderr
+ active_record.mass_assignment_sanitizer: :strict
+ uuid_prefix: zzzzz
+ secret_token: <%= rand(2**512).to_s(36) %>
+ blob_signing_key: zfhgfenhffzltr9dixws36j1yhksjoll2grmku38mi7yxd66h5j4q9w4jzanezacp8s6q0ro3hxakfye02152hncy6zml2ed0uc
+ user_profile_notification_address: arvados@example.com
+ workbench_address: https://localhost:3001/
+ websocket_address: ws://127.0.0.1:3333/websocket
+
+common:
+ uuid_prefix: <%= Digest::MD5.hexdigest(`hostname`).to_i(16).to_s(36)[0..4] %>
+
+ # If not false, this is the hostname that will be used for root_url and
+ # advertised in the discovery document. By default, use the default Rails
+ # logic for deciding on a hostname.
+ host: false
+
+ # If this is not false, HTML requests at the API server's root URL
+ # are redirected to this location, and it is provided in the text of
+ # user activation notification email messages to remind them where
+ # to log in.
+ workbench_address: false
+
+ # Git repositories must be readable by api server, or you won't be
+ # able to submit crunch jobs. To pass the test suites, put a clone
+ # of the arvados tree in {git_repositories_dir}/arvados.git or
+ # {git_repositories_dir}/arvados/.git
+ git_repositories_dir: /var/lib/arvados/git
+
+ # This is a (bare) repository that stores commits used in jobs. When a job
+ # runs, the source commits are first fetched into this repository, then this
+ # repository is used to deploy to compute nodes. This should NOT be a
+ # subdirectory of {git_repositiories_dir}.
+ git_internal_dir: /var/lib/arvados/internal.git
+
+ # :none or :slurm_immediate
+ crunch_job_wrapper: :none
+
+ # username, or false = do not set uid when running jobs.
+ crunch_job_user: crunch
+
+ # The web service must be able to create/write this file, and
+ # crunch-job must be able to stat() it.
+ crunch_refresh_trigger: /tmp/crunch_refresh_trigger
+
+ # These two settings control how frequently log events are flushed to the
+ # database. Log lines are buffered until either crunch_log_bytes_per_event
+ # has been reached or crunch_log_seconds_between_events has elapsed since
+ # the last flush.
+ crunch_log_bytes_per_event: 4096
+ crunch_log_seconds_between_events: 1
+
+ # The sample period for throttling logs, in seconds.
+ crunch_log_throttle_period: 60
+
+ # Maximum number of bytes that job can log over crunch_log_throttle_period
+ # before being silenced until the end of the period.
+ crunch_log_throttle_bytes: 65536
+
+ # Maximum number of lines that job can log over crunch_log_throttle_period
+ # before being silenced until the end of the period.
+ crunch_log_throttle_lines: 1024
+
+ # Maximum bytes that may be logged by a single job. Log bytes that are
+ # silenced by throttling are not counted against this total.
+ crunch_limit_log_bytes_per_job: 67108864
+
+ # Path to dns server configuration directory (e.g. /etc/unbound.d/conf.d),
+ # or false = do not update dns server data.
+ dns_server_conf_dir: false
+
+ # Template for the dns server host snippets. See unbound.template in this directory for
+ # an example. Set to false to disable.
+ dns_server_conf_template: false
+
+ # Dns server reload command, or false = do not reload dns server after data change
+ dns_server_reload_command: false
+
+ # Example for unbound
+ #dns_server_conf_dir: /etc/unbound/conf.d
+ #dns_server_conf_template: /path/to/your/api/server/config/unbound.template
+ #dns_server_reload_command: /etc/init.d/unbound reload
+
+ compute_node_domain: false
+ compute_node_nameservers:
+ - 192.168.1.1
+
+ # The version below is suitable for AWS.
+ # To use it, copy it to your application.yml, uncomment, and change <%# to <%=
+ # compute_node_nameservers: <%#
+ # require 'net/http'
+ # ['local', 'public'].collect do |iface|
+ # Net::HTTP.get(URI("http://169.254.169.254/latest/meta-data/#{iface}-ipv4")).match(/^[\d\.]+$/)[0]
+ # end << '172.16.0.23'
+ # %>
+
+ accept_api_token: {}
+
+ # When new_users_are_active is set to true, the user agreement check is skipped.
+ new_users_are_active: false
+
+ admin_notifier_email_from: arvados@example.com
+ email_subject_prefix: "[ARVADOS] "
+ user_notifier_email_from: arvados@example.com
+ new_user_notification_recipients: [ ]
+ new_inactive_user_notification_recipients: [ ]
+
+ # The e-mail address of the user you would like to become marked as an admin
+ # user on their first login.
+ # In the default configuration, authentication happens through the Arvados SSO
+ # server, which uses openid against Google's servers, so in that case this
+ # should be an address associated with a Google account.
+ auto_admin_user: false
+
+ # If auto_admin_first_user is set to true, the first user to log in when no
+ # other admin users exist will automatically become an admin user.
+ auto_admin_first_user: false
+
+ ## Set Time.zone default to the specified zone and make Active
+ ## Record auto-convert to this zone. Run "rake -D time" for a list
+ ## of tasks for finding time zone names. Default is UTC.
+ #time_zone: Central Time (US & Canada)
+
+ ## Default encoding used in templates for Ruby 1.9.
+ encoding: utf-8
+
+ # Enable the asset pipeline
+ assets.enabled: true
+
+ # Version of your assets, change this if you want to expire all your assets
+ assets.version: "1.0"
+
+ arvados_theme: default
+
+ # The ARVADOS_WEBSOCKETS environment variable determines whether to
+ # serve http, websockets, or both.
+ #
+ # If ARVADOS_WEBSOCKETS="true", http and websockets are both served
+ # from the same process.
+ #
+ # If ARVADOS_WEBSOCKETS="ws-only", only websockets is served.
+ #
+ # If ARVADOS_WEBSOCKETS="false" or not set at all, only http is
+ # served. In this case, you should have a separate process serving
+ # websockets, and the address of that service should be given here
+ # as websocket_address.
+ #
+ # If websocket_address is false (which is the default), the
+ # discovery document will tell clients to use the current server as
+ # the websocket service, or (if the current server does not have
+ # websockets enabled) not to use websockets at all.
+ #
+ # Example: Clients will connect to the specified endpoint.
+ #websocket_address: wss://127.0.0.1:3333/websocket
+ # Default: Clients will connect to this server if it's running
+ # websockets, otherwise none at all.
+ websocket_address: false
+
+ # blob_signing_key is a string of alphanumeric characters used to
+ # generate permission signatures for Keep locators. It must be
+ # identical to the permission key given to Keep. IMPORTANT: This is
+ # a site secret. It should be at least 50 characters.
+ blob_signing_key: ~
+
+ # Amount of time (in seconds) for which a blob permission signature
+ # remains valid. Default: 2 weeks (1209600 seconds)
+ blob_signing_ttl: 1209600
+
+ # Allow clients to create collections by providing a manifest with
+ # unsigned data blob locators. IMPORTANT: This effectively disables
+ # access controls for data stored in Keep: a client who knows a hash
+ # can write a manifest that references the hash, pass it to
+ # collections.create (which will create a permission link), use
+ # collections.get to obtain a signature for that data locator, and
+ # use that signed locator to retrieve the data from Keep. Therefore,
+ # do not turn this on if your users expect to keep data private from
+ # one another!
+ permit_create_collection_with_unsigned_manifest: false
+
+ # secret_token is a string of alphanumeric characters used by Rails
+ # to sign session tokens. IMPORTANT: This is a site secret. It
+ # should be at least 50 characters.
+ secret_token: ~
+
+ # email address to which mail should be sent when the user creates profile for the first time
+ user_profile_notification_address: false
+
+ default_openid_prefix: https://www.google.com/accounts/o8/id
+
+ # Config parameters to automatically setup new users.
+ # The params auto_setup_new_users_with_* are meaningful only when auto_setup_new_users is turned on.
+ # auto_setup_name_blacklist is a list of usernames to be blacklisted for auto setup.
+ auto_setup_new_users: false
+ auto_setup_new_users_with_vm_uuid: false
+ auto_setup_new_users_with_repository: false
+ auto_setup_name_blacklist: [arvados, git, gitolite, gitolite-admin, root, syslog]
+
+ # source_version
+ source_version: "<%= `git log -n 1 --format=%h`.strip %>"
+ local_modified: false
+
+ # Default lifetime for ephemeral collections: 2 weeks.
+ default_trash_lifetime: 1209600
+
+ # Permit insecure (OpenSSL::SSL::VERIFY_NONE) connections to the Single Sign
+ # On (sso) server. Should only be enabled during development when the SSO
+ # server is using a self-signed cert.
+ sso_insecure: false
\ No newline at end of file
--- /dev/null
+require File.expand_path('../boot', __FILE__)
+
+require 'rails/all'
+require 'digest'
+
+if defined?(Bundler)
+ # If you precompile assets before deploying to production, use this line
+ Bundler.require(*Rails.groups(:assets => %w(development test)))
+ # If you want your assets lazily compiled in production, use this line
+ # Bundler.require(:default, :assets, Rails.env)
+end
+
+module Server
+ class Application < Rails::Application
+ # Settings in config/environments/* take precedence over those specified here.
+ # Application configuration should go into files in config/initializers
+ # -- all .rb files in that directory are automatically loaded.
+
+ # Custom directories with classes and modules you want to be autoloadable.
+ # config.autoload_paths += %W(#{config.root}/extras)
+
+ # Only load the plugins named here, in the order given (default is alphabetical).
+ # :all can be used as a placeholder for all plugins not explicitly named.
+ # config.plugins = [ :exception_notification, :ssl_requirement, :all ]
+
+ # Activate observers that should always be running.
+ # config.active_record.observers = :cacher, :garbage_collector, :forum_observer
+ config.active_record.schema_format = :sql
+
+ # The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
+ # config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
+ # config.i18n.default_locale = :de
+
+ # Configure sensitive parameters which will be filtered from the log file.
+ config.filter_parameters += [:password]
+
+ I18n.enforce_available_locales = false
+ end
+end
--- /dev/null
+# Copy this file to application.yml and edit to suit.
+#
+# Consult application.default.yml for the full list of configuration
+# settings.
+#
+# The order of precedence is:
+# 1. config/environments/{RAILS_ENV}.rb (deprecated)
+# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
+# 3. Section in application.yml called "common"
+# 4. Section in application.default.yml corresponding to RAILS_ENV
+# 5. Section in application.default.yml called "common"
+
+development:
+ # Mandatory site secrets. See application.default.yml for more info.
+ secret_token: ~
+ blob_signing_key: ~
+ uuid_prefix: bogus
+ workbench_address: https://localhost:3031
+
+production:
+ # Mandatory site secrets. See application.default.yml for more info.
+ secret_token: ~
+ blob_signing_key: ~
+ uuid_prefix: bogus
+ workbench_address: https://workbench.bogus.arvadosapi.com
+
+test:
+ # Tests should be able to run without further configuration, but if you do
+ # want to change your local test configuration, this is where to do it.
+
+common:
+ # Settings in this section will be used in all environments
+ # (development, production, test) except when overridden in the
+ # environment-specific sections above.
--- /dev/null
+require 'rubygems'
+
+# Set up gems listed in the Gemfile.
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+
+require 'bundler/setup' if File.exists?(ENV['BUNDLE_GEMFILE'])
--- /dev/null
+development:
+ adapter: postgresql
+ encoding: utf8
+ database: arvados_development
+ username: arvados
+ password: xxxxxxxx
+ host: localhost
+
+test:
+ adapter: postgresql
+ encoding: utf8
+ database: arvados_test
+ username: arvados
+ password: xxxxxxxx
+ host: localhost
+
+production:
+ adapter: postgresql
+ encoding: utf8
+ database: arvados_production
+ username: arvados
+ password: xxxxxxxx
+ host: localhost
+
--- /dev/null
+# Load the rails application
+require File.expand_path('../application', __FILE__)
+require 'josh_id'
+
+# Initialize the rails application
+Server::Application.initialize!
+begin
+ Rails.cache.clear
+rescue Errno::ENOENT => e
+ # Cache directory does not exist? Then cache is clear, proceed.
+ Rails.logger.warn "In Rails.cache.clear, ignoring #{e.inspect}"
+end
--- /dev/null
+Server::Application.configure do
+ # Settings specified here will take precedence over those in config/application.rb
+
+ # In the development environment your application's code is reloaded on
+ # every request. This slows down response time but is perfect for development
+ # since you don't have to restart the web server when you make code changes.
+ config.cache_classes = false
+
+ # Log error messages when you accidentally call methods on nil.
+ config.whiny_nils = true
+
+ # Show full error reports and disable caching
+ config.consider_all_requests_local = true
+ config.action_controller.perform_caching = false
+
+ # Don't care if the mailer can't send
+ config.action_mailer.raise_delivery_errors = false
+ config.action_mailer.perform_deliveries = false
+
+ # Print deprecation notices to the Rails logger
+ config.active_support.deprecation = :log
+
+ # Only use best-standards-support built into browsers
+ config.action_dispatch.best_standards_support = :builtin
+
+ # Raise exception on mass assignment protection for Active Record models
+ config.active_record.mass_assignment_sanitizer = :strict
+
+ # Log the query plan for queries taking more than this (works
+ # with SQLite, MySQL, and PostgreSQL)
+ config.active_record.auto_explain_threshold_in_seconds = 0.5
+
+ # Do not compress assets
+ config.assets.compress = false
+
+ # Expands the lines which load the assets
+ config.assets.debug = true
+
+ config.force_ssl = false
+
+end
--- /dev/null
+Server::Application.configure do
+ # Settings specified here will take precedence over those in config/application.rb
+
+ # Code is not reloaded between requests
+ config.cache_classes = true
+
+ # Full error reports are disabled and caching is turned on
+ config.consider_all_requests_local = false
+ config.action_controller.perform_caching = true
+
+ # Disable Rails's static asset server (Apache or nginx will already do this)
+ config.serve_static_assets = false
+
+ # Compress JavaScripts and CSS
+ config.assets.compress = true
+
+ # Don't fallback to assets pipeline if a precompiled asset is missed
+ config.assets.compile = false
+
+ # Generate digests for assets URLs
+ config.assets.digest = true
+
+ # Defaults to Rails.root.join("public/assets")
+ # config.assets.manifest = YOUR_PATH
+
+ # Specifies the header that your server uses for sending files
+ # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
+ # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
+
+ # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
+ # config.force_ssl = true
+
+ # See everything in the log (default is :info)
+ # config.log_level = :debug
+
+ # Use a different logger for distributed setups
+ # config.logger = SyslogLogger.new
+
+ # Use a different cache store in production
+ # config.cache_store = :mem_cache_store
+
+ # Enable serving of images, stylesheets, and JavaScripts from an asset server
+ # config.action_controller.asset_host = "http://assets.example.com"
+
+ # Precompile additional assets (application.js, application.css, and all non-JS/CSS are already added)
+ # config.assets.precompile += %w( search.js )
+
+ # Disable delivery errors, bad email addresses will be ignored
+ # config.action_mailer.raise_delivery_errors = false
+ # config.action_mailer.perform_deliveries = true
+
+ # Enable threaded mode
+ # config.threadsafe!
+
+ # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
+ # the I18n.default_locale when a translation can not be found)
+ config.i18n.fallbacks = true
+
+ # Send deprecation notices to registered listeners
+ config.active_support.deprecation = :notify
+
+end
--- /dev/null
+Server::Application.configure do
+ # Settings specified here will take precedence over those in config/application.rb
+
+ # The test environment is used exclusively to run your application's
+ # test suite. You never need to work with it otherwise. Remember that
+ # your test database is "scratch space" for the test suite and is wiped
+ # and recreated between test runs. Don't rely on the data there!
+ config.cache_classes = true
+
+ # Configure static asset server for tests with Cache-Control for performance
+ config.serve_static_assets = true
+ config.static_cache_control = "public, max-age=3600"
+
+ # Log error messages when you accidentally call methods on nil
+ config.whiny_nils = true
+
+ # Show full error reports and disable caching
+ config.consider_all_requests_local = true
+ config.action_controller.perform_caching = false
+
+ # Raise exceptions instead of rendering exception templates
+ config.action_dispatch.show_exceptions = false
+
+ # Disable request forgery protection in test environment
+ config.action_controller.allow_forgery_protection = false
+
+ # Tell Action Mailer not to deliver emails to the real world.
+ # The :test delivery method accumulates sent emails in the
+ # ActionMailer::Base.deliveries array.
+ config.action_mailer.delivery_method = :test
+
+ # Use SQL instead of Active Record's schema dumper when creating the test database.
+ # This is necessary if your schema can't be completely dumped by the schema dumper,
+ # like if you have constraints or database-specific column types
+ # config.active_record.schema_format = :sql
+
+ # Print deprecation notices to the stderr
+ config.active_support.deprecation = :stderr
+
+ # Raise exception on mass assignment protection for Active Record models
+ config.active_record.mass_assignment_sanitizer = :strict
+
+ # No need for SSL while testing
+ config.force_ssl = false
+
+ # I18n likes to warn when this variable is not set
+ I18n.enforce_available_locales = true
+
+end
--- /dev/null
+require 'andand'
--- /dev/null
+Server::Application.configure do
+ config.middleware.delete ActionDispatch::RemoteIp
+ config.middleware.insert 0, ActionDispatch::RemoteIp
+ config.middleware.insert 1, ArvadosApiToken
+end
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
+# Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
+
+# You can also remove all the silencers if you're trying to debug a problem that might stem from framework code.
+# Rails.backtrace_cleaner.remove_silencers!
--- /dev/null
+require 'common_api_template'
--- /dev/null
+require 'current_api_client'
--- /dev/null
+require 'eventbus'
+
+# See application.yml for details about configuring the websocket service.
+
+Server::Application.configure do
+ # Enables websockets if ARVADOS_WEBSOCKETS is defined with any value. If
+ # ARVADOS_WEBSOCKETS=ws-only, server will only accept websocket connections
+ # and return an error response for all other requests.
+ if ENV['ARVADOS_WEBSOCKETS']
+ config.middleware.insert_after ArvadosApiToken, RackSocket, {
+ :handler => EventBus,
+ :mount => "/websocket",
+ :websocket_only => (ENV['ARVADOS_WEBSOCKETS'] == "ws-only")
+ }
+ Rails.logger.info "Websockets #{ENV['ARVADOS_WEBSOCKETS']}, running at /websocket"
+ else
+ Rails.logger.info "Websockets disabled"
+ end
+end
--- /dev/null
+Server::Application.configure do
+ config.accept_api_token = { 'foobar' => true }
+end
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# Add new inflection rules using the following format
+# (all these examples are active by default):
+# ActiveSupport::Inflector.inflections do |inflect|
+# inflect.plural /^(ox)$/i, '\1en'
+# inflect.singular /^(ox)en/i, '\1'
+# inflect.irregular 'person', 'people'
+# inflect.uncountable %w( fish sheep )
+# end
+
+ActiveSupport::Inflector.inflections do |inflect|
+ inflect.plural /^([Ss]pecimen)$/i, '\1s'
+ inflect.singular /^([Ss]pecimen)s?/i, '\1'
+ inflect.plural /^([Hh]uman)$/i, '\1s'
+ inflect.singular /^([Hh]uman)s?/i, '\1'
+end
--- /dev/null
+require 'kind_and_etag'
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+# Add new mime types for use in respond_to blocks:
+# Mime::Type.register "text/richtext", :rtf
+# Mime::Type.register_alias "text/html", :iphone
--- /dev/null
+require 'net/http'
--- /dev/null
+# Change this omniauth configuration to point to your registered provider
+# Since this is a registered application, add the app id and secret here
+APP_ID = 'arvados-server'
+APP_SECRET = rand(2**512).to_s(36) # CHANGE ME!
+
+# Update your custom Omniauth provider URL here
+CUSTOM_PROVIDER_URL = 'http://localhost:3002'
+
+Rails.application.config.middleware.use OmniAuth::Builder do
+ provider :josh_id, APP_ID, APP_SECRET, CUSTOM_PROVIDER_URL
+end
+
+OmniAuth.config.on_failure = StaticController.action(:login_failure)
--- /dev/null
+# Delete the cached discovery document during startup. Otherwise we
+# might still serve an old discovery document after updating the
+# schema and restarting the server.
+
+Rails.cache.delete 'arvados_v1_rest_discovery'
--- /dev/null
+# Be sure to restart your server when you modify this file.
+
+Server::Application.config.session_store :cookie_store, :key => '_server_session'
+
+# Use the database for sessions instead of the cookie-based default,
+# which shouldn't be used to store highly confidential information
+# (create the session table with "rails generate session_migration")
+# Server::Application.config.session_store :active_record_store
--- /dev/null
+# Be sure to restart your server when you modify this file.
+#
+# This file contains settings for ActionController::ParamsWrapper which
+# is enabled by default.
+
+# Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
+ActiveSupport.on_load(:action_controller) do
+ wrap_parameters :format => [:json]
+end
+
+# Disable root element in JSON by default.
+ActiveSupport.on_load(:active_record) do
+ self.include_root_in_json = false
+end
--- /dev/null
+$application_config = {}
+
+%w(application.default application).each do |cfgfile|
+ path = "#{::Rails.root.to_s}/config/#{cfgfile}.yml"
+ if File.exists? path
+ yaml = ERB.new(IO.read path).result(binding)
+ confs = YAML.load(yaml)
+ $application_config.merge!(confs['common'] || {})
+ $application_config.merge!(confs[::Rails.env.to_s] || {})
+ end
+end
+
+Server::Application.configure do
+ nils = []
+ $application_config.each do |k, v|
+ # "foo.bar: baz" --> { config.foo.bar = baz }
+ cfg = config
+ ks = k.split '.'
+ k = ks.pop
+ ks.each do |kk|
+ cfg = cfg.send(kk)
+ end
+ if cfg.respond_to?(k.to_sym) and !cfg.send(k).nil?
+ # Config must have been set already in environments/*.rb.
+ #
+ # After config files have been migrated, this mechanism should
+ # be deprecated, then removed.
+ elsif v.nil?
+ # Config variables are not allowed to be nil. Make a "naughty"
+ # list, and present it below.
+ nils << k
+ else
+ cfg.send "#{k}=", v
+ end
+ end
+ if !nils.empty?
+ raise <<EOS
+Refusing to start in #{::Rails.env.to_s} mode with missing configuration.
+
+The following configuration settings must be specified in
+config/application.yml:
+* #{nils.join "\n* "}
+
+EOS
+ end
+end
--- /dev/null
+# See http://aaronvb.com/articles/37-rails-caching-and-undefined-class-module
+
+if Rails.env == 'development'
+ Dir.foreach("#{Rails.root}/app/models") do |model_file|
+ require_dependency model_file if model_file.match /\.rb$/
+ end
+end
--- /dev/null
+# Sample localization file for English. Add more files in this directory for other locales.
+# See https://github.com/svenfuchs/rails-i18n/tree/master/rails%2Flocale for starting points.
+
+en:
+ hello: "Hello world"
--- /dev/null
+Server::Application.routes.draw do
+ themes_for_rails
+
+ # See http://guides.rubyonrails.org/routing.html
+
+ # OPTIONS requests are not allowed at routes that use cookies.
+ ['/auth/*a', '/login', '/logout'].each do |nono|
+ match nono, :to => 'user_sessions#cross_origin_forbidden', :via => 'OPTIONS'
+ end
+ # OPTIONS at discovery and API paths get an empty response with CORS headers.
+ match '/discovery/v1/*a', :to => 'static#empty', :via => 'OPTIONS'
+ match '/arvados/v1/*a', :to => 'static#empty', :via => 'OPTIONS'
+
+ namespace :arvados do
+ namespace :v1 do
+ resources :api_client_authorizations do
+ post 'create_system_auth', on: :collection
+ end
+ resources :api_clients
+ resources :authorized_keys
+ resources :collections do
+ get 'provenance', on: :member
+ get 'used_by', on: :member
+ end
+ resources :groups do
+ get 'contents', on: :collection
+ get 'contents', on: :member
+ end
+ resources :humans
+ resources :job_tasks
+ resources :jobs do
+ get 'queue', on: :collection
+ get 'queue_size', on: :collection
+ post 'cancel', on: :member
+ post 'lock', on: :member
+ end
+ resources :keep_disks do
+ post 'ping', on: :collection
+ end
+ resources :keep_services do
+ get 'accessible', on: :collection
+ end
+ resources :links
+ resources :logs
+ resources :nodes do
+ post 'ping', on: :member
+ end
+ resources :pipeline_instances
+ resources :pipeline_templates
+ resources :repositories do
+ get 'get_all_permissions', on: :collection
+ end
+ resources :specimens
+ resources :traits
+ resources :user_agreements do
+ get 'signatures', on: :collection
+ post 'sign', on: :collection
+ end
+ resources :users do
+ get 'current', on: :collection
+ get 'system', on: :collection
+ post 'activate', on: :member
+ post 'setup', on: :collection
+ post 'unsetup', on: :member
+ end
+ resources :virtual_machines do
+ get 'logins', on: :member
+ get 'get_all_logins', on: :collection
+ end
+ get '/permissions/:uuid', :to => 'links#get_permissions'
+ end
+ end
+
+ if Rails.env == 'test'
+ post '/database/reset', to: 'database#reset'
+ end
+
+ # omniauth
+ match '/auth/:provider/callback', :to => 'user_sessions#create'
+ match '/auth/failure', :to => 'user_sessions#failure'
+ # not handled by omniauth provider -> 403 with no CORS headers.
+ get '/auth/*a', :to => 'user_sessions#cross_origin_forbidden'
+
+ # Custom logout
+ match '/login', :to => 'user_sessions#login'
+ match '/logout', :to => 'user_sessions#logout'
+
+ match '/discovery/v1/apis/arvados/v1/rest', :to => 'arvados/v1/schema#index'
+
+ match '/static/login_failure', :to => 'static#login_failure', :as => :login_failure
+
+ # Send unroutable requests to an arbitrary controller
+ # (ends up at ApplicationController#render_not_found)
+ match '*a', :to => 'static#render_not_found'
+
+ root :to => 'static#home'
+end
--- /dev/null
+ local-data: "%{hostname} IN A %{ip_address}"
+ local-data: "%{hostname}.%{uuid_prefix} IN A %{ip_address}"
+ local-data: "%{hostname}.%{uuid_prefix}.arvadosapi.com. IN A %{ip_address}"
+ local-data: "%{ptr_domain}. IN PTR %{hostname}.%{uuid_prefix}.arvadosapi.com"
--- /dev/null
+class CreateCollections < ActiveRecord::Migration
+ def change
+ create_table :collections do |t|
+ t.string :locator
+ t.string :create_by_client
+ t.string :created_by_user
+ t.datetime :created_at
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :portable_data_hash
+ t.string :name
+ t.integer :redundancy
+ t.string :redundancy_confirmed_by_client
+ t.datetime :redundancy_confirmed_at
+ t.integer :redundancy_confirmed_as
+
+ t.timestamps
+ end
+ end
+end
--- /dev/null
+class CreateMetadata < ActiveRecord::Migration
+ def change
+ create_table :metadata do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.datetime :created_at
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :target_uuid
+ t.string :target_kind
+ t.references :native_target, :polymorphic => true
+ t.string :metadatum_class
+ t.string :key
+ t.string :value
+ t.text :info # "unlimited length" in postgresql
+
+ t.timestamps
+ end
+ end
+end
--- /dev/null
+class RenameMetadataClass < ActiveRecord::Migration
+ def up
+ rename_column :metadata, :metadatum_class, :metadata_class
+ end
+
+ def down
+ rename_column :metadata, :metadata_class, :metadatum_class
+ end
+end
--- /dev/null
+class RenameCollectionCreatedByClient < ActiveRecord::Migration
+ def up
+ rename_column :collections, :create_by_client, :created_by_client
+ end
+
+ def down
+ rename_column :collections, :created_by_client, :create_by_client
+ end
+end
--- /dev/null
+class AddUuidToCollections < ActiveRecord::Migration
+ def change
+ add_column :collections, :uuid, :string
+ end
+end
--- /dev/null
+class CreateNodes < ActiveRecord::Migration
+ def up
+ create_table :nodes do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.datetime :created_at
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.integer :slot_number
+ t.string :hostname
+ t.string :domain
+ t.string :ip_address
+ t.datetime :first_ping_at
+ t.datetime :last_ping_at
+ t.text :info
+
+ t.timestamps
+ end
+ add_index :nodes, :uuid, :unique => true
+ add_index :nodes, :slot_number, :unique => true
+ add_index :nodes, :hostname, :unique => true
+ end
+ def down
+ drop_table :nodes
+ end
+end
--- /dev/null
+class CreatePipelines < ActiveRecord::Migration
+ def up
+ create_table :pipelines do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.datetime :created_at
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :name
+ t.text :components
+
+ t.timestamps
+ end
+ add_index :pipelines, :uuid, :unique => true
+ end
+ def down
+ drop_table :pipelines
+ end
+end
--- /dev/null
+class CreatePipelineInvocations < ActiveRecord::Migration
+ def up
+ create_table :pipeline_invocations do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.datetime :created_at
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :pipeline_uuid
+ t.string :name
+ t.text :components
+ t.boolean :success, :null => true
+ t.boolean :active, :default => false
+
+ t.timestamps
+ end
+ add_index :pipeline_invocations, :uuid, :unique => true
+ end
+ def down
+ drop_table :pipeline_invocations
+ end
+end
--- /dev/null
+class AddIndexToCollectionsAndMetadata < ActiveRecord::Migration
+ def up
+ add_index :collections, :uuid, :unique => true
+ add_index :metadata, :uuid, :unique => true
+ end
+ def down
+ remove_index :metadata, :uuid
+ remove_index :collections, :uuid
+ end
+end
--- /dev/null
+class CreateSpecimens < ActiveRecord::Migration
+ def up
+ create_table :specimens do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.datetime :created_at
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :material
+
+ t.timestamps
+ end
+ add_index :specimens, :uuid, :unique => true
+ end
+ def down
+ drop_table :specimens
+ end
+end
--- /dev/null
+class CreateProjects < ActiveRecord::Migration
+ def up
+ create_table :projects do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.datetime :created_at
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :name
+ t.text :description
+
+ t.timestamps
+ end
+ add_index :projects, :uuid, :unique => true
+ end
+ def down
+ drop_table :projects
+ end
+end
--- /dev/null
+class RenameMetadataAttributes < ActiveRecord::Migration
+ def up
+ rename_column :metadata, :target_kind, :tail_kind
+ rename_column :metadata, :target_uuid, :tail
+ rename_column :metadata, :value, :head
+ rename_column :metadata, :key, :name
+ add_column :metadata, :head_kind, :string
+ add_index :metadata, :head
+ add_index :metadata, :head_kind
+ add_index :metadata, :tail
+ add_index :metadata, :tail_kind
+ begin
+ Metadatum.where('head like ?', 'orvos#%').each do |m|
+ kind_uuid = m.head.match /^(orvos\#.*)\#([-0-9a-z]+)$/
+ if kind_uuid
+ m.update_attributes(head_kind: kind_uuid[1],
+ head: kind_uuid[2])
+ end
+ end
+ rescue
+ end
+ end
+
+ def down
+ begin
+ Metadatum.where('head_kind is not null and head_kind <> ? and head is not null', '').each do |m|
+ m.update_attributes(head: m.head_kind + '#' + m.head)
+ end
+ rescue
+ end
+ remove_index :metadata, :tail_kind
+ remove_index :metadata, :tail
+ remove_index :metadata, :head_kind
+ remove_index :metadata, :head
+ rename_column :metadata, :name, :key
+ remove_column :metadata, :head_kind
+ rename_column :metadata, :head, :value
+ rename_column :metadata, :tail, :target_uuid
+ rename_column :metadata, :tail_kind, :target_kind
+ end
+end
--- /dev/null
+class CreateUsers < ActiveRecord::Migration
+ def change
+ create_table :users do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.datetime :created_at
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :email
+ t.string :first_name
+ t.string :last_name
+ t.string :identity_url
+ t.boolean :is_admin
+ t.text :prefs
+
+ t.timestamps
+ end
+ end
+end
--- /dev/null
+class CreateLogs < ActiveRecord::Migration
+ def up
+ create_table :logs do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.string :object_kind
+ t.string :object_uuid
+ t.datetime :event_at
+ t.string :event_type
+ t.text :summary
+ t.text :info
+
+ t.timestamps
+ end
+ add_index :logs, :uuid, :unique => true
+ add_index :logs, :object_kind
+ add_index :logs, :object_uuid
+ add_index :logs, :event_type
+ add_index :logs, :event_at
+ add_index :logs, :summary
+ end
+
+ def down
+ drop_table :logs end
+end
--- /dev/null
+class AddModifiedAtToLogs < ActiveRecord::Migration
+ def change
+ add_column :logs, :modified_at, :datetime
+ end
+end
--- /dev/null
+class AddUuidIndexToUsers < ActiveRecord::Migration
+ def change
+ add_index :users, :uuid, :unique => true
+ end
+end
--- /dev/null
+class CreateApiClients < ActiveRecord::Migration
+ def change
+ create_table :api_clients do |t|
+ t.string :uuid
+ t.string :created_by_client
+ t.string :created_by_user
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :name
+ t.string :url_prefix
+
+ t.timestamps
+ end
+ add_index :api_clients, :uuid, :unique => true
+ end
+end
--- /dev/null
+class CreateApiClientAuthorizations < ActiveRecord::Migration
+ def change
+ create_table :api_client_authorizations do |t|
+ t.string :api_token, :null => false
+ t.references :api_client, :null => false
+ t.references :user, :null => false
+ t.string :created_by_ip_address
+ t.string :last_used_by_ip_address
+ t.datetime :last_used_at
+ t.datetime :expires_at
+
+ t.timestamps
+ end
+ add_index :api_client_authorizations, :api_token, :unique => true
+ add_index :api_client_authorizations, :api_client_id
+ add_index :api_client_authorizations, :user_id
+ add_index :api_client_authorizations, :expires_at
+ end
+end
--- /dev/null
+class RenameCreatedByToOwner < ActiveRecord::Migration
+ def tables
+ %w{api_clients collections logs metadata nodes pipelines pipeline_invocations projects specimens users}
+ end
+
+ def up
+ tables.each do |t|
+ remove_column t.to_sym, :created_by_client
+ rename_column t.to_sym, :created_by_user, :owner
+ end
+ end
+
+ def down
+ tables.reverse.each do |t|
+ rename_column t.to_sym, :owner, :created_by_user
+ add_column t.to_sym, :created_by_client, :string
+ end
+ end
+end
--- /dev/null
+class RenameMetadataToLinks < ActiveRecord::Migration
+ def up
+ rename_table :metadata, :links
+ rename_column :links, :tail, :tail_uuid
+ rename_column :links, :head, :head_uuid
+ rename_column :links, :info, :properties
+ rename_column :links, :metadata_class, :link_class
+ rename_index :links, :index_metadata_on_head_kind, :index_links_on_head_kind
+ rename_index :links, :index_metadata_on_head, :index_links_on_head_uuid
+ rename_index :links, :index_metadata_on_tail_kind, :index_links_on_tail_kind
+ rename_index :links, :index_metadata_on_tail, :index_links_on_tail_uuid
+ rename_index :links, :index_metadata_on_uuid, :index_links_on_uuid
+ end
+
+ def down
+ rename_index :links, :index_links_on_uuid, :index_metadata_on_uuid
+ rename_index :links, :index_links_on_head_kind, :index_metadata_on_head_kind
+ rename_index :links, :index_links_on_head_uuid, :index_metadata_on_head
+ rename_index :links, :index_links_on_tail_kind, :index_metadata_on_tail_kind
+ rename_index :links, :index_links_on_tail_uuid, :index_metadata_on_tail
+ rename_column :links, :link_class, :metadata_class
+ rename_column :links, :properties, :info
+ rename_column :links, :head_uuid, :head
+ rename_column :links, :tail_uuid, :tail
+ rename_table :links, :metadata
+ end
+end
--- /dev/null
+class AddPropertiesToSpecimen < ActiveRecord::Migration
+ def change
+ add_column :specimens, :properties, :text
+ end
+end
--- /dev/null
+class AddManifestTextToCollection < ActiveRecord::Migration
+ def change
+ add_column :collections, :manifest_text, :text
+ end
+end
--- /dev/null
+class CreateJobs < ActiveRecord::Migration
+ def change
+ create_table :jobs do |t|
+ t.string :uuid
+ t.string :owner
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :submit_id
+ t.string :command
+ t.string :command_version
+ t.text :command_parameters
+ t.string :cancelled_by_client
+ t.string :cancelled_by_user
+ t.datetime :cancelled_at
+ t.datetime :started_at
+ t.datetime :finished_at
+ t.boolean :running
+ t.boolean :success
+ t.string :output
+
+ t.timestamps
+ end
+ add_index :jobs, :uuid, :unique => true
+ add_index :jobs, :submit_id, :unique => true
+ add_index :jobs, :command
+ add_index :jobs, :finished_at
+ add_index :jobs, :started_at
+ add_index :jobs, :output
+ end
+end
--- /dev/null
+class CreateJobSteps < ActiveRecord::Migration
+ def change
+ create_table :job_steps do |t|
+ t.string :uuid
+ t.string :owner
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :job_uuid
+ t.integer :sequence
+ t.text :parameters
+ t.text :output
+ t.float :progress
+ t.boolean :success
+
+ t.timestamps
+ end
+ add_index :job_steps, :uuid, :unique => true
+ add_index :job_steps, :job_uuid
+ add_index :job_steps, :sequence
+ add_index :job_steps, :success
+ end
+end
--- /dev/null
+class AddPriorityToJobs < ActiveRecord::Migration
+ def change
+ add_column :jobs, :priority, :string
+ end
+end
--- /dev/null
+class AddIndexOnTimestamps < ActiveRecord::Migration
+ def tables
+ %w{api_clients collections jobs job_steps links logs nodes pipeline_invocations pipelines projects specimens users}
+ end
+
+ def change
+ tables.each do |t|
+ add_index t.to_sym, :created_at
+ add_index t.to_sym, :modified_at
+ end
+ end
+end
--- /dev/null
+class AddPropertiesToPipelineInvocations < ActiveRecord::Migration
+ def change
+ add_column :pipeline_invocations, :properties, :text
+ end
+end
--- /dev/null
+class RemoveNativeTargetFromLinks < ActiveRecord::Migration
+ def up
+ remove_column :links, :native_target_id
+ remove_column :links, :native_target_type
+ end
+ def down
+ add_column :links, :native_target_id, :integer
+ add_column :links, :native_target_type, :string
+ end
+end
--- /dev/null
+class RenameProjectsToGroups < ActiveRecord::Migration
+ def up
+ rename_table :projects, :groups
+ rename_index :groups, :index_projects_on_created_at, :index_groups_on_created_at
+ rename_index :groups, :index_projects_on_modified_at, :index_groups_on_modified_at
+ rename_index :groups, :index_projects_on_uuid, :index_groups_on_uuid
+ Link.update_all({head_kind:'orvos#group'}, ['head_kind=?','orvos#project'])
+ Link.update_all({tail_kind:'orvos#group'}, ['tail_kind=?','orvos#project'])
+ Log.update_all({object_kind:'orvos#group'}, ['object_kind=?','orvos#project'])
+ end
+
+ def down
+ Log.update_all({object_kind:'orvos#project'}, ['object_kind=?','orvos#group'])
+ Link.update_all({tail_kind:'orvos#project'}, ['tail_kind=?','orvos#group'])
+ Link.update_all({head_kind:'orvos#project'}, ['head_kind=?','orvos#group'])
+ rename_index :groups, :index_groups_on_created_at, :index_projects_on_created_at
+ rename_index :groups, :index_groups_on_modified_at, :index_projects_on_modified_at
+ rename_index :groups, :index_groups_on_uuid, :index_projects_on_uuid
+ rename_table :groups, :projects
+ end
+end
--- /dev/null
+class AddIsLockedByToJobs < ActiveRecord::Migration
+ def change
+ add_column :jobs, :is_locked_by, :string
+ end
+end
--- /dev/null
+class AddLogToJobs < ActiveRecord::Migration
+ def change
+ add_column :jobs, :log, :string
+ end
+end
--- /dev/null
+class AddTasksSummaryToJobs < ActiveRecord::Migration
+ def change
+ add_column :jobs, :tasks_summary, :text
+ end
+end
--- /dev/null
+class AddResourceLimitsToJobs < ActiveRecord::Migration
+ def change
+ add_column :jobs, :resource_limits, :text
+ end
+end
--- /dev/null
+class RenameJobCommandToScript < ActiveRecord::Migration
+ def up
+ rename_column :jobs, :command, :script
+ rename_column :jobs, :command_parameters, :script_parameters
+ rename_column :jobs, :command_version, :script_version
+ rename_index :jobs, :index_jobs_on_command, :index_jobs_on_script
+ end
+
+ def down
+ rename_index :jobs, :index_jobs_on_script, :index_jobs_on_command
+ rename_column :jobs, :script_version, :command_version
+ rename_column :jobs, :script_parameters, :command_parameters
+ rename_column :jobs, :script, :command
+ end
+end
--- /dev/null
+class RenamePipelineInvocationToPipelineInstance < ActiveRecord::Migration
+ def up
+ rename_table :pipeline_invocations, :pipeline_instances
+ rename_index :pipeline_instances, :index_pipeline_invocations_on_created_at, :index_pipeline_instances_on_created_at
+ rename_index :pipeline_instances, :index_pipeline_invocations_on_modified_at, :index_pipeline_instances_on_modified_at
+ rename_index :pipeline_instances, :index_pipeline_invocations_on_uuid, :index_pipeline_instances_on_uuid
+ Link.update_all({head_kind:'orvos#pipeline_instance'}, ['head_kind=?','orvos#pipeline_invocation'])
+ Link.update_all({tail_kind:'orvos#pipeline_instance'}, ['tail_kind=?','orvos#pipeline_invocation'])
+ Log.update_all({object_kind:'orvos#pipeline_instance'}, ['object_kind=?','orvos#pipeline_invocation'])
+ end
+
+ def down
+ Link.update_all({head_kind:'orvos#pipeline_invocation'}, ['head_kind=?','orvos#pipeline_instance'])
+ Link.update_all({tail_kind:'orvos#pipeline_invocation'}, ['tail_kind=?','orvos#pipeline_instance'])
+ Log.update_all({object_kind:'orvos#pipeline_invocation'}, ['object_kind=?','orvos#pipeline_instance'])
+ rename_index :pipeline_instances, :index_pipeline_instances_on_created_at, :index_pipeline_invocations_on_created_at
+ rename_index :pipeline_instances, :index_pipeline_instances_on_modified_at, :index_pipeline_invocations_on_modified_at
+ rename_index :pipeline_instances, :index_pipeline_instances_on_uuid, :index_pipeline_invocations_on_uuid
+ rename_table :pipeline_instances, :pipeline_invocations
+ end
+end
--- /dev/null
+class RenamePipelinesToPipelineTemplates < ActiveRecord::Migration
+ def up
+ rename_column :pipeline_instances, :pipeline_uuid, :pipeline_template_uuid
+ rename_table :pipelines, :pipeline_templates
+ rename_index :pipeline_templates, :index_pipelines_on_created_at, :index_pipeline_templates_on_created_at
+ rename_index :pipeline_templates, :index_pipelines_on_modified_at, :index_pipeline_templates_on_modified_at
+ rename_index :pipeline_templates, :index_pipelines_on_uuid, :index_pipeline_templates_on_uuid
+ Link.update_all({head_kind:'orvos#pipeline'}, ['head_kind=?','orvos#pipeline_template'])
+ Link.update_all({tail_kind:'orvos#pipeline'}, ['tail_kind=?','orvos#pipeline_template'])
+ Log.update_all({object_kind:'orvos#pipeline'}, ['object_kind=?','orvos#pipeline_template'])
+ end
+
+ def down
+ Link.update_all({head_kind:'orvos#pipeline_template'}, ['head_kind=?','orvos#pipeline'])
+ Link.update_all({tail_kind:'orvos#pipeline_template'}, ['tail_kind=?','orvos#pipeline'])
+ Log.update_all({object_kind:'orvos#pipeline_template'}, ['object_kind=?','orvos#pipeline'])
+ rename_index :pipeline_templates, :index_pipeline_templates_on_created_at, :index_pipelines_on_created_at
+ rename_index :pipeline_templates, :index_pipeline_templates_on_modified_at, :index_pipelines_on_modified_at
+ rename_index :pipeline_templates, :index_pipeline_templates_on_uuid, :index_pipelines_on_uuid
+ rename_table :pipeline_templates, :pipelines
+ rename_column :pipeline_instances, :pipeline_template_uuid, :pipeline_uuid
+ end
+end
--- /dev/null
+class RenameJobStepsToJobTasks < ActiveRecord::Migration
+ def up
+ rename_table :job_steps, :job_tasks
+ rename_index :job_tasks, :index_job_steps_on_created_at, :index_job_tasks_on_created_at
+ rename_index :job_tasks, :index_job_steps_on_job_uuid, :index_job_tasks_on_job_uuid
+ rename_index :job_tasks, :index_job_steps_on_modified_at, :index_job_tasks_on_modified_at
+ rename_index :job_tasks, :index_job_steps_on_sequence, :index_job_tasks_on_sequence
+ rename_index :job_tasks, :index_job_steps_on_success, :index_job_tasks_on_success
+ rename_index :job_tasks, :index_job_steps_on_uuid, :index_job_tasks_on_uuid
+ end
+
+ def down
+ rename_index :job_steps, :index_job_tasks_on_created_at, :index_job_steps_on_created_at
+ rename_index :job_steps, :index_job_tasks_on_job_uuid, :index_job_steps_on_job_uuid
+ rename_index :job_steps, :index_job_tasks_on_modified_at, :index_job_steps_on_modified_at
+ rename_index :job_steps, :index_job_tasks_on_sequence, :index_job_steps_on_sequence
+ rename_index :job_steps, :index_job_tasks_on_success, :index_job_steps_on_success
+ rename_index :job_steps, :index_job_tasks_on_uuid, :index_job_steps_on_uuid
+ rename_table :job_tasks, :job_steps
+ end
+end
--- /dev/null
+class AddDefaultOwnerToUsers < ActiveRecord::Migration
+ def change
+ add_column :users, :default_owner, :string
+ end
+end
--- /dev/null
+class AddDefaultOwnerToApiClientAuthorizations < ActiveRecord::Migration
+ def change
+ add_column :api_client_authorizations, :default_owner, :string
+ end
+end
--- /dev/null
+class CreateCommits < ActiveRecord::Migration
+ def change
+ create_table :commits do |t|
+ t.string :repository_name
+ t.string :sha1
+ t.string :message
+
+ t.timestamps
+ end
+ add_index :commits, [:repository_name, :sha1], :unique => true
+ end
+end
--- /dev/null
+class CreateCommitAncestors < ActiveRecord::Migration
+ def change
+ create_table :commit_ancestors do |t|
+ t.string :repository_name
+ t.string :descendant, :null => false
+ t.string :ancestor, :null => false
+ t.boolean :is, :default => false, :null => false
+
+ t.timestamps
+ end
+ add_index :commit_ancestors, [:descendant, :ancestor], :unique => true
+ end
+end
--- /dev/null
+class RenameOrvosToArvados < ActiveRecord::Migration
+ def up
+ Link.update_all("head_kind=replace(head_kind,'orvos','arvados')")
+ Link.update_all("tail_kind=replace(tail_kind,'orvos','arvados')")
+ Log.update_all("object_kind=replace(object_kind,'orvos','arvados')")
+ end
+
+ def down
+ Link.update_all("head_kind=replace(head_kind,'arvados','orvos')")
+ Link.update_all("tail_kind=replace(tail_kind,'arvados','orvos')")
+ Log.update_all("object_kind=replace(object_kind,'arvados','orvos')")
+ end
+end
--- /dev/null
+class CreateKeepDisks < ActiveRecord::Migration
+ def change
+ create_table :keep_disks do |t|
+ t.string :uuid, :null => false
+ t.string :owner, :null => false
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :ping_secret, :null => false
+ t.string :node_uuid
+ t.string :filesystem_uuid
+ t.integer :bytes_total
+ t.integer :bytes_free
+ t.boolean :is_readable, :null => false, :default => true
+ t.boolean :is_writable, :null => false, :default => true
+ t.datetime :last_read_at
+ t.datetime :last_write_at
+ t.datetime :last_ping_at
+
+ t.timestamps
+ end
+ add_index :keep_disks, :uuid, :unique => true
+ add_index :keep_disks, :filesystem_uuid
+ add_index :keep_disks, :node_uuid
+ add_index :keep_disks, :last_ping_at
+ end
+end
--- /dev/null
+class AddServiceHostAndServicePortAndServiceSslFlagToKeepDisks < ActiveRecord::Migration
+ def change
+ add_column :keep_disks, :service_host, :string
+ add_column :keep_disks, :service_port, :integer
+ add_column :keep_disks, :service_ssl_flag, :boolean
+ add_index :keep_disks, [:service_host, :service_port, :last_ping_at],
+ name: 'keep_disks_service_host_port_ping_at_index'
+ end
+end
--- /dev/null
+class AddCreatedByJobTaskToJobTasks < ActiveRecord::Migration
+ def change
+ add_column :job_tasks, :created_by_job_task, :string
+ end
+end
--- /dev/null
+class AddQsequenceToJobTasks < ActiveRecord::Migration
+ def change
+ add_column :job_tasks, :qsequence, :integer
+ end
+end
--- /dev/null
+class FixJobTaskQsequenceType < ActiveRecord::Migration
+ def up
+ change_column :job_tasks, :qsequence, :integer, :limit => 8
+ end
+
+ def down
+ change_column :job_tasks, :qsequence, :integer
+ end
+end
--- /dev/null
+class UpdateNodesIndex < ActiveRecord::Migration
+ def up
+ remove_index :nodes, :hostname
+ add_index :nodes, :hostname
+ end
+ def down
+ remove_index :nodes, :hostname
+ add_index :nodes, :hostname, :unique => true
+ end
+end
--- /dev/null
+class CreateAuthorizedKeys < ActiveRecord::Migration
+ def change
+ create_table :authorized_keys do |t|
+ t.string :uuid, :null => false
+ t.string :owner, :null => false
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :name
+ t.string :key_type
+ t.string :authorized_user
+ t.text :public_key
+ t.datetime :expires_at
+
+ t.timestamps
+ end
+ add_index :authorized_keys, :uuid, :unique => true
+ add_index :authorized_keys, [:authorized_user, :expires_at]
+ end
+end
--- /dev/null
+class CreateVirtualMachines < ActiveRecord::Migration
+ def change
+ create_table :virtual_machines do |t|
+ t.string :uuid, :null => false
+ t.string :owner, :null => false
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :hostname
+
+ t.timestamps
+ end
+ add_index :virtual_machines, :uuid, :unique => true
+ add_index :virtual_machines, :hostname
+ end
+end
--- /dev/null
+class CreateRepositories < ActiveRecord::Migration
+ def change
+ create_table :repositories do |t|
+ t.string :uuid, :null => false
+ t.string :owner, :null => false
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :name
+ t.string :fetch_url
+ t.string :push_url
+
+ t.timestamps
+ end
+ add_index :repositories, :uuid, :unique => true
+ add_index :repositories, :name
+ end
+end
--- /dev/null
+class RenameAuthorizedKeyAuthorizedUserToAuthorizedUserUuid < ActiveRecord::Migration
+ def up
+ remove_index :authorized_keys, [:authorized_user, :expires_at]
+ rename_column :authorized_keys, :authorized_user, :authorized_user_uuid
+ add_index :authorized_keys, [:authorized_user_uuid, :expires_at]
+ end
+
+ def down
+ remove_index :authorized_keys, [:authorized_user_uuid, :expires_at]
+ rename_column :authorized_keys, :authorized_user_uuid, :authorized_user
+ add_index :authorized_keys, [:authorized_user, :expires_at]
+ end
+end
--- /dev/null
+class AddNameUniqueIndexToRepositories < ActiveRecord::Migration
+ def up
+ remove_index :repositories, :name
+ add_index :repositories, :name, :unique => true
+ end
+
+ def down
+ remove_index :repositories, :name
+ add_index :repositories, :name
+ end
+end
--- /dev/null
+class AddIsTrustedToApiClients < ActiveRecord::Migration
+ def change
+ add_column :api_clients, :is_trusted, :boolean, :default => false
+ end
+end
--- /dev/null
+class AddIsActiveToUsers < ActiveRecord::Migration
+ def change
+ add_column :users, :is_active, :boolean, :default => false
+ end
+end
--- /dev/null
+class ActivateAllAdmins < ActiveRecord::Migration
+ def up
+ User.update_all({is_active: true}, ['is_admin=?', true])
+ end
+
+ def down
+ end
+end
--- /dev/null
+class CreateTraits < ActiveRecord::Migration
+ def change
+ create_table :traits do |t|
+ t.string :uuid, :null => false
+ t.string :owner, :null => false
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.string :name
+ t.text :properties
+
+ t.timestamps
+ end
+ add_index :traits, :uuid, :unique => true
+ add_index :traits, :name
+ end
+end
--- /dev/null
+class CreateHumans < ActiveRecord::Migration
+ def change
+ create_table :humans do |t|
+ t.string :uuid, :null => false
+ t.string :owner, :null => false
+ t.string :modified_by_client
+ t.string :modified_by_user
+ t.datetime :modified_at
+ t.text :properties
+
+ t.timestamps
+ end
+ add_index :humans, :uuid, :unique => true
+ end
+end
--- /dev/null
+class RenameForeignUuidAttributes < ActiveRecord::Migration
+ def change
+ rename_column :api_client_authorizations, :default_owner, :default_owner_uuid
+ [:api_clients, :authorized_keys, :collections,
+ :groups, :humans, :job_tasks, :jobs, :keep_disks,
+ :links, :logs, :nodes, :pipeline_instances, :pipeline_templates,
+ :repositories, :specimens, :traits, :users, :virtual_machines].each do |t|
+ rename_column t, :owner, :owner_uuid
+ rename_column t, :modified_by_client, :modified_by_client_uuid
+ rename_column t, :modified_by_user, :modified_by_user_uuid
+ end
+ rename_column :collections, :redundancy_confirmed_by_client, :redundancy_confirmed_by_client_uuid
+ rename_column :jobs, :is_locked_by, :is_locked_by_uuid
+ rename_column :job_tasks, :created_by_job_task, :created_by_job_task_uuid
+ end
+end
--- /dev/null
+class RenameJobForeignUuidAttributes < ActiveRecord::Migration
+ def change
+ rename_column :jobs, :cancelled_by_client, :cancelled_by_client_uuid
+ rename_column :jobs, :cancelled_by_user, :cancelled_by_user_uuid
+ end
+end
--- /dev/null
+class RenameUserDefaultOwner < ActiveRecord::Migration
+ def change
+ rename_column :users, :default_owner, :default_owner_uuid
+ end
+end
--- /dev/null
+class AddScopesToApiClientAuthorizations < ActiveRecord::Migration
+ def change
+ add_column :api_client_authorizations, :scopes, :text, :null => false, :default => ['all'].to_yaml
+ end
+end
--- /dev/null
+class RenameResourceLimitsToRuntimeConstraints < ActiveRecord::Migration
+ def change
+ rename_column :jobs, :resource_limits, :runtime_constraints
+ end
+end
--- /dev/null
+class NormalizeCollectionUuid < ActiveRecord::Migration
+ def count_orphans
+ %w(head tail).each do |ht|
+ results = ActiveRecord::Base.connection.execute(<<-EOS)
+SELECT COUNT(links.*)
+ FROM links
+ LEFT JOIN collections c
+ ON links.#{ht}_uuid = c.uuid
+ WHERE (#{ht}_kind='arvados#collection' or #{ht}_uuid ~ '^[0-9a-f]{32,}')
+ AND #{ht}_uuid IS NOT NULL
+ AND #{ht}_uuid NOT IN (SELECT uuid FROM collections)
+EOS
+ puts "#{results.first['count'].to_i} links with #{ht}_uuid pointing nowhere."
+ end
+ end
+
+ def up
+ # Normalize uuids in the collections table to
+ # {hash}+{size}. Existing uuids might be {hash},
+ # {hash}+{size}+K@{instance-name}, {hash}+K@{instance-name}, etc.
+
+ count_orphans
+ puts "Normalizing collection UUIDs."
+
+ update_sql <<-EOS
+UPDATE collections
+ SET uuid = regexp_replace(uuid,'\\+.*','') || '+' || length(manifest_text)
+ WHERE uuid !~ '^[0-9a-f]{32,}\\+[0-9]+$'
+ AND (regexp_replace(uuid,'\\+.*','') || '+' || length(manifest_text))
+ NOT IN (SELECT uuid FROM collections)
+EOS
+
+ count_orphans
+ puts "Updating links by stripping +K@.* from *_uuid attributes."
+
+ update_sql <<-EOS
+UPDATE links
+ SET head_uuid = regexp_replace(head_uuid,'\\+K@.*','')
+ WHERE head_uuid like '%+K@%'
+EOS
+ update_sql <<-EOS
+UPDATE links
+ SET tail_uuid = regexp_replace(tail_uuid,'\\+K@.*','')
+ WHERE tail_uuid like '%+K@%'
+EOS
+
+ count_orphans
+ puts "Updating links by searching bare collection hashes using regexp."
+
+ # Next, update {hash} (and any other non-normalized forms) to
+ # {hash}+{size}. This can only work where the corresponding
+ # collection is found in the collections table (otherwise we can't
+ # know the size).
+ %w(head tail).each do |ht|
+ update_sql <<-EOS
+UPDATE links
+ SET #{ht}_uuid = c.uuid
+ FROM collections c
+ WHERE #{ht}_uuid IS NOT NULL
+ AND (#{ht}_kind='arvados#collection' or #{ht}_uuid ~ '^[0-9a-f]{32,}')
+ AND #{ht}_uuid NOT IN (SELECT uuid FROM collections)
+ AND regexp_replace(#{ht}_uuid,'\\+.*','') = regexp_replace(c.uuid,'\\+.*','')
+ AND c.uuid ~ '^[0-9a-f]{32,}\\+[0-9]+$'
+EOS
+ end
+
+ count_orphans
+ puts "Stripping \"+K@.*\" from jobs.output, jobs.log, job_tasks.output."
+
+ update_sql <<-EOS
+UPDATE jobs
+ SET output = regexp_replace(output,'\\+K@.*','')
+ WHERE output ~ '^[0-9a-f]{32,}\\+[0-9]+\\+K@\\w+$'
+EOS
+ update_sql <<-EOS
+UPDATE jobs
+ SET log = regexp_replace(log,'\\+K@.*','')
+ WHERE log ~ '^[0-9a-f]{32,}\\+[0-9]+\\+K@\\w+$'
+EOS
+ update_sql <<-EOS
+UPDATE job_tasks
+ SET output = regexp_replace(output,'\\+K@.*','')
+ WHERE output ~ '^[0-9a-f]{32,}\\+[0-9]+\\+K@\\w+$'
+EOS
+
+ puts "Done."
+ end
+
+ def down
+ end
+end
--- /dev/null
+class FixLinkKindUnderscores < ActiveRecord::Migration
+ def up
+ update_sql <<-EOS
+UPDATE links
+ SET head_kind = 'arvados#virtualMachine'
+ WHERE head_kind = 'arvados#virtual_machine'
+EOS
+ end
+
+ def down
+ update_sql <<-EOS
+UPDATE links
+ SET head_kind = 'arvados#virtual_machine'
+ WHERE head_kind = 'arvados#virtualMachine'
+EOS
+ end
+end
--- /dev/null
+class NormalizeCollectionUuidsInScriptParameters < ActiveRecord::Migration
+ include CurrentApiClient
+ def up
+ act_as_system_user do
+ PipelineInstance.all.each do |pi|
+ pi.save! if fix_values_recursively(pi.components)
+ end
+ Job.all.each do |j|
+ changed = false
+ j.script_parameters.each do |p, v|
+ if v.is_a? String and v.match /\+K/
+ v.gsub! /\+K\@\w+/, ''
+ changed = true
+ end
+ end
+ j.save! if changed
+ end
+ end
+ end
+
+ def down
+ end
+
+ protected
+ def fix_values_recursively fixme
+ changed = false
+ if fixme.is_a? String
+ if fixme.match /\+K/
+ fixme.gsub! /\+K\@\w+/, ''
+ return true
+ else
+ return false
+ end
+ elsif fixme.is_a? Array
+ fixme.each do |v|
+ changed = fix_values_recursively(v) || changed
+ end
+ elsif fixme.is_a? Hash
+ fixme.each do |p, v|
+ changed = fix_values_recursively(v) || changed
+ end
+ end
+ changed
+ end
+end
--- /dev/null
+class AddNondeterministicColumnToJob < ActiveRecord::Migration
+ def up
+ add_column :jobs, :nondeterministic, :boolean
+ end
+
+ def down
+ remove_column :jobs, :nondeterministic
+ end
+end
--- /dev/null
+class SeparateRepositoryFromScriptVersion < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def fixup pt
+ c = pt.components
+ c.each do |k, v|
+ commit_ish = v["script_version"]
+ if commit_ish.andand.index(':')
+ want_repo, commit_ish = commit_ish.split(':',2)
+ v[:repository] = want_repo
+ v[:script_version] = commit_ish
+ end
+ end
+ pt.save!
+ end
+
+ def up
+ act_as_system_user do
+ PipelineTemplate.all.each do |pt|
+ fixup pt
+ end
+ PipelineInstance.all.each do |pt|
+ fixup pt
+ end
+ end
+ end
+
+ def down
+ raise ActiveRecord::IrreversibleMigration
+ end
+end
--- /dev/null
+class AddRepositoryColumnToJob < ActiveRecord::Migration
+ def up
+ add_column :jobs, :repository, :string
+ end
+
+ def down
+ remove_column :jobs, :repository
+ end
+end
--- /dev/null
+class AddOutputIsPersistentToJob < ActiveRecord::Migration
+ def change
+ add_column :jobs, :output_is_persistent, :boolean, null: false, default: false
+ end
+end
--- /dev/null
+class RemoveKindColumns < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ remove_column :links, :head_kind
+ remove_column :links, :tail_kind
+ remove_column :logs, :object_kind
+ end
+
+ def down
+ add_column :links, :head_kind, :string
+ add_column :links, :tail_kind, :string
+ add_column :logs, :object_kind, :string
+
+ act_as_system_user do
+ Link.all.each do |l|
+ l.head_kind = ArvadosModel::resource_class_for_uuid(l.head_uuid).kind if l.head_uuid
+ l.tail_kind = ArvadosModel::resource_class_for_uuid(l.tail_uuid).kind if l.tail_uuid
+ l.save
+ end
+ Log.all.each do |l|
+ l.object_kind = ArvadosModel::resource_class_for_uuid(l.object_uuid).kind if l.object_uuid
+ l.save
+ end
+ end
+ end
+end
--- /dev/null
+class AddSystemGroup < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ # Make sure the system group exists.
+ system_group
+ end
+
+ def down
+ act_as_system_user do
+ system_group.destroy
+
+ # Destroy the automatically generated links giving system_group
+ # permission on all users.
+ Link.destroy_all(tail_uuid: system_group_uuid, head_kind: 'arvados#user')
+ end
+ end
+end
--- /dev/null
+class RenameLogInfoToProperties < ActiveRecord::Migration
+ def change
+ rename_column :logs, :info, :properties
+ end
+end
--- /dev/null
+class AddGroupClassToGroups < ActiveRecord::Migration
+ def change
+ add_column :groups, :group_class, :string
+ add_index :groups, :group_class
+ end
+end
--- /dev/null
+class RenameAuthKeysUserIndex < ActiveRecord::Migration
+ # Rails' default name for this index is so long, Rails can't modify
+ # the index later, because the autogenerated temporary name exceeds
+ # PostgreSQL's 64-character limit. This migration gives the index
+ # an explicit name to work around that issue.
+ def change
+ rename_index("authorized_keys",
+ "index_authorized_keys_on_authorized_user_uuid_and_expires_at",
+ "index_authkeys_on_user_and_expires_at")
+ end
+end
--- /dev/null
+class TimestampsNotNull < ActiveRecord::Migration
+ def up
+ ActiveRecord::Base.connection.tables.each do |t|
+ next if t == 'schema_migrations'
+ change_column t.to_sym, :created_at, :datetime, :null => false
+ change_column t.to_sym, :updated_at, :datetime, :null => false
+ end
+ end
+ def down
+ # There might have been a NULL constraint before this, depending
+ # on the version of Rails used to build the database.
+ end
+end
--- /dev/null
+class PipelineInstanceState < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ add_column :pipeline_instances, :state, :string
+ add_column :pipeline_instances, :components_summary, :text
+
+ PipelineInstance.reset_column_information
+
+ act_as_system_user do
+ PipelineInstance.all.each do |pi|
+ pi.state = PipelineInstance::New
+
+ if !pi.attribute_present? :success # success is nil
+ if pi[:active] == true
+ pi.state = PipelineInstance::RunningOnServer
+ else
+ if pi.components_look_ready?
+ pi.state = PipelineInstance::Ready
+ else
+ pi.state = PipelineInstance::New
+ end
+ end
+ elsif pi[:success] == true
+ pi.state = PipelineInstance::Complete
+ else
+ pi.state = PipelineInstance::Failed
+ end
+
+ pi.save!
+ end
+ end
+
+# We want to perform addition of state, and removal of active and success in two phases. Hence comment these statements out.
+=begin
+ if column_exists?(:pipeline_instances, :active)
+ remove_column :pipeline_instances, :active
+ end
+
+ if column_exists?(:pipeline_instances, :success)
+ remove_column :pipeline_instances, :success
+ end
+=end
+ end
+
+ def down
+# We want to perform addition of state, and removal of active and success in two phases. Hence comment these statements out.
+=begin
+ add_column :pipeline_instances, :success, :boolean, :null => true
+ add_column :pipeline_instances, :active, :boolean, :default => false
+
+ act_as_system_user do
+ PipelineInstance.all.each do |pi|
+ case pi.state
+ when PipelineInstance::New, PipelineInstance::Ready
+ pi.active = false
+ pi.success = nil
+ when PipelineInstance::RunningOnServer
+ pi.active = true
+ pi.success = nil
+ when PipelineInstance::RunningOnClient
+ pi.active = false
+ pi.success = nil
+ when PipelineInstance::Failed
+ pi.active = false
+ pi.success = false
+ when PipelineInstance::Complete
+ pi.active = false
+ pi.success = true
+ end
+ pi.save!
+ end
+ end
+=end
+
+ if column_exists?(:pipeline_instances, :components_summary)
+ remove_column :pipeline_instances, :components_summary
+ end
+
+ if column_exists?(:pipeline_instances, :state)
+ remove_column :pipeline_instances, :state
+ end
+ end
+end
--- /dev/null
+class AddObjectOwnerToLogs < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ add_column :logs, :object_owner_uuid, :string
+ act_as_system_user do
+ Log.find_in_batches(:batch_size => 500) do |batch|
+ upd = {}
+ ActiveRecord::Base.transaction do
+ batch.each do |log|
+ if log.properties["new_attributes"]
+ log.object_owner_uuid = log.properties['new_attributes']['owner_uuid']
+ log.save
+ elsif log.properties["old_attributes"]
+ log.object_owner_uuid = log.properties['old_attributes']['owner_uuid']
+ log.save
+ end
+ end
+ end
+ end
+ end
+ end
+
+ def down
+ remove_column :logs, :object_owner_uuid
+ end
+end
--- /dev/null
+# At the time we introduced scopes everywhere, VirtualMachinesController
+# recognized scopes that gave the URL for a VM to grant access to that VM's
+# login list. This migration converts those VM-specific scopes to the new
+# general format, and back.
+
+class NewScopeFormat < ActiveRecord::Migration
+ include CurrentApiClient
+
+ VM_PATH_REGEX =
+ %r{(/arvados/v1/virtual_machines/[0-9a-z]{5}-[0-9a-z]{5}-[0-9a-z]{15})}
+ OLD_SCOPE_REGEX = %r{^https?://[^/]+#{VM_PATH_REGEX.source}$}
+ NEW_SCOPE_REGEX = %r{^GET #{VM_PATH_REGEX.source}/logins$}
+
+ def fix_scopes_matching(regex)
+ act_as_system_user
+ ApiClientAuthorization.find_each do |auth|
+ auth.scopes = auth.scopes.map do |scope|
+ if match = regex.match(scope)
+ yield match
+ else
+ scope
+ end
+ end
+ auth.save!
+ end
+ end
+
+ def up
+ fix_scopes_matching(OLD_SCOPE_REGEX) do |match|
+ "GET #{match[1]}/logins"
+ end
+ end
+
+ def down
+ case Rails.env
+ when 'test'
+ hostname = 'www.example.com'
+ else
+ require 'socket'
+ hostname = Socket.gethostname
+ end
+ fix_scopes_matching(NEW_SCOPE_REGEX) do |match|
+ Rails.application.routes.url_for(controller: 'virtual_machines',
+ uuid: match[1].split('/').last,
+ host: hostname, protocol: 'https')
+ end
+ end
+end
--- /dev/null
+class AddUniqueNameIndexToLinks < ActiveRecord::Migration
+ def change
+ # Make sure PgPower is here. Otherwise the "where" will be ignored
+ # and we'll end up with a far too restrictive unique
+ # constraint. (Rails4 should work without PgPower, but that isn't
+ # tested.)
+ if not PgPower then raise "No partial column support" end
+
+ add_index(:links, [:tail_uuid, :name], unique: true,
+ where: "link_class='name'",
+ name: 'links_tail_name_unique_if_link_class_name')
+ end
+end
--- /dev/null
+class CreateKeepServices < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def change
+ act_as_system_user do
+ create_table :keep_services do |t|
+ t.string :uuid, :null => false
+ t.string :owner_uuid, :null => false
+ t.string :modified_by_client_uuid
+ t.string :modified_by_user_uuid
+ t.datetime :modified_at
+ t.string :service_host
+ t.integer :service_port
+ t.boolean :service_ssl_flag
+ t.string :service_type
+
+ t.timestamps
+ end
+ add_index :keep_services, :uuid, :unique => true
+
+ add_column :keep_disks, :keep_service_uuid, :string
+
+ KeepDisk.reset_column_information
+
+ services = {}
+
+ KeepDisk.find_each do |k|
+ services["#{k[:service_host]}_#{k[:service_port]}_#{k[:service_ssl_flag]}"] = {
+ service_host: k[:service_host],
+ service_port: k[:service_port],
+ service_ssl_flag: k[:service_ssl_flag],
+ service_type: 'disk',
+ owner_uuid: k[:owner_uuid]
+ }
+ end
+
+ services.each do |k, v|
+ v['uuid'] = KeepService.create(v).uuid
+ end
+
+ KeepDisk.find_each do |k|
+ k.keep_service_uuid = services["#{k[:service_host]}_#{k[:service_port]}_#{k[:service_ssl_flag]}"]['uuid']
+ k.save
+ end
+
+ remove_column :keep_disks, :service_host
+ remove_column :keep_disks, :service_port
+ remove_column :keep_disks, :service_ssl_flag
+ end
+ end
+end
--- /dev/null
+class AddDescriptionToPipelineTemplates < ActiveRecord::Migration
+ def change
+ add_column :pipeline_templates, :description, :text
+ end
+end
--- /dev/null
+class AddSuppliedScriptVersion < ActiveRecord::Migration
+ def up
+ add_column :jobs, :supplied_script_version, :string
+ end
+
+ def down
+ remove_column :jobs, :supplied_script_version, :string
+ end
+end
--- /dev/null
+class RemoveNameFromCollections < ActiveRecord::Migration
+ def up
+ remove_column :collections, :name
+ end
+
+ def down
+ add_column :collections, :name, :string
+ end
+end
--- /dev/null
+class RemoveActiveAndSuccessFromPipelineInstances < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ if column_exists?(:pipeline_instances, :active)
+ remove_column :pipeline_instances, :active
+ end
+
+ if column_exists?(:pipeline_instances, :success)
+ remove_column :pipeline_instances, :success
+ end
+ end
+
+ def down
+ if !column_exists?(:pipeline_instances, :success)
+ add_column :pipeline_instances, :success, :boolean, :null => true
+ end
+ if !column_exists?(:pipeline_instances, :active)
+ add_column :pipeline_instances, :active, :boolean, :default => false
+ end
+
+ act_as_system_user do
+ PipelineInstance.all.each do |pi|
+ case pi.state
+ when PipelineInstance::New, PipelineInstance::Ready, PipelineInstance::Paused, PipelineInstance::RunningOnClient
+ pi.active = nil
+ pi.success = nil
+ when PipelineInstance::RunningOnServer
+ pi.active = true
+ pi.success = nil
+ when PipelineInstance::Failed
+ pi.active = false
+ pi.success = false
+ when PipelineInstance::Complete
+ pi.active = false
+ pi.success = true
+ end
+ pi.save!
+ end
+ end
+ end
+end
--- /dev/null
+class RenameFolderToProject < ActiveRecord::Migration
+ def up
+ Group.update_all("group_class = 'project'", "group_class = 'folder'")
+ end
+
+ def down
+ Group.update_all("group_class = 'folder'", "group_class = 'project'")
+ end
+end
--- /dev/null
+class AddDockerLocatorToJobs < ActiveRecord::Migration
+ def change
+ add_column :jobs, :docker_image_locator, :string
+ end
+end
--- /dev/null
+class AnonymousGroup < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ # create the anonymous group and user
+ anonymous_group
+ anonymous_user
+ end
+
+ def down
+ act_as_system_user do
+ anonymous_user.destroy
+ anonymous_group.destroy
+ end
+ end
+
+end
--- /dev/null
+class JobTaskSerialQsequence < ActiveRecord::Migration
+ SEQ_NAME = "job_tasks_qsequence_seq"
+
+ def up
+ execute "CREATE SEQUENCE #{SEQ_NAME} OWNED BY job_tasks.qsequence;"
+ end
+
+ def down
+ execute "DROP SEQUENCE #{SEQ_NAME};"
+ end
+end
--- /dev/null
+class EmptyCollection < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ empty_collection
+ end
+
+ def down
+ # do nothing when migrating down (having the empty collection
+ # and a permission link for it is harmless)
+ end
+end
--- /dev/null
+class CollectionUseRegularUuids < ActiveRecord::Migration
+ def up
+ add_column :collections, :name, :string
+ add_column :collections, :description, :string
+ add_column :collections, :properties, :text
+ add_column :collections, :expires_at, :date
+ remove_column :collections, :locator
+
+ say_with_time "Step 1. Move manifest hashes into portable_data_hash field" do
+ ActiveRecord::Base.connection.execute("update collections set portable_data_hash=uuid, uuid=null")
+ end
+
+ say_with_time "Step 2. Create new collection objects from the name links in the table." do
+ from_clause = %{
+from links inner join collections on head_uuid=collections.portable_data_hash
+where link_class='name' and collections.uuid is null
+}
+ links = ActiveRecord::Base.connection.select_all %{
+select links.uuid, head_uuid, tail_uuid, links.name,
+manifest_text, links.created_at, links.modified_at, links.modified_by_client_uuid, links.modified_by_user_uuid
+#{from_clause}
+}
+ links.each do |d|
+ ActiveRecord::Base.connection.execute %{
+insert into collections (uuid, portable_data_hash, owner_uuid, name, manifest_text, created_at, modified_at, modified_by_client_uuid, modified_by_user_uuid, updated_at)
+values (#{ActiveRecord::Base.connection.quote Collection.generate_uuid},
+#{ActiveRecord::Base.connection.quote d['head_uuid']},
+#{ActiveRecord::Base.connection.quote d['tail_uuid']},
+#{ActiveRecord::Base.connection.quote d['name']},
+#{ActiveRecord::Base.connection.quote d['manifest_text']},
+#{ActiveRecord::Base.connection.quote d['created_at']},
+#{ActiveRecord::Base.connection.quote d['modified_at']},
+#{ActiveRecord::Base.connection.quote d['modified_by_client_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_by_user_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_at']})
+}
+ end
+ ActiveRecord::Base.connection.execute "delete from links where links.uuid in (select links.uuid #{from_clause})"
+ end
+
+ say_with_time "Step 3. Create new collection objects from the can_read links in the table." do
+ from_clause = %{
+from links inner join collections on head_uuid=collections.portable_data_hash
+where link_class='permission' and links.name='can_read' and collections.uuid is null
+}
+ links = ActiveRecord::Base.connection.select_all %{
+select links.uuid, head_uuid, tail_uuid, manifest_text, links.created_at, links.modified_at
+#{from_clause}
+}
+ links.each do |d|
+ ActiveRecord::Base.connection.execute %{
+insert into collections (uuid, portable_data_hash, owner_uuid, manifest_text, created_at, modified_at, modified_by_client_uuid, modified_by_user_uuid, updated_at)
+values (#{ActiveRecord::Base.connection.quote Collection.generate_uuid},
+#{ActiveRecord::Base.connection.quote d['head_uuid']},
+#{ActiveRecord::Base.connection.quote d['tail_uuid']},
+#{ActiveRecord::Base.connection.quote d['manifest_text']},
+#{ActiveRecord::Base.connection.quote d['created_at']},
+#{ActiveRecord::Base.connection.quote d['modified_at']},
+#{ActiveRecord::Base.connection.quote d['modified_by_client_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_by_user_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_at']})
+}
+ end
+ ActiveRecord::Base.connection.execute "delete from links where links.uuid in (select links.uuid #{from_clause})"
+ end
+
+ say_with_time "Step 4. Migrate remaining orphan collection objects" do
+ links = ActiveRecord::Base.connection.select_all %{
+select portable_data_hash, owner_uuid, manifest_text, created_at, modified_at
+from collections
+where uuid is null and portable_data_hash not in (select portable_data_hash from collections where uuid is not null)
+}
+ links.each do |d|
+ ActiveRecord::Base.connection.execute %{
+insert into collections (uuid, portable_data_hash, owner_uuid, manifest_text, created_at, modified_at, modified_by_client_uuid, modified_by_user_uuid, updated_at)
+values (#{ActiveRecord::Base.connection.quote Collection.generate_uuid},
+#{ActiveRecord::Base.connection.quote d['portable_data_hash']},
+#{ActiveRecord::Base.connection.quote d['owner_uuid']},
+#{ActiveRecord::Base.connection.quote d['manifest_text']},
+#{ActiveRecord::Base.connection.quote d['created_at']},
+#{ActiveRecord::Base.connection.quote d['modified_at']},
+#{ActiveRecord::Base.connection.quote d['modified_by_client_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_by_user_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_at']})
+}
+ end
+ end
+
+ say_with_time "Step 5. Delete old collection objects." do
+ ActiveRecord::Base.connection.execute("delete from collections where uuid is null")
+ end
+
+ say_with_time "Step 6. Delete permission links where tail_uuid is a collection (invalid records)" do
+ ActiveRecord::Base.connection.execute %{
+delete from links where links.uuid in (select links.uuid
+from links
+where tail_uuid like '________________________________+%' and link_class='permission' )
+}
+ end
+
+ say_with_time "Step 7. Migrate collection -> collection provenance links to jobs" do
+ from_clause = %{
+from links
+where head_uuid like '________________________________+%' and tail_uuid like '________________________________+%' and links.link_class = 'provenance'
+}
+ links = ActiveRecord::Base.connection.select_all %{
+select links.uuid, head_uuid, tail_uuid, links.created_at, links.modified_at, links.modified_by_client_uuid, links.modified_by_user_uuid, links.owner_uuid
+#{from_clause}
+}
+ links.each do |d|
+ newuuid = Job.generate_uuid
+ ActiveRecord::Base.connection.execute %{
+insert into jobs (uuid, script_parameters, output, running, success, created_at, modified_at, modified_by_client_uuid, modified_by_user_uuid, owner_uuid, updated_at)
+values (#{ActiveRecord::Base.connection.quote newuuid},
+#{ActiveRecord::Base.connection.quote "---\ninput: "+d['tail_uuid']},
+#{ActiveRecord::Base.connection.quote d['head_uuid']},
+#{ActiveRecord::Base.connection.quote false},
+#{ActiveRecord::Base.connection.quote true},
+#{ActiveRecord::Base.connection.quote d['created_at']},
+#{ActiveRecord::Base.connection.quote d['modified_at']},
+#{ActiveRecord::Base.connection.quote d['modified_by_client_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_by_user_uuid']},
+#{ActiveRecord::Base.connection.quote d['owner_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_at']})
+}
+ end
+ ActiveRecord::Base.connection.execute "delete from links where links.uuid in (select links.uuid #{from_clause})"
+ end
+
+ say_with_time "Step 8. Migrate remaining links with head_uuid pointing to collections" do
+ from_clause = %{
+from links inner join collections on links.head_uuid=portable_data_hash
+where collections.uuid is not null
+}
+ links = ActiveRecord::Base.connection.select_all %{
+select links.uuid, collections.uuid as collectionuuid, tail_uuid, link_class, links.properties,
+links.name, links.created_at, links.modified_at, links.modified_by_client_uuid, links.modified_by_user_uuid, links.owner_uuid
+#{from_clause}
+}
+ links.each do |d|
+ ActiveRecord::Base.connection.execute %{
+insert into links (uuid, head_uuid, tail_uuid, link_class, name, properties, created_at, modified_at, modified_by_client_uuid, modified_by_user_uuid, owner_uuid, updated_at)
+values (#{ActiveRecord::Base.connection.quote Link.generate_uuid},
+#{ActiveRecord::Base.connection.quote d['collectionuuid']},
+#{ActiveRecord::Base.connection.quote d['tail_uuid']},
+#{ActiveRecord::Base.connection.quote d['link_class']},
+#{ActiveRecord::Base.connection.quote d['name']},
+#{ActiveRecord::Base.connection.quote d['properties']},
+#{ActiveRecord::Base.connection.quote d['created_at']},
+#{ActiveRecord::Base.connection.quote d['modified_at']},
+#{ActiveRecord::Base.connection.quote d['modified_by_client_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_by_user_uuid']},
+#{ActiveRecord::Base.connection.quote d['owner_uuid']},
+#{ActiveRecord::Base.connection.quote d['modified_at']})
+}
+ end
+ ActiveRecord::Base.connection.execute "delete from links where links.uuid in (select links.uuid #{from_clause})"
+ end
+
+ say_with_time "Step 9. Delete any remaining name links" do
+ ActiveRecord::Base.connection.execute("delete from links where link_class='name'")
+ end
+
+ say_with_time "Step 10. Validate links table" do
+ links = ActiveRecord::Base.connection.select_all %{
+select links.uuid, head_uuid, tail_uuid, link_class, name
+from links
+where head_uuid like '________________________________+%' or tail_uuid like '________________________________+%'
+}
+ links.each do |d|
+ raise "Bad row #{d}"
+ end
+ end
+
+ end
+
+ def down
+ raise ActiveRecord::IrreversibleMigration, "Can't downmigrate changes to collections and links without potentially losing data."
+ end
+end
--- /dev/null
+class AddUniqueNameConstraints < ActiveRecord::Migration
+ def change
+ # Ensure uniqueness before adding constraints.
+ ["collections", "pipeline_templates", "groups"].each do |table|
+ rows = ActiveRecord::Base.connection.select_all %{
+select uuid, owner_uuid, name from #{table} order by owner_uuid, name
+}
+ prev = {}
+ n = 1
+ rows.each do |r|
+ if r["owner_uuid"] == prev["owner_uuid"] and !r["name"].nil? and r["name"] == prev["name"]
+ n += 1
+ ActiveRecord::Base.connection.execute %{
+update #{table} set name='#{r["name"]} #{n}' where uuid='#{r["uuid"]}'
+}
+ else
+ n = 1
+ end
+ prev = r
+ end
+ end
+
+ add_index(:collections, [:owner_uuid, :name], unique: true,
+ name: 'collection_owner_uuid_name_unique')
+ add_index(:pipeline_templates, [:owner_uuid, :name], unique: true,
+ name: 'pipeline_template_owner_uuid_name_unique')
+ add_index(:groups, [:owner_uuid, :name], unique: true,
+ name: 'groups_owner_uuid_name_unique')
+ end
+end
--- /dev/null
+class AddNotNullConstraintToGroupName < ActiveRecord::Migration
+ def change
+ ActiveRecord::Base.connection.execute("update groups set name=uuid where name is null or name=''")
+ change_column_null :groups, :name, false
+ end
+end
--- /dev/null
+class RemoveOutputIsPersistentColumn < ActiveRecord::Migration
+ def up
+ remove_column :jobs, :output_is_persistent
+ end
+
+ def down
+ add_column :jobs, :output_is_persistent, :boolean, null: false, default: false
+ end
+end
--- /dev/null
+class JobPriorityFixup < ActiveRecord::Migration
+ def up
+ remove_column :jobs, :priority
+ add_column :jobs, :priority, :integer, null: false, default: 0
+ end
+
+ def down
+ remove_column :jobs, :priority
+ add_column :jobs, :priority, :string, null: true, default: nil
+ end
+end
--- /dev/null
+class AddStartFinishTimeToTasksAndPipelines < ActiveRecord::Migration
+ def up
+ add_column :job_tasks, :started_at, :datetime
+ add_column :job_tasks, :finished_at, :datetime
+ add_column :pipeline_instances, :started_at, :datetime
+ add_column :pipeline_instances, :finished_at, :datetime
+ end
+
+ def down
+ remove_column :job_tasks, :started_at
+ remove_column :job_tasks, :finished_at
+ remove_column :pipeline_instances, :started_at
+ remove_column :pipeline_instances, :finished_at
+ end
+end
--- /dev/null
+class AddDescriptionToPipelineInstancesAndJobs < ActiveRecord::Migration
+ def up
+ add_column :pipeline_instances, :description, :text, null: true
+ add_column :jobs, :description, :text, null: true
+ end
+
+ def down
+ remove_column :jobs, :description
+ remove_column :pipeline_instances, :description
+ end
+end
--- /dev/null
+class ChangeUserOwnerUuidNotNull < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ User.update_all({owner_uuid: system_user_uuid}, 'owner_uuid is null')
+ change_column :users, :owner_uuid, :string, :null => false
+ end
+
+ def down
+ change_column :users, :owner_uuid, :string, :null => true
+ end
+end
--- /dev/null
+class AddPropertiesToNode < ActiveRecord::Migration
+ def up
+ add_column :nodes, :properties, :text
+ end
+
+ def down
+ remove_column :nodes, :properties
+ end
+end
--- /dev/null
+class AddStateToJob < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def up
+ ActiveRecord::Base.transaction do
+ add_column :jobs, :state, :string
+ Job.reset_column_information
+ Job.update_all({state: 'Cancelled'}, ['state is null and cancelled_at is not null'])
+ Job.update_all({state: 'Failed'}, ['state is null and success = ?', false])
+ Job.update_all({state: 'Complete'}, ['state is null and success = ?', true])
+ Job.update_all({state: 'Running'}, ['state is null and running = ?', true])
+ # Locked/started, but not Running/Failed/Complete? Let's assume it failed.
+ Job.update_all({state: 'Failed'}, ['state is null and (is_locked_by_uuid is not null or started_at is not null)'])
+ Job.update_all({state: 'Queued'}, ['state is null'])
+ end
+ end
+
+ def down
+ remove_column :jobs, :state
+ end
+end
--- /dev/null
+class AddJobUuidToNodes < ActiveRecord::Migration
+ def up
+ change_table :nodes do |t|
+ t.column :job_uuid, :string
+ end
+ end
+
+ def down
+ change_table :nodes do |t|
+ t.remove :job_uuid
+ end
+ end
+end
--- /dev/null
+class AddArvadosSdkVersionToJobs < ActiveRecord::Migration
+ def up
+ change_table :jobs do |t|
+ t.column :arvados_sdk_version, :string
+ end
+ end
+
+ def down
+ change_table :jobs do |t|
+ t.remove :arvados_sdk_version
+ end
+ end
+end
--- /dev/null
+class OwnerUuidIndex < ActiveRecord::Migration
+ def tables_with_owner_uuid
+ ActiveRecord::Base.connection.tables.select do |table|
+ columns = ActiveRecord::Base.connection.columns(table)
+ columns.collect(&:name).include? 'owner_uuid'
+ end
+ end
+
+ def up
+ tables_with_owner_uuid.each do |table|
+ add_index table.to_sym, :owner_uuid
+ end
+ end
+
+ def down
+ tables_with_owner_uuid.each do |table|
+ remove_index table.to_sym, :owner_uuid
+ end
+ end
+end
--- /dev/null
+# This file seeds the database with initial/default values.
+#
+# It is invoked by `rake db:seed` and `rake db:setup`.
+
+DatabaseSeeds.install
--- /dev/null
+--
+-- PostgreSQL database dump
+--
+
+SET statement_timeout = 0;
+SET client_encoding = 'UTF8';
+SET standard_conforming_strings = on;
+SET check_function_bodies = false;
+SET client_min_messages = warning;
+
+--
+-- Name: plpgsql; Type: EXTENSION; Schema: -; Owner: -
+--
+
+CREATE EXTENSION IF NOT EXISTS plpgsql WITH SCHEMA pg_catalog;
+
+
+--
+-- Name: EXTENSION plpgsql; Type: COMMENT; Schema: -; Owner: -
+--
+
+COMMENT ON EXTENSION plpgsql IS 'PL/pgSQL procedural language';
+
+
+SET search_path = public, pg_catalog;
+
+SET default_tablespace = '';
+
+SET default_with_oids = false;
+
+--
+-- Name: api_client_authorizations; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE api_client_authorizations (
+ id integer NOT NULL,
+ api_token character varying(255) NOT NULL,
+ api_client_id integer NOT NULL,
+ user_id integer NOT NULL,
+ created_by_ip_address character varying(255),
+ last_used_by_ip_address character varying(255),
+ last_used_at timestamp without time zone,
+ expires_at timestamp without time zone,
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL,
+ default_owner_uuid character varying(255),
+ scopes text DEFAULT '---
+- all
+'::text NOT NULL
+);
+
+
+--
+-- Name: api_client_authorizations_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE api_client_authorizations_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: api_client_authorizations_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE api_client_authorizations_id_seq OWNED BY api_client_authorizations.id;
+
+
+--
+-- Name: api_clients; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE api_clients (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ name character varying(255),
+ url_prefix character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL,
+ is_trusted boolean DEFAULT false
+);
+
+
+--
+-- Name: api_clients_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE api_clients_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: api_clients_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE api_clients_id_seq OWNED BY api_clients.id;
+
+
+--
+-- Name: authorized_keys; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE authorized_keys (
+ id integer NOT NULL,
+ uuid character varying(255) NOT NULL,
+ owner_uuid character varying(255) NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ name character varying(255),
+ key_type character varying(255),
+ authorized_user_uuid character varying(255),
+ public_key text,
+ expires_at timestamp without time zone,
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: authorized_keys_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE authorized_keys_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: authorized_keys_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE authorized_keys_id_seq OWNED BY authorized_keys.id;
+
+
+--
+-- Name: collections; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE collections (
+ id integer NOT NULL,
+ owner_uuid character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ portable_data_hash character varying(255),
+ redundancy integer,
+ redundancy_confirmed_by_client_uuid character varying(255),
+ redundancy_confirmed_at timestamp without time zone,
+ redundancy_confirmed_as integer,
+ updated_at timestamp without time zone NOT NULL,
+ uuid character varying(255),
+ manifest_text text,
+ name character varying(255),
+ description character varying(255),
+ properties text,
+ expires_at date
+);
+
+
+--
+-- Name: collections_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE collections_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: collections_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE collections_id_seq OWNED BY collections.id;
+
+
+--
+-- Name: commit_ancestors; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE commit_ancestors (
+ id integer NOT NULL,
+ repository_name character varying(255),
+ descendant character varying(255) NOT NULL,
+ ancestor character varying(255) NOT NULL,
+ "is" boolean DEFAULT false NOT NULL,
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: commit_ancestors_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE commit_ancestors_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: commit_ancestors_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE commit_ancestors_id_seq OWNED BY commit_ancestors.id;
+
+
+--
+-- Name: commits; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE commits (
+ id integer NOT NULL,
+ repository_name character varying(255),
+ sha1 character varying(255),
+ message character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: commits_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE commits_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: commits_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE commits_id_seq OWNED BY commits.id;
+
+
+--
+-- Name: groups; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE groups (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ name character varying(255) NOT NULL,
+ description text,
+ updated_at timestamp without time zone NOT NULL,
+ group_class character varying(255)
+);
+
+
+--
+-- Name: groups_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE groups_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: groups_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE groups_id_seq OWNED BY groups.id;
+
+
+--
+-- Name: humans; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE humans (
+ id integer NOT NULL,
+ uuid character varying(255) NOT NULL,
+ owner_uuid character varying(255) NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ properties text,
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: humans_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE humans_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: humans_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE humans_id_seq OWNED BY humans.id;
+
+
+--
+-- Name: job_tasks; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE job_tasks (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ job_uuid character varying(255),
+ sequence integer,
+ parameters text,
+ output text,
+ progress double precision,
+ success boolean,
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL,
+ created_by_job_task_uuid character varying(255),
+ qsequence bigint,
+ started_at timestamp without time zone,
+ finished_at timestamp without time zone
+);
+
+
+--
+-- Name: job_tasks_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE job_tasks_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: job_tasks_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE job_tasks_id_seq OWNED BY job_tasks.id;
+
+
+--
+-- Name: job_tasks_qsequence_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE job_tasks_qsequence_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: job_tasks_qsequence_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE job_tasks_qsequence_seq OWNED BY job_tasks.qsequence;
+
+
+--
+-- Name: jobs; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE jobs (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ submit_id character varying(255),
+ script character varying(255),
+ script_version character varying(255),
+ script_parameters text,
+ cancelled_by_client_uuid character varying(255),
+ cancelled_by_user_uuid character varying(255),
+ cancelled_at timestamp without time zone,
+ started_at timestamp without time zone,
+ finished_at timestamp without time zone,
+ running boolean,
+ success boolean,
+ output character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL,
+ is_locked_by_uuid character varying(255),
+ log character varying(255),
+ tasks_summary text,
+ runtime_constraints text,
+ nondeterministic boolean,
+ repository character varying(255),
+ supplied_script_version character varying(255),
+ docker_image_locator character varying(255),
+ priority integer DEFAULT 0 NOT NULL,
+ description text,
+ state character varying(255),
+ arvados_sdk_version character varying(255)
+);
+
+
+--
+-- Name: jobs_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE jobs_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: jobs_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE jobs_id_seq OWNED BY jobs.id;
+
+
+--
+-- Name: keep_disks; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE keep_disks (
+ id integer NOT NULL,
+ uuid character varying(255) NOT NULL,
+ owner_uuid character varying(255) NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ ping_secret character varying(255) NOT NULL,
+ node_uuid character varying(255),
+ filesystem_uuid character varying(255),
+ bytes_total integer,
+ bytes_free integer,
+ is_readable boolean DEFAULT true NOT NULL,
+ is_writable boolean DEFAULT true NOT NULL,
+ last_read_at timestamp without time zone,
+ last_write_at timestamp without time zone,
+ last_ping_at timestamp without time zone,
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL,
+ keep_service_uuid character varying(255)
+);
+
+
+--
+-- Name: keep_disks_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE keep_disks_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: keep_disks_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE keep_disks_id_seq OWNED BY keep_disks.id;
+
+
+--
+-- Name: keep_services; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE keep_services (
+ id integer NOT NULL,
+ uuid character varying(255) NOT NULL,
+ owner_uuid character varying(255) NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ service_host character varying(255),
+ service_port integer,
+ service_ssl_flag boolean,
+ service_type character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: keep_services_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE keep_services_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: keep_services_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE keep_services_id_seq OWNED BY keep_services.id;
+
+
+--
+-- Name: links; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE links (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ tail_uuid character varying(255),
+ link_class character varying(255),
+ name character varying(255),
+ head_uuid character varying(255),
+ properties text,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: links_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE links_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: links_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE links_id_seq OWNED BY links.id;
+
+
+--
+-- Name: logs; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE logs (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ object_uuid character varying(255),
+ event_at timestamp without time zone,
+ event_type character varying(255),
+ summary text,
+ properties text,
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL,
+ modified_at timestamp without time zone,
+ object_owner_uuid character varying(255)
+);
+
+
+--
+-- Name: logs_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE logs_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: logs_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE logs_id_seq OWNED BY logs.id;
+
+
+--
+-- Name: nodes; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE nodes (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ slot_number integer,
+ hostname character varying(255),
+ domain character varying(255),
+ ip_address character varying(255),
+ first_ping_at timestamp without time zone,
+ last_ping_at timestamp without time zone,
+ info text,
+ updated_at timestamp without time zone NOT NULL,
+ properties text,
+ job_uuid character varying(255)
+);
+
+
+--
+-- Name: nodes_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE nodes_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: nodes_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE nodes_id_seq OWNED BY nodes.id;
+
+
+--
+-- Name: pipeline_instances; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE pipeline_instances (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ pipeline_template_uuid character varying(255),
+ name character varying(255),
+ components text,
+ updated_at timestamp without time zone NOT NULL,
+ properties text,
+ state character varying(255),
+ components_summary text,
+ started_at timestamp without time zone,
+ finished_at timestamp without time zone,
+ description text
+);
+
+
+--
+-- Name: pipeline_instances_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE pipeline_instances_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: pipeline_instances_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE pipeline_instances_id_seq OWNED BY pipeline_instances.id;
+
+
+--
+-- Name: pipeline_templates; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE pipeline_templates (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ name character varying(255),
+ components text,
+ updated_at timestamp without time zone NOT NULL,
+ description text
+);
+
+
+--
+-- Name: pipeline_templates_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE pipeline_templates_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: pipeline_templates_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE pipeline_templates_id_seq OWNED BY pipeline_templates.id;
+
+
+--
+-- Name: repositories; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE repositories (
+ id integer NOT NULL,
+ uuid character varying(255) NOT NULL,
+ owner_uuid character varying(255) NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ name character varying(255),
+ fetch_url character varying(255),
+ push_url character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: repositories_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE repositories_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: repositories_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE repositories_id_seq OWNED BY repositories.id;
+
+
+--
+-- Name: schema_migrations; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE schema_migrations (
+ version character varying(255) NOT NULL
+);
+
+
+--
+-- Name: specimens; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE specimens (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ material character varying(255),
+ updated_at timestamp without time zone NOT NULL,
+ properties text
+);
+
+
+--
+-- Name: specimens_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE specimens_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: specimens_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE specimens_id_seq OWNED BY specimens.id;
+
+
+--
+-- Name: traits; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE traits (
+ id integer NOT NULL,
+ uuid character varying(255) NOT NULL,
+ owner_uuid character varying(255) NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ name character varying(255),
+ properties text,
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: traits_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE traits_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: traits_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE traits_id_seq OWNED BY traits.id;
+
+
+--
+-- Name: users; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE users (
+ id integer NOT NULL,
+ uuid character varying(255),
+ owner_uuid character varying(255) NOT NULL,
+ created_at timestamp without time zone NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ email character varying(255),
+ first_name character varying(255),
+ last_name character varying(255),
+ identity_url character varying(255),
+ is_admin boolean,
+ prefs text,
+ updated_at timestamp without time zone NOT NULL,
+ default_owner_uuid character varying(255),
+ is_active boolean DEFAULT false
+);
+
+
+--
+-- Name: users_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE users_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: users_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE users_id_seq OWNED BY users.id;
+
+
+--
+-- Name: virtual_machines; Type: TABLE; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE TABLE virtual_machines (
+ id integer NOT NULL,
+ uuid character varying(255) NOT NULL,
+ owner_uuid character varying(255) NOT NULL,
+ modified_by_client_uuid character varying(255),
+ modified_by_user_uuid character varying(255),
+ modified_at timestamp without time zone,
+ hostname character varying(255),
+ created_at timestamp without time zone NOT NULL,
+ updated_at timestamp without time zone NOT NULL
+);
+
+
+--
+-- Name: virtual_machines_id_seq; Type: SEQUENCE; Schema: public; Owner: -
+--
+
+CREATE SEQUENCE virtual_machines_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
+
+--
+-- Name: virtual_machines_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
+--
+
+ALTER SEQUENCE virtual_machines_id_seq OWNED BY virtual_machines.id;
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY api_client_authorizations ALTER COLUMN id SET DEFAULT nextval('api_client_authorizations_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY api_clients ALTER COLUMN id SET DEFAULT nextval('api_clients_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY authorized_keys ALTER COLUMN id SET DEFAULT nextval('authorized_keys_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY collections ALTER COLUMN id SET DEFAULT nextval('collections_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY commit_ancestors ALTER COLUMN id SET DEFAULT nextval('commit_ancestors_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY commits ALTER COLUMN id SET DEFAULT nextval('commits_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY groups ALTER COLUMN id SET DEFAULT nextval('groups_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY humans ALTER COLUMN id SET DEFAULT nextval('humans_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY job_tasks ALTER COLUMN id SET DEFAULT nextval('job_tasks_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY jobs ALTER COLUMN id SET DEFAULT nextval('jobs_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY keep_disks ALTER COLUMN id SET DEFAULT nextval('keep_disks_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY keep_services ALTER COLUMN id SET DEFAULT nextval('keep_services_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY links ALTER COLUMN id SET DEFAULT nextval('links_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY logs ALTER COLUMN id SET DEFAULT nextval('logs_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY nodes ALTER COLUMN id SET DEFAULT nextval('nodes_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY pipeline_instances ALTER COLUMN id SET DEFAULT nextval('pipeline_instances_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY pipeline_templates ALTER COLUMN id SET DEFAULT nextval('pipeline_templates_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY repositories ALTER COLUMN id SET DEFAULT nextval('repositories_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY specimens ALTER COLUMN id SET DEFAULT nextval('specimens_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY traits ALTER COLUMN id SET DEFAULT nextval('traits_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY users ALTER COLUMN id SET DEFAULT nextval('users_id_seq'::regclass);
+
+
+--
+-- Name: id; Type: DEFAULT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY virtual_machines ALTER COLUMN id SET DEFAULT nextval('virtual_machines_id_seq'::regclass);
+
+
+--
+-- Name: api_client_authorizations_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY api_client_authorizations
+ ADD CONSTRAINT api_client_authorizations_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: api_clients_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY api_clients
+ ADD CONSTRAINT api_clients_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: authorized_keys_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY authorized_keys
+ ADD CONSTRAINT authorized_keys_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: collections_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY collections
+ ADD CONSTRAINT collections_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: commit_ancestors_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY commit_ancestors
+ ADD CONSTRAINT commit_ancestors_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: commits_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY commits
+ ADD CONSTRAINT commits_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: groups_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY groups
+ ADD CONSTRAINT groups_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: humans_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY humans
+ ADD CONSTRAINT humans_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: job_tasks_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY job_tasks
+ ADD CONSTRAINT job_tasks_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: jobs_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY jobs
+ ADD CONSTRAINT jobs_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: keep_disks_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY keep_disks
+ ADD CONSTRAINT keep_disks_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: keep_services_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY keep_services
+ ADD CONSTRAINT keep_services_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: links_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY links
+ ADD CONSTRAINT links_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: logs_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY logs
+ ADD CONSTRAINT logs_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: nodes_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY nodes
+ ADD CONSTRAINT nodes_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: pipeline_instances_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY pipeline_instances
+ ADD CONSTRAINT pipeline_instances_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: pipeline_templates_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY pipeline_templates
+ ADD CONSTRAINT pipeline_templates_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: repositories_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY repositories
+ ADD CONSTRAINT repositories_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: specimens_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY specimens
+ ADD CONSTRAINT specimens_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: traits_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY traits
+ ADD CONSTRAINT traits_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: users_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY users
+ ADD CONSTRAINT users_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: virtual_machines_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace:
+--
+
+ALTER TABLE ONLY virtual_machines
+ ADD CONSTRAINT virtual_machines_pkey PRIMARY KEY (id);
+
+
+--
+-- Name: collection_owner_uuid_name_unique; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX collection_owner_uuid_name_unique ON collections USING btree (owner_uuid, name);
+
+
+--
+-- Name: groups_owner_uuid_name_unique; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX groups_owner_uuid_name_unique ON groups USING btree (owner_uuid, name);
+
+
+--
+-- Name: index_api_client_authorizations_on_api_client_id; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_api_client_authorizations_on_api_client_id ON api_client_authorizations USING btree (api_client_id);
+
+
+--
+-- Name: index_api_client_authorizations_on_api_token; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_api_client_authorizations_on_api_token ON api_client_authorizations USING btree (api_token);
+
+
+--
+-- Name: index_api_client_authorizations_on_expires_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_api_client_authorizations_on_expires_at ON api_client_authorizations USING btree (expires_at);
+
+
+--
+-- Name: index_api_client_authorizations_on_user_id; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_api_client_authorizations_on_user_id ON api_client_authorizations USING btree (user_id);
+
+
+--
+-- Name: index_api_clients_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_api_clients_on_created_at ON api_clients USING btree (created_at);
+
+
+--
+-- Name: index_api_clients_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_api_clients_on_modified_at ON api_clients USING btree (modified_at);
+
+
+--
+-- Name: index_api_clients_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_api_clients_on_owner_uuid ON api_clients USING btree (owner_uuid);
+
+
+--
+-- Name: index_api_clients_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_api_clients_on_uuid ON api_clients USING btree (uuid);
+
+
+--
+-- Name: index_authkeys_on_user_and_expires_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_authkeys_on_user_and_expires_at ON authorized_keys USING btree (authorized_user_uuid, expires_at);
+
+
+--
+-- Name: index_authorized_keys_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_authorized_keys_on_owner_uuid ON authorized_keys USING btree (owner_uuid);
+
+
+--
+-- Name: index_authorized_keys_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_authorized_keys_on_uuid ON authorized_keys USING btree (uuid);
+
+
+--
+-- Name: index_collections_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_collections_on_created_at ON collections USING btree (created_at);
+
+
+--
+-- Name: index_collections_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_collections_on_modified_at ON collections USING btree (modified_at);
+
+
+--
+-- Name: index_collections_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_collections_on_owner_uuid ON collections USING btree (owner_uuid);
+
+
+--
+-- Name: index_collections_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_collections_on_uuid ON collections USING btree (uuid);
+
+
+--
+-- Name: index_commit_ancestors_on_descendant_and_ancestor; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_commit_ancestors_on_descendant_and_ancestor ON commit_ancestors USING btree (descendant, ancestor);
+
+
+--
+-- Name: index_commits_on_repository_name_and_sha1; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_commits_on_repository_name_and_sha1 ON commits USING btree (repository_name, sha1);
+
+
+--
+-- Name: index_groups_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_groups_on_created_at ON groups USING btree (created_at);
+
+
+--
+-- Name: index_groups_on_group_class; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_groups_on_group_class ON groups USING btree (group_class);
+
+
+--
+-- Name: index_groups_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_groups_on_modified_at ON groups USING btree (modified_at);
+
+
+--
+-- Name: index_groups_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_groups_on_owner_uuid ON groups USING btree (owner_uuid);
+
+
+--
+-- Name: index_groups_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_groups_on_uuid ON groups USING btree (uuid);
+
+
+--
+-- Name: index_humans_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_humans_on_owner_uuid ON humans USING btree (owner_uuid);
+
+
+--
+-- Name: index_humans_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_humans_on_uuid ON humans USING btree (uuid);
+
+
+--
+-- Name: index_job_tasks_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_job_tasks_on_created_at ON job_tasks USING btree (created_at);
+
+
+--
+-- Name: index_job_tasks_on_job_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_job_tasks_on_job_uuid ON job_tasks USING btree (job_uuid);
+
+
+--
+-- Name: index_job_tasks_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_job_tasks_on_modified_at ON job_tasks USING btree (modified_at);
+
+
+--
+-- Name: index_job_tasks_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_job_tasks_on_owner_uuid ON job_tasks USING btree (owner_uuid);
+
+
+--
+-- Name: index_job_tasks_on_sequence; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_job_tasks_on_sequence ON job_tasks USING btree (sequence);
+
+
+--
+-- Name: index_job_tasks_on_success; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_job_tasks_on_success ON job_tasks USING btree (success);
+
+
+--
+-- Name: index_job_tasks_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_job_tasks_on_uuid ON job_tasks USING btree (uuid);
+
+
+--
+-- Name: index_jobs_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_jobs_on_created_at ON jobs USING btree (created_at);
+
+
+--
+-- Name: index_jobs_on_finished_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_jobs_on_finished_at ON jobs USING btree (finished_at);
+
+
+--
+-- Name: index_jobs_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_jobs_on_modified_at ON jobs USING btree (modified_at);
+
+
+--
+-- Name: index_jobs_on_output; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_jobs_on_output ON jobs USING btree (output);
+
+
+--
+-- Name: index_jobs_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_jobs_on_owner_uuid ON jobs USING btree (owner_uuid);
+
+
+--
+-- Name: index_jobs_on_script; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_jobs_on_script ON jobs USING btree (script);
+
+
+--
+-- Name: index_jobs_on_started_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_jobs_on_started_at ON jobs USING btree (started_at);
+
+
+--
+-- Name: index_jobs_on_submit_id; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_jobs_on_submit_id ON jobs USING btree (submit_id);
+
+
+--
+-- Name: index_jobs_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_jobs_on_uuid ON jobs USING btree (uuid);
+
+
+--
+-- Name: index_keep_disks_on_filesystem_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_keep_disks_on_filesystem_uuid ON keep_disks USING btree (filesystem_uuid);
+
+
+--
+-- Name: index_keep_disks_on_last_ping_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_keep_disks_on_last_ping_at ON keep_disks USING btree (last_ping_at);
+
+
+--
+-- Name: index_keep_disks_on_node_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_keep_disks_on_node_uuid ON keep_disks USING btree (node_uuid);
+
+
+--
+-- Name: index_keep_disks_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_keep_disks_on_owner_uuid ON keep_disks USING btree (owner_uuid);
+
+
+--
+-- Name: index_keep_disks_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_keep_disks_on_uuid ON keep_disks USING btree (uuid);
+
+
+--
+-- Name: index_keep_services_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_keep_services_on_owner_uuid ON keep_services USING btree (owner_uuid);
+
+
+--
+-- Name: index_keep_services_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_keep_services_on_uuid ON keep_services USING btree (uuid);
+
+
+--
+-- Name: index_links_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_links_on_created_at ON links USING btree (created_at);
+
+
+--
+-- Name: index_links_on_head_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_links_on_head_uuid ON links USING btree (head_uuid);
+
+
+--
+-- Name: index_links_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_links_on_modified_at ON links USING btree (modified_at);
+
+
+--
+-- Name: index_links_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_links_on_owner_uuid ON links USING btree (owner_uuid);
+
+
+--
+-- Name: index_links_on_tail_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_links_on_tail_uuid ON links USING btree (tail_uuid);
+
+
+--
+-- Name: index_links_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_links_on_uuid ON links USING btree (uuid);
+
+
+--
+-- Name: index_logs_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_logs_on_created_at ON logs USING btree (created_at);
+
+
+--
+-- Name: index_logs_on_event_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_logs_on_event_at ON logs USING btree (event_at);
+
+
+--
+-- Name: index_logs_on_event_type; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_logs_on_event_type ON logs USING btree (event_type);
+
+
+--
+-- Name: index_logs_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_logs_on_modified_at ON logs USING btree (modified_at);
+
+
+--
+-- Name: index_logs_on_object_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_logs_on_object_uuid ON logs USING btree (object_uuid);
+
+
+--
+-- Name: index_logs_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_logs_on_owner_uuid ON logs USING btree (owner_uuid);
+
+
+--
+-- Name: index_logs_on_summary; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_logs_on_summary ON logs USING btree (summary);
+
+
+--
+-- Name: index_logs_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_logs_on_uuid ON logs USING btree (uuid);
+
+
+--
+-- Name: index_nodes_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_nodes_on_created_at ON nodes USING btree (created_at);
+
+
+--
+-- Name: index_nodes_on_hostname; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_nodes_on_hostname ON nodes USING btree (hostname);
+
+
+--
+-- Name: index_nodes_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_nodes_on_modified_at ON nodes USING btree (modified_at);
+
+
+--
+-- Name: index_nodes_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_nodes_on_owner_uuid ON nodes USING btree (owner_uuid);
+
+
+--
+-- Name: index_nodes_on_slot_number; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_nodes_on_slot_number ON nodes USING btree (slot_number);
+
+
+--
+-- Name: index_nodes_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_nodes_on_uuid ON nodes USING btree (uuid);
+
+
+--
+-- Name: index_pipeline_instances_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_pipeline_instances_on_created_at ON pipeline_instances USING btree (created_at);
+
+
+--
+-- Name: index_pipeline_instances_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_pipeline_instances_on_modified_at ON pipeline_instances USING btree (modified_at);
+
+
+--
+-- Name: index_pipeline_instances_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_pipeline_instances_on_owner_uuid ON pipeline_instances USING btree (owner_uuid);
+
+
+--
+-- Name: index_pipeline_instances_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_pipeline_instances_on_uuid ON pipeline_instances USING btree (uuid);
+
+
+--
+-- Name: index_pipeline_templates_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_pipeline_templates_on_created_at ON pipeline_templates USING btree (created_at);
+
+
+--
+-- Name: index_pipeline_templates_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_pipeline_templates_on_modified_at ON pipeline_templates USING btree (modified_at);
+
+
+--
+-- Name: index_pipeline_templates_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_pipeline_templates_on_owner_uuid ON pipeline_templates USING btree (owner_uuid);
+
+
+--
+-- Name: index_pipeline_templates_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_pipeline_templates_on_uuid ON pipeline_templates USING btree (uuid);
+
+
+--
+-- Name: index_repositories_on_name; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_repositories_on_name ON repositories USING btree (name);
+
+
+--
+-- Name: index_repositories_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_repositories_on_owner_uuid ON repositories USING btree (owner_uuid);
+
+
+--
+-- Name: index_repositories_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_repositories_on_uuid ON repositories USING btree (uuid);
+
+
+--
+-- Name: index_specimens_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_specimens_on_created_at ON specimens USING btree (created_at);
+
+
+--
+-- Name: index_specimens_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_specimens_on_modified_at ON specimens USING btree (modified_at);
+
+
+--
+-- Name: index_specimens_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_specimens_on_owner_uuid ON specimens USING btree (owner_uuid);
+
+
+--
+-- Name: index_specimens_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_specimens_on_uuid ON specimens USING btree (uuid);
+
+
+--
+-- Name: index_traits_on_name; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_traits_on_name ON traits USING btree (name);
+
+
+--
+-- Name: index_traits_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_traits_on_owner_uuid ON traits USING btree (owner_uuid);
+
+
+--
+-- Name: index_traits_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_traits_on_uuid ON traits USING btree (uuid);
+
+
+--
+-- Name: index_users_on_created_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_users_on_created_at ON users USING btree (created_at);
+
+
+--
+-- Name: index_users_on_modified_at; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_users_on_modified_at ON users USING btree (modified_at);
+
+
+--
+-- Name: index_users_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_users_on_owner_uuid ON users USING btree (owner_uuid);
+
+
+--
+-- Name: index_users_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_users_on_uuid ON users USING btree (uuid);
+
+
+--
+-- Name: index_virtual_machines_on_hostname; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_virtual_machines_on_hostname ON virtual_machines USING btree (hostname);
+
+
+--
+-- Name: index_virtual_machines_on_owner_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE INDEX index_virtual_machines_on_owner_uuid ON virtual_machines USING btree (owner_uuid);
+
+
+--
+-- Name: index_virtual_machines_on_uuid; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX index_virtual_machines_on_uuid ON virtual_machines USING btree (uuid);
+
+
+--
+-- Name: links_tail_name_unique_if_link_class_name; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX links_tail_name_unique_if_link_class_name ON links USING btree (tail_uuid, name) WHERE ((link_class)::text = 'name'::text);
+
+
+--
+-- Name: pipeline_template_owner_uuid_name_unique; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX pipeline_template_owner_uuid_name_unique ON pipeline_templates USING btree (owner_uuid, name);
+
+
+--
+-- Name: unique_schema_migrations; Type: INDEX; Schema: public; Owner: -; Tablespace:
+--
+
+CREATE UNIQUE INDEX unique_schema_migrations ON schema_migrations USING btree (version);
+
+
+--
+-- PostgreSQL database dump complete
+--
+
+SET search_path TO "$user",public;
+
+INSERT INTO schema_migrations (version) VALUES ('20121016005009');
+
+INSERT INTO schema_migrations (version) VALUES ('20130105203021');
+
+INSERT INTO schema_migrations (version) VALUES ('20130105224358');
+
+INSERT INTO schema_migrations (version) VALUES ('20130105224618');
+
+INSERT INTO schema_migrations (version) VALUES ('20130107181109');
+
+INSERT INTO schema_migrations (version) VALUES ('20130107212832');
+
+INSERT INTO schema_migrations (version) VALUES ('20130109175700');
+
+INSERT INTO schema_migrations (version) VALUES ('20130109220548');
+
+INSERT INTO schema_migrations (version) VALUES ('20130113214204');
+
+INSERT INTO schema_migrations (version) VALUES ('20130116024233');
+
+INSERT INTO schema_migrations (version) VALUES ('20130116215213');
+
+INSERT INTO schema_migrations (version) VALUES ('20130118002239');
+
+INSERT INTO schema_migrations (version) VALUES ('20130122020042');
+
+INSERT INTO schema_migrations (version) VALUES ('20130122201442');
+
+INSERT INTO schema_migrations (version) VALUES ('20130122221616');
+
+INSERT INTO schema_migrations (version) VALUES ('20130123174514');
+
+INSERT INTO schema_migrations (version) VALUES ('20130123180224');
+
+INSERT INTO schema_migrations (version) VALUES ('20130123180228');
+
+INSERT INTO schema_migrations (version) VALUES ('20130125220425');
+
+INSERT INTO schema_migrations (version) VALUES ('20130128202518');
+
+INSERT INTO schema_migrations (version) VALUES ('20130128231343');
+
+INSERT INTO schema_migrations (version) VALUES ('20130130205749');
+
+INSERT INTO schema_migrations (version) VALUES ('20130203104818');
+
+INSERT INTO schema_migrations (version) VALUES ('20130203104824');
+
+INSERT INTO schema_migrations (version) VALUES ('20130203115329');
+
+INSERT INTO schema_migrations (version) VALUES ('20130207195855');
+
+INSERT INTO schema_migrations (version) VALUES ('20130218181504');
+
+INSERT INTO schema_migrations (version) VALUES ('20130226170000');
+
+INSERT INTO schema_migrations (version) VALUES ('20130313175417');
+
+INSERT INTO schema_migrations (version) VALUES ('20130315155820');
+
+INSERT INTO schema_migrations (version) VALUES ('20130315183626');
+
+INSERT INTO schema_migrations (version) VALUES ('20130315213205');
+
+INSERT INTO schema_migrations (version) VALUES ('20130318002138');
+
+INSERT INTO schema_migrations (version) VALUES ('20130319165853');
+
+INSERT INTO schema_migrations (version) VALUES ('20130319180730');
+
+INSERT INTO schema_migrations (version) VALUES ('20130319194637');
+
+INSERT INTO schema_migrations (version) VALUES ('20130319201431');
+
+INSERT INTO schema_migrations (version) VALUES ('20130319235957');
+
+INSERT INTO schema_migrations (version) VALUES ('20130320000107');
+
+INSERT INTO schema_migrations (version) VALUES ('20130326173804');
+
+INSERT INTO schema_migrations (version) VALUES ('20130326182917');
+
+INSERT INTO schema_migrations (version) VALUES ('20130415020241');
+
+INSERT INTO schema_migrations (version) VALUES ('20130425024459');
+
+INSERT INTO schema_migrations (version) VALUES ('20130425214427');
+
+INSERT INTO schema_migrations (version) VALUES ('20130523060112');
+
+INSERT INTO schema_migrations (version) VALUES ('20130523060213');
+
+INSERT INTO schema_migrations (version) VALUES ('20130524042319');
+
+INSERT INTO schema_migrations (version) VALUES ('20130528134100');
+
+INSERT INTO schema_migrations (version) VALUES ('20130606183519');
+
+INSERT INTO schema_migrations (version) VALUES ('20130608053730');
+
+INSERT INTO schema_migrations (version) VALUES ('20130610202538');
+
+INSERT INTO schema_migrations (version) VALUES ('20130611163736');
+
+INSERT INTO schema_migrations (version) VALUES ('20130612042554');
+
+INSERT INTO schema_migrations (version) VALUES ('20130617150007');
+
+INSERT INTO schema_migrations (version) VALUES ('20130626002829');
+
+INSERT INTO schema_migrations (version) VALUES ('20130626022810');
+
+INSERT INTO schema_migrations (version) VALUES ('20130627154537');
+
+INSERT INTO schema_migrations (version) VALUES ('20130627184333');
+
+INSERT INTO schema_migrations (version) VALUES ('20130708163414');
+
+INSERT INTO schema_migrations (version) VALUES ('20130708182912');
+
+INSERT INTO schema_migrations (version) VALUES ('20130708185153');
+
+INSERT INTO schema_migrations (version) VALUES ('20130724153034');
+
+INSERT INTO schema_migrations (version) VALUES ('20131007180607');
+
+INSERT INTO schema_migrations (version) VALUES ('20140117231056');
+
+INSERT INTO schema_migrations (version) VALUES ('20140124222114');
+
+INSERT INTO schema_migrations (version) VALUES ('20140129184311');
+
+INSERT INTO schema_migrations (version) VALUES ('20140317135600');
+
+INSERT INTO schema_migrations (version) VALUES ('20140319160547');
+
+INSERT INTO schema_migrations (version) VALUES ('20140321191343');
+
+INSERT INTO schema_migrations (version) VALUES ('20140324024606');
+
+INSERT INTO schema_migrations (version) VALUES ('20140325175653');
+
+INSERT INTO schema_migrations (version) VALUES ('20140402001908');
+
+INSERT INTO schema_migrations (version) VALUES ('20140407184311');
+
+INSERT INTO schema_migrations (version) VALUES ('20140421140924');
+
+INSERT INTO schema_migrations (version) VALUES ('20140421151939');
+
+INSERT INTO schema_migrations (version) VALUES ('20140421151940');
+
+INSERT INTO schema_migrations (version) VALUES ('20140422011506');
+
+INSERT INTO schema_migrations (version) VALUES ('20140423132913');
+
+INSERT INTO schema_migrations (version) VALUES ('20140423133559');
+
+INSERT INTO schema_migrations (version) VALUES ('20140501165548');
+
+INSERT INTO schema_migrations (version) VALUES ('20140519205916');
+
+INSERT INTO schema_migrations (version) VALUES ('20140527152921');
+
+INSERT INTO schema_migrations (version) VALUES ('20140530200539');
+
+INSERT INTO schema_migrations (version) VALUES ('20140601022548');
+
+INSERT INTO schema_migrations (version) VALUES ('20140602143352');
+
+INSERT INTO schema_migrations (version) VALUES ('20140607150616');
+
+INSERT INTO schema_migrations (version) VALUES ('20140611173003');
+
+INSERT INTO schema_migrations (version) VALUES ('20140627210837');
+
+INSERT INTO schema_migrations (version) VALUES ('20140709172343');
+
+INSERT INTO schema_migrations (version) VALUES ('20140714184006');
+
+INSERT INTO schema_migrations (version) VALUES ('20140811184643');
+
+INSERT INTO schema_migrations (version) VALUES ('20140817035914');
+
+INSERT INTO schema_migrations (version) VALUES ('20140818125735');
+
+INSERT INTO schema_migrations (version) VALUES ('20140826180337');
+
+INSERT INTO schema_migrations (version) VALUES ('20140828141043');
+
+INSERT INTO schema_migrations (version) VALUES ('20140909183946');
+
+INSERT INTO schema_migrations (version) VALUES ('20140911221252');
+
+INSERT INTO schema_migrations (version) VALUES ('20140918141529');
+
+INSERT INTO schema_migrations (version) VALUES ('20140918153541');
+
+INSERT INTO schema_migrations (version) VALUES ('20140918153705');
+
+INSERT INTO schema_migrations (version) VALUES ('20140924091559');
+
+INSERT INTO schema_migrations (version) VALUES ('20141111133038');
+
+INSERT INTO schema_migrations (version) VALUES ('20141208164553');
\ No newline at end of file
--- /dev/null
+# Protect referential integrity of owner_uuid columns in other tables
+# that can refer to the uuid column in this table.
+
+module CanBeAnOwner
+
+ def self.included(base)
+ # Rails' "has_many" can prevent us from destroying the owner
+ # record when other objects refer to it.
+ ActiveRecord::Base.connection.tables.each do |t|
+ next if t == base.table_name
+ next if t == 'schema_migrations'
+ klass = t.classify.constantize
+ next unless klass and 'owner_uuid'.in?(klass.columns.collect(&:name))
+ base.has_many(t.to_sym,
+ foreign_key: :owner_uuid,
+ primary_key: :uuid,
+ dependent: :restrict)
+ end
+ # We need custom protection for changing an owner's primary
+ # key. (Apart from this restriction, admins are allowed to change
+ # UUIDs.)
+ base.validate :restrict_uuid_change_breaking_associations
+ end
+
+ protected
+
+ def restrict_uuid_change_breaking_associations
+ return true if new_record? or not uuid_changed?
+
+ # Check for objects that have my old uuid listed as their owner.
+ self.class.reflect_on_all_associations(:has_many).each do |assoc|
+ next unless assoc.foreign_key == :owner_uuid
+ if assoc.klass.where(owner_uuid: uuid_was).any?
+ errors.add(:uuid,
+ "cannot be changed on a #{self.class} that owns objects")
+ return false
+ end
+ end
+
+ # if I owned myself before, I'll just continue to own myself with
+ # my new uuid.
+ if owner_uuid == uuid_was
+ self.owner_uuid = uuid
+ end
+ end
+
+end
--- /dev/null
+module CommonApiTemplate
+ def self.included(base)
+ base.acts_as_api
+ base.class_eval do
+ alias_method :as_api_response_orig, :as_api_response
+ include InstanceMethods
+ end
+ base.extend(ClassMethods)
+ base.api_accessible :common do |t|
+ t.add :href
+ t.add :kind
+ t.add :etag
+ t.add :uuid
+ t.add :owner_uuid
+ t.add :created_at
+ t.add :modified_by_client_uuid
+ t.add :modified_by_user_uuid
+ t.add :modified_at
+ end
+ end
+
+ module InstanceMethods
+ # choose template based on opts[:for_user]
+ def as_api_response(template=nil, opts={})
+ if template.nil?
+ user = opts[:for_user] || current_user
+ if user.andand.is_admin and self.respond_to? :api_accessible_superuser
+ template = :superuser
+ else
+ template = :user
+ end
+ end
+ self.as_api_response_orig(template, opts)
+ end
+ end
+
+ module ClassMethods
+ end
+end
--- /dev/null
+module CurrentApiClient
+ def current_user
+ Thread.current[:user]
+ end
+
+ def current_api_client
+ Thread.current[:api_client]
+ end
+
+ def current_api_client_authorization
+ Thread.current[:api_client_authorization]
+ end
+
+ def current_api_base
+ Thread.current[:api_url_base]
+ end
+
+ def current_default_owner
+ # owner_uuid for newly created objects
+ ((current_api_client_authorization &&
+ current_api_client_authorization.default_owner_uuid) ||
+ (current_user && current_user.default_owner_uuid) ||
+ (current_user && current_user.uuid) ||
+ nil)
+ end
+
+ # Where is the client connecting from?
+ def current_api_client_ip_address
+ Thread.current[:api_client_ip_address]
+ end
+
+ def system_user_uuid
+ [Server::Application.config.uuid_prefix,
+ User.uuid_prefix,
+ '000000000000000'].join('-')
+ end
+
+ def system_group_uuid
+ [Server::Application.config.uuid_prefix,
+ Group.uuid_prefix,
+ '000000000000000'].join('-')
+ end
+
+ def anonymous_group_uuid
+ [Server::Application.config.uuid_prefix,
+ Group.uuid_prefix,
+ 'anonymouspublic'].join('-')
+ end
+
+ def anonymous_user_uuid
+ [Server::Application.config.uuid_prefix,
+ User.uuid_prefix,
+ 'anonymouspublic'].join('-')
+ end
+
+ def system_user
+ if not $system_user
+ real_current_user = Thread.current[:user]
+ Thread.current[:user] = User.new(is_admin: true,
+ is_active: true,
+ uuid: system_user_uuid)
+ $system_user = User.where('uuid=?', system_user_uuid).first
+ if !$system_user
+ $system_user = User.new(uuid: system_user_uuid,
+ is_active: true,
+ is_admin: true,
+ email: 'root',
+ first_name: 'root',
+ last_name: '')
+ $system_user.save!
+ $system_user.reload
+ end
+ Thread.current[:user] = real_current_user
+ end
+ $system_user
+ end
+
+ def system_group
+ if not $system_group
+ act_as_system_user do
+ ActiveRecord::Base.transaction do
+ $system_group = Group.
+ where(uuid: system_group_uuid).first_or_create do |g|
+ g.update_attributes(name: "System group",
+ description: "System group")
+ User.all.collect(&:uuid).each do |user_uuid|
+ Link.create(link_class: 'permission',
+ name: 'can_manage',
+ tail_kind: 'arvados#group',
+ tail_uuid: system_group_uuid,
+ head_kind: 'arvados#user',
+ head_uuid: user_uuid)
+ end
+ end
+ end
+ end
+ end
+ $system_group
+ end
+
+ def all_users_group_uuid
+ [Server::Application.config.uuid_prefix,
+ Group.uuid_prefix,
+ 'fffffffffffffff'].join('-')
+ end
+
+ def all_users_group
+ if not $all_users_group
+ act_as_system_user do
+ ActiveRecord::Base.transaction do
+ $all_users_group = Group.
+ where(uuid: all_users_group_uuid).first_or_create do |g|
+ g.update_attributes(name: "All users",
+ description: "All users",
+ group_class: "role")
+ end
+ end
+ end
+ end
+ $all_users_group
+ end
+
+ def act_as_system_user
+ if block_given?
+ act_as_user system_user do
+ yield
+ end
+ else
+ Thread.current[:user] = system_user
+ end
+ end
+
+ def act_as_user user
+ user_was = Thread.current[:user]
+ Thread.current[:user] = user
+ begin
+ yield
+ ensure
+ Thread.current[:user] = user_was
+ end
+ end
+
+ def anonymous_group
+ if not $anonymous_group
+ act_as_system_user do
+ ActiveRecord::Base.transaction do
+ $anonymous_group = Group.
+ where(uuid: anonymous_group_uuid).first_or_create do |g|
+ g.update_attributes(name: "Anonymous group",
+ description: "Anonymous group")
+ end
+ end
+ end
+ end
+ $anonymous_group
+ end
+
+ def anonymous_user
+ if not $anonymous_user
+ act_as_system_user do
+ $anonymous_user = User.where('uuid=?', anonymous_user_uuid).first
+ if !$anonymous_user
+ $anonymous_user = User.new(uuid: anonymous_user_uuid,
+ is_active: false,
+ is_admin: false,
+ email: 'anonymouspublic',
+ first_name: 'anonymouspublic',
+ last_name: 'anonymouspublic')
+ $anonymous_user.save!
+ $anonymous_user.reload
+ end
+
+ group_perms = Link.where(tail_uuid: anonymous_user_uuid,
+ head_uuid: anonymous_group_uuid,
+ link_class: 'permission',
+ name: 'can_read')
+
+ if !group_perms.any?
+ group_perm = Link.create!(tail_uuid: anonymous_user_uuid,
+ head_uuid: anonymous_group_uuid,
+ link_class: 'permission',
+ name: 'can_read')
+ end
+ end
+ end
+ $anonymous_user
+ end
+
+ def empty_collection_uuid
+ 'd41d8cd98f00b204e9800998ecf8427e+0'
+ end
+
+ def empty_collection
+ if not $empty_collection
+ act_as_system_user do
+ ActiveRecord::Base.transaction do
+ $empty_collection = Collection.
+ where(portable_data_hash: empty_collection_uuid).
+ first_or_create!(manifest_text: '', owner_uuid: anonymous_group.uuid)
+ end
+ end
+ end
+ $empty_collection
+ end
+end
--- /dev/null
+# If any threads raise an unhandled exception, make them all die.
+# We trust a supervisor like runit to restart the server in this case.
+Thread.abort_on_exception = true
+
+require 'eventmachine'
+require 'oj'
+require 'faye/websocket'
+require 'record_filters'
+require 'load_param'
+
+# Patch in user, last_log_id and filters fields into the Faye::Websocket class.
+module Faye
+ class WebSocket
+ attr_accessor :user
+ attr_accessor :last_log_id
+ attr_accessor :filters
+ end
+end
+
+# Store the filters supplied by the user that will be applied to the logs table
+# to determine which events to return to the listener.
+class Filter
+ include LoadParam
+
+ attr_accessor :filters
+
+ def initialize p
+ @params = p
+ load_filters_param
+ end
+
+ def params
+ @params
+ end
+end
+
+# Manages websocket connections, accepts subscription messages and publishes
+# log table events.
+class EventBus
+ include CurrentApiClient
+ include RecordFilters
+
+ # used in RecordFilters
+ def model_class
+ Log
+ end
+
+ # Initialize EventBus. Takes no parameters.
+ def initialize
+ @channel = EventMachine::Channel.new
+ @mtx = Mutex.new
+ @bgthread = false
+ end
+
+ # Push out any pending events to the connection +ws+
+ # +notify_id+ the id of the most recent row in the log table, may be nil
+ #
+ # This accepts a websocket and a notify_id (this is the row id from Postgres
+ # LISTEN/NOTIFY, it may be nil if called from somewhere else)
+ #
+ # It queries the database for log rows that are either
+ # a) greater than ws.last_log_id, which is the last log id which was a candidate to be sent out
+ # b) if ws.last_log_id is nil, then it queries rows starting with notify_id
+ #
+ # Regular Arvados permissions are applied using readable_by() and filters using record_filters()
+ # To avoid clogging up the database, queries are limited to batches of 100. It will schedule a new
+ # push_events call if there are more log rows to send.
+ def push_events ws, notify_id
+ begin
+ if !notify_id.nil? and !ws.last_log_id.nil? and notify_id <= ws.last_log_id
+ # This notify is for a row we've handled already.
+ return
+ end
+
+ # Must have at least one filter set up to receive events
+ if ws.filters.length > 0
+ # Start with log rows readable by user, sorted in ascending order
+ logs = Log.readable_by(ws.user).order("id asc")
+
+ cond_id = nil
+ cond_out = []
+ param_out = []
+
+ if !ws.last_log_id.nil?
+ # Client is only interested in log rows that are newer than the
+ # last log row seen by the client.
+ cond_id = "logs.id > ?"
+ param_out << ws.last_log_id
+ elsif !notify_id.nil?
+ # No last log id, so look at rows starting with notify id
+ cond_id = "logs.id >= ?"
+ param_out << notify_id
+ else
+ # No log id to start from, nothing to do, return
+ return
+ end
+
+ # Now build filters provided by client
+ ws.filters.each do |filter|
+ ft = record_filters filter.filters, Log
+ if ft[:cond_out].any?
+ # Join the clauses within a single subscription filter with AND
+ # so it is consistent with regular queries
+ cond_out << "(#{ft[:cond_out].join ') AND ('})"
+ param_out += ft[:param_out]
+ end
+ end
+
+ # Add filters to query
+ if cond_out.any?
+ # Join subscriptions with OR
+ logs = logs.where(cond_id + " AND ((#{cond_out.join ') OR ('}))", *param_out)
+ else
+ logs = logs.where(cond_id, *param_out)
+ end
+
+ # Execute query and actually send the matching log rows
+ count = 0
+ limit = 20
+
+ logs.limit(limit).each do |l|
+ ws.send(l.as_api_response.to_json)
+ ws.last_log_id = l.id
+ count += 1
+ end
+
+ if count == limit
+ # Number of rows returned was capped by limit(), we need to schedule
+ # another query to get more logs (will start from last_log_id
+ # reported by current query)
+ EventMachine::schedule do
+ push_events ws, nil
+ end
+ elsif !notify_id.nil? and (ws.last_log_id.nil? or notify_id > ws.last_log_id)
+ # Number of rows returned was less than cap, but the notify id is
+ # higher than the last id visible to the client, so update last_log_id
+ ws.last_log_id = notify_id
+ end
+ elsif !notify_id.nil?
+ # No filters set up, so just record the sequence number
+ ws.last_log_id = notify_id
+ end
+ rescue => e
+ Rails.logger.warn "Error publishing event: #{$!}"
+ Rails.logger.warn "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
+ ws.send ({status: 500, message: 'error'}.to_json)
+ ws.close
+ # These exceptions typically indicate serious server trouble:
+ # out of memory issues, database connection problems, etc. Go ahead and
+ # crash; we expect that a supervisor service like runit will restart us.
+ raise
+ end
+ end
+
+ # Handle inbound subscribe or unsubscribe message.
+ def handle_message ws, event
+ begin
+ begin
+ # Parse event data as JSON
+ p = (Oj.load event.data).symbolize_keys
+ filter = Filter.new(p)
+ rescue Oj::Error => e
+ ws.send ({status: 400, message: "malformed request"}.to_json)
+ return
+ end
+
+ if p[:method] == 'subscribe'
+ # Handle subscribe event
+
+ if p[:last_log_id]
+ # Set or reset the last_log_id. The event bus only reports events
+ # for rows that come after last_log_id.
+ ws.last_log_id = p[:last_log_id].to_i
+ end
+
+ if ws.filters.length < MAX_FILTERS
+ # Add a filter. This gets the :filters field which is the same
+ # format as used for regular index queries.
+ ws.filters << filter
+ ws.send ({status: 200, message: 'subscribe ok', filter: p}.to_json)
+
+ # Send any pending events
+ push_events ws, nil
+ else
+ ws.send ({status: 403, message: "maximum of #{MAX_FILTERS} filters allowed per connection"}.to_json)
+ end
+
+ elsif p[:method] == 'unsubscribe'
+ # Handle unsubscribe event
+
+ len = ws.filters.length
+ ws.filters.select! { |f| not ((f.filters == p[:filters]) or (f.filters.empty? and p[:filters].nil?)) }
+ if ws.filters.length < len
+ ws.send ({status: 200, message: 'unsubscribe ok'}.to_json)
+ else
+ ws.send ({status: 404, message: 'filter not found'}.to_json)
+ end
+
+ else
+ ws.send ({status: 400, message: "missing or unrecognized method"}.to_json)
+ end
+ rescue => e
+ Rails.logger.warn "Error handling message: #{$!}"
+ Rails.logger.warn "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
+ ws.send ({status: 500, message: 'error'}.to_json)
+ ws.close
+ end
+ end
+
+ # Constant maximum number of filters, to avoid silly huge database queries.
+ MAX_FILTERS = 16
+
+ # Called by RackSocket when a new websocket connection has been established.
+ def on_connect ws
+
+ # Disconnect if no valid API token.
+ # current_user is included from CurrentApiClient
+ if not current_user
+ ws.send ({status: 401, message: "Valid API token required"}.to_json)
+ ws.close
+ return
+ end
+
+ # Initialize our custom fields on the websocket connection object.
+ ws.user = current_user
+ ws.filters = []
+ ws.last_log_id = nil
+
+ # Subscribe to internal postgres notifications through @channel. This will
+ # call push_events when a notification comes through.
+ sub = @channel.subscribe do |msg|
+ push_events ws, msg
+ end
+
+ # Set up callback for inbound message dispatch.
+ ws.on :message do |event|
+ handle_message ws, event
+ end
+
+ # Set up socket close callback
+ ws.on :close do |event|
+ @channel.unsubscribe sub
+ ws = nil
+ end
+
+ # Start up thread to monitor the Postgres database, if none exists already.
+ @mtx.synchronize do
+ unless @bgthread
+ @bgthread = true
+ Thread.new do
+ # from http://stackoverflow.com/questions/16405520/postgres-listen-notify-rails
+ ActiveRecord::Base.connection_pool.with_connection do |connection|
+ conn = connection.instance_variable_get(:@connection)
+ begin
+ conn.async_exec "LISTEN logs"
+ while true
+ # wait_for_notify will block until there is a change
+ # notification from Postgres about the logs table, then push
+ # the notification into the EventMachine channel. Each
+ # websocket connection subscribes to the other end of the
+ # channel and calls #push_events to actually dispatch the
+ # events to the client.
+ conn.wait_for_notify do |channel, pid, payload|
+ @channel.push payload.to_i
+ end
+ end
+ ensure
+ # Don't want the connection to still be listening once we return
+ # it to the pool - could result in weird behavior for the next
+ # thread to check it out.
+ conn.async_exec "UNLISTEN *"
+ end
+ end
+ @bgthread = false
+ end
+ end
+ end
+
+ # Since EventMachine is an asynchronous event based dispatcher, #on_connect
+ # does not block but instead returns immediately after having set up the
+ # websocket and notification channel callbacks.
+ end
+end
--- /dev/null
+module HasUuid
+
+ UUID_REGEX = /^[0-9a-z]{5}-([0-9a-z]{5})-[0-9a-z]{15}$/
+
+ def self.included(base)
+ base.extend(ClassMethods)
+ base.validate :validate_uuid
+ base.before_create :assign_uuid
+ base.before_destroy :destroy_permission_links
+ base.has_many :links_via_head, class_name: 'Link', foreign_key: :head_uuid, primary_key: :uuid, conditions: "not (link_class = 'permission')", dependent: :restrict
+ base.has_many :links_via_tail, class_name: 'Link', foreign_key: :tail_uuid, primary_key: :uuid, conditions: "not (link_class = 'permission')", dependent: :restrict
+ end
+
+ module ClassMethods
+ def uuid_prefix
+ Digest::MD5.hexdigest(self.to_s).to_i(16).to_s(36)[-5..-1]
+ end
+ def generate_uuid
+ [Server::Application.config.uuid_prefix,
+ self.uuid_prefix,
+ rand(2**256).to_s(36)[-15..-1]].
+ join '-'
+ end
+ end
+
+ protected
+
+ def respond_to_uuid?
+ self.respond_to? :uuid
+ end
+
+ def validate_uuid
+ if self.respond_to_uuid? and self.uuid_changed?
+ if current_user.andand.is_admin and self.uuid.is_a?(String)
+ if (re = self.uuid.match HasUuid::UUID_REGEX)
+ if re[1] == self.class.uuid_prefix
+ return true
+ else
+ self.errors.add(:uuid, "type field is '#{re[1]}', expected '#{self.class.uuid_prefix}'")
+ return false
+ end
+ else
+ self.errors.add(:uuid, "not a valid Arvados uuid '#{self.uuid}'")
+ return false
+ end
+ else
+ if self.new_record?
+ self.errors.add(:uuid, "assignment not permitted")
+ else
+ self.errors.add(:uuid, "change not permitted")
+ end
+ return false
+ end
+ else
+ return true
+ end
+ end
+
+ def assign_uuid
+ if self.respond_to_uuid? and self.uuid.nil? or self.uuid.empty?
+ self.uuid = self.class.generate_uuid
+ end
+ true
+ end
+
+ def destroy_permission_links
+ if uuid
+ Link.destroy_all(['link_class=? and (head_uuid=? or tail_uuid=?)',
+ 'permission', uuid, uuid])
+ end
+ end
+end
--- /dev/null
+require 'omniauth-oauth2'
+module OmniAuth
+ module Strategies
+ class JoshId < OmniAuth::Strategies::OAuth2
+
+ args [:client_id, :client_secret, :custom_provider_url]
+
+ option :custom_provider_url, ''
+
+ uid { raw_info['id'] }
+
+ option :client_options, {}
+
+ info do
+ {
+ :first_name => raw_info['info']['first_name'],
+ :last_name => raw_info['info']['last_name'],
+ :email => raw_info['info']['email'],
+ :identity_url => raw_info['info']['identity_url'],
+ }
+ end
+
+ extra do
+ {
+ 'raw_info' => raw_info
+ }
+ end
+
+ def authorize_params
+ options.authorize_params[:auth_provider] = request.params['auth_provider']
+ super
+ end
+
+ def client
+ options.client_options[:site] = options[:custom_provider_url]
+ options.client_options[:authorize_url] = "#{options[:custom_provider_url]}/auth/josh_id/authorize"
+ options.client_options[:access_token_url] = "#{options[:custom_provider_url]}/auth/josh_id/access_token"
+ if Rails.configuration.sso_insecure
+ options.client_options[:ssl] = {verify_mode: OpenSSL::SSL::VERIFY_NONE}
+ end
+ ::OAuth2::Client.new(options.client_id, options.client_secret, deep_symbolize(options.client_options))
+ end
+
+ def callback_url
+ full_host + script_name + callback_path + "?return_to=" + CGI.escape(request.params['return_to'])
+ end
+
+ def raw_info
+ @raw_info ||= access_token.get("/auth/josh_id/user.json?oauth_token=#{access_token.token}").parsed
+ end
+ end
+ end
+end
--- /dev/null
+module KindAndEtag
+
+ def self.included(base)
+ base.extend(ClassMethods)
+ end
+
+ module ClassMethods
+ def kind
+ 'arvados#' + self.to_s.camelcase(:lower)
+ end
+ end
+
+ def kind
+ self.class.kind
+ end
+
+ def etag
+ Digest::MD5.hexdigest(self.inspect).to_i(16).to_s(36)
+ end
+end
--- /dev/null
+# Mixin module for reading out query parameters from request params.
+#
+# Expects:
+# +params+ Hash
+# Sets:
+# @where, @filters, @limit, @offset, @orders
+module LoadParam
+
+ # Default number of rows to return in a single query.
+ DEFAULT_LIMIT = 100
+
+ # Maximum number of rows to return in a single query, even if the client asks for more.
+ MAX_LIMIT = 1000
+
+ # Load params[:where] into @where
+ def load_where_param
+ if params[:where].nil? or params[:where] == ""
+ @where = {}
+ elsif params[:where].is_a? Hash
+ @where = params[:where]
+ elsif params[:where].is_a? String
+ begin
+ @where = Oj.load(params[:where])
+ raise unless @where.is_a? Hash
+ rescue
+ raise ArgumentError.new("Could not parse \"where\" param as an object")
+ end
+ end
+ @where = @where.with_indifferent_access
+ end
+
+ # Load params[:filters] into @filters
+ def load_filters_param
+ @filters ||= []
+ if params[:filters].is_a? Array
+ @filters += params[:filters]
+ elsif params[:filters].is_a? String and !params[:filters].empty?
+ begin
+ f = Oj.load params[:filters]
+ if not f.nil?
+ raise unless f.is_a? Array
+ @filters += f
+ end
+ rescue
+ raise ArgumentError.new("Could not parse \"filters\" param as an array")
+ end
+ end
+ end
+
+ def default_orders
+ ["#{table_name}.modified_at desc"]
+ end
+
+ # Load params[:limit], params[:offset] and params[:order]
+ # into @limit, @offset, @orders
+ def load_limit_offset_order_params
+ if params[:limit]
+ unless params[:limit].to_s.match(/^\d+$/)
+ raise ArgumentError.new("Invalid value for limit parameter")
+ end
+ @limit = [params[:limit].to_i, MAX_LIMIT].min
+ else
+ @limit = DEFAULT_LIMIT
+ end
+
+ if params[:offset]
+ unless params[:offset].to_s.match(/^\d+$/)
+ raise ArgumentError.new("Invalid value for offset parameter")
+ end
+ @offset = params[:offset].to_i
+ else
+ @offset = 0
+ end
+
+ @orders = []
+ if (params[:order].is_a?(Array) && !params[:order].empty?) || !params[:order].blank?
+ od = []
+ (case params[:order]
+ when String
+ if params[:order].starts_with? '['
+ od = Oj.load(params[:order])
+ raise unless od.is_a? Array
+ od
+ else
+ params[:order].split(',')
+ end
+ when Array
+ params[:order]
+ else
+ []
+ end).each do |order|
+ order = order.to_s
+ attr, direction = order.strip.split " "
+ direction ||= 'asc'
+ # The attr can have its table unspecified if it happens to be for the current "model_class" (the first case)
+ # or it can be fully specified with the database tablename (the second case) (e.g. "collections.name").
+ # NB that the security check for the second case table_name will not work if the model
+ # has used set_table_name to use an alternate table name from the Rails standard.
+ # I could not find a perfect way to handle this well, but ActiveRecord::Base.send(:descendants)
+ # would be a place to start if this ever becomes necessary.
+ if attr.match /^[a-z][_a-z0-9]+$/ and
+ model_class.columns.collect(&:name).index(attr) and
+ ['asc','desc'].index direction.downcase
+ @orders << "#{table_name}.#{attr} #{direction.downcase}"
+ elsif attr.match /^([a-z][_a-z0-9]+)\.([a-z][_a-z0-9]+)$/ and
+ ['asc','desc'].index(direction.downcase) and
+ ActiveRecord::Base.connection.tables.include?($1) and
+ $1.classify.constantize.columns.collect(&:name).index($2)
+ # $1 in the above checks references the first match from the regular expression, which is expected to be the database table name
+ # $2 is of course the actual database column name
+ @orders << "#{attr} #{direction.downcase}"
+ end
+ end
+ end
+
+ if @orders.empty?
+ @orders = default_orders
+ end
+
+ case params[:select]
+ when Array
+ @select = params[:select]
+ when String
+ begin
+ @select = Oj.load params[:select]
+ raise unless @select.is_a? Array or @select.nil?
+ rescue
+ raise ArgumentError.new("Could not parse \"select\" param as an array")
+ end
+ end
+
+ if @select
+ # Any ordering columns must be selected when doing select,
+ # otherwise it is an SQL error, so filter out invaliding orderings.
+ @orders.select! { |o|
+ # match select column against order array entry
+ @select.select { |s| /^#{table_name}.#{s}( (asc|desc))?$/.match o }.any?
+ }
+ end
+
+ @distinct = true if (params[:distinct] == true || params[:distinct] == "true")
+ @distinct = false if (params[:distinct] == false || params[:distinct] == "false")
+ end
+
+end
--- /dev/null
+# Mixin module providing a method to convert filters into a list of SQL
+# fragments suitable to be fed to ActiveRecord #where.
+#
+# Expects:
+# model_class
+# Operates on:
+# @objects
+module RecordFilters
+
+ # Input:
+ # +filters+ array of conditions, each being [column, operator, operand]
+ # +model_class+ subclass of ActiveRecord being filtered
+ #
+ # Output:
+ # Hash with two keys:
+ # :cond_out array of SQL fragments for each filter expression
+ # :param_out array of values for parameter substitution in cond_out
+ def record_filters filters, model_class
+ conds_out = []
+ param_out = []
+
+ ar_table_name = model_class.table_name
+ filters.each do |filter|
+ attrs_in, operator, operand = filter
+ if attrs_in == 'any'
+ attrs = model_class.searchable_columns(operator)
+ elsif attrs_in.is_a? Array
+ attrs = attrs_in
+ else
+ attrs = [attrs_in]
+ end
+ if !filter.is_a? Array
+ raise ArgumentError.new("Invalid element in filters array: #{filter.inspect} is not an array")
+ elsif !operator.is_a? String
+ raise ArgumentError.new("Invalid operator '#{operator}' (#{operator.class}) in filter")
+ end
+ cond_out = []
+ attrs.each do |attr|
+ if !model_class.searchable_columns(operator).index attr.to_s
+ raise ArgumentError.new("Invalid attribute '#{attr}' in filter")
+ end
+ case operator.downcase
+ when '=', '<', '<=', '>', '>=', '!=', 'like', 'ilike'
+ attr_type = model_class.attribute_column(attr).type
+ operator = '<>' if operator == '!='
+ if operand.is_a? String
+ if attr_type == :boolean
+ if not ['=', '<>'].include?(operator)
+ raise ArgumentError.new("Invalid operator '#{operator}' for " \
+ "boolean attribute '#{attr}'")
+ end
+ case operand.downcase
+ when '1', 't', 'true', 'y', 'yes'
+ operand = true
+ when '0', 'f', 'false', 'n', 'no'
+ operand = false
+ else
+ raise ArgumentError("Invalid operand '#{operand}' for " \
+ "boolean attribute '#{attr}'")
+ end
+ end
+ cond_out << "#{ar_table_name}.#{attr} #{operator} ?"
+ if (# any operator that operates on value rather than
+ # representation:
+ operator.match(/[<=>]/) and (attr_type == :datetime))
+ operand = Time.parse operand
+ end
+ param_out << operand
+ elsif operand.nil? and operator == '='
+ cond_out << "#{ar_table_name}.#{attr} is null"
+ elsif operand.nil? and operator == '<>'
+ cond_out << "#{ar_table_name}.#{attr} is not null"
+ elsif (attr_type == :boolean) and ['=', '<>'].include?(operator) and
+ [true, false].include?(operand)
+ cond_out << "#{ar_table_name}.#{attr} #{operator} ?"
+ param_out << operand
+ else
+ raise ArgumentError.new("Invalid operand type '#{operand.class}' "\
+ "for '#{operator}' operator in filters")
+ end
+ when 'in', 'not in'
+ if operand.is_a? Array
+ cond_out << "#{ar_table_name}.#{attr} #{operator} (?)"
+ param_out << operand
+ if operator == 'not in' and not operand.include?(nil)
+ # explicitly allow NULL
+ cond_out[-1] = "(#{cond_out[-1]} OR #{ar_table_name}.#{attr} IS NULL)"
+ end
+ else
+ raise ArgumentError.new("Invalid operand type '#{operand.class}' "\
+ "for '#{operator}' operator in filters")
+ end
+ when 'is_a'
+ operand = [operand] unless operand.is_a? Array
+ cond = []
+ operand.each do |op|
+ cl = ArvadosModel::kind_class op
+ if cl
+ cond << "#{ar_table_name}.#{attr} like ?"
+ param_out << cl.uuid_like_pattern
+ else
+ cond << "1=0"
+ end
+ end
+ cond_out << cond.join(' OR ')
+ end
+ end
+ conds_out << cond_out.join(' OR ') if cond_out.any?
+ end
+
+ {:cond_out => conds_out, :param_out => param_out}
+ end
+
+end
--- /dev/null
+module SimulateJobLog
+ def replay(filename, multiplier = 1, simulated_job_uuid = nil)
+ raise "Environment must be development or test" unless [ 'test', 'development' ].include? ENV['RAILS_ENV']
+
+ multiplier = multiplier.to_f
+ multiplier = 1.0 if multiplier <= 0
+
+ actual_start_time = Time.now
+ log_start_time = nil
+
+ act_as_system_user do
+ File.open(filename).each.with_index do |line, index|
+ cols = {}
+ cols[:timestamp], rest_of_line = line.split(' ', 2)
+ begin
+ cols[:timestamp] = Time.strptime( cols[:timestamp], "%Y-%m-%d_%H:%M:%S" )
+ rescue ArgumentError
+ if line =~ /^((?:Sun|Mon|Tue|Wed|Thu|Fri|Sat) (?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec) \d{1,2} \d\d:\d\d:\d\d \d{4}) (.*)/
+ # Wed Nov 19 07:12:39 2014
+ cols[:timestamp] = Time.strptime( $1, "%a %b %d %H:%M:%S %Y" )
+ rest_of_line = $2
+ else
+ STDERR.puts "Ignoring log line because of unknown time format: #{line}"
+ end
+ end
+ cols[:job_uuid], cols[:pid], cols[:task], cols[:event_type], cols[:message] = rest_of_line.split(' ', 5)
+ # Override job uuid with a simulated one if specified
+ cols[:job_uuid] = simulated_job_uuid || cols[:job_uuid]
+ # determine when we want to simulate this log being created, based on the time multiplier
+ log_start_time = cols[:timestamp] if log_start_time.nil?
+ log_time = cols[:timestamp]
+ actual_elapsed_time = Time.now - actual_start_time
+ log_elapsed_time = log_time - log_start_time
+ modified_elapsed_time = log_elapsed_time / multiplier
+ pause_time = modified_elapsed_time - actual_elapsed_time
+ sleep pause_time if pause_time > 0
+ # output log entry for debugging and create it in the current environment's database
+ puts "#{index} #{cols.to_yaml}\n"
+ Log.new({
+ event_at: Time.zone.local_to_utc(cols[:timestamp]),
+ object_uuid: cols[:job_uuid],
+ event_type: cols[:event_type],
+ properties: { 'text' => line }
+ }).save!
+ end
+ end
+
+ end
+end
--- /dev/null
+namespace :config do
+ desc 'Ensure site configuration has all required settings'
+ task check: :environment do
+ $application_config.sort.each do |k, v|
+ if ENV.has_key?('QUIET') then
+ # Make sure we still check for the variable to exist
+ eval("Rails.configuration.#{k}")
+ else
+ if /(password|secret)/.match(k) then
+ # Make sure we still check for the variable to exist, but don't print the value
+ eval("Rails.configuration.#{k}")
+ $stderr.puts "%-32s %s" % [k, '*********']
+ else
+ $stderr.puts "%-32s %s" % [k, eval("Rails.configuration.#{k}")]
+ end
+ end
+ end
+ # default_trash_lifetime cannot be less than 24 hours
+ if Rails.configuration.default_trash_lifetime < 86400 then
+ raise "default_trash_lifetime is %d, must be at least 86400" % Rails.configuration.default_trash_lifetime
+ end
+ end
+end
--- /dev/null
+require 'simulate_job_log'
+desc 'Simulate job logging from a file. Three arguments: log filename, time multipler (optional), simulated job uuid (optional). E.g. (use quotation marks if using spaces between args): rake "replay_job_log[log.txt, 2.0, qr1hi-8i9sb-nf3qk0xzwwz3lre]"'
+task :replay_job_log, [:filename, :multiplier, :uuid] => :environment do |t, args|
+ include SimulateJobLog
+ abort("No filename specified.") if args[:filename].blank?
+ replay( args[:filename], args[:multiplier].to_f, args[:uuid] )
+end
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+ <title>The page you were looking for doesn't exist (404)</title>
+ <style type="text/css">
+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+ div.dialog {
+ width: 25em;
+ padding: 0 4em;
+ margin: 4em auto 0 auto;
+ border: 1px solid #ccc;
+ border-right-color: #999;
+ border-bottom-color: #999;
+ }
+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+ </style>
+</head>
+
+<body>
+ <!-- This file lives in public/404.html -->
+ <div class="dialog">
+ <h1>The page you were looking for doesn't exist.</h1>
+ <p>You may have mistyped the address or the page may have moved.</p>
+ </div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+ <title>The change you wanted was rejected (422)</title>
+ <style type="text/css">
+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+ div.dialog {
+ width: 25em;
+ padding: 0 4em;
+ margin: 4em auto 0 auto;
+ border: 1px solid #ccc;
+ border-right-color: #999;
+ border-bottom-color: #999;
+ }
+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+ </style>
+</head>
+
+<body>
+ <!-- This file lives in public/422.html -->
+ <div class="dialog">
+ <h1>The change you wanted was rejected.</h1>
+ <p>Maybe you tried to change something you didn't have access to.</p>
+ </div>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+ <title>We're sorry, but something went wrong (500)</title>
+ <style type="text/css">
+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
+ div.dialog {
+ width: 25em;
+ padding: 0 4em;
+ margin: 4em auto 0 auto;
+ border: 1px solid #ccc;
+ border-right-color: #999;
+ border-bottom-color: #999;
+ }
+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
+ </style>
+</head>
+
+<body>
+ <!-- This file lives in public/500.html -->
+ <div class="dialog">
+ <h1>We're sorry, but something went wrong.</h1>
+ <p>We've been notified about this issue and we'll take a look at it shortly.</p>
+ </div>
+</body>
+</html>
--- /dev/null
+# See http://www.robotstxt.org/wc/norobots.html for documentation on how to use the robots.txt file
+#
+# To ban all spiders from the entire site uncomment the next two lines:
+# User-Agent: *
+# Disallow: /
--- /dev/null
+#!/usr/bin/env ruby
+
+
+if ENV["CRUNCH_DISPATCH_LOCKFILE"]
+ lockfilename = ENV.delete "CRUNCH_DISPATCH_LOCKFILE"
+ lockfile = File.open(lockfilename, File::RDWR|File::CREAT, 0644)
+ unless lockfile.flock File::LOCK_EX|File::LOCK_NB
+ abort "Lock unavailable on #{lockfilename} - exit"
+ end
+end
+
+ENV["RAILS_ENV"] = ARGV[0] || ENV["RAILS_ENV"] || "development"
+
+require File.dirname(__FILE__) + '/../config/boot'
+require File.dirname(__FILE__) + '/../config/environment'
+
+class CancelJobs
+ include ApplicationHelper
+
+ def cancel_stale_jobs
+ act_as_system_user do
+ Job.running.each do |jobrecord|
+ f = Log.where("object_uuid=?", jobrecord.uuid).limit(1).order("created_at desc").first
+ if f
+ age = (Time.now - f.created_at)
+ if age > 300
+ $stderr.puts "dispatch: failing orphan job #{jobrecord.uuid}, last log is #{age} seconds old"
+ # job is marked running, but not known to crunch-dispatcher, and
+ # hasn't produced any log entries for 5 minutes, so mark it as failed.
+ jobrecord.running = false
+ jobrecord.cancelled_at ||= Time.now
+ jobrecord.finished_at ||= Time.now
+ if jobrecord.success.nil?
+ jobrecord.success = false
+ end
+ jobrecord.save!
+ end
+ end
+ end
+ end
+ end
+end
+
+CancelJobs.new.cancel_stale_jobs
--- /dev/null
+#!/usr/bin/env ruby
+
+# Install the supplied string (or a randomly generated token, if none
+# is given) as an API token that authenticates to the system user
+# account.
+#
+# Print the token on stdout.
+
+supplied_token = ARGV[0]
+
+require File.dirname(__FILE__) + '/../config/boot'
+require File.dirname(__FILE__) + '/../config/environment'
+
+include ApplicationHelper
+act_as_system_user
+
+if supplied_token
+ api_client_auth = ApiClientAuthorization.
+ where(api_token: supplied_token).
+ first
+ if api_client_auth && !api_client_auth.user.uuid.match(/-000000000000000$/)
+ raise ActiveRecord::RecordNotUnique("Token already exists but is not a superuser token.")
+ end
+end
+
+if !api_client_auth
+ api_client_auth = ApiClientAuthorization.
+ new(user: system_user,
+ api_client_id: 0,
+ created_by_ip_address: '::1',
+ api_token: supplied_token)
+ api_client_auth.save!
+end
+
+puts api_client_auth.api_token
--- /dev/null
+#!/usr/bin/env ruby
+
+require 'shellwords'
+include Process
+
+$options = {}
+(ARGV.any? ? ARGV : ['--jobs', '--pipelines']).each do |arg|
+ case arg
+ when '--jobs'
+ $options[:jobs] = true
+ when '--pipelines'
+ $options[:pipelines] = true
+ else
+ abort "Unrecognized command line option '#{arg}'"
+ end
+end
+if not ($options[:jobs] or $options[:pipelines])
+ abort "Nothing to do. Please specify at least one of: --jobs, --pipelines."
+end
+
+ARGV.reject! { |a| a =~ /--jobs|--pipelines/ }
+
+$warned = {}
+$signal = {}
+%w{TERM INT}.each do |sig|
+ signame = sig
+ Signal.trap(sig) do
+ $stderr.puts "Received #{signame} signal"
+ $signal[:term] = true
+ end
+end
+
+if ENV["CRUNCH_DISPATCH_LOCKFILE"]
+ lockfilename = ENV.delete "CRUNCH_DISPATCH_LOCKFILE"
+ lockfile = File.open(lockfilename, File::RDWR|File::CREAT, 0644)
+ unless lockfile.flock File::LOCK_EX|File::LOCK_NB
+ abort "Lock unavailable on #{lockfilename} - exit"
+ end
+end
+
+ENV["RAILS_ENV"] = ARGV[0] || ENV["RAILS_ENV"] || "development"
+
+require File.dirname(__FILE__) + '/../config/boot'
+require File.dirname(__FILE__) + '/../config/environment'
+require 'open3'
+
+class LogTime < Time
+ def to_s
+ self.utc.strftime "%Y-%m-%d_%H:%M:%S"
+ end
+end
+
+class Dispatcher
+ include ApplicationHelper
+
+ def initialize
+ @crunch_job_bin = (ENV['CRUNCH_JOB_BIN'] || `which arv-crunch-job`.strip)
+ if @crunch_job_bin.empty?
+ raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
+ end
+
+ @arvados_internal = Rails.configuration.git_internal_dir
+ if not File.exists? @arvados_internal
+ $stderr.puts `mkdir -p #{@arvados_internal.shellescape} && git init --bare #{@arvados_internal.shellescape}`
+ raise "No internal git repository available" unless ($? == 0)
+ end
+
+ @repo_root = Rails.configuration.git_repositories_dir
+ @authorizations = {}
+ @did_recently = {}
+ @fetched_commits = {}
+ @git_tags = {}
+ @node_state = {}
+ @pipe_auth_tokens = {}
+ @running = {}
+ @todo = []
+ @todo_pipelines = []
+ end
+
+ def sysuser
+ return act_as_system_user
+ end
+
+ def refresh_todo
+ if $options[:jobs]
+ @todo = Job.queue.select(&:repository)
+ end
+ if $options[:pipelines]
+ @todo_pipelines = PipelineInstance.queue
+ end
+ end
+
+ def each_slurm_line(cmd, outfmt, max_fields=nil)
+ max_fields ||= outfmt.split(":").size
+ max_fields += 1 # To accommodate the node field we add
+ @@slurm_version ||= Gem::Version.new(`sinfo --version`.match(/\b[\d\.]+\b/)[0])
+ if Gem::Version.new('2.3') <= @@slurm_version
+ `#{cmd} --noheader -o '%n:#{outfmt}'`.each_line do |line|
+ yield line.chomp.split(":", max_fields)
+ end
+ else
+ # Expand rows with hostname ranges (like "foo[1-3,5,9-12]:idle")
+ # into multiple rows with one hostname each.
+ `#{cmd} --noheader -o '%N:#{outfmt}'`.each_line do |line|
+ tokens = line.chomp.split(":", max_fields)
+ if (re = tokens[0].match /^(.*?)\[([-,\d]+)\]$/)
+ tokens.shift
+ re[2].split(",").each do |range|
+ range = range.split("-").collect(&:to_i)
+ (range[0]..range[-1]).each do |n|
+ yield [re[1] + n.to_s] + tokens
+ end
+ end
+ else
+ yield tokens
+ end
+ end
+ end
+ end
+
+ def slurm_status
+ slurm_nodes = {}
+ each_slurm_line("sinfo", "%t") do |hostname, state|
+ # Treat nodes in idle* state as down, because the * means that slurm
+ # hasn't been able to communicate with it recently.
+ state.sub!(/^idle\*/, "down")
+ state.sub!(/\W+$/, "")
+ state = "down" unless %w(idle alloc down).include?(state)
+ slurm_nodes[hostname] = {state: state, job: nil}
+ end
+ each_slurm_line("squeue", "%j") do |hostname, job_uuid|
+ slurm_nodes[hostname][:job] = job_uuid if slurm_nodes[hostname]
+ end
+ slurm_nodes
+ end
+
+ def update_node_status
+ return unless Server::Application.config.crunch_job_wrapper.to_s.match /^slurm/
+ slurm_status.each_pair do |hostname, slurmdata|
+ next if @node_state[hostname] == slurmdata
+ begin
+ node = Node.where('hostname=?', hostname).order(:last_ping_at).last
+ if node
+ $stderr.puts "dispatch: update #{hostname} state to #{slurmdata}"
+ node.info["slurm_state"] = slurmdata[:state]
+ node.job_uuid = slurmdata[:job]
+ if node.save
+ @node_state[hostname] = slurmdata
+ else
+ $stderr.puts "dispatch: failed to update #{node.uuid}: #{node.errors.messages}"
+ end
+ elsif slurmdata[:state] != 'down'
+ $stderr.puts "dispatch: SLURM reports '#{hostname}' is not down, but no node has that name"
+ end
+ rescue => error
+ $stderr.puts "dispatch: error updating #{hostname} node status: #{error}"
+ end
+ end
+ end
+
+ def positive_int(raw_value, default=nil)
+ value = begin raw_value.to_i rescue 0 end
+ if value > 0
+ value
+ else
+ default
+ end
+ end
+
+ NODE_CONSTRAINT_MAP = {
+ # Map Job runtime_constraints keys to the corresponding Node info key.
+ 'min_ram_mb_per_node' => 'total_ram_mb',
+ 'min_scratch_mb_per_node' => 'total_scratch_mb',
+ 'min_cores_per_node' => 'total_cpu_cores',
+ }
+
+ def nodes_available_for_job_now(job)
+ # Find Nodes that satisfy a Job's runtime constraints (by building
+ # a list of Procs and using them to test each Node). If there
+ # enough to run the Job, return an array of their names.
+ # Otherwise, return nil.
+ need_procs = NODE_CONSTRAINT_MAP.each_pair.map do |job_key, node_key|
+ Proc.new do |node|
+ positive_int(node.info[node_key], 0) >=
+ positive_int(job.runtime_constraints[job_key], 0)
+ end
+ end
+ min_node_count = positive_int(job.runtime_constraints['min_nodes'], 1)
+ usable_nodes = []
+ Node.find_each do |node|
+ good_node = (node.info['slurm_state'] == 'idle')
+ need_procs.each { |node_test| good_node &&= node_test.call(node) }
+ if good_node
+ usable_nodes << node
+ if usable_nodes.count >= min_node_count
+ return usable_nodes.map { |node| node.hostname }
+ end
+ end
+ end
+ nil
+ end
+
+ def nodes_available_for_job(job)
+ # Check if there are enough idle nodes with the Job's minimum
+ # hardware requirements to run it. If so, return an array of
+ # their names. If not, up to once per hour, signal start_jobs to
+ # hold off launching Jobs. This delay is meant to give the Node
+ # Manager an opportunity to make new resources available for new
+ # Jobs.
+ #
+ # The exact timing parameters here might need to be adjusted for
+ # the best balance between helping the longest-waiting Jobs run,
+ # and making efficient use of immediately available resources.
+ # These are all just first efforts until we have more data to work
+ # with.
+ nodelist = nodes_available_for_job_now(job)
+ if nodelist.nil? and not did_recently(:wait_for_available_nodes, 3600)
+ $stderr.puts "dispatch: waiting for nodes for #{job.uuid}"
+ @node_wait_deadline = Time.now + 5.minutes
+ end
+ nodelist
+ end
+
+ def fail_job job, message
+ $stderr.puts "dispatch: #{job.uuid}: #{message}"
+ begin
+ Log.new(object_uuid: job.uuid,
+ event_type: 'dispatch',
+ owner_uuid: job.owner_uuid,
+ summary: message,
+ properties: {"text" => message}).save!
+ rescue
+ $stderr.puts "dispatch: log.create failed"
+ end
+
+ begin
+ job.lock @authorizations[job.uuid].user.uuid
+ job.state = "Failed"
+ if not job.save
+ $stderr.puts "dispatch: save failed setting job #{job.uuid} to failed"
+ end
+ rescue ArvadosModel::AlreadyLockedError
+ $stderr.puts "dispatch: tried to mark job #{job.uuid} as failed but it was already locked by someone else"
+ end
+ end
+
+ def stdout_s(cmd_a, opts={})
+ IO.popen(cmd_a, "r", opts) do |pipe|
+ return pipe.read.chomp
+ end
+ end
+
+ def git_cmd(*cmd_a)
+ ["git", "--git-dir=#{@arvados_internal}"] + cmd_a
+ end
+
+ def get_authorization(job)
+ if @authorizations[job.uuid] and
+ @authorizations[job.uuid].user.uuid != job.modified_by_user_uuid
+ # We already made a token for this job, but we need a new one
+ # because modified_by_user_uuid has changed (the job will run
+ # as a different user).
+ @authorizations[job.uuid].update_attributes expires_at: Time.now
+ @authorizations[job.uuid] = nil
+ end
+ if not @authorizations[job.uuid]
+ auth = ApiClientAuthorization.
+ new(user: User.where('uuid=?', job.modified_by_user_uuid).first,
+ api_client_id: 0)
+ if not auth.save
+ $stderr.puts "dispatch: auth.save failed for #{job.uuid}"
+ else
+ @authorizations[job.uuid] = auth
+ end
+ end
+ @authorizations[job.uuid]
+ end
+
+ def get_commit(repo_name, commit_hash)
+ # @fetched_commits[V]==true if we know commit V exists in the
+ # arvados_internal git repository.
+ if !@fetched_commits[commit_hash]
+ src_repo = File.join(@repo_root, "#{repo_name}.git")
+ if not File.exists? src_repo
+ src_repo = File.join(@repo_root, repo_name, '.git')
+ if not File.exists? src_repo
+ fail_job job, "No #{repo_name}.git or #{repo_name}/.git at #{@repo_root}"
+ return nil
+ end
+ end
+
+ # check if the commit needs to be fetched or not
+ commit_rev = stdout_s(git_cmd("rev-list", "-n1", commit_hash),
+ err: "/dev/null")
+ unless $? == 0 and commit_rev == commit_hash
+ # commit does not exist in internal repository, so import the source repository using git fetch-pack
+ cmd = git_cmd("fetch-pack", "--no-progress", "--all", src_repo)
+ $stderr.puts "dispatch: #{cmd}"
+ $stderr.puts(stdout_s(cmd))
+ unless $? == 0
+ fail_job job, "git fetch-pack failed"
+ return nil
+ end
+ end
+ @fetched_commits[commit_hash] = true
+ end
+ @fetched_commits[commit_hash]
+ end
+
+ def tag_commit(commit_hash, tag_name)
+ # @git_tags[T]==V if we know commit V has been tagged T in the
+ # arvados_internal repository.
+ if not @git_tags[tag_name]
+ cmd = git_cmd("tag", tag_name, commit_hash)
+ $stderr.puts "dispatch: #{cmd}"
+ $stderr.puts(stdout_s(cmd, err: "/dev/null"))
+ unless $? == 0
+ # git tag failed. This may be because the tag already exists, so check for that.
+ tag_rev = stdout_s(git_cmd("rev-list", "-n1", tag_name))
+ if $? == 0
+ # We got a revision back
+ if tag_rev != commit_hash
+ # Uh oh, the tag doesn't point to the revision we were expecting.
+ # Someone has been monkeying with the job record and/or git.
+ fail_job job, "Existing tag #{tag_name} points to commit #{tag_rev} but expected commit #{commit_hash}"
+ return nil
+ end
+ # we're okay (fall through to setting @git_tags below)
+ else
+ # git rev-list failed for some reason.
+ fail_job job, "'git tag' for #{tag_name} failed but did not find any existing tag using 'git rev-list'"
+ return nil
+ end
+ end
+ # 'git tag' was successful, or there is an existing tag that points to the same revision.
+ @git_tags[tag_name] = commit_hash
+ elsif @git_tags[tag_name] != commit_hash
+ fail_job job, "Existing tag #{tag_name} points to commit #{@git_tags[tag_name]} but this job uses commit #{commit_hash}"
+ return nil
+ end
+ @git_tags[tag_name]
+ end
+
+ def start_jobs
+ @todo.each do |job|
+ next if @running[job.uuid]
+
+ cmd_args = nil
+ case Server::Application.config.crunch_job_wrapper
+ when :none
+ if @running.size > 0
+ # Don't run more than one at a time.
+ return
+ end
+ cmd_args = []
+ when :slurm_immediate
+ nodelist = nodes_available_for_job(job)
+ if nodelist.nil?
+ if Time.now < @node_wait_deadline
+ break
+ else
+ next
+ end
+ end
+ cmd_args = ["salloc",
+ "--chdir=/",
+ "--immediate",
+ "--exclusive",
+ "--no-kill",
+ "--job-name=#{job.uuid}",
+ "--nodelist=#{nodelist.join(',')}"]
+ else
+ raise "Unknown crunch_job_wrapper: #{Server::Application.config.crunch_job_wrapper}"
+ end
+
+ if Server::Application.config.crunch_job_user
+ cmd_args.unshift("sudo", "-E", "-u",
+ Server::Application.config.crunch_job_user,
+ "PATH=#{ENV['PATH']}",
+ "PERLLIB=#{ENV['PERLLIB']}",
+ "PYTHONPATH=#{ENV['PYTHONPATH']}",
+ "RUBYLIB=#{ENV['RUBYLIB']}",
+ "GEM_PATH=#{ENV['GEM_PATH']}")
+ end
+
+ ready = (get_authorization(job) and
+ get_commit(job.repository, job.script_version) and
+ tag_commit(job.script_version, job.uuid))
+ if ready and job.arvados_sdk_version
+ ready = (get_commit("arvados", job.arvados_sdk_version) and
+ tag_commit(job.arvados_sdk_version, "#{job.uuid}-arvados-sdk"))
+ end
+ next unless ready
+
+ cmd_args += [@crunch_job_bin,
+ '--job-api-token', @authorizations[job.uuid].api_token,
+ '--job', job.uuid,
+ '--git-dir', @arvados_internal]
+
+ $stderr.puts "dispatch: #{cmd_args.join ' '}"
+
+ begin
+ i, o, e, t = Open3.popen3(*cmd_args)
+ rescue
+ $stderr.puts "dispatch: popen3: #{$!}"
+ sleep 1
+ next
+ end
+
+ $stderr.puts "dispatch: job #{job.uuid}"
+ start_banner = "dispatch: child #{t.pid} start #{LogTime.now}"
+ $stderr.puts start_banner
+
+ @running[job.uuid] = {
+ stdin: i,
+ stdout: o,
+ stderr: e,
+ wait_thr: t,
+ job: job,
+ buf: {stderr: '', stdout: ''},
+ started: false,
+ sent_int: 0,
+ job_auth: @authorizations[job.uuid],
+ stderr_buf_to_flush: '',
+ stderr_flushed_at: Time.new(0),
+ bytes_logged: 0,
+ events_logged: 0,
+ log_throttle_is_open: true,
+ log_throttle_reset_time: Time.now + Rails.configuration.crunch_log_throttle_period,
+ log_throttle_bytes_so_far: 0,
+ log_throttle_lines_so_far: 0,
+ log_throttle_bytes_skipped: 0,
+ }
+ i.close
+ update_node_status
+ end
+ end
+
+ # Test for hard cap on total output and for log throttling. Returns whether
+ # the log line should go to output or not. Modifies "line" in place to
+ # replace it with an error if a logging limit is tripped.
+ def rate_limit running_job, line
+ message = false
+ linesize = line.size
+ if running_job[:log_throttle_is_open]
+ running_job[:log_throttle_lines_so_far] += 1
+ running_job[:log_throttle_bytes_so_far] += linesize
+ running_job[:bytes_logged] += linesize
+
+ if (running_job[:bytes_logged] >
+ Rails.configuration.crunch_limit_log_bytes_per_job)
+ message = "Exceeded log limit #{Rails.configuration.crunch_limit_log_bytes_per_job} bytes (crunch_limit_log_bytes_per_job). Log will be truncated."
+ running_job[:log_throttle_reset_time] = Time.now + 100.years
+ running_job[:log_throttle_is_open] = false
+
+ elsif (running_job[:log_throttle_bytes_so_far] >
+ Rails.configuration.crunch_log_throttle_bytes)
+ remaining_time = running_job[:log_throttle_reset_time] - Time.now
+ message = "Exceeded rate #{Rails.configuration.crunch_log_throttle_bytes} bytes per #{Rails.configuration.crunch_log_throttle_period} seconds (crunch_log_throttle_bytes). Logging will be silenced for the next #{remaining_time.round} seconds.\n"
+ running_job[:log_throttle_is_open] = false
+
+ elsif (running_job[:log_throttle_lines_so_far] >
+ Rails.configuration.crunch_log_throttle_lines)
+ remaining_time = running_job[:log_throttle_reset_time] - Time.now
+ message = "Exceeded rate #{Rails.configuration.crunch_log_throttle_lines} lines per #{Rails.configuration.crunch_log_throttle_period} seconds (crunch_log_throttle_lines), logging will be silenced for the next #{remaining_time.round} seconds.\n"
+ running_job[:log_throttle_is_open] = false
+ end
+ end
+
+ if not running_job[:log_throttle_is_open]
+ # Don't log anything if any limit has been exceeded. Just count lossage.
+ running_job[:log_throttle_bytes_skipped] += linesize
+ end
+
+ if message
+ # Yes, write to logs, but use our "rate exceeded" message
+ # instead of the log message that exceeded the limit.
+ line.replace message
+ true
+ else
+ running_job[:log_throttle_is_open]
+ end
+ end
+
+ def read_pipes
+ @running.each do |job_uuid, j|
+ job = j[:job]
+
+ now = Time.now
+ if now > j[:log_throttle_reset_time]
+ # It has been more than throttle_period seconds since the last
+ # checkpoint so reset the throttle
+ if j[:log_throttle_bytes_skipped] > 0
+ message = "#{job_uuid} ! Skipped #{j[:log_throttle_bytes_skipped]} bytes of log"
+ $stderr.puts message
+ j[:stderr_buf_to_flush] << "#{LogTime.now} #{message}\n"
+ end
+
+ j[:log_throttle_reset_time] = now + Rails.configuration.crunch_log_throttle_period
+ j[:log_throttle_bytes_so_far] = 0
+ j[:log_throttle_lines_so_far] = 0
+ j[:log_throttle_bytes_skipped] = 0
+ j[:log_throttle_is_open] = true
+ end
+
+ j[:buf].each do |stream, streambuf|
+ # Read some data from the child stream
+ buf = ''
+ begin
+ # It's important to use a big enough buffer here. When we're
+ # being flooded with logs, we must read and discard many
+ # bytes at once. Otherwise, we can easily peg a CPU with
+ # time-checking and other loop overhead. (Quick tests show a
+ # 1MiB buffer working 2.5x as fast as a 64 KiB buffer.)
+ #
+ # So don't reduce this buffer size!
+ buf = j[stream].read_nonblock(2**20)
+ rescue Errno::EAGAIN, EOFError
+ end
+
+ # Short circuit the counting code if we're just going to throw
+ # away the data anyway.
+ if not j[:log_throttle_is_open]
+ j[:log_throttle_bytes_skipped] += streambuf.size + buf.size
+ streambuf.replace ''
+ next
+ elsif buf == ''
+ next
+ end
+
+ # Append to incomplete line from previous read, if any
+ streambuf << buf
+
+ bufend = ''
+ streambuf.each_line do |line|
+ if not line.end_with? $/
+ if line.size > Rails.configuration.crunch_log_throttle_bytes
+ # Without a limit here, we'll use 2x an arbitrary amount
+ # of memory, and waste a lot of time copying strings
+ # around, all without providing any feedback to anyone
+ # about what's going on _or_ hitting any of our throttle
+ # limits.
+ #
+ # Here we leave "line" alone, knowing it will never be
+ # sent anywhere: rate_limit() will reach
+ # crunch_log_throttle_bytes immediately. However, we'll
+ # leave [...] in bufend: if the trailing end of the long
+ # line does end up getting sent anywhere, it will have
+ # some indication that it is incomplete.
+ bufend = "[...]"
+ else
+ # If line length is sane, we'll wait for the rest of the
+ # line to appear in the next read_pipes() call.
+ bufend = line
+ break
+ end
+ end
+ # rate_limit returns true or false as to whether to actually log
+ # the line or not. It also modifies "line" in place to replace
+ # it with an error if a logging limit is tripped.
+ if rate_limit j, line
+ $stderr.print "#{job_uuid} ! " unless line.index(job_uuid)
+ $stderr.puts line
+ pub_msg = "#{LogTime.now} #{line.strip}\n"
+ j[:stderr_buf_to_flush] << pub_msg
+ end
+ end
+
+ # Leave the trailing incomplete line (if any) in streambuf for
+ # next time.
+ streambuf.replace bufend
+ end
+ # Flush buffered logs to the logs table, if appropriate. We have
+ # to do this even if we didn't collect any new logs this time:
+ # otherwise, buffered data older than seconds_between_events
+ # won't get flushed until new data arrives.
+ write_log j
+ end
+ end
+
+ def reap_children
+ return if 0 == @running.size
+ pid_done = nil
+ j_done = nil
+
+ if false
+ begin
+ pid_done = waitpid(-1, Process::WNOHANG | Process::WUNTRACED)
+ if pid_done
+ j_done = @running.values.
+ select { |j| j[:wait_thr].pid == pid_done }.
+ first
+ end
+ rescue SystemCallError
+ # I have @running processes but system reports I have no
+ # children. This is likely to happen repeatedly if it happens at
+ # all; I will log this no more than once per child process I
+ # start.
+ if 0 < @running.select { |uuid,j| j[:warned_waitpid_error].nil? }.size
+ children = @running.values.collect { |j| j[:wait_thr].pid }.join ' '
+ $stderr.puts "dispatch: IPC bug: waitpid() error (#{$!}), but I have children #{children}"
+ end
+ @running.each do |uuid,j| j[:warned_waitpid_error] = true end
+ end
+ else
+ @running.each do |uuid, j|
+ if j[:wait_thr].status == false
+ pid_done = j[:wait_thr].pid
+ j_done = j
+ end
+ end
+ end
+
+ return if !pid_done
+
+ job_done = j_done[:job]
+ $stderr.puts "dispatch: child #{pid_done} exit"
+ $stderr.puts "dispatch: job #{job_done.uuid} end"
+
+ # Ensure every last drop of stdout and stderr is consumed.
+ read_pipes
+ # Reset flush timestamp to make sure log gets written.
+ j_done[:stderr_flushed_at] = Time.new(0)
+ # Write any remaining logs.
+ write_log j_done
+
+ j_done[:buf].each do |stream, streambuf|
+ if streambuf != ''
+ $stderr.puts streambuf + "\n"
+ end
+ end
+
+ # Wait the thread (returns a Process::Status)
+ exit_status = j_done[:wait_thr].value.exitstatus
+
+ jobrecord = Job.find_by_uuid(job_done.uuid)
+ if exit_status != 75 and jobrecord.state == "Running"
+ # crunch-job did not return exit code 75 (see below) and left the job in
+ # the "Running" state, which means there was an unhandled error. Fail
+ # the job.
+ jobrecord.state = "Failed"
+ if not jobrecord.save
+ $stderr.puts "dispatch: jobrecord.save failed"
+ end
+ else
+ # Don't fail the job if crunch-job didn't even get as far as
+ # starting it. If the job failed to run due to an infrastructure
+ # issue with crunch-job or slurm, we want the job to stay in the
+ # queue. If crunch-job exited after losing a race to another
+ # crunch-job process, it exits 75 and we should leave the job
+ # record alone so the winner of the race do its thing.
+ #
+ # There is still an unhandled race condition: If our crunch-job
+ # process is about to lose a race with another crunch-job
+ # process, but crashes before getting to its "exit 75" (for
+ # example, "cannot fork" or "cannot reach API server") then we
+ # will assume incorrectly that it's our process's fault
+ # jobrecord.started_at is non-nil, and mark the job as failed
+ # even though the winner of the race is probably still doing
+ # fine.
+ end
+
+ # Invalidate the per-job auth token, unless the job is still queued and we
+ # might want to try it again.
+ if jobrecord.state != "Queued"
+ j_done[:job_auth].update_attributes expires_at: Time.now
+ end
+
+ @running.delete job_done.uuid
+ end
+
+ def update_pipelines
+ expire_tokens = @pipe_auth_tokens.dup
+ @todo_pipelines.each do |p|
+ pipe_auth = (@pipe_auth_tokens[p.uuid] ||= ApiClientAuthorization.
+ create(user: User.where('uuid=?', p.modified_by_user_uuid).first,
+ api_client_id: 0))
+ puts `export ARVADOS_API_TOKEN=#{pipe_auth.api_token} && arv-run-pipeline-instance --run-pipeline-here --no-wait --instance #{p.uuid}`
+ expire_tokens.delete p.uuid
+ end
+
+ expire_tokens.each do |k, v|
+ v.update_attributes expires_at: Time.now
+ @pipe_auth_tokens.delete k
+ end
+ end
+
+ def run
+ act_as_system_user
+ $stderr.puts "dispatch: ready"
+ while !$signal[:term] or @running.size > 0
+ read_pipes
+ if $signal[:term]
+ @running.each do |uuid, j|
+ if !j[:started] and j[:sent_int] < 2
+ begin
+ Process.kill 'INT', j[:wait_thr].pid
+ rescue Errno::ESRCH
+ # No such pid = race condition + desired result is
+ # already achieved
+ end
+ j[:sent_int] += 1
+ end
+ end
+ else
+ refresh_todo unless did_recently(:refresh_todo, 1.0)
+ update_node_status unless did_recently(:update_node_status, 1.0)
+ unless @todo.empty? or did_recently(:start_jobs, 1.0) or $signal[:term]
+ start_jobs
+ end
+ unless (@todo_pipelines.empty? and @pipe_auth_tokens.empty?) or did_recently(:update_pipelines, 5.0)
+ update_pipelines
+ end
+ end
+ reap_children
+ select(@running.values.collect { |j| [j[:stdout], j[:stderr]] }.flatten,
+ [], [], 1)
+ end
+ end
+
+ protected
+
+ def did_recently(thing, min_interval)
+ if !@did_recently[thing] or @did_recently[thing] < Time.now - min_interval
+ @did_recently[thing] = Time.now
+ false
+ else
+ true
+ end
+ end
+
+ # send message to log table. we want these records to be transient
+ def write_log running_job
+ return if running_job[:stderr_buf_to_flush] == ''
+
+ # Send out to log event if buffer size exceeds the bytes per event or if
+ # it has been at least crunch_log_seconds_between_events seconds since
+ # the last flush.
+ if running_job[:stderr_buf_to_flush].size > Rails.configuration.crunch_log_bytes_per_event or
+ (Time.now - running_job[:stderr_flushed_at]) >= Rails.configuration.crunch_log_seconds_between_events
+ begin
+ log = Log.new(object_uuid: running_job[:job].uuid,
+ event_type: 'stderr',
+ owner_uuid: running_job[:job].owner_uuid,
+ properties: {"text" => running_job[:stderr_buf_to_flush]})
+ log.save!
+ running_job[:events_logged] += 1
+ rescue => exception
+ $stderr.puts "Failed to write logs"
+ $stderr.puts exception.backtrace
+ end
+ running_job[:stderr_buf_to_flush] = ''
+ running_job[:stderr_flushed_at] = Time.now
+ end
+ end
+end
+
+# This is how crunch-job child procs know where the "refresh" trigger file is
+ENV["CRUNCH_REFRESH_TRIGGER"] = Rails.configuration.crunch_refresh_trigger
+
+Dispatcher.new.run
--- /dev/null
+#! /usr/bin/env python
+
+import argparse
+import datetime
+import json
+import re
+import sys
+
+import arvados
+
+# Useful configuration variables:
+
+# Number of log lines to use as context in diagnosing failure.
+LOG_CONTEXT_LINES = 10
+
+# Regex that signifies a failed task.
+FAILED_TASK_REGEX = re.compile(' \d+ failure (.*permanent)')
+
+# Regular expressions used to classify failure types.
+JOB_FAILURE_TYPES = {
+ 'sys/docker': 'Cannot destroy container',
+ 'crunch/node': 'User not found on host',
+ 'slurm/comm': 'Communication connection failure'
+}
+
+def parse_arguments(arguments):
+ arg_parser = argparse.ArgumentParser(
+ description='Produce a report of Crunch failures within a specified time range')
+
+ arg_parser.add_argument(
+ '--start',
+ help='Start date and time')
+ arg_parser.add_argument(
+ '--end',
+ help='End date and time')
+
+ args = arg_parser.parse_args(arguments)
+
+ if args.start and not is_valid_timestamp(args.start):
+ raise ValueError(args.start)
+ if args.end and not is_valid_timestamp(args.end):
+ raise ValueError(args.end)
+
+ return args
+
+
+def api_timestamp(when=None):
+ """Returns a string representing the timestamp 'when' in a format
+ suitable for delivering to the API server. Defaults to the
+ current time.
+ """
+ if when is None:
+ when = datetime.datetime.utcnow()
+ return when.strftime("%Y-%m-%dT%H:%M:%SZ")
+
+
+def is_valid_timestamp(ts):
+ return re.match(r'\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}Z', ts)
+
+
+def jobs_created_between_dates(api, start, end):
+ return arvados.util.list_all(
+ api.jobs().list,
+ filters=json.dumps([ ['created_at', '>=', start],
+ ['created_at', '<=', end] ]))
+
+
+def job_logs(api, job):
+ # Returns the contents of the log for this job (as an array of lines).
+ if job['log']:
+ log_collection = arvados.CollectionReader(job['log'], api)
+ log_filename = "{}.log.txt".format(job['uuid'])
+ return log_collection.open(log_filename).readlines()
+ return []
+
+
+user_names = {}
+def job_user_name(api, user_uuid):
+ def _lookup_user_name(api, user_uuid):
+ try:
+ return api.users().get(uuid=user_uuid).execute()['full_name']
+ except arvados.errors.ApiError:
+ return user_uuid
+
+ if user_uuid not in user_names:
+ user_names[user_uuid] = _lookup_user_name(api, user_uuid)
+ return user_names[user_uuid]
+
+
+job_pipeline_names = {}
+def job_pipeline_name(api, job_uuid):
+ def _lookup_pipeline_name(api, job_uuid):
+ try:
+ pipelines = api.pipeline_instances().list(
+ filters='[["components", "like", "%{}%"]]'.format(job_uuid)).execute()
+ pi = pipelines['items'][0]
+ if pi['name']:
+ return pi['name']
+ else:
+ # Use the pipeline template name
+ pt = api.pipeline_templates().get(uuid=pi['pipeline_template_uuid']).execute()
+ return pt['name']
+ except (TypeError, ValueError, IndexError):
+ return ""
+
+ if job_uuid not in job_pipeline_names:
+ job_pipeline_names[job_uuid] = _lookup_pipeline_name(api, job_uuid)
+ return job_pipeline_names[job_uuid]
+
+
+def is_failed_task(logline):
+ return FAILED_TASK_REGEX.search(logline) != None
+
+
+def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
+ args = parse_arguments(arguments)
+
+ api = arvados.api('v1')
+
+ now = datetime.datetime.utcnow()
+ start_time = args.start or api_timestamp(now - datetime.timedelta(days=1))
+ end_time = args.end or api_timestamp(now)
+
+ # Find all jobs created within the specified window,
+ # and their corresponding job logs.
+ jobs_created = jobs_created_between_dates(api, start_time, end_time)
+ jobs_by_state = {}
+ for job in jobs_created:
+ jobs_by_state.setdefault(job['state'], [])
+ jobs_by_state[job['state']].append(job)
+
+ # Find failed jobs and record the job failure text.
+
+ # failure_stats maps failure types (e.g. "sys/docker") to
+ # a set of job UUIDs that failed for that reason.
+ failure_stats = {}
+ for job in jobs_by_state['Failed']:
+ job_uuid = job['uuid']
+ logs = job_logs(api, job)
+ # Find the first permanent task failure, and collect the
+ # preceding log lines.
+ failure_type = None
+ for i, lg in enumerate(logs):
+ if is_failed_task(lg):
+ # Get preceding log record to provide context.
+ log_start = i - LOG_CONTEXT_LINES if i >= LOG_CONTEXT_LINES else 0
+ log_end = i + 1
+ lastlogs = ''.join(logs[log_start:log_end])
+ # try to identify the type of failure.
+ for key, rgx in JOB_FAILURE_TYPES.iteritems():
+ if re.search(rgx, lastlogs):
+ failure_type = key
+ break
+ if failure_type is not None:
+ break
+ if failure_type is None:
+ failure_type = 'unknown'
+ failure_stats.setdefault(failure_type, set())
+ failure_stats[failure_type].add(job_uuid)
+
+ # Report percentages of successful, failed and unfinished jobs.
+ print "Start: {:20s}".format(start_time)
+ print "End: {:20s}".format(end_time)
+ print ""
+
+ print "Overview"
+ print ""
+
+ job_start_count = len(jobs_created)
+ print " {: <25s} {:4d}".format('Started', job_start_count)
+ for state in ['Complete', 'Failed', 'Queued', 'Cancelled', 'Running']:
+ if state in jobs_by_state:
+ job_count = len(jobs_by_state[state])
+ job_percentage = job_count / float(job_start_count)
+ print " {: <25s} {:4d} ({: >4.0%})".format(state,
+ job_count,
+ job_percentage)
+ print ""
+
+ # Report failure types.
+ failure_summary = ""
+ failure_detail = ""
+
+ # Generate a mapping from failed job uuids to job records, to assist
+ # in generating detailed statistics for job failures.
+ jobs_failed_map = { job['uuid']: job for job in jobs_by_state.get('Failed', []) }
+
+ # sort the failure stats in descending order by occurrence.
+ sorted_failures = sorted(failure_stats,
+ reverse=True,
+ key=lambda failure_type: len(failure_stats[failure_type]))
+ for failtype in sorted_failures:
+ job_uuids = failure_stats[failtype]
+ failstat = " {: <25s} {:4d} ({: >4.0%})\n".format(
+ failtype,
+ len(job_uuids),
+ len(job_uuids) / float(len(jobs_by_state['Failed'])))
+ failure_summary = failure_summary + failstat
+ failure_detail = failure_detail + failstat
+ for j in job_uuids:
+ job_info = jobs_failed_map[j]
+ job_owner = job_user_name(api, job_info['modified_by_user_uuid'])
+ job_name = job_pipeline_name(api, job_info['uuid'])
+ failure_detail = failure_detail + " {} {: <15.15s} {:29.29s}\n".format(j, job_owner, job_name)
+ failure_detail = failure_detail + "\n"
+
+ print "Failures by class"
+ print ""
+ print failure_summary
+
+ print "Failures by class (detail)"
+ print ""
+ print failure_detail
+
+ return 0
+
+
+if __name__ == "__main__":
+ sys.exit(main())
--- /dev/null
+#!/usr/bin/env ruby
+
+# Get or Create an anonymous user token.
+# If get option is used, an existing anonymous user token is returned. If none exist, one is created.
+# If the get option is omitted, a new token is created and returned.
+
+require 'trollop'
+
+opts = Trollop::options do
+ banner ''
+ banner "Usage: get_anonymous_user_token "
+ banner ''
+ opt :get, <<-eos
+Get an existing anonymous user token. If no such token exists \
+or if this option is omitted, a new token is created and returned.
+ eos
+end
+
+get_existing = opts[:get]
+
+require File.dirname(__FILE__) + '/../config/environment'
+
+include ApplicationHelper
+act_as_system_user
+
+def create_api_client_auth
+ api_client_auth = ApiClientAuthorization.
+ new(user: anonymous_user,
+ api_client_id: 0,
+ expires_at: Time.now + 100.years,
+ scopes: ['GET /'])
+ api_client_auth.save!
+ api_client_auth.reload
+end
+
+if get_existing
+ api_client_auth = ApiClientAuthorization.
+ where('user_id=?', anonymous_user.id.to_i).
+ where('expires_at>?', Time.now).
+ select { |auth| auth.scopes == ['GET /'] }.
+ first
+end
+
+# either not a get or no api_client_auth was found
+if !api_client_auth
+ api_client_auth = create_api_client_auth
+end
+
+# print it to the console
+puts api_client_auth.api_token
--- /dev/null
+#!/usr/bin/env ruby
+# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
+
+
+##### SSL - ward, 2012-10-15
+require 'rubygems'
+require 'rails/commands/server'
+require 'rack'
+require 'webrick'
+require 'webrick/https'
+
+module Rails
+ class Server < ::Rack::Server
+ def default_options
+ super.merge({
+ :Port => 3030,
+ :environment => (ENV['RAILS_ENV'] || "development").dup,
+ :daemonize => false,
+ :debugger => false,
+ :pid => File.expand_path("tmp/pids/server.pid"),
+ :config => File.expand_path("config.ru"),
+ :SSLEnable => true,
+ :SSLVerifyClient => OpenSSL::SSL::VERIFY_NONE,
+ :SSLCertName => [["CN", "#{WEBrick::Utils::getservername} #{Time.now().to_s}"]]
+ })
+ end
+ end
+end
+######### /SSL
+
+
+APP_PATH = File.expand_path('../../config/application', __FILE__)
+require File.expand_path('../../config/boot', __FILE__)
+require 'rails/commands'
--- /dev/null
+#! /bin/sh
+
+# This script invokes `rake test' in a fresh Docker instance of the
+# API server, e.g.:
+# docker run -t -i arvados/api /usr/src/arvados/services/api/script/rake_test.sh
+
+/etc/init.d/postgresql start
+
+export RAILS_ENV=test
+cd /usr/src/arvados/services/api
+cp config/environments/test.rb.example config/environments/test.rb
+bundle exec rake db:setup
+bundle exec rake test
--- /dev/null
+#!/usr/bin/env bash
+
+# usage:
+# "restart-dns-server <path-to-restart.txt>" (restart now if needed)
+# or
+# "restart-dns-server <path-to-restart.txt> -d" (wait for restart to be needed, restart, repeat)
+
+RESTART_TXT_PATH=$1
+
+if [[ "$RESTART_TXT_PATH" == "" ]]; then
+ echo
+ echo "Usage: "
+ echo " $0 <path-to-restart.txt> # restart now if needed"
+ echo " $0 <path-to-restart.txt> -d # wait for restart to be needed, restart, repeat"
+ echo
+ exit 1
+fi
+
+while :
+do
+ if [ -e $RESTART_TXT_PATH ]; then
+ RESTART_COMMAND=`cat $RESTART_TXT_PATH`
+ echo "restart command: $RESTART_COMMAND"
+ rm -f "$RESTART_TXT_PATH"
+ echo restarting
+ $RESTART_COMMAND
+ fi
+ if [ "-d" = "$2" ]
+ then
+ sleep 2
+ else
+ exit 0
+ fi
+done
--- /dev/null
+#!/usr/bin/env ruby
+
+abort 'Error: Ruby >= 1.9.3 required.' if RUBY_VERSION < '1.9.3'
+
+require 'logger'
+require 'trollop'
+
+log = Logger.new STDERR
+log.progname = $0.split('/').last
+
+opts = Trollop::options do
+ banner ''
+ banner "Usage: #{log.progname} " +
+ "{user_uuid_or_email} {user_and_repo_name} {vm_uuid}"
+ banner ''
+ opt :debug, <<-eos
+Show debug messages.
+ eos
+ opt :openid_prefix, <<-eos, default: 'https://www.google.com/accounts/o8/id'
+If creating a new user record, require authentication from an OpenID \
+with this OpenID prefix *and* a matching email address in order to \
+claim the account.
+ eos
+ opt :send_notification_email, <<-eos, default: 'true'
+Send notification email after successfully setting up the user.
+ eos
+end
+
+log.level = (ENV['DEBUG'] || opts.debug) ? Logger::DEBUG : Logger::WARN
+
+if ARGV.count != 3
+ Trollop::die "required arguments are missing"
+end
+
+user_arg, user_repo_name, vm_uuid = ARGV
+
+require 'arvados'
+arv = Arvados.new(api_version: 'v1')
+
+# Look up the given user by uuid or, failing that, email address.
+begin
+ found_user = arv.user.get(uuid: user_arg)
+rescue Arvados::TransactionFailedError
+ found = arv.user.list(where: {email: user_arg})[:items]
+
+ if found.count == 0
+ if !user_arg.match(/\w\@\w+\.\w+/)
+ abort "About to create new user, but #{user_arg.inspect} " +
+ "does not look like an email address. Stop."
+ end
+ elsif found.count != 1
+ abort "Found #{found.count} users with email. Stop."
+ else
+ found_user = found.first
+ end
+end
+
+# Invoke user setup method
+if (found_user)
+ user = arv.user.setup uuid: found_user[:uuid], repo_name: user_repo_name,
+ vm_uuid: vm_uuid, openid_prefix: opts.openid_prefix,
+ send_notification_email: opts.send_notification_email
+else
+ user = arv.user.setup user: {email: user_arg}, repo_name: user_repo_name,
+ vm_uuid: vm_uuid, openid_prefix: opts.openid_prefix,
+ send_notification_email: opts.send_notification_email
+end
+
+log.info {"user uuid: " + user[:uuid]}
+
+puts user.inspect
--- /dev/null
+FactoryGirl.define do
+ factory :api_client do
+ is_trusted false
+ to_create do |instance|
+ act_as_system_user do
+ instance.save!
+ end
+ end
+ end
+end
--- /dev/null
+FactoryGirl.define do
+ factory :api_client_authorization do
+ api_client
+ scopes ['all']
+
+ trait :trusted do
+ association :api_client, factory: :api_client, is_trusted: true
+ end
+ factory :token do
+ # Just provides shorthand for "create :api_client_authorization"
+ end
+
+ to_create do |instance|
+ act_as_user instance.user do
+ instance.save!
+ end
+ end
+ end
+end
--- /dev/null
+FactoryGirl.define do
+ factory :group do
+ end
+end
--- /dev/null
+FactoryGirl.define do
+ factory :link do
+ factory :permission_link do
+ link_class 'permission'
+ end
+ end
+end
--- /dev/null
+include CurrentApiClient
+
+FactoryGirl.define do
+ factory :user do
+ ignore do
+ join_groups []
+ end
+ after :create do |user, evaluator|
+ act_as_system_user do
+ evaluator.join_groups.each do |g|
+ Link.create!(tail_uuid: user.uuid,
+ head_uuid: g.uuid,
+ link_class: 'permission',
+ name: 'can_read')
+ Link.create!(tail_uuid: g.uuid,
+ head_uuid: user.uuid,
+ link_class: 'permission',
+ name: 'can_read')
+ end
+ end
+ end
+ first_name "Factory"
+ last_name "Factory"
+ identity_url do
+ "https://example.com/#{rand(2**24).to_s(36)}"
+ end
+ factory :active_user do
+ is_active true
+ after :create do |user|
+ act_as_system_user do
+ Link.create!(tail_uuid: user.uuid,
+ head_uuid: Group.where('uuid ~ ?', '-f+$').first.uuid,
+ link_class: 'permission',
+ name: 'can_read')
+ end
+ end
+ end
+ to_create do |instance|
+ act_as_system_user do
+ instance.save!
+ end
+ end
+ end
+end
--- /dev/null
+# Read about fixtures at http://api.rubyonrails.org/classes/ActiveRecord/Fixtures.html
+
+admin:
+ api_client: untrusted
+ user: admin
+ api_token: 4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h
+ expires_at: 2038-01-01 00:00:00
+
+admin_trustedclient:
+ api_client: trusted_workbench
+ user: admin
+ api_token: 1a9ffdcga2o7cw8q12dndskomgs1ygli3ns9k2o9hgzgmktc78
+ expires_at: 2038-01-01 00:00:00
+
+miniadmin:
+ api_client: untrusted
+ user: miniadmin
+ api_token: 2zb2y9pw3e70270te7oe3ewaantea3adyxjascvkz0zob7q7xb
+ expires_at: 2038-01-01 00:00:00
+
+rominiadmin:
+ api_client: untrusted
+ user: rominiadmin
+ api_token: 5tsb2pc3zlatn1ortl98s2tqsehpby88wmmnzmpsjmzwa6payh
+ expires_at: 2038-01-01 00:00:00
+
+active:
+ api_client: untrusted
+ user: active
+ api_token: 3kg6k6lzmp9kj5cpkcoxie963cmvjahbt2fod9zru30k1jqdmi
+ expires_at: 2038-01-01 00:00:00
+
+active_trustedclient:
+ api_client: trusted_workbench
+ user: active
+ api_token: 27bnddk6x2nmq00a1e3gq43n9tsl5v87a3faqar2ijj8tud5en
+ expires_at: 2038-01-01 00:00:00
+
+active_noscope:
+ api_client: untrusted
+ user: active
+ api_token: activenoscopeabcdefghijklmnopqrstuvwxyz12345678901
+ expires_at: 2038-01-01 00:00:00
+ scopes: []
+
+project_viewer:
+ api_client: untrusted
+ user: project_viewer
+ api_token: projectviewertoken1234567890abcdefghijklmnopqrstuv
+ expires_at: 2038-01-01 00:00:00
+
+project_viewer_trustedclient:
+ api_client: trusted_workbench
+ user: project_viewer
+ api_token: projectviewertrustedtoken1234567890abcdefghijklmno
+ expires_at: 2038-01-01 00:00:00
+
+subproject_admin:
+ api_client: untrusted
+ user: subproject_admin
+ api_token: subprojectadmintoken1234567890abcdefghijklmnopqrst
+ expires_at: 2038-01-01 00:00:00
+
+admin_vm:
+ api_client: untrusted
+ user: admin
+ api_token: adminvirtualmachineabcdefghijklmnopqrstuvwxyz12345
+ expires_at: 2038-01-01 00:00:00
+ # scope refers to the testvm fixture.
+ scopes: ["GET /arvados/v1/virtual_machines/zzzzz-2x53u-382brsig8rp3064/logins"]
+
+admin_noscope:
+ api_client: untrusted
+ user: admin
+ api_token: adminnoscopeabcdefghijklmnopqrstuvwxyz123456789012
+ expires_at: 2038-01-01 00:00:00
+ scopes: []
+
+active_all_collections:
+ api_client: untrusted
+ user: active
+ api_token: activecollectionsabcdefghijklmnopqrstuvwxyz1234567
+ expires_at: 2038-01-01 00:00:00
+ scopes: ["GET /arvados/v1/collections/", "GET /arvados/v1/keep_disks"]
+
+active_userlist:
+ api_client: untrusted
+ user: active
+ api_token: activeuserlistabcdefghijklmnopqrstuvwxyz1234568900
+ expires_at: 2038-01-01 00:00:00
+ scopes: ["GET /arvados/v1/users"]
+
+active_specimens:
+ api_client: untrusted
+ user: active
+ api_token: activespecimensabcdefghijklmnopqrstuvwxyz123456890
+ expires_at: 2038-01-01 00:00:00
+ scopes: ["GET /arvados/v1/specimens/"]
+
+active_apitokens:
+ api_client: trusted_workbench
+ user: active
+ api_token: activeapitokensabcdefghijklmnopqrstuvwxyz123456789
+ expires_at: 2038-01-01 00:00:00
+ scopes: ["GET /arvados/v1/api_client_authorizations",
+ "POST /arvados/v1/api_client_authorizations"]
+
+active_readonly:
+ api_client: untrusted
+ user: active
+ api_token: activereadonlyabcdefghijklmnopqrstuvwxyz1234568790
+ expires_at: 2038-01-01 00:00:00
+ scopes: ["GET /"]
+
+spectator:
+ api_client: untrusted
+ user: spectator
+ api_token: zw2f4gwx8hw8cjre7yp6v1zylhrhn3m5gvjq73rtpwhmknrybu
+ expires_at: 2038-01-01 00:00:00
+
+spectator_specimens:
+ api_client: untrusted
+ user: spectator
+ api_token: spectatorspecimensabcdefghijklmnopqrstuvwxyz123245
+ expires_at: 2038-01-01 00:00:00
+ scopes: ["GET /arvados/v1/specimens", "GET /arvados/v1/specimens/",
+ "POST /arvados/v1/specimens"]
+
+inactive:
+ api_client: untrusted
+ user: inactive
+ api_token: 5s29oj2hzmcmpq80hx9cta0rl5wuf3xfd6r7disusaptz7h9m0
+ expires_at: 2038-01-01 00:00:00
+
+inactive_uninvited:
+ api_client: untrusted
+ user: inactive_uninvited
+ api_token: 62mhllc0otp78v08e3rpa3nsmf8q8ogk47f7u5z4erp5gpj9al
+ expires_at: 2038-01-01 00:00:00
+
+inactive_but_signed_user_agreement:
+ api_client: untrusted
+ user: inactive_but_signed_user_agreement
+ api_token: 64k3bzw37iwpdlexczj02rw3m333rrb8ydvn2qq99ohv68so5k
+ expires_at: 2038-01-01 00:00:00
+
+expired:
+ api_client: untrusted
+ user: active
+ api_token: 2ym314ysp27sk7h943q6vtc378srb06se3pq6ghurylyf3pdmx
+ expires_at: 1970-01-01 00:00:00
+
+expired_trustedclient:
+ api_client: trusted_workbench
+ user: active
+ api_token: 5hpni7izokzcatku2896xxwqdbt5ptomn04r6auc7fohnli82v
+ expires_at: 1970-01-01 00:00:00
+
+valid_token_deleted_user:
+ api_client: trusted_workbench
+ user_id: 1234567
+ api_token: tewfa58099sndckyqhlgd37za6e47o6h03r9l1vpll23hudm8b
+ expires_at: 2038-01-01 00:00:00
+
+anonymous:
+ api_client: untrusted
+ user: anonymous
+ api_token: 4kg6k6lzmp9kj4cpkcoxie964cmvjahbt4fod9zru44k4jqdmi
+ expires_at: 2038-01-01 00:00:00
+ scopes: ["GET /"]
+
+job_reader:
+ api_client: untrusted
+ user: job_reader
+ api_token: e99512cdc0f3415c2428b9758f33bdfb07bc3561b00e86e7e6
+ expires_at: 2038-01-01 00:00:00
+
+active_no_prefs:
+ api_client: untrusted
+ user: active_no_prefs
+ api_token: 3kg612cdc0f3415c2428b9758f33bdfb07bc3561b00e86qdmi
+ expires_at: 2038-01-01 00:00:00
+
+active_no_prefs_profile:
+ api_client: untrusted
+ user: active_no_prefs_profile
+ api_token: 3kg612cdc0f3415c242856758f33bdfb07bc3561b00e86qdmi
+ expires_at: 2038-01-01 00:00:00
+
+user_foo_in_sharing_group:
+ api_client: untrusted
+ user: user_foo_in_sharing_group
+ api_token: 2p1pou8p4ls208mcbedeewlotghppenobcyrmyhq8pyf51xd8u
+ expires_at: 2038-01-01 00:00:00
+
+user1_with_load:
+ api_client: untrusted
+ user: user1_with_load
+ api_token: 1234k6lzmp9kj5cpkcoxie963cmvjahbt2fod9zru30k1jqdmi
+ expires_at: 2038-01-01 00:00:00
+
+fuse:
+ api_client: untrusted
+ user: fuse
+ api_token: 4nagbkv8eap0uok7pxm72nossq5asihls3yn5p4xmvqx5t5e7p
+ expires_at: 2038-01-01 00:00:00
+
--- /dev/null
+# Read about fixtures at http://api.rubyonrails.org/classes/ActiveRecord/Fixtures.html
+
+trusted_workbench:
+ uuid: zzzzz-ozdt8-teyxzyd8qllg11h
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: Official Workbench
+ url_prefix: https://official-workbench.local/
+ is_trusted: true
+
+untrusted:
+ uuid: zzzzz-ozdt8-obw7foaks3qjyej
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: Untrusted
+ url_prefix: https://untrusted.local/
+ is_trusted: false
--- /dev/null
+active:
+ uuid: zzzzz-fngyi-12nc9ov4osp8nae
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ authorized_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ key_type: SSH
+ name: active
+ public_key: ssh-rsa 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 active-user@arvados.local
+
+admin:
+ uuid: zzzzz-fngyi-g290j3i3u701duh
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ authorized_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ key_type: SSH
+ name: admin
+ public_key: ssh-dss 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
+
+spectator:
+ uuid: zzzzz-fngyi-3uze1ipbnz2c2c2
+ owner_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ authorized_user_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ key_type: SSH
+ name: spectator
+ public_key: ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDJK4hxmgXzg1gty+91JfkpgikAZxTvFTQoaFUJYTHIygz2V3FgU64NkK3yfwh+bhs7n8YIMftuCHfojKEJTtedbiv/mYpItetzdOwYONCGSEk1VnfipGhnFvL7FZDESTxLN9KNve3ZmZh8HvO6s8fdlTlqTTNKpsdwLiQn2s3W1TWvru/NP504MD5qPeZ4+8jZEh/uiuRaeXqPDAlE9QGPV4FRAA1xo0dBZIrRMwQC8kOttq/i2pLgHq1xW9p4J23oV68O/kkeBb7VwrX3Av/M61kvRsP8tA5gqh+HMKVO2qTP4yG6eGkAobIokQAcyZetPQIDmfVeoB0NzwPfAy4r
+
+project_viewer:
+ uuid: zzzzz-fngyi-5d3av1396niwcej
+ owner_uuid: zzzzz-tpzed-projectviewer1a
+ authorized_user_uuid: zzzzz-tpzed-projectviewer1a
+ key_type: SSH
+ name: project_viewer
+ public_key: ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDPkOJMQzT9n6RousrLMU7c/KFKTI7I5JifDIEtGJJ1MMZW0GVoxtXALU90HcaRjEOwGPvQPxj7IDYqXs2N9uvm8SUWJMiz6c8NIjhGTkUoOnTFl4E9YTvkkKNs0P+3eT1Y+6zfTcFJHKP3AR4kZX+oiPHowRpCIlnLjXCFxX+E+YI554A7bS4yfOZO9lf6vtiT9I+6EqxC8a0hzZauPC1ZC3d/AFgBnrXJ2fBlAEySznru39quHN1u3v4qHTyaO2pDbG6vdI6O3JDCXCJKRv/B2FLuLTlzB0YesM1FiE6w8QgPxqb42B+uWTZb969UZliH8Pzw/mscOLAjmARDC02z
--- /dev/null
+user_agreement:
+ uuid: zzzzz-4zz18-t68oksiu9m80s4y
+ portable_data_hash: b519d9cb706a29fc7ea24dbea2f05851+93
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2013-12-26T19:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2013-12-26T19:22:54Z
+ updated_at: 2013-12-26T19:22:54Z
+ manifest_text: ". 6a4ff0499484c6c79c95cd8c566bd25f+249025 0:249025:GNU_General_Public_License,_version_3.pdf\n"
+ name: user_agreement
+
+collection_owned_by_active:
+ uuid: zzzzz-4zz18-bv31uwvy3neko21
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:bar\n"
+ name: owned_by_active
+
+foo_file:
+ uuid: zzzzz-4zz18-znfnqtbbv4spc3w
+ portable_data_hash: 1f4b0bc7583c2a7f9102c395f4ffc5e3+45
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo\n"
+ name: foo_file
+
+bar_file:
+ uuid: zzzzz-4zz18-ehbhgtheo8909or
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:bar\n"
+ name: bar_file
+
+baz_file:
+ uuid: zzzzz-4zz18-y9vne9npefyxh8g
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: baz_file
+
+multilevel_collection_1:
+ uuid: zzzzz-4zz18-pyw8yp9g3pr7irn
+ portable_data_hash: 1fd08fc162a5c6413070a8bd0bffc818+150
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 0:0:file1 0:0:file2 0:0:file3\n./dir1 0:0:file1 0:0:file2 0:0:file3\n./dir1/subdir 0:0:file1 0:0:file2 0:0:file3\n./dir2 0:0:file1 0:0:file2 0:0:file3\n"
+ name: multilevel_collection_1
+
+multilevel_collection_2:
+ uuid: zzzzz-4zz18-45xf9hw1sxkhl6q
+ # All of this collection's files are deep in subdirectories.
+ portable_data_hash: 80cf6dd2cf079dd13f272ec4245cb4a8+48
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: "./dir1/sub1 0:0:a 0:0:b\n./dir2/sub2 0:0:c 0:0:d\n"
+ name: multilevel_collection_2
+
+docker_image:
+ uuid: zzzzz-4zz18-1v45jub259sjjgb
+ # This Collection has links with Docker image metadata.
+ portable_data_hash: fa3c1a9cb6783f85f2ecda037e07b8c3+167
+ owner_uuid: qr1hi-tpzed-000000000000000
+ created_at: 2014-06-11T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-06-11T17:22:54Z
+ updated_at: 2014-06-11T17:22:54Z
+ manifest_text: ". d21353cfe035e3e384563ee55eadbb2f+67108864 5c77a43e329b9838cbec18ff42790e57+55605760 0:122714624:d8309758b8fe2c81034ffc8a10c36460b77db7bc5e7b448c4e5b684f9d95a678.tar\n"
+ name: docker_image
+
+unlinked_docker_image:
+ uuid: zzzzz-4zz18-d0d8z5wofvfgwad
+ # This Collection contains a file that looks like a Docker image,
+ # but has no Docker metadata links pointing to it.
+ portable_data_hash: 9ae44d5792468c58bcf85ce7353c7027+124
+ owner_uuid: qr1hi-tpzed-000000000000000
+ created_at: 2014-06-11T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-06-11T17:22:54Z
+ updated_at: 2014-06-11T17:22:54Z
+ manifest_text: ". fca529cfe035e3e384563ee55eadbb2f+67108863 0:67108863:bcd02158b8fe2c81034ffc8a10c36460b77db7bc5e7b448c4e5b684f9d95a678.tar\n"
+ name: unlinked_docker_image
+
+empty:
+ uuid: zzzzz-4zz18-gs9ooj1h9sd5mde
+ # Empty collection owned by anonymous_group is added with rake db:seed.
+ portable_data_hash: d41d8cd98f00b204e9800998ecf8427e+0
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-06-11T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-06-11T17:22:54Z
+ updated_at: 2014-06-11T17:22:54Z
+ manifest_text: ""
+ name: empty_collection
+
+foo_collection_in_aproject:
+ uuid: zzzzz-4zz18-fy296fx3hot09f7
+ portable_data_hash: 1f4b0bc7583c2a7f9102c395f4ffc5e3+45
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ manifest_text: ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo\n"
+ name: "zzzzz-4zz18-fy296fx3hot09f7 added sometime"
+
+user_agreement_in_anonymously_accessible_project:
+ uuid: zzzzz-4zz18-uukreo9rbgwsujr
+ portable_data_hash: b519d9cb706a29fc7ea24dbea2f05851+93
+ owner_uuid: zzzzz-j7d0g-zhxawtyetzwc5f0
+ created_at: 2014-06-13 20:42:26 -0800
+ modified_at: 2014-06-13 20:42:26 -0800
+ updated_at: 2014-06-13 20:42:26 -0800
+ manifest_text: ". 6a4ff0499484c6c79c95cd8c566bd25f+249025 0:249025:GNU_General_Public_License,_version_3.pdf\n"
+ name: GNU General Public License, version 3
+
+baz_collection_name_in_asubproject:
+ uuid: zzzzz-4zz18-lsitwcf548ui4oe
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: "zzzzz-4zz18-lsitwcf548ui4oe added sometime"
+
+empty_collection_name_in_active_user_home_project:
+ uuid: zzzzz-4zz18-5qa38qghh1j3nvv
+ portable_data_hash: d41d8cd98f00b204e9800998ecf8427e+0
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-08-06 22:11:51.242392533 Z
+ modified_at: 2014-08-06 22:11:51.242150425 Z
+ manifest_text: ""
+ name: Empty collection
+
+baz_file_in_asubproject:
+ uuid: zzzzz-4zz18-0mri2x4u7ftngez
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: baz_file
+
+collection_to_move_around_in_aproject:
+ uuid: zzzzz-4zz18-0mri2x4u7ft1234
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: collection_to_move_around
+
+expired_collection:
+ uuid: zzzzz-4zz18-mto52zx1s7sn3ih
+ portable_data_hash: 0b21a217243bfce5617fb9224b95bcb9+49
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ expires_at: 2001-01-01T00:00:00Z
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:expired\n"
+ name: expired_collection
+
+collection_expires_in_future:
+ uuid: zzzzz-4zz18-padkqo7yb8d9i3j
+ portable_data_hash: 0b21a217243bfce5617fb9224b95bcb9+49
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ expires_at: 2038-01-01T00:00:00Z
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:expired\n"
+ name: collection_expires_in_future
+
+# a collection with a log file that can be parsed by the log viewer
+# This collection hash matches the following log text:
+# 2014-01-01_12:00:01 zzzzz-8i9sb-abcdefghijklmno 0 log message 1
+# 2014-01-01_12:00:02 zzzzz-8i9sb-abcdefghijklmno 0 log message 2
+# 2014-01-01_12:00:03 zzzzz-8i9sb-abcdefghijklmno 0 log message 3
+#
+real_log_collection:
+ uuid: zzzzz-4zz18-op4e2lbej01tcvu
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-09-01 12:00:00
+ portable_data_hash: 0b9a7787660e1fce4a93f33e01376ba6+81
+ manifest_text: ". cdd549ae79fe6640fa3d5c6261d8303c+195 0:195:zzzzz-8i9sb-0vsrcqi7whchuil.log.txt\n"
+ name: real_log_collection
+
+collection_in_home_project_with_same_name_as_in_aproject:
+ uuid: zzzzz-4zz18-12342x4u7ftabcd
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: collection_with_same_name_in_aproject_and_home_project
+
+collection_in_aproject_with_same_name_as_in_home_project:
+ uuid: zzzzz-4zz18-56782x4u7ftefgh
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: collection_with_same_name_in_aproject_and_home_project
+
+collection_owned_by_foo:
+ uuid: zzzzz-4zz18-50surkhkbhsp31b
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ owner_uuid: zzzzz-tpzed-81hsbo6mk8nl05c
+ created_at: 2014-02-03T17:22:54Z
+ name: collection_owned_by_foo
+
+collection_to_remove_from_subproject:
+ # The Workbench tests remove this from subproject.
+ uuid: zzzzz-4zz18-subprojgonecoll
+ portable_data_hash: 2386ca6e3fffd4be5e197a72c6c80fb2+51
+ manifest_text: ". 8258b505536a9ab47baa2f4281cb932a+9 0:9:missingno\n"
+ owner_uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ created_at: 2014-10-15T10:45:00
+ name: Collection to remove from subproject
+
+collection_with_files_in_subdir:
+ uuid: zzzzz-4zz18-filesinsubdir00
+ name: collection_files_in_subdir
+ portable_data_hash: 85877ca2d7e05498dd3d109baf2df106+95
+ owner_uuid: zzzzz-tpzed-user1withloadab
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-user1withloadab
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 85877ca2d7e05498dd3d109baf2df106+95+A3a4e26a366ee7e4ed3e476ccf05354761be2e4ae@545a9920 0:95:file_in_subdir1\n./subdir2/subdir3 2bbc341c702df4d8f42ec31f16c10120+64+A315d7e7bad2ce937e711fc454fae2d1194d14d64@545a9920 0:32:file1_in_subdir3.txt 32:32:file2_in_subdir3.txt\n./subdir2/subdir3/subdir4 2bbc341c702df4d8f42ec31f16c10120+64+A315d7e7bad2ce937e711fc454fae2d1194d14d64@545a9920 0:32:file1_in_subdir4.txt 32:32:file2_in_subdir4.txt"
+
+graph_test_collection1:
+ uuid: zzzzz-4zz18-bv31uwvy3neko22
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:bar\n"
+ name: bar_file
+
+graph_test_collection2:
+ uuid: zzzzz-4zz18-uukreo9rbgwsujx
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ portable_data_hash: 65b17c95fdbc9800fc48acda4e9dcd0b+93
+ manifest_text: ". 6a4ff0499484c6c79c95cd8c566bd25f+249025 0:249025:FOO_General_Public_License,_version_3.pdf\n"
+ name: "FOO General Public License, version 3"
+
+graph_test_collection3:
+ uuid: zzzzz-4zz18-uukreo9rbgwsujj
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: "baz file"
+
+collection_1_owned_by_fuse:
+ uuid: zzzzz-4zz18-ovx05bfzormx3bg
+ portable_data_hash: fa7aeb5140e2848d39b416daeef4ffc5+45
+ owner_uuid: zzzzz-tpzed-0fusedrivertest
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 37b51d194a7513e45b56f6524f2d51f2+3 0:3:bar\n"
+ name: "collection #1 owned by FUSE"
+
+collection_2_owned_by_fuse:
+ uuid: zzzzz-4zz18-8ubpy4w74twtwzr
+ portable_data_hash: 1f4b0bc7583c2a7f9102c395f4ffc5e3+45
+ owner_uuid: zzzzz-tpzed-0fusedrivertest
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo\n"
+ name: "collection #2 owned by FUSE"
+
+collection_in_fuse_project:
+ uuid: zzzzz-4zz18-vx4mtkjqfrb534f
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ owner_uuid: zzzzz-j7d0g-0000ownedbyfuse
+ created_at: 2014-02-03T17:22:54Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-02-03T17:22:54Z
+ updated_at: 2014-02-03T17:22:54Z
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ name: "collection in FUSE project"
+
+collection_with_no_name_in_aproject:
+ uuid: zzzzz-4zz18-00000nonamecoll
+ portable_data_hash: 1f4b0bc7583c2a7f9102c395f4ffc5e3+45
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ manifest_text: ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo\n"
+
+collection_to_search_for_in_aproject:
+ uuid: zzzzz-4zz18-abcd6fx123409f7
+ portable_data_hash: 5bd9c1ad0bc8c7f34be170a7b7b39089+45
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ manifest_text: ". juku76584cc2f85cedef654fjyhtgimh+3 0:3:foo\n"
+ name: "zzzzz-4zz18-abcd6fx123409f7 used to search with any"
+
+upload_sandbox:
+ uuid: zzzzz-4zz18-js48y3ykkfdfjd3
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-12-09 15:03:16
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-12-09 15:03:16
+ portable_data_hash: d41d8cd98f00b204e9800998ecf8427e+0
+ updated_at: 2014-12-09 15:03:16
+ manifest_text: ''
+ name: upload sandbox
+
+# Test Helper trims the rest of the file
+
+# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
+
+# collections in project_with_10_collections
+<% for i in 1..10 do %>
+collection_<%=i%>_of_10:
+ name: Collection_<%= i %>
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ uuid: zzzzz-4zz18-10gneyn6brkx<%= i.to_s.rjust(3, '0') %>
+ owner_uuid: zzzzz-j7d0g-0010collections
+ created_at: <%= i.minute.ago.to_s(:db) %>
+<% end %>
+
+# collections in project_with_201_collections
+<% for i in 1..201 do %>
+collection_<%=i%>_of_201:
+ name: Collection_<%= i %>
+ portable_data_hash: ea10d51bcf88862dbcc36eb292017dfd+45
+ manifest_text: ". 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz\n"
+ uuid: zzzzz-4zz18-201gneyn6brd<%= i.to_s.rjust(3, '0') %>
+ owner_uuid: zzzzz-j7d0g-0201collections
+ created_at: <%= i.minute.ago.to_s(:db) %>
+<% end %>
+
+# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
--- /dev/null
+public:
+ uuid: zzzzz-j7d0g-it30l961gq3t0oi
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ name: Public
+ description: Public Group
+ group_class: role
+
+private:
+ uuid: zzzzz-j7d0g-rew6elm53kancon
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: Private
+ description: Private Group
+ group_class: role
+
+private_and_can_read_foofile:
+ uuid: zzzzz-j7d0g-22xp1wpjul508rk
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: Private and Can Read Foofile
+ description: Another Private Group
+ group_class: role
+
+activeandfriends:
+ uuid: zzzzz-j7d0g-swqu6hmi4pa7bk7
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-08-22 14:02:18.481582707 Z
+ modified_by_client_uuid:
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-08-22 14:02:18.481319501 Z
+ name: Active User and friends
+ description:
+ updated_at: 2014-08-22 14:02:18.481166435 Z
+ group_class: role
+
+system_group:
+ uuid: zzzzz-j7d0g-000000000000000
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: System Private
+ description: System-owned Group
+ group_class: role
+
+empty_lonely_group:
+ uuid: zzzzz-j7d0g-jtp06ulmvsezgyu
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: Empty
+ description: Empty Group
+ group_class: role
+
+all_users:
+ uuid: zzzzz-j7d0g-fffffffffffffff
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: All users
+ description: All users
+ group_class: role
+
+testusergroup_admins:
+ uuid: zzzzz-j7d0g-48foin4vonvc2at
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: Administrators of a subset of users
+
+aproject:
+ uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: A Project
+ description: Test project belonging to active user
+ group_class: project
+
+asubproject:
+ uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: A Subproject
+ description: "Test project belonging to active user's first test project"
+ group_class: project
+
+future_project_viewing_group:
+ uuid: zzzzz-j7d0g-futrprojviewgrp
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: Future Project Viewing Group
+ description: "Group used to test granting Group Project viewing"
+ group_class: role
+
+bad_group_has_ownership_cycle_a:
+ uuid: zzzzz-j7d0g-cx2al9cqkmsf1hs
+ owner_uuid: zzzzz-j7d0g-0077nzts8c178lw
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-05-03 18:50:08 -0400
+ modified_at: 2014-05-03 18:50:08 -0400
+ updated_at: 2014-05-03 18:50:08 -0400
+ name: Owned by bad group b
+
+bad_group_has_ownership_cycle_b:
+ uuid: zzzzz-j7d0g-0077nzts8c178lw
+ owner_uuid: zzzzz-j7d0g-cx2al9cqkmsf1hs
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-05-03 18:50:08 -0400
+ modified_at: 2014-05-03 18:50:08 -0400
+ updated_at: 2014-05-03 18:50:08 -0400
+ name: Owned by bad group a
+
+anonymous_group:
+ uuid: zzzzz-j7d0g-anonymouspublic
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: Anonymous group
+ description: Anonymous group
+
+anonymously_accessible_project:
+ uuid: zzzzz-j7d0g-zhxawtyetzwc5f0
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ name: Unrestricted public data
+ group_class: project
+ description: An anonymously accessible project
+
+active_user_has_can_manage:
+ uuid: zzzzz-j7d0g-ptt1ou6a9lxrv07
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ name: Active user has can_manage
+
+# Group for testing granting permission between users who share a group.
+group_for_sharing_tests:
+ uuid: zzzzz-j7d0g-t4ucgncwteul7zt
+ owner_uuid: zzzzz-tpzed-000000000000000
+ name: Group for sharing tests
+ description: Users who can share objects with each other
+ group_class: role
+
+empty_project:
+ uuid: zzzzz-j7d0g-9otoxmrksam74q6
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-12-16 15:56:27.967534940 Z
+ modified_by_client_uuid: ~
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-12-16 15:56:27.967358199 Z
+ name: Empty project
+ description: ~
+ updated_at: 2014-12-16 15:56:27.967242142 Z
+ group_class: project
+
+project_with_10_collections:
+ uuid: zzzzz-j7d0g-0010collections
+ owner_uuid: zzzzz-tpzed-user1withloadab
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-user1withloadab
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: project with 10 collections
+ description: This will result in one page in the display
+ group_class: project
+
+project_with_201_collections:
+ uuid: zzzzz-j7d0g-0201collections
+ owner_uuid: zzzzz-tpzed-user1withloadab
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-user1withloadab
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: project with 201 collections
+ description: This will result in two pages in the display
+ group_class: project
+
+project_with_10_pipelines:
+ uuid: zzzzz-j7d0g-000010pipelines
+ owner_uuid: zzzzz-tpzed-user1withloadab
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-user1withloadab
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: project with 10 pipelines
+ description: project with 10 pipelines
+ group_class: project
+
+project_with_2_pipelines_and_60_jobs:
+ uuid: zzzzz-j7d0g-nnjobspipelines
+ owner_uuid: zzzzz-tpzed-user1withloadab
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-user1withloadab
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: project with 2 pipelines and 60 jobs
+ description: This will result in two pages in the display
+ group_class: project
+
+project_with_25_pipelines:
+ uuid: zzzzz-j7d0g-000025pipelines
+ owner_uuid: zzzzz-tpzed-user1withloadab
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-user1withloadab
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: project with 25 pipelines
+ description: project with 25 pipelines
+ group_class: project
+
+fuse_owned_project:
+ uuid: zzzzz-j7d0g-0000ownedbyfuse
+ owner_uuid: zzzzz-tpzed-0fusedrivertest
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-0fusedrivertest
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ name: FUSE Test Project
+ description: Test project belonging to FUSE test user
+ group_class: project
+
+# This wouldn't pass model validation, but it enables a workbench
+# infinite-loop test. See #4389
+project_owns_itself:
+ uuid: zzzzz-j7d0g-7rqh7hdshd5yp5t
+ owner_uuid: zzzzz-j7d0g-7rqh7hdshd5yp5t
+ created_at: 2014-11-05 22:31:24.258424340 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: 6pbr1-tpzed-000000000000000
+ modified_at: 2014-11-05 22:31:24.258242890 Z
+ name: zzzzz-j7d0g-7rqh7hdshd5yp5t
+ description: ~
+ updated_at: 2014-11-05 22:31:24.258093171 Z
+ group_class: project
--- /dev/null
+running:
+ uuid: zzzzz-8i9sb-pshmckwoma9plh7
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 3.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: ~
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+
+running_cancelled:
+ uuid: zzzzz-8i9sb-4cf0nhn6xte809j
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: <%= 1.minute.ago.to_s(:db) %>
+ cancelled_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_by_client_uuid: zzzzz-ozdt8-obw7foaks3qjyej
+ created_at: <%= 4.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: ~
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Cancelled
+
+uses_nonexistent_script_version:
+ uuid: zzzzz-8i9sb-7m339pu0x9mla88
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ script_version: 7def43a4d3f20789dda4700f703b5514cc3ed250
+ created_at: <%= 5.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: <%= 2.minute.ago.to_s(:db) %>
+ running: false
+ success: true
+ output: d41d8cd98f00b204e9800998ecf8427e+0
+ priority: 0
+ log: d41d8cd98f00b204e9800998ecf8427e+0
+ is_locked_by_uuid: ~
+ tasks_summary:
+ failed: 0
+ todo: 0
+ running: 0
+ done: 1
+ runtime_constraints: {}
+ state: Complete
+
+foobar:
+ uuid: zzzzz-8i9sb-aceg2bnq7jt7kon
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ script_version: 7def43a4d3f20789dda4700f703b5514cc3ed250
+ script_parameters:
+ input: 1f4b0bc7583c2a7f9102c395f4ffc5e3+45
+ created_at: <%= 4.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: <%= 2.minute.ago.to_s(:db) %>
+ running: false
+ success: true
+ output: fa7aeb5140e2848d39b416daeef4ffc5+45
+ priority: 0
+ log: ea10d51bcf88862dbcc36eb292017dfd+45
+ is_locked_by_uuid: ~
+ tasks_summary:
+ failed: 0
+ todo: 0
+ running: 0
+ done: 1
+ runtime_constraints: {}
+ state: Complete
+
+barbaz:
+ uuid: zzzzz-8i9sb-cjs4pklxxjykyuq
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ script_version: 7def43a4d3f20789dda4700f703b5514cc3ed250
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: 1
+ created_at: <%= 4.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: <%= 2.minute.ago.to_s(:db) %>
+ running: false
+ success: true
+ repository: foo
+ output: ea10d51bcf88862dbcc36eb292017dfd+45
+ priority: 0
+ log: d41d8cd98f00b204e9800998ecf8427e+0
+ is_locked_by_uuid: ~
+ tasks_summary:
+ failed: 0
+ todo: 0
+ running: 0
+ done: 1
+ runtime_constraints: {}
+ state: Complete
+
+runningbarbaz:
+ uuid: zzzzz-8i9sb-cjs4pklxxjykyuj
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ script_version: 7def43a4d3f20789dda4700f703b5514cc3ed250
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: 1
+ created_at: <%= 4.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: <%= 2.minute.ago.to_s(:db) %>
+ running: true
+ success: ~
+ repository: foo
+ output: ea10d51bcf88862dbcc36eb292017dfd+45
+ priority: 0
+ log: d41d8cd98f00b204e9800998ecf8427e+0
+ is_locked_by_uuid: ~
+ tasks_summary:
+ failed: 0
+ todo: 0
+ running: 1
+ done: 0
+ runtime_constraints: {}
+ state: Running
+
+previous_job_run:
+ uuid: zzzzz-8i9sb-cjs4pklxxjykqqq
+ created_at: <%= 14.minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ repository: foo
+ script: hash
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: "1"
+ success: true
+ output: ea10d51bcf88862dbcc36eb292017dfd+45
+ state: Complete
+
+previous_docker_job_run:
+ uuid: zzzzz-8i9sb-k6emstgk4kw4yhi
+ created_at: <%= 14.minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ repository: foo
+ script: hash
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: "1"
+ runtime_constraints:
+ docker_image: arvados/test
+ success: true
+ output: ea10d51bcf88862dbcc36eb292017dfd+45
+ docker_image_locator: fa3c1a9cb6783f85f2ecda037e07b8c3+167
+ state: Complete
+
+previous_job_run_with_arvados_sdk_version:
+ uuid: zzzzz-8i9sb-eoo0321or2dw2jg
+ created_at: <%= 14.minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ repository: foo
+ script: hash
+ script_version: 31ce37fe365b3dc204300a3e4c396ad333ed0556
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: "1"
+ runtime_constraints:
+ arvados_sdk_version: commit2
+ arvados_sdk_version: 00634b2b8a492d6f121e3cf1d6587b821136a9a7
+ success: true
+ output: ea10d51bcf88862dbcc36eb292017dfd+45
+ state: Complete
+
+previous_job_run_no_output:
+ uuid: zzzzz-8i9sb-cjs4pklxxjykppp
+ created_at: <%= 14.minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ repository: foo
+ script: hash
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: "2"
+ success: true
+ output: ~
+ state: Complete
+
+nondeterminisic_job_run:
+ uuid: zzzzz-8i9sb-cjs4pklxxjykyyy
+ created_at: <%= 14.minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ repository: foo
+ script: hash2
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: "1"
+ success: true
+ nondeterministic: true
+ state: Complete
+
+nearly_finished_job:
+ uuid: zzzzz-8i9sb-2gx6rz0pjl033w3
+ created_at: <%= 14.minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ repository: arvados
+ script: doesnotexist
+ script_version: 309e25a64fe994867db8459543af372f850e25b9
+ script_parameters:
+ input: b519d9cb706a29fc7ea24dbea2f05851+249025
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: ~
+ running: true
+ success: ~
+ tasks_summary:
+ failed: 0
+ todo: 0
+ running: 1
+ done: 0
+ runtime_constraints: {}
+ state: Complete
+
+queued:
+ uuid: zzzzz-8i9sb-grx15v5mjnsyxk7
+ created_at: <%= 1.minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ started_at: ~
+ finished_at: ~
+ script: foo
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ script_parameters: {}
+ running: ~
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: ~
+ tasks_summary: {}
+ runtime_constraints: {}
+ state: Queued
+
+# A job with a log collection that can be parsed by the log viewer.
+job_with_real_log:
+ uuid: zzzzz-8i9sb-0vsrcqi7whchuil
+ created_at: 2014-09-01 12:00:00
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ log: 0b9a7787660e1fce4a93f33e01376ba6+81
+ script_version: 7def43a4d3f20789dda4700f703b5514cc3ed250
+ state: Complete
+
+cancelled:
+ uuid: zzzzz-8i9sb-4cf0abc123e809j
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: <%= 1.minute.ago.to_s(:db) %>
+ cancelled_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_by_client_uuid: zzzzz-ozdt8-obw7foaks3qjyej
+ created_at: <%= 4.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: ~
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ running: false
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Cancelled
+
+job_in_subproject:
+ uuid: zzzzz-8i9sb-subprojectjob01
+ created_at: 2014-10-15 12:00:00
+ owner_uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ log: ~
+ repository: foo
+ script: hash
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ state: Complete
+
+running_will_be_completed:
+ uuid: zzzzz-8i9sb-rshmckwoma9pjh8
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 3.minute.ago.to_s(:db) %>
+ started_at: <%= 3.minute.ago.to_s(:db) %>
+ finished_at: ~
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+
+graph_stage1:
+ uuid: zzzzz-8i9sb-graphstage10000
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ repository: foo
+ script: hash
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ state: Complete
+ output: fa7aeb5140e2848d39b416daeef4ffc5+45
+
+graph_stage2:
+ uuid: zzzzz-8i9sb-graphstage20000
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ repository: foo
+ script: hash2
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ state: Complete
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ input2: "stuff"
+ output: 65b17c95fdbc9800fc48acda4e9dcd0b+93
+
+graph_stage3:
+ uuid: zzzzz-8i9sb-graphstage30000
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ repository: foo
+ script: hash2
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ state: Complete
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ input2: "stuff2"
+ output: ea10d51bcf88862dbcc36eb292017dfd+45
+
+
+# Test Helper trims the rest of the file
+
+# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
+
+# jobs in project_with_2_pipelines_and_60_jobs
+<% for i in 1..60 do %>
+job_<%=i%>_of_60:
+ uuid: zzzzz-8i9sb-oneof100jobs<%= i.to_s.rjust(3, '0') %>
+ created_at: <%= ((i+5)/5).minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-j7d0g-nnjobspipelines
+ script_version: 7def43a4d3f20789dda4700f703b5514cc3ed250
+ state: Complete
+<% end %>
+
+# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
--- /dev/null
+nonfull:
+ uuid: zzzzz-penuu-5w2o2t1q5wy7fhn
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ node_uuid: zzzzz-7ekkf-53y36l1lu5ijveb
+ keep_service_uuid: zzzzz-bi6l4-6zhilxar6r8ey90
+ last_read_at: <%= 1.minute.ago.to_s(:db) %>
+ last_write_at: <%= 2.minute.ago.to_s(:db) %>
+ last_ping_at: <%= 3.minute.ago.to_s(:db) %>
+ ping_secret: z9xz2tc69dho51g1dmkdy5fnupdhsprahcwxdbjs0zms4eo6i
+
+full:
+ uuid: zzzzz-penuu-4kmq58ui07xuftx
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ node_uuid: zzzzz-7ekkf-53y36l1lu5ijveb
+ keep_service_uuid: zzzzz-bi6l4-6zhilxar6r8ey90
+ last_read_at: <%= 1.minute.ago.to_s(:db) %>
+ last_write_at: <%= 2.day.ago.to_s(:db) %>
+ last_ping_at: <%= 3.minute.ago.to_s(:db) %>
+ ping_secret: xx3ieejcufbjy4lli6yt5ig4e8w5l2hhgmbyzpzuq38gri6lj
+
+nonfull2:
+ uuid: zzzzz-penuu-1ydrih9k2er5j11
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ node_uuid: zzzzz-7ekkf-2z3mc76g2q73aio
+ keep_service_uuid: zzzzz-bi6l4-rsnj3c76ndxb7o0
+ last_read_at: <%= 1.minute.ago.to_s(:db) %>
+ last_write_at: <%= 2.minute.ago.to_s(:db) %>
+ last_ping_at: <%= 3.minute.ago.to_s(:db) %>
+ ping_secret: 4rs260ibhdum1d242xy23qv320rlerc0j7qg9vyqnchbgmjeek
--- /dev/null
+keep0:
+ uuid: zzzzz-bi6l4-6zhilxar6r8ey90
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ service_host: keep0.zzzzz.arvadosapi.com
+ service_port: 25107
+ service_ssl_flag: false
+ service_type: disk
+
+keep1:
+ uuid: zzzzz-bi6l4-rsnj3c76ndxb7o0
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ service_host: keep1.zzzzz.arvadosapi.com
+ service_port: 25107
+ service_ssl_flag: false
+ service_type: disk
+
+proxy:
+ uuid: zzzzz-bi6l4-h0a0xwut9qa6g3a
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ service_host: keep.zzzzz.arvadosapi.com
+ service_port: 25333
+ service_ssl_flag: true
+ service_type: proxy
--- /dev/null
+user_agreement_required:
+ uuid: zzzzz-o0j2j-j2qe76q7s3c8aro
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2013-12-26T19:52:21Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2013-12-26T19:52:21Z
+ updated_at: 2013-12-26T19:52:21Z
+ tail_uuid: zzzzz-tpzed-000000000000000
+ link_class: signature
+ name: require
+ head_uuid: zzzzz-4zz18-t68oksiu9m80s4y
+ properties: {}
+
+user_agreement_readable:
+ uuid: zzzzz-o0j2j-qpf60gg4fwjlmex
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-j7d0g-fffffffffffffff
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-t68oksiu9m80s4y
+ properties: {}
+
+active_user_member_of_all_users_group:
+ uuid: zzzzz-o0j2j-ctbysaduejxfrs5
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-fffffffffffffff
+ properties: {}
+
+active_user_can_manage_group:
+ uuid: zzzzz-o0j2j-3sa30nd3bqn1msh
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-02-03 15:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-02-03 15:42:26 -0800
+ updated_at: 2014-02-03 15:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_manage
+ head_uuid: zzzzz-j7d0g-ptt1ou6a9lxrv07
+ properties: {}
+
+user_agreement_signed_by_active:
+ uuid: zzzzz-o0j2j-4x85a69tqlrud1z
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2013-12-26T20:52:21Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2013-12-26T20:52:21Z
+ updated_at: 2013-12-26T20:52:21Z
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: signature
+ name: click
+ head_uuid: zzzzz-4zz18-t68oksiu9m80s4y
+ properties: {}
+
+user_agreement_signed_by_inactive:
+ uuid: zzzzz-o0j2j-lh7er2o3k6bmetw
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2013-12-26T20:52:21Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-7sg468ezxwnodxs
+ modified_at: 2013-12-26T20:52:21Z
+ updated_at: 2013-12-26T20:52:21Z
+ tail_uuid: zzzzz-tpzed-7sg468ezxwnodxs
+ link_class: signature
+ name: click
+ head_uuid: zzzzz-4zz18-t68oksiu9m80s4y
+ properties: {}
+
+spectator_user_member_of_all_users_group:
+ uuid: zzzzz-o0j2j-0s8ql1redzf8kvn
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-fffffffffffffff
+ properties: {}
+
+inactive_user_member_of_all_users_group:
+ uuid: zzzzz-o0j2j-osckxpy5hl5fjk5
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2013-12-26T20:52:21Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-7sg468ezxwnodxs
+ modified_at: 2013-12-26T20:52:21Z
+ updated_at: 2013-12-26T20:52:21Z
+ tail_uuid: zzzzz-tpzed-x9kqpd79egh49c7
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-fffffffffffffff
+ properties: {}
+
+inactive_signed_ua_user_member_of_all_users_group:
+ uuid: zzzzz-o0j2j-qkhyjcr6tidk652
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2013-12-26T20:52:21Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-7sg468ezxwnodxs
+ modified_at: 2013-12-26T20:52:21Z
+ updated_at: 2013-12-26T20:52:21Z
+ tail_uuid: zzzzz-tpzed-7sg468ezxwnodxs
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-fffffffffffffff
+ properties: {}
+
+foo_file_readable_by_active:
+ uuid: zzzzz-o0j2j-dp1d8395ldqw22r
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-znfnqtbbv4spc3w
+ properties: {}
+
+foo_file_readable_by_active_duplicate_permission:
+ uuid: zzzzz-o0j2j-2qlmhgothiur55r
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-000000000000000
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-znfnqtbbv4spc3w
+ properties: {}
+
+foo_file_readable_by_active_redundant_permission_via_private_group:
+ uuid: zzzzz-o0j2j-5s8ry7sn6bwxb7w
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-000000000000000
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-j7d0g-22xp1wpjul508rk
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-znfnqtbbv4spc3w
+ properties: {}
+
+foo_file_readable_by_aproject:
+ uuid: zzzzz-o0j2j-fp1d8395ldqw22p
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-znfnqtbbv4spc3w
+ properties: {}
+
+bar_file_readable_by_active:
+ uuid: zzzzz-o0j2j-8hppiuduf8eqdng
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-ehbhgtheo8909or
+ properties: {}
+
+bar_file_readable_by_spectator:
+ uuid: zzzzz-o0j2j-0mhldkqozsltcli
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-ehbhgtheo8909or
+ properties: {}
+
+baz_file_publicly_readable:
+ uuid: zzzzz-o0j2j-132ne3lk954vtoc
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-j7d0g-fffffffffffffff
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-y9vne9npefyxh8g
+ properties: {}
+
+barbaz_job_readable_by_spectator:
+ uuid: zzzzz-o0j2j-cpy7p41hpk531e1
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-8i9sb-cjs4pklxxjykyuq
+ properties: {}
+
+runningbarbaz_job_readable_by_spectator:
+ uuid: zzzzz-o0j2j-cpy7p41hpk531e2
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-8i9sb-cjs4pklxxjykyuj
+ properties: {}
+
+arvados_repository_readable_by_all_users:
+ uuid: zzzzz-o0j2j-allcanreadarvrp
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-j7d0g-fffffffffffffff
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-s0uqq-arvadosrepo0123
+ properties: {}
+
+foo_repository_readable_by_spectator:
+ uuid: zzzzz-o0j2j-cpy7p41hpk5xxx
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-s0uqq-382brsig8rp3666
+ properties: {}
+
+foo_repository_manageable_by_active:
+ uuid: zzzzz-o0j2j-8tdfjd8g0s4rn1k
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_manage
+ head_uuid: zzzzz-s0uqq-382brsig8rp3666
+ properties: {}
+
+repository3_readable_by_active:
+ uuid: zzzzz-o0j2j-43iem9bdtefa76g
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-09-23 13:52:46 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-09-23 13:52:46 -0400
+ updated_at: 2014-09-23 13:52:46 -0400
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-s0uqq-38orljkqpyo1j61
+ properties: {}
+
+miniadmin_user_is_a_testusergroup_admin:
+ uuid: zzzzz-o0j2j-38vvkciz7qc12j9
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-04-01 13:53:33 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-04-01 13:53:33 -0400
+ updated_at: 2014-04-01 13:53:33 -0400
+ tail_uuid: zzzzz-tpzed-2bg9x0oeydcw5hm
+ link_class: permission
+ name: can_manage
+ head_uuid: zzzzz-j7d0g-48foin4vonvc2at
+ properties: {}
+
+rominiadmin_user_is_a_testusergroup_admin:
+ uuid: zzzzz-o0j2j-6b0hz5hr107mc90
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-04-01 13:53:33 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-04-01 13:53:33 -0400
+ updated_at: 2014-04-01 13:53:33 -0400
+ tail_uuid: zzzzz-tpzed-4hvxm4n25emegis
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-48foin4vonvc2at
+ properties: {}
+
+testusergroup_can_manage_active_user:
+ uuid: zzzzz-o0j2j-2vaqhxz6hsf4k1d
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-04-01 13:56:10 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-04-01 13:56:10 -0400
+ updated_at: 2014-04-01 13:56:10 -0400
+ tail_uuid: zzzzz-j7d0g-48foin4vonvc2at
+ link_class: permission
+ name: can_manage
+ head_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ properties: {}
+
+test_timestamps:
+ uuid: zzzzz-o0j2j-4abnk2w5t86x4uc
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-15 13:17:14 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-04-15 13:17:14 -0400
+ updated_at: 2014-04-15 13:17:14 -0400
+ link_class: test
+ name: test
+ properties: {}
+
+admin_can_write_aproject:
+ # Yes, this permission is effectively redundant.
+ # We use it to test that other project admins can see
+ # all the project's sharing.
+ uuid: zzzzz-o0j2j-adminmgsproject
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ link_class: permission
+ name: can_write
+ head_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ properties: {}
+
+project_viewer_can_read_project:
+ uuid: zzzzz-o0j2j-projviewerreadp
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-projectviewer1a
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ properties: {}
+
+subproject_admin_can_manage_subproject:
+ uuid: zzzzz-o0j2j-subprojadminlnk
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-10-15 10:00:00 -0000
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-10-15 10:00:00 -0000
+ updated_at: 2014-10-15 10:00:00 -0000
+ tail_uuid: zzzzz-tpzed-subprojectadmin
+ link_class: permission
+ name: can_manage
+ head_uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ properties: {}
+
+foo_collection_tag:
+ uuid: zzzzz-o0j2j-eedahfaho8aphiv
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ tail_uuid: ~
+ head_uuid: zzzzz-4zz18-fy296fx3hot09f7
+ link_class: tag
+ name: foo_tag
+ properties: {}
+
+active_user_can_manage_bad_group_cx2al9cqkmsf1hs:
+ uuid: zzzzz-o0j2j-ezv55ahzc9lvjwe
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-05-03 18:50:08 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-05-03 18:50:08 -0400
+ updated_at: 2014-05-03 18:50:08 -0400
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_manage
+ head_uuid: zzzzz-j7d0g-cx2al9cqkmsf1hs
+ properties: {}
+
+multilevel_collection_1_readable_by_active:
+ uuid: zzzzz-o0j2j-dp1d8395ldqw22j
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-pyw8yp9g3pr7irn
+ properties: {}
+
+has_symbol_keys_in_database_somehow:
+ uuid: zzzzz-o0j2j-enl1wg58310loc6
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-05-28 16:24:02.314722162 Z
+ modified_by_client_uuid:
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-05-28 16:24:02.314484982 Z
+ tail_uuid: ~
+ link_class: test
+ name: ~
+ head_uuid: ~
+ properties:
+ :foo: "bar"
+ baz:
+ - waz
+ - :waz
+ - :waz
+ - 1
+ - ~
+ - false
+ - true
+ updated_at: 2014-05-28 16:24:02.314296411 Z
+
+bug2931_link_with_null_head_uuid:
+ uuid: zzzzz-o0j2j-uru66qok2wruasb
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-05-30 14:30:00.184389725 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-05-30 14:30:00.184019565 Z
+ updated_at: 2014-05-30 14:30:00.183829316 Z
+ link_class: permission
+ name: bug2931
+ tail_uuid: ~
+ head_uuid: ~
+ properties: {}
+
+anonymous_group_can_read_anonymously_accessible_project:
+ uuid: zzzzz-o0j2j-15gpzezqjg4bc4z
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-05-30 14:30:00.184389725 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-05-30 14:30:00.184019565 Z
+ updated_at: 2014-05-30 14:30:00.183829316 Z
+ link_class: permission
+ name: can_read
+ tail_uuid: zzzzz-j7d0g-anonymouspublic
+ head_uuid: zzzzz-j7d0g-zhxawtyetzwc5f0
+ properties: {}
+
+user_agreement_readable_by_anonymously_accessible_project:
+ uuid: zzzzz-o0j2j-o5ds5gvhkztdc8h
+ owner_uuid: zzzzz-j7d0g-zhxawtyetzwc5f0
+ created_at: 2014-06-13 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-06-13 20:42:26 -0800
+ updated_at: 2014-06-13 20:42:26 -0800
+ link_class: permission
+ name: can_read
+
+active_user_permission_to_docker_image_collection:
+ uuid: zzzzz-o0j2j-dp1d8395ldqw33s
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-1v45jub259sjjgb
+ properties: {}
+
+active_user_permission_to_unlinked_docker_image_collection:
+ uuid: zzzzz-o0j2j-g5i0sa8cr3b1psf
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-4zz18-d0d8z5wofvfgwad
+ properties: {}
+
+docker_image_collection_hash:
+ uuid: zzzzz-o0j2j-dockercollhasha
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-06-11 14:30:00.184389725 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-06-11 14:30:00.184019565 Z
+ updated_at: 2014-06-11 14:30:00.183829316 Z
+ link_class: docker_image_hash
+ name: d8309758b8fe2c81034ffc8a10c36460b77db7bc5e7b448c4e5b684f9d95a678
+ tail_uuid: ~
+ head_uuid: zzzzz-4zz18-1v45jub259sjjgb
+ properties:
+ image_timestamp: "2014-06-10T14:30:00.184019565Z"
+
+docker_image_collection_tag:
+ uuid: zzzzz-o0j2j-dockercolltagbb
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-06-11 14:30:00.184389725 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-06-11 14:30:00.184019565 Z
+ updated_at: 2014-06-11 14:30:00.183829316 Z
+ link_class: docker_image_repo+tag
+ name: arvados/apitestfixture:latest
+ tail_uuid: ~
+ head_uuid: zzzzz-4zz18-1v45jub259sjjgb
+ properties:
+ image_timestamp: "2014-06-10T14:30:00.184019565Z"
+
+docker_image_collection_tag2:
+ uuid: zzzzz-o0j2j-dockercolltagbc
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-06-11 14:30:00.184389725 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-06-11 14:30:00.184019565 Z
+ updated_at: 2014-06-11 14:30:00.183829316 Z
+ link_class: docker_image_repo+tag
+ name: arvados/apitestfixture:june10
+ tail_uuid: ~
+ head_uuid: zzzzz-4zz18-1v45jub259sjjgb
+ properties:
+ image_timestamp: "2014-06-10T14:30:00.184019565Z"
+
+ancient_docker_image_collection_hash:
+ # This image helps test that searches for Docker images find
+ # the latest available image: the hash is the same as
+ # docker_image_collection_hash, but it points to a different
+ # Collection and has an older image timestamp.
+ uuid: zzzzz-o0j2j-dockercollhashz
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-06-12 14:30:00.184389725 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-06-12 14:30:00.184019565 Z
+ updated_at: 2014-06-12 14:30:00.183829316 Z
+ link_class: docker_image_hash
+ name: d8309758b8fe2c81034ffc8a10c36460b77db7bc5e7b448c4e5b684f9d95a678
+ tail_uuid: ~
+ head_uuid: zzzzz-4zz18-t68oksiu9m80s4y
+ properties:
+ image_timestamp: "2010-06-10T14:30:00.184019565Z"
+
+job_reader_can_read_previous_job_run:
+ # Permission link giving job_reader permission
+ # to read previous_job_run
+ uuid: zzzzz-o0j2j-8bbd851795ebafd
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-06-13 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-tpzed-000000000000000
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-06-13 20:42:26 -0800
+ updated_at: 2014-06-13 20:42:26 -0800
+ link_class: permission
+ name: can_read
+ tail_uuid: zzzzz-tpzed-905b42d1dd4a354
+ head_uuid: zzzzz-8i9sb-cjs4pklxxjykqqq
+
+job_reader_can_read_foo_repo:
+ # Permission link giving job_reader permission
+ # to read foo_repo
+ uuid: zzzzz-o0j2j-072ec05dc9487f8
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-06-13 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-tpzed-000000000000000
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-06-13 20:42:26 -0800
+ updated_at: 2014-06-13 20:42:26 -0800
+ link_class: permission
+ name: can_read
+ tail_uuid: zzzzz-tpzed-905b42d1dd4a354
+ head_uuid: zzzzz-s0uqq-382brsig8rp3666
+
+baz_collection_name_in_asubproject:
+ uuid: zzzzz-o0j2j-bazprojectname2
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-04-21 15:37:48 -0400
+ updated_at: 2014-04-21 15:37:48 -0400
+ tail_uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ head_uuid: ea10d51bcf88862dbcc36eb292017dfd+45
+ link_class: name
+ # This should resemble the default name assigned when a
+ # Collection is added to a Project.
+ name: "ea10d51bcf88862dbcc36eb292017dfd+45 added sometime"
+ properties: {}
+
+empty_collection_name_in_active_user_home_project:
+ uuid: zzzzz-o0j2j-i3n6m552x6tmoi4
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-08-06 22:11:51.242392533 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ modified_at: 2014-08-06 22:11:51.242150425 Z
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: name
+ name: Empty collection
+ head_uuid: d41d8cd98f00b204e9800998ecf8427e+0
+ properties: {}
+ updated_at: 2014-08-06 22:11:51.242010312 Z
+
+active_user_can_read_activeandfriends:
+ uuid: zzzzz-o0j2j-8184f5vk8c851ts
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-08-22 14:03:46.321059945 Z
+ modified_by_client_uuid:
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-08-22 14:03:46.320865926 Z
+ tail_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-swqu6hmi4pa7bk7
+ properties: {}
+ updated_at: 2014-08-22 14:03:46.320743213 Z
+
+active_user_joined_activeandfriends:
+ uuid: zzzzz-o0j2j-t63rdd7vupqvnco
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-08-22 14:03:28.835064240 Z
+ modified_by_client_uuid:
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-08-22 14:03:28.834849409 Z
+ tail_uuid: zzzzz-j7d0g-swqu6hmi4pa7bk7
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ properties: {}
+ updated_at: 2014-08-22 14:03:28.834720558 Z
+
+future_project_can_read_activeandfriends:
+ uuid: zzzzz-o0j2j-bkdtnddpmwxqiza
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-08-22 14:04:18.811622057 Z
+ modified_by_client_uuid:
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-08-22 14:04:18.811463859 Z
+ tail_uuid: zzzzz-tpzed-futureprojview2
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-swqu6hmi4pa7bk7
+ properties: {}
+ updated_at: 2014-08-22 14:04:18.811387314 Z
+
+future_project_user_joined_activeandfriends:
+ uuid: zzzzz-o0j2j-ksl8bo92eokv332
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-08-22 14:04:24.182103355 Z
+ modified_by_client_uuid:
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-08-22 14:04:24.181939129 Z
+ tail_uuid: zzzzz-j7d0g-swqu6hmi4pa7bk7
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-tpzed-futureprojview2
+ properties: {}
+ updated_at: 2014-08-22 14:04:24.181799856 Z
+
+auto_setup_vm_login_username_can_login_to_test_vm:
+ uuid: zzzzz-o0j2j-i3n6m98766tmoi4
+ owner_uuid: zzzzz-tpzed-xabcdjxw79nv3jz
+ created_at: 2014-08-06 22:11:51.242392533 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xabcdjxw79nv3jz
+ modified_at: 2014-08-06 22:11:51.242150425 Z
+ tail_uuid: zzzzz-tpzed-xabcdjxw79nv3jz
+ link_class: permission
+ name: can_login
+ head_uuid: zzzzz-2x53u-382brsig8rp3064
+ properties: {username: 'auto_setup_vm_login'}
+ updated_at: 2014-08-06 22:11:51.242010312 Z
+
+user_foo_can_read_sharing_group:
+ uuid: zzzzz-o0j2j-gdpvwvpj9kjs5in
+ owner_uuid: zzzzz-tpzed-000000000000000
+ tail_uuid: zzzzz-tpzed-81hsbo6mk8nl05c
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-t4ucgncwteul7zt
+
+user_foo_is_in_sharing_group:
+ uuid: zzzzz-o0j2j-bwmcf9nqwomvtny
+ owner_uuid: zzzzz-tpzed-000000000000000
+ tail_uuid: zzzzz-j7d0g-t4ucgncwteul7zt
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-tpzed-81hsbo6mk8nl05c
+
+user_bar_can_read_sharing_group:
+ uuid: zzzzz-o0j2j-23djaoza9g2zvjx
+ owner_uuid: zzzzz-tpzed-000000000000000
+ tail_uuid: zzzzz-tpzed-n3oaj4sm5fcnwib
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-t4ucgncwteul7zt
+
+user_bar_is_in_sharing_group:
+ uuid: zzzzz-o0j2j-ga7fgy3xsz4hu28
+ owner_uuid: zzzzz-tpzed-000000000000000
+ tail_uuid: zzzzz-j7d0g-t4ucgncwteul7zt
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-tpzed-n3oaj4sm5fcnwib
+
+user1-with-load_member_of_all_users_group:
+ uuid: zzzzz-o0j2j-user1-with-load
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_uuid: zzzzz-tpzed-user1withloadab
+ link_class: permission
+ name: can_read
+ head_uuid: zzzzz-j7d0g-fffffffffffffff
+ properties: {}
+
+empty_collection_name_in_fuse_user_home_project:
+ uuid: zzzzz-o0j2j-hw3mcg3c8pwo6ar
+ owner_uuid: zzzzz-tpzed-0fusedrivertest
+ created_at: 2014-08-06 22:11:51.242392533 Z
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-0fusedrivertest
+ modified_at: 2014-08-06 22:11:51.242150425 Z
+ tail_uuid: zzzzz-tpzed-0fusedrivertest
+ link_class: name
+ name: Empty collection
+ head_uuid: d41d8cd98f00b204e9800998ecf8427e+0
+ properties: {}
+ updated_at: 2014-08-06 22:11:51.242010312 Z
+
--- /dev/null
+log1:
+ id: 1
+ uuid: zzzzz-xxxxx-pshmckwoma9plh7
+ object_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ event_at: <%= 1.minute.ago.to_s(:db) %>
+
+log2: # admin changes repository2, which is owned by active user
+ id: 2
+ uuid: zzzzz-xxxxx-pshmckwoma00002
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f # admin user
+ object_uuid: zzzzz-2x53u-382brsig8rp3667 # repository foo
+ object_owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz # active user
+ event_at: <%= 2.minute.ago.to_s(:db) %>
+
+log3: # admin changes specimen owned_by_spectator
+ id: 3
+ uuid: zzzzz-xxxxx-pshmckwoma00003
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f # admin user
+ object_uuid: zzzzz-2x53u-3b0xxwzlbzxq5yr # specimen owned_by_spectator
+ object_owner_uuid: zzzzz-tpzed-l1s2piq4t4mps8r # spectator user
+ event_at: <%= 3.minute.ago.to_s(:db) %>
+
+log4: # foo collection added, readable by active through link
+ id: 4
+ uuid: zzzzz-xxxxx-pshmckwoma00004
+ owner_uuid: zzzzz-tpzed-000000000000000 # system user
+ object_uuid: zzzzz-4zz18-znfnqtbbv4spc3w # foo file
+ object_owner_uuid: zzzzz-tpzed-000000000000000 # system user
+ event_at: <%= 4.minute.ago.to_s(:db) %>
+
+log5: # baz collection added, readable by active and spectator through group 'all users' group membership
+ id: 5
+ uuid: zzzzz-xxxxx-pshmckwoma00005
+ owner_uuid: zzzzz-tpzed-000000000000000 # system user
+ object_uuid: zzzzz-4zz18-y9vne9npefyxh8g # baz file
+ object_owner_uuid: zzzzz-tpzed-000000000000000 # system user
+ event_at: <%= 5.minute.ago.to_s(:db) %>
+
+log_owned_by_active:
+ id: 6
+ uuid: zzzzz-xxxxx-pshmckwoma12345
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz # active user
+ object_uuid: zzzzz-2x53u-382brsig8rp3667 # repository foo
+ object_owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz # active user
+ event_at: <%= 2.minute.ago.to_s(:db) %>
+ summary: non-admin use can read own logs
--- /dev/null
+busy:
+ uuid: zzzzz-7ekkf-53y36l1lu5ijveb
+ owner_uuid: zzzzz-tpzed-000000000000000
+ hostname: compute0
+ slot_number: 0
+ domain: ""
+ ip_address: 172.17.2.172
+ last_ping_at: <%= 1.minute.ago.to_s(:db) %>
+ first_ping_at: <%= 23.hour.ago.to_s(:db) %>
+ job_uuid: zzzzz-8i9sb-2gx6rz0pjl033w3 # nearly_finished_job
+ info:
+ ping_secret: "48dpm3b8ijyj3jkr2yczxw0844dqd2752bhll7klodvgz9bg80"
+ slurm_state: "alloc"
+
+down:
+ uuid: zzzzz-7ekkf-2vbompg3ecc6e2s
+ owner_uuid: zzzzz-tpzed-000000000000000
+ hostname: compute1
+ slot_number: 1
+ domain: ""
+ ip_address: 172.17.2.173
+ last_ping_at: <%= 1.hour.ago.to_s(:db) %>
+ first_ping_at: <%= 23.hour.ago.to_s(:db) %>
+ job_uuid: ~
+ info:
+ ping_secret: "2k3i71depad36ugwmlgzilbi4e8n0illb2r8l4efg9mzkb3a1k"
+
+idle:
+ uuid: zzzzz-7ekkf-2z3mc76g2q73aio
+ owner_uuid: zzzzz-tpzed-000000000000000
+ hostname: compute2
+ slot_number: 2
+ domain: ""
+ ip_address: 172.17.2.174
+ last_ping_at: <%= 2.minute.ago.to_s(:db) %>
+ first_ping_at: <%= 23.hour.ago.to_s(:db) %>
+ job_uuid: ~
+ info:
+ ping_secret: "69udawxvn3zzj45hs8bumvndricrha4lcpi23pd69e44soanc0"
+ slurm_state: "idle"
+ total_cpu_cores: 16
+
+was_idle_now_down:
+ uuid: zzzzz-7ekkf-xuzpkdasl0uzwyz
+ owner_uuid: zzzzz-tpzed-000000000000000
+ hostname: compute3
+ slot_number: ~
+ domain: ""
+ ip_address: 172.17.2.173
+ last_ping_at: <%= 1.hour.ago.to_s(:db) %>
+ first_ping_at: <%= 23.hour.ago.to_s(:db) %>
+ job_uuid: ~
+ info:
+ ping_secret: "1bd1yi0x4lb5q4gzqqtrnq30oyj08r8dtdimmanbqw49z1anz2"
+ slurm_state: "idle"
+ total_cpu_cores: 16
--- /dev/null
+new_pipeline:
+ state: New
+ uuid: zzzzz-d1hrv-f4gneyn6br1xize
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: <%= 1.minute.ago.to_s(:db) %>
+
+new_pipeline_in_subproject:
+ state: New
+ uuid: zzzzz-d1hrv-subprojpipeline
+ owner_uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ created_at: <%= 1.minute.ago.to_s(:db) %>
+
+has_component_with_no_script_parameters:
+ state: Ready
+ uuid: zzzzz-d1hrv-1xfj6xkicf2muk2
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: <%= 10.minute.ago.to_s(:db) %>
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters: {}
+
+has_component_with_empty_script_parameters:
+ state: Ready
+ uuid: zzzzz-d1hrv-jq16l10gcsnyumo
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: <%= 3.minute.ago.to_s(:db) %>
+ components:
+ foo:
+ script: foo
+ script_version: master
+
+has_component_with_completed_jobs:
+ # Test that the job "started_at" and "finished_at" fields are
+ # parsed into Time fields when rendering. This job must *not*
+ # have its own fixture; the point is to force the
+ # pipeline_instances_controller_test in Workbench to parse
+ # the "components" field.
+ state: Complete
+ uuid: zzzzz-d1hrv-i3e77t9z5y8j9cc
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters: {}
+ job:
+ uuid: zzzzz-8i9sb-rft1xdewxkwgxnz
+ script_version: master
+ started_at: <%= 10.minute.ago.to_s(:db) %>
+ finished_at: <%= 9.minute.ago.to_s(:db) %>
+
+has_job:
+ name: pipeline_with_job
+ state: Ready
+ uuid: zzzzz-d1hrv-1yfj6xkidf2muk3
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: <%= 3.1.minute.ago.to_s(:db) %>
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters: {}
+ job: {
+ uuid: zzzzz-8i9sb-pshmckwoma9plh7,
+ script_version: master
+ }
+
+components_is_jobspec:
+ # Helps test that clients cope with funny-shaped components.
+ # For an example, see #3321.
+ uuid: zzzzz-d1hrv-jobspeccomponts
+ created_at: <%= 30.minute.ago.to_s(:db) %>
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-14 12:35:04 -0400
+ updated_at: 2014-04-14 12:35:04 -0400
+ modified_at: 2014-04-14 12:35:04 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ state: RunningOnServer
+ components:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: "Foo/bar pair"
+ description: "Provide a collection containing at least two files."
+
+pipeline_with_tagged_collection_input:
+ name: pipeline_with_tagged_collection_input
+ state: Ready
+ uuid: zzzzz-d1hrv-1yfj61234abcdk3
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: <%= 3.1.minute.ago.to_s(:db) %>
+ components:
+ part-one:
+ script_parameters:
+ input:
+ value: zzzzz-4zz18-znfnqtbbv4spc3w
+
+pipeline_to_merge_params:
+ name: pipeline_to_merge_params
+ state: Ready
+ uuid: zzzzz-d1hrv-1yfj6dcba4321k3
+ pipeline_template_uuid: zzzzz-p5p6p-aox0k0ofxrystgw
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: <%= 3.1.minute.ago.to_s(:db) %>
+ components:
+ part-one:
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: "Foo/bar pair"
+ description: "Provide a collection containing at least two files."
+ part-two:
+ script_parameters:
+ input:
+ output_of: part-one
+ integer_with_default:
+ default: 123
+ integer_with_value:
+ value: 123
+ string_with_default:
+ default: baz
+ string_with_value:
+ value: baz
+ plain_string: qux
+ array_with_default:
+ default: [1,1,2,3,5]
+ array_with_value:
+ value: [1,1,2,3,5]
+
+pipeline_with_newer_template:
+ state: Complete
+ uuid: zzzzz-d1hrv-9fm8l10i9z2kqc6
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ pipeline_template_uuid: zzzzz-p5p6p-vq4wuvy84xvaq2r
+ created_at: 2014-09-15 12:00:00
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: foo instance input
+
+pipeline_instance_owned_by_fuse:
+ state: Complete
+ uuid: zzzzz-d1hrv-ri9dvgkgqs9y09j
+ owner_uuid: zzzzz-tpzed-0fusedrivertest
+ pipeline_template_uuid: zzzzz-p5p6p-vq4wuvy84xvaq2r
+ created_at: 2014-09-15 12:00:00
+ name: "pipeline instance owned by FUSE"
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: foo instance input
+
+pipeline_instance_in_fuse_project:
+ state: Complete
+ uuid: zzzzz-d1hrv-scarxiyajtshq3l
+ owner_uuid: zzzzz-j7d0g-0000ownedbyfuse
+ pipeline_template_uuid: zzzzz-p5p6p-vq4wuvy84xvaq2r
+ created_at: 2014-09-15 12:00:00
+ name: "pipeline instance in FUSE project"
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: foo instance input
+
+
+# Test Helper trims the rest of the file
+
+# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
+
+# pipelines in project_with_10_pipelines
+<% for i in 1..10 do %>
+pipeline_<%=i%>_of_10:
+ name: pipeline_<%= i %>
+ state: Failed
+ uuid: zzzzz-d1hrv-10pipelines0<%= i.to_s.rjust(3, '0') %>
+ owner_uuid: zzzzz-j7d0g-000010pipelines
+ created_at: <%= (2*(i-1)).hour.ago.to_s(:db) %>
+ started_at: <%= (2*(i-1)).hour.ago.to_s(:db) %>
+ finished_at: <%= (i-1).minute.ago.to_s(:db) %>
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: foo instance input
+<% end %>
+
+# pipelines in project_with_2_pipelines_and_100_jobs
+<% for i in 1..2 do %>
+pipeline_<%=i%>_of_2_pipelines_and_100_jobs:
+ name: pipeline_<%= i %>
+ state: New
+ uuid: zzzzz-d1hrv-abcgneyn6brx<%= i.to_s.rjust(3, '0') %>
+ owner_uuid: zzzzz-j7d0g-nnjobspipelines
+ created_at: <%= i.minute.ago.to_s(:db) %>
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: foo instance input
+<% end %>
+
+# pipelines in project_with_25_pipelines
+<% for i in 1..25 do %>
+pipeline_<%=i%>_of_25:
+ name: pipeline_<%=i%>
+ state: Failed
+ uuid: zzzzz-d1hrv-25pipelines0<%= i.to_s.rjust(3, '0') %>
+ owner_uuid: zzzzz-j7d0g-000025pipelines
+ created_at: <%= i.hour.ago.to_s(:db) %>
+ started_at: <%= i.hour.ago.to_s(:db) %>
+ finished_at: <%= i.minute.ago.to_s(:db) %>
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: foo instance input
+<% end %>
+
+# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
--- /dev/null
+two_part:
+ uuid: zzzzz-p5p6p-aox0k0ofxrystgw
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-04-14 12:35:04 -0400
+ updated_at: 2014-04-14 12:35:04 -0400
+ modified_at: 2014-04-14 12:35:04 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: Two Part Pipeline Template
+ components:
+ part-one:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: "Foo/bar pair"
+ part-two:
+ script: bar
+ script_version: master
+ script_parameters:
+ input:
+ output_of: part-one
+ integer_with_default:
+ default: 123
+ integer_with_value:
+ value: 123
+ string_with_default:
+ default: baz
+ string_with_value:
+ value: baz
+ plain_string: qux
+ array_with_default: # important to test repeating values in the array!
+ default: [1,1,2,3,5]
+ array_with_value: # important to test repeating values in the array!
+ value: [1,1,2,3,5]
+
+components_is_jobspec:
+ # Helps test that clients cope with funny-shaped components.
+ # For an example, see #3321.
+ uuid: zzzzz-p5p6p-jobspeccomponts
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-14 12:35:04 -0400
+ updated_at: 2014-04-14 12:35:04 -0400
+ modified_at: 2014-04-14 12:35:04 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: Pipeline Template with Jobspec Components
+ components:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: "Foo/bar pair"
+ description: "Provide a collection containing at least two files."
+
+parameter_with_search:
+ uuid: zzzzz-p5p6p-paramwsearch345
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-14 12:35:04 -0400
+ updated_at: 2014-04-14 12:35:04 -0400
+ modified_at: 2014-04-14 12:35:04 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: Pipeline Template with Input Parameter with Search
+ components:
+ with-search:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: "Foo/bar pair"
+ description: "Provide a collection containing at least two files."
+ search_for: sometime # Matches baz_collection_in_asubproject
+
+new_pipeline_template:
+ # This template must include components that are not
+ # present in the pipeline instance 'pipeline_with_newer_template',
+ # at least one of which has a script_parameter that is a hash
+ # with a 'dataclass' field (ticket #4000)
+ uuid: zzzzz-p5p6p-vq4wuvy84xvaq2r
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-09-14 12:00:00
+ modified_at: 2014-09-16 12:00:00
+ name: Pipeline Template Newer Than Instance
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: foo template input
+ bar:
+ script: bar
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: bar template input
+
+pipeline_template_in_fuse_project:
+ uuid: zzzzz-p5p6p-templinfuseproj
+ owner_uuid: zzzzz-j7d0g-0000ownedbyfuse
+ created_at: 2014-04-14 12:35:04 -0400
+ updated_at: 2014-04-14 12:35:04 -0400
+ modified_at: 2014-04-14 12:35:04 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-0fusedrivertest
+ name: pipeline template in FUSE project
+ components:
+ foo_component:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: Collection
+ title: "default input"
+ description: "input collection"
+
+template_with_dataclass_file:
+ uuid: zzzzz-p5p6p-k0xoa0ofxrystgw
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-04-14 12:35:04 -0400
+ updated_at: 2014-04-14 12:35:04 -0400
+ modified_at: 2014-04-14 12:35:04 -0400
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: Two Part Template with dataclass File
+ components:
+ part-one:
+ script: foo
+ script_version: master
+ script_parameters:
+ input:
+ required: true
+ dataclass: File
+ title: "Foo/bar pair"
+ description: "Provide an input file"
+ part-two:
+ script: bar
+ script_version: master
+ script_parameters:
+ input:
+ output_of: part-one
+ integer_with_default:
+ default: 123
+ integer_with_value:
+ value: 123
+ string_with_default:
+ default: baz
+ string_with_value:
+ value: baz
+ plain_string: qux
+ array_with_default: # important to test repeating values in the array!
+ default: [1,1,2,3,5]
+ array_with_value: # important to test repeating values in the array!
+ value: [1,1,2,3,5]
--- /dev/null
+crunch_dispatch_test:
+ uuid: zzzzz-s0uqq-382brsig8rp3665
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz # active user
+ name: crunch_dispatch_test
+
+arvados:
+ uuid: zzzzz-s0uqq-arvadosrepo0123
+ owner_uuid: zzzzz-tpzed-000000000000000 # root
+ name: arvados
+
+foo:
+ uuid: zzzzz-s0uqq-382brsig8rp3666
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz # active user
+ name: foo
+
+repository2:
+ uuid: zzzzz-s0uqq-382brsig8rp3667
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz # active user
+ name: foo2
+
+repository3:
+ uuid: zzzzz-s0uqq-38orljkqpyo1j61
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f # admin user
+ name: foo3
+
+auto_setup_repository:
+ uuid: zzzzz-s0uqq-382brabc8rp3667
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz # active user
+ name: auto_setup_repo
--- /dev/null
+owned_by_active_user:
+ uuid: zzzzz-j58dm-3zx463qyo0k4xrn
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
+
+owned_by_private_group:
+ uuid: zzzzz-j58dm-5m3qwg45g3nlpu6
+ owner_uuid: zzzzz-j7d0g-rew6elm53kancon
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
+
+owned_by_spectator:
+ uuid: zzzzz-j58dm-3b0xxwzlbzxq5yr
+ owner_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
+
+in_aproject:
+ uuid: zzzzz-j58dm-7r18rnd5nzhg5yk
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
+
+in_asubproject:
+ uuid: zzzzz-j58dm-c40lddwcqqr1ffs
+ owner_uuid: zzzzz-j7d0g-axqo7eu9pwvna1x
+ created_at: 2014-04-21 15:37:48 -0400
+ modified_at: 2014-04-21 15:37:48 -0400
--- /dev/null
+owned_by_aproject_with_no_name:
+ uuid: zzzzz-q1cn2-ypsjlol9dofwijz
+ owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+ created_at: 2014-05-05 04:11:52 -0400
+ modified_at: 2014-05-05 04:11:52 -0400
--- /dev/null
+# Read about fixtures at http://api.rubyonrails.org/classes/ActiveRecord/Fixtures.html
+
+system_user:
+ uuid: zzzzz-tpzed-000000000000000
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-11-27 06:38:21.215463000 Z
+ modified_by_client_uuid: zzzzz-ozdt8-teyxzyd8qllg11h
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-11-27 06:38:21.208036000 Z
+ email: root
+ first_name: root
+ last_name: ''
+ identity_url:
+ is_admin: true
+ prefs: {}
+ updated_at: 2014-11-27 06:38:21.207873000 Z
+ is_active: true
+
+admin:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-d9tiejq69daie8f
+ email: admin@arvados.local
+ first_name: TestCase
+ last_name: Administrator
+ identity_url: https://admin.openid.local
+ is_active: true
+ is_admin: true
+ prefs:
+ profile:
+ organization: example.com
+ role: IT
+
+miniadmin:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-2bg9x0oeydcw5hm
+ email: miniadmin@arvados.local
+ first_name: TestCase
+ last_name: User Group Administrator
+ identity_url: https://miniadmin.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: IT
+
+rominiadmin:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-4hvxm4n25emegis
+ email: rominiadmin@arvados.local
+ first_name: TestCase
+ last_name: Read-Only User Group Administrator
+ identity_url: https://rominiadmin.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: IT
+
+active:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ email: active-user@arvados.local
+ first_name: Active
+ last_name: User
+ identity_url: https://active-user.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: Computational biologist
+
+project_viewer:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-projectviewer1a
+ email: project-viewer@arvados.local
+ first_name: Project
+ last_name: Viewer
+ identity_url: https://project-viewer.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: Computational biologist
+
+future_project_user:
+ # Workbench tests give this user permission on aproject.
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-futureprojview2
+ email: future-project-user@arvados.local
+ first_name: Future Project
+ last_name: User
+ identity_url: https://future-project-user.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: Computational biologist
+
+subproject_admin:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-subprojectadmin
+ email: subproject-admin@arvados.local
+ first_name: Subproject
+ last_name: Admin
+ identity_url: https://subproject-admin.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: Computational biologist
+
+spectator:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ email: spectator@arvados.local
+ first_name: Spect
+ last_name: Ator
+ identity_url: https://spectator.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: Computational biologist
+
+inactive_uninvited:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-rf2ec3ryh4vb5ma
+ email: inactive-uninvited-user@arvados.local
+ first_name: Inactive and Uninvited
+ last_name: User
+ identity_url: https://inactive-uninvited-user.openid.local
+ is_active: false
+ is_admin: false
+ prefs: {}
+
+inactive:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-x9kqpd79egh49c7
+ email: inactive-user@arvados.local
+ first_name: Inactive
+ last_name: User
+ identity_url: https://inactive-user.openid.local
+ is_active: false
+ is_admin: false
+ prefs: {}
+
+inactive_but_signed_user_agreement:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-7sg468ezxwnodxs
+ email: inactive-user-signed-ua@arvados.local
+ first_name: Inactive But Agreeable
+ last_name: User
+ identity_url: https://inactive-but-agreeable-user.openid.local
+ is_active: false
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: Computational biologist
+
+anonymous:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-anonymouspublic
+ email: anonymouspublic
+ first_name: anonymouspublic
+ last_name: anonymouspublic
+ is_active: false
+ is_admin: false
+ prefs: {}
+
+job_reader:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-905b42d1dd4a354
+ email: jobber@arvados.local
+ first_name: Job
+ last_name: Er
+ identity_url: https://spectator.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: Computational biologist
+
+active_no_prefs:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-a46c42d1td4aoj4
+ email: active_no_prefs@arvados.local
+ first_name: NoPrefs
+ last_name: NoProfile
+ identity_url: https://active_no_prefs.openid.local
+ is_active: true
+ is_admin: false
+ prefs: {}
+
+active_no_prefs_profile:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-a46c98d1td4aoj4
+ email: active_no_prefs_profile@arvados.local
+ first_name: HasPrefs
+ last_name: NoProfile
+ identity_url: https://active_no_prefs_profile.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ test: abc
+
+# Fixtures to test granting and removing permissions.
+
+user_foo_in_sharing_group:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-81hsbo6mk8nl05c
+ email: user_foo_in_sharing_group@arvados.local
+ first_name: Foo
+ last_name: Sharing
+ identity_url: https://user_foo_in_sharing_group.openid.local
+ is_active: true
+ is_admin: false
+
+user_bar_in_sharing_group:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-n3oaj4sm5fcnwib
+ email: user_bar_in_sharing_group@arvados.local
+ first_name: Bar
+ last_name: Sharing
+ identity_url: https://user_bar_in_sharing_group.openid.local
+ is_active: true
+ is_admin: false
+
+user1_with_load:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-user1withloadab
+ email: user1_with_load@arvados.local
+ first_name: user1_with_load
+ last_name: User
+ identity_url: https://user1_with_load.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: IT
+
+fuse:
+ owner_uuid: zzzzz-tpzed-000000000000000
+ uuid: zzzzz-tpzed-0fusedrivertest
+ email: fuse@arvados.local
+ first_name: FUSE
+ last_name: User
+ identity_url: https://fuse.openid.local
+ is_active: true
+ is_admin: false
+ prefs:
+ profile:
+ organization: example.com
+ role: IT
--- /dev/null
+testvm:
+ uuid: zzzzz-2x53u-382brsig8rp3064
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ hostname: testvm.shell
+
+testvm2:
+ uuid: zzzzz-2x53u-382brsig8rp3065
+ owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
+ hostname: testvm2.shell
--- /dev/null
+require 'test_helper'
+
+class ApplicationControllerTest < ActionController::TestCase
+ BAD_UUID = "zzzzz-zzzzz-zzzzzzzzzzzzzzz"
+
+ def now_timestamp
+ Time.now.utc.to_i
+ end
+
+ setup do
+ # These tests are meant to check behavior in ApplicationController.
+ # We instantiate a small concrete controller for convenience.
+ @controller = Arvados::V1::SpecimensController.new
+ @start_stamp = now_timestamp
+ end
+
+ def check_error_token
+ token = json_response['error_token']
+ assert_not_nil token
+ token_time = token.split('+', 2).first.to_i
+ assert_operator(token_time, :>=, @start_stamp, "error token too old")
+ assert_operator(token_time, :<=, now_timestamp, "error token too new")
+ end
+
+ def check_404(errmsg="Path not found")
+ assert_response 404
+ assert_equal([errmsg], json_response['errors'])
+ check_error_token
+ end
+
+ test "requesting nonexistent object returns 404 error" do
+ authorize_with :admin
+ get(:show, id: BAD_UUID)
+ check_404
+ end
+
+ test "requesting object without read permission returns 404 error" do
+ authorize_with :spectator
+ get(:show, id: specimens(:owned_by_active_user).uuid)
+ check_404
+ end
+
+ test "submitting bad object returns error" do
+ authorize_with :spectator
+ post(:create, specimen: {badattr: "badvalue"})
+ assert_response 422
+ check_error_token
+ end
+
+ ['foo', '', 'FALSE', 'TRUE', nil, [true], {a:true}, '"true"'].each do |bogus|
+ test "bogus boolean parameter #{bogus.inspect} returns error" do
+ @controller = Arvados::V1::GroupsController.new
+ authorize_with :active
+ post :create, {
+ group: {},
+ ensure_unique_name: bogus
+ }
+ assert_response 422
+ assert_match(/parameter must be a boolean/, json_response['errors'].first,
+ 'Helpful error message not found')
+ end
+ end
+
+ [[true, [true, 'true', 1, '1']],
+ [false, [false, 'false', 0, '0']]].each do |bool, boolparams|
+ boolparams.each do |boolparam|
+ # Ensure boolparam is acceptable as a boolean
+ test "boolean parameter #{boolparam.inspect} acceptable" do
+ @controller = Arvados::V1::GroupsController.new
+ authorize_with :active
+ post :create, {
+ group: {},
+ ensure_unique_name: boolparam
+ }
+ assert_response :success
+ end
+
+ # Ensure boolparam is acceptable as the _intended_ boolean
+ test "boolean parameter #{boolparam.inspect} accepted as #{bool.inspect}" do
+ @controller = Arvados::V1::GroupsController.new
+ authorize_with :active
+ post :create, {
+ group: {
+ name: groups(:aproject).name,
+ owner_uuid: groups(:aproject).owner_uuid
+ },
+ ensure_unique_name: boolparam
+ }
+ assert_response (bool ? :success : 422)
+ end
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::ApiClientAuthorizationsControllerTest < ActionController::TestCase
+ test "should get index" do
+ authorize_with :active_trustedclient
+ get :index
+ assert_response :success
+ end
+
+ test "should not get index with expired auth" do
+ authorize_with :expired
+ get :index, format: :json
+ assert_response 401
+ end
+
+ test "should not get index from untrusted client" do
+ authorize_with :active
+ get :index
+ assert_response 403
+ end
+
+ test "create system auth" do
+ authorize_with :admin_trustedclient
+ post :create_system_auth, scopes: '["test"]'
+ assert_response :success
+ end
+
+ test "prohibit create system auth with token from non-trusted client" do
+ authorize_with :admin
+ post :create_system_auth, scopes: '["test"]'
+ assert_response 403
+ end
+
+ test "prohibit create system auth by non-admin" do
+ authorize_with :active
+ post :create_system_auth, scopes: '["test"]'
+ assert_response 403
+ end
+
+ def assert_found_tokens(auth, search_params, *expected_tokens)
+ authorize_with auth
+ expected_tokens.map! { |name| api_client_authorizations(name).api_token }
+ get :index, search_params
+ assert_response :success
+ got_tokens = JSON.parse(@response.body)['items']
+ .map { |auth| auth['api_token'] }
+ assert_equal(expected_tokens.sort, got_tokens.sort,
+ "wrong results for #{search_params.inspect}")
+ end
+
+ # Three-tuples with auth to use, scopes to find, and expected tokens.
+ # Make two tests for each tuple, one searching with where and the other
+ # with filter.
+ [[:admin_trustedclient, [], :admin_noscope],
+ [:active_trustedclient, ["GET /arvados/v1/users"], :active_userlist],
+ [:active_trustedclient,
+ ["POST /arvados/v1/api_client_authorizations",
+ "GET /arvados/v1/api_client_authorizations"],
+ :active_apitokens],
+ ].each do |auth, scopes, *expected|
+ test "#{auth.to_s} can find auths where scopes=#{scopes.inspect}" do
+ assert_found_tokens(auth, {where: {scopes: scopes}}, *expected)
+ end
+
+ test "#{auth.to_s} can find auths filtered with scopes=#{scopes.inspect}" do
+ assert_found_tokens(auth, {filters: [['scopes', '=', scopes]]}, *expected)
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::AuthorizedKeysControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::CollectionsControllerTest < ActionController::TestCase
+
+ def permit_unsigned_manifests isok=true
+ # Set security model for the life of a test.
+ Rails.configuration.permit_create_collection_with_unsigned_manifest = isok
+ end
+
+ def assert_signed_manifest manifest_text, label=''
+ assert_not_nil manifest_text, "#{label} manifest_text was nil"
+ manifest_text.scan(/ [[:xdigit:]]{32}\S*/) do |tok|
+ assert_match(/\+A[[:xdigit:]]+@[[:xdigit:]]{8}\b/, tok,
+ "Locator in #{label} manifest_text was not signed")
+ end
+ end
+
+ test "should get index" do
+ authorize_with :active
+ get :index
+ assert_response :success
+ assert(assigns(:objects).andand.any?, "no Collections returned in index")
+ refute(json_response["items"].any? { |c| c.has_key?("manifest_text") },
+ "basic Collections index included manifest_text")
+ end
+
+ test "collections.get returns signed locators" do
+ permit_unsigned_manifests
+ authorize_with :active
+ get :show, {id: collections(:foo_file).uuid}
+ assert_response :success
+ assert_signed_manifest json_response['manifest_text'], 'foo_file'
+ end
+
+ test "index with manifest_text selected returns signed locators" do
+ columns = %w(uuid owner_uuid manifest_text)
+ authorize_with :active
+ get :index, select: columns
+ assert_response :success
+ assert(assigns(:objects).andand.any?,
+ "no Collections returned for index with columns selected")
+ json_response["items"].each do |coll|
+ assert_equal(columns, columns & coll.keys,
+ "Collections index did not respect selected columns")
+ assert_signed_manifest coll['manifest_text'], coll['uuid']
+ end
+ end
+
+ [0,1,2].each do |limit|
+ test "get index with limit=#{limit}" do
+ authorize_with :active
+ get :index, limit: limit
+ assert_response :success
+ assert_equal limit, assigns(:objects).count
+ resp = JSON.parse(@response.body)
+ assert_equal limit, resp['limit']
+ end
+ end
+
+ test "items.count == items_available" do
+ authorize_with :active
+ get :index, limit: 100000
+ assert_response :success
+ resp = JSON.parse(@response.body)
+ assert_equal resp['items_available'], assigns(:objects).length
+ assert_equal resp['items_available'], resp['items'].count
+ unique_uuids = resp['items'].collect { |i| i['uuid'] }.compact.uniq
+ assert_equal unique_uuids.count, resp['items'].count
+ end
+
+ test "items.count == items_available with filters" do
+ authorize_with :active
+ get :index, {
+ limit: 100,
+ filters: [['uuid','=',collections(:foo_file).uuid]]
+ }
+ assert_response :success
+ assert_equal 1, assigns(:objects).length
+ assert_equal 1, json_response['items_available']
+ assert_equal 1, json_response['items'].count
+ end
+
+ test "get index with limit=2 offset=99999" do
+ # Assume there are not that many test fixtures.
+ authorize_with :active
+ get :index, limit: 2, offset: 99999
+ assert_response :success
+ assert_equal 0, assigns(:objects).count
+ resp = JSON.parse(@response.body)
+ assert_equal 2, resp['limit']
+ assert_equal 99999, resp['offset']
+ end
+
+ test "admin can create collection with unsigned manifest" do
+ authorize_with :admin
+ test_collection = {
+ manifest_text: <<-EOS
+. d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo.txt
+. acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:bar.txt
+. acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:bar.txt
+./baz acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:bar.txt
+EOS
+ }
+ test_collection[:portable_data_hash] =
+ Digest::MD5.hexdigest(test_collection[:manifest_text]) +
+ '+' +
+ test_collection[:manifest_text].length.to_s
+
+ # post :create will modify test_collection in place, so we save a copy first.
+ # Hash.deep_dup is not sufficient as it preserves references of strings (??!?)
+ post_collection = Marshal.load(Marshal.dump(test_collection))
+ post :create, {
+ collection: post_collection
+ }
+
+ assert_response :success
+ assert_nil assigns(:objects)
+
+ response_collection = assigns(:object)
+
+ stored_collection = Collection.select([:uuid, :portable_data_hash, :manifest_text]).
+ where(portable_data_hash: response_collection['portable_data_hash']).first
+
+ assert_equal test_collection[:portable_data_hash], stored_collection['portable_data_hash']
+
+ # The manifest in the response will have had permission hints added.
+ # Remove any permission hints in the response before comparing it to the source.
+ stripped_manifest = stored_collection['manifest_text'].gsub(/\+A[A-Za-z0-9@_-]+/, '')
+ assert_equal test_collection[:manifest_text], stripped_manifest
+
+ # TBD: create action should add permission signatures to manifest_text in the response,
+ # and we need to check those permission signatures here.
+ end
+
+ [:admin, :active].each do |user|
+ test "#{user} can get collection using portable data hash" do
+ authorize_with user
+
+ foo_collection = collections(:foo_file)
+
+ # Get foo_file using its portable data hash
+ get :show, {
+ id: foo_collection[:portable_data_hash]
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ resp = assigns(:object)
+ assert_equal foo_collection[:portable_data_hash], resp['portable_data_hash']
+ assert_signed_manifest resp['manifest_text']
+
+ # The manifest in the response will have had permission hints added.
+ # Remove any permission hints in the response before comparing it to the source.
+ stripped_manifest = resp['manifest_text'].gsub(/\+A[A-Za-z0-9@_-]+/, '')
+ assert_equal foo_collection[:manifest_text], stripped_manifest
+ end
+ end
+
+ test "create with owner_uuid set to owned group" do
+ permit_unsigned_manifests
+ authorize_with :active
+ manifest_text = ". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n"
+ post :create, {
+ collection: {
+ owner_uuid: 'zzzzz-j7d0g-rew6elm53kancon',
+ manifest_text: manifest_text,
+ portable_data_hash: "d30fe8ae534397864cb96c544f4cf102+47"
+ }
+ }
+ assert_response :success
+ resp = JSON.parse(@response.body)
+ assert_equal 'zzzzz-j7d0g-rew6elm53kancon', resp['owner_uuid']
+ end
+
+ test "create fails with duplicate name" do
+ permit_unsigned_manifests
+ authorize_with :admin
+ manifest_text = ". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n"
+ post :create, {
+ collection: {
+ owner_uuid: 'zzzzz-tpzed-000000000000000',
+ manifest_text: manifest_text,
+ portable_data_hash: "d30fe8ae534397864cb96c544f4cf102+47",
+ name: "foo_file"
+ }
+ }
+ assert_response 422
+ response_errors = json_response['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert(response_errors.first.include?('duplicate key'),
+ "Expected 'duplicate key' error in #{response_errors.first}")
+ end
+
+ [false, true].each do |unsigned|
+ test "create with duplicate name, ensure_unique_name, unsigned=#{unsigned}" do
+ permit_unsigned_manifests unsigned
+ authorize_with :active
+ manifest_text = ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:foo.txt\n"
+ if !unsigned
+ manifest_text = Collection.sign_manifest manifest_text, api_token(:active)
+ end
+ post :create, {
+ collection: {
+ owner_uuid: users(:active).uuid,
+ manifest_text: manifest_text,
+ name: "owned_by_active"
+ },
+ ensure_unique_name: true
+ }
+ assert_response :success
+ assert_equal 'owned_by_active (2)', json_response['name']
+ end
+ end
+
+ test "create with owner_uuid set to group i can_manage" do
+ permit_unsigned_manifests
+ authorize_with :active
+ manifest_text = ". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n"
+ post :create, {
+ collection: {
+ owner_uuid: groups(:active_user_has_can_manage).uuid,
+ manifest_text: manifest_text,
+ portable_data_hash: "d30fe8ae534397864cb96c544f4cf102+47"
+ }
+ }
+ assert_response :success
+ resp = JSON.parse(@response.body)
+ assert_equal groups(:active_user_has_can_manage).uuid, resp['owner_uuid']
+ end
+
+ test "create with owner_uuid fails on group with only can_read permission" do
+ permit_unsigned_manifests
+ authorize_with :active
+ manifest_text = ". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n"
+ post :create, {
+ collection: {
+ owner_uuid: groups(:all_users).uuid,
+ manifest_text: manifest_text,
+ portable_data_hash: "d30fe8ae534397864cb96c544f4cf102+47"
+ }
+ }
+ assert_response 403
+ end
+
+ test "create with owner_uuid fails on group with no permission" do
+ permit_unsigned_manifests
+ authorize_with :active
+ manifest_text = ". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n"
+ post :create, {
+ collection: {
+ owner_uuid: groups(:public).uuid,
+ manifest_text: manifest_text,
+ portable_data_hash: "d30fe8ae534397864cb96c544f4cf102+47"
+ }
+ }
+ assert_response 422
+ end
+
+ test "admin create with owner_uuid set to group with no permission" do
+ permit_unsigned_manifests
+ authorize_with :admin
+ manifest_text = ". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n"
+ post :create, {
+ collection: {
+ owner_uuid: 'zzzzz-j7d0g-it30l961gq3t0oi',
+ manifest_text: manifest_text,
+ portable_data_hash: "d30fe8ae534397864cb96c544f4cf102+47"
+ }
+ }
+ assert_response :success
+ end
+
+ test "should create with collection passed as json" do
+ permit_unsigned_manifests
+ authorize_with :active
+ post :create, {
+ collection: <<-EOS
+ {
+ "manifest_text":". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n",\
+ "portable_data_hash":"d30fe8ae534397864cb96c544f4cf102+47"\
+ }
+ EOS
+ }
+ assert_response :success
+ end
+
+ test "should fail to create with checksum mismatch" do
+ permit_unsigned_manifests
+ authorize_with :active
+ post :create, {
+ collection: <<-EOS
+ {
+ "manifest_text":". d41d8cd98f00b204e9800998ecf8427e 0:0:bar.txt\n",\
+ "portable_data_hash":"d30fe8ae534397864cb96c544f4cf102+47"\
+ }
+ EOS
+ }
+ assert_response 422
+ end
+
+ test "collection UUID is normalized when created" do
+ permit_unsigned_manifests
+ authorize_with :active
+ post :create, {
+ collection: {
+ manifest_text: ". d41d8cd98f00b204e9800998ecf8427e 0:0:foo.txt\n",
+ portable_data_hash: "d30fe8ae534397864cb96c544f4cf102+47+Khint+Xhint+Zhint"
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ resp = JSON.parse(@response.body)
+ assert_equal "d30fe8ae534397864cb96c544f4cf102+47", resp['portable_data_hash']
+ end
+
+ test "get full provenance for baz file" do
+ authorize_with :active
+ get :provenance, id: 'ea10d51bcf88862dbcc36eb292017dfd+45'
+ assert_response :success
+ resp = JSON.parse(@response.body)
+ assert_not_nil resp['ea10d51bcf88862dbcc36eb292017dfd+45'] # baz
+ assert_not_nil resp['fa7aeb5140e2848d39b416daeef4ffc5+45'] # bar
+ assert_not_nil resp['1f4b0bc7583c2a7f9102c395f4ffc5e3+45'] # foo
+ assert_not_nil resp['zzzzz-8i9sb-cjs4pklxxjykyuq'] # bar->baz
+ assert_not_nil resp['zzzzz-8i9sb-aceg2bnq7jt7kon'] # foo->bar
+ end
+
+ test "get no provenance for foo file" do
+ # spectator user cannot even see baz collection
+ authorize_with :spectator
+ get :provenance, id: '1f4b0bc7583c2a7f9102c395f4ffc5e3+45'
+ assert_response 404
+ end
+
+ test "get partial provenance for baz file" do
+ # spectator user can see bar->baz job, but not foo->bar job
+ authorize_with :spectator
+ get :provenance, id: 'ea10d51bcf88862dbcc36eb292017dfd+45'
+ assert_response :success
+ resp = JSON.parse(@response.body)
+ assert_not_nil resp['ea10d51bcf88862dbcc36eb292017dfd+45'] # baz
+ assert_not_nil resp['fa7aeb5140e2848d39b416daeef4ffc5+45'] # bar
+ assert_not_nil resp['zzzzz-8i9sb-cjs4pklxxjykyuq'] # bar->baz
+ assert_nil resp['zzzzz-8i9sb-aceg2bnq7jt7kon'] # foo->bar
+ assert_nil resp['1f4b0bc7583c2a7f9102c395f4ffc5e3+45'] # foo
+ end
+
+ test "search collections with 'any' operator" do
+ authorize_with :active
+ get :index, {
+ where: { any: ['contains', 'd0bc8c7f34be170a7b7b'] }
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:portable_data_hash)
+ assert_equal 1, found.count
+ assert_equal true, !!found.index('5bd9c1ad0bc8c7f34be170a7b7b39089+45')
+ end
+
+ [false, true].each do |permit_unsigned|
+ test "create collection with signed manifest, permit_unsigned=#{permit_unsigned}" do
+ permit_unsigned_manifests permit_unsigned
+ authorize_with :active
+ locators = %w(
+ d41d8cd98f00b204e9800998ecf8427e+0
+ acbd18db4cc2f85cedef654fccc4a4d8+3
+ ea10d51bcf88862dbcc36eb292017dfd+45)
+
+ unsigned_manifest = locators.map { |loc|
+ ". " + loc + " 0:0:foo.txt\n"
+ }.join()
+ manifest_uuid = Digest::MD5.hexdigest(unsigned_manifest) +
+ '+' +
+ unsigned_manifest.length.to_s
+
+ # Build a manifest with both signed and unsigned locators.
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token(:active),
+ }
+ signed_locators = locators.collect do |x|
+ Blob.sign_locator x, signing_opts
+ end
+ if permit_unsigned
+ # Leave a non-empty blob unsigned.
+ signed_locators[1] = locators[1]
+ else
+ # Leave the empty blob unsigned. This should still be allowed.
+ signed_locators[0] = locators[0]
+ end
+ signed_manifest =
+ ". " + signed_locators[0] + " 0:0:foo.txt\n" +
+ ". " + signed_locators[1] + " 0:0:foo.txt\n" +
+ ". " + signed_locators[2] + " 0:0:foo.txt\n"
+
+ post :create, {
+ collection: {
+ manifest_text: signed_manifest,
+ portable_data_hash: manifest_uuid,
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ resp = JSON.parse(@response.body)
+ assert_equal manifest_uuid, resp['portable_data_hash']
+ # All of the locators in the output must be signed.
+ resp['manifest_text'].lines.each do |entry|
+ m = /([[:xdigit:]]{32}\+\S+)/.match(entry)
+ if m
+ assert Blob.verify_signature m[0], signing_opts
+ end
+ end
+ end
+ end
+
+ test "create collection with signed manifest and explicit TTL" do
+ authorize_with :active
+ locators = %w(
+ d41d8cd98f00b204e9800998ecf8427e+0
+ acbd18db4cc2f85cedef654fccc4a4d8+3
+ ea10d51bcf88862dbcc36eb292017dfd+45)
+
+ unsigned_manifest = locators.map { |loc|
+ ". " + loc + " 0:0:foo.txt\n"
+ }.join()
+ manifest_uuid = Digest::MD5.hexdigest(unsigned_manifest) +
+ '+' +
+ unsigned_manifest.length.to_s
+
+ # build a manifest with both signed and unsigned locators.
+ # TODO(twp): in phase 4, all locators will need to be signed, so
+ # this test should break and will need to be rewritten. Issue #2755.
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token(:active),
+ ttl: 3600 # 1 hour
+ }
+ signed_manifest =
+ ". " + locators[0] + " 0:0:foo.txt\n" +
+ ". " + Blob.sign_locator(locators[1], signing_opts) + " 0:0:foo.txt\n" +
+ ". " + Blob.sign_locator(locators[2], signing_opts) + " 0:0:foo.txt\n"
+
+ post :create, {
+ collection: {
+ manifest_text: signed_manifest,
+ portable_data_hash: manifest_uuid,
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ resp = JSON.parse(@response.body)
+ assert_equal manifest_uuid, resp['portable_data_hash']
+ # All of the locators in the output must be signed.
+ resp['manifest_text'].lines.each do |entry|
+ m = /([[:xdigit:]]{32}\+\S+)/.match(entry)
+ if m
+ assert Blob.verify_signature m[0], signing_opts
+ end
+ end
+ end
+
+ test "create fails with invalid signature" do
+ authorize_with :active
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token(:active),
+ }
+
+ # Generate a locator with a bad signature.
+ unsigned_locator = "d41d8cd98f00b204e9800998ecf8427e+0"
+ bad_locator = unsigned_locator + "+Affffffff@ffffffff"
+ assert !Blob.verify_signature(bad_locator, signing_opts)
+
+ # Creating a collection with this locator should
+ # produce 403 Permission denied.
+ unsigned_manifest = ". #{unsigned_locator} 0:0:foo.txt\n"
+ manifest_uuid = Digest::MD5.hexdigest(unsigned_manifest) +
+ '+' +
+ unsigned_manifest.length.to_s
+
+ bad_manifest = ". #{bad_locator} 0:0:foo.txt\n"
+ post :create, {
+ collection: {
+ manifest_text: bad_manifest,
+ portable_data_hash: manifest_uuid
+ }
+ }
+
+ assert_response 403
+ end
+
+ test "create fails with uuid of signed manifest" do
+ authorize_with :active
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token(:active),
+ }
+
+ unsigned_locator = "d41d8cd98f00b204e9800998ecf8427e+0"
+ signed_locator = Blob.sign_locator(unsigned_locator, signing_opts)
+ signed_manifest = ". #{signed_locator} 0:0:foo.txt\n"
+ manifest_uuid = Digest::MD5.hexdigest(signed_manifest) +
+ '+' +
+ signed_manifest.length.to_s
+
+ post :create, {
+ collection: {
+ manifest_text: signed_manifest,
+ portable_data_hash: manifest_uuid
+ }
+ }
+
+ assert_response 422
+ end
+
+ test "multiple locators per line" do
+ permit_unsigned_manifests
+ authorize_with :active
+ locators = %w(
+ d41d8cd98f00b204e9800998ecf8427e+0
+ acbd18db4cc2f85cedef654fccc4a4d8+3
+ ea10d51bcf88862dbcc36eb292017dfd+45)
+
+ manifest_text = [".", *locators, "0:0:foo.txt\n"].join(" ")
+ manifest_uuid = Digest::MD5.hexdigest(manifest_text) +
+ '+' +
+ manifest_text.length.to_s
+
+ test_collection = {
+ manifest_text: manifest_text,
+ portable_data_hash: manifest_uuid,
+ }
+ post_collection = Marshal.load(Marshal.dump(test_collection))
+ post :create, {
+ collection: post_collection
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ resp = JSON.parse(@response.body)
+ assert_equal manifest_uuid, resp['portable_data_hash']
+
+ # The manifest in the response will have had permission hints added.
+ # Remove any permission hints in the response before comparing it to the source.
+ stripped_manifest = resp['manifest_text'].gsub(/\+A[A-Za-z0-9@_-]+/, '')
+ assert_equal manifest_text, stripped_manifest
+ end
+
+ test "multiple signed locators per line" do
+ permit_unsigned_manifests
+ authorize_with :active
+ locators = %w(
+ d41d8cd98f00b204e9800998ecf8427e+0
+ acbd18db4cc2f85cedef654fccc4a4d8+3
+ ea10d51bcf88862dbcc36eb292017dfd+45)
+
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token(:active),
+ }
+
+ unsigned_manifest = [".", *locators, "0:0:foo.txt\n"].join(" ")
+ manifest_uuid = Digest::MD5.hexdigest(unsigned_manifest) +
+ '+' +
+ unsigned_manifest.length.to_s
+
+ signed_locators = locators.map { |loc| Blob.sign_locator loc, signing_opts }
+ signed_manifest = [".", *signed_locators, "0:0:foo.txt\n"].join(" ")
+
+ post :create, {
+ collection: {
+ manifest_text: signed_manifest,
+ portable_data_hash: manifest_uuid,
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ resp = JSON.parse(@response.body)
+ assert_equal manifest_uuid, resp['portable_data_hash']
+ # All of the locators in the output must be signed.
+ # Each line is of the form "path locator locator ... 0:0:file.txt"
+ # entry.split[1..-2] will yield just the tokens in the middle of the line
+ returned_locator_count = 0
+ resp['manifest_text'].lines.each do |entry|
+ entry.split[1..-2].each do |tok|
+ returned_locator_count += 1
+ assert Blob.verify_signature tok, signing_opts
+ end
+ end
+ assert_equal locators.count, returned_locator_count
+ end
+
+ test 'Reject manifest with unsigned blob' do
+ permit_unsigned_manifests false
+ authorize_with :active
+ unsigned_manifest = ". 0cc175b9c0f1b6a831c399e269772661+1 0:1:a.txt\n"
+ manifest_uuid = Digest::MD5.hexdigest(unsigned_manifest)
+ post :create, {
+ collection: {
+ manifest_text: unsigned_manifest,
+ portable_data_hash: manifest_uuid,
+ }
+ }
+ assert_response 403,
+ "Creating a collection with unsigned blobs should respond 403"
+ assert_empty Collection.where('uuid like ?', manifest_uuid+'%'),
+ "Collection should not exist in database after failed create"
+ end
+
+ test 'List expired collection returns empty list' do
+ authorize_with :active
+ get :index, {
+ where: {name: 'expired_collection'},
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_equal 0, found.count
+ end
+
+ test 'Show expired collection returns 404' do
+ authorize_with :active
+ get :show, {
+ id: 'zzzzz-4zz18-mto52zx1s7sn3ih',
+ }
+ assert_response 404
+ end
+
+ test 'Update expired collection returns 404' do
+ authorize_with :active
+ post :update, {
+ id: 'zzzzz-4zz18-mto52zx1s7sn3ih',
+ collection: {
+ name: "still expired"
+ }
+ }
+ assert_response 404
+ end
+
+ test 'List collection with future expiration time succeeds' do
+ authorize_with :active
+ get :index, {
+ where: {name: 'collection_expires_in_future'},
+ }
+ found = assigns(:objects)
+ assert_equal 1, found.count
+ end
+
+
+ test 'Show collection with future expiration time succeeds' do
+ authorize_with :active
+ get :show, {
+ id: 'zzzzz-4zz18-padkqo7yb8d9i3j',
+ }
+ assert_response :success
+ end
+
+ test 'Update collection with future expiration time succeeds' do
+ authorize_with :active
+ post :update, {
+ id: 'zzzzz-4zz18-padkqo7yb8d9i3j',
+ collection: {
+ name: "still not expired"
+ }
+ }
+ assert_response :success
+ end
+end
--- /dev/null
+require 'test_helper'
+require 'helpers/git_test_helper'
+
+# NOTE: calling Commit.find_commit_range(user, nil, nil, 'rev') will produce
+# an error message "fatal: bad object 'rev'" on stderr if 'rev' does not exist
+# in a given repository. Many of these tests report such errors; their presence
+# does not represent a fatal condition.
+#
+# TODO(twp): consider better error handling of these messages, or
+# decide to abandon it.
+
+class Arvados::V1::CommitsControllerTest < ActionController::TestCase
+ fixtures :repositories, :users
+
+ # See git_setup.rb for the commit log for test.git.tar
+ include GitTestHelper
+
+ test "test_find_commit_range" do
+ authorize_with :active
+
+ # single
+ a = Commit.find_commit_range(users(:active), nil, nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', nil)
+ assert_equal ['31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+
+ #test "test_branch1" do
+ # complains "fatal: bad object 077ba2ad3ea24a929091a9e6ce545c93199b8e57"
+ a = Commit.find_commit_range(users(:active), nil, nil, 'master', nil)
+ assert_includes(a, 'f35f99b7d32bac257f5989df02b9f12ee1a9b0d6')
+ assert_includes(a, '077ba2ad3ea24a929091a9e6ce545c93199b8e57')
+
+ #test "test_branch2" do
+ a = Commit.find_commit_range(users(:active), 'foo', nil, 'b1', nil)
+ assert_equal ['1de84a854e2b440dc53bf42f8548afa4c17da332'], a
+
+ #test "test_branch3" do
+ a = Commit.find_commit_range(users(:active), 'foo', nil, 'HEAD', nil)
+ assert_equal ['1de84a854e2b440dc53bf42f8548afa4c17da332'], a
+
+ #test "test_single_revision_repo" do
+ a = Commit.find_commit_range(users(:active), "foo", nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', nil)
+ assert_equal ['31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+ a = Commit.find_commit_range(users(:active), "bar", nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', nil)
+ assert_equal nil, a
+
+ #test "test_multi_revision" do
+ # complains "fatal: bad object 077ba2ad3ea24a929091a9e6ce545c93199b8e57"
+ a = Commit.find_commit_range(users(:active), nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', '077ba2ad3ea24a929091a9e6ce545c93199b8e57', nil)
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57', '4fe459abe02d9b365932b8f5dc419439ab4e2577', '31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+
+ #test "test_tag" do
+ # complains "fatal: ambiguous argument 'tag1': unknown revision or path
+ # not in the working tree."
+ a = Commit.find_commit_range(users(:active), nil, 'tag1', 'master', nil)
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57', '4fe459abe02d9b365932b8f5dc419439ab4e2577'], a
+
+ #test "test_multi_revision_exclude" do
+ a = Commit.find_commit_range(users(:active), nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', '077ba2ad3ea24a929091a9e6ce545c93199b8e57', ['4fe459abe02d9b365932b8f5dc419439ab4e2577'])
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57', '31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+
+ #test "test_multi_revision_tagged_exclude" do
+ # complains "fatal: bad object 077ba2ad3ea24a929091a9e6ce545c93199b8e57"
+ a = Commit.find_commit_range(users(:active), nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', '077ba2ad3ea24a929091a9e6ce545c93199b8e57', ['tag1'])
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57', '31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+
+ Dir.mktmpdir do |touchdir|
+ # invalid input to maximum
+ a = Commit.find_commit_range(users(:active), nil, nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556 ; touch #{touchdir}/uh_oh", nil)
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to maximum
+ a = Commit.find_commit_range(users(:active), nil, nil, "$(uname>#{touchdir}/uh_oh)", nil)
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to minimum
+ a = Commit.find_commit_range(users(:active), nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556 ; touch #{touchdir}/uh_oh", "31ce37fe365b3dc204300a3e4c396ad333ed0556", nil)
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'minimum' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to minimum
+ a = Commit.find_commit_range(users(:active), nil, "$(uname>#{touchdir}/uh_oh)", "31ce37fe365b3dc204300a3e4c396ad333ed0556", nil)
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'minimum' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to 'excludes'
+ # complains "fatal: bad object 077ba2ad3ea24a929091a9e6ce545c93199b8e57"
+ a = Commit.find_commit_range(users(:active), nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556", "077ba2ad3ea24a929091a9e6ce545c93199b8e57", ["4fe459abe02d9b365932b8f5dc419439ab4e2577 ; touch #{touchdir}/uh_oh"])
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'excludes' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to 'excludes'
+ # complains "fatal: bad object 077ba2ad3ea24a929091a9e6ce545c93199b8e57"
+ a = Commit.find_commit_range(users(:active), nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556", "077ba2ad3ea24a929091a9e6ce545c93199b8e57", ["$(uname>#{touchdir}/uh_oh)"])
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'excludes' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ end
+
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::FiltersTest < ActionController::TestCase
+ test '"not in" filter passes null values' do
+ @controller = Arvados::V1::GroupsController.new
+ authorize_with :admin
+ get :index, {
+ filters: [ ['group_class', 'not in', ['project']] ],
+ controller: 'groups',
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_includes(found.collect(&:group_class), nil,
+ "'group_class not in ['project']' filter should pass null")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::GroupsControllerTest < ActionController::TestCase
+
+ test "attempt to delete group without read or write access" do
+ authorize_with :active
+ post :destroy, id: groups(:empty_lonely_group).uuid
+ assert_response 404
+ end
+
+ test "attempt to delete group without write access" do
+ authorize_with :active
+ post :destroy, id: groups(:all_users).uuid
+ assert_response 403
+ end
+
+ test "get list of projects" do
+ authorize_with :active
+ get :index, filters: [['group_class', '=', 'project']], format: :json
+ assert_response :success
+ group_uuids = []
+ json_response['items'].each do |group|
+ assert_equal 'project', group['group_class']
+ group_uuids << group['uuid']
+ end
+ assert_includes group_uuids, groups(:aproject).uuid
+ assert_includes group_uuids, groups(:asubproject).uuid
+ assert_not_includes group_uuids, groups(:system_group).uuid
+ assert_not_includes group_uuids, groups(:private).uuid
+ end
+
+ test "get list of groups that are not projects" do
+ authorize_with :active
+ get :index, filters: [['group_class', '!=', 'project']], format: :json
+ assert_response :success
+ group_uuids = []
+ json_response['items'].each do |group|
+ assert_not_equal 'project', group['group_class']
+ group_uuids << group['uuid']
+ end
+ assert_not_includes group_uuids, groups(:aproject).uuid
+ assert_not_includes group_uuids, groups(:asubproject).uuid
+ assert_includes group_uuids, groups(:private).uuid
+ end
+
+ test "get list of groups with bogus group_class" do
+ authorize_with :active
+ get :index, {
+ filters: [['group_class', '=', 'nogrouphasthislittleclass']],
+ format: :json,
+ }
+ assert_response :success
+ assert_equal [], json_response['items']
+ assert_equal 0, json_response['items_available']
+ end
+
+ def check_project_contents_response
+ assert_response :success
+ assert_operator 2, :<=, json_response['items_available']
+ assert_operator 2, :<=, json_response['items'].count
+ kinds = json_response['items'].collect { |i| i['kind'] }.uniq
+ expect_kinds = %w'arvados#group arvados#specimen arvados#pipelineTemplate arvados#job'
+ assert_equal expect_kinds, (expect_kinds & kinds)
+
+ json_response['items'].each do |i|
+ if i['kind'] == 'arvados#group'
+ assert(i['group_class'] == 'project',
+ "group#contents returned a non-project group")
+ end
+ end
+ end
+
+ test 'get group-owned objects' do
+ authorize_with :active
+ get :contents, {
+ id: groups(:aproject).uuid,
+ format: :json,
+ include_linked: true,
+ }
+ check_project_contents_response
+ end
+
+ test "user with project read permission can see project objects" do
+ authorize_with :project_viewer
+ get :contents, {
+ id: groups(:aproject).uuid,
+ format: :json,
+ include_linked: true,
+ }
+ check_project_contents_response
+ end
+
+ test "list objects across projects" do
+ authorize_with :project_viewer
+ get :contents, {
+ format: :json,
+ filters: [['uuid', 'is_a', 'arvados#specimen']]
+ }
+ assert_response :success
+ found_uuids = json_response['items'].collect { |i| i['uuid'] }
+ [[:in_aproject, true],
+ [:in_asubproject, true],
+ [:owned_by_private_group, false]].each do |specimen_fixture, should_find|
+ if should_find
+ assert_includes found_uuids, specimens(specimen_fixture).uuid, "did not find specimen fixture '#{specimen_fixture}'"
+ else
+ refute_includes found_uuids, specimens(specimen_fixture).uuid, "found specimen fixture '#{specimen_fixture}'"
+ end
+ end
+ end
+
+ test "list objects in home project" do
+ authorize_with :active
+ get :contents, {
+ format: :json,
+ id: users(:active).uuid
+ }
+ assert_response :success
+ found_uuids = json_response['items'].collect { |i| i['uuid'] }
+ assert_includes found_uuids, specimens(:owned_by_active_user).uuid, "specimen did not appear in home project"
+ refute_includes found_uuids, specimens(:in_asubproject).uuid, "specimen appeared unexpectedly in home project"
+ end
+
+ test "user with project read permission can see project collections" do
+ authorize_with :project_viewer
+ get :contents, {
+ id: groups(:asubproject).uuid,
+ format: :json,
+ }
+ ids = json_response['items'].map { |item| item["uuid"] }
+ assert_includes ids, collections(:baz_file_in_asubproject).uuid
+ end
+
+ [['asc', :<=],
+ ['desc', :>=]].each do |order, operator|
+ test "user with project read permission can sort project collections #{order}" do
+ authorize_with :project_viewer
+ get :contents, {
+ id: groups(:asubproject).uuid,
+ format: :json,
+ filters: [['uuid', 'is_a', "arvados#collection"]],
+ order: "collections.name #{order}"
+ }
+ sorted_names = json_response['items'].collect { |item| item["name"] }
+ # Here we avoid assuming too much about the database
+ # collation. Both "alice"<"Bob" and "alice">"Bob" can be
+ # correct. Hopefully it _is_ safe to assume that if "a" comes
+ # before "b" in the ascii alphabet, "aX">"bY" is never true for
+ # any strings X and Y.
+ reliably_sortable_names = sorted_names.select do |name|
+ name[0] >= 'a' and name[0] <= 'z'
+ end.uniq do |name|
+ name[0]
+ end
+ # Preserve order of sorted_names. But do not use &=. If
+ # sorted_names has out-of-order duplicates, we want to preserve
+ # them here, so we can detect them and fail the test below.
+ sorted_names.select! do |name|
+ reliably_sortable_names.include? name
+ end
+ actually_checked_anything = false
+ previous = nil
+ sorted_names.each do |entry|
+ if previous
+ assert_operator(previous, operator, entry,
+ "Entries sorted incorrectly.")
+ actually_checked_anything = true
+ end
+ previous = entry
+ end
+ assert actually_checked_anything, "Didn't even find two names to compare."
+ end
+ end
+
+ test 'list objects across multiple projects' do
+ authorize_with :project_viewer
+ get :contents, {
+ format: :json,
+ include_linked: false,
+ filters: [['uuid', 'is_a', 'arvados#specimen']]
+ }
+ assert_response :success
+ found_uuids = json_response['items'].collect { |i| i['uuid'] }
+ [[:in_aproject, true],
+ [:in_asubproject, true],
+ [:owned_by_private_group, false]].each do |specimen_fixture, should_find|
+ if should_find
+ assert_includes found_uuids, specimens(specimen_fixture).uuid, "did not find specimen fixture '#{specimen_fixture}'"
+ else
+ refute_includes found_uuids, specimens(specimen_fixture).uuid, "found specimen fixture '#{specimen_fixture}'"
+ end
+ end
+ end
+
+ # Even though the project_viewer tests go through other controllers,
+ # I'm putting them here so they're easy to find alongside the other
+ # project tests.
+ def check_new_project_link_fails(link_attrs)
+ @controller = Arvados::V1::LinksController.new
+ post :create, link: {
+ link_class: "permission",
+ name: "can_read",
+ head_uuid: groups(:aproject).uuid,
+ }.merge(link_attrs)
+ assert_includes(403..422, response.status)
+ end
+
+ test "user with project read permission can't add users to it" do
+ authorize_with :project_viewer
+ check_new_project_link_fails(tail_uuid: users(:spectator).uuid)
+ end
+
+ test "user with project read permission can't add items to it" do
+ authorize_with :project_viewer
+ check_new_project_link_fails(tail_uuid: collections(:baz_file).uuid)
+ end
+
+ test "user with project read permission can't rename items in it" do
+ authorize_with :project_viewer
+ @controller = Arvados::V1::LinksController.new
+ post :update, {
+ id: jobs(:running).uuid,
+ name: "Denied test name",
+ }
+ assert_includes(403..404, response.status)
+ end
+
+ test "user with project read permission can't remove items from it" do
+ @controller = Arvados::V1::PipelineTemplatesController.new
+ authorize_with :project_viewer
+ post :update, {
+ id: pipeline_templates(:two_part).uuid,
+ pipeline_template: {
+ owner_uuid: users(:project_viewer).uuid,
+ }
+ }
+ assert_response 403
+ end
+
+ test "user with project read permission can't delete it" do
+ authorize_with :project_viewer
+ post :destroy, {id: groups(:aproject).uuid}
+ assert_response 403
+ end
+
+ test 'get group-owned objects with limit' do
+ authorize_with :active
+ get :contents, {
+ id: groups(:aproject).uuid,
+ limit: 1,
+ format: :json,
+ }
+ assert_response :success
+ assert_operator 1, :<, json_response['items_available']
+ assert_equal 1, json_response['items'].count
+ end
+
+ test 'get group-owned objects with limit and offset' do
+ authorize_with :active
+ get :contents, {
+ id: groups(:aproject).uuid,
+ limit: 1,
+ offset: 12345,
+ format: :json,
+ }
+ assert_response :success
+ assert_operator 1, :<, json_response['items_available']
+ assert_equal 0, json_response['items'].count
+ end
+
+ test 'get group-owned objects with additional filter matching nothing' do
+ authorize_with :active
+ get :contents, {
+ id: groups(:aproject).uuid,
+ filters: [['uuid', 'in', ['foo_not_a_uuid','bar_not_a_uuid']]],
+ format: :json,
+ }
+ assert_response :success
+ assert_equal [], json_response['items']
+ assert_equal 0, json_response['items_available']
+ end
+
+ %w(offset limit).each do |arg|
+ ['foo', '', '1234five', '0x10', '-8'].each do |val|
+ test "Raise error on bogus #{arg} parameter #{val.inspect}" do
+ authorize_with :active
+ get :contents, {
+ :id => groups(:aproject).uuid,
+ :format => :json,
+ arg => val,
+ }
+ assert_response 422
+ end
+ end
+ end
+
+ test 'get writable_by list for owned group' do
+ authorize_with :active
+ get :show, {
+ id: groups(:aproject).uuid,
+ format: :json
+ }
+ assert_response :success
+ assert_not_nil(json_response['writable_by'],
+ "Should receive uuid list in 'writable_by' field")
+ assert_includes(json_response['writable_by'], users(:active).uuid,
+ "owner should be included in writable_by list")
+ end
+
+ test 'no writable_by list for group with read-only access' do
+ authorize_with :rominiadmin
+ get :show, {
+ id: groups(:testusergroup_admins).uuid,
+ format: :json
+ }
+ assert_response :success
+ assert_equal([json_response['owner_uuid']],
+ json_response['writable_by'],
+ "Should only see owner_uuid in 'writable_by' field")
+ end
+
+ test 'get writable_by list by admin user' do
+ authorize_with :admin
+ get :show, {
+ id: groups(:testusergroup_admins).uuid,
+ format: :json
+ }
+ assert_response :success
+ assert_not_nil(json_response['writable_by'],
+ "Should receive uuid list in 'writable_by' field")
+ assert_includes(json_response['writable_by'],
+ users(:admin).uuid,
+ "Current user should be included in 'writable_by' field")
+ end
+
+ test 'creating subproject with duplicate name fails' do
+ authorize_with :active
+ post :create, {
+ group: {
+ name: 'A Project',
+ owner_uuid: users(:active).uuid,
+ group_class: 'project',
+ },
+ }
+ assert_response 422
+ response_errors = json_response['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert(response_errors.first.include?('duplicate key'),
+ "Expected 'duplicate key' error in #{response_errors.first}")
+ end
+
+ test 'creating duplicate named subproject succeeds with ensure_unique_name' do
+ authorize_with :active
+ post :create, {
+ group: {
+ name: 'A Project',
+ owner_uuid: users(:active).uuid,
+ group_class: 'project',
+ },
+ ensure_unique_name: true
+ }
+ assert_response :success
+ new_project = json_response
+ assert_not_equal(new_project['uuid'],
+ groups(:aproject).uuid,
+ "create returned same uuid as existing project")
+ assert_equal(new_project['name'],
+ 'A Project (2)',
+ "new project name '#{new_project['name']}' was expected to be 'A Project (2)'")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::HumansControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+require 'helpers/git_test_helper'
+
+class Arvados::V1::JobReuseControllerTest < ActionController::TestCase
+ fixtures :repositories, :users, :jobs, :links, :collections
+
+ # See git_setup.rb for the commit log for test.git.tar
+ include GitTestHelper
+
+ setup do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :active
+ end
+
+ test "reuse job with no_reuse=false" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "reuse job with find_or_create=true" do
+ post :create, {
+ job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ find_or_create: true
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "reuse job with symbolic script_version" do
+ post :create, {
+ job: {
+ script: "hash",
+ script_version: "tag1",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ find_or_create: true
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "do not reuse job because no_reuse=true" do
+ post :create, {
+ job: {
+ no_reuse: true,
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ [false, "false"].each do |whichfalse|
+ test "do not reuse job because find_or_create=#{whichfalse.inspect}" do
+ post :create, {
+ job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ find_or_create: whichfalse
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+ end
+
+ test "do not reuse job because output is not readable by user" do
+ authorize_with :job_reader
+ post :create, {
+ job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ find_or_create: true
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_no_output" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '2'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykppp', new_job['uuid']
+ end
+
+ test "test_reuse_job_range" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ minimum_script_version: "tag1",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "cannot_reuse_job_no_minimum_given_so_must_use_specified_commit" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '077ba2ad3ea24a929091a9e6ce545c93199b8e57', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_different_input" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '2'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_different_version" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '2'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '077ba2ad3ea24a929091a9e6ce545c93199b8e57', new_job['script_version']
+ end
+
+ test "test_can_reuse_job_submitted_nondeterministic" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ },
+ nondeterministic: true
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_past_nondeterministic" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash2",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykyyy', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_no_permission" do
+ authorize_with :spectator
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_excluded" do
+ post :create, job: {
+ no_reuse: false,
+ script: "hash",
+ minimum_script_version: "31ce37fe365b3dc204300a3e4c396ad333ed0556",
+ script_version: "master",
+ repository: "foo",
+ exclude_script_versions: ["tag1"],
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_not_equal('4fe459abe02d9b365932b8f5dc419439ab4e2577',
+ new_job['script_version'])
+ end
+
+ test "cannot reuse job with find_or_create but excluded version" do
+ post :create, {
+ job: {
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ find_or_create: true,
+ minimum_script_version: "31ce37fe365b3dc204300a3e4c396ad333ed0556",
+ exclude_script_versions: ["tag1"],
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_not_equal('4fe459abe02d9b365932b8f5dc419439ab4e2577',
+ new_job['script_version'])
+ end
+
+ BASE_FILTERS = {
+ 'repository' => ['=', 'foo'],
+ 'script' => ['=', 'hash'],
+ 'script_version' => ['in git', 'master'],
+ 'docker_image_locator' => ['=', nil],
+ 'arvados_sdk_version' => ['=', nil],
+ }
+
+ def filters_from_hash(hash)
+ hash.each_pair.map { |name, filter| [name] + filter }
+ end
+
+ test "can reuse a Job based on filters" do
+ filters_hash = BASE_FILTERS.
+ merge('script_version' => ['in git', 'tag1'])
+ post(:create, {
+ job: {
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ filters: filters_from_hash(filters_hash),
+ find_or_create: true,
+ })
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "can not reuse a Job based on filters" do
+ filters = filters_from_hash(BASE_FILTERS
+ .reject { |k| k == 'script_version' })
+ filters += [["script_version", "in git",
+ "31ce37fe365b3dc204300a3e4c396ad333ed0556"],
+ ["script_version", "not in git", ["tag1"]]]
+ post(:create, {
+ job: {
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ filters: filters,
+ find_or_create: true,
+ })
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '077ba2ad3ea24a929091a9e6ce545c93199b8e57', new_job['script_version']
+ end
+
+ test "can not reuse a Job based on arbitrary filters" do
+ filters_hash = BASE_FILTERS.
+ merge("created_at" => ["<", "2010-01-01T00:00:00Z"])
+ post(:create, {
+ job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ filters: filters_from_hash(filters_hash),
+ find_or_create: true,
+ })
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "can reuse a Job with a Docker image" do
+ post(:create, {
+ job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ },
+ runtime_constraints: {
+ docker_image: 'arvados/apitestfixture',
+ }
+ },
+ find_or_create: true,
+ })
+ assert_response :success
+ new_job = assigns(:object)
+ assert_not_nil new_job
+ target_job = jobs(:previous_docker_job_run)
+ [:uuid, :script_version, :docker_image_locator].each do |attr|
+ assert_equal(target_job.send(attr), new_job.send(attr))
+ end
+ end
+
+ test "can reuse a Job with a Docker image hash filter" do
+ filters_hash = BASE_FILTERS.
+ merge("script_version" =>
+ ["=", "4fe459abe02d9b365932b8f5dc419439ab4e2577"],
+ "docker_image_locator" =>
+ ["in docker", links(:docker_image_collection_hash).name])
+ post(:create, {
+ job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ },
+ },
+ filters: filters_from_hash(filters_hash),
+ find_or_create: true,
+ })
+ assert_response :success
+ new_job = assigns(:object)
+ assert_not_nil new_job
+ target_job = jobs(:previous_docker_job_run)
+ [:uuid, :script_version, :docker_image_locator].each do |attr|
+ assert_equal(target_job.send(attr), new_job.send(attr))
+ end
+ end
+
+ test "reuse Job with Docker image repo+tag" do
+ filters_hash = BASE_FILTERS.
+ merge("script_version" =>
+ ["=", "4fe459abe02d9b365932b8f5dc419439ab4e2577"],
+ "docker_image_locator" =>
+ ["in docker", links(:docker_image_collection_tag2).name])
+ post(:create, {
+ job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ },
+ },
+ filters: filters_from_hash(filters_hash),
+ find_or_create: true,
+ })
+ assert_response :success
+ new_job = assigns(:object)
+ assert_not_nil new_job
+ target_job = jobs(:previous_docker_job_run)
+ [:uuid, :script_version, :docker_image_locator].each do |attr|
+ assert_equal(target_job.send(attr), new_job.send(attr))
+ end
+ end
+
+ test "new job with unknown Docker image filter" do
+ filters_hash = BASE_FILTERS.
+ merge("docker_image_locator" => ["in docker", "_nonesuchname_"])
+ post(:create, {
+ job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ },
+ },
+ filters: filters_from_hash(filters_hash),
+ find_or_create: true,
+ })
+ assert_response :success
+ new_job = assigns(:object)
+ assert_not_nil new_job
+ assert_not_equal(jobs(:previous_docker_job_run).uuid, new_job.uuid)
+ end
+
+ ["repository", "script"].each do |skip_key|
+ test "missing #{skip_key} filter raises an error" do
+ filters = filters_from_hash(BASE_FILTERS.reject { |k| k == skip_key })
+ post(:create, {
+ job: {
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ },
+ filters: filters,
+ find_or_create: true,
+ })
+ assert_includes(405..599, @response.code.to_i,
+ "bad status code with missing #{skip_key} filter")
+ end
+ end
+
+ test "find Job with script version range" do
+ get :index, filters: [["repository", "=", "foo"],
+ ["script", "=", "hash"],
+ ["script_version", "in git", "tag1"]]
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ assert_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_job_run).uuid)
+ end
+
+ test "find Job with script version range exclusions" do
+ get :index, filters: [["repository", "=", "foo"],
+ ["script", "=", "hash"],
+ ["script_version", "not in git", "tag1"]]
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ refute_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_job_run).uuid)
+ end
+
+ test "find Job with Docker image range" do
+ get :index, filters: [["docker_image_locator", "in docker",
+ "arvados/apitestfixture"]]
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ assert_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_docker_job_run).uuid)
+ refute_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_job_run).uuid)
+ end
+
+ test "find Job with Docker image using reader tokens" do
+ authorize_with :inactive
+ get(:index, {
+ filters: [["docker_image_locator", "in docker",
+ "arvados/apitestfixture"]],
+ reader_tokens: [api_token(:active)],
+ })
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ assert_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_docker_job_run).uuid)
+ refute_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_job_run).uuid)
+ end
+
+ test "'in docker' filter accepts arrays" do
+ get :index, filters: [["docker_image_locator", "in docker",
+ ["_nonesuchname_", "arvados/apitestfixture"]]]
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ assert_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_docker_job_run).uuid)
+ refute_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_job_run).uuid)
+ end
+
+ test "'not in docker' filter accepts arrays" do
+ get :index, filters: [["docker_image_locator", "not in docker",
+ ["_nonesuchname_", "arvados/apitestfixture"]]]
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ assert_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_job_run).uuid)
+ refute_includes(assigns(:objects).map { |job| job.uuid },
+ jobs(:previous_docker_job_run).uuid)
+ end
+
+ def create_foo_hash_job_params(params)
+ if not params.has_key?(:find_or_create)
+ params[:find_or_create] = true
+ end
+ job_attrs = params.delete(:job) || {}
+ params[:job] = {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1',
+ },
+ }.merge(job_attrs)
+ params
+ end
+
+ def check_new_job_created_from(params)
+ start_time = Time.now
+ post(:create, create_foo_hash_job_params(params))
+ assert_response :success
+ new_job = assigns(:object)
+ assert_not_nil new_job
+ assert_operator(start_time, :<=, new_job.created_at)
+ new_job
+ end
+
+ def check_errors_from(params)
+ post(:create, create_foo_hash_job_params(params))
+ assert_includes(405..499, @response.code.to_i)
+ errors = json_response.fetch("errors", [])
+ assert(errors.any?, "no errors assigned from #{params}")
+ refute(errors.any? { |msg| msg =~ /^#<[A-Za-z]+: / },
+ "errors include raw exception")
+ errors
+ end
+
+ # 1de84a8 is on the b1 branch, after master's tip.
+ test "new job created from unsatisfiable minimum version filter" do
+ filters_hash = BASE_FILTERS.merge("script_version" => ["in git", "1de84a8"])
+ check_new_job_created_from(filters: filters_from_hash(filters_hash))
+ end
+
+ test "new job created from unsatisfiable minimum version parameter" do
+ check_new_job_created_from(minimum_script_version: "1de84a8")
+ end
+
+ test "new job created from unsatisfiable minimum version attribute" do
+ check_new_job_created_from(job: {minimum_script_version: "1de84a8"})
+ end
+
+ test "graceful error from nonexistent minimum version filter" do
+ filters_hash = BASE_FILTERS.merge("script_version" =>
+ ["in git", "__nosuchbranch__"])
+ errors = check_errors_from(filters: filters_from_hash(filters_hash))
+ assert(errors.any? { |msg| msg.include? "__nosuchbranch__" },
+ "bad refspec not mentioned in error message")
+ end
+
+ test "graceful error from nonexistent minimum version parameter" do
+ errors = check_errors_from(minimum_script_version: "__nosuchbranch__")
+ assert(errors.any? { |msg| msg.include? "__nosuchbranch__" },
+ "bad refspec not mentioned in error message")
+ end
+
+ test "graceful error from nonexistent minimum version attribute" do
+ errors = check_errors_from(job: {minimum_script_version: "__nosuchbranch__"})
+ assert(errors.any? { |msg| msg.include? "__nosuchbranch__" },
+ "bad refspec not mentioned in error message")
+ end
+
+ test "can't reuse job with older Arvados SDK version" do
+ params = {
+ script_version: "31ce37fe365b3dc204300a3e4c396ad333ed0556",
+ runtime_constraints: {
+ "arvados_sdk_version" => "master",
+ "docker_image" => links(:docker_image_collection_tag).name,
+ },
+ }
+ check_new_job_created_from(job: params)
+ end
+
+ test "reuse job from arvados_sdk_version git filters" do
+ filters_hash = BASE_FILTERS.
+ merge("arvados_sdk_version" => ["in git", "commit2"])
+ filters_hash.delete("script_version")
+ params = create_foo_hash_job_params(filters:
+ filters_from_hash(filters_hash))
+ post(:create, params)
+ assert_response :success
+ assert_equal(jobs(:previous_job_run_with_arvados_sdk_version).uuid,
+ assigns(:object).uuid)
+ end
+
+ test "create new job because of arvados_sdk_version 'not in git' filters" do
+ filters_hash = BASE_FILTERS.reject { |k| k == "script_version" }
+ filters = filters_from_hash(filters_hash)
+ # Allow anything from the root commit, but before commit 2.
+ filters += [["arvados_sdk_version", "in git", "436637c8"],
+ ["arvados_sdk_version", "not in git", "00634b2b"]]
+ check_new_job_created_from(filters: filters)
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::JobTasksControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+require 'helpers/git_test_helper'
+
+class Arvados::V1::JobsControllerTest < ActionController::TestCase
+
+ include GitTestHelper
+
+ test "submit a job" do
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {}
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_nil new_job['uuid']
+ assert_not_nil new_job['script_version'].match(/^[0-9a-f]{40}$/)
+ assert_equal 0, new_job['priority']
+ end
+
+ test "normalize output and log uuids when creating job" do
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ script_version: "master",
+ script_parameters: {},
+ repository: "foo",
+ started_at: Time.now,
+ finished_at: Time.now,
+ running: false,
+ success: true,
+ output: 'd41d8cd98f00b204e9800998ecf8427e+0+K@xyzzy',
+ log: 'd41d8cd98f00b204e9800998ecf8427e+0+K@xyzzy'
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = assigns(:object)
+ assert_equal 'd41d8cd98f00b204e9800998ecf8427e+0', new_job['log']
+ assert_equal 'd41d8cd98f00b204e9800998ecf8427e+0', new_job['output']
+ version = new_job['script_version']
+
+ # Make sure version doesn't get mangled by normalize
+ assert_not_nil version.match(/^[0-9a-f]{40}$/)
+ assert_equal 'master', json_response['supplied_script_version']
+ end
+
+ test "normalize output and log uuids when updating job" do
+ authorize_with :active
+
+ foobar_job = jobs(:foobar)
+
+ new_output = 'd41d8cd98f00b204e9800998ecf8427e+0+K@xyzzy'
+ new_log = 'd41d8cd98f00b204e9800998ecf8427e+0+K@xyzzy'
+ put :update, {
+ id: foobar_job['uuid'],
+ job: {
+ output: new_output,
+ log: new_log
+ }
+ }
+
+ updated_job = json_response
+ assert_not_equal foobar_job['log'], updated_job['log']
+ assert_not_equal new_log, updated_job['log'] # normalized during update
+ assert_equal new_log[0,new_log.rindex('+')], updated_job['log']
+ assert_not_equal foobar_job['output'], updated_job['output']
+ assert_not_equal new_output, updated_job['output'] # normalized during update
+ assert_equal new_output[0,new_output.rindex('+')], updated_job['output']
+ end
+
+ test "cancel a running job" do
+ # We need to verify that "cancel" creates a trigger file, so first
+ # let's make sure there is no stale trigger file.
+ begin
+ File.unlink(Rails.configuration.crunch_refresh_trigger)
+ rescue Errno::ENOENT
+ end
+
+ authorize_with :active
+ put :update, {
+ id: jobs(:running).uuid,
+ job: {
+ cancelled_at: 4.day.ago
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ job = JSON.parse(@response.body)
+ assert_not_nil job['uuid']
+ assert_not_nil job['cancelled_at']
+ assert_not_nil job['cancelled_by_user_uuid']
+ assert_not_nil job['cancelled_by_client_uuid']
+ assert_equal(true, Time.parse(job['cancelled_at']) > 1.minute.ago,
+ 'server should correct bogus cancelled_at ' +
+ job['cancelled_at'])
+ assert_equal(true,
+ File.exists?(Rails.configuration.crunch_refresh_trigger),
+ 'trigger file should be created when job is cancelled')
+ end
+
+ [
+ [:put, :update, {job:{cancelled_at: Time.now}}, :success],
+ [:put, :update, {job:{cancelled_at: nil}}, :unprocessable_entity],
+ [:put, :update, {job:{state: 'Cancelled'}}, :success],
+ [:put, :update, {job:{state: 'Queued'}}, :unprocessable_entity],
+ [:put, :update, {job:{state: 'Running'}}, :unprocessable_entity],
+ [:put, :update, {job:{state: 'Failed'}}, :unprocessable_entity],
+ [:put, :update, {job:{state: 'Complete'}}, :unprocessable_entity],
+ [:post, :cancel, {}, :success],
+ ].each do |http_method, action, params, expected_response|
+ test "cancelled job stays cancelled after #{[http_method, action, params].inspect}" do
+ # We need to verify that "cancel" creates a trigger file, so first
+ # let's make sure there is no stale trigger file.
+ begin
+ File.unlink(Rails.configuration.crunch_refresh_trigger)
+ rescue Errno::ENOENT
+ end
+
+ authorize_with :active
+ self.send http_method, action, { id: jobs(:cancelled).uuid }.merge(params)
+ assert_response expected_response
+ if expected_response == :success
+ job = json_response
+ assert_not_nil job['cancelled_at'], 'job cancelled again using #{attribute}=#{value} did not have cancelled_at value'
+ assert_equal job['state'], 'Cancelled', 'cancelled again job state changed when updated using using #{attribute}=#{value}'
+ end
+ # Verify database record still says Cancelled
+ assert_equal 'Cancelled', Job.find(jobs(:cancelled).id).state, 'job was un-cancelled'
+ end
+ end
+
+ test "cancelled job updated to any other state change results in error" do
+ # We need to verify that "cancel" creates a trigger file, so first
+ # let's make sure there is no stale trigger file.
+ begin
+ File.unlink(Rails.configuration.crunch_refresh_trigger)
+ rescue Errno::ENOENT
+ end
+
+ authorize_with :active
+ put :update, {
+ id: jobs(:running_cancelled).uuid,
+ job: {
+ cancelled_at: nil
+ }
+ }
+ assert_response 422
+ end
+
+ ['abc.py', 'hash.py'].each do |script|
+ test "update job script attribute to #{script} without failing script_version check" do
+ authorize_with :admin
+ put :update, {
+ id: jobs(:uses_nonexistent_script_version).uuid,
+ job: {
+ script: script
+ }
+ }
+ assert_response :success
+ resp = assigns(:object)
+ assert_equal jobs(:uses_nonexistent_script_version).script_version, resp['script_version']
+ end
+ end
+
+ test "search jobs by uuid with >= query" do
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', '>=', 'zzzzz-8i9sb-pshmckwoma9plh7']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ assert_equal false, !!found.index('zzzzz-8i9sb-4cf0nhn6xte809j')
+ end
+
+ test "search jobs by uuid with <= query" do
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', '<=', 'zzzzz-8i9sb-pshmckwoma9plh7']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ assert_equal true, !!found.index('zzzzz-8i9sb-4cf0nhn6xte809j')
+ end
+
+ test "search jobs by uuid with >= and <= query" do
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', '>=', 'zzzzz-8i9sb-pshmckwoma9plh7'],
+ ['uuid', '<=', 'zzzzz-8i9sb-pshmckwoma9plh7']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal found, ['zzzzz-8i9sb-pshmckwoma9plh7']
+ end
+
+ test "search jobs by uuid with < query" do
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', '<', 'zzzzz-8i9sb-pshmckwoma9plh7']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal false, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ assert_equal true, !!found.index('zzzzz-8i9sb-4cf0nhn6xte809j')
+ end
+
+ test "search jobs by uuid with like query" do
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', 'like', '%hmckwoma9pl%']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal found, ['zzzzz-8i9sb-pshmckwoma9plh7']
+ end
+
+ test "search jobs by uuid with 'in' query" do
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', 'in', ['zzzzz-8i9sb-4cf0nhn6xte809j',
+ 'zzzzz-8i9sb-pshmckwoma9plh7']]]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal found.sort, ['zzzzz-8i9sb-4cf0nhn6xte809j',
+ 'zzzzz-8i9sb-pshmckwoma9plh7']
+ end
+
+ test "search jobs by uuid with 'not in' query" do
+ exclude_uuids = [jobs(:running).uuid,
+ jobs(:running_cancelled).uuid]
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', 'not in', exclude_uuids]]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_not_empty found, "'not in' query returned nothing"
+ assert_empty(found & exclude_uuids,
+ "'not in' query returned uuids I asked not to get")
+ end
+
+ ['=', '!='].each do |operator|
+ [['uuid', 'zzzzz-8i9sb-pshmckwoma9plh7'],
+ ['output', nil]].each do |attr, operand|
+ test "search jobs with #{attr} #{operator} #{operand.inspect} query" do
+ authorize_with :active
+ get :index, {
+ filters: [[attr, operator, operand]]
+ }
+ assert_response :success
+ values = assigns(:objects).collect { |x| x.send(attr) }
+ assert_not_empty values, "query should return non-empty result"
+ if operator == '='
+ assert_empty values - [operand], "query results do not satisfy query"
+ else
+ assert_empty values & [operand], "query results do not satisfy query"
+ end
+ end
+ end
+ end
+
+ test "search jobs by started_at with < query" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '<', Time.now.to_s]]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs by started_at with > query" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>', Time.now.to_s]]
+ }
+ assert_response :success
+ assert_equal 0, assigns(:objects).count
+ end
+
+ test "search jobs by started_at with >= query on metric date" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>=', '2014-01-01']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs by started_at with >= query on metric date and time" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>=', '2014-01-01 01:23:45']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs with 'any' operator" do
+ authorize_with :active
+ get :index, {
+ where: { any: ['contains', 'pshmckw'] }
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal 0, found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ assert_equal 1, found.count
+ end
+
+ test "search jobs by nonexistent column with < query" do
+ authorize_with :active
+ get :index, {
+ filters: [['is_borked', '<', 'fizzbuzz']]
+ }
+ assert_response 422
+ end
+
+ test "finish a job" do
+ authorize_with :active
+ put :update, {
+ id: jobs(:nearly_finished_job).uuid,
+ job: {
+ output: '551392cc37a317abf865b95f66f4ef94+101',
+ log: '9215de2a951a721f5f156bc08cf63ad7+93',
+ tasks_summary: {done: 1, running: 0, todo: 0, failed: 0},
+ success: true,
+ running: false,
+ finished_at: Time.now.to_s
+ }
+ }
+ assert_response :success
+ end
+
+ [:spectator, :admin].each_with_index do |which_token, i|
+ test "get job queue as #{which_token} user" do
+ authorize_with which_token
+ get :queue
+ assert_response :success
+ assert_equal i, assigns(:objects).count
+ end
+ end
+
+ test "get job queue as with a = filter" do
+ authorize_with :admin
+ get :queue, { filters: [['script','=','foo']] }
+ assert_response :success
+ assert_equal ['foo'], assigns(:objects).collect(&:script).uniq
+ assert_equal 0, assigns(:objects)[0].queue_position
+ end
+
+ test "get job queue as with a != filter" do
+ authorize_with :admin
+ get :queue, { filters: [['script','!=','foo']] }
+ assert_response :success
+ assert_equal 0, assigns(:objects).count
+ end
+
+ [:spectator, :admin].each do |which_token|
+ test "get queue_size as #{which_token} user" do
+ authorize_with which_token
+ get :queue_size
+ assert_response :success
+ assert_equal 1, JSON.parse(@response.body)["queue_size"]
+ end
+ end
+
+ test "job includes assigned nodes" do
+ authorize_with :active
+ get :show, {id: jobs(:nearly_finished_job).uuid}
+ assert_response :success
+ assert_equal([nodes(:busy).uuid], json_response["node_uuids"])
+ end
+
+ test "job lock success" do
+ authorize_with :active
+ post :lock, {id: jobs(:queued).uuid}
+ assert_response :success
+ job = Job.where(uuid: jobs(:queued).uuid).first
+ assert_equal "Running", job.state
+ end
+
+ test "job lock conflict" do
+ authorize_with :active
+ post :lock, {id: jobs(:running).uuid}
+ assert_response 403 # forbidden
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::KeepDisksControllerTest < ActionController::TestCase
+
+ def default_ping_opts
+ {ping_secret: '', service_ssl_flag: false, service_port: 1234}
+ end
+
+ test "add keep disk with admin token" do
+ authorize_with :admin
+ post :ping, default_ping_opts.
+ merge(filesystem_uuid: 'eb1e77a1-db84-4193-b6e6-ca2894f67d5f')
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_keep_disk = JSON.parse(@response.body)
+ assert_not_nil new_keep_disk['uuid']
+ assert_not_nil new_keep_disk['ping_secret']
+ assert_not_equal '', new_keep_disk['ping_secret']
+ end
+
+ [
+ {},
+ {filesystem_uuid: ''},
+ ].each do |opts|
+ test "add keep disk with[out] filesystem_uuid #{opts}" do
+ authorize_with :admin
+ post :ping, default_ping_opts.merge(opts)
+ assert_response :success
+ assert_not_nil JSON.parse(@response.body)['uuid']
+ end
+ end
+
+ test "refuse to add keep disk without admin token" do
+ post :ping, default_ping_opts
+ assert_response 404
+ end
+
+ test "ping keep disk" do
+ post :ping, default_ping_opts.
+ merge(id: keep_disks(:nonfull).uuid,
+ ping_secret: keep_disks(:nonfull).ping_secret,
+ filesystem_uuid: keep_disks(:nonfull).filesystem_uuid)
+ assert_response :success
+ assert_not_nil assigns(:object)
+ keep_disk = JSON.parse(@response.body)
+ assert_not_nil keep_disk['uuid']
+ assert_not_nil keep_disk['ping_secret']
+ end
+
+ test "admin should get index with ping_secret" do
+ authorize_with :admin
+ get :index
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ items = JSON.parse(@response.body)['items']
+ assert_not_equal 0, items.size
+ assert_not_nil items[0]['ping_secret']
+ end
+
+ # inactive user sees keep disks
+ test "inactive user should get index" do
+ authorize_with :inactive
+ get :index
+ assert_response :success
+ items = JSON.parse(@response.body)['items']
+ assert_not_equal 0, items.size
+
+ # Check these are still included
+ assert items[0]['service_host']
+ assert items[0]['service_port']
+ end
+
+ # active user sees non-secret attributes of keep disks
+ test "active user should get non-empty index with no ping_secret" do
+ authorize_with :active
+ get :index
+ assert_response :success
+ items = JSON.parse(@response.body)['items']
+ assert_not_equal 0, items.size
+ items.each do |item|
+ assert_nil item['ping_secret']
+ assert_not_nil item['is_readable']
+ assert_not_nil item['is_writable']
+ assert_not_nil item['service_host']
+ assert_not_nil item['service_port']
+ end
+ end
+
+ test "search keep_services with 'any' operator" do
+ authorize_with :active
+ get :index, {
+ where: { any: ['contains', 'o2t1q5w'] }
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-penuu-5w2o2t1q5wy7fhn')
+ end
+
+
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::KeepServicesControllerTest < ActionController::TestCase
+
+ test "search keep_services by service_port with < query" do
+ authorize_with :active
+ get :index, {
+ filters: [['service_port', '<', 25107]]
+ }
+ assert_response :success
+ assert_equal false, assigns(:objects).any?
+ end
+
+ test "search keep_disks by service_port with >= query" do
+ authorize_with :active
+ get :index, {
+ filters: [['service_port', '>=', 25107]]
+ }
+ assert_response :success
+ assert_equal true, assigns(:objects).any?
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::LinksControllerTest < ActionController::TestCase
+
+ ['link', 'link_json'].each do |formatted_link|
+ test "no symbol keys in serialized hash #{formatted_link}" do
+ link = {
+ properties: {username: 'testusername'},
+ link_class: 'test',
+ name: 'encoding',
+ tail_uuid: users(:admin).uuid,
+ head_uuid: virtual_machines(:testvm).uuid
+ }
+ authorize_with :admin
+ if formatted_link == 'link_json'
+ post :create, link: link.to_json
+ else
+ post :create, link: link
+ end
+ assert_response :success
+ assert_not_nil assigns(:object)
+ assert_equal 'testusername', assigns(:object).properties['username']
+ assert_equal false, assigns(:object).properties.has_key?(:username)
+ end
+ end
+
+ %w(created_at modified_at).each do |attr|
+ {nil: nil, bogus: 2.days.ago}.each do |bogustype, bogusvalue|
+ test "cannot set #{bogustype} #{attr} in create" do
+ authorize_with :active
+ post :create, {
+ link: {
+ properties: {},
+ link_class: 'test',
+ name: 'test',
+ }.merge(attr => bogusvalue)
+ }
+ assert_response :success
+ resp = JSON.parse @response.body
+ assert_in_delta Time.now, Time.parse(resp[attr]), 3.0
+ end
+ test "cannot set #{bogustype} #{attr} in update" do
+ really_created_at = links(:test_timestamps).created_at
+ authorize_with :active
+ put :update, {
+ id: links(:test_timestamps).uuid,
+ link: {
+ :properties => {test: 'test'},
+ attr => bogusvalue
+ }
+ }
+ assert_response :success
+ resp = JSON.parse @response.body
+ case attr
+ when 'created_at'
+ assert_in_delta really_created_at, Time.parse(resp[attr]), 0.001
+ else
+ assert_in_delta Time.now, Time.parse(resp[attr]), 3.0
+ end
+ end
+ end
+ end
+
+ test "head must exist" do
+ link = {
+ link_class: 'test',
+ name: 'stuff',
+ tail_uuid: users(:active).uuid,
+ head_uuid: 'zzzzz-tpzed-xyzxyzxerrrorxx'
+ }
+ authorize_with :admin
+ post :create, link: link
+ assert_response 422
+ end
+
+ test "tail must exist" do
+ link = {
+ link_class: 'test',
+ name: 'stuff',
+ head_uuid: users(:active).uuid,
+ tail_uuid: 'zzzzz-tpzed-xyzxyzxerrrorxx'
+ }
+ authorize_with :admin
+ post :create, link: link
+ assert_response 422
+ end
+
+ test "head and tail exist, head_kind and tail_kind are returned" do
+ link = {
+ link_class: 'test',
+ name: 'stuff',
+ head_uuid: users(:active).uuid,
+ tail_uuid: users(:spectator).uuid,
+ }
+ authorize_with :admin
+ post :create, link: link
+ assert_response :success
+ l = JSON.parse(@response.body)
+ assert 'arvados#user', l['head_kind']
+ assert 'arvados#user', l['tail_kind']
+ end
+
+ test "can supply head_kind and tail_kind without error" do
+ link = {
+ link_class: 'test',
+ name: 'stuff',
+ head_uuid: users(:active).uuid,
+ tail_uuid: users(:spectator).uuid,
+ head_kind: "arvados#user",
+ tail_kind: "arvados#user",
+ }
+ authorize_with :admin
+ post :create, link: link
+ assert_response :success
+ l = JSON.parse(@response.body)
+ assert 'arvados#user', l['head_kind']
+ assert 'arvados#user', l['tail_kind']
+ end
+
+ test "tail must be visible by user" do
+ link = {
+ link_class: 'test',
+ name: 'stuff',
+ head_uuid: users(:active).uuid,
+ tail_uuid: virtual_machines(:testvm2).uuid
+ }
+ authorize_with :active
+ post :create, link: link
+ assert_response 422
+ end
+
+ test "filter links with 'is_a' operator" do
+ authorize_with :admin
+ get :index, {
+ filters: [ ['tail_uuid', 'is_a', 'arvados#user'] ]
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f| f.tail_uuid.match User.uuid_regex }).count
+ end
+
+ test "filter links with 'is_a' operator with more than one" do
+ authorize_with :admin
+ get :index, {
+ filters: [ ['tail_uuid', 'is_a', ['arvados#user', 'arvados#group'] ] ],
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f|
+ f.tail_uuid.match User.uuid_regex or
+ f.tail_uuid.match Group.uuid_regex
+ }).count
+ end
+
+ test "filter links with 'is_a' operator with bogus type" do
+ authorize_with :admin
+ get :index, {
+ filters: [ ['tail_uuid', 'is_a', ['arvados#bogus'] ] ],
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_equal 0, found.count
+ end
+
+ test "filter links with 'is_a' operator with collection" do
+ authorize_with :admin
+ get :index, {
+ filters: [ ['head_uuid', 'is_a', ['arvados#collection'] ] ],
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f| f.head_uuid.match Collection.uuid_regex}).count
+ end
+
+ test "test can still use where tail_kind" do
+ authorize_with :admin
+ get :index, {
+ where: { tail_kind: 'arvados#user' }
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f| f.tail_uuid.match User.uuid_regex }).count
+ end
+
+ test "test can still use where head_kind" do
+ authorize_with :admin
+ get :index, {
+ where: { head_kind: 'arvados#user' }
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f| f.head_uuid.match User.uuid_regex }).count
+ end
+
+ test "test can still use filter tail_kind" do
+ authorize_with :admin
+ get :index, {
+ filters: [ ['tail_kind', '=', 'arvados#user'] ]
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f| f.tail_uuid.match User.uuid_regex }).count
+ end
+
+ test "test can still use filter head_kind" do
+ authorize_with :admin
+ get :index, {
+ filters: [ ['head_kind', '=', 'arvados#user'] ]
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f| f.head_uuid.match User.uuid_regex }).count
+ end
+
+ test "head_kind matches head_uuid" do
+ link = {
+ link_class: 'test',
+ name: 'stuff',
+ head_uuid: groups(:public).uuid,
+ head_kind: "arvados#user",
+ tail_uuid: users(:spectator).uuid,
+ tail_kind: "arvados#user",
+ }
+ authorize_with :admin
+ post :create, link: link
+ assert_response 422
+ end
+
+ test "tail_kind matches tail_uuid" do
+ link = {
+ link_class: 'test',
+ name: 'stuff',
+ head_uuid: users(:active).uuid,
+ head_kind: "arvados#user",
+ tail_uuid: groups(:public).uuid,
+ tail_kind: "arvados#user",
+ }
+ authorize_with :admin
+ post :create, link: link
+ assert_response 422
+ end
+
+ test "test with virtual_machine" do
+ link = {
+ tail_kind: "arvados#user",
+ tail_uuid: users(:active).uuid,
+ head_kind: "arvados#virtual_machine",
+ head_uuid: virtual_machines(:testvm).uuid,
+ link_class: "permission",
+ name: "can_login",
+ properties: {username: "repo_and_user_name"}
+ }
+ authorize_with :admin
+ post :create, link: link
+ assert_response 422
+ end
+
+ test "test with virtualMachine" do
+ link = {
+ tail_kind: "arvados#user",
+ tail_uuid: users(:active).uuid,
+ head_kind: "arvados#virtualMachine",
+ head_uuid: virtual_machines(:testvm).uuid,
+ link_class: "permission",
+ name: "can_login",
+ properties: {username: "repo_and_user_name"}
+ }
+ authorize_with :admin
+ post :create, link: link
+ assert_response :success
+ end
+
+ test "project owner can show a project permission" do
+ uuid = links(:project_viewer_can_read_project).uuid
+ authorize_with :active
+ get :show, id: uuid
+ assert_response :success
+ assert_equal(uuid, assigns(:object).andand.uuid)
+ end
+
+ test "admin can show a project permission" do
+ uuid = links(:project_viewer_can_read_project).uuid
+ authorize_with :admin
+ get :show, id: uuid
+ assert_response :success
+ assert_equal(uuid, assigns(:object).andand.uuid)
+ end
+
+ test "project viewer can't show others' project permissions" do
+ authorize_with :project_viewer
+ get :show, id: links(:admin_can_write_aproject).uuid
+ assert_response 404
+ end
+
+ test "requesting a nonexistent link returns 404" do
+ authorize_with :active
+ get :show, id: 'zzzzz-zzzzz-zzzzzzzzzzzzzzz'
+ assert_response 404
+ end
+
+ test "retrieve all permissions using generic links index api" do
+ skip "(not implemented)"
+ # Links.readable_by() does not return the full set of permission
+ # links that are visible to a user (i.e., all permission links
+ # whose head_uuid references an object for which the user has
+ # ownership or can_manage permission). Therefore, neither does
+ # /arvados/v1/links.
+ #
+ # It is possible to retrieve the full set of permissions for a
+ # single object via /arvados/v1/permissions.
+ authorize_with :active
+ get :index, filters: [['link_class', '=', 'permission'],
+ ['head_uuid', '=', groups(:aproject).uuid]]
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ assert_includes(assigns(:objects).map(&:uuid),
+ links(:project_viewer_can_read_project).uuid)
+ end
+
+ test "admin can index project permissions" do
+ authorize_with :admin
+ get :index, filters: [['link_class', '=', 'permission'],
+ ['head_uuid', '=', groups(:aproject).uuid]]
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ assert_includes(assigns(:objects).map(&:uuid),
+ links(:project_viewer_can_read_project).uuid)
+ end
+
+ test "project viewer can't index others' project permissions" do
+ authorize_with :project_viewer
+ get :index, filters: [['link_class', '=', 'permission'],
+ ['head_uuid', '=', groups(:aproject).uuid],
+ ['tail_uuid', '!=', users(:project_viewer).uuid]]
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ assert_empty assigns(:objects)
+ end
+
+ # Granting permissions.
+ test "grant can_read on project to other users in group" do
+ authorize_with :user_foo_in_sharing_group
+
+ refute users(:user_bar_in_sharing_group).can?(read: collections(:collection_owned_by_foo).uuid)
+
+ post :create, {
+ link: {
+ tail_uuid: users(:user_bar_in_sharing_group).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:collection_owned_by_foo).uuid,
+ }
+ }
+ assert_response :success
+ assert users(:user_bar_in_sharing_group).can?(read: collections(:collection_owned_by_foo).uuid)
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::LogsControllerTest < ActionController::TestCase
+ fixtures :logs
+
+ test "non-admins can create their own logs" do
+ authorize_with :active
+ post :create, log: {summary: 'test log'}
+ assert_response :success
+ resp = assigns(:object)
+ assert_not_nil resp.uuid
+ assert_equal('test log', resp.summary, "loaded wrong log after creation")
+ end
+
+ test "non-admins can read their own logs" do
+ authorize_with :active
+ my_log = logs(:log_owned_by_active)
+ get :show, {id: my_log[:uuid]}
+ assert_response(:success, "failed to get log")
+ resp = assigns(:object)
+ assert_equal(my_log[:summary], resp.summary, "got wrong log")
+ end
+
+ test "test can still use where object_kind" do
+ authorize_with :admin
+ get :index, {
+ where: { object_kind: 'arvados#user' }
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f| f.object_uuid.match User.uuid_regex }).count
+ l = JSON.parse(@response.body)
+ assert_equal 'arvados#user', l['items'][0]['object_kind']
+ end
+
+ test "test can still use filter object_kind" do
+ authorize_with :admin
+ get :index, {
+ filters: [ ['object_kind', '=', 'arvados#user'] ]
+ }
+ assert_response :success
+ found = assigns(:objects)
+ assert_not_equal 0, found.count
+ assert_equal found.count, (found.select { |f| f.object_uuid.match User.uuid_regex }).count
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::NodesControllerTest < ActionController::TestCase
+
+ test "should get index with ping_secret" do
+ authorize_with :admin
+ get :index
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ node_items = JSON.parse(@response.body)['items']
+ assert_not_equal 0, node_items.size
+ assert_not_nil node_items[0]['info'].andand['ping_secret']
+ end
+
+ # inactive user does not see any nodes
+ test "inactive user should get empty index" do
+ authorize_with :inactive
+ get :index
+ assert_response :success
+ node_items = JSON.parse(@response.body)['items']
+ assert_equal 0, node_items.size
+ end
+
+ # active user sees non-secret attributes of up and recently-up nodes
+ test "active user should get non-empty index with no ping_secret" do
+ authorize_with :active
+ get :index
+ assert_response :success
+ node_items = JSON.parse(@response.body)['items']
+ assert_not_equal 0, node_items.size
+ found_busy_node = false
+ node_items.each do |node|
+ assert_nil node['info'].andand['ping_secret']
+ assert_not_nil node['crunch_worker_state']
+ if node['uuid'] == nodes(:busy).uuid
+ found_busy_node = true
+ assert_equal 'busy', node['crunch_worker_state']
+ end
+ end
+ assert_equal true, found_busy_node
+ end
+
+ test "node should ping with ping_secret and no token" do
+ post :ping, {
+ id: 'zzzzz-7ekkf-2z3mc76g2q73aio',
+ instance_id: 'i-0000000',
+ local_ipv4: '172.17.2.174',
+ ping_secret: '69udawxvn3zzj45hs8bumvndricrha4lcpi23pd69e44soanc0'
+ }
+ assert_response :success
+ response = JSON.parse(@response.body)
+ assert_equal 'zzzzz-7ekkf-2z3mc76g2q73aio', response['uuid']
+ # Ensure we are getting the "superuser" attributes, too
+ assert_not_nil response['first_ping_at'], '"first_ping_at" attr missing'
+ assert_not_nil response['info'], '"info" attr missing'
+ assert_not_nil response['nameservers'], '"nameservers" attr missing'
+ end
+
+ test "node should fail ping with invalid ping_secret" do
+ post :ping, {
+ id: 'zzzzz-7ekkf-2z3mc76g2q73aio',
+ instance_id: 'i-0000000',
+ local_ipv4: '172.17.2.174',
+ ping_secret: 'dricrha4lcpi23pd69e44soanc069udawxvn3zzj45hs8bumvn'
+ }
+ assert_response 401
+ end
+
+ test "create node" do
+ authorize_with :admin
+ post :create, {node: {}}
+ assert_response :success
+ assert_not_nil json_response['uuid']
+ assert_not_nil json_response['info'].is_a? Hash
+ assert_not_nil json_response['info']['ping_secret']
+ end
+
+ test "ping adds node stats to info" do
+ authorize_with :admin
+ node = nodes(:idle)
+ post :ping, {
+ id: node.uuid,
+ ping_secret: node.info['ping_secret'],
+ total_cpu_cores: 32,
+ total_ram_mb: 1024,
+ total_scratch_mb: 2048
+ }
+ assert_response :success
+ info = JSON.parse(@response.body)['info']
+ properties = JSON.parse(@response.body)['properties']
+ assert_equal(node.info['ping_secret'], info['ping_secret'])
+ assert_equal(32, properties['total_cpu_cores'].to_i)
+ assert_equal(1024, properties['total_ram_mb'].to_i)
+ assert_equal(2048, properties['total_scratch_mb'].to_i)
+ end
+
+ test "active user can see their assigned job" do
+ authorize_with :active
+ get :show, {id: nodes(:busy).uuid}
+ assert_response :success
+ assert_equal(jobs(:nearly_finished_job).uuid, json_response["job_uuid"])
+ end
+
+ test "user without job read permission can't see job" do
+ authorize_with :spectator
+ get :show, {id: nodes(:busy).uuid}
+ assert_response :success
+ assert_nil(json_response["job"], "spectator can see node's assigned job")
+ end
+
+ [:admin, :spectator].each do |user|
+ test "select param does not break node list for #{user}" do
+ authorize_with user
+ get :index, {select: ['domain']}
+ assert_response :success
+ end
+ end
+
+ test "admin can associate a job with a node" do
+ changed_node = nodes(:idle)
+ assigned_job = jobs(:queued)
+ authorize_with :admin
+ post :update, {
+ id: changed_node.uuid,
+ node: {job_uuid: assigned_job.uuid},
+ }
+ assert_response :success
+ assert_equal(changed_node.hostname, json_response["hostname"],
+ "hostname mismatch after defining job")
+ assert_equal(assigned_job.uuid, json_response["job_uuid"],
+ "mismatch in node's assigned job UUID")
+ end
+
+ test "non-admin can't associate a job with a node" do
+ authorize_with :active
+ post :update, {
+ id: nodes(:idle).uuid,
+ node: {job_uuid: jobs(:queued).uuid},
+ }
+ assert_response 403
+ end
+
+ test "admin can unassign a job from a node" do
+ changed_node = nodes(:busy)
+ authorize_with :admin
+ post :update, {
+ id: changed_node.uuid,
+ node: {job_uuid: nil},
+ }
+ assert_response :success
+ assert_equal(changed_node.hostname, json_response["hostname"],
+ "hostname mismatch after defining job")
+ assert_nil(json_response["job_uuid"],
+ "node still has job assignment after update")
+ end
+
+ test "non-admin can't unassign a job from a node" do
+ authorize_with :project_viewer
+ post :update, {
+ id: nodes(:busy).uuid,
+ node: {job_uuid: nil},
+ }
+ assert_response 403
+ end
+
+ test "job readable after updating other attributes" do
+ authorize_with :admin
+ post :update, {
+ id: nodes(:busy).uuid,
+ node: {last_ping_at: 1.second.ago},
+ }
+ assert_response :success
+ assert_equal(jobs(:nearly_finished_job).uuid, json_response["job_uuid"],
+ "mismatched job UUID after ping update")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::PipelineInstancesControllerTest < ActionController::TestCase
+
+ test 'create pipeline with components copied from template' do
+ authorize_with :active
+ post :create, {
+ pipeline_instance: {
+ pipeline_template_uuid: pipeline_templates(:two_part).uuid
+ }
+ }
+ assert_response :success
+ assert_equal(pipeline_templates(:two_part).components.to_json,
+ assigns(:object).components.to_json)
+ end
+
+ test 'create pipeline with no template' do
+ authorize_with :active
+ post :create, {
+ pipeline_instance: {
+ components: {}
+ }
+ }
+ assert_response :success
+ assert_equal({}, assigns(:object).components)
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::PipelineTemplatesControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::RepositoriesControllerTest < ActionController::TestCase
+ test "should get_all_logins with admin token" do
+ authorize_with :admin
+ get :get_all_permissions
+ assert_response :success
+ end
+
+ test "should get_all_logins with non-admin token" do
+ authorize_with :active
+ get :get_all_permissions
+ assert_response 403
+ end
+
+ test "get_all_permissions gives RW to repository owner" do
+ authorize_with :admin
+ get :get_all_permissions
+ assert_response :success
+ ok = false
+ json_response['repositories'].each do |repo|
+ if repo['uuid'] == repositories(:repository2).uuid
+ if repo['user_permissions'][users(:active).uuid]['can_write']
+ ok = true
+ end
+ end
+ end
+ assert_equal(true, ok,
+ "No permission on own repo '@{repositories(:repository2).uuid}'")
+ end
+
+ test "get_all_permissions takes into account is_admin flag" do
+ authorize_with :admin
+ get :get_all_permissions
+ assert_response :success
+ json_response['repositories'].each do |repo|
+ assert_not_nil(repo['user_permissions'][users(:admin).uuid],
+ "Admin user is not listed in perms for #{repo['uuid']}")
+ assert_equal(true,
+ repo['user_permissions'][users(:admin).uuid]['can_write'],
+ "Admin has no perms for #{repo['uuid']}")
+ end
+ end
+
+ test "get_all_permissions does not give any access to user without permission" do
+ viewer_uuid = users(:project_viewer).uuid
+ assert_equal(authorized_keys(:project_viewer).authorized_user_uuid,
+ viewer_uuid,
+ "project_viewer must have an authorized_key for this test to work")
+ authorize_with :admin
+ get :get_all_permissions
+ assert_response :success
+ readable_repos = json_response["repositories"].select do |repo|
+ repo["user_permissions"].has_key?(viewer_uuid)
+ end
+ assert_equal(["arvados"], readable_repos.map { |r| r["name"] },
+ "project_viewer should only have permissions on public repos")
+ end
+
+ test "get_all_permissions gives gitolite R to user with read-only access" do
+ authorize_with :admin
+ get :get_all_permissions
+ assert_response :success
+ found_it = false
+ assert_equal(authorized_keys(:spectator).authorized_user_uuid,
+ users(:spectator).uuid,
+ "spectator must have an authorized_key for this test to work")
+ json_response['repositories'].each do |repo|
+ next unless repo['uuid'] == repositories(:foo).uuid
+ assert_equal('R',
+ repo['user_permissions'][users(:spectator).uuid]['gitolite_permissions'],
+ "spectator user should have just R access to #{repo['uuid']}")
+ found_it = true
+ end
+ assert_equal true, found_it, "spectator user does not have R on foo repo"
+ end
+
+ test "get_all_permissions provides admin and active user keys" do
+ authorize_with :admin
+ get :get_all_permissions
+ assert_response :success
+ [:active, :admin].each do |u|
+ assert_equal(1, json_response['user_keys'][users(u).uuid].andand.count,
+ "expected 1 key for #{u} (#{users(u).uuid})")
+ assert_equal(json_response['user_keys'][users(u).uuid][0]['public_key'],
+ authorized_keys(u).public_key,
+ "response public_key does not match fixture #{u}.")
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::SchemaControllerTest < ActionController::TestCase
+
+ test "should get fresh discovery document" do
+ MAX_SCHEMA_AGE = 60
+ get :index
+ assert_response :success
+ discovery_doc = JSON.parse(@response.body)
+ assert_equal 'discovery#restDescription', discovery_doc['kind']
+ assert_equal(true,
+ Time.now - MAX_SCHEMA_AGE.seconds < discovery_doc['generatedAt'],
+ "discovery document was generated >#{MAX_SCHEMA_AGE}s ago")
+ end
+
+ test "discovery document has defaultTrashLifetime" do
+ get :index
+ assert_response :success
+ discovery_doc = JSON.parse(@response.body)
+ assert_includes discovery_doc, 'defaultTrashLifetime'
+ assert_equal discovery_doc['defaultTrashLifetime'], Rails.application.config.default_trash_lifetime
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::SpecimensControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::TraitsControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::UserAgreementsControllerTest < ActionController::TestCase
+
+ test "active user get user agreements" do
+ authorize_with :active
+ get :index
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ agreements_list = JSON.parse(@response.body)
+ assert_not_nil agreements_list['items']
+ assert_not_nil agreements_list['items'][0]
+ end
+
+ test "active user get user agreement signatures" do
+ authorize_with :active
+ get :signatures
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ agreements_list = JSON.parse(@response.body)
+ assert_not_nil agreements_list['items']
+ assert_not_nil agreements_list['items'][0]
+ assert_equal 1, agreements_list['items'].count
+ end
+
+ test "inactive user get user agreements" do
+ authorize_with :inactive
+ get :index
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ agreements_list = JSON.parse(@response.body)
+ assert_not_nil agreements_list['items']
+ assert_not_nil agreements_list['items'][0]
+ end
+
+ test "uninvited user receives empty list of user agreements" do
+ authorize_with :inactive_uninvited
+ get :index
+ assert_response :success
+ assert_not_nil assigns(:objects)
+ agreements_list = JSON.parse(@response.body)
+ assert_not_nil agreements_list['items']
+ assert_nil agreements_list['items'][0]
+ end
+
+end
--- /dev/null
+require 'test_helper'
+require 'helpers/users_test_helper'
+
+class Arvados::V1::UsersControllerTest < ActionController::TestCase
+ include CurrentApiClient
+ include UsersTestHelper
+
+ setup do
+ @all_links_at_start = Link.all
+ @vm_uuid = virtual_machines(:testvm).uuid
+ end
+
+ test "activate a user after signing UA" do
+ authorize_with :inactive_but_signed_user_agreement
+ post :activate, id: users(:inactive_but_signed_user_agreement).uuid
+ assert_response :success
+ assert_not_nil assigns(:object)
+ me = JSON.parse(@response.body)
+ assert_equal true, me['is_active']
+ end
+
+ test "refuse to activate a user before signing UA" do
+ act_as_system_user do
+ required_uuids = Link.where("owner_uuid = ? and link_class = ? and name = ? and tail_uuid = ? and head_uuid like ?",
+ system_user_uuid,
+ 'signature',
+ 'require',
+ system_user_uuid,
+ Collection.uuid_like_pattern).
+ collect(&:head_uuid)
+
+ assert required_uuids.length > 0
+
+ signed_uuids = Link.where(owner_uuid: system_user_uuid,
+ link_class: 'signature',
+ name: 'click',
+ tail_uuid: users(:inactive).uuid,
+ head_uuid: required_uuids).
+ collect(&:head_uuid)
+
+ assert_equal 0, signed_uuids.length
+ end
+
+ authorize_with :inactive
+ assert_equal false, users(:inactive).is_active
+
+ post :activate, id: users(:inactive).uuid
+ assert_response 403
+
+ resp = json_response
+ assert resp['errors'].first.include? 'Cannot activate without user agreements'
+ assert_nil resp['is_active']
+ end
+
+ test "activate an already-active user" do
+ authorize_with :active
+ post :activate, id: users(:active).uuid
+ assert_response :success
+ me = JSON.parse(@response.body)
+ assert_equal true, me['is_active']
+ end
+
+ test "respond 401 if given token exists but user record is missing" do
+ authorize_with :valid_token_deleted_user
+ get :current, {format: :json}
+ assert_response 401
+ end
+
+ test "create new user with user as input" do
+ authorize_with :admin
+ post :create, user: {
+ first_name: "test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ assert_response :success
+ created = JSON.parse(@response.body)
+ assert_equal 'test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected uuid for the newly created user'
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+ end
+
+ test "create user with user, vm and repo as input" do
+ authorize_with :admin
+ repo_name = 'test_repo'
+
+ post :setup, {
+ repo_name: repo_name,
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ user: {
+ uuid: 'zzzzz-tpzed-abcdefghijklmno',
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected non-null uuid for the new user'
+ assert_equal 'zzzzz-tpzed-abcdefghijklmno', created['uuid']
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # arvados#user, repo link and link add user to 'All users' group
+ verify_num_links @all_links_at_start, 4
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ repo_name, created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ verify_system_group_permission_link_for created['uuid']
+ end
+
+ test "setup user with bogus uuid and expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ uuid: 'bogus_uuid',
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid
+ }
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'Path not found'), 'Expected 404'
+ end
+
+ test "setup user with bogus uuid in user and expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ user: {uuid: 'bogus_uuid'},
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'ArgumentError: Require user email'),
+ 'Expected RuntimeError'
+ end
+
+ test "setup user with no uuid and user, expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'Required uuid or user'),
+ 'Expected ArgumentError'
+ end
+
+ test "setup user with no uuid and email, expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ user: {},
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? '<ArgumentError: Require user email'),
+ 'Expected ArgumentError'
+ end
+
+ test "invoke setup with existing uuid, vm and repo and verify links" do
+ authorize_with :admin
+ inactive_user = users(:inactive)
+
+ post :setup, {
+ uuid: users(:inactive).uuid,
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ resp_obj = find_obj_in_resp response_items, 'User', nil
+
+ assert_not_nil resp_obj['uuid'], 'expected uuid for the new user'
+ assert_equal inactive_user['uuid'], resp_obj['uuid']
+ assert_equal inactive_user['email'], resp_obj['email'],
+ 'expecting inactive user email'
+
+ # expect repo and vm links
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ 'test_repo', resp_obj['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ @vm_uuid, resp_obj['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "invoke setup with existing uuid in user, verify response" do
+ authorize_with :admin
+ inactive_user = users(:inactive)
+
+ post :setup, {
+ user: {uuid: inactive_user['uuid']},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ resp_obj = find_obj_in_resp response_items, 'User', nil
+
+ assert_not_nil resp_obj['uuid'], 'expected uuid for the new user'
+ assert_equal inactive_user['uuid'], resp_obj['uuid']
+ assert_equal inactive_user['email'], resp_obj['email'],
+ 'expecting inactive user email'
+ end
+
+ test "invoke setup with existing uuid but different email, expect original email" do
+ authorize_with :admin
+ inactive_user = users(:inactive)
+
+ post :setup, {
+ uuid: inactive_user['uuid'],
+ user: {email: 'junk_email'}
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ resp_obj = find_obj_in_resp response_items, 'User', nil
+
+ assert_not_nil resp_obj['uuid'], 'expected uuid for the new user'
+ assert_equal inactive_user['uuid'], resp_obj['uuid']
+ assert_equal inactive_user['email'], resp_obj['email'],
+ 'expecting inactive user email'
+ end
+
+ test "setup user with valid email and repo as input" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for the new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+
+ # four extra links; system_group, login, group and repo perms
+ verify_num_links @all_links_at_start, 4
+ end
+
+ test "setup user with fake vm and expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ vm_uuid: 'no_such_vm',
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? "No vm found for no_such_vm"),
+ 'Expected RuntimeError: No vm found for no_such_vm'
+ end
+
+ test "setup user with valid email, repo and real vm as input" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ vm_uuid: @vm_uuid,
+ user: {email: 'foo@example.com'}
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for the new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+
+ # five extra links; system_group, login, group, vm, repo
+ verify_num_links @all_links_at_start, 5
+ end
+
+ test "setup user with valid email, no vm and no repo as input" do
+ authorize_with :admin
+
+ post :setup, {
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+
+ # three extra links; system_group, login, and group
+ verify_num_links @all_links_at_start, 3
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ response_object['uuid'], response_object['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', response_object['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', false, 'permission', 'can_manage',
+ 'test_repo', response_object['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, response_object['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "setup user with email, first name, repo name and vm uuid" do
+ authorize_with :admin
+
+ post :setup, {
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ user: {
+ first_name: 'test_first_name',
+ email: 'foo@example.com'
+ }
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+ assert_equal 'test_first_name', response_object['first_name'],
+ 'expecting first name'
+
+ # five extra links; system_group, login, group, repo and vm
+ verify_num_links @all_links_at_start, 5
+ end
+
+ test "setup user with an existing user email and check different object is created" do
+ authorize_with :admin
+ inactive_user = users(:inactive)
+
+ post :setup, {
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ repo_name: 'test_repo',
+ user: {
+ email: inactive_user['email']
+ }
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for new user'
+ assert_not_equal response_object['uuid'], inactive_user['uuid'],
+ 'expected different uuid after create operation'
+ assert_equal inactive_user['email'], response_object['email'], 'expected given email'
+ # system_group, openid, group, and repo. No vm link.
+ verify_num_links @all_links_at_start, 4
+ end
+
+ test "setup user with openid prefix" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ openid_prefix: 'http://www.example.com/account',
+ user: {
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected uuid for new user'
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # verify links
+ # four new links: system_group, arvados#user, repo, and 'All users' group.
+ verify_num_links @all_links_at_start, 4
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ 'test_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "invoke setup with no openid prefix, expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ user: {
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }
+
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'openid_prefix parameter is missing'),
+ 'Expected ArgumentError'
+ end
+
+ test "setup user with user, vm and repo and verify links" do
+ authorize_with :admin
+
+ post :setup, {
+ user: {
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ },
+ vm_uuid: @vm_uuid,
+ repo_name: 'test_repo',
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected uuid for new user'
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # five new links: system_group, arvados#user, repo, vm and 'All
+ # users' group link
+ verify_num_links @all_links_at_start, 5
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ 'test_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ @vm_uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "create user as non admin user and expect error" do
+ authorize_with :active
+
+ post :create, {
+ user: {email: 'foo@example.com'}
+ }
+
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'PermissionDenied'),
+ 'Expected PermissionDeniedError'
+ end
+
+ test "setup user as non admin user and expect error" do
+ authorize_with :active
+
+ post :setup, {
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ user: {email: 'foo@example.com'}
+ }
+
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'Forbidden'),
+ 'Expected Forbidden error'
+ end
+
+ test "setup active user with repo and no vm" do
+ authorize_with :admin
+ active_user = users(:active)
+
+ # invoke setup with a repository
+ post :setup, {
+ repo_name: 'new_repo',
+ uuid: active_user['uuid']
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal active_user[:email], created['email'], 'expected input email'
+
+ # verify links
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ 'new_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "setup active user with vm and no repo" do
+ authorize_with :admin
+ active_user = users(:active)
+
+ # invoke setup with a repository
+ post :setup, {
+ vm_uuid: @vm_uuid,
+ uuid: active_user['uuid'],
+ email: 'junk_email'
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal active_user['email'], created['email'], 'expected original email'
+
+ # verify links
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', false, 'permission', 'can_manage',
+ 'new_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ @vm_uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "unsetup active user" do
+ active_user = users(:active)
+ assert_not_nil active_user['uuid'], 'expected uuid for the active user'
+ assert active_user['is_active'], 'expected is_active for active user'
+
+ verify_link_existence active_user['uuid'], active_user['email'],
+ false, true, false, true, true
+
+ authorize_with :admin
+
+ # now unsetup this user
+ post :unsetup, id: active_user['uuid']
+ assert_response :success
+
+ response_user = JSON.parse(@response.body)
+ assert_not_nil response_user['uuid'], 'expected uuid for the upsetup user'
+ assert_equal active_user['uuid'], response_user['uuid'], 'expected uuid not found'
+ assert !response_user['is_active'], 'expected user to be inactive'
+ assert !response_user['is_invited'], 'expected user to be uninvited'
+
+ verify_link_existence response_user['uuid'], response_user['email'],
+ false, false, false, false, false
+
+ active_user = User.find_by_uuid(users(:active).uuid)
+ readable_groups = active_user.groups_i_can(:read)
+ all_users_group = Group.all.collect(&:uuid).select { |g| g.match /-f+$/ }
+ refute_includes(readable_groups, all_users_group,
+ "active user can read All Users group after being deactivated")
+ assert_equal(false, active_user.is_invited,
+ "active user is_invited after being deactivated & reloaded")
+ end
+
+ test "setup user with send notification param false and verify no email" do
+ authorize_with :admin
+
+ post :setup, {
+ openid_prefix: 'http://www.example.com/account',
+ send_notification_email: 'false',
+ user: {
+ email: "foo@example.com"
+ }
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil created['uuid'], 'expected uuid for the new user'
+ assert_equal created['email'], 'foo@example.com', 'expected given email'
+
+ setup_email = ActionMailer::Base.deliveries.last
+ assert_nil setup_email, 'expected no setup email'
+ end
+
+ test "setup user with send notification param true and verify email" do
+ authorize_with :admin
+
+ post :setup, {
+ openid_prefix: 'http://www.example.com/account',
+ send_notification_email: 'true',
+ user: {
+ email: "foo@example.com"
+ }
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil created['uuid'], 'expected uuid for the new user'
+ assert_equal created['email'], 'foo@example.com', 'expected given email'
+
+ setup_email = ActionMailer::Base.deliveries.last
+ assert_not_nil setup_email, 'Expected email after setup'
+
+ assert_equal Rails.configuration.user_notifier_email_from, setup_email.from[0]
+ assert_equal 'foo@example.com', setup_email.to[0]
+ assert_equal 'Welcome to Curoverse', setup_email.subject
+ assert (setup_email.body.to_s.include? 'Your Arvados account has been set up'),
+ 'Expected Your Arvados account has been set up in email body'
+ assert (setup_email.body.to_s.include? 'foo@example.com'),
+ 'Expected user email in email body'
+ assert (setup_email.body.to_s.include? Rails.configuration.workbench_address),
+ 'Expected workbench url in email body'
+ end
+
+ test "non-admin user can get basic information about readable users" do
+ authorize_with :spectator
+ get(:index)
+ check_non_admin_index
+ check_readable_users_index [:spectator], [:inactive, :active]
+ end
+
+ test "non-admin user gets only safe attributes from users#show" do
+ g = act_as_system_user do
+ create :group
+ end
+ users = create_list :active_user, 2, join_groups: [g]
+ token = create :token, user: users[0]
+ authorize_with_token token
+ get :show, id: users[1].uuid
+ check_non_admin_show
+ end
+
+ [2, 4].each do |limit|
+ test "non-admin user can limit index to #{limit}" do
+ g = act_as_system_user do
+ create :group
+ end
+ users = create_list :active_user, 4, join_groups: [g]
+ token = create :token, user: users[0]
+
+ authorize_with_token token
+ get(:index, limit: limit)
+ check_non_admin_index
+ assert_equal(limit, json_response["items"].size,
+ "non-admin index limit was ineffective")
+ end
+ end
+
+ test "admin has full index powers" do
+ authorize_with :admin
+ check_inactive_user_findable
+ end
+
+ test "reader token can grant admin index powers" do
+ authorize_with :spectator
+ check_inactive_user_findable(reader_tokens: [api_token(:admin)])
+ end
+
+ test "admin can filter on user.is_active" do
+ authorize_with :admin
+ get(:index, filters: [["is_active", "=", "true"]])
+ assert_response :success
+ check_readable_users_index [:active, :spectator], [:inactive]
+ end
+
+ test "admin can search where user.is_active" do
+ authorize_with :admin
+ get(:index, where: {is_active: true})
+ assert_response :success
+ check_readable_users_index [:active, :spectator], [:inactive]
+ end
+
+ test "update active_no_prefs user profile and expect notification email" do
+ authorize_with :admin
+
+ put :update, {
+ id: users(:active_no_prefs).uuid,
+ user: {
+ prefs: {:profile => {'organization' => 'example.com'}}
+ }
+ }
+ assert_response :success
+
+ found_email = false
+ ActionMailer::Base.deliveries.andand.each do |email|
+ if email.subject == "Profile created by #{users(:active_no_prefs).email}"
+ found_email = true
+ break
+ end
+ end
+ assert_equal true, found_email, 'Expected email after creating profile'
+ end
+
+ test "update active_no_prefs_profile user profile and expect notification email" do
+ authorize_with :admin
+
+ user = {}
+ user[:prefs] = users(:active_no_prefs_profile).prefs
+ user[:prefs][:profile] = {:profile => {'organization' => 'example.com'}}
+ put :update, {
+ id: users(:active_no_prefs_profile).uuid,
+ user: user
+ }
+ assert_response :success
+
+ found_email = false
+ ActionMailer::Base.deliveries.andand.each do |email|
+ if email.subject == "Profile created by #{users(:active_no_prefs_profile).email}"
+ found_email = true
+ break
+ end
+ end
+ assert_equal true, found_email, 'Expected email after creating profile'
+ end
+
+ test "update active user profile and expect no notification email" do
+ authorize_with :admin
+
+ put :update, {
+ id: users(:active).uuid,
+ user: {
+ prefs: {:profile => {'organization' => 'anotherexample.com'}}
+ }
+ }
+ assert_response :success
+
+ found_email = false
+ ActionMailer::Base.deliveries.andand.each do |email|
+ if email.subject == "Profile created by #{users(:active).email}"
+ found_email = true
+ break
+ end
+ end
+ assert_equal false, found_email, 'Expected no email after updating profile'
+ end
+
+ test "user API response includes writable_by" do
+ authorize_with :active
+ get :current
+ assert_response :success
+ assert_includes(json_response["writable_by"], users(:active).uuid,
+ "user's writable_by should include self")
+ assert_includes(json_response["writable_by"], users(:active).owner_uuid,
+ "user's writable_by should include its owner_uuid")
+ end
+
+
+ NON_ADMIN_USER_DATA = ["uuid", "kind", "is_active", "email", "first_name",
+ "last_name"].sort
+
+ def check_non_admin_index
+ assert_response :success
+ response_items = json_response["items"]
+ assert_not_nil response_items
+ response_items.each do |user_data|
+ check_non_admin_item user_data
+ assert(user_data["is_active"], "non-admin index returned inactive user")
+ end
+ end
+
+ def check_non_admin_show
+ assert_response :success
+ check_non_admin_item json_response
+ end
+
+ def check_non_admin_item user_data
+ assert_equal(NON_ADMIN_USER_DATA, user_data.keys.sort,
+ "data in response had missing or extra attributes")
+ assert_equal("arvados#user", user_data["kind"])
+ end
+
+
+ def check_readable_users_index expect_present, expect_missing
+ response_uuids = json_response["items"].map { |u| u["uuid"] }
+ expect_present.each do |user_key|
+ assert_includes(response_uuids, users(user_key).uuid,
+ "#{user_key} missing from index")
+ end
+ expect_missing.each do |user_key|
+ refute_includes(response_uuids, users(user_key).uuid,
+ "#{user_key} included in index")
+ end
+ end
+
+ def check_inactive_user_findable(params={})
+ inactive_user = users(:inactive)
+ get(:index, params.merge(filters: [["email", "=", inactive_user.email]]))
+ assert_response :success
+ user_list = json_response["items"]
+ assert_equal(1, user_list.andand.count)
+ # This test needs to check a column non-admins have no access to,
+ # to ensure that admins see all user information.
+ assert_equal(inactive_user.identity_url, user_list.first["identity_url"],
+ "admin's filtered index did not return inactive user")
+ end
+
+ def verify_num_links (original_links, expected_additional_links)
+ links_now = Link.all
+ assert_equal expected_additional_links, Link.all.size-original_links.size,
+ "Expected #{expected_additional_links.inspect} more links"
+ end
+
+ def find_obj_in_resp (response_items, object_type, head_kind=nil)
+ return_obj = nil
+ response_items
+ response_items.each { |x|
+ if !x
+ next
+ end
+
+ if object_type == 'User'
+ if ArvadosModel::resource_class_for_uuid(x['uuid']) == User
+ return_obj = x
+ break
+ end
+ else # looking for a link
+ if x['head_uuid'] and ArvadosModel::resource_class_for_uuid(x['head_uuid']).kind == head_kind
+ return_obj = x
+ break
+ end
+ end
+ }
+ return return_obj
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::VirtualMachinesControllerTest < ActionController::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class DatabaseControllerTest < ActionController::TestCase
+ include CurrentApiClient
+
+ test "reset fails with non-admin token" do
+ authorize_with :active
+ post :reset
+ assert_response 403
+ end
+
+ test "route not found when not in test mode" do
+ authorize_with :admin
+ env_was = Rails.env
+ begin
+ Rails.env = 'production'
+ Rails.application.reload_routes!
+ assert_raises ActionController::RoutingError do
+ post :reset
+ end
+ ensure
+ Rails.env = env_was
+ Rails.application.reload_routes!
+ end
+ end
+
+ test "reset fails when a non-test-fixture user exists" do
+ act_as_system_user do
+ User.create!(uuid: 'abcde-tpzed-123451234512345', email: 'bar@example.net')
+ end
+ authorize_with :admin
+ post :reset
+ assert_response 403
+ end
+
+ test "reset succeeds with admin token" do
+ new_uuid = nil
+ act_as_system_user do
+ new_uuid = Specimen.create.uuid
+ end
+ assert_not_empty Specimen.where(uuid: new_uuid)
+ authorize_with :admin
+ post :reset
+ assert_response 200
+ assert_empty Specimen.where(uuid: new_uuid)
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class UserSessionsControllerTest < ActionController::TestCase
+
+ test "new user from new api client" do
+ authorize_with :inactive
+ api_client_page = 'http://client.example.com/home'
+ get :login, return_to: api_client_page
+ assert_response :redirect
+ assert_equal(0, @response.redirect_url.index(api_client_page + '?'),
+ 'Redirect url ' + @response.redirect_url +
+ ' should start with ' + api_client_page + '?')
+ assert_not_nil assigns(:api_client)
+ end
+
+end
--- /dev/null
+require 'fileutils'
+require 'tmpdir'
+
+# Commit log for "foo" repository in test.git.tar
+# master is the main branch
+# b1 is a branch off of master
+# tag1 is a tag
+#
+# 1de84a8 * b1
+# 077ba2a * master
+# 4fe459a * tag1
+# 31ce37f * foo
+
+module GitTestHelper
+ def self.included base
+ base.setup do
+ @tmpdir = Dir.mktmpdir()
+ system("tar", "-xC", @tmpdir, "-f", "test/test.git.tar")
+ Rails.configuration.git_repositories_dir = "#{@tmpdir}/test"
+ Commit.refresh_repositories
+ end
+
+ base.teardown do
+ FileUtils.remove_entry @tmpdir, true
+ Commit.refresh_repositories
+ end
+ end
+end
--- /dev/null
+module UsersTestHelper
+ def verify_link(response_items, link_object_name, expect_link, link_class,
+ link_name, head_uuid, tail_uuid, head_kind, fetch_object, class_name)
+ link = find_obj_in_resp response_items, 'arvados#link', link_object_name
+
+ if !expect_link
+ assert_nil link, "Expected no link for #{link_object_name}"
+ return
+ end
+
+ assert_not_nil link, "Expected link for #{link_object_name}"
+
+ if fetch_object
+ object = Object.const_get(class_name).where(name: head_uuid)
+ assert [] != object, "expected #{class_name} with name #{head_uuid}"
+ head_uuid = object.first[:uuid]
+ end
+ assert_equal link_class, link['link_class'],
+ "did not find expected link_class for #{link_object_name}"
+
+ assert_equal link_name, link['name'],
+ "did not find expected link_name for #{link_object_name}"
+
+ assert_equal tail_uuid, link['tail_uuid'],
+ "did not find expected tail_uuid for #{link_object_name}"
+
+ assert_equal head_kind, link['head_kind'],
+ "did not find expected head_kind for #{link_object_name}"
+
+ assert_equal head_uuid, link['head_uuid'],
+ "did not find expected head_uuid for #{link_object_name}"
+ end
+
+ def verify_system_group_permission_link_for user_uuid
+ assert_equal 1, Link.where(link_class: 'permission',
+ name: 'can_manage',
+ tail_uuid: system_group_uuid,
+ head_uuid: user_uuid).count
+ end
+
+ def verify_link_existence uuid, email, expect_oid_login_perms,
+ expect_repo_perms, expect_vm_perms, expect_group_perms, expect_signatures
+ # verify that all links are deleted for the user
+ oid_login_perms = Link.where(tail_uuid: email,
+ link_class: 'permission',
+ name: 'can_login').where("head_uuid like ?", User.uuid_like_pattern)
+ if expect_oid_login_perms
+ assert oid_login_perms.any?, "expected oid_login_perms"
+ else
+ assert !oid_login_perms.any?, "expected all oid_login_perms deleted"
+ end
+
+ repo_perms = Link.where(tail_uuid: uuid,
+ link_class: 'permission',
+ name: 'can_manage').where("head_uuid like ?", Repository.uuid_like_pattern)
+ if expect_repo_perms
+ assert repo_perms.any?, "expected repo_perms"
+ else
+ assert !repo_perms.any?, "expected all repo_perms deleted"
+ end
+
+ vm_login_perms = Link.
+ where(tail_uuid: uuid,
+ link_class: 'permission',
+ name: 'can_login').
+ where("head_uuid like ?",
+ VirtualMachine.uuid_like_pattern).
+ where('uuid <> ?',
+ links(:auto_setup_vm_login_username_can_login_to_test_vm).uuid)
+ if expect_vm_perms
+ assert vm_login_perms.any?, "expected vm_login_perms"
+ else
+ assert !vm_login_perms.any?, "expected all vm_login_perms deleted"
+ end
+
+ group = Group.where(name: 'All users').select do |g|
+ g[:uuid].match /-f+$/
+ end.first
+ group_read_perms = Link.where(tail_uuid: uuid,
+ head_uuid: group[:uuid],
+ link_class: 'permission',
+ name: 'can_read')
+ if expect_group_perms
+ assert group_read_perms.any?, "expected all users group read perms"
+ else
+ assert !group_read_perms.any?, "expected all users group perm deleted"
+ end
+
+ signed_uuids = Link.where(link_class: 'signature',
+ tail_uuid: uuid)
+
+ if expect_signatures
+ assert signed_uuids.any?, "expected signatures"
+ else
+ assert !signed_uuids.any?, "expected all signatures deleted"
+ end
+
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class ApiClientAuthorizationsApiTest < ActionDispatch::IntegrationTest
+ fixtures :all
+
+ test "create system auth" do
+ post "/arvados/v1/api_client_authorizations/create_system_auth", {:format => :json, :scopes => ['test'].to_json}, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin_trustedclient).api_token}"}
+ assert_response :success
+ end
+
+ test "create token for different user" do
+ post "/arvados/v1/api_client_authorizations", {
+ :format => :json,
+ :api_client_authorization => {
+ :owner_uuid => users(:spectator).uuid
+ }
+ }, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin_trustedclient).api_token}"}
+ assert_response :success
+
+ get "/arvados/v1/users/current", {
+ :format => :json
+ }, {'HTTP_AUTHORIZATION' => "OAuth2 #{json_response['api_token']}"}
+ @json_response = nil
+ assert_equal users(:spectator).uuid, json_response['uuid']
+ end
+
+ test "refuse to create token for different user if not trusted client" do
+ post "/arvados/v1/api_client_authorizations", {
+ :format => :json,
+ :api_client_authorization => {
+ :owner_uuid => users(:spectator).uuid
+ }
+ }, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin).api_token}"}
+ assert_response 403
+ end
+
+ test "refuse to create token for different user if not admin" do
+ post "/arvados/v1/api_client_authorizations", {
+ :format => :json,
+ :api_client_authorization => {
+ :owner_uuid => users(:spectator).uuid
+ }
+ }, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:active_trustedclient).api_token}"}
+ assert_response 403
+ end
+
+end
--- /dev/null
+# The v1 API uses token scopes to control access to the REST API at the path
+# level. This is enforced in the base ApplicationController, making it a
+# functional test that we can run against many different controllers.
+
+require 'test_helper'
+
+class Arvados::V1::ApiTokensScopeTest < ActionController::IntegrationTest
+ fixtures :all
+
+ def v1_url(*parts)
+ (['arvados', 'v1'] + parts).join('/')
+ end
+
+ test "user list token can only list users" do
+ get_args = [{}, auth(:active_userlist)]
+ get(v1_url('users'), *get_args)
+ assert_response :success
+ get(v1_url('users', ''), *get_args) # Add trailing slash.
+ assert_response :success
+ get(v1_url('users', 'current'), *get_args)
+ assert_response 403
+ get(v1_url('virtual_machines'), *get_args)
+ assert_response 403
+ end
+
+ test "specimens token can see exactly owned specimens" do
+ get_args = [{}, auth(:active_specimens)]
+ get(v1_url('specimens'), *get_args)
+ assert_response 403
+ get(v1_url('specimens', specimens(:owned_by_active_user).uuid), *get_args)
+ assert_response :success
+ get(v1_url('specimens', specimens(:owned_by_spectator).uuid), *get_args)
+ assert_includes(403..404, @response.status)
+ end
+
+ test "token with multiple scopes can use them all" do
+ def get_token_count
+ get(v1_url('api_client_authorizations'), {}, auth(:active_apitokens))
+ assert_response :success
+ token_count = JSON.parse(@response.body)['items_available']
+ assert_not_nil(token_count, "could not find token count")
+ token_count
+ end
+ # Test the GET scope.
+ token_count = get_token_count
+ # Test the POST scope.
+ post(v1_url('api_client_authorizations'),
+ {api_client_authorization: {user_id: users(:active).id}},
+ auth(:active_apitokens))
+ assert_response :success
+ assert_equal(token_count + 1, get_token_count,
+ "token count suggests POST was not accepted")
+ # Test other requests are denied.
+ get(v1_url('api_client_authorizations',
+ api_client_authorizations(:active_apitokens).uuid),
+ {}, auth(:active_apitokens))
+ assert_response 403
+ end
+
+ test "token without scope has no access" do
+ # Logs are good for this test, because logs have relatively
+ # few access controls enforced at the model level.
+ req_args = [{}, auth(:admin_noscope)]
+ get(v1_url('logs'), *req_args)
+ assert_response 403
+ get(v1_url('logs', logs(:log1).uuid), *req_args)
+ assert_response 403
+ post(v1_url('logs'), *req_args)
+ assert_response 403
+ end
+
+ test "VM login scopes work" do
+ # A system administration script makes an API token with limited scope
+ # for virtual machines to let it see logins.
+ def vm_logins_url(name)
+ v1_url('virtual_machines', virtual_machines(name).uuid, 'logins')
+ end
+ get_args = [{}, auth(:admin_vm)]
+ get(vm_logins_url(:testvm), *get_args)
+ assert_response :success
+ get(vm_logins_url(:testvm2), *get_args)
+ assert_includes(400..419, @response.status,
+ "getting testvm2 logins should have failed")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class CollectionsApiTest < ActionDispatch::IntegrationTest
+ fixtures :all
+
+ test "should get index" do
+ get "/arvados/v1/collections", {:format => :json}, auth(:active)
+ assert_response :success
+ assert_equal "arvados#collectionList", json_response['kind']
+ end
+
+ test "get index with filters= (empty string)" do
+ get "/arvados/v1/collections", {:format => :json, :filters => ''}, auth(:active)
+ assert_response :success
+ assert_equal "arvados#collectionList", json_response['kind']
+ end
+
+ test "get index with invalid filters (array of strings) responds 422" do
+ get "/arvados/v1/collections", {
+ :format => :json,
+ :filters => ['uuid', '=', 'ad02e37b6a7f45bbe2ead3c29a109b8a+54'].to_json
+ }, auth(:active)
+ assert_response 422
+ assert_match /nvalid element.*not an array/, json_response['errors'].join(' ')
+ end
+
+ test "get index with invalid filters (unsearchable column) responds 422" do
+ get "/arvados/v1/collections", {
+ :format => :json,
+ :filters => [['this_column_does_not_exist', '=', 'bogus']].to_json
+ }, auth(:active)
+ assert_response 422
+ assert_match /nvalid attribute/, json_response['errors'].join(' ')
+ end
+
+ test "get index with invalid filters (invalid operator) responds 422" do
+ get "/arvados/v1/collections", {
+ :format => :json,
+ :filters => [['uuid', ':-(', 'displeased']].to_json
+ }, auth(:active)
+ assert_response 422
+ assert_match /nvalid operator/, json_response['errors'].join(' ')
+ end
+
+ test "get index with invalid filters (invalid operand type) responds 422" do
+ get "/arvados/v1/collections", {
+ :format => :json,
+ :filters => [['uuid', '=', {foo: 'bar'}]].to_json
+ }, auth(:active)
+ assert_response 422
+ assert_match /nvalid operand type/, json_response['errors'].join(' ')
+ end
+
+ test "get index with where= (empty string)" do
+ get "/arvados/v1/collections", {:format => :json, :where => ''}, auth(:active)
+ assert_response :success
+ assert_equal "arvados#collectionList", json_response['kind']
+ end
+
+ test "controller 404 response is json" do
+ get "/arvados/v1/thingsthatdonotexist", {:format => :xml}, auth(:active)
+ assert_response 404
+ assert_equal 1, json_response['errors'].length
+ assert_equal true, json_response['errors'][0].is_a?(String)
+ end
+
+ test "object 404 response is json" do
+ get "/arvados/v1/groups/zzzzz-j7d0g-o5ba971173cup4f", {}, auth(:active)
+ assert_response 404
+ assert_equal 1, json_response['errors'].length
+ assert_equal true, json_response['errors'][0].is_a?(String)
+ end
+
+ test "store collection as json" do
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token(:active),
+ }
+ signed_locator = Blob.sign_locator('bad42fa702ae3ea7d888fef11b46f450+44',
+ signing_opts)
+ post "/arvados/v1/collections", {
+ format: :json,
+ collection: "{\"manifest_text\":\". #{signed_locator} 0:44:md5sum.txt\\n\",\"portable_data_hash\":\"ad02e37b6a7f45bbe2ead3c29a109b8a+54\"}"
+ }, auth(:active)
+ assert_response 200
+ assert_equal 'ad02e37b6a7f45bbe2ead3c29a109b8a+54', json_response['portable_data_hash']
+ end
+
+ test "store collection with manifest_text only" do
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token(:active),
+ }
+ signed_locator = Blob.sign_locator('bad42fa702ae3ea7d888fef11b46f450+44',
+ signing_opts)
+ post "/arvados/v1/collections", {
+ format: :json,
+ collection: "{\"manifest_text\":\". #{signed_locator} 0:44:md5sum.txt\\n\"}"
+ }, auth(:active)
+ assert_response 200
+ assert_equal 'ad02e37b6a7f45bbe2ead3c29a109b8a+54', json_response['portable_data_hash']
+ end
+
+ test "store collection then update name" do
+ signing_opts = {
+ key: Rails.configuration.blob_signing_key,
+ api_token: api_token(:active),
+ }
+ signed_locator = Blob.sign_locator('bad42fa702ae3ea7d888fef11b46f450+44',
+ signing_opts)
+ post "/arvados/v1/collections", {
+ format: :json,
+ collection: "{\"manifest_text\":\". #{signed_locator} 0:44:md5sum.txt\\n\",\"portable_data_hash\":\"ad02e37b6a7f45bbe2ead3c29a109b8a+54\"}"
+ }, auth(:active)
+ assert_response 200
+ assert_equal 'ad02e37b6a7f45bbe2ead3c29a109b8a+54', json_response['portable_data_hash']
+
+ put "/arvados/v1/collections/#{json_response['uuid']}", {
+ format: :json,
+ collection: { name: "a name" }
+ }, auth(:active)
+
+ assert_response 200
+ assert_equal 'ad02e37b6a7f45bbe2ead3c29a109b8a+54', json_response['portable_data_hash']
+ assert_equal 'a name', json_response['name']
+
+ get "/arvados/v1/collections/#{json_response['uuid']}", {
+ format: :json,
+ }, auth(:active)
+
+ assert_response 200
+ assert_equal 'ad02e37b6a7f45bbe2ead3c29a109b8a+54', json_response['portable_data_hash']
+ assert_equal 'a name', json_response['name']
+ end
+
+
+end
--- /dev/null
+require 'test_helper'
+
+class CrossOriginTest < ActionDispatch::IntegrationTest
+ def options *args
+ # Rails doesn't support OPTIONS the same way as GET, POST, etc.
+ reset! unless integration_session
+ integration_session.__send__(:process, :options, *args).tap do
+ copy_session_variables!
+ end
+ end
+
+ %w(/login /logout /auth/example/callback /auth/joshid).each do |path|
+ test "OPTIONS requests are refused at #{path}" do
+ options path, {}, {}
+ assert_no_cors_headers
+ end
+
+ test "CORS headers do not exist at GET #{path}" do
+ get path, {}, {}
+ assert_no_cors_headers
+ end
+ end
+
+ %w(/discovery/v1/apis/arvados/v1/rest).each do |path|
+ test "CORS headers are set at GET #{path}" do
+ get path, {}, {}
+ assert_response :success
+ assert_cors_headers
+ end
+ end
+
+ ['/arvados/v1/collections',
+ '/arvados/v1/users',
+ '/arvados/v1/api_client_authorizations'].each do |path|
+ test "CORS headers are set and body is stub at OPTIONS #{path}" do
+ options path, {}, {}
+ assert_response :success
+ assert_cors_headers
+ assert_equal '-', response.body
+ end
+
+ test "CORS headers are set at authenticated GET #{path}" do
+ get path, {}, auth(:active_trustedclient)
+ assert_response :success
+ assert_cors_headers
+ end
+
+ # CORS headers are OK only if cookies are *not* used to determine
+ # whether a transaction is allowed. The following is a (far from
+ # perfect) test that the usual Rails cookie->session mechanism
+ # does not grant access to any resources.
+ ['GET', 'POST'].each do |method|
+ test "Session does not work at #{method} #{path}" do
+ send method.downcase, path, {format: 'json'}, {user_id: 1}
+ assert_response 401
+ assert_cors_headers
+ end
+ end
+ end
+
+ protected
+ def assert_cors_headers
+ assert_equal '*', response.headers['Access-Control-Allow-Origin']
+ allowed = response.headers['Access-Control-Allow-Methods'].split(', ')
+ %w(GET HEAD POST PUT DELETE).each do |m|
+ assert_includes allowed, m, "A-C-A-Methods should include #{m}"
+ end
+ assert_equal 'Authorization', response.headers['Access-Control-Allow-Headers']
+ end
+
+ def assert_no_cors_headers
+ response.headers.keys.each do |h|
+ assert_no_match /^Access-Control-/i, h
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+require 'helpers/git_test_helper'
+
+class CrunchDispatchTest < ActionDispatch::IntegrationTest
+ include GitTestHelper
+
+ fixtures :all
+
+ @@crunch_dispatch_pid = nil
+
+ def launch_crunch_dispatch
+ @@crunch_dispatch_pid = Process.fork {
+ ENV['PATH'] = ENV['HOME'] + '/arvados/services/crunch:' + ENV['PATH']
+ exec(ENV['HOME'] + '/arvados/services/api/script/crunch-dispatch.rb')
+ }
+ end
+
+ teardown do
+ if @@crunch_dispatch_pid
+ Process.kill "TERM", @@crunch_dispatch_pid
+ Process.wait
+ @@crunch_dispatch_pid = nil
+ end
+ end
+
+ test "job runs" do
+ post "/arvados/v1/jobs", {
+ format: "json",
+ job: {
+ script: "log",
+ repository: "crunch_dispatch_test",
+ script_version: "f35f99b7d32bac257f5989df02b9f12ee1a9b0d6",
+ script_parameters: "{}"
+ }
+ }, auth(:admin)
+ assert_response :success
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class DatabaseResetTest < ActionDispatch::IntegrationTest
+ self.use_transactional_fixtures = false
+
+ test "reset fails when Rails.env != 'test'" do
+ rails_env_was = Rails.env
+ begin
+ Rails.env = 'production'
+ Rails.application.reload_routes!
+ post '/database/reset', {}, auth(:admin)
+ assert_response 404
+ ensure
+ Rails.env = rails_env_was
+ Rails.application.reload_routes!
+ end
+ end
+
+ test "reset fails with non-admin token" do
+ post '/database/reset', {}, auth(:active)
+ assert_response 403
+ end
+
+ test "database reset doesn't break basic CRUD operations" do
+ active_auth = auth(:active)
+ admin_auth = auth(:admin)
+
+ authorize_with :admin
+ post '/database/reset', {}, admin_auth
+ assert_response :success
+
+ post '/arvados/v1/specimens', {specimen: '{}'}, active_auth
+ assert_response :success
+ new_uuid = json_response['uuid']
+
+ get '/arvados/v1/specimens/'+new_uuid, {}, active_auth
+ assert_response :success
+
+ put('/arvados/v1/specimens/'+new_uuid,
+ {specimen: '{"properties":{}}'}, active_auth)
+ assert_response :success
+
+ delete '/arvados/v1/specimens/'+new_uuid, {}, active_auth
+ assert_response :success
+
+ get '/arvados/v1/specimens/'+new_uuid, {}, active_auth
+ assert_response 404
+ end
+
+ test "roll back database change" do
+ active_auth = auth(:active)
+ admin_auth = auth(:admin)
+
+ old_uuid = specimens(:owned_by_active_user).uuid
+ authorize_with :admin
+ post '/database/reset', {}, admin_auth
+ assert_response :success
+
+ delete '/arvados/v1/specimens/' + old_uuid, {}, active_auth
+ assert_response :success
+ post '/arvados/v1/specimens', {specimen: '{}'}, active_auth
+ assert_response :success
+ new_uuid = json_response['uuid']
+
+ # Reset to fixtures.
+ post '/database/reset', {}, admin_auth
+ assert_response :success
+
+ # New specimen should disappear. Old specimen should reappear.
+ get '/arvados/v1/specimens/'+new_uuid, {}, active_auth
+ assert_response 404
+ get '/arvados/v1/specimens/'+old_uuid, {}, active_auth
+ assert_response :success
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class ErrorsTest < ActionDispatch::IntegrationTest
+ fixtures :api_client_authorizations
+
+ %w(/arvados/v1/shoes /arvados/shoes /shoes /nodes /users).each do |path|
+ test "non-existent route #{path}" do
+ get path, {:format => :json}, auth(:active)
+ assert_nil assigns(:objects)
+ assert_nil assigns(:object)
+ assert_not_nil json_response['errors']
+ assert_response 404
+ end
+ end
+
+ n=0
+ Rails.application.routes.routes.each do |route|
+ test "route #{n += 1} '#{route.path.spec.to_s}' is not an accident" do
+ # Generally, new routes should appear under /arvados/v1/. If
+ # they appear elsewhere, that might have been caused by default
+ # rails generator behavior that we don't want.
+ assert_match(/^\/(|\*a|arvados\/v1\/.*|auth\/.*|login|logout|database\/reset|discovery\/.*|static\/.*|themes\/.*)(\(\.:format\))?$/,
+ route.path.spec.to_s,
+ "Unexpected new route: #{route.path.spec}")
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class GroupsTest < ActionDispatch::IntegrationTest
+
+ test "get all pages of group-owned objects" do
+ limit = 5
+ offset = 0
+ items_available = nil
+ uuid_received = {}
+ owner_received = {}
+ while true
+ @json_response = nil
+
+ get "/arvados/v1/groups/contents", {
+ id: groups(:aproject).uuid,
+ limit: limit,
+ offset: offset,
+ format: :json,
+ }, auth(:active)
+
+ assert_response :success
+ assert_operator(0, :<, json_response['items'].count,
+ "items_available=#{items_available} but received 0 "\
+ "items with offset=#{offset}")
+ items_available ||= json_response['items_available']
+ assert_equal(items_available, json_response['items_available'],
+ "items_available changed between page #{offset/limit} "\
+ "and page #{1+offset/limit}")
+ json_response['items'].each do |item|
+ uuid = item['uuid']
+ assert_equal(nil, uuid_received[uuid],
+ "Received '#{uuid}' again on page #{1+offset/limit}")
+ uuid_received[uuid] = true
+ owner_received[item['owner_uuid']] = true
+ offset += 1
+ assert_equal groups(:aproject).uuid, item['owner_uuid']
+ end
+ break if offset >= items_available
+ end
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class JobsApiTest < ActionDispatch::IntegrationTest
+ fixtures :all
+
+ test "cancel job" do
+ post "/arvados/v1/jobs/#{jobs(:running).uuid}/cancel", {:format => :json}, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:active).api_token}"}
+ assert_response :success
+ assert_equal "arvados#job", json_response['kind']
+ assert_not_nil json_response['cancelled_at']
+ end
+
+ test "cancel someone else's visible job" do
+ post "/arvados/v1/jobs/#{jobs(:runningbarbaz).uuid}/cancel", {:format => :json}, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:spectator).api_token}"}
+ assert_response 403
+ end
+
+ test "cancel someone else's invisible job" do
+ post "/arvados/v1/jobs/#{jobs(:running).uuid}/cancel", {:format => :json}, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:spectator).api_token}"}
+ assert_response 404
+ end
+
+ test "task qsequence values automatically increase monotonically" do
+ post_args = ["/arvados/v1/job_tasks",
+ {job_task: {
+ job_uuid: jobs(:running).uuid,
+ sequence: 1,
+ }},
+ auth(:active)]
+ last_qsequence = -1
+ (1..3).each do |task_num|
+ @response = nil
+ post(*post_args)
+ assert_response :success
+ qsequence = json_response["qsequence"]
+ assert_not_nil(qsequence, "task not assigned qsequence")
+ assert_operator(qsequence, :>, last_qsequence,
+ "qsequence did not increase between tasks")
+ last_qsequence = qsequence
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class KeepProxyTest < ActionDispatch::IntegrationTest
+ test "request keep disks" do
+ get "/arvados/v1/keep_services/accessible", {:format => :json}, auth(:active)
+ assert_response :success
+ services = json_response['items']
+
+ assert_operator 2, :<=, services.length
+ services.each do |service|
+ assert_equal 'disk', service['service_type']
+ end
+ end
+
+ test "request keep proxy" do
+ get "/arvados/v1/keep_services/accessible", {:format => :json}, auth(:active).merge({'HTTP_X_EXTERNAL_CLIENT' => '1'})
+ assert_response :success
+ services = json_response['items']
+
+ assert_equal 1, services.length
+
+ assert_equal keep_services(:proxy).uuid, services[0]['uuid']
+ assert_equal keep_services(:proxy).service_host, services[0]['service_host']
+ assert_equal keep_services(:proxy).service_port, services[0]['service_port']
+ assert_equal keep_services(:proxy).service_ssl_flag, services[0]['service_ssl_flag']
+ assert_equal 'proxy', services[0]['service_type']
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class LoginWorkflowTest < ActionDispatch::IntegrationTest
+ test "default prompt to login is JSON" do
+ post('/arvados/v1/specimens', {specimen: {}},
+ {'HTTP_ACCEPT' => ''})
+ assert_response 401
+ assert_includes(json_response['errors'], "Not logged in")
+ end
+
+ test "login prompt respects JSON Accept header" do
+ post('/arvados/v1/specimens', {specimen: {}},
+ {'HTTP_ACCEPT' => 'application/json'})
+ assert_response 401
+ assert_includes(json_response['errors'], "Not logged in")
+ end
+
+ test "login prompt respects HTML Accept header" do
+ post('/arvados/v1/specimens', {specimen: {}},
+ {'HTTP_ACCEPT' => 'text/html'})
+ assert_response 302
+ assert_match(%r{/auth/joshid$}, @response.headers['Location'],
+ "HTML login prompt did not include expected redirect")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class PermissionsTest < ActionDispatch::IntegrationTest
+ include CurrentApiClient # for empty_collection
+ fixtures :users, :groups, :api_client_authorizations, :collections
+
+ test "adding and removing direct can_read links" do
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+
+ # try to add permission as spectator
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, auth(:spectator)
+ assert_response 422
+
+ # add permission as admin
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ u = json_response['uuid']
+ assert_response :success
+
+ # read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response :success
+
+ # try to delete permission as spectator
+ delete "/arvados/v1/links/#{u}", {:format => :json}, auth(:spectator)
+ assert_response 403
+
+ # delete permission as admin
+ delete "/arvados/v1/links/#{u}", {:format => :json}, auth(:admin)
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+ end
+
+
+ test "adding can_read links from user to group, group to collection" do
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+
+ # add permission for spectator to read group
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: groups(:private).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+
+ # add permission for group to read collection
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: groups(:private).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ u = json_response['uuid']
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response :success
+
+ # delete permission for group to read collection
+ delete "/arvados/v1/links/#{u}", {:format => :json}, auth(:admin)
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+
+ end
+
+
+ test "adding can_read links from group to collection, user to group" do
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+
+ # add permission for group to read collection
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: groups(:private).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+
+ # add permission for spectator to read group
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: groups(:private).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ u = json_response['uuid']
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response :success
+
+ # delete permission for spectator to read group
+ delete "/arvados/v1/links/#{u}", {:format => :json}, auth(:admin)
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+
+ end
+
+ test "adding can_read links from user to group, group to group, group to collection" do
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+
+ # add permission for user to read group
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: groups(:private).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ assert_response :success
+
+ # add permission for group to read group
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: groups(:private).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: groups(:empty_lonely_group).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ assert_response :success
+
+ # add permission for group to read collection
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: groups(:empty_lonely_group).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ u = json_response['uuid']
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response :success
+
+ # delete permission for group to read collection
+ delete "/arvados/v1/links/#{u}", {:format => :json}, auth(:admin)
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth(:spectator)
+ assert_response 404
+ end
+
+ test "read-only group-admin cannot modify administered user" do
+ put "/arvados/v1/users/#{users(:active).uuid}", {
+ :user => {
+ first_name: 'KilroyWasHere'
+ },
+ :format => :json
+ }, auth(:rominiadmin)
+ assert_response 403
+ end
+
+ test "read-only group-admin cannot read or update non-administered user" do
+ get "/arvados/v1/users/#{users(:spectator).uuid}", {
+ :format => :json
+ }, auth(:rominiadmin)
+ assert_response 404
+
+ put "/arvados/v1/users/#{users(:spectator).uuid}", {
+ :user => {
+ first_name: 'KilroyWasHere'
+ },
+ :format => :json
+ }, auth(:rominiadmin)
+ assert_response 404
+ end
+
+ test "RO group-admin finds user's specimens, RW group-admin can update" do
+ [[:rominiadmin, false],
+ [:miniadmin, true]].each do |which_user, update_should_succeed|
+ get "/arvados/v1/specimens", {:format => :json}, auth(which_user)
+ assert_response :success
+ resp_uuids = json_response['items'].collect { |i| i['uuid'] }
+ [[true, specimens(:owned_by_active_user).uuid],
+ [true, specimens(:owned_by_private_group).uuid],
+ [false, specimens(:owned_by_spectator).uuid],
+ ].each do |should_find, uuid|
+ assert_equal(should_find, !resp_uuids.index(uuid).nil?,
+ "%s should%s see %s in specimen list" %
+ [which_user.to_s,
+ should_find ? '' : 'not ',
+ uuid])
+ put "/arvados/v1/specimens/#{uuid}", {
+ :specimen => {
+ properties: {
+ miniadmin_was_here: true
+ }
+ },
+ :format => :json
+ }, auth(which_user)
+ if !should_find
+ assert_response 404
+ elsif !update_should_succeed
+ assert_response 403
+ else
+ assert_response :success
+ end
+ end
+ end
+ end
+
+ test "get_permissions returns list" do
+ # First confirm that user :active cannot get permissions on group :public
+ get "/arvados/v1/permissions/#{groups(:public).uuid}", nil, auth(:active)
+ assert_response 404
+
+ # add some permissions, including can_manage
+ # permission for user :active
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: groups(:public).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ assert_response :success
+ can_read_uuid = json_response['uuid']
+
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:inactive).uuid,
+ link_class: 'permission',
+ name: 'can_write',
+ head_uuid: groups(:public).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ assert_response :success
+ can_write_uuid = json_response['uuid']
+
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_uuid: users(:active).uuid,
+ link_class: 'permission',
+ name: 'can_manage',
+ head_uuid: groups(:public).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ assert_response :success
+ can_manage_uuid = json_response['uuid']
+
+ # Now user :active should be able to retrieve permissions
+ # on group :public.
+ get("/arvados/v1/permissions/#{groups(:public).uuid}",
+ { :format => :json },
+ auth(:active))
+ assert_response :success
+
+ perm_uuids = json_response['items'].map { |item| item['uuid'] }
+ assert_includes perm_uuids, can_read_uuid, "can_read_uuid not found"
+ assert_includes perm_uuids, can_write_uuid, "can_write_uuid not found"
+ assert_includes perm_uuids, can_manage_uuid, "can_manage_uuid not found"
+ end
+
+ test "get_permissions returns 404 for nonexistent uuid" do
+ nonexistent = Group.generate_uuid
+ # make sure it really doesn't exist
+ get "/arvados/v1/groups/#{nonexistent}", nil, auth(:admin)
+ assert_response 404
+
+ get "/arvados/v1/permissions/#{nonexistent}", nil, auth(:active)
+ assert_response 404
+ end
+
+ test "get_permissions returns 404 for unreadable uuid" do
+ get "/arvados/v1/permissions/#{groups(:public).uuid}", nil, auth(:active)
+ assert_response 404
+ end
+
+ test "get_permissions returns 403 if user can read but not manage" do
+ post "/arvados/v1/links", {
+ :link => {
+ tail_uuid: users(:active).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_uuid: groups(:public).uuid,
+ properties: {}
+ }
+ }, auth(:admin)
+ assert_response :success
+
+ get "/arvados/v1/permissions/#{groups(:public).uuid}", nil, auth(:active)
+ assert_response 403
+ end
+
+ test "active user can read the empty collection" do
+ # The active user should be able to read the empty collection.
+
+ get("/arvados/v1/collections/#{empty_collection_uuid}",
+ { :format => :json },
+ auth(:active))
+ assert_response :success
+ assert_empty json_response['manifest_text'], "empty collection manifest_text is not empty"
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineTest < ActionDispatch::IntegrationTest
+ # These tests simulate the workflow of arv-run-pipeline-instance
+ # and other pipeline-running code.
+
+ def check_component_match(comp_key, comp_hash)
+ assert_response :success
+ built_json = json_response
+ built_component = built_json["components"][comp_key]
+ comp_hash.each_pair do |key, expected|
+ assert_equal(expected, built_component[key.to_s],
+ "component's #{key} field changed")
+ end
+ end
+
+ test "creating a pipeline instance preserves required component parameters" do
+ comp_name = "test_component"
+ component = {
+ repository: "test_repo",
+ script: "test_script",
+ script_version: "test_refspec",
+ script_parameters: {},
+ }
+
+ post("/arvados/v1/pipeline_instances",
+ {pipeline_instance: {components: {comp_name => component}}.to_json},
+ auth(:active))
+ check_component_match(comp_name, component)
+ pi_uuid = json_response["uuid"]
+
+ @response = nil
+ get("/arvados/v1/pipeline_instances/#{pi_uuid}", {}, auth(:active))
+ check_component_match(comp_name, component)
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class Arvados::V1::ReaderTokensTest < ActionController::IntegrationTest
+ fixtures :all
+
+ def spectator_specimen
+ specimens(:owned_by_spectator).uuid
+ end
+
+ def get_specimens(main_auth, read_auth, formatter=:to_a)
+ params = {}
+ params[:reader_tokens] = [api_token(read_auth)].send(formatter) if read_auth
+ headers = {}
+ headers.merge!(auth(main_auth)) if main_auth
+ get('/arvados/v1/specimens', params, headers)
+ end
+
+ def get_specimen_uuids(main_auth, read_auth, formatter=:to_a)
+ get_specimens(main_auth, read_auth, formatter)
+ assert_response :success
+ json_response['items'].map { |spec| spec['uuid'] }
+ end
+
+ def assert_post_denied(main_auth, read_auth, formatter=:to_a)
+ if main_auth
+ headers = auth(main_auth)
+ expected = 403
+ else
+ headers = {}
+ expected = 401
+ end
+ post('/arvados/v1/specimens.json',
+ {specimen: {}, reader_tokens: [api_token(read_auth)].send(formatter)},
+ headers)
+ assert_response expected
+ end
+
+ test "active user can't see spectator specimen" do
+ # Other tests in this suite assume that the active user doesn't
+ # have read permission to the owned_by_spectator specimen.
+ # This test checks that this assumption still holds.
+ refute_includes(get_specimen_uuids(:active, nil), spectator_specimen,
+ ["active user can read the owned_by_spectator specimen",
+ "other tests will return false positives"].join(" - "))
+ end
+
+ [nil, :active_noscope].each do |main_auth|
+ [:spectator, :spectator_specimens].each do |read_auth|
+ test "#{main_auth} auth with reader token #{read_auth} can read" do
+ assert_includes(get_specimen_uuids(main_auth, read_auth),
+ spectator_specimen, "did not find spectator specimen")
+ end
+
+ test "#{main_auth} auth with JSON read token #{read_auth} can read" do
+ assert_includes(get_specimen_uuids(main_auth, read_auth, :to_json),
+ spectator_specimen, "did not find spectator specimen")
+ end
+
+ test "#{main_auth} auth with reader token #{read_auth} can't write" do
+ assert_post_denied(main_auth, read_auth)
+ end
+
+ test "#{main_auth} auth with JSON read token #{read_auth} can't write" do
+ assert_post_denied(main_auth, read_auth, :to_json)
+ end
+ end
+ end
+
+ test "scopes are still limited with reader tokens" do
+ get('/arvados/v1/collections',
+ {reader_tokens: [api_token(:spectator_specimens)]},
+ auth(:active_noscope))
+ assert_response 403
+ end
+
+ test "reader tokens grant no permissions when expired" do
+ get_specimens(:active_noscope, :expired)
+ assert_response 403
+ end
+
+ test "reader tokens grant no permissions outside their scope" do
+ refute_includes(get_specimen_uuids(:active, :admin_vm), spectator_specimen,
+ "scoped reader token granted permissions out of scope")
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class SelectTest < ActionDispatch::IntegrationTest
+ test "should select just two columns" do
+ get "/arvados/v1/links", {:format => :json, :select => ['uuid', 'link_class']}, auth(:active)
+ assert_response :success
+ assert_equal json_response['items'].count, json_response['items'].select { |i|
+ i.count == 3 and i['uuid'] != nil and i['link_class'] != nil
+ }.count
+ end
+
+ test "fewer distinct than total count" do
+ get "/arvados/v1/links", {:format => :json, :select => ['link_class'], :distinct => false}, auth(:active)
+ assert_response :success
+ links = json_response['items']
+
+ get "/arvados/v1/links", {:format => :json, :select => ['link_class'], :distinct => true}, auth(:active)
+ assert_response :success
+ distinct = json_response['items']
+
+ assert_operator(distinct.count, :<, links.count,
+ "distinct count should be less than link count")
+ assert_equal links.uniq.count, distinct.count
+ end
+
+ test "select with order" do
+ get "/arvados/v1/links", {:format => :json, :select => ['uuid'], :order => ["uuid asc"]}, auth(:active)
+ assert_response :success
+
+ assert json_response['items'].length > 0
+
+ p = ""
+ json_response['items'].each do |i|
+ assert i['uuid'] > p
+ p = i['uuid']
+ end
+ end
+
+ def assert_link_classes_ascend(current_class, prev_class)
+ # Databases and Ruby don't always agree about string ordering with
+ # punctuation. If the strings aren't ascending normally, check
+ # that they're equal up to punctuation.
+ if current_class < prev_class
+ class_prefix = current_class.split(/\W/).first
+ assert prev_class.start_with?(class_prefix)
+ end
+ end
+
+ test "select two columns with order" do
+ get "/arvados/v1/links", {:format => :json, :select => ['link_class', 'uuid'], :order => ['link_class asc', "uuid desc"]}, auth(:active)
+ assert_response :success
+
+ assert json_response['items'].length > 0
+
+ prev_link_class = ""
+ prev_uuid = "zzzzz-zzzzz-zzzzzzzzzzzzzzz"
+
+ json_response['items'].each do |i|
+ if prev_link_class != i['link_class']
+ prev_uuid = "zzzzz-zzzzz-zzzzzzzzzzzzzzz"
+ end
+
+ assert_link_classes_ascend(i['link_class'], prev_link_class)
+ assert i['uuid'] < prev_uuid
+
+ prev_link_class = i['link_class']
+ prev_uuid = i['uuid']
+ end
+ end
+
+ test "select two columns with old-style order syntax" do
+ get "/arvados/v1/links", {:format => :json, :select => ['link_class', 'uuid'], :order => 'link_class asc, uuid desc'}, auth(:active)
+ assert_response :success
+
+ assert json_response['items'].length > 0
+
+ prev_link_class = ""
+ prev_uuid = "zzzzz-zzzzz-zzzzzzzzzzzzzzz"
+
+ json_response['items'].each do |i|
+ if prev_link_class != i['link_class']
+ prev_uuid = "zzzzz-zzzzz-zzzzzzzzzzzzzzz"
+ end
+
+ assert_link_classes_ascend(i['link_class'], prev_link_class)
+ assert i['uuid'] < prev_uuid
+
+ prev_link_class = i['link_class']
+ prev_uuid = i['uuid']
+ end
+ end
+
+end
--- /dev/null
+require 'test_helper'
+require 'helpers/git_test_helper'
+
+class SerializedEncodingTest < ActionDispatch::IntegrationTest
+ include GitTestHelper
+
+ fixtures :all
+
+ {
+ api_client_authorization: {scopes: []},
+
+ human: {properties: {eye_color: 'gray'}},
+
+ job: {
+ repository: 'foo',
+ runtime_constraints: {docker_image: 'arvados/apitestfixture'},
+ script: 'hash',
+ script_version: 'master',
+ script_parameters: {pattern: 'foobar'},
+ tasks_summary: {todo: 0},
+ },
+
+ job_task: {parameters: {pattern: 'foo'}},
+
+ link: {link_class: 'test', name: 'test', properties: {foo: :bar}},
+
+ node: {info: {uptime: 1234}},
+
+ pipeline_instance: {
+ components: {"job1" => {parameters: {pattern: "xyzzy"}}},
+ components_summary: {todo: 0},
+ properties: {test: true},
+ },
+
+ pipeline_template: {
+ components: {"job1" => {parameters: {pattern: "xyzzy"}}},
+ },
+
+ specimen: {properties: {eye_color: 'meringue'}},
+
+ trait: {properties: {eye_color: 'brown'}},
+
+ user: {prefs: {cookies: 'thin mint'}},
+ }.each_pair do |resource, postdata|
+ test "create json-encoded #{resource.to_s}" do
+ post("/arvados/v1/#{resource.to_s.pluralize}",
+ {resource => postdata.to_json}, auth(:admin_trustedclient))
+ assert_response :success
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class UserSessionsApiTest < ActionDispatch::IntegrationTest
+ def client_url
+ 'https://wb.example.com'
+ end
+
+ def mock_auth_with_email email
+ mock = {
+ 'provider' => 'josh_id',
+ 'uid' => 'https://edward.example.com',
+ 'info' => {
+ 'identity_url' => 'https://edward.example.com',
+ 'name' => 'Edward Example',
+ 'first_name' => 'Edward',
+ 'last_name' => 'Example',
+ 'email' => email,
+ },
+ }
+ post('/auth/josh_id/callback',
+ {return_to: client_url},
+ {'omniauth.auth' => mock})
+ assert_response :redirect, 'Did not redirect to client with token'
+ end
+
+ test 'create new user during omniauth callback' do
+ mock_auth_with_email 'edward@example.com'
+ assert_equal(0, @response.redirect_url.index(client_url),
+ 'Redirected to wrong address after succesful login: was ' +
+ @response.redirect_url + ', expected ' + client_url + '[...]')
+ assert_not_nil(@response.redirect_url.index('api_token='),
+ 'Expected api_token in query string of redirect url ' +
+ @response.redirect_url)
+ end
+
+ # Test various combinations of auto_setup configuration and email
+ # address provided during a new user's first session setup.
+ [{result: :nope, email: nil, cfg: {auto: true, repo: true, vm: true}},
+ {result: :yup, email: nil, cfg: {auto: true}},
+ {result: :nope, email: '@example.com', cfg: {auto: true, repo: true, vm: true}},
+ {result: :yup, email: '@example.com', cfg: {auto: true}},
+ {result: :nope, email: 'root@', cfg: {auto: true, repo: true, vm: true}},
+ {result: :nope, email: 'root@', cfg: {auto: true, repo: true}},
+ {result: :nope, email: 'root@', cfg: {auto: true, vm: true}},
+ {result: :yup, email: 'root@', cfg: {auto: true}},
+ {result: :nope, email: 'gitolite@', cfg: {auto: true, repo: true}},
+ {result: :nope, email: '*_*@', cfg: {auto: true, vm: true}},
+ {result: :yup, email: 'toor@', cfg: {auto: true, vm: true, repo: true}},
+ {result: :yup, email: 'foo@', cfg: {auto: true, vm: true},
+ uniqprefix: 'foo'},
+ {result: :yup, email: 'foo@', cfg: {auto: true, repo: true},
+ uniqprefix: 'foo'},
+ {result: :yup, email: 'auto_setup_vm_login@', cfg: {auto: true, repo: true},
+ uniqprefix: 'auto_setup_vm_login'},
+ ].each do |testcase|
+ test "user auto-activate #{testcase.inspect}" do
+ # Configure auto_setup behavior according to testcase[:cfg]
+ Rails.configuration.auto_setup_new_users = testcase[:cfg][:auto]
+ Rails.configuration.auto_setup_new_users_with_vm_uuid =
+ (testcase[:cfg][:vm] ? virtual_machines(:testvm).uuid : false)
+ Rails.configuration.auto_setup_new_users_with_repository =
+ testcase[:cfg][:repo]
+
+ mock_auth_with_email testcase[:email]
+ u = assigns(:user)
+ vm_links = Link.where('link_class=? and tail_uuid=? and head_uuid like ?',
+ 'permission', u.uuid,
+ '%-' + VirtualMachine.uuid_prefix + '-%')
+ repo_links = Link.where('link_class=? and tail_uuid=? and head_uuid like ?',
+ 'permission', u.uuid,
+ '%-' + Repository.uuid_prefix + '-%')
+ repos = Repository.where('uuid in (?)', repo_links.collect(&:head_uuid))
+ case u[:result]
+ when :nope
+ assert_equal false, u.is_invited, "should not have been set up"
+ assert_empty vm_links, "should not have VM login permission"
+ assert_empty repo_links, "should not have repo permission"
+ when :yup
+ assert_equal true, u.is_invited
+ if testcase[:cfg][:vm]
+ assert_equal 1, vm_links.count, "wrong number of VM perm links"
+ else
+ assert_empty vm_links, "should not have VM login permission"
+ end
+ if testcase[:cfg][:repo]
+ assert_equal 1, repo_links.count, "wrong number of repo perm links"
+ assert_equal 1, repos.count, "wrong number of repos"
+ assert_equal 'can_manage', repo_links.first.name, "wrong perm type"
+ else
+ assert_empty repo_links, "should not have repo permission"
+ end
+ end
+ if (prefix = testcase[:uniqprefix])
+ # This email address conflicts with a test fixture. Make sure
+ # every VM login and repository name got digits added to make
+ # it unique.
+ (repos.collect(&:name) +
+ vm_links.collect { |link| link.properties['username'] }
+ ).each do |name|
+ r = name.match /^(.{#{prefix.length}})(\d+)$/
+ assert_not_nil r, "#{name.inspect} does not match {prefix}\\d+"
+ assert_equal(prefix, r[1],
+ "#{name.inspect} was not {#{prefix.inspect} plus digits}")
+ end
+ end
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+require 'helpers/users_test_helper'
+
+class UsersTest < ActionDispatch::IntegrationTest
+ include UsersTestHelper
+
+ test "setup user multiple times" do
+ repo_name = 'test_repo'
+
+ post "/arvados/v1/users/setup", {
+ repo_name: repo_name,
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ user: {
+ uuid: 'zzzzz-tpzed-abcdefghijklmno',
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }, auth(:admin)
+
+ assert_response :success
+
+ response_items = json_response['items']
+
+ created = find_obj_in_resp response_items, 'arvados#user', nil
+
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected non-null uuid for the new user'
+ assert_equal 'zzzzz-tpzed-abcdefghijklmno', created['uuid']
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # arvados#user, repo link and link add user to 'All users' group
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'arvados#user'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ repo_name, created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ verify_system_group_permission_link_for created['uuid']
+
+ # invoke setup again with the same data
+ post "/arvados/v1/users/setup", {
+ repo_name: repo_name,
+ vm_uuid: virtual_machines(:testvm).uuid,
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ user: {
+ uuid: 'zzzzz-tpzed-abcdefghijklmno',
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }, auth(:admin)
+
+ assert_response :success
+
+ response_items = json_response['items']
+
+ created = find_obj_in_resp response_items, 'arvados#user', nil
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected non-null uuid for the new user'
+ assert_equal 'zzzzz-tpzed-abcdefghijklmno', created['uuid']
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # arvados#user, repo link and link add user to 'All users' group
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ repo_name, created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ virtual_machines(:testvm).uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ verify_system_group_permission_link_for created['uuid']
+ end
+
+ test "setup user in multiple steps and verify response" do
+ post "/arvados/v1/users/setup", {
+ openid_prefix: 'http://www.example.com/account',
+ user: {
+ email: "foo@example.com"
+ }
+ }, auth(:admin)
+
+ assert_response :success
+ response_items = json_response['items']
+ created = find_obj_in_resp response_items, 'arvados#user', nil
+
+ assert_not_nil created['uuid'], 'expected uuid for new user'
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_equal created['email'], 'foo@example.com', 'expected input email'
+
+ # three new links: system_group, arvados#user, and 'All users' group.
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'arvados#user'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', false, 'permission', 'can_manage',
+ 'test_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ # invoke setup with a repository
+ post "/arvados/v1/users/setup", {
+ openid_prefix: 'http://www.example.com/account',
+ repo_name: 'new_repo',
+ uuid: created['uuid']
+ }, auth(:admin)
+
+ assert_response :success
+
+ response_items = json_response['items']
+ created = find_obj_in_resp response_items, 'arvados#user', nil
+
+ assert_equal 'foo@example.com', created['email'], 'expected input email'
+
+ # verify links
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ 'new_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ # invoke setup with a vm_uuid
+ post "/arvados/v1/users/setup", {
+ vm_uuid: virtual_machines(:testvm).uuid,
+ openid_prefix: 'http://www.example.com/account',
+ user: {
+ email: 'junk_email'
+ },
+ uuid: created['uuid']
+ }, auth(:admin)
+
+ assert_response :success
+
+ response_items = json_response['items']
+ created = find_obj_in_resp response_items, 'arvados#user', nil
+
+ assert_equal created['email'], 'foo@example.com', 'expected original email'
+
+ # verify links
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ # since no repo name in input, we won't get any; even though user has one
+ verify_link response_items, 'arvados#repository', false, 'permission', 'can_manage',
+ 'new_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ virtual_machines(:testvm).uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "setup and unsetup user" do
+ post "/arvados/v1/users/setup", {
+ repo_name: 'test_repo',
+ vm_uuid: virtual_machines(:testvm).uuid,
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }, auth(:admin)
+
+ assert_response :success
+ response_items = json_response['items']
+ created = find_obj_in_resp response_items, 'arvados#user', nil
+ assert_not_nil created['uuid'], 'expected uuid for the new user'
+ assert_equal created['email'], 'foo@example.com', 'expected given email'
+
+ # five extra links: system_group, login, group, repo and vm
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'arvados#user'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_manage',
+ 'test_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ virtual_machines(:testvm).uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ verify_link_existence created['uuid'], created['email'], true, true, true, true, false
+
+ post "/arvados/v1/users/#{created['uuid']}/unsetup", {}, auth(:admin)
+
+ assert_response :success
+
+ created2 = json_response
+ assert_not_nil created2['uuid'], 'expected uuid for the newly created user'
+ assert_equal created['uuid'], created2['uuid'], 'expected uuid not found'
+
+ verify_link_existence created['uuid'], created['email'], false, false, false, false, false
+ end
+
+ def find_obj_in_resp (response_items, kind, head_kind=nil)
+ response_items.each do |x|
+ if x && x['kind']
+ return x if (x['kind'] == kind && x['head_kind'] == head_kind)
+ end
+ end
+ nil
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class ValidLinksTest < ActionDispatch::IntegrationTest
+ fixtures :all
+
+ test "tail must exist on update" do
+ admin_auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin).api_token}"}
+
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ link_class: 'test',
+ name: 'stuff',
+ head_uuid: users(:active).uuid,
+ tail_uuid: virtual_machines(:testvm).uuid
+ }
+ }, admin_auth
+ assert_response :success
+ u = json_response['uuid']
+
+ put "/arvados/v1/links/#{u}", {
+ :format => :json,
+ :link => {
+ tail_uuid: virtual_machines(:testvm2).uuid
+ }
+ }, admin_auth
+ assert_response :success
+ assert_equal virtual_machines(:testvm2).uuid, (ActiveSupport::JSON.decode @response.body)['tail_uuid']
+
+ put "/arvados/v1/links/#{u}", {
+ :format => :json,
+ :link => {
+ tail_uuid: 'zzzzz-tpzed-xyzxyzxerrrorxx'
+ }
+ }, admin_auth
+ assert_response 422
+ end
+
+end
--- /dev/null
+require 'test_helper'
+require 'websocket_runner'
+require 'oj'
+require 'database_cleaner'
+
+DatabaseCleaner.strategy = :deletion
+
+class WebsocketTest < ActionDispatch::IntegrationTest
+ self.use_transactional_fixtures = false
+
+ setup do
+ DatabaseCleaner.start
+ end
+
+ teardown do
+ DatabaseCleaner.clean
+ end
+
+ def ws_helper (token = nil, timeout = true)
+ opened = false
+ close_status = nil
+ too_long = false
+
+ EM.run {
+ if token
+ ws = Faye::WebSocket::Client.new("ws://localhost:3002/websocket?api_token=#{api_client_authorizations(token).api_token}")
+ else
+ ws = Faye::WebSocket::Client.new("ws://localhost:3002/websocket")
+ end
+
+ ws.on :open do |event|
+ opened = true
+ if timeout
+ EM::Timer.new 4 do
+ too_long = true if close_status.nil?
+ EM.stop_event_loop
+ end
+ end
+ end
+
+ ws.on :close do |event|
+ close_status = [:close, event.code, event.reason]
+ EM.stop_event_loop
+ end
+
+ yield ws
+ }
+
+ assert opened, "Should have opened web socket"
+ assert (not too_long), "Test took too long"
+ assert_equal 1000, close_status[1], "Connection closed unexpectedly (check log for errors)"
+ end
+
+ test "connect with no token" do
+ status = nil
+
+ ws_helper do |ws|
+ ws.on :message do |event|
+ d = Oj.load event.data
+ status = d["status"]
+ ws.close
+ end
+ end
+
+ assert_equal 401, status
+ end
+
+
+ test "connect, subscribe and get response" do
+ status = nil
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe'}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ status = d["status"]
+ ws.close
+ end
+ end
+
+ assert_equal 200, status
+ end
+
+ test "connect, subscribe, get event" do
+ state = 1
+ spec = nil
+ ev_uuid = nil
+
+ authorize_with :admin
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe'}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ spec = Specimen.create
+ state = 2
+ when 2
+ ev_uuid = d["object_uuid"]
+ ws.close
+ end
+ end
+
+ end
+
+ assert_not_nil spec
+ assert_equal spec.uuid, ev_uuid
+ end
+
+ test "connect, subscribe, get two events" do
+ state = 1
+ spec = nil
+ human = nil
+ spec_ev_uuid = nil
+ human_ev_uuid = nil
+
+ authorize_with :admin
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe'}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ spec = Specimen.create
+ human = Human.create
+ state = 2
+ when 2
+ spec_ev_uuid = d["object_uuid"]
+ state = 3
+ when 3
+ human_ev_uuid = d["object_uuid"]
+ state = 4
+ ws.close
+ when 4
+ assert false, "Should not get any more events"
+ end
+ end
+
+ end
+
+ assert_not_nil spec
+ assert_not_nil human
+ assert_equal spec.uuid, spec_ev_uuid
+ assert_equal human.uuid, human_ev_uuid
+ end
+
+ test "connect, subscribe, filter events" do
+ state = 1
+ human = nil
+ human_ev_uuid = nil
+
+ authorize_with :admin
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#human']]}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ Specimen.create
+ human = Human.create
+ state = 2
+ when 2
+ human_ev_uuid = d["object_uuid"]
+ state = 3
+ ws.close
+ when 3
+ assert false, "Should not get any more events"
+ end
+ end
+
+ end
+
+ assert_not_nil human
+ assert_equal human.uuid, human_ev_uuid
+ end
+
+
+ test "connect, subscribe, multiple filters" do
+ state = 1
+ spec = nil
+ human = nil
+ spec_ev_uuid = nil
+ human_ev_uuid = nil
+
+ authorize_with :admin
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#human']]}.to_json)
+ ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#specimen']]}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ state = 2
+ when 2
+ assert_equal 200, d["status"]
+ spec = Specimen.create
+ Trait.create # not part of filters, should not be received
+ human = Human.create
+ state = 3
+ when 3
+ spec_ev_uuid = d["object_uuid"]
+ state = 4
+ when 4
+ human_ev_uuid = d["object_uuid"]
+ state = 5
+ ws.close
+ when 5
+ assert false, "Should not get any more events"
+ end
+ end
+
+ end
+
+ assert_not_nil spec
+ assert_not_nil human
+ assert_equal spec.uuid, spec_ev_uuid
+ assert_equal human.uuid, human_ev_uuid
+ end
+
+
+ test "connect, subscribe, compound filter" do
+ state = 1
+ t1 = nil
+
+ authorize_with :admin
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#trait'], ['event_type', '=', 'update']]}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ t1 = Trait.create("name" => "foo")
+ t1.name = "bar"
+ t1.save!
+ state = 2
+ when 2
+ assert_equal 'update', d['event_type']
+ state = 3
+ ws.close
+ when 3
+ assert false, "Should not get any more events"
+ end
+ end
+
+ end
+
+ assert_equal 3, state
+ assert_not_nil t1
+ end
+
+ test "connect, subscribe, ask events starting at seq num" do
+ state = 1
+ human = nil
+ human_ev_uuid = nil
+
+ authorize_with :admin
+
+ lastid = logs(:log3).id
+ l1 = nil
+ l2 = nil
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe', last_log_id: lastid}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ state = 2
+ when 2
+ l1 = d["object_uuid"]
+ assert_not_nil l1, "Unexpected message: #{d}"
+ state = 3
+ when 3
+ l2 = d["object_uuid"]
+ assert_not_nil l2, "Unexpected message: #{d}"
+ state = 4
+ ws.close
+ when 4
+ assert false, "Should not get any more events"
+ end
+ end
+
+ end
+
+ assert_equal logs(:log4).object_uuid, l1
+ assert_equal logs(:log5).object_uuid, l2
+ end
+
+ test "connect, subscribe, get event, unsubscribe" do
+ state = 1
+ spec = nil
+ spec_ev_uuid = nil
+ filter_id = nil
+
+ authorize_with :admin
+
+ ws_helper :admin, false do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe'}.to_json)
+ EM::Timer.new 3 do
+ # Set a time limit on the test because after unsubscribing the server
+ # still has to process the next event (and then hopefully correctly
+ # decides not to send it because we unsubscribed.)
+ ws.close
+ end
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ spec = Specimen.create
+ state = 2
+ when 2
+ spec_ev_uuid = d["object_uuid"]
+ ws.send ({method: 'unsubscribe'}.to_json)
+
+ EM::Timer.new 1 do
+ Specimen.create
+ end
+
+ state = 3
+ when 3
+ assert_equal 200, d["status"]
+ state = 4
+ when 4
+ assert false, "Should not get any more events"
+ end
+ end
+
+ end
+
+ assert_not_nil spec
+ assert_equal spec.uuid, spec_ev_uuid
+ end
+
+ test "connect, subscribe, get event, unsubscribe with filter" do
+ state = 1
+ spec = nil
+ spec_ev_uuid = nil
+
+ authorize_with :admin
+
+ ws_helper :admin, false do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#human']]}.to_json)
+ EM::Timer.new 3 do
+ # Set a time limit on the test because after unsubscribing the server
+ # still has to process the next event (and then hopefully correctly
+ # decides not to send it because we unsubscribed.)
+ ws.close
+ end
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ spec = Human.create
+ state = 2
+ when 2
+ spec_ev_uuid = d["object_uuid"]
+ ws.send ({method: 'unsubscribe', filters: [['object_uuid', 'is_a', 'arvados#human']]}.to_json)
+
+ EM::Timer.new 1 do
+ Human.create
+ end
+
+ state = 3
+ when 3
+ assert_equal 200, d["status"]
+ state = 4
+ when 4
+ assert false, "Should not get any more events"
+ end
+ end
+
+ end
+
+ assert_not_nil spec
+ assert_equal spec.uuid, spec_ev_uuid
+ end
+
+
+ test "connect, subscribe, get event, try to unsubscribe with bogus filter" do
+ state = 1
+ spec = nil
+ spec_ev_uuid = nil
+ human = nil
+ human_ev_uuid = nil
+
+ authorize_with :admin
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe'}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ spec = Specimen.create
+ state = 2
+ when 2
+ spec_ev_uuid = d["object_uuid"]
+ ws.send ({method: 'unsubscribe', filters: [['foo', 'bar', 'baz']]}.to_json)
+
+ EM::Timer.new 1 do
+ human = Human.create
+ end
+
+ state = 3
+ when 3
+ assert_equal 404, d["status"]
+ state = 4
+ when 4
+ human_ev_uuid = d["object_uuid"]
+ state = 5
+ ws.close
+ when 5
+ assert false, "Should not get any more events"
+ end
+ end
+
+ end
+
+ assert_not_nil spec
+ assert_not_nil human
+ assert_equal spec.uuid, spec_ev_uuid
+ assert_equal human.uuid, human_ev_uuid
+ end
+
+
+
+ test "connected, not subscribed, no event" do
+ authorize_with :admin
+
+ ws_helper :admin, false do |ws|
+ ws.on :open do |event|
+ EM::Timer.new 1 do
+ Specimen.create
+ end
+
+ EM::Timer.new 3 do
+ ws.close
+ end
+ end
+
+ ws.on :message do |event|
+ assert false, "Should not get any messages, message was #{event.data}"
+ end
+ end
+ end
+
+ test "connected, not authorized to see event" do
+ state = 1
+
+ authorize_with :admin
+
+ ws_helper :active, false do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe'}.to_json)
+
+ EM::Timer.new 3 do
+ ws.close
+ end
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ Specimen.create
+ state = 2
+ when 2
+ assert false, "Should not get any messages, message was #{event.data}"
+ end
+ end
+
+ end
+
+ end
+
+ test "connect, try bogus method" do
+ status = nil
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({method: 'frobnabble'}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ status = d["status"]
+ ws.close
+ end
+ end
+
+ assert_equal 400, status
+ end
+
+ test "connect, missing method" do
+ status = nil
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send ({fizzbuzz: 'frobnabble'}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ status = d["status"]
+ ws.close
+ end
+ end
+
+ assert_equal 400, status
+ end
+
+ test "connect, send malformed request" do
+ status = nil
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ ws.send '<XML4EVER></XML4EVER>'
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ status = d["status"]
+ ws.close
+ end
+ end
+
+ assert_equal 400, status
+ end
+
+
+ test "connect, try subscribe too many filters" do
+ state = 1
+
+ authorize_with :admin
+
+ ws_helper :admin do |ws|
+ ws.on :open do |event|
+ (1..17).each do |i|
+ ws.send ({method: 'subscribe', filters: [['object_uuid', '=', i]]}.to_json)
+ end
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when (1..EventBus::MAX_FILTERS)
+ assert_equal 200, d["status"]
+ state += 1
+ when (EventBus::MAX_FILTERS+1)
+ assert_equal 403, d["status"]
+ ws.close
+ end
+ end
+
+ end
+
+ assert_equal 17, state
+
+ end
+
+ test "connect, subscribe, lots of events" do
+ state = 1
+ event_count = 0
+ log_start = Log.order(:id).last.id
+
+ authorize_with :admin
+
+ ws_helper :admin, false do |ws|
+ EM::Timer.new 45 do
+ # Needs a longer timeout than the default
+ ws.close
+ end
+
+ ws.on :open do |event|
+ ws.send ({method: 'subscribe'}.to_json)
+ end
+
+ ws.on :message do |event|
+ d = Oj.load event.data
+ case state
+ when 1
+ assert_equal 200, d["status"]
+ ActiveRecord::Base.transaction do
+ (1..202).each do
+ spec = Specimen.create
+ end
+ end
+ state = 2
+ when 2
+ event_count += 1
+ assert_equal d['id'], event_count+log_start
+ if event_count == 202
+ ws.close
+ end
+ end
+ end
+
+ end
+
+ assert_equal 202, event_count
+ end
+
+
+end
--- /dev/null
+2014-11-07_23:33:51 qr1hi-8i9sb-nf3qk0xzwwz3lre 31708 1 stderr crunchstat: cpu 1970.8200 user 60.2700 sys 8 cpus -- interval 10.0002 seconds 35.3900 user 0.8600 sys
--- /dev/null
+require 'test_helper'
+require 'rails/performance_test_help'
+
+class BrowsingTest < ActionDispatch::PerformanceTest
+ # Refer to the documentation for all available options
+ # self.profile_options = { :runs => 5, :metrics => [:wall_time, :memory]
+ # :output => 'tmp/performance', :formats => [:flat] }
+
+ def test_homepage
+ get '/'
+ end
+end
--- /dev/null
+ENV["RAILS_ENV"] = "test"
+unless ENV["NO_COVERAGE_TEST"]
+ begin
+ require 'simplecov'
+ require 'simplecov-rcov'
+ class SimpleCov::Formatter::MergedFormatter
+ def format(result)
+ SimpleCov::Formatter::HTMLFormatter.new.format(result)
+ SimpleCov::Formatter::RcovFormatter.new.format(result)
+ end
+ end
+ SimpleCov.formatter = SimpleCov::Formatter::MergedFormatter
+ SimpleCov.start do
+ add_filter '/test/'
+ add_filter 'initializers/secret_token'
+ add_filter 'initializers/omniauth'
+ end
+ rescue Exception => e
+ $stderr.puts "SimpleCov unavailable (#{e}). Proceeding without."
+ end
+end
+
+require File.expand_path('../../config/environment', __FILE__)
+require 'rails/test_help'
+
+module ArvadosTestSupport
+ def json_response
+ ActiveSupport::JSON.decode @response.body
+ end
+
+ def api_token(api_client_auth_name)
+ api_client_authorizations(api_client_auth_name).api_token
+ end
+
+ def auth(api_client_auth_name)
+ {'HTTP_AUTHORIZATION' => "OAuth2 #{api_token(api_client_auth_name)}"}
+ end
+end
+
+class ActiveSupport::TestCase
+ include FactoryGirl::Syntax::Methods
+ fixtures :all
+
+ include ArvadosTestSupport
+
+ teardown do
+ Thread.current[:api_client_ip_address] = nil
+ Thread.current[:api_client_authorization] = nil
+ Thread.current[:api_client_uuid] = nil
+ Thread.current[:api_client] = nil
+ Thread.current[:user] = nil
+ restore_configuration
+ end
+
+ def restore_configuration
+ # Restore configuration settings changed during tests
+ $application_config.each do |k,v|
+ if k.match /^[^.]*$/
+ Rails.configuration.send (k + '='), v
+ end
+ end
+ end
+
+ def set_user_from_auth(auth_name)
+ client_auth = api_client_authorizations(auth_name)
+ Thread.current[:api_client_authorization] = client_auth
+ Thread.current[:api_client] = client_auth.api_client
+ Thread.current[:user] = client_auth.user
+ end
+
+ def expect_json
+ self.request.headers["Accept"] = "text/json"
+ end
+
+ def authorize_with api_client_auth_name
+ authorize_with_token api_client_authorizations(api_client_auth_name).api_token
+ end
+
+ def authorize_with_token token
+ t = token
+ t = t.api_token if t.respond_to? :api_token
+ ArvadosApiToken.new.call("rack.input" => "",
+ "HTTP_AUTHORIZATION" => "OAuth2 #{t}")
+ end
+end
+
+class ActionController::TestCase
+ setup do
+ @counter = 0
+ end
+
+ def check_counter action
+ @counter += 1
+ if @counter == 2
+ assert_equal 1, 2, "Multiple actions in functional test"
+ end
+ end
+
+ [:get, :post, :put, :patch, :delete].each do |method|
+ define_method method do |action, *args|
+ check_counter action
+ super action, *args
+ end
+ end
+end
+
+class ActionDispatch::IntegrationTest
+ teardown do
+ Thread.current[:api_client_ip_address] = nil
+ Thread.current[:api_client_authorization] = nil
+ Thread.current[:api_client_uuid] = nil
+ Thread.current[:api_client] = nil
+ Thread.current[:user] = nil
+ end
+end
+
+# Ensure permissions are computed from the test fixtures.
+User.invalidate_permissions_cache
--- /dev/null
+require 'test_helper'
+
+class ApiClientAuthorizationTest < ActiveSupport::TestCase
+ include CurrentApiClient
+
+ [:admin_trustedclient, :active_trustedclient].each do |token|
+ test "ApiClientAuthorization can be created then deleted by #{token}" do
+ set_user_from_auth token
+ x = ApiClientAuthorization.create!(user_id: current_user.id,
+ api_client_id: 0,
+ scopes: [])
+ newtoken = x.api_token
+ assert x.destroy, "Failed to destroy new ApiClientAuth"
+ assert_empty ApiClientAuthorization.where(api_token: newtoken), "Destroyed ApiClientAuth is still in database"
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class ApiClientTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class ApplicationTest < ActiveSupport::TestCase
+ include CurrentApiClient
+
+ test "test act_as_system_user" do
+ Thread.current[:user] = users(:active)
+ assert_equal users(:active), Thread.current[:user]
+ act_as_system_user do
+ assert_not_equal users(:active), Thread.current[:user]
+ assert_equal system_user, Thread.current[:user]
+ end
+ assert_equal users(:active), Thread.current[:user]
+ end
+
+ test "test act_as_system_user is exception safe" do
+ Thread.current[:user] = users(:active)
+ assert_equal users(:active), Thread.current[:user]
+ caught = false
+ begin
+ act_as_system_user do
+ assert_not_equal users(:active), Thread.current[:user]
+ assert_equal system_user, Thread.current[:user]
+ raise "Fail"
+ end
+ rescue
+ caught = true
+ end
+ assert caught
+ assert_equal users(:active), Thread.current[:user]
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class ArvadosModelTest < ActiveSupport::TestCase
+ fixtures :all
+
+ def create_with_attrs attrs
+ a = Specimen.create({material: 'caloric'}.merge(attrs))
+ a if a.valid?
+ end
+
+ test 'non-admin cannot assign uuid' do
+ set_user_from_auth :active_trustedclient
+ want_uuid = Specimen.generate_uuid
+ a = create_with_attrs(uuid: want_uuid)
+ assert_nil a, "Non-admin should not assign uuid."
+ end
+
+ test 'admin can assign valid uuid' do
+ set_user_from_auth :admin_trustedclient
+ want_uuid = Specimen.generate_uuid
+ a = create_with_attrs(uuid: want_uuid)
+ assert_equal want_uuid, a.uuid, "Admin should assign valid uuid."
+ assert a.uuid.length==27, "Auto assigned uuid length is wrong."
+ end
+
+ test 'admin cannot assign uuid with wrong object type' do
+ set_user_from_auth :admin_trustedclient
+ want_uuid = Human.generate_uuid
+ a = create_with_attrs(uuid: want_uuid)
+ assert_nil a, "Admin should not be able to assign invalid uuid."
+ end
+
+ test 'admin cannot assign badly formed uuid' do
+ set_user_from_auth :admin_trustedclient
+ a = create_with_attrs(uuid: "ntoheunthaoesunhasoeuhtnsaoeunhtsth")
+ assert_nil a, "Admin should not be able to assign invalid uuid."
+ end
+
+ test 'admin cannot assign empty uuid' do
+ set_user_from_auth :admin_trustedclient
+ a = create_with_attrs(uuid: "")
+ assert_nil a, "Admin cannot assign empty uuid."
+ end
+
+ [ {:a => 'foo'},
+ {'a' => :foo},
+ {:a => ['foo', 'bar']},
+ {'a' => [:foo, 'bar']},
+ {'a' => ['foo', :bar]},
+ {:a => [:foo, :bar]},
+ {:a => {'foo' => {'bar' => 'baz'}}},
+ {'a' => {:foo => {'bar' => 'baz'}}},
+ {'a' => {'foo' => {:bar => 'baz'}}},
+ {'a' => {'foo' => {'bar' => :baz}}},
+ {'a' => {'foo' => ['bar', :baz]}},
+ {'a' => {['foo', :foo] => ['bar', 'baz']}},
+ ].each do |x|
+ test "refuse symbol keys in serialized attribute: #{x.inspect}" do
+ set_user_from_auth :admin_trustedclient
+ assert_nothing_raised do
+ Link.create!(link_class: 'test',
+ properties: {})
+ end
+ assert_raises ActiveRecord::RecordInvalid do
+ Link.create!(link_class: 'test',
+ properties: x)
+ end
+ end
+ end
+
+ test "Stringify symbols coming from serialized attribute in database" do
+ set_user_from_auth :admin_trustedclient
+ fixed = Link.find_by_uuid(links(:has_symbol_keys_in_database_somehow).uuid)
+ assert_equal(["baz", "foo"], fixed.properties.keys.sort,
+ "Hash symbol keys from DB did not get stringified.")
+ assert_equal(['waz', 'waz', 'waz', 1, nil, false, true],
+ fixed.properties['baz'],
+ "Array symbol values from DB did not get stringified.")
+ assert_equal true, fixed.save, "Failed to save fixed model back to db."
+ end
+
+ test "No HashWithIndifferentAccess in database" do
+ set_user_from_auth :admin_trustedclient
+ assert_raises ActiveRecord::RecordInvalid do
+ Link.create!(link_class: 'test',
+ properties: {'foo' => 'bar'}.with_indifferent_access)
+ end
+ end
+
+ [['uuid', {unique: true}],
+ ['owner_uuid', {}]].each do |the_column, requires|
+ test "unique index on all models with #{the_column}" do
+ checked = 0
+ ActiveRecord::Base.connection.tables.each do |table|
+ columns = ActiveRecord::Base.connection.columns(table)
+
+ next unless columns.collect(&:name).include? the_column
+
+ indexes = ActiveRecord::Base.connection.indexes(table).reject do |index|
+ requires.map do |key, val|
+ index.send(key) == val
+ end.include? false
+ end
+ assert_includes indexes.collect(&:columns), [the_column], 'no index'
+ checked += 1
+ end
+ # Sanity check: make sure we didn't just systematically miss everything.
+ assert_operator(10, :<, checked,
+ "Only #{checked} tables have a #{the_column}?!")
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class AuthorizedKeyTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class BlobTest < ActiveSupport::TestCase
+ @@api_token = rand(2**512).to_s(36)[0..49]
+ @@key = rand(2**2048).to_s(36)
+ @@blob_data = 'foo'
+ @@blob_locator = Digest::MD5.hexdigest(@@blob_data) +
+ '+' + @@blob_data.size.to_s
+
+ @@known_locator = 'acbd18db4cc2f85cedef654fccc4a4d8+3'
+ @@known_token = 'hocfupkn2pjhrpgp2vxv8rsku7tvtx49arbc9s4bvu7p7wxqvk'
+ @@known_key = '13u9fkuccnboeewr0ne3mvapk28epf68a3bhj9q8sb4l6e4e5mkk' +
+ 'p6nhj2mmpscgu1zze5h5enydxfe3j215024u16ij4hjaiqs5u4pzsl3nczmaoxnc' +
+ 'ljkm4875xqn4xv058koz3vkptmzhyheiy6wzevzjmdvxhvcqsvr5abhl15c2d4o4' +
+ 'jhl0s91lojy1mtrzqqvprqcverls0xvy9vai9t1l1lvvazpuadafm71jl4mrwq2y' +
+ 'gokee3eamvjy8qq1fvy238838enjmy5wzy2md7yvsitp5vztft6j4q866efym7e6' +
+ 'vu5wm9fpnwjyxfldw3vbo01mgjs75rgo7qioh8z8ij7jpyp8508okhgbbex3ceei' +
+ '786u5rw2a9gx743dj3fgq2irk'
+ @@known_signed_locator = 'acbd18db4cc2f85cedef654fccc4a4d8+3' +
+ '+A257f3f5f5f0a4e4626a18fc74bd42ec34dcb228a@7fffffff'
+
+ test 'generate predictable invincible signature' do
+ signed = Blob.sign_locator @@known_locator, {
+ api_token: @@known_token,
+ key: @@known_key,
+ expire: 0x7fffffff,
+ }
+ assert_equal @@known_signed_locator, signed
+ end
+
+ test 'verify predictable invincible signature' do
+ assert_equal true, Blob.verify_signature!(@@known_signed_locator,
+ api_token: @@known_token,
+ key: @@known_key)
+ end
+
+ test 'correct' do
+ signed = Blob.sign_locator @@blob_locator, api_token: @@api_token, key: @@key
+ assert_equal true, Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+
+ test 'expired' do
+ signed = Blob.sign_locator @@blob_locator, api_token: @@api_token, key: @@key, ttl: -1
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'expired, but no raise' do
+ signed = Blob.sign_locator @@blob_locator, api_token: @@api_token, key: @@key, ttl: -1
+ assert_equal false, Blob.verify_signature(signed,
+ api_token: @@api_token,
+ key: @@key)
+ end
+
+ test 'bogus, wrong block hash' do
+ signed = Blob.sign_locator @@blob_locator, api_token: @@api_token, key: @@key
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed.sub('acbd','abcd'), api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, expired' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+Aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa@531641bf'
+ assert_raises Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, wrong key' do
+ signed = Blob.sign_locator(@@blob_locator,
+ api_token: @@api_token,
+ key: (@@key+'x'))
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, wrong api token' do
+ signed = Blob.sign_locator(@@blob_locator,
+ api_token: @@api_token.reverse,
+ key: @@key)
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, signature format 1' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+Aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa@'
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, signature format 2' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+A@531641bf'
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, signature format 3' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+Axyzzy@531641bf'
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, timestamp format' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+Aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa@xyzzy'
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'no signature at all' do
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(@@blob_locator, api_token: @@api_token, key: @@key)
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class CollectionTest < ActiveSupport::TestCase
+ def create_collection name, enc=nil
+ txt = ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:#{name}.txt\n"
+ txt.force_encoding(enc) if enc
+ return Collection.create(manifest_text: txt)
+ end
+
+ test 'accept ASCII manifest_text' do
+ act_as_system_user do
+ c = create_collection 'foo', Encoding::US_ASCII
+ assert c.valid?
+ end
+ end
+
+ test 'accept UTF-8 manifest_text' do
+ act_as_system_user do
+ c = create_collection "f\xc3\x98\xc3\x98", Encoding::UTF_8
+ assert c.valid?
+ end
+ end
+
+ test 'refuse manifest_text with invalid UTF-8 byte sequence' do
+ act_as_system_user do
+ c = create_collection "f\xc8o", Encoding::UTF_8
+ assert !c.valid?
+ assert_equal [:manifest_text], c.errors.messages.keys
+ assert_match /UTF-8/, c.errors.messages[:manifest_text].first
+ end
+ end
+
+ test 'refuse manifest_text with non-UTF-8 encoding' do
+ act_as_system_user do
+ c = create_collection "f\xc8o", Encoding::ASCII_8BIT
+ assert !c.valid?
+ assert_equal [:manifest_text], c.errors.messages.keys
+ assert_match /UTF-8/, c.errors.messages[:manifest_text].first
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class CommitAncestorTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class CommitTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class GroupTest < ActiveSupport::TestCase
+
+ test "cannot set owner_uuid to object with existing ownership cycle" do
+ set_user_from_auth :active_trustedclient
+
+ # First make sure we have lots of permission on the bad group by
+ # renaming it to "{current name} is mine all mine"
+ g = groups(:bad_group_has_ownership_cycle_b)
+ g.name += " is mine all mine"
+ assert g.save, "active user should be able to modify group #{g.uuid}"
+
+ # Use the group as the owner of a new object
+ s = Specimen.
+ create(owner_uuid: groups(:bad_group_has_ownership_cycle_b).uuid)
+ assert s.valid?, "ownership should pass validation #{s.errors.messages}"
+ assert_equal false, s.save, "should not save object with #{g.uuid} as owner"
+
+ # Use the group as the new owner of an existing object
+ s = specimens(:in_aproject)
+ s.owner_uuid = groups(:bad_group_has_ownership_cycle_b).uuid
+ assert s.valid?, "ownership should pass validation"
+ assert_equal false, s.save, "should not save object with #{g.uuid} as owner"
+ end
+
+ test "cannot create a new ownership cycle" do
+ set_user_from_auth :active_trustedclient
+
+ g_foo = Group.create!(name: "foo")
+ g_bar = Group.create!(name: "bar")
+
+ g_foo.owner_uuid = g_bar.uuid
+ assert g_foo.save, lambda { g_foo.errors.messages }
+ g_bar.owner_uuid = g_foo.uuid
+ assert g_bar.valid?, "ownership cycle should not prevent validation"
+ assert_equal false, g_bar.save, "should not create an ownership loop"
+ assert g_bar.errors.messages[:owner_uuid].join(" ").match(/ownership cycle/)
+ end
+
+ test "cannot create a single-object ownership cycle" do
+ set_user_from_auth :active_trustedclient
+
+ g_foo = Group.create!(name: "foo")
+ assert g_foo.save
+
+ # Ensure I have permission to manage this group even when its owner changes
+ perm_link = Link.create!(tail_uuid: users(:active).uuid,
+ head_uuid: g_foo.uuid,
+ link_class: 'permission',
+ name: 'can_manage')
+ assert perm_link.save
+
+ g_foo.owner_uuid = g_foo.uuid
+ assert_equal false, g_foo.save, "should not create an ownership loop"
+ assert g_foo.errors.messages[:owner_uuid].join(" ").match(/ownership cycle/)
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class ApiClientAuthorizationsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class ApiClientsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class AuthorizedKeysHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class CollectionsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class CommitAncestorsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class CommitsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class GroupsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class HumansHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class JobTasksHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class JobsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class KeepDisksHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class LinksHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class LogsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class NodesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineInstancesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class PipelinesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class RepositoriesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class SpecimensHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class TraitsHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class VirtualMachinesHelperTest < ActionView::TestCase
+end
--- /dev/null
+require 'test_helper'
+
+class HumanTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class JobTaskTest < ActiveSupport::TestCase
+ test "new tasks get an assigned qsequence" do
+ set_user_from_auth :active
+ task = JobTask.create
+ assert_not_nil task.qsequence
+ assert_operator(task.qsequence, :>=, 0)
+ end
+
+ test "assigned qsequence is not overwritten" do
+ set_user_from_auth :active
+ task = JobTask.create!(qsequence: 99)
+ assert_equal(99, task.qsequence)
+ end
+end
--- /dev/null
+require 'test_helper'
+require 'helpers/git_test_helper'
+
+class JobTest < ActiveSupport::TestCase
+ include GitTestHelper
+
+ BAD_COLLECTION = "#{'f' * 32}+0"
+
+ setup do
+ set_user_from_auth :active
+ end
+
+ def job_attrs merge_me={}
+ # Default (valid) set of attributes, with given overrides
+ {
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ }.merge(merge_me)
+ end
+
+ test "Job without Docker image doesn't get locator" do
+ job = Job.new job_attrs
+ assert job.valid?, job.errors.full_messages.to_s
+ assert_nil job.docker_image_locator
+ end
+
+ { 'name' => [:links, :docker_image_collection_tag, :name],
+ 'hash' => [:links, :docker_image_collection_hash, :name],
+ 'locator' => [:collections, :docker_image, :portable_data_hash],
+ }.each_pair do |spec_type, (fixture_type, fixture_name, fixture_attr)|
+ test "Job initialized with Docker image #{spec_type} gets locator" do
+ image_spec = send(fixture_type, fixture_name).send(fixture_attr)
+ job = Job.new job_attrs(runtime_constraints:
+ {'docker_image' => image_spec})
+ assert job.valid?, job.errors.full_messages.to_s
+ assert_equal(collections(:docker_image).portable_data_hash, job.docker_image_locator)
+ end
+
+ test "Job modified with Docker image #{spec_type} gets locator" do
+ job = Job.new job_attrs
+ assert job.valid?, job.errors.full_messages.to_s
+ assert_nil job.docker_image_locator
+ image_spec = send(fixture_type, fixture_name).send(fixture_attr)
+ job.runtime_constraints['docker_image'] = image_spec
+ assert job.valid?, job.errors.full_messages.to_s
+ assert_equal(collections(:docker_image).portable_data_hash, job.docker_image_locator)
+ end
+ end
+
+ test "removing a Docker runtime constraint removes the locator" do
+ image_locator = collections(:docker_image).portable_data_hash
+ job = Job.new job_attrs(runtime_constraints:
+ {'docker_image' => image_locator})
+ assert job.valid?, job.errors.full_messages.to_s
+ assert_equal(image_locator, job.docker_image_locator)
+ job.runtime_constraints = {}
+ assert job.valid?, job.errors.full_messages.to_s + "after clearing runtime constraints"
+ assert_nil job.docker_image_locator
+ end
+
+ test "locate a Docker image with a repository + tag" do
+ image_repo, image_tag =
+ links(:docker_image_collection_tag2).name.split(':', 2)
+ job = Job.new job_attrs(runtime_constraints:
+ {'docker_image' => image_repo,
+ 'docker_image_tag' => image_tag})
+ assert job.valid?, job.errors.full_messages.to_s
+ assert_equal(collections(:docker_image).portable_data_hash, job.docker_image_locator)
+ end
+
+ test "can't locate a Docker image with a nonexistent tag" do
+ image_repo = links(:docker_image_collection_tag).name
+ image_tag = '__nonexistent tag__'
+ job = Job.new job_attrs(runtime_constraints:
+ {'docker_image' => image_repo,
+ 'docker_image_tag' => image_tag})
+ assert(job.invalid?, "Job with bad Docker tag valid")
+ end
+
+ test "locate a Docker image with a partial hash" do
+ image_hash = links(:docker_image_collection_hash).name[0..24]
+ job = Job.new job_attrs(runtime_constraints:
+ {'docker_image' => image_hash})
+ assert job.valid?, job.errors.full_messages.to_s + " with partial hash #{image_hash}"
+ assert_equal(collections(:docker_image).portable_data_hash, job.docker_image_locator)
+ end
+
+ { 'name' => 'arvados_test_nonexistent',
+ 'hash' => 'f' * 64,
+ 'locator' => BAD_COLLECTION,
+ }.each_pair do |spec_type, image_spec|
+ test "Job validation fails with nonexistent Docker image #{spec_type}" do
+ job = Job.new job_attrs(runtime_constraints:
+ {'docker_image' => image_spec})
+ assert(job.invalid?, "nonexistent Docker image #{spec_type} was valid")
+ end
+ end
+
+ test "Job validation fails with non-Docker Collection constraint" do
+ job = Job.new job_attrs(runtime_constraints:
+ {'docker_image' => collections(:foo_file).uuid})
+ assert(job.invalid?, "non-Docker Collection constraint was valid")
+ end
+
+ test "can create Job with Docker image Collection without Docker links" do
+ image_uuid = collections(:unlinked_docker_image).portable_data_hash
+ job = Job.new job_attrs(runtime_constraints: {"docker_image" => image_uuid})
+ assert(job.valid?, "Job created with unlinked Docker image was invalid")
+ assert_equal(image_uuid, job.docker_image_locator)
+ end
+
+ def check_attrs_unset(job, attrs)
+ assert_empty(attrs.each_key.map { |key| job.send(key) }.compact,
+ "job has values for #{attrs.keys}")
+ end
+
+ def check_creation_prohibited(attrs)
+ begin
+ job = Job.new(job_attrs(attrs))
+ rescue ActiveModel::MassAssignmentSecurity::Error
+ # Test passes - expected attribute protection
+ else
+ check_attrs_unset(job, attrs)
+ end
+ end
+
+ def check_modification_prohibited(attrs)
+ job = Job.new(job_attrs)
+ attrs.each_pair do |key, value|
+ assert_raises(NoMethodError) { job.send("{key}=".to_sym, value) }
+ end
+ check_attrs_unset(job, attrs)
+ end
+
+ test "can't create Job with Docker image locator" do
+ check_creation_prohibited(docker_image_locator: BAD_COLLECTION)
+ end
+
+ test "can't assign Docker image locator to Job" do
+ check_modification_prohibited(docker_image_locator: BAD_COLLECTION)
+ end
+
+ [
+ {script_parameters: ""},
+ {script_parameters: []},
+ {script_parameters: {symbols: :are_not_allowed_here}},
+ {runtime_constraints: ""},
+ {runtime_constraints: []},
+ {tasks_summary: ""},
+ {tasks_summary: []},
+ {script_version: "no/branch/could/ever/possibly/have/this/name"},
+ ].each do |invalid_attrs|
+ test "validation failures set error messages: #{invalid_attrs.to_json}" do
+ # Ensure valid_attrs doesn't produce errors -- otherwise we will
+ # not know whether errors reported below are actually caused by
+ # invalid_attrs.
+ dummy = Job.create! job_attrs
+
+ job = Job.create job_attrs(invalid_attrs)
+ assert_raises(ActiveRecord::RecordInvalid, ArgumentError,
+ "save! did not raise the expected exception") do
+ job.save!
+ end
+ assert_not_empty job.errors, "validation failure did not provide errors"
+ end
+ end
+
+ [
+ # Each test case is of the following format
+ # Array of parameters where each parameter is of the format:
+ # attr name to be changed, attr value, and array of expectations (where each expectation is an array)
+ [['running', false, [['state', 'Queued']]]],
+ [['state', 'Running', [['started_at', 'not_nil']]]],
+ [['is_locked_by_uuid', 'use_current_user_uuid', [['state', 'Queued']]], ['state', 'Running', [['running', true], ['started_at', 'not_nil'], ['success', 'nil']]]],
+ [['running', false, [['state', 'Queued']]], ['state', 'Complete', [['success', true]]]],
+ [['running', true, [['state', 'Running']]], ['cancelled_at', Time.now, [['state', 'Cancelled']]]],
+ [['running', true, [['state', 'Running']]], ['state', 'Cancelled', [['cancelled_at', 'not_nil']]]],
+ [['running', true, [['state', 'Running']]], ['success', true, [['state', 'Complete']]]],
+ [['running', true, [['state', 'Running']]], ['success', false, [['state', 'Failed']]]],
+ [['running', true, [['state', 'Running']]], ['state', 'Complete', [['success', true],['finished_at', 'not_nil']]]],
+ [['running', true, [['state', 'Running']]], ['state', 'Failed', [['success', false],['finished_at', 'not_nil']]]],
+ [['cancelled_at', Time.now, [['state', 'Cancelled']]], ['success', false, [['state', 'Cancelled'],['finished_at', 'nil'], ['cancelled_at', 'not_nil']]]],
+ [['cancelled_at', Time.now, [['state', 'Cancelled'],['running', false]]], ['success', true, [['state', 'Cancelled'],['running', false],['finished_at', 'nil'],['cancelled_at', 'not_nil']]]],
+ # potential migration cases
+ [['state', nil, [['state', 'Queued']]]],
+ [['state', nil, [['state', 'Queued']]], ['cancelled_at', Time.now, [['state', 'Cancelled']]]],
+ [['running', true, [['state', 'Running']]], ['state', nil, [['state', 'Running']]]],
+ ].each do |parameters|
+ test "verify job status #{parameters}" do
+ job = Job.create! job_attrs
+ assert_equal 'Queued', job.state, "job.state"
+
+ parameters.each do |parameter|
+ expectations = parameter[2]
+ if parameter[1] == 'use_current_user_uuid'
+ parameter[1] = Thread.current[:user].uuid
+ end
+
+ if expectations.instance_of? Array
+ job[parameter[0]] = parameter[1]
+ assert_equal true, job.save, job.errors.full_messages.to_s
+ expectations.each do |expectation|
+ if expectation[1] == 'not_nil'
+ assert_not_nil job[expectation[0]], expectation[0]
+ elsif expectation[1] == 'nil'
+ assert_nil job[expectation[0]], expectation[0]
+ else
+ assert_equal expectation[1], job[expectation[0]], expectation[0]
+ end
+ end
+ else
+ raise 'I do not know how to handle this expectation'
+ end
+ end
+ end
+ end
+
+ test "Test job state changes" do
+ all = ["Queued", "Running", "Complete", "Failed", "Cancelled"]
+ valid = {"Queued" => all, "Running" => ["Complete", "Failed", "Cancelled"]}
+ all.each do |start|
+ all.each do |finish|
+ if start != finish
+ job = Job.create! job_attrs(state: start)
+ assert_equal start, job.state
+ job.state = finish
+ job.save
+ job.reload
+ if valid[start] and valid[start].include? finish
+ assert_equal finish, job.state
+ else
+ assert_equal start, job.state
+ end
+ end
+ end
+ end
+ end
+
+ test "Test job locking" do
+ set_user_from_auth :active_trustedclient
+ job = Job.create! job_attrs
+
+ assert_equal "Queued", job.state
+
+ # Should be able to lock successfully
+ job.lock current_user.uuid
+ assert_equal "Running", job.state
+
+ assert_raises ArvadosModel::AlreadyLockedError do
+ # Can't lock it again
+ job.lock current_user.uuid
+ end
+ job.reload
+ assert_equal "Running", job.state
+
+ set_user_from_auth :project_viewer
+ assert_raises ArvadosModel::AlreadyLockedError do
+ # Can't lock it as a different user either
+ job.lock current_user.uuid
+ end
+ job.reload
+ assert_equal "Running", job.state
+
+ assert_raises ArvadosModel::PermissionDeniedError do
+ # Can't update fields as a different user
+ job.update_attributes(state: "Failed")
+ end
+ job.reload
+ assert_equal "Running", job.state
+
+
+ set_user_from_auth :active_trustedclient
+
+ # Can update fields as the locked_by user
+ job.update_attributes(state: "Failed")
+ assert_equal "Failed", job.state
+ end
+
+ test "verify job queue position" do
+ job1 = Job.create! job_attrs
+ assert_equal 'Queued', job1.state, "Incorrect job state for newly created job1"
+
+ job2 = Job.create! job_attrs
+ assert_equal 'Queued', job2.state, "Incorrect job state for newly created job2"
+
+ assert_not_nil job1.queue_position, "Expected non-nil queue position for job1"
+ assert_not_nil job2.queue_position, "Expected non-nil queue position for job2"
+ assert_not_equal job1.queue_position, job2.queue_position
+ end
+
+ SDK_MASTER = "ca68b24e51992e790f29df5cc4bc54ce1da4a1c2"
+ SDK_TAGGED = "00634b2b8a492d6f121e3cf1d6587b821136a9a7"
+
+ def sdk_constraint(version)
+ {runtime_constraints: {
+ "arvados_sdk_version" => version,
+ "docker_image" => links(:docker_image_collection_tag).name,
+ }}
+ end
+
+ def check_job_sdk_version(expected)
+ job = yield
+ if expected.nil?
+ refute(job.valid?, "job valid with bad Arvados SDK version")
+ else
+ assert(job.valid?, "job not valid with good Arvados SDK version")
+ assert_equal(expected, job.arvados_sdk_version)
+ end
+ end
+
+ { "master" => SDK_MASTER,
+ "commit2" => SDK_TAGGED,
+ SDK_TAGGED[0, 8] => SDK_TAGGED,
+ "__nonexistent__" => nil,
+ }.each_pair do |search, commit_hash|
+ test "creating job with SDK version '#{search}'" do
+ check_job_sdk_version(commit_hash) do
+ Job.new(job_attrs(sdk_constraint(search)))
+ end
+ end
+
+ test "updating job from no SDK to version '#{search}'" do
+ job = Job.create!(job_attrs)
+ assert_nil job.arvados_sdk_version
+ check_job_sdk_version(commit_hash) do
+ job.runtime_constraints = sdk_constraint(search)[:runtime_constraints]
+ job
+ end
+ end
+
+ test "updating job from SDK version 'master' to '#{search}'" do
+ job = Job.create!(job_attrs(sdk_constraint("master")))
+ assert_equal(SDK_MASTER, job.arvados_sdk_version)
+ check_job_sdk_version(commit_hash) do
+ job.runtime_constraints = sdk_constraint(search)[:runtime_constraints]
+ job
+ end
+ end
+ end
+
+ test "clear the SDK version" do
+ job = Job.create!(job_attrs(sdk_constraint("master")))
+ assert_equal(SDK_MASTER, job.arvados_sdk_version)
+ job.runtime_constraints = {}
+ assert(job.valid?, "job invalid after clearing SDK version")
+ assert_nil(job.arvados_sdk_version)
+ end
+
+ test "job with SDK constraint, without Docker image is invalid" do
+ sdk_attrs = sdk_constraint("master")
+ sdk_attrs[:runtime_constraints].delete("docker_image")
+ job = Job.create(job_attrs(sdk_attrs))
+ refute(job.valid?, "Job valid with SDK version, without Docker image")
+ sdk_errors = job.errors.messages[:arvados_sdk_version] || []
+ refute_empty(sdk_errors.grep(/\bDocker\b/),
+ "no Job SDK errors mention that Docker is required")
+ end
+
+ test "invalid to clear Docker image constraint when SDK constraint exists" do
+ job = Job.create!(job_attrs(sdk_constraint("master")))
+ job.runtime_constraints.delete("docker_image")
+ refute(job.valid?,
+ "Job with SDK constraint valid after clearing Docker image")
+ end
+
+ test "can't create job with SDK version assigned directly" do
+ check_creation_prohibited(arvados_sdk_version: SDK_MASTER)
+ end
+
+ test "can't modify job to assign SDK version directly" do
+ check_modification_prohibited(arvados_sdk_version: SDK_MASTER)
+ end
+
+ test "job validation fails when collection uuid found in script_parameters" do
+ bad_params = {
+ script_parameters: {
+ 'input' => {
+ 'param1' => 'the collection uuid zzzzz-4zz18-012345678901234'
+ }
+ }
+ }
+ assert_raises(ActiveRecord::RecordInvalid,
+ "created job with a collection uuid in script_parameters") do
+ job = Job.create!(job_attrs(bad_params))
+ end
+ end
+
+ test "job validation succeeds when no collection uuid in script_parameters" do
+ good_params = {
+ script_parameters: {
+ 'arg1' => 'foo',
+ 'arg2' => [ 'bar', 'baz' ],
+ 'arg3' => {
+ 'a' => 1,
+ 'b' => [2, 3, 4],
+ }
+ }
+ }
+ job = Job.create!(job_attrs(good_params))
+ assert job.valid?
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class KeepDiskTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class KeepServiceTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class LinkTest < ActiveSupport::TestCase
+ fixtures :all
+
+ setup do
+ set_user_from_auth :admin_trustedclient
+ end
+
+ test "cannot delete an object referenced by links" do
+ ob = Specimen.create
+ link = Link.create(tail_uuid: users(:active).uuid,
+ head_uuid: ob.uuid,
+ link_class: 'test',
+ name: 'test')
+ assert_equal users(:admin).uuid, link.owner_uuid
+ assert_raises(ActiveRecord::DeleteRestrictionError,
+ "should not delete #{ob.uuid} with link #{link.uuid}") do
+ ob.destroy
+ end
+ end
+
+ def new_active_link_valid?(link_attrs)
+ set_user_from_auth :active
+ begin
+ Link.
+ create({link_class: "permission",
+ name: "can_read",
+ head_uuid: groups(:aproject).uuid,
+ }.merge(link_attrs)).
+ valid?
+ rescue ArvadosModel::PermissionDeniedError
+ false
+ end
+ end
+
+ test "link granting permission to nonexistent user is invalid" do
+ refute new_active_link_valid?(tail_uuid:
+ users(:active).uuid.sub(/-\w+$/, "-#{'z' * 15}"))
+ end
+
+ test "link granting non-project permission to unreadable user is invalid" do
+ refute new_active_link_valid?(tail_uuid: users(:admin).uuid,
+ head_uuid: collections(:bar_file).uuid)
+ end
+
+ test "user can't add a Collection to a Project without permission" do
+ refute new_active_link_valid?(link_class: "name",
+ name: "Permission denied test name",
+ tail_uuid: collections(:bar_file).uuid)
+ end
+
+ test "user can't add a User to a Project" do
+ # Users *can* give other users permissions to projects.
+ # This test helps ensure that that exception is specific to permissions.
+ refute new_active_link_valid?(link_class: "name",
+ name: "Permission denied test name",
+ tail_uuid: users(:admin).uuid)
+ end
+
+ test "link granting project permissions to unreadable user is invalid" do
+ refute new_active_link_valid?(tail_uuid: users(:admin).uuid)
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class LogTest < ActiveSupport::TestCase
+ include CurrentApiClient
+
+ EVENT_TEST_METHODS = {
+ :create => [:created_at, :assert_nil, :assert_not_nil],
+ :update => [:modified_at, :assert_not_nil, :assert_not_nil],
+ :destroy => [nil, :assert_not_nil, :assert_nil],
+ }
+
+ def setup
+ @start_time = Time.now
+ @log_count = 1
+ end
+
+ def assert_properties(test_method, event, props, *keys)
+ verb = (test_method == :assert_nil) ? 'have nil' : 'define'
+ keys.each do |prop_name|
+ assert_includes(props, prop_name, "log properties missing #{prop_name}")
+ self.send(test_method, props[prop_name],
+ "#{event.to_s} log should #{verb} #{prop_name}")
+ end
+ end
+
+ def get_logs_about(thing)
+ Log.where(object_uuid: thing.uuid).order("created_at ASC").all
+ end
+
+ def assert_logged(thing, event_type)
+ logs = get_logs_about(thing)
+ assert_equal(@log_count, logs.size, "log count mismatch")
+ @log_count += 1
+ log = logs.last
+ props = log.properties
+ assert_equal(current_user.andand.uuid, log.owner_uuid,
+ "log is not owned by current user")
+ assert_equal(current_user.andand.uuid, log.modified_by_user_uuid,
+ "log is not 'modified by' current user")
+ assert_equal(current_api_client.andand.uuid, log.modified_by_client_uuid,
+ "log is not 'modified by' current client")
+ assert_equal(thing.uuid, log.object_uuid, "log UUID mismatch")
+ assert_equal(event_type.to_s, log.event_type, "log event type mismatch")
+ time_method, old_props_test, new_props_test = EVENT_TEST_METHODS[event_type]
+ if time_method.nil? or (timestamp = thing.send(time_method)).nil?
+ assert(log.event_at >= @start_time, "log timestamp too old")
+ else
+ assert_in_delta(timestamp, log.event_at, 1, "log timestamp mismatch")
+ end
+ assert_properties(old_props_test, event_type, props,
+ 'old_etag', 'old_attributes')
+ assert_properties(new_props_test, event_type, props,
+ 'new_etag', 'new_attributes')
+ yield props if block_given?
+ end
+
+ def assert_auth_logged_with_clean_properties(auth, event_type)
+ assert_logged(auth, event_type) do |props|
+ ['old_attributes', 'new_attributes'].map { |k| props[k] }.compact
+ .each do |attributes|
+ refute_includes(attributes, 'api_token',
+ "auth log properties include sensitive API token")
+ end
+ yield props if block_given?
+ end
+ end
+
+ test "creating a user makes a log" do
+ set_user_from_auth :admin_trustedclient
+ u = User.new(first_name: "Log", last_name: "Test")
+ u.save!
+ assert_logged(u, :create) do |props|
+ assert_equal(u.etag, props['new_etag'], "new user etag mismatch")
+ assert_equal(u.first_name, props['new_attributes']['first_name'],
+ "new user first name mismatch")
+ assert_equal(u.last_name, props['new_attributes']['last_name'],
+ "new user first name mismatch")
+ end
+ end
+
+ test "updating a virtual machine makes a log" do
+ set_user_from_auth :admin_trustedclient
+ vm = virtual_machines(:testvm)
+ orig_etag = vm.etag
+ vm.hostname = 'testvm.testshell'
+ vm.save!
+ assert_logged(vm, :update) do |props|
+ assert_equal(orig_etag, props['old_etag'], "updated VM old etag mismatch")
+ assert_equal(vm.etag, props['new_etag'], "updated VM new etag mismatch")
+ assert_equal('testvm.shell', props['old_attributes']['hostname'],
+ "updated VM old name mismatch")
+ assert_equal('testvm.testshell', props['new_attributes']['hostname'],
+ "updated VM new name mismatch")
+ end
+ end
+
+ test "destroying an authorization makes a log" do
+ set_user_from_auth :admin_trustedclient
+ auth = api_client_authorizations(:spectator)
+ orig_etag = auth.etag
+ orig_attrs = auth.attributes
+ orig_attrs.delete 'api_token'
+ auth.destroy
+ assert_logged(auth, :destroy) do |props|
+ assert_equal(orig_etag, props['old_etag'], "destroyed auth etag mismatch")
+ assert_equal(orig_attrs, props['old_attributes'],
+ "destroyed auth attributes mismatch")
+ end
+ end
+
+ test "saving an unchanged client still makes a log" do
+ set_user_from_auth :admin_trustedclient
+ client = api_clients(:untrusted)
+ client.is_trusted = client.is_trusted
+ client.save!
+ assert_logged(client, :update) do |props|
+ ['old', 'new'].each do |age|
+ assert_equal(client.etag, props["#{age}_etag"],
+ "unchanged client #{age} etag mismatch")
+ assert_equal(client.attributes, props["#{age}_attributes"],
+ "unchanged client #{age} attributes mismatch")
+ end
+ end
+ end
+
+ test "updating a group twice makes two logs" do
+ set_user_from_auth :admin_trustedclient
+ group = groups(:empty_lonely_group)
+ name1 = group.name
+ name2 = "#{name1} under test"
+ group.name = name2
+ group.save!
+ assert_logged(group, :update) do |props|
+ assert_equal(name1, props['old_attributes']['name'],
+ "group start name mismatch")
+ assert_equal(name2, props['new_attributes']['name'],
+ "group updated name mismatch")
+ end
+ group.name = name1
+ group.save!
+ assert_logged(group, :update) do |props|
+ assert_equal(name2, props['old_attributes']['name'],
+ "group pre-revert name mismatch")
+ assert_equal(name1, props['new_attributes']['name'],
+ "group final name mismatch")
+ end
+ end
+
+ test "making a log doesn't get logged" do
+ set_user_from_auth :active_trustedclient
+ log = Log.new
+ log.save!
+ assert_equal(0, get_logs_about(log).size, "made a Log about a Log")
+ end
+
+ test "non-admins can't modify or delete logs" do
+ set_user_from_auth :active_trustedclient
+ log = Log.new(summary: "immutable log test")
+ assert_nothing_raised { log.save! }
+ log.summary = "log mutation test should fail"
+ assert_raise(ArvadosModel::PermissionDeniedError) { log.save! }
+ assert_raise(ArvadosModel::PermissionDeniedError) { log.destroy }
+ end
+
+ test "admins can modify and delete logs" do
+ set_user_from_auth :admin_trustedclient
+ log = Log.new(summary: "admin log mutation test")
+ assert_nothing_raised { log.save! }
+ log.summary = "admin mutated log test"
+ assert_nothing_raised { log.save! }
+ assert_nothing_raised { log.destroy }
+ end
+
+ test "failure saving log causes failure saving object" do
+ Log.class_eval do
+ alias_method :_orig_validations, :perform_validations
+ def perform_validations(options)
+ false
+ end
+ end
+ begin
+ set_user_from_auth :active_trustedclient
+ user = users(:active)
+ user.first_name = 'Test'
+ assert_raise(ActiveRecord::RecordInvalid) { user.save! }
+ ensure
+ Log.class_eval do
+ alias_method :perform_validations, :_orig_validations
+ end
+ end
+ end
+
+ test "don't log changes only to ApiClientAuthorization.last_used_*" do
+ set_user_from_auth :admin_trustedclient
+ auth = api_client_authorizations(:spectator)
+ start_log_count = get_logs_about(auth).size
+ auth.last_used_at = Time.now
+ auth.last_used_by_ip_address = '::1'
+ auth.save!
+ assert_equal(start_log_count, get_logs_about(auth).size,
+ "log count changed after 'using' ApiClientAuthorization")
+ auth.created_by_ip_address = '::1'
+ auth.save!
+ assert_logged(auth, :update)
+ end
+
+ test "token isn't included in ApiClientAuthorization logs" do
+ set_user_from_auth :admin_trustedclient
+ auth = ApiClientAuthorization.new
+ auth.user = users(:spectator)
+ auth.api_client = api_clients(:untrusted)
+ auth.save!
+ assert_auth_logged_with_clean_properties(auth, :create)
+ auth.expires_at = Time.now
+ auth.save!
+ assert_auth_logged_with_clean_properties(auth, :update)
+ auth.destroy
+ assert_auth_logged_with_clean_properties(auth, :destroy)
+ end
+
+ test "use ownership and permission links to determine which logs a user can see" do
+ c = Log.readable_by(users(:admin)).order("id asc").each.to_a
+ assert_equal 6, c.size
+ assert_equal 1, c[0].id # no-op
+ assert_equal 2, c[1].id # admin changes repository foo, which is owned by active user
+ assert_equal 3, c[2].id # admin changes specimen owned_by_spectator
+ assert_equal 4, c[3].id # foo collection added, readable by active through link
+ assert_equal 5, c[4].id # baz collection added, readable by active and spectator through group 'all users' group membership
+ assert_equal 6, c[5].id # log_owned_by_active
+
+ c = Log.readable_by(users(:active)).order("id asc").each.to_a
+ assert_equal 4, c.size
+ assert_equal 2, c[0].id # admin changes repository foo, which is owned by active user
+ assert_equal 4, c[1].id # foo collection added, readable by active through link
+ assert_equal 5, c[2].id # baz collection added, readable by active and spectator through group 'all users' group membership
+ assert_equal 6, c[3].id # log_owned_by_active
+
+ c = Log.readable_by(users(:spectator)).order("id asc").each.to_a
+ assert_equal 2, c.size
+ assert_equal 3, c[0].id # admin changes specimen owned_by_spectator
+ assert_equal 5, c[1].id # baz collection added, readable by active and spectator through group 'all users' group membership
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class NodeTest < ActiveSupport::TestCase
+ def ping_node(node_name, ping_data)
+ set_user_from_auth :admin
+ node = nodes(node_name)
+ node.ping({ping_secret: node.info['ping_secret'],
+ ip: node.ip_address}.merge(ping_data))
+ node
+ end
+
+ test "pinging a node can add and update stats" do
+ node = ping_node(:idle, {total_cpu_cores: '12', total_ram_mb: '512'})
+ assert_equal(12, node.properties['total_cpu_cores'])
+ assert_equal(512, node.properties['total_ram_mb'])
+ end
+
+ test "stats disappear if not in a ping" do
+ node = ping_node(:idle, {total_ram_mb: '256'})
+ refute_includes(node.properties, 'total_cpu_cores')
+ assert_equal(256, node.properties['total_ram_mb'])
+ end
+
+ test "worker state is down for node with no slot" do
+ node = nodes(:was_idle_now_down)
+ assert_nil node.slot_number, "fixture is not what I expected"
+ assert_equal 'down', node.crunch_worker_state, "wrong worker state"
+ end
+end
--- /dev/null
+require 'test_helper'
+
+# Test referential integrity: ensure we cannot leave any object
+# without owners by deleting a user or group.
+#
+# "o" is an owner.
+# "i" is an item.
+
+class OwnerTest < ActiveSupport::TestCase
+ fixtures :users, :groups, :specimens
+
+ setup do
+ set_user_from_auth :admin_trustedclient
+ end
+
+ User.all
+ Group.all
+ [User, Group].each do |o_class|
+ test "create object with legit #{o_class} owner" do
+ o = o_class.create!
+ i = Specimen.create(owner_uuid: o.uuid)
+ assert i.valid?, "new item should pass validation"
+ assert i.uuid, "new item should have an ID"
+ assert Specimen.where(uuid: i.uuid).any?, "new item should really be in DB"
+ end
+
+ test "create object with non-existent #{o_class} owner" do
+ assert_raises(ActiveRecord::RecordInvalid,
+ "create should fail with random owner_uuid") do
+ i = Specimen.create!(owner_uuid: o_class.generate_uuid)
+ end
+
+ i = Specimen.create(owner_uuid: o_class.generate_uuid)
+ assert !i.valid?, "object with random owner_uuid should not be valid?"
+
+ i = Specimen.new(owner_uuid: o_class.generate_uuid)
+ assert !i.valid?, "new item should not pass validation"
+ assert !i.uuid, "new item should not have an ID"
+ end
+
+ [User, Group].each do |new_o_class|
+ test "change owner from legit #{o_class} to legit #{new_o_class} owner" do
+ o = o_class.create!
+ i = Specimen.create!(owner_uuid: o.uuid)
+ new_o = new_o_class.create!
+ assert(Specimen.where(uuid: i.uuid).any?,
+ "new item should really be in DB")
+ assert(i.update_attributes(owner_uuid: new_o.uuid),
+ "should change owner_uuid from #{o.uuid} to #{new_o.uuid}")
+ end
+ end
+
+ test "delete #{o_class} that owns nothing" do
+ o = o_class.create!
+ assert(o_class.where(uuid: o.uuid).any?,
+ "new #{o_class} should really be in DB")
+ assert(o.destroy, "should delete #{o_class} that owns nothing")
+ assert_equal(false, o_class.where(uuid: o.uuid).any?,
+ "#{o.uuid} should not be in DB after deleting")
+ end
+
+ test "change uuid of #{o_class} that owns nothing" do
+ # (we're relying on our admin credentials here)
+ o = o_class.create!
+ assert(o_class.where(uuid: o.uuid).any?,
+ "new #{o_class} should really be in DB")
+ old_uuid = o.uuid
+ new_uuid = o.uuid.sub(/..........$/, rand(2**256).to_s(36)[0..9])
+ assert(o.update_attributes(uuid: new_uuid),
+ "should change #{o_class} uuid from #{old_uuid} to #{new_uuid}")
+ assert_equal(false, o_class.where(uuid: old_uuid).any?,
+ "#{old_uuid} should disappear when renamed to #{new_uuid}")
+ end
+ end
+
+ ['users(:active)', 'groups(:aproject)'].each do |ofixt|
+ test "delete #{ofixt} that owns other objects" do
+ o = eval ofixt
+ assert_equal(true, Specimen.where(owner_uuid: o.uuid).any?,
+ "need something to be owned by #{o.uuid} for this test")
+
+ assert_raises(ActiveRecord::DeleteRestrictionError,
+ "should not delete #{ofixt} that owns objects") do
+ o.destroy
+ end
+ end
+
+ test "change uuid of #{ofixt} that owns other objects" do
+ o = eval ofixt
+ assert_equal(true, Specimen.where(owner_uuid: o.uuid).any?,
+ "need something to be owned by #{o.uuid} for this test")
+ old_uuid = o.uuid
+ new_uuid = o.uuid.sub(/..........$/, rand(2**256).to_s(36)[0..9])
+ assert(!o.update_attributes(uuid: new_uuid),
+ "should not change uuid of #{ofixt} that owns objects")
+ end
+ end
+
+ test "delete User that owns self" do
+ o = User.create!
+ assert User.where(uuid: o.uuid).any?, "new User should really be in DB"
+ assert_equal(true, o.update_attributes(owner_uuid: o.uuid),
+ "setting owner to self should work")
+ assert(o.destroy, "should delete User that owns self")
+ assert_equal(false, User.where(uuid: o.uuid).any?,
+ "#{o.uuid} should not be in DB after deleting")
+ end
+
+ test "change uuid of User that owns self" do
+ o = User.create!
+ assert User.where(uuid: o.uuid).any?, "new User should really be in DB"
+ assert_equal(true, o.update_attributes(owner_uuid: o.uuid),
+ "setting owner to self should work")
+ old_uuid = o.uuid
+ new_uuid = o.uuid.sub(/..........$/, rand(2**256).to_s(36)[0..9])
+ assert(o.update_attributes(uuid: new_uuid),
+ "should change uuid of User that owns self")
+ assert_equal(false, User.where(uuid: old_uuid).any?,
+ "#{old_uuid} should not be in DB after deleting")
+ assert_equal(true, User.where(uuid: new_uuid).any?,
+ "#{new_uuid} should be in DB after renaming")
+ assert_equal(new_uuid, User.where(uuid: new_uuid).first.owner_uuid,
+ "#{new_uuid} should be its own owner in DB after renaming")
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class PermissionTest < ActiveSupport::TestCase
+ include CurrentApiClient
+
+ test "Grant permissions on an object I own" do
+ set_user_from_auth :active_trustedclient
+
+ ob = Specimen.create
+ assert ob.save
+
+ # Ensure I have permission to manage this group even when its owner changes
+ perm_link = Link.create(tail_uuid: users(:active).uuid,
+ head_uuid: ob.uuid,
+ link_class: 'permission',
+ name: 'can_manage')
+ assert perm_link.save, "should give myself permission on my own object"
+ end
+
+ test "Delete permission links when deleting an object" do
+ set_user_from_auth :active_trustedclient
+
+ ob = Specimen.create!
+ Link.create!(tail_uuid: users(:active).uuid,
+ head_uuid: ob.uuid,
+ link_class: 'permission',
+ name: 'can_manage')
+ ob_uuid = ob.uuid
+ assert ob.destroy, "Could not destroy object with 1 permission link"
+ assert_empty(Link.where(head_uuid: ob_uuid),
+ "Permission link was not deleted when object was deleted")
+ end
+
+ test "permission links owned by root" do
+ set_user_from_auth :active_trustedclient
+ ob = Specimen.create!
+ perm_link = Link.create!(tail_uuid: users(:active).uuid,
+ head_uuid: ob.uuid,
+ link_class: 'permission',
+ name: 'can_read')
+ assert_equal system_user_uuid, perm_link.owner_uuid
+ end
+
+ test "readable_by" do
+ set_user_from_auth :active_trustedclient
+
+ ob = Specimen.create!
+ Link.create!(tail_uuid: users(:active).uuid,
+ head_uuid: ob.uuid,
+ link_class: 'permission',
+ name: 'can_read')
+ assert Specimen.readable_by(users(:active)).where(uuid: ob.uuid).any?, "user does not have read permission"
+ end
+
+ test "writable_by" do
+ set_user_from_auth :active_trustedclient
+
+ ob = Specimen.create!
+ Link.create!(tail_uuid: users(:active).uuid,
+ head_uuid: ob.uuid,
+ link_class: 'permission',
+ name: 'can_write')
+ assert ob.writable_by.include?(users(:active).uuid), "user does not have write permission"
+ end
+
+ test "writable_by reports requesting user's own uuid for a writable project" do
+ invited_to_write = users(:project_viewer)
+ group = groups(:asubproject)
+
+ # project_view can read, but cannot see write or see writers list
+ set_user_from_auth :project_viewer
+ assert_equal([group.owner_uuid],
+ group.writable_by,
+ "writers list should just have owner_uuid")
+
+ # allow project_viewer to write for the remainder of the test
+ set_user_from_auth :admin
+ Link.create!(tail_uuid: invited_to_write.uuid,
+ head_uuid: group.uuid,
+ link_class: 'permission',
+ name: 'can_write')
+ group.permissions.reload
+
+ # project_viewer should see self in writers list (but not all writers)
+ set_user_from_auth :project_viewer
+ assert_not_nil(group.writable_by,
+ "can write but cannot see writers list")
+ assert_includes(group.writable_by, invited_to_write.uuid,
+ "self missing from writers list")
+ assert_includes(group.writable_by, group.owner_uuid,
+ "project owner missing from writers list")
+ refute_includes(group.writable_by, users(:active).uuid,
+ "saw :active user in writers list")
+
+ # active user should see full writers list
+ set_user_from_auth :active
+ assert_includes(group.writable_by, invited_to_write.uuid,
+ "permission just added, but missing from writers list")
+
+ # allow project_viewer to manage for the remainder of the test
+ set_user_from_auth :admin
+ Link.create!(tail_uuid: invited_to_write.uuid,
+ head_uuid: group.uuid,
+ link_class: 'permission',
+ name: 'can_manage')
+ # invite another writer we can test for
+ Link.create!(tail_uuid: users(:spectator).uuid,
+ head_uuid: group.uuid,
+ link_class: 'permission',
+ name: 'can_write')
+ group.permissions.reload
+
+ set_user_from_auth :project_viewer
+ assert_not_nil(group.writable_by,
+ "can manage but cannot see writers list")
+ assert_includes(group.writable_by, users(:spectator).uuid,
+ ":spectator missing from writers list")
+ end
+
+ test "user owns group, group can_manage object's group, user can add permissions" do
+ set_user_from_auth :admin
+
+ owner_grp = Group.create!(owner_uuid: users(:active).uuid)
+
+ sp_grp = Group.create!
+ sp = Specimen.create!(owner_uuid: sp_grp.uuid)
+
+ manage_perm = Link.create!(link_class: 'permission',
+ name: 'can_manage',
+ tail_uuid: owner_grp.uuid,
+ head_uuid: sp_grp.uuid)
+
+ # active user owns owner_grp, which has can_manage permission on sp_grp
+ # user should be able to add permissions on sp.
+ set_user_from_auth :active_trustedclient
+ test_perm = Link.create(tail_uuid: users(:active).uuid,
+ head_uuid: sp.uuid,
+ link_class: 'permission',
+ name: 'can_write')
+ test_uuid = test_perm.uuid
+ assert test_perm.save, "could not save new permission on target object"
+ assert test_perm.destroy, "could not delete new permission on target object"
+ end
+
+ # TODO(twp): fix bug #3091, which should fix this test.
+ test "can_manage permission on a non-group object" do
+ skip
+ set_user_from_auth :admin
+
+ ob = Specimen.create!
+ # grant can_manage permission to active
+ perm_link = Link.create!(tail_uuid: users(:active).uuid,
+ head_uuid: ob.uuid,
+ link_class: 'permission',
+ name: 'can_manage')
+ # ob is owned by :admin, the link is owned by root
+ assert_equal users(:admin).uuid, ob.owner_uuid
+ assert_equal system_user_uuid, perm_link.owner_uuid
+
+ # user "active" can modify the permission link
+ set_user_from_auth :active_trustedclient
+ perm_link.properties["foo"] = 'bar'
+ assert perm_link.save, "could not save modified link"
+
+ assert_equal 'bar', perm_link.properties['foo'], "link properties do not include foo = bar"
+ end
+
+ test "user without can_manage permission may not modify permission link" do
+ set_user_from_auth :admin
+
+ ob = Specimen.create!
+ # grant can_manage permission to active
+ perm_link = Link.create!(tail_uuid: users(:active).uuid,
+ head_uuid: ob.uuid,
+ link_class: 'permission',
+ name: 'can_read')
+ # ob is owned by :admin, the link is owned by root
+ assert_equal ob.owner_uuid, users(:admin).uuid
+ assert_equal perm_link.owner_uuid, system_user_uuid
+
+ # user "active" may not modify the permission link
+ set_user_from_auth :active_trustedclient
+ perm_link.name = 'can_manage'
+ assert_raises ArvadosModel::PermissionDeniedError do
+ perm_link.save
+ end
+ end
+
+ test "manager user gets permission to minions' articles via can_manage link" do
+ manager = create :active_user, first_name: "Manage", last_name: "Er"
+ minion = create :active_user, first_name: "Min", last_name: "Ion"
+ minions_specimen = act_as_user minion do
+ Specimen.create!
+ end
+ # Manager creates a group. (Make sure it doesn't magically give
+ # anyone any additional permissions.)
+ g = nil
+ act_as_user manager do
+ g = create :group, name: "NoBigSecret Lab"
+ assert_empty(User.readable_by(manager).where(uuid: minion.uuid),
+ "saw a user I shouldn't see")
+ assert_raises(ArvadosModel::PermissionDeniedError,
+ ActiveRecord::RecordInvalid,
+ "gave can_read permission to a user I shouldn't see") do
+ create(:permission_link,
+ name: 'can_read', tail_uuid: minion.uuid, head_uuid: g.uuid)
+ end
+ %w(can_manage can_write can_read).each do |perm_type|
+ assert_raises(ArvadosModel::PermissionDeniedError,
+ ActiveRecord::RecordInvalid,
+ "escalated privileges") do
+ create(:permission_link,
+ name: perm_type, tail_uuid: g.uuid, head_uuid: minion.uuid)
+ end
+ end
+ assert_empty(User.readable_by(manager).where(uuid: minion.uuid),
+ "manager saw minion too soon")
+ assert_empty(User.readable_by(minion).where(uuid: manager.uuid),
+ "minion saw manager too soon")
+ assert_empty(Group.readable_by(minion).where(uuid: g.uuid),
+ "minion saw manager's new NoBigSecret Lab group too soon")
+
+ # Manager declares everybody on the system should be able to see
+ # the NoBigSecret Lab group.
+ create(:permission_link,
+ name: 'can_read',
+ tail_uuid: 'zzzzz-j7d0g-fffffffffffffff',
+ head_uuid: g.uuid)
+ # ...but nobody has joined the group yet. Manager still can't see
+ # minion.
+ assert_empty(User.readable_by(manager).where(uuid: minion.uuid),
+ "manager saw minion too soon")
+ end
+
+ act_as_user minion do
+ # Minion can see the group.
+ assert_not_empty(Group.readable_by(minion).where(uuid: g.uuid),
+ "minion could not see the NoBigSecret Lab group")
+ # Minion joins the group.
+ create(:permission_link,
+ name: 'can_read',
+ tail_uuid: g.uuid,
+ head_uuid: minion.uuid)
+ end
+
+ act_as_user manager do
+ # Now, manager can see minion.
+ assert_not_empty(User.readable_by(manager).where(uuid: minion.uuid),
+ "manager could not see minion")
+ # But cannot obtain further privileges this way.
+ assert_raises(ArvadosModel::PermissionDeniedError,
+ "escalated privileges") do
+ create(:permission_link,
+ name: 'can_manage', tail_uuid: manager.uuid, head_uuid: minion.uuid)
+ end
+ assert_empty(Specimen
+ .readable_by(manager)
+ .where(uuid: minions_specimen.uuid),
+ "manager saw the minion's private stuff")
+ assert_raises(ArvadosModel::PermissionDeniedError,
+ "manager could update minion's private stuff") do
+ minions_specimen.update_attributes(properties: {'x' => 'y'})
+ end
+ end
+
+ act_as_system_user do
+ # Root can give Manager more privileges over Minion.
+ create(:permission_link,
+ name: 'can_manage', tail_uuid: g.uuid, head_uuid: minion.uuid)
+ end
+
+ act_as_user manager do
+ # Now, manager can read and write Minion's stuff.
+ assert_not_empty(Specimen
+ .readable_by(manager)
+ .where(uuid: minions_specimen.uuid),
+ "manager could not find minion's specimen by uuid")
+ assert_equal(true,
+ minions_specimen.update_attributes(properties: {'x' => 'y'}),
+ "manager could not update minion's specimen object")
+ end
+ end
+
+ test "users with bidirectional read permission in group can see each other, but cannot see each other's private articles" do
+ a = create :active_user, first_name: "A"
+ b = create :active_user, first_name: "B"
+ other = create :active_user, first_name: "OTHER"
+ act_as_system_user do
+ g = create :group
+ [a,b].each do |u|
+ create(:permission_link,
+ name: 'can_read', tail_uuid: u.uuid, head_uuid: g.uuid)
+ create(:permission_link,
+ name: 'can_read', head_uuid: u.uuid, tail_uuid: g.uuid)
+ end
+ end
+ a_specimen = act_as_user a do
+ Specimen.create!
+ end
+ assert_not_empty(Specimen.readable_by(a).where(uuid: a_specimen.uuid),
+ "A cannot read own Specimen, following test probably useless.")
+ assert_empty(Specimen.readable_by(b).where(uuid: a_specimen.uuid),
+ "B can read A's Specimen")
+ [a,b].each do |u|
+ assert_empty(User.readable_by(u).where(uuid: other.uuid),
+ "#{u.first_name} can see OTHER in the user list")
+ assert_empty(User.readable_by(other).where(uuid: u.uuid),
+ "OTHER can see #{u.first_name} in the user list")
+ act_as_user u do
+ assert_raises ArvadosModel::PermissionDeniedError, "wrote without perm" do
+ other.update_attributes!(prefs: {'pwned' => true})
+ end
+ assert_equal(true, u.update_attributes!(prefs: {'thisisme' => true}),
+ "#{u.first_name} can't update its own prefs")
+ end
+ act_as_user other do
+ assert_raises(ArvadosModel::PermissionDeniedError,
+ "OTHER wrote #{u.first_name} without perm") do
+ u.update_attributes!(prefs: {'pwned' => true})
+ end
+ assert_equal(true, other.update_attributes!(prefs: {'thisisme' => true}),
+ "OTHER can't update its own prefs")
+ end
+ end
+ end
+
+ test "cannot create with owner = unwritable user" do
+ set_user_from_auth :rominiadmin
+ assert_raises ArvadosModel::PermissionDeniedError, "created with owner = unwritable user" do
+ Specimen.create!(owner_uuid: users(:active).uuid)
+ end
+ end
+
+ test "cannot change owner to unwritable user" do
+ set_user_from_auth :rominiadmin
+ ob = Specimen.create!
+ assert_raises ArvadosModel::PermissionDeniedError, "changed owner to unwritable user" do
+ ob.update_attributes!(owner_uuid: users(:active).uuid)
+ end
+ end
+
+ test "cannot create with owner = unwritable group" do
+ set_user_from_auth :rominiadmin
+ assert_raises ArvadosModel::PermissionDeniedError, "created with owner = unwritable group" do
+ Specimen.create!(owner_uuid: groups(:aproject).uuid)
+ end
+ end
+
+ test "cannot change owner to unwritable group" do
+ set_user_from_auth :rominiadmin
+ ob = Specimen.create!
+ assert_raises ArvadosModel::PermissionDeniedError, "changed owner to unwritable group" do
+ ob.update_attributes!(owner_uuid: groups(:aproject).uuid)
+ end
+ end
+
+ test "active user cannot write admin's repo" do
+ set_user_from_auth :active
+ assert_raises ArvadosModel::PermissionDeniedError, "pwned" do
+ repositories(:repository3).update_attributes(name: "kilroy")
+ end
+ end
+
+ test "active user cannot change repo name via can_manage permission" do
+ set_user_from_auth :active
+ assert_raises ArvadosModel::PermissionDeniedError, "pwned" do
+ repositories(:foo).update_attributes(name: "arvados")
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineInstanceTest < ActiveSupport::TestCase
+
+ test "check active and success for a pipeline in new state" do
+ pi = pipeline_instances :new_pipeline
+
+ assert_equal 'New', pi.state, 'expected state to be New for :new_pipeline'
+
+ # save the pipeline and expect state to be New
+ Thread.current[:user] = users(:admin)
+
+ pi.save
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::New, pi.state, 'expected state to be New for new pipeline'
+ end
+
+ test "check active and success for a newly created pipeline" do
+ set_user_from_auth :active
+
+ pi = PipelineInstance.create(state: 'Ready')
+ pi.save
+
+ assert pi.valid?, 'expected newly created empty pipeline to be valid ' + pi.errors.messages.to_s
+ assert_equal 'Ready', pi.state, 'expected state to be Ready for a new empty pipeline'
+ end
+
+ test "update attributes for pipeline" do
+ Thread.current[:user] = users(:admin)
+
+ pi = pipeline_instances :new_pipeline
+
+ # add a component with no input and expect state to be New
+ component = {'script_parameters' => {"input_not_provided" => {"required" => true}}}
+ pi.components['first'] = component
+ components = pi.components
+ pi.update_attribute 'components', pi.components
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::New, pi.state, 'expected state to be New after adding component with input'
+ assert_equal pi.components.size, 1, 'expected one component'
+
+ # add a component with no input not required
+ component = {'script_parameters' => {"input_not_provided" => {"required" => false}}}
+ pi.components['first'] = component
+ components = pi.components
+ pi.update_attribute 'components', pi.components
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::Ready, pi.state, 'expected state to be Ready after adding component with input'
+ assert_equal pi.components.size, 1, 'expected one component'
+
+ # add a component with input and expect state to become Ready
+ component = {'script_parameters' => {"input" => "yyyad4b39ca5a924e481008009d94e32+210"}}
+ pi.components['first'] = component
+ components = pi.components
+ pi.update_attribute 'components', pi.components
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::Ready, pi.state, 'expected state to be Ready after adding component with input'
+ assert_equal pi.components.size, 1, 'expected one component'
+
+ pi.state = PipelineInstance::RunningOnServer
+ pi.save
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::RunningOnServer, pi.state, 'expected state to be RunningOnServer after updating state to RunningOnServer'
+
+ pi.state = PipelineInstance::Paused
+ pi.save
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::Paused, pi.state, 'expected state to be Paused after updating state to Paused'
+
+ pi.state = PipelineInstance::Complete
+ pi.save
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::Complete, pi.state, 'expected state to be Complete after updating state to Complete'
+
+ pi.state = 'bogus'
+ pi.save
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::Complete, pi.state, 'expected state to be unchanged with set to a bogus value'
+
+ pi.state = PipelineInstance::Failed
+ pi.save
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::Failed, pi.state, 'expected state to be Failed after updating state to Failed'
+ end
+
+ test "update attributes for pipeline with two components" do
+ pi = pipeline_instances :new_pipeline
+
+ # add two components, one with input and one with no input and expect state to be New
+ component1 = {'script_parameters' => {"something" => "xxxad4b39ca5a924e481008009d94e32+210", "input" => "c1bad4b39ca5a924e481008009d94e32+210"}}
+ component2 = {'script_parameters' => {"something_else" => "xxxad4b39ca5a924e481008009d94e32+210", "input_missing" => {"required" => true}}}
+ pi.components['first'] = component1
+ pi.components['second'] = component2
+ components = pi.components
+
+ Thread.current[:user] = users(:admin)
+ pi.update_attribute 'components', pi.components
+
+ pi = PipelineInstance.find_by_uuid 'zzzzz-d1hrv-f4gneyn6br1xize'
+ assert_equal PipelineInstance::New, pi.state, 'expected state to be New after adding component with input'
+ assert_equal pi.components.size, 2, 'expected two components'
+ end
+
+ [:has_component_with_no_script_parameters,
+ :has_component_with_empty_script_parameters].each do |pi_name|
+ test "update pipeline that #{pi_name}" do
+ pi = pipeline_instances pi_name
+
+ Thread.current[:user] = users(:active)
+ assert_equal PipelineInstance::Ready, pi.state
+ end
+ end
+end
--- /dev/null
+require 'test_helper'
+
+class PipelineTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class RepositoryTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class SpecimenTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class TraitTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'test_helper'
+
+class UserNotifierTest < ActionMailer::TestCase
+
+ # Send the email, then test that it got queued
+ test "account is setup" do
+ user = users :active
+ email = UserNotifier.account_is_setup user
+
+ assert_not_nil email
+
+ # Test the body of the sent email contains what we expect it to
+ assert_equal Rails.configuration.user_notifier_email_from, email.from.first
+ assert_equal user.email, email.to.first
+ assert_equal 'Welcome to Curoverse', email.subject
+ assert (email.body.to_s.include? 'Your Arvados account has been set up'),
+ 'Expected Your Arvados account has been set up in email body'
+ assert (email.body.to_s.include? user.email),
+ 'Expected user email in email body'
+ assert (email.body.to_s.include? Rails.configuration.workbench_address),
+ 'Expected workbench url in email body'
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class UserTest < ActiveSupport::TestCase
+ include CurrentApiClient
+
+ # The fixture services/api/test/fixtures/users.yml serves as the input for this test case
+ setup do
+ # Make sure system_user exists before making "pre-test users" list
+ system_user
+ end
+
+ [[false, 'foo@example.com', true, nil],
+ [false, 'bar@example.com', nil, true],
+ [true, 'foo@example.com', true, nil],
+ [true, 'bar@example.com', true, true],
+ [false, false, nil, nil],
+ [true, false, true, nil]
+ ].each do |auto_admin_first_user_config, auto_admin_user_config, foo_should_be_admin, bar_should_be_admin|
+ # In each case, 'foo' is created first, then 'bar', then 'bar2', then 'baz'.
+ test "auto admin with auto_admin_first=#{auto_admin_first_user_config} auto_admin=#{auto_admin_user_config}" do
+
+ if auto_admin_first_user_config
+ # This test requires no admin users exist (except for the system user)
+ users(:admin).delete
+ @all_users = User.where("uuid not like '%-000000000000000'").where(:is_admin => true).find(:all)
+ assert_equal 0, @all_users.size, "No admin users should exist (except for the system user)"
+ end
+
+ Rails.configuration.auto_admin_first_user = auto_admin_first_user_config
+ Rails.configuration.auto_admin_user = auto_admin_user_config
+
+ # See if the foo user has is_admin
+ foo = User.new
+ foo.first_name = 'foo'
+ foo.email = 'foo@example.com'
+
+ act_as_system_user do
+ foo.save!
+ end
+
+ foo = User.find(foo.id) # get the user back
+ assert_equal foo_should_be_admin, foo.is_admin, "is_admin is wrong for user foo"
+ assert_equal 'foo', foo.first_name
+
+ # See if the bar user has is_admin
+ bar = User.new
+ bar.first_name = 'bar'
+ bar.email = 'bar@example.com'
+
+ act_as_system_user do
+ bar.save!
+ end
+
+ bar = User.find(bar.id) # get the user back
+ assert_equal bar_should_be_admin, bar.is_admin, "is_admin is wrong for user bar"
+ assert_equal 'bar', bar.first_name
+
+ # A subsequent user with the bar@example.com address should never be
+ # elevated to admin
+ bar2 = User.new
+ bar2.first_name = 'bar2'
+ bar2.email = 'bar@example.com'
+
+ act_as_system_user do
+ bar2.save!
+ end
+
+ bar2 = User.find(bar2.id) # get the user back
+ assert !bar2.is_admin, "is_admin is wrong for user bar2"
+ assert_equal 'bar2', bar2.first_name
+
+ # An ordinary new user should not be elevated to admin
+ baz = User.new
+ baz.first_name = 'baz'
+ baz.email = 'baz@example.com'
+
+ act_as_system_user do
+ baz.save!
+ end
+
+ baz = User.find(baz.id) # get the user back
+ assert !baz.is_admin
+ assert_equal 'baz', baz.first_name
+
+ end
+ end
+
+ test "check non-admin active user properties" do
+ @active_user = users(:active) # get the active user
+ assert !@active_user.is_admin, 'is_admin should not be set for a non-admin user'
+ assert @active_user.is_active, 'user should be active'
+ assert @active_user.is_invited, 'is_invited should be set'
+ assert_not_nil @active_user.prefs, "user's preferences should be non-null, but may be size zero"
+ assert (@active_user.can? :read=>"#{@active_user.uuid}"), "user should be able to read own object"
+ assert (@active_user.can? :write=>"#{@active_user.uuid}"), "user should be able to write own object"
+ assert (@active_user.can? :manage=>"#{@active_user.uuid}"), "user should be able to manage own object"
+
+ assert @active_user.groups_i_can(:read).size > 0, "active user should be able read at least one group"
+
+ # non-admin user cannot manage or write other user objects
+ @uninvited_user = users(:inactive_uninvited) # get the uninvited user
+ assert !(@active_user.can? :read=>"#{@uninvited_user.uuid}")
+ assert !(@active_user.can? :write=>"#{@uninvited_user.uuid}")
+ assert !(@active_user.can? :manage=>"#{@uninvited_user.uuid}")
+ end
+
+ test "check admin user properties" do
+ @admin_user = users(:admin) # get the admin user
+ assert @admin_user.is_admin, 'is_admin should be set for admin user'
+ assert @admin_user.is_active, 'admin user cannot be inactive'
+ assert @admin_user.is_invited, 'is_invited should be set'
+ assert_not_nil @admin_user.uuid.size, "user's uuid should be non-null"
+ assert_not_nil @admin_user.prefs, "user's preferences should be non-null, but may be size zero"
+ assert @admin_user.identity_url.size > 0, "user's identity url is expected"
+ assert @admin_user.can? :read=>"#{@admin_user.uuid}"
+ assert @admin_user.can? :write=>"#{@admin_user.uuid}"
+ assert @admin_user.can? :manage=>"#{@admin_user.uuid}"
+
+ assert @admin_user.groups_i_can(:read).size > 0, "admin active user should be able read at least one group"
+ assert @admin_user.groups_i_can(:write).size > 0, "admin active user should be able write to at least one group"
+ assert @admin_user.groups_i_can(:manage).size > 0, "admin active user should be able manage at least one group"
+
+ # admin user can also write or manage other users
+ @uninvited_user = users(:inactive_uninvited) # get the uninvited user
+ assert @admin_user.can? :read=>"#{@uninvited_user.uuid}"
+ assert @admin_user.can? :write=>"#{@uninvited_user.uuid}"
+ assert @admin_user.can? :manage=>"#{@uninvited_user.uuid}"
+ end
+
+ test "check inactive and uninvited user properties" do
+ @uninvited_user = users(:inactive_uninvited) # get the uninvited user
+ assert !@uninvited_user.is_admin, 'is_admin should not be set for a non-admin user'
+ assert !@uninvited_user.is_active, 'user should be inactive'
+ assert !@uninvited_user.is_invited, 'is_invited should not be set'
+ assert @uninvited_user.can? :read=>"#{@uninvited_user.uuid}"
+ assert @uninvited_user.can? :write=>"#{@uninvited_user.uuid}"
+ assert @uninvited_user.can? :manage=>"#{@uninvited_user.uuid}"
+
+ assert @uninvited_user.groups_i_can(:read).size == 1, "inactive and uninvited user can only read anonymous user group"
+ assert @uninvited_user.groups_i_can(:read).first.ends_with? 'anonymouspublic' , "inactive and uninvited user can only read anonymous user group"
+ assert @uninvited_user.groups_i_can(:write).size == 0, "inactive and uninvited user should not be able write to any groups"
+ assert @uninvited_user.groups_i_can(:manage).size == 0, "inactive and uninvited user should not be able manage any groups"
+ end
+
+ test "find user method checks" do
+ User.find(:all).each do |user|
+ assert_not_nil user.uuid, "non-null uuid expected for " + user.full_name
+ end
+
+ user = users(:active) # get the active user
+
+ found_user = User.find(user.id) # find a user by the row id
+
+ assert_equal found_user.full_name, user.first_name + ' ' + user.last_name
+ assert_equal found_user.identity_url, user.identity_url
+ end
+
+ test "full name should not contain spurious whitespace" do
+ set_user_from_auth :admin
+
+ user = User.create ({uuid: 'zzzzz-tpzed-abcdefghijklmno', email: 'foo@example.com' })
+
+ assert_equal '', user.full_name
+
+ user.first_name = 'John'
+ user.last_name = 'Smith'
+
+ assert_equal user.first_name + ' ' + user.last_name, user.full_name
+ end
+
+ test "create new user" do
+ set_user_from_auth :admin
+
+ @all_users = User.find(:all)
+
+ user = User.new
+ user.first_name = "first_name_for_newly_created_user"
+ user.save
+
+ # verify there is one extra user in the db now
+ assert_equal @all_users.size+1, User.find(:all).size
+
+ user = User.find(user.id) # get the user back
+ assert_equal(user.first_name, 'first_name_for_newly_created_user')
+ assert_not_nil user.uuid, 'uuid should be set for newly created user'
+ assert_nil user.email, 'email should be null for newly created user, because it was not passed in'
+ assert_nil user.identity_url, 'identity_url should be null for newly created user, because it was not passed in'
+
+ user.first_name = 'first_name_for_newly_created_user_updated'
+ user.save
+ user = User.find(user.id) # get the user back
+ assert_equal(user.first_name, 'first_name_for_newly_created_user_updated')
+ end
+
+ test "create new user with notifications" do
+ set_user_from_auth :admin
+
+ create_user_and_verify_setup_and_notifications true, 'active-notify-address@example.com', 'inactive-notify-address@example.com', nil, false
+ create_user_and_verify_setup_and_notifications true, 'active-notify-address@example.com', [], nil, false
+ create_user_and_verify_setup_and_notifications true, [], [], nil, false
+ create_user_and_verify_setup_and_notifications false, 'active-notify-address@example.com', 'inactive-notify-address@example.com', nil, false
+ create_user_and_verify_setup_and_notifications false, [], 'inactive-notify-address@example.com', nil, false
+ create_user_and_verify_setup_and_notifications false, [], [], nil, false
+ end
+
+ [
+ [false, [], [], 'inactive-none@example.com', false, false, true],
+ [false, [], [], 'inactive-vm@example.com', true, false, true],
+ [false, [], [], 'inactive-repo@example.com', false, true, true],
+ [false, [], [], 'inactive-both@example.com', true, true, true],
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'active-none@example.com', false, false, true],
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'active-vm@example.com', true, false, true],
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'active-repo@example.com', false, true, true],
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'active-both@example.com', true, true, true],
+
+ [false, [], [], nil, true, true, false],
+
+ [false, [], [], 'arvados', true, true, false],
+ [false, [], [], 'arvados', true, false, false], # blacklisted username
+ [false, [], [], 'arvados', false, false, true], # since we are not creating repo and vm login, this blacklisted name is not a problem
+
+ [false, [], [], 'arvados@example.com', false, false, true], # since we are not creating repo and vm login, this blacklisted name is not a problem
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'arvados@example.com', false, false, true], # since we are not creating repo and vm login, this blacklisted name is not a problem
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'root@example.com', true, false, false], # blacklisted name
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', 'root@example.com', true, false, false], # blacklisted name
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'roo_t@example.com', false, true, true], # not blacklisted name
+
+ [false, [], [], '@example.com', true, false, false], # incorrect format
+ [false, [], [], '@example.com', false, true, false],
+ [false, [], [], '@example.com', false, false, true], # no repo and vm login, so no issue with email format
+
+ [false, [], [], '^^incorrect_format@example.com', true, true, false],
+
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', 'auto_setup_repo@example.com', true, true, true], # existing repository name 'auto_setup_repo'
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'auto_setup_repo@example.com', true, false, true], # existing repository name 'auto_setup_repo'
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', 'auto_setup_repo@example.com', false, true, true], # existing repository name 'auto_setup_repo'
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', 'auto_setup_repo@example.com', false, false, true], # existing repository name 'auto_setup_repo', but we are not creating repo or login link
+
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', 'auto_setup_vm_login@example.com', true, true, true], # existing vm login name
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'auto_setup_vm_login@example.com', true, false, true], # existing vm login name
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', 'auto_setup_vm_login@example.com', false, true, true], # existing vm login name
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', 'auto_setup_vm_login@example.com', false, false, true], # existing vm login name, but we are not creating repo or login link
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', '*!*@example.com', true, false, false], # username is invalid format
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', '*!*@example.com', false, false, true], # since no repo and vm login, username is ok (not validated)
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', '*!*@example.com', false, false, true], # since no repo and vm login, username is ok (not validated)
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', '&4ad@example.com', true, true, false], # username is invalid format
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', '&4ad@example.com', false, false, true], # no repo or vm login, so format not checked
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', '&4ad@example.com', true, true, false], # username is invalid format
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', '&4ad@example.com', false, false, true], # no repo or vm login, so format not checked
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', '4ad@example.com', true, true, false], # username is invalid format
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', '4ad@example.com', false, false, true], # no repo or vm login, so format not checked
+ [false, 'active-notify@example.com', 'inactive-notify@example.com', '4ad@example.com', false, false, true], # no repo or vm login, so format not checked
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', '.foo@example.com', false, false, true], # no repo or vm login, so format not checked
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', '.foo@example.com', true, false, false], # invalid format
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'bar.@example.com', false, false, true], # no repo or vm login, so format not checked
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'bar.@example.com', true, false, false], # valid format
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'ice9@example.com', false, false, true], # no repo or vm login, so format not checked
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'ice9@example.com', true, false, true], # valid format
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'o_o@example.com', false, false, true], # no repo or vm login, so format not checked
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'o_o@example.com', true, false, true], # valid format
+
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'r00t@example.com', false, false, true], # no repo or vm login, so format not checked
+ [true, 'active-notify@example.com', 'inactive-notify@example.com', 'r00t@example.com', true, false, true], # valid format
+
+ ].each do |active, new_user_recipients, inactive_recipients, email, auto_setup_vm, auto_setup_repo, ok_to_auto_setup|
+ test "create new user with auto setup #{active} #{email} #{auto_setup_vm} #{auto_setup_repo}" do
+ auto_setup_new_users = Rails.configuration.auto_setup_new_users
+ auto_setup_new_users_with_vm_uuid = Rails.configuration.auto_setup_new_users_with_vm_uuid
+ auto_setup_new_users_with_repository = Rails.configuration.auto_setup_new_users_with_repository
+
+ begin
+ set_user_from_auth :admin
+
+ Rails.configuration.auto_setup_new_users = true
+
+ if auto_setup_vm
+ Rails.configuration.auto_setup_new_users_with_vm_uuid = virtual_machines(:testvm)['uuid']
+ else
+ Rails.configuration.auto_setup_new_users_with_vm_uuid = false
+ end
+
+ Rails.configuration.auto_setup_new_users_with_repository = auto_setup_repo
+
+ create_user_and_verify_setup_and_notifications active, new_user_recipients, inactive_recipients, email, ok_to_auto_setup
+ ensure
+ Rails.configuration.auto_setup_new_users = auto_setup_new_users
+ Rails.configuration.auto_setup_new_users_with_vm_uuid = auto_setup_new_users_with_vm_uuid
+ Rails.configuration.auto_setup_new_users_with_repository = auto_setup_new_users_with_repository
+ end
+ end
+ end
+
+ test "update existing user" do
+ set_user_from_auth :active # set active user as current user
+
+ @active_user = users(:active) # get the active user
+
+ @active_user.first_name = "first_name_changed"
+ @active_user.save
+
+ @active_user = User.find(@active_user.id) # get the user back
+ assert_equal(@active_user.first_name, 'first_name_changed')
+
+ # admin user also should be able to update the "active" user info
+ set_user_from_auth :admin # set admin user as current user
+ @active_user.first_name = "first_name_changed_by_admin_for_active_user"
+ @active_user.save
+
+ @active_user = User.find(@active_user.id) # get the user back
+ assert_equal(@active_user.first_name, 'first_name_changed_by_admin_for_active_user')
+ end
+
+ test "delete a user and verify" do
+ @active_user = users(:active) # get the active user
+ active_user_uuid = @active_user.uuid
+
+ set_user_from_auth :admin
+ @active_user.delete
+
+ found_deleted_user = false
+ User.find(:all).each do |user|
+ if user.uuid == active_user_uuid
+ found_deleted_user = true
+ break
+ end
+ end
+ assert !found_deleted_user, "found deleted user: "+active_user_uuid
+
+ end
+
+ test "create new user as non-admin user" do
+ set_user_from_auth :active
+
+ begin
+ user = User.new
+ user.save
+ rescue ArvadosModel::PermissionDeniedError => e
+ end
+ assert (e.message.include? 'PermissionDeniedError'),
+ 'Expected PermissionDeniedError'
+ end
+
+ test "setup new user" do
+ set_user_from_auth :admin
+
+ email = 'foo@example.com'
+ openid_prefix = 'http://openid/prefix'
+
+ user = User.create ({uuid: 'zzzzz-tpzed-abcdefghijklmno', email: email})
+
+ vm = VirtualMachine.create
+
+ response = User.setup user, openid_prefix, 'test_repo', vm.uuid
+
+ resp_user = find_obj_in_resp response, 'User'
+ verify_user resp_user, email
+
+ oid_login_perm = find_obj_in_resp response, 'Link', 'arvados#user'
+
+ verify_link oid_login_perm, 'permission', 'can_login', resp_user[:email],
+ resp_user[:uuid]
+
+ assert_equal openid_prefix, oid_login_perm[:properties]['identity_url_prefix'],
+ 'expected identity_url_prefix not found for oid_login_perm'
+
+ group_perm = find_obj_in_resp response, 'Link', 'arvados#group'
+ verify_link group_perm, 'permission', 'can_read', resp_user[:uuid], nil
+
+ repo_perm = find_obj_in_resp response, 'Link', 'arvados#repository'
+ verify_link repo_perm, 'permission', 'can_manage', resp_user[:uuid], nil
+
+ vm_perm = find_obj_in_resp response, 'Link', 'arvados#virtualMachine'
+ verify_link vm_perm, 'permission', 'can_login', resp_user[:uuid], vm.uuid
+ end
+
+ test "setup new user with junk in database" do
+ set_user_from_auth :admin
+
+ email = 'foo@example.com'
+ openid_prefix = 'http://openid/prefix'
+
+ user = User.create ({uuid: 'zzzzz-tpzed-abcdefghijklmno', email: email})
+
+ vm = VirtualMachine.create
+
+ # Set up the bogus Link
+ bad_uuid = 'zzzzz-tpzed-xyzxyzxyzxyzxyz'
+
+ resp_link = Link.create ({tail_uuid: email, link_class: 'permission',
+ name: 'can_login', head_uuid: bad_uuid})
+ resp_link.save(validate: false)
+
+ verify_link resp_link, 'permission', 'can_login', email, bad_uuid
+
+ response = User.setup user, openid_prefix, 'test_repo', vm.uuid
+
+ resp_user = find_obj_in_resp response, 'User'
+ verify_user resp_user, email
+
+ oid_login_perm = find_obj_in_resp response, 'Link', 'arvados#user'
+
+ verify_link oid_login_perm, 'permission', 'can_login', resp_user[:email],
+ resp_user[:uuid]
+
+ assert_equal openid_prefix, oid_login_perm[:properties]['identity_url_prefix'],
+ 'expected identity_url_prefix not found for oid_login_perm'
+
+ group_perm = find_obj_in_resp response, 'Link', 'arvados#group'
+ verify_link group_perm, 'permission', 'can_read', resp_user[:uuid], nil
+
+ repo_perm = find_obj_in_resp response, 'Link', 'arvados#repository'
+ verify_link repo_perm, 'permission', 'can_manage', resp_user[:uuid], nil
+
+ vm_perm = find_obj_in_resp response, 'Link', 'arvados#virtualMachine'
+ verify_link vm_perm, 'permission', 'can_login', resp_user[:uuid], vm.uuid
+ end
+
+ test "setup new user in multiple steps" do
+ set_user_from_auth :admin
+
+ email = 'foo@example.com'
+ openid_prefix = 'http://openid/prefix'
+
+ user = User.create ({uuid: 'zzzzz-tpzed-abcdefghijklmno', email: email})
+
+ response = User.setup user, openid_prefix
+
+ resp_user = find_obj_in_resp response, 'User'
+ verify_user resp_user, email
+
+ oid_login_perm = find_obj_in_resp response, 'Link', 'arvados#user'
+ verify_link oid_login_perm, 'permission', 'can_login', resp_user[:email],
+ resp_user[:uuid]
+ assert_equal openid_prefix, oid_login_perm[:properties]['identity_url_prefix'],
+ 'expected identity_url_prefix not found for oid_login_perm'
+
+ group_perm = find_obj_in_resp response, 'Link', 'arvados#group'
+ verify_link group_perm, 'permission', 'can_read', resp_user[:uuid], nil
+
+ # invoke setup again with repo_name
+ response = User.setup user, openid_prefix, 'test_repo'
+ resp_user = find_obj_in_resp response, 'User', nil
+ verify_user resp_user, email
+ assert_equal user.uuid, resp_user[:uuid], 'expected uuid not found'
+
+ group_perm = find_obj_in_resp response, 'Link', 'arvados#group'
+ verify_link group_perm, 'permission', 'can_read', resp_user[:uuid], nil
+
+ repo_perm = find_obj_in_resp response, 'Link', 'arvados#repository'
+ verify_link repo_perm, 'permission', 'can_manage', resp_user[:uuid], nil
+
+ # invoke setup again with a vm_uuid
+ vm = VirtualMachine.create
+
+ response = User.setup user, openid_prefix, 'test_repo', vm.uuid
+
+ resp_user = find_obj_in_resp response, 'User', nil
+ verify_user resp_user, email
+ assert_equal user.uuid, resp_user[:uuid], 'expected uuid not found'
+
+ group_perm = find_obj_in_resp response, 'Link', 'arvados#group'
+ verify_link group_perm, 'permission', 'can_read', resp_user[:uuid], nil
+
+ repo_perm = find_obj_in_resp response, 'Link', 'arvados#repository'
+ verify_link repo_perm, 'permission', 'can_manage', resp_user[:uuid], nil
+
+ vm_perm = find_obj_in_resp response, 'Link', 'arvados#virtualMachine'
+ verify_link vm_perm, 'permission', 'can_login', resp_user[:uuid], vm.uuid
+ end
+
+ def find_obj_in_resp (response_items, object_type, head_kind=nil)
+ return_obj = nil
+ response_items.each { |x|
+ if !x
+ next
+ end
+
+ if object_type == 'User'
+ if ArvadosModel::resource_class_for_uuid(x['uuid']) == User
+ return_obj = x
+ break
+ end
+ else # looking for a link
+ if ArvadosModel::resource_class_for_uuid(x['head_uuid']).kind == head_kind
+ return_obj = x
+ break
+ end
+ end
+ }
+ return return_obj
+ end
+
+ def verify_user (resp_user, email)
+ assert_not_nil resp_user, 'expected user object'
+ assert_not_nil resp_user['uuid'], 'expected user object'
+ assert_equal email, resp_user['email'], 'expected email not found'
+
+ end
+
+ def verify_link (link_object, link_class, link_name, tail_uuid, head_uuid)
+ assert_not_nil link_object, "expected link for #{link_class} #{link_name}"
+ assert_not_nil link_object[:uuid],
+ "expected non-nil uuid for link for #{link_class} #{link_name}"
+ assert_equal link_class, link_object[:link_class],
+ "expected link_class not found for #{link_class} #{link_name}"
+ assert_equal link_name, link_object[:name],
+ "expected link_name not found for #{link_class} #{link_name}"
+ assert_equal tail_uuid, link_object[:tail_uuid],
+ "expected tail_uuid not found for #{link_class} #{link_name}"
+ if head_uuid
+ assert_equal head_uuid, link_object[:head_uuid],
+ "expected head_uuid not found for #{link_class} #{link_name}"
+ end
+ end
+
+ def create_user_and_verify_setup_and_notifications (active, new_user_recipients, inactive_recipients, email, ok_to_auto_setup)
+ Rails.configuration.new_user_notification_recipients = new_user_recipients
+ Rails.configuration.new_inactive_user_notification_recipients = inactive_recipients
+
+ assert_equal new_user_recipients, Rails.configuration.new_user_notification_recipients
+ assert_equal inactive_recipients, Rails.configuration.new_inactive_user_notification_recipients
+
+ ActionMailer::Base.deliveries = []
+
+ user = User.new
+ user.first_name = "first_name_for_newly_created_user"
+ user.email = email
+ user.is_active = active
+ user.save!
+
+ # check user setup
+ group = Group.where(name: 'All users').select do |g|
+ g[:uuid].match /-f+$/
+ end.first
+
+ if !Rails.configuration.auto_setup_new_users || !ok_to_auto_setup
+ # verify that the user is not added to "All groups" by auto_setup
+ verify_link_exists false, group[:uuid], user.uuid, 'permission', 'can_read', nil, nil
+
+ # check oid login link not created by auto_setup
+ verify_link_exists false, user.uuid, user.email, 'permission', 'can_login', nil, nil
+ else
+ # verify that auto_setup took place
+ # verify that the user is added to "All groups"
+ verify_link_exists true, group[:uuid], user.uuid, 'permission', 'can_read', nil, nil
+
+ # check oid login link
+ verify_link_exists true, user.uuid, user.email, 'permission', 'can_login', nil, nil
+
+ username = user.email.partition('@')[0] if email
+
+ # check repo
+ repo_names = []
+ if Rails.configuration.auto_setup_new_users_with_repository
+ repos = Repository.where('name like ?', "%#{username}%")
+ assert_not_nil repos, 'repository not found'
+ assert_equal true, repos.any?, 'repository not found'
+ repo_uuids = []
+ repos.each do |repo|
+ repo_uuids << repo[:uuid]
+ repo_names << repo[:name]
+ end
+ if username == 'auto_setup_repo'
+ begin
+ repo_names.delete('auto_setup_repo')
+ ensure
+ assert_equal true, repo_names.any?, 'Repository name for username foo is not unique'
+ end
+ end
+ verify_link_exists true, repo_uuids, user.uuid, 'permission', 'can_manage', nil, nil
+ end
+
+ # if username is existing vm login name, make sure the username used to generate any repo is unique
+ if username == 'auto_setup_vm_login' || username == 'auto_setup_repo'
+ if repo_names.any?
+ assert repo_names.first.start_with? username
+ assert_not_nil /\d$/.match(repo_names.first)
+ end
+ end
+
+ # check vm uuid
+ vm_uuid = Rails.configuration.auto_setup_new_users_with_vm_uuid
+ if vm_uuid
+ verify_link_exists true, vm_uuid, user.uuid, 'permission', 'can_login', 'username', (username == 'auto_setup_repo' ? repo_names.first : username)
+ else
+ verify_link_exists false, vm_uuid, user.uuid, 'permission', 'can_login', 'username', (username == 'auto_setup_repo' ? repo_names.first : username)
+ end
+ end
+
+ # check email notifications
+ new_user_email = nil
+ new_inactive_user_email = nil
+
+ new_user_email_subject = "#{Rails.configuration.email_subject_prefix}New user created notification"
+ if Rails.configuration.auto_setup_new_users
+ new_user_email_subject = (ok_to_auto_setup || active) ?
+ "#{Rails.configuration.email_subject_prefix}New user created and setup notification" :
+ "#{Rails.configuration.email_subject_prefix}New user created, but not setup notification"
+ end
+
+ ActionMailer::Base.deliveries.each do |d|
+ if d.subject == new_user_email_subject then
+ new_user_email = d
+ elsif d.subject == "#{Rails.configuration.email_subject_prefix}New inactive user notification" then
+ new_inactive_user_email = d
+ end
+ end
+
+ # both active and inactive user creations should result in new user creation notification mails,
+ # if the new user email recipients config parameter is set
+ if not new_user_recipients.empty? then
+ assert_not_nil new_user_email, 'Expected new user email after setup'
+ assert_equal Rails.configuration.user_notifier_email_from, new_user_email.from[0]
+ assert_equal new_user_recipients, new_user_email.to[0]
+ assert_equal new_user_email_subject, new_user_email.subject
+ else
+ assert_nil new_user_email, 'Did not expect new user email after setup'
+ end
+
+ if not active
+ if not inactive_recipients.empty? then
+ assert_not_nil new_inactive_user_email, 'Expected new inactive user email after setup'
+ assert_equal Rails.configuration.user_notifier_email_from, new_inactive_user_email.from[0]
+ assert_equal inactive_recipients, new_inactive_user_email.to[0]
+ assert_equal "#{Rails.configuration.email_subject_prefix}New inactive user notification", new_inactive_user_email.subject
+ else
+ assert_nil new_inactive_user_email, 'Did not expect new inactive user email after setup'
+ end
+ else
+ assert_nil new_inactive_user_email, 'Expected no inactive user email after setting up active user'
+ end
+ ActionMailer::Base.deliveries = []
+
+ end
+
+ def verify_link_exists link_exists, head_uuid, tail_uuid, link_class, link_name, property_name, property_value
+ all_links = Link.where(head_uuid: head_uuid,
+ tail_uuid: tail_uuid,
+ link_class: link_class,
+ name: link_name)
+ assert_equal link_exists, all_links.any?, "Link #{'not' if link_exists} found for #{link_name} #{link_class} #{property_value}"
+ if link_exists && property_name && property_value
+ all_links.each do |link|
+ assert_equal true, all_links.first.properties[property_name].start_with?(property_value), 'Property not found in link'
+ end
+ end
+ end
+
+end
--- /dev/null
+require 'test_helper'
+
+class VirtualMachineTest < ActiveSupport::TestCase
+ # test "the truth" do
+ # assert true
+ # end
+end
--- /dev/null
+require 'bundler'
+
+$ARV_API_SERVER_DIR = File.expand_path('../..', __FILE__)
+SERVER_PID_PATH = 'tmp/pids/passenger.3002.pid'
+
+class WebsocketTestRunner < MiniTest::Unit
+ def _system(*cmd)
+ Bundler.with_clean_env do
+ if not system({'ARVADOS_WEBSOCKETS' => 'ws-only', 'RAILS_ENV' => 'test'}, *cmd)
+ raise RuntimeError, "#{cmd[0]} returned exit code #{$?.exitstatus}"
+ end
+ end
+ end
+
+ def _run(args=[])
+ server_pid = Dir.chdir($ARV_API_SERVER_DIR) do |apidir|
+ # Only passenger seems to be able to run the websockets server successfully.
+ _system('passenger', 'start', '-d', '-p3002')
+ timeout = Time.now.tv_sec + 10
+ begin
+ sleep 0.2
+ begin
+ server_pid = IO.read(SERVER_PID_PATH).to_i
+ good_pid = (server_pid > 0) and (Process.kill(0, pid) rescue false)
+ rescue Errno::ENOENT
+ good_pid = false
+ end
+ end while (not good_pid) and (Time.now.tv_sec < timeout)
+ if not good_pid
+ raise RuntimeError, "could not find API server Rails pid"
+ end
+ server_pid
+ end
+ begin
+ super(args)
+ ensure
+ Process.kill('TERM', server_pid)
+ end
+ end
+end
+
+MiniTest::Unit.runner = WebsocketTestRunner.new
--- /dev/null
+../../sdk/cli/bin/arv-crunch-job
\ No newline at end of file
--- /dev/null
+package main
+
+import (
+ "bufio"
+ "bytes"
+ "errors"
+ "flag"
+ "fmt"
+ "io"
+ "io/ioutil"
+ "log"
+ "os"
+ "os/exec"
+ "os/signal"
+ "strconv"
+ "strings"
+ "syscall"
+ "time"
+)
+
+/*
+#include <unistd.h>
+#include <sys/types.h>
+#include <pwd.h>
+#include <stdlib.h>
+*/
+import "C"
+
+// The above block of magic allows us to look up user_hz via _SC_CLK_TCK.
+
+type Cgroup struct {
+ root string
+ parent string
+ cid string
+}
+
+func CopyPipeToChan(in io.Reader, out chan string, done chan<- bool) {
+ s := bufio.NewScanner(in)
+ for s.Scan() {
+ out <- s.Text()
+ }
+ done <- true
+}
+
+func CopyChanToPipe(in <-chan string, out io.Writer) {
+ for s := range in {
+ fmt.Fprintln(out, s)
+ }
+}
+
+var logChan chan string
+func LogPrintf(format string, args ...interface{}) {
+ if logChan == nil {
+ return
+ }
+ logChan <- fmt.Sprintf("crunchstat: " + format, args...)
+}
+
+func ReadAllOrWarn(in *os.File) ([]byte, error) {
+ content, err := ioutil.ReadAll(in)
+ if err != nil {
+ LogPrintf("read %s: %s", in.Name(), err)
+ }
+ return content, err
+}
+
+var reportedStatFile = map[string]string{}
+
+// Open the cgroup stats file in /sys/fs corresponding to the target
+// cgroup, and return an *os.File. If no stats file is available,
+// return nil.
+//
+// TODO: Instead of trying all options, choose a process in the
+// container, and read /proc/PID/cgroup to determine the appropriate
+// cgroup root for the given statgroup. (This will avoid falling back
+// to host-level stats during container setup and teardown.)
+func OpenStatFile(cgroup Cgroup, statgroup string, stat string) (*os.File, error) {
+ var paths = []string{
+ fmt.Sprintf("%s/%s/%s/%s/%s", cgroup.root, statgroup, cgroup.parent, cgroup.cid, stat),
+ fmt.Sprintf("%s/%s/%s/%s", cgroup.root, cgroup.parent, cgroup.cid, stat),
+ fmt.Sprintf("%s/%s/%s", cgroup.root, statgroup, stat),
+ fmt.Sprintf("%s/%s", cgroup.root, stat),
+ }
+ var path string
+ var file *os.File
+ var err error
+ for _, path = range paths {
+ file, err = os.Open(path)
+ if err == nil {
+ break
+ } else {
+ path = ""
+ }
+ }
+ if pathWas, ok := reportedStatFile[stat]; !ok || pathWas != path {
+ // Log whenever we start using a new/different cgroup
+ // stat file for a given statistic. This typically
+ // happens 1 to 3 times per statistic, depending on
+ // whether we happen to collect stats [a] before any
+ // processes have been created in the container and
+ // [b] after all contained processes have exited.
+ reportedStatFile[stat] = path
+ if path == "" {
+ LogPrintf("did not find stats file: stat %s, statgroup %s, cid %s, parent %s, root %s", stat, statgroup, cgroup.cid, cgroup.parent, cgroup.root)
+ } else {
+ LogPrintf("reading stats from %s", path)
+ }
+ }
+ return file, err
+}
+
+func GetContainerNetStats(cgroup Cgroup) (io.Reader, error) {
+ procsFile, err := OpenStatFile(cgroup, "cpuacct", "cgroup.procs")
+ if err != nil {
+ return nil, err
+ }
+ defer procsFile.Close()
+ reader := bufio.NewScanner(procsFile)
+ for reader.Scan() {
+ taskPid := reader.Text()
+ statsFilename := fmt.Sprintf("/proc/%s/net/dev", taskPid)
+ stats, err := ioutil.ReadFile(statsFilename)
+ if err != nil {
+ LogPrintf("read %s: %s", statsFilename, err)
+ continue
+ }
+ return strings.NewReader(string(stats)), nil
+ }
+ return nil, errors.New("Could not read stats for any proc in container")
+}
+
+type IoSample struct {
+ sampleTime time.Time
+ txBytes int64
+ rxBytes int64
+}
+
+func DoBlkIoStats(cgroup Cgroup, lastSample map[string]IoSample) {
+ c, err := OpenStatFile(cgroup, "blkio", "blkio.io_service_bytes")
+ if err != nil {
+ return
+ }
+ defer c.Close()
+ b := bufio.NewScanner(c)
+ var sampleTime = time.Now()
+ newSamples := make(map[string]IoSample)
+ for b.Scan() {
+ var device, op string
+ var val int64
+ if _, err := fmt.Sscanf(string(b.Text()), "%s %s %d", &device, &op, &val); err != nil {
+ continue
+ }
+ var thisSample IoSample
+ var ok bool
+ if thisSample, ok = newSamples[device]; !ok {
+ thisSample = IoSample{sampleTime, -1, -1}
+ }
+ switch op {
+ case "Read":
+ thisSample.rxBytes = val
+ case "Write":
+ thisSample.txBytes = val
+ }
+ newSamples[device] = thisSample
+ }
+ for dev, sample := range newSamples {
+ if sample.txBytes < 0 || sample.rxBytes < 0 {
+ continue
+ }
+ delta := ""
+ if prev, ok := lastSample[dev]; ok {
+ delta = fmt.Sprintf(" -- interval %.4f seconds %d write %d read",
+ sample.sampleTime.Sub(prev.sampleTime).Seconds(),
+ sample.txBytes-prev.txBytes,
+ sample.rxBytes-prev.rxBytes)
+ }
+ LogPrintf("blkio:%s %d write %d read%s", dev, sample.txBytes, sample.rxBytes, delta)
+ lastSample[dev] = sample
+ }
+}
+
+type MemSample struct {
+ sampleTime time.Time
+ memStat map[string]int64
+}
+
+func DoMemoryStats(cgroup Cgroup) {
+ c, err := OpenStatFile(cgroup, "memory", "memory.stat")
+ if err != nil {
+ return
+ }
+ defer c.Close()
+ b := bufio.NewScanner(c)
+ thisSample := MemSample{time.Now(), make(map[string]int64)}
+ wantStats := [...]string{"cache", "swap", "pgmajfault", "rss"}
+ for b.Scan() {
+ var stat string
+ var val int64
+ if _, err := fmt.Sscanf(string(b.Text()), "%s %d", &stat, &val); err != nil {
+ continue
+ }
+ thisSample.memStat[stat] = val
+ }
+ var outstat bytes.Buffer
+ for _, key := range wantStats {
+ if val, ok := thisSample.memStat[key]; ok {
+ outstat.WriteString(fmt.Sprintf(" %d %s", val, key))
+ }
+ }
+ LogPrintf("mem%s", outstat.String())
+}
+
+func DoNetworkStats(cgroup Cgroup, lastSample map[string]IoSample) {
+ sampleTime := time.Now()
+ stats, err := GetContainerNetStats(cgroup)
+ if err != nil {
+ return
+ }
+
+ scanner := bufio.NewScanner(stats)
+ for scanner.Scan() {
+ var ifName string
+ var rx, tx int64
+ words := strings.Fields(scanner.Text())
+ if len(words) != 17 {
+ // Skip lines with wrong format
+ continue
+ }
+ ifName = strings.TrimRight(words[0], ":")
+ if ifName == "lo" || ifName == "" {
+ // Skip loopback interface and lines with wrong format
+ continue
+ }
+ if tx, err = strconv.ParseInt(words[9], 10, 64); err != nil {
+ continue
+ }
+ if rx, err = strconv.ParseInt(words[1], 10, 64); err != nil {
+ continue
+ }
+ nextSample := IoSample{}
+ nextSample.sampleTime = sampleTime
+ nextSample.txBytes = tx
+ nextSample.rxBytes = rx
+ var delta string
+ if prev, ok := lastSample[ifName]; ok {
+ interval := nextSample.sampleTime.Sub(prev.sampleTime).Seconds()
+ delta = fmt.Sprintf(" -- interval %.4f seconds %d tx %d rx",
+ interval,
+ tx-prev.txBytes,
+ rx-prev.rxBytes)
+ }
+ LogPrintf("net:%s %d tx %d rx%s", ifName, tx, rx, delta)
+ lastSample[ifName] = nextSample
+ }
+}
+
+type CpuSample struct {
+ hasData bool // to distinguish the zero value from real data
+ sampleTime time.Time
+ user float64
+ sys float64
+ cpus int64
+}
+
+// Return the number of CPUs available in the container. Return 0 if
+// we can't figure out the real number of CPUs.
+func GetCpuCount(cgroup Cgroup) int64 {
+ cpusetFile, err := OpenStatFile(cgroup, "cpuset", "cpuset.cpus")
+ if err != nil {
+ return 0
+ }
+ defer cpusetFile.Close()
+ b, err := ReadAllOrWarn(cpusetFile)
+ sp := strings.Split(string(b), ",")
+ cpus := int64(0)
+ for _, v := range sp {
+ var min, max int64
+ n, _ := fmt.Sscanf(v, "%d-%d", &min, &max)
+ if n == 2 {
+ cpus += (max - min) + 1
+ } else {
+ cpus += 1
+ }
+ }
+ return cpus
+}
+
+func DoCpuStats(cgroup Cgroup, lastSample *CpuSample) {
+ statFile, err := OpenStatFile(cgroup, "cpuacct", "cpuacct.stat")
+ if err != nil {
+ return
+ }
+ defer statFile.Close()
+ b, err := ReadAllOrWarn(statFile)
+ if err != nil {
+ return
+ }
+
+ nextSample := CpuSample{true, time.Now(), 0, 0, GetCpuCount(cgroup)}
+ var userTicks, sysTicks int64
+ fmt.Sscanf(string(b), "user %d\nsystem %d", &userTicks, &sysTicks)
+ user_hz := float64(C.sysconf(C._SC_CLK_TCK))
+ nextSample.user = float64(userTicks) / user_hz
+ nextSample.sys = float64(sysTicks) / user_hz
+
+ delta := ""
+ if lastSample.hasData {
+ delta = fmt.Sprintf(" -- interval %.4f seconds %.4f user %.4f sys",
+ nextSample.sampleTime.Sub(lastSample.sampleTime).Seconds(),
+ nextSample.user-lastSample.user,
+ nextSample.sys-lastSample.sys)
+ }
+ LogPrintf("cpu %.4f user %.4f sys %d cpus%s",
+ nextSample.user, nextSample.sys, nextSample.cpus, delta)
+ *lastSample = nextSample
+}
+
+func PollCgroupStats(cgroup Cgroup, poll int64, stop_poll_chan <-chan bool) {
+ var lastNetSample = map[string]IoSample{}
+ var lastDiskSample = map[string]IoSample{}
+ var lastCpuSample = CpuSample{}
+
+ poll_chan := make(chan bool, 1)
+ go func() {
+ // Send periodic poll events.
+ poll_chan <- true
+ for {
+ time.Sleep(time.Duration(poll) * time.Millisecond)
+ poll_chan <- true
+ }
+ }()
+ for {
+ select {
+ case <-stop_poll_chan:
+ return
+ case <-poll_chan:
+ // Emit stats, then select again.
+ }
+ DoMemoryStats(cgroup)
+ DoCpuStats(cgroup, &lastCpuSample)
+ DoBlkIoStats(cgroup, lastDiskSample)
+ DoNetworkStats(cgroup, lastNetSample)
+ }
+}
+
+func run(logger *log.Logger) error {
+
+ var (
+ cgroup_root string
+ cgroup_parent string
+ cgroup_cidfile string
+ wait int64
+ poll int64
+ )
+
+ flag.StringVar(&cgroup_root, "cgroup-root", "", "Root of cgroup tree")
+ flag.StringVar(&cgroup_parent, "cgroup-parent", "", "Name of container parent under cgroup")
+ flag.StringVar(&cgroup_cidfile, "cgroup-cid", "", "Path to container id file")
+ flag.Int64Var(&wait, "wait", 5, "Maximum time (in seconds) to wait for cid file to show up")
+ flag.Int64Var(&poll, "poll", 1000, "Polling frequency, in milliseconds")
+
+ flag.Parse()
+
+ if cgroup_root == "" {
+ logger.Fatal("Must provide -cgroup-root")
+ }
+
+ logChan = make(chan string, 1)
+ defer close(logChan)
+ finish_chan := make(chan bool)
+ defer close(finish_chan)
+
+ go CopyChanToPipe(logChan, os.Stderr)
+
+ var cmd *exec.Cmd
+
+ if len(flag.Args()) > 0 {
+ // Set up subprocess
+ cmd = exec.Command(flag.Args()[0], flag.Args()[1:]...)
+
+ logger.Print("Running ", flag.Args())
+
+ // Child process will use our stdin and stdout pipes
+ // (we close our copies below)
+ cmd.Stdin = os.Stdin
+ cmd.Stdout = os.Stdout
+
+ // Forward SIGINT and SIGTERM to inner process
+ term := make(chan os.Signal, 1)
+ go func(sig <-chan os.Signal) {
+ catch := <-sig
+ if cmd.Process != nil {
+ cmd.Process.Signal(catch)
+ }
+ logger.Print("caught signal: ", catch)
+ }(term)
+ signal.Notify(term, syscall.SIGTERM)
+ signal.Notify(term, syscall.SIGINT)
+
+ // Funnel stderr through our channel
+ stderr_pipe, err := cmd.StderrPipe()
+ if err != nil {
+ logger.Fatal(err)
+ }
+ go CopyPipeToChan(stderr_pipe, logChan, finish_chan)
+
+ // Run subprocess
+ if err := cmd.Start(); err != nil {
+ logger.Fatal(err)
+ }
+
+ // Close stdin/stdout in this (parent) process
+ os.Stdin.Close()
+ os.Stdout.Close()
+ }
+
+ // Read the cid file
+ var container_id string
+ if cgroup_cidfile != "" {
+ // wait up to 'wait' seconds for the cid file to appear
+ ok := false
+ var i time.Duration
+ for i = 0; i < time.Duration(wait)*time.Second; i += (100 * time.Millisecond) {
+ cid, err := ioutil.ReadFile(cgroup_cidfile)
+ if err == nil && len(cid) > 0 {
+ ok = true
+ container_id = string(cid)
+ break
+ }
+ time.Sleep(100 * time.Millisecond)
+ }
+ if !ok {
+ logger.Printf("Could not read cid file %s", cgroup_cidfile)
+ }
+ }
+
+ stop_poll_chan := make(chan bool, 1)
+ cgroup := Cgroup{cgroup_root, cgroup_parent, container_id}
+ go PollCgroupStats(cgroup, poll, stop_poll_chan)
+
+ // When the child exits, tell the polling goroutine to stop.
+ defer func() { stop_poll_chan <- true }()
+
+ // Wait for CopyPipeToChan to consume child's stderr pipe
+ <-finish_chan
+
+ return cmd.Wait()
+}
+
+func main() {
+ logger := log.New(os.Stderr, "crunchstat: ", 0)
+ if err := run(logger); err != nil {
+ if exiterr, ok := err.(*exec.ExitError); ok {
+ // The program has exited with an exit code != 0
+
+ // This works on both Unix and
+ // Windows. Although package syscall is
+ // generally platform dependent, WaitStatus is
+ // defined for both Unix and Windows and in
+ // both cases has an ExitStatus() method with
+ // the same signature.
+ if status, ok := exiterr.Sys().(syscall.WaitStatus); ok {
+ os.Exit(status.ExitStatus())
+ }
+ } else {
+ logger.Fatalf("cmd.Wait: %v", err)
+ }
+ }
+}
--- /dev/null
+package main
+
+import (
+ "os"
+ "regexp"
+ "testing"
+)
+
+func TestReadAllOrWarnFail(t *testing.T) {
+ logChan = make(chan string)
+ go func() {
+ defer close(logChan)
+ // The special file /proc/self/mem can be opened for
+ // reading, but reading from byte 0 returns an error.
+ f, err := os.Open("/proc/self/mem")
+ if err != nil {
+ t.Fatalf("Opening /proc/self/mem: %s", err)
+ }
+ if x, err := ReadAllOrWarn(f); err == nil {
+ t.Fatalf("Expected error, got %v", x)
+ }
+ }()
+ if _, ok := <-logChan; !ok {
+ t.Fatalf("Expected error message about nonexistent file")
+ }
+ if msg, ok := <-logChan; ok {
+ t.Fatalf("Expected channel to close, got %s", msg)
+ }
+}
+
+func TestReadAllOrWarnSuccess(t *testing.T) {
+ logChan = make(chan string)
+ go func() {
+ defer close(logChan)
+ f, err := os.Open("./crunchstat_test.go")
+ if err != nil {
+ t.Fatalf("Opening ./crunchstat_test.go: %s", err)
+ }
+ data, err := ReadAllOrWarn(f)
+ if err != nil {
+ t.Fatalf("got error %s", err)
+ }
+ if matched, err := regexp.MatchString("^package main\n", string(data)); err != nil || !matched {
+ t.Fatalf("data failed regexp: %s", err)
+ }
+ }()
+ if msg, ok := <-logChan; ok {
+ t.Fatalf("Expected channel to close, got %s", msg)
+ }
+}
--- /dev/null
+#! /usr/bin/env python
+
+import arvados
+
+import argparse
+import cgi
+import csv
+import json
+import logging
+import math
+import pprint
+import re
+import threading
+import urllib2
+
+from BaseHTTPServer import HTTPServer, BaseHTTPRequestHandler
+from collections import defaultdict, Counter
+from functools import partial
+from operator import itemgetter
+from SocketServer import ThreadingMixIn
+
+arv = arvados.api('v1')
+
+# Adapted from http://stackoverflow.com/questions/4180980/formatting-data-quantity-capacity-as-string
+byteunits = ('B', 'KiB', 'MiB', 'GiB', 'TiB', 'PiB', 'EiB', 'ZiB', 'YiB')
+def fileSizeFormat(value):
+ exponent = 0 if value == 0 else int(math.log(value, 1024))
+ return "%7.2f %-3s" % (float(value) / pow(1024, exponent),
+ byteunits[exponent])
+
+def percentageFloor(x):
+ """ Returns a float which is the input rounded down to the neared 0.01.
+
+e.g. precentageFloor(0.941354) = 0.94
+"""
+ return math.floor(x*100) / 100.0
+
+
+def byteSizeFromValidUuid(valid_uuid):
+ return int(valid_uuid.split('+')[1])
+
+class maxdict(dict):
+ """A dictionary that holds the largest value entered for each key."""
+ def addValue(self, key, value):
+ dict.__setitem__(self, key, max(dict.get(self, key), value))
+ def addValues(self, kv_pairs):
+ for key,value in kv_pairs:
+ self.addValue(key, value)
+ def addDict(self, d):
+ self.addValues(d.items())
+
+class CollectionInfo:
+ DEFAULT_PERSISTER_REPLICATION_LEVEL=2
+ all_by_uuid = {}
+
+ def __init__(self, uuid):
+ if CollectionInfo.all_by_uuid.has_key(uuid):
+ raise ValueError('Collection for uuid "%s" already exists.' % uuid)
+ self.uuid = uuid
+ self.block_uuids = set() # uuids of keep blocks in this collection
+ self.reader_uuids = set() # uuids of users who can read this collection
+ self.persister_uuids = set() # uuids of users who want this collection saved
+ # map from user uuid to replication level they desire
+ self.persister_replication = maxdict()
+
+ # The whole api response in case we need anything else later.
+ self.api_response = []
+ CollectionInfo.all_by_uuid[uuid] = self
+
+ def byteSize(self):
+ return sum(map(byteSizeFromValidUuid, self.block_uuids))
+
+ def __str__(self):
+ return ('CollectionInfo uuid: %s\n'
+ ' %d block(s) containing %s\n'
+ ' reader_uuids: %s\n'
+ ' persister_replication: %s' %
+ (self.uuid,
+ len(self.block_uuids),
+ fileSizeFormat(self.byteSize()),
+ pprint.pformat(self.reader_uuids, indent = 15),
+ pprint.pformat(self.persister_replication, indent = 15)))
+
+ @staticmethod
+ def get(uuid):
+ if not CollectionInfo.all_by_uuid.has_key(uuid):
+ CollectionInfo(uuid)
+ return CollectionInfo.all_by_uuid[uuid]
+
+
+def extractUuid(candidate):
+ """ Returns a canonical (hash+size) uuid from a valid uuid, or None if candidate is not a valid uuid."""
+ match = re.match('([0-9a-fA-F]{32}\+[0-9]+)(\+[^+]+)*$', candidate)
+ return match and match.group(1)
+
+def checkUserIsAdmin():
+ current_user = arv.users().current().execute()
+
+ if not current_user['is_admin']:
+ log.warning('Current user %s (%s - %s) does not have '
+ 'admin access and will not see much of the data.',
+ current_user['full_name'],
+ current_user['email'],
+ current_user['uuid'])
+ if args.require_admin_user:
+ log.critical('Exiting, rerun with --no-require-admin-user '
+ 'if you wish to continue.')
+ exit(1)
+
+def buildCollectionsList():
+ if args.uuid:
+ return [args.uuid,]
+ else:
+ collections_list_response = arv.collections().list(limit=args.max_api_results).execute()
+
+ print ('Returned %d of %d collections.' %
+ (len(collections_list_response['items']),
+ collections_list_response['items_available']))
+
+ return [item['uuid'] for item in collections_list_response['items']]
+
+
+def readCollections(collection_uuids):
+ for collection_uuid in collection_uuids:
+ collection_block_uuids = set()
+ collection_response = arv.collections().get(uuid=collection_uuid).execute()
+ collection_info = CollectionInfo.get(collection_uuid)
+ collection_info.api_response = collection_response
+ manifest_lines = collection_response['manifest_text'].split('\n')
+
+ if args.verbose:
+ print 'Manifest text for %s:' % collection_uuid
+ pprint.pprint(manifest_lines)
+
+ for manifest_line in manifest_lines:
+ if manifest_line:
+ manifest_tokens = manifest_line.split(' ')
+ if args.verbose:
+ print 'manifest tokens: ' + pprint.pformat(manifest_tokens)
+ stream_name = manifest_tokens[0]
+
+ line_block_uuids = set(filter(None,
+ [extractUuid(candidate)
+ for candidate in manifest_tokens[1:]]))
+ collection_info.block_uuids.update(line_block_uuids)
+
+ # file_tokens = [token
+ # for token in manifest_tokens[1:]
+ # if extractUuid(token) is None]
+
+ # # Sort file tokens by start position in case they aren't already
+ # file_tokens.sort(key=lambda file_token: int(file_token.split(':')[0]))
+
+ # if args.verbose:
+ # print 'line_block_uuids: ' + pprint.pformat(line_block_uuids)
+ # print 'file_tokens: ' + pprint.pformat(file_tokens)
+
+
+def readLinks():
+ link_classes = set()
+
+ for collection_uuid,collection_info in CollectionInfo.all_by_uuid.items():
+ # TODO(misha): We may not be seing all the links, but since items
+ # available does not return an accurate number, I don't knos how
+ # to confirm that we saw all of them.
+ collection_links_response = arv.links().list(where={'head_uuid':collection_uuid}).execute()
+ link_classes.update([link['link_class'] for link in collection_links_response['items']])
+ for link in collection_links_response['items']:
+ if link['link_class'] == 'permission':
+ collection_info.reader_uuids.add(link['tail_uuid'])
+ elif link['link_class'] == 'resources':
+ replication_level = link['properties'].get(
+ 'replication',
+ CollectionInfo.DEFAULT_PERSISTER_REPLICATION_LEVEL)
+ collection_info.persister_replication.addValue(
+ link['tail_uuid'],
+ replication_level)
+ collection_info.persister_uuids.add(link['tail_uuid'])
+
+ print 'Found the following link classes:'
+ pprint.pprint(link_classes)
+
+def reportMostPopularCollections():
+ most_popular_collections = sorted(
+ CollectionInfo.all_by_uuid.values(),
+ key=lambda info: len(info.reader_uuids) + 10 * len(info.persister_replication),
+ reverse=True)[:10]
+
+ print 'Most popular Collections:'
+ for collection_info in most_popular_collections:
+ print collection_info
+
+
+def buildMaps():
+ for collection_uuid,collection_info in CollectionInfo.all_by_uuid.items():
+ # Add the block holding the manifest itself for all calculations
+ block_uuids = collection_info.block_uuids.union([collection_uuid,])
+ for block_uuid in block_uuids:
+ block_to_collections[block_uuid].add(collection_uuid)
+ block_to_readers[block_uuid].update(collection_info.reader_uuids)
+ block_to_persisters[block_uuid].update(collection_info.persister_uuids)
+ block_to_persister_replication[block_uuid].addDict(
+ collection_info.persister_replication)
+ for reader_uuid in collection_info.reader_uuids:
+ reader_to_collections[reader_uuid].add(collection_uuid)
+ reader_to_blocks[reader_uuid].update(block_uuids)
+ for persister_uuid in collection_info.persister_uuids:
+ persister_to_collections[persister_uuid].add(collection_uuid)
+ persister_to_blocks[persister_uuid].update(block_uuids)
+
+
+def itemsByValueLength(original):
+ return sorted(original.items(),
+ key=lambda item:len(item[1]),
+ reverse=True)
+
+
+def reportBusiestUsers():
+ busiest_readers = itemsByValueLength(reader_to_collections)
+ print 'The busiest readers are:'
+ for reader,collections in busiest_readers:
+ print '%s reading %d collections.' % (reader, len(collections))
+ busiest_persisters = itemsByValueLength(persister_to_collections)
+ print 'The busiest persisters are:'
+ for persister,collections in busiest_persisters:
+ print '%s reading %d collections.' % (persister, len(collections))
+
+
+def blockDiskUsage(block_uuid):
+ """Returns the disk usage of a block given its uuid.
+
+ Will return 0 before reading the contents of the keep servers.
+ """
+ return byteSizeFromValidUuid(block_uuid) * block_to_replication[block_uuid]
+
+def blockPersistedUsage(user_uuid, block_uuid):
+ return (byteSizeFromValidUuid(block_uuid) *
+ block_to_persister_replication[block_uuid].get(user_uuid, 0))
+
+memo_computeWeightedReplicationCosts = {}
+def computeWeightedReplicationCosts(replication_levels):
+ """Computes the relative cost of varied replication levels.
+
+ replication_levels: a tuple of integers representing the desired
+ replication level. If n users want a replication level of x then x
+ should appear n times in replication_levels.
+
+ Returns a dictionary from replication level to cost.
+
+ The basic thinking is that the cost of replicating at level x should
+ be shared by everyone who wants replication of level x or higher.
+
+ For example, if we have two users who want 1 copy, one user who
+ wants 3 copies and two users who want 6 copies:
+ the input would be [1, 1, 3, 6, 6] (or any permutation)
+
+ The cost of the first copy is shared by all 5 users, so they each
+ pay 1 copy / 5 users = 0.2.
+ The cost of the second and third copies shared by 3 users, so they
+ each pay 2 copies / 3 users = 0.67 (plus the above costs)
+ The cost of the fourth, fifth and sixth copies is shared by two
+ users, so they each pay 3 copies / 2 users = 1.5 (plus the above costs)
+
+ Here are some other examples:
+ computeWeightedReplicationCosts([1,]) -> {1:1.0}
+ computeWeightedReplicationCosts([2,]) -> {2:2.0}
+ computeWeightedReplicationCosts([1,1]) -> {1:0.5}
+ computeWeightedReplicationCosts([2,2]) -> {1:1.0}
+ computeWeightedReplicationCosts([1,2]) -> {1:0.5,2:1.5}
+ computeWeightedReplicationCosts([1,3]) -> {1:0.5,2:2.5}
+ computeWeightedReplicationCosts([1,3,6,6,10]) -> {1:0.2,3:0.7,6:1.7,10:5.7}
+ """
+ replication_level_counts = sorted(Counter(replication_levels).items())
+
+ memo_key = str(replication_level_counts)
+
+ if not memo_key in memo_computeWeightedReplicationCosts:
+ last_level = 0
+ current_cost = 0
+ total_interested = float(sum(map(itemgetter(1), replication_level_counts)))
+ cost_for_level = {}
+ for replication_level, count in replication_level_counts:
+ copies_added = replication_level - last_level
+ # compute marginal cost from last level and add it to the last cost
+ current_cost += copies_added / total_interested
+ cost_for_level[replication_level] = current_cost
+ # update invariants
+ last_level = replication_level
+ total_interested -= count
+ memo_computeWeightedReplicationCosts[memo_key] = cost_for_level
+
+ return memo_computeWeightedReplicationCosts[memo_key]
+
+def blockPersistedWeightedUsage(user_uuid, block_uuid):
+ persister_replication_for_block = block_to_persister_replication[block_uuid]
+ user_replication = persister_replication_for_block[user_uuid]
+ return (
+ byteSizeFromValidUuid(block_uuid) *
+ computeWeightedReplicationCosts(
+ persister_replication_for_block.values())[user_replication])
+
+
+def computeUserStorageUsage():
+ for user, blocks in reader_to_blocks.items():
+ user_to_usage[user][UNWEIGHTED_READ_SIZE_COL] = sum(map(
+ byteSizeFromValidUuid,
+ blocks))
+ user_to_usage[user][WEIGHTED_READ_SIZE_COL] = sum(map(
+ lambda block_uuid:(float(byteSizeFromValidUuid(block_uuid))/
+ len(block_to_readers[block_uuid])),
+ blocks))
+ for user, blocks in persister_to_blocks.items():
+ user_to_usage[user][UNWEIGHTED_PERSIST_SIZE_COL] = sum(map(
+ partial(blockPersistedUsage, user),
+ blocks))
+ user_to_usage[user][WEIGHTED_PERSIST_SIZE_COL] = sum(map(
+ partial(blockPersistedWeightedUsage, user),
+ blocks))
+
+def printUserStorageUsage():
+ print ('user: unweighted readable block size, weighted readable block size, '
+ 'unweighted persisted block size, weighted persisted block size:')
+ for user, usage in user_to_usage.items():
+ print ('%s: %s %s %s %s' %
+ (user,
+ fileSizeFormat(usage[UNWEIGHTED_READ_SIZE_COL]),
+ fileSizeFormat(usage[WEIGHTED_READ_SIZE_COL]),
+ fileSizeFormat(usage[UNWEIGHTED_PERSIST_SIZE_COL]),
+ fileSizeFormat(usage[WEIGHTED_PERSIST_SIZE_COL])))
+
+def logUserStorageUsage():
+ for user, usage in user_to_usage.items():
+ body = {}
+ # user could actually represent a user or a group. We don't set
+ # the object_type field since we don't know which we have.
+ body['object_uuid'] = user
+ body['event_type'] = args.user_storage_log_event_type
+ properties = {}
+ properties['read_collections_total_bytes'] = usage[UNWEIGHTED_READ_SIZE_COL]
+ properties['read_collections_weighted_bytes'] = (
+ usage[WEIGHTED_READ_SIZE_COL])
+ properties['persisted_collections_total_bytes'] = (
+ usage[UNWEIGHTED_PERSIST_SIZE_COL])
+ properties['persisted_collections_weighted_bytes'] = (
+ usage[WEIGHTED_PERSIST_SIZE_COL])
+ body['properties'] = properties
+ # TODO(misha): Confirm that this will throw an exception if it
+ # fails to create the log entry.
+ arv.logs().create(body=body).execute()
+
+def getKeepServers():
+ response = arv.keep_disks().list().execute()
+ return [[keep_server['service_host'], keep_server['service_port']]
+ for keep_server in response['items']]
+
+
+def getKeepBlocks(keep_servers):
+ blocks = []
+ for host,port in keep_servers:
+ response = urllib2.urlopen('http://%s:%d/index' % (host, port))
+ server_blocks = [line.split(' ')
+ for line in response.read().split('\n')
+ if line]
+ server_blocks = [(block_id, int(mtime))
+ for block_id, mtime in server_blocks]
+ blocks.append(server_blocks)
+ return blocks
+
+def getKeepStats(keep_servers):
+ MOUNT_COLUMN = 5
+ TOTAL_COLUMN = 1
+ FREE_COLUMN = 3
+ DISK_BLOCK_SIZE = 1024
+ stats = []
+ for host,port in keep_servers:
+ response = urllib2.urlopen('http://%s:%d/status.json' % (host, port))
+
+ parsed_json = json.load(response)
+ df_entries = [line.split()
+ for line in parsed_json['df'].split('\n')
+ if line]
+ keep_volumes = [columns
+ for columns in df_entries
+ if 'keep' in columns[MOUNT_COLUMN]]
+ total_space = DISK_BLOCK_SIZE*sum(map(int,map(itemgetter(TOTAL_COLUMN),
+ keep_volumes)))
+ free_space = DISK_BLOCK_SIZE*sum(map(int,map(itemgetter(FREE_COLUMN),
+ keep_volumes)))
+ stats.append([total_space, free_space])
+ return stats
+
+
+def computeReplication(keep_blocks):
+ for server_blocks in keep_blocks:
+ for block_uuid, _ in server_blocks:
+ block_to_replication[block_uuid] += 1
+ log.debug('Seeing the following replication levels among blocks: %s',
+ str(set(block_to_replication.values())))
+
+
+def computeGarbageCollectionCandidates():
+ for server_blocks in keep_blocks:
+ block_to_latest_mtime.addValues(server_blocks)
+ empty_set = set()
+ garbage_collection_priority = sorted(
+ [(block,mtime)
+ for block,mtime in block_to_latest_mtime.items()
+ if len(block_to_persisters.get(block,empty_set)) == 0],
+ key = itemgetter(1))
+ global garbage_collection_report
+ garbage_collection_report = []
+ cumulative_disk_size = 0
+ for block,mtime in garbage_collection_priority:
+ disk_size = blockDiskUsage(block)
+ cumulative_disk_size += disk_size
+ garbage_collection_report.append(
+ (block,
+ mtime,
+ disk_size,
+ cumulative_disk_size,
+ float(free_keep_space + cumulative_disk_size)/total_keep_space))
+
+ print 'The oldest Garbage Collection Candidates: '
+ pprint.pprint(garbage_collection_report[:20])
+
+
+def outputGarbageCollectionReport(filename):
+ with open(filename, 'wb') as csvfile:
+ gcwriter = csv.writer(csvfile)
+ gcwriter.writerow(['block uuid', 'latest mtime', 'disk size',
+ 'cumulative size', 'disk free'])
+ for line in garbage_collection_report:
+ gcwriter.writerow(line)
+
+def computeGarbageCollectionHistogram():
+ # TODO(misha): Modify this to allow users to specify the number of
+ # histogram buckets through a flag.
+ histogram = []
+ last_percentage = -1
+ for _,mtime,_,_,disk_free in garbage_collection_report:
+ curr_percentage = percentageFloor(disk_free)
+ if curr_percentage > last_percentage:
+ histogram.append( (mtime, curr_percentage) )
+ last_percentage = curr_percentage
+
+ log.info('Garbage collection histogram is: %s', histogram)
+
+ return histogram
+
+
+def logGarbageCollectionHistogram():
+ body = {}
+ # TODO(misha): Decide whether we should specify an object_uuid in
+ # the body and if so, which uuid to use.
+ body['event_type'] = args.block_age_free_space_histogram_log_event_type
+ properties = {}
+ properties['histogram'] = garbage_collection_histogram
+ body['properties'] = properties
+ # TODO(misha): Confirm that this will throw an exception if it
+ # fails to create the log entry.
+ arv.logs().create(body=body).execute()
+
+
+def detectReplicationProblems():
+ blocks_not_in_any_collections.update(
+ set(block_to_replication.keys()).difference(block_to_collections.keys()))
+ underreplicated_persisted_blocks.update(
+ [uuid
+ for uuid, persister_replication in block_to_persister_replication.items()
+ if len(persister_replication) > 0 and
+ block_to_replication[uuid] < max(persister_replication.values())])
+ overreplicated_persisted_blocks.update(
+ [uuid
+ for uuid, persister_replication in block_to_persister_replication.items()
+ if len(persister_replication) > 0 and
+ block_to_replication[uuid] > max(persister_replication.values())])
+
+ log.info('Found %d blocks not in any collections, e.g. %s...',
+ len(blocks_not_in_any_collections),
+ ','.join(list(blocks_not_in_any_collections)[:5]))
+ log.info('Found %d underreplicated blocks, e.g. %s...',
+ len(underreplicated_persisted_blocks),
+ ','.join(list(underreplicated_persisted_blocks)[:5]))
+ log.info('Found %d overreplicated blocks, e.g. %s...',
+ len(overreplicated_persisted_blocks),
+ ','.join(list(overreplicated_persisted_blocks)[:5]))
+
+ # TODO:
+ # Read blocks sorted by mtime
+ # Cache window vs % free space
+ # Collections which candidates will appear in
+ # Youngest underreplicated read blocks that appear in collections.
+ # Report Collections that have blocks which are missing from (or
+ # underreplicated in) keep.
+
+
+# This is the main flow here
+
+parser = argparse.ArgumentParser(description='Report on keep disks.')
+"""The command line argument parser we use.
+
+We only use it in the __main__ block, but leave it outside the block
+in case another package wants to use it or customize it by specifying
+it as a parent to their commandline parser.
+"""
+parser.add_argument('-m',
+ '--max-api-results',
+ type=int,
+ default=5000,
+ help=('The max results to get at once.'))
+parser.add_argument('-p',
+ '--port',
+ type=int,
+ default=9090,
+ help=('The port number to serve on. 0 means no server.'))
+parser.add_argument('-v',
+ '--verbose',
+ help='increase output verbosity',
+ action='store_true')
+parser.add_argument('-u',
+ '--uuid',
+ help='uuid of specific collection to process')
+parser.add_argument('--require-admin-user',
+ action='store_true',
+ default=True,
+ help='Fail if the user is not an admin [default]')
+parser.add_argument('--no-require-admin-user',
+ dest='require_admin_user',
+ action='store_false',
+ help=('Allow users without admin permissions with '
+ 'only a warning.'))
+parser.add_argument('--log-to-workbench',
+ action='store_true',
+ default=False,
+ help='Log findings to workbench')
+parser.add_argument('--no-log-to-workbench',
+ dest='log_to_workbench',
+ action='store_false',
+ help='Don\'t log findings to workbench [default]')
+parser.add_argument('--user-storage-log-event-type',
+ default='user-storage-report',
+ help=('The event type to set when logging user '
+ 'storage usage to workbench.'))
+parser.add_argument('--block-age-free-space-histogram-log-event-type',
+ default='block-age-free-space-histogram',
+ help=('The event type to set when logging user '
+ 'storage usage to workbench.'))
+parser.add_argument('--garbage-collection-file',
+ default='',
+ help=('The file to write a garbage collection report, or '
+ 'leave empty for no report.'))
+
+args = None
+
+# TODO(misha): Think about moving some of this to the __main__ block.
+log = logging.getLogger('arvados.services.datamanager')
+stderr_handler = logging.StreamHandler()
+log.setLevel(logging.INFO)
+stderr_handler.setFormatter(
+ logging.Formatter('%(asctime)-15s %(levelname)-8s %(message)s'))
+log.addHandler(stderr_handler)
+
+# Global Data - don't try this at home
+collection_uuids = []
+
+# These maps all map from uuids to a set of uuids
+block_to_collections = defaultdict(set) # keep blocks
+reader_to_collections = defaultdict(set) # collection(s) for which the user has read access
+persister_to_collections = defaultdict(set) # collection(s) which the user has persisted
+block_to_readers = defaultdict(set)
+block_to_persisters = defaultdict(set)
+block_to_persister_replication = defaultdict(maxdict)
+reader_to_blocks = defaultdict(set)
+persister_to_blocks = defaultdict(set)
+
+UNWEIGHTED_READ_SIZE_COL = 0
+WEIGHTED_READ_SIZE_COL = 1
+UNWEIGHTED_PERSIST_SIZE_COL = 2
+WEIGHTED_PERSIST_SIZE_COL = 3
+NUM_COLS = 4
+user_to_usage = defaultdict(lambda : [0,]*NUM_COLS)
+
+keep_servers = []
+keep_blocks = []
+keep_stats = []
+total_keep_space = 0
+free_keep_space = 0
+
+block_to_replication = defaultdict(lambda: 0)
+block_to_latest_mtime = maxdict()
+
+garbage_collection_report = []
+"""A list of non-persisted blocks, sorted by increasing mtime
+
+Each entry is of the form (block uuid, latest mtime, disk size,
+cumulative size)
+
+* block uuid: The id of the block we want to delete
+* latest mtime: The latest mtime of the block across all keep servers.
+* disk size: The total disk space used by this block (block size
+multiplied by current replication level)
+* cumulative disk size: The sum of this block's disk size and all the
+blocks listed above it
+* disk free: The proportion of our disk space that would be free if we
+deleted this block and all the above. So this is (free disk space +
+cumulative disk size) / total disk capacity
+"""
+
+garbage_collection_histogram = []
+""" Shows the tradeoff of keep block age vs keep disk free space.
+
+Each entry is of the form (mtime, Disk Proportion).
+
+An entry of the form (1388747781, 0.52) means that if we deleted the
+oldest non-presisted blocks until we had 52% of the disk free, then
+all blocks with an mtime greater than 1388747781 would be preserved.
+"""
+
+# Stuff to report on
+blocks_not_in_any_collections = set()
+underreplicated_persisted_blocks = set()
+overreplicated_persisted_blocks = set()
+
+all_data_loaded = False
+
+def loadAllData():
+ checkUserIsAdmin()
+
+ log.info('Building Collection List')
+ global collection_uuids
+ collection_uuids = filter(None, [extractUuid(candidate)
+ for candidate in buildCollectionsList()])
+
+ log.info('Reading Collections')
+ readCollections(collection_uuids)
+
+ if args.verbose:
+ pprint.pprint(CollectionInfo.all_by_uuid)
+
+ log.info('Reading Links')
+ readLinks()
+
+ reportMostPopularCollections()
+
+ log.info('Building Maps')
+ buildMaps()
+
+ reportBusiestUsers()
+
+ log.info('Getting Keep Servers')
+ global keep_servers
+ keep_servers = getKeepServers()
+
+ print keep_servers
+
+ log.info('Getting Blocks from each Keep Server.')
+ global keep_blocks
+ keep_blocks = getKeepBlocks(keep_servers)
+
+ log.info('Getting Stats from each Keep Server.')
+ global keep_stats, total_keep_space, free_keep_space
+ keep_stats = getKeepStats(keep_servers)
+
+ total_keep_space = sum(map(itemgetter(0), keep_stats))
+ free_keep_space = sum(map(itemgetter(1), keep_stats))
+
+ # TODO(misha): Delete this hack when the keep servers are fixed!
+ # This hack deals with the fact that keep servers report each other's disks.
+ total_keep_space /= len(keep_stats)
+ free_keep_space /= len(keep_stats)
+
+ log.info('Total disk space: %s, Free disk space: %s (%d%%).' %
+ (fileSizeFormat(total_keep_space),
+ fileSizeFormat(free_keep_space),
+ 100*free_keep_space/total_keep_space))
+
+ computeReplication(keep_blocks)
+
+ log.info('average replication level is %f',
+ (float(sum(block_to_replication.values())) /
+ len(block_to_replication)))
+
+ computeGarbageCollectionCandidates()
+
+ if args.garbage_collection_file:
+ log.info('Writing garbage Collection report to %s',
+ args.garbage_collection_file)
+ outputGarbageCollectionReport(args.garbage_collection_file)
+
+ global garbage_collection_histogram
+ garbage_collection_histogram = computeGarbageCollectionHistogram()
+
+ if args.log_to_workbench:
+ logGarbageCollectionHistogram()
+
+ detectReplicationProblems()
+
+ computeUserStorageUsage()
+ printUserStorageUsage()
+ if args.log_to_workbench:
+ logUserStorageUsage()
+
+ global all_data_loaded
+ all_data_loaded = True
+
+
+class DataManagerHandler(BaseHTTPRequestHandler):
+ USER_PATH = 'user'
+ COLLECTION_PATH = 'collection'
+ BLOCK_PATH = 'block'
+
+ def userLink(self, uuid):
+ return ('<A HREF="/%(path)s/%(uuid)s">%(uuid)s</A>' %
+ {'uuid': uuid,
+ 'path': DataManagerHandler.USER_PATH})
+
+ def collectionLink(self, uuid):
+ return ('<A HREF="/%(path)s/%(uuid)s">%(uuid)s</A>' %
+ {'uuid': uuid,
+ 'path': DataManagerHandler.COLLECTION_PATH})
+
+ def blockLink(self, uuid):
+ return ('<A HREF="/%(path)s/%(uuid)s">%(uuid)s</A>' %
+ {'uuid': uuid,
+ 'path': DataManagerHandler.BLOCK_PATH})
+
+ def writeTop(self, title):
+ self.wfile.write('<HTML><HEAD><TITLE>%s</TITLE></HEAD>\n<BODY>' % title)
+
+ def writeBottom(self):
+ self.wfile.write('</BODY></HTML>\n')
+
+ def writeHomePage(self):
+ self.send_response(200)
+ self.end_headers()
+ self.writeTop('Home')
+ self.wfile.write('<TABLE>')
+ self.wfile.write('<TR><TH>user'
+ '<TH>unweighted readable block size'
+ '<TH>weighted readable block size'
+ '<TH>unweighted persisted block size'
+ '<TH>weighted persisted block size</TR>\n')
+ for user, usage in user_to_usage.items():
+ self.wfile.write('<TR><TD>%s<TD>%s<TD>%s<TD>%s<TD>%s</TR>\n' %
+ (self.userLink(user),
+ fileSizeFormat(usage[UNWEIGHTED_READ_SIZE_COL]),
+ fileSizeFormat(usage[WEIGHTED_READ_SIZE_COL]),
+ fileSizeFormat(usage[UNWEIGHTED_PERSIST_SIZE_COL]),
+ fileSizeFormat(usage[WEIGHTED_PERSIST_SIZE_COL])))
+ self.wfile.write('</TABLE>\n')
+ self.writeBottom()
+
+ def userExists(self, uuid):
+ # Currently this will return false for a user who exists but
+ # doesn't appear on any manifests.
+ # TODO(misha): Figure out if we need to fix this.
+ return user_to_usage.has_key(uuid)
+
+ def writeUserPage(self, uuid):
+ if not self.userExists(uuid):
+ self.send_error(404,
+ 'User (%s) Not Found.' % cgi.escape(uuid, quote=False))
+ else:
+ # Here we assume that since a user exists, they don't need to be
+ # html escaped.
+ self.send_response(200)
+ self.end_headers()
+ self.writeTop('User %s' % uuid)
+ self.wfile.write('<TABLE>')
+ self.wfile.write('<TR><TH>user'
+ '<TH>unweighted readable block size'
+ '<TH>weighted readable block size'
+ '<TH>unweighted persisted block size'
+ '<TH>weighted persisted block size</TR>\n')
+ usage = user_to_usage[uuid]
+ self.wfile.write('<TR><TD>%s<TD>%s<TD>%s<TD>%s<TD>%s</TR>\n' %
+ (self.userLink(uuid),
+ fileSizeFormat(usage[UNWEIGHTED_READ_SIZE_COL]),
+ fileSizeFormat(usage[WEIGHTED_READ_SIZE_COL]),
+ fileSizeFormat(usage[UNWEIGHTED_PERSIST_SIZE_COL]),
+ fileSizeFormat(usage[WEIGHTED_PERSIST_SIZE_COL])))
+ self.wfile.write('</TABLE>\n')
+ self.wfile.write('<P>Persisting Collections: %s\n' %
+ ', '.join(map(self.collectionLink,
+ persister_to_collections[uuid])))
+ self.wfile.write('<P>Reading Collections: %s\n' %
+ ', '.join(map(self.collectionLink,
+ reader_to_collections[uuid])))
+ self.writeBottom()
+
+ def collectionExists(self, uuid):
+ return CollectionInfo.all_by_uuid.has_key(uuid)
+
+ def writeCollectionPage(self, uuid):
+ if not self.collectionExists(uuid):
+ self.send_error(404,
+ 'Collection (%s) Not Found.' % cgi.escape(uuid, quote=False))
+ else:
+ collection = CollectionInfo.get(uuid)
+ # Here we assume that since a collection exists, its id doesn't
+ # need to be html escaped.
+ self.send_response(200)
+ self.end_headers()
+ self.writeTop('Collection %s' % uuid)
+ self.wfile.write('<H1>Collection %s</H1>\n' % uuid)
+ self.wfile.write('<P>Total size %s (not factoring in replication).\n' %
+ fileSizeFormat(collection.byteSize()))
+ self.wfile.write('<P>Readers: %s\n' %
+ ', '.join(map(self.userLink, collection.reader_uuids)))
+
+ if len(collection.persister_replication) == 0:
+ self.wfile.write('<P>No persisters\n')
+ else:
+ replication_to_users = defaultdict(set)
+ for user,replication in collection.persister_replication.items():
+ replication_to_users[replication].add(user)
+ replication_levels = sorted(replication_to_users.keys())
+
+ self.wfile.write('<P>%d persisters in %d replication level(s) maxing '
+ 'out at %dx replication:\n' %
+ (len(collection.persister_replication),
+ len(replication_levels),
+ replication_levels[-1]))
+
+ # TODO(misha): This code is used twice, let's move it to a method.
+ self.wfile.write('<TABLE><TR><TH>%s</TR>\n' %
+ '<TH>'.join(['Replication Level ' + str(x)
+ for x in replication_levels]))
+ self.wfile.write('<TR>\n')
+ for replication_level in replication_levels:
+ users = replication_to_users[replication_level]
+ self.wfile.write('<TD valign="top">%s\n' % '<BR>\n'.join(
+ map(self.userLink, users)))
+ self.wfile.write('</TR></TABLE>\n')
+
+ replication_to_blocks = defaultdict(set)
+ for block in collection.block_uuids:
+ replication_to_blocks[block_to_replication[block]].add(block)
+ replication_levels = sorted(replication_to_blocks.keys())
+ self.wfile.write('<P>%d blocks in %d replication level(s):\n' %
+ (len(collection.block_uuids), len(replication_levels)))
+ self.wfile.write('<TABLE><TR><TH>%s</TR>\n' %
+ '<TH>'.join(['Replication Level ' + str(x)
+ for x in replication_levels]))
+ self.wfile.write('<TR>\n')
+ for replication_level in replication_levels:
+ blocks = replication_to_blocks[replication_level]
+ self.wfile.write('<TD valign="top">%s\n' % '<BR>\n'.join(blocks))
+ self.wfile.write('</TR></TABLE>\n')
+
+
+ def do_GET(self):
+ if not all_data_loaded:
+ self.send_error(503,
+ 'Sorry, but I am still loading all the data I need.')
+ else:
+ # Removing leading '/' and process request path
+ split_path = self.path[1:].split('/')
+ request_type = split_path[0]
+ log.debug('path (%s) split as %s with request_type %s' % (self.path,
+ split_path,
+ request_type))
+ if request_type == '':
+ self.writeHomePage()
+ elif request_type == DataManagerHandler.USER_PATH:
+ self.writeUserPage(split_path[1])
+ elif request_type == DataManagerHandler.COLLECTION_PATH:
+ self.writeCollectionPage(split_path[1])
+ else:
+ self.send_error(404, 'Unrecognized request path.')
+ return
+
+class ThreadedHTTPServer(ThreadingMixIn, HTTPServer):
+ """Handle requests in a separate thread."""
+
+
+if __name__ == '__main__':
+ args = parser.parse_args()
+
+ if args.port == 0:
+ loadAllData()
+ else:
+ loader = threading.Thread(target = loadAllData, name = 'loader')
+ loader.start()
+
+ server = ThreadedHTTPServer(('localhost', args.port), DataManagerHandler)
+ server.serve_forever()
--- /dev/null
+#! /usr/bin/env python
+
+import datamanager
+import unittest
+
+class TestComputeWeightedReplicationCosts(unittest.TestCase):
+ def test_obvious(self):
+ self.assertEqual(datamanager.computeWeightedReplicationCosts([1,]),
+ {1:1.0})
+
+ def test_simple(self):
+ self.assertEqual(datamanager.computeWeightedReplicationCosts([2,]),
+ {2:2.0})
+
+ def test_even_split(self):
+ self.assertEqual(datamanager.computeWeightedReplicationCosts([1,1]),
+ {1:0.5})
+
+ def test_even_split_bigger(self):
+ self.assertEqual(datamanager.computeWeightedReplicationCosts([2,2]),
+ {2:1.0})
+
+ def test_uneven_split(self):
+ self.assertEqual(datamanager.computeWeightedReplicationCosts([1,2]),
+ {1:0.5, 2:1.5})
+
+ def test_uneven_split_bigger(self):
+ self.assertEqual(datamanager.computeWeightedReplicationCosts([1,3]),
+ {1:0.5, 3:2.5})
+
+ def test_uneven_split_jumble(self):
+ self.assertEqual(datamanager.computeWeightedReplicationCosts([1,3,6,6,10]),
+ {1:0.2, 3:0.7, 6:1.7, 10:5.7})
+
+ def test_documentation_example(self):
+ self.assertEqual(datamanager.computeWeightedReplicationCosts([1,1,3,6,6]),
+ {1:0.2, 3: 0.2 + 2.0 / 3, 6: 0.2 + 2.0 / 3 + 1.5})
+
+
+if __name__ == '__main__':
+ unittest.main()
--- /dev/null
+../../sdk/python/.gitignore
\ No newline at end of file
--- /dev/null
+include README.rst
--- /dev/null
+========================
+Arvados Keep FUSE Driver
+========================
+
+Overview
+--------
+
+This package provides a FUSE driver for Keep, the Arvados_ storage
+system. It allows you to read data from your collections as if they
+were on the local filesystem.
+
+.. _Arvados: https://arvados.org/
+
+Installation
+------------
+
+Installing under your user account
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This method lets you install the package without root access.
+However, other users on the same system won't be able to use it.
+
+1. Run ``pip install --user arvados_fuse``.
+
+2. In your shell configuration, make sure you add ``$HOME/.local/bin``
+ to your PATH environment variable. For example, you could add the
+ command ``PATH=$PATH:$HOME/.local/bin`` to your ``.bashrc`` file.
+
+3. Reload your shell configuration. For example, bash users could run
+ ``source ~/.bashrc``.
+
+Installing on Debian systems
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+1. Add this Arvados repository to your sources list::
+
+ deb http://apt.arvados.org/ wheezy main
+
+2. Update your package list.
+
+3. Install the ``python-arvados-fuse`` package.
+
+Configuration
+-------------
+
+This driver needs two pieces of information to connect to
+Arvados: the DNS name of the API server, and an API authorization
+token. You can set these in environment variables, or the file
+``$HOME/.config/arvados/settings.conf``. `The Arvados user
+documentation
+<http://doc.arvados.org/user/reference/api-tokens.html>`_ describes
+how to find this information in the Arvados Workbench, and install it
+on your system.
+
+Testing and Development
+-----------------------
+
+This package is one part of the Arvados source package, and it has
+integration tests to check interoperability with other Arvados
+components. Our `hacking guide
+<https://arvados.org/projects/arvados/wiki/Hacking_Python_SDK>`_
+describes how to set up a development environment and run tests.
--- /dev/null
+#
+# FUSE driver for Arvados Keep
+#
+
+import os
+import sys
+import llfuse
+import errno
+import stat
+import threading
+import arvados
+import pprint
+import arvados.events
+import re
+import apiclient
+import json
+import logging
+import time
+import _strptime
+import calendar
+import threading
+import itertools
+
+from arvados.util import portable_data_hash_pattern, uuid_pattern, collection_uuid_pattern, group_uuid_pattern, user_uuid_pattern, link_uuid_pattern
+
+_logger = logging.getLogger('arvados.arvados_fuse')
+
+# Match any character which FUSE or Linux cannot accommodate as part
+# of a filename. (If present in a collection filename, they will
+# appear as underscores in the fuse mount.)
+_disallowed_filename_characters = re.compile('[\x00/]')
+
+class SafeApi(object):
+ '''Threadsafe wrapper for API object. This stores and returns a different api
+ object per thread, because httplib2 which underlies apiclient is not
+ threadsafe.
+ '''
+
+ def __init__(self, config):
+ self.host = config.get('ARVADOS_API_HOST')
+ self.api_token = config.get('ARVADOS_API_TOKEN')
+ self.insecure = config.flag_is_true('ARVADOS_API_HOST_INSECURE')
+ self.local = threading.local()
+ self.block_cache = arvados.KeepBlockCache()
+
+ def localapi(self):
+ if 'api' not in self.local.__dict__:
+ self.local.api = arvados.api('v1', False, self.host,
+ self.api_token, self.insecure)
+ return self.local.api
+
+ def localkeep(self):
+ if 'keep' not in self.local.__dict__:
+ self.local.keep = arvados.KeepClient(api_client=self.localapi(), block_cache=self.block_cache)
+ return self.local.keep
+
+ def __getattr__(self, name):
+ # Proxy nonexistent attributes to the local API client.
+ try:
+ return getattr(self.localapi(), name)
+ except AttributeError:
+ return super(SafeApi, self).__getattr__(name)
+
+
+def convertTime(t):
+ '''Parse Arvados timestamp to unix time.'''
+ try:
+ return calendar.timegm(time.strptime(t, "%Y-%m-%dT%H:%M:%SZ"))
+ except (TypeError, ValueError):
+ return 0
+
+def sanitize_filename(dirty):
+ '''Replace disallowed filename characters with harmless "_".'''
+ if dirty is None:
+ return None
+ elif dirty == '':
+ return '_'
+ elif dirty == '.':
+ return '_'
+ elif dirty == '..':
+ return '__'
+ else:
+ return _disallowed_filename_characters.sub('_', dirty)
+
+
+class FreshBase(object):
+ '''Base class for maintaining fresh/stale state to determine when to update.'''
+ def __init__(self):
+ self._stale = True
+ self._poll = False
+ self._last_update = time.time()
+ self._atime = time.time()
+ self._poll_time = 60
+
+ # Mark the value as stale
+ def invalidate(self):
+ self._stale = True
+
+ # Test if the entries dict is stale.
+ def stale(self):
+ if self._stale:
+ return True
+ if self._poll:
+ return (self._last_update + self._poll_time) < self._atime
+ return False
+
+ def fresh(self):
+ self._stale = False
+ self._last_update = time.time()
+
+ def atime(self):
+ return self._atime
+
+class File(FreshBase):
+ '''Base for file objects.'''
+
+ def __init__(self, parent_inode, _mtime=0):
+ super(File, self).__init__()
+ self.inode = None
+ self.parent_inode = parent_inode
+ self._mtime = _mtime
+
+ def size(self):
+ return 0
+
+ def readfrom(self, off, size):
+ return ''
+
+ def mtime(self):
+ return self._mtime
+
+
+class StreamReaderFile(File):
+ '''Wraps a StreamFileReader as a file.'''
+
+ def __init__(self, parent_inode, reader, _mtime):
+ super(StreamReaderFile, self).__init__(parent_inode, _mtime)
+ self.reader = reader
+
+ def size(self):
+ return self.reader.size()
+
+ def readfrom(self, off, size):
+ return self.reader.readfrom(off, size)
+
+ def stale(self):
+ return False
+
+
+class StringFile(File):
+ '''Wrap a simple string as a file'''
+ def __init__(self, parent_inode, contents, _mtime):
+ super(StringFile, self).__init__(parent_inode, _mtime)
+ self.contents = contents
+
+ def size(self):
+ return len(self.contents)
+
+ def readfrom(self, off, size):
+ return self.contents[off:(off+size)]
+
+
+class ObjectFile(StringFile):
+ '''Wrap a dict as a serialized json object.'''
+
+ def __init__(self, parent_inode, obj):
+ super(ObjectFile, self).__init__(parent_inode, "", 0)
+ self.uuid = obj['uuid']
+ self.update(obj)
+
+ def update(self, obj):
+ self._mtime = convertTime(obj['modified_at']) if 'modified_at' in obj else 0
+ self.contents = json.dumps(obj, indent=4, sort_keys=True) + "\n"
+
+
+class Directory(FreshBase):
+ '''Generic directory object, backed by a dict.
+ Consists of a set of entries with the key representing the filename
+ and the value referencing a File or Directory object.
+ '''
+
+ def __init__(self, parent_inode):
+ super(Directory, self).__init__()
+
+ '''parent_inode is the integer inode number'''
+ self.inode = None
+ if not isinstance(parent_inode, int):
+ raise Exception("parent_inode should be an int")
+ self.parent_inode = parent_inode
+ self._entries = {}
+ self._mtime = time.time()
+
+ # Overriden by subclasses to implement logic to update the entries dict
+ # when the directory is stale
+ def update(self):
+ pass
+
+ # Only used when computing the size of the disk footprint of the directory
+ # (stub)
+ def size(self):
+ return 0
+
+ def checkupdate(self):
+ if self.stale():
+ try:
+ self.update()
+ except apiclient.errors.HttpError as e:
+ _logger.debug(e)
+
+ def __getitem__(self, item):
+ self.checkupdate()
+ return self._entries[item]
+
+ def items(self):
+ self.checkupdate()
+ return self._entries.items()
+
+ def __iter__(self):
+ self.checkupdate()
+ return self._entries.iterkeys()
+
+ def __contains__(self, k):
+ self.checkupdate()
+ return k in self._entries
+
+ def merge(self, items, fn, same, new_entry):
+ '''Helper method for updating the contents of the directory. Takes a list
+ describing the new contents of the directory, reuse entries that are
+ the same in both the old and new lists, create new entries, and delete
+ old entries missing from the new list.
+
+ items: iterable with new directory contents
+
+ fn: function to take an entry in 'items' and return the desired file or
+ directory name, or None if this entry should be skipped
+
+ same: function to compare an existing entry (a File or Directory
+ object) with an entry in the items list to determine whether to keep
+ the existing entry.
+
+ new_entry: function to create a new directory entry (File or Directory
+ object) from an entry in the items list.
+
+ '''
+
+ oldentries = self._entries
+ self._entries = {}
+ changed = False
+ for i in items:
+ name = sanitize_filename(fn(i))
+ if name:
+ if name in oldentries and same(oldentries[name], i):
+ # move existing directory entry over
+ self._entries[name] = oldentries[name]
+ del oldentries[name]
+ else:
+ # create new directory entry
+ ent = new_entry(i)
+ if ent is not None:
+ self._entries[name] = self.inodes.add_entry(ent)
+ changed = True
+
+ # delete any other directory entries that were not in found in 'items'
+ for i in oldentries:
+ llfuse.invalidate_entry(self.inode, str(i))
+ self.inodes.del_entry(oldentries[i])
+ changed = True
+
+ if changed:
+ self._mtime = time.time()
+
+ self.fresh()
+
+ def clear(self):
+ '''Delete all entries'''
+ oldentries = self._entries
+ self._entries = {}
+ for n in oldentries:
+ if isinstance(n, Directory):
+ n.clear()
+ llfuse.invalidate_entry(self.inode, str(n))
+ self.inodes.del_entry(oldentries[n])
+ self.invalidate()
+
+ def mtime(self):
+ return self._mtime
+
+
+class CollectionDirectory(Directory):
+ '''Represents the root of a directory tree holding a collection.'''
+
+ def __init__(self, parent_inode, inodes, api, num_retries, collection):
+ super(CollectionDirectory, self).__init__(parent_inode)
+ self.inodes = inodes
+ self.api = api
+ self.num_retries = num_retries
+ self.collection_object_file = None
+ self.collection_object = None
+ if isinstance(collection, dict):
+ self.collection_locator = collection['uuid']
+ else:
+ self.collection_locator = collection
+
+ def same(self, i):
+ return i['uuid'] == self.collection_locator or i['portable_data_hash'] == self.collection_locator
+
+ def new_collection(self, new_collection_object, coll_reader):
+ self.collection_object = new_collection_object
+
+ if self.collection_object_file is not None:
+ self.collection_object_file.update(self.collection_object)
+
+ self.clear()
+ for s in coll_reader.all_streams():
+ cwd = self
+ for part in s.name().split('/'):
+ if part != '' and part != '.':
+ partname = sanitize_filename(part)
+ if partname not in cwd._entries:
+ cwd._entries[partname] = self.inodes.add_entry(Directory(cwd.inode))
+ cwd = cwd._entries[partname]
+ for k, v in s.files().items():
+ cwd._entries[sanitize_filename(k)] = self.inodes.add_entry(StreamReaderFile(cwd.inode, v, self.mtime()))
+
+ def update(self):
+ try:
+ if self.collection_object is not None and portable_data_hash_pattern.match(self.collection_locator):
+ return True
+
+ with llfuse.lock_released:
+ coll_reader = arvados.CollectionReader(
+ self.collection_locator, self.api, self.api.localkeep(),
+ num_retries=self.num_retries)
+ new_collection_object = coll_reader.api_response() or {}
+ # If the Collection only exists in Keep, there will be no API
+ # response. Fill in the fields we need.
+ if 'uuid' not in new_collection_object:
+ new_collection_object['uuid'] = self.collection_locator
+ if "portable_data_hash" not in new_collection_object:
+ new_collection_object["portable_data_hash"] = new_collection_object["uuid"]
+ if 'manifest_text' not in new_collection_object:
+ new_collection_object['manifest_text'] = coll_reader.manifest_text()
+ coll_reader.normalize()
+ # end with llfuse.lock_released, re-acquire lock
+
+ if self.collection_object is None or self.collection_object["portable_data_hash"] != new_collection_object["portable_data_hash"]:
+ self.new_collection(new_collection_object, coll_reader)
+
+ self.fresh()
+ return True
+ except apiclient.errors.NotFoundError:
+ _logger.exception("arv-mount %s: error", self.collection_locator)
+ except arvados.errors.ArgumentError as detail:
+ _logger.warning("arv-mount %s: error %s", self.collection_locator, detail)
+ if self.collection_object is not None and "manifest_text" in self.collection_object:
+ _logger.warning("arv-mount manifest_text is: %s", self.collection_object["manifest_text"])
+ except Exception:
+ _logger.exception("arv-mount %s: error", self.collection_locator)
+ if self.collection_object is not None and "manifest_text" in self.collection_object:
+ _logger.error("arv-mount manifest_text is: %s", self.collection_object["manifest_text"])
+ return False
+
+ def __getitem__(self, item):
+ self.checkupdate()
+ if item == '.arvados#collection':
+ if self.collection_object_file is None:
+ self.collection_object_file = ObjectFile(self.inode, self.collection_object)
+ self.inodes.add_entry(self.collection_object_file)
+ return self.collection_object_file
+ else:
+ return super(CollectionDirectory, self).__getitem__(item)
+
+ def __contains__(self, k):
+ if k == '.arvados#collection':
+ return True
+ else:
+ return super(CollectionDirectory, self).__contains__(k)
+
+ def mtime(self):
+ self.checkupdate()
+ return convertTime(self.collection_object["modified_at"]) if self.collection_object is not None and 'modified_at' in self.collection_object else 0
+
+
+class MagicDirectory(Directory):
+ '''A special directory that logically contains the set of all extant keep
+ locators. When a file is referenced by lookup(), it is tested to see if it
+ is a valid keep locator to a manifest, and if so, loads the manifest
+ contents as a subdirectory of this directory with the locator as the
+ directory name. Since querying a list of all extant keep locators is
+ impractical, only collections that have already been accessed are visible
+ to readdir().
+ '''
+
+ README_TEXT = '''
+This directory provides access to Arvados collections as subdirectories listed
+by uuid (in the form 'zzzzz-4zz18-1234567890abcde') or portable data hash (in
+the form '1234567890abcdefghijklmnopqrstuv+123').
+
+Note that this directory will appear empty until you attempt to access a
+specific collection subdirectory (such as trying to 'cd' into it), at which
+point the collection will actually be looked up on the server and the directory
+will appear if it exists.
+'''.lstrip()
+
+ def __init__(self, parent_inode, inodes, api, num_retries):
+ super(MagicDirectory, self).__init__(parent_inode)
+ self.inodes = inodes
+ self.api = api
+ self.num_retries = num_retries
+
+ def __setattr__(self, name, value):
+ super(MagicDirectory, self).__setattr__(name, value)
+ # When we're assigned an inode, add a README.
+ if ((name == 'inode') and (self.inode is not None) and
+ (not self._entries)):
+ self._entries['README'] = self.inodes.add_entry(
+ StringFile(self.inode, self.README_TEXT, time.time()))
+ # If we're the root directory, add an identical by_id subdirectory.
+ if self.inode == llfuse.ROOT_INODE:
+ self._entries['by_id'] = self.inodes.add_entry(MagicDirectory(
+ self.inode, self.inodes, self.api, self.num_retries))
+
+ def __contains__(self, k):
+ if k in self._entries:
+ return True
+
+ if not portable_data_hash_pattern.match(k) and not uuid_pattern.match(k):
+ return False
+
+ try:
+ e = self.inodes.add_entry(CollectionDirectory(
+ self.inode, self.inodes, self.api, self.num_retries, k))
+ if e.update():
+ self._entries[k] = e
+ return True
+ else:
+ return False
+ except Exception as e:
+ _logger.debug('arv-mount exception keep %s', e)
+ return False
+
+ def __getitem__(self, item):
+ if item in self:
+ return self._entries[item]
+ else:
+ raise KeyError("No collection with id " + item)
+
+
+class RecursiveInvalidateDirectory(Directory):
+ def invalidate(self):
+ if self.inode == llfuse.ROOT_INODE:
+ llfuse.lock.acquire()
+ try:
+ super(RecursiveInvalidateDirectory, self).invalidate()
+ for a in self._entries:
+ self._entries[a].invalidate()
+ except Exception:
+ _logger.exception()
+ finally:
+ if self.inode == llfuse.ROOT_INODE:
+ llfuse.lock.release()
+
+
+class TagsDirectory(RecursiveInvalidateDirectory):
+ '''A special directory that contains as subdirectories all tags visible to the user.'''
+
+ def __init__(self, parent_inode, inodes, api, num_retries, poll_time=60):
+ super(TagsDirectory, self).__init__(parent_inode)
+ self.inodes = inodes
+ self.api = api
+ self.num_retries = num_retries
+ self._poll = True
+ self._poll_time = poll_time
+
+ def update(self):
+ with llfuse.lock_released:
+ tags = self.api.links().list(
+ filters=[['link_class', '=', 'tag']],
+ select=['name'], distinct=True
+ ).execute(num_retries=self.num_retries)
+ if "items" in tags:
+ self.merge(tags['items'],
+ lambda i: i['name'] if 'name' in i else i['uuid'],
+ lambda a, i: a.tag == i,
+ lambda i: TagDirectory(self.inode, self.inodes, self.api, self.num_retries, i['name'], poll=self._poll, poll_time=self._poll_time))
+
+
+class TagDirectory(Directory):
+ '''A special directory that contains as subdirectories all collections visible
+ to the user that are tagged with a particular tag.
+ '''
+
+ def __init__(self, parent_inode, inodes, api, num_retries, tag,
+ poll=False, poll_time=60):
+ super(TagDirectory, self).__init__(parent_inode)
+ self.inodes = inodes
+ self.api = api
+ self.num_retries = num_retries
+ self.tag = tag
+ self._poll = poll
+ self._poll_time = poll_time
+
+ def update(self):
+ with llfuse.lock_released:
+ taggedcollections = self.api.links().list(
+ filters=[['link_class', '=', 'tag'],
+ ['name', '=', self.tag],
+ ['head_uuid', 'is_a', 'arvados#collection']],
+ select=['head_uuid']
+ ).execute(num_retries=self.num_retries)
+ self.merge(taggedcollections['items'],
+ lambda i: i['head_uuid'],
+ lambda a, i: a.collection_locator == i['head_uuid'],
+ lambda i: CollectionDirectory(self.inode, self.inodes, self.api, self.num_retries, i['head_uuid']))
+
+
+class ProjectDirectory(Directory):
+ '''A special directory that contains the contents of a project.'''
+
+ def __init__(self, parent_inode, inodes, api, num_retries, project_object,
+ poll=False, poll_time=60):
+ super(ProjectDirectory, self).__init__(parent_inode)
+ self.inodes = inodes
+ self.api = api
+ self.num_retries = num_retries
+ self.project_object = project_object
+ self.project_object_file = None
+ self.uuid = project_object['uuid']
+ self._poll = poll
+ self._poll_time = poll_time
+
+ def createDirectory(self, i):
+ if collection_uuid_pattern.match(i['uuid']):
+ return CollectionDirectory(self.inode, self.inodes, self.api, self.num_retries, i)
+ elif group_uuid_pattern.match(i['uuid']):
+ return ProjectDirectory(self.inode, self.inodes, self.api, self.num_retries, i, self._poll, self._poll_time)
+ elif link_uuid_pattern.match(i['uuid']):
+ if i['head_kind'] == 'arvados#collection' or portable_data_hash_pattern.match(i['head_uuid']):
+ return CollectionDirectory(self.inode, self.inodes, self.api, self.num_retries, i['head_uuid'])
+ else:
+ return None
+ elif uuid_pattern.match(i['uuid']):
+ return ObjectFile(self.parent_inode, i)
+ else:
+ return None
+
+ def update(self):
+ if self.project_object_file == None:
+ self.project_object_file = ObjectFile(self.inode, self.project_object)
+ self.inodes.add_entry(self.project_object_file)
+
+ def namefn(i):
+ if 'name' in i:
+ if i['name'] is None or len(i['name']) == 0:
+ return None
+ elif collection_uuid_pattern.match(i['uuid']) or group_uuid_pattern.match(i['uuid']):
+ # collection or subproject
+ return i['name']
+ elif link_uuid_pattern.match(i['uuid']) and i['head_kind'] == 'arvados#collection':
+ # name link
+ return i['name']
+ elif 'kind' in i and i['kind'].startswith('arvados#'):
+ # something else
+ return "{}.{}".format(i['name'], i['kind'][8:])
+ else:
+ return None
+
+ def samefn(a, i):
+ if isinstance(a, CollectionDirectory):
+ return a.collection_locator == i['uuid']
+ elif isinstance(a, ProjectDirectory):
+ return a.uuid == i['uuid']
+ elif isinstance(a, ObjectFile):
+ return a.uuid == i['uuid'] and not a.stale()
+ return False
+
+ with llfuse.lock_released:
+ if group_uuid_pattern.match(self.uuid):
+ self.project_object = self.api.groups().get(
+ uuid=self.uuid).execute(num_retries=self.num_retries)
+ elif user_uuid_pattern.match(self.uuid):
+ self.project_object = self.api.users().get(
+ uuid=self.uuid).execute(num_retries=self.num_retries)
+
+ contents = arvados.util.list_all(self.api.groups().contents,
+ self.num_retries, uuid=self.uuid)
+ # Name links will be obsolete soon, take this out when there are no more pre-#3036 in use.
+ contents += arvados.util.list_all(
+ self.api.links().list, self.num_retries,
+ filters=[['tail_uuid', '=', self.uuid],
+ ['link_class', '=', 'name']])
+
+ # end with llfuse.lock_released, re-acquire lock
+
+ self.merge(contents,
+ namefn,
+ samefn,
+ self.createDirectory)
+
+ def __getitem__(self, item):
+ self.checkupdate()
+ if item == '.arvados#project':
+ return self.project_object_file
+ else:
+ return super(ProjectDirectory, self).__getitem__(item)
+
+ def __contains__(self, k):
+ if k == '.arvados#project':
+ return True
+ else:
+ return super(ProjectDirectory, self).__contains__(k)
+
+
+class SharedDirectory(Directory):
+ '''A special directory that represents users or groups who have shared projects with me.'''
+
+ def __init__(self, parent_inode, inodes, api, num_retries, exclude,
+ poll=False, poll_time=60):
+ super(SharedDirectory, self).__init__(parent_inode)
+ self.inodes = inodes
+ self.api = api
+ self.num_retries = num_retries
+ self.current_user = api.users().current().execute(num_retries=num_retries)
+ self._poll = True
+ self._poll_time = poll_time
+
+ def update(self):
+ with llfuse.lock_released:
+ all_projects = arvados.util.list_all(
+ self.api.groups().list, self.num_retries,
+ filters=[['group_class','=','project']])
+ objects = {}
+ for ob in all_projects:
+ objects[ob['uuid']] = ob
+
+ roots = []
+ root_owners = {}
+ for ob in all_projects:
+ if ob['owner_uuid'] != self.current_user['uuid'] and ob['owner_uuid'] not in objects:
+ roots.append(ob)
+ root_owners[ob['owner_uuid']] = True
+
+ lusers = arvados.util.list_all(
+ self.api.users().list, self.num_retries,
+ filters=[['uuid','in', list(root_owners)]])
+ lgroups = arvados.util.list_all(
+ self.api.groups().list, self.num_retries,
+ filters=[['uuid','in', list(root_owners)]])
+
+ users = {}
+ groups = {}
+
+ for l in lusers:
+ objects[l["uuid"]] = l
+ for l in lgroups:
+ objects[l["uuid"]] = l
+
+ contents = {}
+ for r in root_owners:
+ if r in objects:
+ obr = objects[r]
+ if "name" in obr:
+ contents[obr["name"]] = obr
+ if "first_name" in obr:
+ contents[u"{} {}".format(obr["first_name"], obr["last_name"])] = obr
+
+ for r in roots:
+ if r['owner_uuid'] not in objects:
+ contents[r['name']] = r
+
+ # end with llfuse.lock_released, re-acquire lock
+
+ try:
+ self.merge(contents.items(),
+ lambda i: i[0],
+ lambda a, i: a.uuid == i[1]['uuid'],
+ lambda i: ProjectDirectory(self.inode, self.inodes, self.api, self.num_retries, i[1], poll=self._poll, poll_time=self._poll_time))
+ except Exception:
+ _logger.exception()
+
+
+class FileHandle(object):
+ '''Connects a numeric file handle to a File or Directory object that has
+ been opened by the client.'''
+
+ def __init__(self, fh, entry):
+ self.fh = fh
+ self.entry = entry
+
+
+class Inodes(object):
+ '''Manage the set of inodes. This is the mapping from a numeric id
+ to a concrete File or Directory object'''
+
+ def __init__(self):
+ self._entries = {}
+ self._counter = itertools.count(llfuse.ROOT_INODE)
+
+ def __getitem__(self, item):
+ return self._entries[item]
+
+ def __setitem__(self, key, item):
+ self._entries[key] = item
+
+ def __iter__(self):
+ return self._entries.iterkeys()
+
+ def items(self):
+ return self._entries.items()
+
+ def __contains__(self, k):
+ return k in self._entries
+
+ def add_entry(self, entry):
+ entry.inode = next(self._counter)
+ self._entries[entry.inode] = entry
+ return entry
+
+ def del_entry(self, entry):
+ llfuse.invalidate_inode(entry.inode)
+ del self._entries[entry.inode]
+
+class Operations(llfuse.Operations):
+ '''This is the main interface with llfuse. The methods on this object are
+ called by llfuse threads to service FUSE events to query and read from
+ the file system.
+
+ llfuse has its own global lock which is acquired before calling a request handler,
+ so request handlers do not run concurrently unless the lock is explicitly released
+ using "with llfuse.lock_released:"'''
+
+ def __init__(self, uid, gid, encoding="utf-8", set_executable_bit=False):
+ super(Operations, self).__init__()
+
+ self.inodes = Inodes()
+ self.uid = uid
+ self.gid = gid
+ self.encoding = encoding
+ self.set_executable_bit = set_executable_bit
+
+ # dict of inode to filehandle
+ self._filehandles = {}
+ self._filehandles_counter = 1
+
+ # Other threads that need to wait until the fuse driver
+ # is fully initialized should wait() on this event object.
+ self.initlock = threading.Event()
+
+ def init(self):
+ # Allow threads that are waiting for the driver to be finished
+ # initializing to continue
+ self.initlock.set()
+
+ def access(self, inode, mode, ctx):
+ return True
+
+ def getattr(self, inode):
+ if inode not in self.inodes:
+ raise llfuse.FUSEError(errno.ENOENT)
+
+ e = self.inodes[inode]
+
+ entry = llfuse.EntryAttributes()
+ entry.st_ino = inode
+ entry.generation = 0
+ entry.entry_timeout = 300
+ entry.attr_timeout = 300
+
+ entry.st_mode = stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH
+ if isinstance(e, Directory):
+ entry.st_mode |= stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH | stat.S_IFDIR
+ elif isinstance(e, StreamReaderFile) and self.set_executable_bit:
+ entry.st_mode |= stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH | stat.S_IFREG
+ else:
+ entry.st_mode |= stat.S_IFREG
+
+ entry.st_nlink = 1
+ entry.st_uid = self.uid
+ entry.st_gid = self.gid
+ entry.st_rdev = 0
+
+ entry.st_size = e.size()
+
+ entry.st_blksize = 512
+ entry.st_blocks = (e.size()/512)+1
+ entry.st_atime = int(e.atime())
+ entry.st_mtime = int(e.mtime())
+ entry.st_ctime = int(e.mtime())
+
+ return entry
+
+ def lookup(self, parent_inode, name):
+ name = unicode(name, self.encoding)
+ _logger.debug("arv-mount lookup: parent_inode %i name %s",
+ parent_inode, name)
+ inode = None
+
+ if name == '.':
+ inode = parent_inode
+ else:
+ if parent_inode in self.inodes:
+ p = self.inodes[parent_inode]
+ if name == '..':
+ inode = p.parent_inode
+ elif isinstance(p, Directory) and name in p:
+ inode = p[name].inode
+
+ if inode != None:
+ return self.getattr(inode)
+ else:
+ raise llfuse.FUSEError(errno.ENOENT)
+
+ def open(self, inode, flags):
+ if inode in self.inodes:
+ p = self.inodes[inode]
+ else:
+ raise llfuse.FUSEError(errno.ENOENT)
+
+ if (flags & os.O_WRONLY) or (flags & os.O_RDWR):
+ raise llfuse.FUSEError(errno.EROFS)
+
+ if isinstance(p, Directory):
+ raise llfuse.FUSEError(errno.EISDIR)
+
+ fh = self._filehandles_counter
+ self._filehandles_counter += 1
+ self._filehandles[fh] = FileHandle(fh, p)
+ return fh
+
+ def read(self, fh, off, size):
+ _logger.debug("arv-mount read %i %i %i", fh, off, size)
+ if fh in self._filehandles:
+ handle = self._filehandles[fh]
+ else:
+ raise llfuse.FUSEError(errno.EBADF)
+
+ # update atime
+ handle.entry._atime = time.time()
+
+ try:
+ with llfuse.lock_released:
+ return handle.entry.readfrom(off, size)
+ except arvados.errors.NotFoundError as e:
+ _logger.warning("Block not found: " + str(e))
+ raise llfuse.FUSEError(errno.EIO)
+ except Exception:
+ _logger.exception()
+ raise llfuse.FUSEError(errno.EIO)
+
+ def release(self, fh):
+ if fh in self._filehandles:
+ del self._filehandles[fh]
+
+ def opendir(self, inode):
+ _logger.debug("arv-mount opendir: inode %i", inode)
+
+ if inode in self.inodes:
+ p = self.inodes[inode]
+ else:
+ raise llfuse.FUSEError(errno.ENOENT)
+
+ if not isinstance(p, Directory):
+ raise llfuse.FUSEError(errno.ENOTDIR)
+
+ fh = self._filehandles_counter
+ self._filehandles_counter += 1
+ if p.parent_inode in self.inodes:
+ parent = self.inodes[p.parent_inode]
+ else:
+ raise llfuse.FUSEError(errno.EIO)
+
+ # update atime
+ p._atime = time.time()
+
+ self._filehandles[fh] = FileHandle(fh, [('.', p), ('..', parent)] + list(p.items()))
+ return fh
+
+ def readdir(self, fh, off):
+ _logger.debug("arv-mount readdir: fh %i off %i", fh, off)
+
+ if fh in self._filehandles:
+ handle = self._filehandles[fh]
+ else:
+ raise llfuse.FUSEError(errno.EBADF)
+
+ _logger.debug("arv-mount handle.entry %s", handle.entry)
+
+ e = off
+ while e < len(handle.entry):
+ if handle.entry[e][1].inode in self.inodes:
+ try:
+ yield (handle.entry[e][0].encode(self.encoding), self.getattr(handle.entry[e][1].inode), e+1)
+ except UnicodeEncodeError:
+ pass
+ e += 1
+
+ def releasedir(self, fh):
+ del self._filehandles[fh]
+
+ def statfs(self):
+ st = llfuse.StatvfsData()
+ st.f_bsize = 64 * 1024
+ st.f_blocks = 0
+ st.f_files = 0
+
+ st.f_bfree = 0
+ st.f_bavail = 0
+
+ st.f_ffree = 0
+ st.f_favail = 0
+
+ st.f_frsize = 0
+ return st
+
+ # The llfuse documentation recommends only overloading functions that
+ # are actually implemented, as the default implementation will raise ENOSYS.
+ # However, there is a bug in the llfuse default implementation of create()
+ # "create() takes exactly 5 positional arguments (6 given)" which will crash
+ # arv-mount.
+ # The workaround is to implement it with the proper number of parameters,
+ # and then everything works out.
+ def create(self, p1, p2, p3, p4, p5):
+ raise llfuse.FUSEError(errno.EROFS)
--- /dev/null
+#!/usr/bin/env python
+
+import argparse
+import arvados
+import daemon
+import logging
+import os
+import signal
+import subprocess
+import time
+
+import arvados.commands._util as arv_cmd
+from arvados_fuse import *
+
+logger = logging.getLogger('arvados.arv-mount')
+
+if __name__ == '__main__':
+ # Handle command line parameters
+ parser = argparse.ArgumentParser(
+ parents=[arv_cmd.retry_opt],
+ description='''Mount Keep data under the local filesystem. Default mode is --home''',
+ epilog="""
+Note: When using the --exec feature, you must either specify the
+mountpoint before --exec, or mark the end of your --exec arguments
+with "--".
+""")
+ parser.add_argument('mountpoint', type=str, help="""Mount point.""")
+ parser.add_argument('--allow-other', action='store_true',
+ help="""Let other users read the mount""")
+
+ mount_mode = parser.add_mutually_exclusive_group()
+
+ mount_mode.add_argument('--all', action='store_true', help="""Mount a subdirectory for each mode: home, shared, by_tag, by_id (default).""")
+ mount_mode.add_argument('--home', action='store_true', help="""Mount only the user's home project.""")
+ mount_mode.add_argument('--shared', action='store_true', help="""Mount only list of projects shared with the user.""")
+ mount_mode.add_argument('--by-tag', action='store_true',
+ help="""Mount subdirectories listed by tag.""")
+ mount_mode.add_argument('--by-id', action='store_true',
+ help="""Mount subdirectories listed by portable data hash or uuid.""")
+ mount_mode.add_argument('--project', type=str, help="""Mount a specific project.""")
+ mount_mode.add_argument('--collection', type=str, help="""Mount only the specified collection.""")
+
+ parser.add_argument('--debug', action='store_true', help="""Debug mode""")
+ parser.add_argument('--logfile', help="""Write debug logs and errors to the specified file (default stderr).""")
+ parser.add_argument('--foreground', action='store_true', help="""Run in foreground (default is to daemonize unless --exec specified)""", default=False)
+ parser.add_argument('--encoding', type=str, help="Character encoding to use for filesystem, default is utf-8 (see Python codec registry for list of available encodings)", default="utf-8")
+ parser.add_argument('--exec', type=str, nargs=argparse.REMAINDER,
+ dest="exec_args", metavar=('command', 'args', '...', '--'),
+ help="""Mount, run a command, then unmount and exit""")
+ parser.add_argument('--set-executable-bit', action='store_true', help="""Set executable bit on collection files""")
+
+ args = parser.parse_args()
+ args.mountpoint = os.path.realpath(args.mountpoint)
+ if args.logfile:
+ args.logfile = os.path.realpath(args.logfile)
+
+ # Daemonize as early as possible, so we don't accidentally close
+ # file descriptors we're using.
+ if not (args.exec_args or args.foreground):
+ os.chdir(args.mountpoint)
+ daemon_ctx = daemon.DaemonContext(working_directory='.')
+ daemon_ctx.open()
+ else:
+ daemon_ctx = None
+
+ # Configure a log handler based on command-line switches.
+ if args.logfile:
+ log_handler = logging.FileHandler(args.logfile)
+ elif daemon_ctx:
+ log_handler = logging.NullHandler()
+ else:
+ log_handler = None
+
+ if log_handler is not None:
+ arvados.logger.removeHandler(arvados.log_handler)
+ arvados.logger.addHandler(log_handler)
+
+ if args.debug:
+ arvados.logger.setLevel(logging.DEBUG)
+ logger.debug("arv-mount debugging enabled")
+
+ try:
+ # Create the request handler
+ operations = Operations(os.getuid(), os.getgid(), args.encoding, args.set_executable_bit)
+ api = SafeApi(arvados.config)
+
+ usr = api.users().current().execute(num_retries=args.retries)
+ now = time.time()
+ dir_class = None
+ dir_args = [llfuse.ROOT_INODE, operations.inodes, api, args.retries]
+ if args.by_id:
+ # Set up the request handler with the 'magic directory' at the root
+ dir_class = MagicDirectory
+ elif args.by_tag:
+ dir_class = TagsDirectory
+ elif args.shared:
+ dir_class = SharedDirectory
+ dir_args.append(usr)
+ elif args.home:
+ dir_class = ProjectDirectory
+ dir_args.append(usr)
+ dir_args.append(True)
+ elif args.collection is not None:
+ # Set up the request handler with the collection at the root
+ dir_class = CollectionDirectory
+ dir_args.append(args.collection)
+ elif args.project is not None:
+ dir_class = ProjectDirectory
+ dir_args.append(api.groups().get(uuid=args.project).execute(
+ num_retries=args.retries))
+
+ if dir_class is not None:
+ operations.inodes.add_entry(dir_class(*dir_args))
+ else:
+ e = operations.inodes.add_entry(Directory(llfuse.ROOT_INODE))
+ dir_args[0] = e.inode
+
+ e._entries['by_id'] = operations.inodes.add_entry(MagicDirectory(*dir_args))
+ e._entries['by_tag'] = operations.inodes.add_entry(TagsDirectory(*dir_args))
+
+ dir_args.append(usr)
+ dir_args.append(True)
+ e._entries['home'] = operations.inodes.add_entry(ProjectDirectory(*dir_args))
+ e._entries['shared'] = operations.inodes.add_entry(SharedDirectory(*dir_args))
+
+ text = '''
+Welcome to Arvados! This directory provides file system access to files and objects
+available on the Arvados installation located at '{}'
+using credentials for user '{}'.
+
+From here, the following directories are available:
+
+ by_id/ Access to Keep collections by uuid or portable data hash (see by_id/README for details).
+ by_tag/ Access to Keep collections organized by tag.
+ home/ The contents of your home project.
+ shared/ Projects shared with you.
+'''.format(arvados.config.get('ARVADOS_API_HOST'), usr['email'])
+
+ e._entries["README"] = operations.inodes.add_entry(StringFile(e.inode, text, now))
+
+
+ except Exception:
+ logger.exception("arv-mount: exception during API setup")
+ exit(1)
+
+ # FUSE options, see mount.fuse(8)
+ opts = [optname for optname in ['allow_other', 'debug']
+ if getattr(args, optname)]
+
+ if args.exec_args:
+ # Initialize the fuse connection
+ llfuse.init(operations, args.mountpoint, opts)
+
+ t = threading.Thread(None, lambda: llfuse.main())
+ t.start()
+
+ # wait until the driver is finished initializing
+ operations.initlock.wait()
+
+ rc = 255
+ try:
+ sp = subprocess.Popen(args.exec_args, shell=False)
+
+ # forward signals to the process.
+ signal.signal(signal.SIGINT, lambda signum, frame: sp.send_signal(signum))
+ signal.signal(signal.SIGTERM, lambda signum, frame: sp.send_signal(signum))
+ signal.signal(signal.SIGQUIT, lambda signum, frame: sp.send_signal(signum))
+
+ # wait for process to complete.
+ rc = sp.wait()
+
+ # restore default signal handlers.
+ signal.signal(signal.SIGINT, signal.SIG_DFL)
+ signal.signal(signal.SIGTERM, signal.SIG_DFL)
+ signal.signal(signal.SIGQUIT, signal.SIG_DFL)
+ except Exception as e:
+ logger.exception('arv-mount: exception during exec %s',
+ args.exec_args)
+ try:
+ rc = e.errno
+ except AttributeError:
+ pass
+ finally:
+ subprocess.call(["fusermount", "-u", "-z", args.mountpoint])
+
+ exit(rc)
+ else:
+ try:
+ llfuse.init(operations, args.mountpoint, opts)
+ llfuse.main()
+ except Exception as e:
+ logger.exception('arv-mount: exception during mount')
+ exit(getattr(e, 'errno', 1))
--- /dev/null
+#!/usr/bin/env python
+
+import os
+import subprocess
+import time
+
+from setuptools import setup, find_packages
+from setuptools.command.egg_info import egg_info
+
+SETUP_DIR = os.path.dirname(__file__)
+README = os.path.join(SETUP_DIR, 'README.rst')
+
+class TagBuildWithCommit(egg_info):
+ """Tag the build with the sha1 and date of the last git commit.
+
+ If a build tag has already been set (e.g., "egg_info -b", building
+ from source package), leave it alone.
+ """
+ def tags(self):
+ if self.tag_build is None:
+ git_tags = subprocess.check_output(
+ ['git', 'log', '--first-parent', '--max-count=1',
+ '--format=format:%ct %h', SETUP_DIR]).split()
+ assert len(git_tags) == 2
+ git_tags[0] = time.strftime(
+ '%Y%m%d%H%M%S', time.gmtime(int(git_tags[0])))
+ self.tag_build = '.{}+{}'.format(*git_tags)
+ return egg_info.tags(self)
+
+
+setup(name='arvados_fuse',
+ version='0.1',
+ description='Arvados FUSE driver',
+ long_description=open(README).read(),
+ author='Arvados',
+ author_email='info@arvados.org',
+ url="https://arvados.org",
+ download_url="https://github.com/curoverse/arvados.git",
+ license='GNU Affero General Public License, version 3.0',
+ packages=['arvados_fuse'],
+ scripts=[
+ 'bin/arv-mount'
+ ],
+ install_requires=[
+ 'arvados-python-client>=0.1.20141203150737.277b3c7',
+ 'llfuse',
+ 'python-daemon'
+ ],
+ test_suite='tests',
+ tests_require=['PyYAML'],
+ zip_safe=False,
+ cmdclass={'egg_info': TagBuildWithCommit},
+ )
--- /dev/null
+../../../sdk/python/tests/run_test_server.py
\ No newline at end of file
--- /dev/null
+import unittest
+import arvados
+import arvados_fuse as fuse
+import threading
+import time
+import os
+import llfuse
+import tempfile
+import shutil
+import subprocess
+import glob
+import run_test_server
+import json
+
+class MountTestBase(unittest.TestCase):
+ def setUp(self):
+ self.keeptmp = tempfile.mkdtemp()
+ os.environ['KEEP_LOCAL_STORE'] = self.keeptmp
+ self.mounttmp = tempfile.mkdtemp()
+ run_test_server.run(False)
+ run_test_server.authorize_with("admin")
+ self.api = api = fuse.SafeApi(arvados.config)
+
+ def make_mount(self, root_class, *root_args):
+ operations = fuse.Operations(os.getuid(), os.getgid())
+ operations.inodes.add_entry(root_class(
+ llfuse.ROOT_INODE, operations.inodes, self.api, 0, *root_args))
+ llfuse.init(operations, self.mounttmp, [])
+ threading.Thread(None, llfuse.main).start()
+ # wait until the driver is finished initializing
+ operations.initlock.wait()
+
+ def tearDown(self):
+ run_test_server.stop()
+
+ # llfuse.close is buggy, so use fusermount instead.
+ #llfuse.close(unmount=True)
+ count = 0
+ success = 1
+ while (count < 9 and success != 0):
+ success = subprocess.call(["fusermount", "-u", self.mounttmp])
+ time.sleep(0.5)
+ count += 1
+
+ os.rmdir(self.mounttmp)
+ shutil.rmtree(self.keeptmp)
+
+ def assertDirContents(self, subdir, expect_content):
+ path = self.mounttmp
+ if subdir:
+ path = os.path.join(path, subdir)
+ self.assertEqual(sorted(expect_content), sorted(os.listdir(path)))
+
+
+class FuseMountTest(MountTestBase):
+ def setUp(self):
+ super(FuseMountTest, self).setUp()
+
+ cw = arvados.CollectionWriter()
+
+ cw.start_new_file('thing1.txt')
+ cw.write("data 1")
+ cw.start_new_file('thing2.txt')
+ cw.write("data 2")
+ cw.start_new_stream('dir1')
+
+ cw.start_new_file('thing3.txt')
+ cw.write("data 3")
+ cw.start_new_file('thing4.txt')
+ cw.write("data 4")
+
+ cw.start_new_stream('dir2')
+ cw.start_new_file('thing5.txt')
+ cw.write("data 5")
+ cw.start_new_file('thing6.txt')
+ cw.write("data 6")
+
+ cw.start_new_stream('dir2/dir3')
+ cw.start_new_file('thing7.txt')
+ cw.write("data 7")
+
+ cw.start_new_file('thing8.txt')
+ cw.write("data 8")
+
+ cw.start_new_stream('edgecases')
+ for f in ":/./../.../-/*/\x01\\/ ".split("/"):
+ cw.start_new_file(f)
+ cw.write('x')
+
+ for f in ":/../.../-/*/\x01\\/ ".split("/"):
+ cw.start_new_stream('edgecases/dirs/' + f)
+ cw.start_new_file('x/x')
+ cw.write('x')
+
+ self.testcollection = cw.finish()
+ self.api.collections().create(body={"manifest_text":cw.manifest_text()}).execute()
+
+ def runTest(self):
+ self.make_mount(fuse.CollectionDirectory, self.testcollection)
+
+ self.assertDirContents(None, ['thing1.txt', 'thing2.txt',
+ 'edgecases', 'dir1', 'dir2'])
+ self.assertDirContents('dir1', ['thing3.txt', 'thing4.txt'])
+ self.assertDirContents('dir2', ['thing5.txt', 'thing6.txt', 'dir3'])
+ self.assertDirContents('dir2/dir3', ['thing7.txt', 'thing8.txt'])
+ self.assertDirContents('edgecases',
+ "dirs/:/_/__/.../-/*/\x01\\/ ".split("/"))
+ self.assertDirContents('edgecases/dirs',
+ ":/__/.../-/*/\x01\\/ ".split("/"))
+
+ files = {'thing1.txt': 'data 1',
+ 'thing2.txt': 'data 2',
+ 'dir1/thing3.txt': 'data 3',
+ 'dir1/thing4.txt': 'data 4',
+ 'dir2/thing5.txt': 'data 5',
+ 'dir2/thing6.txt': 'data 6',
+ 'dir2/dir3/thing7.txt': 'data 7',
+ 'dir2/dir3/thing8.txt': 'data 8'}
+
+ for k, v in files.items():
+ with open(os.path.join(self.mounttmp, k)) as f:
+ self.assertEqual(v, f.read())
+
+
+class FuseNoAPITest(MountTestBase):
+ def setUp(self):
+ super(FuseNoAPITest, self).setUp()
+ keep = arvados.keep.KeepClient(local_store=self.keeptmp)
+ self.file_data = "API-free text\n"
+ self.file_loc = keep.put(self.file_data)
+ self.coll_loc = keep.put(". {} 0:{}:api-free.txt\n".format(
+ self.file_loc, len(self.file_data)))
+
+ def runTest(self):
+ self.make_mount(fuse.MagicDirectory)
+ self.assertDirContents(self.coll_loc, ['api-free.txt'])
+ with open(os.path.join(
+ self.mounttmp, self.coll_loc, 'api-free.txt')) as keep_file:
+ actual = keep_file.read(-1)
+ self.assertEqual(self.file_data, actual)
+
+
+class FuseMagicTest(MountTestBase):
+ def setUp(self):
+ super(FuseMagicTest, self).setUp()
+
+ cw = arvados.CollectionWriter()
+
+ cw.start_new_file('thing1.txt')
+ cw.write("data 1")
+
+ self.testcollection = cw.finish()
+ self.api.collections().create(body={"manifest_text":cw.manifest_text()}).execute()
+
+ def runTest(self):
+ self.make_mount(fuse.MagicDirectory)
+
+ mount_ls = os.listdir(self.mounttmp)
+ self.assertIn('README', mount_ls)
+ self.assertFalse(any(arvados.util.keep_locator_pattern.match(fn) or
+ arvados.util.uuid_pattern.match(fn)
+ for fn in mount_ls),
+ "new FUSE MagicDirectory lists Collection")
+ self.assertDirContents(self.testcollection, ['thing1.txt'])
+ self.assertDirContents(os.path.join('by_id', self.testcollection),
+ ['thing1.txt'])
+ mount_ls = os.listdir(self.mounttmp)
+ self.assertIn('README', mount_ls)
+ self.assertIn(self.testcollection, mount_ls)
+ self.assertIn(self.testcollection,
+ os.listdir(os.path.join(self.mounttmp, 'by_id')))
+
+ files = {}
+ files[os.path.join(self.mounttmp, self.testcollection, 'thing1.txt')] = 'data 1'
+
+ for k, v in files.items():
+ with open(os.path.join(self.mounttmp, k)) as f:
+ self.assertEqual(v, f.read())
+
+
+class FuseTagsTest(MountTestBase):
+ def runTest(self):
+ self.make_mount(fuse.TagsDirectory)
+
+ d1 = os.listdir(self.mounttmp)
+ d1.sort()
+ self.assertEqual(['foo_tag'], d1)
+
+ d2 = os.listdir(os.path.join(self.mounttmp, 'foo_tag'))
+ d2.sort()
+ self.assertEqual(['zzzzz-4zz18-fy296fx3hot09f7'], d2)
+
+ d3 = os.listdir(os.path.join(self.mounttmp, 'foo_tag', 'zzzzz-4zz18-fy296fx3hot09f7'))
+ d3.sort()
+ self.assertEqual(['foo'], d3)
+
+
+class FuseTagsUpdateTest(MountTestBase):
+ def tag_collection(self, coll_uuid, tag_name):
+ return self.api.links().create(
+ body={'link': {'head_uuid': coll_uuid,
+ 'link_class': 'tag',
+ 'name': tag_name,
+ }}).execute()
+
+ def runTest(self):
+ operations = fuse.Operations(os.getuid(), os.getgid())
+ e = operations.inodes.add_entry(fuse.TagsDirectory(llfuse.ROOT_INODE, operations.inodes, self.api, 0, poll_time=1))
+
+ llfuse.init(operations, self.mounttmp, [])
+ t = threading.Thread(None, lambda: llfuse.main())
+ t.start()
+
+ # wait until the driver is finished initializing
+ operations.initlock.wait()
+ self.assertIn('foo_tag', os.listdir(self.mounttmp))
+
+ bar_uuid = run_test_server.fixture('collections')['bar_file']['uuid']
+ self.tag_collection(bar_uuid, 'fuse_test_tag')
+ time.sleep(1)
+ self.assertIn('fuse_test_tag', os.listdir(self.mounttmp))
+ self.assertDirContents('fuse_test_tag', [bar_uuid])
+
+ baz_uuid = run_test_server.fixture('collections')['baz_file']['uuid']
+ l = self.tag_collection(baz_uuid, 'fuse_test_tag')
+ time.sleep(1)
+ self.assertDirContents('fuse_test_tag', [bar_uuid, baz_uuid])
+
+ self.api.links().delete(uuid=l['uuid']).execute()
+ time.sleep(1)
+ self.assertDirContents('fuse_test_tag', [bar_uuid])
+
+
+class FuseSharedTest(MountTestBase):
+ def runTest(self):
+ self.make_mount(fuse.SharedDirectory,
+ self.api.users().current().execute()['uuid'])
+
+ # shared_dirs is a list of the directories exposed
+ # by fuse.SharedDirectory (i.e. any object visible
+ # to the current user)
+ shared_dirs = os.listdir(self.mounttmp)
+ shared_dirs.sort()
+ self.assertIn('FUSE User', shared_dirs)
+
+ # fuse_user_objs is a list of the objects owned by the FUSE
+ # test user (which present as files in the 'FUSE User'
+ # directory)
+ fuse_user_objs = os.listdir(os.path.join(self.mounttmp, 'FUSE User'))
+ fuse_user_objs.sort()
+ self.assertEqual(['Empty collection.link', # permission link on collection
+ 'FUSE Test Project', # project owned by user
+ 'collection #1 owned by FUSE', # collection owned by user
+ 'collection #2 owned by FUSE', # collection owned by user
+ 'pipeline instance owned by FUSE.pipelineInstance', # pipeline instance owned by user
+ ], fuse_user_objs)
+
+ # test_proj_files is a list of the files in the FUSE Test Project.
+ test_proj_files = os.listdir(os.path.join(self.mounttmp, 'FUSE User', 'FUSE Test Project'))
+ test_proj_files.sort()
+ self.assertEqual(['collection in FUSE project',
+ 'pipeline instance in FUSE project.pipelineInstance',
+ 'pipeline template in FUSE project.pipelineTemplate'
+ ], test_proj_files)
+
+ # Double check that we can open and read objects in this folder as a file,
+ # and that its contents are what we expect.
+ with open(os.path.join(
+ self.mounttmp,
+ 'FUSE User',
+ 'FUSE Test Project',
+ 'pipeline template in FUSE project.pipelineTemplate')) as f:
+ j = json.load(f)
+ self.assertEqual("pipeline template in FUSE project", j['name'])
+
+
+class FuseHomeTest(MountTestBase):
+ def runTest(self):
+ self.make_mount(fuse.ProjectDirectory,
+ self.api.users().current().execute())
+
+ d1 = os.listdir(self.mounttmp)
+ self.assertIn('Unrestricted public data', d1)
+
+ d2 = os.listdir(os.path.join(self.mounttmp, 'Unrestricted public data'))
+ self.assertEqual(['GNU General Public License, version 3'], d2)
+
+ d3 = os.listdir(os.path.join(self.mounttmp, 'Unrestricted public data', 'GNU General Public License, version 3'))
+ self.assertEqual(["GNU_General_Public_License,_version_3.pdf"], d3)
+
+
+class FuseUnitTest(unittest.TestCase):
+ def test_sanitize_filename(self):
+ acceptable = [
+ "foo.txt",
+ ".foo",
+ "..foo",
+ "...",
+ "foo...",
+ "foo..",
+ "foo.",
+ "-",
+ "\x01\x02\x03",
+ ]
+ unacceptable = [
+ "f\00",
+ "\00\00",
+ "/foo",
+ "foo/",
+ "//",
+ ]
+ for f in acceptable:
+ self.assertEqual(f, fuse.sanitize_filename(f))
+ for f in unacceptable:
+ self.assertNotEqual(f, fuse.sanitize_filename(f))
+ # The sanitized filename should be the same length, though.
+ self.assertEqual(len(f), len(fuse.sanitize_filename(f)))
+ # Special cases
+ self.assertEqual("_", fuse.sanitize_filename(""))
+ self.assertEqual("_", fuse.sanitize_filename("."))
+ self.assertEqual("__", fuse.sanitize_filename(".."))
--- /dev/null
+#! /usr/bin/env python
+
+# traffic_test.py
+#
+# Launch a test Keep and API server and PUT and GET a bunch of blocks.
+# Can be used to simulate client traffic in Keep to evaluate memory usage,
+# error logging, performance, etc.
+#
+# This script is warty and is relatively environment-specific, but the
+# example run described below should execute cleanly.
+#
+# Usage:
+# traffic_test.py start
+# Starts the test servers.
+# traffic_test.py put file1 file2 file3 ....
+# Runs arv-put on each file.
+# traffic_test.py get hash1 hash2 hash3 ....
+# Loops forever issuing GET requests for specified blocks.
+# traffic_test.py stop
+# Stops the test servers.
+#
+# Example:
+#
+# $ ./traffic_test.py start
+# $ ./traffic_test.py put GS00253-DNA_A02_200_37.tsv.bz2 \
+# GS00253-DNA_B01_200_37.tsv.bz2 \
+# GS00253-DNA_B02_200_37.tsv.bz2
+# $ ./traffic_test.py get $(find /tmp/tmp* -type f -printf "%f ")
+# [loops forever]
+# ^C
+# $ ./traffic_test.py stop
+#
+# Multiple "get" runs may be run concurrently to evaluate Keep's handling
+# of additional concurrent clients.
+
+PYSDK_DIR = "../../../sdk/python"
+PYTEST_DIR = PYSDK_DIR + "/tests"
+ARV_PUT_PATH = PYSDK_DIR + "/bin/arv-put"
+ARV_GET_PATH = PYSDK_DIR + "/bin/arv-get"
+SECONDS_BETWEEN_GETS = 1
+
+import argparse
+import httplib2
+import os
+import random
+import subprocess
+import sys
+import time
+
+# for run_test_server.py
+sys.path.insert(0, PYSDK_DIR)
+sys.path.insert(0, PYTEST_DIR)
+import arvados
+import run_test_server
+
+def arv_cmd(*args):
+ p = subprocess.Popen([sys.executable] + list(args),
+ stdout=subprocess.PIPE)
+ (arvout, arverr) = p.communicate()
+ if p.returncode != 0:
+ print "error {} from {} {}: {}".format(
+ p.returncode, sys.executable, args, arverr)
+ sys.exit(p.returncode)
+ return arvout
+
+def start():
+ run_test_server.run()
+ run_test_server.run_keep()
+
+def put(files):
+ os.environ["ARVADOS_API_HOST"] = "127.0.0.1:3000"
+ run_test_server.authorize_with('active')
+ for v in ["ARVADOS_API_HOST",
+ "ARVADOS_API_HOST_INSECURE",
+ "ARVADOS_API_TOKEN"]:
+ os.environ[v] = arvados.config.settings()[v]
+
+ if not os.environ.has_key('PYTHONPATH'):
+ os.environ['PYTHONPATH'] = ''
+ os.environ['PYTHONPATH'] = "{}:{}:{}".format(
+ PYSDK_DIR, PYTEST_DIR, os.environ['PYTHONPATH'])
+
+ for c in files:
+ manifest_uuid = arv_cmd(ARV_PUT_PATH, c)
+
+def get(blocks):
+ os.environ["ARVADOS_API_HOST"] = "127.0.0.1:3000"
+
+ run_test_server.authorize_with('active')
+ for v in ["ARVADOS_API_HOST",
+ "ARVADOS_API_HOST_INSECURE",
+ "ARVADOS_API_TOKEN"]:
+ os.environ[v] = arvados.config.settings()[v]
+
+ nqueries = 0
+ while True:
+ b = random.choice(blocks)
+ print "GET /" + b
+ body = arv_cmd(ARV_GET_PATH, b)
+ print "got {} bytes".format(len(body))
+ time.sleep(SECONDS_BETWEEN_GETS)
+ nqueries = nqueries + 1
+
+def stop():
+ run_test_server.stop_keep()
+ run_test_server.stop()
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+ parser.add_argument('action',
+ type=str,
+ nargs='+',
+ help='''"start", "put", "get", "stop"''')
+ args = parser.parse_args()
+
+ if args.action[0] == 'start':
+ start()
+ elif args.action[0] == 'put':
+ put(args.action[1:])
+ elif args.action[0] == 'get':
+ get(args.action[1:])
+ elif args.action[0] == 'stop':
+ stop()
+ else:
+ print('Unrecognized action "{}"'.format(args.action))
+ print('actions are "start", "put", "get", "stop"')
--- /dev/null
+package main
+
+import (
+ "flag"
+ "fmt"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/keepclient"
+ "github.com/gorilla/mux"
+ "io"
+ "io/ioutil"
+ "log"
+ "net"
+ "net/http"
+ "os"
+ "os/signal"
+ "sync"
+ "syscall"
+ "time"
+)
+
+// Default TCP address on which to listen for requests.
+// Initialized by the -listen flag.
+const DEFAULT_ADDR = ":25107"
+
+var listener net.Listener
+
+func main() {
+ var (
+ listen string
+ no_get bool
+ no_put bool
+ default_replicas int
+ timeout int64
+ pidfile string
+ )
+
+ flagset := flag.NewFlagSet("default", flag.ExitOnError)
+
+ flagset.StringVar(
+ &listen,
+ "listen",
+ DEFAULT_ADDR,
+ "Interface on which to listen for requests, in the format "+
+ "ipaddr:port. e.g. -listen=10.0.1.24:8000. Use -listen=:port "+
+ "to listen on all network interfaces.")
+
+ flagset.BoolVar(
+ &no_get,
+ "no-get",
+ false,
+ "If set, disable GET operations")
+
+ flagset.BoolVar(
+ &no_put,
+ "no-put",
+ false,
+ "If set, disable PUT operations")
+
+ flagset.IntVar(
+ &default_replicas,
+ "default-replicas",
+ 2,
+ "Default number of replicas to write if not specified by the client.")
+
+ flagset.Int64Var(
+ &timeout,
+ "timeout",
+ 15,
+ "Timeout on requests to internal Keep services (default 15 seconds)")
+
+ flagset.StringVar(
+ &pidfile,
+ "pid",
+ "",
+ "Path to write pid file")
+
+ flagset.Parse(os.Args[1:])
+
+ arv, err := arvadosclient.MakeArvadosClient()
+ if err != nil {
+ log.Fatalf("Error setting up arvados client %s", err.Error())
+ }
+
+ kc, err := keepclient.MakeKeepClient(&arv)
+ if err != nil {
+ log.Fatalf("Error setting up keep client %s", err.Error())
+ }
+
+ if pidfile != "" {
+ f, err := os.Create(pidfile)
+ if err != nil {
+ log.Fatalf("Error writing pid file (%s): %s", pidfile, err.Error())
+ }
+ fmt.Fprint(f, os.Getpid())
+ f.Close()
+ defer os.Remove(pidfile)
+ }
+
+ kc.Want_replicas = default_replicas
+
+ kc.Client.Timeout = time.Duration(timeout) * time.Second
+
+ listener, err = net.Listen("tcp", listen)
+ if err != nil {
+ log.Fatalf("Could not listen on %v", listen)
+ }
+
+ go RefreshServicesList(&kc)
+
+ // Shut down the server gracefully (by closing the listener)
+ // if SIGTERM is received.
+ term := make(chan os.Signal, 1)
+ go func(sig <-chan os.Signal) {
+ s := <-sig
+ log.Println("caught signal:", s)
+ listener.Close()
+ }(term)
+ signal.Notify(term, syscall.SIGTERM)
+ signal.Notify(term, syscall.SIGINT)
+
+ log.Printf("Arvados Keep proxy started listening on %v with server list %v", listener.Addr(), kc.ServiceRoots())
+
+ // Start listening for requests.
+ http.Serve(listener, MakeRESTRouter(!no_get, !no_put, &kc))
+
+ log.Println("shutting down")
+}
+
+type ApiTokenCache struct {
+ tokens map[string]int64
+ lock sync.Mutex
+ expireTime int64
+}
+
+// Refresh the keep service list every five minutes.
+func RefreshServicesList(kc *keepclient.KeepClient) {
+ for {
+ time.Sleep(300 * time.Second)
+ oldservices := kc.ServiceRoots()
+ kc.DiscoverKeepServers()
+ newservices := kc.ServiceRoots()
+ s1 := fmt.Sprint(oldservices)
+ s2 := fmt.Sprint(newservices)
+ if s1 != s2 {
+ log.Printf("Updated server list to %v", s2)
+ }
+ }
+}
+
+// Cache the token and set an expire time. If we already have an expire time
+// on the token, it is not updated.
+func (this *ApiTokenCache) RememberToken(token string) {
+ this.lock.Lock()
+ defer this.lock.Unlock()
+
+ now := time.Now().Unix()
+ if this.tokens[token] == 0 {
+ this.tokens[token] = now + this.expireTime
+ }
+}
+
+// Check if the cached token is known and still believed to be valid.
+func (this *ApiTokenCache) RecallToken(token string) bool {
+ this.lock.Lock()
+ defer this.lock.Unlock()
+
+ now := time.Now().Unix()
+ if this.tokens[token] == 0 {
+ // Unknown token
+ return false
+ } else if now < this.tokens[token] {
+ // Token is known and still valid
+ return true
+ } else {
+ // Token is expired
+ this.tokens[token] = 0
+ return false
+ }
+}
+
+func GetRemoteAddress(req *http.Request) string {
+ if realip := req.Header.Get("X-Real-IP"); realip != "" {
+ if forwarded := req.Header.Get("X-Forwarded-For"); forwarded != realip {
+ return fmt.Sprintf("%s (X-Forwarded-For %s)", realip, forwarded)
+ } else {
+ return realip
+ }
+ }
+ return req.RemoteAddr
+}
+
+func CheckAuthorizationHeader(kc keepclient.KeepClient, cache *ApiTokenCache, req *http.Request) (pass bool, tok string) {
+ var auth string
+ if auth = req.Header.Get("Authorization"); auth == "" {
+ return false, ""
+ }
+
+ _, err := fmt.Sscanf(auth, "OAuth2 %s", &tok)
+ if err != nil {
+ // Scanning error
+ return false, ""
+ }
+
+ if cache.RecallToken(tok) {
+ // Valid in the cache, short circut
+ return true, tok
+ }
+
+ arv := *kc.Arvados
+ arv.ApiToken = tok
+ if err := arv.Call("HEAD", "users", "", "current", nil, nil); err != nil {
+ log.Printf("%s: CheckAuthorizationHeader error: %v", GetRemoteAddress(req), err)
+ return false, ""
+ }
+
+ // Success! Update cache
+ cache.RememberToken(tok)
+
+ return true, tok
+}
+
+type GetBlockHandler struct {
+ *keepclient.KeepClient
+ *ApiTokenCache
+}
+
+type PutBlockHandler struct {
+ *keepclient.KeepClient
+ *ApiTokenCache
+}
+
+type InvalidPathHandler struct{}
+
+type OptionsHandler struct{}
+
+// MakeRESTRouter
+// Returns a mux.Router that passes GET and PUT requests to the
+// appropriate handlers.
+//
+func MakeRESTRouter(
+ enable_get bool,
+ enable_put bool,
+ kc *keepclient.KeepClient) *mux.Router {
+
+ t := &ApiTokenCache{tokens: make(map[string]int64), expireTime: 300}
+
+ rest := mux.NewRouter()
+
+ if enable_get {
+ rest.Handle(`/{hash:[0-9a-f]{32}}+{hints}`,
+ GetBlockHandler{kc, t}).Methods("GET", "HEAD")
+ rest.Handle(`/{hash:[0-9a-f]{32}}`, GetBlockHandler{kc, t}).Methods("GET", "HEAD")
+ }
+
+ if enable_put {
+ rest.Handle(`/{hash:[0-9a-f]{32}}+{hints}`, PutBlockHandler{kc, t}).Methods("PUT")
+ rest.Handle(`/{hash:[0-9a-f]{32}}`, PutBlockHandler{kc, t}).Methods("PUT")
+ rest.Handle(`/`, PutBlockHandler{kc, t}).Methods("POST")
+ rest.Handle(`/{any}`, OptionsHandler{}).Methods("OPTIONS")
+ rest.Handle(`/`, OptionsHandler{}).Methods("OPTIONS")
+ }
+
+ rest.NotFoundHandler = InvalidPathHandler{}
+
+ return rest
+}
+
+func SetCorsHeaders(resp http.ResponseWriter) {
+ resp.Header().Set("Access-Control-Allow-Methods", "GET, HEAD, POST, PUT, OPTIONS")
+ resp.Header().Set("Access-Control-Allow-Origin", "*")
+ resp.Header().Set("Access-Control-Allow-Headers", "Authorization, Content-Length, Content-Type, X-Keep-Desired-Replicas")
+ resp.Header().Set("Access-Control-Max-Age", "86486400")
+}
+
+func (this InvalidPathHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ log.Printf("%s: %s %s unroutable", GetRemoteAddress(req), req.Method, req.URL.Path)
+ http.Error(resp, "Bad request", http.StatusBadRequest)
+}
+
+func (this OptionsHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ log.Printf("%s: %s %s", GetRemoteAddress(req), req.Method, req.URL.Path)
+ SetCorsHeaders(resp)
+}
+
+func (this GetBlockHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ SetCorsHeaders(resp)
+
+ kc := *this.KeepClient
+
+ hash := mux.Vars(req)["hash"]
+ hints := mux.Vars(req)["hints"]
+
+ locator := keepclient.MakeLocator2(hash, hints)
+
+ log.Printf("%s: %s %s begin", GetRemoteAddress(req), req.Method, hash)
+
+ var pass bool
+ var tok string
+ if pass, tok = CheckAuthorizationHeader(kc, this.ApiTokenCache, req); !pass {
+ http.Error(resp, "Missing or invalid Authorization header", http.StatusForbidden)
+ return
+ }
+
+ // Copy ArvadosClient struct and use the client's API token
+ arvclient := *kc.Arvados
+ arvclient.ApiToken = tok
+ kc.Arvados = &arvclient
+
+ var reader io.ReadCloser
+ var err error
+ var blocklen int64
+
+ if req.Method == "GET" {
+ reader, blocklen, _, err = kc.AuthorizedGet(hash, locator.Signature, locator.Timestamp)
+ defer reader.Close()
+ } else if req.Method == "HEAD" {
+ blocklen, _, err = kc.AuthorizedAsk(hash, locator.Signature, locator.Timestamp)
+ }
+
+ if blocklen > -1 {
+ resp.Header().Set("Content-Length", fmt.Sprint(blocklen))
+ } else {
+ log.Printf("%s: %s %s Keep server did not return Content-Length",
+ GetRemoteAddress(req), req.Method, hash)
+ }
+
+ var status = 0
+ switch err {
+ case nil:
+ status = http.StatusOK
+ if reader != nil {
+ n, err2 := io.Copy(resp, reader)
+ if blocklen > -1 && n != blocklen {
+ log.Printf("%s: %s %s %v %v mismatched copy size expected Content-Length: %v",
+ GetRemoteAddress(req), req.Method, hash, status, n, blocklen)
+ } else if err2 == nil {
+ log.Printf("%s: %s %s %v %v",
+ GetRemoteAddress(req), req.Method, hash, status, n)
+ } else {
+ log.Printf("%s: %s %s %v %v copy error: %v",
+ GetRemoteAddress(req), req.Method, hash, status, n, err2.Error())
+ }
+ } else {
+ log.Printf("%s: %s %s %v 0", GetRemoteAddress(req), req.Method, hash, status)
+ }
+ case keepclient.BlockNotFound:
+ status = http.StatusNotFound
+ http.Error(resp, "Not found", http.StatusNotFound)
+ default:
+ status = http.StatusBadGateway
+ http.Error(resp, err.Error(), http.StatusBadGateway)
+ }
+
+ if err != nil {
+ log.Printf("%s: %s %s %v error: %v",
+ GetRemoteAddress(req), req.Method, hash, status, err.Error())
+ }
+}
+
+func (this PutBlockHandler) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ SetCorsHeaders(resp)
+
+ kc := *this.KeepClient
+
+ hash := mux.Vars(req)["hash"]
+ hints := mux.Vars(req)["hints"]
+
+ locator := keepclient.MakeLocator2(hash, hints)
+
+ var contentLength int64 = -1
+ if req.Header.Get("Content-Length") != "" {
+ _, err := fmt.Sscanf(req.Header.Get("Content-Length"), "%d", &contentLength)
+ if err != nil {
+ resp.Header().Set("Content-Length", fmt.Sprintf("%d", contentLength))
+ }
+
+ }
+
+ log.Printf("%s: %s %s Content-Length %v", GetRemoteAddress(req), req.Method, hash, contentLength)
+
+ if contentLength < 0 {
+ http.Error(resp, "Must include Content-Length header", http.StatusLengthRequired)
+ return
+ }
+
+ if locator.Size > 0 && int64(locator.Size) != contentLength {
+ http.Error(resp, "Locator size hint does not match Content-Length header", http.StatusBadRequest)
+ return
+ }
+
+ var pass bool
+ var tok string
+ if pass, tok = CheckAuthorizationHeader(kc, this.ApiTokenCache, req); !pass {
+ http.Error(resp, "Missing or invalid Authorization header", http.StatusForbidden)
+ return
+ }
+
+ // Copy ArvadosClient struct and use the client's API token
+ arvclient := *kc.Arvados
+ arvclient.ApiToken = tok
+ kc.Arvados = &arvclient
+
+ // Check if the client specified the number of replicas
+ if req.Header.Get("X-Keep-Desired-Replicas") != "" {
+ var r int
+ _, err := fmt.Sscanf(req.Header.Get(keepclient.X_Keep_Desired_Replicas), "%d", &r)
+ if err != nil {
+ kc.Want_replicas = r
+ }
+ }
+
+ // Now try to put the block through
+ var replicas int
+ var put_err error
+ if hash == "" {
+ if bytes, err := ioutil.ReadAll(req.Body); err != nil {
+ msg := fmt.Sprintf("Error reading request body: %s", err)
+ log.Printf(msg)
+ http.Error(resp, msg, http.StatusInternalServerError)
+ return
+ } else {
+ hash, replicas, put_err = kc.PutB(bytes)
+ }
+ } else {
+ hash, replicas, put_err = kc.PutHR(hash, req.Body, contentLength)
+ }
+
+ // Tell the client how many successful PUTs we accomplished
+ resp.Header().Set(keepclient.X_Keep_Replicas_Stored, fmt.Sprintf("%d", replicas))
+
+ switch put_err {
+ case nil:
+ // Default will return http.StatusOK
+ log.Printf("%s: %s %s finished, stored %v replicas (desired %v)", GetRemoteAddress(req), req.Method, hash, replicas, kc.Want_replicas)
+ n, err2 := io.WriteString(resp, hash)
+ if err2 != nil {
+ log.Printf("%s: wrote %v bytes to response body and got error %v", n, err2.Error())
+ }
+
+ case keepclient.OversizeBlockError:
+ // Too much data
+ http.Error(resp, fmt.Sprintf("Exceeded maximum blocksize %d", keepclient.BLOCKSIZE), http.StatusRequestEntityTooLarge)
+
+ case keepclient.InsufficientReplicasError:
+ if replicas > 0 {
+ // At least one write is considered success. The
+ // client can decide if getting less than the number of
+ // replications it asked for is a fatal error.
+ // Default will return http.StatusOK
+ n, err2 := io.WriteString(resp, hash)
+ if err2 != nil {
+ log.Printf("%s: wrote %v bytes to response body and got error %v", n, err2.Error())
+ }
+ } else {
+ http.Error(resp, put_err.Error(), http.StatusServiceUnavailable)
+ }
+
+ default:
+ http.Error(resp, put_err.Error(), http.StatusBadGateway)
+ }
+
+ if put_err != nil {
+ log.Printf("%s: %s %s stored %v replicas (desired %v) got error %v", GetRemoteAddress(req), req.Method, hash, replicas, kc.Want_replicas, put_err.Error())
+ }
+
+}
--- /dev/null
+package main
+
+import (
+ "crypto/md5"
+ "crypto/tls"
+ "fmt"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/keepclient"
+ . "gopkg.in/check.v1"
+ "io"
+ "io/ioutil"
+ "log"
+ "net/http"
+ "net/url"
+ "os"
+ "os/exec"
+ "strings"
+ "testing"
+ "time"
+)
+
+// Gocheck boilerplate
+func Test(t *testing.T) {
+ TestingT(t)
+}
+
+// Gocheck boilerplate
+var _ = Suite(&ServerRequiredSuite{})
+
+// Tests that require the Keep server running
+type ServerRequiredSuite struct{}
+
+func pythonDir() string {
+ cwd, _ := os.Getwd()
+ return fmt.Sprintf("%s/../../sdk/python/tests", cwd)
+}
+
+// Wait (up to 1 second) for keepproxy to listen on a port. This
+// avoids a race condition where we hit a "connection refused" error
+// because we start testing the proxy too soon.
+func waitForListener() {
+ const (
+ ms = 5
+ )
+ for i := 0; listener == nil && i < 1000; i += ms {
+ time.Sleep(ms * time.Millisecond)
+ }
+ if listener == nil {
+ log.Fatalf("Timed out waiting for listener to start")
+ }
+}
+
+func closeListener() {
+ if listener != nil {
+ listener.Close()
+ }
+}
+
+func (s *ServerRequiredSuite) SetUpSuite(c *C) {
+ cwd, _ := os.Getwd()
+ defer os.Chdir(cwd)
+
+ os.Chdir(pythonDir())
+ {
+ cmd := exec.Command("python", "run_test_server.py", "start")
+ stderr, err := cmd.StderrPipe()
+ if err != nil {
+ log.Fatalf("Setting up stderr pipe: %s", err)
+ }
+ go io.Copy(os.Stderr, stderr)
+ if err := cmd.Run(); err != nil {
+ panic(fmt.Sprintf("'python run_test_server.py start' returned error %s", err))
+ }
+ }
+ {
+ cmd := exec.Command("python", "run_test_server.py", "start_keep")
+ stderr, err := cmd.StderrPipe()
+ if err != nil {
+ log.Fatalf("Setting up stderr pipe: %s", err)
+ }
+ go io.Copy(os.Stderr, stderr)
+ if err := cmd.Run(); err != nil {
+ panic(fmt.Sprintf("'python run_test_server.py start_keep' returned error %s", err))
+ }
+ }
+
+ os.Setenv("ARVADOS_API_HOST", "localhost:3000")
+ os.Setenv("ARVADOS_API_TOKEN", "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ os.Setenv("ARVADOS_API_HOST_INSECURE", "true")
+}
+
+func (s *ServerRequiredSuite) TearDownSuite(c *C) {
+ cwd, _ := os.Getwd()
+ defer os.Chdir(cwd)
+
+ os.Chdir(pythonDir())
+ exec.Command("python", "run_test_server.py", "stop_keep").Run()
+ exec.Command("python", "run_test_server.py", "stop").Run()
+}
+
+func setupProxyService() {
+
+ client := &http.Client{Transport: &http.Transport{
+ TLSClientConfig: &tls.Config{InsecureSkipVerify: true}}}
+
+ var req *http.Request
+ var err error
+ if req, err = http.NewRequest("POST", fmt.Sprintf("https://%s/arvados/v1/keep_services", os.Getenv("ARVADOS_API_HOST")), nil); err != nil {
+ panic(err.Error())
+ }
+ req.Header.Add("Authorization", fmt.Sprintf("OAuth2 %s", os.Getenv("ARVADOS_API_TOKEN")))
+
+ reader, writer := io.Pipe()
+
+ req.Body = reader
+
+ go func() {
+ data := url.Values{}
+ data.Set("keep_service", `{
+ "service_host": "localhost",
+ "service_port": 29950,
+ "service_ssl_flag": false,
+ "service_type": "proxy"
+}`)
+
+ writer.Write([]byte(data.Encode()))
+ writer.Close()
+ }()
+
+ var resp *http.Response
+ if resp, err = client.Do(req); err != nil {
+ panic(err.Error())
+ }
+ if resp.StatusCode != 200 {
+ panic(resp.Status)
+ }
+}
+
+func runProxy(c *C, args []string, token string, port int) keepclient.KeepClient {
+ os.Args = append(args, fmt.Sprintf("-listen=:%v", port))
+ os.Setenv("ARVADOS_API_TOKEN", "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+
+ listener = nil
+ go main()
+ time.Sleep(100 * time.Millisecond)
+
+ os.Setenv("ARVADOS_KEEP_PROXY", fmt.Sprintf("http://localhost:%v", port))
+ os.Setenv("ARVADOS_API_TOKEN", token)
+ arv, err := arvadosclient.MakeArvadosClient()
+ c.Assert(err, Equals, nil)
+ kc, err := keepclient.MakeKeepClient(&arv)
+ c.Assert(err, Equals, nil)
+ c.Check(kc.Using_proxy, Equals, true)
+ c.Check(len(kc.ServiceRoots()), Equals, 1)
+ for _, root := range kc.ServiceRoots() {
+ c.Check(root, Equals, fmt.Sprintf("http://localhost:%v", port))
+ }
+ os.Setenv("ARVADOS_KEEP_PROXY", "")
+ log.Print("keepclient created")
+ return kc
+}
+
+func (s *ServerRequiredSuite) TestPutAskGet(c *C) {
+ log.Print("TestPutAndGet start")
+
+ os.Args = []string{"keepproxy", "-listen=:29950"}
+ os.Setenv("ARVADOS_API_TOKEN", "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ listener = nil
+ go main()
+ time.Sleep(100 * time.Millisecond)
+
+ setupProxyService()
+
+ os.Setenv("ARVADOS_EXTERNAL_CLIENT", "true")
+ arv, err := arvadosclient.MakeArvadosClient()
+ c.Assert(err, Equals, nil)
+ kc, err := keepclient.MakeKeepClient(&arv)
+ c.Assert(err, Equals, nil)
+ c.Check(kc.Arvados.External, Equals, true)
+ c.Check(kc.Using_proxy, Equals, true)
+ c.Check(len(kc.ServiceRoots()), Equals, 1)
+ for _, root := range kc.ServiceRoots() {
+ c.Check(root, Equals, "http://localhost:29950")
+ }
+ os.Setenv("ARVADOS_EXTERNAL_CLIENT", "")
+ log.Print("keepclient created")
+
+ waitForListener()
+ defer closeListener()
+
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
+ var hash2 string
+
+ {
+ _, _, err := kc.Ask(hash)
+ c.Check(err, Equals, keepclient.BlockNotFound)
+ log.Print("Ask 1")
+ }
+
+ {
+ var rep int
+ var err error
+ hash2, rep, err = kc.PutB([]byte("foo"))
+ c.Check(hash2, Matches, fmt.Sprintf(`^%s\+3(\+.+)?$`, hash))
+ c.Check(rep, Equals, 2)
+ c.Check(err, Equals, nil)
+ log.Print("PutB")
+ }
+
+ {
+ blocklen, _, err := kc.Ask(hash2)
+ c.Assert(err, Equals, nil)
+ c.Check(blocklen, Equals, int64(3))
+ log.Print("Ask 2")
+ }
+
+ {
+ reader, blocklen, _, err := kc.Get(hash2)
+ c.Assert(err, Equals, nil)
+ all, err := ioutil.ReadAll(reader)
+ c.Check(all, DeepEquals, []byte("foo"))
+ c.Check(blocklen, Equals, int64(3))
+ log.Print("Get")
+ }
+
+ {
+ var rep int
+ var err error
+ hash2, rep, err = kc.PutB([]byte(""))
+ c.Check(hash2, Matches, `^d41d8cd98f00b204e9800998ecf8427e\+0(\+.+)?$`)
+ c.Check(rep, Equals, 2)
+ c.Check(err, Equals, nil)
+ log.Print("PutB zero block")
+ }
+
+ {
+ reader, blocklen, _, err := kc.Get("d41d8cd98f00b204e9800998ecf8427e")
+ c.Assert(err, Equals, nil)
+ all, err := ioutil.ReadAll(reader)
+ c.Check(all, DeepEquals, []byte(""))
+ c.Check(blocklen, Equals, int64(0))
+ log.Print("Get zero block")
+ }
+
+ log.Print("TestPutAndGet done")
+}
+
+func (s *ServerRequiredSuite) TestPutAskGetForbidden(c *C) {
+ log.Print("TestPutAskGetForbidden start")
+
+ kc := runProxy(c, []string{"keepproxy"}, "123abc", 29951)
+ waitForListener()
+ defer closeListener()
+
+ log.Print("keepclient created")
+
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("bar")))
+
+ {
+ _, _, err := kc.Ask(hash)
+ c.Check(err, Equals, keepclient.BlockNotFound)
+ log.Print("Ask 1")
+ }
+
+ {
+ hash2, rep, err := kc.PutB([]byte("bar"))
+ c.Check(hash2, Equals, "")
+ c.Check(rep, Equals, 0)
+ c.Check(err, Equals, keepclient.InsufficientReplicasError)
+ log.Print("PutB")
+ }
+
+ {
+ blocklen, _, err := kc.Ask(hash)
+ c.Assert(err, Equals, keepclient.BlockNotFound)
+ c.Check(blocklen, Equals, int64(0))
+ log.Print("Ask 2")
+ }
+
+ {
+ _, blocklen, _, err := kc.Get(hash)
+ c.Assert(err, Equals, keepclient.BlockNotFound)
+ c.Check(blocklen, Equals, int64(0))
+ log.Print("Get")
+ }
+
+ log.Print("TestPutAskGetForbidden done")
+}
+
+func (s *ServerRequiredSuite) TestGetDisabled(c *C) {
+ log.Print("TestGetDisabled start")
+
+ kc := runProxy(c, []string{"keepproxy", "-no-get"}, "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h", 29952)
+ waitForListener()
+ defer closeListener()
+
+ hash := fmt.Sprintf("%x", md5.Sum([]byte("baz")))
+
+ {
+ _, _, err := kc.Ask(hash)
+ c.Check(err, Equals, keepclient.BlockNotFound)
+ log.Print("Ask 1")
+ }
+
+ {
+ hash2, rep, err := kc.PutB([]byte("baz"))
+ c.Check(hash2, Matches, fmt.Sprintf(`^%s\+3(\+.+)?$`, hash))
+ c.Check(rep, Equals, 2)
+ c.Check(err, Equals, nil)
+ log.Print("PutB")
+ }
+
+ {
+ blocklen, _, err := kc.Ask(hash)
+ c.Assert(err, Equals, keepclient.BlockNotFound)
+ c.Check(blocklen, Equals, int64(0))
+ log.Print("Ask 2")
+ }
+
+ {
+ _, blocklen, _, err := kc.Get(hash)
+ c.Assert(err, Equals, keepclient.BlockNotFound)
+ c.Check(blocklen, Equals, int64(0))
+ log.Print("Get")
+ }
+
+ log.Print("TestGetDisabled done")
+}
+
+func (s *ServerRequiredSuite) TestPutDisabled(c *C) {
+ log.Print("TestPutDisabled start")
+
+ kc := runProxy(c, []string{"keepproxy", "-no-put"}, "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h", 29953)
+ waitForListener()
+ defer closeListener()
+
+ {
+ hash2, rep, err := kc.PutB([]byte("quux"))
+ c.Check(hash2, Equals, "")
+ c.Check(rep, Equals, 0)
+ c.Check(err, Equals, keepclient.InsufficientReplicasError)
+ log.Print("PutB")
+ }
+
+ log.Print("TestPutDisabled done")
+}
+
+func (s *ServerRequiredSuite) TestCorsHeaders(c *C) {
+ runProxy(c, []string{"keepproxy"}, "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h", 29954)
+ waitForListener()
+ defer closeListener()
+
+ {
+ client := http.Client{}
+ req, err := http.NewRequest("OPTIONS",
+ fmt.Sprintf("http://localhost:29954/%x+3",
+ md5.Sum([]byte("foo"))),
+ nil)
+ req.Header.Add("Access-Control-Request-Method", "PUT")
+ req.Header.Add("Access-Control-Request-Headers", "Authorization, X-Keep-Desired-Replicas")
+ resp, err := client.Do(req)
+ c.Check(err, Equals, nil)
+ c.Check(resp.StatusCode, Equals, 200)
+ body, err := ioutil.ReadAll(resp.Body)
+ c.Check(string(body), Equals, "")
+ c.Check(resp.Header.Get("Access-Control-Allow-Methods"), Equals, "GET, HEAD, POST, PUT, OPTIONS")
+ c.Check(resp.Header.Get("Access-Control-Allow-Origin"), Equals, "*")
+ }
+
+ {
+ resp, err := http.Get(
+ fmt.Sprintf("http://localhost:29954/%x+3",
+ md5.Sum([]byte("foo"))))
+ c.Check(err, Equals, nil)
+ c.Check(resp.Header.Get("Access-Control-Allow-Headers"), Equals, "Authorization, Content-Length, Content-Type, X-Keep-Desired-Replicas")
+ c.Check(resp.Header.Get("Access-Control-Allow-Origin"), Equals, "*")
+ }
+}
+
+func (s *ServerRequiredSuite) TestPostWithoutHash(c *C) {
+ runProxy(c, []string{"keepproxy"}, "4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h", 29955)
+ waitForListener()
+ defer closeListener()
+
+ {
+ client := http.Client{}
+ req, err := http.NewRequest("POST",
+ "http://localhost:29955/",
+ strings.NewReader("qux"))
+ req.Header.Add("Authorization", "OAuth2 4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h")
+ req.Header.Add("Content-Type", "application/octet-stream")
+ resp, err := client.Do(req)
+ c.Check(err, Equals, nil)
+ body, err := ioutil.ReadAll(resp.Body)
+ c.Check(err, Equals, nil)
+ c.Check(string(body), Equals,
+ fmt.Sprintf("%x+%d", md5.Sum([]byte("qux")), 3))
+ }
+}
--- /dev/null
+// Tests for Keep HTTP handlers:
+//
+// GetBlockHandler
+// PutBlockHandler
+// IndexHandler
+//
+// The HTTP handlers are responsible for enforcing permission policy,
+// so these tests must exercise all possible permission permutations.
+
+package main
+
+import (
+ "bytes"
+ "encoding/json"
+ "fmt"
+ "net/http"
+ "net/http/httptest"
+ "os"
+ "regexp"
+ "strings"
+ "testing"
+ "time"
+)
+
+// A RequestTester represents the parameters for an HTTP request to
+// be issued on behalf of a unit test.
+type RequestTester struct {
+ uri string
+ api_token string
+ method string
+ request_body []byte
+}
+
+// Test GetBlockHandler on the following situations:
+// - permissions off, unauthenticated request, unsigned locator
+// - permissions on, authenticated request, signed locator
+// - permissions on, authenticated request, unsigned locator
+// - permissions on, unauthenticated request, signed locator
+// - permissions on, authenticated request, expired locator
+//
+func TestGetHandler(t *testing.T) {
+ defer teardown()
+
+ // Prepare two test Keep volumes. Our block is stored on the second volume.
+ KeepVM = MakeTestVolumeManager(2)
+ defer KeepVM.Quit()
+
+ vols := KeepVM.Volumes()
+ if err := vols[0].Put(TEST_HASH, TEST_BLOCK); err != nil {
+ t.Error(err)
+ }
+
+ // Create locators for testing.
+ // Turn on permission settings so we can generate signed locators.
+ enforce_permissions = true
+ PermissionSecret = []byte(known_key)
+ permission_ttl = time.Duration(300) * time.Second
+
+ var (
+ unsigned_locator = "/" + TEST_HASH
+ valid_timestamp = time.Now().Add(permission_ttl)
+ expired_timestamp = time.Now().Add(-time.Hour)
+ signed_locator = "/" + SignLocator(TEST_HASH, known_token, valid_timestamp)
+ expired_locator = "/" + SignLocator(TEST_HASH, known_token, expired_timestamp)
+ )
+
+ // -----------------
+ // Test unauthenticated request with permissions off.
+ enforce_permissions = false
+
+ // Unauthenticated request, unsigned locator
+ // => OK
+ response := IssueRequest(
+ &RequestTester{
+ method: "GET",
+ uri: unsigned_locator,
+ })
+ ExpectStatusCode(t,
+ "Unauthenticated request, unsigned locator", http.StatusOK, response)
+ ExpectBody(t,
+ "Unauthenticated request, unsigned locator",
+ string(TEST_BLOCK),
+ response)
+
+ received_cl := response.Header().Get("Content-Length")
+ expected_cl := fmt.Sprintf("%d", len(TEST_BLOCK))
+ if received_cl != expected_cl {
+ t.Errorf("expected Content-Length %s, got %s", expected_cl, received_cl)
+ }
+
+ // ----------------
+ // Permissions: on.
+ enforce_permissions = true
+
+ // Authenticated request, signed locator
+ // => OK
+ response = IssueRequest(&RequestTester{
+ method: "GET",
+ uri: signed_locator,
+ api_token: known_token,
+ })
+ ExpectStatusCode(t,
+ "Authenticated request, signed locator", http.StatusOK, response)
+ ExpectBody(t,
+ "Authenticated request, signed locator", string(TEST_BLOCK), response)
+
+ received_cl = response.Header().Get("Content-Length")
+ expected_cl = fmt.Sprintf("%d", len(TEST_BLOCK))
+ if received_cl != expected_cl {
+ t.Errorf("expected Content-Length %s, got %s", expected_cl, received_cl)
+ }
+
+ // Authenticated request, unsigned locator
+ // => PermissionError
+ response = IssueRequest(&RequestTester{
+ method: "GET",
+ uri: unsigned_locator,
+ api_token: known_token,
+ })
+ ExpectStatusCode(t, "unsigned locator", PermissionError.HTTPCode, response)
+
+ // Unauthenticated request, signed locator
+ // => PermissionError
+ response = IssueRequest(&RequestTester{
+ method: "GET",
+ uri: signed_locator,
+ })
+ ExpectStatusCode(t,
+ "Unauthenticated request, signed locator",
+ PermissionError.HTTPCode, response)
+
+ // Authenticated request, expired locator
+ // => ExpiredError
+ response = IssueRequest(&RequestTester{
+ method: "GET",
+ uri: expired_locator,
+ api_token: known_token,
+ })
+ ExpectStatusCode(t,
+ "Authenticated request, expired locator",
+ ExpiredError.HTTPCode, response)
+}
+
+// Test PutBlockHandler on the following situations:
+// - no server key
+// - with server key, authenticated request, unsigned locator
+// - with server key, unauthenticated request, unsigned locator
+//
+func TestPutHandler(t *testing.T) {
+ defer teardown()
+
+ // Prepare two test Keep volumes.
+ KeepVM = MakeTestVolumeManager(2)
+ defer KeepVM.Quit()
+
+ // --------------
+ // No server key.
+
+ // Unauthenticated request, no server key
+ // => OK (unsigned response)
+ unsigned_locator := "/" + TEST_HASH
+ response := IssueRequest(
+ &RequestTester{
+ method: "PUT",
+ uri: unsigned_locator,
+ request_body: TEST_BLOCK,
+ })
+
+ ExpectStatusCode(t,
+ "Unauthenticated request, no server key", http.StatusOK, response)
+ ExpectBody(t,
+ "Unauthenticated request, no server key",
+ TEST_HASH_PUT_RESPONSE, response)
+
+ // ------------------
+ // With a server key.
+
+ PermissionSecret = []byte(known_key)
+ permission_ttl = time.Duration(300) * time.Second
+
+ // When a permission key is available, the locator returned
+ // from an authenticated PUT request will be signed.
+
+ // Authenticated PUT, signed locator
+ // => OK (signed response)
+ response = IssueRequest(
+ &RequestTester{
+ method: "PUT",
+ uri: unsigned_locator,
+ request_body: TEST_BLOCK,
+ api_token: known_token,
+ })
+
+ ExpectStatusCode(t,
+ "Authenticated PUT, signed locator, with server key",
+ http.StatusOK, response)
+ response_locator := strings.TrimSpace(response.Body.String())
+ if !VerifySignature(response_locator, known_token) {
+ t.Errorf("Authenticated PUT, signed locator, with server key:\n"+
+ "response '%s' does not contain a valid signature",
+ response_locator)
+ }
+
+ // Unauthenticated PUT, unsigned locator
+ // => OK
+ response = IssueRequest(
+ &RequestTester{
+ method: "PUT",
+ uri: unsigned_locator,
+ request_body: TEST_BLOCK,
+ })
+
+ ExpectStatusCode(t,
+ "Unauthenticated PUT, unsigned locator, with server key",
+ http.StatusOK, response)
+ ExpectBody(t,
+ "Unauthenticated PUT, unsigned locator, with server key",
+ TEST_HASH_PUT_RESPONSE, response)
+}
+
+// Test /index requests:
+// - unauthenticated /index request
+// - unauthenticated /index/prefix request
+// - authenticated /index request | non-superuser
+// - authenticated /index/prefix request | non-superuser
+// - authenticated /index request | superuser
+// - authenticated /index/prefix request | superuser
+//
+// The only /index requests that should succeed are those issued by the
+// superuser. They should pass regardless of the value of enforce_permissions.
+//
+func TestIndexHandler(t *testing.T) {
+ defer teardown()
+
+ // Set up Keep volumes and populate them.
+ // Include multiple blocks on different volumes, and
+ // some metadata files (which should be omitted from index listings)
+ KeepVM = MakeTestVolumeManager(2)
+ defer KeepVM.Quit()
+
+ vols := KeepVM.Volumes()
+ vols[0].Put(TEST_HASH, TEST_BLOCK)
+ vols[1].Put(TEST_HASH_2, TEST_BLOCK_2)
+ vols[0].Put(TEST_HASH+".meta", []byte("metadata"))
+ vols[1].Put(TEST_HASH_2+".meta", []byte("metadata"))
+
+ data_manager_token = "DATA MANAGER TOKEN"
+
+ unauthenticated_req := &RequestTester{
+ method: "GET",
+ uri: "/index",
+ }
+ authenticated_req := &RequestTester{
+ method: "GET",
+ uri: "/index",
+ api_token: known_token,
+ }
+ superuser_req := &RequestTester{
+ method: "GET",
+ uri: "/index",
+ api_token: data_manager_token,
+ }
+ unauth_prefix_req := &RequestTester{
+ method: "GET",
+ uri: "/index/" + TEST_HASH[0:3],
+ }
+ auth_prefix_req := &RequestTester{
+ method: "GET",
+ uri: "/index/" + TEST_HASH[0:3],
+ api_token: known_token,
+ }
+ superuser_prefix_req := &RequestTester{
+ method: "GET",
+ uri: "/index/" + TEST_HASH[0:3],
+ api_token: data_manager_token,
+ }
+
+ // -------------------------------------------------------------
+ // Only the superuser should be allowed to issue /index requests.
+
+ // ---------------------------
+ // enforce_permissions enabled
+ // This setting should not affect tests passing.
+ enforce_permissions = true
+
+ // unauthenticated /index request
+ // => UnauthorizedError
+ response := IssueRequest(unauthenticated_req)
+ ExpectStatusCode(t,
+ "enforce_permissions on, unauthenticated request",
+ UnauthorizedError.HTTPCode,
+ response)
+
+ // unauthenticated /index/prefix request
+ // => UnauthorizedError
+ response = IssueRequest(unauth_prefix_req)
+ ExpectStatusCode(t,
+ "permissions on, unauthenticated /index/prefix request",
+ UnauthorizedError.HTTPCode,
+ response)
+
+ // authenticated /index request, non-superuser
+ // => UnauthorizedError
+ response = IssueRequest(authenticated_req)
+ ExpectStatusCode(t,
+ "permissions on, authenticated request, non-superuser",
+ UnauthorizedError.HTTPCode,
+ response)
+
+ // authenticated /index/prefix request, non-superuser
+ // => UnauthorizedError
+ response = IssueRequest(auth_prefix_req)
+ ExpectStatusCode(t,
+ "permissions on, authenticated /index/prefix request, non-superuser",
+ UnauthorizedError.HTTPCode,
+ response)
+
+ // superuser /index request
+ // => OK
+ response = IssueRequest(superuser_req)
+ ExpectStatusCode(t,
+ "permissions on, superuser request",
+ http.StatusOK,
+ response)
+
+ // ----------------------------
+ // enforce_permissions disabled
+ // Valid Request should still pass.
+ enforce_permissions = false
+
+ // superuser /index request
+ // => OK
+ response = IssueRequest(superuser_req)
+ ExpectStatusCode(t,
+ "permissions on, superuser request",
+ http.StatusOK,
+ response)
+
+ expected := `^` + TEST_HASH + `\+\d+ \d+\n` +
+ TEST_HASH_2 + `\+\d+ \d+\n$`
+ match, _ := regexp.MatchString(expected, response.Body.String())
+ if !match {
+ t.Errorf(
+ "permissions on, superuser request: expected %s, got:\n%s",
+ expected, response.Body.String())
+ }
+
+ // superuser /index/prefix request
+ // => OK
+ response = IssueRequest(superuser_prefix_req)
+ ExpectStatusCode(t,
+ "permissions on, superuser request",
+ http.StatusOK,
+ response)
+
+ expected = `^` + TEST_HASH + `\+\d+ \d+\n$`
+ match, _ = regexp.MatchString(expected, response.Body.String())
+ if !match {
+ t.Errorf(
+ "permissions on, superuser /index/prefix request: expected %s, got:\n%s",
+ expected, response.Body.String())
+ }
+}
+
+// TestDeleteHandler
+//
+// Cases tested:
+//
+// With no token and with a non-data-manager token:
+// * Delete existing block
+// (test for 403 Forbidden, confirm block not deleted)
+//
+// With data manager token:
+//
+// * Delete existing block
+// (test for 200 OK, response counts, confirm block deleted)
+//
+// * Delete nonexistent block
+// (test for 200 OK, response counts)
+//
+// TODO(twp):
+//
+// * Delete block on read-only and read-write volume
+// (test for 200 OK, response with copies_deleted=1,
+// copies_failed=1, confirm block deleted only on r/w volume)
+//
+// * Delete block on read-only volume only
+// (test for 200 OK, response with copies_deleted=0, copies_failed=1,
+// confirm block not deleted)
+//
+func TestDeleteHandler(t *testing.T) {
+ defer teardown()
+
+ // Set up Keep volumes and populate them.
+ // Include multiple blocks on different volumes, and
+ // some metadata files (which should be omitted from index listings)
+ KeepVM = MakeTestVolumeManager(2)
+ defer KeepVM.Quit()
+
+ vols := KeepVM.Volumes()
+ vols[0].Put(TEST_HASH, TEST_BLOCK)
+
+ // Explicitly set the permission_ttl to 0 for these
+ // tests, to ensure the MockVolume deletes the blocks
+ // even though they have just been created.
+ permission_ttl = time.Duration(0)
+
+ var user_token = "NOT DATA MANAGER TOKEN"
+ data_manager_token = "DATA MANAGER TOKEN"
+
+ unauth_req := &RequestTester{
+ method: "DELETE",
+ uri: "/" + TEST_HASH,
+ }
+
+ user_req := &RequestTester{
+ method: "DELETE",
+ uri: "/" + TEST_HASH,
+ api_token: user_token,
+ }
+
+ superuser_existing_block_req := &RequestTester{
+ method: "DELETE",
+ uri: "/" + TEST_HASH,
+ api_token: data_manager_token,
+ }
+
+ superuser_nonexistent_block_req := &RequestTester{
+ method: "DELETE",
+ uri: "/" + TEST_HASH_2,
+ api_token: data_manager_token,
+ }
+
+ // Unauthenticated request returns PermissionError.
+ var response *httptest.ResponseRecorder
+ response = IssueRequest(unauth_req)
+ ExpectStatusCode(t,
+ "unauthenticated request",
+ PermissionError.HTTPCode,
+ response)
+
+ // Authenticated non-admin request returns PermissionError.
+ response = IssueRequest(user_req)
+ ExpectStatusCode(t,
+ "authenticated non-admin request",
+ PermissionError.HTTPCode,
+ response)
+
+ // Authenticated admin request for nonexistent block.
+ type deletecounter struct {
+ Deleted int `json:"copies_deleted"`
+ Failed int `json:"copies_failed"`
+ }
+ var response_dc, expected_dc deletecounter
+
+ response = IssueRequest(superuser_nonexistent_block_req)
+ ExpectStatusCode(t,
+ "data manager request, nonexistent block",
+ http.StatusNotFound,
+ response)
+
+ // Authenticated admin request for existing block while never_delete is set.
+ never_delete = true
+ response = IssueRequest(superuser_existing_block_req)
+ ExpectStatusCode(t,
+ "authenticated request, existing block, method disabled",
+ MethodDisabledError.HTTPCode,
+ response)
+ never_delete = false
+
+ // Authenticated admin request for existing block.
+ response = IssueRequest(superuser_existing_block_req)
+ ExpectStatusCode(t,
+ "data manager request, existing block",
+ http.StatusOK,
+ response)
+ // Expect response {"copies_deleted":1,"copies_failed":0}
+ expected_dc = deletecounter{1, 0}
+ json.NewDecoder(response.Body).Decode(&response_dc)
+ if response_dc != expected_dc {
+ t.Errorf("superuser_existing_block_req\nexpected: %+v\nreceived: %+v",
+ expected_dc, response_dc)
+ }
+ // Confirm the block has been deleted
+ _, err := vols[0].Get(TEST_HASH)
+ var block_deleted = os.IsNotExist(err)
+ if !block_deleted {
+ t.Error("superuser_existing_block_req: block not deleted")
+ }
+
+ // A DELETE request on a block newer than permission_ttl should return
+ // success but leave the block on the volume.
+ vols[0].Put(TEST_HASH, TEST_BLOCK)
+ permission_ttl = time.Duration(1) * time.Hour
+
+ response = IssueRequest(superuser_existing_block_req)
+ ExpectStatusCode(t,
+ "data manager request, existing block",
+ http.StatusOK,
+ response)
+ // Expect response {"copies_deleted":1,"copies_failed":0}
+ expected_dc = deletecounter{1, 0}
+ json.NewDecoder(response.Body).Decode(&response_dc)
+ if response_dc != expected_dc {
+ t.Errorf("superuser_existing_block_req\nexpected: %+v\nreceived: %+v",
+ expected_dc, response_dc)
+ }
+ // Confirm the block has NOT been deleted.
+ _, err = vols[0].Get(TEST_HASH)
+ if err != nil {
+ t.Errorf("testing delete on new block: %s\n", err)
+ }
+}
+
+// TestPullHandler
+//
+// Test handling of the PUT /pull statement.
+//
+// Cases tested: syntactically valid and invalid pull lists, from the
+// data manager and from unprivileged users:
+//
+// 1. Valid pull list from an ordinary user
+// (expected result: 401 Unauthorized)
+//
+// 2. Invalid pull request from an ordinary user
+// (expected result: 401 Unauthorized)
+//
+// 3. Valid pull request from the data manager
+// (expected result: 200 OK with request body "Received 3 pull
+// requests"
+//
+// 4. Invalid pull request from the data manager
+// (expected result: 400 Bad Request)
+//
+// Test that in the end, the pull manager received a good pull list with
+// the expected number of requests.
+//
+// TODO(twp): test concurrency: launch 100 goroutines to update the
+// pull list simultaneously. Make sure that none of them return 400
+// Bad Request and that pullq.GetList() returns a valid list.
+//
+func TestPullHandler(t *testing.T) {
+ defer teardown()
+
+ var user_token = "USER TOKEN"
+ data_manager_token = "DATA MANAGER TOKEN"
+
+ good_json := []byte(`[
+ {
+ "locator":"locator_with_two_servers",
+ "servers":[
+ "server1",
+ "server2"
+ ]
+ },
+ {
+ "locator":"locator_with_no_servers",
+ "servers":[]
+ },
+ {
+ "locator":"",
+ "servers":["empty_locator"]
+ }
+ ]`)
+
+ bad_json := []byte(`{ "key":"I'm a little teapot" }`)
+
+ type pullTest struct {
+ name string
+ req RequestTester
+ response_code int
+ response_body string
+ }
+ var testcases = []pullTest{
+ {
+ "Valid pull list from an ordinary user",
+ RequestTester{"/pull", user_token, "PUT", good_json},
+ http.StatusUnauthorized,
+ "Unauthorized\n",
+ },
+ {
+ "Invalid pull request from an ordinary user",
+ RequestTester{"/pull", user_token, "PUT", bad_json},
+ http.StatusUnauthorized,
+ "Unauthorized\n",
+ },
+ {
+ "Valid pull request from the data manager",
+ RequestTester{"/pull", data_manager_token, "PUT", good_json},
+ http.StatusOK,
+ "Received 3 pull requests\n",
+ },
+ {
+ "Invalid pull request from the data manager",
+ RequestTester{"/pull", data_manager_token, "PUT", bad_json},
+ http.StatusBadRequest,
+ "Bad Request\n",
+ },
+ }
+
+ for _, tst := range testcases {
+ response := IssueRequest(&tst.req)
+ ExpectStatusCode(t, tst.name, tst.response_code, response)
+ ExpectBody(t, tst.name, tst.response_body, response)
+ }
+
+ // The Keep pull manager should have received one good list with 3
+ // requests on it.
+ for i := 0; i < 3; i++ {
+ item := <-pullq.NextItem
+ if _, ok := item.(PullRequest); !ok {
+ t.Errorf("item %v could not be parsed as a PullRequest", item)
+ }
+ }
+
+ expectChannelEmpty(t, pullq.NextItem)
+}
+
+// TestTrashHandler
+//
+// Test cases:
+//
+// Cases tested: syntactically valid and invalid trash lists, from the
+// data manager and from unprivileged users:
+//
+// 1. Valid trash list from an ordinary user
+// (expected result: 401 Unauthorized)
+//
+// 2. Invalid trash list from an ordinary user
+// (expected result: 401 Unauthorized)
+//
+// 3. Valid trash list from the data manager
+// (expected result: 200 OK with request body "Received 3 trash
+// requests"
+//
+// 4. Invalid trash list from the data manager
+// (expected result: 400 Bad Request)
+//
+// Test that in the end, the trash collector received a good list
+// trash list with the expected number of requests.
+//
+// TODO(twp): test concurrency: launch 100 goroutines to update the
+// pull list simultaneously. Make sure that none of them return 400
+// Bad Request and that replica.Dump() returns a valid list.
+//
+func TestTrashHandler(t *testing.T) {
+ defer teardown()
+
+ var user_token = "USER TOKEN"
+ data_manager_token = "DATA MANAGER TOKEN"
+
+ good_json := []byte(`[
+ {
+ "locator":"block1",
+ "block_mtime":1409082153
+ },
+ {
+ "locator":"block2",
+ "block_mtime":1409082153
+ },
+ {
+ "locator":"block3",
+ "block_mtime":1409082153
+ }
+ ]`)
+
+ bad_json := []byte(`I am not a valid JSON string`)
+
+ type trashTest struct {
+ name string
+ req RequestTester
+ response_code int
+ response_body string
+ }
+
+ var testcases = []trashTest{
+ {
+ "Valid trash list from an ordinary user",
+ RequestTester{"/trash", user_token, "PUT", good_json},
+ http.StatusUnauthorized,
+ "Unauthorized\n",
+ },
+ {
+ "Invalid trash list from an ordinary user",
+ RequestTester{"/trash", user_token, "PUT", bad_json},
+ http.StatusUnauthorized,
+ "Unauthorized\n",
+ },
+ {
+ "Valid trash list from the data manager",
+ RequestTester{"/trash", data_manager_token, "PUT", good_json},
+ http.StatusOK,
+ "Received 3 trash requests\n",
+ },
+ {
+ "Invalid trash list from the data manager",
+ RequestTester{"/trash", data_manager_token, "PUT", bad_json},
+ http.StatusBadRequest,
+ "Bad Request\n",
+ },
+ }
+
+ for _, tst := range testcases {
+ response := IssueRequest(&tst.req)
+ ExpectStatusCode(t, tst.name, tst.response_code, response)
+ ExpectBody(t, tst.name, tst.response_body, response)
+ }
+
+ // The trash collector should have received one good list with 3
+ // requests on it.
+ for i := 0; i < 3; i++ {
+ item := <-trashq.NextItem
+ if _, ok := item.(TrashRequest); !ok {
+ t.Errorf("item %v could not be parsed as a TrashRequest", item)
+ }
+ }
+
+ expectChannelEmpty(t, trashq.NextItem)
+}
+
+// ====================
+// Helper functions
+// ====================
+
+// IssueTestRequest executes an HTTP request described by rt, to a
+// REST router. It returns the HTTP response to the request.
+func IssueRequest(rt *RequestTester) *httptest.ResponseRecorder {
+ response := httptest.NewRecorder()
+ body := bytes.NewReader(rt.request_body)
+ req, _ := http.NewRequest(rt.method, rt.uri, body)
+ if rt.api_token != "" {
+ req.Header.Set("Authorization", "OAuth2 "+rt.api_token)
+ }
+ loggingRouter := MakeLoggingRESTRouter()
+ loggingRouter.ServeHTTP(response, req)
+ return response
+}
+
+// ExpectStatusCode checks whether a response has the specified status code,
+// and reports a test failure if not.
+func ExpectStatusCode(
+ t *testing.T,
+ testname string,
+ expected_status int,
+ response *httptest.ResponseRecorder) {
+ if response.Code != expected_status {
+ t.Errorf("%s: expected status %s, got %+v",
+ testname, expected_status, response)
+ }
+}
+
+func ExpectBody(
+ t *testing.T,
+ testname string,
+ expected_body string,
+ response *httptest.ResponseRecorder) {
+ if response.Body.String() != expected_body {
+ t.Errorf("%s: expected response body '%s', got %+v",
+ testname, expected_body, response)
+ }
+}
--- /dev/null
+package main
+
+// REST handlers for Keep are implemented here.
+//
+// GetBlockHandler (GET /locator)
+// PutBlockHandler (PUT /locator)
+// IndexHandler (GET /index, GET /index/prefix)
+// StatusHandler (GET /status.json)
+
+import (
+ "bufio"
+ "bytes"
+ "container/list"
+ "crypto/md5"
+ "encoding/json"
+ "fmt"
+ "github.com/gorilla/mux"
+ "io"
+ "log"
+ "net/http"
+ "os"
+ "regexp"
+ "runtime"
+ "strconv"
+ "strings"
+ "syscall"
+ "time"
+)
+
+// MakeRESTRouter returns a new mux.Router that forwards all Keep
+// requests to the appropriate handlers.
+//
+func MakeRESTRouter() *mux.Router {
+ rest := mux.NewRouter()
+
+ rest.HandleFunc(
+ `/{hash:[0-9a-f]{32}}`, GetBlockHandler).Methods("GET", "HEAD")
+ rest.HandleFunc(
+ `/{hash:[0-9a-f]{32}}+{hints}`,
+ GetBlockHandler).Methods("GET", "HEAD")
+
+ rest.HandleFunc(`/{hash:[0-9a-f]{32}}`, PutBlockHandler).Methods("PUT")
+ rest.HandleFunc(`/{hash:[0-9a-f]{32}}`, DeleteHandler).Methods("DELETE")
+
+ // For IndexHandler we support:
+ // /index - returns all locators
+ // /index/{prefix} - returns all locators that begin with {prefix}
+ // {prefix} is a string of hexadecimal digits between 0 and 32 digits.
+ // If {prefix} is the empty string, return an index of all locators
+ // (so /index and /index/ behave identically)
+ // A client may supply a full 32-digit locator string, in which
+ // case the server will return an index with either zero or one
+ // entries. This usage allows a client to check whether a block is
+ // present, and its size and upload time, without retrieving the
+ // entire block.
+ //
+ rest.HandleFunc(`/index`, IndexHandler).Methods("GET", "HEAD")
+ rest.HandleFunc(
+ `/index/{prefix:[0-9a-f]{0,32}}`, IndexHandler).Methods("GET", "HEAD")
+ rest.HandleFunc(`/status.json`, StatusHandler).Methods("GET", "HEAD")
+
+ // The PullHandler and TrashHandler process "PUT /pull" and "PUT
+ // /trash" requests from Data Manager. These requests instruct
+ // Keep to replicate or delete blocks; see
+ // https://arvados.org/projects/arvados/wiki/Keep_Design_Doc
+ // for more details.
+ //
+ // Each handler parses the JSON list of block management requests
+ // in the message body, and replaces any existing pull queue or
+ // trash queue with their contentes.
+ //
+ rest.HandleFunc(`/pull`, PullHandler).Methods("PUT")
+ rest.HandleFunc(`/trash`, TrashHandler).Methods("PUT")
+
+ // Any request which does not match any of these routes gets
+ // 400 Bad Request.
+ rest.NotFoundHandler = http.HandlerFunc(BadRequestHandler)
+
+ return rest
+}
+
+func BadRequestHandler(w http.ResponseWriter, r *http.Request) {
+ http.Error(w, BadRequestError.Error(), BadRequestError.HTTPCode)
+}
+
+// FindKeepVolumes scans all mounted volumes on the system for Keep
+// volumes, and returns a list of matching paths.
+//
+// A device is assumed to be a Keep volume if it is a normal or tmpfs
+// volume and has a "/keep" directory directly underneath the mount
+// point.
+//
+func FindKeepVolumes() []string {
+ vols := make([]string, 0)
+
+ if f, err := os.Open(PROC_MOUNTS); err != nil {
+ log.Fatalf("opening %s: %s\n", PROC_MOUNTS, err)
+ } else {
+ scanner := bufio.NewScanner(f)
+ for scanner.Scan() {
+ args := strings.Fields(scanner.Text())
+ dev, mount := args[0], args[1]
+ if mount != "/" &&
+ (dev == "tmpfs" || strings.HasPrefix(dev, "/dev/")) {
+ keep := mount + "/keep"
+ if st, err := os.Stat(keep); err == nil && st.IsDir() {
+ vols = append(vols, keep)
+ }
+ }
+ }
+ if err := scanner.Err(); err != nil {
+ log.Fatal(err)
+ }
+ }
+ return vols
+}
+
+func GetBlockHandler(resp http.ResponseWriter, req *http.Request) {
+ hash := mux.Vars(req)["hash"]
+
+ hints := mux.Vars(req)["hints"]
+
+ // Parse the locator string and hints from the request.
+ // TODO(twp): implement a Locator type.
+ var signature, timestamp string
+ if hints != "" {
+ signature_pat, _ := regexp.Compile("^A([[:xdigit:]]+)@([[:xdigit:]]{8})$")
+ for _, hint := range strings.Split(hints, "+") {
+ if match, _ := regexp.MatchString("^[[:digit:]]+$", hint); match {
+ // Server ignores size hints
+ } else if m := signature_pat.FindStringSubmatch(hint); m != nil {
+ signature = m[1]
+ timestamp = m[2]
+ } else if match, _ := regexp.MatchString("^[[:upper:]]", hint); match {
+ // Any unknown hint that starts with an uppercase letter is
+ // presumed to be valid and ignored, to permit forward compatibility.
+ } else {
+ // Unknown format; not a valid locator.
+ http.Error(resp, BadRequestError.Error(), BadRequestError.HTTPCode)
+ return
+ }
+ }
+ }
+
+ // If permission checking is in effect, verify this
+ // request's permission signature.
+ if enforce_permissions {
+ if signature == "" || timestamp == "" {
+ http.Error(resp, PermissionError.Error(), PermissionError.HTTPCode)
+ return
+ } else if IsExpired(timestamp) {
+ http.Error(resp, ExpiredError.Error(), ExpiredError.HTTPCode)
+ return
+ } else {
+ req_locator := req.URL.Path[1:] // strip leading slash
+ if !VerifySignature(req_locator, GetApiToken(req)) {
+ http.Error(resp, PermissionError.Error(), PermissionError.HTTPCode)
+ return
+ }
+ }
+ }
+
+ block, err := GetBlock(hash, false)
+
+ // Garbage collect after each GET. Fixes #2865.
+ // TODO(twp): review Keep memory usage and see if there's
+ // a better way to do this than blindly garbage collecting
+ // after every block.
+ defer runtime.GC()
+
+ if err != nil {
+ // This type assertion is safe because the only errors
+ // GetBlock can return are DiskHashError or NotFoundError.
+ http.Error(resp, err.Error(), err.(*KeepError).HTTPCode)
+ return
+ }
+
+ resp.Header().Set("Content-Length", fmt.Sprintf("%d", len(block)))
+
+ _, err = resp.Write(block)
+
+ return
+}
+
+func PutBlockHandler(resp http.ResponseWriter, req *http.Request) {
+ // Garbage collect after each PUT. Fixes #2865.
+ // See also GetBlockHandler.
+ defer runtime.GC()
+
+ hash := mux.Vars(req)["hash"]
+
+ // Read the block data to be stored.
+ // If the request exceeds BLOCKSIZE bytes, issue a HTTP 500 error.
+ //
+ if req.ContentLength > BLOCKSIZE {
+ http.Error(resp, TooLongError.Error(), TooLongError.HTTPCode)
+ return
+ }
+
+ buf := make([]byte, req.ContentLength)
+ nread, err := io.ReadFull(req.Body, buf)
+ if err != nil {
+ http.Error(resp, err.Error(), 500)
+ } else if int64(nread) < req.ContentLength {
+ http.Error(resp, "request truncated", 500)
+ } else {
+ if err := PutBlock(buf, hash); err == nil {
+ // Success; add a size hint, sign the locator if
+ // possible, and return it to the client.
+ return_hash := fmt.Sprintf("%s+%d", hash, len(buf))
+ api_token := GetApiToken(req)
+ if PermissionSecret != nil && api_token != "" {
+ expiry := time.Now().Add(permission_ttl)
+ return_hash = SignLocator(return_hash, api_token, expiry)
+ }
+ resp.Write([]byte(return_hash + "\n"))
+ } else {
+ ke := err.(*KeepError)
+ http.Error(resp, ke.Error(), ke.HTTPCode)
+ }
+ }
+ return
+}
+
+// IndexHandler
+// A HandleFunc to address /index and /index/{prefix} requests.
+//
+func IndexHandler(resp http.ResponseWriter, req *http.Request) {
+ // Reject unauthorized requests.
+ if !IsDataManagerToken(GetApiToken(req)) {
+ http.Error(resp, UnauthorizedError.Error(), UnauthorizedError.HTTPCode)
+ return
+ }
+
+ prefix := mux.Vars(req)["prefix"]
+
+ var index string
+ for _, vol := range KeepVM.Volumes() {
+ index = index + vol.Index(prefix)
+ }
+ resp.Write([]byte(index))
+}
+
+// StatusHandler
+// Responds to /status.json requests with the current node status,
+// described in a JSON structure.
+//
+// The data given in a status.json response includes:
+// volumes - a list of Keep volumes currently in use by this server
+// each volume is an object with the following fields:
+// * mount_point
+// * device_num (an integer identifying the underlying filesystem)
+// * bytes_free
+// * bytes_used
+//
+type VolumeStatus struct {
+ MountPoint string `json:"mount_point"`
+ DeviceNum uint64 `json:"device_num"`
+ BytesFree uint64 `json:"bytes_free"`
+ BytesUsed uint64 `json:"bytes_used"`
+}
+
+type NodeStatus struct {
+ Volumes []*VolumeStatus `json:"volumes"`
+}
+
+func StatusHandler(resp http.ResponseWriter, req *http.Request) {
+ st := GetNodeStatus()
+ if jstat, err := json.Marshal(st); err == nil {
+ resp.Write(jstat)
+ } else {
+ log.Printf("json.Marshal: %s\n", err)
+ log.Printf("NodeStatus = %v\n", st)
+ http.Error(resp, err.Error(), 500)
+ }
+}
+
+// GetNodeStatus
+// Returns a NodeStatus struct describing this Keep
+// node's current status.
+//
+func GetNodeStatus() *NodeStatus {
+ st := new(NodeStatus)
+
+ st.Volumes = make([]*VolumeStatus, len(KeepVM.Volumes()))
+ for i, vol := range KeepVM.Volumes() {
+ st.Volumes[i] = vol.Status()
+ }
+ return st
+}
+
+// GetVolumeStatus
+// Returns a VolumeStatus describing the requested volume.
+//
+func GetVolumeStatus(volume string) *VolumeStatus {
+ var fs syscall.Statfs_t
+ var devnum uint64
+
+ if fi, err := os.Stat(volume); err == nil {
+ devnum = fi.Sys().(*syscall.Stat_t).Dev
+ } else {
+ log.Printf("GetVolumeStatus: os.Stat: %s\n", err)
+ return nil
+ }
+
+ err := syscall.Statfs(volume, &fs)
+ if err != nil {
+ log.Printf("GetVolumeStatus: statfs: %s\n", err)
+ return nil
+ }
+ // These calculations match the way df calculates disk usage:
+ // "free" space is measured by fs.Bavail, but "used" space
+ // uses fs.Blocks - fs.Bfree.
+ free := fs.Bavail * uint64(fs.Bsize)
+ used := (fs.Blocks - fs.Bfree) * uint64(fs.Bsize)
+ return &VolumeStatus{volume, devnum, free, used}
+}
+
+// DeleteHandler processes DELETE requests.
+//
+// DELETE /{hash:[0-9a-f]{32} will delete the block with the specified hash
+// from all connected volumes.
+//
+// Only the Data Manager, or an Arvados admin with scope "all", are
+// allowed to issue DELETE requests. If a DELETE request is not
+// authenticated or is issued by a non-admin user, the server returns
+// a PermissionError.
+//
+// Upon receiving a valid request from an authorized user,
+// DeleteHandler deletes all copies of the specified block on local
+// writable volumes.
+//
+// Response format:
+//
+// If the requested blocks was not found on any volume, the response
+// code is HTTP 404 Not Found.
+//
+// Otherwise, the response code is 200 OK, with a response body
+// consisting of the JSON message
+//
+// {"copies_deleted":d,"copies_failed":f}
+//
+// where d and f are integers representing the number of blocks that
+// were successfully and unsuccessfully deleted.
+//
+func DeleteHandler(resp http.ResponseWriter, req *http.Request) {
+ hash := mux.Vars(req)["hash"]
+
+ // Confirm that this user is an admin and has a token with unlimited scope.
+ var tok = GetApiToken(req)
+ if tok == "" || !CanDelete(tok) {
+ http.Error(resp, PermissionError.Error(), PermissionError.HTTPCode)
+ return
+ }
+
+ if never_delete {
+ http.Error(resp, MethodDisabledError.Error(), MethodDisabledError.HTTPCode)
+ return
+ }
+
+ // Delete copies of this block from all available volumes. Report
+ // how many blocks were successfully and unsuccessfully
+ // deleted.
+ var result struct {
+ Deleted int `json:"copies_deleted"`
+ Failed int `json:"copies_failed"`
+ }
+ for _, vol := range KeepVM.Volumes() {
+ if err := vol.Delete(hash); err == nil {
+ result.Deleted++
+ } else if os.IsNotExist(err) {
+ continue
+ } else {
+ result.Failed++
+ log.Println("DeleteHandler:", err)
+ }
+ }
+
+ var st int
+
+ if result.Deleted == 0 && result.Failed == 0 {
+ st = http.StatusNotFound
+ } else {
+ st = http.StatusOK
+ }
+
+ resp.WriteHeader(st)
+
+ if st == http.StatusOK {
+ if body, err := json.Marshal(result); err == nil {
+ resp.Write(body)
+ } else {
+ log.Printf("json.Marshal: %s (result = %v)\n", err, result)
+ http.Error(resp, err.Error(), 500)
+ }
+ }
+}
+
+/* PullHandler processes "PUT /pull" requests for the data manager.
+ The request body is a JSON message containing a list of pull
+ requests in the following format:
+
+ [
+ {
+ "locator":"e4d909c290d0fb1ca068ffaddf22cbd0+4985",
+ "servers":[
+ "keep0.qr1hi.arvadosapi.com:25107",
+ "keep1.qr1hi.arvadosapi.com:25108"
+ ]
+ },
+ {
+ "locator":"55ae4d45d2db0793d53f03e805f656e5+658395",
+ "servers":[
+ "10.0.1.5:25107",
+ "10.0.1.6:25107",
+ "10.0.1.7:25108"
+ ]
+ },
+ ...
+ ]
+
+ Each pull request in the list consists of a block locator string
+ and an ordered list of servers. Keepstore should try to fetch the
+ block from each server in turn.
+
+ If the request has not been sent by the Data Manager, return 401
+ Unauthorized.
+
+ If the JSON unmarshalling fails, return 400 Bad Request.
+*/
+
+type PullRequest struct {
+ Locator string `json:"locator"`
+ Servers []string `json:"servers"`
+}
+
+func PullHandler(resp http.ResponseWriter, req *http.Request) {
+ // Reject unauthorized requests.
+ if !IsDataManagerToken(GetApiToken(req)) {
+ http.Error(resp, UnauthorizedError.Error(), UnauthorizedError.HTTPCode)
+ return
+ }
+
+ // Parse the request body.
+ var pr []PullRequest
+ r := json.NewDecoder(req.Body)
+ if err := r.Decode(&pr); err != nil {
+ http.Error(resp, BadRequestError.Error(), BadRequestError.HTTPCode)
+ return
+ }
+
+ // We have a properly formatted pull list sent from the data
+ // manager. Report success and send the list to the pull list
+ // manager for further handling.
+ resp.WriteHeader(http.StatusOK)
+ resp.Write([]byte(
+ fmt.Sprintf("Received %d pull requests\n", len(pr))))
+
+ plist := list.New()
+ for _, p := range pr {
+ plist.PushBack(p)
+ }
+
+ if pullq == nil {
+ pullq = NewWorkQueue()
+ }
+ pullq.ReplaceQueue(plist)
+}
+
+type TrashRequest struct {
+ Locator string `json:"locator"`
+ BlockMtime int64 `json:"block_mtime"`
+}
+
+func TrashHandler(resp http.ResponseWriter, req *http.Request) {
+ // Reject unauthorized requests.
+ if !IsDataManagerToken(GetApiToken(req)) {
+ http.Error(resp, UnauthorizedError.Error(), UnauthorizedError.HTTPCode)
+ return
+ }
+
+ // Parse the request body.
+ var trash []TrashRequest
+ r := json.NewDecoder(req.Body)
+ if err := r.Decode(&trash); err != nil {
+ http.Error(resp, BadRequestError.Error(), BadRequestError.HTTPCode)
+ return
+ }
+
+ // We have a properly formatted trash list sent from the data
+ // manager. Report success and send the list to the trash work
+ // queue for further handling.
+ resp.WriteHeader(http.StatusOK)
+ resp.Write([]byte(
+ fmt.Sprintf("Received %d trash requests\n", len(trash))))
+
+ tlist := list.New()
+ for _, t := range trash {
+ tlist.PushBack(t)
+ }
+
+ if trashq == nil {
+ trashq = NewWorkQueue()
+ }
+ trashq.ReplaceQueue(tlist)
+}
+
+// ==============================
+// GetBlock and PutBlock implement lower-level code for handling
+// blocks by rooting through volumes connected to the local machine.
+// Once the handler has determined that system policy permits the
+// request, it calls these methods to perform the actual operation.
+//
+// TODO(twp): this code would probably be better located in the
+// VolumeManager interface. As an abstraction, the VolumeManager
+// should be the only part of the code that cares about which volume a
+// block is stored on, so it should be responsible for figuring out
+// which volume to check for fetching blocks, storing blocks, etc.
+
+// ==============================
+// GetBlock fetches and returns the block identified by "hash". If
+// the update_timestamp argument is true, GetBlock also updates the
+// block's file modification time (for the sake of PutBlock, which
+// must update the file's timestamp when the block already exists).
+//
+// On success, GetBlock returns a byte slice with the block data, and
+// a nil error.
+//
+// If the block cannot be found on any volume, returns NotFoundError.
+//
+// If the block found does not have the correct MD5 hash, returns
+// DiskHashError.
+//
+
+func GetBlock(hash string, update_timestamp bool) ([]byte, error) {
+ // Attempt to read the requested hash from a keep volume.
+ error_to_caller := NotFoundError
+
+ for _, vol := range KeepVM.Volumes() {
+ if buf, err := vol.Get(hash); err != nil {
+ // IsNotExist is an expected error and may be ignored.
+ // (If all volumes report IsNotExist, we return a NotFoundError)
+ // All other errors should be logged but we continue trying to
+ // read.
+ switch {
+ case os.IsNotExist(err):
+ continue
+ default:
+ log.Printf("GetBlock: reading %s: %s\n", hash, err)
+ }
+ } else {
+ // Double check the file checksum.
+ //
+ filehash := fmt.Sprintf("%x", md5.Sum(buf))
+ if filehash != hash {
+ // TODO(twp): this condition probably represents a bad disk and
+ // should raise major alarm bells for an administrator: e.g.
+ // they should be sent directly to an event manager at high
+ // priority or logged as urgent problems.
+ //
+ log.Printf("%s: checksum mismatch for request %s (actual %s)\n",
+ vol, hash, filehash)
+ error_to_caller = DiskHashError
+ } else {
+ // Success!
+ if error_to_caller != NotFoundError {
+ log.Printf("%s: checksum mismatch for request %s but a good copy was found on another volume and returned\n",
+ vol, hash)
+ }
+ // Update the timestamp if the caller requested.
+ // If we could not update the timestamp, continue looking on
+ // other volumes.
+ if update_timestamp {
+ if vol.Touch(hash) != nil {
+ continue
+ }
+ }
+ return buf, nil
+ }
+ }
+ }
+
+ if error_to_caller != NotFoundError {
+ log.Printf("%s: checksum mismatch, no good copy found\n", hash)
+ }
+ return nil, error_to_caller
+}
+
+/* PutBlock(block, hash)
+ Stores the BLOCK (identified by the content id HASH) in Keep.
+
+ The MD5 checksum of the block must be identical to the content id HASH.
+ If not, an error is returned.
+
+ PutBlock stores the BLOCK on the first Keep volume with free space.
+ A failure code is returned to the user only if all volumes fail.
+
+ On success, PutBlock returns nil.
+ On failure, it returns a KeepError with one of the following codes:
+
+ 500 Collision
+ A different block with the same hash already exists on this
+ Keep server.
+ 422 MD5Fail
+ The MD5 hash of the BLOCK does not match the argument HASH.
+ 503 Full
+ There was not enough space left in any Keep volume to store
+ the object.
+ 500 Fail
+ The object could not be stored for some other reason (e.g.
+ all writes failed). The text of the error message should
+ provide as much detail as possible.
+*/
+
+func PutBlock(block []byte, hash string) error {
+ // Check that BLOCK's checksum matches HASH.
+ blockhash := fmt.Sprintf("%x", md5.Sum(block))
+ if blockhash != hash {
+ log.Printf("%s: MD5 checksum %s did not match request", hash, blockhash)
+ return RequestHashError
+ }
+
+ // If we already have a block on disk under this identifier, return
+ // success (but check for MD5 collisions). While fetching the block,
+ // update its timestamp.
+ // The only errors that GetBlock can return are DiskHashError and NotFoundError.
+ // In either case, we want to write our new (good) block to disk,
+ // so there is nothing special to do if err != nil.
+ //
+ if oldblock, err := GetBlock(hash, true); err == nil {
+ if bytes.Compare(block, oldblock) == 0 {
+ // The block already exists; return success.
+ return nil
+ } else {
+ return CollisionError
+ }
+ }
+
+ // Choose a Keep volume to write to.
+ // If this volume fails, try all of the volumes in order.
+ vol := KeepVM.Choose()
+ if err := vol.Put(hash, block); err == nil {
+ return nil // success!
+ } else {
+ allFull := true
+ for _, vol := range KeepVM.Volumes() {
+ err := vol.Put(hash, block)
+ if err == nil {
+ return nil // success!
+ }
+ if err != FullError {
+ // The volume is not full but the write did not succeed.
+ // Report the error and continue trying.
+ allFull = false
+ log.Printf("%s: Write(%s): %s\n", vol, hash, err)
+ }
+ }
+
+ if allFull {
+ log.Printf("all Keep volumes full")
+ return FullError
+ } else {
+ log.Printf("all Keep volumes failed")
+ return GenericError
+ }
+ }
+}
+
+// IsValidLocator
+// Return true if the specified string is a valid Keep locator.
+// When Keep is extended to support hash types other than MD5,
+// this should be updated to cover those as well.
+//
+func IsValidLocator(loc string) bool {
+ match, err := regexp.MatchString(`^[0-9a-f]{32}$`, loc)
+ if err == nil {
+ return match
+ }
+ log.Printf("IsValidLocator: %s\n", err)
+ return false
+}
+
+// GetApiToken returns the OAuth2 token from the Authorization
+// header of a HTTP request, or an empty string if no matching
+// token is found.
+func GetApiToken(req *http.Request) string {
+ if auth, ok := req.Header["Authorization"]; ok {
+ if pat, err := regexp.Compile(`^OAuth2\s+(.*)`); err != nil {
+ log.Println(err)
+ } else if match := pat.FindStringSubmatch(auth[0]); match != nil {
+ return match[1]
+ }
+ }
+ return ""
+}
+
+// IsExpired returns true if the given Unix timestamp (expressed as a
+// hexadecimal string) is in the past, or if timestamp_hex cannot be
+// parsed as a hexadecimal string.
+func IsExpired(timestamp_hex string) bool {
+ ts, err := strconv.ParseInt(timestamp_hex, 16, 0)
+ if err != nil {
+ log.Printf("IsExpired: %s\n", err)
+ return true
+ }
+ return time.Unix(ts, 0).Before(time.Now())
+}
+
+// CanDelete returns true if the user identified by api_token is
+// allowed to delete blocks.
+func CanDelete(api_token string) bool {
+ if api_token == "" {
+ return false
+ }
+ // Blocks may be deleted only when Keep has been configured with a
+ // data manager.
+ if IsDataManagerToken(api_token) {
+ return true
+ }
+ // TODO(twp): look up api_token with the API server
+ // return true if is_admin is true and if the token
+ // has unlimited scope
+ return false
+}
+
+// IsDataManagerToken returns true if api_token represents the data
+// manager's token.
+func IsDataManagerToken(api_token string) bool {
+ return data_manager_token != "" && api_token == data_manager_token
+}
--- /dev/null
+package main
+
+import (
+ "bytes"
+ "flag"
+ "fmt"
+ "io/ioutil"
+ "log"
+ "net"
+ "net/http"
+ "os"
+ "os/signal"
+ "strings"
+ "syscall"
+ "time"
+)
+
+// ======================
+// Configuration settings
+//
+// TODO(twp): make all of these configurable via command line flags
+// and/or configuration file settings.
+
+// Default TCP address on which to listen for requests.
+// Initialized by the --listen flag.
+const DEFAULT_ADDR = ":25107"
+
+// A Keep "block" is 64MB.
+const BLOCKSIZE = 64 * 1024 * 1024
+
+// A Keep volume must have at least MIN_FREE_KILOBYTES available
+// in order to permit writes.
+const MIN_FREE_KILOBYTES = BLOCKSIZE / 1024
+
+var PROC_MOUNTS = "/proc/mounts"
+
+// enforce_permissions controls whether permission signatures
+// should be enforced (affecting GET and DELETE requests).
+// Initialized by the --enforce-permissions flag.
+var enforce_permissions bool
+
+// permission_ttl is the time duration for which new permission
+// signatures (returned by PUT requests) will be valid.
+// Initialized by the --permission-ttl flag.
+var permission_ttl time.Duration
+
+// data_manager_token represents the API token used by the
+// Data Manager, and is required on certain privileged operations.
+// Initialized by the --data-manager-token-file flag.
+var data_manager_token string
+
+// never_delete can be used to prevent the DELETE handler from
+// actually deleting anything.
+var never_delete = false
+
+// ==========
+// Error types.
+//
+type KeepError struct {
+ HTTPCode int
+ ErrMsg string
+}
+
+var (
+ BadRequestError = &KeepError{400, "Bad Request"}
+ UnauthorizedError = &KeepError{401, "Unauthorized"}
+ CollisionError = &KeepError{500, "Collision"}
+ RequestHashError = &KeepError{422, "Hash mismatch in request"}
+ PermissionError = &KeepError{403, "Forbidden"}
+ DiskHashError = &KeepError{500, "Hash mismatch in stored data"}
+ ExpiredError = &KeepError{401, "Expired permission signature"}
+ NotFoundError = &KeepError{404, "Not Found"}
+ GenericError = &KeepError{500, "Fail"}
+ FullError = &KeepError{503, "Full"}
+ TooLongError = &KeepError{504, "Timeout"}
+ MethodDisabledError = &KeepError{405, "Method disabled"}
+)
+
+func (e *KeepError) Error() string {
+ return e.ErrMsg
+}
+
+// ========================
+// Internal data structures
+//
+// These global variables are used by multiple parts of the
+// program. They are good candidates for moving into their own
+// packages.
+
+// The Keep VolumeManager maintains a list of available volumes.
+// Initialized by the --volumes flag (or by FindKeepVolumes).
+var KeepVM VolumeManager
+
+// The pull list manager and trash queue are threadsafe queues which
+// support atomic update operations. The PullHandler and TrashHandler
+// store results from Data Manager /pull and /trash requests here.
+//
+// See the Keep and Data Manager design documents for more details:
+// https://arvados.org/projects/arvados/wiki/Keep_Design_Doc
+// https://arvados.org/projects/arvados/wiki/Data_Manager_Design_Doc
+//
+var pullq *WorkQueue
+var trashq *WorkQueue
+
+// TODO(twp): continue moving as much code as possible out of main
+// so it can be effectively tested. Esp. handling and postprocessing
+// of command line flags (identifying Keep volumes and initializing
+// permission arguments).
+
+func main() {
+ log.Println("Keep started: pid", os.Getpid())
+
+ // Parse command-line flags:
+ //
+ // -listen=ipaddr:port
+ // Interface on which to listen for requests. Use :port without
+ // an ipaddr to listen on all network interfaces.
+ // Examples:
+ // -listen=127.0.0.1:4949
+ // -listen=10.0.1.24:8000
+ // -listen=:25107 (to listen to port 25107 on all interfaces)
+ //
+ // -volumes
+ // A comma-separated list of directories to use as Keep volumes.
+ // Example:
+ // -volumes=/var/keep01,/var/keep02,/var/keep03/subdir
+ //
+ // If -volumes is empty or is not present, Keep will select volumes
+ // by looking at currently mounted filesystems for /keep top-level
+ // directories.
+
+ var (
+ data_manager_token_file string
+ listen string
+ permission_key_file string
+ permission_ttl_sec int
+ serialize_io bool
+ volumearg string
+ pidfile string
+ )
+ flag.StringVar(
+ &data_manager_token_file,
+ "data-manager-token-file",
+ "",
+ "File with the API token used by the Data Manager. All DELETE "+
+ "requests or GET /index requests must carry this token.")
+ flag.BoolVar(
+ &enforce_permissions,
+ "enforce-permissions",
+ false,
+ "Enforce permission signatures on requests.")
+ flag.StringVar(
+ &listen,
+ "listen",
+ DEFAULT_ADDR,
+ "Interface on which to listen for requests, in the format "+
+ "ipaddr:port. e.g. -listen=10.0.1.24:8000. Use -listen=:port "+
+ "to listen on all network interfaces.")
+ flag.BoolVar(
+ &never_delete,
+ "never-delete",
+ false,
+ "If set, nothing will be deleted. HTTP 405 will be returned "+
+ "for valid DELETE requests.")
+ flag.StringVar(
+ &permission_key_file,
+ "permission-key-file",
+ "",
+ "File containing the secret key for generating and verifying "+
+ "permission signatures.")
+ flag.IntVar(
+ &permission_ttl_sec,
+ "permission-ttl",
+ 1209600,
+ "Expiration time (in seconds) for newly generated permission "+
+ "signatures.")
+ flag.BoolVar(
+ &serialize_io,
+ "serialize",
+ false,
+ "If set, all read and write operations on local Keep volumes will "+
+ "be serialized.")
+ flag.StringVar(
+ &volumearg,
+ "volumes",
+ "",
+ "Comma-separated list of directories to use for Keep volumes, "+
+ "e.g. -volumes=/var/keep1,/var/keep2. If empty or not "+
+ "supplied, Keep will scan mounted filesystems for volumes "+
+ "with a /keep top-level directory.")
+
+ flag.StringVar(
+ &pidfile,
+ "pid",
+ "",
+ "Path to write pid file")
+
+ flag.Parse()
+
+ // Look for local keep volumes.
+ var keepvols []string
+ if volumearg == "" {
+ // TODO(twp): decide whether this is desirable default behavior.
+ // In production we may want to require the admin to specify
+ // Keep volumes explicitly.
+ keepvols = FindKeepVolumes()
+ } else {
+ keepvols = strings.Split(volumearg, ",")
+ }
+
+ // Check that the specified volumes actually exist.
+ var goodvols []Volume = nil
+ for _, v := range keepvols {
+ if _, err := os.Stat(v); err == nil {
+ log.Println("adding Keep volume:", v)
+ newvol := MakeUnixVolume(v, serialize_io)
+ goodvols = append(goodvols, &newvol)
+ } else {
+ log.Printf("bad Keep volume: %s\n", err)
+ }
+ }
+
+ if len(goodvols) == 0 {
+ log.Fatal("could not find any keep volumes")
+ }
+
+ // Initialize data manager token and permission key.
+ // If these tokens are specified but cannot be read,
+ // raise a fatal error.
+ if data_manager_token_file != "" {
+ if buf, err := ioutil.ReadFile(data_manager_token_file); err == nil {
+ data_manager_token = strings.TrimSpace(string(buf))
+ } else {
+ log.Fatalf("reading data manager token: %s\n", err)
+ }
+ }
+ if permission_key_file != "" {
+ if buf, err := ioutil.ReadFile(permission_key_file); err == nil {
+ PermissionSecret = bytes.TrimSpace(buf)
+ } else {
+ log.Fatalf("reading permission key: %s\n", err)
+ }
+ }
+
+ // Initialize permission TTL
+ permission_ttl = time.Duration(permission_ttl_sec) * time.Second
+
+ // If --enforce-permissions is true, we must have a permission key
+ // to continue.
+ if PermissionSecret == nil {
+ if enforce_permissions {
+ log.Fatal("--enforce-permissions requires a permission key")
+ } else {
+ log.Println("Running without a PermissionSecret. Block locators " +
+ "returned by this server will not be signed, and will be rejected " +
+ "by a server that enforces permissions.")
+ log.Println("To fix this, run Keep with --permission-key-file=<path> " +
+ "to define the location of a file containing the permission key.")
+ }
+ }
+
+ // Start a round-robin VolumeManager with the volumes we have found.
+ KeepVM = MakeRRVolumeManager(goodvols)
+
+ // Tell the built-in HTTP server to direct all requests to the REST router.
+ loggingRouter := MakeLoggingRESTRouter()
+ http.HandleFunc("/", func(resp http.ResponseWriter, req *http.Request) {
+ loggingRouter.ServeHTTP(resp, req)
+ })
+
+ // Set up a TCP listener.
+ listener, err := net.Listen("tcp", listen)
+ if err != nil {
+ log.Fatal(err)
+ }
+
+ // Shut down the server gracefully (by closing the listener)
+ // if SIGTERM is received.
+ term := make(chan os.Signal, 1)
+ go func(sig <-chan os.Signal) {
+ s := <-sig
+ log.Println("caught signal:", s)
+ listener.Close()
+ }(term)
+ signal.Notify(term, syscall.SIGTERM)
+
+ if pidfile != "" {
+ f, err := os.Create(pidfile)
+ if err == nil {
+ fmt.Fprint(f, os.Getpid())
+ f.Close()
+ } else {
+ log.Printf("Error writing pid file (%s): %s", pidfile, err.Error())
+ }
+ }
+
+ // Start listening for requests.
+ srv := &http.Server{Addr: listen}
+ srv.Serve(listener)
+
+ log.Println("shutting down")
+
+ if pidfile != "" {
+ os.Remove(pidfile)
+ }
+}
--- /dev/null
+package main
+
+import (
+ "bytes"
+ "fmt"
+ "io/ioutil"
+ "os"
+ "path"
+ "regexp"
+ "sort"
+ "strings"
+ "testing"
+)
+
+var TEST_BLOCK = []byte("The quick brown fox jumps over the lazy dog.")
+var TEST_HASH = "e4d909c290d0fb1ca068ffaddf22cbd0"
+var TEST_HASH_PUT_RESPONSE = "e4d909c290d0fb1ca068ffaddf22cbd0+44\n"
+
+var TEST_BLOCK_2 = []byte("Pack my box with five dozen liquor jugs.")
+var TEST_HASH_2 = "f15ac516f788aec4f30932ffb6395c39"
+
+var TEST_BLOCK_3 = []byte("Now is the time for all good men to come to the aid of their country.")
+var TEST_HASH_3 = "eed29bbffbc2dbe5e5ee0bb71888e61f"
+
+// BAD_BLOCK is used to test collisions and corruption.
+// It must not match any test hashes.
+var BAD_BLOCK = []byte("The magic words are squeamish ossifrage.")
+
+// TODO(twp): Tests still to be written
+//
+// * TestPutBlockFull
+// - test that PutBlock returns 503 Full if the filesystem is full.
+// (must mock FreeDiskSpace or Statfs? use a tmpfs?)
+//
+// * TestPutBlockWriteErr
+// - test the behavior when Write returns an error.
+// - Possible solutions: use a small tmpfs and a high
+// MIN_FREE_KILOBYTES to trick PutBlock into attempting
+// to write a block larger than the amount of space left
+// - use an interface to mock ioutil.TempFile with a File
+// object that always returns an error on write
+//
+// ========================================
+// GetBlock tests.
+// ========================================
+
+// TestGetBlock
+// Test that simple block reads succeed.
+//
+func TestGetBlock(t *testing.T) {
+ defer teardown()
+
+ // Prepare two test Keep volumes. Our block is stored on the second volume.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ vols := KeepVM.Volumes()
+ if err := vols[1].Put(TEST_HASH, TEST_BLOCK); err != nil {
+ t.Error(err)
+ }
+
+ // Check that GetBlock returns success.
+ result, err := GetBlock(TEST_HASH, false)
+ if err != nil {
+ t.Errorf("GetBlock error: %s", err)
+ }
+ if fmt.Sprint(result) != fmt.Sprint(TEST_BLOCK) {
+ t.Errorf("expected %s, got %s", TEST_BLOCK, result)
+ }
+}
+
+// TestGetBlockMissing
+// GetBlock must return an error when the block is not found.
+//
+func TestGetBlockMissing(t *testing.T) {
+ defer teardown()
+
+ // Create two empty test Keep volumes.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ // Check that GetBlock returns failure.
+ result, err := GetBlock(TEST_HASH, false)
+ if err != NotFoundError {
+ t.Errorf("Expected NotFoundError, got %v", result)
+ }
+}
+
+// TestGetBlockCorrupt
+// GetBlock must return an error when a corrupted block is requested
+// (the contents of the file do not checksum to its hash).
+//
+func TestGetBlockCorrupt(t *testing.T) {
+ defer teardown()
+
+ // Create two test Keep volumes and store a corrupt block in one.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ vols := KeepVM.Volumes()
+ vols[0].Put(TEST_HASH, BAD_BLOCK)
+
+ // Check that GetBlock returns failure.
+ result, err := GetBlock(TEST_HASH, false)
+ if err != DiskHashError {
+ t.Errorf("Expected DiskHashError, got %v (buf: %v)", err, result)
+ }
+}
+
+// ========================================
+// PutBlock tests
+// ========================================
+
+// TestPutBlockOK
+// PutBlock can perform a simple block write and returns success.
+//
+func TestPutBlockOK(t *testing.T) {
+ defer teardown()
+
+ // Create two test Keep volumes.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ // Check that PutBlock stores the data as expected.
+ if err := PutBlock(TEST_BLOCK, TEST_HASH); err != nil {
+ t.Fatalf("PutBlock: %v", err)
+ }
+
+ vols := KeepVM.Volumes()
+ result, err := vols[0].Get(TEST_HASH)
+ if err != nil {
+ t.Fatalf("Volume #0 Get returned error: %v", err)
+ }
+ if string(result) != string(TEST_BLOCK) {
+ t.Fatalf("PutBlock stored '%s', Get retrieved '%s'",
+ string(TEST_BLOCK), string(result))
+ }
+}
+
+// TestPutBlockOneVol
+// PutBlock still returns success even when only one of the known
+// volumes is online.
+//
+func TestPutBlockOneVol(t *testing.T) {
+ defer teardown()
+
+ // Create two test Keep volumes, but cripple one of them.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ vols := KeepVM.Volumes()
+ vols[0].(*MockVolume).Bad = true
+
+ // Check that PutBlock stores the data as expected.
+ if err := PutBlock(TEST_BLOCK, TEST_HASH); err != nil {
+ t.Fatalf("PutBlock: %v", err)
+ }
+
+ result, err := GetBlock(TEST_HASH, false)
+ if err != nil {
+ t.Fatalf("GetBlock: %v", err)
+ }
+ if string(result) != string(TEST_BLOCK) {
+ t.Error("PutBlock/GetBlock mismatch")
+ t.Fatalf("PutBlock stored '%s', GetBlock retrieved '%s'",
+ string(TEST_BLOCK), string(result))
+ }
+}
+
+// TestPutBlockMD5Fail
+// Check that PutBlock returns an error if passed a block and hash that
+// do not match.
+//
+func TestPutBlockMD5Fail(t *testing.T) {
+ defer teardown()
+
+ // Create two test Keep volumes.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ // Check that PutBlock returns the expected error when the hash does
+ // not match the block.
+ if err := PutBlock(BAD_BLOCK, TEST_HASH); err != RequestHashError {
+ t.Error("Expected RequestHashError, got %v", err)
+ }
+
+ // Confirm that GetBlock fails to return anything.
+ if result, err := GetBlock(TEST_HASH, false); err != NotFoundError {
+ t.Errorf("GetBlock succeeded after a corrupt block store (result = %s, err = %v)",
+ string(result), err)
+ }
+}
+
+// TestPutBlockCorrupt
+// PutBlock should overwrite corrupt blocks on disk when given
+// a PUT request with a good block.
+//
+func TestPutBlockCorrupt(t *testing.T) {
+ defer teardown()
+
+ // Create two test Keep volumes.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ // Store a corrupted block under TEST_HASH.
+ vols := KeepVM.Volumes()
+ vols[0].Put(TEST_HASH, BAD_BLOCK)
+ if err := PutBlock(TEST_BLOCK, TEST_HASH); err != nil {
+ t.Errorf("PutBlock: %v", err)
+ }
+
+ // The block on disk should now match TEST_BLOCK.
+ if block, err := GetBlock(TEST_HASH, false); err != nil {
+ t.Errorf("GetBlock: %v", err)
+ } else if bytes.Compare(block, TEST_BLOCK) != 0 {
+ t.Errorf("GetBlock returned: '%s'", string(block))
+ }
+}
+
+// TestPutBlockCollision
+// PutBlock returns a 400 Collision error when attempting to
+// store a block that collides with another block on disk.
+//
+func TestPutBlockCollision(t *testing.T) {
+ defer teardown()
+
+ // These blocks both hash to the MD5 digest cee9a457e790cf20d4bdaa6d69f01e41.
+ var b1 = []byte("\x0e0eaU\x9a\xa7\x87\xd0\x0b\xc6\xf7\x0b\xbd\xfe4\x04\xcf\x03e\x9epO\x854\xc0\x0f\xfbe\x9cL\x87@\xcc\x94/\xeb-\xa1\x15\xa3\xf4\x15\\\xbb\x86\x07Is\x86em}\x1f4\xa4 Y\xd7\x8fZ\x8d\xd1\xef")
+ var b2 = []byte("\x0e0eaU\x9a\xa7\x87\xd0\x0b\xc6\xf7\x0b\xbd\xfe4\x04\xcf\x03e\x9etO\x854\xc0\x0f\xfbe\x9cL\x87@\xcc\x94/\xeb-\xa1\x15\xa3\xf4\x15\xdc\xbb\x86\x07Is\x86em}\x1f4\xa4 Y\xd7\x8fZ\x8d\xd1\xef")
+ var locator = "cee9a457e790cf20d4bdaa6d69f01e41"
+
+ // Prepare two test Keep volumes.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ // Store one block, then attempt to store the other. Confirm that
+ // PutBlock reported a CollisionError.
+ if err := PutBlock(b1, locator); err != nil {
+ t.Error(err)
+ }
+ if err := PutBlock(b2, locator); err == nil {
+ t.Error("PutBlock did not report a collision")
+ } else if err != CollisionError {
+ t.Errorf("PutBlock returned %v", err)
+ }
+}
+
+// TestPutBlockTouchFails
+// When PutBlock is asked to PUT an existing block, but cannot
+// modify the timestamp, it should write a second block.
+//
+func TestPutBlockTouchFails(t *testing.T) {
+ defer teardown()
+
+ // Prepare two test Keep volumes.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+ vols := KeepVM.Volumes()
+
+ // Store a block and then make the underlying volume bad,
+ // so a subsequent attempt to update the file timestamp
+ // will fail.
+ vols[0].Put(TEST_HASH, BAD_BLOCK)
+ old_mtime, err := vols[0].Mtime(TEST_HASH)
+ if err != nil {
+ t.Fatalf("vols[0].Mtime(%s): %s\n", TEST_HASH, err)
+ }
+
+ // vols[0].Touch will fail on the next call, so the volume
+ // manager will store a copy on vols[1] instead.
+ vols[0].(*MockVolume).Touchable = false
+ if err := PutBlock(TEST_BLOCK, TEST_HASH); err != nil {
+ t.Fatalf("PutBlock: %v", err)
+ }
+ vols[0].(*MockVolume).Touchable = true
+
+ // Now the mtime on the block on vols[0] should be unchanged, and
+ // there should be a copy of the block on vols[1].
+ new_mtime, err := vols[0].Mtime(TEST_HASH)
+ if err != nil {
+ t.Fatalf("vols[0].Mtime(%s): %s\n", TEST_HASH, err)
+ }
+ if !new_mtime.Equal(old_mtime) {
+ t.Errorf("mtime was changed on vols[0]:\nold_mtime = %v\nnew_mtime = %v\n",
+ old_mtime, new_mtime)
+ }
+ result, err := vols[1].Get(TEST_HASH)
+ if err != nil {
+ t.Fatalf("vols[1]: %v", err)
+ }
+ if bytes.Compare(result, TEST_BLOCK) != 0 {
+ t.Errorf("new block does not match test block\nnew block = %v\n", result)
+ }
+}
+
+// ========================================
+// FindKeepVolumes tests.
+// ========================================
+
+// TestFindKeepVolumes
+// Confirms that FindKeepVolumes finds tmpfs volumes with "/keep"
+// directories at the top level.
+//
+func TestFindKeepVolumes(t *testing.T) {
+ var tempVols [2]string
+ var err error
+
+ defer func() {
+ for _, path := range tempVols {
+ os.RemoveAll(path)
+ }
+ }()
+
+ // Create two directories suitable for using as keep volumes.
+ for i := range tempVols {
+ if tempVols[i], err = ioutil.TempDir("", "findvol"); err != nil {
+ t.Fatal(err)
+ }
+ tempVols[i] = tempVols[i] + "/keep"
+ if err = os.Mkdir(tempVols[i], 0755); err != nil {
+ t.Fatal(err)
+ }
+ }
+
+ // Set up a bogus PROC_MOUNTS file.
+ if f, err := ioutil.TempFile("", "keeptest"); err == nil {
+ for _, vol := range tempVols {
+ fmt.Fprintf(f, "tmpfs %s tmpfs opts\n", path.Dir(vol))
+ }
+ f.Close()
+ PROC_MOUNTS = f.Name()
+
+ // Check that FindKeepVolumes finds the temp volumes.
+ resultVols := FindKeepVolumes()
+ if len(tempVols) != len(resultVols) {
+ t.Fatalf("set up %d volumes, FindKeepVolumes found %d\n",
+ len(tempVols), len(resultVols))
+ }
+ for i := range tempVols {
+ if tempVols[i] != resultVols[i] {
+ t.Errorf("FindKeepVolumes returned %s, expected %s\n",
+ resultVols[i], tempVols[i])
+ }
+ }
+
+ os.Remove(f.Name())
+ }
+}
+
+// TestFindKeepVolumesFail
+// When no Keep volumes are present, FindKeepVolumes returns an empty slice.
+//
+func TestFindKeepVolumesFail(t *testing.T) {
+ defer teardown()
+
+ // Set up a bogus PROC_MOUNTS file with no Keep vols.
+ if f, err := ioutil.TempFile("", "keeptest"); err == nil {
+ fmt.Fprintln(f, "rootfs / rootfs opts 0 0")
+ fmt.Fprintln(f, "sysfs /sys sysfs opts 0 0")
+ fmt.Fprintln(f, "proc /proc proc opts 0 0")
+ fmt.Fprintln(f, "udev /dev devtmpfs opts 0 0")
+ fmt.Fprintln(f, "devpts /dev/pts devpts opts 0 0")
+ f.Close()
+ PROC_MOUNTS = f.Name()
+
+ // Check that FindKeepVolumes returns an empty array.
+ resultVols := FindKeepVolumes()
+ if len(resultVols) != 0 {
+ t.Fatalf("FindKeepVolumes returned %v", resultVols)
+ }
+
+ os.Remove(PROC_MOUNTS)
+ }
+}
+
+// TestIndex
+// Test an /index request.
+func TestIndex(t *testing.T) {
+ defer teardown()
+
+ // Set up Keep volumes and populate them.
+ // Include multiple blocks on different volumes, and
+ // some metadata files.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ vols := KeepVM.Volumes()
+ vols[0].Put(TEST_HASH, TEST_BLOCK)
+ vols[1].Put(TEST_HASH_2, TEST_BLOCK_2)
+ vols[0].Put(TEST_HASH_3, TEST_BLOCK_3)
+ vols[0].Put(TEST_HASH+".meta", []byte("metadata"))
+ vols[1].Put(TEST_HASH_2+".meta", []byte("metadata"))
+
+ index := vols[0].Index("") + vols[1].Index("")
+ index_rows := strings.Split(index, "\n")
+ sort.Strings(index_rows)
+ sorted_index := strings.Join(index_rows, "\n")
+ expected := `^\n` + TEST_HASH + `\+\d+ \d+\n` +
+ TEST_HASH_3 + `\+\d+ \d+\n` +
+ TEST_HASH_2 + `\+\d+ \d+$`
+
+ match, err := regexp.MatchString(expected, sorted_index)
+ if err == nil {
+ if !match {
+ t.Errorf("IndexLocators returned:\n%s", index)
+ }
+ } else {
+ t.Errorf("regexp.MatchString: %s", err)
+ }
+}
+
+// TestNodeStatus
+// Test that GetNodeStatus returns valid info about available volumes.
+//
+// TODO(twp): set up appropriate interfaces to permit more rigorous
+// testing.
+//
+func TestNodeStatus(t *testing.T) {
+ defer teardown()
+
+ // Set up test Keep volumes with some blocks.
+ KeepVM = MakeTestVolumeManager(2)
+ defer func() { KeepVM.Quit() }()
+
+ vols := KeepVM.Volumes()
+ vols[0].Put(TEST_HASH, TEST_BLOCK)
+ vols[1].Put(TEST_HASH_2, TEST_BLOCK_2)
+
+ // Get node status and make a basic sanity check.
+ st := GetNodeStatus()
+ for i := range vols {
+ volinfo := st.Volumes[i]
+ mtp := volinfo.MountPoint
+ if mtp != "/bogo" {
+ t.Errorf("GetNodeStatus mount_point %s, expected /bogo", mtp)
+ }
+ if volinfo.DeviceNum == 0 {
+ t.Errorf("uninitialized device_num in %v", volinfo)
+ }
+ if volinfo.BytesFree == 0 {
+ t.Errorf("uninitialized bytes_free in %v", volinfo)
+ }
+ if volinfo.BytesUsed == 0 {
+ t.Errorf("uninitialized bytes_used in %v", volinfo)
+ }
+ }
+}
+
+// ========================================
+// Helper functions for unit tests.
+// ========================================
+
+// MakeTestVolumeManager
+// Creates and returns a RRVolumeManager with the specified number
+// of MockVolumes.
+//
+func MakeTestVolumeManager(num_volumes int) VolumeManager {
+ vols := make([]Volume, num_volumes)
+ for i := range vols {
+ vols[i] = CreateMockVolume()
+ }
+ return MakeRRVolumeManager(vols)
+}
+
+// teardown
+// Cleanup to perform after each test.
+//
+func teardown() {
+ data_manager_token = ""
+ enforce_permissions = false
+ PermissionSecret = nil
+ KeepVM = nil
+}
--- /dev/null
+package main
+
+// LoggingRESTRouter
+// LoggingResponseWriter
+
+import (
+ "github.com/gorilla/mux"
+ "log"
+ "net/http"
+ "strings"
+)
+
+type LoggingResponseWriter struct {
+ Status int
+ Length int
+ http.ResponseWriter
+ ResponseBody string
+}
+
+func (loggingWriter *LoggingResponseWriter) WriteHeader(code int) {
+ loggingWriter.Status = code
+ loggingWriter.ResponseWriter.WriteHeader(code)
+}
+
+func (loggingWriter *LoggingResponseWriter) Write(data []byte) (int, error) {
+ loggingWriter.Length += len(data)
+ if loggingWriter.Status >= 400 {
+ loggingWriter.ResponseBody += string(data)
+ }
+ return loggingWriter.ResponseWriter.Write(data)
+}
+
+type LoggingRESTRouter struct {
+ router *mux.Router
+}
+
+func MakeLoggingRESTRouter() *LoggingRESTRouter {
+ router := MakeRESTRouter()
+ return (&LoggingRESTRouter{router})
+}
+
+func (loggingRouter *LoggingRESTRouter) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
+ loggingWriter := LoggingResponseWriter{200, 0, resp, ""}
+ loggingRouter.router.ServeHTTP(&loggingWriter, req)
+ statusText := "OK"
+ if loggingWriter.Status >= 400 {
+ statusText = strings.Replace(loggingWriter.ResponseBody, "\n", "", -1)
+ }
+ log.Printf("[%s] %s %s %d %d \"%s\"", req.RemoteAddr, req.Method, req.URL.Path[1:], loggingWriter.Status, loggingWriter.Length, statusText)
+
+}
--- /dev/null
+/*
+Permissions management on Arvados locator hashes.
+
+The permissions structure for Arvados is as follows (from
+https://arvados.org/issues/2328)
+
+A Keep locator string has the following format:
+
+ [hash]+[size]+A[signature]@[timestamp]
+
+The "signature" string here is a cryptographic hash, expressed as a
+string of hexadecimal digits, and timestamp is a 32-bit Unix timestamp
+expressed as a hexadecimal number. e.g.:
+
+ acbd18db4cc2f85cedef654fccc4a4d8+3+A257f3f5f5f0a4e4626a18fc74bd42ec34dcb228a@7fffffff
+
+The signature represents a guarantee that this locator was generated
+by either Keep or the API server for use with the supplied API token.
+If a request to Keep includes a locator with a valid signature and is
+accompanied by the proper API token, the user has permission to GET
+that object.
+
+The signature may be generated either by Keep (after the user writes a
+block) or by the API server (if the user has can_read permission on
+the specified object). Keep and API server share a secret that is used
+to generate signatures.
+
+To verify a permission hint, Keep generates a new hint for the
+requested object (using the locator string, the timestamp, the
+permission secret and the user's API token, which must appear in the
+request headers) and compares it against the hint included in the
+request. If the permissions do not match, or if the API token is not
+present, Keep returns a 401 error.
+*/
+
+package main
+
+import (
+ "crypto/hmac"
+ "crypto/sha1"
+ "fmt"
+ "regexp"
+ "strconv"
+ "strings"
+ "time"
+)
+
+// The PermissionSecret is the secret key used to generate SHA1
+// digests for permission hints. apiserver and Keep must use the same
+// key.
+var PermissionSecret []byte
+
+// MakePermSignature returns a string representing the signed permission
+// hint for the blob identified by blob_hash, api_token and expiration timestamp.
+func MakePermSignature(blob_hash string, api_token string, expiry string) string {
+ hmac := hmac.New(sha1.New, PermissionSecret)
+ hmac.Write([]byte(blob_hash))
+ hmac.Write([]byte("@"))
+ hmac.Write([]byte(api_token))
+ hmac.Write([]byte("@"))
+ hmac.Write([]byte(expiry))
+ digest := hmac.Sum(nil)
+ return fmt.Sprintf("%x", digest)
+}
+
+// SignLocator takes a blob_locator, an api_token and an expiry time, and
+// returns a signed locator string.
+func SignLocator(blob_locator string, api_token string, expiry time.Time) string {
+ // If no permission secret or API token is available,
+ // return an unsigned locator.
+ if PermissionSecret == nil || api_token == "" {
+ return blob_locator
+ }
+ // Extract the hash from the blob locator, omitting any size hint that may be present.
+ blob_hash := strings.Split(blob_locator, "+")[0]
+ // Return the signed locator string.
+ timestamp_hex := fmt.Sprintf("%08x", expiry.Unix())
+ return blob_locator +
+ "+A" + MakePermSignature(blob_hash, api_token, timestamp_hex) +
+ "@" + timestamp_hex
+}
+
+var signedLocatorRe = regexp.MustCompile(`^([[:xdigit:]]{32}).*\+A([[:xdigit:]]{40})@([[:xdigit:]]{8})`)
+
+// VerifySignature returns true if the signature on the signed_locator
+// can be verified using the given api_token.
+func VerifySignature(signed_locator string, api_token string) bool {
+ matches := signedLocatorRe.FindStringSubmatch(signed_locator)
+ if matches == nil {
+ // Could not find a permission signature at all
+ return false
+ }
+ blob_hash := matches[1]
+ sig_hex := matches[2]
+ exp_hex := matches[3]
+ if exp_time, err := ParseHexTimestamp(exp_hex); err != nil || exp_time.Before(time.Now()) {
+ // Signature is expired, or timestamp is unparseable
+ return false
+ }
+ return sig_hex == MakePermSignature(blob_hash, api_token, exp_hex)
+}
+
+func ParseHexTimestamp(timestamp_hex string) (ts time.Time, err error) {
+ if ts_int, e := strconv.ParseInt(timestamp_hex, 16, 0); e == nil {
+ ts = time.Unix(ts_int, 0)
+ } else {
+ err = e
+ }
+ return ts, err
+}
--- /dev/null
+package main
+
+import (
+ "testing"
+ "time"
+)
+
+const (
+ known_hash = "acbd18db4cc2f85cedef654fccc4a4d8"
+ known_locator = known_hash + "+3"
+ known_token = "hocfupkn2pjhrpgp2vxv8rsku7tvtx49arbc9s4bvu7p7wxqvk"
+ known_key = "13u9fkuccnboeewr0ne3mvapk28epf68a3bhj9q8sb4l6e4e5mkk" +
+ "p6nhj2mmpscgu1zze5h5enydxfe3j215024u16ij4hjaiqs5u4pzsl3nczmaoxnc" +
+ "ljkm4875xqn4xv058koz3vkptmzhyheiy6wzevzjmdvxhvcqsvr5abhl15c2d4o4" +
+ "jhl0s91lojy1mtrzqqvprqcverls0xvy9vai9t1l1lvvazpuadafm71jl4mrwq2y" +
+ "gokee3eamvjy8qq1fvy238838enjmy5wzy2md7yvsitp5vztft6j4q866efym7e6" +
+ "vu5wm9fpnwjyxfldw3vbo01mgjs75rgo7qioh8z8ij7jpyp8508okhgbbex3ceei" +
+ "786u5rw2a9gx743dj3fgq2irk"
+ known_signature = "257f3f5f5f0a4e4626a18fc74bd42ec34dcb228a"
+ known_timestamp = "7fffffff"
+ known_sig_hint = "+A" + known_signature + "@" + known_timestamp
+ known_signed_locator = known_locator + known_sig_hint
+)
+
+func TestSignLocator(t *testing.T) {
+ PermissionSecret = []byte(known_key)
+ defer func() { PermissionSecret = nil }()
+
+ if ts, err := ParseHexTimestamp(known_timestamp); err != nil {
+ t.Errorf("bad known_timestamp %s", known_timestamp)
+ } else {
+ if known_signed_locator != SignLocator(known_locator, known_token, ts) {
+ t.Fail()
+ }
+ }
+}
+
+func TestVerifySignature(t *testing.T) {
+ PermissionSecret = []byte(known_key)
+ defer func() { PermissionSecret = nil }()
+
+ if !VerifySignature(known_signed_locator, known_token) {
+ t.Fail()
+ }
+}
+
+func TestVerifySignatureExtraHints(t *testing.T) {
+ PermissionSecret = []byte(known_key)
+ defer func() { PermissionSecret = nil }()
+
+ if !VerifySignature(known_locator + "+K@xyzzy" + known_sig_hint, known_token) {
+ t.Fatal("Verify cannot handle hint before permission signature")
+ }
+
+ if !VerifySignature(known_locator + known_sig_hint + "+Zfoo", known_token) {
+ t.Fatal("Verify cannot handle hint after permission signature")
+ }
+
+ if !VerifySignature(known_locator + "+K@xyzzy" + known_sig_hint + "+Zfoo", known_token) {
+ t.Fatal("Verify cannot handle hints around permission signature")
+ }
+}
+
+// The size hint on the locator string should not affect signature validation.
+func TestVerifySignatureWrongSize(t *testing.T) {
+ PermissionSecret = []byte(known_key)
+ defer func() { PermissionSecret = nil }()
+
+ if !VerifySignature(known_hash + "+999999" + known_sig_hint, known_token) {
+ t.Fatal("Verify cannot handle incorrect size hint")
+ }
+
+ if !VerifySignature(known_hash + known_sig_hint, known_token) {
+ t.Fatal("Verify cannot handle missing size hint")
+ }
+}
+
+func TestVerifySignatureBadSig(t *testing.T) {
+ PermissionSecret = []byte(known_key)
+ defer func() { PermissionSecret = nil }()
+
+ bad_locator := known_locator + "+Aaaaaaaaaaaaaaaa@" + known_timestamp
+ if VerifySignature(bad_locator, known_token) {
+ t.Fail()
+ }
+}
+
+func TestVerifySignatureBadTimestamp(t *testing.T) {
+ PermissionSecret = []byte(known_key)
+ defer func() { PermissionSecret = nil }()
+
+ bad_locator := known_locator + "+A" + known_signature + "@00000000"
+ if VerifySignature(bad_locator, known_token) {
+ t.Fail()
+ }
+}
+
+func TestVerifySignatureBadSecret(t *testing.T) {
+ PermissionSecret = []byte("00000000000000000000")
+ defer func() { PermissionSecret = nil }()
+
+ if VerifySignature(known_signed_locator, known_token) {
+ t.Fail()
+ }
+}
+
+func TestVerifySignatureBadToken(t *testing.T) {
+ PermissionSecret = []byte(known_key)
+ defer func() { PermissionSecret = nil }()
+
+ if VerifySignature(known_signed_locator, "00000000") {
+ t.Fail()
+ }
+}
+
+func TestVerifySignatureExpired(t *testing.T) {
+ PermissionSecret = []byte(known_key)
+ defer func() { PermissionSecret = nil }()
+
+ yesterday := time.Now().AddDate(0, 0, -1)
+ expired_locator := SignLocator(known_hash, known_token, yesterday)
+ if VerifySignature(expired_locator, known_token) {
+ t.Fail()
+ }
+}
--- /dev/null
+// A Volume is an interface representing a Keep back-end storage unit:
+// for example, a single mounted disk, a RAID array, an Amazon S3 volume,
+// etc.
+
+package main
+
+import (
+ "errors"
+ "fmt"
+ "os"
+ "strings"
+ "time"
+)
+
+type Volume interface {
+ Get(loc string) ([]byte, error)
+ Put(loc string, block []byte) error
+ Touch(loc string) error
+ Mtime(loc string) (time.Time, error)
+ Index(prefix string) string
+ Delete(loc string) error
+ Status() *VolumeStatus
+ String() string
+}
+
+// MockVolumes are Volumes used to test the Keep front end.
+//
+// If the Bad field is true, this volume should return an error
+// on all writes and puts.
+//
+// The Touchable field signifies whether the Touch method will
+// succeed. Defaults to true. Note that Bad and Touchable are
+// independent: a MockVolume may be set up so that Put fails but Touch
+// works or vice versa.
+//
+// TODO(twp): rename Bad to something more descriptive, e.g. Writable,
+// and make sure that the tests that rely on it are testing the right
+// thing. We may need to simulate Writable, Touchable and Corrupt
+// volumes in different ways.
+//
+type MockVolume struct {
+ Store map[string][]byte
+ Timestamps map[string]time.Time
+ Bad bool
+ Touchable bool
+}
+
+func CreateMockVolume() *MockVolume {
+ return &MockVolume{
+ Store: make(map[string][]byte),
+ Timestamps: make(map[string]time.Time),
+ Bad: false,
+ Touchable: true,
+ }
+}
+
+func (v *MockVolume) Get(loc string) ([]byte, error) {
+ if v.Bad {
+ return nil, errors.New("Bad volume")
+ } else if block, ok := v.Store[loc]; ok {
+ return block, nil
+ }
+ return nil, os.ErrNotExist
+}
+
+func (v *MockVolume) Put(loc string, block []byte) error {
+ if v.Bad {
+ return errors.New("Bad volume")
+ }
+ v.Store[loc] = block
+ return v.Touch(loc)
+}
+
+func (v *MockVolume) Touch(loc string) error {
+ if v.Touchable {
+ v.Timestamps[loc] = time.Now()
+ return nil
+ }
+ return errors.New("Touch failed")
+}
+
+func (v *MockVolume) Mtime(loc string) (time.Time, error) {
+ var mtime time.Time
+ var err error
+ if v.Bad {
+ err = errors.New("Bad volume")
+ } else if t, ok := v.Timestamps[loc]; ok {
+ mtime = t
+ } else {
+ err = os.ErrNotExist
+ }
+ return mtime, err
+}
+
+func (v *MockVolume) Index(prefix string) string {
+ var result string
+ for loc, block := range v.Store {
+ if IsValidLocator(loc) && strings.HasPrefix(loc, prefix) {
+ result = result + fmt.Sprintf("%s+%d %d\n",
+ loc, len(block), 123456789)
+ }
+ }
+ return result
+}
+
+func (v *MockVolume) Delete(loc string) error {
+ if _, ok := v.Store[loc]; ok {
+ if time.Since(v.Timestamps[loc]) < permission_ttl {
+ return nil
+ }
+ delete(v.Store, loc)
+ return nil
+ }
+ return os.ErrNotExist
+}
+
+func (v *MockVolume) Status() *VolumeStatus {
+ var used uint64
+ for _, block := range v.Store {
+ used = used + uint64(len(block))
+ }
+ return &VolumeStatus{"/bogo", 123, 1000000 - used, used}
+}
+
+func (v *MockVolume) String() string {
+ return "[MockVolume]"
+}
+
+// A VolumeManager manages a collection of volumes.
+//
+// - Volumes is a slice of available Volumes.
+// - Choose() returns a Volume suitable for writing to.
+// - Quit() instructs the VolumeManager to shut down gracefully.
+//
+type VolumeManager interface {
+ Volumes() []Volume
+ Choose() Volume
+ Quit()
+}
+
+type RRVolumeManager struct {
+ volumes []Volume
+ nextwrite chan Volume
+ quit chan int
+}
+
+func MakeRRVolumeManager(vols []Volume) *RRVolumeManager {
+ // Create a new VolumeManager struct with the specified volumes,
+ // and with new Nextwrite and Quit channels.
+ // The Quit channel is buffered with a capacity of 1 so that
+ // another routine may write to it without blocking.
+ vm := &RRVolumeManager{vols, make(chan Volume), make(chan int, 1)}
+
+ // This goroutine implements round-robin volume selection.
+ // It sends each available Volume in turn to the Nextwrite
+ // channel, until receiving a notification on the Quit channel
+ // that it should terminate.
+ go func() {
+ var i int = 0
+ for {
+ select {
+ case <-vm.quit:
+ return
+ case vm.nextwrite <- vm.volumes[i]:
+ i = (i + 1) % len(vm.volumes)
+ }
+ }
+ }()
+
+ return vm
+}
+
+func (vm *RRVolumeManager) Volumes() []Volume {
+ return vm.volumes
+}
+
+func (vm *RRVolumeManager) Choose() Volume {
+ return <-vm.nextwrite
+}
+
+func (vm *RRVolumeManager) Quit() {
+ vm.quit <- 1
+}
--- /dev/null
+// A UnixVolume is a Volume backed by a locally mounted disk.
+//
+package main
+
+import (
+ "fmt"
+ "io/ioutil"
+ "log"
+ "os"
+ "path/filepath"
+ "strconv"
+ "strings"
+ "syscall"
+ "time"
+)
+
+// IORequests are encapsulated Get or Put requests. They are used to
+// implement serialized I/O (i.e. only one read/write operation per
+// volume). When running in serialized mode, the Keep front end sends
+// IORequests on a channel to an IORunner, which handles them one at a
+// time and returns an IOResponse.
+//
+type IOMethod int
+
+const (
+ KeepGet IOMethod = iota
+ KeepPut
+)
+
+type IORequest struct {
+ method IOMethod
+ loc string
+ data []byte
+ reply chan *IOResponse
+}
+
+type IOResponse struct {
+ data []byte
+ err error
+}
+
+// A UnixVolume has the following properties:
+//
+// root
+// the path to the volume's root directory
+// queue
+// A channel of IORequests. If non-nil, all I/O requests for
+// this volume should be queued on this channel; the result
+// will be delivered on the IOResponse channel supplied in the
+// request.
+//
+type UnixVolume struct {
+ root string // path to this volume
+ queue chan *IORequest
+}
+
+func (v *UnixVolume) IOHandler() {
+ for req := range v.queue {
+ var result IOResponse
+ switch req.method {
+ case KeepGet:
+ result.data, result.err = v.Read(req.loc)
+ case KeepPut:
+ result.err = v.Write(req.loc, req.data)
+ }
+ req.reply <- &result
+ }
+}
+
+func MakeUnixVolume(root string, serialize bool) (v UnixVolume) {
+ if serialize {
+ v = UnixVolume{root, make(chan *IORequest)}
+ go v.IOHandler()
+ } else {
+ v = UnixVolume{root, nil}
+ }
+ return
+}
+
+func (v *UnixVolume) Get(loc string) ([]byte, error) {
+ if v.queue == nil {
+ return v.Read(loc)
+ }
+ reply := make(chan *IOResponse)
+ v.queue <- &IORequest{KeepGet, loc, nil, reply}
+ response := <-reply
+ return response.data, response.err
+}
+
+func (v *UnixVolume) Put(loc string, block []byte) error {
+ if v.queue == nil {
+ return v.Write(loc, block)
+ }
+ reply := make(chan *IOResponse)
+ v.queue <- &IORequest{KeepPut, loc, block, reply}
+ response := <-reply
+ return response.err
+}
+
+func (v *UnixVolume) Touch(loc string) error {
+ p := v.blockPath(loc)
+ f, err := os.OpenFile(p, os.O_RDWR|os.O_APPEND, 0644)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ if e := lockfile(f); e != nil {
+ return e
+ }
+ defer unlockfile(f)
+ now := time.Now().Unix()
+ utime := syscall.Utimbuf{now, now}
+ return syscall.Utime(p, &utime)
+}
+
+func (v *UnixVolume) Mtime(loc string) (time.Time, error) {
+ p := v.blockPath(loc)
+ if fi, err := os.Stat(p); err != nil {
+ return time.Time{}, err
+ } else {
+ return fi.ModTime(), nil
+ }
+}
+
+// Read retrieves a block identified by the locator string "loc", and
+// returns its contents as a byte slice.
+//
+// If the block could not be opened or read, Read returns a nil slice
+// and the os.Error that was generated.
+//
+// If the block is present but its content hash does not match loc,
+// Read returns the block and a CorruptError. It is the caller's
+// responsibility to decide what (if anything) to do with the
+// corrupted data block.
+//
+func (v *UnixVolume) Read(loc string) ([]byte, error) {
+ buf, err := ioutil.ReadFile(v.blockPath(loc))
+ return buf, err
+}
+
+// Write stores a block of data identified by the locator string
+// "loc". It returns nil on success. If the volume is full, it
+// returns a FullError. If the write fails due to some other error,
+// that error is returned.
+//
+func (v *UnixVolume) Write(loc string, block []byte) error {
+ if v.IsFull() {
+ return FullError
+ }
+ bdir := v.blockDir(loc)
+ if err := os.MkdirAll(bdir, 0755); err != nil {
+ log.Printf("%s: could not create directory %s: %s",
+ loc, bdir, err)
+ return err
+ }
+
+ tmpfile, tmperr := ioutil.TempFile(bdir, "tmp"+loc)
+ if tmperr != nil {
+ log.Printf("ioutil.TempFile(%s, tmp%s): %s", bdir, loc, tmperr)
+ return tmperr
+ }
+ bpath := v.blockPath(loc)
+
+ if _, err := tmpfile.Write(block); err != nil {
+ log.Printf("%s: writing to %s: %s\n", v, bpath, err)
+ return err
+ }
+ if err := tmpfile.Close(); err != nil {
+ log.Printf("closing %s: %s\n", tmpfile.Name(), err)
+ os.Remove(tmpfile.Name())
+ return err
+ }
+ if err := os.Rename(tmpfile.Name(), bpath); err != nil {
+ log.Printf("rename %s %s: %s\n", tmpfile.Name(), bpath, err)
+ os.Remove(tmpfile.Name())
+ return err
+ }
+ return nil
+}
+
+// Status returns a VolumeStatus struct describing the volume's
+// current state.
+//
+func (v *UnixVolume) Status() *VolumeStatus {
+ var fs syscall.Statfs_t
+ var devnum uint64
+
+ if fi, err := os.Stat(v.root); err == nil {
+ devnum = fi.Sys().(*syscall.Stat_t).Dev
+ } else {
+ log.Printf("%s: os.Stat: %s\n", v, err)
+ return nil
+ }
+
+ err := syscall.Statfs(v.root, &fs)
+ if err != nil {
+ log.Printf("%s: statfs: %s\n", v, err)
+ return nil
+ }
+ // These calculations match the way df calculates disk usage:
+ // "free" space is measured by fs.Bavail, but "used" space
+ // uses fs.Blocks - fs.Bfree.
+ free := fs.Bavail * uint64(fs.Bsize)
+ used := (fs.Blocks - fs.Bfree) * uint64(fs.Bsize)
+ return &VolumeStatus{v.root, devnum, free, used}
+}
+
+// Index returns a list of blocks found on this volume which begin with
+// the specified prefix. If the prefix is an empty string, Index returns
+// a complete list of blocks.
+//
+// The return value is a multiline string (separated by
+// newlines). Each line is in the format
+//
+// locator+size modification-time
+//
+// e.g.:
+//
+// e4df392f86be161ca6ed3773a962b8f3+67108864 1388894303
+// e4d41e6fd68460e0e3fc18cc746959d2+67108864 1377796043
+// e4de7a2810f5554cd39b36d8ddb132ff+67108864 1388701136
+//
+func (v *UnixVolume) Index(prefix string) (output string) {
+ filepath.Walk(v.root,
+ func(path string, info os.FileInfo, err error) error {
+ // This WalkFunc inspects each path in the volume
+ // and prints an index line for all files that begin
+ // with prefix.
+ if err != nil {
+ log.Printf("IndexHandler: %s: walking to %s: %s",
+ v, path, err)
+ return nil
+ }
+ locator := filepath.Base(path)
+ // Skip directories that do not match prefix.
+ // We know there is nothing interesting inside.
+ if info.IsDir() &&
+ !strings.HasPrefix(locator, prefix) &&
+ !strings.HasPrefix(prefix, locator) {
+ return filepath.SkipDir
+ }
+ // Skip any file that is not apparently a locator, e.g. .meta files
+ if !IsValidLocator(locator) {
+ return nil
+ }
+ // Print filenames beginning with prefix
+ if !info.IsDir() && strings.HasPrefix(locator, prefix) {
+ output = output + fmt.Sprintf(
+ "%s+%d %d\n", locator, info.Size(), info.ModTime().Unix())
+ }
+ return nil
+ })
+
+ return
+}
+
+func (v *UnixVolume) Delete(loc string) error {
+ p := v.blockPath(loc)
+ f, err := os.OpenFile(p, os.O_RDWR|os.O_APPEND, 0644)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ if e := lockfile(f); e != nil {
+ return e
+ }
+ defer unlockfile(f)
+
+ // If the block has been PUT more recently than -permission_ttl,
+ // return success without removing the block. This guards against
+ // a race condition where a block is old enough that Data Manager
+ // has added it to the trash list, but the user submitted a PUT
+ // for the block since then.
+ if fi, err := os.Stat(p); err != nil {
+ return err
+ } else {
+ if time.Since(fi.ModTime()) < permission_ttl {
+ return nil
+ }
+ }
+ return os.Remove(p)
+}
+
+// blockDir returns the fully qualified directory name for the directory
+// where loc is (or would be) stored on this volume.
+func (v *UnixVolume) blockDir(loc string) string {
+ return filepath.Join(v.root, loc[0:3])
+}
+
+// blockPath returns the fully qualified pathname for the path to loc
+// on this volume.
+func (v *UnixVolume) blockPath(loc string) string {
+ return filepath.Join(v.blockDir(loc), loc)
+}
+
+// IsFull returns true if the free space on the volume is less than
+// MIN_FREE_KILOBYTES.
+//
+func (v *UnixVolume) IsFull() (isFull bool) {
+ fullSymlink := v.root + "/full"
+
+ // Check if the volume has been marked as full in the last hour.
+ if link, err := os.Readlink(fullSymlink); err == nil {
+ if ts, err := strconv.Atoi(link); err == nil {
+ fulltime := time.Unix(int64(ts), 0)
+ if time.Since(fulltime).Hours() < 1.0 {
+ return true
+ }
+ }
+ }
+
+ if avail, err := v.FreeDiskSpace(); err == nil {
+ isFull = avail < MIN_FREE_KILOBYTES
+ } else {
+ log.Printf("%s: FreeDiskSpace: %s\n", v, err)
+ isFull = false
+ }
+
+ // If the volume is full, timestamp it.
+ if isFull {
+ now := fmt.Sprintf("%d", time.Now().Unix())
+ os.Symlink(now, fullSymlink)
+ }
+ return
+}
+
+// FreeDiskSpace returns the number of unused 1k blocks available on
+// the volume.
+//
+func (v *UnixVolume) FreeDiskSpace() (free uint64, err error) {
+ var fs syscall.Statfs_t
+ err = syscall.Statfs(v.root, &fs)
+ if err == nil {
+ // Statfs output is not guaranteed to measure free
+ // space in terms of 1K blocks.
+ free = fs.Bavail * uint64(fs.Bsize) / 1024
+ }
+ return
+}
+
+func (v *UnixVolume) String() string {
+ return fmt.Sprintf("[UnixVolume %s]", v.root)
+}
+
+// lockfile and unlockfile use flock(2) to manage kernel file locks.
+func lockfile(f *os.File) error {
+ return syscall.Flock(int(f.Fd()), syscall.LOCK_EX)
+}
+
+func unlockfile(f *os.File) error {
+ return syscall.Flock(int(f.Fd()), syscall.LOCK_UN)
+}
--- /dev/null
+package main
+
+import (
+ "bytes"
+ "fmt"
+ "io/ioutil"
+ "os"
+ "syscall"
+ "testing"
+ "time"
+)
+
+func TempUnixVolume(t *testing.T, serialize bool) UnixVolume {
+ d, err := ioutil.TempDir("", "volume_test")
+ if err != nil {
+ t.Fatal(err)
+ }
+ return MakeUnixVolume(d, serialize)
+}
+
+func _teardown(v UnixVolume) {
+ if v.queue != nil {
+ close(v.queue)
+ }
+ os.RemoveAll(v.root)
+}
+
+// store writes a Keep block directly into a UnixVolume, for testing
+// UnixVolume methods.
+//
+func _store(t *testing.T, vol UnixVolume, filename string, block []byte) {
+ blockdir := fmt.Sprintf("%s/%s", vol.root, filename[:3])
+ if err := os.MkdirAll(blockdir, 0755); err != nil {
+ t.Fatal(err)
+ }
+
+ blockpath := fmt.Sprintf("%s/%s", blockdir, filename)
+ if f, err := os.Create(blockpath); err == nil {
+ f.Write(block)
+ f.Close()
+ } else {
+ t.Fatal(err)
+ }
+}
+
+func TestGet(t *testing.T) {
+ v := TempUnixVolume(t, false)
+ defer _teardown(v)
+ _store(t, v, TEST_HASH, TEST_BLOCK)
+
+ buf, err := v.Get(TEST_HASH)
+ if err != nil {
+ t.Error(err)
+ }
+ if bytes.Compare(buf, TEST_BLOCK) != 0 {
+ t.Errorf("expected %s, got %s", string(TEST_BLOCK), string(buf))
+ }
+}
+
+func TestGetNotFound(t *testing.T) {
+ v := TempUnixVolume(t, false)
+ defer _teardown(v)
+ _store(t, v, TEST_HASH, TEST_BLOCK)
+
+ buf, err := v.Get(TEST_HASH_2)
+ switch {
+ case os.IsNotExist(err):
+ break
+ case err == nil:
+ t.Errorf("Read should have failed, returned %s", string(buf))
+ default:
+ t.Errorf("Read expected ErrNotExist, got: %s", err)
+ }
+}
+
+func TestPut(t *testing.T) {
+ v := TempUnixVolume(t, false)
+ defer _teardown(v)
+
+ err := v.Put(TEST_HASH, TEST_BLOCK)
+ if err != nil {
+ t.Error(err)
+ }
+ p := fmt.Sprintf("%s/%s/%s", v.root, TEST_HASH[:3], TEST_HASH)
+ if buf, err := ioutil.ReadFile(p); err != nil {
+ t.Error(err)
+ } else if bytes.Compare(buf, TEST_BLOCK) != 0 {
+ t.Errorf("Write should have stored %s, did store %s",
+ string(TEST_BLOCK), string(buf))
+ }
+}
+
+func TestPutBadVolume(t *testing.T) {
+ v := TempUnixVolume(t, false)
+ defer _teardown(v)
+
+ os.Chmod(v.root, 000)
+ err := v.Put(TEST_HASH, TEST_BLOCK)
+ if err == nil {
+ t.Error("Write should have failed")
+ }
+}
+
+// TestPutTouch
+// Test that when applying PUT to a block that already exists,
+// the block's modification time is updated.
+func TestPutTouch(t *testing.T) {
+ v := TempUnixVolume(t, false)
+ defer _teardown(v)
+
+ if err := v.Put(TEST_HASH, TEST_BLOCK); err != nil {
+ t.Error(err)
+ }
+
+ // We'll verify { t0 < threshold < t1 }, where t0 is the
+ // existing block's timestamp on disk before Put() and t1 is
+ // its timestamp after Put().
+ threshold := time.Now().Add(-time.Second)
+
+ // Set the stored block's mtime far enough in the past that we
+ // can see the difference between "timestamp didn't change"
+ // and "timestamp granularity is too low".
+ {
+ oldtime := time.Now().Add(-20 * time.Second).Unix()
+ if err := syscall.Utime(v.blockPath(TEST_HASH),
+ &syscall.Utimbuf{oldtime, oldtime}); err != nil {
+ t.Error(err)
+ }
+
+ // Make sure v.Mtime() agrees the above Utime really worked.
+ if t0, err := v.Mtime(TEST_HASH); err != nil || t0.IsZero() || !t0.Before(threshold) {
+ t.Errorf("Setting mtime failed: %v, %v", t0, err)
+ }
+ }
+
+ // Write the same block again.
+ if err := v.Put(TEST_HASH, TEST_BLOCK); err != nil {
+ t.Error(err)
+ }
+
+ // Verify threshold < t1
+ t1, err := v.Mtime(TEST_HASH)
+ if err != nil {
+ t.Error(err)
+ }
+ if t1.Before(threshold) {
+ t.Errorf("t1 %v must be >= threshold %v after v.Put ",
+ t1, threshold)
+ }
+}
+
+// Serialization tests: launch a bunch of concurrent
+//
+// TODO(twp): show that the underlying Read/Write operations executed
+// serially and not concurrently. The easiest way to do this is
+// probably to activate verbose or debug logging, capture log output
+// and examine it to confirm that Reads and Writes did not overlap.
+//
+// TODO(twp): a proper test of I/O serialization requires that a
+// second request start while the first one is still underway.
+// Guaranteeing that the test behaves this way requires some tricky
+// synchronization and mocking. For now we'll just launch a bunch of
+// requests simultaenously in goroutines and demonstrate that they
+// return accurate results.
+//
+func TestGetSerialized(t *testing.T) {
+ // Create a volume with I/O serialization enabled.
+ v := TempUnixVolume(t, true)
+ defer _teardown(v)
+
+ _store(t, v, TEST_HASH, TEST_BLOCK)
+ _store(t, v, TEST_HASH_2, TEST_BLOCK_2)
+ _store(t, v, TEST_HASH_3, TEST_BLOCK_3)
+
+ sem := make(chan int)
+ go func(sem chan int) {
+ buf, err := v.Get(TEST_HASH)
+ if err != nil {
+ t.Errorf("err1: %v", err)
+ }
+ if bytes.Compare(buf, TEST_BLOCK) != 0 {
+ t.Errorf("buf should be %s, is %s", string(TEST_BLOCK), string(buf))
+ }
+ sem <- 1
+ }(sem)
+
+ go func(sem chan int) {
+ buf, err := v.Get(TEST_HASH_2)
+ if err != nil {
+ t.Errorf("err2: %v", err)
+ }
+ if bytes.Compare(buf, TEST_BLOCK_2) != 0 {
+ t.Errorf("buf should be %s, is %s", string(TEST_BLOCK_2), string(buf))
+ }
+ sem <- 1
+ }(sem)
+
+ go func(sem chan int) {
+ buf, err := v.Get(TEST_HASH_3)
+ if err != nil {
+ t.Errorf("err3: %v", err)
+ }
+ if bytes.Compare(buf, TEST_BLOCK_3) != 0 {
+ t.Errorf("buf should be %s, is %s", string(TEST_BLOCK_3), string(buf))
+ }
+ sem <- 1
+ }(sem)
+
+ // Wait for all goroutines to finish
+ for done := 0; done < 3; {
+ done += <-sem
+ }
+}
+
+func TestPutSerialized(t *testing.T) {
+ // Create a volume with I/O serialization enabled.
+ v := TempUnixVolume(t, true)
+ defer _teardown(v)
+
+ sem := make(chan int)
+ go func(sem chan int) {
+ err := v.Put(TEST_HASH, TEST_BLOCK)
+ if err != nil {
+ t.Errorf("err1: %v", err)
+ }
+ sem <- 1
+ }(sem)
+
+ go func(sem chan int) {
+ err := v.Put(TEST_HASH_2, TEST_BLOCK_2)
+ if err != nil {
+ t.Errorf("err2: %v", err)
+ }
+ sem <- 1
+ }(sem)
+
+ go func(sem chan int) {
+ err := v.Put(TEST_HASH_3, TEST_BLOCK_3)
+ if err != nil {
+ t.Errorf("err3: %v", err)
+ }
+ sem <- 1
+ }(sem)
+
+ // Wait for all goroutines to finish
+ for done := 0; done < 2; {
+ done += <-sem
+ }
+
+ // Double check that we actually wrote the blocks we expected to write.
+ buf, err := v.Get(TEST_HASH)
+ if err != nil {
+ t.Errorf("Get #1: %v", err)
+ }
+ if bytes.Compare(buf, TEST_BLOCK) != 0 {
+ t.Errorf("Get #1: expected %s, got %s", string(TEST_BLOCK), string(buf))
+ }
+
+ buf, err = v.Get(TEST_HASH_2)
+ if err != nil {
+ t.Errorf("Get #2: %v", err)
+ }
+ if bytes.Compare(buf, TEST_BLOCK_2) != 0 {
+ t.Errorf("Get #2: expected %s, got %s", string(TEST_BLOCK_2), string(buf))
+ }
+
+ buf, err = v.Get(TEST_HASH_3)
+ if err != nil {
+ t.Errorf("Get #3: %v", err)
+ }
+ if bytes.Compare(buf, TEST_BLOCK_3) != 0 {
+ t.Errorf("Get #3: expected %s, got %s", string(TEST_BLOCK_3), string(buf))
+ }
+}
+
+func TestIsFull(t *testing.T) {
+ v := TempUnixVolume(t, false)
+ defer _teardown(v)
+
+ full_path := v.root + "/full"
+ now := fmt.Sprintf("%d", time.Now().Unix())
+ os.Symlink(now, full_path)
+ if !v.IsFull() {
+ t.Errorf("%s: claims not to be full", v)
+ }
+ os.Remove(full_path)
+
+ // Test with an expired /full link.
+ expired := fmt.Sprintf("%d", time.Now().Unix()-3605)
+ os.Symlink(expired, full_path)
+ if v.IsFull() {
+ t.Errorf("%s: should no longer be full", v)
+ }
+}
--- /dev/null
+package main
+
+/* A WorkQueue is an asynchronous thread-safe queue manager. It
+ provides a channel from which items can be read off the queue, and
+ permits replacing the contents of the queue at any time.
+
+ The overall work flow for a WorkQueue is as follows:
+
+ 1. A WorkQueue is created with NewWorkQueue(). This
+ function instantiates a new WorkQueue and starts a manager
+ goroutine. The manager listens on an input channel
+ (manager.newlist) and an output channel (manager.NextItem).
+
+ 2. The manager first waits for a new list of requests on the
+ newlist channel. When another goroutine calls
+ manager.ReplaceQueue(lst), it sends lst over the newlist
+ channel to the manager. The manager goroutine now has
+ ownership of the list.
+
+ 3. Once the manager has this initial list, it listens on both the
+ input and output channels for one of the following to happen:
+
+ a. A worker attempts to read an item from the NextItem
+ channel. The manager sends the next item from the list
+ over this channel to the worker, and loops.
+
+ b. New data is sent to the manager on the newlist channel.
+ This happens when another goroutine calls
+ manager.ReplaceItem() with a new list. The manager
+ discards the current list, replaces it with the new one,
+ and begins looping again.
+
+ c. The input channel is closed. The manager closes its
+ output channel (signalling any workers to quit) and
+ terminates.
+
+ Tasks currently handled by WorkQueue:
+ * the pull list
+ * the trash list
+
+ Example usage:
+
+ // Any kind of user-defined type can be used with the
+ // WorkQueue.
+ type FrobRequest struct {
+ frob string
+ }
+
+ // Make a work list.
+ froblist := NewWorkQueue()
+
+ // Start a concurrent worker to read items from the NextItem
+ // channel until it is closed, deleting each one.
+ go func(list WorkQueue) {
+ for i := range list.NextItem {
+ req := i.(FrobRequest)
+ frob.Run(req)
+ }
+ }(froblist)
+
+ // Set up a HTTP handler for PUT /frob
+ router.HandleFunc(`/frob`,
+ func(w http.ResponseWriter, req *http.Request) {
+ // Parse the request body into a list.List
+ // of FrobRequests, and give this list to the
+ // frob manager.
+ newfrobs := parseBody(req.Body)
+ froblist.ReplaceQueue(newfrobs)
+ }).Methods("PUT")
+
+ Methods available on a WorkQueue:
+
+ ReplaceQueue(list)
+ Replaces the current item list with a new one. The list
+ manager discards any unprocessed items on the existing
+ list and replaces it with the new one. If the worker is
+ processing a list item when ReplaceQueue is called, it
+ finishes processing before receiving items from the new
+ list.
+ Close()
+ Shuts down the manager goroutine. When Close is called,
+ the manager closes the NextItem channel.
+*/
+
+import "container/list"
+
+type WorkQueue struct {
+ newlist chan *list.List
+ NextItem chan interface{}
+}
+
+// NewWorkQueue returns a new worklist, and launches a listener
+// goroutine that waits for work and farms it out to workers.
+//
+func NewWorkQueue() *WorkQueue {
+ b := WorkQueue{
+ newlist: make(chan *list.List),
+ NextItem: make(chan interface{}),
+ }
+ go b.listen()
+ return &b
+}
+
+// ReplaceQueue sends a new list of pull requests to the manager goroutine.
+// The manager will discard any outstanding pull list and begin
+// working on the new list.
+//
+func (b *WorkQueue) ReplaceQueue(list *list.List) {
+ b.newlist <- list
+}
+
+// Close shuts down the manager and terminates the goroutine, which
+// completes any pull request in progress and abandons any pending
+// requests.
+//
+func (b *WorkQueue) Close() {
+ close(b.newlist)
+}
+
+// listen is run in a goroutine. It reads new pull lists from its
+// input queue until the queue is closed.
+// listen takes ownership of the list that is passed to it.
+//
+// Note that the routine does not ever need to access the list
+// itself once the current_item has been initialized, so we do
+// not bother to keep a pointer to the list. Because it is a
+// doubly linked list, holding on to the current item will keep
+// it from garbage collection.
+//
+func (b *WorkQueue) listen() {
+ var current_item *list.Element
+
+ // When we're done, close the output channel to shut down any
+ // workers.
+ defer close(b.NextItem)
+
+ for {
+ // If the current list is empty, wait for a new list before
+ // even checking if workers are ready.
+ if current_item == nil {
+ if p, ok := <-b.newlist; ok {
+ current_item = p.Front()
+ } else {
+ // The channel was closed; shut down.
+ return
+ }
+ }
+ select {
+ case p, ok := <-b.newlist:
+ if ok {
+ current_item = p.Front()
+ } else {
+ // The input channel is closed; time to shut down
+ return
+ }
+ case b.NextItem <- current_item.Value:
+ current_item = current_item.Next()
+ }
+ }
+}
--- /dev/null
+package main
+
+import (
+ "container/list"
+ "testing"
+)
+
+func makeTestWorkList(ary []int) *list.List {
+ l := list.New()
+ for _, n := range ary {
+ l.PushBack(n)
+ }
+ return l
+}
+
+func expectChannelEmpty(t *testing.T, c <-chan interface{}) {
+ select {
+ case item := <-c:
+ t.Fatalf("Received value (%v) from channel that we expected to be empty", item)
+ default:
+ // no-op
+ }
+}
+
+func expectChannelNotEmpty(t *testing.T, c <-chan interface{}) {
+ if item, ok := <-c; !ok {
+ t.Fatal("expected data on a closed channel")
+ } else if item == nil {
+ t.Fatal("expected data on an empty channel")
+ }
+}
+
+func expectChannelClosed(t *testing.T, c <-chan interface{}) {
+ received, ok := <-c
+ if ok {
+ t.Fatalf("Expected channel to be closed, but received %v instead", received)
+ }
+}
+
+func expectFromChannel(t *testing.T, c <-chan interface{}, expected []int) {
+ for i := range expected {
+ actual, ok := <-c
+ t.Logf("received %v", actual)
+ if !ok {
+ t.Fatalf("Expected %v but channel was closed after receiving the first %d elements correctly.", expected, i)
+ } else if actual.(int) != expected[i] {
+ t.Fatalf("Expected %v but received '%v' after receiving the first %d elements correctly.", expected[i], actual, i)
+ }
+ }
+}
+
+// Create a WorkQueue, generate a list for it, and instantiate a worker.
+func TestWorkQueueReadWrite(t *testing.T) {
+ var input = []int{1, 1, 2, 3, 5, 8, 13, 21, 34}
+
+ b := NewWorkQueue()
+ b.ReplaceQueue(makeTestWorkList(input))
+
+ expectFromChannel(t, b.NextItem, input)
+ expectChannelEmpty(t, b.NextItem)
+ b.Close()
+}
+
+// Start a worker before the list has any input.
+func TestWorkQueueEarlyRead(t *testing.T) {
+ var input = []int{1, 1, 2, 3, 5, 8, 13, 21, 34}
+
+ b := NewWorkQueue()
+
+ // First, demonstrate that nothing is available on the NextItem
+ // channel.
+ expectChannelEmpty(t, b.NextItem)
+
+ // Start a reader in a goroutine. The reader will block until the
+ // block work list has been initialized.
+ //
+ done := make(chan int)
+ go func() {
+ expectFromChannel(t, b.NextItem, input)
+ b.Close()
+ done <- 1
+ }()
+
+ // Feed the blocklist a new worklist, and wait for the worker to
+ // finish.
+ b.ReplaceQueue(makeTestWorkList(input))
+ <-done
+
+ expectChannelClosed(t, b.NextItem)
+}
+
+// Show that a reader may block when the manager's list is exhausted,
+// and that the reader resumes automatically when new data is
+// available.
+func TestWorkQueueReaderBlocks(t *testing.T) {
+ var (
+ inputBeforeBlock = []int{1, 2, 3, 4, 5}
+ inputAfterBlock = []int{6, 7, 8, 9, 10}
+ )
+
+ b := NewWorkQueue()
+ sendmore := make(chan int)
+ done := make(chan int)
+ go func() {
+ expectFromChannel(t, b.NextItem, inputBeforeBlock)
+
+ // Confirm that the channel is empty, so a subsequent read
+ // on it will block.
+ expectChannelEmpty(t, b.NextItem)
+
+ // Signal that we're ready for more input.
+ sendmore <- 1
+ expectFromChannel(t, b.NextItem, inputAfterBlock)
+ b.Close()
+ done <- 1
+ }()
+
+ // Write a slice of the first five elements and wait for the
+ // reader to signal that it's ready for us to send more input.
+ b.ReplaceQueue(makeTestWorkList(inputBeforeBlock))
+ <-sendmore
+
+ b.ReplaceQueue(makeTestWorkList(inputAfterBlock))
+
+ // Wait for the reader to complete.
+ <-done
+}
+
+// Replace one active work list with another.
+func TestWorkQueueReplaceQueue(t *testing.T) {
+ var firstInput = []int{1, 1, 2, 3, 5, 8, 13, 21, 34}
+ var replaceInput = []int{1, 4, 9, 16, 25, 36, 49, 64, 81}
+
+ b := NewWorkQueue()
+ b.ReplaceQueue(makeTestWorkList(firstInput))
+
+ // Read just the first five elements from the work list.
+ // Confirm that the channel is not empty.
+ expectFromChannel(t, b.NextItem, firstInput[0:5])
+ expectChannelNotEmpty(t, b.NextItem)
+
+ // Replace the work list and read five more elements.
+ // The old list should have been discarded and all new
+ // elements come from the new list.
+ b.ReplaceQueue(makeTestWorkList(replaceInput))
+ expectFromChannel(t, b.NextItem, replaceInput[0:5])
+
+ b.Close()
+}
--- /dev/null
+../../sdk/python/.gitignore
\ No newline at end of file
--- /dev/null
+====================
+Arvados Node Manager
+====================
+
+Overview
+--------
+
+This package provides ``arvados-node-manager``. It dynamically starts
+and stops compute nodes on an Arvados_ cloud installation based on job
+demand.
+
+.. _Arvados: https://arvados.org/
+
+Setup
+-----
+
+1. Install the package.
+
+2. Write a configuration file. ``doc/ec2.example.cfg`` documents all
+ of the options available, with specific tunables for EC2 clouds.
+
+3. Run ``arvados-node-manager --config YOURCONFIGFILE`` using whatever
+ supervisor you like (e.g., runit).
+
+Testing and Development
+-----------------------
+
+To run tests, just run::
+
+ python setup.py test
+
+Our `hacking guide
+<https://arvados.org/projects/arvados/wiki/Hacking_Node_Manager>`_
+provides an architectural overview of the Arvados Node Manager to help
+you find your way around the source. The `Lifecycle of an Arvados
+compute node
+<https://arvados.org/projects/arvados/wiki/Lifecycle_of_an_Arvados_compute_node>`_
+page explains how it works in concert with other Arvados components to
+prepare a node for compute work.
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import _strptime # See <http://bugs.python.org/issue7980#msg221094>.
+import logging
+
+logger = logging.getLogger('arvnodeman')
+logger.addHandler(logging.NullHandler())
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import logging
+import time
+
+import pykka
+
+from .config import actor_class
+
+def _notify_subscribers(response, subscribers):
+ """Send the response to all the subscriber methods.
+
+ If any of the subscriber actors have stopped, remove them from the
+ subscriber set.
+ """
+ dead_subscribers = set()
+ for subscriber in subscribers:
+ try:
+ subscriber(response)
+ except pykka.ActorDeadError:
+ dead_subscribers.add(subscriber)
+ subscribers.difference_update(dead_subscribers)
+
+class RemotePollLoopActor(actor_class):
+ """Abstract actor class to regularly poll a remote service.
+
+ This actor sends regular requests to a remote service, and sends each
+ response to subscribers. It takes care of error handling, and retrying
+ requests with exponential backoff.
+
+ To use this actor, define the _send_request method. If you also
+ define an _item_key method, this class will support subscribing to
+ a specific item by key in responses.
+ """
+ def __init__(self, client, timer_actor, poll_wait=60, max_poll_wait=180):
+ super(RemotePollLoopActor, self).__init__()
+ self._client = client
+ self._timer = timer_actor
+ self._logger = logging.getLogger(self.LOGGER_NAME)
+ self._later = self.actor_ref.proxy()
+ self._polling_started = False
+ self.log_prefix = "{} (at {})".format(self.__class__.__name__, id(self))
+ self.min_poll_wait = poll_wait
+ self.max_poll_wait = max_poll_wait
+ self.poll_wait = self.min_poll_wait
+ self.all_subscribers = set()
+ self.key_subscribers = {}
+ if hasattr(self, '_item_key'):
+ self.subscribe_to = self._subscribe_to
+
+ def _start_polling(self):
+ if not self._polling_started:
+ self._polling_started = True
+ self._later.poll()
+
+ def subscribe(self, subscriber):
+ self.all_subscribers.add(subscriber)
+ self._logger.debug("%r subscribed to all events", subscriber)
+ self._start_polling()
+
+ # __init__ exposes this method to the proxy if the subclass defines
+ # _item_key.
+ def _subscribe_to(self, key, subscriber):
+ self.key_subscribers.setdefault(key, set()).add(subscriber)
+ self._logger.debug("%r subscribed to events for '%s'", subscriber, key)
+ self._start_polling()
+
+ def _send_request(self):
+ raise NotImplementedError("subclasses must implement request method")
+
+ def _got_response(self, response):
+ self._logger.debug("%s got response with %d items",
+ self.log_prefix, len(response))
+ self.poll_wait = self.min_poll_wait
+ _notify_subscribers(response, self.all_subscribers)
+ if hasattr(self, '_item_key'):
+ items = {self._item_key(x): x for x in response}
+ for key, subscribers in self.key_subscribers.iteritems():
+ _notify_subscribers(items.get(key), subscribers)
+
+ def _got_error(self, error):
+ self.poll_wait = min(self.poll_wait * 2, self.max_poll_wait)
+ return "{} got error: {} - waiting {} seconds".format(
+ self.log_prefix, error, self.poll_wait)
+
+ def is_common_error(self, exception):
+ return False
+
+ def poll(self, scheduled_start=None):
+ self._logger.debug("%s sending poll", self.log_prefix)
+ start_time = time.time()
+ if scheduled_start is None:
+ scheduled_start = start_time
+ try:
+ response = self._send_request()
+ except Exception as error:
+ errmsg = self._got_error(error)
+ if self.is_common_error(error):
+ self._logger.warning(errmsg)
+ else:
+ self._logger.exception(errmsg)
+ next_poll = start_time + self.poll_wait
+ else:
+ self._got_response(response)
+ next_poll = scheduled_start + self.poll_wait
+ end_time = time.time()
+ if next_poll < end_time: # We've drifted too much; start fresh.
+ next_poll = end_time + self.poll_wait
+ self._timer.schedule(next_poll, self._later.poll, next_poll)
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import itertools
+import time
+
+def arvados_node_fqdn(arvados_node, default_hostname='dynamic.compute'):
+ hostname = arvados_node.get('hostname') or default_hostname
+ return '{}.{}'.format(hostname, arvados_node['domain'])
+
+def arvados_node_mtime(node):
+ return time.mktime(time.strptime(node['modified_at'] + 'UTC',
+ '%Y-%m-%dT%H:%M:%SZ%Z')) - time.timezone
+
+def timestamp_fresh(timestamp, fresh_time):
+ return (time.time() - timestamp) < fresh_time
+
+class ShutdownTimer(object):
+ """Keep track of a cloud node's shutdown windows.
+
+ Instantiate this class with a timestamp of when a cloud node started,
+ and a list of durations (in minutes) of when the node must not and may
+ be shut down, alternating. The class will tell you when a shutdown
+ window is open, and when the next open window will start.
+ """
+ def __init__(self, start_time, shutdown_windows):
+ # The implementation is easiest if we have an even number of windows,
+ # because then windows always alternate between open and closed.
+ # Rig that up: calculate the first shutdown window based on what's
+ # passed in. Then, if we were given an odd number of windows, merge
+ # that first window into the last one, since they both# represent
+ # closed state.
+ first_window = shutdown_windows[0]
+ shutdown_windows = list(shutdown_windows[1:])
+ self._next_opening = start_time + (60 * first_window)
+ if len(shutdown_windows) % 2:
+ shutdown_windows.append(first_window)
+ else:
+ shutdown_windows[-1] += first_window
+ self.shutdown_windows = itertools.cycle([60 * n
+ for n in shutdown_windows])
+ self._open_start = self._next_opening
+ self._open_for = next(self.shutdown_windows)
+
+ def _advance_opening(self):
+ while self._next_opening < time.time():
+ self._open_start = self._next_opening
+ self._next_opening += self._open_for + next(self.shutdown_windows)
+ self._open_for = next(self.shutdown_windows)
+
+ def next_opening(self):
+ self._advance_opening()
+ return self._next_opening
+
+ def window_open(self):
+ self._advance_opening()
+ return 0 < (time.time() - self._open_start) < self._open_for
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import functools
+import logging
+import time
+
+import libcloud.common.types as cloud_types
+import pykka
+
+from .. import arvados_node_fqdn, arvados_node_mtime, timestamp_fresh
+from ...clientactor import _notify_subscribers
+from ... import config
+
+class ComputeNodeStateChangeBase(config.actor_class):
+ """Base class for actors that change a compute node's state.
+
+ This base class takes care of retrying changes and notifying
+ subscribers when the change is finished.
+ """
+ def __init__(self, logger_name, cloud_client, timer_actor,
+ retry_wait, max_retry_wait):
+ super(ComputeNodeStateChangeBase, self).__init__()
+ self._later = self.actor_ref.proxy()
+ self._logger = logging.getLogger(logger_name)
+ self._cloud = cloud_client
+ self._timer = timer_actor
+ self.min_retry_wait = retry_wait
+ self.max_retry_wait = max_retry_wait
+ self.retry_wait = retry_wait
+ self.subscribers = set()
+
+ @staticmethod
+ def _retry(errors=()):
+ """Retry decorator for an actor method that makes remote requests.
+
+ Use this function to decorator an actor method, and pass in a
+ tuple of exceptions to catch. This decorator will schedule
+ retries of that method with exponential backoff if the
+ original method raises a known cloud driver error, or any of the
+ given exception types.
+ """
+ def decorator(orig_func):
+ @functools.wraps(orig_func)
+ def retry_wrapper(self, *args, **kwargs):
+ start_time = time.time()
+ try:
+ orig_func(self, *args, **kwargs)
+ except Exception as error:
+ if not (isinstance(error, errors) or
+ self._cloud.is_cloud_exception(error)):
+ raise
+ self._logger.warning(
+ "Client error: %s - waiting %s seconds",
+ error, self.retry_wait)
+ self._timer.schedule(start_time + self.retry_wait,
+ getattr(self._later,
+ orig_func.__name__),
+ *args, **kwargs)
+ self.retry_wait = min(self.retry_wait * 2,
+ self.max_retry_wait)
+ else:
+ self.retry_wait = self.min_retry_wait
+ return retry_wrapper
+ return decorator
+
+ def _finished(self):
+ _notify_subscribers(self._later, self.subscribers)
+ self.subscribers = None
+
+ def subscribe(self, subscriber):
+ if self.subscribers is None:
+ try:
+ subscriber(self._later)
+ except pykka.ActorDeadError:
+ pass
+ else:
+ self.subscribers.add(subscriber)
+
+
+class ComputeNodeSetupActor(ComputeNodeStateChangeBase):
+ """Actor to create and set up a cloud compute node.
+
+ This actor prepares an Arvados node record for a new compute node
+ (either creating one or cleaning one passed in), then boots the
+ actual compute node. It notifies subscribers when the cloud node
+ is successfully created (the last step in the process for Node
+ Manager to handle).
+ """
+ def __init__(self, timer_actor, arvados_client, cloud_client,
+ cloud_size, arvados_node=None,
+ retry_wait=1, max_retry_wait=180):
+ super(ComputeNodeSetupActor, self).__init__(
+ 'arvnodeman.nodeup', cloud_client, timer_actor,
+ retry_wait, max_retry_wait)
+ self._arvados = arvados_client
+ self.cloud_size = cloud_size
+ self.arvados_node = None
+ self.cloud_node = None
+ if arvados_node is None:
+ self._later.create_arvados_node()
+ else:
+ self._later.prepare_arvados_node(arvados_node)
+
+ @ComputeNodeStateChangeBase._retry()
+ def create_arvados_node(self):
+ self.arvados_node = self._arvados.nodes().create(body={}).execute()
+ self._later.create_cloud_node()
+
+ @ComputeNodeStateChangeBase._retry()
+ def prepare_arvados_node(self, node):
+ self.arvados_node = self._arvados.nodes().update(
+ uuid=node['uuid'],
+ body={'hostname': None,
+ 'ip_address': None,
+ 'slot_number': None,
+ 'first_ping_at': None,
+ 'last_ping_at': None,
+ 'info': {'ec2_instance_id': None,
+ 'last_action': "Prepared by Node Manager"}}
+ ).execute()
+ self._later.create_cloud_node()
+
+ @ComputeNodeStateChangeBase._retry()
+ def create_cloud_node(self):
+ self._logger.info("Creating cloud node with size %s.",
+ self.cloud_size.name)
+ self.cloud_node = self._cloud.create_node(self.cloud_size,
+ self.arvados_node)
+ self._logger.info("Cloud node %s created.", self.cloud_node.id)
+ self._later.post_create()
+
+ @ComputeNodeStateChangeBase._retry()
+ def post_create(self):
+ self._cloud.post_create_node(self.cloud_node)
+ self._logger.info("%s post-create work done.", self.cloud_node.id)
+ self._finished()
+
+ def stop_if_no_cloud_node(self):
+ if self.cloud_node is None:
+ self.stop()
+
+
+class ComputeNodeShutdownActor(ComputeNodeStateChangeBase):
+ """Actor to shut down a compute node.
+
+ This actor simply destroys a cloud node, retrying as needed.
+ """
+ def __init__(self, timer_actor, cloud_client, node_monitor,
+ cancellable=True, retry_wait=1, max_retry_wait=180):
+ # If a ShutdownActor is cancellable, it will ask the
+ # ComputeNodeMonitorActor if it's still eligible before taking each
+ # action, and stop the shutdown process if the node is no longer
+ # eligible. Normal shutdowns based on job demand should be
+ # cancellable; shutdowns based on node misbehavior should not.
+ super(ComputeNodeShutdownActor, self).__init__(
+ 'arvnodeman.nodedown', cloud_client, timer_actor,
+ retry_wait, max_retry_wait)
+ self._monitor = node_monitor.proxy()
+ self.cloud_node = self._monitor.cloud_node.get()
+ self.cancellable = cancellable
+ self.success = None
+
+ def on_start(self):
+ self._later.shutdown_node()
+
+ def cancel_shutdown(self):
+ self.success = False
+ self._finished()
+
+ def _stop_if_window_closed(orig_func):
+ @functools.wraps(orig_func)
+ def stop_wrapper(self, *args, **kwargs):
+ if (self.cancellable and
+ (not self._monitor.shutdown_eligible().get())):
+ self._logger.info(
+ "Cloud node %s shutdown cancelled - no longer eligible.",
+ self.cloud_node.id)
+ self._later.cancel_shutdown()
+ return None
+ else:
+ return orig_func(self, *args, **kwargs)
+ return stop_wrapper
+
+ @_stop_if_window_closed
+ @ComputeNodeStateChangeBase._retry()
+ def shutdown_node(self):
+ if self._cloud.destroy_node(self.cloud_node):
+ self._logger.info("Cloud node %s shut down.", self.cloud_node.id)
+ self.success = True
+ self._finished()
+ else:
+ # Force a retry.
+ raise cloud_types.LibcloudError("destroy_node failed")
+
+ # Make the decorator available to subclasses.
+ _stop_if_window_closed = staticmethod(_stop_if_window_closed)
+
+
+class ComputeNodeUpdateActor(config.actor_class):
+ """Actor to dispatch one-off cloud management requests.
+
+ This actor receives requests for small cloud updates, and
+ dispatches them to a real driver. ComputeNodeMonitorActors use
+ this to perform maintenance tasks on themselves. Having a
+ dedicated actor for this gives us the opportunity to control the
+ flow of requests; e.g., by backing off when errors occur.
+
+ This actor is most like a "traditional" Pykka actor: there's no
+ subscribing, but instead methods return real driver results. If
+ you're interested in those results, you should get them from the
+ Future that the proxy method returns. Be prepared to handle exceptions
+ from the cloud driver when you do.
+ """
+ def __init__(self, cloud_factory, max_retry_wait=180):
+ super(ComputeNodeUpdateActor, self).__init__()
+ self._cloud = cloud_factory()
+ self.max_retry_wait = max_retry_wait
+ self.error_streak = 0
+ self.next_request_time = time.time()
+
+ def _throttle_errors(orig_func):
+ @functools.wraps(orig_func)
+ def throttle_wrapper(self, *args, **kwargs):
+ throttle_time = self.next_request_time - time.time()
+ if throttle_time > 0:
+ time.sleep(throttle_time)
+ self.next_request_time = time.time()
+ try:
+ result = orig_func(self, *args, **kwargs)
+ except Exception as error:
+ self.error_streak += 1
+ self.next_request_time += min(2 ** self.error_streak,
+ self.max_retry_wait)
+ raise
+ else:
+ self.error_streak = 0
+ return result
+ return throttle_wrapper
+
+ @_throttle_errors
+ def sync_node(self, cloud_node, arvados_node):
+ return self._cloud.sync_node(cloud_node, arvados_node)
+
+
+class ComputeNodeMonitorActor(config.actor_class):
+ """Actor to manage a running compute node.
+
+ This actor gets updates about a compute node's cloud and Arvados records.
+ It uses this information to notify subscribers when the node is eligible
+ for shutdown.
+ """
+ def __init__(self, cloud_node, cloud_node_start_time, shutdown_timer,
+ timer_actor, update_actor, arvados_node=None,
+ poll_stale_after=600, node_stale_after=3600):
+ super(ComputeNodeMonitorActor, self).__init__()
+ self._later = self.actor_ref.proxy()
+ self._logger = logging.getLogger('arvnodeman.computenode')
+ self._last_log = None
+ self._shutdowns = shutdown_timer
+ self._timer = timer_actor
+ self._update = update_actor
+ self.cloud_node = cloud_node
+ self.cloud_node_start_time = cloud_node_start_time
+ self.poll_stale_after = poll_stale_after
+ self.node_stale_after = node_stale_after
+ self.subscribers = set()
+ self.arvados_node = None
+ self._later.update_arvados_node(arvados_node)
+ self.last_shutdown_opening = None
+ self._later.consider_shutdown()
+
+ def subscribe(self, subscriber):
+ self.subscribers.add(subscriber)
+
+ def _debug(self, msg, *args):
+ if msg == self._last_log:
+ return
+ self._last_log = msg
+ self._logger.debug(msg, *args)
+
+ def in_state(self, *states):
+ # Return a boolean to say whether or not our Arvados node record is in
+ # one of the given states. If state information is not
+ # available--because this node has no Arvados record, the record is
+ # stale, or the record has no state information--return None.
+ if (self.arvados_node is None) or not timestamp_fresh(
+ arvados_node_mtime(self.arvados_node), self.node_stale_after):
+ return None
+ state = self.arvados_node['info'].get('slurm_state')
+ if not state:
+ return None
+ result = state in states
+ if state == 'idle':
+ result = result and not self.arvados_node['job_uuid']
+ return result
+
+ def shutdown_eligible(self):
+ if not self._shutdowns.window_open():
+ return False
+ elif self.arvados_node is None:
+ # If this is a new, unpaired node, it's eligible for
+ # shutdown--we figure there was an error during bootstrap.
+ return timestamp_fresh(self.cloud_node_start_time,
+ self.node_stale_after)
+ else:
+ return self.in_state('idle')
+
+ def consider_shutdown(self):
+ next_opening = self._shutdowns.next_opening()
+ if self.shutdown_eligible():
+ self._debug("Node %s suggesting shutdown.", self.cloud_node.id)
+ _notify_subscribers(self._later, self.subscribers)
+ elif self._shutdowns.window_open():
+ self._debug("Node %s shutdown window open but node busy.",
+ self.cloud_node.id)
+ elif self.last_shutdown_opening != next_opening:
+ self._debug("Node %s shutdown window closed. Next at %s.",
+ self.cloud_node.id, time.ctime(next_opening))
+ self._timer.schedule(next_opening, self._later.consider_shutdown)
+ self.last_shutdown_opening = next_opening
+
+ def offer_arvados_pair(self, arvados_node):
+ if self.arvados_node is not None:
+ return None
+ elif arvados_node['ip_address'] in self.cloud_node.private_ips:
+ self._later.update_arvados_node(arvados_node)
+ return self.cloud_node.id
+ else:
+ return None
+
+ def update_cloud_node(self, cloud_node):
+ if cloud_node is not None:
+ self.cloud_node = cloud_node
+ self._later.consider_shutdown()
+
+ def update_arvados_node(self, arvados_node):
+ if arvados_node is not None:
+ self.arvados_node = arvados_node
+ new_hostname = arvados_node_fqdn(self.arvados_node)
+ if new_hostname != self.cloud_node.name:
+ self._update.sync_node(self.cloud_node, self.arvados_node)
+ self._later.consider_shutdown()
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import subprocess
+import time
+
+from . import \
+ ComputeNodeSetupActor, ComputeNodeUpdateActor, ComputeNodeMonitorActor
+from . import ComputeNodeShutdownActor as ShutdownActorBase
+
+class ComputeNodeShutdownActor(ShutdownActorBase):
+ SLURM_END_STATES = frozenset(['down\n', 'down*\n', 'drain\n', 'fail\n'])
+
+ def on_start(self):
+ arv_node = self._monitor.arvados_node.get()
+ if arv_node is None:
+ return super(ComputeNodeShutdownActor, self).on_start()
+ else:
+ self._nodename = arv_node['hostname']
+ self._logger.info("Draining SLURM node %s", self._nodename)
+ self._later.issue_slurm_drain()
+
+ def _set_node_state(self, state, *args):
+ cmd = ['scontrol', 'update', 'NodeName=' + self._nodename,
+ 'State=' + state]
+ cmd.extend(args)
+ subprocess.check_output(cmd)
+
+ @ShutdownActorBase._retry((subprocess.CalledProcessError,))
+ def cancel_shutdown(self):
+ self._set_node_state('RESUME')
+ return super(ComputeNodeShutdownActor, self).cancel_shutdown()
+
+ @ShutdownActorBase._stop_if_window_closed
+ @ShutdownActorBase._retry((subprocess.CalledProcessError,))
+ def issue_slurm_drain(self):
+ self._set_node_state('DRAIN', 'Reason=Node Manager shutdown')
+ self._logger.info("Waiting for SLURM node %s to drain", self._nodename)
+ self._later.await_slurm_drain()
+
+ @ShutdownActorBase._stop_if_window_closed
+ @ShutdownActorBase._retry((subprocess.CalledProcessError,))
+ def await_slurm_drain(self):
+ output = subprocess.check_output(
+ ['sinfo', '--noheader', '-o', '%t', '-n', self._nodename])
+ if output in self.SLURM_END_STATES:
+ self._later.shutdown_node()
+ else:
+ self._timer.schedule(time.time() + 10,
+ self._later.await_slurm_drain)
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import libcloud.common.types as cloud_types
+
+from ...config import NETWORK_ERRORS
+
+class BaseComputeNodeDriver(object):
+ """Abstract base class for compute node drivers.
+
+ libcloud abstracts away many of the differences between cloud providers,
+ but managing compute nodes requires some cloud-specific features (e.g.,
+ on EC2 we use tags to identify compute nodes). Compute node drivers
+ are responsible for translating the node manager's cloud requests to a
+ specific cloud's vocabulary.
+
+ Subclasses must implement arvados_create_kwargs (to update node
+ creation kwargs with information about the specific Arvados node
+ record), sync_node, and node_start_time.
+ """
+ CLOUD_ERRORS = NETWORK_ERRORS + (cloud_types.LibcloudError,)
+
+ def __init__(self, auth_kwargs, list_kwargs, create_kwargs, driver_class):
+ self.real = driver_class(**auth_kwargs)
+ self.list_kwargs = list_kwargs
+ self.create_kwargs = create_kwargs
+
+ def __getattr__(self, name):
+ # Proxy non-extension methods to the real driver.
+ if (not name.startswith('_') and not name.startswith('ex_')
+ and hasattr(self.real, name)):
+ return getattr(self.real, name)
+ else:
+ return super(BaseComputeNodeDriver, self).__getattr__(name)
+
+ def search_for(self, term, list_method, key=lambda item: item.id):
+ cache_key = (list_method, term)
+ if cache_key not in self.SEARCH_CACHE:
+ results = [item for item in getattr(self.real, list_method)()
+ if key(item) == term]
+ count = len(results)
+ if count != 1:
+ raise ValueError("{} returned {} results for '{}'".format(
+ list_method, count, term))
+ self.SEARCH_CACHE[cache_key] = results[0]
+ return self.SEARCH_CACHE[cache_key]
+
+ def list_nodes(self):
+ return self.real.list_nodes(**self.list_kwargs)
+
+ def arvados_create_kwargs(self, arvados_node):
+ raise NotImplementedError("BaseComputeNodeDriver.arvados_create_kwargs")
+
+ def create_node(self, size, arvados_node):
+ kwargs = self.create_kwargs.copy()
+ kwargs.update(self.arvados_create_kwargs(arvados_node))
+ kwargs['size'] = size
+ return self.real.create_node(**kwargs)
+
+ def post_create_node(self, cloud_node):
+ # ComputeNodeSetupActor calls this method after the cloud node is
+ # created. Any setup tasks that need to happen afterward (e.g.,
+ # tagging) should be done in this method.
+ pass
+
+ def sync_node(self, cloud_node, arvados_node):
+ # When a compute node first pings the API server, the API server
+ # will automatically assign some attributes on the corresponding
+ # node record, like hostname. This method should propagate that
+ # information back to the cloud node appropriately.
+ raise NotImplementedError("BaseComputeNodeDriver.sync_node")
+
+ @classmethod
+ def node_start_time(cls, node):
+ raise NotImplementedError("BaseComputeNodeDriver.node_start_time")
+
+ @classmethod
+ def is_cloud_exception(cls, exception):
+ # libcloud compute drivers typically raise bare Exceptions to
+ # represent API errors. Return True for any exception that is
+ # exactly an Exception, or a better-known higher-level exception.
+ return (isinstance(exception, cls.CLOUD_ERRORS) or
+ getattr(exception, '__class__', None) is Exception)
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import time
+
+import libcloud.compute.providers as cloud_provider
+import libcloud.compute.types as cloud_types
+
+from . import BaseComputeNodeDriver
+from .. import arvados_node_fqdn
+
+class ComputeNodeDriver(BaseComputeNodeDriver):
+ """Compute node driver wrapper for libcloud's dummy driver.
+
+ This class provides the glue necessary to run the node manager with a
+ dummy cloud. It's useful for testing.
+ """
+ DEFAULT_DRIVER = cloud_provider.get_driver(cloud_types.Provider.DUMMY)
+ DEFAULT_REAL = DEFAULT_DRIVER('ComputeNodeDriver')
+ DUMMY_START_TIME = time.time()
+
+ def __init__(self, auth_kwargs, list_kwargs, create_kwargs,
+ driver_class=DEFAULT_DRIVER):
+ super(ComputeNodeDriver, self).__init__(
+ auth_kwargs, list_kwargs, create_kwargs, driver_class)
+ if driver_class is self.DEFAULT_DRIVER:
+ self.real = self.DEFAULT_REAL
+
+ def _ensure_private_ip(self, node):
+ if not node.private_ips:
+ node.private_ips = ['10.10.0.{}'.format(node.id)]
+
+ def arvados_create_kwargs(self, arvados_node):
+ return {}
+
+ def list_nodes(self):
+ nodelist = super(ComputeNodeDriver, self).list_nodes()
+ for node in nodelist:
+ self._ensure_private_ip(node)
+ return nodelist
+
+ def create_node(self, size, arvados_node):
+ node = super(ComputeNodeDriver, self).create_node(size, arvados_node)
+ self._ensure_private_ip(node)
+ return node
+
+ def sync_node(self, cloud_node, arvados_node):
+ cloud_node.name = arvados_node_fqdn(arvados_node)
+
+ @classmethod
+ def node_start_time(cls, node):
+ return cls.DUMMY_START_TIME
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import time
+
+import libcloud.compute.base as cloud_base
+import libcloud.compute.providers as cloud_provider
+import libcloud.compute.types as cloud_types
+from libcloud.compute.drivers import ec2 as cloud_ec2
+
+from . import BaseComputeNodeDriver
+from .. import arvados_node_fqdn
+
+### Monkeypatch libcloud to support AWS' new SecurityGroup API.
+# These classes can be removed when libcloud support specifying
+# security groups with the SecurityGroupId parameter.
+class ANMEC2Connection(cloud_ec2.EC2Connection):
+ def request(self, *args, **kwargs):
+ params = kwargs.get('params')
+ if (params is not None) and (params.get('Action') == 'RunInstances'):
+ for key in params.keys():
+ if key.startswith('SecurityGroup.'):
+ new_key = key.replace('Group.', 'GroupId.', 1)
+ params[new_key] = params.pop(key).id
+ kwargs['params'] = params
+ return super(ANMEC2Connection, self).request(*args, **kwargs)
+
+
+class ANMEC2NodeDriver(cloud_ec2.EC2NodeDriver):
+ connectionCls = ANMEC2Connection
+
+
+class ComputeNodeDriver(BaseComputeNodeDriver):
+ """Compute node driver wrapper for EC2.
+
+ This translates cloud driver requests to EC2's specific parameters.
+ """
+ DEFAULT_DRIVER = ANMEC2NodeDriver
+### End monkeypatch
+ SEARCH_CACHE = {}
+
+ def __init__(self, auth_kwargs, list_kwargs, create_kwargs,
+ driver_class=DEFAULT_DRIVER):
+ # We need full lists of keys up front because these loops modify
+ # dictionaries in-place.
+ for key in list_kwargs.keys():
+ list_kwargs[key.replace('_', ':')] = list_kwargs.pop(key)
+ self.tags = {key[4:]: value
+ for key, value in list_kwargs.iteritems()
+ if key.startswith('tag:')}
+ super(ComputeNodeDriver, self).__init__(
+ auth_kwargs, {'ex_filters': list_kwargs}, create_kwargs,
+ driver_class)
+ for key in self.create_kwargs.keys():
+ init_method = getattr(self, '_init_' + key, None)
+ if init_method is not None:
+ new_pair = init_method(self.create_kwargs.pop(key))
+ if new_pair is not None:
+ self.create_kwargs[new_pair[0]] = new_pair[1]
+
+ def _init_image_id(self, image_id):
+ return 'image', self.search_for(image_id, 'list_images')
+
+ def _init_ping_host(self, ping_host):
+ self.ping_host = ping_host
+
+ def _init_security_groups(self, group_names):
+ return 'ex_security_groups', [
+ self.search_for(gname.strip(), 'ex_get_security_groups')
+ for gname in group_names.split(',')]
+
+ def _init_subnet_id(self, subnet_id):
+ return 'ex_subnet', self.search_for(subnet_id, 'ex_list_subnets')
+
+ def _init_ssh_key(self, filename):
+ with open(filename) as ssh_file:
+ key = cloud_base.NodeAuthSSHKey(ssh_file.read())
+ return 'auth', key
+
+ def arvados_create_kwargs(self, arvados_node):
+ result = {'name': arvados_node_fqdn(arvados_node)}
+ ping_secret = arvados_node['info'].get('ping_secret')
+ if ping_secret is not None:
+ ping_url = ('https://{}/arvados/v1/nodes/{}/ping?ping_secret={}'.
+ format(self.ping_host, arvados_node['uuid'],
+ ping_secret))
+ result['ex_userdata'] = ping_url
+ return result
+
+ def post_create_node(self, cloud_node):
+ self.real.ex_create_tags(cloud_node, self.tags)
+
+ def sync_node(self, cloud_node, arvados_node):
+ self.real.ex_create_tags(cloud_node,
+ {'Name': arvados_node_fqdn(arvados_node)})
+
+ @classmethod
+ def node_start_time(cls, node):
+ time_str = node.extra['launch_time'].split('.', 2)[0] + 'UTC'
+ return time.mktime(time.strptime(
+ time_str,'%Y-%m-%dT%H:%M:%S%Z')) - time.timezone
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import ConfigParser
+import importlib
+import logging
+import ssl
+import sys
+
+import arvados
+import httplib2
+import pykka
+from apiclient import errors as apierror
+
+# IOError is the base class for socket.error and friends.
+# It seems like it hits the sweet spot for operations we want to retry:
+# it's low-level, but unlikely to catch code bugs.
+NETWORK_ERRORS = (IOError, ssl.SSLError)
+ARVADOS_ERRORS = NETWORK_ERRORS + (apierror.Error,)
+
+actor_class = pykka.ThreadingActor
+
+class NodeManagerConfig(ConfigParser.SafeConfigParser):
+ """Node Manager Configuration class.
+
+ This a standard Python ConfigParser, with additional helper methods to
+ create objects instantiated with configuration information.
+ """
+
+ LOGGING_NONLEVELS = frozenset(['file'])
+
+ def __init__(self, *args, **kwargs):
+ # Can't use super() because SafeConfigParser is an old-style class.
+ ConfigParser.SafeConfigParser.__init__(self, *args, **kwargs)
+ for sec_name, settings in {
+ 'Arvados': {'insecure': 'no',
+ 'timeout': '15'},
+ 'Daemon': {'min_nodes': '0',
+ 'max_nodes': '1',
+ 'poll_time': '60',
+ 'max_poll_time': '300',
+ 'poll_stale_after': '600',
+ 'boot_fail_after': str(sys.maxint),
+ 'node_stale_after': str(60 * 60 * 2)},
+ 'Logging': {'file': '/dev/stderr',
+ 'level': 'WARNING'},
+ }.iteritems():
+ if not self.has_section(sec_name):
+ self.add_section(sec_name)
+ for opt_name, value in settings.iteritems():
+ if not self.has_option(sec_name, opt_name):
+ self.set(sec_name, opt_name, value)
+
+ def get_section(self, section, transformer=None):
+ result = self._dict()
+ for key, value in self.items(section):
+ if transformer is not None:
+ try:
+ value = transformer(value)
+ except (TypeError, ValueError):
+ pass
+ result[key] = value
+ return result
+
+ def log_levels(self):
+ return {key: getattr(logging, self.get('Logging', key).upper())
+ for key in self.options('Logging')
+ if key not in self.LOGGING_NONLEVELS}
+
+ def dispatch_classes(self):
+ mod_name = 'arvnodeman.computenode.dispatch'
+ if self.has_option('Daemon', 'dispatcher'):
+ mod_name = '{}.{}'.format(mod_name,
+ self.get('Daemon', 'dispatcher'))
+ module = importlib.import_module(mod_name)
+ return (module.ComputeNodeSetupActor,
+ module.ComputeNodeShutdownActor,
+ module.ComputeNodeUpdateActor,
+ module.ComputeNodeMonitorActor)
+
+ def new_arvados_client(self):
+ if self.has_option('Daemon', 'certs_file'):
+ certs_file = self.get('Daemon', 'certs_file')
+ else:
+ certs_file = None
+ insecure = self.getboolean('Arvados', 'insecure')
+ http = httplib2.Http(timeout=self.getint('Arvados', 'timeout'),
+ ca_certs=certs_file,
+ disable_ssl_certificate_validation=insecure)
+ return arvados.api('v1',
+ cache=False, # Don't reuse an existing client.
+ host=self.get('Arvados', 'host'),
+ token=self.get('Arvados', 'token'),
+ insecure=insecure,
+ http=http)
+
+ def new_cloud_client(self):
+ module = importlib.import_module('arvnodeman.computenode.driver.' +
+ self.get('Cloud', 'provider'))
+ auth_kwargs = self.get_section('Cloud Credentials')
+ if 'timeout' in auth_kwargs:
+ auth_kwargs['timeout'] = int(auth_kwargs['timeout'])
+ return module.ComputeNodeDriver(auth_kwargs,
+ self.get_section('Cloud List'),
+ self.get_section('Cloud Create'))
+
+ def node_sizes(self, all_sizes):
+ size_kwargs = {}
+ for sec_name in self.sections():
+ sec_words = sec_name.split(None, 2)
+ if sec_words[0] != 'Size':
+ continue
+ size_kwargs[sec_words[1]] = self.get_section(sec_name, int)
+ return [(size, size_kwargs[size.id]) for size in all_sizes
+ if size.id in size_kwargs]
+
+ def shutdown_windows(self):
+ return [int(n)
+ for n in self.get('Cloud', 'shutdown_windows').split(',')]
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import functools
+import logging
+import time
+
+import pykka
+
+from . import computenode as cnode
+from .computenode import dispatch
+from .config import actor_class
+
+class _ComputeNodeRecord(object):
+ def __init__(self, actor=None, cloud_node=None, arvados_node=None,
+ assignment_time=float('-inf')):
+ self.actor = actor
+ self.cloud_node = cloud_node
+ self.arvados_node = arvados_node
+ self.assignment_time = assignment_time
+
+
+class _BaseNodeTracker(object):
+ def __init__(self):
+ self.nodes = {}
+ self.orphans = {}
+
+ # Proxy the methods listed below to self.nodes.
+ def _proxy_method(name):
+ method = getattr(dict, name)
+ @functools.wraps(method, ('__name__', '__doc__'))
+ def wrapper(self, *args, **kwargs):
+ return method(self.nodes, *args, **kwargs)
+ return wrapper
+
+ for _method_name in ['__contains__', '__getitem__', '__len__', 'get']:
+ locals()[_method_name] = _proxy_method(_method_name)
+
+ def record_key(self, record):
+ return self.item_key(getattr(record, self.RECORD_ATTR))
+
+ def add(self, record):
+ self.nodes[self.record_key(record)] = record
+
+ def update_record(self, key, item):
+ setattr(self.nodes[key], self.RECORD_ATTR, item)
+
+ def update_from(self, response):
+ unseen = set(self.nodes.iterkeys())
+ for item in response:
+ key = self.item_key(item)
+ if key in unseen:
+ unseen.remove(key)
+ self.update_record(key, item)
+ else:
+ yield key, item
+ self.orphans = {key: self.nodes.pop(key) for key in unseen}
+
+ def unpaired(self):
+ return (record for record in self.nodes.itervalues()
+ if getattr(record, self.PAIR_ATTR) is None)
+
+
+class _CloudNodeTracker(_BaseNodeTracker):
+ RECORD_ATTR = 'cloud_node'
+ PAIR_ATTR = 'arvados_node'
+ item_key = staticmethod(lambda cloud_node: cloud_node.id)
+
+
+class _ArvadosNodeTracker(_BaseNodeTracker):
+ RECORD_ATTR = 'arvados_node'
+ PAIR_ATTR = 'cloud_node'
+ item_key = staticmethod(lambda arvados_node: arvados_node['uuid'])
+
+ def find_stale_node(self, stale_time):
+ for record in self.nodes.itervalues():
+ node = record.arvados_node
+ if (not cnode.timestamp_fresh(cnode.arvados_node_mtime(node),
+ stale_time) and
+ not cnode.timestamp_fresh(record.assignment_time,
+ stale_time)):
+ return node
+ return None
+
+
+class NodeManagerDaemonActor(actor_class):
+ """Node Manager daemon.
+
+ This actor subscribes to all information polls about cloud nodes,
+ Arvados nodes, and the job queue. It creates a ComputeNodeMonitorActor
+ for every cloud node, subscribing them to poll updates
+ appropriately. It creates and destroys cloud nodes based on job queue
+ demand, and stops the corresponding ComputeNode actors when their work
+ is done.
+ """
+ def __init__(self, server_wishlist_actor, arvados_nodes_actor,
+ cloud_nodes_actor, cloud_update_actor, timer_actor,
+ arvados_factory, cloud_factory,
+ shutdown_windows, min_size, min_nodes, max_nodes,
+ poll_stale_after=600,
+ boot_fail_after=1800,
+ node_stale_after=7200,
+ node_setup_class=dispatch.ComputeNodeSetupActor,
+ node_shutdown_class=dispatch.ComputeNodeShutdownActor,
+ node_actor_class=dispatch.ComputeNodeMonitorActor):
+ super(NodeManagerDaemonActor, self).__init__()
+ self._node_setup = node_setup_class
+ self._node_shutdown = node_shutdown_class
+ self._node_actor = node_actor_class
+ self._cloud_updater = cloud_update_actor
+ self._timer = timer_actor
+ self._new_arvados = arvados_factory
+ self._new_cloud = cloud_factory
+ self._cloud_driver = self._new_cloud()
+ self._logger = logging.getLogger('arvnodeman.daemon')
+ self._later = self.actor_ref.proxy()
+ self.shutdown_windows = shutdown_windows
+ self.min_cloud_size = min_size
+ self.min_nodes = min_nodes
+ self.max_nodes = max_nodes
+ self.poll_stale_after = poll_stale_after
+ self.boot_fail_after = boot_fail_after
+ self.node_stale_after = node_stale_after
+ self.last_polls = {}
+ for poll_name in ['server_wishlist', 'arvados_nodes', 'cloud_nodes']:
+ poll_actor = locals()[poll_name + '_actor']
+ poll_actor.subscribe(getattr(self._later, 'update_' + poll_name))
+ setattr(self, '_{}_actor'.format(poll_name), poll_actor)
+ self.last_polls[poll_name] = -self.poll_stale_after
+ self.cloud_nodes = _CloudNodeTracker()
+ self.arvados_nodes = _ArvadosNodeTracker()
+ self.booting = {} # Actor IDs to ComputeNodeSetupActors
+ self.booted = {} # Cloud node IDs to _ComputeNodeRecords
+ self.shutdowns = {} # Cloud node IDs to ComputeNodeShutdownActors
+ self._logger.debug("Daemon initialized")
+
+ def _update_poll_time(self, poll_key):
+ self.last_polls[poll_key] = time.time()
+
+ def _pair_nodes(self, node_record, arvados_node):
+ self._logger.info("Cloud node %s has associated with Arvados node %s",
+ node_record.cloud_node.id, arvados_node['uuid'])
+ self._arvados_nodes_actor.subscribe_to(
+ arvados_node['uuid'], node_record.actor.update_arvados_node)
+ node_record.arvados_node = arvados_node
+ self.arvados_nodes.add(node_record)
+
+ def _new_node(self, cloud_node):
+ start_time = self._cloud_driver.node_start_time(cloud_node)
+ shutdown_timer = cnode.ShutdownTimer(start_time,
+ self.shutdown_windows)
+ actor = self._node_actor.start(
+ cloud_node=cloud_node,
+ cloud_node_start_time=start_time,
+ shutdown_timer=shutdown_timer,
+ update_actor=self._cloud_updater,
+ timer_actor=self._timer,
+ arvados_node=None,
+ poll_stale_after=self.poll_stale_after,
+ node_stale_after=self.node_stale_after).proxy()
+ actor.subscribe(self._later.node_can_shutdown)
+ self._cloud_nodes_actor.subscribe_to(cloud_node.id,
+ actor.update_cloud_node)
+ record = _ComputeNodeRecord(actor, cloud_node)
+ return record
+
+ def update_cloud_nodes(self, nodelist):
+ self._update_poll_time('cloud_nodes')
+ for key, node in self.cloud_nodes.update_from(nodelist):
+ self._logger.info("Registering new cloud node %s", key)
+ if key in self.booted:
+ record = self.booted.pop(key)
+ else:
+ record = self._new_node(node)
+ self.cloud_nodes.add(record)
+ for arv_rec in self.arvados_nodes.unpaired():
+ if record.actor.offer_arvados_pair(arv_rec.arvados_node).get():
+ self._pair_nodes(record, arv_rec.arvados_node)
+ break
+ for key, record in self.cloud_nodes.orphans.iteritems():
+ record.actor.stop()
+ record.cloud_node = None
+ self.shutdowns.pop(key, None)
+
+ def update_arvados_nodes(self, nodelist):
+ self._update_poll_time('arvados_nodes')
+ for key, node in self.arvados_nodes.update_from(nodelist):
+ self._logger.info("Registering new Arvados node %s", key)
+ record = _ComputeNodeRecord(arvados_node=node)
+ self.arvados_nodes.add(record)
+ for arv_rec in self.arvados_nodes.unpaired():
+ arv_node = arv_rec.arvados_node
+ for cloud_rec in self.cloud_nodes.unpaired():
+ if cloud_rec.actor.offer_arvados_pair(arv_node).get():
+ self._pair_nodes(cloud_rec, arv_node)
+ break
+
+ def _nodes_up(self):
+ return sum(len(nodelist) for nodelist in
+ [self.cloud_nodes, self.booted, self.booting])
+
+ def _nodes_busy(self):
+ return sum(1 for idle in
+ pykka.get_all(rec.actor.in_state('idle') for rec in
+ self.cloud_nodes.nodes.itervalues())
+ if idle is False)
+
+ def _nodes_wanted(self):
+ up_count = self._nodes_up()
+ under_min = self.min_nodes - up_count
+ over_max = up_count - self.max_nodes
+ if over_max >= 0:
+ return -over_max
+ elif under_min > 0:
+ return under_min
+ else:
+ up_count -= len(self.shutdowns) + self._nodes_busy()
+ return len(self.last_wishlist) - up_count
+
+ def _nodes_excess(self):
+ up_count = self._nodes_up() - len(self.shutdowns)
+ over_min = up_count - self.min_nodes
+ if over_min <= 0:
+ return over_min
+ else:
+ return up_count - self._nodes_busy() - len(self.last_wishlist)
+
+ def update_server_wishlist(self, wishlist):
+ self._update_poll_time('server_wishlist')
+ self.last_wishlist = wishlist
+ nodes_wanted = self._nodes_wanted()
+ if nodes_wanted > 0:
+ self._later.start_node()
+ elif (nodes_wanted < 0) and self.booting:
+ self._later.stop_booting_node()
+
+ def _check_poll_freshness(orig_func):
+ """Decorator to inhibit a method when poll information is stale.
+
+ This decorator checks the timestamps of all the poll information the
+ daemon has received. The decorated method is only called if none
+ of the timestamps are considered stale.
+ """
+ @functools.wraps(orig_func)
+ def wrapper(self, *args, **kwargs):
+ now = time.time()
+ if all(now - t < self.poll_stale_after
+ for t in self.last_polls.itervalues()):
+ return orig_func(self, *args, **kwargs)
+ else:
+ return None
+ return wrapper
+
+ @_check_poll_freshness
+ def start_node(self):
+ nodes_wanted = self._nodes_wanted()
+ if nodes_wanted < 1:
+ return None
+ arvados_node = self.arvados_nodes.find_stale_node(self.node_stale_after)
+ try:
+ cloud_size = self.last_wishlist[self._nodes_up()]
+ except IndexError:
+ cloud_size = self.min_cloud_size
+ self._logger.info("Want %s more nodes. Booting a %s node.",
+ nodes_wanted, cloud_size.name)
+ new_setup = self._node_setup.start(
+ timer_actor=self._timer,
+ arvados_client=self._new_arvados(),
+ arvados_node=arvados_node,
+ cloud_client=self._new_cloud(),
+ cloud_size=cloud_size).proxy()
+ self.booting[new_setup.actor_ref.actor_urn] = new_setup
+ if arvados_node is not None:
+ self.arvados_nodes[arvados_node['uuid']].assignment_time = (
+ time.time())
+ new_setup.subscribe(self._later.node_up)
+ if nodes_wanted > 1:
+ self._later.start_node()
+
+ def _get_actor_attrs(self, actor, *attr_names):
+ return pykka.get_all([getattr(actor, name) for name in attr_names])
+
+ def node_up(self, setup_proxy):
+ cloud_node = setup_proxy.cloud_node.get()
+ del self.booting[setup_proxy.actor_ref.actor_urn]
+ setup_proxy.stop()
+ record = self.cloud_nodes.get(cloud_node.id)
+ if record is None:
+ record = self._new_node(cloud_node)
+ self.booted[cloud_node.id] = record
+ self._timer.schedule(time.time() + self.boot_fail_after,
+ self._later.shutdown_unpaired_node, cloud_node.id)
+
+ @_check_poll_freshness
+ def stop_booting_node(self):
+ nodes_excess = self._nodes_excess()
+ if (nodes_excess < 1) or not self.booting:
+ return None
+ for key, node in self.booting.iteritems():
+ node.stop_if_no_cloud_node().get()
+ if not node.actor_ref.is_alive():
+ del self.booting[key]
+ if nodes_excess > 1:
+ self._later.stop_booting_node()
+ break
+
+ def _begin_node_shutdown(self, node_actor, cancellable):
+ cloud_node_id = node_actor.cloud_node.get().id
+ if cloud_node_id in self.shutdowns:
+ return None
+ shutdown = self._node_shutdown.start(
+ timer_actor=self._timer, cloud_client=self._new_cloud(),
+ node_monitor=node_actor.actor_ref, cancellable=cancellable).proxy()
+ self.shutdowns[cloud_node_id] = shutdown
+ shutdown.subscribe(self._later.node_finished_shutdown)
+
+ @_check_poll_freshness
+ def node_can_shutdown(self, node_actor):
+ if self._nodes_excess() > 0:
+ self._begin_node_shutdown(node_actor, cancellable=True)
+
+ def shutdown_unpaired_node(self, cloud_node_id):
+ for record_dict in [self.cloud_nodes, self.booted]:
+ if cloud_node_id in record_dict:
+ record = record_dict[cloud_node_id]
+ break
+ else:
+ return None
+ if record.arvados_node is None:
+ self._begin_node_shutdown(record.actor, cancellable=False)
+
+ def node_finished_shutdown(self, shutdown_actor):
+ success, cloud_node = self._get_actor_attrs(shutdown_actor, 'success',
+ 'cloud_node')
+ shutdown_actor.stop()
+ cloud_node_id = cloud_node.id
+ if not success:
+ del self.shutdowns[cloud_node_id]
+ elif cloud_node_id in self.booted:
+ self.booted.pop(cloud_node_id).actor.stop()
+ del self.shutdowns[cloud_node_id]
+
+ def shutdown(self):
+ self._logger.info("Shutting down after signal.")
+ self.poll_stale_after = -1 # Inhibit starting/stopping nodes
+ for bootnode in self.booting.itervalues():
+ bootnode.stop_if_no_cloud_node()
+ self._later.await_shutdown()
+
+ def await_shutdown(self):
+ if any(node.actor_ref.is_alive() for node in self.booting.itervalues()):
+ self._timer.schedule(time.time() + 1, self._later.await_shutdown)
+ else:
+ self.stop()
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import logging
+
+from . import clientactor
+from .config import ARVADOS_ERRORS
+
+class ServerCalculator(object):
+ """Generate cloud server wishlists from an Arvados job queue.
+
+ Instantiate this class with a list of cloud node sizes you're willing to
+ use, plus keyword overrides from the configuration. Then you can pass
+ job queues to servers_for_queue. It will return a list of node sizes
+ that would best satisfy the jobs, choosing the cheapest size that
+ satisfies each job, and ignoring jobs that can't be satisfied.
+ """
+
+ class CloudSizeWrapper(object):
+ def __init__(self, real_size, **kwargs):
+ self.real = real_size
+ for name in ['id', 'name', 'ram', 'disk', 'bandwidth', 'price',
+ 'extra']:
+ setattr(self, name, getattr(self.real, name))
+ self.cores = kwargs.pop('cores')
+ self.scratch = self.disk
+ for name, override in kwargs.iteritems():
+ if not hasattr(self, name):
+ raise ValueError("unrecognized size field '%s'" % (name,))
+ setattr(self, name, override)
+
+ def meets_constraints(self, **kwargs):
+ for name, want_value in kwargs.iteritems():
+ have_value = getattr(self, name)
+ if (have_value != 0) and (have_value < want_value):
+ return False
+ return True
+
+
+ def __init__(self, server_list, max_nodes=None):
+ self.cloud_sizes = [self.CloudSizeWrapper(s, **kws)
+ for s, kws in server_list]
+ self.cloud_sizes.sort(key=lambda s: s.price)
+ self.max_nodes = max_nodes or float('inf')
+ self.logger = logging.getLogger('arvnodeman.jobqueue')
+ self.logged_jobs = set()
+
+ @staticmethod
+ def coerce_int(x, fallback):
+ try:
+ return int(x)
+ except (TypeError, ValueError):
+ return fallback
+
+ def cloud_size_for_constraints(self, constraints):
+ want_value = lambda key: self.coerce_int(constraints.get(key), 0)
+ wants = {'cores': want_value('min_cores_per_node'),
+ 'ram': want_value('min_ram_mb_per_node'),
+ 'scratch': want_value('min_scratch_mb_per_node')}
+ for size in self.cloud_sizes:
+ if size.meets_constraints(**wants):
+ return size
+ return None
+
+ def servers_for_queue(self, queue):
+ servers = []
+ seen_jobs = set()
+ for job in queue:
+ seen_jobs.add(job['uuid'])
+ constraints = job['runtime_constraints']
+ want_count = self.coerce_int(constraints.get('min_nodes'), 1)
+ cloud_size = self.cloud_size_for_constraints(constraints)
+ if cloud_size is None:
+ if job['uuid'] not in self.logged_jobs:
+ self.logged_jobs.add(job['uuid'])
+ self.logger.debug("job %s not satisfiable", job['uuid'])
+ elif (want_count <= self.max_nodes):
+ servers.extend([cloud_size.real] * max(1, want_count))
+ self.logged_jobs.intersection_update(seen_jobs)
+ return servers
+
+ def cheapest_size(self):
+ return self.cloud_sizes[0]
+
+
+class JobQueueMonitorActor(clientactor.RemotePollLoopActor):
+ """Actor to generate server wishlists from the job queue.
+
+ This actor regularly polls Arvados' job queue, and uses the provided
+ ServerCalculator to turn that into a list of requested node sizes. That
+ list is sent to subscribers on every poll.
+ """
+
+ CLIENT_ERRORS = ARVADOS_ERRORS
+ LOGGER_NAME = 'arvnodeman.jobqueue'
+
+ def __init__(self, client, timer_actor, server_calc, *args, **kwargs):
+ super(JobQueueMonitorActor, self).__init__(
+ client, timer_actor, *args, **kwargs)
+ self._calculator = server_calc
+
+ def _send_request(self):
+ return self._client.jobs().queue().execute()['items']
+
+ def _got_response(self, queue):
+ server_list = self._calculator.servers_for_queue(queue)
+ self._logger.debug("Sending server wishlist: %s",
+ ', '.join(s.name for s in server_list) or "(empty)")
+ return super(JobQueueMonitorActor, self)._got_response(server_list)
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import argparse
+import logging
+import signal
+import sys
+import time
+
+import daemon
+import pykka
+
+from . import config as nmconfig
+from .daemon import NodeManagerDaemonActor
+from .jobqueue import JobQueueMonitorActor, ServerCalculator
+from .nodelist import ArvadosNodeListMonitorActor, CloudNodeListMonitorActor
+from .timedcallback import TimedCallBackActor
+
+node_daemon = None
+
+def abort(msg, code=1):
+ print("arvados-node-manager: " + msg)
+ sys.exit(code)
+
+def parse_cli(args):
+ parser = argparse.ArgumentParser(
+ prog='arvados-node-manager',
+ description="Dynamically allocate Arvados cloud compute nodes")
+ parser.add_argument(
+ '--foreground', action='store_true', default=False,
+ help="Run in the foreground. Don't daemonize.")
+ parser.add_argument(
+ '--config', help="Path to configuration file")
+ return parser.parse_args(args)
+
+def load_config(path):
+ if not path:
+ abort("No --config file specified", 2)
+ config = nmconfig.NodeManagerConfig()
+ try:
+ with open(path) as config_file:
+ config.readfp(config_file)
+ except (IOError, OSError) as error:
+ abort("Error reading configuration file {}: {}".format(path, error))
+ return config
+
+def setup_logging(path, level, **sublevels):
+ handler = logging.FileHandler(path)
+ handler.setFormatter(logging.Formatter(
+ '%(asctime)s %(name)s[%(process)d] %(levelname)s: %(message)s',
+ '%Y-%m-%d %H:%M:%S'))
+ root_logger = logging.getLogger()
+ root_logger.addHandler(handler)
+ root_logger.setLevel(level)
+ for logger_name, sublevel in sublevels.iteritems():
+ sublogger = logging.getLogger(logger_name)
+ sublogger.setLevel(sublevel)
+
+def build_server_calculator(config):
+ cloud_size_list = config.node_sizes(config.new_cloud_client().list_sizes())
+ if not cloud_size_list:
+ abort("No valid node sizes configured")
+ return ServerCalculator(cloud_size_list,
+ config.getint('Daemon', 'max_nodes'))
+
+def launch_pollers(config, server_calculator):
+ poll_time = config.getint('Daemon', 'poll_time')
+ max_poll_time = config.getint('Daemon', 'max_poll_time')
+
+ timer = TimedCallBackActor.start(poll_time / 10.0).proxy()
+ cloud_node_poller = CloudNodeListMonitorActor.start(
+ config.new_cloud_client(), timer, poll_time, max_poll_time).proxy()
+ arvados_node_poller = ArvadosNodeListMonitorActor.start(
+ config.new_arvados_client(), timer, poll_time, max_poll_time).proxy()
+ job_queue_poller = JobQueueMonitorActor.start(
+ config.new_arvados_client(), timer, server_calculator,
+ poll_time, max_poll_time).proxy()
+ return timer, cloud_node_poller, arvados_node_poller, job_queue_poller
+
+_caught_signals = {}
+def shutdown_signal(signal_code, frame):
+ current_count = _caught_signals.get(signal_code, 0)
+ _caught_signals[signal_code] = current_count + 1
+ if node_daemon is None:
+ pykka.ActorRegistry.stop_all()
+ sys.exit(-signal_code)
+ elif current_count == 0:
+ node_daemon.shutdown()
+ elif current_count == 1:
+ pykka.ActorRegistry.stop_all()
+ else:
+ sys.exit(-signal_code)
+
+def main(args=None):
+ global node_daemon
+ args = parse_cli(args)
+ config = load_config(args.config)
+
+ if not args.foreground:
+ daemon.DaemonContext().open()
+ for sigcode in [signal.SIGINT, signal.SIGQUIT, signal.SIGTERM]:
+ signal.signal(sigcode, shutdown_signal)
+
+ setup_logging(config.get('Logging', 'file'), **config.log_levels())
+ node_setup, node_shutdown, node_update, node_monitor = \
+ config.dispatch_classes()
+ server_calculator = build_server_calculator(config)
+ timer, cloud_node_poller, arvados_node_poller, job_queue_poller = \
+ launch_pollers(config, server_calculator)
+ cloud_node_updater = node_update.start(config.new_cloud_client).proxy()
+ node_daemon = NodeManagerDaemonActor.start(
+ job_queue_poller, arvados_node_poller, cloud_node_poller,
+ cloud_node_updater, timer,
+ config.new_arvados_client, config.new_cloud_client,
+ config.shutdown_windows(),
+ server_calculator.cheapest_size(),
+ config.getint('Daemon', 'min_nodes'),
+ config.getint('Daemon', 'max_nodes'),
+ config.getint('Daemon', 'poll_stale_after'),
+ config.getint('Daemon', 'boot_fail_after'),
+ config.getint('Daemon', 'node_stale_after'),
+ node_setup, node_shutdown, node_monitor).proxy()
+
+ signal.pause()
+ daemon_stopped = node_daemon.actor_ref.actor_stopped.is_set
+ while not daemon_stopped():
+ time.sleep(1)
+ pykka.ActorRegistry.stop_all()
+
+
+if __name__ == '__main__':
+ main()
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+from . import clientactor
+from . import config
+
+class ArvadosNodeListMonitorActor(clientactor.RemotePollLoopActor):
+ """Actor to poll the Arvados node list.
+
+ This actor regularly polls the list of Arvados node records, and
+ sends it to subscribers.
+ """
+ LOGGER_NAME = 'arvnodeman.arvados_nodes'
+
+ def is_common_error(self, exception):
+ return isinstance(exception, config.ARVADOS_ERRORS)
+
+ def _item_key(self, node):
+ return node['uuid']
+
+ def _send_request(self):
+ return self._client.nodes().list(limit=10000).execute()['items']
+
+
+class CloudNodeListMonitorActor(clientactor.RemotePollLoopActor):
+ """Actor to poll the cloud node list.
+
+ This actor regularly polls the cloud to get a list of running compute
+ nodes, and sends it to subscribers.
+ """
+ LOGGER_NAME = 'arvnodeman.cloud_nodes'
+
+ def is_common_error(self, exception):
+ return self._client.is_cloud_exception(exception)
+
+ def _item_key(self, node):
+ return node.id
+
+ def _send_request(self):
+ return self._client.list_nodes()
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import heapq
+import time
+
+import pykka
+
+from .config import actor_class
+
+class TimedCallBackActor(actor_class):
+ """Send messages to other actors on a schedule.
+
+ Other actors can call the schedule() method to schedule delivery of a
+ message at a later time. This actor runs the necessary event loop for
+ delivery.
+ """
+ def __init__(self, max_sleep=1):
+ super(TimedCallBackActor, self).__init__()
+ self._proxy = self.actor_ref.proxy()
+ self.messages = []
+ self.max_sleep = max_sleep
+
+ def schedule(self, delivery_time, receiver, *args, **kwargs):
+ if not self.messages:
+ self._proxy.deliver()
+ heapq.heappush(self.messages, (delivery_time, receiver, args, kwargs))
+
+ def deliver(self):
+ if not self.messages:
+ return None
+ til_next = self.messages[0][0] - time.time()
+ if til_next < 0:
+ t, receiver, args, kwargs = heapq.heappop(self.messages)
+ try:
+ receiver(*args, **kwargs)
+ except pykka.ActorDeadError:
+ pass
+ else:
+ time.sleep(min(til_next, self.max_sleep))
+ self._proxy.deliver()
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+from arvnodeman.launcher import main
+main()
--- /dev/null
+# EC2 configuration for Arvados Node Manager.
+# All times are in seconds unless specified otherwise.
+
+[Daemon]
+# The dispatcher can customize the start and stop procedure for
+# cloud nodes. For example, the SLURM dispatcher drains nodes
+# through SLURM before shutting them down.
+#dispatcher = slurm
+
+# Node Manager will ensure that there are at least this many nodes
+# running at all times.
+min_nodes = 0
+
+# Node Manager will not start any compute nodes when at least this
+# many are running.
+max_nodes = 8
+
+# Poll EC2 nodes and Arvados for new information every N seconds.
+poll_time = 60
+
+# Polls have exponential backoff when services fail to respond.
+# This is the longest time to wait between polls.
+max_poll_time = 300
+
+# If Node Manager can't succesfully poll a service for this long,
+# it will never start or stop compute nodes, on the assumption that its
+# information is too outdated.
+poll_stale_after = 600
+
+# If Node Manager boots a cloud node, and it does not pair with an Arvados
+# node before this long, assume that there was a cloud bootstrap failure and
+# shut it down. Note that normal shutdown windows apply (see the Cloud
+# section), so this should be shorter than the first shutdown window value.
+boot_fail_after = 1800
+
+# "Node stale time" affects two related behaviors.
+# 1. If a compute node has been running for at least this long, but it
+# isn't paired with an Arvados node, do not shut it down, but leave it alone.
+# This prevents the node manager from shutting down a node that might
+# actually be doing work, but is having temporary trouble contacting the
+# API server.
+# 2. When the Node Manager starts a new compute node, it will try to reuse
+# an Arvados node that hasn't been updated for this long.
+node_stale_after = 14400
+
+# File path for Certificate Authorities
+certs_file = /etc/ssl/certs/ca-certificates.crt
+
+[Logging]
+# Log file path
+file = /var/log/arvados/node-manager.log
+
+# Log level for most Node Manager messages.
+# Choose one of DEBUG, INFO, WARNING, ERROR, or CRITICAL.
+# WARNING lets you know when polling a service fails.
+# INFO additionally lets you know when a compute node is started or stopped.
+level = INFO
+
+# You can also set different log levels for specific libraries.
+# Pykka is the Node Manager's actor library.
+# Setting this to DEBUG will display tracebacks for uncaught
+# exceptions in the actors, but it's also very chatty.
+pykka = WARNING
+
+# Setting apiclient to INFO will log the URL of every Arvados API request.
+apiclient = WARNING
+
+[Arvados]
+host = zyxwv.arvadosapi.com
+token = ARVADOS_TOKEN
+timeout = 15
+
+# Accept an untrusted SSL certificate from the API server?
+insecure = no
+
+[Cloud]
+provider = ec2
+
+# It's usually most cost-effective to shut down compute nodes during narrow
+# windows of time. For example, EC2 bills each node by the hour, so the best
+# time to shut down a node is right before a new hour of uptime starts.
+# Shutdown windows define these periods of time. These are windows in
+# full minutes, separated by commas. Counting from the time the node is
+# booted, the node WILL NOT shut down for N1 minutes; then it MAY shut down
+# for N2 minutes; then it WILL NOT shut down for N3 minutes; and so on.
+# For example, "54, 5, 1" means the node may shut down from the 54th to the
+# 59th minute of each hour of uptime.
+# Specify at least two windows. You can add as many as you need beyond that.
+shutdown_windows = 54, 5, 1
+
+[Cloud Credentials]
+key = KEY
+secret = SECRET_KEY
+region = us-east-1
+timeout = 60
+
+[Cloud List]
+# This section defines filters that find compute nodes.
+# Tags that you specify here will automatically be added to nodes you create.
+# Replace colons in Amazon filters with underscores
+# (e.g., write "tag:mytag" as "tag_mytag").
+instance-state-name = running
+tag_arvados-class = dynamic-compute
+tag_cluster = zyxwv
+
+[Cloud Create]
+# New compute nodes will send pings to Arvados at this host.
+# You may specify a port, and use brackets to disambiguate IPv6 addresses.
+ping_host = hostname:port
+
+# Give the name of an SSH key on AWS...
+ex_keyname = string
+
+# ... or a file path for an SSH key that can log in to the compute node.
+# (One or the other, not both.)
+# ssh_key = path
+
+# The EC2 IDs of the image and subnet compute nodes should use.
+image_id = idstring
+subnet_id = idstring
+
+# Comma-separated EC2 IDs for the security group(s) assigned to each
+# compute node.
+security_groups = idstring1, idstring2
+
+[Size t2.medium]
+# You can define any number of Size sections to list EC2 sizes you're
+# willing to use. The Node Manager should boot the cheapest size(s) that
+# can run jobs in the queue (N.B.: defining more than one size has not been
+# tested yet).
+# Each size section MUST define the number of cores it has. You may also
+# want to define the number of mebibytes of scratch space for Crunch jobs.
+# You can also override Amazon's provided data fields by setting the same
+# names here.
+cores = 2
+scratch = 100
\ No newline at end of file
--- /dev/null
+# You can use this configuration to run a development Node Manager for
+# testing. It uses libcloud's dummy driver and your own development API server.
+# When new cloud nodes are created, you'll need to simulate the ping that
+# they send to the Arvados API server. The easiest way I've found to do that
+# is through the API server Rails console: load the Node object, set its
+# IP address to 10.10.0.N (where N is the cloud node's ID), and save.
+
+[Daemon]
+min_nodes = 0
+max_nodes = 8
+poll_time = 15
+max_poll_time = 60
+poll_stale_after = 600
+node_stale_after = 300
+certs_file = /etc/ssl/certs/ca-certificates.crt
+
+[Logging]
+level = DEBUG
+pykka = DEBUG
+apiclient = WARNING
+
+[Arvados]
+host = localhost:3030
+# This is the token for the text fixture's admin user.
+token = 4axaw8zxe0qm22wa6urpp5nskcne8z88cvbupv653y1njyi05h
+insecure = yes
+timeout = 15
+
+[Cloud]
+provider = dummy
+shutdown_windows = 1, 1
+timeout = 15
+
+[Cloud Credentials]
+creds = dummycreds
+
+[Cloud List]
+[Cloud Create]
+
+[Size 2]
+cores = 4
+scratch = 1234
--- /dev/null
+#!/usr/bin/env python
+
+import os
+import subprocess
+import time
+
+from setuptools import setup, find_packages
+from setuptools.command.egg_info import egg_info
+
+SETUP_DIR = os.path.dirname(__file__) or "."
+
+class TagBuildWithCommit(egg_info):
+ """Tag the build with the sha1 and date of the last git commit.
+
+ If a build tag has already been set (e.g., "egg_info -b", building
+ from source package), leave it alone.
+ """
+ def tags(self):
+ if self.tag_build is None:
+ git_tags = subprocess.check_output(
+ ['git', 'log', '--first-parent', '--max-count=1',
+ '--format=format:%ct %h', SETUP_DIR]).split()
+ assert len(git_tags) == 2
+ git_tags[0] = time.strftime(
+ '%Y%m%d%H%M%S', time.gmtime(int(git_tags[0])))
+ self.tag_build = '.{}+{}'.format(*git_tags)
+ return egg_info.tags(self)
+
+
+setup(name='arvados-node-manager',
+ version='0.1',
+ description='Arvados compute node manager',
+ long_description=open(os.path.join(SETUP_DIR, 'README.rst')).read(),
+ author='Arvados',
+ author_email='info@arvados.org',
+ url="https://arvados.org",
+ license='GNU Affero General Public License, version 3.0',
+ packages=find_packages(),
+ install_requires=[
+ 'apache-libcloud',
+ 'arvados-python-client',
+ 'pykka',
+ 'python-daemon',
+ ],
+ scripts=['bin/arvados-node-manager'],
+ test_suite='tests',
+ tests_require=['mock>=1.0'],
+ zip_safe=False,
+ cmdclass={'egg_info': TagBuildWithCommit},
+ )
--- /dev/null
+#!/usr/bin/env python
+
+import logging
+import os
+
+# Set the ANMTEST_LOGLEVEL environment variable to enable logging at that level.
+loglevel = os.environ.get('ANMTEST_LOGLEVEL', 'CRITICAL')
+logging.basicConfig(level=getattr(logging, loglevel.upper()))
+
+# Set the ANM_TIMEOUT environment variable to the maximum amount of time to
+# wait for tested actors to respond to important messages. The default value
+# is very conservative, because a small value may produce false negatives on
+# slower systems. If you're debugging a known timeout issue, however, you may
+# want to set this lower to speed up tests.
+pykka_timeout = int(os.environ.get('ANMTEST_TIMEOUT', '10'))
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import unittest
+
+import mock
+import pykka
+
+import arvnodeman.clientactor as clientactor
+from . import testutil
+
+class RemotePollLoopActorTestCase(testutil.RemotePollLoopActorTestMixin,
+ unittest.TestCase):
+ class MockClientError(Exception):
+ pass
+
+ class TestActor(clientactor.RemotePollLoopActor):
+ LOGGER_NAME = 'arvnodeman.testpoll'
+
+ def _send_request(self):
+ return self._client()
+ TestActor.CLIENT_ERRORS = (MockClientError,)
+ TEST_CLASS = TestActor
+
+
+ def build_monitor(self, side_effect, *args, **kwargs):
+ super(RemotePollLoopActorTestCase, self).build_monitor(*args, **kwargs)
+ self.client.side_effect = side_effect
+
+ def test_poll_loop_starts_after_subscription(self):
+ self.build_monitor(['test1'])
+ self.monitor.subscribe(self.subscriber).get(self.TIMEOUT)
+ self.stop_proxy(self.monitor)
+ self.subscriber.assert_called_with('test1')
+ self.assertTrue(self.timer.schedule.called)
+
+ def test_poll_loop_continues_after_failure(self):
+ self.build_monitor(self.MockClientError)
+ self.monitor.subscribe(self.subscriber).get(self.TIMEOUT)
+ self.assertTrue(self.stop_proxy(self.monitor),
+ "poll loop died after error")
+ self.assertTrue(self.timer.schedule.called,
+ "poll loop did not reschedule after error")
+ self.assertFalse(self.subscriber.called,
+ "poll loop notified subscribers after error")
+
+ def test_late_subscribers_get_responses(self):
+ self.build_monitor(['pre_late_test', 'late_test'])
+ self.monitor.subscribe(lambda response: None).get(self.TIMEOUT)
+ self.monitor.subscribe(self.subscriber)
+ self.monitor.poll().get(self.TIMEOUT)
+ self.stop_proxy(self.monitor)
+ self.subscriber.assert_called_with('late_test')
+
+ def test_survive_dead_subscriptions(self):
+ self.build_monitor(['survive1', 'survive2'])
+ dead_subscriber = mock.Mock(name='dead_subscriber')
+ dead_subscriber.side_effect = pykka.ActorDeadError
+ self.monitor.subscribe(dead_subscriber)
+ self.monitor.subscribe(self.subscriber)
+ self.monitor.poll().get(self.TIMEOUT)
+ self.assertTrue(self.stop_proxy(self.monitor),
+ "poll loop died from dead subscriber")
+ self.subscriber.assert_called_with('survive2')
+
+ def check_poll_timers(self, *test_times):
+ schedule_mock = self.timer.schedule
+ last_expect = None
+ with mock.patch('time.time') as time_mock:
+ for fake_time, expect_next in test_times:
+ time_mock.return_value = fake_time
+ self.monitor.poll(last_expect).get(self.TIMEOUT)
+ self.assertTrue(schedule_mock.called)
+ self.assertEqual(expect_next, schedule_mock.call_args[0][0])
+ schedule_mock.reset_mock()
+ last_expect = expect_next
+
+ def test_poll_timing_on_consecutive_successes_with_drift(self):
+ self.build_monitor(['1', '2'], poll_wait=3, max_poll_wait=14)
+ self.check_poll_timers((0, 3), (4, 6))
+
+ def test_poll_backoff_on_failures(self):
+ self.build_monitor(self.MockClientError, poll_wait=3, max_poll_wait=14)
+ self.check_poll_timers((0, 6), (6, 18), (18, 32))
+
+ def test_poll_timing_after_error_recovery(self):
+ self.build_monitor(['a', self.MockClientError(), 'b'],
+ poll_wait=3, max_poll_wait=14)
+ self.check_poll_timers((0, 3), (4, 10), (10, 13))
+
+ def test_no_subscriptions_by_key_without_support(self):
+ self.build_monitor([])
+ with self.assertRaises(AttributeError):
+ self.monitor.subscribe_to('key')
+
+
+class RemotePollLoopActorWithKeysTestCase(testutil.RemotePollLoopActorTestMixin,
+ unittest.TestCase):
+ class TestActor(RemotePollLoopActorTestCase.TestActor):
+ def _item_key(self, item):
+ return item['key']
+ TEST_CLASS = TestActor
+
+
+ def build_monitor(self, side_effect, *args, **kwargs):
+ super(RemotePollLoopActorWithKeysTestCase, self).build_monitor(
+ *args, **kwargs)
+ self.client.side_effect = side_effect
+
+ def test_key_subscription(self):
+ self.build_monitor([[{'key': 1}, {'key': 2}]])
+ self.monitor.subscribe_to(2, self.subscriber).get(self.TIMEOUT)
+ self.stop_proxy(self.monitor)
+ self.subscriber.assert_called_with({'key': 2})
+
+ def test_survive_dead_key_subscriptions(self):
+ item = {'key': 3}
+ self.build_monitor([[item], [item]])
+ dead_subscriber = mock.Mock(name='dead_subscriber')
+ dead_subscriber.side_effect = pykka.ActorDeadError
+ self.monitor.subscribe_to(3, dead_subscriber)
+ self.monitor.subscribe_to(3, self.subscriber)
+ self.monitor.poll().get(self.TIMEOUT)
+ self.assertTrue(self.stop_proxy(self.monitor),
+ "poll loop died from dead key subscriber")
+ self.subscriber.assert_called_with(item)
+
+ def test_mixed_subscriptions(self):
+ item = {'key': 4}
+ self.build_monitor([[item], [item]])
+ key_subscriber = mock.Mock(name='key_subscriber')
+ self.monitor.subscribe(self.subscriber)
+ self.monitor.subscribe_to(4, key_subscriber)
+ self.monitor.poll().get(self.TIMEOUT)
+ self.stop_proxy(self.monitor)
+ self.subscriber.assert_called_with([item])
+ key_subscriber.assert_called_with(item)
+
+ def test_subscription_to_missing_key(self):
+ self.build_monitor([[]])
+ self.monitor.subscribe_to('nonesuch', self.subscriber).get(self.TIMEOUT)
+ self.stop_proxy(self.monitor)
+ self.subscriber.assert_called_with(None)
+
+
+if __name__ == '__main__':
+ unittest.main()
+
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import time
+import unittest
+
+import arvados.errors as arverror
+import mock
+
+import arvnodeman.computenode as cnode
+from . import testutil
+
+@mock.patch('time.time', return_value=1)
+class ShutdownTimerTestCase(unittest.TestCase):
+ def test_two_length_window(self, time_mock):
+ timer = cnode.ShutdownTimer(time_mock.return_value, [8, 2])
+ self.assertEqual(481, timer.next_opening())
+ self.assertFalse(timer.window_open())
+ time_mock.return_value += 500
+ self.assertEqual(1081, timer.next_opening())
+ self.assertTrue(timer.window_open())
+ time_mock.return_value += 200
+ self.assertEqual(1081, timer.next_opening())
+ self.assertFalse(timer.window_open())
+
+ def test_three_length_window(self, time_mock):
+ timer = cnode.ShutdownTimer(time_mock.return_value, [6, 3, 1])
+ self.assertEqual(361, timer.next_opening())
+ self.assertFalse(timer.window_open())
+ time_mock.return_value += 400
+ self.assertEqual(961, timer.next_opening())
+ self.assertTrue(timer.window_open())
+ time_mock.return_value += 200
+ self.assertEqual(961, timer.next_opening())
+ self.assertFalse(timer.window_open())
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import time
+import unittest
+
+import arvados.errors as arverror
+import httplib2
+import mock
+import pykka
+
+import arvnodeman.computenode.dispatch as dispatch
+from . import testutil
+
+class ComputeNodeSetupActorTestCase(testutil.ActorTestMixin, unittest.TestCase):
+ def make_mocks(self, arvados_effect=None):
+ if arvados_effect is None:
+ arvados_effect = [testutil.arvados_node_mock()]
+ self.arvados_effect = arvados_effect
+ self.timer = testutil.MockTimer()
+ self.api_client = mock.MagicMock(name='api_client')
+ self.api_client.nodes().create().execute.side_effect = arvados_effect
+ self.api_client.nodes().update().execute.side_effect = arvados_effect
+ self.cloud_client = mock.MagicMock(name='cloud_client')
+ self.cloud_client.create_node.return_value = testutil.cloud_node_mock(1)
+
+ def make_actor(self, arv_node=None):
+ if not hasattr(self, 'timer'):
+ self.make_mocks(arvados_effect=[arv_node])
+ self.setup_actor = dispatch.ComputeNodeSetupActor.start(
+ self.timer, self.api_client, self.cloud_client,
+ testutil.MockSize(1), arv_node).proxy()
+
+ def test_creation_without_arvados_node(self):
+ self.make_actor()
+ self.assertEqual(self.arvados_effect[-1],
+ self.setup_actor.arvados_node.get(self.TIMEOUT))
+ self.assertTrue(self.api_client.nodes().create().execute.called)
+ self.assertEqual(self.cloud_client.create_node(),
+ self.setup_actor.cloud_node.get(self.TIMEOUT))
+
+ def test_creation_with_arvados_node(self):
+ self.make_actor(testutil.arvados_node_mock())
+ self.assertEqual(self.arvados_effect[-1],
+ self.setup_actor.arvados_node.get(self.TIMEOUT))
+ self.assertTrue(self.api_client.nodes().update().execute.called)
+ self.assertEqual(self.cloud_client.create_node(),
+ self.setup_actor.cloud_node.get(self.TIMEOUT))
+
+ def test_failed_arvados_calls_retried(self):
+ self.make_mocks([
+ arverror.ApiError(httplib2.Response({'status': '500'}), ""),
+ testutil.arvados_node_mock(),
+ ])
+ self.make_actor()
+ self.wait_for_assignment(self.setup_actor, 'arvados_node')
+
+ def test_failed_cloud_calls_retried(self):
+ self.make_mocks()
+ self.cloud_client.create_node.side_effect = [
+ Exception("test cloud creation error"),
+ self.cloud_client.create_node.return_value,
+ ]
+ self.make_actor()
+ self.wait_for_assignment(self.setup_actor, 'cloud_node')
+
+ def test_failed_post_create_retried(self):
+ self.make_mocks()
+ self.cloud_client.post_create_node.side_effect = [
+ Exception("test cloud post-create error"), None]
+ self.make_actor()
+ done = self.FUTURE_CLASS()
+ self.setup_actor.subscribe(done.set)
+ done.get(self.TIMEOUT)
+ self.assertEqual(2, self.cloud_client.post_create_node.call_count)
+
+ def test_stop_when_no_cloud_node(self):
+ self.make_mocks(
+ arverror.ApiError(httplib2.Response({'status': '500'}), ""))
+ self.make_actor()
+ self.setup_actor.stop_if_no_cloud_node()
+ self.assertTrue(
+ self.setup_actor.actor_ref.actor_stopped.wait(self.TIMEOUT))
+
+ def test_no_stop_when_cloud_node(self):
+ self.make_actor()
+ self.wait_for_assignment(self.setup_actor, 'cloud_node')
+ self.setup_actor.stop_if_no_cloud_node().get(self.TIMEOUT)
+ self.assertTrue(self.stop_proxy(self.setup_actor),
+ "actor was stopped by stop_if_no_cloud_node")
+
+ def test_subscribe(self):
+ self.make_mocks(
+ arverror.ApiError(httplib2.Response({'status': '500'}), ""))
+ self.make_actor()
+ subscriber = mock.Mock(name='subscriber_mock')
+ self.setup_actor.subscribe(subscriber)
+ self.api_client.nodes().create().execute.side_effect = [
+ testutil.arvados_node_mock()]
+ self.wait_for_assignment(self.setup_actor, 'cloud_node')
+ self.assertEqual(self.setup_actor.actor_ref.actor_urn,
+ subscriber.call_args[0][0].actor_ref.actor_urn)
+
+ def test_late_subscribe(self):
+ self.make_actor()
+ subscriber = mock.Mock(name='subscriber_mock')
+ self.wait_for_assignment(self.setup_actor, 'cloud_node')
+ self.setup_actor.subscribe(subscriber).get(self.TIMEOUT)
+ self.stop_proxy(self.setup_actor)
+ self.assertEqual(self.setup_actor.actor_ref.actor_urn,
+ subscriber.call_args[0][0].actor_ref.actor_urn)
+
+
+class ComputeNodeShutdownActorMixin(testutil.ActorTestMixin):
+ def make_mocks(self, cloud_node=None, arvados_node=None,
+ shutdown_open=True):
+ self.timer = testutil.MockTimer()
+ self.shutdowns = testutil.MockShutdownTimer()
+ self.shutdowns._set_state(shutdown_open, 300)
+ self.cloud_client = mock.MagicMock(name='cloud_client')
+ self.updates = mock.MagicMock(name='update_mock')
+ if cloud_node is None:
+ cloud_node = testutil.cloud_node_mock()
+ self.cloud_node = cloud_node
+ self.arvados_node = arvados_node
+
+ def make_actor(self, cancellable=True):
+ if not hasattr(self, 'timer'):
+ self.make_mocks()
+ monitor_actor = dispatch.ComputeNodeMonitorActor.start(
+ self.cloud_node, time.time(), self.shutdowns, self.timer,
+ self.updates, self.arvados_node)
+ self.shutdown_actor = self.ACTOR_CLASS.start(
+ self.timer, self.cloud_client, monitor_actor, cancellable).proxy()
+ self.monitor_actor = monitor_actor.proxy()
+
+ def check_success_flag(self, expected, allow_msg_count=1):
+ # allow_msg_count is the number of internal messages that may
+ # need to be handled for shutdown to finish.
+ for try_num in range(1 + allow_msg_count):
+ last_flag = self.shutdown_actor.success.get(self.TIMEOUT)
+ if last_flag is expected:
+ break
+ else:
+ self.fail("success flag {} is not {}".format(last_flag, expected))
+
+ def test_uncancellable_shutdown(self, *mocks):
+ self.make_mocks(shutdown_open=False)
+ self.cloud_client.destroy_node.return_value = False
+ self.make_actor(cancellable=False)
+ self.check_success_flag(None, 0)
+ self.shutdowns._set_state(True, 600)
+ self.cloud_client.destroy_node.return_value = True
+ self.check_success_flag(True)
+
+
+class ComputeNodeShutdownActorTestCase(ComputeNodeShutdownActorMixin,
+ unittest.TestCase):
+ ACTOR_CLASS = dispatch.ComputeNodeShutdownActor
+
+ def test_easy_shutdown(self):
+ self.make_actor()
+ self.check_success_flag(True)
+ self.assertTrue(self.cloud_client.destroy_node.called)
+
+ def test_shutdown_cancelled_when_window_closes(self):
+ self.make_mocks(shutdown_open=False)
+ self.make_actor()
+ self.check_success_flag(False, 2)
+ self.assertFalse(self.cloud_client.destroy_node.called)
+
+ def test_shutdown_retries_when_cloud_fails(self):
+ self.make_mocks()
+ self.cloud_client.destroy_node.return_value = False
+ self.make_actor()
+ self.assertIsNone(self.shutdown_actor.success.get(self.TIMEOUT))
+ self.cloud_client.destroy_node.return_value = True
+ self.check_success_flag(True)
+
+ def test_late_subscribe(self):
+ self.make_actor()
+ subscriber = mock.Mock(name='subscriber_mock')
+ self.shutdown_actor.subscribe(subscriber).get(self.TIMEOUT)
+ self.stop_proxy(self.shutdown_actor)
+ self.assertTrue(subscriber.called)
+ self.assertEqual(self.shutdown_actor.actor_ref.actor_urn,
+ subscriber.call_args[0][0].actor_ref.actor_urn)
+
+
+class ComputeNodeUpdateActorTestCase(testutil.ActorTestMixin,
+ unittest.TestCase):
+ def make_actor(self):
+ self.driver = mock.MagicMock(name='driver_mock')
+ self.updater = dispatch.ComputeNodeUpdateActor.start(self.driver).proxy()
+
+ def test_node_sync(self):
+ self.make_actor()
+ cloud_node = testutil.cloud_node_mock()
+ arv_node = testutil.arvados_node_mock()
+ self.updater.sync_node(cloud_node, arv_node).get(self.TIMEOUT)
+ self.driver().sync_node.assert_called_with(cloud_node, arv_node)
+
+
+class ComputeNodeMonitorActorTestCase(testutil.ActorTestMixin,
+ unittest.TestCase):
+ def make_mocks(self, node_num):
+ self.shutdowns = testutil.MockShutdownTimer()
+ self.shutdowns._set_state(False, 300)
+ self.timer = mock.MagicMock(name='timer_mock')
+ self.updates = mock.MagicMock(name='update_mock')
+ self.cloud_mock = testutil.cloud_node_mock(node_num)
+ self.subscriber = mock.Mock(name='subscriber_mock')
+
+ def make_actor(self, node_num=1, arv_node=None, start_time=None):
+ if not hasattr(self, 'cloud_mock'):
+ self.make_mocks(node_num)
+ if start_time is None:
+ start_time = time.time()
+ self.node_actor = dispatch.ComputeNodeMonitorActor.start(
+ self.cloud_mock, start_time, self.shutdowns, self.timer,
+ self.updates, arv_node).proxy()
+ self.node_actor.subscribe(self.subscriber).get(self.TIMEOUT)
+
+ def node_state(self, *states):
+ return self.node_actor.in_state(*states).get(self.TIMEOUT)
+
+ def test_in_state_when_unpaired(self):
+ self.make_actor()
+ self.assertIsNone(self.node_state('idle', 'alloc'))
+
+ def test_in_state_when_pairing_stale(self):
+ self.make_actor(arv_node=testutil.arvados_node_mock(
+ job_uuid=None, age=90000))
+ self.assertIsNone(self.node_state('idle', 'alloc'))
+
+ def test_in_state_when_no_state_available(self):
+ self.make_actor(arv_node=testutil.arvados_node_mock(info={}))
+ self.assertIsNone(self.node_state('idle', 'alloc'))
+
+ def test_in_idle_state(self):
+ self.make_actor(2, arv_node=testutil.arvados_node_mock(job_uuid=None))
+ self.assertTrue(self.node_state('idle'))
+ self.assertFalse(self.node_state('alloc'))
+ self.assertTrue(self.node_state('idle', 'alloc'))
+
+ def test_in_alloc_state(self):
+ self.make_actor(3, arv_node=testutil.arvados_node_mock(job_uuid=True))
+ self.assertFalse(self.node_state('idle'))
+ self.assertTrue(self.node_state('alloc'))
+ self.assertTrue(self.node_state('idle', 'alloc'))
+
+ def test_init_shutdown_scheduling(self):
+ self.make_actor()
+ self.assertTrue(self.timer.schedule.called)
+ self.assertEqual(300, self.timer.schedule.call_args[0][0])
+
+ def test_shutdown_window_close_scheduling(self):
+ self.make_actor()
+ self.shutdowns._set_state(False, 600)
+ self.timer.schedule.reset_mock()
+ self.node_actor.consider_shutdown().get(self.TIMEOUT)
+ self.stop_proxy(self.node_actor)
+ self.assertTrue(self.timer.schedule.called)
+ self.assertEqual(600, self.timer.schedule.call_args[0][0])
+ self.assertFalse(self.subscriber.called)
+
+ def test_shutdown_subscription(self):
+ self.make_actor()
+ self.shutdowns._set_state(True, 600)
+ self.node_actor.consider_shutdown().get(self.TIMEOUT)
+ self.assertTrue(self.subscriber.called)
+ self.assertEqual(self.node_actor.actor_ref.actor_urn,
+ self.subscriber.call_args[0][0].actor_ref.actor_urn)
+
+ def test_shutdown_without_arvados_node(self):
+ self.make_actor()
+ self.shutdowns._set_state(True, 600)
+ self.assertTrue(self.node_actor.shutdown_eligible().get(self.TIMEOUT))
+
+ def test_no_shutdown_without_arvados_node_and_old_cloud_node(self):
+ self.make_actor(start_time=0)
+ self.shutdowns._set_state(True, 600)
+ self.assertFalse(self.node_actor.shutdown_eligible().get(self.TIMEOUT))
+
+ def test_no_shutdown_when_window_closed(self):
+ self.make_actor(3, testutil.arvados_node_mock(3, job_uuid=None))
+ self.assertFalse(self.node_actor.shutdown_eligible().get(self.TIMEOUT))
+
+ def test_no_shutdown_when_node_running_job(self):
+ self.make_actor(4, testutil.arvados_node_mock(4, job_uuid=True))
+ self.shutdowns._set_state(True, 600)
+ self.assertFalse(self.node_actor.shutdown_eligible().get(self.TIMEOUT))
+
+ def test_no_shutdown_when_node_state_unknown(self):
+ self.make_actor(5, testutil.arvados_node_mock(5, info={}))
+ self.shutdowns._set_state(True, 600)
+ self.assertFalse(self.node_actor.shutdown_eligible().get(self.TIMEOUT))
+
+ def test_no_shutdown_when_node_state_stale(self):
+ self.make_actor(6, testutil.arvados_node_mock(6, age=90000))
+ self.shutdowns._set_state(True, 600)
+ self.assertFalse(self.node_actor.shutdown_eligible().get(self.TIMEOUT))
+
+ def test_arvados_node_match(self):
+ self.make_actor(2)
+ arv_node = testutil.arvados_node_mock(
+ 2, hostname='compute-two.zzzzz.arvadosapi.com')
+ pair_id = self.node_actor.offer_arvados_pair(arv_node).get(self.TIMEOUT)
+ self.assertEqual(self.cloud_mock.id, pair_id)
+ self.stop_proxy(self.node_actor)
+ self.updates.sync_node.assert_called_with(self.cloud_mock, arv_node)
+
+ def test_arvados_node_mismatch(self):
+ self.make_actor(3)
+ arv_node = testutil.arvados_node_mock(1)
+ self.assertIsNone(
+ self.node_actor.offer_arvados_pair(arv_node).get(self.TIMEOUT))
+
+ def test_update_cloud_node(self):
+ self.make_actor(1)
+ self.make_mocks(2)
+ self.cloud_mock.id = '1'
+ self.node_actor.update_cloud_node(self.cloud_mock)
+ current_cloud = self.node_actor.cloud_node.get(self.TIMEOUT)
+ self.assertEqual([testutil.ip_address_mock(2)],
+ current_cloud.private_ips)
+
+ def test_missing_cloud_node_update(self):
+ self.make_actor(1)
+ self.node_actor.update_cloud_node(None)
+ current_cloud = self.node_actor.cloud_node.get(self.TIMEOUT)
+ self.assertEqual([testutil.ip_address_mock(1)],
+ current_cloud.private_ips)
+
+ def test_update_arvados_node(self):
+ self.make_actor(3)
+ job_uuid = 'zzzzz-jjjjj-updatejobnode00'
+ new_arvados = testutil.arvados_node_mock(3, job_uuid)
+ self.node_actor.update_arvados_node(new_arvados)
+ current_arvados = self.node_actor.arvados_node.get(self.TIMEOUT)
+ self.assertEqual(job_uuid, current_arvados['job_uuid'])
+
+ def test_missing_arvados_node_update(self):
+ self.make_actor(4, testutil.arvados_node_mock(4))
+ self.node_actor.update_arvados_node(None)
+ current_arvados = self.node_actor.arvados_node.get(self.TIMEOUT)
+ self.assertEqual(testutil.ip_address_mock(4),
+ current_arvados['ip_address'])
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import subprocess
+import unittest
+
+import mock
+
+import arvnodeman.computenode.dispatch.slurm as slurm_dispatch
+from . import testutil
+from .test_computenode_dispatch import ComputeNodeShutdownActorMixin
+
+@mock.patch('subprocess.check_output')
+class SLURMComputeNodeShutdownActorTestCase(ComputeNodeShutdownActorMixin,
+ unittest.TestCase):
+ ACTOR_CLASS = slurm_dispatch.ComputeNodeShutdownActor
+
+ def check_slurm_got_args(self, proc_mock, *args):
+ self.assertTrue(proc_mock.called)
+ slurm_cmd = proc_mock.call_args[0][0]
+ for s in args:
+ self.assertIn(s, slurm_cmd)
+
+ def check_success_after_reset(self, proc_mock, end_state='drain\n'):
+ self.make_mocks(arvados_node=testutil.arvados_node_mock(63))
+ self.make_actor()
+ self.check_success_flag(None, 0)
+ self.check_success_flag(None, 0)
+ # Order is critical here: if the mock gets called when no return value
+ # or side effect is set, we may invoke a real subprocess.
+ proc_mock.return_value = end_state
+ proc_mock.side_effect = None
+ self.check_success_flag(True, 3)
+ self.check_slurm_got_args(proc_mock, 'compute63')
+
+ def make_wait_state_test(start_state='drng\n', end_state='drain\n'):
+ def test(self, proc_mock):
+ proc_mock.return_value = start_state
+ self.check_success_after_reset(proc_mock, end_state)
+ return test
+
+ for wait_state in ['alloc\n', 'drng\n', 'idle*\n']:
+ locals()['test_wait_while_' + wait_state.strip()
+ ] = make_wait_state_test(start_state=wait_state)
+
+ for end_state in ['down\n', 'down*\n', 'drain\n', 'fail\n']:
+ locals()['test_wait_until_' + end_state.strip()
+ ] = make_wait_state_test(end_state=end_state)
+
+ def test_retry_failed_slurm_calls(self, proc_mock):
+ proc_mock.side_effect = subprocess.CalledProcessError(1, ["mock"])
+ self.check_success_after_reset(proc_mock)
+
+ def test_slurm_bypassed_when_no_arvados_node(self, proc_mock):
+ # Test we correctly handle a node that failed to bootstrap.
+ proc_mock.return_value = 'idle\n'
+ self.make_actor()
+ self.check_success_flag(True)
+ self.assertFalse(proc_mock.called)
+
+ def test_node_undrained_when_shutdown_window_closes(self, proc_mock):
+ proc_mock.return_value = 'alloc\n'
+ self.make_mocks(arvados_node=testutil.arvados_node_mock(job_uuid=True))
+ self.make_actor()
+ self.check_success_flag(False, 2)
+ self.check_slurm_got_args(proc_mock, 'NodeName=compute99',
+ 'State=RESUME')
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import ssl
+import time
+import unittest
+
+import libcloud.common.types as cloud_types
+import mock
+
+import arvnodeman.computenode.driver.ec2 as ec2
+from . import testutil
+
+class EC2ComputeNodeDriverTestCase(unittest.TestCase):
+ def setUp(self):
+ self.driver_mock = mock.MagicMock(name='driver_mock')
+
+ def new_driver(self, auth_kwargs={}, list_kwargs={}, create_kwargs={}):
+ create_kwargs.setdefault('ping_host', '100::')
+ return ec2.ComputeNodeDriver(
+ auth_kwargs, list_kwargs, create_kwargs,
+ driver_class=self.driver_mock)
+
+ def test_driver_instantiation(self):
+ kwargs = {'key': 'testkey'}
+ driver = self.new_driver(auth_kwargs=kwargs)
+ self.assertTrue(self.driver_mock.called)
+ self.assertEqual(kwargs, self.driver_mock.call_args[1])
+
+ def test_list_kwargs_become_filters(self):
+ # We're also testing tag name translation.
+ driver = self.new_driver(list_kwargs={'tag_test': 'true'})
+ driver.list_nodes()
+ list_method = self.driver_mock().list_nodes
+ self.assertTrue(list_method.called)
+ self.assertEqual({'tag:test': 'true'},
+ list_method.call_args[1].get('ex_filters'))
+
+ def test_create_location_loaded_at_initialization(self):
+ kwargs = {'location': 'testregion'}
+ driver = self.new_driver(create_kwargs=kwargs)
+ self.assertTrue(self.driver_mock().list_locations)
+
+ def test_create_image_loaded_at_initialization(self):
+ kwargs = {'image': 'testimage'}
+ driver = self.new_driver(create_kwargs=kwargs)
+ self.assertTrue(self.driver_mock().list_images)
+
+ def test_create_includes_ping_secret(self):
+ arv_node = testutil.arvados_node_mock(info={'ping_secret': 'ssshh'})
+ driver = self.new_driver()
+ driver.create_node(testutil.MockSize(1), arv_node)
+ create_method = self.driver_mock().create_node
+ self.assertTrue(create_method.called)
+ self.assertIn('ping_secret=ssshh',
+ create_method.call_args[1].get('ex_userdata',
+ 'arg missing'))
+
+ def test_hostname_from_arvados_node(self):
+ arv_node = testutil.arvados_node_mock(8)
+ driver = self.new_driver()
+ self.assertEqual('compute8.zzzzz.arvadosapi.com',
+ driver.arvados_create_kwargs(arv_node)['name'])
+
+ def test_default_hostname_from_new_arvados_node(self):
+ arv_node = testutil.arvados_node_mock(hostname=None)
+ driver = self.new_driver()
+ self.assertEqual('dynamic.compute.zzzzz.arvadosapi.com',
+ driver.arvados_create_kwargs(arv_node)['name'])
+
+ def check_node_tagged(self, cloud_node, expected_tags):
+ tag_mock = self.driver_mock().ex_create_tags
+ self.assertTrue(tag_mock.called)
+ self.assertIs(cloud_node, tag_mock.call_args[0][0])
+ self.assertEqual(expected_tags, tag_mock.call_args[0][1])
+
+ def test_post_create_node_tags_from_list_kwargs(self):
+ expect_tags = {'key1': 'test value 1', 'key2': 'test value 2'}
+ list_kwargs = {('tag_' + key): value
+ for key, value in expect_tags.iteritems()}
+ list_kwargs['instance-state-name'] = 'running'
+ cloud_node = testutil.cloud_node_mock()
+ driver = self.new_driver(list_kwargs=list_kwargs)
+ driver.post_create_node(cloud_node)
+ self.check_node_tagged(cloud_node, expect_tags)
+
+ def test_sync_node(self):
+ arv_node = testutil.arvados_node_mock(1)
+ cloud_node = testutil.cloud_node_mock(2)
+ driver = self.new_driver()
+ driver.sync_node(cloud_node, arv_node)
+ self.check_node_tagged(cloud_node,
+ {'Name': 'compute1.zzzzz.arvadosapi.com'})
+
+ def test_node_create_time(self):
+ refsecs = int(time.time())
+ reftuple = time.gmtime(refsecs)
+ node = testutil.cloud_node_mock()
+ node.extra = {'launch_time': time.strftime('%Y-%m-%dT%H:%M:%S.000Z',
+ reftuple)}
+ self.assertEqual(refsecs, ec2.ComputeNodeDriver.node_start_time(node))
+
+ def test_cloud_exceptions(self):
+ for error in [Exception("test exception"),
+ IOError("test exception"),
+ ssl.SSLError("test exception"),
+ cloud_types.LibcloudError("test exception")]:
+ self.assertTrue(ec2.ComputeNodeDriver.is_cloud_exception(error),
+ "{} not flagged as cloud exception".format(error))
+
+ def test_noncloud_exceptions(self):
+ self.assertFalse(
+ ec2.ComputeNodeDriver.is_cloud_exception(ValueError("test error")),
+ "ValueError flagged as cloud exception")
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import io
+import logging
+import unittest
+
+import arvnodeman.computenode.dispatch as dispatch
+import arvnodeman.computenode.dispatch.slurm as slurm_dispatch
+import arvnodeman.config as nmconfig
+
+class NodeManagerConfigTestCase(unittest.TestCase):
+ TEST_CONFIG = u"""
+[Cloud]
+provider = dummy
+shutdown_windows = 52, 6, 2
+
+[Cloud Credentials]
+creds = dummy_creds
+
+[Cloud List]
+[Cloud Create]
+
+[Size 1]
+cores = 1
+
+[Logging]
+file = /dev/null
+level = DEBUG
+testlogger = INFO
+"""
+
+ def load_config(self, config=None, config_str=None):
+ if config is None:
+ config = nmconfig.NodeManagerConfig()
+ if config_str is None:
+ config_str = self.TEST_CONFIG
+ with io.StringIO(config_str) as config_fp:
+ config.readfp(config_fp)
+ return config
+
+ def test_seeded_defaults(self):
+ config = nmconfig.NodeManagerConfig()
+ sec_names = set(config.sections())
+ self.assertIn('Arvados', sec_names)
+ self.assertIn('Daemon', sec_names)
+ self.assertFalse(any(name.startswith('Size ') for name in sec_names))
+
+ def test_list_sizes(self):
+ config = self.load_config()
+ client = config.new_cloud_client()
+ sizes = config.node_sizes(client.list_sizes())
+ self.assertEqual(1, len(sizes))
+ size, kwargs = sizes[0]
+ self.assertEqual('Small', size.name)
+ self.assertEqual(1, kwargs['cores'])
+
+ def test_shutdown_windows(self):
+ config = self.load_config()
+ self.assertEqual([52, 6, 2], config.shutdown_windows())
+
+ def test_log_levels(self):
+ config = self.load_config()
+ self.assertEqual({'level': logging.DEBUG,
+ 'testlogger': logging.INFO},
+ config.log_levels())
+
+ def check_dispatch_classes(self, config, module):
+ setup, shutdown, update, monitor = config.dispatch_classes()
+ self.assertIs(setup, module.ComputeNodeSetupActor)
+ self.assertIs(shutdown, module.ComputeNodeShutdownActor)
+ self.assertIs(update, module.ComputeNodeUpdateActor)
+ self.assertIs(monitor, module.ComputeNodeMonitorActor)
+
+ def test_default_dispatch(self):
+ config = self.load_config()
+ self.check_dispatch_classes(config, dispatch)
+
+ def test_custom_dispatch(self):
+ config = self.load_config(
+ config_str=self.TEST_CONFIG + "[Daemon]\ndispatcher=slurm\n")
+ self.check_dispatch_classes(config, slurm_dispatch)
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import time
+import unittest
+
+import mock
+import pykka
+
+import arvnodeman.daemon as nmdaemon
+from arvnodeman.computenode.dispatch import ComputeNodeMonitorActor
+from . import testutil
+
+class NodeManagerDaemonActorTestCase(testutil.ActorTestMixin,
+ unittest.TestCase):
+ def new_setup_proxy(self):
+ # Make sure that every time the daemon starts a setup actor,
+ # it gets a new mock object back.
+ self.last_setup = mock.MagicMock(name='setup_proxy_mock')
+ return self.last_setup
+
+ def make_daemon(self, cloud_nodes=[], arvados_nodes=[], want_sizes=[],
+ min_size=testutil.MockSize(1), min_nodes=0, max_nodes=8):
+ for name in ['cloud_nodes', 'arvados_nodes', 'server_wishlist']:
+ setattr(self, name + '_poller', mock.MagicMock(name=name + '_mock'))
+ self.arv_factory = mock.MagicMock(name='arvados_mock')
+ self.cloud_factory = mock.MagicMock(name='cloud_mock')
+ self.cloud_factory().node_start_time.return_value = time.time()
+ self.cloud_updates = mock.MagicMock(name='updates_mock')
+ self.timer = testutil.MockTimer(deliver_immediately=False)
+ self.node_setup = mock.MagicMock(name='setup_mock')
+ self.node_setup.start().proxy.side_effect = self.new_setup_proxy
+ self.node_setup.reset_mock()
+ self.node_shutdown = mock.MagicMock(name='shutdown_mock')
+ self.daemon = nmdaemon.NodeManagerDaemonActor.start(
+ self.server_wishlist_poller, self.arvados_nodes_poller,
+ self.cloud_nodes_poller, self.cloud_updates, self.timer,
+ self.arv_factory, self.cloud_factory,
+ [54, 5, 1], min_size, min_nodes, max_nodes, 600, 1800, 3600,
+ self.node_setup, self.node_shutdown).proxy()
+ if cloud_nodes is not None:
+ self.daemon.update_cloud_nodes(cloud_nodes).get(self.TIMEOUT)
+ if arvados_nodes is not None:
+ self.daemon.update_arvados_nodes(arvados_nodes).get(self.TIMEOUT)
+ if want_sizes is not None:
+ self.daemon.update_server_wishlist(want_sizes).get(self.TIMEOUT)
+
+ def monitor_list(self):
+ return pykka.ActorRegistry.get_by_class(ComputeNodeMonitorActor)
+
+ def alive_monitor_count(self):
+ return sum(1 for actor in self.monitor_list() if actor.is_alive())
+
+ def assertShutdownCancellable(self, expected=True):
+ self.assertTrue(self.node_shutdown.start.called)
+ self.assertIs(expected,
+ self.node_shutdown.start.call_args[1]['cancellable'],
+ "ComputeNodeShutdownActor incorrectly cancellable")
+
+ def test_easy_node_creation(self):
+ size = testutil.MockSize(1)
+ self.make_daemon(want_sizes=[size])
+ self.stop_proxy(self.daemon)
+ self.assertTrue(self.node_setup.start.called)
+
+ def check_monitors_arvados_nodes(self, *arv_nodes):
+ pairings = [monitor.proxy().arvados_node
+ for monitor in self.monitor_list() if monitor.is_alive()]
+ self.assertItemsEqual(arv_nodes, pykka.get_all(pairings, self.TIMEOUT))
+
+ def test_node_pairing(self):
+ cloud_node = testutil.cloud_node_mock(1)
+ arv_node = testutil.arvados_node_mock(1)
+ self.make_daemon([cloud_node], [arv_node])
+ self.stop_proxy(self.daemon)
+ self.check_monitors_arvados_nodes(arv_node)
+
+ def test_node_pairing_after_arvados_update(self):
+ cloud_node = testutil.cloud_node_mock(2)
+ self.make_daemon([cloud_node],
+ [testutil.arvados_node_mock(2, ip_address=None)])
+ arv_node = testutil.arvados_node_mock(2)
+ self.daemon.update_arvados_nodes([arv_node]).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.check_monitors_arvados_nodes(arv_node)
+
+ def test_arvados_node_un_and_re_paired(self):
+ arv_node = testutil.arvados_node_mock(3)
+ self.make_daemon([testutil.cloud_node_mock(3)], [arv_node])
+ self.check_monitors_arvados_nodes(arv_node)
+ self.daemon.update_cloud_nodes([]).get(self.TIMEOUT)
+ self.assertEqual(0, self.alive_monitor_count())
+ self.daemon.update_cloud_nodes([testutil.cloud_node_mock(3)])
+ self.stop_proxy(self.daemon)
+ self.check_monitors_arvados_nodes(arv_node)
+
+ def test_old_arvados_node_not_double_assigned(self):
+ arv_node = testutil.arvados_node_mock(3, age=9000)
+ size = testutil.MockSize(3)
+ self.make_daemon(arvados_nodes=[arv_node])
+ self.daemon.update_server_wishlist([size]).get(self.TIMEOUT)
+ self.daemon.update_server_wishlist([size, size]).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ used_nodes = [call[1].get('arvados_node')
+ for call in self.node_setup.start.call_args_list]
+ self.assertEqual(2, len(used_nodes))
+ self.assertIn(arv_node, used_nodes)
+ self.assertIn(None, used_nodes)
+
+ def test_node_count_satisfied(self):
+ self.make_daemon([testutil.cloud_node_mock()],
+ want_sizes=[testutil.MockSize(1)])
+ self.stop_proxy(self.daemon)
+ self.assertFalse(self.node_setup.called)
+
+ def test_booting_nodes_counted(self):
+ cloud_node = testutil.cloud_node_mock(1)
+ arv_node = testutil.arvados_node_mock(1)
+ server_wishlist = [testutil.MockSize(1)] * 2
+ self.make_daemon([cloud_node], [arv_node], server_wishlist)
+ self.daemon.max_nodes.get(self.TIMEOUT)
+ self.assertTrue(self.node_setup.start.called)
+ self.daemon.update_server_wishlist(server_wishlist).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertEqual(1, self.node_setup.start.call_count)
+
+ def test_boot_new_node_when_all_nodes_busy(self):
+ arv_node = testutil.arvados_node_mock(2, job_uuid=True)
+ self.make_daemon([testutil.cloud_node_mock(2)], [arv_node],
+ [testutil.MockSize(2)])
+ self.stop_proxy(self.daemon)
+ self.assertTrue(self.node_setup.start.called)
+
+ def test_boot_new_node_below_min_nodes(self):
+ min_size = testutil.MockSize(1)
+ wish_size = testutil.MockSize(3)
+ self.make_daemon([], [], None, min_size=min_size, min_nodes=2)
+ self.daemon.update_server_wishlist([wish_size]).get(self.TIMEOUT)
+ self.daemon.update_cloud_nodes([]).get(self.TIMEOUT)
+ self.daemon.update_server_wishlist([wish_size]).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertEqual([wish_size, min_size],
+ [call[1].get('cloud_size')
+ for call in self.node_setup.start.call_args_list])
+
+ def test_no_new_node_when_ge_min_nodes_busy(self):
+ cloud_nodes = [testutil.cloud_node_mock(n) for n in range(1, 4)]
+ arv_nodes = [testutil.arvados_node_mock(n, job_uuid=True)
+ for n in range(1, 4)]
+ self.make_daemon(cloud_nodes, arv_nodes, [], min_nodes=2)
+ self.stop_proxy(self.daemon)
+ self.assertEqual(0, self.node_setup.start.call_count)
+
+ def test_no_new_node_when_max_nodes_busy(self):
+ self.make_daemon([testutil.cloud_node_mock(3)],
+ [testutil.arvados_node_mock(3, job_uuid=True)],
+ [testutil.MockSize(3)],
+ max_nodes=1)
+ self.stop_proxy(self.daemon)
+ self.assertFalse(self.node_setup.start.called)
+
+ def start_node_boot(self, cloud_node=None, arv_node=None, id_num=1):
+ if cloud_node is None:
+ cloud_node = testutil.cloud_node_mock(id_num)
+ if arv_node is None:
+ arv_node = testutil.arvados_node_mock(id_num)
+ self.make_daemon(want_sizes=[testutil.MockSize(id_num)])
+ self.daemon.max_nodes.get(self.TIMEOUT)
+ self.assertEqual(1, self.node_setup.start.call_count)
+ self.last_setup.cloud_node.get.return_value = cloud_node
+ self.last_setup.arvados_node.get.return_value = arv_node
+ return self.last_setup
+
+ def test_no_duplication_when_booting_node_listed_fast(self):
+ # Test that we don't start two ComputeNodeMonitorActors when
+ # we learn about a booting node through a listing before we
+ # get the "node up" message from CloudNodeSetupActor.
+ cloud_node = testutil.cloud_node_mock(1)
+ setup = self.start_node_boot(cloud_node)
+ self.daemon.update_cloud_nodes([cloud_node])
+ self.daemon.node_up(setup).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+
+ def test_no_duplication_when_booted_node_listed(self):
+ cloud_node = testutil.cloud_node_mock(2)
+ setup = self.start_node_boot(cloud_node, id_num=2)
+ self.daemon.node_up(setup)
+ self.daemon.update_cloud_nodes([cloud_node]).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+
+ def test_node_counted_after_boot_with_slow_listing(self):
+ # Test that, after we boot a compute node, we assume it exists
+ # even it doesn't appear in the listing (e.g., because of delays
+ # propagating tags).
+ setup = self.start_node_boot()
+ self.daemon.node_up(setup).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+ self.daemon.update_cloud_nodes([]).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+
+ def test_booted_unlisted_node_counted(self):
+ setup = self.start_node_boot(id_num=1)
+ self.daemon.node_up(setup)
+ self.daemon.update_server_wishlist(
+ [testutil.MockSize(1)]).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertEqual(1, self.node_setup.start.call_count)
+
+ def test_booted_node_can_shutdown(self):
+ setup = self.start_node_boot()
+ self.daemon.node_up(setup).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+ monitor = self.monitor_list()[0].proxy()
+ self.daemon.update_server_wishlist([])
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertTrue(self.node_shutdown.start.called,
+ "daemon did not shut down booted node on offer")
+
+ def test_booted_node_lifecycle(self):
+ cloud_node = testutil.cloud_node_mock(6)
+ setup = self.start_node_boot(cloud_node, id_num=6)
+ self.daemon.node_up(setup).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+ monitor = self.monitor_list()[0].proxy()
+ self.daemon.update_server_wishlist([])
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.assertShutdownCancellable(True)
+ shutdown = self.node_shutdown.start().proxy()
+ shutdown.cloud_node.get.return_value = cloud_node
+ self.daemon.node_finished_shutdown(shutdown).get(self.TIMEOUT)
+ self.assertTrue(shutdown.stop.called,
+ "shutdown actor not stopped after finishing")
+ self.assertTrue(monitor.actor_ref.actor_stopped.wait(self.TIMEOUT),
+ "monitor for booted node not stopped after shutdown")
+ self.daemon.update_server_wishlist(
+ [testutil.MockSize(2)]).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertTrue(self.node_setup.start.called,
+ "second node not started after booted node stopped")
+
+ def test_booted_node_shut_down_when_never_listed(self):
+ setup = self.start_node_boot()
+ self.daemon.node_up(setup).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+ self.assertFalse(self.node_shutdown.start.called)
+ self.timer.deliver()
+ self.stop_proxy(self.daemon)
+ self.assertShutdownCancellable(False)
+
+ def test_booted_node_shut_down_when_never_paired(self):
+ cloud_node = testutil.cloud_node_mock(2)
+ setup = self.start_node_boot(cloud_node)
+ self.daemon.node_up(setup).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+ self.daemon.update_cloud_nodes([cloud_node])
+ self.timer.deliver()
+ self.stop_proxy(self.daemon)
+ self.assertShutdownCancellable(False)
+
+ def test_node_that_pairs_not_considered_failed_boot(self):
+ cloud_node = testutil.cloud_node_mock(3)
+ arv_node = testutil.arvados_node_mock(3)
+ setup = self.start_node_boot(cloud_node, arv_node)
+ self.daemon.node_up(setup).get(self.TIMEOUT)
+ self.assertEqual(1, self.alive_monitor_count())
+ self.daemon.update_cloud_nodes([cloud_node])
+ self.daemon.update_arvados_nodes([arv_node]).get(self.TIMEOUT)
+ self.timer.deliver()
+ self.stop_proxy(self.daemon)
+ self.assertFalse(self.node_shutdown.start.called)
+
+ def test_booting_nodes_shut_down(self):
+ self.make_daemon(want_sizes=[testutil.MockSize(1)])
+ self.daemon.update_server_wishlist([]).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertTrue(self.last_setup.stop_if_no_cloud_node.called)
+
+ def test_shutdown_declined_at_wishlist_capacity(self):
+ cloud_node = testutil.cloud_node_mock(1)
+ size = testutil.MockSize(1)
+ self.make_daemon(cloud_nodes=[cloud_node], want_sizes=[size])
+ self.assertEqual(1, self.alive_monitor_count())
+ monitor = self.monitor_list()[0].proxy()
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertFalse(self.node_shutdown.start.called)
+
+ def test_shutdown_declined_below_min_nodes(self):
+ cloud_node = testutil.cloud_node_mock(1)
+ self.make_daemon(cloud_nodes=[cloud_node], min_nodes=1)
+ self.assertEqual(1, self.alive_monitor_count())
+ monitor = self.monitor_list()[0].proxy()
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertFalse(self.node_shutdown.start.called)
+
+ def test_shutdown_accepted_below_capacity(self):
+ self.make_daemon(cloud_nodes=[testutil.cloud_node_mock()])
+ self.assertEqual(1, self.alive_monitor_count())
+ monitor = self.monitor_list()[0].proxy()
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertTrue(self.node_shutdown.start.called)
+
+ def test_shutdown_declined_when_idle_and_job_queued(self):
+ cloud_nodes = [testutil.cloud_node_mock(n) for n in [3, 4]]
+ arv_nodes = [testutil.arvados_node_mock(3, job_uuid=True),
+ testutil.arvados_node_mock(4, job_uuid=None)]
+ self.make_daemon(cloud_nodes, arv_nodes, [testutil.MockSize(1)])
+ self.assertEqual(2, self.alive_monitor_count())
+ for mon_ref in self.monitor_list():
+ monitor = mon_ref.proxy()
+ if monitor.cloud_node.get(self.TIMEOUT) is cloud_nodes[-1]:
+ break
+ else:
+ self.fail("monitor for idle node not found")
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertFalse(self.node_shutdown.start.called)
+
+ def test_node_shutdown_after_cancelled_shutdown(self):
+ cloud_node = testutil.cloud_node_mock(5)
+ self.make_daemon([cloud_node], [testutil.arvados_node_mock(5)])
+ self.assertEqual(1, self.alive_monitor_count())
+ monitor = self.monitor_list()[0].proxy()
+ shutdown_proxy = self.node_shutdown.start().proxy
+ shutdown_proxy().cloud_node.get.return_value = cloud_node
+ shutdown_proxy().success.get.return_value = False
+ shutdown_proxy.reset_mock()
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.assertTrue(shutdown_proxy.called)
+ self.daemon.node_finished_shutdown(shutdown_proxy()).get(self.TIMEOUT)
+ shutdown_proxy().success.get.return_value = True
+ shutdown_proxy.reset_mock()
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.assertTrue(shutdown_proxy.called)
+
+ def test_nodes_shutting_down_replaced_below_max_nodes(self):
+ cloud_node = testutil.cloud_node_mock(6)
+ self.make_daemon([cloud_node], [testutil.arvados_node_mock(6)])
+ self.assertEqual(1, self.alive_monitor_count())
+ monitor = self.monitor_list()[0].proxy()
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.assertTrue(self.node_shutdown.start.called)
+ self.daemon.update_server_wishlist(
+ [testutil.MockSize(6)]).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertTrue(self.node_setup.start.called)
+
+ def test_nodes_shutting_down_not_replaced_at_max_nodes(self):
+ cloud_node = testutil.cloud_node_mock(7)
+ self.make_daemon([cloud_node], [testutil.arvados_node_mock(7)],
+ max_nodes=1)
+ self.assertEqual(1, self.alive_monitor_count())
+ monitor = self.monitor_list()[0].proxy()
+ self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
+ self.assertTrue(self.node_shutdown.start.called)
+ self.daemon.update_server_wishlist(
+ [testutil.MockSize(7)]).get(self.TIMEOUT)
+ self.stop_proxy(self.daemon)
+ self.assertFalse(self.node_setup.start.called)
+
+ def test_nodes_shutting_down_count_against_excess(self):
+ cloud_nodes = [testutil.cloud_node_mock(n) for n in [8, 9]]
+ arv_nodes = [testutil.arvados_node_mock(n) for n in [8, 9]]
+ self.make_daemon(cloud_nodes, arv_nodes, [testutil.MockSize(8)])
+ self.assertEqual(2, self.alive_monitor_count())
+ for mon_ref in self.monitor_list():
+ self.daemon.node_can_shutdown(mon_ref.proxy()).get(self.TIMEOUT)
+ self.assertEqual(1, self.node_shutdown.start.call_count)
+
+ def test_clean_shutdown_waits_for_node_setup_finish(self):
+ new_node = self.start_node_boot()
+ self.daemon.shutdown().get(self.TIMEOUT)
+ self.assertTrue(new_node.stop_if_no_cloud_node.called)
+ self.daemon.node_up(new_node).get(self.TIMEOUT)
+ self.assertTrue(new_node.stop.called)
+ self.timer.deliver()
+ self.assertTrue(
+ self.daemon.actor_ref.actor_stopped.wait(self.TIMEOUT))
+
+ def test_wishlist_ignored_after_shutdown(self):
+ size = testutil.MockSize(2)
+ self.make_daemon(want_sizes=[size])
+ self.daemon.shutdown().get(self.TIMEOUT)
+ self.daemon.update_server_wishlist([size] * 2).get(self.TIMEOUT)
+ self.timer.deliver()
+ self.stop_proxy(self.daemon)
+ self.assertEqual(1, self.node_setup.start.call_count)
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import unittest
+
+import arvnodeman.jobqueue as jobqueue
+from . import testutil
+
+class ServerCalculatorTestCase(unittest.TestCase):
+ def make_calculator(self, factors, **kwargs):
+ return jobqueue.ServerCalculator(
+ [(testutil.MockSize(n), {'cores': n}) for n in factors], **kwargs)
+
+ def calculate(self, servcalc, *constraints):
+ return servcalc.servers_for_queue(
+ [{'uuid': 'zzzzz-jjjjj-{:015x}'.format(index),
+ 'runtime_constraints': cdict}
+ for index, cdict in enumerate(constraints)])
+
+ def test_empty_queue_needs_no_servers(self):
+ servcalc = self.make_calculator([1])
+ self.assertEqual([], servcalc.servers_for_queue([]))
+
+ def test_easy_server_count(self):
+ servcalc = self.make_calculator([1])
+ servlist = self.calculate(servcalc, {'min_nodes': 3})
+ self.assertEqual(3, len(servlist))
+
+ def test_implicit_server_count(self):
+ servcalc = self.make_calculator([1])
+ servlist = self.calculate(servcalc, {}, {'min_nodes': 3})
+ self.assertEqual(4, len(servlist))
+
+ def test_bad_min_nodes_override(self):
+ servcalc = self.make_calculator([1])
+ servlist = self.calculate(servcalc,
+ {'min_nodes': -2}, {'min_nodes': 'foo'})
+ self.assertEqual(2, len(servlist))
+
+ def test_ignore_unsatisfiable_jobs(self):
+ servcalc = self.make_calculator([1], max_nodes=9)
+ servlist = self.calculate(servcalc,
+ {'min_cores_per_node': 2},
+ {'min_ram_mb_per_node': 256},
+ {'min_nodes': 6},
+ {'min_nodes': 12},
+ {'min_scratch_mb_per_node': 200})
+ self.assertEqual(6, len(servlist))
+
+ def test_job_requesting_max_nodes_accepted(self):
+ servcalc = self.make_calculator([1], max_nodes=4)
+ servlist = self.calculate(servcalc, {'min_nodes': 4})
+ self.assertEqual(4, len(servlist))
+
+ def test_cheapest_size(self):
+ servcalc = self.make_calculator([2, 4, 1, 3])
+ self.assertEqual(testutil.MockSize(1), servcalc.cheapest_size())
+
+
+class JobQueueMonitorActorTestCase(testutil.RemotePollLoopActorTestMixin,
+ unittest.TestCase):
+ TEST_CLASS = jobqueue.JobQueueMonitorActor
+
+ class MockCalculator(object):
+ @staticmethod
+ def servers_for_queue(queue):
+ return [testutil.MockSize(n) for n in queue]
+
+
+ def build_monitor(self, side_effect, *args, **kwargs):
+ super(JobQueueMonitorActorTestCase, self).build_monitor(*args, **kwargs)
+ self.client.jobs().queue().execute.side_effect = side_effect
+
+ def test_subscribers_get_server_lists(self):
+ self.build_monitor([{'items': [1, 2]}], self.MockCalculator())
+ self.monitor.subscribe(self.subscriber).get(self.TIMEOUT)
+ self.stop_proxy(self.monitor)
+ self.subscriber.assert_called_with([testutil.MockSize(1),
+ testutil.MockSize(2)])
+
+
+if __name__ == '__main__':
+ unittest.main()
+
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import unittest
+
+import arvnodeman.nodelist as nodelist
+from . import testutil
+
+class ArvadosNodeListMonitorActorTestCase(testutil.RemotePollLoopActorTestMixin,
+ unittest.TestCase):
+ TEST_CLASS = nodelist.ArvadosNodeListMonitorActor
+
+ def build_monitor(self, side_effect, *args, **kwargs):
+ super(ArvadosNodeListMonitorActorTestCase, self).build_monitor(
+ *args, **kwargs)
+ self.client.nodes().list().execute.side_effect = side_effect
+
+ def test_uuid_is_subscription_key(self):
+ node = testutil.arvados_node_mock()
+ self.build_monitor([{'items': [node]}])
+ self.monitor.subscribe_to(node['uuid'],
+ self.subscriber).get(self.TIMEOUT)
+ self.stop_proxy(self.monitor)
+ self.subscriber.assert_called_with(node)
+
+
+class CloudNodeListMonitorActorTestCase(testutil.RemotePollLoopActorTestMixin,
+ unittest.TestCase):
+ TEST_CLASS = nodelist.CloudNodeListMonitorActor
+
+ class MockNode(object):
+ def __init__(self, count):
+ self.id = str(count)
+ self.name = 'test{}.example.com'.format(count)
+ self.private_ips = ['10.0.0.{}'.format(count)]
+ self.public_ips = []
+ self.size = None
+ self.state = 0
+
+
+ def build_monitor(self, side_effect, *args, **kwargs):
+ super(CloudNodeListMonitorActorTestCase, self).build_monitor(
+ *args, **kwargs)
+ self.client.list_nodes.side_effect = side_effect
+
+ def test_id_is_subscription_key(self):
+ node = self.MockNode(1)
+ self.build_monitor([[node]])
+ self.monitor.subscribe_to('1', self.subscriber).get(self.TIMEOUT)
+ self.stop_proxy(self.monitor)
+ self.subscriber.assert_called_with(node)
+
+
+if __name__ == '__main__':
+ unittest.main()
+
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import time
+import unittest
+
+import mock
+import pykka
+
+import arvnodeman.timedcallback as timedcallback
+from . import testutil
+
+@testutil.no_sleep
+class TimedCallBackActorTestCase(testutil.ActorTestMixin, unittest.TestCase):
+ def test_immediate_turnaround(self):
+ receiver = mock.Mock()
+ deliverer = timedcallback.TimedCallBackActor.start().proxy()
+ deliverer.schedule(time.time() - 1, receiver,
+ 'immediate').get(self.TIMEOUT)
+ self.stop_proxy(deliverer)
+ receiver.assert_called_with('immediate')
+
+ def test_delayed_turnaround(self):
+ receiver = mock.Mock()
+ with mock.patch('time.time', return_value=0) as mock_now:
+ deliverer = timedcallback.TimedCallBackActor.start().proxy()
+ deliverer.schedule(1, receiver, 'delayed')
+ deliverer.schedule(3, receiver, 'failure').get(self.TIMEOUT)
+ self.assertFalse(receiver.called)
+ mock_now.return_value = 2
+ deliverer.schedule(3, receiver, 'failure').get(self.TIMEOUT)
+ self.stop_proxy(deliverer)
+ receiver.assert_called_with('delayed')
+
+ def test_out_of_order_scheduling(self):
+ receiver = mock.Mock()
+ with mock.patch('time.time', return_value=1.5) as mock_now:
+ deliverer = timedcallback.TimedCallBackActor.start().proxy()
+ deliverer.schedule(2, receiver, 'second')
+ deliverer.schedule(1, receiver, 'first')
+ deliverer.schedule(3, receiver, 'failure').get(self.TIMEOUT)
+ receiver.assert_called_with('first')
+ mock_now.return_value = 2.5
+ deliverer.schedule(3, receiver, 'failure').get(self.TIMEOUT)
+ self.stop_proxy(deliverer)
+ receiver.assert_called_with('second')
+
+ def test_dead_actors_ignored(self):
+ receiver = mock.Mock(name='dead_actor', spec=pykka.ActorRef)
+ receiver.tell.side_effect = pykka.ActorDeadError
+ deliverer = timedcallback.TimedCallBackActor.start().proxy()
+ deliverer.schedule(time.time() - 1, receiver.tell,
+ 'error').get(self.TIMEOUT)
+ self.assertTrue(self.stop_proxy(deliverer), "deliverer died")
+ receiver.tell.assert_called_with('error')
+
+
+if __name__ == '__main__':
+ unittest.main()
+
--- /dev/null
+#!/usr/bin/env python
+
+from __future__ import absolute_import, print_function
+
+import threading
+import time
+
+import mock
+import pykka
+
+from . import pykka_timeout
+
+no_sleep = mock.patch('time.sleep', lambda n: None)
+
+def arvados_node_mock(node_num=99, job_uuid=None, age=0, **kwargs):
+ if job_uuid is True:
+ job_uuid = 'zzzzz-jjjjj-jobjobjobjobjob'
+ slurm_state = 'idle' if (job_uuid is None) else 'alloc'
+ node = {'uuid': 'zzzzz-yyyyy-{:015x}'.format(node_num),
+ 'created_at': '2014-01-01T01:02:03Z',
+ 'modified_at': time.strftime('%Y-%m-%dT%H:%M:%SZ',
+ time.gmtime(time.time() - age)),
+ 'hostname': 'compute{}'.format(node_num),
+ 'domain': 'zzzzz.arvadosapi.com',
+ 'ip_address': ip_address_mock(node_num),
+ 'job_uuid': job_uuid,
+ 'info': {'slurm_state': slurm_state}}
+ node.update(kwargs)
+ return node
+
+def cloud_node_mock(node_num=99):
+ node = mock.NonCallableMagicMock(
+ ['id', 'name', 'state', 'public_ips', 'private_ips', 'driver', 'size',
+ 'image', 'extra'],
+ name='cloud_node')
+ node.id = str(node_num)
+ node.name = node.id
+ node.public_ips = []
+ node.private_ips = [ip_address_mock(node_num)]
+ return node
+
+def ip_address_mock(last_octet):
+ return '10.20.30.{}'.format(last_octet)
+
+class MockShutdownTimer(object):
+ def _set_state(self, is_open, next_opening):
+ self.window_open = lambda: is_open
+ self.next_opening = lambda: next_opening
+
+
+class MockSize(object):
+ def __init__(self, factor):
+ self.id = 'z{}.test'.format(factor)
+ self.name = self.id
+ self.ram = 128 * factor
+ self.disk = 100 * factor
+ self.bandwidth = 16 * factor
+ self.price = float(factor)
+ self.extra = {}
+
+ def __eq__(self, other):
+ return self.id == other.id
+
+
+class MockTimer(object):
+ def __init__(self, deliver_immediately=True):
+ self.deliver_immediately = deliver_immediately
+ self.messages = []
+ self.lock = threading.Lock()
+
+ def deliver(self):
+ with self.lock:
+ to_deliver = self.messages
+ self.messages = []
+ for callback, args, kwargs in to_deliver:
+ callback(*args, **kwargs)
+
+ def schedule(self, want_time, callback, *args, **kwargs):
+ with self.lock:
+ self.messages.append((callback, args, kwargs))
+ if self.deliver_immediately:
+ self.deliver()
+
+
+class ActorTestMixin(object):
+ FUTURE_CLASS = pykka.ThreadingFuture
+ TIMEOUT = pykka_timeout
+
+ def tearDown(self):
+ pykka.ActorRegistry.stop_all()
+
+ def stop_proxy(self, proxy):
+ return proxy.actor_ref.stop(timeout=self.TIMEOUT)
+
+ def wait_for_assignment(self, proxy, attr_name, unassigned=None,
+ timeout=TIMEOUT):
+ deadline = time.time() + timeout
+ while True:
+ loop_timeout = deadline - time.time()
+ if loop_timeout <= 0:
+ self.fail("actor did not assign {} in time".format(attr_name))
+ result = getattr(proxy, attr_name).get(loop_timeout)
+ if result is not unassigned:
+ return result
+
+
+class RemotePollLoopActorTestMixin(ActorTestMixin):
+ def build_monitor(self, *args, **kwargs):
+ self.timer = mock.MagicMock(name='timer_mock')
+ self.client = mock.MagicMock(name='client_mock')
+ self.subscriber = mock.Mock(name='subscriber_mock')
+ self.monitor = self.TEST_CLASS.start(
+ self.client, self.timer, *args, **kwargs).proxy()
projects / arvados.git / commitdiff
