arvados.git
10 years agoRefresh dashboard with AJAX every 60 seconds.
Tom Clegg [Mon, 3 Feb 2014 08:45:11 +0000 (00:45 -0800)]
Refresh dashboard with AJAX every 60 seconds.

refs #1976
closes #2004

10 years agoUse AJAX/remote requests when deleting objects. Add delete button to
Tom Clegg [Mon, 3 Feb 2014 08:21:52 +0000 (00:21 -0800)]
Use AJAX/remote requests when deleting objects. Add delete button to
pipeline_instances index.

refs #1976

10 years agoImprove progress view on pipeline_instances.show page and add AJAX
Tom Clegg [Mon, 3 Feb 2014 08:07:24 +0000 (00:07 -0800)]
Improve progress view on pipeline_instances.show page and add AJAX
auto-refresh.

refs #1976
refs #2004

10 years agoAdd arv-mount.
Tom Clegg [Mon, 3 Feb 2014 01:49:24 +0000 (17:49 -0800)]
Add arv-mount.

10 years agoAdd StreamFileReader.seek() method.
Tom Clegg [Mon, 3 Feb 2014 01:27:26 +0000 (17:27 -0800)]
Add StreamFileReader.seek() method.

10 years agoFix scoping for error classes.
Tom Clegg [Mon, 3 Feb 2014 01:26:59 +0000 (17:26 -0800)]
Fix scoping for error classes.

10 years agoFix crash when component has missing attributes (e.g., no job was run).
Tom Clegg [Sun, 2 Feb 2014 00:06:33 +0000 (16:06 -0800)]
Fix crash when component has missing attributes (e.g., no job was run).

refs #1978

10 years agoAdd basic select-and-compare interface to pipeline_instances#index.
Tom Clegg [Sun, 2 Feb 2014 00:05:55 +0000 (16:05 -0800)]
Add basic select-and-compare interface to pipeline_instances#index.

refs #1978

10 years agoMerge branch 'master' into 1978-compare-pipelines
Tom Clegg [Sat, 1 Feb 2014 23:34:44 +0000 (15:34 -0800)]
Merge branch 'master' into 1978-compare-pipelines

Conflicts:
apps/workbench/app/controllers/pipeline_instances_controller.rb
apps/workbench/app/views/pipeline_instances/compare.html.erb

10 years agoRemove extra breadcrumbs bar.
Tom Clegg [Sat, 1 Feb 2014 23:17:10 +0000 (15:17 -0800)]
Remove extra breadcrumbs bar.

10 years agoAllow controller to override page name for breadcrumbs.
Tom Clegg [Sat, 1 Feb 2014 23:16:52 +0000 (15:16 -0800)]
Allow controller to override page name for breadcrumbs.

10 years agoAdd breadcrumbs bar to #index and #show pages.
Tom Clegg [Fri, 31 Jan 2014 21:59:33 +0000 (13:59 -0800)]
Add breadcrumbs bar to #index and #show pages.

10 years agoUse generic index page for /users
Tom Clegg [Fri, 31 Jan 2014 21:32:39 +0000 (13:32 -0800)]
Use generic index page for /users

10 years agoShow condensed data about pipeline instances side by side on "compare"
Tom Clegg [Wed, 29 Jan 2014 02:15:43 +0000 (18:15 -0800)]
Show condensed data about pipeline instances side by side on "compare"
page.

refs #1978

10 years agoAdd pipeline_instances/compare page
Tom Clegg [Tue, 28 Jan 2014 15:57:47 +0000 (07:57 -0800)]
Add pipeline_instances/compare page

10 years agoFix "show all pipeline templates" link target on dashboard page.
Tom Clegg [Fri, 31 Jan 2014 20:50:35 +0000 (12:50 -0800)]
Fix "show all pipeline templates" link target on dashboard page.

10 years agoFix some arv unit tests.
Tim Pierce [Fri, 31 Jan 2014 22:59:04 +0000 (17:59 -0500)]
Fix some arv unit tests.

10 years agoMerge branch '2036-fix-python-sdk' of git.clinicalfuture.com:arvados into 2036-fix...
Tim Pierce [Thu, 30 Jan 2014 20:42:13 +0000 (15:42 -0500)]
Merge branch '2036-fix-python-sdk' of git.clinicalfuture.com:arvados into 2036-fix-python-sdk

Conflicts:
sdk/python/arvados/__init__.py
sdk/python/arvados/api.py
sdk/python/arvados/collection.py
sdk/python/arvados/keep.py

10 years agoResolving scoping problems. Python unit tests now pass. (fixes #2036)
Tim Pierce [Thu, 30 Jan 2014 20:37:39 +0000 (15:37 -0500)]
Resolving scoping problems. Python unit tests now pass. (fixes #2036)

10 years agoRearranging modules to eliminate recursive imports.
Tim Pierce [Wed, 29 Jan 2014 23:07:22 +0000 (18:07 -0500)]
Rearranging modules to eliminate recursive imports.

10 years agoRearranging modules to eliminate recursive imports.
Tim Pierce [Wed, 29 Jan 2014 23:07:22 +0000 (18:07 -0500)]
Rearranging modules to eliminate recursive imports.

10 years agoAdd functional test for "skip script_version validation when not
Tom Clegg [Wed, 29 Jan 2014 20:08:54 +0000 (12:08 -0800)]
Add functional test for "skip script_version validation when not
changing that attribute".

10 years agoSkip "specified commit exists" validation when updating an existing
Tom Clegg [Wed, 29 Jan 2014 19:52:59 +0000 (11:52 -0800)]
Skip "specified commit exists" validation when updating an existing
job without modifying script_version.

10 years agoFix jobs.cancelled_by_*_changed? calls to jobs.cancelled_by_*_uuid_changed?
Tom Clegg [Wed, 29 Jan 2014 19:37:32 +0000 (11:37 -0800)]
Fix jobs.cancelled_by_*_changed? calls to jobs.cancelled_by_*_uuid_changed?

Missed in 64f3cccd176b214b2e9a571c54973c4e546c606a

10 years agoRemove +K@foo parts from collection uuids in jobs' script_parameters
Tom Clegg [Wed, 29 Jan 2014 19:04:12 +0000 (11:04 -0800)]
Remove +K@foo parts from collection uuids in jobs' script_parameters
and other job fields cached in PipelineInstances.

refs #1881

10 years agoFix regular expressions in database migration.
Tom Clegg [Wed, 29 Jan 2014 18:41:19 +0000 (10:41 -0800)]
Fix regular expressions in database migration.

refs #1881

10 years agoShow condensed data about pipeline instances side by side on "compare"
Tom Clegg [Wed, 29 Jan 2014 02:15:43 +0000 (18:15 -0800)]
Show condensed data about pipeline instances side by side on "compare"
page.

refs #1978

10 years agoPython SDK uses ~/.config/arvados/settings.conf like other SDKs.
Tim Pierce [Tue, 28 Jan 2014 22:31:39 +0000 (17:31 -0500)]
Python SDK uses ~/.config/arvados/settings.conf like other SDKs.

Also: Update ~/.config/arvados/settings.conf when docker images are restarted.

10 years agoUpdating dependencies.
Tim Pierce [Tue, 28 Jan 2014 21:11:38 +0000 (16:11 -0500)]
Updating dependencies.

10 years agoUpdating dependencies to satisfy RubyGems.
Tim Pierce [Tue, 28 Jan 2014 21:05:01 +0000 (16:05 -0500)]
Updating dependencies to satisfy RubyGems.

10 years agoClean up /arvados/v1/../../discovery/v1/ hack before sending request
Tom Clegg [Tue, 28 Jan 2014 16:04:48 +0000 (08:04 -0800)]
Clean up /arvados/v1/../../discovery/v1/ hack before sending request
to server.

10 years agoAdd pipeline_instances/compare page
Tom Clegg [Tue, 28 Jan 2014 15:57:47 +0000 (07:57 -0800)]
Add pipeline_instances/compare page

10 years agoLeft navbar uses bootstrap "nav-header" class for section headers.
Peter Amstutz [Mon, 27 Jan 2014 21:44:44 +0000 (16:44 -0500)]
Left navbar uses bootstrap "nav-header" class for section headers.

10 years agoMerge branch '1946-request-body-vs-parameters'
Tom Clegg [Mon, 27 Jan 2014 21:17:55 +0000 (13:17 -0800)]
Merge branch '1946-request-body-vs-parameters'

closes #1946

10 years agoRemove request body object from parameters lists in *.create and
Tom Clegg [Mon, 27 Jan 2014 20:43:50 +0000 (12:43 -0800)]
Remove request body object from parameters lists in *.create and
*.update -- mark it required in the request body instead.

refs #1946

10 years agoAdd version string to arv (assume "gem install" makes the version
Tom Clegg [Mon, 27 Jan 2014 20:31:59 +0000 (12:31 -0800)]
Add version string to arv (assume "gem install" makes the version
apparent in the executable path).

10 years agoDo not add body object to discovery parameters.
Tom Clegg [Mon, 27 Jan 2014 20:11:08 +0000 (12:11 -0800)]
Do not add body object to discovery parameters.

10 years agoFix up dependencies, pin google-api-client at 0.6.x
Tom Clegg [Mon, 27 Jan 2014 20:10:34 +0000 (12:10 -0800)]
Fix up dependencies, pin google-api-client at 0.6.x

10 years agoAdd Gemfile.lock
Tom Clegg [Mon, 27 Jan 2014 19:25:19 +0000 (11:25 -0800)]
Add Gemfile.lock

10 years agoSend parameters in the request body instead of query parameters if
Tom Clegg [Mon, 27 Jan 2014 19:23:07 +0000 (11:23 -0800)]
Send parameters in the request body instead of query parameters if
discovery document specifies request.properties.(key).$ref.

refs #1946

10 years agoAdd tests, fix dependencies so "bundle exec rake test" runs.
Tom Clegg [Mon, 27 Jan 2014 19:17:27 +0000 (11:17 -0800)]
Add tests, fix dependencies so "bundle exec rake test" runs.

10 years agoFix crash when no config file exists, and fix config access from Model
Tom Clegg [Mon, 27 Jan 2014 17:39:47 +0000 (09:39 -0800)]
Fix crash when no config file exists, and fix config access from Model
class.

refs #1943

10 years agoRemove Keep prototype (moved to branch 1747-keep-prototype-ruby).
Tom Clegg [Mon, 27 Jan 2014 15:58:00 +0000 (07:58 -0800)]
Remove Keep prototype (moved to branch 1747-keep-prototype-ruby).

refs #1747

10 years agoDo not offer to let non-admin users create new keepDisks and nodes.
Tom Clegg [Sat, 25 Jan 2014 06:43:36 +0000 (22:43 -0800)]
Do not offer to let non-admin users create new keepDisks and nodes.

10 years agoChange underscores to camelcase in "kind" strings as documented.
Tom Clegg [Sat, 25 Jan 2014 06:41:29 +0000 (22:41 -0800)]
Change underscores to camelcase in "kind" strings as documented.

10 years agoAdd virtualMachine test fixture.
Tom Clegg [Sat, 25 Jan 2014 06:40:37 +0000 (22:40 -0800)]
Add virtualMachine test fixture.

10 years agoReplace Admin menu with System menu (users can see those things too).
Tom Clegg [Sat, 25 Jan 2014 06:38:54 +0000 (22:38 -0800)]
Replace Admin menu with System menu (users can see those things too).

10 years agoAlways use symbol keys for object attribute names and string keys
Tom Clegg [Sat, 25 Jan 2014 06:24:37 +0000 (22:24 -0800)]
Always use symbol keys for object attribute names and string keys
inside serialized hashes, rather than HashWithIndifferentAccess.

This ensures serialized attributes go into the database as plain
hashes with string keys, even when Rails was responsible for
unserializing the data coming from the client.

refs #1944
refs #1987

10 years agoEnsure we always respond with json (except the redirect at the root
Tom Clegg [Sat, 25 Jan 2014 05:42:04 +0000 (21:42 -0800)]
Ensure we always respond with json (except the redirect at the root
URI).

closes #1739

10 years agoDo not run ec2 commands in test mode.
Tom Clegg [Sat, 25 Jan 2014 05:31:29 +0000 (21:31 -0800)]
Do not run ec2 commands in test mode.

10 years agoUpdate tests to match recent permission changes; dry up "404 if no
Tom Clegg [Sat, 25 Jan 2014 05:08:58 +0000 (21:08 -0800)]
Update tests to match recent permission changes; dry up "404 if no
object found" logic; fix status codes in some error responses.

10 years agoUse discovery document to build infix->kind map instead of using a
Tom Clegg [Fri, 24 Jan 2014 22:59:51 +0000 (14:59 -0800)]
Use discovery document to build infix->kind map instead of using a
hard-coded list.

10 years agoProvide UUID prefix used for each schema in discovery document.
Tom Clegg [Fri, 24 Jan 2014 22:59:07 +0000 (14:59 -0800)]
Provide UUID prefix used for each schema in discovery document.

10 years agoFix crash on error pages by removing before_filters that assume there
Tom Clegg [Fri, 24 Jan 2014 22:57:21 +0000 (14:57 -0800)]
Fix crash on error pages by removing before_filters that assume there
is a current_user.

10 years agoChange underscores to camelcase in "kind" strings as documented.
Tom Clegg [Fri, 24 Jan 2014 22:54:38 +0000 (14:54 -0800)]
Change underscores to camelcase in "kind" strings as documented.

10 years agoAdd /keep_disks page to Admin menu.
Tom Clegg [Fri, 24 Jan 2014 18:17:21 +0000 (10:17 -0800)]
Add /keep_disks page to Admin menu.

10 years agoFix keep_disks.ping to accept a correct ping_secret in lieu of a
Tom Clegg [Fri, 24 Jan 2014 16:45:36 +0000 (08:45 -0800)]
Fix keep_disks.ping to accept a correct ping_secret in lieu of a
sufficiently authorized token.

10 years agoUpdate schema migration version.
Tom Clegg [Fri, 24 Jan 2014 16:45:17 +0000 (08:45 -0800)]
Update schema migration version.

10 years agoAlways accept properties and info as serialized attributes.
Tom Clegg [Fri, 24 Jan 2014 16:36:00 +0000 (08:36 -0800)]
Always accept properties and info as serialized attributes.

refs #1944
refs #1987

10 years agoAlways use string keys instead of symbol keys for serialized attributes.
Tom Clegg [Fri, 24 Jan 2014 16:35:08 +0000 (08:35 -0800)]
Always use string keys instead of symbol keys for serialized attributes.

refs #1944
refs #1987

10 years agoTweaked running external program tutorial to make it more explicit that md5sum is...
Peter Amstutz [Fri, 24 Jan 2014 16:00:34 +0000 (11:00 -0500)]
Tweaked running external program tutorial to make it more explicit that md5sum is the external program used in the example.

10 years agoGemfile now just points to gemspec so same dependency information is not listed twice.
Peter Amstutz [Thu, 23 Jan 2014 20:37:21 +0000 (15:37 -0500)]
Gemfile now just points to gemspec so same dependency information is not listed twice.

10 years agoAdded doc/_site to gitignore
Peter Amstutz [Thu, 23 Jan 2014 20:36:57 +0000 (15:36 -0500)]
Added doc/_site to gitignore

10 years agoAll git access should happen via git@ urls, not git://
Ward Vandewege [Thu, 23 Jan 2014 16:34:42 +0000 (11:34 -0500)]
All git access should happen via git@ urls, not git://

10 years agoCache the API discovery doc for at least 24 hours (refs #1923)
Tim Pierce [Wed, 22 Jan 2014 00:19:49 +0000 (19:19 -0500)]
Cache the API discovery doc for at least 24 hours (refs #1923)

10 years agoadd list-inactive-users.rb script.
Tom Clegg [Tue, 21 Jan 2014 22:30:07 +0000 (14:30 -0800)]
add list-inactive-users.rb script.

closes #1817

10 years agoMerge branch '1943-client-sdk-config-files'
Tim Pierce [Tue, 21 Jan 2014 22:14:40 +0000 (17:14 -0500)]
Merge branch '1943-client-sdk-config-files'

Conflicts:
sdk/python/arvados/__init__.py

10 years agoClients use $HOME/.config/arvados/settings.conf for configuration. (fixes #1943)
Tim Pierce [Tue, 21 Jan 2014 22:09:00 +0000 (17:09 -0500)]
Clients use $HOME/.config/arvados/settings.conf for configuration. (fixes #1943)

10 years agoMerge branch '1881-normalize-collection-uuids'
Tom Clegg [Tue, 21 Jan 2014 22:07:39 +0000 (14:07 -0800)]
Merge branch '1881-normalize-collection-uuids'

closes #1881

10 years agoMerge branch '1922-cache-discovery-python'
Tom Clegg [Tue, 21 Jan 2014 22:04:30 +0000 (14:04 -0800)]
Merge branch '1922-cache-discovery-python'

10 years agoMerge branch '1868-tutorial-running-binary-progs'
Peter Amstutz [Tue, 21 Jan 2014 22:04:11 +0000 (17:04 -0500)]
Merge branch '1868-tutorial-running-binary-progs'

10 years agoMerge branch '1911-python-sdk-pydoc'
Peter Amstutz [Tue, 21 Jan 2014 22:03:38 +0000 (17:03 -0500)]
Merge branch '1911-python-sdk-pydoc'

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Tue, 21 Jan 2014 22:03:00 +0000 (17:03 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoFixed import problems due to splitting module into multiple files
Peter Amstutz [Tue, 21 Jan 2014 21:57:53 +0000 (16:57 -0500)]
Fixed import problems due to splitting module into multiple files

10 years agoNew tutorial for running external programs
Peter Amstutz [Tue, 21 Jan 2014 21:38:23 +0000 (16:38 -0500)]
New tutorial for running external programs

10 years agoRemoved "Tutorial:" from titles since that was an artifact from before we had improve...
Peter Amstutz [Tue, 21 Jan 2014 21:35:37 +0000 (16:35 -0500)]
Removed "Tutorial:" from titles since that was an artifact from before we had improved the navbar.  Also fixed typo in tutorial-trait-search.

10 years agocollection.py import stream
Peter Amstutz [Tue, 21 Jan 2014 20:29:25 +0000 (15:29 -0500)]
collection.py import stream

10 years agoUpdating API parameter documentation (refs #1901)
Tim Pierce [Tue, 21 Jan 2014 20:28:19 +0000 (15:28 -0500)]
Updating API parameter documentation (refs #1901)

Removed unused parameters.
More docs for the "list" command.
Use only the first line of the parameter documentation in "arv resource help".

10 years agoStarted tutorial on running external programs
Peter Amstutz [Tue, 21 Jan 2014 19:19:37 +0000 (14:19 -0500)]
Started tutorial on running external programs

10 years agoFixed path to glyphicons
Peter Amstutz [Tue, 21 Jan 2014 19:15:08 +0000 (14:15 -0500)]
Fixed path to glyphicons

10 years agoMoved Python SDK and crunch utility scripts pages to SDK Reference section.
Peter Amstutz [Tue, 21 Jan 2014 19:06:35 +0000 (14:06 -0500)]
Moved Python SDK and crunch utility scripts pages to SDK Reference section.

10 years agoFix circumventing usual permission mechanism in nodes.ping.
Tom Clegg [Tue, 21 Jan 2014 18:53:02 +0000 (10:53 -0800)]
Fix circumventing usual permission mechanism in nodes.ping.

10 years agoAdd section about adding Keep disks during install.
Tom Clegg [Tue, 21 Jan 2014 18:19:20 +0000 (10:19 -0800)]
Add section about adding Keep disks during install.

10 years agoUpdate bundle. Avoid google-api-client 0.7.0 (rc2 is incompatible) and
Tom Clegg [Tue, 21 Jan 2014 17:01:31 +0000 (09:01 -0800)]
Update bundle. Avoid google-api-client 0.7.0 (rc2 is incompatible) and
ensure minitest >= 5.0.

10 years agoAdd link to "create standard objects", and delete obsolete tutorial
Tom Clegg [Tue, 21 Jan 2014 16:58:00 +0000 (08:58 -0800)]
Add link to "create standard objects", and delete obsolete tutorial
instructions.

10 years agoScript to build python documentation (requires epydoc)
Peter Amstutz [Tue, 21 Jan 2014 16:51:34 +0000 (11:51 -0500)]
Script to build python documentation (requires epydoc)

10 years agoAdded Python SDK section to documentation
Peter Amstutz [Tue, 21 Jan 2014 16:45:40 +0000 (11:45 -0500)]
Added Python SDK section to documentation

10 years agoFix error message when the all-users group can not be found.
Ward Vandewege [Tue, 21 Jan 2014 16:36:46 +0000 (11:36 -0500)]
Fix error message when the all-users group can not be found.

10 years agoRenamed Keep/Stream/Collection submodules to keep/stream/collection (lower case)
Peter Amstutz [Tue, 21 Jan 2014 15:15:48 +0000 (10:15 -0500)]
Renamed Keep/Stream/Collection submodules to keep/stream/collection (lower case)

10 years agoMoving Collection, Stream and Keep classes into their own files
Peter Amstutz [Tue, 21 Jan 2014 14:06:00 +0000 (09:06 -0500)]
Moving Collection, Stream and Keep classes into their own files

10 years agoRender token with ApplicationController#show instead of calling
Tom Clegg [Mon, 20 Jan 2014 18:16:55 +0000 (10:16 -0800)]
Render token with ApplicationController#show instead of calling
as_api_response directly from
api_client_authorizations.create_system_auth.

Resolves:

Error: #<ActsAsApi::TemplateNotFoundError: acts_as_api template
:superuser was not found for model ApiClientAuthorization>

10 years agoCache discovery document in ~/.cache/arvados/discovery/.
Tom Clegg [Mon, 20 Jan 2014 15:41:39 +0000 (07:41 -0800)]
Cache discovery document in ~/.cache/arvados/discovery/.

refs #1922

10 years agoSet cache expiry time on discovery document.
Tom Clegg [Mon, 20 Jan 2014 15:41:12 +0000 (07:41 -0800)]
Set cache expiry time on discovery document.

refs #1922

10 years agoRemove +K@{name} hints from collection uuid, link head/tail, job
Tom Clegg [Mon, 20 Jan 2014 07:55:55 +0000 (23:55 -0800)]
Remove +K@{name} hints from collection uuid, link head/tail, job
output/log, and job_task output.

refs #1881

10 years agoNormalize collection UUID to {hash}+{size} before save and lookup.
Tom Clegg [Mon, 20 Jan 2014 07:34:20 +0000 (23:34 -0800)]
Normalize collection UUID to {hash}+{size} before save and lookup.

refs #1881

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Tim Pierce [Fri, 17 Jan 2014 22:35:34 +0000 (17:35 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoUpdated `arv' command line format options. Default now generates JSON. (refs #1889)
Tim Pierce [Fri, 17 Jan 2014 22:33:00 +0000 (17:33 -0500)]
Updated `arv' command line format options. Default now generates JSON. (refs #1889)

Replaced --pretty, --json, --uuid, --yaml, --human with
--format={json,uuid,yaml}, and added --short for --format=uuid.

Default output format is now JSON (pretty-printed).

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Fri, 17 Jan 2014 21:58:41 +0000 (16:58 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoChanged upload path in scp command to load to /scratch/you instead of just /scratch...
Peter Amstutz [Fri, 17 Jan 2014 21:58:07 +0000 (16:58 -0500)]
Changed upload path in scp command to load to /scratch/you instead of just /scratch, tweaked markup to try and emphasize that "you" that should be replaced by your own username.

10 years agoMerge branch '1880-check-duplicate-public-key'
Tom Clegg [Fri, 17 Jan 2014 21:50:19 +0000 (13:50 -0800)]
Merge branch '1880-check-duplicate-public-key'

closes #1880