arvados.git
10 years ago2809: Merge branch 'master' refs #2809
Tom Clegg [Fri, 9 May 2014 18:38:39 +0000 (14:38 -0400)]
2809: Merge branch 'master' refs #2809

Conflicts:
apps/workbench/Gemfile.lock
apps/workbench/app/controllers/application_controller.rb
apps/workbench/app/models/arvados_api_client.rb
apps/workbench/app/models/group.rb
apps/workbench/app/models/user.rb
apps/workbench/app/views/layouts/application.html.erb

10 years agoFix whitespace.
Ward Vandewege [Fri, 9 May 2014 13:23:00 +0000 (09:23 -0400)]
Fix whitespace.

10 years agoFix Python SDK test suite issues.
Tom Clegg [Fri, 9 May 2014 08:12:44 +0000 (04:12 -0400)]
Fix Python SDK test suite issues.

10 years agoFix python SDK test suite issues.
Tom Clegg [Fri, 9 May 2014 06:57:27 +0000 (02:57 -0400)]
Fix python SDK test suite issues.

10 years agoFix pipeline instance state tests.
Tom Clegg [Fri, 9 May 2014 02:33:12 +0000 (22:33 -0400)]
Fix pipeline instance state tests.

10 years agoDo not blindly overwrite GOPATH if it exists.
Ward Vandewege [Fri, 9 May 2014 02:05:12 +0000 (22:05 -0400)]
Do not blindly overwrite GOPATH if it exists.

10 years agoMerge branch '2638-add-cache-age-disk-usage-histogram-to-workbench' closes #2638
Misha Zatsman [Fri, 9 May 2014 01:08:46 +0000 (01:08 +0000)]
Merge branch '2638-add-cache-age-disk-usage-histogram-to-workbench' closes #2638

10 years agoFixed stop_keep(). Updated test_mount because the fixture changed (again).
Peter Amstutz [Thu, 8 May 2014 21:10:07 +0000 (17:10 -0400)]
Fixed stop_keep().  Updated test_mount because the fixture changed (again).

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Thu, 8 May 2014 20:54:18 +0000 (16:54 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

10 years ago- Added MANIFEST.in to include setup_header.py in the source package. Now gets
Peter Amstutz [Thu, 8 May 2014 20:52:45 +0000 (16:52 -0400)]
- Added MANIFEST.in to include setup_header.py in the source package.  Now gets
the version number from PKG-INFO metadata if available, or git if not, which
should handle all the cases of using sdist, pip install, or install from git
checkout.
- Improved run_test_server.py and fixed Python SDK tests to use it.

10 years agoTrim newline from logfile hash emerging from `arv keep put`.
Tom Clegg [Thu, 8 May 2014 20:45:47 +0000 (16:45 -0400)]
Trim newline from logfile hash emerging from `arv keep put`.

10 years agoMerge branch '2525-java-sdk'
radhika [Thu, 8 May 2014 20:40:48 +0000 (16:40 -0400)]
Merge branch '2525-java-sdk'

10 years ago2759: Workbench shouldn't try to make links from Link names.
Brett Smith [Thu, 8 May 2014 20:38:46 +0000 (16:38 -0400)]
2759: Workbench shouldn't try to make links from Link names.

Because the name attribute can include arbitrary text, it might
resemble an Arvados object UUID.  If that happens, the
_arvados_attr_value partial will try to make a link from it.  All
sorts of weirdness could happen as a result (our specific bug was a
bad URL fed to Workbench's API client), so don't even try.  Just
render the name directly as editable text.

Closes #2759.

10 years agoMerge branch 'master' of git.curoverse.com:arvados into 2638-add-cache-age-disk-usage...
Misha Zatsman [Thu, 8 May 2014 20:10:04 +0000 (20:10 +0000)]
Merge branch 'master' of git.curoverse.com:arvados into 2638-add-cache-age-disk-usage-histogram-to-workbench

10 years agoAdded some documentation and renamed variables after Tim's review.
Misha Zatsman [Thu, 8 May 2014 20:09:07 +0000 (20:09 +0000)]
Added some documentation and renamed variables after Tim's review.

10 years agoRemove now-superfluous build.sh step from the documentation to build the
Ward Vandewege [Thu, 8 May 2014 19:04:41 +0000 (15:04 -0400)]
Remove now-superfluous build.sh step from the documentation to build the
Python SDK from source.

10 years ago2525: update available params method
radhika [Thu, 8 May 2014 18:25:43 +0000 (14:25 -0400)]
2525: update available params method

10 years ago2525: getAvailableParametersForMethod includes properties from request also.
radhika [Thu, 8 May 2014 18:06:04 +0000 (14:06 -0400)]
2525: getAvailableParametersForMethod includes properties from request also.
This is required for create and update methods which have no other parameters.

10 years agoMerge branch '2352-use-state'
radhika [Thu, 8 May 2014 17:42:50 +0000 (13:42 -0400)]
Merge branch '2352-use-state'

10 years agoMerge branch '2739-fix-100-task-limit-wip'
Brett Smith [Thu, 8 May 2014 17:22:04 +0000 (13:22 -0400)]
Merge branch '2739-fix-100-task-limit-wip'

Closes #2739.

10 years ago2739: Ensure crunch-job spawns all new tasks.
Brett Smith [Thu, 8 May 2014 17:19:27 +0000 (13:19 -0400)]
2739: Ensure crunch-job spawns all new tasks.

Without this fix, crunch-job would only spawn tasks up to the API
server default result limit (currently 100).  Refs #2739.

10 years agoBugfix: Don't crash trying to render a new log buffer.
Brett Smith [Thu, 8 May 2014 17:15:16 +0000 (13:15 -0400)]
Bugfix: Don't crash trying to render a new log buffer.

If you submit a Job and then try to load your Workbench Dashboard,
Workbench will likely crash because the log_buffer is a symbol at that
time.  This check guards to make sure that we only try to render
actual log content.

10 years ago2352: when a running pipeline_instance is stopped in workbench, put it in Paused...
radhika [Thu, 8 May 2014 17:02:55 +0000 (13:02 -0400)]
2352: when a running pipeline_instance is stopped in workbench, put it in Paused state.
Similar behavior as when run with --run-here at command prompt.

10 years agoMerge branch 'master' into 2352-use-state
radhika [Thu, 8 May 2014 14:45:00 +0000 (10:45 -0400)]
Merge branch 'master' into 2352-use-state

10 years ago2352: fix issue with setting active during save
radhika [Thu, 8 May 2014 14:40:53 +0000 (10:40 -0400)]
2352: fix issue with setting active during save

10 years ago2492: Properly escape Docker image name in Crunch.
Brett Smith [Thu, 8 May 2014 13:34:33 +0000 (09:34 -0400)]
2492: Properly escape Docker image name in Crunch.

10 years ago2492: Crunch respects the maximum length of Docker image hashes.
Brett Smith [Thu, 8 May 2014 13:28:23 +0000 (09:28 -0400)]
2492: Crunch respects the maximum length of Docker image hashes.

10 years ago2352: look for only RunningOnServer in queue method in pipeline_instance
radhika [Thu, 8 May 2014 12:23:11 +0000 (08:23 -0400)]
2352: look for only RunningOnServer in queue method in pipeline_instance

10 years ago2352: set active to nil when Ready
radhika [Wed, 7 May 2014 23:54:23 +0000 (19:54 -0400)]
2352: set active to nil when Ready

10 years ago2352: when --submit is used, set the state to Ready, not RunningOnClient.
radhika [Wed, 7 May 2014 23:34:24 +0000 (19:34 -0400)]
2352: when --submit is used, set the state to Ready, not RunningOnClient.
And do not set Active to true.

10 years agoMerge branch 'master' into 2352-use-state
radhika [Wed, 7 May 2014 19:04:40 +0000 (15:04 -0400)]
Merge branch 'master' into 2352-use-state

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Wed, 7 May 2014 16:11:22 +0000 (12:11 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years ago2525: prompt example
radhika [Wed, 7 May 2014 16:10:47 +0000 (12:10 -0400)]
2525: prompt example

10 years ago2525: list resources, methods, and parameters in prompt example to improve user exper...
radhika [Wed, 7 May 2014 16:09:07 +0000 (12:09 -0400)]
2525: list resources, methods, and parameters in prompt example to improve user experience.

10 years ago2525: Expand prompt example to list the available resources and methods. This can...
radhika [Wed, 7 May 2014 15:58:23 +0000 (11:58 -0400)]
2525: Expand prompt example to list the available resources and methods. This can help enhance user experience.

10 years agoMerge branch 'origin-2035-arv-mount-tags-folders'
Peter Amstutz [Wed, 7 May 2014 15:53:13 +0000 (11:53 -0400)]
Merge branch 'origin-2035-arv-mount-tags-folders'

Conflicts:
sdk/python/bin/arv-mount

10 years agoMerge branch '2035-arv-mount-tags-folders' into origin-2035-arv-mount-tags-folders
Peter Amstutz [Wed, 7 May 2014 15:39:55 +0000 (11:39 -0400)]
Merge branch '2035-arv-mount-tags-folders' into origin-2035-arv-mount-tags-folders

10 years agoMerge branch '2492-docker-crunch-jobs'
Brett Smith [Wed, 7 May 2014 15:32:18 +0000 (11:32 -0400)]
Merge branch '2492-docker-crunch-jobs'

Closes #2492.

10 years agocrunch: Install Docker images on demand.
Brett Smith [Wed, 7 May 2014 15:28:16 +0000 (11:28 -0400)]
crunch: Install Docker images on demand.

Ward requested this to simplify the installation and testing
procedure.  This is sort of temporary scaffolding; we expect that in
the future Docker images will be stored in, and read from, Keep.

10 years agocrunch-job: Support runtime Docker image.
Brett Smith [Wed, 7 May 2014 15:24:21 +0000 (11:24 -0400)]
crunch-job: Support runtime Docker image.

This adds support for the allow_other mount option in arv-mount to
make the Keep mount available to the container.

10 years agodocker: Build base container for Crunch jobs.
Brett Smith [Fri, 4 Apr 2014 16:00:57 +0000 (12:00 -0400)]
docker: Build base container for Crunch jobs.

10 years ago2525: refactor response printing
radhika [Wed, 7 May 2014 15:23:01 +0000 (11:23 -0400)]
2525: refactor response printing

10 years agoMerge branch '2744-update-dev-docs'
Tom Clegg [Wed, 7 May 2014 15:15:37 +0000 (11:15 -0400)]
Merge branch '2744-update-dev-docs'

closes #2744

10 years ago2525: update java sdk documentation to include ArvadosSDKJavaExampleWithPrompt
radhika [Wed, 7 May 2014 15:07:42 +0000 (11:07 -0400)]
2525: update java sdk documentation to include ArvadosSDKJavaExampleWithPrompt

10 years agoImprove tests: multiple values for "not in", check =, != results more carefully.
Tom Clegg [Wed, 7 May 2014 15:05:22 +0000 (11:05 -0400)]
Improve tests: multiple values for "not in", check =, != results more carefully.

10 years agoMerge branch 'master' into origin-2035-arv-mount-tags-folders
Peter Amstutz [Wed, 7 May 2014 15:05:21 +0000 (11:05 -0400)]
Merge branch 'master' into origin-2035-arv-mount-tags-folders

10 years ago2525: more testing. also "=" works in place of "is_a" for a filter.
radhika [Wed, 7 May 2014 14:55:03 +0000 (10:55 -0400)]
2525: more testing. also "=" works in place of "is_a" for a filter.

10 years agoEliminated build.sh and sed in favor of a common setup_header.py script which
Peter Amstutz [Wed, 7 May 2014 14:32:54 +0000 (10:32 -0400)]
Eliminated build.sh and sed in favor of a common setup_header.py script which
call popen to get the git revision directly.  Removed spurious server_pid > 0
and added except Execption: on run_test_server.py.

10 years ago2525: example param parsing
radhika [Wed, 7 May 2014 12:22:55 +0000 (08:22 -0400)]
2525: example param parsing

10 years ago2525: example
radhika [Wed, 7 May 2014 12:03:40 +0000 (08:03 -0400)]
2525: example

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Wed, 7 May 2014 10:49:07 +0000 (06:49 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years ago2525: improve response printing in the examples for readability.
radhika [Wed, 7 May 2014 10:47:47 +0000 (06:47 -0400)]
2525: improve response printing in the examples for readability.

10 years agoMerge branch 'master' of git.curoverse.com:arvados into 2638-add-cache-age-disk-usage...
Misha Zatsman [Wed, 7 May 2014 06:15:18 +0000 (06:15 +0000)]
Merge branch 'master' of git.curoverse.com:arvados into 2638-add-cache-age-disk-usage-histogram-to-workbench

10 years agoClarify log methods page: say "log entry" instead of "log".
Tom Clegg [Wed, 7 May 2014 04:16:30 +0000 (00:16 -0400)]
Clarify log methods page: say "log entry" instead of "log".

10 years agoDocument "filters" feature. Add missing "!=" and "not in" operators.
Tom Clegg [Wed, 7 May 2014 04:12:12 +0000 (00:12 -0400)]
Document "filters" feature. Add missing "!=" and "not in" operators.

10 years agoRefuse to run rake tasks without "bundle exec".
Tom Clegg [Wed, 7 May 2014 03:15:40 +0000 (23:15 -0400)]
Refuse to run rake tasks without "bundle exec".

Otherwise you can accidentally load (or dump) schemas without having
the pg_power gem loaded, which will leave you with incorrect indexes
in your database (or schema.rb).

10 years ago2525: Add ArvadosSDKJavaExampleWithPrompt.java to serve as an easier tool to make...
radhika [Wed, 7 May 2014 02:59:11 +0000 (22:59 -0400)]
2525: Add ArvadosSDKJavaExampleWithPrompt.java to serve as an easier tool to make quick calls to API server.

10 years agoAvoided printing graph if no data. Added date histogram was generated.
Misha Zatsman [Wed, 7 May 2014 02:48:40 +0000 (02:48 +0000)]
Avoided printing graph if no data. Added date histogram was generated.

10 years agoAdded cache age histogram!
Misha Zatsman [Wed, 7 May 2014 02:33:06 +0000 (02:33 +0000)]
Added cache age histogram!

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Wed, 7 May 2014 01:47:04 +0000 (21:47 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years agoFix crash creating new user during initial login. Add test.
Tom Clegg [Wed, 7 May 2014 01:46:04 +0000 (21:46 -0400)]
Fix crash creating new user during initial login. Add test.

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Wed, 7 May 2014 01:34:04 +0000 (21:34 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years ago2525: Address review feedback.
radhika [Wed, 7 May 2014 01:33:26 +0000 (21:33 -0400)]
2525: Address review feedback.

10 years agoFix up workbench and apiserver install docs.
Tom Clegg [Tue, 6 May 2014 23:40:27 +0000 (19:40 -0400)]
Fix up workbench and apiserver install docs.

10 years agoFix prompt paths.
Tom Clegg [Tue, 6 May 2014 23:40:19 +0000 (19:40 -0400)]
Fix prompt paths.

10 years agoAdded printing of histogram json.
Misha Zatsman [Tue, 6 May 2014 23:30:26 +0000 (23:30 +0000)]
Added printing of histogram json.

10 years agoClean up install docs
Tom Clegg [Tue, 6 May 2014 22:42:41 +0000 (18:42 -0400)]
Clean up install docs

10 years agoAdd wait_for_ajax after using x-editable in tests.
Tom Clegg [Tue, 6 May 2014 22:27:01 +0000 (18:27 -0400)]
Add wait_for_ajax after using x-editable in tests.

10 years agoFix Perl and Python SDK instructions on crunch install page
Tom Clegg [Tue, 6 May 2014 21:38:38 +0000 (17:38 -0400)]
Fix Perl and Python SDK instructions on crunch install page

10 years agoMerge branch 'master' into 2744-update-dev-docs
Tom Clegg [Tue, 6 May 2014 21:32:35 +0000 (17:32 -0400)]
Merge branch 'master' into 2744-update-dev-docs

10 years agoFix dead links
Tom Clegg [Tue, 6 May 2014 21:28:12 +0000 (17:28 -0400)]
Fix dead links

10 years agoAdded div for histogram and style for it.
Misha Zatsman [Tue, 6 May 2014 21:13:07 +0000 (21:13 +0000)]
Added div for histogram and style for it.

10 years agoMerge branch '2733-coverage-report'
Tom Clegg [Tue, 6 May 2014 20:54:12 +0000 (16:54 -0400)]
Merge branch '2733-coverage-report'

closes #2733

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Tue, 6 May 2014 20:30:39 +0000 (16:30 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years agoSynchronize repository and crunch setup instructions with current behavior.
Tom Clegg [Tue, 6 May 2014 20:17:58 +0000 (16:17 -0400)]
Synchronize repository and crunch setup instructions with current behavior.

10 years agoFix copy/paste error in gem build instructions.
Tom Clegg [Tue, 6 May 2014 19:53:10 +0000 (15:53 -0400)]
Fix copy/paste error in gem build instructions.

10 years agoRemove Gemfile.lock from repo
Tom Clegg [Tue, 6 May 2014 19:52:10 +0000 (15:52 -0400)]
Remove Gemfile.lock from repo

see http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/

10 years agoRemove stray debug puts.
Tom Clegg [Tue, 6 May 2014 17:10:05 +0000 (13:10 -0400)]
Remove stray debug puts.

10 years agoMerge branch '1970-folder-view'
Tom Clegg [Tue, 6 May 2014 17:01:44 +0000 (13:01 -0400)]
Merge branch '1970-folder-view'

closes #1970

10 years agoMerge branch 'master' into 1970-folder-view
Tom Clegg [Tue, 6 May 2014 17:01:34 +0000 (13:01 -0400)]
Merge branch 'master' into 1970-folder-view

10 years agoAdd find?() method so "assert find?(...), msg" can be used in test cases.
Tom Clegg [Tue, 6 May 2014 16:58:14 +0000 (12:58 -0400)]
Add find?() method so "assert find?(...), msg" can be used in test cases.

10 years agoReplace unfailable assert() with a comment explaining what it means
Tom Clegg [Tue, 6 May 2014 16:37:29 +0000 (12:37 -0400)]
Replace unfailable assert() with a comment explaining what it means
for find() to raise an exception.

10 years ago2525: correct indentation for pom.xml
radhika [Tue, 6 May 2014 16:28:17 +0000 (12:28 -0400)]
2525: correct indentation for pom.xml

10 years ago2525: use -Dmaven.test.skip=true when packaging the SDK.
radhika [Tue, 6 May 2014 16:08:40 +0000 (12:08 -0400)]
2525: use -Dmaven.test.skip=true when packaging the SDK.

10 years agoAdded test for group mount. Passes.
Peter Amstutz [Tue, 6 May 2014 15:43:31 +0000 (11:43 -0400)]
Added test for group mount.  Passes.

10 years agoImproved fresh/stale handling with base class, added property fuse inode cache
Peter Amstutz [Tue, 6 May 2014 15:25:34 +0000 (11:25 -0400)]
Improved fresh/stale handling with base class, added property fuse inode cache
invalidation.  Added common merge function for handling directory updates.
arv-mount now daemonizes by default.

10 years agoMerge branch 'master' into 2525-java-sdk
radhika [Tue, 6 May 2014 14:54:54 +0000 (10:54 -0400)]
Merge branch 'master' into 2525-java-sdk

10 years ago2352: initial tests for arv-run-pipeline-instance
radhika [Tue, 6 May 2014 14:47:06 +0000 (10:47 -0400)]
2352: initial tests for arv-run-pipeline-instance

10 years agoMerge branch 'master' into 2352-use-state
radhika [Tue, 6 May 2014 13:57:07 +0000 (09:57 -0400)]
Merge branch 'master' into 2352-use-state

10 years agoAdding support for groups and viewing arvados objects as files (serialized
Peter Amstutz [Tue, 6 May 2014 02:42:55 +0000 (22:42 -0400)]
Adding support for groups and viewing arvados objects as files (serialized
json).  Work in progress.

10 years agoMerge branch 'master' into origin-2035-arv-mount-tags-folders
Peter Amstutz [Tue, 6 May 2014 01:25:20 +0000 (21:25 -0400)]
Merge branch 'master' into origin-2035-arv-mount-tags-folders

10 years agoFix so that a present but empty select parameter in queries no longer yields
Peter Amstutz [Tue, 6 May 2014 01:24:45 +0000 (21:24 -0400)]
Fix so that a present but empty select parameter in queries no longer yields
an error.

10 years agoAdded PyYAML to requirements.txt
Peter Amstutz [Tue, 6 May 2014 01:15:47 +0000 (21:15 -0400)]
Added PyYAML to requirements.txt

10 years agoMerge branch 'master' into origin-2035-arv-mount-tags-folders
Peter Amstutz [Tue, 6 May 2014 00:41:45 +0000 (20:41 -0400)]
Merge branch 'master' into origin-2035-arv-mount-tags-folders

10 years agoRemove duplicate ERROR_ACTIONS constant from merge.
Tom Clegg [Tue, 6 May 2014 00:31:45 +0000 (20:31 -0400)]
Remove duplicate ERROR_ACTIONS constant from merge.

10 years agoEnsure edited description really gets saved.
Tom Clegg [Tue, 6 May 2014 00:31:18 +0000 (20:31 -0400)]
Ensure edited description really gets saved.

10 years agoUse send(symbol) instead of send(string).
Tom Clegg [Tue, 6 May 2014 00:22:38 +0000 (20:22 -0400)]
Use send(symbol) instead of send(string).

10 years agoChange icon for virtual machines nav.
Tom Clegg [Tue, 6 May 2014 00:21:08 +0000 (20:21 -0400)]
Change icon for virtual machines nav.

10 years agoRemove confusing return value.
Tom Clegg [Tue, 6 May 2014 00:20:46 +0000 (20:20 -0400)]
Remove confusing return value.

10 years agoMerge branch '2640-folder-api' into 1970-folder-view
Tom Clegg [Mon, 5 May 2014 22:33:04 +0000 (18:33 -0400)]
Merge branch '2640-folder-api' into 1970-folder-view

Conflicts:
apps/workbench/app/controllers/application_controller.rb
services/api/app/controllers/application_controller.rb