Tom Clegg [Tue, 22 Apr 2014 16:09:00 +0000 (12:09 -0400)]
Add two missing sudo.
Tim Pierce [Tue, 22 Apr 2014 15:20:02 +0000 (11:20 -0400)]
Bug fix: GetBlock must report a CorruptError immediately.
Refs #2620.
Peter Amstutz [Tue, 22 Apr 2014 13:47:38 +0000 (09:47 -0400)]
Moved application-specific code out from rack_socket to lib/eventbus.rb
radhika chippada [Tue, 22 Apr 2014 04:59:53 +0000 (00:59 -0400)]
Set state during save
Tom Clegg [Tue, 22 Apr 2014 04:52:42 +0000 (00:52 -0400)]
Build response objects based on item type rather than list type.
Tom Clegg [Tue, 22 Apr 2014 04:51:56 +0000 (00:51 -0400)]
Add unit test for User#owned_items.
radhika chippada [Tue, 22 Apr 2014 04:20:56 +0000 (00:20 -0400)]
2352: Add state to pipeline_instance. Db migration and unit testing.
Tom Clegg [Tue, 22 Apr 2014 03:55:06 +0000 (23:55 -0400)]
Add docs for owned_items.
Tom Clegg [Tue, 22 Apr 2014 03:50:22 +0000 (23:50 -0400)]
Rename include_managed to include_indirect.
Tom Clegg [Tue, 22 Apr 2014 03:39:20 +0000 (23:39 -0400)]
Support limit and offset params in owned_items.
Tom Clegg [Mon, 21 Apr 2014 21:50:49 +0000 (17:50 -0400)]
Add owned_items action for groups and users.
Peter Amstutz [Mon, 21 Apr 2014 20:53:42 +0000 (16:53 -0400)]
Added code to properly initialize EventMachine to deal with Passenger forking.
Added postgres NOTIFY to ArvadosModel#log_change
Added postgres LISTEN to background thread, which posts a message to the websocket.
Notification works!
Tom Clegg [Mon, 21 Apr 2014 19:46:19 +0000 (15:46 -0400)]
Fill in "I'm in a folder" fixtures
Tom Clegg [Mon, 21 Apr 2014 19:43:34 +0000 (15:43 -0400)]
Improve permission link examples.
Peter Amstutz [Mon, 21 Apr 2014 18:28:33 +0000 (14:28 -0400)]
Proof of concept echo server based on rack middleware that hijacks websocket connections.
Tom Clegg [Mon, 21 Apr 2014 17:46:30 +0000 (13:46 -0400)]
Add some test fixtures that are owned by folders.
Peter Amstutz [Mon, 21 Apr 2014 17:31:39 +0000 (13:31 -0400)]
Websocket event testing page.
Tom Clegg [Mon, 21 Apr 2014 16:15:56 +0000 (12:15 -0400)]
Set :null=>false explicitly on timestamp columns.
New versions of Rails do this automatically, but dev instances keep
having edit wars because some of them have never been told to add the
not-null constraint.
Tom Clegg [Mon, 21 Apr 2014 15:32:35 +0000 (11:32 -0400)]
Remove _kind columns from schema.
(Seemingly reintroduced by accident in
cc5023d40182e503e8ba109fc86e09efd6337836)
Tom Clegg [Mon, 21 Apr 2014 15:16:33 +0000 (11:16 -0400)]
Expose generate_uuid class method, e.g., for making test fixtures.
Tom Clegg [Mon, 21 Apr 2014 15:00:10 +0000 (11:00 -0400)]
Add group_class attribute.
Tom Clegg [Sun, 20 Apr 2014 03:14:24 +0000 (23:14 -0400)]
Tom Clegg [Sun, 20 Apr 2014 02:50:54 +0000 (22:50 -0400)]
Permit a job to update its output and log attributes even if those
collections have not yet been registered with apiserver.
Tom Clegg [Sat, 19 Apr 2014 17:57:47 +0000 (13:57 -0400)]
Hide refresh button on "show pipeline instance" page.
Tom Clegg [Sat, 19 Apr 2014 06:39:11 +0000 (02:39 -0400)]
Fix configuration behavior in Ruby SDK.
API_VERSION is not configuration: it indicates how a client program
expects the API server to behave. (No environment variable or config
file should try to override that.)
Do not invoke insecure behavior unless API_HOST_INSECURE is "1",
"true", or "yes".
If API_HOST and API_TOKEN environment variables are set, do not bother
reading the configuration file at all.
Strip spaces so "API_TOKEN = foo" works in the configuration file.
Tom Clegg [Sat, 19 Apr 2014 03:46:21 +0000 (23:46 -0400)]
Add dependency info to Workbench install page. Fix "is_trusted" recipe.
Tom Clegg [Sat, 19 Apr 2014 02:36:05 +0000 (22:36 -0400)]
Remove updated_at from API responses.
Tom Clegg [Sat, 19 Apr 2014 02:29:00 +0000 (22:29 -0400)]
Describe logins and get_all_logins methods.
Tom Clegg [Sat, 19 Apr 2014 02:24:51 +0000 (22:24 -0400)]
Fix up job create/cancel descriptions.
Tom Clegg [Sat, 19 Apr 2014 02:18:32 +0000 (22:18 -0400)]
Clean up API schema and method pages.
Fill in missing object descriptions.
Remove redundant updated_at attributes.
Move methods sections from schema pages to method pages.
Remove some unnecessary empty sections.
Remove obsolete Commit and CommitAncestor.
Tom Clegg [Sat, 19 Apr 2014 01:23:08 +0000 (21:23 -0400)]
Remove spurious "destroy" methods from API docs.
Tom Clegg [Sat, 19 Apr 2014 01:21:24 +0000 (21:21 -0400)]
Remove spurious "show" methods from API docs.
Tom Clegg [Sat, 19 Apr 2014 01:16:36 +0000 (21:16 -0400)]
Use "filters" instead of "where" in examples and docs. Remove
references to unsupported "q" and "pageToken" parameters.
Tom Clegg [Sat, 19 Apr 2014 01:00:31 +0000 (21:00 -0400)]
Accept minimum_script_version, excluded_script_versions, and
find_or_create flag as parameters to create, instead of treating them
as if they were attributes of the Job resource.
Accept find_or_create as a positive flag, rather than no_reuse as a
negative flag.
Behave as requested by the find_or_create flag even if
nondeterministic=true in the submitted job: i.e., a client can use the
find_or_create feature when submitting a job which itself will never
be reused. (It's up to the client to decide whether this is ever
useful.)
For now, both old and new flag names/locations are accepted and
supplied by API server and arv-run-pipeline-instance respectively.
Tom Clegg [Fri, 18 Apr 2014 23:36:59 +0000 (19:36 -0400)]
Extricate flags controlling jobs.create behavior from the Job resource itself.
Tom Clegg [Fri, 18 Apr 2014 22:27:46 +0000 (18:27 -0400)]
Fix here-doc usage.
Tom Clegg [Fri, 18 Apr 2014 22:27:22 +0000 (18:27 -0400)]
Clean up .gitignore files
Tim Pierce [Fri, 18 Apr 2014 20:54:46 +0000 (16:54 -0400)]
Adding a Volume interface and UnixVolume implementation.
refs #2620
Tim Pierce [Fri, 18 Apr 2014 20:00:59 +0000 (16:00 -0400)]
Reorganize Keep code in preparation for dividing into modules.
Refs #2620
Tom Clegg [Fri, 18 Apr 2014 17:44:11 +0000 (13:44 -0400)]
Add Postgres setup instructions. Fix missing "bundle exec".
Tom Clegg [Fri, 18 Apr 2014 17:08:18 +0000 (13:08 -0400)]
Fix missing --format=uuid, fix obsolete version=repo:commit example.
Tom Clegg [Fri, 18 Apr 2014 16:57:16 +0000 (12:57 -0400)]
Fix up MD5 and Git capitalization/typeface and some Git vocabulary
Tom Clegg [Fri, 18 Apr 2014 16:34:47 +0000 (12:34 -0400)]
Fix up SSH capitalization/typeface
Tom Clegg [Fri, 18 Apr 2014 16:05:49 +0000 (12:05 -0400)]
Add missing </span> tag.
Tom Clegg [Fri, 18 Apr 2014 16:04:27 +0000 (12:04 -0400)]
Add instructions for Ruby and bundler. Add missing dependencies.
Tom Clegg [Fri, 18 Apr 2014 15:48:26 +0000 (11:48 -0400)]
Fix typo
Peter Amstutz [Thu, 17 Apr 2014 15:17:47 +0000 (11:17 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Conflicts:
apps/workbench/app/helpers/application_helper.rb
Peter Amstutz [Thu, 17 Apr 2014 14:06:36 +0000 (10:06 -0400)]
Thumbnail behavior now conforms to original story
Added documentation to a few methods
Tom Clegg [Thu, 17 Apr 2014 14:06:25 +0000 (10:06 -0400)]
Merge branch '2596-refactor-pipeline-create'
closes #2596
Peter Amstutz [Thu, 17 Apr 2014 12:50:39 +0000 (08:50 -0400)]
Merge remote-tracking branch 'origin/master' into 1971-show-image-thumbnails
Tom Clegg [Thu, 17 Apr 2014 01:48:47 +0000 (21:48 -0400)]
Fix errant use of symbol vs. string
Tom Clegg [Thu, 17 Apr 2014 00:43:56 +0000 (20:43 -0400)]
Fix unwarranted use of instance variable.
Tom Clegg [Thu, 17 Apr 2014 00:42:51 +0000 (20:42 -0400)]
Merge back-to-back condition blocks with the same condition.
Tom Clegg [Thu, 17 Apr 2014 00:38:28 +0000 (20:38 -0400)]
Merge branch 'master' into 2596-refactor-pipeline-create
Conflicts:
apps/workbench/app/helpers/application_helper.rb
Tom Clegg [Thu, 17 Apr 2014 00:21:42 +0000 (20:21 -0400)]
Remove bootstrap_components logic from Workbench, now that it happens
automatically on the API server side.
Tom Clegg [Thu, 17 Apr 2014 00:19:45 +0000 (20:19 -0400)]
Fix, and tests for, PipelineInstance#bootstrap_components
Tim Pierce [Wed, 16 Apr 2014 18:57:51 +0000 (14:57 -0400)]
Merge branch '2449-keep-index-status-handlers'
Closes #2449, closes #2603, closes #2561.
Peter Amstutz [Wed, 16 Apr 2014 18:29:22 +0000 (14:29 -0400)]
Increased wait time on capybara test to reduce chance of failure.
Peter Amstutz [Wed, 16 Apr 2014 18:11:44 +0000 (14:11 -0400)]
Merge branch '2376-show-collection-tags-everywhere'
Conflicts:
apps/workbench/app/controllers/actions_controller.rb
Tim Pierce [Wed, 16 Apr 2014 17:45:22 +0000 (13:45 -0400)]
Check that specified Keep volumes actually exist.
Incorporates code review for #2449. Refs #2561.
Peter Amstutz [Wed, 16 Apr 2014 13:48:57 +0000 (09:48 -0400)]
Fixed error reporting when head/tail_uuid don't match head/tail_kind for links.
Added a couple more tests.
Peter Amstutz [Wed, 16 Apr 2014 12:48:16 +0000 (08:48 -0400)]
Merge branch '2488-jobs-pipeline-doc'
Peter Amstutz [Wed, 16 Apr 2014 12:42:54 +0000 (08:42 -0400)]
Fixed typo in application_helper.rb
Removed commented out line in application.html.erb
Tim Pierce [Tue, 15 Apr 2014 21:20:12 +0000 (17:20 -0400)]
Merge branch 'master' into 2449-keep-index-status-handlers
Tim Pierce [Tue, 15 Apr 2014 21:18:22 +0000 (17:18 -0400)]
Add a device_num field to status.json output.
Include the underlying device number (as returned by stat(2)) in
status.json output, so clients can see if two Keep directories are
located on the same underlying volume. Refs #2561.
Peter Amstutz [Tue, 15 Apr 2014 21:10:02 +0000 (17:10 -0400)]
Parameterize the 'arv' command so that it can be specified with an environment
variable to make it easier to run with the right environment for development.
Tim Pierce [Tue, 15 Apr 2014 20:46:57 +0000 (16:46 -0400)]
Added IsValidLocator to filter /index output.
IndexHandler should skip metadata files and anything else that isn't a
valid locator, so call IsValidLocator before including the file in the
index output. Refs #2561.
Tom Clegg [Tue, 15 Apr 2014 17:47:52 +0000 (13:47 -0400)]
Merge branch 'master' into 2596-refactor-pipeline-create
Conflicts:
apps/workbench/test/functional/users_controller_test.rb
services/api/app/controllers/arvados/v1/jobs_controller.rb
services/api/test/functional/arvados/v1/links_controller_test.rb
Tom Clegg [Tue, 15 Apr 2014 17:36:12 +0000 (13:36 -0400)]
Ensure created/modified/updated_at are correct, add tests.
Tom Clegg [Tue, 15 Apr 2014 17:03:44 +0000 (13:03 -0400)]
Update local copy of updated_at if the server provides it.
Tom Clegg [Tue, 15 Apr 2014 16:22:57 +0000 (12:22 -0400)]
Add tests, enable environments/test.rb to prevent CSRF checks in tests
Tom Clegg [Sun, 13 Apr 2014 19:38:00 +0000 (15:38 -0400)]
Fix exception when valid token points to missing user
Tom Clegg [Sun, 13 Apr 2014 05:39:35 +0000 (01:39 -0400)]
Add tests to expose some token handling bugs.
Tom Clegg [Sun, 13 Apr 2014 05:33:33 +0000 (01:33 -0400)]
Move test-api-server framework so it works in functional and unit tests too.
Tom Clegg [Sun, 13 Apr 2014 05:15:23 +0000 (01:15 -0400)]
Add token that is valid except that it points to a missing user.
Tom Clegg [Sun, 13 Apr 2014 05:14:05 +0000 (01:14 -0400)]
Send HTTP 500 if we end up in render_error without a more specific status.
Peter Amstutz [Tue, 15 Apr 2014 15:11:49 +0000 (11:11 -0400)]
Job reuse bugfix: do not reuse completed jobs that have NULL output.
Peter Amstutz [Tue, 15 Apr 2014 14:58:13 +0000 (10:58 -0400)]
Added thumbnail option to #link_to_if_arvados_object, enabled on pipeline instance and job pages.
Refactored #is_image and #file_path to CollectionsHelper.
Peter Amstutz [Tue, 15 Apr 2014 14:04:54 +0000 (10:04 -0400)]
Merge branch '2376-show-collection-tags-everywhere' into 1971-show-image-thumbnails
Conflicts:
apps/workbench/app/controllers/actions_controller.rb
apps/workbench/app/views/collections/_show_files.html.erb
Peter Amstutz [Tue, 15 Apr 2014 14:02:02 +0000 (10:02 -0400)]
Merge branch 'master' into 1971-show-image-thumbnails
Conflicts:
apps/workbench/app/views/collections/_show_files.html.erb
Tom Clegg [Tue, 15 Apr 2014 03:56:04 +0000 (23:56 -0400)]
Merge branch '2388-bogus-token-error-page'
closes #2388
radhika chippada [Tue, 15 Apr 2014 01:51:04 +0000 (21:51 -0400)]
Merge branch 'master' into 1776-setup-user-email
Tim Pierce [Mon, 14 Apr 2014 20:41:33 +0000 (16:41 -0400)]
Merge branch 'master' into 2449-keep-index-status-handlers
Tim Pierce [Mon, 14 Apr 2014 20:39:52 +0000 (16:39 -0400)]
Merge branch '2449-keep-write-blocks'
Closes #2449, closes #2292, closes #2507.
Ward Vandewege [Mon, 14 Apr 2014 20:31:07 +0000 (16:31 -0400)]
Do not blow up when HOME is not set.
Peter Amstutz [Mon, 14 Apr 2014 20:29:34 +0000 (16:29 -0400)]
Javascript to replace <span> tags used for labels to square brackets for
selection lists that can't handle HTML.
Some output sanitization in case a tag has HTML in it.
Tim Pierce [Mon, 14 Apr 2014 19:54:26 +0000 (15:54 -0400)]
Added rudimentary GetNodeStatus test. (refs #2561)
Added GetNodeStatus unit test.
Revised structure of NodeStatus struct to reflect the desired output format.
radhika chippada [Mon, 14 Apr 2014 19:38:32 +0000 (15:38 -0400)]
Merge branch 'master' into 1776-setup-user-email
Conflicts:
services/api/app/controllers/arvados/v1/users_controller.rb
Tim Pierce [Mon, 14 Apr 2014 19:23:34 +0000 (15:23 -0400)]
Merge branch '2449-keep-write-blocks' into 2449-keep-index-status-handlers
Tim Pierce [Mon, 14 Apr 2014 19:23:04 +0000 (15:23 -0400)]
Merge branch 'master' into 2449-keep-write-blocks
Peter Amstutz [Mon, 14 Apr 2014 18:50:41 +0000 (14:50 -0400)]
Reverted Gemfile.lock
Peter Amstutz [Mon, 14 Apr 2014 18:48:09 +0000 (14:48 -0400)]
Removes spurious whitespace.
Peter Amstutz [Mon, 14 Apr 2014 18:47:42 +0000 (14:47 -0400)]
Adds tags to link text for anything using #link_to_if_arvados_object for a collection
Changed breadcrumb at top of page to use #link_to_if_arvados_object
Adding a collection to selection list includes tags in item text
Tim Pierce [Mon, 14 Apr 2014 18:14:22 +0000 (14:14 -0400)]
Simplify GetNodeStatus to return only disk usage stats for volumes (refs #2561)
GetNodeStatus now only collects volume mount point, bytes free and bytes used.
More stats will be added as we find them necessary.
Peter Amstutz [Mon, 14 Apr 2014 15:22:41 +0000 (11:22 -0400)]
Links controller checks that head/tail_kind matches head/tail_uuid.
Added test.
Tim Pierce [Mon, 14 Apr 2014 15:19:36 +0000 (11:19 -0400)]
Merge branch '2449-keep-write-blocks' into 2449-keep-index-status-handlers
Peter Amstutz [Fri, 11 Apr 2014 19:45:08 +0000 (15:45 -0400)]
Reverted accidental change to Gemfile.
Restored parameter check in load_filters_param.
Removed spurious commented-out code from test.
Peter Amstutz [Mon, 14 Apr 2014 13:54:10 +0000 (09:54 -0400)]
Merge remote-tracking branch 'origin/master' into origin-2228-check-filter-uuid-columns
Peter Amstutz [Mon, 14 Apr 2014 13:53:02 +0000 (09:53 -0400)]
Improved language about git revisions a bit based on review feeback.
Peter Amstutz [Mon, 14 Apr 2014 13:31:42 +0000 (09:31 -0400)]
* Refactored to remove load_kind_params filter and instead override load_where_param and load_filters_param in the links and logs controllers to add the _kind functionality.
* Removed 'rescue' clause. I think I left that in from debugging.
* Fixed :log -> :logs
* filters: ['tail_kind','=','arvados#user'] works
* Added more tests.
* Added equivalent logic and tests for logs controller for object_kind