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.
Tim Pierce [Fri, 18 Apr 2014 20:00:59 +0000 (16:00 -0400)]
Reorganize Keep code in preparation for dividing into modules.
Refs #2620
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
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.
Tom Clegg [Sun, 13 Apr 2014 00:57:28 +0000 (20:57 -0400)]
Make arrays non-editable on pipeline instance page.
(This is better than offering to edit them but mangling them in the
process.)
Tom Clegg [Sun, 13 Apr 2014 00:50:23 +0000 (20:50 -0400)]
Do not reuse cancelled jobs. Do not consider nil outputs from
incomplete jobs when deciding whether a script is deterministic.
Tom Clegg [Sun, 13 Apr 2014 00:19:35 +0000 (20:19 -0400)]
Ignore jobs with no repository specified, instead of crashing.
Tom Clegg [Sun, 13 Apr 2014 00:09:01 +0000 (20:09 -0400)]
Refactor pipeline_template -> pipeline_instance process.
Copy components from template to instance during #create, not #show.
Maintain script_parameters information in pipeline_instance. When
editing, use that instead of relying on the original template.
Add a generic "merge parameters in update" param, instead of altering
default behavior for pipeline instances. Use Rails deep_merge instead
of gem.
Maintain original component order instead of applying tsort.
Tim Pierce [Sat, 12 Apr 2014 18:26:43 +0000 (14:26 -0400)]
Merge branch 'master' into 2449-keep-write-blocks
Tim Pierce [Sat, 12 Apr 2014 18:24:49 +0000 (14:24 -0400)]
Clean up error handling (refs #2292).
Tim Pierce [Sat, 12 Apr 2014 04:41:56 +0000 (00:41 -0400)]
Code review comments (refs #2292)
Tim Pierce [Fri, 11 Apr 2014 22:01:14 +0000 (18:01 -0400)]
Fix nil map bug and status.json route. (refs #2561)
Tim Pierce [Fri, 11 Apr 2014 21:51:04 +0000 (17:51 -0400)]
Merge branch '2449-keep-write-blocks' into 2449-keep-index-status-handlers
Tim Pierce [Fri, 11 Apr 2014 21:28:39 +0000 (17:28 -0400)]
Merge branch 'master' into 2449-keep-write-blocks
Peter Amstutz [Fri, 11 Apr 2014 20:58:20 +0000 (16:58 -0400)]
Reorganized job/pipeline docs into relevant API reference sections
Peter Amstutz [Fri, 11 Apr 2014 20:29:38 +0000 (16:29 -0400)]
Updated Job section of API documentation regarding repository and
nondeterministic attributes. refs #2488
Tim Pierce [Fri, 11 Apr 2014 20:15:36 +0000 (16:15 -0400)]
Merge branch 'master' into 2449-keep-index-status-handlers
Tim Pierce [Fri, 11 Apr 2014 20:05:45 +0000 (16:05 -0400)]
Update documentation for command-line flags (closes #2463, closes #2591).
Peter Amstutz [Fri, 11 Apr 2014 20:04:28 +0000 (16:04 -0400)]
Merge remote-tracking branch 'origin/master' into origin-2228-check-filter-uuid-columns
Conflicts:
services/api/app/models/arvados_model.rb
Peter Amstutz [Fri, 11 Apr 2014 19:45:08 +0000 (15:45 -0400)]
API server tests pass, workbench tests are failing
Tim Pierce [Fri, 11 Apr 2014 19:44:27 +0000 (15:44 -0400)]
Added ReadAtMost function for reading request data (refs #2292)
ReadAtMost will read up to the specified number of bytes, returning
an error if the request is larger than that limit.
Tim Pierce [Fri, 11 Apr 2014 18:48:14 +0000 (14:48 -0400)]
Updating docs for code review (refs #2463)
Tim Pierce [Fri, 11 Apr 2014 17:34:43 +0000 (13:34 -0400)]
Merge branch 'master' into 2449-keep-flags
Tim Pierce [Fri, 11 Apr 2014 17:33:05 +0000 (13:33 -0400)]
Merge branch 'master' into 2449-keep-write-blocks
Brett Smith [Fri, 11 Apr 2014 17:02:25 +0000 (13:02 -0400)]
Merge branch '2375-log-table' into master
We add a log to the Log table whenever another model is created,
updated, or destroyed. Closes #2375, #2559.
Tom Clegg [Fri, 11 Apr 2014 16:59:04 +0000 (12:59 -0400)]
Merge branch '2246-fix-git-clone-race'
closes #2246
Tim Pierce [Fri, 11 Apr 2014 15:30:25 +0000 (11:30 -0400)]
Merge branch '2449-keep-write-blocks' into 2449-keep-index-status-handlers
Tim Pierce [Fri, 11 Apr 2014 15:29:04 +0000 (11:29 -0400)]
Merge branch '2449-keep-write-blocks' into 2449-keep-flags
Tim Pierce [Fri, 11 Apr 2014 14:43:56 +0000 (10:43 -0400)]
Added todo for TestPutBlockWriteErr (refs #2292)
Tim Pierce [Fri, 11 Apr 2014 14:27:11 +0000 (10:27 -0400)]
Merge branch 'master' into 2449-keep-write-blocks
Tim Pierce [Fri, 11 Apr 2014 14:25:51 +0000 (10:25 -0400)]
Added TestPutBlockCollision (refs #2292).
Brett Smith [Fri, 11 Apr 2014 14:14:12 +0000 (10:14 -0400)]
api: Don't include API tokens in logs.
Refs #2375. See Tom's comments.
I also renamed UNLOGGED_ATTRIBUTES to UNLOGGED_CHANGES to help clarify
that it's not used by logged_attributes.
Peter Amstutz [Fri, 11 Apr 2014 13:44:13 +0000 (09:44 -0400)]
Merged master
Brett Smith [Fri, 11 Apr 2014 13:35:49 +0000 (09:35 -0400)]
api: More robust tests for log properties.
This ensures that logs always have the old/new_etag/attributes
properties, even if they're expressly set to nil.
Brett Smith [Fri, 11 Apr 2014 13:20:35 +0000 (09:20 -0400)]
api: Improve test for selective API auth logging.
radhika chippada [Fri, 11 Apr 2014 13:17:48 +0000 (09:17 -0400)]
Merge branch '2272-fix-setup-user-in-workbench'
radhika chippada [Fri, 11 Apr 2014 13:09:59 +0000 (09:09 -0400)]
Merge branch 'master' of git.curoverse.com:arvados
Tim Pierce [Fri, 11 Apr 2014 11:02:42 +0000 (07:02 -0400)]
Write status output in JSON. (refs #2561)
Tom Clegg [Fri, 11 Apr 2014 03:55:20 +0000 (23:55 -0400)]
Merge branch '2338-maintain-active-tab'
closes #2338
Tom Clegg [Fri, 11 Apr 2014 03:47:10 +0000 (23:47 -0400)]
Add/fix some shell quoting.
Tom Clegg [Fri, 11 Apr 2014 03:46:42 +0000 (23:46 -0400)]
Add comments to explain different ways we choose $repo.
projects / arvados.git / log