radhika [Fri, 6 Jun 2014 03:55:17 +0000 (23:55 -0400)]
2872: all tests are updated to reflect the new ui.
Peter Amstutz [Fri, 6 Jun 2014 02:02:30 +0000 (22:02 -0400)]
2961: Now loads tab panes (past the first one) in the background.
Automatically triggers reload of tab panes when receiving a changed event from
websocket.
Peter Amstutz [Thu, 5 Jun 2014 20:31:18 +0000 (16:31 -0400)]
2961: Removed spurious elementId from subscribeToEventLog(). Added arv-log-event-listener[data-object-type="xxxxx"] to
match on uuid types.
Peter Amstutz [Thu, 5 Jun 2014 19:50:26 +0000 (15:50 -0400)]
Fixes PipelineInstancesControllerTest. application_controller#create now does
the right thing based on requested response format. refs #2882
Tim Pierce [Thu, 5 Jun 2014 19:42:06 +0000 (15:42 -0400)]
2857: fix flaky time-sensitive tests
Allow tests to inject a mock Time object into Blob, in order to generate
consistent behavior for tests that rely on permission signatures.
Closes #2857.
radhika [Thu, 5 Jun 2014 19:36:50 +0000 (15:36 -0400)]
2872: update tests to match the new ui
Peter Amstutz [Thu, 5 Jun 2014 18:49:35 +0000 (14:49 -0400)]
Merge branch '2882-job-process-stats' refs #2882
Peter Amstutz [Thu, 5 Jun 2014 18:44:51 +0000 (14:44 -0400)]
2955: Renamed script to "cancel_stale_jobs". Fixed spelling canceled_at -> cancelled_at.
radhika [Thu, 5 Jun 2014 17:54:56 +0000 (13:54 -0400)]
2872: fix test
Peter Amstutz [Thu, 5 Jun 2014 17:20:39 +0000 (13:20 -0400)]
2961: Added tab_pane query parameter which returns just the desired tab pane partial.
Peter Amstutz [Thu, 5 Jun 2014 16:43:09 +0000 (12:43 -0400)]
2955: Moved logic to clean jobs table from crunch-dispatch into a standalone
script.
Tom Clegg [Thu, 5 Jun 2014 15:17:59 +0000 (11:17 -0400)]
2872: Merge branch 'master' into 2872-folder-nav
Conflicts:
apps/workbench/app/controllers/application_controller.rb
apps/workbench/app/helpers/application_helper.rb
apps/workbench/app/models/authorized_key.rb
apps/workbench/app/models/job.rb
apps/workbench/app/models/pipeline_instance.rb
apps/workbench/app/models/user.rb
apps/workbench/app/models/virtual_machine.rb
Tom Clegg [Thu, 5 Jun 2014 15:15:02 +0000 (11:15 -0400)]
2872: Make Show button say Show again. Fix links on collections index.
radhika [Thu, 5 Jun 2014 15:03:11 +0000 (11:03 -0400)]
2871: handle if there is no friendly_link_name in link
radhika [Thu, 5 Jun 2014 14:25:19 +0000 (10:25 -0400)]
2871: remove trailing white space
radhika [Thu, 5 Jun 2014 14:04:32 +0000 (10:04 -0400)]
2871: some more comments
radhika [Thu, 5 Jun 2014 13:45:43 +0000 (09:45 -0400)]
2871: preload objects for dashboard
radhika [Thu, 5 Jun 2014 12:52:01 +0000 (08:52 -0400)]
Merge branch 'master' into 2871-preload-objects
radhika [Thu, 5 Jun 2014 12:47:32 +0000 (08:47 -0400)]
2871: preload_objects_for_dataclass for pipeline instances in dashboard
radhika [Thu, 5 Jun 2014 12:35:11 +0000 (08:35 -0400)]
2871: add preload_objects_for_dataclass method to application_controller
radhika [Wed, 4 Jun 2014 22:24:26 +0000 (18:24 -0400)]
2871: improved link_name retrieval
Tim Pierce [Wed, 4 Jun 2014 21:24:49 +0000 (17:24 -0400)]
2865: add traffic_test.py for testing Keep performance.
Refs #2865.
radhika [Wed, 4 Jun 2014 21:13:15 +0000 (17:13 -0400)]
2871: metadata tab using preloaded objects. wow, i can't believe how many api calls are cut down with this :)
radhika [Wed, 4 Jun 2014 21:01:03 +0000 (17:01 -0400)]
2871: add link head_uuids to the list of to be preloaded uuids
Peter Amstutz [Wed, 4 Jun 2014 20:24:07 +0000 (16:24 -0400)]
2882: Removed unnecessary no_reuse options
radhika [Wed, 4 Jun 2014 20:17:06 +0000 (16:17 -0400)]
Merge branch 'master' into 2871-preload-objects
Peter Amstutz [Wed, 4 Jun 2014 20:00:03 +0000 (16:00 -0400)]
2955: Sets jobrecord.canceled_at when canceling/failing an orphan job.
arv-run-pipeline-instance recognizes canceled jobs when counting the number of ended jobs.
radhika [Wed, 4 Jun 2014 19:53:46 +0000 (15:53 -0400)]
Merge branch 'master' into 2919-provenance-graph-cutoff
radhika [Wed, 4 Jun 2014 19:53:17 +0000 (15:53 -0400)]
Merge branch 'master' into 2871-preload-objects
radhika [Wed, 4 Jun 2014 19:50:50 +0000 (15:50 -0400)]
2871: metadata page updated to use some preloaded collections and links; not fully done yet.
Peter Amstutz [Wed, 4 Jun 2014 19:23:31 +0000 (15:23 -0400)]
Merge remote-tracking branch 'origin/master' into 2882-job-process-stats
Peter Amstutz [Wed, 4 Jun 2014 19:23:11 +0000 (15:23 -0400)]
2882: Improved re-run job buttons on job status page
Peter Amstutz [Wed, 4 Jun 2014 19:19:10 +0000 (15:19 -0400)]
Merge branch 'master' into 2882-job-process-stats refs #2882
Peter Amstutz [Wed, 4 Jun 2014 19:03:37 +0000 (15:03 -0400)]
Merge branch 'origin-2939-re-run-job-button' into 2882-job-process-stats
Peter Amstutz [Wed, 4 Jun 2014 18:52:07 +0000 (14:52 -0400)]
2882: arv-mount restores signal handlers after sp.wait(). Fixed spelling ellapsed -> elapsed.
radhika [Wed, 4 Jun 2014 17:58:36 +0000 (13:58 -0400)]
2871: rename get collections and log collections method names to match the format of links method.
Brett Smith [Wed, 4 Jun 2014 14:30:16 +0000 (10:30 -0400)]
2933: Add Keep signing key configuration to Docker.
This is a little hypothetical until we Dockerize the new Keep server,
but it's necessary to get the API server running.
Refs #2933.
Brett Smith [Wed, 4 Jun 2014 14:29:05 +0000 (10:29 -0400)]
2933: Update Docker to use new Python package build process.
Refs #2933.
radhika [Wed, 4 Jun 2014 17:37:00 +0000 (13:37 -0400)]
2871: get collections methods return all collections for the given uuid.
radhika [Wed, 4 Jun 2014 15:29:04 +0000 (11:29 -0400)]
Merge branch 'master' into 2871-preload-objects
radhika [Wed, 4 Jun 2014 15:17:31 +0000 (11:17 -0400)]
Merge branch 'master' into 2895-no-more-redis
radhika [Wed, 4 Jun 2014 15:16:30 +0000 (11:16 -0400)]
Merge branch 'master' into 2871-preload-objects
radhika [Wed, 4 Jun 2014 15:15:24 +0000 (11:15 -0400)]
2871: add preload methods for collections and logs in application_controller. Use the preload methods in dashboard.
Peter Amstutz [Wed, 4 Jun 2014 14:09:51 +0000 (10:09 -0400)]
2955: Fixed query of log table that checks for age of last log by an orphan
job.
Peter Amstutz [Mon, 2 Jun 2014 20:44:26 +0000 (16:44 -0400)]
2955: crunch-dispatch now sends a clean environment to crunch-job. (cherry-picked from #2882)
Conflicts:
services/api/script/crunch-dispatch.rb
Peter Amstutz [Wed, 4 Jun 2014 13:55:24 +0000 (09:55 -0400)]
2955: Added check that an orphan job hasn't produces any logs for 5 minutes
before automatically failing it. arv-run-pipeline-instance will identify jobs
that are running=false and success=false as failed even if finished_at is null.
Peter Amstutz [Tue, 3 Jun 2014 21:10:45 +0000 (17:10 -0400)]
2955: Fixed refresh_running to set finished_at on failed jobs. Increased
polling period to 30 seconds.
Tim Pierce [Tue, 3 Jun 2014 20:53:50 +0000 (16:53 -0400)]
2865: reduce Keep memory usage.
Eliminate ioutil.ReadAll to reduce unnecessary 2x memory allocations.
* PutBlockHandler allocates a buffer exactly as long as
req.ContentLength and fills it with io.ReadFull.
* GetBlock uses ioutil.ReadFile (which it arguably should have been
doing in the first place).
Refs #2865.
Peter Amstutz [Tue, 3 Jun 2014 20:50:48 +0000 (16:50 -0400)]
2955: Periodically compare Job.running to @running and fail any jobs not in
@running.
Tom Clegg [Tue, 3 Jun 2014 20:21:32 +0000 (16:21 -0400)]
2872: Fix breadcrumbs on pipeline instance compare page.
Peter Amstutz [Tue, 3 Jun 2014 20:10:29 +0000 (16:10 -0400)]
2882: Explicit polling frequency
Tom Clegg [Tue, 3 Jun 2014 20:08:49 +0000 (16:08 -0400)]
2872: Fix links to collections from folder view.
Brett Smith [Tue, 3 Jun 2014 20:07:55 +0000 (16:07 -0400)]
2953: crunch-job strips permission hints from output manifests.
The API server also strips permission hints from submitted
collections, and will reject it if the specified UUID doesn't match
that result. As a consequence, this is necessary for crunch-job to
register output with the API server.
Closes #2953.
Peter Amstutz [Tue, 3 Jun 2014 19:22:33 +0000 (15:22 -0400)]
Merge remote-tracking branch 'origin/master' into origin-2939-re-run-job-button refs #2939
Conflicts:
services/api/db/schema.rb
Tom Clegg [Tue, 3 Jun 2014 19:13:32 +0000 (15:13 -0400)]
2872: Do not try to add name links for objects that have their own names
Tom Clegg [Tue, 3 Jun 2014 19:12:50 +0000 (15:12 -0400)]
2872: Fix syntax
Peter Amstutz [Tue, 3 Jun 2014 19:09:42 +0000 (15:09 -0400)]
2882: Added crunchstat service to collect cgroup stats, and added support to
crunch-job.
radhika [Tue, 3 Jun 2014 18:57:02 +0000 (14:57 -0400)]
2895: remove arvados.jobs.log_stream from arv
radhika [Tue, 3 Jun 2014 18:46:45 +0000 (14:46 -0400)]
Merge branch 'master' into 2895-no-more-redis
radhika [Tue, 3 Jun 2014 18:44:32 +0000 (14:44 -0400)]
2871: add helper method to get "n" number of objects of specific dataclass
Tom Clegg [Tue, 3 Jun 2014 18:43:48 +0000 (14:43 -0400)]
2872: Fix up log message display on pipeline instance page.
Tom Clegg [Tue, 3 Jun 2014 18:40:19 +0000 (14:40 -0400)]
2872: Check "optional" flag too when looking for required inputs.
Tom Clegg [Tue, 3 Jun 2014 17:18:41 +0000 (13:18 -0400)]
2872: Fix empty name placeholders.
radhika [Tue, 3 Jun 2014 15:27:41 +0000 (11:27 -0400)]
Merge branch 'master' into 2871-preload-objects
radhika [Tue, 3 Jun 2014 15:26:23 +0000 (11:26 -0400)]
2871: preload links helper method is added to workbench application_controller.
Tom Clegg [Tue, 3 Jun 2014 15:14:39 +0000 (11:14 -0400)]
2872: Fix crash on missing object.
Tom Clegg [Tue, 3 Jun 2014 15:09:11 +0000 (11:09 -0400)]
2872: Fix total_bytes returning nil.
Ward Vandewege [Tue, 3 Jun 2014 15:01:00 +0000 (11:01 -0400)]
Fix workbench URL in inactive user notification e-mail.
refs #2681
Tom Clegg [Tue, 3 Jun 2014 14:18:54 +0000 (10:18 -0400)]
2872: Treat HEAD same as GET in case we are behind a proxy.
Ward Vandewege [Tue, 3 Jun 2014 13:50:32 +0000 (09:50 -0400)]
Merge branch '2951-more-robust-fuse-test-teardown'
refs #2951
Ward Vandewege [Tue, 3 Jun 2014 13:40:54 +0000 (09:40 -0400)]
Retry the fusermount call up to 10 times with a small pause between
calls if it is not successful. This should make the teardown of the fuse
mount more reliable in automated testing.
refs #2951
Tom Clegg [Tue, 3 Jun 2014 09:01:20 +0000 (05:01 -0400)]
2872: Filter by tail instead of owner in case api server rule is not in yet.
Tom Clegg [Tue, 3 Jun 2014 08:51:28 +0000 (04:51 -0400)]
2872: Ensure friendly_name is always a string.
Tom Clegg [Tue, 3 Jun 2014 08:17:32 +0000 (04:17 -0400)]
2872: Add selection checkboxes to folder view. Compare pipeline instances and remove multiple items.
Tom Clegg [Tue, 3 Jun 2014 06:51:39 +0000 (02:51 -0400)]
2872: Make infinite scroll work with regular window scrollbars too.
Tom Clegg [Tue, 3 Jun 2014 06:12:43 +0000 (02:12 -0400)]
2872: Add "clone and edit" button to pipeline instance page.
Tom Clegg [Tue, 3 Jun 2014 05:00:39 +0000 (01:00 -0400)]
2872: Add free text search in chooser.
Tom Clegg [Tue, 3 Jun 2014 00:35:49 +0000 (20:35 -0400)]
2872: Fix attribute_editable? to play nicer with group ownership. refs #2872
Brett Smith [Mon, 2 Jun 2014 21:26:50 +0000 (17:26 -0400)]
2893: API server accepts all serialized parameters as JSON.
This commit takes the bugfix that was applied in
135f306e, and ensures
it's applied to all serialized attributes.
Peter Amstutz [Mon, 2 Jun 2014 20:44:26 +0000 (16:44 -0400)]
2882: crunch-dispatch now sends a clean environment to crunch-job.
Tom Clegg [Mon, 2 Jun 2014 19:14:15 +0000 (15:14 -0400)]
2872: Change default order of folder contents. refs #2872
Tom Clegg [Mon, 2 Jun 2014 19:13:52 +0000 (15:13 -0400)]
2872: Ensure name link tail_uuid == owner_uuid. refs #2872
Ward Vandewege [Mon, 2 Jun 2014 19:17:44 +0000 (15:17 -0400)]
Merge branch '2681-new-inactive-user-notification'
refs #2681
Ward Vandewege [Mon, 2 Jun 2014 19:15:42 +0000 (15:15 -0400)]
Merge branch 'master' into 2681-new-inactive-user-notification
radhika [Mon, 2 Jun 2014 18:52:54 +0000 (14:52 -0400)]
Merge branch 'master' into 2919-provenance-graph-cutoff
Peter Amstutz [Mon, 2 Jun 2014 18:47:33 +0000 (14:47 -0400)]
2882: Added button to cancel a running job.
Peter Amstutz [Mon, 2 Jun 2014 18:22:00 +0000 (14:22 -0400)]
2882: arv-mount --exec forwards SIGINT and SIGTERM to the underlying subprocess.
radhika [Mon, 2 Jun 2014 17:56:50 +0000 (13:56 -0400)]
2903: rename db migrate script with clear description
radhika [Mon, 2 Jun 2014 17:51:03 +0000 (13:51 -0400)]
Merge branch 'master' into 2903-remove-pi-active-and-success
Conflicts:
services/api/db/schema.rb
Peter Amstutz [Mon, 2 Jun 2014 17:32:23 +0000 (13:32 -0400)]
Merge branch 'master' into 2882-job-process-stats refs #2882
Ward Vandewege [Mon, 2 Jun 2014 17:31:33 +0000 (13:31 -0400)]
Merge branch 'master' into 2681-new-inactive-user-notification
Ward Vandewege [Mon, 2 Jun 2014 17:02:30 +0000 (13:02 -0400)]
DTRT with system_user in our user test case. Partial revocation of
commit:
e9fc734b
radhika [Mon, 2 Jun 2014 17:00:28 +0000 (13:00 -0400)]
Merge branch 'master' into 2919-provenance-graph-cutoff
radhika [Mon, 2 Jun 2014 16:59:10 +0000 (12:59 -0400)]
2919: set the left postitioning for the provenance graph calculated based on the left-nav size
Tom Clegg [Mon, 2 Jun 2014 16:04:07 +0000 (12:04 -0400)]
2872: Fix up tests
Tom Clegg [Mon, 2 Jun 2014 15:36:45 +0000 (11:36 -0400)]
2872: Add job summary partial.
Tom Clegg [Mon, 2 Jun 2014 15:07:47 +0000 (11:07 -0400)]
2872: Fix bugs
Tom Clegg [Mon, 2 Jun 2014 15:03:50 +0000 (11:03 -0400)]
2872: Fix some tests and bugs
Brett Smith [Mon, 2 Jun 2014 14:55:15 +0000 (10:55 -0400)]
2752: Show arv-put output on stdin test failure.
Brett Smith [Mon, 2 Jun 2014 14:54:43 +0000 (10:54 -0400)]
2755: Adjust arv-put test invocation.
This method works better with the new test layout.