radhika [Sat, 7 Jun 2014 13:03:19 +0000 (09:03 -0400)]
Merge branch 'master' into 2871-preload-objects
Tim Pierce [Fri, 6 Jun 2014 21:37:18 +0000 (17:37 -0400)]
Merge branch '2857-collection-tests'
Closes #2857.
radhika [Fri, 6 Jun 2014 19:57:19 +0000 (15:57 -0400)]
Merge branch 'master' into 2871-preload-objects
Tim Pierce [Fri, 6 Jun 2014 19:48:43 +0000 (15:48 -0400)]
2857: strip signatures from manifests before testing equality.
As Brett observed, the "post" method in these tests mutates its
argument. For a valid test, we must ensure that the source data has not
been transformed into the result data.
For tests which do not care about validating the signatures, we just
strip out the signatures from the result manifest before comparing it to
the source.
Refs #2857.
Tim Pierce [Fri, 6 Jun 2014 15:31:59 +0000 (11:31 -0400)]
Merge branch 'master' into 2857-collection-tests
Peter Amstutz [Fri, 6 Jun 2014 14:40:59 +0000 (10:40 -0400)]
Merge branch '2955-fail-orphan-jobs' closes #2955
Peter Amstutz [Fri, 6 Jun 2014 14:39:39 +0000 (10:39 -0400)]
Reverted change
a0aba6d "crunch-dispatch now sends a clean environment to crunch-job"
Peter Amstutz [Fri, 6 Jun 2014 14:31:18 +0000 (10:31 -0400)]
Merge branch 'master' into 2955-fail-orphan-jobs
Peter Amstutz [Fri, 6 Jun 2014 14:30:06 +0000 (10:30 -0400)]
Reverted change
a0aba6d "crunch-dispatch now sends a clean environment to crunch-job" refs #2882.
Brett Smith [Fri, 6 Jun 2014 13:47:11 +0000 (09:47 -0400)]
Merge branch '2880-compute-ping-stats'
Closes #2967, #2975.
Brett Smith [Thu, 5 Jun 2014 15:38:46 +0000 (11:38 -0400)]
2880: API server saves node statistics from pings.
Crunch will use this information when scheduling Jobs, to satisfy
specified runtime constraints. Getting this data into the pings is
the responsibility of the node's ping script.
Brett Smith [Fri, 6 Jun 2014 13:38:25 +0000 (09:38 -0400)]
2882: Workbench generic create controller adds JSON href attribute.
This is a bugfix commit. This detail got lost when create stopped
calling show to render the object. Refs #2882.
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.
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.
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.
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.
Peter Amstutz [Tue, 3 Jun 2014 20:10:29 +0000 (16:10 -0400)]
2882: Explicit polling frequency
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
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
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.
Ward Vandewege [Tue, 3 Jun 2014 15:01:00 +0000 (11:01 -0400)]
Fix workbench URL in inactive user notification e-mail.
refs #2681
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 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
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.
Peter Amstutz [Mon, 2 Jun 2014 14:30:57 +0000 (10:30 -0400)]
2919: Reinstated absolute positioning, changed font size so that text is no
longer overflowing the graph boxes and ovals.
Brett Smith [Mon, 2 Jun 2014 14:23:42 +0000 (10:23 -0400)]
2752: arv-put works when it can't write a cache file.
Brett Smith [Mon, 2 Jun 2014 14:03:30 +0000 (10:03 -0400)]
2752: Rename test_arv_put.py.
This allows us to run specific test cases from the command-line. The
hyphen in the filename prevented that before.
Brett Smith [Mon, 2 Jun 2014 13:48:58 +0000 (09:48 -0400)]
2752/2755: Move test_cmdline code to test_arv-put.
Tim and I wrote tests for arv-put simultaneously. This commit merges
them together.
Peter Amstutz [Mon, 2 Jun 2014 13:21:56 +0000 (09:21 -0400)]
2939: Use JSON.dump instead of Oj.dump, solves the symbol keys problem.
Peter Amstutz [Mon, 2 Jun 2014 12:52:06 +0000 (08:52 -0400)]
Merge remote-tracking branch 'origin/master' into origin-2939-re-run-job-button refs #2939
Conflicts:
services/api/db/schema.rb
Peter Amstutz [Mon, 2 Jun 2014 12:50:33 +0000 (08:50 -0400)]
2939: Added repository to re-run with latest button label
Tom Clegg [Sun, 1 Jun 2014 04:13:33 +0000 (00:13 -0400)]
2872: Remove name column from collections table.
Peter Amstutz [Sat, 31 May 2014 01:52:49 +0000 (21:52 -0400)]
2939: Added generic "options" parameter to #create to allow workbench pages to
specify additional parameters to be passed through to the API server.
Peter Amstutz [Sat, 31 May 2014 01:02:59 +0000 (21:02 -0400)]
Merge remote-tracking branch 'refs/remotes/origin/2939-create-params' into origin-2939-re-run-job-button
Peter Amstutz [Sat, 31 May 2014 00:54:54 +0000 (20:54 -0400)]
2939: added no_reuse, nondeterministic
radhika [Fri, 30 May 2014 21:42:22 +0000 (17:42 -0400)]
2903: merge master
radhika [Fri, 30 May 2014 21:39:44 +0000 (17:39 -0400)]
Merge branch 'master' into 2903-remove-pi-active-and-success
radhika [Fri, 30 May 2014 21:29:04 +0000 (17:29 -0400)]
Merge branch 'master' into 2895-no-more-redis
Tom Clegg [Fri, 30 May 2014 21:22:33 +0000 (17:22 -0400)]
2939: Allow caller to pass additional parameters to create API.
radhika [Fri, 30 May 2014 21:18:17 +0000 (17:18 -0400)]
2895: remove redis gem
projects / arvados.git / log