Peter Amstutz [Wed, 14 Sep 2016 15:38:13 +0000 (11:38 -0400)]
9766: Rename metavar. Post packed yaml text instead of json. Adjust fixture
to have similar form as posted by --create-workflow. Fix fixture to be a
string instead of structured text.
Peter Amstutz [Wed, 14 Sep 2016 12:35:15 +0000 (08:35 -0400)]
Merge branch 'master' into 9766-register-workflow
radhika [Tue, 13 Sep 2016 23:52:40 +0000 (19:52 -0400)]
closes #9836
Merge branch '9836-workflows-doc'
radhika [Tue, 13 Sep 2016 23:51:45 +0000 (19:51 -0400)]
Merge branch 'master' into 9836-workflows-doc
radhika [Tue, 13 Sep 2016 23:50:47 +0000 (19:50 -0400)]
closes #9835
Merge branch '9835-container-api-doc'
radhika [Tue, 13 Sep 2016 23:50:27 +0000 (19:50 -0400)]
Merge branch 'master' into 9835-container-api-doc
Peter Amstutz [Tue, 13 Sep 2016 18:40:16 +0000 (14:40 -0400)]
Fix typo, updated version on wrong package, refs #10013
Peter Amstutz [Tue, 13 Sep 2016 17:14:24 +0000 (13:14 -0400)]
Update cwltool version, refs #10013
radhika [Tue, 13 Sep 2016 16:32:20 +0000 (12:32 -0400)]
9836: Remove the workflow definition related discussion and provide a link to CWL instead.
radhika [Tue, 13 Sep 2016 16:17:34 +0000 (12:17 -0400)]
9835: mount_types improvements.
Peter Amstutz [Tue, 13 Sep 2016 14:05:09 +0000 (10:05 -0400)]
Merge branch '9924-revoked-working-slots' closes #9924
Peter Amstutz [Tue, 13 Sep 2016 14:04:43 +0000 (10:04 -0400)]
9924: Tweak comment and remove superfluous variable assignment.
Peter Amstutz [Tue, 13 Sep 2016 02:13:11 +0000 (22:13 -0400)]
9924: Mark all slots as "failed" on "Unable to confirm allocation" error.
Peter Amstutz [Tue, 13 Sep 2016 01:53:59 +0000 (21:53 -0400)]
Merge branch '10001-cwl-scatter' closes #10001
Peter Amstutz [Tue, 13 Sep 2016 01:53:35 +0000 (21:53 -0400)]
10001: Update cwltool dependency to get parallel scatter fixes.
Peter Amstutz [Tue, 13 Sep 2016 01:42:53 +0000 (21:42 -0400)]
Merge branch '10004-check-sinfo' closes #10004
Peter Amstutz [Tue, 13 Sep 2016 01:42:26 +0000 (21:42 -0400)]
10004: Add comment documenting reason why check_sinfo is needed.
Tom Clegg [Mon, 12 Sep 2016 20:53:55 +0000 (16:53 -0400)]
Fix crash when pipeline template is not readable. refs #10003
Peter Amstutz [Mon, 12 Sep 2016 19:17:23 +0000 (15:17 -0400)]
10004: Add check_sinfo() to end srun_sync() if any of the allocated nodes are
no longer "alloc" according to sinfo.
radhika [Mon, 12 Sep 2016 17:49:35 +0000 (13:49 -0400)]
9836: Add workflow to api documentation.
radhika [Fri, 9 Sep 2016 21:01:31 +0000 (17:01 -0400)]
closes #10005
Merge branch '10005-rename-workflow-in-workflow-as-definition'
radhika [Fri, 9 Sep 2016 19:58:44 +0000 (15:58 -0400)]
10005: update workflow fixture name and description as well and update workbench invocations of workflow.workflow.
radhika [Fri, 9 Sep 2016 19:06:29 +0000 (15:06 -0400)]
10005: Rename workflow attribute in workflow object as definition.
radhika [Fri, 9 Sep 2016 00:48:30 +0000 (20:48 -0400)]
9835: more details such as mount_types added.
Tom Clegg [Thu, 8 Sep 2016 23:19:42 +0000 (19:19 -0400)]
Merge branch '9898-container-lock-api'
closes #9898
Tom Clegg [Thu, 8 Sep 2016 21:09:26 +0000 (17:09 -0400)]
9898: Update test for new response code.
Tom Clegg [Thu, 8 Sep 2016 21:06:58 +0000 (17:06 -0400)]
Merge branch '9996-stop-on-error'
closes #9996
Tom Clegg [Thu, 8 Sep 2016 21:06:03 +0000 (17:06 -0400)]
Merge branch '9888-unit-tests'
closes #9888
Tom Clegg [Thu, 8 Sep 2016 21:02:22 +0000 (17:02 -0400)]
9996: Stop retrieving collections if a fatal error makes any further work futile.
Tom Clegg [Thu, 8 Sep 2016 20:56:42 +0000 (16:56 -0400)]
9888: Add find_reusable unit test.
Tom Clegg [Thu, 8 Sep 2016 20:53:24 +0000 (16:53 -0400)]
9898: Fix broken test.
Peter Amstutz [Thu, 8 Sep 2016 20:30:16 +0000 (16:30 -0400)]
Restore use of --build-arg COMMIT in arvados/jobs Dockerfile to select "cut"
above which layers must be rebuilt. no issue #
Tom Clegg [Thu, 8 Sep 2016 20:15:11 +0000 (16:15 -0400)]
9898: Code cleanup.
Tom Clegg [Thu, 8 Sep 2016 20:14:22 +0000 (16:14 -0400)]
9898: Check previous state after obtaining row lock.
Tom Clegg [Thu, 8 Sep 2016 20:13:29 +0000 (16:13 -0400)]
9898: Change state transition error responses from 403 to 422.
Tom Clegg [Thu, 8 Sep 2016 20:11:59 +0000 (16:11 -0400)]
9898: Remove unused code
radhika [Thu, 8 Sep 2016 19:33:05 +0000 (15:33 -0400)]
9898: add unlock method also on the container model.
Peter Amstutz [Thu, 8 Sep 2016 17:58:56 +0000 (13:58 -0400)]
Merge branch 'master' into 9766-register-workflow
radhika [Thu, 8 Sep 2016 16:53:54 +0000 (12:53 -0400)]
9898: add Lock and Unlock methods to dispatch go sdk.
Peter Amstutz [Thu, 8 Sep 2016 16:07:28 +0000 (12:07 -0400)]
Don't use cached layers and always delete intermediate containers when building
arvados/jobs Docker image. no issue #
radhika [Thu, 8 Sep 2016 15:02:39 +0000 (11:02 -0400)]
Merge branch 'master' into 9898-container-lock-api
Conflicts:
services/api/app/models/container.rb
Peter Amstutz [Thu, 8 Sep 2016 02:02:20 +0000 (22:02 -0400)]
Add -f argument to curl to exit nonzero and try mirror if primary
rpmforge-release url fails, refs #9944
radhika [Wed, 7 Sep 2016 23:18:40 +0000 (19:18 -0400)]
9835: Container and ContainerRequest documentation.
Peter Amstutz [Wed, 7 Sep 2016 20:53:10 +0000 (16:53 -0400)]
Don't pass work_api twice in ArvadosCommandTool constructor. Bump arvados-python-client minimum dependency because tests depend on it. refs #9944
Peter Amstutz [Wed, 7 Sep 2016 20:19:50 +0000 (16:19 -0400)]
Merge branch '9944-cwl-lockfile-packaging' closes #9944
Peter Amstutz [Wed, 7 Sep 2016 20:12:47 +0000 (16:12 -0400)]
Merge branch 'master' into 9944-cwl-lockfile-packaging
Peter Amstutz [Wed, 7 Sep 2016 19:58:50 +0000 (15:58 -0400)]
9944: Tweak centos6 Dockerfiles to fall back to mirror if repoforge main is
unavailable.
Peter Amstutz [Wed, 7 Sep 2016 19:58:13 +0000 (15:58 -0400)]
9944: Fix schema-salad 'lockfile' dependency to account for different package
names between centos & debian/ubuntu.
Peter Amstutz [Tue, 6 Sep 2016 20:56:53 +0000 (16:56 -0400)]
9944: Add 'lockfile' to backports and update cwltool dependency
Tom Clegg [Wed, 7 Sep 2016 16:05:29 +0000 (12:05 -0400)]
Merge branch '9679-dispatch-event-logs'
refs #9679
Tom Clegg [Wed, 7 Sep 2016 15:57:17 +0000 (11:57 -0400)]
9679: Add trailing newline to log text if necessary.
Peter Amstutz [Tue, 6 Sep 2016 20:56:53 +0000 (16:56 -0400)]
Merge branch '9932-cwl-style' closes #9932
Peter Amstutz [Tue, 6 Sep 2016 20:56:32 +0000 (16:56 -0400)]
9932: Copyedits
Peter Amstutz [Tue, 6 Sep 2016 16:07:51 +0000 (12:07 -0400)]
Merge branch 'master' into 9766-register-workflow
Conflicts:
build/run-build-packages.sh
sdk/cwl/setup.py
sdk/cwl/tests/test_job.py
Tom Clegg [Tue, 6 Sep 2016 14:11:25 +0000 (10:11 -0400)]
9679: Mention container state changes in container [request] log messages.
Tom Clegg [Mon, 5 Sep 2016 20:23:48 +0000 (16:23 -0400)]
9679: Extricate container/job log code from pipeline-specific code.
Tom Clegg [Mon, 5 Sep 2016 20:19:31 +0000 (16:19 -0400)]
Merge branch '9799-nonadmin-logs'
closes #9799
Tom Clegg [Mon, 5 Sep 2016 20:19:06 +0000 (16:19 -0400)]
9931: Fix missing include in workbench test support.
refs #9931
Tom Clegg [Mon, 5 Sep 2016 17:47:54 +0000 (13:47 -0400)]
9799: Merge branch 'master' into 9799-nonadmin-logs
Conflicts:
apps/workbench/test/integration/application_layout_test.rb
Peter Amstutz [Mon, 5 Sep 2016 15:46:09 +0000 (11:46 -0400)]
9932: Add CWL best practices guide
Tom Clegg [Mon, 5 Sep 2016 15:15:10 +0000 (11:15 -0400)]
9799: Remove duplicate uuids from db queries.
Tom Clegg [Mon, 5 Sep 2016 14:45:39 +0000 (10:45 -0400)]
9799: Fix method def style
Lucas Di Pentima [Mon, 5 Sep 2016 14:09:00 +0000 (11:09 -0300)]
Merge branch '9858-selenium-locking-port-binding'
Closes #9858
radhika [Sat, 3 Sep 2016 02:15:54 +0000 (22:15 -0400)]
9898: update crunch-dispatch-local tests to be in sync with api server updates.
Lucas Di Pentima [Fri, 2 Sep 2016 20:16:00 +0000 (17:16 -0300)]
9858: Added Errno::EACCES exception handling just in case it tries to open a low port as a user.
radhika [Fri, 2 Sep 2016 20:08:58 +0000 (16:08 -0400)]
9898: test updates
Tom Clegg [Fri, 2 Sep 2016 20:03:54 +0000 (16:03 -0400)]
9931: Fix missing module. Remove global "include" in tests, so bugs like this can be caught in tests.
refs #9931
refs #9875
Lucas Di Pentima [Fri, 2 Sep 2016 19:41:27 +0000 (16:41 -0300)]
9858: Check if port-1 is available, retry if not when asking an available port for selenium.
radhika [Fri, 2 Sep 2016 19:34:59 +0000 (15:34 -0400)]
9898: controller test with lock / unlock state transitions.
Peter Amstutz [Fri, 2 Sep 2016 17:47:04 +0000 (13:47 -0400)]
Merge branch '9923-cwl-collection-dir' refs #9923
radhika [Fri, 2 Sep 2016 15:42:35 +0000 (11:42 -0400)]
9898: update crunch-dispatch to use lock and unlock apis instead of setting state directly.
Tom Clegg [Fri, 2 Sep 2016 02:12:22 +0000 (22:12 -0400)]
Merge branch '9875-fix-params-digest'
refs #9875
Tom Clegg [Fri, 2 Sep 2016 02:05:51 +0000 (22:05 -0400)]
9875: Fix script_parameters_digest to sort hashes hiding inside arrays, too.
radhika [Fri, 2 Sep 2016 00:42:16 +0000 (20:42 -0400)]
9898: add lock and unlock endpoints to containers_controller.
Peter Amstutz [Thu, 1 Sep 2016 21:37:08 +0000 (17:37 -0400)]
9923: Fix instanceof() to check correct base class
Tom Clegg [Thu, 1 Sep 2016 19:40:03 +0000 (15:40 -0400)]
Merge branch '9888-move-job-reuse-code'
refs #9888
Tom Clegg [Thu, 1 Sep 2016 14:25:14 +0000 (10:25 -0400)]
9888: Move record-filtering code into model classes.
Peter Amstutz [Thu, 1 Sep 2016 19:24:29 +0000 (15:24 -0400)]
Add cachecontrol and cwltest to PYTHON_BACKPORTS for latest cwltool refs #9850
Tom Clegg [Thu, 1 Sep 2016 15:45:20 +0000 (11:45 -0400)]
Add max_request_log_params_size config (was hardcoded to 1000).
No issue #
Peter Amstutz [Thu, 1 Sep 2016 16:51:41 +0000 (12:51 -0400)]
Add README describing scripts in build/ no issue #
Peter Amstutz [Thu, 1 Sep 2016 14:32:43 +0000 (10:32 -0400)]
Fix tests refs #9850
Peter Amstutz [Thu, 1 Sep 2016 14:06:32 +0000 (10:06 -0400)]
Merge branch '9850-cwl-js' closes #9850
Peter Amstutz [Thu, 1 Sep 2016 13:52:11 +0000 (09:52 -0400)]
9850: Update cwltool to get javascript evaluation performance improvements.
Tom Clegg [Wed, 31 Aug 2016 15:32:05 +0000 (11:32 -0400)]
Make flaky test fail less often.
No issue #
radhika [Wed, 31 Aug 2016 15:09:33 +0000 (11:09 -0400)]
closes #9893
Merge branch '9893-java-sdk'
Tom Clegg [Wed, 31 Aug 2016 02:34:03 +0000 (22:34 -0400)]
9799: Update tests: non-admin user can see container assigned to committed CR.
Tom Clegg [Tue, 30 Aug 2016 21:34:42 +0000 (17:34 -0400)]
9799: Fix bootstrap markup.
Tom Clegg [Tue, 30 Aug 2016 20:30:17 +0000 (16:30 -0400)]
9799: Fix up live_log_lines so it works for all work units.
Tom Clegg [Tue, 30 Aug 2016 20:35:32 +0000 (16:35 -0400)]
9799: Remove bogus bootstrap classes and fix html syntax.
Tom Clegg [Tue, 30 Aug 2016 20:23:59 +0000 (16:23 -0400)]
9799: Move work unit tests from application_layout_test to work_units_test.
Tom Clegg [Tue, 30 Aug 2016 15:36:28 +0000 (11:36 -0400)]
9799: Fix show/hide "cancel container req" button: check ArvadosBase#editable?, and use CR priority instead of container priority.
Tom Clegg [Tue, 30 Aug 2016 15:14:55 +0000 (11:14 -0400)]
9799: Add forgotten serialized column.
Tom Clegg [Tue, 30 Aug 2016 03:29:57 +0000 (23:29 -0400)]
9799: Use more realistic log entries in Workbench live-logging tests. Remove redundant test.
Tom Clegg [Sun, 28 Aug 2016 03:31:37 +0000 (23:31 -0400)]
9799: Add missing container request, so container fixture is visible to test user.
Tom Clegg [Sat, 27 Aug 2016 03:34:14 +0000 (23:34 -0400)]
9799: Clean up permission code and comments.
Tom Clegg [Sat, 27 Aug 2016 03:16:15 +0000 (23:16 -0400)]
9799: Fix test order dependency.
Tom Clegg [Sat, 27 Aug 2016 03:06:11 +0000 (23:06 -0400)]
9799: Remove redundant test.
Tom Clegg [Tue, 30 Aug 2016 03:11:34 +0000 (23:11 -0400)]
9799: Restore permission on Log entries via owner_uuid.
Tom Clegg [Sat, 27 Aug 2016 03:06:01 +0000 (23:06 -0400)]
9799: Dry up SQL statements using named bind parameters.
Tom Clegg [Sat, 27 Aug 2016 01:46:10 +0000 (21:46 -0400)]
9799: Update test: "spectator" user is now allowed to read log entries about itself.
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