Lucas Di Pentima [Tue, 6 Dec 2016 22:54:04 +0000 (19:54 -0300)]
10587: Added tests to Python commands to check for the --version argument.
Peter Amstutz [Tue, 6 Dec 2016 20:59:14 +0000 (15:59 -0500)]
10576: Bump cwltool, schema-salad and rdflib-jsonld package versions.
radhika [Tue, 6 Dec 2016 20:40:49 +0000 (15:40 -0500)]
10300: old pipeline display is failing due to min_nodes in runtime_constraints being a string; convert to integer to be able to view it.
Peter Amstutz [Tue, 6 Dec 2016 20:05:15 +0000 (15:05 -0500)]
10576: Bump cwltool and schema-salad versions.
Ward Vandewege [Tue, 6 Dec 2016 19:56:10 +0000 (14:56 -0500)]
README.md: add link to the Go Report Card for Arvados.
No issue #
radhika [Tue, 6 Dec 2016 18:58:18 +0000 (13:58 -0500)]
closes #10215
Merge branch '10215-arvados-cwl-runner-version'
radhika [Tue, 6 Dec 2016 18:57:55 +0000 (13:57 -0500)]
Merge branch 'master' into 10215-arvados-cwl-runner-version
Tom Clegg [Tue, 6 Dec 2016 18:29:26 +0000 (13:29 -0500)]
8460: Add install doc page.
Tom Clegg [Tue, 6 Dec 2016 16:07:00 +0000 (11:07 -0500)]
8460: Add json mime type.
Tom Clegg [Tue, 6 Dec 2016 16:06:44 +0000 (11:06 -0500)]
8460: Fix binary path.
radhika [Tue, 6 Dec 2016 15:46:45 +0000 (10:46 -0500)]
closes #10604
Merge branch '10604-crunch2-user-guide'
radhika [Tue, 6 Dec 2016 15:44:41 +0000 (10:44 -0500)]
10604: rename tutorial-pipeline-workbench.html as tutorial-workbench-workbench.html
radhika [Tue, 6 Dec 2016 15:31:50 +0000 (10:31 -0500)]
Merge branch 'master' into 10604-crunch2-user-guide
Peter Amstutz [Tue, 6 Dec 2016 14:46:11 +0000 (09:46 -0500)]
Merge branch '10519-cr-fiddlesticks' closes #10519
Peter Amstutz [Tue, 6 Dec 2016 14:40:12 +0000 (09:40 -0500)]
Merge branch '10658-crunch-run-missing-files' closes #10658
Peter Amstutz [Tue, 6 Dec 2016 14:39:09 +0000 (09:39 -0500)]
Merge branch '10649-squeue-stderr' closes #10649
Ward Vandewege [Mon, 5 Dec 2016 22:13:22 +0000 (17:13 -0500)]
Fix typo in comment.
No issue #
Peter Amstutz [Mon, 5 Dec 2016 22:06:37 +0000 (17:06 -0500)]
10576: Running jobs from keep: and arv: prefixes WIP. Tests passing, needs some integration testing.
Tom Clegg [Mon, 5 Dec 2016 20:40:25 +0000 (15:40 -0500)]
8460: golint fixes.
Tom Clegg [Mon, 5 Dec 2016 20:20:16 +0000 (15:20 -0500)]
8460: Log entry at startup.
Tom Clegg [Mon, 5 Dec 2016 20:20:03 +0000 (15:20 -0500)]
8460: Cancel context before returning from handler.
Tom Clegg [Mon, 5 Dec 2016 19:36:15 +0000 (14:36 -0500)]
8460: Merge branch 'master' into 8460-websocket-go
Tom Clegg [Mon, 5 Dec 2016 19:35:25 +0000 (14:35 -0500)]
8460: Add simple /status.json
radhika [Mon, 5 Dec 2016 18:23:42 +0000 (13:23 -0500)]
10215: if version arg is used, just display version info and exit.
Peter Amstutz [Mon, 5 Dec 2016 15:40:42 +0000 (10:40 -0500)]
10576: Add resolver to execute from keep references and arvados workflow
records. Add test for keep references in workflow default input.
Tom Clegg [Sat, 3 Dec 2016 08:52:43 +0000 (03:52 -0500)]
8460: status.json -> debug.json
Tom Clegg [Sat, 3 Dec 2016 08:44:45 +0000 (03:44 -0500)]
8460: Rename pg -> event_source.go
Peter Amstutz [Fri, 2 Dec 2016 22:17:25 +0000 (17:17 -0500)]
10576: Tests & fixes for keep ref url join.
Peter Amstutz [Fri, 2 Dec 2016 21:50:06 +0000 (16:50 -0500)]
10576: Working on fetch & url join for keep references.
radhika [Fri, 2 Dec 2016 20:09:14 +0000 (15:09 -0500)]
10519: added a test to check Run button when an empty workflow is used with no required inputs.
Peter Amstutz [Fri, 2 Dec 2016 20:05:08 +0000 (15:05 -0500)]
Bump package iteration on arvados-docker-cleaner for dependency fix. no issue #
Peter Amstutz [Fri, 2 Dec 2016 19:47:01 +0000 (14:47 -0500)]
Pin websocket-client backport dependency to 0.37.0 to avoid tertiary dependency
problems on debian7 and ubuntu1204. no issue #
radhika [Fri, 2 Dec 2016 18:52:52 +0000 (13:52 -0500)]
Merge branch 'master' into 10519-cr-fiddlesticks
radhika [Fri, 2 Dec 2016 18:52:13 +0000 (13:52 -0500)]
refs #10293
Merge branch '10293-cr-log-and-output-in-wb'
Lucas Di Pentima [Fri, 2 Dec 2016 18:48:40 +0000 (15:48 -0300)]
Merge branch '5737-fix-broken-test-with-231'
refs #5737
radhika [Fri, 2 Dec 2016 18:48:12 +0000 (13:48 -0500)]
10293: update test assertion to expect output collection name, instead of pdh.
Lucas Di Pentima [Fri, 2 Dec 2016 18:45:19 +0000 (15:45 -0300)]
5737: Updated test so it pass on both 2.1 and 2.3 ruby versions.
radhika [Fri, 2 Dec 2016 18:33:20 +0000 (13:33 -0500)]
Merge branch 'master' into 10293-cr-log-and-output-in-wb
Peter Amstutz [Fri, 2 Dec 2016 18:23:48 +0000 (13:23 -0500)]
Use regex to determine whether to print help text for arvbash.sh. refs #10655
Peter Amstutz [Fri, 2 Dec 2016 18:17:33 +0000 (13:17 -0500)]
Merge branch '10655-arvbash' closes #10655
Peter Amstutz [Fri, 2 Dec 2016 18:15:47 +0000 (13:15 -0500)]
Merge branch '10647-dev-jobs-image' closes #10647
radhika [Fri, 2 Dec 2016 17:27:24 +0000 (12:27 -0500)]
10604: add crunch1 only note to arv-copy documentation.
Peter Amstutz [Fri, 2 Dec 2016 15:50:15 +0000 (10:50 -0500)]
Update arvbox to work with passenger 5.0, refs #5737
Peter Amstutz [Fri, 2 Dec 2016 16:58:28 +0000 (11:58 -0500)]
10519: Don't fiddlesticks on uncomitted container request page if workflow or
cwl.input.json are missing.
Peter Amstutz [Fri, 2 Dec 2016 16:07:08 +0000 (11:07 -0500)]
Fix bug done.done() not returning output value. refs #10293
radhika [Fri, 2 Dec 2016 16:02:07 +0000 (11:02 -0500)]
10293: update container_work_unit to look for output_uuid and log_uuid for a container_request, rather than using those from the associated container.
Peter Amstutz [Fri, 2 Dec 2016 15:20:19 +0000 (10:20 -0500)]
10658: Put container into cancelled state on error during docker load or mount
setup.
Peter Amstutz [Fri, 2 Dec 2016 14:59:38 +0000 (09:59 -0500)]
10658: Flush logs even when maintaining container in queued state.
Peter Amstutz [Thu, 1 Dec 2016 17:56:17 +0000 (12:56 -0500)]
10649: Make errors emitted by squeue and scancel show up in logs.
Peter Amstutz [Thu, 1 Dec 2016 22:22:30 +0000 (17:22 -0500)]
10655: Add arvbash to tools/
radhika [Thu, 1 Dec 2016 21:23:33 +0000 (16:23 -0500)]
10604: add pages to write and run workflows.
Lucas Di Pentima [Thu, 1 Dec 2016 20:35:30 +0000 (17:35 -0300)]
Merge branch '5737-ruby231'
refs #5737
Lucas Di Pentima [Thu, 1 Dec 2016 19:34:10 +0000 (16:34 -0300)]
5737: Merge branch 'master' into 5737-ruby231
Peter Amstutz [Thu, 1 Dec 2016 19:00:11 +0000 (14:00 -0500)]
Merge branch '10651-cwl-submit-runner-ram' refs #10651
Peter Amstutz [Thu, 1 Dec 2016 18:59:45 +0000 (13:59 -0500)]
Merge branch 'origin-10293-cwl-cr-output' closes #10293
Peter Amstutz [Thu, 1 Dec 2016 18:54:53 +0000 (13:54 -0500)]
10293: Update test_done to test more stuff and remove redundant test_done_use_existing_collection.
Peter Amstutz [Thu, 1 Dec 2016 18:36:55 +0000 (13:36 -0500)]
10651: Check --submit-runner-ram has a valid value. Add tests.
Peter Amstutz [Thu, 1 Dec 2016 18:11:24 +0000 (13:11 -0500)]
10293: Fix error message when wrong --api provided.
Peter Amstutz [Thu, 1 Dec 2016 17:34:20 +0000 (12:34 -0500)]
10651: Add --submit-runner-ram to specify amount of RAM that should be
allocated for workflow runner job or container.
Tom Clegg [Thu, 1 Dec 2016 15:35:50 +0000 (10:35 -0500)]
8460: fixup
15aca78 stats.Duration
Tom Clegg [Thu, 1 Dec 2016 07:29:11 +0000 (02:29 -0500)]
8460: Add godoc page.
Tom Clegg [Thu, 1 Dec 2016 07:28:38 +0000 (02:28 -0500)]
8460: Add systemd unit file.
Tom Clegg [Thu, 1 Dec 2016 06:33:55 +0000 (01:33 -0500)]
8460: Move loggedDuration from keepstore to sdk pkg as stats.Duration.
Peter Amstutz [Wed, 30 Nov 2016 22:12:42 +0000 (17:12 -0500)]
10293: Avoid noisy and unhelpful error when cwl.output.json is missing.
Lucas Di Pentima [Wed, 30 Nov 2016 21:51:46 +0000 (18:51 -0300)]
10587: Add --version argument to arvados-node-manager.
Peter Amstutz [Wed, 30 Nov 2016 21:39:14 +0000 (16:39 -0500)]
10293: Improve error messages for --api and unsupported InitialWorkDirRequirement.
Peter Amstutz [Wed, 30 Nov 2016 21:04:00 +0000 (16:04 -0500)]
10293: Don't try to json decode empty output file to reduce spurious errors.
Peter Amstutz [Wed, 30 Nov 2016 20:52:38 +0000 (15:52 -0500)]
10293: Override workflow runner done() to get container from container request.
Peter Amstutz [Wed, 30 Nov 2016 20:26:30 +0000 (15:26 -0500)]
10293: Bug fixes
* Now polling state on self.poll_api.container_requests() table
* Runner object puts "self" into processes table
* Don't report spurious ApiError when not running in container
Lucas Di Pentima [Wed, 30 Nov 2016 21:24:15 +0000 (18:24 -0300)]
10587: Added --version to arv-mount command.
Lucas Di Pentima [Wed, 30 Nov 2016 20:56:11 +0000 (17:56 -0300)]
10587: Adding --version argument to Python SDK cli commands
radhika [Wed, 30 Nov 2016 20:46:02 +0000 (15:46 -0500)]
10604: Update the "Running a pipeline using Workbench" to talk about "workflows"
Tom Clegg [Wed, 30 Nov 2016 20:09:13 +0000 (15:09 -0500)]
8460: Merge branch 'master' into 8460-websocket-go
Peter Amstutz [Wed, 30 Nov 2016 19:40:53 +0000 (14:40 -0500)]
10647: Get necessary version of cwltool from sdk/cwl/setup.py instead of
listing it in two places.
Peter Amstutz [Wed, 30 Nov 2016 19:36:36 +0000 (14:36 -0500)]
10647: Image tag is most recent git hash of python sdk or arvados-cwl-runner.
Peter Amstutz [Wed, 30 Nov 2016 19:25:58 +0000 (14:25 -0500)]
10647: Script + Dockerfile to build arvados/jobs image from local git checkout, for development.
Lucas Di Pentima [Tue, 29 Nov 2016 15:52:05 +0000 (12:52 -0300)]
5737: Merge branch 'master' into 5737-ruby231
radhika [Tue, 29 Nov 2016 15:48:17 +0000 (10:48 -0500)]
closes #10518
Merge branch '10518-crunch2-only-wb'
Peter Amstutz [Tue, 29 Nov 2016 14:38:41 +0000 (09:38 -0500)]
Merge branch '10599-run-build-packages' closes #10599
Peter Amstutz [Wed, 23 Nov 2016 18:58:37 +0000 (13:58 -0500)]
10599: Add run-build-packages-one-target.sh --only-build, run-build-packages looks for $ONLY_BUILD in its environment.
radhika [Tue, 29 Nov 2016 02:27:32 +0000 (21:27 -0500)]
10518: update API groups_controller.contents method to exclude classes with index disabled and update user guide to use "Run a process" instead of "Run a pipeline"
Lucas Di Pentima [Mon, 28 Nov 2016 23:18:15 +0000 (20:18 -0300)]
5737: Fixed unused variable declarations.
Lucas Di Pentima [Mon, 28 Nov 2016 22:48:10 +0000 (19:48 -0300)]
5737: Fixed several warning messages from running tests.
Lucas Di Pentima [Mon, 28 Nov 2016 22:45:55 +0000 (19:45 -0300)]
5737: Fixed a bug in container reuse test code.
Peter Amstutz [Mon, 28 Nov 2016 20:58:51 +0000 (15:58 -0500)]
Merge branch '10630-no-json-debug-dump' refs #10630
Peter Amstutz [Mon, 28 Nov 2016 20:56:23 +0000 (15:56 -0500)]
10630: Bump cwltool version to completely skip debug statements that make
expensive json.dumps() calls.
Tom Clegg [Mon, 28 Nov 2016 20:02:51 +0000 (15:02 -0500)]
10467: Update var names in parameterized test func.
Tom Clegg [Mon, 28 Nov 2016 19:59:05 +0000 (14:59 -0500)]
10467: Add "context canceled" tests for PUT and HEAD.
Lucas Di Pentima [Mon, 28 Nov 2016 19:54:25 +0000 (16:54 -0300)]
5737: Fixes to remove ruby warnings when running collection api integration tests
Tom Clegg [Mon, 28 Nov 2016 19:46:26 +0000 (14:46 -0500)]
Merge branch '10586-writer-pool-deadlock' refs #10586
Tom Clegg [Mon, 28 Nov 2016 19:45:30 +0000 (14:45 -0500)]
10467: Add "client disconnect" test.
Lucas Di Pentima [Mon, 28 Nov 2016 19:29:17 +0000 (16:29 -0300)]
5737: Fixes to remove ruby warnings when running websocket integration tests.
Tom Clegg [Mon, 28 Nov 2016 18:46:28 +0000 (13:46 -0500)]
10586: Add extra notify_all() as deadlock insurance.
Tom Clegg [Mon, 28 Nov 2016 18:46:10 +0000 (13:46 -0500)]
10586: Fix misuse of "!=" to mean "is not".
Tom Clegg [Mon, 28 Nov 2016 18:44:52 +0000 (13:44 -0500)]
10586: Do not pile on more errors in the service.finished() case.
Lucas Di Pentima [Mon, 28 Nov 2016 17:50:44 +0000 (14:50 -0300)]
5737: Explicitly passing PID file path to passenger so that the tests pass again.
Lucas Di Pentima [Mon, 28 Nov 2016 17:49:23 +0000 (14:49 -0300)]
5737: Removed minitest: it wasn't really running the tests.
Peter Amstutz [Mon, 28 Nov 2016 14:50:41 +0000 (09:50 -0500)]
Install upgraded setuptools in arvbox, refs #10583
radhika [Mon, 28 Nov 2016 13:12:48 +0000 (08:12 -0500)]
Merge branch 'master' into 10293-cwl-cr-output
Tom Clegg [Fri, 25 Nov 2016 23:21:51 +0000 (18:21 -0500)]
10586: Suppress stack traces for expected http errors.