Peter Amstutz [Fri, 30 Nov 2018 20:32:27 +0000 (15:32 -0500)]
14558: Version dependency fixes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 30 Nov 2018 16:58:20 +0000 (11:58 -0500)]
Merge branch '14510-cwl-perf' refs #14510
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 30 Nov 2018 15:50:20 +0000 (10:50 -0500)]
14510: Bugfix order of precedence for setting collection cache size
Fix a couple other buggy tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 30 Nov 2018 14:25:47 +0000 (09:25 -0500)]
14510: Don't initialize workflow redundantly.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Fri, 30 Nov 2018 02:08:05 +0000 (21:08 -0500)]
Make sure the dev version prefix is based on the latest tag in the repo, not
the latest tag on the master branch (part 3). Make sure the change also works
in Python 3.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 29 Nov 2018 19:49:31 +0000 (14:49 -0500)]
Make sure the dev version prefix is based on the latest tag in the repo,
not the latest tag on the master branch (part 2).
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 29 Nov 2018 14:27:59 +0000 (09:27 -0500)]
Make sure the dev version prefix is based on the latest tag in the repo,
not the latest tag on the master branch.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 29 Nov 2018 03:23:34 +0000 (22:23 -0500)]
Work around ruamel.yaml packaging issue.
closes #14552
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 28 Nov 2018 20:12:19 +0000 (15:12 -0500)]
Stop relying on the keyservers during arvbox docker image build, they are too
unreliable.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Wed, 28 Nov 2018 19:42:06 +0000 (14:42 -0500)]
14510: Set collection metadata cache size as 150% of sum of inputs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Wed, 28 Nov 2018 19:19:23 +0000 (14:19 -0500)]
Release 1.2.1 does not require special attention when upgrading.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 28 Nov 2018 18:32:11 +0000 (13:32 -0500)]
Merge branch '14345-add-webdav-user-doc'
refs #14345
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 28 Nov 2018 18:29:43 +0000 (13:29 -0500)]
Merge branch 'master' into 14345-add-webdav-user-doc
refs #14345
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 28 Nov 2018 18:29:14 +0000 (13:29 -0500)]
14345: Some more language tweaks.
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Tom Morris [Wed, 28 Nov 2018 18:19:00 +0000 (13:19 -0500)]
Add OS X description & tweak Windows
refs #14345
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Ward Vandewege [Wed, 28 Nov 2018 18:12:34 +0000 (13:12 -0500)]
14535: fix typos.
refs #14535
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 28 Nov 2018 16:40:53 +0000 (11:40 -0500)]
Add user documentation for accessing Keep from Windows.
refs #14345
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Tue, 27 Nov 2018 23:13:30 +0000 (18:13 -0500)]
14510: Estimate collection cache size wip
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 27 Nov 2018 22:26:07 +0000 (17:26 -0500)]
14510: Update tests/docs for --collection-cache-size
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 27 Nov 2018 20:53:07 +0000 (15:53 -0500)]
14510: Setting collection cache wip
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 20 Nov 2018 19:33:53 +0000 (14:33 -0500)]
14510: Perfomance fixes
* Add --collection-cache to enable users to workaround cache thrashing
* Limit task queue size. Release workflow lock when attempting to
enqueue a task (which now may block).
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 27 Nov 2018 20:54:37 +0000 (15:54 -0500)]
Restore default value of --on-error to 'continue' refs #14440
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 27 Nov 2018 19:18:31 +0000 (14:18 -0500)]
Merge branch '14440-fed-user-doc' refs #14440
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 27 Nov 2018 19:14:54 +0000 (14:14 -0500)]
14440: Fix formatting of cwl-run-options table.
Also expand help text of --on-error option a bit.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Nico Cesar [Tue, 27 Nov 2018 18:15:18 +0000 (13:15 -0500)]
Merge branch '14535-ruamel-dependencies'
refs #14535
Arvados-DCO-1.1-Signed-off-by: Nico Cesar <ncesar@veritasgenetics.com>
Nico Cesar [Tue, 27 Nov 2018 18:06:36 +0000 (13:06 -0500)]
14535: bumping package revision up for python-ruamel.yaml
refs #14535
Arvados-DCO-1.1-Signed-off-by: Nico Cesar <ncesar@veritasgenetics.com>
Peter Amstutz [Tue, 27 Nov 2018 17:47:11 +0000 (12:47 -0500)]
14440: Refresh cwl-run-options, add note about dockerCollectionPDH
Also add note about workbench not displaying remote steps.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Nico Cesar [Tue, 27 Nov 2018 16:27:44 +0000 (11:27 -0500)]
14535: add dependencies for ruamel.yaml
refs #14535
Arvados-DCO-1.1-Signed-off-by: Nico Cesar <ncesar@veritasgenetics.com>
Lucas Di Pentima [Mon, 26 Nov 2018 19:43:29 +0000 (16:43 -0300)]
Merge branch '14519-wb-textile-issues'
Closes #14519
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 26 Nov 2018 19:42:11 +0000 (16:42 -0300)]
14519: Adds more table related tags to the whitelist
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 21 Nov 2018 22:32:23 +0000 (19:32 -0300)]
14519: Fixes bug by adding table tags to the sanitizer white list
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 21 Nov 2018 22:31:51 +0000 (19:31 -0300)]
14519: Test exposing the regression
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Mon, 26 Nov 2018 17:37:07 +0000 (12:37 -0500)]
14440: Add discussion of federation features.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 21:24:31 +0000 (16:24 -0500)]
14440: Federated workflow diagram.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 21:23:59 +0000 (16:23 -0500)]
14440: Comments on how federated.cwl works
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 19:46:06 +0000 (14:46 -0500)]
14440: Add project
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 18:42:38 +0000 (13:42 -0500)]
14440: Add project_uuid to ClusterTarget example
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 16:33:40 +0000 (11:33 -0500)]
14440: Federated workflow docs WIP
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 20 Nov 2018 22:20:52 +0000 (17:20 -0500)]
14440: Working on docs for federated workflows.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 26 Nov 2018 15:42:02 +0000 (10:42 -0500)]
Merge branch '14198-make-builder' refs #14198
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 26 Nov 2018 15:13:39 +0000 (10:13 -0500)]
14198: Restore behavior of creating an empty Builder object
Used for do_eval() on set_cluster_target(). Calling _init_job() turns
out to have some unintended side effects as well as doing redundant
work.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 21:39:59 +0000 (16:39 -0500)]
Finish fixing setting project_uuid from runtimeContext, fix tests.
refs #14198
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 19:46:38 +0000 (14:46 -0500)]
Fix ClusterTarget.project_uuid to correctly set the project uuid
refs #14198
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 21 Nov 2018 19:44:23 +0000 (14:44 -0500)]
Merge branch '14345-nginx-proxy-request-buffering'
refs #14345
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 21 Nov 2018 19:34:17 +0000 (14:34 -0500)]
14345: Disable proxy request buffering in Nginx keepproxy example.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 21 Nov 2018 19:14:04 +0000 (14:14 -0500)]
14345: Disable Nginx proxy request buffering for keep-web requests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 19:00:04 +0000 (14:00 -0500)]
Fix --submit-runner-cluster tests refs #14198
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 21 Nov 2018 18:28:00 +0000 (13:28 -0500)]
Merge branch '14345-proppatch'
refs #14345
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 18:06:00 +0000 (13:06 -0500)]
Merge branch '14198-fed-testing' refs #14198
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 21 Nov 2018 17:41:11 +0000 (12:41 -0500)]
14198: Call validate_cluster_target on --submit-runner-cluster
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 20 Nov 2018 22:26:17 +0000 (17:26 -0500)]
14198: Add check for uuidPrefix if local cluster isn't in the remoteHosts.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 20 Nov 2018 18:30:40 +0000 (13:30 -0500)]
14198: Update build.list for latest cwltool/schema-salad
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 19 Nov 2018 20:05:01 +0000 (15:05 -0500)]
14198: Fix secondaryFile tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Sat, 17 Nov 2018 03:01:45 +0000 (22:01 -0500)]
14198: Tests for hints in different places
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 21:39:09 +0000 (16:39 -0500)]
14198: Tests prefer setting ClusterTarget hint on the workflow step.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 21:18:19 +0000 (16:18 -0500)]
14198: Test cases for places that ClusterTarget can appear
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 15:59:52 +0000 (10:59 -0500)]
14198: Set ClusterTarget hint on steps instead of tools
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 14 Nov 2018 19:44:19 +0000 (14:44 -0500)]
14198: Rewrite README
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 14 Nov 2018 04:10:07 +0000 (23:10 -0500)]
14198: Connect test cases to outputs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 14 Nov 2018 03:56:56 +0000 (22:56 -0500)]
14198: Add threestep-remote
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 14 Nov 2018 03:06:36 +0000 (22:06 -0500)]
14198: Add scatter-gather
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 13 Nov 2018 22:28:59 +0000 (17:28 -0500)]
14198: Add test twostep-remote-copy-to-home
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 13 Nov 2018 21:37:34 +0000 (16:37 -0500)]
14198: Fix collection PDHs for remote-case
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Nov 2018 20:48:14 +0000 (15:48 -0500)]
14198: Add some basic doc comments.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Nov 2018 20:33:05 +0000 (15:33 -0500)]
14198: Add remote-case and twostep-both-remote
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Nov 2018 20:02:50 +0000 (15:02 -0500)]
14198: Add more twostep tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Nov 2018 15:47:23 +0000 (10:47 -0500)]
14198: Working on two step test cases
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Nov 2018 03:19:15 +0000 (22:19 -0500)]
14198: Refactor arvbox federation setup
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 21:15:11 +0000 (16:15 -0500)]
14198: Federation feature and testing
* Evaluate ClusterTarget in the job step that declares it
* Don't use get_requirement to inherit ClusterTarget.
* Workflow to start and configure a federation of N arvboxes, initialize test user
* Test cases.
* Prepare/scrub before running test
* Use --always-submit-runner
* Tests use isolated inputs. Return success boolean
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 19:21:07 +0000 (14:21 -0500)]
14198: Set arvrunner before calling super constructor
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 19:12:51 +0000 (14:12 -0500)]
14198: Set arvrunner on ArvadosWorkflowStep
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 18:55:49 +0000 (13:55 -0500)]
14198: Set fake 'class' so _init_job is happy
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 16:44:55 +0000 (11:44 -0500)]
14198: Fix jobstep builder init
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 16:28:27 +0000 (11:28 -0500)]
14198: Fix ruamel.yaml versioning
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 16:26:51 +0000 (11:26 -0500)]
14198: Construct ArvadosWorkflowStep
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Nov 2018 15:28:24 +0000 (10:28 -0500)]
14198: Update version deps for schema-salad, cwltool, ruamel.yaml, requests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 14 Nov 2018 18:22:16 +0000 (13:22 -0500)]
14198: Update cwltool and schema-salad
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 7 Nov 2018 21:24:02 +0000 (16:24 -0500)]
14198: Add --always-submit-runner
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 5 Nov 2018 22:44:23 +0000 (17:44 -0500)]
14198: Add --submit-runner-cluster test
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 5 Nov 2018 15:16:48 +0000 (10:16 -0500)]
14198: Unit tests pass again
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 2 Nov 2018 21:05:20 +0000 (17:05 -0400)]
14198: test_submit passes
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 2 Nov 2018 20:41:01 +0000 (16:41 -0400)]
14198: More test updates
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 2 Nov 2018 20:05:29 +0000 (16:05 -0400)]
14198: Bringing unit tests up to date WIP
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 1 Nov 2018 18:42:12 +0000 (14:42 -0400)]
14198: Add paging on container list, check for valid cluster id
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 31 Oct 2018 17:25:24 +0000 (13:25 -0400)]
14198: Use ArvRuntimeContext.submit_runner_cluster for target cluster
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 25 Oct 2018 21:21:05 +0000 (17:21 -0400)]
14198: Fix typo current -> current_container, add copyright header
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 25 Oct 2018 21:11:59 +0000 (17:11 -0400)]
14198: Log current container
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 25 Oct 2018 20:14:50 +0000 (16:14 -0400)]
14198: Support expressions in TargetCluster[clusterID, ownerUUID]
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 25 Oct 2018 19:19:05 +0000 (15:19 -0400)]
14198: Resolve to Docker images to PDH and set "arvados.org/cwl#dockerCollectionPDH"
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 25 Oct 2018 19:02:23 +0000 (15:02 -0400)]
14198: Refactor and add support for --submit-runner-cluster
Rename ArvCwlRunner to ArvCwlExecutor and move into its own file.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 25 Oct 2018 14:36:47 +0000 (10:36 -0400)]
14198: Use PDH for container_image instead of docker repo+tag
Needed to support federated container requests.
This reverts
6ea807b2caf6c934f170b2e4d89c23c4a08ca69c
Based on the commit comment, that change was made to accomodate the
Docker v1 to v2 image format migration (to enable the API server to
select the image with the correct format). However, the API server
subsequently gained the ability to detect if it needed to substitute a
PDH with a migrated image PDH in commit
a72205728f94f5261b657766e01f5767dc15d4b5 so now we want restore the
original behavior of locally resolving the image PDH and using that in
the container request.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 24 Oct 2018 18:45:21 +0000 (14:45 -0400)]
14198: Initial support ClusterTarget hint
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 21 Nov 2018 16:46:34 +0000 (11:46 -0500)]
14345: Support PROPPATCH method.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Ward Vandewege [Tue, 20 Nov 2018 18:45:14 +0000 (13:45 -0500)]
14516: when calculating the next available username, make sure to take merged
accounts into consideration - they have usernames too, and we have a unique
index on username in the users table.
refs #14516
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Tue, 20 Nov 2018 14:23:25 +0000 (09:23 -0500)]
CWL arvados-tests.sh uses --api=containers no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Fri, 16 Nov 2018 16:44:42 +0000 (13:44 -0300)]
Merge branch '14497-rack-upgrade'
Closes #14497
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 16 Nov 2018 15:07:32 +0000 (12:07 -0300)]
14497: Upgrades rack to 1.6.11 on api & workbench.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Wed, 14 Nov 2018 21:35:30 +0000 (16:35 -0500)]
Add --no-tty to apt-key in arvbox dockerfile. no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 14 Nov 2018 21:05:34 +0000 (16:05 -0500)]
Merge branch '14419-concurrent-map-write'
fixes #14419
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Ward Vandewege [Wed, 14 Nov 2018 20:57:32 +0000 (15:57 -0500)]
The Dockerfiles for package building and testing on debian 9 seem to want
--no-tty as an argument to gpg calls now.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
projects / arvados.git / log