Tom Clegg [Tue, 27 Sep 2016 16:49:49 +0000 (12:49 -0400)]
9848: Set expiry time on container output and log collections.
Tom Clegg [Tue, 27 Sep 2016 16:48:16 +0000 (12:48 -0400)]
9848: Use pointer receiver for all arvadosclient.ArvadosClient methods.
This makes it possible for all methods to satisfy a single interface.
Tom Clegg [Tue, 27 Sep 2016 03:18:24 +0000 (23:18 -0400)]
9848: Copy the output and log collections (if any) when finalizing a container request.
When reusing a container, ensure log and output are readable.
Tom Clegg [Tue, 27 Sep 2016 03:23:01 +0000 (23:23 -0400)]
9848: group some assertions into bigger test cases.
Peter Amstutz [Mon, 26 Sep 2016 21:17:35 +0000 (17:17 -0400)]
Merge branch '10081-update-cwl-runner' refs #10081
Peter Amstutz [Mon, 26 Sep 2016 21:04:29 +0000 (17:04 -0400)]
10081: Fix renamed methods.
radhika [Mon, 26 Sep 2016 20:03:17 +0000 (16:03 -0400)]
closes #9514
Merge branch '9514-only-delete-old-container-logs'
Peter Amstutz [Mon, 26 Sep 2016 19:30:39 +0000 (15:30 -0400)]
Merge branch '9988-cwl-arv-hints' closes #9988
Peter Amstutz [Mon, 26 Sep 2016 19:30:17 +0000 (15:30 -0400)]
Fix typo.
Tom Clegg [Mon, 26 Sep 2016 17:44:16 +0000 (13:44 -0400)]
Merge branch '9950-arv-git-httpd-config' closes #9950
Tom Clegg [Mon, 26 Sep 2016 16:24:46 +0000 (12:24 -0400)]
9950: Remove uses of environment variables.
Tom Clegg [Wed, 21 Sep 2016 18:34:05 +0000 (14:34 -0400)]
9950: Propagate Client.Insecure config to arvadosclient library via ARVADOS_API_HOST_INSECURE env var.
Tom Clegg [Wed, 21 Sep 2016 01:28:00 +0000 (21:28 -0400)]
9950: Add systemd unit file arv-git-httpd.service.
Tom Clegg [Wed, 21 Sep 2016 13:35:27 +0000 (09:35 -0400)]
9950: Rename Root config to RepoRoot.
Tom Clegg [Wed, 21 Sep 2016 01:27:32 +0000 (21:27 -0400)]
9950: Load config from /etc/arvados/arv-git-httpd/config.json.
radhika [Mon, 26 Sep 2016 14:53:38 +0000 (10:53 -0400)]
refs #10028
Merge branch '10028-search-uuid-prefix'
radhika [Mon, 26 Sep 2016 14:15:33 +0000 (10:15 -0400)]
9514: update delete_old_job_logs task also to use the better performing sql.
Peter Amstutz [Mon, 26 Sep 2016 12:42:43 +0000 (08:42 -0400)]
Merge branch '10081-cwl-run-same-job' closes #10081
radhika [Sat, 24 Sep 2016 23:31:09 +0000 (19:31 -0400)]
9514: Use sql to issue delete sql without getting ids in batch.
Tom Clegg [Sat, 24 Sep 2016 02:31:54 +0000 (22:31 -0400)]
Merge branch '10124-fix-sleepy-tests' closes #10124
Tom Clegg [Fri, 23 Sep 2016 18:50:23 +0000 (14:50 -0400)]
10124: Replace "sleep 1, then assert" with "retry assertion for up to 10 seconds".
Peter Amstutz [Fri, 23 Sep 2016 20:22:10 +0000 (16:22 -0400)]
Bump cwltool version in fpm_build refs #10088
Peter Amstutz [Fri, 23 Sep 2016 20:20:07 +0000 (16:20 -0400)]
Merge branch '10081-cwl-run-same-job' into 9988-cwl-arv-hints
Peter Amstutz [Fri, 23 Sep 2016 20:18:39 +0000 (16:18 -0400)]
Merge branch 'master' into 10081-cwl-run-same-job
Conflicts:
sdk/cwl/arvados_cwl/runner.py
Peter Amstutz [Fri, 23 Sep 2016 20:14:06 +0000 (16:14 -0400)]
Merge branch '10088-cwl-dedup-deps' refs #10088
Peter Amstutz [Fri, 23 Sep 2016 18:27:35 +0000 (14:27 -0400)]
10081: Change logical identifier for Arvados schema to arvados.org/cwl.
Improve exception text when checking that locations are keep references.
radhika [Fri, 23 Sep 2016 18:09:20 +0000 (14:09 -0400)]
9514: if logs are not found in logs table, do not show the log div for a completed container.
Peter Amstutz [Fri, 23 Sep 2016 02:38:06 +0000 (22:38 -0400)]
10088: Updated cwltool deduplicates dependencies to avoid creating separate
collections for subdirectories. Don't try to update file literals that arn't
in scandeps.
Tom Clegg [Fri, 23 Sep 2016 16:06:54 +0000 (12:06 -0400)]
Use longer timeout for flaky test.
No issue #
Tom Clegg [Fri, 23 Sep 2016 15:34:14 +0000 (11:34 -0400)]
gofmt. refs #9955
radhika [Fri, 23 Sep 2016 15:31:00 +0000 (11:31 -0400)]
9514: fixture correction
Tom Clegg [Fri, 23 Sep 2016 15:00:05 +0000 (11:00 -0400)]
Merge branch '9955-keepproxy-config' closes #9955
radhika [Fri, 23 Sep 2016 14:09:13 +0000 (10:09 -0400)]
Merge branch 'master' into 9514-only-delete-old-container-logs
radhika [Thu, 22 Sep 2016 23:16:12 +0000 (19:16 -0400)]
10028: replace _____-uuid-prefix with site_config_uuid_prefix-uuid-prefix
radhika [Thu, 22 Sep 2016 18:32:16 +0000 (14:32 -0400)]
closes #10036
Merge branch '10036-canceled-container-state'
radhika [Thu, 22 Sep 2016 02:50:24 +0000 (22:50 -0400)]
10036: Use status label "Ready" for a canceled container request (priority 0), when it's container_uuid is in Queued or Locked states.
Lucas Di Pentima [Thu, 22 Sep 2016 17:02:34 +0000 (14:02 -0300)]
Merge branch '10037-useless-progress-bar'
Closes #10037
Lucas Di Pentima [Thu, 22 Sep 2016 17:01:40 +0000 (14:01 -0300)]
10037: Merge branch 'master' into 10037-useless-progress-bar
Lucas Di Pentima [Thu, 22 Sep 2016 17:00:37 +0000 (14:00 -0300)]
10037: Changed test name to something more appropiate.
Peter Amstutz [Thu, 22 Sep 2016 16:29:33 +0000 (12:29 -0400)]
9988: Add arvados-specfic hints RuntimeConstraints and APIRequirement.
Peter Amstutz [Thu, 22 Sep 2016 16:39:44 +0000 (12:39 -0400)]
Merge branch '10117-fuse-refcount' refs #10117
Peter Amstutz [Thu, 22 Sep 2016 16:38:17 +0000 (12:38 -0400)]
10117: Revert mistaken change to Gemfile.lock.
Peter Amstutz [Thu, 22 Sep 2016 16:32:32 +0000 (12:32 -0400)]
10081: Rename cwl.input.json to cwl.input.yml, fix test.
Peter Amstutz [Thu, 22 Sep 2016 15:38:21 +0000 (11:38 -0400)]
10117: Tweak behavior of has_ref(). Fix naming of CacheTest.
Lucas Di Pentima [Thu, 22 Sep 2016 15:31:23 +0000 (12:31 -0300)]
10037: Test enhancement to check for other statuses on the dashboard, also adding pipeline instances on those checks.
Peter Amstutz [Thu, 22 Sep 2016 13:58:57 +0000 (09:58 -0400)]
Merge branch 'master' into 10081-cwl-run-same-job
Peter Amstutz [Thu, 22 Sep 2016 13:57:56 +0000 (09:57 -0400)]
Update cwltool again for bugfix, refs #10088
Lucas Di Pentima [Thu, 22 Sep 2016 13:20:32 +0000 (10:20 -0300)]
10037: Fixed alignment issues on the dashboard
Peter Amstutz [Wed, 21 Sep 2016 22:10:54 +0000 (18:10 -0400)]
10117: The check needs to be between clear() and the deletion from entries.
Peter Amstutz [Wed, 21 Sep 2016 21:58:29 +0000 (17:58 -0400)]
10117: Check that inode is in entries before trying to remove it, along with
explanation why it is necessary.
Lucas Di Pentima [Wed, 21 Sep 2016 21:37:07 +0000 (18:37 -0300)]
Merge branch '10029-wb-send-request-id'
Closes #10029
Lucas Di Pentima [Wed, 21 Sep 2016 21:36:04 +0000 (18:36 -0300)]
10029: Merge branch 'master' into 10029-wb-send-request-id
Lucas Di Pentima [Wed, 21 Sep 2016 21:20:20 +0000 (18:20 -0300)]
10037: Fixed test because of the fixture dates changes made to allow some containers to appear on the recent pipelines and processes list on the dashboard
Lucas Di Pentima [Wed, 21 Sep 2016 21:19:23 +0000 (18:19 -0300)]
10037: Added test to check for progress bar showing only on running containers
Peter Amstutz [Wed, 21 Sep 2016 19:51:34 +0000 (15:51 -0400)]
10117: OrderedDict preserves insertion order, so use inode as key instead of cache_priority.
Peter Amstutz [Wed, 21 Sep 2016 18:55:53 +0000 (14:55 -0400)]
10117: Restore original semantics of invalidate() and add code comment, add
kernel_invalidate().
Peter Amstutz [Wed, 21 Sep 2016 18:17:51 +0000 (14:17 -0400)]
10117: Additional refinement: a directory not in use but still referenced needs
to be invalidated before it can be cleared so that the kernel releases its
references.
Tom Clegg [Wed, 21 Sep 2016 18:07:30 +0000 (14:07 -0400)]
9955: Add keepproxy config file and systemd unit file.
Peter Amstutz [Wed, 21 Sep 2016 15:13:32 +0000 (11:13 -0400)]
10117: Consider both use_count and ref_count and check subdirectories to determine if it is safe to evict directory contents from cache.
Lucas Di Pentima [Wed, 21 Sep 2016 15:14:13 +0000 (12:14 -0300)]
10029: Some changes/improvements described as follows:
* client_session_id renamed to current_request_id
* before_filter moved to be the first one
* request id clearing after lograge is done logging it
* added test to check for the request being cleared correctly
* corrected test that check for request_id being passed to the api server
Tom Clegg [Wed, 21 Sep 2016 15:09:04 +0000 (11:09 -0400)]
9955: 9950: Add shim for using an arvados.Client to configure an arvadosclient.ArvadosClient.
Lucas Di Pentima [Wed, 21 Sep 2016 13:36:04 +0000 (10:36 -0300)]
10037: Avoid showing progressbar on Workbench's Dashboard when a container is not running, instead show it's state label.
Tom Clegg [Wed, 21 Sep 2016 02:39:22 +0000 (22:39 -0400)]
Merge branch '9957-keep-web-config' closes #9957
Tom Clegg [Mon, 19 Sep 2016 18:16:14 +0000 (14:16 -0400)]
9957: Clarify AuthToken is not used.
Tom Clegg [Mon, 19 Sep 2016 17:55:08 +0000 (13:55 -0400)]
9957: Clarify anonymous token explanation.
Tom Clegg [Fri, 16 Sep 2016 03:41:39 +0000 (23:41 -0400)]
9957: Refactor keep-web to load config from a file, with legacy support for command line flags.
Add systemd unit file.
Peter Amstutz [Tue, 20 Sep 2016 19:48:30 +0000 (15:48 -0400)]
Update cwltool version pin, refs #10088
Peter Amstutz [Tue, 20 Sep 2016 12:22:25 +0000 (08:22 -0400)]
Merge branch '10088-raw-files' refs #10088
Peter Amstutz [Tue, 20 Sep 2016 01:47:52 +0000 (21:47 -0400)]
10081: Upload dependencies. Fix keep paths. Ensure correct quoting.
Peter Amstutz [Mon, 19 Sep 2016 20:08:56 +0000 (16:08 -0400)]
10081: Fix quoting issue with workflow & input object documents. Improve test
for single-container subworkflow dispatch.
Peter Amstutz [Mon, 19 Sep 2016 18:58:55 +0000 (14:58 -0400)]
10081: Dump as yaml instead of json. Add test for extracted subworkflow.
Tom Clegg [Mon, 19 Sep 2016 17:49:13 +0000 (13:49 -0400)]
Merge branch '9954-keep-balance-systemd' closes #9954
Tom Clegg [Mon, 19 Sep 2016 17:46:32 +0000 (13:46 -0400)]
Merge branch '10014-collection-error-detail' closes #10014
Lucas Di Pentima [Mon, 19 Sep 2016 17:43:12 +0000 (14:43 -0300)]
10029: Added test to check for client_session_id parameter existence and format.
Tom Clegg [Fri, 16 Sep 2016 15:05:48 +0000 (11:05 -0400)]
10014: Add error details. Use filesystem language ("directory") instead of "subcollection".
Tom Clegg [Tue, 13 Sep 2016 20:25:36 +0000 (16:25 -0400)]
10014: Add details to various error messages.
Peter Amstutz [Mon, 19 Sep 2016 16:04:30 +0000 (12:04 -0400)]
10081: Mock Collection class in TestWorkflow
Peter Amstutz [Mon, 19 Sep 2016 15:56:21 +0000 (11:56 -0400)]
Merge branch '10088-raw-files' into 10081-cwl-run-same-job
Peter Amstutz [Mon, 19 Sep 2016 15:35:17 +0000 (11:35 -0400)]
10088: Bump cwltool dependency for another bugfix to scandeps.
Peter Amstutz [Sun, 18 Sep 2016 01:26:36 +0000 (21:26 -0400)]
10088: Bump cwltool dependency for bugfix to scandeps.
Peter Amstutz [Fri, 16 Sep 2016 21:37:13 +0000 (17:37 -0400)]
10088: upload_dependencies reads raw files to find actual dependencies
Lucas Di Pentima [Fri, 16 Sep 2016 17:59:12 +0000 (14:59 -0300)]
10029: Added client_session_id to Workbench's client request log.
Peter Amstutz [Fri, 16 Sep 2016 15:01:59 +0000 (11:01 -0400)]
10081: Fix RunInSingleContainer test
Peter Amstutz [Fri, 16 Sep 2016 14:54:14 +0000 (10:54 -0400)]
10081: Custom extension of v1.0 schema to recognize RunInSingleContainer.
Peter Amstutz [Fri, 16 Sep 2016 13:54:45 +0000 (09:54 -0400)]
10081: Add test for recursively calling cwltool when arv:RunInSingleContainer
is provided.
radhika [Thu, 15 Sep 2016 22:30:31 +0000 (18:30 -0400)]
9514: add rake task to delete logs for old containers whose log is already stored in keep.
Peter Amstutz [Thu, 15 Sep 2016 21:04:22 +0000 (17:04 -0400)]
10081: Update cwltool version for bugfix.
Peter Amstutz [Thu, 15 Sep 2016 21:00:08 +0000 (17:00 -0400)]
10081: Quote expression interpolations. Set hints and requirements.
Lucas Di Pentima [Thu, 15 Sep 2016 20:53:40 +0000 (17:53 -0300)]
10029: Added a session id for every new workbench request, to be sent as a parameter to the API server.
Peter Amstutz [Thu, 15 Sep 2016 20:13:08 +0000 (16:13 -0400)]
10081: Submitting whole workflows as jobs WIP
radhika [Thu, 15 Sep 2016 15:33:52 +0000 (11:33 -0400)]
refs #9835
Merge branch '9835-container-reuse-doc'
radhika [Wed, 14 Sep 2016 13:14:28 +0000 (09:14 -0400)]
9836: Add container reuse to ContainerRequest documentation.
Peter Amstutz [Thu, 15 Sep 2016 15:29:09 +0000 (11:29 -0400)]
Fix arvados-cwl-runner tests, refs #9766
Peter Amstutz [Thu, 15 Sep 2016 14:27:12 +0000 (10:27 -0400)]
Fix misake in arvados-cwl-runner upload_dependencies refactor. refs #9766
Tom Clegg [Thu, 15 Sep 2016 14:27:32 +0000 (10:27 -0400)]
9954: Add systemd unit keep-balance.service.
Tom Clegg [Thu, 15 Sep 2016 13:50:15 +0000 (09:50 -0400)]
Merge branch '9986-fuse-retry-if-killed' closes #9986
Tom Clegg [Wed, 14 Sep 2016 20:34:05 +0000 (16:34 -0400)]
9986: Retry (up to 2 times) any python test suite killed by SIGKILL.
Peter Amstutz [Wed, 14 Sep 2016 21:14:07 +0000 (17:14 -0400)]
Merge branch '100032-cwl-metrics' refs #100032
Peter Amstutz [Wed, 14 Sep 2016 21:13:35 +0000 (17:13 -0400)]
100032: Add metrics to job submission in --debug mode.
Peter Amstutz [Wed, 14 Sep 2016 16:30:56 +0000 (12:30 -0400)]
Merge branch '9766-register-workflow' closes #9766
projects / arvados.git / log