Jiayong Li [Mon, 22 May 2017 20:46:02 +0000 (16:46 -0400)]
Change statfile in run.py to raise exception when a reference file is not found, and add test in test_pathmapper.py
Peter Amstutz [Mon, 22 May 2017 15:10:50 +0000 (11:10 -0400)]
Merge branch '11369-crunchv2-notes' refs #11369
Peter Amstutz [Mon, 22 May 2017 14:57:35 +0000 (10:57 -0400)]
11369: Add migration notes about crunchv1-to-crunchv2
Tom Clegg [Sun, 21 May 2017 18:33:08 +0000 (14:33 -0400)]
Merge branch '11720-govendor'
closes #11720
Tom Clegg [Fri, 19 May 2017 23:36:56 +0000 (19:36 -0400)]
Merge branch '11590-log-reuse'
closes #11590
Tom Clegg [Fri, 19 May 2017 23:17:22 +0000 (19:17 -0400)]
Merge branch '9005-disable-keepalive'
refs #9005
refs #11726
refs #11729
Tom Clegg [Fri, 19 May 2017 23:11:05 +0000 (19:11 -0400)]
9005: 11726: 11729: Disable http keepalive.
The previous workaround for #9005 did not account for the prefetch
feature: if a goroutine is using the HTTP client to prefetch data at
the moment the handler exits, CloseIdleConnections() does not close
that connection, so it stays open indefinitely.
Tom Clegg [Fri, 19 May 2017 20:23:39 +0000 (16:23 -0400)]
Merge branch '9005-conn-leak'
refs #9005
Tom Clegg [Fri, 19 May 2017 19:55:40 +0000 (15:55 -0400)]
9005: Fix missing error checks.
Tom Clegg [Fri, 19 May 2017 19:55:22 +0000 (15:55 -0400)]
9005: Fix missing Close().
radhika [Fri, 19 May 2017 19:34:32 +0000 (15:34 -0400)]
closes #11710
Merge branch '11710-container-request-show-perf'
radhika [Fri, 19 May 2017 18:30:58 +0000 (14:30 -0400)]
11710: fix typo in finding children
radhika [Thu, 18 May 2017 19:38:52 +0000 (15:38 -0400)]
11710: fetching requesting containers
radhika [Thu, 18 May 2017 15:42:25 +0000 (11:42 -0400)]
11710: preload / batch retrieval of children of a container_work_unit
Tom Clegg [Fri, 19 May 2017 17:47:52 +0000 (13:47 -0400)]
9005: Remove debug printf.
Tom Clegg [Thu, 18 May 2017 21:25:20 +0000 (17:25 -0400)]
11590: Dry up log_reuse_info() calls.
radhika [Thu, 18 May 2017 19:46:15 +0000 (15:46 -0400)]
refs #9587
Merge branch '9587-include-trash-in-group-contents'
radhika [Thu, 18 May 2017 01:47:52 +0000 (21:47 -0400)]
9587: add support for include_trash in groups_controller -> contents method
Tom Clegg [Thu, 18 May 2017 18:53:38 +0000 (14:53 -0400)]
11590: Add container logging tests.
Tom Clegg [Thu, 18 May 2017 18:45:00 +0000 (14:45 -0400)]
Merge branch '11644-mounts-api'
closes #11644
Tom Clegg [Thu, 18 May 2017 17:26:36 +0000 (13:26 -0400)]
11644: Add DeviceID() to Volume interface.
Tom Clegg [Thu, 18 May 2017 17:22:54 +0000 (13:22 -0400)]
11644: Unify block-index handlers. Move prefix arg to query string.
Tom Clegg [Thu, 18 May 2017 16:19:13 +0000 (12:19 -0400)]
11590: Log container reuse decisions.
Tom Clegg [Thu, 18 May 2017 14:26:53 +0000 (10:26 -0400)]
Merge branch '11590-log-reuse'
refs #11590
Tom Clegg [Thu, 18 May 2017 14:26:35 +0000 (10:26 -0400)]
11590: Clarify "job state" condition in log message.
Tom Clegg [Thu, 18 May 2017 14:21:56 +0000 (10:21 -0400)]
11720: Add vendor/.gitignore.
Tom Clegg [Wed, 17 May 2017 21:07:41 +0000 (17:07 -0400)]
11720: Update Go dependencies.
Tom Clegg [Wed, 17 May 2017 20:48:09 +0000 (16:48 -0400)]
11720: Merge branch 'master' into 11720-govendor
Tom Clegg [Wed, 17 May 2017 20:47:20 +0000 (16:47 -0400)]
Merge branch '11546-fast-lock'
closes #11546
Tom Clegg [Wed, 17 May 2017 19:26:26 +0000 (15:26 -0400)]
11720: Control dependencies with govendor.
radhika [Wed, 17 May 2017 18:28:43 +0000 (14:28 -0400)]
closes #11580
Merge branch '11580-container-requests'
Tom Clegg [Wed, 17 May 2017 18:28:33 +0000 (14:28 -0400)]
11546: Wrap lock/unlock in transactions.
radhika [Tue, 16 May 2017 19:33:31 +0000 (15:33 -0400)]
11580: preload containers
radhika [Tue, 16 May 2017 00:09:25 +0000 (20:09 -0400)]
11580: add container_requests index page
Tom Clegg [Wed, 17 May 2017 17:51:57 +0000 (13:51 -0400)]
11546: Avoid loading/saving non-essential fields in /arvados/v1/containers/lock.
Peter Amstutz [Wed, 17 May 2017 17:50:03 +0000 (13:50 -0400)]
Merge branch '11714-crunch-run-cgroup-parent' closes #11714
Peter Amstutz [Wed, 17 May 2017 15:07:46 +0000 (11:07 -0400)]
11714: Set CgroupParent under Resources because setting Cgroup in HostConfig
doesn't work.
Peter Amstutz [Wed, 17 May 2017 17:08:35 +0000 (13:08 -0400)]
Merge branch '11718-crunch-run-docker-wait' closes #11718
Peter Amstutz [Wed, 17 May 2017 15:04:06 +0000 (11:04 -0400)]
11718: Update crunch-run for docker client API change in ContainerWait().
Tom Clegg [Tue, 16 May 2017 17:31:27 +0000 (13:31 -0400)]
11644: Test fields in /mounts response.
Tom Clegg [Tue, 16 May 2017 17:23:02 +0000 (13:23 -0400)]
11644: Ensure generated UUIDs are always 27 chars.
Tom Clegg [Tue, 16 May 2017 17:22:42 +0000 (13:22 -0400)]
11644: Add volume replication level to /mounts response.
Tom Clegg [Tue, 16 May 2017 17:11:45 +0000 (13:11 -0400)]
11644: Replace linear search with map for looking up mounts by UUID.
Tom Clegg [Tue, 16 May 2017 17:03:14 +0000 (13:03 -0400)]
11644: Test non-empty MountUUID in trash list.
Tom Clegg [Tue, 16 May 2017 16:43:39 +0000 (12:43 -0400)]
11644: Add pull-to-mount-UUID test. Tidy up pull worker and tests.
Peter Amstutz [Tue, 16 May 2017 14:52:04 +0000 (10:52 -0400)]
Merge branch '11693-crunch2-output-symlinks' closes #11693
Peter Amstutz [Tue, 16 May 2017 14:38:55 +0000 (10:38 -0400)]
11693: Only check collection mounts when determining whether to call
getCollectionManifestForPath to merge files into output collection. Remove
redundant assignment of outputSuffix.
Lucas Di Pentima [Tue, 16 May 2017 14:32:48 +0000 (11:32 -0300)]
Merge branch '10111-collection-labels'
Closes #10111
Lucas Di Pentima [Tue, 16 May 2017 14:32:11 +0000 (11:32 -0300)]
10111: Merge branch 'master' into 10111-collection-labels
Peter Amstutz [Tue, 16 May 2017 13:12:58 +0000 (09:12 -0400)]
11693: Detect and error on symlinks pointing to locations outside the output directory.
Tom Clegg [Mon, 15 May 2017 19:36:02 +0000 (15:36 -0400)]
11644: Accept index/pull/trash requests for a specific mount.
Peter Amstutz [Mon, 15 May 2017 20:58:05 +0000 (16:58 -0400)]
11693: Add test that error capturing output results in cancelled container.
Peter Amstutz [Mon, 15 May 2017 20:25:39 +0000 (16:25 -0400)]
11693: Add test cases for symlinks to directories and symlinks inside subdirectories.
Lucas Di Pentima [Mon, 15 May 2017 20:08:11 +0000 (17:08 -0300)]
10111: Moved the api request related code to the controller.
Peter Amstutz [Mon, 15 May 2017 19:52:00 +0000 (15:52 -0400)]
11693: Add tests.
Peter Amstutz [Mon, 15 May 2017 18:06:33 +0000 (14:06 -0400)]
11693: Dereference symlinks to input files and add incorporate them into output collection manifest.
Peter Amstutz [Mon, 15 May 2017 14:19:20 +0000 (10:19 -0400)]
11693: Mark container as cancelled if there is an error during finalization.
Tom Clegg [Mon, 15 May 2017 14:11:20 +0000 (10:11 -0400)]
11644: Use storage account and bucket name as DeviceID for Azure volumes.
Tom Clegg [Mon, 15 May 2017 14:10:55 +0000 (10:10 -0400)]
11644: Use endpoint and bucket name as DeviceID for S3 volumes.
Tom Clegg [Mon, 15 May 2017 05:59:39 +0000 (01:59 -0400)]
11644: Use filesystem UUID and path as DeviceID for local disk volumes.
Tom Clegg [Fri, 12 May 2017 21:21:00 +0000 (17:21 -0400)]
11644: Add /mounts endpoint using random mount UUIDs assigned at runtime.
Tom Clegg [Fri, 12 May 2017 14:45:20 +0000 (10:45 -0400)]
Merge branch '11590-log-reuse'
refs #11590
Tom Clegg [Fri, 12 May 2017 14:34:29 +0000 (10:34 -0400)]
11590: Reword log messages.
Lucas Di Pentima [Fri, 12 May 2017 14:29:01 +0000 (11:29 -0300)]
Merge branch '11647-no-perm-tokens'
Refs #11647
Lucas Di Pentima [Fri, 12 May 2017 14:28:00 +0000 (11:28 -0300)]
11647: Merge branch 'master' into 11647-no-perm-tokens
Lucas Di Pentima [Fri, 12 May 2017 14:00:55 +0000 (11:00 -0300)]
11647: When repacking small blocks into big ones, commit them synchronously.
Lucas Di Pentima [Fri, 12 May 2017 13:57:58 +0000 (10:57 -0300)]
11647: Test proving that when small blocks get repacked and the resulting big block is
committed asynchronously, it doesn't get the permission token on the manifest.
Peter Amstutz [Thu, 11 May 2017 21:27:27 +0000 (17:27 -0400)]
Merge branch '11681-str-newstr' refs #11681
Peter Amstutz [Thu, 11 May 2017 21:25:34 +0000 (17:25 -0400)]
11681: Return native str type from Collection.portable_data_hash() (previous commit was actually for CollectionWriter)
Tom Clegg [Thu, 11 May 2017 20:35:24 +0000 (16:35 -0400)]
Merge branch '11681-str-newstr'
refs #11681
Tom Clegg [Thu, 11 May 2017 19:37:32 +0000 (15:37 -0400)]
11681: Return native str type from KeepLocator.__str__() and Collection.portable_data_hash()
radhika [Thu, 11 May 2017 16:54:53 +0000 (12:54 -0400)]
closes #10645
Merge branch '10645-cr-mounts-display'
radhika [Thu, 11 May 2017 16:54:19 +0000 (12:54 -0400)]
Merge branch 'master' into 10645-cr-mounts-display
Tom Clegg [Thu, 11 May 2017 15:38:37 +0000 (11:38 -0400)]
11590: Add "reuse jobs even if conflicting outputs exist" and "log reuse decisions" config options.
Peter Amstutz [Thu, 11 May 2017 15:00:38 +0000 (11:00 -0400)]
Merge branch '11369-cwl-keepcache-ram' refs #11369
Peter Amstutz [Thu, 11 May 2017 14:19:32 +0000 (10:19 -0400)]
Merge branch '11626-crunch2-log-slurm-errors' closes #11626
Peter Amstutz [Thu, 11 May 2017 14:19:05 +0000 (10:19 -0400)]
11626: Fix log.Printf -> log.Print
radhika [Thu, 11 May 2017 12:54:59 +0000 (08:54 -0400)]
10645: display collection link with disposition. preload mount and command collections.
Ward Vandewege [Thu, 11 May 2017 01:10:02 +0000 (21:10 -0400)]
Be smarter about how we handle packages built in previous runs.
This commit fixes a bug: packages that were built but failed testing
will no longer be uploaded later, when a subsequent set of packages
passes the tests.
No issue #
Ward Vandewege [Wed, 10 May 2017 21:09:06 +0000 (17:09 -0400)]
The Workbench package has a build-time dependency on tzdata for
Ubuntu1604, which is not included in the default upstream docker image.
Add it to our list of dependencies.
Also tweak Workbench package dependencies, no need to expliclitly list
g++ for CentOS7.
No issue #
Ward Vandewege [Wed, 10 May 2017 20:21:45 +0000 (16:21 -0400)]
Fix Workbench package dependency.
No issue #
Ward Vandewege [Wed, 10 May 2017 19:11:26 +0000 (15:11 -0400)]
Our API server and Workbench packages depend on 2 gems that compile
native objects, which require g++ to build them: event-machine and
therubyracer. For our debian-based distros, that package is not
necessarily installed, so we're adding it to the dependency list.
No issue #
Peter Amstutz [Wed, 10 May 2017 18:57:23 +0000 (14:57 -0400)]
11369: Add keep_cache to base RAM request.
Peter Amstutz [Wed, 10 May 2017 18:50:15 +0000 (14:50 -0400)]
Merge branch '10827-checker-cwltool-update' refs #10827
Peter Amstutz [Wed, 10 May 2017 15:16:18 +0000 (11:16 -0400)]
10827: Bump cwltool & schema salad dependency.
radhika [Wed, 10 May 2017 16:56:30 +0000 (12:56 -0400)]
closes #10112
Merge branch '10112-workflow-show'
radhika [Wed, 10 May 2017 16:55:21 +0000 (12:55 -0400)]
Merge branch 'master' into 10112-workflow-show
radhika [Wed, 10 May 2017 15:45:23 +0000 (11:45 -0400)]
10112: preload collections
Peter Amstutz [Wed, 10 May 2017 15:08:36 +0000 (11:08 -0400)]
10827: Add --validate, --print-dot and --enable-dev options (pass through to
existing cwltool functionality).
Tom Clegg [Wed, 10 May 2017 14:23:20 +0000 (10:23 -0400)]
Merge branch '11629-groups-contents-memory'
refs #11629
refs #11458
Tom Clegg [Wed, 10 May 2017 14:22:42 +0000 (10:22 -0400)]
11629: Fix ambiguous column reference.
Tom Clegg [Tue, 9 May 2017 20:37:47 +0000 (16:37 -0400)]
Merge branch '11634-bundler-cache'
closes #11634
Tom Clegg [Tue, 9 May 2017 20:33:31 +0000 (16:33 -0400)]
Merge branch '11629-groups-contents-memory'
closes #11629
Peter Amstutz [Fri, 5 May 2017 21:11:39 +0000 (17:11 -0400)]
11626: Log sbatch errors where the user can see them. Fix tests so there is no lingering goroutines.
Peter Amstutz [Tue, 9 May 2017 20:00:39 +0000 (16:00 -0400)]
Add libgnutls28-dev and python3-dev to install package list to satisfy
run-tests.sh dependencies. refs #11308
Tom Clegg [Tue, 9 May 2017 19:49:41 +0000 (15:49 -0400)]
Merge branch '11308-collection-keys'
refs #11308
Tom Clegg [Tue, 9 May 2017 19:31:44 +0000 (15:31 -0400)]
11308: Fix modes not tested in test case.
Tom Clegg [Tue, 9 May 2017 19:30:19 +0000 (15:30 -0400)]
11308: collection.keys() supports indexing for python2 callers.
radhika [Tue, 9 May 2017 15:29:02 +0000 (11:29 -0400)]
10112: use show_text_with_locators partial to display the various attributes of the definition
radhika [Tue, 9 May 2017 14:35:38 +0000 (10:35 -0400)]
Merge branch 'master' into 10112-workflow-show
projects / arvados.git / log