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 15:04:06 +0000 (11:04 -0400)]
11718: Update crunch-run for docker client API change in ContainerWait().
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.
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 [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
radhika [Tue, 9 May 2017 14:31:06 +0000 (10:31 -0400)]
refs #10645
Merge branch '10645-cr-mounts-display'
radhika [Tue, 9 May 2017 14:28:23 +0000 (10:28 -0400)]
10645: added comment
radhika [Tue, 9 May 2017 11:35:16 +0000 (07:35 -0400)]
Merge branch 'master' into 10645-cr-mounts-display
radhika [Tue, 9 May 2017 11:33:51 +0000 (07:33 -0400)]
10645: refactor the display of text with locators into a partial
radhika [Tue, 9 May 2017 01:58:07 +0000 (21:58 -0400)]
10645: collection links in command
radhika [Tue, 9 May 2017 01:21:02 +0000 (21:21 -0400)]
10645: regexp for keep_locator_in_json format
radhika [Mon, 8 May 2017 22:56:53 +0000 (18:56 -0400)]
10645: test update
radhika [Mon, 8 May 2017 22:43:54 +0000 (18:43 -0400)]
10645: display PDHs in command as clickable collections.
radhika [Mon, 8 May 2017 21:34:01 +0000 (17:34 -0400)]
10645: display keep locator in mounts as pdh/file_name
Tom Clegg [Mon, 8 May 2017 20:04:59 +0000 (16:04 -0400)]
Merge branch '11638-limit-conns'
closes #11638
Tom Clegg [Mon, 8 May 2017 20:04:01 +0000 (16:04 -0400)]
11638: Log a warning if Postgres pool size is unlimited.
Peter Amstutz [Mon, 8 May 2017 19:14:58 +0000 (15:14 -0400)]
10645: Tweak so that left column is col-md-6 (instead of col-md-5). Also tweak
full width part to be col-md-12. Move "priority" back to right hand column.
Tom Clegg [Mon, 8 May 2017 19:02:54 +0000 (15:02 -0400)]
11638: Add PostgresPool config option, and default application_name
Tom Clegg [Mon, 8 May 2017 18:17:46 +0000 (14:17 -0400)]
11629: Apply memory limits to job/pipeline "components" fields.
Tom Clegg [Mon, 8 May 2017 18:17:16 +0000 (14:17 -0400)]
11629: Fix items_available in groups#contents response.
radhika [Mon, 8 May 2017 17:59:35 +0000 (13:59 -0400)]
10645: L&F improvements
radhika [Mon, 8 May 2017 16:42:10 +0000 (12:42 -0400)]
Merge branch 'master' into 10645-cr-mounts-display
Tom Clegg [Mon, 8 May 2017 16:06:00 +0000 (12:06 -0400)]
Merge branch '11308-python3'
refs #11308
Tom Clegg [Mon, 8 May 2017 16:05:31 +0000 (12:05 -0400)]
11308: Merge branch 'master' into 11308-python3
Lucas Di Pentima [Mon, 8 May 2017 14:52:55 +0000 (11:52 -0300)]
10111: When dealing with output collection nodes, render the specific collection url instead of use its pdh
Lucas Di Pentima [Mon, 8 May 2017 14:31:06 +0000 (11:31 -0300)]
10111: Refactored the graph creation code to minimize the amount of API calls neeeded.
Tom Clegg [Mon, 8 May 2017 14:07:21 +0000 (10:07 -0400)]
11634: Prevent bundler from trying to use/update system gem cache.
Tom Clegg [Mon, 8 May 2017 13:59:35 +0000 (09:59 -0400)]
11634: Fix whitespace.
radhika [Mon, 8 May 2017 13:18:19 +0000 (09:18 -0400)]
10645: improve location regex usage
radhika [Fri, 5 May 2017 19:35:32 +0000 (15:35 -0400)]
10645: table width 100%
Tom Clegg [Fri, 5 May 2017 18:09:54 +0000 (14:09 -0400)]
11629: Limit database reads for all list responses, not just index.
radhika [Fri, 5 May 2017 19:30:46 +0000 (15:30 -0400)]
10112: add Definition tab to workflow page
radhika [Fri, 5 May 2017 17:38:21 +0000 (13:38 -0400)]
Merge branch 'master' into 10112-workflow-show
radhika [Fri, 5 May 2017 17:30:38 +0000 (13:30 -0400)]
Merge branch 'master' into 10645-cr-mounts-display
radhika [Fri, 5 May 2017 17:29:59 +0000 (13:29 -0400)]
10645: corrections to test fixture
radhika [Fri, 5 May 2017 16:05:11 +0000 (12:05 -0400)]
closes #8019
Merge branch '8019-crunchrun-log-throttle'
radhika [Fri, 5 May 2017 16:02:36 +0000 (12:02 -0400)]
Merge branch 'master' into 8019-crunchrun-log-throttle
Peter Amstutz [Fri, 5 May 2017 15:54:13 +0000 (11:54 -0400)]
8019: Make flush channel buffered again (because we want to be able to do back-to-back flushes).
Fix "> crunchLogBytesPerEvent" to ">= crunchLogBytesPerEvent" for consistency.
radhika [Fri, 5 May 2017 15:12:48 +0000 (11:12 -0400)]
10645: small style updates
Lucas Di Pentima [Fri, 5 May 2017 14:43:47 +0000 (11:43 -0300)]
10111: On output collections, name the collection node after the output_uuid reference.
Lucas Di Pentima [Fri, 5 May 2017 13:49:49 +0000 (10:49 -0300)]
10111: Fix integration test
radhika [Fri, 5 May 2017 13:44:53 +0000 (09:44 -0400)]
Merge branch 'master' into 10645-cr-mounts-display
radhika [Fri, 5 May 2017 01:32:37 +0000 (21:32 -0400)]
Merge branch 'master' into 10645-cr-mounts-display
radhika [Fri, 5 May 2017 01:31:18 +0000 (21:31 -0400)]
10645: mount inputs display
Lucas Di Pentima [Thu, 4 May 2017 21:37:09 +0000 (18:37 -0300)]
10111: Better labels on collection on the provenance graph.
Lucas Di Pentima [Thu, 4 May 2017 18:30:52 +0000 (15:30 -0300)]
Merge branch '10111-cr-prov-regression-fixes'
Refs #10111
Lucas Di Pentima [Thu, 4 May 2017 18:26:48 +0000 (15:26 -0300)]
10111: Flipped arrow between the cr and its childs cr.
radhika [Thu, 4 May 2017 17:32:34 +0000 (13:32 -0400)]
8019: uncomment the test statement
Lucas Di Pentima [Thu, 4 May 2017 17:17:54 +0000 (14:17 -0300)]
10111: Only add cr input collections by PDH.
Tom Clegg [Thu, 4 May 2017 17:02:40 +0000 (13:02 -0400)]
8019: Use tl.stopping channel instead of tl.flush to signal Close. Use unbuffered channel to signal flush.
Lucas Di Pentima [Thu, 4 May 2017 15:42:19 +0000 (12:42 -0300)]
10111: Skip log outputs from the provenance graph.
Container request's outputs are now added to the graph by their PDHs so that they connect with the CR childs inputs.
Tom Clegg [Thu, 4 May 2017 15:16:42 +0000 (11:16 -0400)]
11308: Merge branch 'master' into 11308-python3
Tom Clegg [Thu, 4 May 2017 15:09:41 +0000 (11:09 -0400)]
11308: Fix bytes vs. strings from recent merge.
projects / arvados.git / log