Lucas Di Pentima [Thu, 27 Apr 2017 20:15:53 +0000 (17:15 -0300)]
11579: Explicitly following links on test.
Lucas Di Pentima [Thu, 27 Apr 2017 20:12:56 +0000 (17:12 -0300)]
11579: Tests added.
Lucas Di Pentima [Thu, 27 Apr 2017 19:51:31 +0000 (16:51 -0300)]
11579: Added symlinked dir traversal as the default behavior.
Added flag to disable this and ignore symlinked dirs: --no-follow-links.
Lucas Di Pentima [Thu, 27 Apr 2017 16:54:32 +0000 (13:54 -0300)]
11579: Test proving the bug: arv-put does not follow symlinks.
Lucas Di Pentima [Wed, 26 Apr 2017 18:56:00 +0000 (15:56 -0300)]
Merge branch '10111-cr-provenance-graph'
Closes #10111
Lucas Di Pentima [Wed, 26 Apr 2017 18:55:03 +0000 (15:55 -0300)]
10111: Merge branch 'master' into 10111-cr-provenance-graph
Lucas Di Pentima [Wed, 26 Apr 2017 18:29:20 +0000 (15:29 -0300)]
10111: Replaced graph edges names: cr->child & mounts->input.
Nico Cesar [Wed, 26 Apr 2017 18:25:22 +0000 (14:25 -0400)]
Merge branch '11305-migrate-docker19-doc'
Documentation for the migration process from Docker 1.9 or less to Docker 1.10+
Docker changed the format of the images, and there is an arvados tool arvados-migrate-docker19,
this commit explains how to migrate
refs #11305
Lucas Di Pentima [Wed, 26 Apr 2017 16:28:06 +0000 (13:28 -0300)]
10111: If there is no cwl.input.json object as part of a CR mount list, search for input PDHs on the entire mount list
Lucas Di Pentima [Wed, 26 Apr 2017 11:56:01 +0000 (08:56 -0300)]
10111: Only include those mounts that are declared on the cwl input definition.
Removed trailing spaces.
Lucas Di Pentima [Tue, 25 Apr 2017 19:26:38 +0000 (16:26 -0300)]
10111: Added "child" CRs to the graph, and removed container image and requesting container elements.
Tom Clegg [Tue, 25 Apr 2017 17:22:44 +0000 (13:22 -0400)]
Merge branch '11544-bad-collection-id-500'
closes #11544
Tom Clegg [Tue, 25 Apr 2017 16:57:11 +0000 (12:57 -0400)]
11544: Return 404 instead of 500 for malformed collection IDs.
Peter Amstutz [Tue, 25 Apr 2017 15:58:34 +0000 (11:58 -0400)]
Merge branch '11507-deleted-bufferblocks' refs #11507
Peter Amstutz [Fri, 21 Apr 2017 20:36:21 +0000 (16:36 -0400)]
11507: Move repack_writes() method from ArvadosFile to BufferBlock.
Lucas Di Pentima [Tue, 25 Apr 2017 03:50:31 +0000 (00:50 -0300)]
10111: Tests added
Lucas Di Pentima [Mon, 24 Apr 2017 20:07:19 +0000 (17:07 -0300)]
10111: Merge branch 'master' into 10111-cr-provenance-graph
Lucas Di Pentima [Mon, 24 Apr 2017 19:30:00 +0000 (16:30 -0300)]
10111: Added provenance graph for container requests.
Tom Clegg [Mon, 24 Apr 2017 18:57:41 +0000 (14:57 -0400)]
Fix panic in test case (overwriting a locked sync.Mutex with an unlocked one).
No issue #
Tom Clegg [Mon, 24 Apr 2017 18:05:20 +0000 (14:05 -0400)]
Merge branch '11517-no-count-logs'
refs #11517
Tom Clegg [Mon, 24 Apr 2017 18:02:54 +0000 (14:02 -0400)]
11517: Add test for count=none.
Tom Clegg [Mon, 24 Apr 2017 18:00:45 +0000 (14:00 -0400)]
11517: Skip database reset in some workbench unit tests.
Reduces unit test suite time by half.
Tom Clegg [Mon, 24 Apr 2017 17:42:31 +0000 (13:42 -0400)]
11517: Comment with_count() method
Nico Cesar [Mon, 24 Apr 2017 17:02:15 +0000 (13:02 -0400)]
11305: added kernel and module dependency for docker migration in doc
refs #11305
Tom Clegg [Fri, 21 Apr 2017 19:17:46 +0000 (15:17 -0400)]
11517: Use count=none when retrieving logs.
Nico Cesar [Mon, 24 Apr 2017 12:43:55 +0000 (08:43 -0400)]
we need the tagged image to do this
Peter Amstutz [Fri, 21 Apr 2017 18:48:15 +0000 (14:48 -0400)]
11507: Put self._pending_write_size update back under the lock.
Peter Amstutz [Fri, 21 Apr 2017 18:31:49 +0000 (14:31 -0400)]
11507: More small block packing fixes:
* Repack writes before small block merging.
* Update segments of file with new locator/segment offset instead of replacing
entire file contents.
Peter Amstutz [Fri, 21 Apr 2017 13:55:00 +0000 (09:55 -0400)]
11507: Cleanup
Peter Amstutz [Thu, 20 Apr 2017 21:45:37 +0000 (17:45 -0400)]
11507: Put bufferblocks into DELETED state when deleted so they don't get
reused accidentally if there are dangling references. When packing small
blocks, update segments with the block hash instead of the bufferblock id to
avoid dangling references.
Peter Amstutz [Thu, 20 Apr 2017 21:10:30 +0000 (17:10 -0400)]
11507: Test cases that reproduce bug
Peter Amstutz [Thu, 20 Apr 2017 18:18:44 +0000 (14:18 -0400)]
Merge branch '11510-sdk-extend-files' refs #11510
Peter Amstutz [Thu, 20 Apr 2017 18:15:49 +0000 (14:15 -0400)]
11510: Tweak interface to better match Pythons "io.IOBase" class.
Tom Clegg [Thu, 20 Apr 2017 18:10:50 +0000 (14:10 -0400)]
Merge branch '11470-update-task-fields'
refs #11470
Peter Amstutz [Thu, 20 Apr 2017 17:25:56 +0000 (13:25 -0400)]
11510: Fix truncate() to not change file pointer. Additional tests.
Peter Amstutz [Thu, 20 Apr 2017 14:41:05 +0000 (10:41 -0400)]
11510: Repack writes any time there's more than one segment referencing the same bufferblock.
Peter Amstutz [Tue, 18 Apr 2017 21:54:57 +0000 (17:54 -0400)]
11510: Fix longstanding bug in replace_range() when appending data from a buffer that was written out of order.
Tom Clegg [Thu, 20 Apr 2017 02:12:42 +0000 (22:12 -0400)]
11470: Fix identifiers to conventional Go.
Tom Clegg [Thu, 20 Apr 2017 02:09:45 +0000 (22:09 -0400)]
11470: Fix accidentally cleared fields during job_task update.
Updating with a Task struct had the effect of clearing job_uuid,
created_by_job_task_uuid, and parameters fields, and resetting
sequence to 0.
Lucas Di Pentima [Wed, 19 Apr 2017 20:42:26 +0000 (17:42 -0300)]
Merge branch '11502-unstripped-manifest-fix'
Closes #11502, #11511
Lucas Di Pentima [Wed, 19 Apr 2017 19:38:30 +0000 (16:38 -0300)]
11502: Merge branch 'master' into 11502-unstripped-manifest-fix
Lucas Di Pentima [Wed, 19 Apr 2017 19:28:26 +0000 (16:28 -0300)]
11502: Instead of asking for a stripped manifest, replace the tokens with some constant string to do the comparison.
Tom Clegg [Wed, 19 Apr 2017 19:04:20 +0000 (15:04 -0400)]
Merge branch '11517-indexes'
refs #11517
Tom Clegg [Wed, 19 Apr 2017 18:00:01 +0000 (14:00 -0400)]
11517: Add indexes to help slow queries.
radhika [Wed, 19 Apr 2017 15:27:33 +0000 (11:27 -0400)]
closes #11450
Merge branch '11450-workflows-page'
radhika [Fri, 14 Apr 2017 17:29:54 +0000 (13:29 -0400)]
11450: workflows index page
Peter Amstutz [Tue, 18 Apr 2017 20:40:51 +0000 (16:40 -0400)]
11510: Add support for sparse writes to ArvadosFile.
Allow seeking past end of file. Allow using truncate() to extend file size. Add zero padding to fill in gaps.
Tom Clegg [Tue, 18 Apr 2017 18:01:47 +0000 (14:01 -0400)]
11459: Move RAILS_PACKAGE_ITERATION to run-library.
Otherwise, the SSO build script cannot see it.
refs #11459
Tom Clegg [Tue, 18 Apr 2017 17:01:01 +0000 (13:01 -0400)]
Merge branch '11509-keep-web-cors-range'
closes #11509
Tom Clegg [Tue, 18 Apr 2017 17:00:27 +0000 (13:00 -0400)]
11509: Add comments.
Lucas Di Pentima [Tue, 18 Apr 2017 16:45:39 +0000 (13:45 -0300)]
11502: Use os.path.join instead of formatting path-like strings on tests.
Lucas Di Pentima [Tue, 18 Apr 2017 16:36:44 +0000 (13:36 -0300)]
11502: Avoid races on test by getting the unstripped manifest version before the comparison.
Lucas Di Pentima [Tue, 18 Apr 2017 15:31:48 +0000 (12:31 -0300)]
11502: Fix regression by writing a collection manifest with its access tokens in place when asked by PDH & UUID.
Added --strip-manifest argument to allow writing manifests without tokens.
Updated tests accordingly.
Tom Clegg [Tue, 18 Apr 2017 15:25:15 +0000 (11:25 -0400)]
Fix ignored symlink failure.
No issue #
radhika [Tue, 18 Apr 2017 13:57:55 +0000 (09:57 -0400)]
refs #11465
Merge branch '11465-disabled-collection-file-tooltips'
radhika [Tue, 18 Apr 2017 13:56:48 +0000 (09:56 -0400)]
11465: tooltip on disabled pencil icon
Tom Clegg [Mon, 17 Apr 2017 23:19:10 +0000 (19:19 -0400)]
11509: Allow cross-origin requests with Range headers.
radhika [Mon, 17 Apr 2017 19:17:13 +0000 (15:17 -0400)]
closes #11465
Merge branch '11465-disabled-collection-file-tooltips'
radhika [Mon, 17 Apr 2017 17:34:44 +0000 (13:34 -0400)]
11465: correct disabled tooltip behavior on image types
Tom Clegg [Mon, 17 Apr 2017 14:01:06 +0000 (10:01 -0400)]
Fix crunch-run tests.
refs #11209
radhika [Mon, 17 Apr 2017 01:20:11 +0000 (21:20 -0400)]
11465: add tooltips to disabled collection file controls
Tom Clegg [Fri, 14 Apr 2017 20:42:12 +0000 (16:42 -0400)]
Merge branch '11209-crunch-unmount-all'
refs #11209
Lucas Di Pentima [Fri, 14 Apr 2017 20:26:29 +0000 (17:26 -0300)]
Merge branch '11502-arvget-flaky-test'
Closes #11502
Lucas Di Pentima [Fri, 14 Apr 2017 20:04:35 +0000 (17:04 -0300)]
11502: When getting a manifest using a PDH, the manifest is stripped.
Corrected test so that when comparing manifests, it does so by comparing stripped ones so that it doesn't intermittently fail.
Tom Clegg [Fri, 14 Apr 2017 17:19:16 +0000 (13:19 -0400)]
11209: Use arv-mount --unmount-all instead of mount|awk|xargs script to clean up stale mounts from previous jobs.
Peter Amstutz [Fri, 14 Apr 2017 15:17:46 +0000 (11:17 -0400)]
Merge branch '11462-cwl-cache-collectionreader' refs #11462
Peter Amstutz [Fri, 14 Apr 2017 15:08:01 +0000 (11:08 -0400)]
11462: Log ArgumentError in make_output_collection. Add test for CollectionCache.
Peter Amstutz [Fri, 14 Apr 2017 14:21:33 +0000 (10:21 -0400)]
Fix regression, restore a line that shouldn't have been removed. refs #10401
Peter Amstutz [Thu, 13 Apr 2017 21:32:44 +0000 (17:32 -0400)]
11462: Fix crunch script for fetcher_constructor constructor change.
Peter Amstutz [Thu, 13 Apr 2017 19:48:50 +0000 (15:48 -0400)]
Add missing test file. refs #10401
Peter Amstutz [Thu, 13 Apr 2017 19:54:15 +0000 (15:54 -0400)]
11462: Runner asks for 3000 MB of RAM by default instead of 1024.
Peter Amstutz [Thu, 13 Apr 2017 19:48:50 +0000 (15:48 -0400)]
11462: Add missing test file.
Peter Amstutz [Thu, 13 Apr 2017 19:46:05 +0000 (15:46 -0400)]
11462: Bump cwltool version for mergedirs() fix
Peter Amstutz [Thu, 13 Apr 2017 19:11:39 +0000 (15:11 -0400)]
11462: Store CollectionReader objects in a central cache to avoid redundant
fetches & storing multiple copies. On pipeline with large inputs, reduced
memory usage by up to 70%.
radhika [Thu, 13 Apr 2017 18:20:32 +0000 (14:20 -0400)]
11465: add tooltips to disabled collection file controls
Peter Amstutz [Thu, 13 Apr 2017 15:40:27 +0000 (11:40 -0400)]
Merge branch '11493-cwl-six' refs #11493
Peter Amstutz [Thu, 13 Apr 2017 15:13:41 +0000 (11:13 -0400)]
11493: Bump cwltool version for relaxed dependency on 'six'
Peter Amstutz [Wed, 12 Apr 2017 20:10:13 +0000 (16:10 -0400)]
Merge branch '8567-moar-docker' refs #8567
Peter Amstutz [Wed, 12 Apr 2017 18:45:24 +0000 (14:45 -0400)]
Merge branch '10401-limit-dir-expansion' closes #10401
Peter Amstutz [Wed, 12 Apr 2017 18:38:33 +0000 (18:38 +0000)]
8567: Migrate unnamed images
Lucas Di Pentima [Wed, 12 Apr 2017 18:37:03 +0000 (15:37 -0300)]
Merge branch '11341-arvput-resume-error'
Closes #11341
Peter Amstutz [Wed, 12 Apr 2017 18:27:15 +0000 (14:27 -0400)]
Merge branch '8465-cwl-containers-stdin-stderr' closes #8465
radhika [Wed, 12 Apr 2017 16:42:16 +0000 (12:42 -0400)]
closes #11365
Merge branch '11365-collection-lock-button'
Lucas Di Pentima [Wed, 12 Apr 2017 16:34:49 +0000 (13:34 -0300)]
11341: Fixed log message
Lucas Di Pentima [Wed, 12 Apr 2017 16:32:49 +0000 (13:32 -0300)]
11341: Added additional information log for cases when the user ask to not use any cache.
Peter Amstutz [Wed, 12 Apr 2017 16:22:25 +0000 (12:22 -0400)]
10401: Document LoadListingRequirement in Arvados extensions.
radhika [Fri, 7 Apr 2017 21:08:14 +0000 (17:08 -0400)]
11365: "lock" collection to prevent user from deleting / renaming files until user explicitly unlocks by clicking the button.
Peter Amstutz [Wed, 12 Apr 2017 16:08:52 +0000 (12:08 -0400)]
10401: Add integration tests for directory listing behavior.
Lucas Di Pentima [Wed, 12 Apr 2017 16:07:05 +0000 (13:07 -0300)]
11341: Use NamedTemporaryFile instead of mkstemp for cache saving.
Added logging messages to inform the user what's happening with the cache file.
Tom Clegg [Wed, 12 Apr 2017 15:37:54 +0000 (11:37 -0400)]
11349: Fix section name in example configs.
refs #11349
Peter Amstutz [Wed, 12 Apr 2017 14:33:25 +0000 (10:33 -0400)]
8465: Add unit test for generating container request with std* redirection.
Peter Amstutz [Wed, 12 Apr 2017 14:12:06 +0000 (10:12 -0400)]
Merge branch 'master' into 10401-limit-dir-expansion
Peter Amstutz [Tue, 11 Apr 2017 23:03:52 +0000 (19:03 -0400)]
cwl/test_with_arvbox.sh pulls arvados/jobs:latest refs #11457
Peter Amstutz [Tue, 11 Apr 2017 22:00:25 +0000 (18:00 -0400)]
Build SSO packages for Ubuntu 1604. refs #11457
Peter Amstutz [Tue, 11 Apr 2017 19:56:56 +0000 (15:56 -0400)]
10401: Get structure.sql from master.
Peter Amstutz [Tue, 11 Apr 2017 19:55:30 +0000 (15:55 -0400)]
Merge branch 'master' into 10401-limit-dir-expansion
Tom Clegg [Tue, 11 Apr 2017 18:31:42 +0000 (14:31 -0400)]
Build packages for python "future" module.
refs #11349
refs #11308
radhika [Tue, 11 Apr 2017 18:34:46 +0000 (14:34 -0400)]
refs #8465
Merge branch '8465-stderr-redirection'
radhika [Tue, 11 Apr 2017 18:08:21 +0000 (14:08 -0400)]
Merge branch 'master' into 8465-stderr-redirection
Peter Amstutz [Tue, 11 Apr 2017 17:40:30 +0000 (13:40 -0400)]
8465: arvados-cwl-runner support for stdin and stderr redirection with containers.
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