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.
radhika [Tue, 18 Apr 2017 20:35:08 +0000 (16:35 -0400)]
8019: expose crunch log throttling config parameters via discovery document
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.
Tom Clegg [Tue, 11 Apr 2017 15:33:17 +0000 (11:33 -0400)]
Merge branch '11349-nodemanager-status-api'
refs #11349
Tom Clegg [Tue, 11 Apr 2017 15:17:05 +0000 (11:17 -0400)]
11349: Move assertion outside loop for clarity.
Tom Clegg [Tue, 11 Apr 2017 15:16:50 +0000 (11:16 -0400)]
11349: Warn if management/status server is not enabled.
Tom Clegg [Mon, 10 Apr 2017 20:56:37 +0000 (16:56 -0400)]
7709: Clear deliveries before each test. Fixes flaky test.
Tom Clegg [Mon, 10 Apr 2017 18:57:56 +0000 (14:57 -0400)]
7709: Remove Ruby websocket server.
Lucas Di Pentima [Tue, 11 Apr 2017 13:33:24 +0000 (10:33 -0300)]
Merge branch '6304-dns-update-fix'
Closes #6304
Lucas Di Pentima [Tue, 11 Apr 2017 13:32:10 +0000 (10:32 -0300)]
6304: Change assertion type for better failure message.
Tom Clegg [Mon, 10 Apr 2017 19:45:40 +0000 (15:45 -0400)]
Secure link to google search.
No issue #
Lucas Di Pentima [Mon, 10 Apr 2017 17:58:08 +0000 (14:58 -0300)]
6304: Merge branch 'master' into 6304-dns-update-fix
Lucas Di Pentima [Mon, 10 Apr 2017 17:56:04 +0000 (14:56 -0300)]
6304: Corrected test setup to make it pass.
Added a separator to the temp file so that its name is more readable.
radhika [Mon, 10 Apr 2017 17:33:11 +0000 (13:33 -0400)]
Merge branch '8465-stdin-redirection' into 8465-stderr-redirection
radhika [Mon, 10 Apr 2017 17:32:22 +0000 (13:32 -0400)]
8465: test cleanup
Tom Clegg [Mon, 10 Apr 2017 17:07:07 +0000 (13:07 -0400)]
7709: Fix ActiveRecord::ImmutableRelation.
Lucas Di Pentima [Mon, 10 Apr 2017 16:51:28 +0000 (13:51 -0300)]
6304: Clean up temp files that could exist in case of writing errors.
Also added a test for this case, not working properly atm.
Tom Clegg [Mon, 10 Apr 2017 16:37:42 +0000 (12:37 -0400)]
7709: Merge branch 'master' into 7709-api-rails4
Conflicts:
services/api/app/controllers/arvados/v1/nodes_controller.rb
services/api/app/models/container_request.rb
services/api/db/structure.sql
Peter Amstutz [Mon, 10 Apr 2017 14:59:05 +0000 (10:59 -0400)]
Merge branch '11332-cwl-url-quoting' refs #11332
Peter Amstutz [Mon, 10 Apr 2017 14:58:33 +0000 (10:58 -0400)]
11332: Add @ to quote safelist.
Tom Clegg [Mon, 10 Apr 2017 14:20:31 +0000 (10:20 -0400)]
11349: Report wishlist size in status["nodes_wish"].
Peter Amstutz [Mon, 10 Apr 2017 14:07:23 +0000 (10:07 -0400)]
11332: Use urllib quote/unquote to handle special chars (e.g. '#')
Tom Clegg [Fri, 7 Apr 2017 19:20:04 +0000 (15:20 -0400)]
11349: Add management server with /status.json
Peter Amstutz [Fri, 7 Apr 2017 21:06:01 +0000 (17:06 -0400)]
8465: Set proper container flags to provide data on stdin.
Peter Amstutz [Fri, 7 Apr 2017 19:26:54 +0000 (15:26 -0400)]
Merge branch '11237-google-api-python-client' refs #11237
Peter Amstutz [Fri, 7 Apr 2017 18:31:21 +0000 (14:31 -0400)]
11237: Tweak version dependencies.
Peter Amstutz [Fri, 7 Apr 2017 18:21:35 +0000 (14:21 -0400)]
11237: Don't build oauth2client on ubuntu1604
Peter Amstutz [Fri, 7 Apr 2017 18:18:57 +0000 (14:18 -0400)]
11237: Bump google-api-python-client to 1.6.2 for better compatability across
oauth2client and Python versions.
Tom Clegg [Fri, 7 Apr 2017 17:23:57 +0000 (13:23 -0400)]
Merge branch '11209-unmount-subtype'
refs #11209
Peter Amstutz [Fri, 7 Apr 2017 15:43:56 +0000 (11:43 -0400)]
Increase ping delay in WatchdogActorTest to try and reduce spurious test failures. no issue #
Peter Amstutz [Fri, 7 Apr 2017 15:36:30 +0000 (11:36 -0400)]
Add check that gnutls.h is available so pycurl can compile. no issue #
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