Tom Clegg [Fri, 21 Apr 2017 20:02:50 +0000 (16:02 -0400)]
11308: Merge branch 'master' into 11308-python3
Conflicts:
sdk/python/arvados/arvfile.py
sdk/python/arvados/commands/get.py
sdk/python/arvados/commands/migrate19.py
sdk/python/tests/test_arv_get.py
sdk/python/tests/test_arvfile.py
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
Tom Clegg [Fri, 14 Apr 2017 20:16:58 +0000 (16:16 -0400)]
11308: Stop if fuse.h or gnutls.h sanity check fails.
Tom Clegg [Fri, 14 Apr 2017 20:12:55 +0000 (16:12 -0400)]
11308: Add sanity check for python3-dev.
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 18:45:01 +0000 (14:45 -0400)]
11308: Fix bytes vs. strings in arv-get command and tests.
Tom Clegg [Fri, 14 Apr 2017 18:44:23 +0000 (14:44 -0400)]
11308: Remove unused import.
Tom Clegg [Fri, 14 Apr 2017 17:52:57 +0000 (13:52 -0400)]
11308: Futurize test_arv_get.py and commands/get.py
Tom Clegg [Fri, 14 Apr 2017 17:43:10 +0000 (13:43 -0400)]
11308: Fix whitespace
Tom Clegg [Fri, 14 Apr 2017 17:52:26 +0000 (13:52 -0400)]
11308: Restore dependency lost in merge.
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
Tom Clegg [Wed, 12 Apr 2017 19:01:07 +0000 (15:01 -0400)]
11308: Merge branch 'master' into 11308-python3
Conflicts:
sdk/python/arvados/__init__.py
sdk/python/arvados/api.py
sdk/python/arvados/commands/ls.py
sdk/python/arvados/keep.py
sdk/python/setup.py
sdk/python/tests/test_arv_ls.py
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 16:02:14 +0000 (12:02 -0400)]
11308: Remove unused import.
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.
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 [Tue, 11 Apr 2017 02:04:00 +0000 (22:04 -0400)]
11308: Fix bytes vs. strings in test case.
Tom Clegg [Tue, 11 Apr 2017 00:23:04 +0000 (20:23 -0400)]
11308: Remove superfluous parens.
Tom Clegg [Tue, 11 Apr 2017 00:22:42 +0000 (20:22 -0400)]
11308: Avoid Python2-inefficient list() operations.
Tom Clegg [Tue, 11 Apr 2017 00:22:03 +0000 (20:22 -0400)]
11308: Fix futurize misinterpretation.
Tom Clegg [Tue, 11 Apr 2017 00:21:19 +0000 (20:21 -0400)]
11308: Put back exception handling
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
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.
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
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