Tom Clegg [Thu, 31 May 2018 21:06:32 +0000 (17:06 -0400)]
12061: Poll aggressively in integration tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 31 May 2018 21:01:15 +0000 (17:01 -0400)]
12061: Allow sub-second poll times and sub-minute shutdown windows.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 31 May 2018 19:05:47 +0000 (15:05 -0400)]
Merge branch '13517-buffer-leak'
refs #13517
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 31 May 2018 18:39:41 +0000 (14:39 -0400)]
Merge branch '12061-flaky-tests'
refs #12061
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 31 May 2018 18:26:59 +0000 (14:26 -0400)]
12061: Explicitly join actor thread after stopping.
Fixes the "nonfatal" test case the same way the "fatal" test case was
fixed in
6706c6d46c6cfb080371b147b60fcaa191bd55a6.
Since the nonfatal case just tests that kill_mock did *not* get
called, the race condition used to make the test ineffectual
occasionally, instead of failing occasionally.
The race condition became visible only after the status reporting test
was added.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 31 May 2018 17:44:18 +0000 (13:44 -0400)]
13517: Fix leaked goroutine and buffer on failed S3 write.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 30 May 2018 20:32:20 +0000 (16:32 -0400)]
12061: Don't round down to 1s in timestamp parser.
ComputeNodeMonitorActor.offer_arvados_pair() pairs nodes only if
first_ping_time >= cloud_node_start_time
However, first_ping_time is passed through arvados_timestamp() before
this comparison, which was truncating the subsecond part -- so the
comparison was effectively
floor(first_ping_time) >= cloud_node_start_time
When FPT and CNST differed only in the subsecond part, this comparison
failed, and the nodes could never be paired. This caused sporadic
failures in tests, where the two values are often separated by less
than a second.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 30 May 2018 20:30:45 +0000 (16:30 -0400)]
12061: Change busywait approach to preserve assertion messages.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 30 May 2018 11:39:30 +0000 (07:39 -0400)]
Merge branch '11162-wes-support' refs #11162
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 29 May 2018 20:05:27 +0000 (16:05 -0400)]
Merge branch '13513-balance-deadlock'
fixes #13513
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 29 May 2018 17:16:55 +0000 (13:16 -0400)]
11162: Remove debugging check
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 29 May 2018 13:46:04 +0000 (09:46 -0400)]
13513: Fix deadlocked workers.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Sat, 26 May 2018 02:04:21 +0000 (22:04 -0400)]
Fix crunch_script for jobs api refs #13516
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Sat, 26 May 2018 01:49:14 +0000 (21:49 -0400)]
Replace unicode copyright character with ASCII in README.Rmd
Fix documentation generation
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 25 May 2018 20:45:12 +0000 (16:45 -0400)]
11162: Add tests for http_to_keep.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 25 May 2018 14:16:07 +0000 (10:16 -0400)]
11162: Add test for --submit-request-uuid
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 25 May 2018 13:55:13 +0000 (09:55 -0400)]
11162: Fix tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 23 May 2018 20:56:40 +0000 (16:56 -0400)]
11162: Bump cwltool for fix in generating basename from url
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 23 May 2018 19:23:44 +0000 (15:23 -0400)]
11162: Smarter http downloads.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 23 May 2018 17:17:40 +0000 (13:17 -0400)]
11162: Add logging about checking cache
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 23 May 2018 16:52:22 +0000 (12:52 -0400)]
11162: Set a default cache time of 24 hours for files fetched over http.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 23 May 2018 00:45:58 +0000 (20:45 -0400)]
11162: Add progress for http data download.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 22 May 2018 20:53:16 +0000 (16:53 -0400)]
11162: Add --submit-request-uuid
Allows container request to be created separately from initialization
that occurs prior to actually committing the container to run.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 14 May 2018 16:02:51 +0000 (12:02 -0400)]
11162: Handle missing git
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 11 May 2018 20:36:54 +0000 (16:36 -0400)]
11162: Support public http and https file references
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Thu, 24 May 2018 15:30:58 +0000 (11:30 -0400)]
2411: Merge branch '2411-another-pass'
refs #2411
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 24 May 2018 02:26:25 +0000 (22:26 -0400)]
2411: Add a bunch of exceptions to .licenseignore for our R sdk
refs #2411
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 24 May 2018 02:26:05 +0000 (22:26 -0400)]
2411: Add license header to sdk/R/README.Rmd
refs #2411
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 24 May 2018 02:17:25 +0000 (22:17 -0400)]
2411: add copyright headers to our R files.
refs #2411
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 24 May 2018 02:16:58 +0000 (22:16 -0400)]
2411: Add support for R source files to build/check-copyright-notices
refs #2411
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 23 May 2018 21:50:16 +0000 (17:50 -0400)]
2411: another pass at adding copyright headers where missing.
refs #2411
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 23 May 2018 14:04:13 +0000 (10:04 -0400)]
Add Veritas Genetics to the AUTHORS file.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Fuad Muhic [Wed, 23 May 2018 13:07:39 +0000 (15:07 +0200)]
Merge branch '13430-allow-storage-classes'
refs #13430
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Wed, 23 May 2018 10:15:31 +0000 (12:15 +0200)]
Merge branch '13453-r-sdk-incorrect-rest-call-fix'
refs #13453
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Wed, 23 May 2018 10:05:41 +0000 (12:05 +0200)]
Added test that checks that saving a committed collection updates the storage_classes_desired
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Wed, 23 May 2018 01:25:58 +0000 (21:25 -0400)]
Tweak arvados-cwl-runner subprocess32 version dependency refs #13516
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 22 May 2018 23:19:21 +0000 (19:19 -0400)]
Fix tests refs #13516
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 22 May 2018 21:08:13 +0000 (17:08 -0400)]
Merge branch '13516-fix-cwl-tests' refs #13516
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 22 May 2018 17:55:54 +0000 (13:55 -0400)]
13516: Bump cwltool, cwltest and subprocess32 versions
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Tue, 22 May 2018 16:08:36 +0000 (18:08 +0200)]
Updated save method of Collection class to always update when
storage_classes is specified.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Tue, 22 May 2018 15:40:15 +0000 (17:40 +0200)]
Added tests and documentation for save and save_new methods in
Collection class.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Ward Vandewege [Tue, 22 May 2018 13:58:52 +0000 (09:58 -0400)]
9918: Merge branch '9918-index-timeout'
refs #9918
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Tue, 22 May 2018 13:47:40 +0000 (09:47 -0400)]
9918: Merge branch 'master' into 9918-index-timeout
refs #9918
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Fuad Muhic [Tue, 22 May 2018 10:25:28 +0000 (12:25 +0200)]
Added tests to arv-put to cover storage classes feature.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Mon, 21 May 2018 17:54:19 +0000 (13:54 -0400)]
Merge branch '12995-wb-merge-acct' refs #12995
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 21 May 2018 16:29:19 +0000 (12:29 -0400)]
12995: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Mon, 21 May 2018 15:18:37 +0000 (17:18 +0200)]
Added --storage-classes argument to arv-put.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Mon, 21 May 2018 15:08:17 +0000 (11:08 -0400)]
12995: Add username to link_accounts page.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 21 May 2018 14:59:47 +0000 (10:59 -0400)]
12995: Add user and admin documentation pages.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 18 May 2018 20:57:21 +0000 (16:57 -0400)]
12995: Do nested logout/login to workaround SSO session.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 18 May 2018 20:28:44 +0000 (16:28 -0400)]
12995: Bugfix to support following chained user uuid redirection.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 18 May 2018 19:50:15 +0000 (15:50 -0400)]
9918: Add RequestTimeout config for keep-balance.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 18 May 2018 19:37:23 +0000 (15:37 -0400)]
12995: Don't let admins lose admin privs by linking a non-admin account.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 18 May 2018 19:10:53 +0000 (15:10 -0400)]
Merge branch '13164-container-deadlock'
refs #13164
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 18 May 2018 18:34:43 +0000 (14:34 -0400)]
12995: Add testing
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 18 May 2018 18:29:34 +0000 (14:29 -0400)]
13164: Lock tables in order when locking a container.
Locking involves assigning auth_uuid, which involves looking up
container requests, so both tables must be locked in order to avoid
deadlock.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 18 May 2018 18:02:29 +0000 (14:02 -0400)]
13164: Lock tables in order for container updates.
Otherwise, a container update can lock a container row, then perform
container request queries, which can deadlock with another thread that
locked container_requests first.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Fri, 18 May 2018 13:30:48 +0000 (10:30 -0300)]
Merge branch '12737-wb-rails42-upgrade'
Closes #12737
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 17 May 2018 21:41:01 +0000 (17:41 -0400)]
12995: Can now merge with inactive accounts.
Checks that the remaining account is active so users don't lock
themselves out by accident.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Thu, 17 May 2018 20:25:21 +0000 (17:25 -0300)]
12737: Fix integration tests
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 17 May 2018 19:45:59 +0000 (15:45 -0400)]
12995: Can merge accounts in both directions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Thu, 17 May 2018 17:47:37 +0000 (14:47 -0300)]
12737: Fix controller tests
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 17 May 2018 17:00:36 +0000 (13:00 -0400)]
12995: Linking alternate login works.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 17 May 2018 16:07:06 +0000 (12:07 -0400)]
12995: Add link account page with confirmation.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Wed, 16 May 2018 20:59:29 +0000 (16:59 -0400)]
Fix another ineffassign warning in our golang code.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Lucas Di Pentima [Wed, 16 May 2018 20:20:20 +0000 (17:20 -0300)]
12737: Assign empty default values on serialized attributes
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 16 May 2018 13:24:12 +0000 (10:24 -0300)]
12737: Send serialized attributes when save()
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 15 May 2018 18:36:42 +0000 (14:36 -0400)]
Merge branch '12708-report-storage-classes'
refs #12708
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 15 May 2018 18:35:55 +0000 (14:35 -0400)]
Merge branch '13164-container-locking'
refs #13164
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 14 May 2018 19:32:26 +0000 (15:32 -0400)]
12737: Rename config serve_static_assets to serve_static_files.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 14 May 2018 19:32:23 +0000 (15:32 -0400)]
12737: Fix serialized column setup.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Mon, 14 May 2018 15:40:25 +0000 (12:40 -0300)]
12737: Remove attribute from previous tests
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 14 May 2018 14:28:36 +0000 (10:28 -0400)]
13164: Lock tables when updating multiple containers + CRs.
Avoid database inconsistencies after update races.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Mon, 14 May 2018 14:17:35 +0000 (11:17 -0300)]
12737: Upgrade workbench from rails 4.1 to 4.2 (WIP)
Serialization isn't working properly, Hash & Array columns happily receive
these types but return their text versions when accessed.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Fri, 11 May 2018 20:54:16 +0000 (16:54 -0400)]
Merge branch '13473-no-cpu-constraints'
refs #13473
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 11 May 2018 19:38:51 +0000 (15:38 -0400)]
13473: Tidy up slurmConstraintArgs func.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 11 May 2018 19:25:36 +0000 (15:25 -0400)]
13473: Drop slurm resource constraints when using instancetype=X.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Ward Vandewege [Fri, 11 May 2018 00:31:11 +0000 (20:31 -0400)]
Merge branch 'thehyve/fix-crunch-documentation' Fix a typo in Crunch Dispatch installation manual
No issue #, github PR 66
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Tom Clegg [Thu, 10 May 2018 20:07:33 +0000 (16:07 -0400)]
Merge branch '13446-keepstore-tls'
refs #13446
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 10 May 2018 20:07:16 +0000 (16:07 -0400)]
Merge branch '9918-index-error'
refs #9918
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 10 May 2018 20:05:30 +0000 (16:05 -0400)]
9918: Don't mask http/network error with response body format error.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 10 May 2018 18:12:16 +0000 (14:12 -0400)]
Bump package iteration for a-c-r in run-build-docker-jobs-image.sh
refs #13435
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 10 May 2018 15:41:17 +0000 (11:41 -0400)]
Bump arvados-python-client version for consistent dependencies
refs #13435
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 10 May 2018 15:38:13 +0000 (11:38 -0400)]
Merge branch '12256-cwl-defaults' closes #12256
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 10 May 2018 15:03:29 +0000 (11:03 -0400)]
12256: Comments about workflow references / extra files.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Thu, 10 May 2018 09:05:29 +0000 (11:05 +0200)]
Replaced call to non-existent method execute in RESTService class with
correct call to exec method.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Wed, 9 May 2018 19:56:20 +0000 (15:56 -0400)]
13446: Enable TLS if given TLSCertificateFile and TLSKeyFile.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 9 May 2018 19:24:55 +0000 (15:24 -0400)]
12256: Only scan for referenced files first time after packing
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 9 May 2018 18:44:42 +0000 (14:44 -0400)]
12256: Pull up minimum ruamel.yaml version to get consistent output.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 9 May 2018 18:28:14 +0000 (14:28 -0400)]
12256: Bump cwltool version for workflow packing bugfix.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 4 May 2018 20:44:29 +0000 (16:44 -0400)]
12256: Handle default references in RunInSingleContainer
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 3 May 2018 16:34:05 +0000 (12:34 -0400)]
12256: Add a bunch of test cases.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 3 May 2018 14:37:44 +0000 (10:37 -0400)]
12256: Fix anonymous directory default inputs with file literals
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Wed, 9 May 2018 18:19:10 +0000 (15:19 -0300)]
Merge branch '12737-api-security-deps-fixes'
Refs #12737
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Wed, 9 May 2018 17:53:11 +0000 (13:53 -0400)]
Fix subprocess32 version constraint, refs #13435
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 9 May 2018 17:47:11 +0000 (13:47 -0400)]
Avoid copying mutex after first use.
refs #13455
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 9 May 2018 17:11:55 +0000 (13:11 -0400)]
Avoid http client race in test case.
If we don't wait for Put() to return before returning from the test
case, CloseIdleConnections can cause Put() to fail, and the resulting
call to t.Error() panics the testing package.
"errType *url.Error, err Put
http://fakeaccountname.blob.127.0.0.1:42861/fakecontainername/
e4d909c290d0fb1ca068ffaddf22cbd0:
net/http: HTTP/1.x transport connection broken: http:
CloseIdleConnections called"
"panic: Fail in goroutine after TestAzureBlobVolumeCreateBlobRace has completed"
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Wed, 9 May 2018 17:03:04 +0000 (14:03 -0300)]
12737: Updated gem dependencies, adressing a couple of known vulnerabilities.
* https://nvd.nist.gov/vuln/detail/CVE-2018-3741
* https://github.com/flavorjones/loofah/issues/144
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 8 May 2018 21:34:39 +0000 (17:34 -0400)]
12708: Log desired/short/surplus figures for each storage class.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 8 May 2018 13:30:15 +0000 (09:30 -0400)]
Merge branch '12626-merge-accounts'
refs #12626
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
projects / arvados.git / log