Tom Clegg [Tue, 9 Jan 2018 15:54:50 +0000 (10:54 -0500)]
Merge branch '12702-migrate-user'
closes #12702
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 9 Jan 2018 14:50:17 +0000 (09:50 -0500)]
Merge branch '12913-secondary-mounts' refs #12913
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 9 Jan 2018 14:31:39 +0000 (09:31 -0500)]
12913: Add integration test for fix
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 8 Jan 2018 21:39:15 +0000 (16:39 -0500)]
12913: Apply secondaryFiles to inputs to RunInSingleContainer
Fixes bug where mounts mismatch cwl.input.yml due to discovering
secondaryFiles during workflow execution.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 20:53:28 +0000 (15:53 -0500)]
12876: Update govendor bundle.
refs #12876
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 20:51:08 +0000 (15:51 -0500)]
Merge branch '12876-arvados-client'
refs #12876
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 18:30:55 +0000 (13:30 -0500)]
12702: Disallow updating sys/anon UUIDs. Test updating current user.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 16:10:00 +0000 (11:10 -0500)]
Update govendor bundle.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 16:02:51 +0000 (11:02 -0500)]
Merge branch '12908-slurm-cons-res'
fixes #12908
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 16:01:55 +0000 (11:01 -0500)]
12908: Mention SelectType=select/cons_res in slurm config advice.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 15:34:01 +0000 (10:34 -0500)]
Merge branch '12720-systemd-compat'
fixes #12720
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 15 Dec 2017 19:08:16 +0000 (14:08 -0500)]
12720: Invoke StartLimitInterval three different ways.
Needed to convince various versions of systemd not to go into "leave
service down and wait for manual intervention" mode automatically.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Ward Vandewege [Mon, 8 Jan 2018 02:38:29 +0000 (21:38 -0500)]
Add systemd unit file for arvados-health.
refs #12260
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 01:40:32 +0000 (20:40 -0500)]
12876: Call attention to missing python and ruby dependencies.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 01:16:46 +0000 (20:16 -0500)]
12876: Recover from more symlink confusion.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 01:14:02 +0000 (20:14 -0500)]
12876: List subcommands like "arvados-client keep get" in main usage.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 8 Jan 2018 01:01:05 +0000 (20:01 -0500)]
12876: Merge branch 'master' into 12876-arvados-client
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 5 Jan 2018 22:13:39 +0000 (17:13 -0500)]
Merge branch '12870-fuse-binds-invalidate'
refs #12870
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 5 Jan 2018 20:13:25 +0000 (20:13 +0000)]
12870: Fix test
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 5 Jan 2018 20:07:25 +0000 (15:07 -0500)]
12702: Add API docs for users#update_uuid.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 5 Jan 2018 19:39:51 +0000 (19:39 +0000)]
12870: Don't send invalidation for inodes still referenced by kernel
When trying to flush cached inode contents, invalidating dentries
which are still referenced can race with lookups, causing the kernel to return
spurious "not found" errors.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 5 Jan 2018 15:38:04 +0000 (10:38 -0500)]
12702: Add /arvados/v1/users/{uuid}/update_uuid API.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 2 Jan 2018 19:17:16 +0000 (14:17 -0500)]
Drop superfluous "node-info" prefix in node-info.txt log file.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 2 Jan 2018 05:47:04 +0000 (00:47 -0500)]
12876: Pass commands through to ruby/python programs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 27 Dec 2017 07:19:17 +0000 (02:19 -0500)]
12876: Simplify legacy option parsing.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sun, 24 Dec 2017 19:44:36 +0000 (14:44 -0500)]
12876: Fix up error/usage messages.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sat, 23 Dec 2017 06:26:28 +0000 (01:26 -0500)]
12876: More compatibility with "arv get".
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sat, 23 Dec 2017 06:14:11 +0000 (01:14 -0500)]
12876: Util to accept subcommand after initial args.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 22 Dec 2017 14:45:58 +0000 (09:45 -0500)]
12876: arvados-client get [-format=yaml] uuid
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 22 Dec 2017 19:32:24 +0000 (14:32 -0500)]
Merge branch '12755-python3-centos7'
fixes #12755
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 22 Dec 2017 19:31:36 +0000 (14:31 -0500)]
12755: Resume packaging arvados-docker-cleaner for centos7.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 22 Dec 2017 16:16:48 +0000 (11:16 -0500)]
12755: Revert
ce0a973 for python33 packages.
They started trying to claim directories like /opt/rh/python33 and
became uninstallable as a result.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fernando Monserrat [Fri, 22 Dec 2017 15:18:01 +0000 (12:18 -0300)]
refs #12850 Merge branch '12850-docker-tag-version'
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Tom Clegg [Thu, 21 Dec 2017 18:48:54 +0000 (13:48 -0500)]
Note DCO requirement.
Fix some typos.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 21 Dec 2017 18:25:18 +0000 (13:25 -0500)]
Fix copyright header, and copyright header checker exit code.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 21 Dec 2017 17:41:19 +0000 (12:41 -0500)]
Merge branch '12844-webdav-move-into-self'
fixes #12844
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 21 Dec 2017 16:53:26 +0000 (11:53 -0500)]
Merge branch 'patch-2' of https://github.com/jrandall/arvados
fixes #11621
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Joshua C. Randall [Thu, 21 Dec 2017 14:54:13 +0000 (14:54 +0000)]
fix bwa-mem.cwl docker repo
Change from missing `biodckr/bwa` repo to minimal bwa docker image `lh3lh3/bwa`
The new docker image has `bwa` set as entrypoint, so also change `baseCommand` from `[bwa, mem]` to `[mem]`
Fixes 11621
Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>
Tom Clegg [Thu, 21 Dec 2017 15:21:04 +0000 (10:21 -0500)]
12844: Refuse to unreference a directory by moving it into itself.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fernando Monserrat [Thu, 21 Dec 2017 15:14:35 +0000 (12:14 -0300)]
#12850 trim whitespaces for lint
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Wed, 20 Dec 2017 20:25:23 +0000 (17:25 -0300)]
#12850 add tag as input for docker tag
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Tom Clegg [Tue, 19 Dec 2017 21:46:29 +0000 (16:46 -0500)]
Merge branch '12848-python-versions'
refs #12848
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 19 Dec 2017 21:41:52 +0000 (16:41 -0500)]
12848: Fix python builder ignoring --build-version.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 19 Dec 2017 16:19:00 +0000 (11:19 -0500)]
12755: Stop building arvados-docker-cleaner for centos7.
(until we make the package installable again)
refs #12755
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 19 Dec 2017 09:14:55 +0000 (04:14 -0500)]
12377: Update workbench test breaking since
484246ac0.
refs #12377
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 19 Dec 2017 03:21:39 +0000 (22:21 -0500)]
Merge branch '12715-slow-propfind'
fixes #12715
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 18 Dec 2017 22:04:36 +0000 (17:04 -0500)]
Merge branch '12822-keepproxy-token-scope'
refs #12822
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 18 Dec 2017 20:36:10 +0000 (15:36 -0500)]
Merge branch '12377-workbench-composer-link' refs #12377
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 18 Dec 2017 17:52:09 +0000 (12:52 -0500)]
Merge branch '12821-sbatch-script-race'
refs #12821
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sat, 16 Dec 2017 00:13:24 +0000 (19:13 -0500)]
12821: Fix race in concurrent calls to submit().
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 15 Dec 2017 20:21:26 +0000 (15:21 -0500)]
Merge branch '12721-build-test-version'
refs #12721
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 15 Dec 2017 17:51:07 +0000 (12:51 -0500)]
12721: Add run-build-test-packages-one-target.sh --build-version arg
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 15 Dec 2017 15:14:13 +0000 (10:14 -0500)]
12715: Rename flag !reading => alwaysReadEOF.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 15 Dec 2017 14:25:32 +0000 (09:25 -0500)]
Add composer_url to arvbox workbench config refs #12377
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 15 Dec 2017 03:25:38 +0000 (22:25 -0500)]
12715: Fix slow PROPFIND by avoiding content probing.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 15 Dec 2017 03:13:17 +0000 (22:13 -0500)]
12822: Allow reading from keepproxy with collection sharing tokens.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 14 Dec 2017 23:05:23 +0000 (18:05 -0500)]
12377: Add link to composer on workbench
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 21:52:50 +0000 (16:52 -0500)]
Merge branch '8311-mount-git'
closes #8311
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 21:22:08 +0000 (16:22 -0500)]
8311: Fix gitUrl discovery doc for config git_repo_https_base: true.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 21:14:00 +0000 (16:14 -0500)]
8311: Ensure git tree is readable even with umask 077.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 21:01:19 +0000 (16:01 -0500)]
8311: Remove support for writable git_tree mount.
Feature is of dubious value, and expected behavior isn't clear --
e.g., should all files be world-writable?
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 20:56:18 +0000 (15:56 -0500)]
8311: Ensure git tree tmpdir is readable by container.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 14 Dec 2017 20:22:24 +0000 (15:22 -0500)]
8311: Pass in container token to extractTree
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 20:22:18 +0000 (15:22 -0500)]
8311: Ensure gitUrl is always a string in the discovery doc.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 18:17:12 +0000 (13:17 -0500)]
8311: Fix API tests broken in
4343e1f.
* Restore arvados repo dropped from tarball.
* Fix git repo fixtures being removed in API test teardown.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 17:14:48 +0000 (12:14 -0500)]
8311: Tidy up integration test services.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 16:37:10 +0000 (11:37 -0500)]
8311: Update docs to describe current implementation.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 16:26:02 +0000 (11:26 -0500)]
8311: Reject invalid/unsupported git mounts. Default to path="/".
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 13 Dec 2017 22:13:42 +0000 (17:13 -0500)]
8311: Try some git_tree mounts in TestSetupMounts.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 12 Dec 2017 23:56:07 +0000 (18:56 -0500)]
8311: Add git_tree mount type.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 15:29:10 +0000 (10:29 -0500)]
8311: Add auth handler tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 12 Dec 2017 23:58:15 +0000 (18:58 -0500)]
8311: Access git repos by UUID.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 15:26:08 +0000 (10:26 -0500)]
8311: Fix "read" or "write" mistakenly appended to response data.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 14 Dec 2017 15:25:14 +0000 (10:25 -0500)]
8311: Remove debug printf.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 14 Dec 2017 14:41:03 +0000 (09:41 -0500)]
Fix Access-Control-Allow-Headers CORS header tests refs #12060
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Dec 2017 21:17:43 +0000 (16:17 -0500)]
Add Content-Type to Access-Control-Allow-Headers CORS headers refs #12060
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Dec 2017 16:12:56 +0000 (11:12 -0500)]
Merge branch '4019-query-properties' closes #4019
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Dec 2017 15:01:38 +0000 (10:01 -0500)]
4019: More tests for error cases
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Dec 2017 14:50:53 +0000 (09:50 -0500)]
4019: Improve error checking, add tests for some error cases
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Dec 2017 14:12:42 +0000 (09:12 -0500)]
Merge branch '12614-node-states' refs #12614
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 12 Dec 2017 21:19:37 +0000 (16:19 -0500)]
Tag arvados/jobs image with $cwl_runner_version instead of git hash refs #12811
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 12 Dec 2017 20:39:30 +0000 (15:39 -0500)]
12614: Can shutdown failed nodes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 12 Dec 2017 18:58:16 +0000 (13:58 -0500)]
12614: Support daemon actor aware of 'fail' node state
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 12 Dec 2017 18:35:21 +0000 (13:35 -0500)]
12614: Make node manager aware of "fail" node state.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 12 Dec 2017 16:51:44 +0000 (11:51 -0500)]
Merge branch '12803-unescaped-colon-filename'
fixes #12803
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 12 Dec 2017 16:29:48 +0000 (11:29 -0500)]
Merge branch '12765-workbench-404-trashed' refs #12765
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 12 Dec 2017 16:29:37 +0000 (11:29 -0500)]
12803: Accept unescaped colons in filenames.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 12 Dec 2017 15:40:40 +0000 (10:40 -0500)]
4019: Add index for efficient jsonb query on collection properties
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 12 Dec 2017 15:32:15 +0000 (10:32 -0500)]
4019: Add URI quoting option for keys. Update docs. Fix tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 11 Dec 2017 22:50:00 +0000 (17:50 -0500)]
4019: Update docs. Tweak syntax of 'exists' and add alternate form.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 11 Dec 2017 22:00:40 +0000 (17:00 -0500)]
Merge branch '12550-crunch1-exit-race'
refs #12550
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 11 Dec 2017 21:34:37 +0000 (16:34 -0500)]
Merge branch '12511-is-trashed-query' refs #12511
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 11 Dec 2017 21:33:12 +0000 (16:33 -0500)]
4019: Expand testing. Make behavior consistent for != and "not in"
Rename "?" to "exists" and add "not exists".
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 11 Dec 2017 21:16:13 +0000 (16:16 -0500)]
Merge branch '12167-python-request-id'
refs #12167
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 11 Dec 2017 20:43:04 +0000 (15:43 -0500)]
12167: Allow --silent to be combined with -*-progress flags.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 11 Dec 2017 19:32:01 +0000 (14:32 -0500)]
12167: Test arv-get and arv-put X-Request-Id logging.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 11 Dec 2017 16:54:52 +0000 (11:54 -0500)]
12511: readable_by filters on is_trashed directly
Fix performance problem in the negative join NOT EXISTS(...) used to filter out
trashed items for admin users. The clause
(uuid = target_uuid OR owner_uuid = target_uuid) doesn't use the index
efficiently and results in a very expensive seq scan.
However, the "OR" in the negative clause is not necessary. We only need
materialized_permission_view to know if "owner_uuid" is trashed (directly or
indirectly), not "uuid". If the record type has an is_trashed flag (currently
only collections and groups) then it is more efficient to filter on that
directly.
This commit refactors the readable_by query to only check owner_uuid, and
additionally filter on "is_trashed" for collections and groups.
As an additional cleanup, because "readable_by" now explicitly knows to filter
on "is_trashed" this makes the default_scope in Collections redundant. This
commit also removes default_scope & various uses of unscoped reduces complexity.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 11 Dec 2017 17:42:57 +0000 (12:42 -0500)]
12550: Fix race: read buffered data from stderr after child exits.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 11 Dec 2017 02:52:41 +0000 (21:52 -0500)]
12721: Add missing _version.py, now part of source tree.
refs #12721
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Sat, 9 Dec 2017 18:59:23 +0000 (13:59 -0500)]
4019: Initial support for queries on jsonb subproperties.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
projects / arvados.git / log