Lucas Di Pentima [Mon, 8 Jan 2018 14:44:38 +0000 (11:44 -0300)]
12479: Merge branch 'master' into 12479-wb-structured-vocabulary
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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 [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>
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>
Lucas Di Pentima [Fri, 5 Jan 2018 19:34:35 +0000 (16:34 -0300)]
12479: Allow the user to edit the currently accepted value on a
selectize field.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 5 Jan 2018 16:19:54 +0000 (13:19 -0300)]
12479: Selectize tweaks to enhance usability. Removed all table
borders. When no vocabulary is defined, switch to simple input fields
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 3 Jan 2018 21:38:34 +0000 (18:38 -0300)]
12479: Removed table border. Fixed indentation.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 3 Jan 2018 21:12:04 +0000 (18:12 -0300)]
12749: Several fixes and enhancements:
* Removed the "add new tag" button, a new empty row is added on demand
* Fixed widget auto-focus when adding new tag names and values
* Fixed conditional usages
* Simplified vocabulary definition format
* Renamed example vocabulary file
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 2 Jan 2018 20:19:06 +0000 (17:19 -0300)]
12479: Renamed 'overridable' property to 'strict'. Both toplevel
and type specific 'strict' properties are assumed false by default.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Tue, 2 Jan 2018 17:47:18 +0000 (14:47 -0300)]
12479: Removed commented out test
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 2 Jan 2018 17:14:35 +0000 (14:14 -0300)]
12479: Removed tags related code on wb, not needed with the new
tag editor. Removed related tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 2 Jan 2018 16:19:07 +0000 (13:19 -0300)]
12479: Old tag editor files removal. Tests commented out.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Fri, 22 Dec 2017 16:41:58 +0000 (13:41 -0300)]
12479: Syntax error fixed.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Fri, 22 Dec 2017 15:11:59 +0000 (12:11 -0300)]
12479: Avoid saving tags with name and/or value being empty string.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 22 Dec 2017 12:53:16 +0000 (09:53 -0300)]
12479: Add placeholder messages on selectize boxes. Filter keys/values
when being empty strings (ie: when adding new tags).
Fixed bug that made the Save button behave incorrectly.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Wed, 20 Dec 2017 22:24:45 +0000 (19:24 -0300)]
Merge branch 'master' into 12479-wb-structured-vocabulary
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Wed, 20 Dec 2017 19:13:14 +0000 (16:13 -0300)]
12479: When requesting the collection, only ask the api server for the
properties.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 20 Dec 2017 18:38:04 +0000 (15:38 -0300)]
12479: Save button changes state when having changes to save and after
saving. When no tags, show a proper message.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 20 Dec 2017 16:13:14 +0000 (13:13 -0300)]
12479: Replacing isDirty flag with dirty stream
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 20 Dec 2017 16:00:21 +0000 (13:00 -0300)]
12479: WIP making the save objject show the save state
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 19 Dec 2017 22:04:10 +0000 (19:04 -0300)]
12479: Properties saving working. Remove tag button styling.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Tue, 19 Dec 2017 18:45:30 +0000 (15:45 -0300)]
12479: Remove tag button working.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 19 Dec 2017 18:16:30 +0000 (15:16 -0300)]
12479: Refactoring to simplify the code.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Mon, 18 Dec 2017 22:12:04 +0000 (19:12 -0300)]
12479: Add Selectize via npm package
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Mon, 18 Dec 2017 19:42:19 +0000 (16:42 -0300)]
12479: Passing UUID & controller name data from data-mount-mithril element
instead of parsing URL.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
Lucas Di Pentima [Mon, 18 Dec 2017 13:57:34 +0000 (10:57 -0300)]
12479: Assign default vocabulary on model instantiation
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 18 Dec 2017 13:06:03 +0000 (10:06 -0300)]
12479: Get remote vocabulary definition, use a fallback is it doesn't exist.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 18 Dec 2017 11:10:21 +0000 (08:10 -0300)]
12479: New tag editor for structured vocabulary. There are pending
issues to be solved.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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>
projects / arvados.git / log