arvados.git
6 years agoMerge branch '12702-migrate-user'
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>

6 years agoMerge branch '12913-secondary-mounts' refs #12913
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>

6 years ago12913: Add integration test for fix
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>

6 years ago12913: Apply secondaryFiles to inputs to RunInSingleContainer
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>

6 years ago12876: Update govendor bundle.
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>

6 years agoMerge branch '12876-arvados-client'
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>

6 years ago12702: Disallow updating sys/anon UUIDs. Test updating current user.
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>

6 years agoUpdate govendor bundle.
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>

6 years agoMerge branch '12908-slurm-cons-res'
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>

6 years ago12908: Mention SelectType=select/cons_res in slurm config advice.
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>

6 years agoMerge branch '12720-systemd-compat'
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>

6 years ago12720: Invoke StartLimitInterval three different ways.
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>

6 years agoAdd systemd unit file for arvados-health.
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>

6 years ago12876: Call attention to missing python and ruby dependencies.
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>

6 years ago12876: Recover from more symlink confusion.
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>

6 years ago12876: List subcommands like "arvados-client keep get" in main usage.
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>

6 years ago12876: Merge branch 'master' into 12876-arvados-client
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>

6 years agoMerge branch '12870-fuse-binds-invalidate'
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>

6 years ago12870: Fix test
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>

6 years ago12702: Add API docs for users#update_uuid.
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>

6 years ago12870: Don't send invalidation for inodes still referenced by kernel
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>

6 years ago12702: Add /arvados/v1/users/{uuid}/update_uuid API.
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>

6 years agoDrop superfluous "node-info" prefix in node-info.txt log file.
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>

6 years ago12876: Pass commands through to ruby/python programs.
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>

6 years ago12876: Simplify legacy option parsing.
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>

6 years ago12876: Fix up error/usage messages.
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>

6 years ago12876: More compatibility with "arv get".
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>

6 years ago12876: Util to accept subcommand after initial args.
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>

6 years ago12876: arvados-client get [-format=yaml] uuid
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>

6 years agoMerge branch '12755-python3-centos7'
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>

6 years ago12755: Resume packaging arvados-docker-cleaner for centos7.
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>

6 years ago12755: Revert ce0a973 for python33 packages.
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>

6 years agorefs #12850 Merge branch '12850-docker-tag-version'
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>

6 years agoNote DCO requirement.
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>

6 years agoFix copyright header, and copyright header checker exit code.
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>

6 years agoMerge branch '12844-webdav-move-into-self'
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>

6 years agoMerge branch 'patch-2' of https://github.com/jrandall/arvados
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>

6 years agofix bwa-mem.cwl docker repo
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>

6 years ago12844: Refuse to unreference a directory by moving it into itself.
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>

6 years ago#12850 trim whitespaces for lint
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>

6 years ago#12850 add tag as input for docker tag
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>

6 years agoMerge branch '12848-python-versions' 1.1.2
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>

6 years ago12848: Fix python builder ignoring --build-version.
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>

6 years ago12755: Stop building arvados-docker-cleaner for centos7.
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>

6 years ago12377: Update workbench test breaking since 484246ac0.
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>

6 years agoMerge branch '12715-slow-propfind'
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>

6 years agoMerge branch '12822-keepproxy-token-scope'
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>

6 years agoMerge branch '12377-workbench-composer-link' refs #12377
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>

6 years agoMerge branch '12821-sbatch-script-race'
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>

6 years ago12821: Fix race in concurrent calls to submit().
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>

6 years agoMerge branch '12721-build-test-version'
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>

6 years ago12721: Add run-build-test-packages-one-target.sh --build-version arg
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>

6 years ago12715: Rename flag !reading => alwaysReadEOF.
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>

6 years agoAdd composer_url to arvbox workbench config refs #12377
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>

6 years ago12715: Fix slow PROPFIND by avoiding content probing.
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>

6 years ago12822: Allow reading from keepproxy with collection sharing tokens.
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>

6 years ago12377: Add link to composer on workbench
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>

6 years agoMerge branch '8311-mount-git'
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>

6 years ago8311: Fix gitUrl discovery doc for config git_repo_https_base: true.
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>

6 years ago8311: Ensure git tree is readable even with umask 077.
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>

6 years ago8311: Remove support for writable git_tree mount.
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>

6 years ago8311: Ensure git tree tmpdir is readable by container.
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>

6 years ago8311: Pass in container token to extractTree
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>

6 years ago8311: Ensure gitUrl is always a string in the discovery doc.
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>

6 years ago8311: Fix API tests broken in 4343e1f.
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>

6 years ago8311: Tidy up integration test services.
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>

6 years ago8311: Update docs to describe current implementation.
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>

6 years ago8311: Reject invalid/unsupported git mounts. Default to path="/".
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>

6 years ago8311: Try some git_tree mounts in TestSetupMounts.
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>

6 years ago8311: Add git_tree mount type.
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>

6 years ago8311: Add auth handler tests.
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>

6 years ago8311: Access git repos by UUID.
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>

6 years ago8311: Fix "read" or "write" mistakenly appended to response data.
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>

6 years ago8311: Remove debug printf.
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>

6 years agoFix Access-Control-Allow-Headers CORS header tests refs #12060
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>

6 years agoAdd Content-Type to Access-Control-Allow-Headers CORS headers refs #12060
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>

6 years agoMerge branch '4019-query-properties' closes #4019
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>

6 years ago4019: More tests for error cases
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>

6 years ago4019: Improve error checking, add tests for some error cases
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>

6 years agoMerge branch '12614-node-states' refs #12614
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>

6 years agoTag arvados/jobs image with $cwl_runner_version instead of git hash refs #12811
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>

6 years ago12614: Can shutdown failed nodes.
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>

6 years ago12614: Support daemon actor aware of 'fail' node state
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>

6 years ago12614: Make node manager aware of "fail" node state.
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>

6 years agoMerge branch '12803-unescaped-colon-filename'
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>

6 years agoMerge branch '12765-workbench-404-trashed' refs #12765
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>

6 years ago12803: Accept unescaped colons in filenames.
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>

6 years ago4019: Add index for efficient jsonb query on collection properties
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>

6 years ago4019: Add URI quoting option for keys. Update docs. Fix tests.
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>

6 years ago4019: Update docs. Tweak syntax of 'exists' and add alternate form.
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>

6 years agoMerge branch '12550-crunch1-exit-race'
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>

6 years agoMerge branch '12511-is-trashed-query' refs #12511
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>

6 years ago4019: Expand testing. Make behavior consistent for != and "not in"
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>

6 years agoMerge branch '12167-python-request-id'
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>

6 years ago12167: Allow --silent to be combined with -*-progress flags.
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>

6 years ago12167: Test arv-get and arv-put X-Request-Id logging.
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>

6 years ago12511: readable_by filters on is_trashed directly
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>

6 years ago12550: Fix race: read buffered data from stderr after child exits.
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>

6 years ago12721: Add missing _version.py, now part of source tree.
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>

6 years ago4019: Initial support for queries on jsonb subproperties.
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>