arvados.git
4 years agosetuptools >=44 doesn't support Python 3.4 on Debian jessie 1.4.3
Peter Amstutz [Fri, 3 Jan 2020 20:44:28 +0000 (15:44 -0500)]
setuptools >=44 doesn't support Python 3.4 on Debian jessie

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years agoUpdate bundles to a commit that can be installed with git 2.1.4.
Tom Clegg [Fri, 3 Jan 2020 20:40:02 +0000 (15:40 -0500)]
Update bundles to a commit that can be installed with git 2.1.4.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoUpdate version number script to work with git 2.1.4.
Tom Clegg [Fri, 3 Jan 2020 20:24:08 +0000 (15:24 -0500)]
Update version number script to work with git 2.1.4.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years ago15965: Decode as UTF-8 to avoid "not ASCII" error on Python 2
Peter Amstutz [Thu, 2 Jan 2020 20:53:56 +0000 (15:53 -0500)]
15965: Decode as UTF-8 to avoid "not ASCII" error on Python 2

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago15942: Fix deadlock caused by unclosed "done" channel.
Tom Clegg [Sun, 22 Dec 2019 00:20:45 +0000 (19:20 -0500)]
15942: Fix deadlock caused by unclosed "done" channel.

Also, stop relying on the flushing goroutine to set flushing=nil when
finished; closing the channel is now enough to indicate work is done.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoUpdate CI url, and add Curii Corporation to the AUTHORS file.
Ward Vandewege [Tue, 17 Dec 2019 20:54:12 +0000 (15:54 -0500)]
Update CI url, and add Curii Corporation to the AUTHORS file.

No issue #

4 years ago15928: Fix deadlock.
Tom Clegg [Wed, 11 Dec 2019 15:40:01 +0000 (10:40 -0500)]
15928: Fix deadlock.

Locking the parent dir isn't necessary to finish async writes, and
deadlocks if a waitPrune() is waiting for the async writes to finish.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoUpdate gitter link to arvados/community
Peter Amstutz [Mon, 9 Dec 2019 20:43:52 +0000 (15:43 -0500)]
Update gitter link to arvados/community

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years agoRemove biostars link
Peter Amstutz [Mon, 9 Dec 2019 19:38:09 +0000 (14:38 -0500)]
Remove biostars link

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years agoFix support links
Peter Amstutz [Mon, 9 Dec 2019 19:26:31 +0000 (14:26 -0500)]
Fix support links

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

4 years ago15910: Fix races in collectionfs flush/sync.
Tom Clegg [Wed, 4 Dec 2019 16:28:38 +0000 (11:28 -0500)]
15910: Fix races in collectionfs flush/sync.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15900-gem-version-142' into 1.4-dev
Tom Clegg [Wed, 4 Dec 2019 18:55:49 +0000 (13:55 -0500)]
Merge branch '15900-gem-version-142' into 1.4-dev

refs #15900

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15900: Update bundle to commits that report stable versions.
Tom Clegg [Tue, 3 Dec 2019 16:34:36 +0000 (11:34 -0500)]
15900: Update bundle to commits that report stable versions.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15900: Report stable gem version for a given commit.
Tom Clegg [Tue, 3 Dec 2019 16:25:27 +0000 (11:25 -0500)]
15900: Report stable gem version for a given commit.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '1.4-dev' of git.curoverse.com:arvados into 1.4-dev 1.4.2
Ward Vandewege [Thu, 21 Nov 2019 21:39:20 +0000 (16:39 -0500)]
Merge branch '1.4-dev' of git.curoverse.com:arvados into 1.4-dev

4 years agoMerge branch '15497-reuse-fix' 15800-arvados-1-4-2
Lucas Di Pentima [Thu, 24 Oct 2019 20:51:05 +0000 (17:51 -0300)]
Merge branch '15497-reuse-fix'
Closes #15497

4 years agoMerge branch '15793-cache-results-in-each'
Tom Clegg [Tue, 5 Nov 2019 19:29:29 +0000 (14:29 -0500)]
Merge branch '15793-cache-results-in-each'

refs #15793

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15680-arv-put-retry'
Tom Clegg [Mon, 21 Oct 2019 15:42:39 +0000 (11:42 -0400)]
Merge branch '15680-arv-put-retry'

fixes #15680

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15652-crunch-run-memory-use'
Tom Clegg [Tue, 22 Oct 2019 20:09:02 +0000 (16:09 -0400)]
Merge branch '15652-crunch-run-memory-use'

refs #15652

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15699-update-gem'
Tom Clegg [Mon, 21 Oct 2019 20:59:58 +0000 (16:59 -0400)]
Merge branch '15699-update-gem'

refs #15699

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15699-update-gem'
Tom Clegg [Mon, 21 Oct 2019 14:38:48 +0000 (10:38 -0400)]
Merge branch '15699-update-gem'

refs #15699

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15699: Fix fencepost error at end of stream.
Tom Clegg [Sat, 19 Oct 2019 02:53:25 +0000 (22:53 -0400)]
15699: Fix fencepost error at end of stream.

refs #15699

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15699: Update arvados-cli to latest arvados gem.
Tom Clegg [Thu, 17 Oct 2019 14:57:11 +0000 (10:57 -0400)]
15699: Update arvados-cli to latest arvados gem.

refs #15699

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15699-workbench-copy-fail'
Tom Clegg [Tue, 15 Oct 2019 19:21:55 +0000 (15:21 -0400)]
Merge branch '15699-workbench-copy-fail'

refs #15699

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15656-user-delete-container'
Tom Clegg [Tue, 1 Oct 2019 14:29:07 +0000 (10:29 -0400)]
Merge branch '15656-user-delete-container'

refs #15656

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15655-logtail-encoding'
Eric Biagiotti [Wed, 9 Oct 2019 13:31:06 +0000 (09:31 -0400)]
Merge branch '15655-logtail-encoding'

refs #15655

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

4 years agoMerge branch '15496-wb1-group-membership-admin'
Lucas Di Pentima [Fri, 26 Jul 2019 20:17:26 +0000 (17:17 -0300)]
Merge branch '15496-wb1-group-membership-admin'
Closes #15496

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15673: Pin faraday below 0.16.
Tom Clegg [Mon, 30 Sep 2019 19:33:53 +0000 (15:33 -0400)]
15673: Pin faraday below 0.16.

This allows arvados-cli and login-sync to install correctly even if an
older arvados gem (without the faraday pin) is already installed.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15673: Pin faraday gem version.
Tom Clegg [Mon, 30 Sep 2019 19:03:06 +0000 (15:03 -0400)]
15673: Pin faraday gem version.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15649: Revert python-arvados-sdk dependency change accidentally 1.4.1
Ward Vandewege [Sat, 21 Sep 2019 13:30:59 +0000 (09:30 -0400)]
15649: Revert python-arvados-sdk dependency change accidentally
introduced in commit ce4e615391bfda40400fd1ca6e03eab6aa4fd77e

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years ago15648: update documentation adding upgrade to rh-python36
Fernando Monserrat [Fri, 20 Sep 2019 15:49:15 +0000 (12:49 -0300)]
15648: update documentation adding upgrade to rh-python36

Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

4 years ago15648: update to rh-python36
Fernando Monserrat [Thu, 19 Sep 2019 18:57:59 +0000 (15:57 -0300)]
15648: update to rh-python36

Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

4 years ago15649: Pin libcloud 2.5.0.
Tom Clegg [Fri, 20 Sep 2019 15:16:04 +0000 (11:16 -0400)]
15649: Pin libcloud 2.5.0.

libcloud 2.6.0 uses an incorrect blob storage URL when creating Azure
nodes.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoSkip failing crunch-job test no issue #
Peter Amstutz [Thu, 12 Sep 2019 19:42:15 +0000 (15:42 -0400)]
Skip failing crunch-job test no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoReformat for newer gofmt no issue #
Peter Amstutz [Thu, 12 Sep 2019 19:10:49 +0000 (15:10 -0400)]
Reformat for newer gofmt no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoPins mithril version to fix CI pipeline.
Lucas Di Pentima [Wed, 24 Jul 2019 21:31:46 +0000 (18:31 -0300)]
Pins mithril version to fix CI pipeline.
No issue #

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago14946: Fixes 'gem install' invocation.
Lucas Di Pentima [Tue, 28 May 2019 19:23:42 +0000 (16:23 -0300)]
14946: Fixes 'gem install' invocation.

Params --no-ri and --no-rdoc are no longer valid.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15583: Adds more with_counts to queries
Eric Biagiotti [Wed, 28 Aug 2019 13:26:50 +0000 (09:26 -0400)]
15583: Adds more with_counts to queries

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

4 years ago15583: Add with_count('none') more places
Peter Amstutz [Thu, 22 Aug 2019 19:04:14 +0000 (15:04 -0400)]
15583: Add with_count('none') more places

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15583: Set with_count('none') on wb page notification tests
Peter Amstutz [Thu, 22 Aug 2019 18:47:44 +0000 (14:47 -0400)]
15583: Set with_count('none') on wb page notification tests

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15605: Updates vendor.json to use the latest goamz version.
Lucas Di Pentima [Thu, 5 Sep 2019 14:40:37 +0000 (11:40 -0300)]
15605: Updates vendor.json to use the latest goamz version.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15554 - Don't depend on latest version of Arvados Python SDK
Tom Morris [Tue, 10 Sep 2019 18:19:39 +0000 (14:19 -0400)]
15554 - Don't depend on latest version of Arvados Python SDK

Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>

4 years ago15554 - Fix Crunch1 child jobs
Tom Morris [Fri, 6 Sep 2019 15:58:12 +0000 (11:58 -0400)]
15554 - Fix Crunch1 child jobs

Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>

4 years ago15554 - Fix crunchstat-summary for running containers
Tom Morris [Mon, 19 Aug 2019 21:11:44 +0000 (17:11 -0400)]
15554 - Fix crunchstat-summary for running containers

Change the decision logic for when to use the live logs to account for
the fact that the log collection exists now before the container completes.

Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>

4 years ago15554 - Add Python SDK constants for container request states
Tom Morris [Wed, 28 Aug 2019 15:13:21 +0000 (11:13 -0400)]
15554 - Add Python SDK constants for container request states

Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>

4 years ago15499: Only create additional log collection when container is Complete
Peter Amstutz [Tue, 10 Sep 2019 15:25:58 +0000 (11:25 -0400)]
15499: Only create additional log collection when container is Complete

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15499: Create additional unmodified log collection on finalize!
Peter Amstutz [Mon, 9 Sep 2019 19:37:32 +0000 (15:37 -0400)]
15499: Create additional unmodified log collection on finalize!

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15499: Make reuse tests fail to expose the bug.
Lucas Di Pentima [Fri, 6 Sep 2019 21:28:39 +0000 (18:28 -0300)]
15499: Make reuse tests fail to expose the bug.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agodoc: on the config migration page, make sure to include RAILS_ENV in the bundle
Ward Vandewege [Thu, 11 Jul 2019 19:45:16 +0000 (15:45 -0400)]
doc: on the config migration page, make sure to include RAILS_ENV in the bundle
commands.

No issue #

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoKeep relative URL when switching between versions in our documentation.
Ward Vandewege [Wed, 19 Jun 2019 19:02:10 +0000 (15:02 -0400)]
Keep relative URL when switching between versions in our documentation.

refs #15138

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years ago15138: Include logic to support building multiple versions of our documentation.
Ward Vandewege [Tue, 11 Jun 2019 17:42:40 +0000 (13:42 -0400)]
15138: Include logic to support building multiple versions of our documentation.

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years ago15138: Show the TM notice a little bit higher.
Ward Vandewege [Mon, 10 Jun 2019 14:41:22 +0000 (10:41 -0400)]
15138: Show the TM notice a little bit higher.

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoCrunch-job needs to call the python executable from our sdk package for 1.4.0
Ward Vandewege [Wed, 5 Jun 2019 16:49:27 +0000 (12:49 -0400)]
Crunch-job needs to call the python executable from our sdk package for
collating job output.

refs #9945

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoDo not blow up when Rails.configuration.Users.UserProfileNotificationAddress is 15286-defaults-fix
Ward Vandewege [Mon, 3 Jun 2019 19:14:37 +0000 (15:14 -0400)]
Do not blow up when Rails.configuration.Users.UserProfileNotificationAddress is
set to the empty string, which is the default since #13996 (it defaulted to a
dummy e-mail adress before).

refs #15286
refs #13996

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoUpdate the 'upgrading' documentation to reflect the v1.4.0 release, and warn
Ward Vandewege [Fri, 31 May 2019 19:42:37 +0000 (15:42 -0400)]
Update the 'upgrading' documentation to reflect the v1.4.0 release, and warn
about the db migration that can take some time during upgrade.

refs #15093

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoMerge branch '15093-move-collection-update-out-of-band' into 1.4-dev
Ward Vandewege [Fri, 31 May 2019 19:30:34 +0000 (15:30 -0400)]
Merge branch '15093-move-collection-update-out-of-band' into 1.4-dev

closes #15093

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoAddress review comments. 15093-move-collection-update-out-of-band
Ward Vandewege [Fri, 31 May 2019 19:27:38 +0000 (15:27 -0400)]
Address review comments.

refs #15093

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoMove the population of the new columns on the collections table to a standalone
Ward Vandewege [Fri, 31 May 2019 18:51:50 +0000 (14:51 -0400)]
Move the population of the new columns on the collections table to a standalone
script that should be run separate from the migration. Add a note to the
upgrade documentation along those lines. Make the script not blow up on
collections with invalid manifests, but rather just skip them.

refs #15093
refs #14484

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoFix reporting logs on container requests refs #15028
Peter Amstutz [Tue, 23 Apr 2019 22:01:55 +0000 (18:01 -0400)]
Fix reporting logs on container requests refs #15028

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoMerge branch '14878-priority-race'
Tom Clegg [Tue, 28 May 2019 18:05:47 +0000 (14:05 -0400)]
Merge branch '14878-priority-race'

fixes #14878

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago14878: Add comment.
Tom Clegg [Tue, 28 May 2019 18:05:05 +0000 (14:05 -0400)]
14878: Add comment.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15275-attribute-dirtyness-bugfix'
Lucas Di Pentima [Tue, 28 May 2019 15:41:51 +0000 (12:41 -0300)]
Merge branch '15275-attribute-dirtyness-bugfix'
Closes #15275

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago14878: Skip flock() when testing priority updater.
Tom Clegg [Tue, 28 May 2019 15:04:35 +0000 (11:04 -0400)]
14878: Skip flock() when testing priority updater.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15275: Adds test for different jsonb properties comparisons cases.
Lucas Di Pentima [Tue, 28 May 2019 14:27:43 +0000 (11:27 -0300)]
15275: Adds test for different jsonb properties comparisons cases.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Checks for jsonb types changes by comparing deserialized values.
Lucas Di Pentima [Fri, 24 May 2019 21:11:23 +0000 (18:11 -0300)]
15275: Checks for jsonb types changes by comparing deserialized values.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoarvbox use lowercase keys for database connection params refs #15273
Peter Amstutz [Fri, 24 May 2019 20:31:49 +0000 (16:31 -0400)]
arvbox use lowercase keys for database connection params refs #15273

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoMerge branch 'master' into 15275-attribute-dirtyness-bugfix
Lucas Di Pentima [Fri, 24 May 2019 18:34:01 +0000 (15:34 -0300)]
Merge branch 'master' into 15275-attribute-dirtyness-bugfix

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Re-adds the test exposing this branch's particular bug.
Lucas Di Pentima [Fri, 24 May 2019 18:33:13 +0000 (15:33 -0300)]
15275: Re-adds the test exposing this branch's particular bug.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoMerge branch '15275-collection-delete-bugfix'. Refs #15275
Lucas Di Pentima [Fri, 24 May 2019 18:11:34 +0000 (15:11 -0300)]
Merge branch '15275-collection-delete-bugfix'. Refs #15275

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Simplifies method code.
Lucas Di Pentima [Fri, 24 May 2019 18:00:40 +0000 (15:00 -0300)]
15275: Simplifies method code.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Don't create snapshots whenever is_trashed is true.
Lucas Di Pentima [Fri, 24 May 2019 17:58:59 +0000 (14:58 -0300)]
15275: Don't create snapshots whenever is_trashed is true.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Don't create snapshot when trashing collection.
Lucas Di Pentima [Fri, 24 May 2019 15:36:54 +0000 (12:36 -0300)]
15275: Don't create snapshot when trashing collection.

Also, skips test about bogus properties field changes, for now.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Adds another test exposing the jsonb changed field bug.
Lucas Di Pentima [Fri, 24 May 2019 13:55:14 +0000 (10:55 -0300)]
15275: Adds another test exposing the jsonb changed field bug.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Moves comment to its proper place.
Lucas Di Pentima [Fri, 24 May 2019 13:31:40 +0000 (10:31 -0300)]
15275: Moves comment to its proper place.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Avoids running manage_versioning when not needed.
Lucas Di Pentima [Fri, 24 May 2019 01:22:02 +0000 (22:22 -0300)]
15275: Avoids running manage_versioning when not needed.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15275: Saves snapshot as system user instead of assigning a signed manifest to it
Lucas Di Pentima [Thu, 23 May 2019 23:07:13 +0000 (20:07 -0300)]
15275: Saves snapshot as system user instead of assigning a signed manifest to it

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15725: Adds test exposing 2 issues when trashing collections with versioning
Lucas Di Pentima [Thu, 23 May 2019 22:53:12 +0000 (19:53 -0300)]
15725: Adds test exposing 2 issues when trashing collections with versioning

1) Snapshot being created when deleting a collection
2) Permission denied error when trying to create the new snapshot

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoMake sure that the libpam-arvados package puts its various files in the place
Ward Vandewege [Thu, 23 May 2019 18:45:35 +0000 (14:45 -0400)]
Make sure that the libpam-arvados package puts its various files in the place
where the pam subsystem will expect them, not inside the virtualenv.

Also, remove the code from sdk/pam/setup.py that installed a copy of the
libpam-arvados.py file under /usr/data/lib/security/libpam_arvados.py for
legacy reasons.

refs #9945
refs #15186

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoMerge branch '15273-db-conn-keys'
Tom Clegg [Thu, 23 May 2019 18:23:54 +0000 (14:23 -0400)]
Merge branch '15273-db-conn-keys'

fixes #15273

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15273: Fix key-conflict test.
Tom Clegg [Thu, 23 May 2019 18:23:26 +0000 (14:23 -0400)]
15273: Fix key-conflict test.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15273: Use lowercase keys for database connection params.
Tom Clegg [Thu, 23 May 2019 17:42:37 +0000 (13:42 -0400)]
15273: Use lowercase keys for database connection params.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15003-disable-config-warnings'
Tom Clegg [Thu, 23 May 2019 15:27:26 +0000 (11:27 -0400)]
Merge branch '15003-disable-config-warnings'

refs #15003

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15258-wb-report-issue-bugfix'
Lucas Di Pentima [Thu, 23 May 2019 14:03:13 +0000 (11:03 -0300)]
Merge branch '15258-wb-report-issue-bugfix'
Closes #15258

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15003: Temporarily disable config warnings.
Tom Clegg [Thu, 23 May 2019 13:31:40 +0000 (09:31 -0400)]
15003: Temporarily disable config warnings.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15258: Explicitly require libs instead of relying on autoloading.
Lucas Di Pentima [Thu, 23 May 2019 13:14:21 +0000 (10:14 -0300)]
15258: Explicitly require libs instead of relying on autoloading.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15258: Removes /lib from eager load paths because of failing integration tests.
Lucas Di Pentima [Thu, 23 May 2019 12:52:10 +0000 (09:52 -0300)]
15258: Removes /lib from eager load paths because of failing integration tests.

PhantomJS started to randomly fail, maybe because of memory or timing reasons.
This change exposes the bug observed on production, on development & test envs.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoIncrease client_max_body_size in arvbox to support file uploads.
Peter Amstutz [Wed, 22 May 2019 21:31:48 +0000 (17:31 -0400)]
Increase client_max_body_size in arvbox to support file uploads.

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15258: Adds /lib to the eager_load paths.
Lucas Di Pentima [Wed, 22 May 2019 19:57:19 +0000 (16:57 -0300)]
15258: Adds /lib to the eager_load paths.

On rails 5.0 the autoload paths stopped working on production environments
for thread safety concerns.
See: https://github.com/rails/rails/commit/a71350cae0082193ad8c66d65ab62e8bb0b7853b

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoWhile our Python SDK now supports Python 3.4+, our FUSE driver does not yet. On
Ward Vandewege [Tue, 21 May 2019 17:27:41 +0000 (13:27 -0400)]
While our Python SDK now supports Python 3.4+, our FUSE driver does not yet. On
the FUSE driver installation page, we should be mentioning the latter, not the
former.

No issue #

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoOur Python SDK now also supports version 3.4+, update the fuse drive doc page
Ward Vandewege [Tue, 21 May 2019 14:36:24 +0000 (10:36 -0400)]
Our Python SDK now also supports version 3.4+, update the fuse drive doc page
accordingly.

No issue #

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoFix cwl tests refs #15241
Peter Amstutz [Mon, 20 May 2019 20:42:11 +0000 (16:42 -0400)]
Fix cwl tests refs #15241

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoMerge branch '15241-collection-input' refs #15241
Peter Amstutz [Mon, 20 May 2019 19:48:27 +0000 (15:48 -0400)]
Merge branch '15241-collection-input' refs #15241

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15241: Fix input bare collection as directory
Peter Amstutz [Mon, 20 May 2019 19:46:17 +0000 (15:46 -0400)]
15241: Fix input bare collection as directory

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoMerge branch '14988-wb-rails5-upgrade'
Lucas Di Pentima [Fri, 17 May 2019 17:31:29 +0000 (14:31 -0300)]
Merge branch '14988-wb-rails5-upgrade'
Closes #14988

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoMerge branch '15227-apiserver-properties-bugfix'
Lucas Di Pentima [Fri, 17 May 2019 17:30:33 +0000 (14:30 -0300)]
Merge branch '15227-apiserver-properties-bugfix'
Closes #15227

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoUpdate the note about supported Python versions for Arv SDK.
Peter Amstutz [Fri, 17 May 2019 15:55:31 +0000 (11:55 -0400)]
Update the note about supported Python versions for Arv SDK.

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago14988: Restores debug message when accessing non-loaded attributes.
Lucas Di Pentima [Fri, 17 May 2019 14:42:19 +0000 (11:42 -0300)]
14988: Restores debug message when accessing non-loaded attributes.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoAdd user email and cancel button to federated user redirect page
Peter Amstutz [Fri, 17 May 2019 14:18:13 +0000 (10:18 -0400)]
Add user email and cancel button to federated user redirect page

refs #15061

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago14988: Fixes destroyed? method to return false on new records.
Lucas Di Pentima [Fri, 17 May 2019 13:28:13 +0000 (10:28 -0300)]
14988: Fixes destroyed? method to return false on new records.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15227: Fixes type checking on json attributes.
Lucas Di Pentima [Fri, 17 May 2019 00:20:33 +0000 (21:20 -0300)]
15227: Fixes type checking on json attributes.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>