arvados.git
3 years ago18076: Fixes the bug by assigning a different (and random) username.
Lucas Di Pentima [Mon, 6 Sep 2021 19:41:40 +0000 (16:41 -0300)]
18076: Fixes the bug by assigning a different (and random) username.

If the renamed user does exist on the LoginCluster, it'll eventually be named
correctly, and it is a stale record, it'll get a username that gives the admin
a clue about what happened to it.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago18076: Expands test case exposing a related issue with users with a repository.
Lucas Di Pentima [Mon, 6 Sep 2021 19:28:42 +0000 (16:28 -0300)]
18076: Expands test case exposing a related issue with users with a repository.

The previous fix set the conflicting user's username to null but this isn't
possible when the user record is linked to a repository.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago18102: Fix double-unlock in scheduler.
Tom Clegg [Mon, 6 Sep 2021 18:47:03 +0000 (14:47 -0400)]
18102: Fix double-unlock in scheduler.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago18078: Fix tests
Peter Amstutz [Fri, 3 Sep 2021 21:22:14 +0000 (17:22 -0400)]
18078: Fix tests

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

3 years ago18094: Removes update_uuid from the R SDK.
Lucas Di Pentima [Fri, 3 Sep 2021 19:04:34 +0000 (16:04 -0300)]
18094: Removes update_uuid from the R SDK.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years agoMerge branch '17755-add-singularity-to-compute-image'
Ward Vandewege [Fri, 3 Sep 2021 18:43:11 +0000 (14:43 -0400)]
Merge branch '17755-add-singularity-to-compute-image'

closes #17755

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

3 years ago18094: Removes update_uuid code & tests from railsAPI.
Lucas Di Pentima [Fri, 3 Sep 2021 18:39:05 +0000 (15:39 -0300)]
18094: Removes update_uuid code & tests from railsAPI.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago18027: Kill arv-mount directly if arv-mount --unmount cannot run.
Tom Clegg [Fri, 3 Sep 2021 14:29:05 +0000 (10:29 -0400)]
18027: Kill arv-mount directly if arv-mount --unmount cannot run.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago18027: Fix crash when reporting error during --unmount.
Tom Clegg [Fri, 3 Sep 2021 14:26:36 +0000 (10:26 -0400)]
18027: Fix crash when reporting error during --unmount.

Traceback (most recent call last):
  File "/usr/bin/arv-mount", line 10, in <module>
    arvados_fuse.command.Mount(args).run()
  File "/usr/share/python3/dist/python3-arvados-fuse/lib/python3.7/site-packages/arvados_fuse/command.py", line 172, in run
    recursive=self.args.unmount_all)
  File "/usr/share/python3/dist/python3-arvados-fuse/lib/python3.7/site-packages/arvados_fuse/unmount.py", line 162, in unmount
    sys.stderr.write(fusermount_output)
TypeError: write() argument must be str, not bytes

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17755: Merge branch 'main' into 17755-add-singularity-to-compute-image
Ward Vandewege [Fri, 3 Sep 2021 14:03:20 +0000 (10:03 -0400)]
17755: Merge branch 'main' into 17755-add-singularity-to-compute-image

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

3 years ago18094: Removes update_uuid from GoSDK & controller.
Lucas Di Pentima [Fri, 3 Sep 2021 00:01:17 +0000 (21:01 -0300)]
18094: Removes update_uuid from GoSDK & controller.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago18094: Updates documentation, adding an upgrade note.
Lucas Di Pentima [Thu, 2 Sep 2021 20:37:21 +0000 (17:37 -0300)]
18094: Updates documentation, adding an upgrade note.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years agoMerge branch '18076-stale-cached-users-handling' into main. Closes #18076
Lucas Di Pentima [Thu, 2 Sep 2021 20:07:28 +0000 (17:07 -0300)]
Merge branch '18076-stale-cached-users-handling' into main. Closes #18076

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago18076: Improves test.
Lucas Di Pentima [Thu, 2 Sep 2021 20:06:38 +0000 (17:06 -0300)]
18076: Improves test.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago18076: Fixes the bug, expands the test with additional checks.
Lucas Di Pentima [Thu, 2 Sep 2021 18:54:23 +0000 (15:54 -0300)]
18076: Fixes the bug, expands the test with additional checks.

If there's a stale cached user record that's creating the username collision,
set it to nil before retrying the update. There're two scenarios this is
covering:

1. The stale user record belongs to an existing user on LoginCluster. Its
   username was taken by other user so the new username is coming in the
   batch_update operation -- it's ok to temporarily have it set to nil.
2. The stale user record doesn't exist on LoginCluster anymore, so having
   it being reset to nil isn't harmful and avoids future collisions.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago18076: Adds test exposing the issue.
Lucas Di Pentima [Wed, 1 Sep 2021 20:41:01 +0000 (17:41 -0300)]
18076: Adds test exposing the issue.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago14018: Setting process properties WIP
Peter Amstutz [Thu, 2 Sep 2021 17:51:04 +0000 (13:51 -0400)]
14018: Setting process properties WIP

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

3 years ago14018: Setting process properties WIP
Peter Amstutz [Thu, 2 Sep 2021 17:15:52 +0000 (13:15 -0400)]
14018: Setting process properties WIP

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

3 years ago18078: Reacquire llfuse lock before populating collection directory
Peter Amstutz [Thu, 2 Sep 2021 15:20:12 +0000 (11:20 -0400)]
18078: Reacquire llfuse lock before populating collection directory

Updates the test for generating "conflict" files.

I don't have a test case for the reported bug, however this is the
only place I could find where _entries was being modified without the
lock held.  By reacquiring the lock, it should no longer be possible
to read _entries at the same time as it is being updated.

Also clean up a few "from future" bits that are no longer needed
because we're python 3 only.

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

3 years agoMerge branch '17696-gosdk-default-storage-class' into main. Closes #17696
Lucas Di Pentima [Wed, 1 Sep 2021 20:00:45 +0000 (17:00 -0300)]
Merge branch '17696-gosdk-default-storage-class' into main. Closes #17696

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17995: Fix merge error.
Tom Clegg [Wed, 1 Sep 2021 18:38:40 +0000 (14:38 -0400)]
17995: Fix merge error.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17995: Merge branch 'main'
Tom Clegg [Wed, 1 Sep 2021 18:24:47 +0000 (14:24 -0400)]
17995: Merge branch 'main'

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17995: Accept boolean expressions as strings without ["...",=,true].
Tom Clegg [Wed, 1 Sep 2021 18:22:59 +0000 (14:22 -0400)]
17995: Accept boolean expressions as strings without ["...",=,true].

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoUpdate test to accept non-empty default BsubArgumentsList.
Tom Clegg [Wed, 1 Sep 2021 13:18:29 +0000 (09:18 -0400)]
Update test to accept non-empty default BsubArgumentsList.

refs #17857

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoUpdate default bsub arguments to save stdout/stderr in /tmp.
Tom Clegg [Tue, 31 Aug 2021 20:43:17 +0000 (16:43 -0400)]
Update default bsub arguments to save stdout/stderr in /tmp.

refs #17857

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoFix misleading log message.
Tom Clegg [Tue, 31 Aug 2021 20:22:09 +0000 (16:22 -0400)]
Fix misleading log message.

refs #17857

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17696: Updates tests to check for backwards compatibility.
Lucas Di Pentima [Mon, 30 Aug 2021 20:19:11 +0000 (17:19 -0300)]
17696: Updates tests to check for backwards compatibility.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17696: Moves default storage classes loading to keepclient.New().
Lucas Di Pentima [Thu, 26 Aug 2021 21:02:01 +0000 (18:02 -0300)]
17696: Moves default storage classes loading to keepclient.New().

Also adds integration test that proves that a collection and its keepclient
use the same default storage classes list.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17696: Adds default storage classes config loading to KeepClient, with tests.
Lucas Di Pentima [Mon, 23 Aug 2021 16:08:35 +0000 (13:08 -0300)]
17696: Adds default storage classes config loading to KeepClient, with tests.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17696: Adds ArvadosClient.ClusterConfig() to get the exported cluster's config.
Lucas Di Pentima [Fri, 20 Aug 2021 16:09:39 +0000 (13:09 -0300)]
17696: Adds ArvadosClient.ClusterConfig() to get the exported cluster's config.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17995: Merge branch 'main'
Tom Clegg [Mon, 30 Aug 2021 18:02:46 +0000 (14:02 -0400)]
17995: Merge branch 'main'

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17995: Rephrase filter expression docs.
Tom Clegg [Mon, 30 Aug 2021 18:02:03 +0000 (14:02 -0400)]
17995: Rephrase filter expression docs.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoMerge branch '17217-collection-signatures' into main
Tom Clegg [Mon, 30 Aug 2021 17:29:33 +0000 (13:29 -0400)]
Merge branch '17217-collection-signatures' into main

closes #17217

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoMerge branch '17994-filter-by-storage-classes' into main
Tom Clegg [Mon, 30 Aug 2021 17:27:03 +0000 (13:27 -0400)]
Merge branch '17994-filter-by-storage-classes' into main

closes #17994

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoFix whitespace.
Ward Vandewege [Mon, 30 Aug 2021 14:59:33 +0000 (10:59 -0400)]
Fix whitespace.

No issue #

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

3 years ago17217: Sign locators in CollectionCreate and Update.
Tom Clegg [Mon, 30 Aug 2021 14:07:33 +0000 (10:07 -0400)]
17217: Sign locators in CollectionCreate and Update.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17217: Update RailsAPI tests to not expect signatures.
Tom Clegg [Thu, 26 Aug 2021 20:02:10 +0000 (16:02 -0400)]
17217: Update RailsAPI tests to not expect signatures.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17217: Test signature expiry times.
Tom Clegg [Thu, 26 Aug 2021 18:36:18 +0000 (14:36 -0400)]
17217: Test signature expiry times.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17217: Skip signatures when BlobSigning=false.
Tom Clegg [Thu, 26 Aug 2021 04:10:52 +0000 (00:10 -0400)]
17217: Skip signatures when BlobSigning=false.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoMerge branch '17696-pysdk-default-storage-class' into main. Refs #17696
Lucas Di Pentima [Fri, 27 Aug 2021 15:22:47 +0000 (12:22 -0300)]
Merge branch '17696-pysdk-default-storage-class' into main. Refs #17696

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17994: Document new filtering capabilities.
Tom Clegg [Fri, 27 Aug 2021 15:18:08 +0000 (11:18 -0400)]
17994: Document new filtering capabilities.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17994: Document filtering by comparing two attributes.
Tom Clegg [Fri, 27 Aug 2021 14:19:17 +0000 (10:19 -0400)]
17994: Document filtering by comparing two attributes.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17994: Accept a few very specific expressions as filters.
Tom Clegg [Thu, 26 Aug 2021 20:34:42 +0000 (16:34 -0400)]
17994: Accept a few very specific expressions as filters.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoNeed to match the regex again
Peter Amstutz [Thu, 26 Aug 2021 22:45:56 +0000 (18:45 -0400)]
Need to match the regex again

no issue #

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

3 years agoMerge branch '15159-export-trustallcontent' into main. Closes #15159
Stephen Smith [Thu, 26 Aug 2021 16:52:20 +0000 (12:52 -0400)]
Merge branch '15159-export-trustallcontent' into main. Closes #15159

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

3 years ago17696: Updates API documentation adding storage_classes_* fields.
Lucas Di Pentima [Thu, 19 Aug 2021 22:27:12 +0000 (19:27 -0300)]
17696: Updates API documentation adding storage_classes_* fields.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17696: Updates docstring on arvados.Collection class.
Lucas Di Pentima [Thu, 19 Aug 2021 21:29:19 +0000 (18:29 -0300)]
17696: Updates docstring on arvados.Collection class.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17696: KeepClient uses default storage classes when none is required explicitly
Lucas Di Pentima [Thu, 19 Aug 2021 21:08:39 +0000 (18:08 -0300)]
17696: KeepClient uses default storage classes when none is required explicitly

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17217: Add signatures test for groups/contents.
Tom Clegg [Thu, 26 Aug 2021 04:04:30 +0000 (00:04 -0400)]
17217: Add signatures test for groups/contents.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17217: Update tests, remove unused code.
Tom Clegg [Thu, 26 Aug 2021 04:04:26 +0000 (00:04 -0400)]
17217: Update tests, remove unused code.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17217: Remove crufty test util funcs.
Tom Clegg [Tue, 24 Aug 2021 20:07:43 +0000 (16:07 -0400)]
17217: Remove crufty test util funcs.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17217: Sign manifests in controller instead of RailsAPI.
Tom Clegg [Tue, 24 Aug 2021 20:07:34 +0000 (16:07 -0400)]
17217: Sign manifests in controller instead of RailsAPI.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoMerge branch '17755-singularity-race' into main refs #17755
Peter Amstutz [Wed, 25 Aug 2021 19:34:04 +0000 (15:34 -0400)]
Merge branch '17755-singularity-race' into main refs #17755

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

3 years ago17755: Fix os.Stat
Peter Amstutz [Wed, 25 Aug 2021 17:01:45 +0000 (13:01 -0400)]
17755: Fix os.Stat

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

3 years ago17755: Add ensure_unique_name to avoid collisions on creating cache collection
Peter Amstutz [Tue, 24 Aug 2021 20:46:21 +0000 (16:46 -0400)]
17755: Add ensure_unique_name to avoid collisions on creating cache collection

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

3 years agoMerge branch '17948-test-collection-tool' into main. Closes #17948
Lucas Di Pentima [Tue, 24 Aug 2021 20:18:19 +0000 (17:18 -0300)]
Merge branch '17948-test-collection-tool' into main. Closes #17948

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years agoarvbox ensures workbench2 development server doesn't run with HTTPS
Peter Amstutz [Tue, 24 Aug 2021 17:51:12 +0000 (13:51 -0400)]
arvbox ensures workbench2 development server doesn't run with HTTPS

This is because it is already proxied through nginx, which is set up
with the correct certificates.

Also install 'vim-tiny' to have a way to edit files inside the container.

no issue #

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

3 years agoMerge branch '18004-cached-token-race-condition' into main. Closes #18004
Lucas Di Pentima [Tue, 24 Aug 2021 15:31:11 +0000 (12:31 -0300)]
Merge branch '18004-cached-token-race-condition' into main. Closes #18004

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17994: Update comment.
Tom Clegg [Tue, 24 Aug 2021 13:57:10 +0000 (09:57 -0400)]
17994: Update comment.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17994: Support filtering by element/key presence in jsonb columns.
Tom Clegg [Tue, 24 Aug 2021 13:47:04 +0000 (09:47 -0400)]
17994: Support filtering by element/key presence in jsonb columns.

Remove storage_classes_* from searchable_columns so that filters with
the magic attr "any" don't try to search them.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoMerge branch '15430-fts-operator-removal' into main. Closes #15430
Lucas Di Pentima [Mon, 23 Aug 2021 21:47:29 +0000 (18:47 -0300)]
Merge branch '15430-fts-operator-removal' into main. Closes #15430

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago15430: Improves upgrade notes.
Lucas Di Pentima [Mon, 23 Aug 2021 21:37:12 +0000 (18:37 -0300)]
15430: Improves upgrade notes.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years agoMerge branch '17698-keepstore-concurrent-writes'
Tom Clegg [Mon, 23 Aug 2021 18:22:35 +0000 (14:22 -0400)]
Merge branch '17698-keepstore-concurrent-writes'

closes #17698

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17994: Allow filtering on storage_classes_desired/confirmed fields.
Tom Clegg [Mon, 23 Aug 2021 18:21:36 +0000 (14:21 -0400)]
17994: Allow filtering on storage_classes_desired/confirmed fields.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17698: Merge branch 'main' into 17698-keepstore-concurrent-writes
Tom Clegg [Mon, 23 Aug 2021 17:45:06 +0000 (13:45 -0400)]
17698: Merge branch 'main' into 17698-keepstore-concurrent-writes

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17698: Test "no writable volumes" case.
Tom Clegg [Mon, 23 Aug 2021 14:28:17 +0000 (10:28 -0400)]
17698: Test "no writable volumes" case.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17698: Add comment to clarify locking.
Tom Clegg [Mon, 23 Aug 2021 14:01:40 +0000 (10:01 -0400)]
17698: Add comment to clarify locking.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17698: Update PutBlock comment.
Tom Clegg [Mon, 23 Aug 2021 14:01:32 +0000 (10:01 -0400)]
17698: Update PutBlock comment.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17698: Rename newPutResult to match new putProgress type name.
Tom Clegg [Mon, 23 Aug 2021 14:00:50 +0000 (10:00 -0400)]
17698: Rename newPutResult to match new putProgress type name.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17698: Fix AllWritable panic when no volumes are writable.
Tom Clegg [Mon, 23 Aug 2021 14:00:01 +0000 (10:00 -0400)]
17698: Fix AllWritable panic when no volumes are writable.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years agoMerge branch '17535-test-provision-jenkins'
Javier Bértoli [Fri, 20 Aug 2021 00:57:19 +0000 (21:57 -0300)]
Merge branch '17535-test-provision-jenkins'

closes #17535
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

3 years ago17755: Merge branch 'main' into 17755-add-singularity-to-compute-image
Ward Vandewege [Tue, 17 Aug 2021 20:12:10 +0000 (16:12 -0400)]
17755: Merge branch 'main' into 17755-add-singularity-to-compute-image

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

3 years ago18004: Fixes a couple of race condition bugs related to caching remote users.
Lucas Di Pentima [Tue, 17 Aug 2021 18:20:59 +0000 (15:20 -0300)]
18004: Fixes a couple of race condition bugs related to caching remote users.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years agoMerge branch '17983-fuse-unlock-relock' into main refs #17983
Peter Amstutz [Tue, 17 Aug 2021 15:08:11 +0000 (11:08 -0400)]
Merge branch '17983-fuse-unlock-relock' into main refs #17983

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

3 years ago17948: Adds info to error messaging.
Lucas Di Pentima [Thu, 12 Aug 2021 14:01:52 +0000 (11:01 -0300)]
17948: Adds info to error messaging.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17948: Adds arguments to allow specifying how many subdirs to create.
Lucas Di Pentima [Tue, 10 Aug 2021 20:05:54 +0000 (17:05 -0300)]
17948: Adds arguments to allow specifying how many subdirs to create.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17948: Splits adjectives & nouns list into multiple lines.
Lucas Di Pentima [Tue, 10 Aug 2021 19:22:54 +0000 (16:22 -0300)]
17948: Splits adjectives & nouns list into multiple lines.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17948: Fixes conditional.
Lucas Di Pentima [Fri, 6 Aug 2021 20:26:10 +0000 (17:26 -0300)]
17948: Fixes conditional.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17948: Optimizes tool to stop adding data to a big enough manifest.
Lucas Di Pentima [Fri, 6 Aug 2021 19:55:16 +0000 (16:55 -0300)]
17948: Optimizes tool to stop adding data to a big enough manifest.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17948: First working implementation (WIP)
Lucas Di Pentima [Thu, 5 Aug 2021 14:42:09 +0000 (11:42 -0300)]
17948: First working implementation (WIP)

There're some issues: RailsAPI's full text search index on collections
returns an error when creating collection with >~36k files. Also, PySDK
is returning a socket read timeout error, seemilngly disregarding the
'timeout' setting on the arvados.api() object.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago15430: Adds an upgrade note warning that @@ won't work anymore.
Lucas Di Pentima [Mon, 16 Aug 2021 20:09:24 +0000 (17:09 -0300)]
15430: Adds an upgrade note warning that @@ won't work anymore.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago15430: Drops FTS indexes, removes unneeded test.
Lucas Di Pentima [Mon, 16 Aug 2021 19:44:49 +0000 (16:44 -0300)]
15430: Drops FTS indexes, removes unneeded test.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago17983: Fix writable fuse deadlock
Peter Amstutz [Mon, 16 Aug 2021 19:33:10 +0000 (15:33 -0400)]
17983: Fix writable fuse deadlock

Resulting from threads competing for llfuse.lock and collection lock
and one code path locking in the wrong order.

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

3 years ago15430: Fixes updated wb1 test that was migrated from using '@@' to 'ilike'.
Lucas Di Pentima [Mon, 16 Aug 2021 18:31:56 +0000 (15:31 -0300)]
15430: Fixes updated wb1 test that was migrated from using '@@' to 'ilike'.

It seems that the ordering isn't the same when using both operators as one
pipeline instance object wasn't getting listed after migration. Had to both
change the created_at and uuid fields to make it appear on the all_processes
page when passing 'ilike'.

This shouldn't be a problem, as we're actually using 'ilike' on the real wb1
page, it was just the test what was outdated.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago15430: Updates wb1 test so that it exercises the ilike operator instead of @@
Lucas Di Pentima [Thu, 12 Aug 2021 15:50:55 +0000 (12:50 -0300)]
15430: Updates wb1 test so that it exercises the ilike operator instead of @@

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago15430: Removes support for the '@@' full text search operator.
Lucas Di Pentima [Thu, 12 Aug 2021 15:03:30 +0000 (12:03 -0300)]
15430: Removes support for the '@@' full text search operator.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas.dipentima@curii.com>

3 years ago15159: Export TrustAllContent for use in wb2
Stephen Smith [Mon, 16 Aug 2021 18:52:54 +0000 (14:52 -0400)]
15159: Export TrustAllContent for use in wb2

Arvados-DCO-1.1-Signed-off-by: Stephen Smith <stephen@curii.com>

3 years agoMerge branch '18001-add-UserNotifierEmailBcc'
Ward Vandewege [Fri, 13 Aug 2021 19:35:05 +0000 (15:35 -0400)]
Merge branch '18001-add-UserNotifierEmailBcc'

closes #18001

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

3 years ago18001: Merge branch 'main' into 18001-add-UserNotifierEmailBcc
Ward Vandewege [Fri, 13 Aug 2021 19:33:46 +0000 (15:33 -0400)]
18001: Merge branch 'main' into 18001-add-UserNotifierEmailBcc

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

3 years ago18001: address review comments.
Ward Vandewege [Fri, 13 Aug 2021 19:33:17 +0000 (15:33 -0400)]
18001: address review comments.

No issue #

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

3 years agoMerge branch '17390-cwl-storage-classes' into main
Peter Amstutz [Fri, 13 Aug 2021 18:21:57 +0000 (14:21 -0400)]
Merge branch '17390-cwl-storage-classes' into main

refs #17390

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

3 years ago17390: Document arv:OutputStorageClass extension
Peter Amstutz [Fri, 13 Aug 2021 18:11:33 +0000 (14:11 -0400)]
17390: Document arv:OutputStorageClass extension

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

3 years ago17698: Do concurrent writes when multiple volumes are needed.
Tom Clegg [Fri, 13 Aug 2021 15:06:34 +0000 (11:06 -0400)]
17698: Do concurrent writes when multiple volumes are needed.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 years ago17390: Update arvados-cwl-runner docs
Peter Amstutz [Fri, 13 Aug 2021 14:33:34 +0000 (10:33 -0400)]
17390: Update arvados-cwl-runner docs

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

3 years ago17390: Add unit tests for storage classes
Peter Amstutz [Thu, 12 Aug 2021 19:24:14 +0000 (15:24 -0400)]
17390: Add unit tests for storage classes

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

3 years ago17390: Use cluster-configured default
Peter Amstutz [Tue, 10 Aug 2021 20:59:21 +0000 (16:59 -0400)]
17390: Use cluster-configured default

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

3 years ago17390: setting intermediate/final storage classes WIP
Peter Amstutz [Tue, 10 Aug 2021 20:54:40 +0000 (16:54 -0400)]
17390: setting intermediate/final storage classes WIP

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

3 years agoMerge branch '17984-cwl-project-uuid-users' into main
Peter Amstutz [Fri, 13 Aug 2021 14:13:54 +0000 (10:13 -0400)]
Merge branch '17984-cwl-project-uuid-users' into main

refs #17984

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

3 years agoMerge branch '18013-token-rake-task-fix'
Ward Vandewege [Thu, 12 Aug 2021 20:22:51 +0000 (16:22 -0400)]
Merge branch '18013-token-rake-task-fix'

closes #18013

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

3 years ago18013: Merge branch 'main' into 18013-token-rake-task-fix
Ward Vandewege [Thu, 12 Aug 2021 20:22:20 +0000 (16:22 -0400)]
18013: Merge branch 'main' into 18013-token-rake-task-fix

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>