arvados.git
6 years ago12995: Can merge accounts in both directions.
Peter Amstutz [Thu, 17 May 2018 19:45:59 +0000 (15:45 -0400)]
12995: Can merge accounts in both directions.

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

6 years ago12995: Linking alternate login works.
Peter Amstutz [Thu, 17 May 2018 17:00:36 +0000 (13:00 -0400)]
12995: Linking alternate login works.

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

6 years ago12995: Add link account page with confirmation.
Peter Amstutz [Thu, 17 May 2018 16:07:06 +0000 (12:07 -0400)]
12995: Add link account page with confirmation.

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

6 years agoFix another ineffassign warning in our golang code.
Ward Vandewege [Wed, 16 May 2018 20:59:29 +0000 (16:59 -0400)]
Fix another ineffassign warning in our golang code.

No issue #

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

6 years agoMerge branch '12708-report-storage-classes'
Tom Clegg [Tue, 15 May 2018 18:36:42 +0000 (14:36 -0400)]
Merge branch '12708-report-storage-classes'

refs #12708

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

6 years agoMerge branch '13164-container-locking'
Tom Clegg [Tue, 15 May 2018 18:35:55 +0000 (14:35 -0400)]
Merge branch '13164-container-locking'

refs #13164

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

6 years ago13164: Lock tables when updating multiple containers + CRs.
Tom Clegg [Mon, 14 May 2018 14:28:36 +0000 (10:28 -0400)]
13164: Lock tables when updating multiple containers + CRs.

Avoid database inconsistencies after update races.

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

6 years agoMerge branch '13473-no-cpu-constraints'
Tom Clegg [Fri, 11 May 2018 20:54:16 +0000 (16:54 -0400)]
Merge branch '13473-no-cpu-constraints'

refs #13473

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

6 years ago13473: Tidy up slurmConstraintArgs func.
Tom Clegg [Fri, 11 May 2018 19:38:51 +0000 (15:38 -0400)]
13473: Tidy up slurmConstraintArgs func.

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

6 years ago13473: Drop slurm resource constraints when using instancetype=X.
Tom Clegg [Fri, 11 May 2018 19:25:36 +0000 (15:25 -0400)]
13473: Drop slurm resource constraints when using instancetype=X.

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

6 years agoMerge branch 'thehyve/fix-crunch-documentation' Fix a typo in Crunch Dispatch install...
Ward Vandewege [Fri, 11 May 2018 00:31:11 +0000 (20:31 -0400)]
Merge branch 'thehyve/fix-crunch-documentation' Fix a typo in Crunch Dispatch installation manual

No issue #, github PR 66

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

6 years agoMerge branch '13446-keepstore-tls'
Tom Clegg [Thu, 10 May 2018 20:07:33 +0000 (16:07 -0400)]
Merge branch '13446-keepstore-tls'

refs #13446

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

6 years agoMerge branch '9918-index-error'
Tom Clegg [Thu, 10 May 2018 20:07:16 +0000 (16:07 -0400)]
Merge branch '9918-index-error'

refs #9918

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

6 years ago9918: Don't mask http/network error with response body format error.
Tom Clegg [Thu, 10 May 2018 20:05:30 +0000 (16:05 -0400)]
9918: Don't mask http/network error with response body format error.

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

6 years agoBump package iteration for a-c-r in run-build-docker-jobs-image.sh
Peter Amstutz [Thu, 10 May 2018 18:12:16 +0000 (14:12 -0400)]
Bump package iteration for a-c-r in run-build-docker-jobs-image.sh

refs #13435

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

6 years agoBump arvados-python-client version for consistent dependencies
Peter Amstutz [Thu, 10 May 2018 15:41:17 +0000 (11:41 -0400)]
Bump arvados-python-client version for consistent dependencies

refs #13435

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

6 years agoMerge branch '12256-cwl-defaults' closes #12256
Peter Amstutz [Thu, 10 May 2018 15:38:13 +0000 (11:38 -0400)]
Merge branch '12256-cwl-defaults' closes #12256

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

6 years ago12256: Comments about workflow references / extra files.
Peter Amstutz [Thu, 10 May 2018 15:03:29 +0000 (11:03 -0400)]
12256: Comments about workflow references / extra files.

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

6 years ago13446: Enable TLS if given TLSCertificateFile and TLSKeyFile.
Tom Clegg [Wed, 9 May 2018 19:56:20 +0000 (15:56 -0400)]
13446: Enable TLS if given TLSCertificateFile and TLSKeyFile.

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

6 years ago12256: Only scan for referenced files first time after packing
Peter Amstutz [Wed, 9 May 2018 19:24:55 +0000 (15:24 -0400)]
12256: Only scan for referenced files first time after packing

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

6 years ago12256: Pull up minimum ruamel.yaml version to get consistent output.
Peter Amstutz [Wed, 9 May 2018 18:44:42 +0000 (14:44 -0400)]
12256: Pull up minimum ruamel.yaml version to get consistent output.

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

6 years ago12256: Bump cwltool version for workflow packing bugfix.
Peter Amstutz [Wed, 9 May 2018 18:28:14 +0000 (14:28 -0400)]
12256: Bump cwltool version for workflow packing bugfix.

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

6 years ago12256: Handle default references in RunInSingleContainer
Peter Amstutz [Fri, 4 May 2018 20:44:29 +0000 (16:44 -0400)]
12256: Handle default references in RunInSingleContainer

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

6 years ago12256: Add a bunch of test cases.
Peter Amstutz [Thu, 3 May 2018 16:34:05 +0000 (12:34 -0400)]
12256: Add a bunch of test cases.

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

6 years ago12256: Fix anonymous directory default inputs with file literals
Peter Amstutz [Thu, 3 May 2018 14:37:44 +0000 (10:37 -0400)]
12256: Fix anonymous directory default inputs with file literals

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

6 years agoMerge branch '12737-api-security-deps-fixes'
Lucas Di Pentima [Wed, 9 May 2018 18:19:10 +0000 (15:19 -0300)]
Merge branch '12737-api-security-deps-fixes'
Refs #12737

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

6 years agoFix subprocess32 version constraint, refs #13435
Peter Amstutz [Wed, 9 May 2018 17:53:11 +0000 (13:53 -0400)]
Fix subprocess32 version constraint, refs #13435

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

6 years agoAvoid copying mutex after first use.
Tom Clegg [Wed, 9 May 2018 17:47:11 +0000 (13:47 -0400)]
Avoid copying mutex after first use.

refs #13455

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

6 years agoAvoid http client race in test case.
Tom Clegg [Wed, 9 May 2018 17:11:55 +0000 (13:11 -0400)]
Avoid http client race in test case.

If we don't wait for Put() to return before returning from the test
case, CloseIdleConnections can cause Put() to fail, and the resulting
call to t.Error() panics the testing package.

"errType *url.Error, err Put
http://fakeaccountname.blob.127.0.0.1:42861/fakecontainername/e4d909c290d0fb1ca068ffaddf22cbd0:
net/http: HTTP/1.x transport connection broken: http:
CloseIdleConnections called"

"panic: Fail in goroutine after TestAzureBlobVolumeCreateBlobRace has completed"

No issue #

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

6 years ago12737: Updated gem dependencies, adressing a couple of known vulnerabilities.
Lucas Di Pentima [Wed, 9 May 2018 17:03:04 +0000 (14:03 -0300)]
12737: Updated gem dependencies, adressing a couple of known vulnerabilities.

* https://nvd.nist.gov/vuln/detail/CVE-2018-3741
* https://github.com/flavorjones/loofah/issues/144

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

6 years ago12708: Log desired/short/surplus figures for each storage class.
Tom Clegg [Tue, 8 May 2018 21:34:39 +0000 (17:34 -0400)]
12708: Log desired/short/surplus figures for each storage class.

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

6 years agoMerge branch '12626-merge-accounts'
Tom Clegg [Tue, 8 May 2018 13:30:15 +0000 (09:30 -0400)]
Merge branch '12626-merge-accounts'

refs #12626

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

6 years agoFix run script syntax.
Tom Clegg [Tue, 8 May 2018 13:06:20 +0000 (09:06 -0400)]
Fix run script syntax.

fixes #8348

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

6 years ago12626: Merge branch 'master' into 12626-merge-accounts
Tom Clegg [Mon, 7 May 2018 22:14:16 +0000 (18:14 -0400)]
12626: Merge branch 'master' into 12626-merge-accounts

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

6 years agoTweak tests for slightly different ruamel.yaml behavior, refs #13435
Peter Amstutz [Mon, 7 May 2018 19:37:28 +0000 (15:37 -0400)]
Tweak tests for slightly different ruamel.yaml behavior, refs #13435

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

6 years ago12626: Copy omniauth info into auth account, not target account.
Tom Clegg [Mon, 7 May 2018 19:11:58 +0000 (15:11 -0400)]
12626: Copy omniauth info into auth account, not target account.

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

6 years ago12626: Update permission graph after user merge.
Tom Clegg [Mon, 7 May 2018 19:10:24 +0000 (15:10 -0400)]
12626: Update permission graph after user merge.

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

6 years agoMerge branch '13435-ruamel-yaml-ver' closes #13435
Peter Amstutz [Mon, 7 May 2018 18:46:11 +0000 (14:46 -0400)]
Merge branch '13435-ruamel-yaml-ver' closes #13435

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

6 years ago13435: Build scandir to satisfy pathlib2 dependency of a-c-r
Peter Amstutz [Mon, 7 May 2018 14:59:58 +0000 (10:59 -0400)]
13435: Build scandir to satisfy pathlib2 dependency of a-c-r

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

6 years ago13435: Update ruamel.yaml and ciso8601 versions.
Peter Amstutz [Mon, 7 May 2018 14:20:57 +0000 (10:20 -0400)]
13435: Update ruamel.yaml and ciso8601 versions.

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

6 years agoMerge branch '13278-launch-failed'
Tom Clegg [Mon, 7 May 2018 14:40:17 +0000 (10:40 -0400)]
Merge branch '13278-launch-failed'

refs #13278
refs #13399

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

6 years ago13278: Release jobs that are pending because "launch failed".
Tom Clegg [Tue, 27 Mar 2018 17:01:38 +0000 (13:01 -0400)]
13278: Release jobs that are pending because "launch failed".

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

6 years agoMerge branch '13365-default-secondaryFiles' refs #13365
Peter Amstutz [Mon, 7 May 2018 13:49:30 +0000 (09:49 -0400)]
Merge branch '13365-default-secondaryFiles' refs #13365

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

6 years agoMerge branch '13383-trash-workers'
Tom Clegg [Mon, 7 May 2018 13:31:57 +0000 (09:31 -0400)]
Merge branch '13383-trash-workers'

closes #13383
refs #13335

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

6 years ago13383: Implement EmptyTrashWorkers in azure and filesystem backends.
Tom Clegg [Fri, 4 May 2018 20:48:50 +0000 (16:48 -0400)]
13383: Implement EmptyTrashWorkers in azure and filesystem backends.

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

6 years ago13383: Fix warning about expected 404 error.
Tom Clegg [Tue, 24 Apr 2018 21:03:50 +0000 (17:03 -0400)]
13383: Fix warning about expected 404 error.

The expected error (object not found immediately after deleting it)
was being logged as a warning, and the warning erroneously stated the
error was from "HEAD recent/X" rather than "HEAD X".

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

6 years ago13383: Add PullWorkers, TrashWorkers, EmptyTrashWorkers configs.
Tom Clegg [Tue, 24 Apr 2018 20:32:24 +0000 (16:32 -0400)]
13383: Add PullWorkers, TrashWorkers, EmptyTrashWorkers configs.

EmptyTrashWorkers only applies to S3 volumes.

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

6 years agoMerge branch '12167-go-request-id'
Tom Clegg [Fri, 4 May 2018 19:47:13 +0000 (15:47 -0400)]
Merge branch '12167-go-request-id'

refs #12167

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

6 years agoMerge branch 'tests-cleanup'
Tom Clegg [Fri, 4 May 2018 19:44:56 +0000 (15:44 -0400)]
Merge branch 'tests-cleanup'

No issue #

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

6 years ago12626: Add tests for missing new_owner_uuid.
Tom Clegg [Fri, 4 May 2018 19:19:14 +0000 (15:19 -0400)]
12626: Add tests for missing new_owner_uuid.

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

6 years ago12626: Advertise required params for users#merge in discovery doc.
Tom Clegg [Fri, 4 May 2018 19:09:46 +0000 (15:09 -0400)]
12626: Advertise required params for users#merge in discovery doc.

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

6 years ago12626: Improve error message.
Tom Clegg [Fri, 4 May 2018 19:09:36 +0000 (15:09 -0400)]
12626: Improve error message.

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

6 years ago12626: Change variable dst_user -> new_user for consistency.
Tom Clegg [Fri, 4 May 2018 18:59:41 +0000 (14:59 -0400)]
12626: Change variable dst_user -> new_user for consistency.

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

6 years ago12626: Be more selective/explicit about changing various UUIDs.
Tom Clegg [Fri, 4 May 2018 18:56:23 +0000 (14:56 -0400)]
12626: Be more selective/explicit about changing various UUIDs.

Update comments.

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

6 years ago12626: Update pg_terminate_backend recipe for PostgreSQL >= 9.2.
Tom Clegg [Fri, 4 May 2018 18:41:39 +0000 (14:41 -0400)]
12626: Update pg_terminate_backend recipe for PostgreSQL >= 9.2.

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

6 years agoAvoid broken llfuse 1.3.4 ("pip install" fails).
Tom Clegg [Fri, 4 May 2018 17:26:04 +0000 (13:26 -0400)]
Avoid broken llfuse 1.3.4 ("pip install" fails).

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

6 years ago13365: Remove check for callback that now happens in a different place.
Peter Amstutz [Fri, 4 May 2018 14:50:52 +0000 (10:50 -0400)]
13365: Remove check for callback that now happens in a different place.

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

6 years ago13365: Add tests to confirm regressions are fixed.
Peter Amstutz [Fri, 4 May 2018 14:29:44 +0000 (10:29 -0400)]
13365: Add tests to confirm regressions are fixed.

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

6 years ago13365: clean up discover_secondary_files
Peter Amstutz [Fri, 4 May 2018 14:13:05 +0000 (10:13 -0400)]
13365: clean up discover_secondary_files

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

6 years ago13365: Fix state logging
Peter Amstutz [Thu, 3 May 2018 20:18:12 +0000 (16:18 -0400)]
13365: Fix state logging

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

6 years agoSkip some unnecessary pip invocations.
Tom Clegg [Thu, 3 May 2018 20:09:37 +0000 (16:09 -0400)]
Skip some unnecessary pip invocations.

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

6 years ago13365: Further fixes to ensure output callback only happens once
Peter Amstutz [Thu, 3 May 2018 19:48:16 +0000 (15:48 -0400)]
13365: Further fixes to ensure output callback only happens once

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

6 years agoFix gopath/govendor recipe.
Tom Clegg [Wed, 25 Apr 2018 17:31:11 +0000 (13:31 -0400)]
Fix gopath/govendor recipe.

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

6 years agoSkip explicit libcloud preinstall when not using a fork.
Tom Clegg [Wed, 25 Apr 2018 17:30:27 +0000 (13:30 -0400)]
Skip explicit libcloud preinstall when not using a fork.

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

6 years agoFix wrong temp path in govendor recipe.
Tom Clegg [Sun, 8 Apr 2018 00:49:21 +0000 (20:49 -0400)]
Fix wrong temp path in govendor recipe.

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

6 years agoUse released version of llfuse for tests.
Tom Clegg [Sun, 8 Apr 2018 00:48:03 +0000 (20:48 -0400)]
Use released version of llfuse for tests.

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

6 years ago12167: Test X-Request-ID headers.
Tom Clegg [Thu, 3 May 2018 18:24:45 +0000 (14:24 -0400)]
12167: Test X-Request-ID headers.

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

6 years ago12167: Generate only one request ID per get/put.
Tom Clegg [Thu, 3 May 2018 18:03:40 +0000 (14:03 -0400)]
12167: Generate only one request ID per get/put.

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

6 years ago13365: Fix race condition between job submitted and event monitor threads
Peter Amstutz [Thu, 3 May 2018 17:46:57 +0000 (13:46 -0400)]
13365: Fix race condition between job submitted and event monitor threads

Don't call "done" if work reuse means a container request or job
immediately comes back as Completed because it might get called
twice.

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

6 years agoMerge branch '13365-note-bug-in-docs' refs #13365
Peter Amstutz [Thu, 3 May 2018 17:07:31 +0000 (13:07 -0400)]
Merge branch '13365-note-bug-in-docs' refs #13365

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

6 years ago13365: Add example error messages and highlight the changes.
Peter Amstutz [Thu, 3 May 2018 15:13:38 +0000 (11:13 -0400)]
13365: Add example error messages and highlight the changes.

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

6 years ago12167: Generate a new request ID if caller explicitly uses "".
Tom Clegg [Thu, 3 May 2018 14:21:05 +0000 (10:21 -0400)]
12167: Generate a new request ID if caller explicitly uses "".

Skip invoking unique ID generator if ID is already set.

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

6 years ago12167: Merge branch 'master'
Tom Clegg [Thu, 3 May 2018 14:10:11 +0000 (10:10 -0400)]
12167: Merge branch 'master'

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

6 years ago12626: Log UUID of auth record (if any) instead of supplied token.
Tom Clegg [Thu, 3 May 2018 14:05:40 +0000 (10:05 -0400)]
12626: Log UUID of auth record (if any) instead of supplied token.

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

6 years ago13365: Bump cwltool, 3rd party package versions.
Peter Amstutz [Wed, 2 May 2018 23:49:12 +0000 (19:49 -0400)]
13365: Bump cwltool, 3rd party package versions.

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

6 years ago12626: Check for scoped tokens.
Tom Clegg [Wed, 2 May 2018 20:54:45 +0000 (16:54 -0400)]
12626: Check for scoped tokens.

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

6 years ago12626: Add arvados/v1/users/merge API.
Tom Clegg [Wed, 2 May 2018 20:12:15 +0000 (16:12 -0400)]
12626: Add arvados/v1/users/merge API.

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

6 years ago13365: Bump schema-salad for better error formatting.
Peter Amstutz [Tue, 1 May 2018 21:37:02 +0000 (17:37 -0400)]
13365: Bump schema-salad for better error formatting.

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

6 years agoBump cwltool version for secondaryFile checker support.
Peter Amstutz [Tue, 1 May 2018 20:30:02 +0000 (16:30 -0400)]
Bump cwltool version for secondaryFile checker support.

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

6 years ago13365: Reintroduce secondaryFile discovery.
Peter Amstutz [Tue, 1 May 2018 20:09:38 +0000 (16:09 -0400)]
13365: Reintroduce secondaryFile discovery.

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

6 years ago13365: Discover secondaryFiles associated with default files inputs
Peter Amstutz [Tue, 17 Apr 2018 19:23:46 +0000 (15:23 -0400)]
13365: Discover secondaryFiles associated with default files inputs

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

6 years agoMerge branch '13111-no-anonymous-sitefs'
Tom Clegg [Tue, 1 May 2018 18:06:15 +0000 (14:06 -0400)]
Merge branch '13111-no-anonymous-sitefs'

refs #13111

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

6 years agoMerge branch '13338-wb-run-wf-proj' refs #13338
Peter Amstutz [Tue, 1 May 2018 17:35:05 +0000 (13:35 -0400)]
Merge branch '13338-wb-run-wf-proj' refs #13338

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

6 years ago12167: Pass request ID via keepclient instead of custom code.
Tom Clegg [Tue, 1 May 2018 15:16:47 +0000 (11:16 -0400)]
12167: Pass request ID via keepclient instead of custom code.

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

6 years agoFix #ZgotmplZ in dir listing page when filename contains a colon.
Tom Clegg [Mon, 30 Apr 2018 14:03:11 +0000 (10:03 -0400)]
Fix #ZgotmplZ in dir listing page when filename contains a colon.

refs #8784

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

6 years ago13365: Tweak text.
Peter Amstutz [Mon, 30 Apr 2018 21:31:47 +0000 (17:31 -0400)]
13365: Tweak text.

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

6 years ago13365: Update release notes about a-c-r bug in v1.1.4.
Peter Amstutz [Mon, 30 Apr 2018 21:29:36 +0000 (17:29 -0400)]
13365: Update release notes about a-c-r bug in v1.1.4.

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

6 years agoFix wrong event_type when getting buffered live logs for crunch2.
Tom Clegg [Mon, 30 Apr 2018 20:37:12 +0000 (16:37 -0400)]
Fix wrong event_type when getting buffered live logs for crunch2.

refs #12690

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

6 years ago13111: Disable siteFS routes for anonymous requests.
Tom Clegg [Fri, 27 Apr 2018 20:45:28 +0000 (16:45 -0400)]
13111: Disable siteFS routes for anonymous requests.

This enables dav clients to use HTTP authentication even when
anonymous tokens are configured.

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

6 years agoDocumentation: update PostgreSQL installation instructions
Ward Vandewege [Fri, 27 Apr 2018 15:46:02 +0000 (11:46 -0400)]
Documentation: update PostgreSQL installation instructions

refs #13165

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

6 years agoNode manager integration test writes to stderr in chunks.
Peter Amstutz [Fri, 27 Apr 2018 15:51:51 +0000 (11:51 -0400)]
Node manager integration test writes to stderr in chunks.

Handles EAGAIN when getting pipe buffer backpressure.  no issue #

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

6 years agoAvoid dangling child procs in test suite.
Tom Clegg [Thu, 26 Apr 2018 20:51:53 +0000 (16:51 -0400)]
Avoid dangling child procs in test suite.

In go 1.10.1, these seem to make "go test" hang sometimes.

https://github.com/golang/go/issues/24050

No issue #

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

6 years ago13338: Running workflow from workbench puts collections in correct project.
Peter Amstutz [Thu, 26 Apr 2018 20:45:01 +0000 (16:45 -0400)]
13338: Running workflow from workbench puts collections in correct project.

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

6 years agoMerge branch '13377-block-sig-time' refs #13377
Peter Amstutz [Thu, 26 Apr 2018 20:11:37 +0000 (16:11 -0400)]
Merge branch '13377-block-sig-time' refs #13377

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

6 years ago13377: Ensure that collection fetched by PDH has longest available lifetime.
Peter Amstutz [Thu, 26 Apr 2018 20:00:11 +0000 (16:00 -0400)]
13377: Ensure that collection fetched by PDH has longest available lifetime.

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

6 years agoMerge branch '12708-balance-storage-classes'
Tom Clegg [Thu, 26 Apr 2018 19:34:06 +0000 (15:34 -0400)]
Merge branch '12708-balance-storage-classes'

refs #12708

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

6 years agoMerge branch '13399-log-low-priority'
Tom Clegg [Thu, 26 Apr 2018 19:30:03 +0000 (15:30 -0400)]
Merge branch '13399-log-low-priority'

refs #13399

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

6 years ago13399: Log when a slurm job's priority is unrealistically low.
Tom Clegg [Thu, 26 Apr 2018 18:54:24 +0000 (14:54 -0400)]
13399: Log when a slurm job's priority is unrealistically low.

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

6 years agoMerge branch '13282-admin-docs' refs #13282
Peter Amstutz [Thu, 26 Apr 2018 18:30:29 +0000 (14:30 -0400)]
Merge branch '13282-admin-docs' refs #13282

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

6 years ago13282: doc updates
Peter Amstutz [Thu, 26 Apr 2018 18:13:27 +0000 (14:13 -0400)]
13282: doc updates

* Improve presentation of R SDK
* Move obsolete crunch1 documentation to "Obsolete" section.

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