arvados.git
6 years agoMerge branch 'master' into 7478-anm-spot-instances
Lucas Di Pentima [Fri, 25 May 2018 15:42:25 +0000 (12:42 -0300)]
Merge branch 'master' into 7478-anm-spot-instances

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

6 years ago7478: On EC2 driver ask for a spot instance when needed.
Lucas Di Pentima [Fri, 25 May 2018 14:10:00 +0000 (11:10 -0300)]
7478: On EC2 driver ask for a spot instance when needed.

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

6 years ago7478: Allow different configured node sizes to refer to the same instance type
Lucas Di Pentima [Thu, 24 May 2018 21:31:37 +0000 (18:31 -0300)]
7478: Allow different configured node sizes to refer to the same instance type

Add 'preemptable' attribute to every node size configuration, being False
by default.
Add 'instance_type' config attribute to store the real node size name. By
default this value will be the same as the size name, so that it's compatible
with current config files.

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

6 years ago2411: Merge branch '2411-another-pass'
Ward Vandewege [Thu, 24 May 2018 15:30:58 +0000 (11:30 -0400)]
2411: Merge branch '2411-another-pass'

refs #2411

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

6 years ago2411: Add a bunch of exceptions to .licenseignore for our R sdk
Ward Vandewege [Thu, 24 May 2018 02:26:25 +0000 (22:26 -0400)]
2411: Add a bunch of exceptions to .licenseignore for our R sdk

refs #2411

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

6 years ago2411: Add license header to sdk/R/README.Rmd
Ward Vandewege [Thu, 24 May 2018 02:26:05 +0000 (22:26 -0400)]
2411: Add license header to sdk/R/README.Rmd

refs #2411

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

6 years ago2411: add copyright headers to our R files.
Ward Vandewege [Thu, 24 May 2018 02:17:25 +0000 (22:17 -0400)]
2411: add copyright headers to our R files.

refs #2411

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

6 years ago2411: Add support for R source files to build/check-copyright-notices
Ward Vandewege [Thu, 24 May 2018 02:16:58 +0000 (22:16 -0400)]
2411: Add support for R source files to build/check-copyright-notices

refs #2411

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

6 years ago2411: another pass at adding copyright headers where missing.
Ward Vandewege [Wed, 23 May 2018 21:50:16 +0000 (17:50 -0400)]
2411: another pass at adding copyright headers where missing.

refs #2411

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

6 years ago7478: Preemptable instances support on GoSDK & dispatchcloud instance chooser
Lucas Di Pentima [Wed, 23 May 2018 19:13:04 +0000 (16:13 -0300)]
7478: Preemptable instances support on GoSDK & dispatchcloud instance chooser

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

6 years agoAdd Veritas Genetics to the AUTHORS file.
Ward Vandewege [Wed, 23 May 2018 14:04:13 +0000 (10:04 -0400)]
Add Veritas Genetics to the AUTHORS file.

No issue #

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

6 years agoMerge branch '13430-allow-storage-classes'
Fuad Muhic [Wed, 23 May 2018 13:07:39 +0000 (15:07 +0200)]
Merge branch '13430-allow-storage-classes'

refs #13430

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMerge branch '13453-r-sdk-incorrect-rest-call-fix'
Fuad Muhic [Wed, 23 May 2018 10:15:31 +0000 (12:15 +0200)]
Merge branch '13453-r-sdk-incorrect-rest-call-fix'

refs #13453

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoAdded test that checks that saving a committed collection updates the storage_classes...
Fuad Muhic [Wed, 23 May 2018 10:05:41 +0000 (12:05 +0200)]
Added test that checks that saving a committed collection updates the storage_classes_desired

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoTweak arvados-cwl-runner subprocess32 version dependency refs #13516
Peter Amstutz [Wed, 23 May 2018 01:25:58 +0000 (21:25 -0400)]
Tweak arvados-cwl-runner subprocess32 version dependency refs #13516

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

6 years agoFix tests refs #13516
Peter Amstutz [Tue, 22 May 2018 23:19:21 +0000 (19:19 -0400)]
Fix tests refs #13516

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

6 years agoMerge branch '13516-fix-cwl-tests' refs #13516
Peter Amstutz [Tue, 22 May 2018 21:08:13 +0000 (17:08 -0400)]
Merge branch '13516-fix-cwl-tests' refs #13516

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

6 years ago13516: Bump cwltool, cwltest and subprocess32 versions
Peter Amstutz [Tue, 22 May 2018 17:55:54 +0000 (13:55 -0400)]
13516: Bump cwltool, cwltest and subprocess32 versions

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

6 years ago7478: Preemptable instances scheduling parameter on API server
Lucas Di Pentima [Tue, 22 May 2018 17:49:44 +0000 (14:49 -0300)]
7478: Preemptable instances scheduling parameter on API server

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

6 years agoUpdated save method of Collection class to always update when
Fuad Muhic [Tue, 22 May 2018 16:08:36 +0000 (18:08 +0200)]
Updated save method of Collection class to always update when
storage_classes is specified.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoAdded tests and documentation for save and save_new methods in
Fuad Muhic [Tue, 22 May 2018 15:40:15 +0000 (17:40 +0200)]
Added tests and documentation for save and save_new methods in
Collection class.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago9918: Merge branch '9918-index-timeout'
Ward Vandewege [Tue, 22 May 2018 13:58:52 +0000 (09:58 -0400)]
9918: Merge branch '9918-index-timeout'

refs #9918

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

6 years ago9918: Merge branch 'master' into 9918-index-timeout
Ward Vandewege [Tue, 22 May 2018 13:47:40 +0000 (09:47 -0400)]
9918: Merge branch 'master' into 9918-index-timeout

refs #9918

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

6 years agoAdded tests to arv-put to cover storage classes feature.
Fuad Muhic [Tue, 22 May 2018 10:25:28 +0000 (12:25 +0200)]
Added tests to arv-put to cover storage classes feature.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMerge branch '12995-wb-merge-acct' refs #12995
Peter Amstutz [Mon, 21 May 2018 17:54:19 +0000 (13:54 -0400)]
Merge branch '12995-wb-merge-acct' refs #12995

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

6 years ago12995: Fix tests
Peter Amstutz [Mon, 21 May 2018 16:29:19 +0000 (12:29 -0400)]
12995: Fix tests

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

6 years agoAdded --storage-classes argument to arv-put.
Fuad Muhic [Mon, 21 May 2018 15:18:37 +0000 (17:18 +0200)]
Added --storage-classes argument to arv-put.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago12995: Add username to link_accounts page.
Peter Amstutz [Mon, 21 May 2018 15:08:17 +0000 (11:08 -0400)]
12995: Add username to link_accounts page.

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

6 years ago12995: Add user and admin documentation pages.
Peter Amstutz [Mon, 21 May 2018 14:59:47 +0000 (10:59 -0400)]
12995: Add user and admin documentation pages.

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

6 years ago7478: Use our libcloud fork
Lucas Di Pentima [Fri, 18 May 2018 21:32:31 +0000 (18:32 -0300)]
7478: Use our libcloud fork

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

6 years ago12995: Do nested logout/login to workaround SSO session.
Peter Amstutz [Fri, 18 May 2018 20:57:21 +0000 (16:57 -0400)]
12995: Do nested logout/login to workaround SSO session.

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

6 years ago12995: Bugfix to support following chained user uuid redirection.
Peter Amstutz [Fri, 18 May 2018 20:28:44 +0000 (16:28 -0400)]
12995: Bugfix to support following chained user uuid redirection.

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

6 years ago9918: Add RequestTimeout config for keep-balance.
Tom Clegg [Fri, 18 May 2018 19:50:15 +0000 (15:50 -0400)]
9918: Add RequestTimeout config for keep-balance.

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

6 years ago12995: Don't let admins lose admin privs by linking a non-admin account.
Peter Amstutz [Fri, 18 May 2018 19:37:23 +0000 (15:37 -0400)]
12995: Don't let admins lose admin privs by linking a non-admin account.

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

6 years agoMerge branch '13164-container-deadlock'
Tom Clegg [Fri, 18 May 2018 19:10:53 +0000 (15:10 -0400)]
Merge branch '13164-container-deadlock'

refs #13164

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

6 years ago12995: Add testing
Peter Amstutz [Fri, 18 May 2018 18:34:43 +0000 (14:34 -0400)]
12995: Add testing

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

6 years ago13164: Lock tables in order when locking a container.
Tom Clegg [Fri, 18 May 2018 18:29:34 +0000 (14:29 -0400)]
13164: Lock tables in order when locking a container.

Locking involves assigning auth_uuid, which involves looking up
container requests, so both tables must be locked in order to avoid
deadlock.

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

6 years ago13164: Lock tables in order for container updates.
Tom Clegg [Fri, 18 May 2018 18:02:29 +0000 (14:02 -0400)]
13164: Lock tables in order for container updates.

Otherwise, a container update can lock a container row, then perform
container request queries, which can deadlock with another thread that
locked container_requests first.

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

6 years agoMerge branch '12737-wb-rails42-upgrade'
Lucas Di Pentima [Fri, 18 May 2018 13:30:48 +0000 (10:30 -0300)]
Merge branch '12737-wb-rails42-upgrade'
Closes #12737

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

6 years ago12995: Can now merge with inactive accounts.
Peter Amstutz [Thu, 17 May 2018 21:41:01 +0000 (17:41 -0400)]
12995: Can now merge with inactive accounts.

Checks that the remaining account is active so users don't lock
themselves out by accident.

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

6 years ago12737: Fix integration tests
Lucas Di Pentima [Thu, 17 May 2018 20:25:21 +0000 (17:25 -0300)]
12737: Fix integration tests

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

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 ago12737: Fix controller tests
Lucas Di Pentima [Thu, 17 May 2018 17:47:37 +0000 (14:47 -0300)]
12737: Fix controller tests

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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 ago12737: Assign empty default values on serialized attributes
Lucas Di Pentima [Wed, 16 May 2018 20:20:20 +0000 (17:20 -0300)]
12737: Assign empty default values on serialized attributes

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

6 years ago12737: Send serialized attributes when save()
Lucas Di Pentima [Wed, 16 May 2018 13:24:12 +0000 (10:24 -0300)]
12737: Send serialized attributes when save()

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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 ago12737: Rename config serve_static_assets to serve_static_files.
Tom Clegg [Mon, 14 May 2018 19:32:26 +0000 (15:32 -0400)]
12737: Rename config serve_static_assets to serve_static_files.

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

6 years ago12737: Fix serialized column setup.
Tom Clegg [Mon, 14 May 2018 19:32:23 +0000 (15:32 -0400)]
12737: Fix serialized column setup.

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

6 years ago12737: Remove attribute from previous tests
Lucas Di Pentima [Mon, 14 May 2018 15:40:25 +0000 (12:40 -0300)]
12737: Remove attribute from previous tests

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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 ago12737: Upgrade workbench from rails 4.1 to 4.2 (WIP)
Lucas Di Pentima [Mon, 14 May 2018 14:17:35 +0000 (11:17 -0300)]
12737: Upgrade workbench from rails 4.1 to 4.2 (WIP)

Serialization isn't working properly, Hash & Array columns happily receive
these types but return their text versions when accessed.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@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 agoReplaced call to non-existent method execute in RESTService class with
Fuad Muhic [Thu, 10 May 2018 09:05:29 +0000 (11:05 +0200)]
Replaced call to non-existent method execute in RESTService class with
correct call to exec method.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.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>