arvados.git
5 years ago14325: Propagate API env vars to crunch-run.
Tom Clegg [Tue, 18 Dec 2018 20:50:17 +0000 (15:50 -0500)]
14325: Propagate API env vars to crunch-run.

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

5 years agoMerge branch '14324-cdc-azure' refs #14324
Peter Amstutz [Tue, 15 Jan 2019 18:40:34 +0000 (13:40 -0500)]
Merge branch '14324-cdc-azure' refs #14324

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

5 years ago14324: Embed test public key instead of reading from file
Peter Amstutz [Tue, 15 Jan 2019 18:29:30 +0000 (13:29 -0500)]
14324: Embed test public key instead of reading from file

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

5 years ago14324: Fix API throttling header fallbacks. Add gocheck_test
Peter Amstutz [Mon, 14 Jan 2019 19:13:20 +0000 (14:13 -0500)]
14324:  Fix API throttling header fallbacks.  Add gocheck_test

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

5 years agoFix arvbox demo for workbench2 no issue #
Peter Amstutz [Mon, 14 Jan 2019 16:00:12 +0000 (11:00 -0500)]
Fix arvbox demo for workbench2 no issue #

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

5 years ago14324: Fix tests
Peter Amstutz [Fri, 11 Jan 2019 19:04:06 +0000 (14:04 -0500)]
14324: Fix tests

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

5 years ago14324: Use logrus in Azure driver. Fix Sirupsen->sirupsen in imports
Peter Amstutz [Fri, 11 Jan 2019 15:08:37 +0000 (10:08 -0500)]
14324: Use logrus in Azure driver.  Fix Sirupsen->sirupsen in imports

"It's in the past been possible to import Logrus as both upper- and
lower-case. Due to the Go package environment, this caused issues in
the community and we needed a standard. Some environments experienced
problems with the upper-case variant, so the lower-case was
decided. Everything using logrus will need to use the lower-case:
github.com/sirupsen/logrus. Any package that isn't, should be
changed."

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

5 years ago14324: Remove context from interface, use Stop() instead
Peter Amstutz [Thu, 10 Jan 2019 18:33:50 +0000 (13:33 -0500)]
14324: Remove context from interface, use Stop() instead

Remove 'Context' passed into methods of the InstanceSet interface,
instead the AzureInstanceSet creates its own cancellable background
context.  The Stop() method now cancels the context and waits for any
outstanding cloud driver work to complete before returning.

* Fix test
* Document how to run individual test cases against real cloud
* ManageBlobs runs periodically in the background
* Logging cleaned up

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

5 years ago14324: Azure driver for crunch-dispatch-cloud
Peter Amstutz [Wed, 9 Jan 2019 21:13:56 +0000 (16:13 -0500)]
14324: Azure driver for crunch-dispatch-cloud

* Adds context parameter to methods of InstanceSet interface that may block
* Fix tests

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

5 years ago14324: Azure driver WIP
Peter Amstutz [Wed, 9 Jan 2019 16:35:55 +0000 (11:35 -0500)]
14324: Azure driver WIP

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

5 years ago13964: Fail on missing node-token tag
Peter Amstutz [Fri, 31 Aug 2018 20:41:07 +0000 (16:41 -0400)]
13964: Fail on missing node-token tag

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

5 years ago13964: Forget the node token once the key fingerprint is known
Peter Amstutz [Fri, 31 Aug 2018 20:27:08 +0000 (16:27 -0400)]
13964: Forget the node token once the key fingerprint is known

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

5 years ago13964: Fix string pointer capture
Peter Amstutz [Fri, 31 Aug 2018 20:15:55 +0000 (16:15 -0400)]
13964: Fix string pointer capture

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

5 years ago13964: Trim space
Peter Amstutz [Fri, 31 Aug 2018 20:11:12 +0000 (16:11 -0400)]
13964: Trim space

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

5 years ago13964: ssh key checking
Peter Amstutz [Fri, 31 Aug 2018 19:55:43 +0000 (15:55 -0400)]
13964: ssh key checking

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

5 years ago13964: ssh key verification wip
Peter Amstutz [Fri, 31 Aug 2018 19:11:58 +0000 (15:11 -0400)]
13964: ssh key verification wip

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

5 years ago13964: Set and check node-token WIP
Peter Amstutz [Fri, 31 Aug 2018 18:47:28 +0000 (14:47 -0400)]
13964: Set and check node-token WIP

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

5 years ago13964: Tweak test
Peter Amstutz [Fri, 31 Aug 2018 18:24:28 +0000 (14:24 -0400)]
13964: Tweak test

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

5 years ago13964: SSH access WIP
Peter Amstutz [Fri, 31 Aug 2018 15:42:01 +0000 (11:42 -0400)]
13964: SSH access WIP

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

5 years ago13964: InstanceTags type
Peter Amstutz [Thu, 23 Aug 2018 20:38:28 +0000 (16:38 -0400)]
13964: InstanceTags type

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

5 years ago13964: VM names are namespaced. Can set/get tags.
Peter Amstutz [Thu, 23 Aug 2018 20:22:12 +0000 (16:22 -0400)]
13964: VM names are namespaced.  Can set/get tags.

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

5 years ago13964: Don't panic running tests on stubs
Peter Amstutz [Thu, 23 Aug 2018 19:21:05 +0000 (15:21 -0400)]
13964: Don't panic running tests on stubs

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

5 years ago13964: Detect and report rate limit and quota exceeded errors
Peter Amstutz [Thu, 23 Aug 2018 19:15:42 +0000 (15:15 -0400)]
13964: Detect and report rate limit and quota exceeded errors

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

5 years ago13964: Return Arvados instance type
Peter Amstutz [Thu, 23 Aug 2018 02:42:26 +0000 (22:42 -0400)]
13964: Return Arvados instance type

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

5 years ago13964: Full lifecycle for NICs/VHDs/VMs
Peter Amstutz [Thu, 23 Aug 2018 02:13:23 +0000 (22:13 -0400)]
13964: Full lifecycle for NICs/VHDs/VMs

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

5 years ago13964: Can successfully create a VM, list existing VMs
Peter Amstutz [Tue, 21 Aug 2018 15:28:37 +0000 (11:28 -0400)]
13964: Can successfully create a VM, list existing VMs

Cleanup unused NICs.  Blob cleanup in progress.

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

5 years ago13964: Azure provider WIP
Peter Amstutz [Mon, 20 Aug 2018 13:41:16 +0000 (09:41 -0400)]
13964: Azure provider WIP

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

5 years agoarvbox uses 'down: ready' as ready condition no issue #
Peter Amstutz [Wed, 9 Jan 2019 19:39:43 +0000 (14:39 -0500)]
arvbox uses 'down: ready' as ready condition no issue #

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

5 years agoConfigure UTF-8 locale inside arvbox, no issue #
Peter Amstutz [Wed, 9 Jan 2019 15:13:56 +0000 (10:13 -0500)]
Configure UTF-8 locale inside arvbox, no issue #

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

5 years agoMerge branch '14660-arvbox-workbench2' refs #14660
Peter Amstutz [Tue, 8 Jan 2019 22:00:24 +0000 (17:00 -0500)]
Merge branch '14660-arvbox-workbench2' refs #14660

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

5 years ago14660: make "sv restart" work for workbench2, prevent fail loop
Peter Amstutz [Tue, 8 Jan 2019 21:57:56 +0000 (16:57 -0500)]
14660: make "sv restart" work for workbench2, prevent fail loop

Print out https url for workbench2 on start.

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

5 years agoMerge branch '14691-suggested-ssh-config-update'
Ward Vandewege [Fri, 4 Jan 2019 22:28:56 +0000 (17:28 -0500)]
Merge branch '14691-suggested-ssh-config-update'

closes #14691

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

5 years ago14691: workbench update, bring in line with documentation
Ward Vandewege [Fri, 4 Jan 2019 21:02:54 +0000 (16:02 -0500)]
14691: workbench update, bring in line with documentation

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

5 years ago14691: documentation update
Ward Vandewege [Fri, 4 Jan 2019 15:29:43 +0000 (10:29 -0500)]
14691: documentation update

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

5 years ago14660: Enable workbench2 to connect to development server via websockets.
Peter Amstutz [Fri, 4 Jan 2019 19:30:39 +0000 (14:30 -0500)]
14660: Enable workbench2 to connect to development server via websockets.

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

5 years ago14660: Proxy keep-web for https. Install root cert inside the container.
Peter Amstutz [Fri, 4 Jan 2019 16:28:12 +0000 (11:28 -0500)]
14660: Proxy keep-web for https.  Install root cert inside the container.

Now services inside the container can talk to each other without the
"insecure" flag.

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

5 years ago14660: Add workbench2 to arvbox. Improve SSL support in arvbox.
Peter Amstutz [Thu, 3 Jan 2019 19:53:25 +0000 (14:53 -0500)]
14660: Add workbench2 to arvbox.  Improve SSL support in arvbox.

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

5 years agoMerge branch '14360-dispatch-cloud'
Tom Clegg [Thu, 20 Dec 2018 19:02:05 +0000 (14:02 -0500)]
Merge branch '14360-dispatch-cloud'

closes #14360

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

5 years ago14360: Merge branch 'master' into 14360-dispatch-cloud
Tom Clegg [Thu, 20 Dec 2018 18:58:26 +0000 (13:58 -0500)]
14360: Merge branch 'master' into 14360-dispatch-cloud

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

5 years ago14360: Fix error log level on first probe after boot.
Tom Clegg [Thu, 20 Dec 2018 18:57:27 +0000 (13:57 -0500)]
14360: Fix error log level on first probe after boot.

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

5 years ago14360: Test for errant Create calls after failure.
Tom Clegg [Thu, 20 Dec 2018 16:00:10 +0000 (11:00 -0500)]
14360: Test for errant Create calls after failure.

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

5 years ago14360: Fix test case.
Tom Clegg [Thu, 20 Dec 2018 15:03:19 +0000 (10:03 -0500)]
14360: Fix test case.

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

5 years ago14360: Fix instance creation limiting.
Tom Clegg [Thu, 20 Dec 2018 14:44:45 +0000 (09:44 -0500)]
14360: Fix instance creation limiting.

Scheduler was claiming one of its unalloc instances only if the
container could be scheduled, so the "need new instance" condition was
not triggered for lower-priority containers needing the same instance
type.

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

5 years ago14360: Fix panic in test when last container is run twice.
Tom Clegg [Thu, 20 Dec 2018 14:42:49 +0000 (09:42 -0500)]
14360: Fix panic in test when last container is run twice.

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

5 years ago14360: Debug log when acquiring lock.
Tom Clegg [Thu, 20 Dec 2018 14:27:37 +0000 (09:27 -0500)]
14360: Debug log when acquiring lock.

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

5 years ago14360: Shutdown pool between tests to eliminate leaking logs.
Tom Clegg [Thu, 20 Dec 2018 14:25:56 +0000 (09:25 -0500)]
14360: Shutdown pool between tests to eliminate leaking logs.

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

5 years ago14360: Replace OnComplete/OnCancel with ExecuteContainer callback.
Tom Clegg [Tue, 18 Dec 2018 20:08:57 +0000 (15:08 -0500)]
14360: Replace OnComplete/OnCancel with ExecuteContainer callback.

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

5 years agoMerge branch '14327-cwl-unnecessary-collections' refs #14327
Peter Amstutz [Tue, 18 Dec 2018 19:14:58 +0000 (14:14 -0500)]
Merge branch '14327-cwl-unnecessary-collections' refs #14327

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

5 years ago14360: Call ChooseType just once per container.
Tom Clegg [Tue, 18 Dec 2018 19:11:23 +0000 (14:11 -0500)]
14360: Call ChooseType just once per container.

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

5 years ago14327: Add comments
Peter Amstutz [Tue, 18 Dec 2018 19:08:58 +0000 (14:08 -0500)]
14327: Add comments

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

5 years ago14360: Remove log spam.
Tom Clegg [Tue, 18 Dec 2018 18:54:40 +0000 (13:54 -0500)]
14360: Remove log spam.

Just don't reserve space for an image if there is no image.

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

5 years agoMerge branch '14640-api-wb-activejob-upgrade'
Lucas Di Pentima [Tue, 18 Dec 2018 17:02:05 +0000 (14:02 -0300)]
Merge branch '14640-api-wb-activejob-upgrade'
Closes #14640

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

5 years agoFix test_with_arvbox.sh to use https://versions.arvados.org no issue #
Peter Amstutz [Tue, 18 Dec 2018 16:50:51 +0000 (11:50 -0500)]
Fix test_with_arvbox.sh to use https://versions.arvados.org no issue #

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

5 years ago14640: Upgrades WB rails to 4.2.11
Lucas Di Pentima [Tue, 18 Dec 2018 16:17:24 +0000 (13:17 -0300)]
14640: Upgrades WB rails to 4.2.11

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

5 years ago14640: Upgrades API to rails 4.2.11
Lucas Di Pentima [Tue, 18 Dec 2018 16:02:41 +0000 (13:02 -0300)]
14640: Upgrades API to rails 4.2.11

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

5 years agoMerge branch 'master' into 14360-dispatch-cloud
Tom Clegg [Tue, 18 Dec 2018 15:02:55 +0000 (10:02 -0500)]
Merge branch 'master' into 14360-dispatch-cloud

refs #14360

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

5 years ago14360: Shutdown between tests to eliminate leaking logs.
Tom Clegg [Tue, 18 Dec 2018 07:59:05 +0000 (02:59 -0500)]
14360: Shutdown between tests to eliminate leaking logs.

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

5 years ago14360: Clean up stub driver.
Tom Clegg [Tue, 18 Dec 2018 07:27:27 +0000 (02:27 -0500)]
14360: Clean up stub driver.

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

5 years ago14360: Avoid overreporting instances during Create/List race.
Tom Clegg [Tue, 18 Dec 2018 04:37:47 +0000 (23:37 -0500)]
14360: Avoid overreporting instances during Create/List race.

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

5 years ago14327: Don't create new collection if source has expected secondaryFiles
Peter Amstutz [Mon, 17 Dec 2018 21:23:07 +0000 (16:23 -0500)]
14327: Don't create new collection if source has expected secondaryFiles

If all secondary files/directories are located in the same collection
as the primary file and the paths and names that are consistent with
staging, don't create a new collection.

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

5 years agoWe've moved the chat/community support channel from IRC to gitter.im.
Ward Vandewege [Mon, 17 Dec 2018 20:53:43 +0000 (15:53 -0500)]
We've moved the chat/community support channel from IRC to gitter.im.

No issue #

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

5 years ago14360: Comment stubServer.
Tom Clegg [Mon, 17 Dec 2018 20:14:11 +0000 (15:14 -0500)]
14360: Comment stubServer.

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

5 years agoUpdate cwltool refs #14510
Peter Amstutz [Mon, 17 Dec 2018 17:46:54 +0000 (12:46 -0500)]
Update cwltool refs #14510

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

5 years ago14360: Locking comment.
Tom Clegg [Mon, 17 Dec 2018 18:49:43 +0000 (13:49 -0500)]
14360: Locking comment.

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

5 years ago14360: Fix log spam on normal race condition.
Tom Clegg [Mon, 17 Dec 2018 18:47:14 +0000 (13:47 -0500)]
14360: Fix log spam on normal race condition.

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

5 years agoUpdate README and community doc page. refs #14617
Peter Amstutz [Mon, 17 Dec 2018 16:31:52 +0000 (11:31 -0500)]
Update README and community doc page.  refs #14617

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

5 years ago14360: Comment TestDispatchToStubDriver.
Tom Clegg [Mon, 17 Dec 2018 15:57:40 +0000 (10:57 -0500)]
14360: Comment TestDispatchToStubDriver.

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

5 years ago11419: Read JSON files in binary mode.
Tom Clegg [Fri, 14 Dec 2018 20:59:34 +0000 (15:59 -0500)]
11419: Read JSON files in binary mode.

Files opened in text mode do not have a size() method.

refs #11419

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

5 years agoSet DBName correctly for arvbox demo, hopefully fix ci.commonwl.org
Peter Amstutz [Fri, 14 Dec 2018 21:36:50 +0000 (16:36 -0500)]
Set DBName correctly for arvbox demo, hopefully fix ci.commonwl.org

no issue #

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

5 years agoMerge branch '14596-check-container-locked'
Tom Clegg [Fri, 14 Dec 2018 17:54:00 +0000 (12:54 -0500)]
Merge branch '14596-check-container-locked'

closes #14596

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

5 years agono issue # Fix and update rvm GPG Key signature issue on test dockerfiles
Fernando Monserrat [Fri, 14 Dec 2018 16:17:23 +0000 (13:17 -0300)]
no issue # Fix and update rvm GPG Key signature issue on test dockerfiles
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

5 years agoMerge branch '13006-sync-groups-is_a-filter'
Lucas Di Pentima [Fri, 14 Dec 2018 16:03:29 +0000 (13:03 -0300)]
Merge branch '13006-sync-groups-is_a-filter'
Closes #13006

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

5 years agoMerge branch '13006-api-is_a-filter'
Lucas Di Pentima [Fri, 14 Dec 2018 16:02:46 +0000 (13:02 -0300)]
Merge branch '13006-api-is_a-filter'
Refs #13006

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

5 years agoMerge branch '13006-api-is_a-filter' into 13006-sync-groups-is_a-filter
Lucas Di Pentima [Fri, 14 Dec 2018 15:54:49 +0000 (12:54 -0300)]
Merge branch '13006-api-is_a-filter' into 13006-sync-groups-is_a-filter

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

5 years ago13006: Uses 'is_a' filter again because it's being fixed on the API server.
Lucas Di Pentima [Thu, 13 Dec 2018 21:03:24 +0000 (18:03 -0300)]
13006: Uses 'is_a' filter again because it's being fixed on the API server.

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

5 years agono issue # Fix and update rvm GPG Key signature issue
Fernando Monserrat [Thu, 13 Dec 2018 21:02:53 +0000 (18:02 -0300)]
no issue # Fix and update rvm GPG Key signature issue
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

5 years ago13006: Fail when using is_a filter on uuid attr and prefix_uuid doesn't match.
Lucas Di Pentima [Thu, 13 Dec 2018 20:53:33 +0000 (17:53 -0300)]
13006: Fail when using is_a filter on uuid attr and prefix_uuid doesn't match.

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

5 years ago14596: crunch-run: don't do anything unless container is Locked.
Tom Clegg [Thu, 13 Dec 2018 20:16:42 +0000 (15:16 -0500)]
14596: crunch-run: don't do anything unless container is Locked.

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

5 years agoMerge branch '14595-leave-modified-at' refs #14595
Peter Amstutz [Thu, 13 Dec 2018 20:09:12 +0000 (15:09 -0500)]
Merge branch '14595-leave-modified-at' refs #14595

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

5 years ago14595: Fix comment.
Peter Amstutz [Thu, 13 Dec 2018 20:08:53 +0000 (15:08 -0500)]
14595: Fix comment.

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

5 years ago14595: Add leave_modified_at_alone
Peter Amstutz [Thu, 13 Dec 2018 19:37:29 +0000 (14:37 -0500)]
14595: Add leave_modified_at_alone

leave_modified_by_user_alone does not affect modified_at

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

5 years agoMerge branch '14012-arvput-check-cache'
Lucas Di Pentima [Thu, 13 Dec 2018 19:34:21 +0000 (16:34 -0300)]
Merge branch '14012-arvput-check-cache'
Closes #14012

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

5 years ago13006: Adds expression index on links.[tail|head]_uuid
Lucas Di Pentima [Thu, 13 Dec 2018 19:21:38 +0000 (16:21 -0300)]
13006: Adds expression index on links.[tail|head]_uuid

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

5 years agoMerge branch '14596-no-requeue'
Tom Clegg [Thu, 13 Dec 2018 18:16:29 +0000 (13:16 -0500)]
Merge branch '14596-no-requeue'

fixes #14596

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

5 years ago13006: Changes is_a filter to use a substring query to support remote UUIDs.
Lucas Di Pentima [Thu, 13 Dec 2018 17:28:28 +0000 (14:28 -0300)]
13006: Changes is_a filter to use a substring query to support remote UUIDs.

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

5 years ago14596: Use sbatch --no-requeue to avoid bogus container re-runs.
Tom Clegg [Thu, 13 Dec 2018 17:10:52 +0000 (12:10 -0500)]
14596: Use sbatch --no-requeue to avoid bogus container re-runs.

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

5 years ago13006: Test exposing the bug
Lucas Di Pentima [Thu, 13 Dec 2018 16:11:04 +0000 (13:11 -0300)]
13006: Test exposing the bug

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

5 years agoMerge branch '14495-crunch-docker-space' refs #14495
Peter Amstutz [Thu, 13 Dec 2018 15:38:35 +0000 (10:38 -0500)]
Merge branch '14495-crunch-docker-space' refs #14495

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

5 years ago14495: Add warnings when estimateDockerImageSize gets bad input
Peter Amstutz [Thu, 13 Dec 2018 15:37:26 +0000 (10:37 -0500)]
14495: Add warnings when estimateDockerImageSize gets bad input

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

5 years ago14360: Fix race between per-container lock and garbage collection.
Tom Clegg [Wed, 12 Dec 2018 20:21:51 +0000 (15:21 -0500)]
14360: Fix race between per-container lock and garbage collection.

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

5 years agoMerge branch '11419-text-mode'
Tom Clegg [Mon, 10 Dec 2018 21:18:35 +0000 (16:18 -0500)]
Merge branch '11419-text-mode'

closes #11419

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

5 years ago14012: Enhance test coverage on _cached_manifest_valid() method
Lucas Di Pentima [Mon, 10 Dec 2018 20:55:58 +0000 (17:55 -0300)]
14012: Enhance test coverage on _cached_manifest_valid() method

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

5 years ago14012: Split cache file name generation for readability
Lucas Di Pentima [Mon, 10 Dec 2018 20:55:11 +0000 (17:55 -0300)]
14012: Split cache file name generation for readability

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

5 years agoMerge branch '14594-update-cwltool' refs #14594
Peter Amstutz [Mon, 10 Dec 2018 19:06:34 +0000 (14:06 -0500)]
Merge branch '14594-update-cwltool' refs #14594

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

5 years agoMerge branch '14538-async-write'
Tom Clegg [Mon, 10 Dec 2018 16:41:12 +0000 (11:41 -0500)]
Merge branch '14538-async-write'

fixes #14538

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

5 years ago14594: Update to latest cwltool
Peter Amstutz [Mon, 10 Dec 2018 16:40:13 +0000 (11:40 -0500)]
14594: Update to latest cwltool

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

5 years ago14538: Merge branch 'master' into 14538-async-write
Tom Clegg [Mon, 10 Dec 2018 16:38:35 +0000 (11:38 -0500)]
14538: Merge branch 'master' into 14538-async-write

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

5 years ago11419: Merge branch 'master' into 11419-text-mode
Tom Clegg [Mon, 10 Dec 2018 16:37:40 +0000 (11:37 -0500)]
11419: Merge branch 'master' into 11419-text-mode

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

5 years ago14360: Merge branch 'master' into 14360-dispatch-cloud
Tom Clegg [Mon, 10 Dec 2018 16:31:14 +0000 (11:31 -0500)]
14360: Merge branch 'master' into 14360-dispatch-cloud

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

5 years agoMerge branch '14476-cwl-missing-input' refs #14476
Peter Amstutz [Mon, 10 Dec 2018 16:25:38 +0000 (11:25 -0500)]
Merge branch '14476-cwl-missing-input' refs #14476

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