arvados.git
3 months ago19070: Still trying to fix test_with_arvbox
Peter Amstutz [Tue, 17 May 2022 18:45:28 +0000 (14:45 -0400)]
19070: Still trying to fix test_with_arvbox

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

3 months ago19070: Fixing CWL tests
Peter Amstutz [Tue, 17 May 2022 18:20:24 +0000 (14:20 -0400)]
19070: Fixing CWL tests

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

3 months agoMerge branch '19081-singularity-no-eval'
Tom Clegg [Tue, 17 May 2022 18:13:34 +0000 (14:13 -0400)]
Merge branch '19081-singularity-no-eval'

refs #19081

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

3 months agoMerge branch '19094-log-versions'
Tom Clegg [Tue, 17 May 2022 17:25:54 +0000 (13:25 -0400)]
Merge branch '19094-log-versions'

closes #19094

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

3 months ago19081: Disable singularity env var eval behavior if possible.
Tom Clegg [Tue, 17 May 2022 15:41:40 +0000 (11:41 -0400)]
19081: Disable singularity env var eval behavior if possible.

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

3 months ago19094: Note docker/singularity/arv-mount versions in container log.
Tom Clegg [Tue, 17 May 2022 06:17:39 +0000 (02:17 -0400)]
19094: Note docker/singularity/arv-mount versions in container log.

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

3 months agoBash syntax in arvados-tests.sh requires bash, fixed.
Peter Amstutz [Mon, 16 May 2022 20:11:28 +0000 (16:11 -0400)]
Bash syntax in arvados-tests.sh requires bash, fixed.

refs #19109

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

3 months agoFix set_secondary recursion error
Peter Amstutz [Mon, 16 May 2022 18:51:20 +0000 (14:51 -0400)]
Fix set_secondary recursion error

skip some problematic conformance tests in test_with_arvbox

refs #19109

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

3 months agoFix arvados-tests.sh to use python from a-c-r package if available.
Peter Amstutz [Mon, 16 May 2022 17:20:29 +0000 (13:20 -0400)]
Fix arvados-tests.sh to use python from a-c-r package if available.

Add note about the purpose of arvados-tests.sh

refs #19070

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

3 months agoMerge branch '18947-dispatch-slurm'
Tom Clegg [Fri, 13 May 2022 20:53:27 +0000 (16:53 -0400)]
Merge branch '18947-dispatch-slurm'

refs #18947

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

3 months ago18947: Merge branch 'main'
Tom Clegg [Fri, 13 May 2022 20:52:43 +0000 (16:52 -0400)]
18947: Merge branch 'main'

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

3 months agoMerge branch '18947-health'
Tom Clegg [Fri, 13 May 2022 20:50:00 +0000 (16:50 -0400)]
Merge branch '18947-health'

refs #18947

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

3 months ago18947: Merge branch 'main'
Tom Clegg [Fri, 13 May 2022 20:48:36 +0000 (16:48 -0400)]
18947: Merge branch 'main'

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

3 months agoMerge branch '19126-nginx-proxy-settings-change'
Ward Vandewege [Fri, 13 May 2022 18:46:48 +0000 (14:46 -0400)]
Merge branch '19126-nginx-proxy-settings-change'

closes #19126

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

3 months ago19126: Merge branch 'main' into 19126-nginx-proxy-settings-change
Ward Vandewege [Fri, 13 May 2022 18:46:17 +0000 (14:46 -0400)]
19126: Merge branch 'main' into 19126-nginx-proxy-settings-change

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

3 months agoMerge branch '19109-upload-secondary' refs #19109
Peter Amstutz [Fri, 13 May 2022 15:08:31 +0000 (11:08 -0400)]
Merge branch '19109-upload-secondary' refs #19109

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

3 months agoMerge branch '19070-update-workflow-deps' refs #19070
Peter Amstutz [Fri, 13 May 2022 15:08:08 +0000 (11:08 -0400)]
Merge branch '19070-update-workflow-deps' refs #19070

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

3 months ago19126: disable all nginx proxy caching for controller in the templates used by the...
Ward Vandewege [Fri, 13 May 2022 14:56:07 +0000 (10:56 -0400)]
19126: disable all nginx proxy caching for controller in the templates used by the installer.

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

3 months ago19126: disable all proxy caching in the nginx template used by our tests
Ward Vandewege [Fri, 13 May 2022 14:36:07 +0000 (10:36 -0400)]
19126: disable all proxy caching in the nginx template used by our tests
       and arvados-server boot.

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

3 months ago19126: Merge branch 'main' into 19126-nginx-proxy-settings-change
Ward Vandewege [Fri, 13 May 2022 14:33:06 +0000 (10:33 -0400)]
19126: Merge branch 'main' into 19126-nginx-proxy-settings-change

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

3 months agoMerge branch '16345-check-clock-skew'
Tom Clegg [Fri, 13 May 2022 14:25:41 +0000 (10:25 -0400)]
Merge branch '16345-check-clock-skew'

refs #16345

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

3 months agoMerge branch '19127-remove-warnings'
Ward Vandewege [Fri, 13 May 2022 14:13:29 +0000 (10:13 -0400)]
Merge branch '19127-remove-warnings'

closes #19127

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

3 months ago19126: disable all nginx proxy caching for controller.
Ward Vandewege [Fri, 13 May 2022 11:57:00 +0000 (07:57 -0400)]
19126: disable all nginx proxy caching for controller.

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

3 months ago19127: remove config file support for InstanceTypes specified as an
Ward Vandewege [Thu, 12 May 2022 18:31:53 +0000 (14:31 -0400)]
19127: remove config file support for InstanceTypes specified as an
       array (deprecated since Arvados 1.2.0). Remove support for
       InstanceType "Scratch" field from config file (deprecated since
       Arvados 1.4.0).

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

3 months ago19109: Avoid recursion fail mode
Peter Amstutz [Thu, 12 May 2022 21:20:55 +0000 (17:20 -0400)]
19109: Avoid recursion fail mode

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

3 months ago19070: Add documentation notes about --copy-deps
Peter Amstutz [Thu, 12 May 2022 20:55:57 +0000 (16:55 -0400)]
19070: Add documentation notes about --copy-deps

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

3 months ago19070: Fix --update-workflow
Peter Amstutz [Thu, 12 May 2022 18:31:57 +0000 (14:31 -0400)]
19070: Fix --update-workflow

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

3 months ago19127: Update test to catch InstanceTypes computed fields.
Tom Clegg [Wed, 11 May 2022 23:40:43 +0000 (19:40 -0400)]
19127: Update test to catch InstanceTypes computed fields.

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

3 months ago19070: Prefer to use the passed-in runtimeContext
Peter Amstutz [Wed, 11 May 2022 21:19:51 +0000 (17:19 -0400)]
19070: Prefer to use the passed-in runtimeContext

Code cleanup, change most places to use the passed-in runtimeContext
instead of the ArvRunner top level runtimeContext.

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

3 months ago19070: Fix tests
Peter Amstutz [Fri, 6 May 2022 19:24:23 +0000 (15:24 -0400)]
19070: Fix tests

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

3 months ago19070: --create/update-workflow also implies --match-submitter-images
Peter Amstutz [Fri, 6 May 2022 14:23:03 +0000 (10:23 -0400)]
19070: --create/update-workflow also implies --match-submitter-images

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

3 months ago19070: Add integration test for copying dependencies
Peter Amstutz [Wed, 4 May 2022 20:57:01 +0000 (16:57 -0400)]
19070: Add integration test for copying dependencies

Fix python tests

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

3 months ago19070: Fix test_arvados_jobs_image
Peter Amstutz [Wed, 4 May 2022 18:17:18 +0000 (14:17 -0400)]
19070: Fix test_arvados_jobs_image

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

3 months ago19070: Fix most tests
Peter Amstutz [Tue, 3 May 2022 22:05:43 +0000 (18:05 -0400)]
19070: Fix most tests

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

3 months ago19070: Add --copy-deps/--no-copy-deps
Peter Amstutz [Tue, 3 May 2022 21:01:26 +0000 (17:01 -0400)]
19070: Add --copy-deps/--no-copy-deps

Copies dependencies by default using --create-workflow and --update
workflow

Keeps old behavior by default when running from the command line (can
get new behavior with --copy-deps).

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

3 months ago19070: Always make copy of Docker images with --project-uuid
Peter Amstutz [Thu, 28 Apr 2022 16:53:55 +0000 (12:53 -0400)]
19070: Always make copy of Docker images with --project-uuid

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

3 months ago19070: keepdocker will use image in arvados
Peter Amstutz [Thu, 28 Apr 2022 16:44:10 +0000 (12:44 -0400)]
19070: keepdocker will use image in arvados

If not available in Docker

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

3 months ago19127: do not dump InstanceTypes...Name and InstanceTypes...Scratch,
Ward Vandewege [Wed, 11 May 2022 21:03:07 +0000 (17:03 -0400)]
19127: do not dump InstanceTypes...Name and InstanceTypes...Scratch,
       they are computed fields.

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

3 months ago19109: Fix integration test
Peter Amstutz [Wed, 11 May 2022 19:57:06 +0000 (15:57 -0400)]
19109: Fix integration test

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

3 months ago19109: test/fix for related bug, finding secondary files with expressions
Peter Amstutz [Wed, 11 May 2022 19:42:28 +0000 (15:42 -0400)]
19109: test/fix for related bug, finding secondary files with expressions

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

3 months ago19126: update the nginx template used by our tests and arvados-server
Ward Vandewege [Wed, 11 May 2022 18:45:39 +0000 (14:45 -0400)]
19126: update the nginx template used by our tests and arvados-server
       boot.

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

3 months ago19126: update documentation to reflect nginx proxy configuration for
Ward Vandewege [Wed, 11 May 2022 18:44:08 +0000 (14:44 -0400)]
19126: update documentation to reflect nginx proxy configuration for
       controller.

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

3 months agoMerge branch '19103-aca-list-default-limit'. Closes #19103
Lucas Di Pentima [Wed, 11 May 2022 14:02:50 +0000 (11:02 -0300)]
Merge branch '19103-aca-list-default-limit'. Closes #19103

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

3 months ago19109: Add test case for discovering & uploading secondary files
Peter Amstutz [Tue, 10 May 2022 19:34:07 +0000 (15:34 -0400)]
19109: Add test case for discovering & uploading secondary files

Correctly find secondary files in the optional "File?" case

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

3 months ago19103: Fixes the default Limit param for ACA list requests.
Lucas Di Pentima [Wed, 11 May 2022 13:02:00 +0000 (10:02 -0300)]
19103: Fixes the default Limit param for ACA list requests.

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

3 months ago19103: Exposes the bug with a test.
Lucas Di Pentima [Wed, 11 May 2022 12:48:48 +0000 (09:48 -0300)]
19103: Exposes the bug with a test.

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

3 months ago16345: "arvados-server check" detects clock skew.
Tom Clegg [Thu, 5 May 2022 19:37:06 +0000 (15:37 -0400)]
16345: "arvados-server check" detects clock skew.

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

3 months ago18947: Move arvados-dispatch-slurm into arvados-server binary.
Tom Clegg [Tue, 10 May 2022 17:55:20 +0000 (13:55 -0400)]
18947: Move arvados-dispatch-slurm into arvados-server binary.

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

3 months agoMerge branch '19095-singularity-bugfix'
Tom Clegg [Tue, 10 May 2022 14:04:34 +0000 (10:04 -0400)]
Merge branch '19095-singularity-bugfix'

fixes #19095

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

3 months ago19095: Link build script doc page.
Tom Clegg [Tue, 10 May 2022 14:02:45 +0000 (10:02 -0400)]
19095: Link build script doc page.

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

3 months ago19095: Add upgrade note about singularity version.
Tom Clegg [Tue, 10 May 2022 14:00:27 +0000 (10:00 -0400)]
19095: Add upgrade note about singularity version.

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

3 months ago18947: Move arvados-health command into arvados-server binary.
Tom Clegg [Tue, 10 May 2022 13:43:02 +0000 (09:43 -0400)]
18947: Move arvados-health command into arvados-server binary.

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

3 months agoMerge branch '18794-config-health'
Tom Clegg [Mon, 9 May 2022 18:53:19 +0000 (14:53 -0400)]
Merge branch '18794-config-health'

closes #18794

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

3 months ago18794: Increase timeout and logging for rails restart test.
Tom Clegg [Mon, 9 May 2022 14:42:34 +0000 (10:42 -0400)]
18794: Increase timeout and logging for rails restart test.

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

3 months ago18794: Merge branch 'main'
Tom Clegg [Mon, 9 May 2022 13:49:36 +0000 (09:49 -0400)]
18794: Merge branch 'main'

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

3 months agoMerge branch '18947-keep-balance'
Tom Clegg [Fri, 6 May 2022 13:49:13 +0000 (09:49 -0400)]
Merge branch '18947-keep-balance'

refs #18947

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

3 months ago19095: Update singularity install doc link to 3.9.
Tom Clegg [Fri, 6 May 2022 13:26:20 +0000 (09:26 -0400)]
19095: Update singularity install doc link to 3.9.

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

3 months agoMerge branch '18995-code-cleanup-5'
Ward Vandewege [Fri, 6 May 2022 12:47:39 +0000 (08:47 -0400)]
Merge branch '18995-code-cleanup-5'

refs #18995

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

3 months ago18995: Merge branch 'main' into 18995-code-cleanup-5
Ward Vandewege [Fri, 6 May 2022 12:47:11 +0000 (08:47 -0400)]
18995: Merge branch 'main' into 18995-code-cleanup-5

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

3 months agoMerge branch '19015-rvm-gemset-passenger-fix'
Ward Vandewege [Fri, 6 May 2022 12:20:49 +0000 (08:20 -0400)]
Merge branch '19015-rvm-gemset-passenger-fix'

closes #19015

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

3 months ago19015: Merge branch 'main' into 19015-rvm-gemset-passenger-fix
Ward Vandewege [Fri, 6 May 2022 12:19:56 +0000 (08:19 -0400)]
19015: Merge branch 'main' into 19015-rvm-gemset-passenger-fix

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

3 months ago18794: Make "touch restart.txt" recipe work when owned by root.
Tom Clegg [Thu, 5 May 2022 21:42:46 +0000 (17:42 -0400)]
18794: Make "touch restart.txt" recipe work when owned by root.

If root has done "touch {tmp}/restart.txt", then the www-data user
cannot utime() or write() the existing file, but can remove it and
create a new one.

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

3 months ago18794: Auto-reload workbench1 config, too.
Tom Clegg [Thu, 5 May 2022 21:21:33 +0000 (17:21 -0400)]
18794: Auto-reload workbench1 config, too.

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

3 months ago18794: Fix wb1 health-check tests, add metrics tests.
Tom Clegg [Thu, 5 May 2022 18:14:57 +0000 (14:14 -0400)]
18794: Fix wb1 health-check tests, add metrics tests.

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

3 months ago18794: Fix reload_config: don't assume restart.txt already exists.
Tom Clegg [Thu, 5 May 2022 16:59:45 +0000 (12:59 -0400)]
18794: Fix reload_config: don't assume restart.txt already exists.

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

3 months ago18794: Merge branch 'main'
Tom Clegg [Thu, 5 May 2022 15:25:13 +0000 (11:25 -0400)]
18794: Merge branch 'main'

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

3 months ago18794: Wait up to 10s for rails to notice config change.
Tom Clegg [Thu, 5 May 2022 15:23:56 +0000 (11:23 -0400)]
18794: Wait up to 10s for rails to notice config change.

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

3 months ago18794: Add version metric to RailsAPI.
Tom Clegg [Thu, 5 May 2022 14:53:53 +0000 (10:53 -0400)]
18794: Add version metric to RailsAPI.

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

3 months ago18794: Add version and config metrics to workbench1.
Tom Clegg [Thu, 5 May 2022 14:53:32 +0000 (10:53 -0400)]
18794: Add version and config metrics to workbench1.

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

3 months ago18995: add a few missing alt texts to image.
Ward Vandewege [Thu, 5 May 2022 14:40:30 +0000 (10:40 -0400)]
18995: add a few missing alt texts to image.

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

3 months ago18947: Update keep-balance package script.
Tom Clegg [Mon, 2 May 2022 19:18:51 +0000 (15:18 -0400)]
18947: Update keep-balance package script.

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

3 months ago18947: Update boot recipe for keep-balance.
Tom Clegg [Mon, 2 May 2022 19:18:10 +0000 (15:18 -0400)]
18947: Update boot recipe for keep-balance.

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

3 months ago19095: Remove bit about loopback device errors in singularity 3.9.1.
Tom Clegg [Thu, 5 May 2022 13:55:59 +0000 (09:55 -0400)]
19095: Remove bit about loopback device errors in singularity 3.9.1.

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

3 months ago19095: Update singularity to 3.9.9 to get loopback device bugfix.
Tom Clegg [Thu, 5 May 2022 13:44:41 +0000 (09:44 -0400)]
19095: Update singularity to 3.9.9 to get loopback device bugfix.

https://github.com/sylabs/singularity/pull/458

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

3 months ago15730: Add rsync dependency in dev/test env.
Tom Clegg [Wed, 4 May 2022 20:46:45 +0000 (16:46 -0400)]
15730: Add rsync dependency in dev/test env.

Now needed by arvados-server boot to run passenger in test mode.

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

3 months agoMerge branch '19077-arvbox-fixes' refs #19077
Peter Amstutz [Mon, 2 May 2022 21:32:13 +0000 (17:32 -0400)]
Merge branch '19077-arvbox-fixes' refs #19077

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

3 months ago19077: yarn is already installed
Peter Amstutz [Mon, 2 May 2022 21:31:49 +0000 (17:31 -0400)]
19077: yarn is already installed

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

3 months ago19077: Remove Composer & default to singularity
Peter Amstutz [Mon, 2 May 2022 20:47:32 +0000 (16:47 -0400)]
19077: Remove Composer & default to singularity

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

3 months ago18947: Move keep-balance systemd unit file.
Tom Clegg [Mon, 2 May 2022 19:17:18 +0000 (15:17 -0400)]
18947: Move keep-balance systemd unit file.

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

3 months ago18947: Refactor keep-balance as arvados-server subcommand.
Tom Clegg [Thu, 28 Apr 2022 19:17:05 +0000 (15:17 -0400)]
18947: Refactor keep-balance as arvados-server subcommand.

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

3 months agoMerge branch '18947-keep-web'
Tom Clegg [Mon, 2 May 2022 19:12:52 +0000 (15:12 -0400)]
Merge branch '18947-keep-web'

refs #18947

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

3 months ago18947: Update description field in keep-web systemd unit file.
Tom Clegg [Mon, 2 May 2022 19:12:05 +0000 (15:12 -0400)]
18947: Update description field in keep-web systemd unit file.

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

3 months ago19015: update the nginx override so that systemd is happy even when RVM
Ward Vandewege [Fri, 29 Apr 2022 18:55:04 +0000 (14:55 -0400)]
19015: update the nginx override so that systemd is happy even when RVM
       is not installed. We don't install the override when RVM is not
       present, so this is a "just in case".

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

3 months ago18947: Refactor keep-web as arvados-server command.
Tom Clegg [Fri, 29 Apr 2022 00:20:05 +0000 (20:20 -0400)]
18947: Refactor keep-web as arvados-server command.

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

3 months agoAdd a 2 minute lock timeout to the first invocation of apt. This is
Ward Vandewege [Thu, 28 Apr 2022 15:15:44 +0000 (11:15 -0400)]
Add a 2 minute lock timeout to the first invocation of apt. This is
supported from apt 1.9.1 (i.e Debian 11, ubuntu 20.04 and up). It avoids
race conditions, e.g. caused by cloud-init running apt on a node that
has just booted.

No issue #

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

3 months ago19075: When constructing a workflow request, set use_existing=false
Peter Amstutz [Wed, 27 Apr 2022 20:18:57 +0000 (16:18 -0400)]
19075: When constructing a workflow request, set use_existing=false

refs #19075

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

3 months agoDo not pipe into `grep -q`, because that stops reading as soon as a
Ward Vandewege [Thu, 28 Apr 2022 14:43:02 +0000 (10:43 -0400)]
Do not pipe into `grep -q`, because that stops reading as soon as a
match is found, which can cause a SIGPIPE.

No issue #

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

3 months ago19015: installer fix: work around a Passenger issue with the detection of RVM
Ward Vandewege [Wed, 27 Apr 2022 21:56:26 +0000 (17:56 -0400)]
19015: installer fix: work around a Passenger issue with the detection of RVM

This fixes the on-demand building of passenger_native_support.so when
RVM is in use.

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

3 months ago19075 When constructing a workflow request, set use_existing=false
Peter Amstutz [Wed, 27 Apr 2022 20:18:57 +0000 (16:18 -0400)]
19075 When constructing a workflow request, set use_existing=false

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

3 months ago18794: Fix "check" command test.
Tom Clegg [Wed, 27 Apr 2022 17:33:40 +0000 (13:33 -0400)]
18794: Fix "check" command test.

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

3 months ago18794: Fix routing test.
Tom Clegg [Wed, 27 Apr 2022 17:21:14 +0000 (13:21 -0400)]
18794: Fix routing test.

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

3 months ago18794: Remove passenger --no-install-runtime args in test env.
Tom Clegg [Wed, 27 Apr 2022 15:07:44 +0000 (11:07 -0400)]
18794: Remove passenger --no-install-runtime args in test env.

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

3 months agoMerge branch '18947-githttpd'
Tom Clegg [Wed, 27 Apr 2022 14:07:50 +0000 (10:07 -0400)]
Merge branch '18947-githttpd'

refs #18947

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

3 months agoMerge branch '18696-rnaseq-training' refs #18696
Peter Amstutz [Wed, 27 Apr 2022 13:50:44 +0000 (09:50 -0400)]
Merge branch '18696-rnaseq-training' refs #18696

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

3 months ago18794: Don't restart if new config is unreadable or unchanged.
Tom Clegg [Tue, 26 Apr 2022 19:46:16 +0000 (15:46 -0400)]
18794: Don't restart if new config is unreadable or unchanged.

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

3 months ago18794: Don't start config-check thread in packaging tasks.
Tom Clegg [Tue, 26 Apr 2022 19:32:24 +0000 (15:32 -0400)]
18794: Don't start config-check thread in packaging tasks.

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

3 months ago18794: Recommend "arvados-server check" after upgrade/config change.
Tom Clegg [Tue, 26 Apr 2022 19:14:50 +0000 (15:14 -0400)]
18794: Recommend "arvados-server check" after upgrade/config change.

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

3 months ago18794: "check" defaults to succinct human-readable output.
Tom Clegg [Tue, 26 Apr 2022 19:04:31 +0000 (15:04 -0400)]
18794: "check" defaults to succinct human-readable output.

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

3 months ago18696: Integrate RNASeq-cwl-training into user guide
Peter Amstutz [Tue, 26 Apr 2022 18:41:42 +0000 (14:41 -0400)]
18696: Integrate RNASeq-cwl-training into user guide

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

3 months ago18794: Restart RailsAPI workers when config file changes.
Tom Clegg [Tue, 26 Apr 2022 15:16:26 +0000 (11:16 -0400)]
18794: Restart RailsAPI workers when config file changes.

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