arvados.git
23 months ago17004: Set default collection output name "Output from workflow XYZ"
Peter Amstutz [Fri, 13 May 2022 20:41:19 +0000 (16:41 -0400)]
17004: Set default collection output name "Output from workflow XYZ"

Previously this wasn't set, so the output collection would be called
"Container output for request XYZ" which is pretty meaningless to
humans.

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

23 months agoUpdate tests related to make_output_collection
Peter Amstutz [Tue, 10 May 2022 18:48:49 +0000 (14:48 -0400)]
Update tests related to make_output_collection

Also update API revision to reflect addition of output_properties

Check API revision before adding output_properties.

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

23 months ago17004: Allow output_properties to override the default metadata
Peter Amstutz [Tue, 10 May 2022 15:26:44 +0000 (11:26 -0400)]
17004: Allow output_properties to override the default metadata

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

23 months ago17004: Work on CWL side
Peter Amstutz [Fri, 6 May 2022 21:12:04 +0000 (17:12 -0400)]
17004: Work on CWL side

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

23 months ago17004: Add API server tests for output_properties
Peter Amstutz [Fri, 6 May 2022 20:10:21 +0000 (16:10 -0400)]
17004: Add API server tests for output_properties

Fix migration to update the trigram index

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

23 months ago17004: Add migration
Peter Amstutz [Fri, 6 May 2022 19:04:25 +0000 (15:04 -0400)]
17004: Add migration

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

23 months ago17004: Setting intermediate collection fields
Peter Amstutz [Fri, 6 May 2022 14:20:47 +0000 (10:20 -0400)]
17004: Setting intermediate collection fields

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

23 months ago17004: Initial CWL support for setting output properties
Peter Amstutz [Thu, 5 May 2022 20:00:37 +0000 (16:00 -0400)]
17004: Initial CWL support for setting output properties

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

23 months ago17004: Initial API server support for output_properties
Peter Amstutz [Thu, 5 May 2022 15:49:48 +0000 (11:49 -0400)]
17004: Initial API server support for output_properties

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

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 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>

23 months ago18794: Export current version as metric (Go services only).
Tom Clegg [Mon, 25 Apr 2022 18:17:45 +0000 (14:17 -0400)]
18794: Export current version as metric (Go services only).

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

23 months ago18794: Avoid failing health check on incomplete-but-working config.
Tom Clegg [Wed, 13 Apr 2022 19:11:56 +0000 (15:11 -0400)]
18794: Avoid failing health check on incomplete-but-working config.

It is typical to have some InternalURLs that are only reachable by
from the same node (not necessarily where health-check runs) or are
missing entirely because only Nginx needs to know where they are.

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

23 months ago18794: Add /metrics endpoint to RailsAPI.
Tom Clegg [Mon, 11 Apr 2022 18:35:03 +0000 (14:35 -0400)]
18794: Add /metrics endpoint to RailsAPI.

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

23 months ago18794: Fail health check on mismatched configs.
Tom Clegg [Mon, 11 Apr 2022 15:18:50 +0000 (11:18 -0400)]
18794: Fail health check on mismatched configs.

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

23 months ago18794: Export config load time as prometheus metric.
Tom Clegg [Fri, 8 Apr 2022 21:48:21 +0000 (17:48 -0400)]
18794: Export config load time as prometheus metric.

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

23 months ago18794: Export config timestamp/hash as prometheus metric.
Tom Clegg [Fri, 8 Apr 2022 20:05:26 +0000 (16:05 -0400)]
18794: Export config timestamp/hash as prometheus metric.

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

23 months ago18794: Add SourceTimestamp and SourceSHA256 to config-dump output.
Tom Clegg [Fri, 8 Apr 2022 15:08:14 +0000 (11:08 -0400)]
18794: Add SourceTimestamp and SourceSHA256 to config-dump output.

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

23 months ago18794: Add "arvados-server check" subcommand.
Tom Clegg [Thu, 7 Apr 2022 20:11:55 +0000 (16:11 -0400)]
18794: Add "arvados-server check" subcommand.

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

23 months agoMerge branch '18835-uploadfiles-test' refs #18835
Peter Amstutz [Tue, 26 Apr 2022 13:28:43 +0000 (09:28 -0400)]
Merge branch '18835-uploadfiles-test' refs #18835

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

23 months agoSalt installer multinode AWS example: modernize Arvados config a bit,
Ward Vandewege [Tue, 26 Apr 2022 12:52:53 +0000 (08:52 -0400)]
Salt installer multinode AWS example: modernize Arvados config a bit,
switch to using one S3 bucket for simplicity, make sure that the default
setting for CloudVMs/DriverParameters/IAMInstanceProfile matches
Volumes/DriverParameters/IAMRole.

refs #19054

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

23 months ago18835: Add a test for the is_in_collection feature of PathMapper
Peter Amstutz [Mon, 25 Apr 2022 21:00:53 +0000 (17:00 -0400)]
18835: Add a test for the is_in_collection feature of PathMapper

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

23 months agoMerge branch '19054-local-keepstore-aws-doc-update'
Ward Vandewege [Mon, 25 Apr 2022 20:52:18 +0000 (16:52 -0400)]
Merge branch '19054-local-keepstore-aws-doc-update'

closes #19054

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

23 months ago19054: Merge branch 'main' into 19054-local-keepstore-aws-doc-update
Ward Vandewege [Mon, 25 Apr 2022 20:51:22 +0000 (16:51 -0400)]
19054: Merge branch 'main' into 19054-local-keepstore-aws-doc-update

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

23 months ago19054: more doc changes.
Ward Vandewege [Mon, 25 Apr 2022 20:32:52 +0000 (16:32 -0400)]
19054: more doc changes.

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