arvados.git
2 years ago18308: reduce the default value for PreserveVersionIfIdle to 10s.
Ward Vandewege [Thu, 18 Nov 2021 21:20:22 +0000 (16:20 -0500)]
18308: reduce the default value for PreserveVersionIfIdle to 10s.

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

2 years ago18308: enable collection versioning by default, with a 30s idle timeout.
Ward Vandewege [Mon, 15 Nov 2021 17:31:31 +0000 (12:31 -0500)]
18308: enable collection versioning by default, with a 30s idle timeout.

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

2 years agoMerge branch '18346-crunchrun-no-events' refs #18346
Peter Amstutz [Fri, 12 Nov 2021 14:38:05 +0000 (09:38 -0500)]
Merge branch '18346-crunchrun-no-events' refs #18346

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

2 years ago18346: Only disable websockets when all container mounts are by PDH
Peter Amstutz [Thu, 11 Nov 2021 22:32:01 +0000 (17:32 -0500)]
18346: Only disable websockets when all container mounts are by PDH

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

2 years ago18346: Fix tests
Peter Amstutz [Thu, 11 Nov 2021 21:13:44 +0000 (16:13 -0500)]
18346: Fix tests

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

2 years ago18346: Add arv-mount --disable-event-listening
Peter Amstutz [Thu, 11 Nov 2021 21:10:54 +0000 (16:10 -0500)]
18346: Add arv-mount --disable-event-listening

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

2 years agoMerge branch '16817-users-visible-upon-activation'
Tom Clegg [Thu, 11 Nov 2021 20:47:05 +0000 (15:47 -0500)]
Merge branch '16817-users-visible-upon-activation'

closes #16817

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

2 years ago16817: Merge branch 'main'
Tom Clegg [Thu, 11 Nov 2021 19:54:03 +0000 (14:54 -0500)]
16817: Merge branch 'main'

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

2 years agoMerge branch '17944-backend-vocabulary-validation-rebased' into main.
Lucas Di Pentima [Thu, 11 Nov 2021 17:51:31 +0000 (14:51 -0300)]
Merge branch '17944-backend-vocabulary-validation-rebased' into main.

Refs #17944

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

2 years ago17944: Removes link to old doc version, so that tests pass.
Lucas Di Pentima [Thu, 11 Nov 2021 17:39:51 +0000 (14:39 -0300)]
17944: Removes link to old doc version, so that tests pass.

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

2 years ago17944: Undo changes on tests.
Lucas Di Pentima [Thu, 11 Nov 2021 17:04:45 +0000 (14:04 -0300)]
17944: Undo changes on tests.

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

2 years ago17944: Adds upgrade notes.
Lucas Di Pentima [Wed, 10 Nov 2021 20:48:50 +0000 (17:48 -0300)]
17944: Adds upgrade notes.

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

2 years agoMerge branch '18346-container-token'
Tom Clegg [Wed, 10 Nov 2021 20:11:57 +0000 (15:11 -0500)]
Merge branch '18346-container-token'

refs #18346

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

2 years ago17944: Only check for value aliases collision between different values.
Lucas Di Pentima [Wed, 10 Nov 2021 19:31:12 +0000 (16:31 -0300)]
17944: Only check for value aliases collision between different values.

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

2 years ago17944: Improves error reporting on invalid value types.
Lucas Di Pentima [Wed, 10 Nov 2021 18:21:17 +0000 (15:21 -0300)]
17944: Improves error reporting on invalid value types.

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

2 years ago18346: Do not forward locally-issued token to own login cluster.
Tom Clegg [Wed, 10 Nov 2021 16:13:09 +0000 (11:13 -0500)]
18346: Do not forward locally-issued token to own login cluster.

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

2 years ago17944: Fixes tests.
Lucas Di Pentima [Tue, 9 Nov 2021 22:35:18 +0000 (19:35 -0300)]
17944: Fixes tests.

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

2 years ago17944: Fixes logging on vocabulary reload.
Lucas Di Pentima [Tue, 9 Nov 2021 21:59:23 +0000 (18:59 -0300)]
17944: Fixes logging on vocabulary reload.

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

2 years ago17944: Adds a case-insensitive check for key/value against labels.
Lucas Di Pentima [Tue, 9 Nov 2021 21:45:31 +0000 (18:45 -0300)]
17944: Adds a case-insensitive check for key/value against labels.

Also, improves tests.

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

2 years ago17944: Improves keys & value collision validation against aliases. Adds tests.
Lucas Di Pentima [Tue, 9 Nov 2021 21:01:12 +0000 (18:01 -0300)]
17944: Improves keys & value collision validation against aliases. Adds tests.

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

2 years ago17944: Fixes test. Avoids unnecessary Validate() call.
Lucas Di Pentima [Tue, 9 Nov 2021 19:36:51 +0000 (16:36 -0300)]
17944: Fixes test. Avoids unnecessary Validate() call.

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

2 years ago17944: Improves error messages.
Lucas Di Pentima [Tue, 9 Nov 2021 19:10:01 +0000 (16:10 -0300)]
17944: Improves error messages.

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

2 years ago17944: Fixes premature vocabulary check success.
Lucas Di Pentima [Tue, 9 Nov 2021 18:24:47 +0000 (15:24 -0300)]
17944: Fixes premature vocabulary check success.

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

2 years ago17944: Fixes tests. Improves health funcs handling.
Lucas Di Pentima [Fri, 5 Nov 2021 19:54:44 +0000 (16:54 -0300)]
17944: Fixes tests. Improves health funcs handling.

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

2 years ago17944: Adds /_health/vocabulary health endpoint. Improves cache refreshing.
Lucas Di Pentima [Fri, 5 Nov 2021 19:07:37 +0000 (16:07 -0300)]
17944: Adds /_health/vocabulary health endpoint. Improves cache refreshing.

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

2 years agoRemve last reference to terraform for now.
Ward Vandewege [Thu, 4 Nov 2021 20:06:03 +0000 (16:06 -0400)]
Remve last reference to terraform for now.

refs #17450

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

2 years agoRemove reference to terraform code that was never checked in.
Ward Vandewege [Thu, 4 Nov 2021 19:59:26 +0000 (15:59 -0400)]
Remove reference to terraform code that was never checked in.

refs #17450

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

2 years agoMake the linkchecker more strict so it objects to relative links within
Ward Vandewege [Thu, 4 Nov 2021 19:55:17 +0000 (15:55 -0400)]
Make the linkchecker more strict so it objects to relative links within
our doc tree that do not have the {{ site.baseurl }} prefix.

Fix all the links that were incorrect that way.

No issue #

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

2 years agoFix failing "apt-get update" in test.
Tom Clegg [Thu, 4 Nov 2021 17:27:38 +0000 (13:27 -0400)]
Fix failing "apt-get update" in test.

refs #18334

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

2 years ago17944: Adds vocabulary checking support to links.
Lucas Di Pentima [Wed, 3 Nov 2021 15:55:44 +0000 (12:55 -0300)]
17944: Adds vocabulary checking support to links.

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

2 years agoMerge branch '12859-keepstore-fd-leak'
Tom Clegg [Wed, 3 Nov 2021 20:33:19 +0000 (16:33 -0400)]
Merge branch '12859-keepstore-fd-leak'

fixes #12859

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

2 years ago17944: Makes returning an empty Vocabulary also include an empty "tags".
Lucas Di Pentima [Tue, 2 Nov 2021 20:03:49 +0000 (17:03 -0300)]
17944: Makes returning an empty Vocabulary also include an empty "tags".

...instead of returning "tags":null which makes workbench2's code to fail.

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

2 years ago17944: Forces vocabulary checking at startup time.
Lucas Di Pentima [Mon, 1 Nov 2021 20:12:14 +0000 (17:12 -0300)]
17944: Forces vocabulary checking at startup time.

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

2 years ago17944: Vocabulary check errors return status 400 instead of 500.
Lucas Di Pentima [Mon, 1 Nov 2021 19:02:20 +0000 (16:02 -0300)]
17944: Vocabulary check errors return status 400 instead of 500.

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

2 years ago17944: Vocabulary loading, monitoring and checking on several object types.
Lucas Di Pentima [Mon, 25 Oct 2021 16:05:31 +0000 (13:05 -0300)]
17944: Vocabulary loading, monitoring and checking on several object types.

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

2 years ago17944: Updates config knobs and documentation.
Lucas Di Pentima [Thu, 21 Oct 2021 18:16:14 +0000 (15:16 -0300)]
17944: Updates config knobs and documentation.

Workbench.VocabularyURL will be auto-exported providing the new vocabulary
endpoint, for backwards compatibility.

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

2 years agoMerge branch '18313-arvbox-bootstrap-go-version'
Ward Vandewege [Tue, 2 Nov 2021 16:53:31 +0000 (12:53 -0400)]
Merge branch '18313-arvbox-bootstrap-go-version'

closes #18313

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

2 years ago18313: Merge branch 'main' into 18313-arvbox-bootstrap-go-version
Ward Vandewege [Tue, 2 Nov 2021 16:53:02 +0000 (12:53 -0400)]
18313: Merge branch 'main' into 18313-arvbox-bootstrap-go-version

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

2 years ago18313: remove leftover grep from Dockerfile.base
Ward Vandewege [Tue, 2 Nov 2021 14:04:02 +0000 (10:04 -0400)]
18313: remove leftover grep from Dockerfile.base

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

2 years agoMerge branch '18318-nokogiri-updates' into main. Closes #18318
Lucas Di Pentima [Tue, 2 Nov 2021 13:54:40 +0000 (10:54 -0300)]
Merge branch '18318-nokogiri-updates' into main. Closes #18318

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

2 years ago18318: Updates the nokogiri dependency on API & WB1.
Lucas Di Pentima [Tue, 2 Nov 2021 13:04:48 +0000 (10:04 -0300)]
18318: Updates the nokogiri dependency on API & WB1.

Addresses https://nvd.nist.gov/vuln/detail/CVE-2021-41098

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

2 years ago18313: add a test for the grep/awk command used in the arvbox code.
Ward Vandewege [Mon, 1 Nov 2021 21:56:50 +0000 (17:56 -0400)]
18313: add a test for the grep/awk command used in the arvbox code.

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

2 years ago12859: Fix unclosed file descriptors in local filesystem driver.
Tom Clegg [Mon, 1 Nov 2021 18:49:29 +0000 (14:49 -0400)]
12859: Fix unclosed file descriptors in local filesystem driver.

Temporary file was not being closed/removed in the case where client
disconnection is detected while waiting for the volume-level serialize
lock.

Also, GetDeviceID was leaking one file descriptor per volume at
startup time.

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

2 years agoTweak docker image tagging
Peter Amstutz [Thu, 9 Sep 2021 14:16:49 +0000 (10:16 -0400)]
Tweak docker image tagging

no issue #

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

2 years ago18313: make the arvbox build scripts look up the Go compiler version to
Ward Vandewege [Fri, 29 Oct 2021 17:47:00 +0000 (13:47 -0400)]
18313: make the arvbox build scripts look up the Go compiler version to
       use for bootstrapping by pulling it from lib/install/deps.go

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

2 years agoMerge branch '18309-faraday-dependency'
Ward Vandewege [Fri, 29 Oct 2021 17:22:43 +0000 (13:22 -0400)]
Merge branch '18309-faraday-dependency'

closes #18309

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

2 years ago18309: remove faraday dependency in the arvados-login-sync gem, instead
Ward Vandewege [Fri, 29 Oct 2021 15:29:34 +0000 (11:29 -0400)]
18309: remove faraday dependency in the arvados-login-sync gem, instead
       depend on the correct version of the arvados-google-api-client
       gem.

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

2 years agoMerge branch '18273-java-timeout' refs #18273
Peter Amstutz [Fri, 29 Oct 2021 15:17:36 +0000 (11:17 -0400)]
Merge branch '18273-java-timeout' refs #18273

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

2 years ago18273: Tweak java sdk example
Peter Amstutz [Fri, 29 Oct 2021 14:54:19 +0000 (10:54 -0400)]
18273: Tweak java sdk example

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

2 years ago16817: Add Users.ActivatedUsersAreVisibleToOthers config.
Tom Clegg [Fri, 29 Oct 2021 14:08:48 +0000 (10:08 -0400)]
16817: Add Users.ActivatedUsersAreVisibleToOthers config.

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

2 years agoWe now rely on Go 1.16. Unbreak the arvbox build toolchain by switching
Ward Vandewege [Fri, 29 Oct 2021 13:29:29 +0000 (09:29 -0400)]
We now rely on Go 1.16. Unbreak the arvbox build toolchain by switching
to upstream Golang, the buster-backports version is too old.

No issue #

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

2 years agoController test fix.
Ward Vandewege [Thu, 28 Oct 2021 23:47:05 +0000 (19:47 -0400)]
Controller test fix.

refs #18183

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

2 years ago18273: simplify and use version-at-commit.sh
Peter Amstutz [Thu, 28 Oct 2021 18:57:04 +0000 (14:57 -0400)]
18273: simplify and use version-at-commit.sh

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

2 years ago18273: Set docker gradle version
Peter Amstutz [Thu, 28 Oct 2021 18:37:28 +0000 (14:37 -0400)]
18273: Set docker gradle version

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

2 years agoAnother rails test fix.
Ward Vandewege [Thu, 28 Oct 2021 18:10:40 +0000 (14:10 -0400)]
Another rails test fix.

refs #18183

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

2 years agoMerge branch '18264-cwl-test-running-improvements'
Ward Vandewege [Thu, 28 Oct 2021 17:40:31 +0000 (13:40 -0400)]
Merge branch '18264-cwl-test-running-improvements'

refs #18264

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

2 years ago18264: Merge branch 'main' into 18264-cwl-test-running-improvements
Ward Vandewege [Thu, 28 Oct 2021 17:40:12 +0000 (13:40 -0400)]
18264: Merge branch 'main' into 18264-cwl-test-running-improvements

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

2 years agoUpdate the test db structure.
Ward Vandewege [Thu, 28 Oct 2021 16:48:02 +0000 (12:48 -0400)]
Update the test db structure.

refs #18183

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

2 years ago18273: Increase default java sdk timeouts & make them configuable
Peter Amstutz [Thu, 14 Oct 2021 19:09:00 +0000 (15:09 -0400)]
18273: Increase default java sdk timeouts & make them configuable

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

2 years agoFix up "upgrading to {earlier version}" links.
Tom Clegg [Thu, 28 Oct 2021 14:28:44 +0000 (10:28 -0400)]
Fix up "upgrading to {earlier version}" links.

No issue #

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

2 years agoMerge branch '16347-container-local-keepstore'
Tom Clegg [Thu, 28 Oct 2021 14:14:09 +0000 (10:14 -0400)]
Merge branch '16347-container-local-keepstore'

closes #16347

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

2 years ago16347: Clarify upgrade note.
Tom Clegg [Thu, 28 Oct 2021 13:58:36 +0000 (09:58 -0400)]
16347: Clarify upgrade note.

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

2 years agoMerge branch '18183-revoke-tokens-when-user-is-disabled'
Ward Vandewege [Wed, 27 Oct 2021 21:33:37 +0000 (17:33 -0400)]
Merge branch '18183-revoke-tokens-when-user-is-disabled'

closes #18183

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

2 years ago18183: Merge branch 'main' into 18183-revoke-tokens-when-user-is-disabled
Ward Vandewege [Wed, 27 Oct 2021 21:32:57 +0000 (17:32 -0400)]
18183: Merge branch 'main' into 18183-revoke-tokens-when-user-is-disabled

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

2 years agoFix top of upgrade notes to 2.3.0
Peter Amstutz [Wed, 27 Oct 2021 18:37:47 +0000 (14:37 -0400)]
Fix top of upgrade notes to 2.3.0

refs #18130

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

2 years ago18183: add a database migration that deletes tokens and ssh keys that
Ward Vandewege [Wed, 27 Oct 2021 19:48:54 +0000 (15:48 -0400)]
18183: add a database migration that deletes tokens and ssh keys that
       belong to inactive users.

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

2 years ago18183: When the user unsetup api endpoint is hit, any tokens owned by
Ward Vandewege [Wed, 27 Oct 2021 19:05:00 +0000 (15:05 -0400)]
18183: When the user unsetup api endpoint is hit, any tokens owned by
       the user should be deleted.

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

2 years ago16347: Fix race in test helper func.
Tom Clegg [Wed, 27 Oct 2021 19:33:09 +0000 (15:33 -0400)]
16347: Fix race in test helper func.

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

2 years ago16347: Add upgrade note.
Tom Clegg [Wed, 27 Oct 2021 18:34:47 +0000 (14:34 -0400)]
16347: Add upgrade note.

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

2 years ago16347: Merge branch 'main'
Tom Clegg [Wed, 27 Oct 2021 18:12:56 +0000 (14:12 -0400)]
16347: Merge branch 'main'

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

2 years ago18264: add a script that uses the existing version logic in the build
Ward Vandewege [Tue, 26 Oct 2021 18:52:32 +0000 (14:52 -0400)]
18264: add a script that uses the existing version logic in the build
       scripts to generate a package version string from a local Arvados
       git checkout.

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

2 years agoSince CWL defaults to 256M of ram, make that the suggested amount for
Ward Vandewege [Tue, 26 Oct 2021 18:28:23 +0000 (14:28 -0400)]
Since CWL defaults to 256M of ram, make that the suggested amount for
the `mksquashfs mem` setting in singularity.conf.

No issue #

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

2 years agoMerge branch '18290-lsf-bsub-args-template'
Ward Vandewege [Mon, 25 Oct 2021 15:28:09 +0000 (11:28 -0400)]
Merge branch '18290-lsf-bsub-args-template'

closes #18290

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

2 years ago18290: Merge branch 'main' into 18290-lsf-bsub-args-template
Ward Vandewege [Mon, 25 Oct 2021 15:27:37 +0000 (11:27 -0400)]
18290: Merge branch 'main' into 18290-lsf-bsub-args-template

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

2 years ago18290: address review comments.
Ward Vandewege [Mon, 25 Oct 2021 14:15:21 +0000 (10:15 -0400)]
18290: address review comments.

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

2 years ago18290: LSF: make the bsub arguments completely configurable.
Ward Vandewege [Sat, 23 Oct 2021 15:42:14 +0000 (11:42 -0400)]
18290: LSF: make the bsub arguments completely configurable.

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

2 years agoMerge branch '18287-external-url-defaults'
Tom Clegg [Fri, 22 Oct 2021 19:29:04 +0000 (15:29 -0400)]
Merge branch '18287-external-url-defaults'

fixes #18287

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

2 years agoMerge branch '18289-only-pass-allow-other-when-running-docker'
Ward Vandewege [Fri, 22 Oct 2021 18:19:19 +0000 (14:19 -0400)]
Merge branch '18289-only-pass-allow-other-when-running-docker'

closes #18289

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

2 years ago18289: add support to set `mksquashfs mem` for Singularity in our
Ward Vandewege [Fri, 22 Oct 2021 16:47:17 +0000 (12:47 -0400)]
18289: add support to set `mksquashfs mem` for Singularity in our
       compute node image builder for cloud setups.

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

2 years ago18289: Address review comments (documentation).
Ward Vandewege [Fri, 22 Oct 2021 16:46:45 +0000 (12:46 -0400)]
18289: Address review comments (documentation).

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

2 years ago18289: Documentation changes to reflect we support both Slurm and LSF.
Ward Vandewege [Fri, 22 Oct 2021 14:29:16 +0000 (10:29 -0400)]
18289: Documentation changes to reflect we support both Slurm and LSF.
       Refactor the compute node installation instructions. Fix a few
       linkchecker warnings.

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

2 years ago18289: documentation: singularity refinements.
Ward Vandewege [Thu, 21 Oct 2021 23:33:48 +0000 (19:33 -0400)]
18289: documentation: singularity refinements.

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

2 years ago18289: only pass the --allow-other argument to arv-mount when the
Ward Vandewege [Thu, 21 Oct 2021 20:53:03 +0000 (16:53 -0400)]
18289: only pass the --allow-other argument to arv-mount when the
       runtime is Docker.

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

2 years agoMerge branch '18288-fix-anonymouspublic-token-expiration'
Ward Vandewege [Thu, 21 Oct 2021 20:42:37 +0000 (16:42 -0400)]
Merge branch '18288-fix-anonymouspublic-token-expiration'

closes #18288

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

2 years ago18288: when storing the anonymous user token, make sure to clear the
Ward Vandewege [Thu, 21 Oct 2021 20:27:59 +0000 (16:27 -0400)]
18288: when storing the anonymous user token, make sure to clear the
       expires_at field.

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

2 years ago18288: when running the db:check_long_lived_tokens and
Ward Vandewege [Thu, 21 Oct 2021 20:16:04 +0000 (16:16 -0400)]
18288: when running the db:check_long_lived_tokens and
       db:fix_long_lived_tokens rake tasks, do not expire the
       anonymouspublic token.

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

2 years agoMerge branch '17742-provide-custom-certs'
Javier Bértoli [Thu, 21 Oct 2021 19:00:13 +0000 (16:00 -0300)]
Merge branch '17742-provide-custom-certs'

closes #17742
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

2 years ago17742: update documentation addressing review suggestions
Javier Bértoli [Thu, 21 Oct 2021 18:59:04 +0000 (15:59 -0300)]
17742: update documentation addressing review suggestions

Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@curii.com>

2 years agoMerge branch '18281-login-sync-expired-tokens'
Ward Vandewege [Thu, 21 Oct 2021 18:47:04 +0000 (14:47 -0400)]
Merge branch '18281-login-sync-expired-tokens'

closes #18281

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

2 years agoMerge branch 'main' into 18281-login-sync-expired-tokens
Ward Vandewege [Thu, 21 Oct 2021 18:46:26 +0000 (14:46 -0400)]
Merge branch 'main' into 18281-login-sync-expired-tokens

closes #18281

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

2 years agoMerge branch '18286-lsf-doc'
Tom Clegg [Thu, 21 Oct 2021 18:37:23 +0000 (14:37 -0400)]
Merge branch '18286-lsf-doc'

refs #18286

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

2 years ago18287: Remove superfluous {ExternalURL: "-"} values.
Tom Clegg [Thu, 21 Oct 2021 18:35:43 +0000 (14:35 -0400)]
18287: Remove superfluous {ExternalURL: "-"} values.

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

2 years ago18281: Rephrase the help text for --force-rotate option.
Ward Vandewege [Thu, 21 Oct 2021 18:19:42 +0000 (14:19 -0400)]
18281: Rephrase the help text for --force-rotate option.

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

2 years ago18286: Document requirement to add Services.DispatchLSF section.
Tom Clegg [Thu, 21 Oct 2021 18:00:45 +0000 (14:00 -0400)]
18286: Document requirement to add Services.DispatchLSF section.

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

2 years ago18281: make arvados-login-sync smart enough to replace expired tokens.
Ward Vandewege [Wed, 20 Oct 2021 20:28:30 +0000 (16:28 -0400)]
18281: make arvados-login-sync smart enough to replace expired tokens.
       Also add a --debug parameter and some debug output.

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

2 years agoMerge branch '18260-update-cwltool' refs #18260
Peter Amstutz [Wed, 20 Oct 2021 18:28:23 +0000 (14:28 -0400)]
Merge branch '18260-update-cwltool' refs #18260

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

2 years ago18260: Update when we're going to actually run the workflow
Peter Amstutz [Wed, 20 Oct 2021 01:11:05 +0000 (21:11 -0400)]
18260: Update when we're going to actually run the workflow

Update cwltool version for bugfixes.

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

2 years agoDocumentation: when starting the Arvados k8s helm chart on GKE, do not
Ward Vandewege [Tue, 19 Oct 2021 20:03:53 +0000 (16:03 -0400)]
Documentation: when starting the Arvados k8s helm chart on GKE, do not
specify the k8s version (use the default).

refs #18278

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

2 years ago18260: Update cwltool for fix for integration test 35
Peter Amstutz [Tue, 19 Oct 2021 20:04:29 +0000 (16:04 -0400)]
18260: Update cwltool for fix for integration test 35

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

2 years agoMerge branch '18259-doc-architecture-singularity'
Ward Vandewege [Tue, 19 Oct 2021 20:02:14 +0000 (16:02 -0400)]
Merge branch '18259-doc-architecture-singularity'

closes #18259

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