arvados.git
3 years agoMerge branch '17118-arvput-fix'
Lucas Di Pentima [Wed, 23 Dec 2020 15:27:35 +0000 (12:27 -0300)]
Merge branch '17118-arvput-fix'
Closes #17118

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years agoFix detection of packages that were already built.
Ward Vandewege [Wed, 23 Dec 2020 02:16:41 +0000 (21:16 -0500)]
Fix detection of packages that were already built.

refs #17218

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

3 years agoMerge branch '17218-repository-update'
Ward Vandewege [Tue, 22 Dec 2020 22:10:27 +0000 (17:10 -0500)]
Merge branch '17218-repository-update'

closes #17218

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

3 years agoWe've made a change in the structure of our apt repositories.
Ward Vandewege [Tue, 22 Dec 2020 19:52:26 +0000 (14:52 -0500)]
We've made a change in the structure of our apt repositories.

refs #17218

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

3 years ago17118: Changes the way exception raising is done on PySDK's KeepWriterThread.
Lucas Di Pentima [Tue, 22 Dec 2020 15:41:01 +0000 (12:41 -0300)]
17118: Changes the way exception raising is done on PySDK's KeepWriterThread.

This solves the OOM bug where some keepstores fail when uploading data.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years agoFix a few staticcheck warnings.
Ward Vandewege [Mon, 21 Dec 2020 02:55:19 +0000 (21:55 -0500)]
Fix a few staticcheck warnings.

No issue #

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

3 years agoFix a few more golint warnings.
Ward Vandewege [Fri, 18 Dec 2020 22:55:50 +0000 (17:55 -0500)]
Fix a few more golint warnings.

No issue #

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

3 years agoFix another golint warning.
Ward Vandewege [Fri, 18 Dec 2020 02:38:02 +0000 (21:38 -0500)]
Fix another golint warning.

No issue #

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

3 years agoMerge branch '17208-s3-signature-double-slash'
Tom Clegg [Tue, 15 Dec 2020 05:31:48 +0000 (00:31 -0500)]
Merge branch '17208-s3-signature-double-slash'

fixes #17208

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

3 years agoFix a few more golint warnings.
Ward Vandewege [Tue, 15 Dec 2020 00:42:44 +0000 (19:42 -0500)]
Fix a few more golint warnings.

No issue #

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

3 years agoMerge branch '17152-collection-preserve-version-changes'
Lucas Di Pentima [Mon, 14 Dec 2020 21:35:29 +0000 (18:35 -0300)]
Merge branch '17152-collection-preserve-version-changes'
Refs #17152

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years ago17208: Update test for s3cmd's new console output.
Tom Clegg [Mon, 14 Dec 2020 20:41:33 +0000 (15:41 -0500)]
17208: Update test for s3cmd's new console output.

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

3 years ago17152: Improves modified_at conditional update check.
Lucas Di Pentima [Mon, 14 Dec 2020 13:31:14 +0000 (10:31 -0300)]
17152: Improves modified_at conditional update check.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years agoFix more golint warnings.
Ward Vandewege [Sun, 13 Dec 2020 19:26:57 +0000 (14:26 -0500)]
Fix more golint warnings.

No issue #

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

3 years agoFix more golint warnings.
Ward Vandewege [Sat, 12 Dec 2020 20:09:48 +0000 (15:09 -0500)]
Fix more golint warnings.

No issue #

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

3 years ago17152: Moves conditional preserve_version disabling to collection's controller.
Lucas Di Pentima [Fri, 11 Dec 2020 15:28:22 +0000 (12:28 -0300)]
17152: Moves conditional preserve_version disabling to collection's controller.

There was a bug that flipped preserve_version to false after creating a new
version even though the update request included preserve_version=true.
This happened because the logic was at model level, and was incorrect because
at that level we cannot know if the client included the attribute on its
request.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years ago17208: Add test case.
Tom Clegg [Fri, 11 Dec 2020 05:43:40 +0000 (00:43 -0500)]
17208: Add test case.

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

3 years ago17208: Merge branch 'master'
Tom Clegg [Fri, 11 Dec 2020 01:32:29 +0000 (20:32 -0500)]
17208: Merge branch 'master'

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

3 years ago17152: Avoids creating audit logs when only 'preserve_version' is updated.
Lucas Di Pentima [Thu, 10 Dec 2020 20:58:58 +0000 (17:58 -0300)]
17152: Avoids creating audit logs when only 'preserve_version' is updated.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years ago17152: Changes preserve_version semantics, updates related documentation.
Lucas Di Pentima [Thu, 10 Dec 2020 19:53:49 +0000 (16:53 -0300)]
17152: Changes preserve_version semantics, updates related documentation.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years ago17152: Updates collection tests to reflect the new behavior.
Lucas Di Pentima [Thu, 10 Dec 2020 19:04:52 +0000 (16:04 -0300)]
17152: Updates collection tests to reflect the new behavior.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years ago17152: Updates API revision number.
Lucas Di Pentima [Thu, 10 Dec 2020 19:04:05 +0000 (16:04 -0300)]
17152: Updates API revision number.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years ago17208: Use normalized path to compute signatures.
Tom Clegg [Thu, 10 Dec 2020 21:41:41 +0000 (16:41 -0500)]
17208: Use normalized path to compute signatures.

Transparently clean paths containing "//".

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

3 years agoCostanalyzer bugfix: when a collection uuid is supplied, write the csv
Ward Vandewege [Thu, 10 Dec 2020 15:33:57 +0000 (10:33 -0500)]
Costanalyzer bugfix: when a collection uuid is supplied, write the csv
files with the name of the associated container request uuid, not the
collection uuid. Also change tests to use a proper temporary directory
for the outputs, and do not reuse that directory between tests (which
hid the bug this commit fixed).

refs #17187

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

3 years agoMerge branch '17202-no-redir-crossorigin'
Tom Clegg [Wed, 9 Dec 2020 23:47:15 +0000 (18:47 -0500)]
Merge branch '17202-no-redir-crossorigin'

refs #17202

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

3 years agoFix ineffassign warning.
Ward Vandewege [Wed, 9 Dec 2020 22:06:06 +0000 (17:06 -0500)]
Fix ineffassign warning.

No issue #

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

3 years agoMerge branch '17152-collection-versions-fixes'
Lucas Di Pentima [Wed, 9 Dec 2020 21:31:33 +0000 (18:31 -0300)]
Merge branch '17152-collection-versions-fixes'
Refs #17152

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years ago17202: Test avoiding redirect for cross-origin inline images.
Tom Clegg [Wed, 9 Dec 2020 20:44:57 +0000 (15:44 -0500)]
17202: Test avoiding redirect for cross-origin inline images.

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

3 years agoMerge branch '17199-available-port-race'
Tom Clegg [Wed, 9 Dec 2020 14:45:09 +0000 (09:45 -0500)]
Merge branch '17199-available-port-race'

fixes #17199

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years ago17202: Use explicit SameSite=Lax for 303-with-cookie.
Tom Clegg [Wed, 9 Dec 2020 14:34:14 +0000 (09:34 -0500)]
17202: Use explicit SameSite=Lax for 303-with-cookie.

This improves XSS protection on some browsers, including Safari and
Firefox for Android.

On most browsers, Lax is already the default.

https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Set-Cookie/SameSite

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years ago17202: Bypass 303-with-token on cross-origin requests.
Tom Clegg [Wed, 9 Dec 2020 00:52:36 +0000 (19:52 -0500)]
17202: Bypass 303-with-token on cross-origin requests.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years agoMerge branch '17187-costanalyzer-updates'
Ward Vandewege [Tue, 8 Dec 2020 18:05:07 +0000 (13:05 -0500)]
Merge branch '17187-costanalyzer-updates'

closes #17187

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

3 years ago17187: Merge branch 'master' into 17187-costanalyzer-updates
Ward Vandewege [Tue, 8 Dec 2020 18:04:29 +0000 (13:04 -0500)]
17187: Merge branch 'master' into 17187-costanalyzer-updates

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

3 years agoMerge branch '17161-doc-system-root-token'
Tom Clegg [Tue, 8 Dec 2020 15:59:32 +0000 (10:59 -0500)]
Merge branch '17161-doc-system-root-token'

fixes #17161

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years ago17199: Avoid returning same port twice from find_available_port().
Tom Clegg [Mon, 7 Dec 2020 18:43:23 +0000 (13:43 -0500)]
17199: Avoid returning same port twice from find_available_port().

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years ago17187: implement review feedback:
Ward Vandewege [Tue, 8 Dec 2020 00:36:54 +0000 (19:36 -0500)]
17187: implement review feedback:

* uuids are now specified at the end of the option list
* invalid uuids will cause the command to error out
* output directory is now optional

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

3 years agoMerge branch '17009-s3-vhost-list'
Tom Clegg [Mon, 7 Dec 2020 20:08:25 +0000 (15:08 -0500)]
Merge branch '17009-s3-vhost-list'

refs #17009

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years agoFix tests.
Tom Clegg [Mon, 7 Dec 2020 19:20:27 +0000 (14:20 -0500)]
Fix tests.

refs #17022

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years agoMerge branch '17177-use-newly-created-ca'
Javier Bértoli [Mon, 7 Dec 2020 16:34:37 +0000 (13:34 -0300)]
Merge branch '17177-use-newly-created-ca'

closes #17177

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

3 years agofix(provision): update arvados-formula's version
Javier Bértoli [Mon, 7 Dec 2020 15:46:06 +0000 (12:46 -0300)]
fix(provision): update arvados-formula's version

refs #17177

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

3 years agofix(provision): pin arvados-formula
Javier Bértoli [Mon, 7 Dec 2020 14:22:08 +0000 (11:22 -0300)]
fix(provision): pin arvados-formula

refs #17177

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

3 years agofix(provision): add port to workbench2 nginx's stanza
Javier Bértoli [Mon, 7 Dec 2020 12:20:29 +0000 (09:20 -0300)]
fix(provision): add port to workbench2 nginx's stanza

refs #17177

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

3 years ago17187: costanalyzer: print the total from the aggregate cost accounting
Ward Vandewege [Sun, 6 Dec 2020 15:54:11 +0000 (10:54 -0500)]
17187: costanalyzer: print the total from the aggregate cost accounting
       across all uuids to stdout.

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

3 years ago17187: costanalyzer: allow specifying multiple comma-separated uuids via
Ward Vandewege [Sun, 6 Dec 2020 15:26:39 +0000 (10:26 -0500)]
17187: costanalyzer: allow specifying multiple comma-separated uuids via
       one -uuid argument

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

3 years ago17187: costanalyzer: add support for collection uuids.
Ward Vandewege [Sat, 5 Dec 2020 21:37:00 +0000 (16:37 -0500)]
17187: costanalyzer: add support for collection uuids.

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

3 years agofix(provision): pin formulas' versions
Javier Bértoli [Fri, 4 Dec 2020 16:22:38 +0000 (13:22 -0300)]
fix(provision): pin formulas' versions

* Pin formulas versions, to prevent changes upstream breaking the installer
* Remove verbose/debug flags
* Remove unused entries in the config pillars

refs #17177

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

3 years agofix(provision): Document CA certificate purpose and installation
Javier Bértoli [Fri, 4 Dec 2020 12:17:34 +0000 (09:17 -0300)]
fix(provision): Document CA certificate purpose and installation

refs #17177

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

3 years agofix(provision): Add a CA and sign certificates with it
Javier Bértoli [Thu, 3 Dec 2020 23:00:46 +0000 (20:00 -0300)]
fix(provision): Add a CA and sign certificates with it

refs #17177

As discussed [here](https://forum.arvados.org/t/debugging-arvados-deployed-with-salt/58/8)
and [here](https://gitter.im/arvados/community?at=5fc65683496ca3372e3474a3), Arvados needs
certs signed by a known CA to work correctly.

This PR adds a CA and leaves a copy of the certificate in the installer directory.

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

3 years ago17009: Fix s3 ListObjects endpoint with vhost-style requests.
Tom Clegg [Wed, 2 Dec 2020 22:36:35 +0000 (17:36 -0500)]
17009: Fix s3 ListObjects endpoint with vhost-style requests.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years ago17009: Test virtual host-style S3 requests.
Tom Clegg [Thu, 3 Dec 2020 21:24:37 +0000 (16:24 -0500)]
17009: Test virtual host-style S3 requests.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years ago17152: Adds migration to fix collection versions' modified_at timestamps.
Lucas Di Pentima [Thu, 3 Dec 2020 20:42:22 +0000 (17:42 -0300)]
17152: Adds migration to fix collection versions' modified_at timestamps.

Also, with test.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years ago17152: Publishes the arvbox WebDAV download port.
Lucas Di Pentima [Thu, 3 Dec 2020 18:18:19 +0000 (15:18 -0300)]
17152: Publishes the arvbox WebDAV download port.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years agoUpgrade script/create_superuser_token.rb in the api server codebase to
Ward Vandewege [Thu, 3 Dec 2020 14:13:36 +0000 (09:13 -0500)]
Upgrade script/create_superuser_token.rb in the api server codebase to
generate v2 tokens.

refs #17022

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

3 years agoClarify token details for the arv-user-activity tool.
Ward Vandewege [Thu, 3 Dec 2020 01:13:01 +0000 (20:13 -0500)]
Clarify token details for the arv-user-activity tool.

refs #17022

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

3 years ago17161: Improve SystemRootToken docs.
Tom Clegg [Wed, 2 Dec 2020 22:14:37 +0000 (17:14 -0500)]
17161: Improve SystemRootToken docs.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years agoUpdate error regexp in test case.
Tom Clegg [Wed, 2 Dec 2020 14:30:55 +0000 (09:30 -0500)]
Update error regexp in test case.

refs #17009

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years agofix(docs): broken link
Javier Bértoli [Wed, 2 Dec 2020 13:44:27 +0000 (10:44 -0300)]
fix(docs): broken link

reported on [github](https://github.com/arvados/arvados-formula/issues/3#issuecomment-733019750)

No issue #

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

3 years ago17152: Fixes old collection versions' modified_at handling and test.
Lucas Di Pentima [Tue, 1 Dec 2020 22:17:01 +0000 (19:17 -0300)]
17152: Fixes old collection versions' modified_at handling and test.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>

3 years agoMerge branch '17072-update-cwltool' refs #17072
Peter Amstutz [Tue, 1 Dec 2020 21:16:05 +0000 (16:16 -0500)]
Merge branch '17072-update-cwltool' refs #17072

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

3 years agoMerge branch '17022-user-activity-report' refs #17022
Peter Amstutz [Mon, 30 Nov 2020 22:03:33 +0000 (17:03 -0500)]
Merge branch '17022-user-activity-report' refs #17022

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

3 years ago17022: Update install docs & fix Marc's email.
Peter Amstutz [Mon, 30 Nov 2020 19:16:56 +0000 (14:16 -0500)]
17022: Update install docs & fix Marc's email.

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

3 years agoNow that our k8s helm charts retain state, update the documentation
Ward Vandewege [Mon, 30 Nov 2020 16:55:41 +0000 (11:55 -0500)]
Now that our k8s helm charts retain state, update the documentation
accordingly.

No issue #

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

3 years agoMerge branch '16774-keep-web-errors' refs #16774
Peter Amstutz [Mon, 30 Nov 2020 16:03:53 +0000 (11:03 -0500)]
Merge branch '16774-keep-web-errors' refs #16774

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

3 years agoFix more golint warnings - update crunchrun tests.
Ward Vandewege [Mon, 30 Nov 2020 01:51:27 +0000 (20:51 -0500)]
Fix more golint warnings - update crunchrun tests.

No issue #

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

3 years agoFix more golint warnings.
Ward Vandewege [Sun, 29 Nov 2020 02:26:28 +0000 (21:26 -0500)]
Fix more golint warnings.

No issue #

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

3 years agoFix more golint warnings.
Ward Vandewege [Fri, 27 Nov 2020 13:28:41 +0000 (08:28 -0500)]
Fix more golint warnings.

No issue #

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

3 years agoFix more golint warnings.
Ward Vandewege [Thu, 26 Nov 2020 22:17:10 +0000 (17:17 -0500)]
Fix more golint warnings.

No issue #

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

3 years agoMerge branch 'pvanheus-fix_cluster_test' from github.com/pvanheus:fix_cluster_test
Javier Bértoli [Thu, 26 Nov 2020 18:49:50 +0000 (15:49 -0300)]
Merge branch 'pvanheus-fix_cluster_test' from github.com/pvanheus:fix_cluster_test

No issue #

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

3 years agoFix hardcoded initial user name and email
Peter van Heusden [Thu, 26 Nov 2020 18:35:16 +0000 (20:35 +0200)]
Fix hardcoded initial user name and email

Arvados-DCO-1.1-Signed-off-by: Peter Van Heusden <vh@sanbi.ac.za>

3 years agoFix more golint warnings.
Ward Vandewege [Wed, 25 Nov 2020 22:24:35 +0000 (17:24 -0500)]
Fix more golint warnings.

No issue #

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

3 years ago17072: Fix for added args on cwltool.docker.get_image
Peter Amstutz [Wed, 25 Nov 2020 21:45:53 +0000 (16:45 -0500)]
17072: Fix for added args on cwltool.docker.get_image

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

3 years ago17072: Increase default submit thread concurrency to 4
Peter Amstutz [Wed, 25 Nov 2020 21:13:58 +0000 (16:13 -0500)]
17072: Increase default submit thread concurrency to 4

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

3 years ago17072: Fix imports. Use task_queue from cwltool.
Peter Amstutz [Wed, 25 Nov 2020 21:10:57 +0000 (16:10 -0500)]
17072: Fix imports.  Use task_queue from cwltool.

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

3 years ago17072: Bump cwltool version for unbound 'result' fix
Peter Amstutz [Wed, 25 Nov 2020 20:42:08 +0000 (15:42 -0500)]
17072: Bump cwltool version for unbound 'result' fix

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

3 years agoMerge branch '17150-system-root-token'
Javier Bértoli [Wed, 25 Nov 2020 18:06:50 +0000 (15:06 -0300)]
Merge branch '17150-system-root-token'

closes #17146, #17147, #17150

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

3 years ago17009: Fix bucket-level ops using virtual host-style requests.
Tom Clegg [Wed, 25 Nov 2020 17:14:34 +0000 (12:14 -0500)]
17009: Fix bucket-level ops using virtual host-style requests.

refs #17009

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years agofix(test): wrong variable comparison
Javier Bértoli [Wed, 25 Nov 2020 02:03:37 +0000 (23:03 -0300)]
fix(test): wrong variable comparison

refs #17146, #17147, #17150

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

3 years agofix(docker): formula upgraded
Javier Bértoli [Wed, 25 Nov 2020 02:02:31 +0000 (23:02 -0300)]
fix(docker): formula upgraded

refs #17146, #17147, #17150

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

3 years ago17022: Add example usage of keyset_list_all to code cookbook.
Peter Amstutz [Tue, 24 Nov 2020 23:00:12 +0000 (18:00 -0500)]
17022: Add example usage of keyset_list_all to code cookbook.

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

3 years ago17022: Add test cases for keyset_list_all
Peter Amstutz [Tue, 24 Nov 2020 22:51:21 +0000 (17:51 -0500)]
17022: Add test cases for keyset_list_all

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

3 years ago17022: Improve output. Added documentation page.
Peter Amstutz [Tue, 24 Nov 2020 22:03:32 +0000 (17:03 -0500)]
17022: Improve output.  Added documentation page.

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

3 years agoFix salt-install and test scripts
Javier Bértoli [Tue, 24 Nov 2020 20:17:25 +0000 (17:17 -0300)]
Fix salt-install and test scripts

* add checks to find existing resources
* run some shellcheck

refs #17146, #17147, #17150

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

3 years ago16774: text/plain response uses crlf. Tests check error codes.
Peter Amstutz [Tue, 24 Nov 2020 18:40:21 +0000 (13:40 -0500)]
16774: text/plain response uses crlf.  Tests check error codes.

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

3 years agoDocumentation cleanups.
Ward Vandewege [Tue, 24 Nov 2020 18:17:44 +0000 (13:17 -0500)]
Documentation cleanups.

No issue #

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

3 years agoMake run-build-packages-python-and-ruby.sh say so when it decides to
Ward Vandewege [Tue, 24 Nov 2020 18:17:06 +0000 (13:17 -0500)]
Make run-build-packages-python-and-ruby.sh say so when it decides to
skip building Python packages.

No issue #

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

3 years agoMerge branch '17106-s3-fed-token'
Tom Clegg [Tue, 24 Nov 2020 16:55:48 +0000 (11:55 -0500)]
Merge branch '17106-s3-fed-token'

fixes #17106

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years ago17106: Add examples to S3 auth instructions.
Tom Clegg [Tue, 24 Nov 2020 15:26:36 +0000 (10:26 -0500)]
17106: Add examples to S3 auth instructions.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years agoFix salt-install's crunch-dispatch-local config and tests
Peter van Heusden [Wed, 18 Nov 2020 14:01:32 +0000 (16:01 +0200)]
Fix salt-install's crunch-dispatch-local config and tests

* added [@pvanheus fix]:https://github.com/arvados/arvados/pull/140
* added [a debug parameter to the provision script](https://gitter.im/arvados/community?at=5fb54b4bd37a1a13d6b46a05)
* added a test script to verify the cluster is able to run a CWL workflow
* document salt-install's workflow test

refs #17146, #17147, #17150

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

3 years ago17106: Fix key unescape: don't convert + to space.
Tom Clegg [Tue, 24 Nov 2020 04:45:47 +0000 (23:45 -0500)]
17106: Fix key unescape: don't convert + to space.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years ago16774: Fix tests. Use encoder for xml error response.
Peter Amstutz [Mon, 23 Nov 2020 20:04:48 +0000 (15:04 -0500)]
16774: Fix tests.  Use encoder for xml error response.

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

3 years ago17106: Allow use of URL-encoded token as S3 access/secret key.
Tom Clegg [Mon, 23 Nov 2020 19:52:57 +0000 (14:52 -0500)]
17106: Allow use of URL-encoded token as S3 access/secret key.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

3 years agoFix OS package iteration number in run-build-docker-jobs-image.sh
Ward Vandewege [Mon, 23 Nov 2020 19:48:35 +0000 (14:48 -0500)]
Fix OS package iteration number in run-build-docker-jobs-image.sh

refs #17012

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

3 years agoUpdate error checking in run-build-docker-jobs-image.sh
Ward Vandewege [Mon, 23 Nov 2020 16:51:21 +0000 (11:51 -0500)]
Update error checking in run-build-docker-jobs-image.sh

refs #17012

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

3 years agoRemove now-unneeded code from sdk/cwl/test_with_arvbox.sh, add comment
Ward Vandewege [Mon, 23 Nov 2020 16:47:53 +0000 (11:47 -0500)]
Remove now-unneeded code from sdk/cwl/test_with_arvbox.sh, add comment
to clarify that calculate_python_sdk_cwl_package_versions now outputs
python-style package suffixes.

refs #17012

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

3 years agoMerge branch '17154-wb-profile' refs #17154
Peter Amstutz [Mon, 23 Nov 2020 16:23:51 +0000 (11:23 -0500)]
Merge branch '17154-wb-profile' refs #17154

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

3 years ago17154: Add comment. Use strings.HasPrefix
Peter Amstutz [Mon, 23 Nov 2020 15:59:06 +0000 (10:59 -0500)]
17154: Add comment.  Use strings.HasPrefix

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

3 years agoNow that calculate_python_sdk_cwl_package_versions returns python-style
Ward Vandewege [Mon, 23 Nov 2020 14:20:56 +0000 (09:20 -0500)]
Now that calculate_python_sdk_cwl_package_versions returns python-style
version string suffixes (.dev/rc), make sure the 2 scripts that use that
function are adapted accordingly.

refs #17012

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

3 years agoMove the handle_python_package() function from run-library.sh to
Ward Vandewege [Sun, 22 Nov 2020 13:35:06 +0000 (08:35 -0500)]
Move the handle_python_package() function from run-library.sh to
run-build-packages-python-and-ruby.sh, it is only used in the latter.
Update it to call python3 instead of just 'python'.

refs #15888

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

3 years agoFix more golint warnings.
Ward Vandewege [Sat, 21 Nov 2020 20:53:01 +0000 (15:53 -0500)]
Fix more golint warnings.

No issue #

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

3 years ago16774: Keep-web errors include messages
Peter Amstutz [Fri, 20 Nov 2020 23:03:30 +0000 (18:03 -0500)]
16774: Keep-web errors include messages

Errors on the regular keep-web side return plain text responses.

Errors on the S3 side return XML error responses that S3 clients
expect.

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