arvados.git
4 years ago16470: Bumps dependency on activesupport for rails upgrade.
Lucas Di Pentima [Wed, 1 Jul 2020 21:42:41 +0000 (18:42 -0300)]
16470: Bumps dependency on activesupport for rails upgrade.

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

4 years agoThe arvados-docker-cleaner packages on Debian 10 and Ubuntu
Ward Vandewege [Thu, 23 Jul 2020 13:13:53 +0000 (09:13 -0400)]
The arvados-docker-cleaner packages on Debian 10 and Ubuntu
18.04 (and later, presumably) have a dependency on the python3-distutils
package.

closes #16611

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

4 years ago16623: Add NetworkResourceGroup to install-dispatch-cloud
Peter Amstutz [Wed, 22 Jul 2020 20:28:57 +0000 (16:28 -0400)]
16623: Add NetworkResourceGroup to install-dispatch-cloud

refs #16623

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

4 years ago16623: Add NetworkResourceGroup option for Azure
Peter Amstutz [Wed, 22 Jul 2020 18:58:59 +0000 (14:58 -0400)]
16623: Add NetworkResourceGroup option for Azure

refs #16623

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

4 years agoMerge branch '16585-keep-exercise-improvements'
Ward Vandewege [Wed, 22 Jul 2020 20:09:53 +0000 (16:09 -0400)]
Merge branch '16585-keep-exercise-improvements'

closes #16585

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

4 years agoMerge branch 'master' into 16585-keep-exercise-improvements
Ward Vandewege [Wed, 22 Jul 2020 20:09:19 +0000 (16:09 -0400)]
Merge branch 'master' into 16585-keep-exercise-improvements

refs #16585

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

4 years ago16585: implement review feedback.
Ward Vandewege [Tue, 21 Jul 2020 21:10:40 +0000 (17:10 -0400)]
16585: implement review feedback.

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

4 years agoMerge branch '16584-with-schemas' refs #16584
Peter Amstutz [Tue, 21 Jul 2020 21:02:11 +0000 (17:02 -0400)]
Merge branch '16584-with-schemas' refs #16584

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

4 years agoMerge branch '16377-missing-default' refs #16377
Peter Amstutz [Tue, 21 Jul 2020 21:01:57 +0000 (17:01 -0400)]
Merge branch '16377-missing-default' refs #16377

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

4 years agoMerge branch '16353-cwl-1.2' refs #16353
Peter Amstutz [Tue, 21 Jul 2020 20:59:14 +0000 (16:59 -0400)]
Merge branch '16353-cwl-1.2' refs #16353

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

4 years ago16585: fix memory leak when -repeat is specified and -rthreads is not
Ward Vandewege [Mon, 20 Jul 2020 23:21:14 +0000 (19:21 -0400)]
16585: fix memory leak when -repeat is specified and -rthreads is not
       zero. Always skip warmup phase when -rthreads is zero.

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

4 years ago16353: Handle a few mount point edge cases.
Peter Amstutz [Mon, 20 Jul 2020 22:11:18 +0000 (18:11 -0400)]
16353: Handle a few mount point edge cases.

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

4 years ago16353: Support CWL 1.2 behavior for mounting at arbitrary container path
Peter Amstutz [Mon, 20 Jul 2020 19:59:29 +0000 (15:59 -0400)]
16353: Support CWL 1.2 behavior for mounting at arbitrary container path

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

4 years agoMerge branch 'golharam-use_mktemp'
Ward Vandewege [Fri, 17 Jul 2020 13:34:33 +0000 (09:34 -0400)]
Merge branch 'golharam-use_mktemp'

No issue #

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

4 years agoMerge branch 'use_mktemp' of https://github.com/golharam/arvados into golharam-use_mktemp
Ward Vandewege [Fri, 17 Jul 2020 13:33:19 +0000 (09:33 -0400)]
Merge branch 'use_mktemp' of https://github.com/golharam/arvados into golharam-use_mktemp

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

4 years agoMerge branch 'mr-c-patch-1'
Ward Vandewege [Fri, 17 Jul 2020 13:28:56 +0000 (09:28 -0400)]
Merge branch 'mr-c-patch-1'

No issue #

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

4 years agoMerge branch 'patch-1' of https://github.com/mr-c/arvados into mr-c-patch-1
Ward Vandewege [Fri, 17 Jul 2020 13:14:59 +0000 (09:14 -0400)]
Merge branch 'patch-1' of https://github.com/mr-c/arvados into mr-c-patch-1

No issue #

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

4 years agoMerge branch '16589-arv-fed-migrate-fixes'
Lucas Di Pentima [Tue, 14 Jul 2020 21:42:56 +0000 (18:42 -0300)]
Merge branch '16589-arv-fed-migrate-fixes'
Closes #16589

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

4 years ago16589: Changes error message wording.
Lucas Di Pentima [Tue, 14 Jul 2020 21:33:17 +0000 (18:33 -0300)]
16589: Changes error message wording.

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

4 years ago16377: Fix CollectionFsAccess.exists to catch IOError & return False
Peter Amstutz [Thu, 25 Jun 2020 21:36:19 +0000 (17:36 -0400)]
16377: Fix CollectionFsAccess.exists to catch IOError & return False

Add test to reproduce

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

4 years ago16584: Fix http tests for change in naming
Peter Amstutz [Tue, 14 Jul 2020 17:19:14 +0000 (13:19 -0400)]
16584: Fix http tests for change in naming

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

4 years ago16584: Add --skip-schemas (passthrough to cwltool)
Peter Amstutz [Mon, 13 Jul 2020 21:39:50 +0000 (17:39 -0400)]
16584: Add --skip-schemas (passthrough to cwltool)

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

4 years ago16584: collection name quote slashes in http_to_keep
Peter Amstutz [Mon, 13 Jul 2020 21:36:45 +0000 (17:36 -0400)]
16584: collection name quote slashes in http_to_keep

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

4 years ago16584: Don't consume exception in set_crunch_output
Peter Amstutz [Tue, 14 Jul 2020 17:19:14 +0000 (13:19 -0400)]
16584: Don't consume exception in set_crunch_output

Fix a couple of incorrect tests that were hidden by this.

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

4 years ago16589: Fixes name collision error matching, enhances admin migration message.
Lucas Di Pentima [Tue, 14 Jul 2020 16:43:47 +0000 (13:43 -0300)]
16589: Fixes name collision error matching, enhances admin migration message.

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

4 years ago16589: Properly reports error when a name collision happens.
Lucas Di Pentima [Mon, 13 Jul 2020 21:58:47 +0000 (18:58 -0300)]
16589: Properly reports error when a name collision happens.

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

4 years ago16589: Changes default data migration behavior.
Lucas Di Pentima [Mon, 13 Jul 2020 21:31:23 +0000 (18:31 -0300)]
16589: Changes default data migration behavior.

Now all users' data will be moved to the target account's home project unless
--data-into-subproject is used.

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

4 years ago16589: Enhances error message when admin status doesn't match.
Lucas Di Pentima [Mon, 13 Jul 2020 21:03:44 +0000 (18:03 -0300)]
16589: Enhances error message when admin status doesn't match.

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

4 years agoMerge branch '16534-testable'
Tom Clegg [Mon, 13 Jul 2020 18:12:26 +0000 (14:12 -0400)]
Merge branch '16534-testable'

refs #16534

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

4 years ago16353: Bump cwltool version
Peter Amstutz [Mon, 13 Jul 2020 15:20:10 +0000 (11:20 -0400)]
16353: Bump cwltool version

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

4 years agoMerge branch '16573-keep-deduplication-reporting-tool'
Ward Vandewege [Mon, 13 Jul 2020 13:26:53 +0000 (09:26 -0400)]
Merge branch '16573-keep-deduplication-reporting-tool'

closes #16573

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

4 years ago16573: address a few more review comments.
Ward Vandewege [Mon, 13 Jul 2020 13:25:11 +0000 (09:25 -0400)]
16573: address a few more review comments.

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

4 years ago16573: address review comments.
Ward Vandewege [Mon, 13 Jul 2020 01:34:02 +0000 (21:34 -0400)]
16573: address review comments.

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

4 years ago16589: Removes debugging import.
Lucas Di Pentima [Fri, 10 Jul 2020 17:09:36 +0000 (14:09 -0300)]
16589: Removes debugging import.

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

4 years ago16589: Fixes test check.
Lucas Di Pentima [Fri, 10 Jul 2020 16:17:22 +0000 (13:17 -0300)]
16589: Fixes test check.

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

4 years ago16589: Migrates users' first & last names.
Lucas Di Pentima [Fri, 10 Jul 2020 15:22:39 +0000 (12:22 -0300)]
16589: Migrates users' first & last names.

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

4 years ago16573: Merge branch 'master' into 16573-keep-deduplication-reporting-tool
Ward Vandewege [Fri, 10 Jul 2020 14:53:46 +0000 (10:53 -0400)]
16573: Merge branch 'master' into 16573-keep-deduplication-reporting-tool

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

4 years ago16589: Adds checks testing that migrated users get their first & last names.
Lucas Di Pentima [Fri, 10 Jul 2020 14:05:41 +0000 (11:05 -0300)]
16589: Adds checks testing that migrated users get their first & last names.

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

4 years ago16585: add -useIndex flag. Remove global variables.
Ward Vandewege [Thu, 9 Jul 2020 21:31:46 +0000 (17:31 -0400)]
16585: add -useIndex flag. Remove global variables.

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

4 years ago16589: Fixes dry-run mode. Adds command arg to avoid subproject creation.
Lucas Di Pentima [Thu, 9 Jul 2020 21:00:17 +0000 (18:00 -0300)]
16589: Fixes dry-run mode. Adds command arg to avoid subproject creation.

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

4 years ago16534: Merge branch 'master'
Tom Clegg [Thu, 9 Jul 2020 15:09:18 +0000 (11:09 -0400)]
16534: Merge branch 'master'

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

4 years ago16534: Get ready to pass parent handle to controllers.
Tom Clegg [Thu, 9 Jul 2020 14:24:55 +0000 (10:24 -0400)]
16534: Get ready to pass parent handle to controllers.

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

4 years ago16534: Move RoutableFunc to lib/controller/api.
Tom Clegg [Thu, 9 Jul 2020 14:07:59 +0000 (10:07 -0400)]
16534: Move RoutableFunc to lib/controller/api.

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

4 years ago16573: add a deduplication-report command to arvados-client
Ward Vandewege [Mon, 29 Jun 2020 20:53:38 +0000 (16:53 -0400)]
16573: add a deduplication-report command to arvados-client

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

4 years ago16585: simplify the code: use a context instead of a channel for the
Ward Vandewege [Tue, 7 Jul 2020 20:56:21 +0000 (16:56 -0400)]
16585: simplify the code: use a context instead of a channel for the
       timer and catching signals.

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

4 years ago16534: Add/fix comments.
Tom Clegg [Tue, 7 Jul 2020 18:40:08 +0000 (14:40 -0400)]
16534: Add/fix comments.

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

4 years ago16353: Initialize 'builder' with document version
Peter Amstutz [Tue, 7 Jul 2020 17:55:04 +0000 (13:55 -0400)]
16353: Initialize 'builder' with document version

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

4 years ago16353: Bump schema salad and cwltool versions for v1.2.0-dev4 support
Peter Amstutz [Tue, 7 Jul 2020 17:23:11 +0000 (13:23 -0400)]
16353: Bump schema salad and cwltool versions for v1.2.0-dev4 support

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

4 years ago16585: Add --repeat cli argument, which automatically repeats an
Ward Vandewege [Mon, 6 Jul 2020 13:37:32 +0000 (09:37 -0400)]
16585: Add --repeat cli argument, which automatically repeats an
expirement N times. Add warmup phase to ensure there are always
sufficient blocks available for all read threads. Refactor nextLocator
to be an atomic.Value instead of a channel, to avoid read starvation.

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

4 years agoInstall old version of XML package from source.
Tom Clegg [Tue, 7 Jul 2020 14:51:31 +0000 (10:51 -0400)]
Install old version of XML package from source.

refs #16586

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

4 years agoDocumentation: fix nginx snippets, remove warnings.
Ward Vandewege [Tue, 7 Jul 2020 13:27:43 +0000 (09:27 -0400)]
Documentation: fix nginx snippets, remove warnings.

No issue #

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

4 years ago16534: Move controller transaction/context code to its own package.
Tom Clegg [Mon, 6 Jul 2020 20:00:35 +0000 (16:00 -0400)]
16534: Move controller transaction/context code to its own package.

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

4 years agoMerge branch '15348-pam-module'
Tom Clegg [Mon, 6 Jul 2020 18:18:18 +0000 (14:18 -0400)]
Merge branch '15348-pam-module'

refs #15348

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

4 years ago16534: Exempt go.mod and go.sum from license header check.
Tom Clegg [Mon, 6 Jul 2020 13:51:12 +0000 (09:51 -0400)]
16534: Exempt go.mod and go.sum from license header check.

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

4 years ago16534: Supply *sqlx.Tx to controller handlers.
Tom Clegg [Mon, 6 Jul 2020 13:47:46 +0000 (09:47 -0400)]
16534: Supply *sqlx.Tx to controller handlers.

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

4 years ago15348: Fix packaging bug that was ignoring fpm-info.sh for Go progs.
Tom Clegg [Thu, 2 Jul 2020 20:53:51 +0000 (16:53 -0400)]
15348: Fix packaging bug that was ignoring fpm-info.sh for Go progs.

Until now, the libpam-arvados-go dependency on ca-certificates and the
keep-web dependency on mailcap/mime-support were listed correctly in
fpm-info.sh, but they weren't expressed in the packages because
run-library.sh was looking for fpm-info.sh in the wrong place.

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

4 years ago15348: Tweak README wording.
Tom Clegg [Thu, 2 Jul 2020 15:20:16 +0000 (11:20 -0400)]
15348: Tweak README wording.

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

4 years ago15348: Look up hostname if not provided in config args.
Tom Clegg [Thu, 2 Jul 2020 14:48:15 +0000 (10:48 -0400)]
15348: Look up hostname if not provided in config args.

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

4 years ago15348: Add README to libpam-arvados-go package.
Tom Clegg [Wed, 1 Jul 2020 19:28:47 +0000 (15:28 -0400)]
15348: Add README to libpam-arvados-go package.

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

4 years ago15348: Update webshell install docs to use new pam package.
Tom Clegg [Wed, 1 Jul 2020 19:05:28 +0000 (15:05 -0400)]
15348: Update webshell install docs to use new pam package.

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

4 years ago15348: Merge branch 'master'
Tom Clegg [Wed, 1 Jul 2020 19:01:38 +0000 (15:01 -0400)]
15348: Merge branch 'master'

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

4 years ago15348: Rename libpam-arvados-experimental -> libpam-arvados-go.
Tom Clegg [Wed, 1 Jul 2020 18:49:49 +0000 (14:49 -0400)]
15348: Rename libpam-arvados-experimental -> libpam-arvados-go.

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

4 years ago15348: Use normal (packaged) path in docker test case.
Tom Clegg [Wed, 1 Jul 2020 18:48:29 +0000 (14:48 -0400)]
15348: Use normal (packaged) path in docker test case.

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

4 years ago15348: Add config example to libpam-arvados package.
Tom Clegg [Wed, 1 Jul 2020 18:46:02 +0000 (14:46 -0400)]
15348: Add config example to libpam-arvados package.

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

4 years ago15348: Add ca-certificates as pam package dependency.
Tom Clegg [Wed, 1 Jul 2020 18:23:54 +0000 (14:23 -0400)]
15348: Add ca-certificates as pam package dependency.

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

4 years agoMerge branch '16534-localdb-postgresql'
Tom Clegg [Wed, 1 Jul 2020 03:56:40 +0000 (23:56 -0400)]
Merge branch '16534-localdb-postgresql'

refs #16534

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

4 years agoFix broken link in 'Link user accounts' documentation page.
Ward Vandewege [Tue, 30 Jun 2020 21:02:22 +0000 (17:02 -0400)]
Fix broken link in 'Link user accounts' documentation page.

refs #16441

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

4 years ago16534: Test goroutine safety.
Tom Clegg [Tue, 30 Jun 2020 21:01:54 +0000 (17:01 -0400)]
16534: Test goroutine safety.

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

4 years ago16534: Rename Transaction -> ContextWithTransaction.
Tom Clegg [Tue, 30 Jun 2020 20:29:02 +0000 (16:29 -0400)]
16534: Rename Transaction -> ContextWithTransaction.

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

4 years agoMerge branch '16441-user-merge-doc' refs #16441
Peter Amstutz [Mon, 29 Jun 2020 21:09:39 +0000 (17:09 -0400)]
Merge branch '16441-user-merge-doc' refs #16441

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

4 years ago16441: Typo fix, used 'zzzzz' in examples.
Peter Amstutz [Mon, 29 Jun 2020 21:06:51 +0000 (17:06 -0400)]
16441: Typo fix, used 'zzzzz' in examples.

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

4 years agoRestore check for 'id' field for CWL v1.0 only
Peter Amstutz [Mon, 29 Jun 2020 18:55:55 +0000 (14:55 -0400)]
Restore check for 'id' field for CWL v1.0 only

On further research, I realized why the check for 'id' on embedded
process objects was in place (to catch potential id conflicts earlier
instead of later), however the underlying problem is resolved in cwl
1.1+

refs #16382

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

4 years agoFixed default value bug, don't expect test to fail any more
Peter Amstutz [Mon, 29 Jun 2020 18:45:10 +0000 (14:45 -0400)]
Fixed default value bug, don't expect test to fail any more

refs #16382

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

4 years agoMerge branch '16568-python3-arvados-python-client-package-test'
Ward Vandewege [Mon, 29 Jun 2020 15:17:52 +0000 (11:17 -0400)]
Merge branch '16568-python3-arvados-python-client-package-test'

closes #16568

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

4 years ago16568: add package test files for the python3 arvados python client
Ward Vandewege [Mon, 29 Jun 2020 15:16:21 +0000 (11:16 -0400)]
16568: add package test files for the python3 arvados python client
       packages.

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

4 years agoMerge branch '6649-document-webshell'
Ward Vandewege [Mon, 29 Jun 2020 13:00:48 +0000 (09:00 -0400)]
Merge branch '6649-document-webshell'

closes #6649

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

4 years ago6649: Merge branch 'master' into 6649-document-webshell
Ward Vandewege [Mon, 29 Jun 2020 13:00:28 +0000 (09:00 -0400)]
6649: Merge branch 'master' into 6649-document-webshell

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

4 years ago6649: Document webshell installation.
Ward Vandewege [Thu, 25 Jun 2020 16:04:20 +0000 (12:04 -0400)]
6649: Document webshell installation.

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

4 years ago16534: Add database access in lib/controller/localdb.
Tom Clegg [Fri, 26 Jun 2020 21:15:30 +0000 (17:15 -0400)]
16534: Add database access in lib/controller/localdb.

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

4 years ago15348: Change "no such vm" error message to "permission denied".
Tom Clegg [Fri, 26 Jun 2020 20:28:06 +0000 (16:28 -0400)]
15348: Change "no such vm" error message to "permission denied".

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

4 years agoMerge branch '16382-cwl-path-in-default' refs #16382
Peter Amstutz [Fri, 26 Jun 2020 14:28:53 +0000 (10:28 -0400)]
Merge branch '16382-cwl-path-in-default' refs #16382

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

4 years agoDon't validate links in 'fix roles' migration refs #16007
Peter Amstutz [Fri, 26 Jun 2020 14:26:32 +0000 (10:26 -0400)]
Don't validate links in 'fix roles' migration refs #16007

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

4 years agoMerge branch '16522-python3-arvados-fuse'
Ward Vandewege [Fri, 26 Jun 2020 13:54:44 +0000 (09:54 -0400)]
Merge branch '16522-python3-arvados-fuse'

closes #16522

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

4 years ago16522: Merge branch 'master' into 16522-python3-arvados-fuse
Ward Vandewege [Fri, 26 Jun 2020 13:54:00 +0000 (09:54 -0400)]
16522: Merge branch 'master' into 16522-python3-arvados-fuse

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

4 years agoDocumentation: add missing span in the 'Set up a shell node' page, to
Ward Vandewege [Fri, 26 Jun 2020 00:38:04 +0000 (20:38 -0400)]
Documentation: add missing span in the 'Set up a shell node' page, to
fix coloration bug in the 'Create scoped token' section.

No issue #

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

4 years ago16382: Extra handling for secondaryFiles containing expressions
Peter Amstutz [Thu, 25 Jun 2020 18:23:04 +0000 (14:23 -0400)]
16382: Extra handling for secondaryFiles containing expressions

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

4 years ago16382: When packing workflow convert "path" to "location"
Peter Amstutz [Wed, 24 Jun 2020 20:29:42 +0000 (16:29 -0400)]
16382: When packing workflow convert "path" to "location"

Previously it was being modified in-place and the modification was
propagated to the packed version, that no longer happens so it needs
to re-apply the path->location fix here.

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

4 years agorequire 'update_permissions' fix for migration refs #16007
Peter Amstutz [Thu, 25 Jun 2020 20:04:51 +0000 (16:04 -0400)]
require 'update_permissions' fix for migration refs #16007

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

4 years agoMerge branch '16476-upgrade-arvados-jobs-to-buster'
Ward Vandewege [Thu, 25 Jun 2020 18:40:46 +0000 (14:40 -0400)]
Merge branch '16476-upgrade-arvados-jobs-to-buster'

closes #16476

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

4 years ago16476: Merge branch 'master' into 16476-upgrade-arvados-jobs-to-buster
Ward Vandewege [Thu, 25 Jun 2020 18:39:44 +0000 (14:39 -0400)]
16476: Merge branch 'master' into 16476-upgrade-arvados-jobs-to-buster

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

4 years agoMerge branch '16564-rack-upgrade'
Lucas Di Pentima [Thu, 25 Jun 2020 16:42:04 +0000 (13:42 -0300)]
Merge branch '16564-rack-upgrade'
Closes #16564

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

4 years ago16564: Upgrades rack to address CVE-2020-8184.
Lucas Di Pentima [Thu, 25 Jun 2020 13:36:01 +0000 (10:36 -0300)]
16564: Upgrades rack to address CVE-2020-8184.

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

4 years ago16441: Document how to link accounts as admin, also API method
Peter Amstutz [Tue, 23 Jun 2020 20:40:45 +0000 (16:40 -0400)]
16441: Document how to link accounts as admin, also API method

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

4 years ago15348: Fix test suite crash after skipping docker tests.
Tom Clegg [Tue, 23 Jun 2020 15:13:17 +0000 (11:13 -0400)]
15348: Fix test suite crash after skipping docker tests.

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

4 years ago15348: Add pam_sm_setcred stub.
Tom Clegg [Tue, 23 Jun 2020 14:00:45 +0000 (10:00 -0400)]
15348: Add pam_sm_setcred stub.

Otherwise, auth fails: "PAM unable to resolve symbol: pam_sm_setcred"

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

4 years ago15348: Add debug flag & installation note.
Tom Clegg [Tue, 23 Jun 2020 04:55:47 +0000 (00:55 -0400)]
15348: Add debug flag & installation note.

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

4 years ago15348: Add libpam-arvados-experimental package.
Tom Clegg [Tue, 23 Jun 2020 04:40:14 +0000 (00:40 -0400)]
15348: Add libpam-arvados-experimental package.

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

4 years ago15348: Add Go-based PAM module.
Tom Clegg [Mon, 22 Jun 2020 20:58:14 +0000 (16:58 -0400)]
15348: Add Go-based PAM module.

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

4 years agoRestore link to fix test refs #16007
Peter Amstutz [Mon, 22 Jun 2020 20:06:22 +0000 (16:06 -0400)]
Restore link to fix test refs #16007

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

4 years agoMake it clear that the API token is used by all Arvados command line
Ward Vandewege [Mon, 22 Jun 2020 16:08:24 +0000 (12:08 -0400)]
Make it clear that the API token is used by all Arvados command line
tools, not just the 'arv' tool.

No issue #

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