arvados.git
3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 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>

3 years agoMerge branch '16480-keep-balance-index-timeout'
Tom Clegg [Mon, 22 Jun 2020 15:36:11 +0000 (11:36 -0400)]
Merge branch '16480-keep-balance-index-timeout'

fixes #16480

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

3 years ago16480: Merge branch 'master'
Tom Clegg [Mon, 22 Jun 2020 15:35:35 +0000 (11:35 -0400)]
16480: Merge branch 'master'

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

3 years agoAdd links to the Arvados forum refs #16521
Peter Amstutz [Fri, 19 Jun 2020 21:20:59 +0000 (17:20 -0400)]
Add links to the Arvados forum refs #16521

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

3 years agoMerge branch '16007-validate-group-class' refs #16007
Peter Amstutz [Fri, 19 Jun 2020 15:38:18 +0000 (11:38 -0400)]
Merge branch '16007-validate-group-class' refs #16007

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

3 years ago16007: Fix typo
Peter Amstutz [Fri, 19 Jun 2020 15:37:57 +0000 (11:37 -0400)]
16007: Fix typo

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

3 years agoMerge branch '16513-keep-exercise-improvements'
Ward Vandewege [Fri, 19 Jun 2020 15:37:42 +0000 (11:37 -0400)]
Merge branch '16513-keep-exercise-improvements'

refs #16513

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

3 years ago16513: Merge branch 'master' into 16513-keep-exercise-improvements
Ward Vandewege [Fri, 19 Jun 2020 15:36:55 +0000 (11:36 -0400)]
16513: Merge branch 'master' into 16513-keep-exercise-improvements

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

3 years agoMerge branch '16526-ruby-and-python-build-script-updates'
Ward Vandewege [Fri, 19 Jun 2020 15:33:20 +0000 (11:33 -0400)]
Merge branch '16526-ruby-and-python-build-script-updates'

closes #16526

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

3 years ago16526: Merge branch 'master' into 16526-ruby-and-python-build-script-updates
Ward Vandewege [Fri, 19 Jun 2020 15:31:54 +0000 (11:31 -0400)]
16526: Merge branch 'master' into 16526-ruby-and-python-build-script-updates

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

3 years ago16522: add package test symlink for the python3 fuse tests.
Ward Vandewege [Fri, 19 Jun 2020 15:29:41 +0000 (11:29 -0400)]
16522: add package test symlink for the python3 fuse tests.

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

3 years ago16480: Configurable timeout for entire keep-balance iteration.
Tom Clegg [Fri, 19 Jun 2020 14:34:01 +0000 (10:34 -0400)]
16480: Configurable timeout for entire keep-balance iteration.

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

3 years ago16007: note about sharing with anonymous users, and renaming roles
Peter Amstutz [Thu, 18 Jun 2020 16:15:57 +0000 (12:15 -0400)]
16007: note about sharing with anonymous users, and renaming roles

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

3 years ago16007: Doc updates/clarifications from feedback
Peter Amstutz [Thu, 18 Jun 2020 16:04:46 +0000 (12:04 -0400)]
16007: Doc updates/clarifications from feedback

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

3 years agoMerge branch '16482-bump-cwltool-version'
Ward Vandewege [Thu, 18 Jun 2020 15:53:41 +0000 (11:53 -0400)]
Merge branch '16482-bump-cwltool-version'

closes #16482

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

3 years ago16482: Merge branch 'master' into 16482-bump-cwltool-version
Ward Vandewege [Thu, 18 Jun 2020 15:52:23 +0000 (11:52 -0400)]
16482: Merge branch 'master' into 16482-bump-cwltool-version

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

3 years ago16007: Update docs, restore empty_collection, fix tests
Peter Amstutz [Wed, 17 Jun 2020 21:34:34 +0000 (17:34 -0400)]
16007: Update docs, restore empty_collection, fix tests

Also include link uuid in migration log message

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

3 years ago16522: add a python3 package for arvados-fuse.
Ward Vandewege [Wed, 17 Jun 2020 19:41:02 +0000 (15:41 -0400)]
16522: add a python3 package for arvados-fuse.

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

3 years ago16007: Migration works with large database
Peter Amstutz [Mon, 8 Jun 2020 14:43:47 +0000 (10:43 -0400)]
16007: Migration works with large database

Changing individual permissions on groups that affect a lot of objects
is expensive.  The migration now suppresses permission updates and
does a batch update at the end.

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

3 years ago16007: Fix FUSE test
Peter Amstutz [Tue, 2 Jun 2020 20:49:38 +0000 (16:49 -0400)]
16007: Fix FUSE test

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

3 years ago16007: Add migration to fix invalid groups & permission links
Peter Amstutz [Tue, 2 Jun 2020 20:45:21 +0000 (16:45 -0400)]
16007: Add migration to fix invalid groups & permission links

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

3 years ago16007: Reenable updating the permission level of a link
Peter Amstutz [Tue, 2 Jun 2020 17:26:48 +0000 (13:26 -0400)]
16007: Reenable updating the permission level of a link

Add test to ensure permission table is synchronized when updating the
level of an existing permission link.

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

3 years ago16007: Update group-sync tool for new restrictions on roles
Peter Amstutz [Tue, 2 Jun 2020 14:09:29 +0000 (10:09 -0400)]
16007: Update group-sync tool for new restrictions on roles

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

3 years ago16007: Roles are owned by system user
Peter Amstutz [Mon, 1 Jun 2020 22:03:56 +0000 (18:03 -0400)]
16007: Roles are owned by system user

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

3 years ago16007: Only users and roles can be granted permission
Peter Amstutz [Mon, 1 Jun 2020 18:59:51 +0000 (14:59 -0400)]
16007: Only users and roles can be granted permission

Permission link tail_uuid must be a user or group_class role.

Also disallow modifying permission links.

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

3 years ago16007: Make it so that only projects can own things
Peter Amstutz [Fri, 29 May 2020 21:25:05 +0000 (17:25 -0400)]
16007: Make it so that only projects can own things

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

3 years ago16007: Validate group_class is set to 'project' or 'role'
Peter Amstutz [Fri, 29 May 2020 04:04:12 +0000 (00:04 -0400)]
16007: Validate group_class is set to 'project' or 'role'

Fix tests.

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

3 years ago16513: switch to CSV output only, send CSV to stdout and logs to stderr,
Ward Vandewege [Wed, 17 Jun 2020 16:31:39 +0000 (12:31 -0400)]
16513: switch to CSV output only, send CSV to stdout and logs to stderr,
       abort on ctrl-c, print final CSV line when ending.

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

3 years agoMerge branch '16171-oidc-config'
Tom Clegg [Wed, 17 Jun 2020 16:35:32 +0000 (12:35 -0400)]
Merge branch '16171-oidc-config'

closes #16171

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

3 years ago16171: Link install docs to additional OpenIDConnect configs.
Tom Clegg [Wed, 17 Jun 2020 16:34:41 +0000 (12:34 -0400)]
16171: Link install docs to additional OpenIDConnect configs.

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

3 years ago16171: Fix typo.
Tom Clegg [Wed, 17 Jun 2020 14:24:38 +0000 (10:24 -0400)]
16171: Fix typo.

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

3 years agoMerge branch '16007-permission-table-rb' refs #16007
Peter Amstutz [Tue, 16 Jun 2020 21:25:38 +0000 (17:25 -0400)]
Merge branch '16007-permission-table-rb' refs #16007

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

3 years ago16007: Update comments to discuss edge_id
Peter Amstutz [Tue, 16 Jun 2020 19:52:43 +0000 (15:52 -0400)]
16007: Update comments to discuss edge_id

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

3 years ago16480: Use longer timeout for keepstore index requests.
Tom Clegg [Tue, 16 Jun 2020 14:10:53 +0000 (10:10 -0400)]
16480: Use longer timeout for keepstore index requests.

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

3 years ago16007: Handle overlapping permissions correctly
Peter Amstutz [Mon, 15 Jun 2020 22:17:09 +0000 (18:17 -0400)]
16007: Handle overlapping permissions correctly

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

3 years ago16007: Add tests for overlapping permission links
Peter Amstutz [Mon, 15 Jun 2020 18:25:30 +0000 (14:25 -0400)]
16007: Add tests for overlapping permission links

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

3 years agoMerge branch '16425-skip-unused-dirs'
Tom Clegg [Mon, 15 Jun 2020 15:17:48 +0000 (11:17 -0400)]
Merge branch '16425-skip-unused-dirs'

fixes #16425

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

3 years agoMerge branch '16427-undelete'
Tom Clegg [Fri, 12 Jun 2020 20:25:47 +0000 (16:25 -0400)]
Merge branch '16427-undelete'

closes #16427

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

3 years ago16425: Don't scan dirs that we don't write in.
Tom Clegg [Fri, 12 Jun 2020 20:14:20 +0000 (16:14 -0400)]
16425: Don't scan dirs that we don't write in.

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

3 years ago16526: update the run-build-packages-python-and-ruby.sh script so that
Ward Vandewege [Fri, 12 Jun 2020 15:26:24 +0000 (11:26 -0400)]
16526: update the run-build-packages-python-and-ruby.sh script so that
it can be asked to do ruby gems or python packages alone. The default
behavior remains unchanged: both ruby gems and python packages will be
built.Some bash comparison cleanups.

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

3 years ago16171: Merge branch 'master'
Tom Clegg [Fri, 12 Jun 2020 15:18:45 +0000 (11:18 -0400)]
16171: Merge branch 'master'

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

3 years ago16427: Merge branch 'master'
Tom Clegg [Fri, 12 Jun 2020 15:17:41 +0000 (11:17 -0400)]
16427: Merge branch 'master'

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

3 years agoMerge branch 'master' into 16007-permission-table-rb
Peter Amstutz [Fri, 12 Jun 2020 14:43:53 +0000 (10:43 -0400)]
Merge branch 'master' into 16007-permission-table-rb

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

3 years ago16513: add an option to keep-exercise for a timed run, with a CSV output
Ward Vandewege [Fri, 12 Jun 2020 14:47:26 +0000 (10:47 -0400)]
16513: add an option to keep-exercise for a timed run, with a CSV output
       printed at the end.

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

3 years ago16524: Pin rsa package to < 4.1
Peter Amstutz [Fri, 12 Jun 2020 14:13:24 +0000 (10:13 -0400)]
16524: Pin rsa package to < 4.1

Because >= 4.1 does not support python 2 any more.  refs #16524

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

3 years ago16427: Option to recover from given collection's last log entry.
Tom Clegg [Thu, 11 Jun 2020 20:29:33 +0000 (16:29 -0400)]
16427: Option to recover from given collection's last log entry.

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

3 years agoFix double slash in URL.
Tom Clegg [Thu, 11 Jun 2020 19:26:06 +0000 (15:26 -0400)]
Fix double slash in URL.

refs #16523

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

3 years ago16007: Add REVOKE_PERM and CAN_MANAGE_PERM constants
Peter Amstutz [Thu, 11 Jun 2020 17:12:04 +0000 (13:12 -0400)]
16007: Add REVOKE_PERM and CAN_MANAGE_PERM constants

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

3 years ago16427: Rename undelete -> recover-collection.
Tom Clegg [Wed, 10 Jun 2020 14:26:18 +0000 (10:26 -0400)]
16427: Rename undelete -> recover-collection.

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

3 years ago16171: Add new config keys to export list.
Tom Clegg [Tue, 9 Jun 2020 17:47:45 +0000 (13:47 -0400)]
16171: Add new config keys to export list.

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