arvados.git
4 years ago15572: Many small doc tweaks as part of review.
Ward Vandewege [Fri, 20 Dec 2019 16:17:36 +0000 (11:17 -0500)]
15572: Many small doc tweaks as part of review.

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

4 years ago15572: add note that mount tmp device_type is not implemented
Peter Amstutz [Wed, 18 Dec 2019 21:38:45 +0000 (16:38 -0500)]
15572: add note that mount tmp device_type is not implemented

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

4 years ago15572: Fix healthcheck doc to refer to Services instead NodeProfiles
Peter Amstutz [Wed, 18 Dec 2019 21:36:07 +0000 (16:36 -0500)]
15572: Fix healthcheck doc to refer to Services instead NodeProfiles

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

4 years ago15572: Fix Services.Workbench1 typo
Peter Amstutz [Wed, 18 Dec 2019 20:01:59 +0000 (15:01 -0500)]
15572: Fix Services.Workbench1 typo

Add redirect http-to-https blocks for workbench.

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

4 years ago15572: Add notes about keep-web and compute node image configuration
Peter Amstutz [Wed, 18 Dec 2019 18:22:18 +0000 (13:22 -0500)]
15572: Add notes about keep-web and compute node image configuration

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

4 years ago15572: GitSSH should have leading ssh://
Peter Amstutz [Tue, 17 Dec 2019 18:24:40 +0000 (13:24 -0500)]
15572: GitSSH should have leading ssh://

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

4 years ago15572: More information about setting up Azure credentials
Peter Amstutz [Tue, 17 Dec 2019 17:14:17 +0000 (12:14 -0500)]
15572: More information about setting up Azure credentials

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

4 years ago15572: Make note that secret inputs must be submitted on command line
Peter Amstutz [Tue, 17 Dec 2019 16:59:19 +0000 (11:59 -0500)]
15572: Make note that secret inputs must be submitted on command line

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

4 years ago15572: Reorganize and update version migration documentation
Peter Amstutz [Tue, 17 Dec 2019 16:43:42 +0000 (11:43 -0500)]
15572: Reorganize and update version migration documentation

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

4 years ago15572: WebDAV ExternalURL expected to have trailing slash
Peter Amstutz [Mon, 16 Dec 2019 21:22:44 +0000 (16:22 -0500)]
15572: WebDAV ExternalURL expected to have trailing slash

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

4 years ago15572: Update gitolite install instructions
Peter Amstutz [Mon, 16 Dec 2019 20:24:12 +0000 (15:24 -0500)]
15572: Update gitolite install instructions

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

4 years ago15572: Install doc updates for workbench, ws, dispatcher
Peter Amstutz [Mon, 16 Dec 2019 16:58:29 +0000 (11:58 -0500)]
15572: Install doc updates for workbench, ws, dispatcher

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

4 years ago15572: Documentation tweaks from experience installing dev cluster
Peter Amstutz [Sun, 15 Dec 2019 05:02:02 +0000 (00:02 -0500)]
15572: Documentation tweaks from experience installing dev cluster

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

4 years ago15572: Add missing file
Peter Amstutz [Fri, 13 Dec 2019 17:06:11 +0000 (12:06 -0500)]
15572: Add missing file

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

4 years ago15572: Passes link checking
Peter Amstutz [Fri, 13 Dec 2019 16:43:57 +0000 (11:43 -0500)]
15572: Passes link checking

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

4 years ago15572: Add hypothes.is annotations to docs
Peter Amstutz [Fri, 13 Dec 2019 05:06:00 +0000 (00:06 -0500)]
15572: Add hypothes.is annotations to docs

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

4 years ago15572: Make notes on cloud/slurm dispatcher install to set up VM / compute nodes.
Peter Amstutz [Thu, 12 Dec 2019 22:32:10 +0000 (17:32 -0500)]
15572: Make notes on cloud/slurm dispatcher install to set up VM / compute nodes.

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

4 years ago15572: Epic documentation commit
Peter Amstutz [Thu, 12 Dec 2019 22:21:56 +0000 (17:21 -0500)]
15572: Epic documentation commit

* Revise dispatcher install
* Revise shell and compute node install
* Fix up Python and CLI SDK install docs
* Refactor boilerplate sections into parameterized liquid template include

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

4 years ago15572: Fix up left nav rendering highlighting
Peter Amstutz [Wed, 11 Dec 2019 21:06:06 +0000 (16:06 -0500)]
15572: Fix up left nav rendering highlighting

Do the right thing with pages that are symlinks.

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

4 years ago15572: Updating dispatcher install
Peter Amstutz [Tue, 10 Dec 2019 21:40:35 +0000 (16:40 -0500)]
15572: Updating dispatcher install

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

4 years agoMerge branch 'master' into 15572-new-install-docs
Peter Amstutz [Tue, 10 Dec 2019 21:14:00 +0000 (16:14 -0500)]
Merge branch 'master' into 15572-new-install-docs

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

4 years ago15572: Update workbench, composer, websocket, git, shell install docs
Peter Amstutz [Tue, 10 Dec 2019 20:40:53 +0000 (15:40 -0500)]
15572: Update workbench, composer, websocket, git, shell install docs

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

4 years agoMerge branch 'MajewskiKrzysztof-file-token-error'
Lucas Di Pentima [Tue, 10 Dec 2019 18:29:59 +0000 (15:29 -0300)]
Merge branch 'MajewskiKrzysztof-file-token-error'
Closes #15919

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

4 years agoMerge branch 'file-token-error' of git://github.com/MajewskiKrzysztof/arvados into...
Lucas Di Pentima [Tue, 10 Dec 2019 17:40:16 +0000 (14:40 -0300)]
Merge branch 'file-token-error' of git://github.com/MajewskiKrzysztof/arvados into MajewskiKrzysztof-file-token-error

4 years agoMerge branch 'MajewskiKrzysztof-exists-filter'
Lucas Di Pentima [Tue, 10 Dec 2019 17:33:45 +0000 (14:33 -0300)]
Merge branch 'MajewskiKrzysztof-exists-filter'
Closes #15920

4 years agoAdd missing EXISTS filter.
Krzysztof Majewski [Fri, 15 Nov 2019 09:05:24 +0000 (10:05 +0100)]
Add missing EXISTS filter.

Arvados-DCO-1.1-Signed-off-by: Krzysztof Majewski <majewski.kielce@gmail.com>

4 years ago15572: Updated install docs for keep components, login/SSO
Peter Amstutz [Thu, 5 Dec 2019 21:43:04 +0000 (16:43 -0500)]
15572: Updated install docs for keep components, login/SSO

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

4 years agoAdd Curii Corporation to AUTHORS
Peter Amstutz [Mon, 9 Dec 2019 21:06:28 +0000 (16:06 -0500)]
Add Curii Corporation to AUTHORS

no issue #

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

4 years agoUpdate gitter link to arvados/community
Peter Amstutz [Mon, 9 Dec 2019 20:43:52 +0000 (15:43 -0500)]
Update gitter link to arvados/community

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

4 years agoRemove biostars link
Peter Amstutz [Mon, 9 Dec 2019 19:38:09 +0000 (14:38 -0500)]
Remove biostars link

no issue #

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

4 years agoFix support links
Peter Amstutz [Mon, 9 Dec 2019 19:26:31 +0000 (14:26 -0500)]
Fix support links

no issue #

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

4 years agoarvbox uses "go install" instead of "go get" no issue #
Peter Amstutz [Sun, 8 Dec 2019 21:33:51 +0000 (16:33 -0500)]
arvbox uses "go install" instead of "go get" no issue #

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

4 years agoMerge branch '15910-crunch-run-crash'
Tom Clegg [Thu, 5 Dec 2019 15:45:02 +0000 (10:45 -0500)]
Merge branch '15910-crunch-run-crash'

refs #15910

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15572: Documentation WIP
Peter Amstutz [Wed, 4 Dec 2019 23:30:56 +0000 (18:30 -0500)]
15572: Documentation WIP

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoMove all api server packages dependencies into the packages.
Ward Vandewege [Wed, 4 Dec 2019 19:51:18 +0000 (14:51 -0500)]
Move all api server packages dependencies into the packages.

closes #15905

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoMerge branch '15900-gem-version'
Tom Clegg [Wed, 4 Dec 2019 18:56:50 +0000 (13:56 -0500)]
Merge branch '15900-gem-version'

refs #15900

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15904-remove-old-config-files-from-rails-packages'
Ward Vandewege [Wed, 4 Dec 2019 16:43:56 +0000 (11:43 -0500)]
Merge branch '15904-remove-old-config-files-from-rails-packages'

closes #15904

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years ago15910: Fix races in collectionfs flush/sync.
Tom Clegg [Wed, 4 Dec 2019 16:28:38 +0000 (11:28 -0500)]
15910: Fix races in collectionfs flush/sync.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoStop adding application.yml and database.yml symlinks on fresh installs of the
Ward Vandewege [Wed, 4 Dec 2019 14:35:16 +0000 (09:35 -0500)]
Stop adding application.yml and database.yml symlinks on fresh installs of the
rails packages.

refs #15904

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years ago15572: List nginx under external dependencies
Peter Amstutz [Tue, 3 Dec 2019 23:08:05 +0000 (18:08 -0500)]
15572: List nginx under external dependencies

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15572: Add nginx install page
Peter Amstutz [Tue, 3 Dec 2019 23:07:02 +0000 (18:07 -0500)]
15572: Add nginx install page

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15572: Ongoing install guide refresh/refactor
Peter Amstutz [Tue, 3 Dec 2019 23:06:27 +0000 (18:06 -0500)]
15572: Ongoing install guide refresh/refactor

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15572: API server and controller install docs
Peter Amstutz [Tue, 3 Dec 2019 20:58:38 +0000 (15:58 -0500)]
15572: API server and controller install docs

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15900: Report stable gem version for a given commit.
Tom Clegg [Tue, 3 Dec 2019 16:39:29 +0000 (11:39 -0500)]
15900: Report stable gem version for a given commit.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoFix file token error
Krzysztof Majewski [Tue, 3 Dec 2019 13:11:42 +0000 (14:11 +0100)]
Fix file token error
Arvados-DCO-1.1-Signed-off-by: Krzysztof Majewski <majewski.kielce@gmail.com>

4 years ago15572: Start describing config file
Peter Amstutz [Mon, 2 Dec 2019 23:13:31 +0000 (18:13 -0500)]
15572: Start describing config file

Move the "choose components" table into prereqs

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15572: First pass on new prereqs/planning page
Peter Amstutz [Mon, 2 Dec 2019 19:24:13 +0000 (14:24 -0500)]
15572: First pass on new prereqs/planning page

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoAdd PATCH to allowed CORS methods.
Tom Clegg [Sat, 30 Nov 2019 04:08:44 +0000 (23:08 -0500)]
Add PATCH to allowed CORS methods.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoTest X-Http-Method-Override.
Tom Clegg [Sat, 30 Nov 2019 04:08:23 +0000 (23:08 -0500)]
Test X-Http-Method-Override.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoFix Rails package version calculation again.
Tom Clegg [Fri, 29 Nov 2019 19:16:39 +0000 (14:16 -0500)]
Fix Rails package version calculation again.

refs #15819
refs #15863

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15864-controller-fixes'
Tom Clegg [Fri, 29 Nov 2019 07:46:15 +0000 (02:46 -0500)]
Merge branch '15864-controller-fixes'

refs #15864

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15864: Use POST/X-Http-Method-Override instead of long request URLs.
Tom Clegg [Fri, 29 Nov 2019 07:42:09 +0000 (02:42 -0500)]
15864: Use POST/X-Http-Method-Override instead of long request URLs.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15864: Support X-Http-Method-Override header used by Python SDK.
Tom Clegg [Fri, 29 Nov 2019 07:38:35 +0000 (02:38 -0500)]
15864: Support X-Http-Method-Override header used by Python SDK.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15864: Fix error response when requesting nonexistent UUIDs.
Tom Clegg [Fri, 29 Nov 2019 07:37:41 +0000 (02:37 -0500)]
15864: Fix error response when requesting nonexistent UUIDs.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoFix rails package versions for dev builds.
Tom Clegg [Thu, 28 Nov 2019 18:04:11 +0000 (13:04 -0500)]
Fix rails package versions for dev builds.

[ $goversion > $railsversion ] doesn't compare versions, it just
creates an empty file called $railsversion and returns success.  As a
result, the arvados-api-server and arvados-workbench package
numbers (and the rebuild-or-reuse decisions) were based only on the
last change to cmd/arvados-server, disregarding more recent changes in
the respective Rails projects.

refs #15819
refs #15863

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15795-sys-root-token'
Tom Clegg [Thu, 28 Nov 2019 15:19:46 +0000 (10:19 -0500)]
Merge branch '15795-sys-root-token'

refs #15795

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoAdd Debian 10 ("buster") to the supported GNU/Linux distributions list.
Ward Vandewege [Wed, 27 Nov 2019 20:20:21 +0000 (15:20 -0500)]
Add Debian 10 ("buster") to the supported GNU/Linux distributions list.

No issue #

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

4 years agoMerge branch '15877-accept-json-in-json'
Tom Clegg [Tue, 26 Nov 2019 21:16:27 +0000 (16:16 -0500)]
Merge branch '15877-accept-json-in-json'

fixes #15877

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15877: Accept JSON-encoded param values in JSON request body.
Tom Clegg [Tue, 26 Nov 2019 20:32:30 +0000 (15:32 -0500)]
15877: Accept JSON-encoded param values in JSON request body.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15849-vocab-migration-example'
Lucas Di Pentima [Tue, 26 Nov 2019 20:08:07 +0000 (17:08 -0300)]
Merge branch '15849-vocab-migration-example'
Closes #15849

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoMerge branch '15795-sys-root-token' refs #15795
Peter Amstutz [Tue, 26 Nov 2019 20:06:42 +0000 (15:06 -0500)]
Merge branch '15795-sys-root-token' refs #15795

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15849: Adds a message for dry-run mode when nothing should be migrated.
Lucas Di Pentima [Tue, 26 Nov 2019 20:06:03 +0000 (17:06 -0300)]
15849: Adds a message for dry-run mode when nothing should be migrated.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15849: Removes default value setting to required argument.
Lucas Di Pentima [Tue, 26 Nov 2019 19:51:20 +0000 (16:51 -0300)]
15849: Removes default value setting to required argument.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15849: Adds symlink to script from doc's includes subdir.
Lucas Di Pentima [Tue, 26 Nov 2019 19:49:31 +0000 (16:49 -0300)]
15849: Adds symlink to script from doc's includes subdir.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15849: Moves script to 'tools/' subdir, with some fixes.
Lucas Di Pentima [Tue, 26 Nov 2019 19:46:14 +0000 (16:46 -0300)]
15849: Moves script to 'tools/' subdir, with some fixes.

* Fixed --vocabulary-file argument requirement check
* Modified API server querying to get stable listings

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoMerge branch '15803-unsetup' refs #15803
Peter Amstutz [Tue, 26 Nov 2019 19:17:10 +0000 (14:17 -0500)]
Merge branch '15803-unsetup' refs #15803

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoRevert requirement for bundler upgrade.
Tom Clegg [Tue, 26 Nov 2019 18:55:14 +0000 (13:55 -0500)]
Revert requirement for bundler upgrade.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoInstall bundler 2 in package build images.
Tom Clegg [Tue, 26 Nov 2019 16:21:09 +0000 (11:21 -0500)]
Install bundler 2 in package build images.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoUpdate Go.
Tom Clegg [Tue, 26 Nov 2019 16:20:44 +0000 (11:20 -0500)]
Update Go.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15795: Ensure dispatcher can use SystemRootToken to lock containers.
Tom Clegg [Tue, 26 Nov 2019 15:54:48 +0000 (10:54 -0500)]
15795: Ensure dispatcher can use SystemRootToken to lock containers.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15803: Add test that inactive user is not activated on remote.
Peter Amstutz [Tue, 26 Nov 2019 15:13:43 +0000 (10:13 -0500)]
15803: Add test that inactive user is not activated on remote.

Add links to documentation.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoUpdate token in keepproxy test.
Tom Clegg [Tue, 26 Nov 2019 15:10:01 +0000 (10:10 -0500)]
Update token in keepproxy test.

Fixes commit b047cc92acab06d4c1f1d80173486f951b63d729.

refs #15720

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15849: Moves script to the documentation, includes it on the admin section.
Lucas Di Pentima [Tue, 26 Nov 2019 14:35:10 +0000 (11:35 -0300)]
15849: Moves script to the documentation, includes it on the admin section.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15849: Errors out when a duplicated label is detected on the vocabulary.
Lucas Di Pentima [Tue, 26 Nov 2019 14:16:18 +0000 (11:16 -0300)]
15849: Errors out when a duplicated label is detected on the vocabulary.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15849: Fixes file paths on wb2's arvbox config.
Lucas Di Pentima [Tue, 26 Nov 2019 14:14:56 +0000 (11:14 -0300)]
15849: Fixes file paths on wb2's arvbox config.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years ago15849: Adds vocabulary migration example script.
Lucas Di Pentima [Mon, 25 Nov 2019 23:49:35 +0000 (20:49 -0300)]
15849: Adds vocabulary migration example script.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

4 years agoMerge branch 'master' into 15803-unsetup
Peter Amstutz [Mon, 25 Nov 2019 22:37:25 +0000 (17:37 -0500)]
Merge branch 'master' into 15803-unsetup

4 years ago15795: Accept SystemRootToken from configuration
Peter Amstutz [Sat, 23 Nov 2019 02:33:25 +0000 (21:33 -0500)]
15795: Accept SystemRootToken from configuration

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoMerge branch '15720-fed-user-list'
Tom Clegg [Mon, 25 Nov 2019 21:58:52 +0000 (16:58 -0500)]
Merge branch '15720-fed-user-list'

closes #15720

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15720: Warn about empty ManagementToken or SystemRootToken.
Tom Clegg [Mon, 25 Nov 2019 20:32:21 +0000 (15:32 -0500)]
15720: Warn about empty ManagementToken or SystemRootToken.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15720: Update generated code.
Tom Clegg [Mon, 25 Nov 2019 21:14:47 +0000 (16:14 -0500)]
15720: Update generated code.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15720: Merge branch 'master' into 15720-fed-user-list
Tom Clegg [Mon, 25 Nov 2019 20:20:21 +0000 (15:20 -0500)]
15720: Merge branch 'master' into 15720-fed-user-list

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15851-bundle'
Tom Clegg [Fri, 22 Nov 2019 20:35:25 +0000 (15:35 -0500)]
Merge branch '15851-bundle'

refs #15851

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15851: Update expected versions in Gemfile.lock files.
Tom Clegg [Fri, 22 Nov 2019 20:31:23 +0000 (15:31 -0500)]
15851: Update expected versions in Gemfile.lock files.

Bundler won't install a gem whose *.gemspec file doesn't match the
expected version number, even when Gemfile.lock specifies a git
repo+commit.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15851: Explicit path to bundle executable.
Tom Clegg [Fri, 22 Nov 2019 19:34:43 +0000 (14:34 -0500)]
15851: Explicit path to bundle executable.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoMerge branch '15851-empty-items-array'
Tom Clegg [Fri, 22 Nov 2019 19:04:52 +0000 (14:04 -0500)]
Merge branch '15851-empty-items-array'

fixes #15851

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15851: Merge branch 'master' into 15851-empty-items-array
Tom Clegg [Fri, 22 Nov 2019 19:04:27 +0000 (14:04 -0500)]
15851: Merge branch 'master' into 15851-empty-items-array

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15866: Install bundler in GEMHOME.
Tom Clegg [Fri, 22 Nov 2019 18:59:26 +0000 (13:59 -0500)]
15866: Install bundler in GEMHOME.

refs #15866

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15866: Abandon services/api install if bundle fails.
Tom Clegg [Fri, 22 Nov 2019 17:54:32 +0000 (12:54 -0500)]
15866: Abandon services/api install if bundle fails.

refs #15866

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoUpdate to bundler 2.0.2
Tom Clegg [Fri, 22 Nov 2019 17:49:21 +0000 (12:49 -0500)]
Update to bundler 2.0.2

refs #15866

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15867: Don't pass blank remote param.
Tom Clegg [Fri, 22 Nov 2019 17:14:26 +0000 (12:14 -0500)]
15867: Don't pass blank remote param.

fixes #15867

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoActivate new users created on the login cluster by federation-migrate
Peter Amstutz [Fri, 22 Nov 2019 15:37:02 +0000 (10:37 -0500)]
Activate new users created on the login cluster by federation-migrate

Users are activated if they were active on their original cluster.

Update check script part of federation-migrate test to check
is_active.

Also add assertions to permission test "users with bidirectional read
permission in group can see each other" to explictly check that the
other user appears in user's user listing.

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoDon't set AnonymousUserToken in arvbox
Peter Amstutz [Thu, 21 Nov 2019 22:37:48 +0000 (17:37 -0500)]
Don't set AnonymousUserToken in arvbox

Definitely don't want to set it to superuser!

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoMerge branch '15848-controller-list-sort'
Tom Clegg [Thu, 21 Nov 2019 20:33:10 +0000 (15:33 -0500)]
Merge branch '15848-controller-list-sort'

refs #15848

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoRefactor arvbox federation test scripts, no issue #
Peter Amstutz [Thu, 21 Nov 2019 19:47:46 +0000 (14:47 -0500)]
Refactor arvbox federation test scripts, no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years ago15848: Convert timestamps from pointer to value fields.
Tom Clegg [Thu, 21 Nov 2019 19:24:19 +0000 (14:24 -0500)]
15848: Convert timestamps from pointer to value fields.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15848: Fix incorrect order in federation query response.
Tom Clegg [Thu, 21 Nov 2019 17:34:45 +0000 (12:34 -0500)]
15848: Fix incorrect order in federation query response.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years agoFix arvbox "go get" for arvados-server no issue #
Peter Amstutz [Thu, 21 Nov 2019 17:17:16 +0000 (12:17 -0500)]
Fix arvbox "go get" for arvados-server no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

4 years agoMerge branch '15854-filter-container-fields'
Tom Clegg [Thu, 21 Nov 2019 16:13:08 +0000 (11:13 -0500)]
Merge branch '15854-filter-container-fields'

closes #15854

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

4 years ago15851: Return items [], not null, in empty set responses.
Tom Clegg [Thu, 21 Nov 2019 15:49:56 +0000 (10:49 -0500)]
15851: Return items [], not null, in empty set responses.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>