arvados.git
5 years agoMerge branch '15275-attribute-dirtyness-bugfix'
Lucas Di Pentima [Tue, 28 May 2019 15:41:51 +0000 (12:41 -0300)]
Merge branch '15275-attribute-dirtyness-bugfix'
Closes #15275

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

5 years ago15275: Adds test for different jsonb properties comparisons cases.
Lucas Di Pentima [Tue, 28 May 2019 14:27:43 +0000 (11:27 -0300)]
15275: Adds test for different jsonb properties comparisons cases.

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

5 years ago15275: Checks for jsonb types changes by comparing deserialized values.
Lucas Di Pentima [Fri, 24 May 2019 21:11:23 +0000 (18:11 -0300)]
15275: Checks for jsonb types changes by comparing deserialized values.

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

5 years agoarvbox use lowercase keys for database connection params refs #15273
Peter Amstutz [Fri, 24 May 2019 20:31:49 +0000 (16:31 -0400)]
arvbox use lowercase keys for database connection params refs #15273

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

5 years agoMerge branch 'master' into 15275-attribute-dirtyness-bugfix
Lucas Di Pentima [Fri, 24 May 2019 18:34:01 +0000 (15:34 -0300)]
Merge branch 'master' into 15275-attribute-dirtyness-bugfix

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

5 years ago15275: Re-adds the test exposing this branch's particular bug.
Lucas Di Pentima [Fri, 24 May 2019 18:33:13 +0000 (15:33 -0300)]
15275: Re-adds the test exposing this branch's particular bug.

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

5 years agoMerge branch '15275-collection-delete-bugfix'. Refs #15275
Lucas Di Pentima [Fri, 24 May 2019 18:11:34 +0000 (15:11 -0300)]
Merge branch '15275-collection-delete-bugfix'. Refs #15275

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

5 years ago15275: Simplifies method code.
Lucas Di Pentima [Fri, 24 May 2019 18:00:40 +0000 (15:00 -0300)]
15275: Simplifies method code.

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

5 years ago15275: Don't create snapshots whenever is_trashed is true.
Lucas Di Pentima [Fri, 24 May 2019 17:58:59 +0000 (14:58 -0300)]
15275: Don't create snapshots whenever is_trashed is true.

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

5 years ago15275: Don't create snapshot when trashing collection.
Lucas Di Pentima [Fri, 24 May 2019 15:36:54 +0000 (12:36 -0300)]
15275: Don't create snapshot when trashing collection.

Also, skips test about bogus properties field changes, for now.

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

5 years ago15275: Adds another test exposing the jsonb changed field bug.
Lucas Di Pentima [Fri, 24 May 2019 13:55:14 +0000 (10:55 -0300)]
15275: Adds another test exposing the jsonb changed field bug.

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

5 years ago15275: Moves comment to its proper place.
Lucas Di Pentima [Fri, 24 May 2019 13:31:40 +0000 (10:31 -0300)]
15275: Moves comment to its proper place.

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

5 years ago15275: Avoids running manage_versioning when not needed.
Lucas Di Pentima [Fri, 24 May 2019 01:22:02 +0000 (22:22 -0300)]
15275: Avoids running manage_versioning when not needed.

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

5 years ago15275: Saves snapshot as system user instead of assigning a signed manifest to it
Lucas Di Pentima [Thu, 23 May 2019 23:07:13 +0000 (20:07 -0300)]
15275: Saves snapshot as system user instead of assigning a signed manifest to it

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

5 years ago15725: Adds test exposing 2 issues when trashing collections with versioning
Lucas Di Pentima [Thu, 23 May 2019 22:53:12 +0000 (19:53 -0300)]
15725: Adds test exposing 2 issues when trashing collections with versioning

1) Snapshot being created when deleting a collection
2) Permission denied error when trying to create the new snapshot

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

5 years agoMake sure that the libpam-arvados package puts its various files in the place
Ward Vandewege [Thu, 23 May 2019 18:45:35 +0000 (14:45 -0400)]
Make sure that the libpam-arvados package puts its various files in the place
where the pam subsystem will expect them, not inside the virtualenv.

Also, remove the code from sdk/pam/setup.py that installed a copy of the
libpam-arvados.py file under /usr/data/lib/security/libpam_arvados.py for
legacy reasons.

refs #9945
refs #15186

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

5 years agoMerge branch '15273-db-conn-keys'
Tom Clegg [Thu, 23 May 2019 18:23:54 +0000 (14:23 -0400)]
Merge branch '15273-db-conn-keys'

fixes #15273

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

5 years ago15273: Fix key-conflict test.
Tom Clegg [Thu, 23 May 2019 18:23:26 +0000 (14:23 -0400)]
15273: Fix key-conflict test.

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

5 years ago15273: Use lowercase keys for database connection params.
Tom Clegg [Thu, 23 May 2019 17:42:37 +0000 (13:42 -0400)]
15273: Use lowercase keys for database connection params.

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

5 years agoMerge branch '15003-disable-config-warnings'
Tom Clegg [Thu, 23 May 2019 15:27:26 +0000 (11:27 -0400)]
Merge branch '15003-disable-config-warnings'

refs #15003

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

5 years agoMerge branch '15258-wb-report-issue-bugfix'
Lucas Di Pentima [Thu, 23 May 2019 14:03:13 +0000 (11:03 -0300)]
Merge branch '15258-wb-report-issue-bugfix'
Closes #15258

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

5 years ago15003: Temporarily disable config warnings.
Tom Clegg [Thu, 23 May 2019 13:31:40 +0000 (09:31 -0400)]
15003: Temporarily disable config warnings.

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

5 years ago15258: Explicitly require libs instead of relying on autoloading.
Lucas Di Pentima [Thu, 23 May 2019 13:14:21 +0000 (10:14 -0300)]
15258: Explicitly require libs instead of relying on autoloading.

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

5 years ago15258: Removes /lib from eager load paths because of failing integration tests.
Lucas Di Pentima [Thu, 23 May 2019 12:52:10 +0000 (09:52 -0300)]
15258: Removes /lib from eager load paths because of failing integration tests.

PhantomJS started to randomly fail, maybe because of memory or timing reasons.
This change exposes the bug observed on production, on development & test envs.

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

5 years agoIncrease client_max_body_size in arvbox to support file uploads.
Peter Amstutz [Wed, 22 May 2019 21:31:48 +0000 (17:31 -0400)]
Increase client_max_body_size in arvbox to support file uploads.

no issue #

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

5 years ago15258: Adds /lib to the eager_load paths.
Lucas Di Pentima [Wed, 22 May 2019 19:57:19 +0000 (16:57 -0300)]
15258: Adds /lib to the eager_load paths.

On rails 5.0 the autoload paths stopped working on production environments
for thread safety concerns.
See: https://github.com/rails/rails/commit/a71350cae0082193ad8c66d65ab62e8bb0b7853b

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

5 years agoWhile our Python SDK now supports Python 3.4+, our FUSE driver does not yet. On
Ward Vandewege [Tue, 21 May 2019 17:27:41 +0000 (13:27 -0400)]
While our Python SDK now supports Python 3.4+, our FUSE driver does not yet. On
the FUSE driver installation page, we should be mentioning the latter, not the
former.

No issue #

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

5 years agoOur Python SDK now also supports version 3.4+, update the fuse drive doc page
Ward Vandewege [Tue, 21 May 2019 14:36:24 +0000 (10:36 -0400)]
Our Python SDK now also supports version 3.4+, update the fuse drive doc page
accordingly.

No issue #

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

5 years agoFix cwl tests refs #15241
Peter Amstutz [Mon, 20 May 2019 20:42:11 +0000 (16:42 -0400)]
Fix cwl tests refs #15241

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

5 years agoMerge branch '15241-collection-input' refs #15241
Peter Amstutz [Mon, 20 May 2019 19:48:27 +0000 (15:48 -0400)]
Merge branch '15241-collection-input' refs #15241

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

5 years ago15241: Fix input bare collection as directory
Peter Amstutz [Mon, 20 May 2019 19:46:17 +0000 (15:46 -0400)]
15241: Fix input bare collection as directory

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

5 years agoMerge branch '14988-wb-rails5-upgrade'
Lucas Di Pentima [Fri, 17 May 2019 17:31:29 +0000 (14:31 -0300)]
Merge branch '14988-wb-rails5-upgrade'
Closes #14988

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

5 years agoMerge branch '15227-apiserver-properties-bugfix'
Lucas Di Pentima [Fri, 17 May 2019 17:30:33 +0000 (14:30 -0300)]
Merge branch '15227-apiserver-properties-bugfix'
Closes #15227

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

5 years agoUpdate the note about supported Python versions for Arv SDK.
Peter Amstutz [Fri, 17 May 2019 15:55:31 +0000 (11:55 -0400)]
Update the note about supported Python versions for Arv SDK.

no issue #

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

5 years ago14988: Restores debug message when accessing non-loaded attributes.
Lucas Di Pentima [Fri, 17 May 2019 14:42:19 +0000 (11:42 -0300)]
14988: Restores debug message when accessing non-loaded attributes.

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

5 years agoAdd user email and cancel button to federated user redirect page
Peter Amstutz [Fri, 17 May 2019 14:18:13 +0000 (10:18 -0400)]
Add user email and cancel button to federated user redirect page

refs #15061

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

5 years ago14988: Fixes destroyed? method to return false on new records.
Lucas Di Pentima [Fri, 17 May 2019 13:28:13 +0000 (10:28 -0300)]
14988: Fixes destroyed? method to return false on new records.

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

5 years ago15227: Fixes type checking on json attributes.
Lucas Di Pentima [Fri, 17 May 2019 00:20:33 +0000 (21:20 -0300)]
15227: Fixes type checking on json attributes.

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

5 years ago15227: More tests to expose the bug.
Lucas Di Pentima [Fri, 17 May 2019 00:19:57 +0000 (21:19 -0300)]
15227: More tests to expose the bug.

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

5 years agoMerge branch '15232-blobttl-suffix'
Tom Clegg [Wed, 15 May 2019 21:05:55 +0000 (17:05 -0400)]
Merge branch '15232-blobttl-suffix'

fixes #15232

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

5 years agoSyncs up generated config.
Lucas Di Pentima [Wed, 15 May 2019 20:25:01 +0000 (17:25 -0300)]
Syncs up generated config.

No issue #

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

5 years agoMerge branch '15061-fed-migrate' refs #15061
Peter Amstutz [Wed, 15 May 2019 20:09:48 +0000 (16:09 -0400)]
Merge branch '15061-fed-migrate' refs #15061

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

5 years ago15061: Code cleanup, improve validity checking & error handling
Peter Amstutz [Wed, 15 May 2019 18:38:15 +0000 (14:38 -0400)]
15061: Code cleanup, improve validity checking & error handling

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

5 years ago15227: Adds test exposing bug.
Lucas Di Pentima [Wed, 15 May 2019 18:50:24 +0000 (15:50 -0300)]
15227: Adds test exposing bug.

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

5 years ago15232: Fix type of Collections.BlobSigningTTL config key.
Tom Clegg [Wed, 15 May 2019 18:02:33 +0000 (14:02 -0400)]
15232: Fix type of Collections.BlobSigningTTL config key.

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

5 years agoMerge branch '15167-unlogged-attrs-api-docs'
Lucas Di Pentima [Wed, 15 May 2019 16:54:22 +0000 (13:54 -0300)]
Merge branch '15167-unlogged-attrs-api-docs'
Closes #15167

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

5 years agoMerge branch '15003-preprocess-config'
Tom Clegg [Wed, 15 May 2019 14:59:46 +0000 (10:59 -0400)]
Merge branch '15003-preprocess-config'

refs #15003

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

5 years ago15003: Merge branch 'master' into 15003-preprocess-config
Tom Clegg [Wed, 15 May 2019 13:57:36 +0000 (09:57 -0400)]
15003: Merge branch 'master' into 15003-preprocess-config

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

5 years agoReset the rails package iteration to 1
Ward Vandewege [Tue, 14 May 2019 21:33:33 +0000 (17:33 -0400)]
Reset the rails package iteration to 1

No issue #

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

5 years agoMerge branch '15200-fix-blobsigning-config-migration'
Ward Vandewege [Tue, 14 May 2019 21:30:04 +0000 (17:30 -0400)]
Merge branch '15200-fix-blobsigning-config-migration'

closes #15200

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

5 years agoWhen specified in the api configuration,
Ward Vandewege [Tue, 14 May 2019 21:16:28 +0000 (17:16 -0400)]
When specified in the api configuration,

  permit_create_collection_with_unsigned_manifest: false

needs to be translated to

  BlobSigning: true

refs #15200

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

5 years ago15061: Add warning about clusters that are not in tokens file.
Peter Amstutz [Tue, 14 May 2019 20:17:23 +0000 (16:17 -0400)]
15061: Add warning about clusters that are not in tokens file.

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

5 years ago15061: Check well-connectedness. Fix typos.
Peter Amstutz [Tue, 14 May 2019 18:12:25 +0000 (14:12 -0400)]
15061: Check well-connectedness.  Fix typos.

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

5 years agoBump the rails package iteration to 9, for the packaging fix in commit
Ward Vandewege [Tue, 14 May 2019 16:37:43 +0000 (12:37 -0400)]
Bump the rails package iteration to 9, for the packaging fix in commit
b4fabf39c7cb1c48a2ba09ba2f45da45b6c4574

refs #15225

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

5 years ago14988: Fixes bootstrap import issue
Lucas Di Pentima [Tue, 14 May 2019 14:29:04 +0000 (11:29 -0300)]
14988: Fixes bootstrap import issue

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

5 years agoFix the api server package postinstall script to use `rake config:dump` to get a
Ward Vandewege [Tue, 14 May 2019 14:21:08 +0000 (10:21 -0400)]
Fix the api server package postinstall script to use `rake config:dump` to get a
value, rather than `rake config:check` which no longer produces output.

closes #15225

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

5 years ago14988: Upgrades bootstrap-sass to deal with CVE-2019-8331.
Lucas Di Pentima [Tue, 14 May 2019 14:15:50 +0000 (11:15 -0300)]
14988: Upgrades bootstrap-sass to deal with CVE-2019-8331.

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

5 years ago14988: Fixes pipeline instance controller's param handling.
Lucas Di Pentima [Mon, 13 May 2019 14:41:38 +0000 (11:41 -0300)]
14988: Fixes pipeline instance controller's param handling.

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

5 years agoAdd workbench2Url to discovery document refs #15064
Peter Amstutz [Mon, 13 May 2019 14:00:47 +0000 (10:00 -0400)]
Add workbench2Url to discovery document refs #15064

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

5 years agoMigrate arvbox api application.yml settings to config.yml
Peter Amstutz [Mon, 13 May 2019 13:58:39 +0000 (09:58 -0400)]
Migrate arvbox api application.yml settings to config.yml

To set workbench2 url.  refs #15064

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

5 years ago14988: Fixes assert_equal param ordering for proper error messages.
Lucas Di Pentima [Mon, 13 May 2019 13:56:21 +0000 (10:56 -0300)]
14988: Fixes assert_equal param ordering for proper error messages.

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

5 years agoMerge branch 'master' into 14988-wb-rails5-upgrade
Lucas Di Pentima [Mon, 13 May 2019 12:25:01 +0000 (09:25 -0300)]
Merge branch 'master' into 14988-wb-rails5-upgrade

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

5 years agoLog if client hangs up while waiting for unix volume Serialize lock.
Tom Clegg [Fri, 10 May 2019 20:36:39 +0000 (16:36 -0400)]
Log if client hangs up while waiting for unix volume Serialize lock.

No issue #

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

5 years agoRemove extra \n from log.Printf formats
Tom Clegg [Fri, 10 May 2019 20:07:47 +0000 (16:07 -0400)]
Remove extra \n from log.Printf formats

No issue #

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

5 years agoMerge branch '15061-fed-login' refs #15061
Peter Amstutz [Thu, 9 May 2019 20:57:08 +0000 (16:57 -0400)]
Merge branch '15061-fed-login' refs #15061

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

5 years ago15061: Add documentation for using arv-federation-migrate
Peter Amstutz [Thu, 9 May 2019 19:25:23 +0000 (15:25 -0400)]
15061: Add documentation for using arv-federation-migrate

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

5 years ago15061: Move federation migrate script into sdk
Peter Amstutz [Thu, 9 May 2019 14:59:56 +0000 (10:59 -0400)]
15061: Move federation migrate script into sdk

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

5 years ago15061: add federation-migrate script
Peter Amstutz [Wed, 8 May 2019 21:25:06 +0000 (17:25 -0400)]
15061: add federation-migrate script

Produces a report, users can edit the report to choose which cluster
each user should belong to, then run the report back through to
perform the migration.

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

5 years ago15061: Add missing file
Peter Amstutz [Thu, 9 May 2019 19:27:07 +0000 (15:27 -0400)]
15061: Add missing file

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

5 years ago15061: Implement admin variant of user merge by uuid
Peter Amstutz [Tue, 7 May 2019 22:00:57 +0000 (18:00 -0400)]
15061: Implement admin variant of user merge by uuid

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

5 years ago15061: API support for linking local account to remote user
Peter Amstutz [Tue, 7 May 2019 20:31:21 +0000 (16:31 -0400)]
15061: API support for linking local account to remote user

Adds page to login process to redirect user to log in to home cluster.

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

5 years ago15061: Correctly filter out "*" from RemoteClusters
Peter Amstutz [Mon, 6 May 2019 19:35:42 +0000 (15:35 -0400)]
15061: Correctly filter out "*" from RemoteClusters

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

5 years agoPin pykka < 2 for nodemanager no issue #
Peter Amstutz [Thu, 9 May 2019 14:37:36 +0000 (10:37 -0400)]
Pin pykka < 2 for nodemanager no issue #

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

5 years ago14988: Fixes merge conflict
Lucas Di Pentima [Wed, 8 May 2019 21:50:26 +0000 (18:50 -0300)]
14988: Fixes merge conflict

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

5 years agoFix unit error in the node manager documentation for EC2.
Ward Vandewege [Wed, 8 May 2019 20:39:17 +0000 (16:39 -0400)]
Fix unit error in the node manager documentation for EC2.

refs #15199

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

5 years agoarvbox crunch-run and certificate fixes
Peter Amstutz [Fri, 3 May 2019 20:21:06 +0000 (16:21 -0400)]
arvbox crunch-run and certificate fixes

arvbox crunch-run change to -container-enable-networking=default

Previously was "always" which causes CWL tests that checked that
networking was disabled to fail.

arvbox root-cert creates file with .crt instead of .pem, because
that's the file extension update-ca-certificates looks for.

Add cluster id and timestamp to arvbox test certificate common name to
prevents collisions on the certificate subject.

Arvbox sets trusted api_client for workbench2.

refs #15028 refs #15061

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

5 years agoMerge branch 'master' into 14988-wb-rails5-upgrade
Lucas Di Pentima [Wed, 8 May 2019 19:25:57 +0000 (16:25 -0300)]
Merge branch 'master' into 14988-wb-rails5-upgrade

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

5 years ago14988: Fixes exception raising due to a change in rails5 behavior.
Lucas Di Pentima [Wed, 8 May 2019 13:10:48 +0000 (10:10 -0300)]
14988: Fixes exception raising due to a change in rails5 behavior.

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

5 years ago14988: Adds empty subdir to test/ as it's required by rails.
Lucas Di Pentima [Wed, 8 May 2019 13:09:58 +0000 (10:09 -0300)]
14988: Adds empty subdir to test/ as it's required by rails.

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

5 years ago14988: Fixes .dup method behavior on ArvadosBase.
Lucas Di Pentima [Tue, 7 May 2019 20:26:33 +0000 (17:26 -0300)]
14988: Fixes .dup method behavior on ArvadosBase.

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

5 years agoMerge branch '15112-rerun-containers' refs #15112
Peter Amstutz [Tue, 7 May 2019 15:55:11 +0000 (11:55 -0400)]
Merge branch '15112-rerun-containers' refs #15112

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

5 years ago14988: Fixes exception raising when logging out.
Lucas Di Pentima [Tue, 7 May 2019 13:53:24 +0000 (10:53 -0300)]
14988: Fixes exception raising when logging out.

See: https://stackoverflow.com/a/41266746

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

5 years ago14988: Disables wiselinks gem. Testing if it's really needed.
Lucas Di Pentima [Mon, 6 May 2019 20:56:00 +0000 (17:56 -0300)]
14988: Disables wiselinks gem. Testing if it's really needed.

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

5 years ago14988: Removes deprecation warning about rendering nothing.
Lucas Di Pentima [Mon, 6 May 2019 20:52:20 +0000 (17:52 -0300)]
14988: Removes deprecation warning about rendering nothing.

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

5 years ago14988: Fixes anonymous config & token usage issues on tests.
Lucas Di Pentima [Mon, 6 May 2019 20:12:30 +0000 (17:12 -0300)]
14988: Fixes anonymous config & token usage issues on tests.

After calling post/get it seems that the token is reset, so on tests with
multiple controller/api calls there were some problems with authentication.

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

5 years ago14988: Adds missing create!() method to ArvadosBase.
Lucas Di Pentima [Mon, 6 May 2019 18:08:25 +0000 (15:08 -0300)]
14988: Adds missing create!() method to ArvadosBase.

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

5 years ago14988: Fixes CSS syntax error on Jobs controller tests.
Lucas Di Pentima [Mon, 6 May 2019 15:16:54 +0000 (12:16 -0300)]
14988: Fixes CSS syntax error on Jobs controller tests.

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

5 years ago15003: Merge branch 'master' into 15003-preprocess-config
Tom Clegg [Mon, 6 May 2019 15:16:15 +0000 (11:16 -0400)]
15003: Merge branch 'master' into 15003-preprocess-config

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

5 years ago14988: Fixes CSS syntax issue.
Lucas Di Pentima [Mon, 6 May 2019 15:07:12 +0000 (12:07 -0300)]
14988: Fixes CSS syntax issue.

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

5 years ago14988: Fixes unit test by adding 'x-python' type to the preview-allowed list.
Lucas Di Pentima [Mon, 6 May 2019 14:30:49 +0000 (11:30 -0300)]
14988: Fixes unit test by adding 'x-python' type to the preview-allowed list.

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

5 years ago14988: Fixes functionals tests (WIP)
Lucas Di Pentima [Mon, 6 May 2019 12:23:36 +0000 (09:23 -0300)]
14988: Fixes functionals tests (WIP)

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

5 years agoFix mistake setting container_count_max from wrong config parameter
Peter Amstutz [Fri, 3 May 2019 15:40:43 +0000 (11:40 -0400)]
Fix mistake setting container_count_max from wrong config parameter

refs #13996

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

5 years agoMerge branch '15164-cr-finalize-lock' closes #15164
Peter Amstutz [Thu, 2 May 2019 14:13:26 +0000 (10:13 -0400)]
Merge branch '15164-cr-finalize-lock' closes #15164

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

5 years ago15112: log root user. log progress.
Peter Amstutz [Thu, 2 May 2019 13:22:12 +0000 (09:22 -0400)]
15112: log root user.  log progress.

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

5 years ago15112: Rename since it doesn't rerun anything
Peter Amstutz [Wed, 1 May 2019 20:39:06 +0000 (16:39 -0400)]
15112: Rename since it doesn't rerun anything

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

5 years ago15112: Don't submit anything, just produce a csv file with results
Peter Amstutz [Wed, 1 May 2019 20:30:31 +0000 (16:30 -0400)]
15112: Don't submit anything, just produce a csv file with results

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

5 years agoFix typo.
Ward Vandewege [Wed, 1 May 2019 20:18:51 +0000 (16:18 -0400)]
Fix typo.

No issue #

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

5 years agoFix debug setup accidentally committed.
Tom Morris [Wed, 1 May 2019 18:56:35 +0000 (14:56 -0400)]
Fix debug setup accidentally committed.

refs #14670

Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>

5 years ago15112: Script to re-run containers
Peter Amstutz [Tue, 30 Apr 2019 22:06:54 +0000 (18:06 -0400)]
15112: Script to re-run containers

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

5 years agoMerge branch '15161-config-check-rake-fix'
Lucas Di Pentima [Tue, 30 Apr 2019 19:55:35 +0000 (16:55 -0300)]
Merge branch '15161-config-check-rake-fix'
Refs #15161

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