Peter Amstutz [Thu, 5 Mar 2020 23:00:15 +0000 (18:00 -0500)]
Pin version of launchy gem while we still support Ruby 2.3
refs #16215
Need to do it for login-sync too.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 5 Mar 2020 21:27:33 +0000 (16:27 -0500)]
Pin version of launchy gem while we still support Ruby 2.3
refs #16215
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Mon, 13 Apr 2020 18:34:12 +0000 (15:34 -0300)]
16313: Updates minimum requestd ram on docker containers from 4 to 16 MB.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Mon, 13 Apr 2020 18:38:15 +0000 (14:38 -0400)]
Bump mithril for advisory https://npmjs.com/advisories/1094
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 13 Apr 2020 18:00:32 +0000 (14:00 -0400)]
Pin jssha to 2.4.2
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 13 Apr 2020 14:25:11 +0000 (10:25 -0400)]
16263: Add test for BypassFederation
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Mon, 6 Apr 2020 14:01:18 +0000 (11:01 -0300)]
16263: Pulls from official git repo when running federation tests.
This is helpful to ask for specific branches that aren't published on github.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Thu, 2 Apr 2020 14:52:44 +0000 (10:52 -0400)]
16263: User migration test also checks federated user behavior
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Wed, 1 Apr 2020 01:03:42 +0000 (21:03 -0400)]
16263: Tweak federation tests, use CWL 1.1
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 31 Mar 2020 21:42:03 +0000 (17:42 -0400)]
16263: Add bypass_federation test
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 31 Mar 2020 21:16:57 +0000 (17:16 -0400)]
16263: Fix no_federation -> bypass_federation in boolParms
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 31 Mar 2020 21:12:31 +0000 (17:12 -0400)]
16263: Fix only_admin_can_bypass_federation
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 31 Mar 2020 20:45:49 +0000 (16:45 -0400)]
16263: Missed rename
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 31 Mar 2020 20:33:27 +0000 (16:33 -0400)]
16263: Rename no_federation -> bypass_federation
Enforce if bypass_federation is true that user is admin.
Update API revision and make federation migrate check for it.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 31 Mar 2020 18:42:46 +0000 (14:42 -0400)]
16263: Add no_federation to user update
We might agree on a different API but try this and see if it helps
pass the test.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 31 Mar 2020 02:30:10 +0000 (22:30 -0400)]
16263: local_user_list -> no_federation in boolParams
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 31 Mar 2020 02:14:23 +0000 (22:14 -0400)]
16263: Generalize "local_user_list" flag to "no_federation"
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 30 Mar 2020 21:12:17 +0000 (17:12 -0400)]
16263: UserMerge shouldn't be federated
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 30 Mar 2020 18:50:06 +0000 (14:50 -0400)]
16263: Fix omitempty placement
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 30 Mar 2020 18:43:36 +0000 (14:43 -0400)]
16263: Add omitempty to GetOptions
Don't try to migrate if activate_remote_user fails.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Sat, 28 Mar 2020 01:36:09 +0000 (21:36 -0400)]
16263: Add local_user_list to boolParams
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Fri, 27 Mar 2020 21:08:48 +0000 (17:08 -0400)]
16263: Add local_user_list flag to bypass LoginCluster behavior
Required by federation migrate script.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Thu, 26 Mar 2020 14:46:34 +0000 (11:46 -0300)]
16263: Decodes JSON numbers as strings instead of float64.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Wed, 25 Mar 2020 19:35:18 +0000 (16:35 -0300)]
16263: Adds unit test case confirming 'limit' bug.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Wed, 25 Mar 2020 14:26:55 +0000 (11:26 -0300)]
16263: Adds test exposing a bug when using 'limit' with the max int64 value.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Tue, 24 Mar 2020 20:39:01 +0000 (17:39 -0300)]
16263: Bool filter bug fix.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Tue, 24 Mar 2020 21:03:34 +0000 (18:03 -0300)]
16263: Adds test exposing a bug on filter unmarshalling.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Mon, 23 Mar 2020 19:20:41 +0000 (16:20 -0300)]
16263: Makes gofmt happy.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Mon, 23 Mar 2020 18:32:59 +0000 (15:32 -0300)]
16263: Don't cache modified_by_*_uuid fields when using LoginCluster.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Mon, 23 Mar 2020 15:27:18 +0000 (12:27 -0300)]
16263: Adds nullify behavior to users's batch_update endpoint.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 19 Mar 2020 21:15:52 +0000 (18:15 -0300)]
16263: Assigns nil to select attributes when receiving empty values.
Controller may translate NULL values to "" on certain object string fields.
The same with integers, NULLs are converted to 0.
When controller retrieves objects from railsAPI and uses the data to create
or update objects, some of those fields should get converted back to NULL.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Ward Vandewege [Fri, 10 Apr 2020 12:56:56 +0000 (08:56 -0400)]
Fix tests.
refs #16326
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@jhvc.com>
Ward Vandewege [Thu, 9 Apr 2020 21:53:31 +0000 (17:53 -0400)]
documentation: update descriptions for MaxKeepBlobBuffers and MaxConcurrentRequests
keepstore: MaxConcurrentRequests set to zero should mean no limit
refs #16326
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@jhvc.com>
Tom Clegg [Thu, 9 Apr 2020 20:58:36 +0000 (16:58 -0400)]
Warn if MaxKeepBlobBuffers > MaxConcurrentRequests.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 21:42:39 +0000 (16:42 -0500)]
16219: Test populated container fields.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 19:44:22 +0000 (14:44 -0500)]
16219: Load all fields needed to compute node size.
Without ContainerImage and Mounts, the scratch size requirement can't
be computed correctly.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 12 Mar 2020 04:15:16 +0000 (00:15 -0400)]
16221: Fix test for config endpoint.
x['configs'] raises KeyError on an old discovery doc -- test
x.get('configs', False) instead.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 20:52:04 +0000 (16:52 -0400)]
Fix instance IDs in arvados-dispatch-cloud log messages.
Some logs had {"Instance": {}} instead of the provider's instance ID.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 1 Apr 2020 20:44:02 +0000 (16:44 -0400)]
16270: Fill in missing scratch fields on InstanceType entries.
Previously they were being filled in correctly when written as an
array in the config file, but not when written as a map.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
dependabot[bot] [Tue, 3 Mar 2020 21:27:27 +0000 (21:27 +0000)]
Bump rake from 12.3.2 to 13.0.1 in /services/api
Bumps [rake](https://github.com/ruby/rake) from 12.3.2 to 13.0.1.
- [Release notes](https://github.com/ruby/rake/releases)
- [Changelog](https://github.com/ruby/rake/blob/master/History.rdoc)
- [Commits](https://github.com/ruby/rake/compare/v12.3.2...v13.0.1)
Signed-off-by: dependabot[bot] <support@github.com>
dependabot[bot] [Tue, 3 Mar 2020 21:27:30 +0000 (21:27 +0000)]
Bump rake from 12.3.2 to 13.0.1 in /apps/workbench
Bumps [rake](https://github.com/ruby/rake) from 12.3.2 to 13.0.1.
- [Release notes](https://github.com/ruby/rake/releases)
- [Changelog](https://github.com/ruby/rake/blob/master/History.rdoc)
- [Commits](https://github.com/ruby/rake/compare/v12.3.2...v13.0.1)
Signed-off-by: dependabot[bot] <support@github.com>
dependabot[bot] [Tue, 25 Feb 2020 08:04:58 +0000 (08:04 +0000)]
Bump nokogiri from 1.10.4 to 1.10.8 in /apps/workbench
Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.10.4 to 1.10.8.
- [Release notes](https://github.com/sparklemotion/nokogiri/releases)
- [Changelog](https://github.com/sparklemotion/nokogiri/blob/master/CHANGELOG.md)
- [Commits](https://github.com/sparklemotion/nokogiri/compare/v1.10.4...v1.10.8)
Signed-off-by: dependabot[bot] <support@github.com>
dependabot[bot] [Fri, 8 Nov 2019 21:48:47 +0000 (21:48 +0000)]
Bump loofah from 2.2.3 to 2.3.1 in /apps/workbench
Bumps [loofah](https://github.com/flavorjones/loofah) from 2.2.3 to 2.3.1.
- [Release notes](https://github.com/flavorjones/loofah/releases)
- [Changelog](https://github.com/flavorjones/loofah/blob/master/CHANGELOG.md)
- [Commits](https://github.com/flavorjones/loofah/compare/v2.2.3...v2.3.1)
Signed-off-by: dependabot[bot] <support@github.com>
dependabot[bot] [Tue, 25 Feb 2020 08:04:57 +0000 (08:04 +0000)]
Bump nokogiri from 1.10.2 to 1.10.8 in /services/api
Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.10.2 to 1.10.8.
- [Release notes](https://github.com/sparklemotion/nokogiri/releases)
- [Changelog](https://github.com/sparklemotion/nokogiri/blob/master/CHANGELOG.md)
- [Commits](https://github.com/sparklemotion/nokogiri/compare/v1.10.2...v1.10.8)
Signed-off-by: dependabot[bot] <support@github.com>
Lucas Di Pentima [Mon, 23 Mar 2020 21:07:56 +0000 (18:07 -0300)]
16266: Applies monkeypatch to fix CVE-2020-5267 on workbench1.
As adviced on https://github.com/advisories/GHSA-65cv-r6x7-79hv
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Thu, 26 Mar 2020 16:29:40 +0000 (13:29 -0300)]
16266: Adds tests exposing potential XSS vulnerability on escape_javascript()
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Tue, 24 Mar 2020 19:35:38 +0000 (15:35 -0400)]
16138: Remove additional/code references to copying pipelines
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 23 Mar 2020 15:00:07 +0000 (11:00 -0400)]
16138: Remove additional pipelines related code
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Fri, 20 Mar 2020 19:47:00 +0000 (15:47 -0400)]
16138: whitelist fields for arv-copy
Also removed code for copying
PipelineTemplate/PipelineInstance (obsolete jobs API).
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 3 Mar 2020 21:17:38 +0000 (16:17 -0500)]
Remove Gemfile.lock from login-sync
no issue #
To be consistent with sdk/ruby sdk/cli behavior.
There's a circular dependency where the version number of the gem is
embedded in Gemfile.lock, but the version number is derived from the
git commit timestamp, so when it updates Gemfile.lock it creates a new
version, which requires a updating Gemfile.lock, and so on.
However, unlike the Ruby on Rails deb/rpm packages, when we create
gems (dev or production) it does not include Gemfile.lock, so there's
no benefit to having it checked in.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 3 Mar 2020 20:34:05 +0000 (15:34 -0500)]
Ruby gems respect ARVADOS_BUILDING_VERSION
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 27 Feb 2020 18:56:49 +0000 (13:56 -0500)]
Nodemanager and crunchstat-summary sync with pysdk version
refs #16151
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Fri, 28 Feb 2020 17:07:35 +0000 (12:07 -0500)]
16169: Monkey patch load_tool.resolve_and_validate_document to fix bug
There is a bug in upstream cwltool where the version updater needs to
replace the document fragments in the loader index with the updated
ones, but actually it only does it for the root document. Normally we
just fix the bug in upstream but that's challenging because current
cwltool dropped support for Python 2.7 and we're still supporting py2
in Arvados 2.0 (although py2 support will most likely be dropped in
Arvados 2.1). Making a bugfix fork comes with its own
complications (it would need to be added to PyPi) so monkey patching
is the least disruptive fix (and is relatively safe because our
cwltool dependency is pinned to a specific version). This
should be removed as soon as a bugfix goes into upstream cwltool and
we upgrade to it.
Lucas Di Pentima [Wed, 26 Feb 2020 23:58:59 +0000 (20:58 -0300)]
16169: Adds test exposing the requirement propagation bug.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Thu, 27 Feb 2020 17:21:34 +0000 (12:21 -0500)]
16177: Fix tests, test server config now has TrustAllContent: false
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Wed, 26 Feb 2020 20:31:58 +0000 (15:31 -0500)]
16177: Use correct config item Collections.TrustAllContent
Also added fallback error handler, if view or download link doesn't
work, render error text (otherwise you get a very confusing Rails
crash page).
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Wed, 26 Feb 2020 21:12:22 +0000 (16:12 -0500)]
16202: Add Workbench.SSHHelpHostSuffix
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Ward Vandewege [Wed, 26 Feb 2020 18:49:28 +0000 (13:49 -0500)]
Fix web shell.
refs #16203
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@jhvc.com>
Tom Clegg [Tue, 25 Feb 2020 17:14:32 +0000 (12:14 -0500)]
15954: Propagate remote param.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 20 Feb 2020 20:43:50 +0000 (15:43 -0500)]
16101: Redirect logout to Workbench if return_to param missing.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 17 Feb 2020 18:55:27 +0000 (13:55 -0500)]
16101: Handle logout without sso-provider.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Sat, 15 Feb 2020 21:47:34 +0000 (16:47 -0500)]
16100: Move test to integration suite to avoid logging errors.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 14 Feb 2020 18:40:01 +0000 (13:40 -0500)]
16100: Add package dependency for /etc/mime.types.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 14 Feb 2020 18:39:38 +0000 (13:39 -0500)]
16100: Log a warning if /etc/mime.types is missing.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 14 Feb 2020 18:25:30 +0000 (13:25 -0500)]
16100: Test content-type detection.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 13 Feb 2020 07:29:22 +0000 (02:29 -0500)]
16100: Fix bogus timing stats for empty responses.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 13 Feb 2020 02:50:07 +0000 (21:50 -0500)]
16039: Touch python clients so they run tests with the latest SDK.
Otherwise, "pip install" (during "install services/nodemanager", for
example) downgrades the SDK from the current version to the latest
version published on pip, and all test suites run with that version,
instead of the version we think we're testing.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 13 Feb 2020 02:47:44 +0000 (21:47 -0500)]
16039: Install missing python dep.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 12 Feb 2020 18:49:50 +0000 (13:49 -0500)]
16039: Use current python sdk in py3 tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 12 Feb 2020 15:48:05 +0000 (10:48 -0500)]
16039: Fix & add test for sanitized/unsanitized name conflict.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 12 Feb 2020 15:37:48 +0000 (10:37 -0500)]
16039: Accommodate API servers with no config export.
Add more checks in test cases.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 11 Feb 2020 15:58:28 +0000 (10:58 -0500)]
16039: Obey ForwardSlashNameSubstitution config in arv-mount.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Fri, 14 Feb 2020 18:54:08 +0000 (13:54 -0500)]
Tweak upgrade notes
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Fri, 14 Feb 2020 00:22:45 +0000 (19:22 -0500)]
Merge branch '16152-keep-balance-http-crash'
fixes #16152
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 13 Feb 2020 20:58:09 +0000 (15:58 -0500)]
16152: Fix nil http handler and ignored config args.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Wed, 12 Feb 2020 03:37:44 +0000 (22:37 -0500)]
Merge branch '16144-nil-checks' refs #16144
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Tue, 11 Feb 2020 23:14:42 +0000 (20:14 -0300)]
16144: Adds more checks and simplifies nested conditionals.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Tue, 11 Feb 2020 22:22:24 +0000 (19:22 -0300)]
16144: Fixes the bug.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Tue, 11 Feb 2020 22:21:09 +0000 (19:21 -0300)]
16144: Adds tests exposing the bug.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Tue, 11 Feb 2020 17:57:54 +0000 (14:57 -0300)]
Merge branch '16141-gosdk-missing-fields'
Closes #16141
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Tue, 11 Feb 2020 17:10:48 +0000 (14:10 -0300)]
16141: Fixes User type, adjusts fixture to make the test pass.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Tue, 11 Feb 2020 16:41:41 +0000 (13:41 -0300)]
16141: Updates the test to use a different, more complete collection fixture.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Tue, 11 Feb 2020 16:41:17 +0000 (13:41 -0300)]
16141: Fixes GoSDK's Collection type.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Mon, 10 Feb 2020 19:22:07 +0000 (16:22 -0300)]
16141: Fixes test to use the 1st keep_service's uuid the test server returns.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Mon, 10 Feb 2020 18:40:47 +0000 (15:40 -0300)]
16141: Adds better message on test in failing situations.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Tom Clegg [Mon, 10 Feb 2020 18:03:15 +0000 (13:03 -0500)]
Merge branch '15835-metrics-docs'
closes #15835
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Mon, 10 Feb 2020 17:54:49 +0000 (12:54 -0500)]
Pin virtualenv<20
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Mon, 10 Feb 2020 17:41:44 +0000 (14:41 -0300)]
16141: Fixes GoSDK's User type.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Mon, 10 Feb 2020 17:41:10 +0000 (14:41 -0300)]
16141: Expands test for other object types.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Mon, 10 Feb 2020 16:11:26 +0000 (11:11 -0500)]
Set upper version of setuptools for Python 2 in Centos7 container
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 10 Feb 2020 16:09:36 +0000 (11:09 -0500)]
Set upper version of setuptools for Python 2 support
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Mon, 10 Feb 2020 15:41:12 +0000 (12:41 -0300)]
16141: Fixes Collection type on Go SDK. Adjusts test.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Mon, 10 Feb 2020 15:14:05 +0000 (10:14 -0500)]
Merge branch '16139-cwl-secondaryfiles-fix'
fixes #16139
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 10 Feb 2020 15:13:07 +0000 (10:13 -0500)]
Annotate notify uses localStorage instead of sessionStorage
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Sun, 9 Feb 2020 23:07:15 +0000 (18:07 -0500)]
16139: Add test
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Fri, 7 Feb 2020 23:40:51 +0000 (20:40 -0300)]
16141: Adds missing collection fields to GoSDK.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Lucas Di Pentima [Fri, 7 Feb 2020 23:40:17 +0000 (20:40 -0300)]
16141: Exposes the bug.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Fri, 7 Feb 2020 20:59:10 +0000 (15:59 -0500)]
16139: Fix secondaryFile errors when running --submit --no-wait
When submitting, we want to preserve the original CWL version of the
document.
However, when it creates a RunnerContainer (a cwltool.Process) it
examines the input interface and expects it to be in the 1.1 data
model. But if we preserve/reload the original document, it is still
in the 1.0 data model. This causes
The code was deliberately overriding the CWL version in metadata to
make this work. This results in the problem reported on this ticket.
The fix is to maintain both the updated and preserved documents, and
use them appropriately where they are expected.
refs #16139
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Fri, 7 Feb 2020 21:07:06 +0000 (16:07 -0500)]
15835: Update metrics docs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Fri, 7 Feb 2020 16:36:53 +0000 (11:36 -0500)]
Add note that some services require a minimal config.yml to start.
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
projects / arvados.git / log