arvados.git
4 years agoPin jssha to 2.4.2
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>

4 years ago16263: Add test for BypassFederation
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>

4 years ago16263: Pulls from official git repo when running federation tests.
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>

4 years ago16263: User migration test also checks federated user behavior
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>

4 years ago16263: Tweak federation tests, use CWL 1.1
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>

4 years ago16263: Add bypass_federation test
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>

4 years ago16263: Fix no_federation -> bypass_federation in boolParms
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>

4 years ago16263: Fix only_admin_can_bypass_federation
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>

4 years ago16263: Missed rename
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>

4 years ago16263: Rename no_federation -> bypass_federation
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>

4 years ago16263: Add no_federation to user update
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>

4 years ago16263: local_user_list -> no_federation in boolParams
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>

4 years ago16263: Generalize "local_user_list" flag to "no_federation"
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>

4 years ago16263: UserMerge shouldn't be federated
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>

4 years ago16263: Fix omitempty placement
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>

4 years ago16263: Add omitempty to GetOptions
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>

4 years ago16263: Add local_user_list to boolParams
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>

4 years ago16263: Add local_user_list flag to bypass LoginCluster behavior
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>

4 years ago16263: Decodes JSON numbers as strings instead of float64.
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>

4 years ago16263: Adds unit test case confirming 'limit' bug.
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>

4 years ago16263: Adds test exposing a bug when using 'limit' with the max int64 value.
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>

4 years ago16263: Bool filter bug fix.
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>

4 years ago16263: Adds test exposing a bug on filter unmarshalling.
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>

4 years ago16263: Makes gofmt happy.
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>

4 years ago16263: Don't cache modified_by_*_uuid fields when using LoginCluster.
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>

4 years ago16263: Adds nullify behavior to users's batch_update endpoint.
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>

4 years ago16263: Assigns nil to select attributes when receiving empty values.
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>

4 years agoFix tests.
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>

4 years agodocumentation: update descriptions for MaxKeepBlobBuffers and MaxConcurrentRequests
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>

4 years agoWarn if MaxKeepBlobBuffers > MaxConcurrentRequests.
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>

4 years ago16219: Test populated container fields.
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>

4 years ago16219: Load all fields needed to compute node size.
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>

4 years ago16221: Fix test for config endpoint.
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>

4 years agoFix instance IDs in arvados-dispatch-cloud log messages.
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>

4 years ago16270: Fill in missing scratch fields on InstanceType entries.
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>

4 years agoBump rake from 12.3.2 to 13.0.1 in /services/api
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>
4 years agoBump rake from 12.3.2 to 13.0.1 in /apps/workbench
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>
4 years agoBump nokogiri from 1.10.4 to 1.10.8 in /apps/workbench
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>
4 years agoBump loofah from 2.2.3 to 2.3.1 in /apps/workbench
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>
4 years agoBump nokogiri from 1.10.2 to 1.10.8 in /services/api
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>
4 years ago16266: Applies monkeypatch to fix CVE-2020-5267 on workbench1.
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>

4 years ago16266: Adds tests exposing potential XSS vulnerability on escape_javascript()
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>

4 years ago16138: Remove additional/code references to copying pipelines
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>

4 years ago16138: Remove additional pipelines related code
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>

4 years ago16138: whitelist fields for arv-copy
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>

4 years agoRemove Gemfile.lock from login-sync 2.0.1
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>

4 years agoRuby gems respect ARVADOS_BUILDING_VERSION
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>

4 years agoNodemanager and crunchstat-summary sync with pysdk version
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>

4 years ago16169: Monkey patch load_tool.resolve_and_validate_document to fix bug
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.

4 years ago16169: Adds test exposing the requirement propagation bug.
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>

4 years ago16177: Fix tests, test server config now has TrustAllContent: false
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>

4 years ago16177: Use correct config item Collections.TrustAllContent
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>

4 years ago16202: Add Workbench.SSHHelpHostSuffix
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>

4 years agoFix web shell.
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>

4 years ago15954: Propagate remote param.
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>

4 years ago16101: Redirect logout to Workbench if return_to param missing.
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>

4 years ago16101: Handle logout without sso-provider.
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>

4 years ago16100: Move test to integration suite to avoid logging errors.
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>

4 years ago16100: Add package dependency for /etc/mime.types.
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>

4 years ago16100: Log a warning if /etc/mime.types is missing.
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>

4 years ago16100: Test content-type detection.
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>

4 years ago16100: Fix bogus timing stats for empty responses.
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>

4 years ago16039: Touch python clients so they run tests with the latest SDK.
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>

4 years ago16039: Install missing python dep.
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>

4 years ago16039: Use current python sdk in py3 tests.
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>

4 years ago16039: Fix & add test for sanitized/unsanitized name conflict.
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>

4 years ago16039: Accommodate API servers with no config export.
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>

4 years ago16039: Obey ForwardSlashNameSubstitution config in arv-mount.
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>

4 years agoTweak upgrade notes
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>

4 years agoMerge branch '16152-keep-balance-http-crash' 2.0.0
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>

4 years ago16152: Fix nil http handler and ignored config args.
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>

4 years agoMerge branch '16144-nil-checks' refs #16144
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>

4 years ago16144: Adds more checks and simplifies nested conditionals.
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>

4 years ago16144: Fixes the bug.
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>

4 years ago16144: Adds tests exposing the bug.
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>

4 years agoMerge branch '16141-gosdk-missing-fields'
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>

4 years ago16141: Fixes User type, adjusts fixture to make the test pass.
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>

4 years ago16141: Updates the test to use a different, more complete collection fixture.
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>

4 years ago16141: Fixes GoSDK's Collection type.
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>

4 years ago16141: Fixes test to use the 1st keep_service's uuid the test server returns.
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>

4 years ago16141: Adds better message on test in failing situations.
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>

4 years agoMerge branch '15835-metrics-docs'
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>

4 years agoPin virtualenv<20
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>

4 years ago16141: Fixes GoSDK's User type.
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>

4 years ago16141: Expands test for other object types.
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>

4 years agoSet upper version of setuptools for Python 2 in Centos7 container
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>

4 years agoSet upper version of setuptools for Python 2 support
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>

4 years ago16141: Fixes Collection type on Go SDK. Adjusts test.
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>

4 years agoMerge branch '16139-cwl-secondaryfiles-fix'
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>

4 years agoAnnotate notify uses localStorage instead of sessionStorage
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>

4 years ago16139: Add test
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>

4 years ago16141: Adds missing collection fields to GoSDK.
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>

4 years ago16141: Exposes the bug.
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>

4 years ago16139: Fix secondaryFile errors when running --submit --no-wait
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>

4 years ago15835: Update metrics docs.
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>

4 years agoAdd note that some services require a minimal config.yml to start.
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>

4 years agoImprove readability of upgrade notes
Peter Amstutz [Thu, 6 Feb 2020 22:36:12 +0000 (17:36 -0500)]
Improve readability of upgrade notes

no issue #

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

4 years agoMerge branch '16133-federation-loop'
Tom Clegg [Thu, 6 Feb 2020 19:59:07 +0000 (14:59 -0500)]
Merge branch '16133-federation-loop'

fixes #16133

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

4 years ago16133: Don't take multiple federation hops.
Tom Clegg [Thu, 6 Feb 2020 19:16:55 +0000 (14:16 -0500)]
16133: Don't take multiple federation hops.

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

4 years agoMerge branch '16136-original-owner' closes #16136
Peter Amstutz [Thu, 6 Feb 2020 17:25:54 +0000 (12:25 -0500)]
Merge branch '16136-original-owner' closes #16136

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