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>
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>
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>
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>
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>
Peter Amstutz [Thu, 6 Feb 2020 16:42:59 +0000 (11:42 -0500)]
16136: Prioritize 'Function' over 'Value' and ignore null
Because arvados-server config-dump will emit "Value: null" even if the
original config file didn't provide it.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Thu, 6 Feb 2020 16:09:32 +0000 (11:09 -0500)]
16133: Don't take multiple hops when getting collections.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 6 Feb 2020 15:45:48 +0000 (10:45 -0500)]
16133: Avoid cycle between old and new controllers.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 6 Feb 2020 15:19:04 +0000 (10:19 -0500)]
16133: Avoid cycle when searching federation for PDH.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Wed, 5 Feb 2020 18:33:02 +0000 (13:33 -0500)]
Add a note to the install section
Add note that you should look in the SDKs section for client tools.
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Tue, 4 Feb 2020 14:43:36 +0000 (09:43 -0500)]
Merge branch '16111-ssh-help' closes #16111
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Mon, 3 Feb 2020 22:04:16 +0000 (17:04 -0500)]
Merge branch '16104-select-uuid'
refs #16104
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Peter Amstutz [Mon, 3 Feb 2020 21:02:36 +0000 (16:02 -0500)]
16111: Add SSHHelpPageHTML so admin can provide custom instructions
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Tom Clegg [Mon, 3 Feb 2020 20:28:04 +0000 (15:28 -0500)]
16104: Don't impose federated query limitations on local-only query.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Ward Vandewege [Mon, 3 Feb 2020 19:39:20 +0000 (14:39 -0500)]
In our systemd service files, set a reasonable default for the open file
limit (65536).
refs #16089
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@jhvc.com>
Peter Amstutz [Mon, 3 Feb 2020 19:35:42 +0000 (14:35 -0500)]
Merge branch '16108-favorites' refs #16108
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 3 Feb 2020 19:34:53 +0000 (14:34 -0500)]
16108: Use zzzzz- in examples
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Sun, 2 Feb 2020 17:58:16 +0000 (12:58 -0500)]
16108: Change wb1 'favorites' to filter on user_uuid instead of tail_uuid
Fixes potential exploit by which a malicious user could inject
favorites into another user's favorites list.
Public favorites owned by "All Users" will now appear in wb1.
Move documentation about 'star' links from admin section to API
documentation.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Ward Vandewege [Sun, 2 Feb 2020 15:55:17 +0000 (10:55 -0500)]
Update maintainer and vendor for our OS packages.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@jhvc.com>
Peter Amstutz [Thu, 30 Jan 2020 23:28:41 +0000 (18:28 -0500)]
Workbench 2 isn't really beta if we're telling people to use it.
refs #16015
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 30 Jan 2020 23:17:43 +0000 (18:17 -0500)]
Update more documentation for new config file, add 'group favorites'
refs #16015
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 30 Jan 2020 21:57:08 +0000 (16:57 -0500)]
Workbench1 package depends on graphviz
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Thu, 30 Jan 2020 19:52:17 +0000 (16:52 -0300)]
Adds information about the new vocabulary format on the release notes.
No issue #
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Thu, 30 Jan 2020 18:00:31 +0000 (13:00 -0500)]
Pin bundler to version compatible with all Rubies we support
refs #16015
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Thu, 30 Jan 2020 15:50:38 +0000 (10:50 -0500)]
Update text to refer to Arvados 2.0
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Tue, 28 Jan 2020 22:06:50 +0000 (19:06 -0300)]
Merge branch '15902-slow-query'
Closes #15902
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Tom Clegg [Tue, 28 Jan 2020 20:05:02 +0000 (15:05 -0500)]
15902: Adjust order to avoid poorly optimized query.
When many requesting_container_uuid values are passed in this query,
the default order (["modified_at desc", "uuid"]) sometimes causes
PostgreSQL to begin with the timestamp index, which results in a slow
query. The requesting_container_uuid index makes the query much
faster.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Lucas Di Pentima [Tue, 28 Jan 2020 18:51:35 +0000 (15:51 -0300)]
Merge branch '15944-arvbox-publicdev-fix'
Closes #15944
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Mon, 27 Jan 2020 23:05:23 +0000 (18:05 -0500)]
arvados/jobs image uses python3 for arvados-cwl-runner
This avoids the deprecation warning from cwltool.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Mon, 27 Jan 2020 18:31:49 +0000 (13:31 -0500)]
Add python3 build of arvados-cwl-runner
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Fri, 24 Jan 2020 22:22:06 +0000 (19:22 -0300)]
15944: Takes arvbox container's default gw IP as internal client.
This makes Keep work on 'publicdev' mode.
Also, turns off nginx's response caching for easier debugging.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas@di-pentima.com.ar>
Peter Amstutz [Fri, 24 Jan 2020 20:22:48 +0000 (15:22 -0500)]
Add a bit more discussion about DNS on compute node images closes #16085
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Peter Amstutz [Fri, 24 Jan 2020 16:36:30 +0000 (11:36 -0500)]
Use updated run_upload_packages
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Lucas Di Pentima [Fri, 24 Jan 2020 14:41:05 +0000 (11:41 -0300)]
15944: Merge branch 'master' into 15944-arvbox-publicdev-fix
Peter Amstutz [Thu, 23 Jan 2020 22:09:59 +0000 (17:09 -0500)]
Fix setting workflow label field from record name fixes #16083
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
projects / arvados.git / log