arvados.git
5 years ago15340: Skip metrics update when running tests with no registry.
Tom Clegg [Fri, 14 Jun 2019 20:52:36 +0000 (16:52 -0400)]
15340: Skip metrics update when running tests with no registry.

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

5 years ago15340: Add metrics for cloud ops/errors and instance disappearances.
Tom Clegg [Fri, 14 Jun 2019 19:27:30 +0000 (15:27 -0400)]
15340: Add metrics for cloud ops/errors and instance disappearances.

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

5 years agoMerge branch '15000-config-api'
Tom Clegg [Fri, 14 Jun 2019 18:28:49 +0000 (14:28 -0400)]
Merge branch '15000-config-api'

refs #15000

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

5 years ago15000: Recommend checking config publication errors during install.
Tom Clegg [Fri, 14 Jun 2019 18:21:18 +0000 (14:21 -0400)]
15000: Recommend checking config publication errors during install.

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

5 years agoMerge branch '15368-python-deps' closes #15368
Peter Amstutz [Fri, 14 Jun 2019 17:35:51 +0000 (13:35 -0400)]
Merge branch '15368-python-deps' closes #15368

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

5 years ago15368: Don't require git to install arvados-python-client
Peter Amstutz [Fri, 14 Jun 2019 17:10:57 +0000 (13:10 -0400)]
15368: Don't require git to install arvados-python-client

It was catching CalledProcessError but if git is not installed the
error is actually OSError.

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

5 years ago15368: Change doc references from "arv keep put/get" to "arv-put/get"
Peter Amstutz [Fri, 14 Jun 2019 17:07:17 +0000 (13:07 -0400)]
15368: Change doc references from "arv keep put/get" to "arv-put/get"

Since the "arv" frontend just adds overhead and requires installing
both ruby and python SDK instead of just the python sdk.

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

5 years ago15368: Add note about debian dependencies for installing from pip
Peter Amstutz [Fri, 14 Jun 2019 17:06:08 +0000 (13:06 -0400)]
15368: Add note about debian dependencies for installing from pip

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

5 years ago15000: Update test.
Tom Clegg [Thu, 13 Jun 2019 21:03:50 +0000 (17:03 -0400)]
15000: Update test.

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

5 years ago15000: Move exported config threshold to "needed by clients".
Tom Clegg [Thu, 13 Jun 2019 19:46:01 +0000 (15:46 -0400)]
15000: Move exported config threshold to "needed by clients".

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

5 years ago15000: Remove example image ID.
Tom Clegg [Thu, 13 Jun 2019 19:45:38 +0000 (15:45 -0400)]
15000: Remove example image ID.

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

5 years agoMerge branch '15332-fed-demo' refs #15332
Peter Amstutz [Thu, 13 Jun 2019 19:14:46 +0000 (15:14 -0400)]
Merge branch '15332-fed-demo' refs #15332

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

5 years ago15332: Updated federation demo to do something a little more interesting.
Peter Amstutz [Mon, 10 Jun 2019 21:25:17 +0000 (17:25 -0400)]
15332: Updated federation demo to do something a little more interesting.

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

5 years agoMerge branch '15003-config-default-location'
Tom Clegg [Thu, 13 Jun 2019 14:25:35 +0000 (10:25 -0400)]
Merge branch '15003-config-default-location'

refs #15003

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

5 years ago15000: Include bad value in error message.
Tom Clegg [Thu, 13 Jun 2019 13:32:02 +0000 (09:32 -0400)]
15000: Include bad value in error message.

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

5 years ago15003: Load config from default location or -config arg, not stdin.
Tom Clegg [Wed, 12 Jun 2019 20:27:07 +0000 (16:27 -0400)]
15003: Load config from default location or -config arg, not stdin.

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

5 years agoMerge branch '15138-version-our-documentation'
Ward Vandewege [Wed, 12 Jun 2019 18:02:08 +0000 (14:02 -0400)]
Merge branch '15138-version-our-documentation'

refs #15138

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

5 years ago15138: Include logic to support building multiple versions of our documentation.
Ward Vandewege [Tue, 11 Jun 2019 17:42:40 +0000 (13:42 -0400)]
15138: Include logic to support building multiple versions of our documentation.

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

5 years agoMerge branch '14930-arvput-trash-at'
Lucas Di Pentima [Tue, 11 Jun 2019 19:13:19 +0000 (16:13 -0300)]
Merge branch '14930-arvput-trash-at'
Closes #14930

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

5 years agoTest setUp sets cwltool global names set used to ensure unique names
Peter Amstutz [Tue, 11 Jun 2019 18:08:26 +0000 (14:08 -0400)]
Test setUp sets cwltool global names set used to ensure unique names

no issue #

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

5 years agoMerge branch '15350-pysdk-cookbook-recipe'
Lucas Di Pentima [Tue, 11 Jun 2019 18:49:16 +0000 (15:49 -0300)]
Merge branch '15350-pysdk-cookbook-recipe'
Closes #15350

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

5 years ago15350: Simplifies recipe code.
Lucas Di Pentima [Tue, 11 Jun 2019 18:32:15 +0000 (15:32 -0300)]
15350: Simplifies recipe code.

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

5 years ago15138: Show the TM notice a little bit higher.
Ward Vandewege [Mon, 10 Jun 2019 14:41:22 +0000 (10:41 -0400)]
15138: Show the TM notice a little bit higher.

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

5 years ago15350: Adds PySDK recipe to get a container request's state.
Lucas Di Pentima [Tue, 11 Jun 2019 16:55:34 +0000 (13:55 -0300)]
15350: Adds PySDK recipe to get a container request's state.

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

5 years ago15350: Fixes unnecessary api client instantiations on examples.
Lucas Di Pentima [Tue, 11 Jun 2019 16:49:16 +0000 (13:49 -0300)]
15350: Fixes unnecessary api client instantiations on examples.

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

5 years agoMerge branch 'master' into 14930-arvput-trash-at
Lucas Di Pentima [Mon, 10 Jun 2019 23:15:23 +0000 (20:15 -0300)]
Merge branch 'master' into 14930-arvput-trash-at

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

5 years ago14930: Don't ignore DST settings.
Lucas Di Pentima [Mon, 10 Jun 2019 22:44:47 +0000 (19:44 -0300)]
14930: Don't ignore DST settings.

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

5 years agoFix whitespace for gofmt 1.12.
Tom Clegg [Mon, 10 Jun 2019 20:12:51 +0000 (16:12 -0400)]
Fix whitespace for gofmt 1.12.

No issue #

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

5 years agoMerge branch '15028-fix-tests' refs #15028
Peter Amstutz [Mon, 10 Jun 2019 18:10:36 +0000 (14:10 -0400)]
Merge branch '15028-fix-tests' refs #15028

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

5 years ago15028: Fix test
Peter Amstutz [Mon, 10 Jun 2019 18:09:56 +0000 (14:09 -0400)]
15028: Fix test

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

5 years agoMerge branch '14946-ruby-2.5'
Lucas Di Pentima [Mon, 10 Jun 2019 17:46:52 +0000 (14:46 -0300)]
Merge branch '14946-ruby-2.5'
Refs #14946

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

5 years agoMerge branch 'master' into 14946-ruby-2.5
Lucas Di Pentima [Mon, 10 Jun 2019 17:45:54 +0000 (14:45 -0300)]
Merge branch 'master' into 14946-ruby-2.5

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

5 years ago15028: Make sure tests use a version that supports CWL v1.1
Peter Amstutz [Mon, 10 Jun 2019 15:37:12 +0000 (11:37 -0400)]
15028: Make sure tests use a version that supports CWL v1.1

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

5 years ago15028: Bump cwltool version for bugfix.
Peter Amstutz [Fri, 7 Jun 2019 19:27:05 +0000 (15:27 -0400)]
15028: Bump cwltool version for bugfix.

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

5 years agoMake debian9 the default target for our package building scripts.
Ward Vandewege [Fri, 7 Jun 2019 18:12:38 +0000 (14:12 -0400)]
Make debian9 the default target for our package building scripts.

No issue #

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

5 years ago15000: Add Workbench configs.
Tom Clegg [Thu, 6 Jun 2019 21:08:23 +0000 (17:08 -0400)]
15000: Add Workbench configs.

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

5 years ago15000: Accept byte size suffixes (KB, KiB, ...) for numeric configs.
Tom Clegg [Thu, 6 Jun 2019 20:03:10 +0000 (16:03 -0400)]
15000: Accept byte size suffixes (KB, KiB, ...) for numeric configs.

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

5 years ago15000: Accept negative durations in config, fix crashing error log.
Tom Clegg [Thu, 6 Jun 2019 20:02:35 +0000 (16:02 -0400)]
15000: Accept negative durations in config, fix crashing error log.

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

5 years ago15000: Ensure all config defaults are captured in config struct.
Tom Clegg [Thu, 6 Jun 2019 17:44:23 +0000 (13:44 -0400)]
15000: Ensure all config defaults are captured in config struct.

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

5 years ago15000: Export safe parts of cluster config at /arvados/v1/config.
Tom Clegg [Thu, 6 Jun 2019 14:54:26 +0000 (10:54 -0400)]
15000: Export safe parts of cluster config at /arvados/v1/config.

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

5 years ago14930: Adds expiration notice in local time at the end of the run.
Lucas Di Pentima [Fri, 7 Jun 2019 16:27:22 +0000 (13:27 -0300)]
14930: Adds expiration notice in local time at the end of the run.

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

5 years ago14930: Assumes end-of-day datetime when --trash-at YYYY-MM-DD only.
Lucas Di Pentima [Fri, 7 Jun 2019 15:00:15 +0000 (12:00 -0300)]
14930: Assumes end-of-day datetime when --trash-at YYYY-MM-DD only.

Also:
* Refuses day-less dates on --trash-at
* Enhances readability on utc offset usage
* Adds tests

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

5 years agoarvbox certificates should be valid for 1 year not 30 days. no issue #
Peter Amstutz [Fri, 7 Jun 2019 14:59:17 +0000 (10:59 -0400)]
arvbox certificates should be valid for 1 year not 30 days. no issue #

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

5 years agoMerge branch '15311-api-no-colons' refs #15311
Peter Amstutz [Fri, 7 Jun 2019 14:41:23 +0000 (10:41 -0400)]
Merge branch '15311-api-no-colons' refs #15311

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

5 years ago15311: Remove stringify-symbol behavior on database load
Peter Amstutz [Thu, 6 Jun 2019 15:36:34 +0000 (11:36 -0400)]
15311: Remove stringify-symbol behavior on database load

* Add test case demonstrating bug

* Remove convert_serialized_symbols_to_strings hook

* Add "rake symbols:check" to warn you if there are any serialized
columns that may have legacy symbols.

* Add "rake symbols:stringify" to warn you if there are any serialized
columns that may have legacy symbols.

* Add release notes for checking and stringifying symbols.

* Add table of contents to upgrading doc page.

* Add note about the has_symbol_keys_in_database_somehow fixture.

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

5 years agoMake sdk/cli testable in interactive mode.
Ward Vandewege [Fri, 7 Jun 2019 01:26:27 +0000 (21:26 -0400)]
Make sdk/cli testable in interactive mode.

No issue #

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

5 years agoFix the build by disabling an old crunch-job (jobs api) test that now
Ward Vandewege [Fri, 7 Jun 2019 01:16:30 +0000 (21:16 -0400)]
Fix the build by disabling an old crunch-job (jobs api) test that now
depends on the presence of a post 1.3 version of the
python-arvados-python-client package being present.

refs #9945

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

5 years agoMerge branch '15306-api-nonjson-params'
Lucas Di Pentima [Thu, 6 Jun 2019 17:37:49 +0000 (14:37 -0300)]
Merge branch '15306-api-nonjson-params'
Closes #15306

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

5 years ago15306: Adds warning log message when parameter isn't boolean.
Lucas Di Pentima [Thu, 6 Jun 2019 16:55:19 +0000 (13:55 -0300)]
15306: Adds warning log message when parameter isn't boolean.

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

5 years ago15306: Moves include_trash param declaration to the controller.
Lucas Di Pentima [Thu, 6 Jun 2019 16:48:47 +0000 (13:48 -0300)]
15306: Moves include_trash param declaration to the controller.

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

5 years ago15306: Adds include_trash param definition to container requests.
Lucas Di Pentima [Thu, 6 Jun 2019 12:44:31 +0000 (09:44 -0300)]
15306: Adds include_trash param definition to container requests.

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

5 years agoCorrect the release date for 1.4.0 in our documentation.
Ward Vandewege [Wed, 5 Jun 2019 20:59:37 +0000 (16:59 -0400)]
Correct the release date for 1.4.0 in our documentation.

No issue #

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

5 years ago15306: Fixes tests to POST form & json encoded params.
Lucas Di Pentima [Wed, 5 Jun 2019 20:52:48 +0000 (17:52 -0300)]
15306: Fixes tests to POST form & json encoded params.

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

5 years ago15306: Don't interpret include_trash="false" as include_trash=true.
Lucas Di Pentima [Wed, 5 Jun 2019 19:59:29 +0000 (16:59 -0300)]
15306: Don't interpret include_trash="false" as include_trash=true.

The same goes to include_old_versions params at find_objects_for_index().
If any of those params aren't declared as boolean, assume false.

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

5 years agoMerge branch '9945-crunch-job-python-path'
Ward Vandewege [Wed, 5 Jun 2019 17:53:28 +0000 (13:53 -0400)]
Merge branch '9945-crunch-job-python-path'

refs #9945

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

5 years agoCrunch-job needs to call the python executable from our sdk package for
Ward Vandewege [Wed, 5 Jun 2019 16:49:27 +0000 (12:49 -0400)]
Crunch-job needs to call the python executable from our sdk package for
collating job output.

refs #9945

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

5 years ago15306: Fixes issue on groups controller.
Lucas Di Pentima [Wed, 5 Jun 2019 13:08:10 +0000 (10:08 -0300)]
15306: Fixes issue on groups controller.

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

5 years ago15306: Adds similar test to groups, exposing the same issue as collections.
Lucas Di Pentima [Wed, 5 Jun 2019 13:07:44 +0000 (10:07 -0300)]
15306: Adds similar test to groups, exposing the same issue as collections.

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

5 years ago15306: Fixes the bug.
Lucas Di Pentima [Tue, 4 Jun 2019 23:34:21 +0000 (20:34 -0300)]
15306: Fixes the bug.

The problem was coming from 2 sides:

1) The collections#show action didn't have the required parameters definitions.
2) The load_required_parameters callback was being called after the object
   lookup callback.

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

5 years ago15306: Adds more test cases confirming the issue is encoding independent.
Lucas Di Pentima [Tue, 4 Jun 2019 23:32:13 +0000 (20:32 -0300)]
15306: Adds more test cases confirming the issue is encoding independent.

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

5 years ago15306: Removes trailing slash on test.
Lucas Di Pentima [Tue, 4 Jun 2019 19:36:19 +0000 (16:36 -0300)]
15306: Removes trailing slash on test.

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

5 years ago15306: Adds testing on collections#show that expose the bug.
Lucas Di Pentima [Tue, 4 Jun 2019 19:30:01 +0000 (16:30 -0300)]
15306: Adds testing on collections#show that expose the bug.

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

5 years ago15306: Don't check for empty responses now that we use a filter.
Lucas Di Pentima [Tue, 4 Jun 2019 18:23:47 +0000 (15:23 -0300)]
15306: Don't check for empty responses now that we use a filter.

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

5 years ago15306: Avoid paging in query string tests, too.
Tom Clegg [Tue, 4 Jun 2019 18:08:34 +0000 (14:08 -0400)]
15306: Avoid paging in query string tests, too.

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

5 years ago15306: Adjust tests: check ?include_trash= and avoid paging.
Tom Clegg [Tue, 4 Jun 2019 18:02:02 +0000 (14:02 -0400)]
15306: Adjust tests: check ?include_trash= and avoid paging.

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

5 years ago15306: Adds integration tests with query string & form encoded params.
Lucas Di Pentima [Tue, 4 Jun 2019 17:39:21 +0000 (14:39 -0300)]
15306: Adds integration tests with query string & form encoded params.

Specifically testing include_trash on collections.

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

5 years agoMerge branch '15028-cwl-v1.1' refs #15028
Peter Amstutz [Tue, 4 Jun 2019 17:20:24 +0000 (13:20 -0400)]
Merge branch '15028-cwl-v1.1' refs #15028

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

5 years ago14930: Adds trash_at syncing when updating a collection with '--trash-after N'
Lucas Di Pentima [Tue, 4 Jun 2019 13:37:49 +0000 (10:37 -0300)]
14930: Adds trash_at syncing when updating a collection with '--trash-after N'

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

5 years agoMerge branch '15003-duration-format'
Tom Clegg [Tue, 4 Jun 2019 13:28:04 +0000 (09:28 -0400)]
Merge branch '15003-duration-format'

refs #15003

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

5 years ago14930: Fixes utc offset calculation when naive datetime provided & adds tests.
Lucas Di Pentima [Tue, 4 Jun 2019 12:34:53 +0000 (09:34 -0300)]
14930: Fixes utc offset calculation when naive datetime provided & adds tests.

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

5 years ago15028: Update to latest cwltool.
Peter Amstutz [Mon, 3 Jun 2019 21:08:19 +0000 (17:08 -0400)]
15028: Update to latest cwltool.

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

5 years agoMerge branch '15286-fixes'
Ward Vandewege [Mon, 3 Jun 2019 20:51:19 +0000 (16:51 -0400)]
Merge branch '15286-fixes'

Fixes from the 1.4 branch.

refs #15286

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

5 years ago14930: Removes unused variable assignments on tests.
Lucas Di Pentima [Mon, 3 Jun 2019 20:42:07 +0000 (17:42 -0300)]
14930: Removes unused variable assignments on tests.

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

5 years agoDo not blow up when Rails.configuration.Users.UserProfileNotificationAddress is
Ward Vandewege [Mon, 3 Jun 2019 19:14:37 +0000 (15:14 -0400)]
Do not blow up when Rails.configuration.Users.UserProfileNotificationAddress is
set to the empty string, which is the default since #13996 (it defaulted to a
dummy e-mail adress before).

refs #15286
refs #13996

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

5 years agoUpdate the 'upgrading' documentation to reflect the v1.4.0 release, and warn
Ward Vandewege [Fri, 31 May 2019 19:42:37 +0000 (15:42 -0400)]
Update the 'upgrading' documentation to reflect the v1.4.0 release, and warn
about the db migration that can take some time during upgrade.

refs #15093

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

5 years agoAddress review comments.
Ward Vandewege [Fri, 31 May 2019 19:27:38 +0000 (15:27 -0400)]
Address review comments.

refs #15093

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

5 years agoMove the population of the new columns on the collections table to a standalone
Ward Vandewege [Fri, 31 May 2019 18:51:50 +0000 (14:51 -0400)]
Move the population of the new columns on the collections table to a standalone
script that should be run separate from the migration. Add a note to the
upgrade documentation along those lines. Make the script not blow up on
collections with invalid manifests, but rather just skip them.

refs #15093
refs #14484

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

5 years ago14930: Assumes timezone-less provided trash datetimes as local.
Lucas Di Pentima [Mon, 3 Jun 2019 19:28:06 +0000 (16:28 -0300)]
14930: Assumes timezone-less provided trash datetimes as local.

Depending of the local system's clock setting, it makes the necessary
correction to express it as UTC.
Also, provides examples on the command's help output.

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

5 years agoMerge branch '14931-custom-tags'
Tom Clegg [Mon, 3 Jun 2019 18:59:56 +0000 (14:59 -0400)]
Merge branch '14931-custom-tags'

closes #14931

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

5 years ago14930: Moves the trash_at compute logic into its own method.
Lucas Di Pentima [Mon, 3 Jun 2019 17:05:46 +0000 (14:05 -0300)]
14930: Moves the trash_at compute logic into its own method.

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

5 years ago14931: Change default tag prefix to "Arvados".
Tom Clegg [Mon, 3 Jun 2019 15:58:55 +0000 (11:58 -0400)]
14931: Change default tag prefix to "Arvados".

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

5 years ago14930: Adds --trash-at & --trash-after arguments to arv-put (WIP)
Lucas Di Pentima [Fri, 31 May 2019 21:40:43 +0000 (18:40 -0300)]
14930: Adds --trash-at & --trash-after arguments to arv-put (WIP)

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

5 years ago15003: Format durations as "336h", not "336h0m0s".
Tom Clegg [Fri, 31 May 2019 20:15:05 +0000 (16:15 -0400)]
15003: Format durations as "336h", not "336h0m0s".

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

5 years ago14931: Pass custom tags to cloud driver for shared resources.
Tom Clegg [Thu, 30 May 2019 14:49:57 +0000 (10:49 -0400)]
14931: Pass custom tags to cloud driver for shared resources.

Neither driver uses them yet: the only shared resources being created
are AWS key pairs, which don't support tags.

https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/Using_Tags.html

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

5 years ago14931: Add configurable prefix for built-in tags.
Tom Clegg [Thu, 30 May 2019 14:13:07 +0000 (10:13 -0400)]
14931: Add configurable prefix for built-in tags.

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

5 years ago14931: Tag and filter instances by SetID, so driver doesn't need to.
Tom Clegg [Wed, 29 May 2019 20:01:36 +0000 (16:01 -0400)]
14931: Tag and filter instances by SetID, so driver doesn't need to.

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

5 years ago14931: Support extra tags on resources created by dispatchcloud.
Tom Clegg [Tue, 28 May 2019 19:39:11 +0000 (15:39 -0400)]
14931: Support extra tags on resources created by dispatchcloud.

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

5 years agoMerge branch '15003-new-config-struct'
Tom Clegg [Fri, 31 May 2019 17:54:57 +0000 (13:54 -0400)]
Merge branch '15003-new-config-struct'

refs #15003

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

5 years ago15003: Merge branch 'master'
Tom Clegg [Fri, 31 May 2019 17:54:10 +0000 (13:54 -0400)]
15003: Merge branch 'master'

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

5 years ago15003: Update doc comment on Map, and use it in lib/service.
Tom Clegg [Fri, 31 May 2019 17:28:03 +0000 (13:28 -0400)]
15003: Update doc comment on Map, and use it in lib/service.

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

5 years ago15028: Fix bashism
Peter Amstutz [Fri, 31 May 2019 16:04:18 +0000 (12:04 -0400)]
15028: Fix bashism

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

5 years ago15028: Move 'conformance' default to v1.0 fallback
Peter Amstutz [Fri, 31 May 2019 15:53:41 +0000 (11:53 -0400)]
15028: Move 'conformance' default to v1.0 fallback

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

5 years ago15028: 'conformance' changed to 'conformance-v1.0'
Peter Amstutz [Fri, 31 May 2019 15:30:48 +0000 (11:30 -0400)]
15028: 'conformance' changed to 'conformance-v1.0'

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

5 years ago15028: Fix test on python3. Add conformance-v1.1 to run_in_arvbox suites.
Peter Amstutz [Fri, 31 May 2019 15:28:21 +0000 (11:28 -0400)]
15028: Fix test on python3.  Add conformance-v1.1 to run_in_arvbox suites.

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

5 years ago15028: Fix tests
Peter Amstutz [Thu, 30 May 2019 21:05:29 +0000 (17:05 -0400)]
15028: Fix tests

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

5 years ago14946: Removes shadowed Collection.uuid method as it isn't being used.
Lucas Di Pentima [Thu, 30 May 2019 20:44:53 +0000 (17:44 -0300)]
14946: Removes shadowed Collection.uuid method as it isn't being used.

Ruby 2.5 started to warn about this method being redefined at
ArvadosBase.columns

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

5 years agoFix syntax for python3.
Tom Clegg [Thu, 30 May 2019 18:25:23 +0000 (14:25 -0400)]
Fix syntax for python3.

refs #14964

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

5 years ago14946: Fixes Fixnum deprecation warning.
Lucas Di Pentima [Thu, 30 May 2019 16:48:52 +0000 (13:48 -0300)]
14946: Fixes Fixnum deprecation warning.

See https://bugs.ruby-lang.org/issues/12005

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

5 years ago14946: Fixes warnings related to uninitialized instance variables, and others.
Lucas Di Pentima [Thu, 30 May 2019 15:43:46 +0000 (12:43 -0300)]
14946: Fixes warnings related to uninitialized instance variables, and others.

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

5 years agoMerge branch 'master' into 14946-ruby-2.5
Lucas Di Pentima [Tue, 28 May 2019 21:59:16 +0000 (18:59 -0300)]
Merge branch 'master' into 14946-ruby-2.5

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