Lucas Di Pentima [Thu, 28 Mar 2019 21:06:37 +0000 (18:06 -0300)]
14873: Fixes unit tests.
JSONB columns shouldn't be declared as 'serialized' because their content
get encoded twice.
When not declaring them as serialized, their default values (eg: [], {})
should be explicitly set.
Fixes on fixtures when default JSONB values are not defined on the schema.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 27 Mar 2019 18:20:05 +0000 (15:20 -0300)]
Merge branch 'master' into 14873-api-rails5-upgrade
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 27 Mar 2019 18:09:52 +0000 (15:09 -0300)]
14873: Adds headers to controller tests' requests.
API server logs used to report 'format: html' when running functional tests.
With these additions, it now reports 'json', but this is not enough to fix
the issue about nested arrays being flattened when running tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 27 Mar 2019 18:07:09 +0000 (15:07 -0300)]
14873: Gets rid of yet another deprecation warning.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 27 Mar 2019 18:02:11 +0000 (15:02 -0300)]
14873: Skips indexes which 'columns' attribute isn't an Array.
ActiveRecord::Base.connection.indexes(table) didn't seem to return these
previous to rails 5.0 upgrade.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Wed, 27 Mar 2019 15:15:15 +0000 (11:15 -0400)]
Accept :py3 modifier for any Python suite in interactive mode.
(even ones that aren't normally run with python3 by jenkins)
refs #14939
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Wed, 27 Mar 2019 02:41:10 +0000 (23:41 -0300)]
14873: Marks past migrations with version 4.2
Rails 5 migration API changes, so to be able to run past migrations
with newer rails, it's required to mark them.
This isn't documented on the Rails 5.0 upgrade notes, but it's mentioned on some
blogs, like this one:
https://blog.bigbinary.com/2016/03/01/migrations-are-versioned-in-rails-5.html
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 27 Mar 2019 01:38:43 +0000 (22:38 -0300)]
14873: Fixes parameter handling (WIP)
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 26 Mar 2019 20:46:42 +0000 (17:46 -0300)]
14873: Fixes integration tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Fernando Monserrat [Tue, 26 Mar 2019 20:29:45 +0000 (17:29 -0300)]
no issue # Remove jessie-updates from sources.list as it is no longer supported
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Tue, 26 Mar 2019 20:09:31 +0000 (16:09 -0400)]
arvbox nginx redirects http to https
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 26 Mar 2019 18:33:15 +0000 (15:33 -0300)]
14873: Fixes deprecation warnings on integration tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 26 Mar 2019 16:18:00 +0000 (13:18 -0300)]
14873: Upgrades 'pg' gem & solves an issue related to a new internal table.
Rails 5 includes an undocumented internal table called 'ar_internal_metadata'
used to record the environment that the current system is on, so that it can
avoid accidental database wipes when in production.
Our code iterates over the tables so this one needs to be skipped.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 26 Mar 2019 14:28:19 +0000 (10:28 -0400)]
Merge branch '14807-prod-blockers'
refs #14807
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 25 Mar 2019 14:47:37 +0000 (10:47 -0400)]
14807: Move "fallback to ARVADOS_*" logic out to lib/service.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Mon, 25 Mar 2019 14:44:49 +0000 (11:44 -0300)]
14873: Removes legacy setting as all controllers were migrated.
When needing to stop the callback chain, instead of returning false
now we need to call: throw(:abort)
The removed setting allowed the old behavior, and it isn't neede anymore.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 25 Mar 2019 14:33:30 +0000 (11:33 -0300)]
14873: Adds new abstract class ApplicationRecord.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 22 Mar 2019 21:25:14 +0000 (18:25 -0300)]
14783: Fixes more deprecation warnings from functional tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Fri, 22 Mar 2019 20:20:29 +0000 (16:20 -0400)]
14807: Add lib/service test.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 22 Mar 2019 19:25:47 +0000 (15:25 -0400)]
14807: Fix go vet warnings about %s args.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Fri, 22 Mar 2019 18:56:02 +0000 (15:56 -0300)]
14873: Fixes deprecation notes on functional tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Fri, 22 Mar 2019 18:44:03 +0000 (14:44 -0400)]
14807: Pass token to service handlers explicitly, not via context.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Fri, 22 Mar 2019 16:40:36 +0000 (13:40 -0300)]
14873: Adds missing copyright notices
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 22 Mar 2019 16:30:54 +0000 (13:30 -0300)]
14873: Fixes all deprecation notes on unit tests
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 22 Mar 2019 13:20:54 +0000 (10:20 -0300)]
14873: Replaces *_filter with *_action
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 22 Mar 2019 12:42:44 +0000 (09:42 -0300)]
14873: Rails 5 upgrade. Some tests still failing. (WIP)
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Thu, 21 Mar 2019 18:47:53 +0000 (14:47 -0400)]
14807: Refuse to create instance with AddedScratch>0.
The resulting VM would be the wrong size because dynamically attached
scratch space is not implemented.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 21 Mar 2019 18:36:29 +0000 (14:36 -0400)]
14807: Load API host/token from cluster config if present.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 21 Mar 2019 20:55:00 +0000 (16:55 -0400)]
Merge branch '15007-azure-panic'
fixes #15007
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 21 Mar 2019 20:54:49 +0000 (16:54 -0400)]
15007: Fix crash when Azure nic has IP config but no IP address.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 21 Mar 2019 20:50:32 +0000 (16:50 -0400)]
Merge branch '14807-prod-blockers'
refs #14807
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Morris [Thu, 21 Mar 2019 20:02:20 +0000 (16:02 -0400)]
Merge branch '14451-crunchstat-summary-cache-ram'
Fix three small crunchstat-summary issues:
- Use default of 1 if no cores requested. fixes #12026
- Don't recommend RAM or CPU changes based on zero usage. fixes #10570
- Remove extra MB (2**20) factor in Keep cache recommendation. Fixes #14451
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Fri, 15 Mar 2019 05:11:59 +0000 (01:11 -0400)]
Improve wording with direction of recommendation change.
No issue.
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Fri, 15 Mar 2019 04:47:38 +0000 (00:47 -0400)]
Use default of 1 if no cores requested. refs #12026
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Fri, 15 Mar 2019 04:10:06 +0000 (00:10 -0400)]
Don't recommend RAM or CPU changes based on zero usage. refs #10570
Never recommend 0 MB RAM. If CPU usage is zero, don't make any
CPU recommendations.
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Fri, 15 Mar 2019 04:03:59 +0000 (00:03 -0400)]
Fix Keep cache recommendation calculation.
Remove extra MB (2**20) factor. Refs #14451
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Fri, 15 Mar 2019 02:11:45 +0000 (22:11 -0400)]
Spell MB consistently.
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Eric Biagiotti [Thu, 21 Mar 2019 19:52:26 +0000 (15:52 -0400)]
Merge branch '14645-fuse-operations-reporting'
refs #14645
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Tom Morris [Thu, 21 Mar 2019 19:47:54 +0000 (15:47 -0400)]
Merge branch '14939-crunchstat-summary-python3'
Fixes #14939
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Thu, 14 Mar 2019 22:47:20 +0000 (18:47 -0400)]
Resolve deprecation warnings
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Thu, 14 Mar 2019 22:30:52 +0000 (18:30 -0400)]
Fix resource leak warned by Python 3
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Wed, 13 Mar 2019 23:33:03 +0000 (19:33 -0400)]
Add crunchstat-summary to Python 3 tests. refs #14939
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Wed, 13 Mar 2019 23:26:00 +0000 (19:26 -0400)]
Fix test Python 3 integer divide difference.
Use float for both Python 2 & 3 like the rest of the metrics.
refs #14393
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Morris [Fri, 8 Mar 2019 23:40:24 +0000 (18:40 -0500)]
Update crunchstat-summary to Python 3. Refs #14939
Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>
Tom Clegg [Thu, 21 Mar 2019 18:12:54 +0000 (14:12 -0400)]
14807: Allow some fake nodes to remain unbroken.
If every fake node hits a fake failure mode in 200-400 ms, throughput
can fall below 20 containers per second and fail the test.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Eric Biagiotti [Thu, 21 Mar 2019 18:03:16 +0000 (14:03 -0400)]
Merge remote-tracking branch 'origin/master' into 14645-fuse-operations-reporting
refs #14645
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 21 Mar 2019 14:49:31 +0000 (10:49 -0400)]
14645: Updates crunchstat format for fuse ops
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Wed, 20 Mar 2019 20:17:07 +0000 (17:17 -0300)]
Merge branch '14873-google-api-client-update'
Refs #14873
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Wed, 20 Mar 2019 05:50:10 +0000 (01:50 -0400)]
14807: Give up if initial keep services list isn't loaded in 60s.
Otherwise, MakeKeepClient blocks forever when ARVADOS_* env vars are
bad.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 19 Mar 2019 21:02:05 +0000 (17:02 -0400)]
14807: Report queue metrics.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 19 Mar 2019 17:40:10 +0000 (13:40 -0400)]
14807: Add "kill instance" management API.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 21:27:40 +0000 (17:27 -0400)]
14807: Configurable rate limit for cloud provider API calls.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 20:32:58 +0000 (16:32 -0400)]
14807: Drain instances that crunch-run reports broken.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 20 Mar 2019 19:24:02 +0000 (15:24 -0400)]
Merge branch '14807-escalate-sigterm'
refs #14807
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 20 Mar 2019 19:20:57 +0000 (15:20 -0400)]
14807: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 20 Mar 2019 19:20:38 +0000 (15:20 -0400)]
14807: Tweak log message.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 20 Mar 2019 18:07:06 +0000 (14:07 -0400)]
Merge branch '14947-run-tests-interactive'
closes #14947
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Mon, 18 Mar 2019 20:10:04 +0000 (17:10 -0300)]
14873: Removes activerecord-deprecated_finders gem dependency.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 18 Mar 2019 18:49:51 +0000 (15:49 -0300)]
14873: Removes protected_attributes gem dependency.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Wed, 20 Mar 2019 17:41:35 +0000 (13:41 -0400)]
14947: Ignore --only / --skip args in interactive mode.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Wed, 20 Mar 2019 17:39:03 +0000 (14:39 -0300)]
14873: Updates arvados & arvados-cli gems dependency on google-api-client.
Start using our own fork arvados-google-api-client that ask for activesupport
version <5.1 so that it doesn't block the rails 5 upgrade.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Wed, 20 Mar 2019 17:37:28 +0000 (13:37 -0400)]
14947: Fix controller install in deps.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 20 Mar 2019 13:28:24 +0000 (09:28 -0400)]
14947: Accept test suite options in interactive mode.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Eric Biagiotti [Tue, 19 Mar 2019 20:27:00 +0000 (16:27 -0400)]
14645: Adds op counts to reporting
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Tom Clegg [Tue, 19 Mar 2019 20:23:55 +0000 (16:23 -0400)]
14947: Install controller (cmd/arvados-server) for integration tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 19 Mar 2019 17:28:39 +0000 (13:28 -0400)]
14807: Don't send SIGKILL to crunch-run processes.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Eric Biagiotti [Tue, 19 Mar 2019 17:26:26 +0000 (13:26 -0400)]
14645: Adds individual ops time output
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Tom Clegg [Tue, 19 Mar 2019 15:57:32 +0000 (11:57 -0400)]
14807: Add comments to "error indicates success" code.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 19 Mar 2019 14:30:36 +0000 (10:30 -0400)]
14947: Suggest "install deps" as first interactive command.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 18 Mar 2019 20:13:35 +0000 (16:13 -0400)]
Move back arvbox version of nodejs to fix composer compile issue
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 19:16:25 +0000 (15:16 -0400)]
14807: Update tests to new worker/pool interface.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 19:08:19 +0000 (15:08 -0400)]
14807: Lengthen kill delays in stub driver to test term-kill-drain.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 18 Mar 2019 18:43:31 +0000 (14:43 -0400)]
Merge branch '14322-cwl-uuid-input' refs #14322
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 18 Mar 2019 18:04:19 +0000 (14:04 -0400)]
14322: Tweak JSON_KEEP_LOCATOR_REGEXP and comment
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 15:09:09 +0000 (11:09 -0400)]
14807: Escalate sigterm->sigkill->drain instance.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 15:44:19 +0000 (11:44 -0400)]
14807: Fail test if a container gets run twice.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 15:44:07 +0000 (11:44 -0400)]
14807: Fix unreliable test.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 15:11:56 +0000 (11:11 -0400)]
Merge branch '14977-kill-if-not-in-queue'
fixes #14977
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 18 Mar 2019 13:42:27 +0000 (09:42 -0400)]
14977: Re-order statements for clarity.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 15 Mar 2019 20:19:51 +0000 (16:19 -0400)]
14977: Don't try fixStaleLocks until worker pool state is loaded.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 15 Mar 2019 20:11:48 +0000 (16:11 -0400)]
14977: Kill containers that don't exist according to controller.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 15 Mar 2019 19:21:39 +0000 (15:21 -0400)]
14977: Drop containers when the controller says they don't exist.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 15 Mar 2019 14:54:59 +0000 (10:54 -0400)]
14322: Fix noisy unicode logging error in tests, add comments
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 21:30:57 +0000 (17:30 -0400)]
14322: Add missing test files
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 21:26:07 +0000 (17:26 -0400)]
14322: Workbench links collection uuids in workflow inputs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 21:20:22 +0000 (17:20 -0400)]
14322: Update comment on bwa-mem-input-mixed.yml
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 20:40:33 +0000 (16:40 -0400)]
14322: Add additional example input files
* with uuids
* with both portable data hashes and uuids
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 20:19:37 +0000 (16:19 -0400)]
14322: Tweak workbench support from manual testing
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 19:52:20 +0000 (15:52 -0400)]
14322: Update workbench to use new collectionUUID
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 19:25:33 +0000 (15:25 -0400)]
14322: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 18:57:53 +0000 (14:57 -0400)]
14322: Tweak documentation to mention uuid keep URI form
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 13 Mar 2019 18:57:20 +0000 (14:57 -0400)]
14322: CollectionFsAccess accepts UUIDs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 12 Mar 2019 20:39:12 +0000 (16:39 -0400)]
14322: Tests for edge cases
Report unknown uuids and mismatches between current collection
PDH (from API server lookup) and location PDH.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 11 Mar 2019 21:42:09 +0000 (17:42 -0400)]
14322: Propagate collection UUID to container mount
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 11 Mar 2019 21:02:14 +0000 (17:02 -0400)]
14322: Convert uuids on input to portable data hashes
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 15 Mar 2019 14:10:15 +0000 (10:10 -0400)]
Fix a-c-r printing logs on error refs #14870
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 14 Mar 2019 20:24:18 +0000 (16:24 -0400)]
14947: run-tests: add --interactive, skip deps on --skip-install.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Thu, 14 Mar 2019 19:42:18 +0000 (16:42 -0300)]
Merge branch '14966-api-test-hang-fix'
Closes #14966
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 7 Feb 2019 22:07:08 +0000 (17:07 -0500)]
Arvbox updates, no issue #
* Bump Go version, add openjdk.
* Bump node version. Make sure node is in path.
* Fix $HOME in setup scripts.
* Add "arvbox devenv" command which creates and enters a container
environment suitable for interactively running development tools
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Thu, 14 Mar 2019 18:56:00 +0000 (15:56 -0300)]
14966: Implements cleanup on test case teardown.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
projects / arvados.git / log