Peter Amstutz [Thu, 18 Sep 2014 17:47:52 +0000 (13:47 -0400)]
Merge branch '3605-queue-position-size' refs #3605
Peter Amstutz [Thu, 18 Sep 2014 17:38:05 +0000 (13:38 -0400)]
3605: Use #each_with_index instead of #each_index
Peter Amstutz [Thu, 18 Sep 2014 17:33:03 +0000 (13:33 -0400)]
Merge branch '3605-node-info-field' refs #3605
Conflicts:
services/api/db/structure.sql
Peter Amstutz [Thu, 18 Sep 2014 17:29:23 +0000 (13:29 -0400)]
3605: Do .to_i on total_cpu_cores, total_ram_mb, and total_scratch_mb in Node#ping.
Peter Amstutz [Thu, 18 Sep 2014 16:11:43 +0000 (12:11 -0400)]
3605: Add properties column to node. Put public-facing node information (cpu
cores, RAM, scratch space) into properties field. Info field is back to being
admin-only.
Tim Pierce [Thu, 18 Sep 2014 14:54:32 +0000 (10:54 -0400)]
Bug fix: Added missing owner_uuid to user fixture.
No issue #.
Tim Pierce [Thu, 18 Sep 2014 14:46:32 +0000 (10:46 -0400)]
Merge branch '3927-user-owner-uuid-not-null'
Closes #3927.
Tim Pierce [Thu, 18 Sep 2014 14:35:05 +0000 (10:35 -0400)]
3927: add NOT NULL constraint to User.owner_uuid
Added a migration setting all users with null owner_uuid to
system_user_uuid, and enforced a NOT NULL constraint on that column.
Tom Clegg [Thu, 18 Sep 2014 00:11:40 +0000 (20:11 -0400)]
Update Gemfiles to use latest arvados gem. refs #3550
Tom Clegg [Wed, 17 Sep 2014 22:01:03 +0000 (18:01 -0400)]
Merge branch '3550-local-pipeline' closes #3550
Tom Clegg [Wed, 17 Sep 2014 22:00:25 +0000 (18:00 -0400)]
3550: Merge branch 'master' into 3550-local-pipeline
Conflicts:
sdk/cli/bin/arv-run-pipeline-instance
Peter Amstutz [Wed, 17 Sep 2014 19:00:02 +0000 (15:00 -0400)]
3605: Test queue_size method and queue_position field. Adjust "GET queue"
tests for jobs controller to test that users don't see queue items for which
they do not have permissions.
radhika [Wed, 17 Sep 2014 18:56:02 +0000 (14:56 -0400)]
closes #2761
Merge branch '2761-diagnostic-suite'
radhika [Wed, 17 Sep 2014 18:55:17 +0000 (14:55 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
mishaz [Wed, 17 Sep 2014 18:24:51 +0000 (18:24 +0000)]
Merge branch 'update-go-sdk-documentation'
Updating Go SDK Documentation,
no issue #
radhika [Wed, 17 Sep 2014 18:10:40 +0000 (14:10 -0400)]
no issue # - fix couple more places where description is failing on nil template name.
Tim Pierce [Wed, 17 Sep 2014 17:55:23 +0000 (13:55 -0400)]
3411: fix failing tests
The FuseSharedTest requires "pipeline_with_template.pipelineInstance" on
my machine, but not on Jenkins. Puzzling.
No issue # -- bug fix
Tim Pierce [Wed, 17 Sep 2014 15:46:38 +0000 (11:46 -0400)]
Merge branch '3411-expire-collections'
Refs #3411.
Tim Pierce [Wed, 17 Sep 2014 15:45:38 +0000 (11:45 -0400)]
3411: added new collection fixtures owned by active_user
radhika [Wed, 17 Sep 2014 15:38:37 +0000 (11:38 -0400)]
no issue # : fix nil issue in pipeline_templates page
Tom Clegg [Wed, 17 Sep 2014 15:13:14 +0000 (11:13 -0400)]
3550: Fix race conditions: avoid setting running/success/finished_at
attributes until output and log have been saved.
Tim Pierce [Wed, 17 Sep 2014 14:59:23 +0000 (10:59 -0400)]
Merge branch '3411-expire-collections'
Closes #3411.
Tom Clegg [Wed, 17 Sep 2014 14:57:41 +0000 (10:57 -0400)]
3550: Fix running local job repeatedly on subsequent loop iterations.
Tom Clegg [Wed, 17 Sep 2014 14:48:13 +0000 (10:48 -0400)]
3550: Add missing .andand
Tim Pierce [Wed, 17 Sep 2014 14:20:48 +0000 (10:20 -0400)]
3411: code review feedback
* Ensure each functional test issues only one request to the controller
* $application_config['default_trash_lifetime'] -> Rails.configuration.default_trash_lifetime
radhika [Wed, 17 Sep 2014 14:10:16 +0000 (10:10 -0400)]
2761: added some comments
radhika [Wed, 17 Sep 2014 14:04:49 +0000 (10:04 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
Tom Clegg [Wed, 17 Sep 2014 13:49:43 +0000 (09:49 -0400)]
3550: Add missing .andand
Peter Amstutz [Wed, 17 Sep 2014 13:29:32 +0000 (09:29 -0400)]
3605: Add "queue_position" to jobs. Also add a route on jobs controller to get
the true size of the job queue.
Peter Amstutz [Wed, 17 Sep 2014 13:11:36 +0000 (09:11 -0400)]
Merge branch '3605-node-info-field' refs #3605
Peter Amstutz [Wed, 17 Sep 2014 01:00:14 +0000 (21:00 -0400)]
Fix test
Tim Pierce [Wed, 17 Sep 2014 02:40:16 +0000 (22:40 -0400)]
Merge branch '3705-keep-blockworklist'
Closes #3705.
radhika [Wed, 17 Sep 2014 02:36:08 +0000 (22:36 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
radhika [Wed, 17 Sep 2014 02:35:12 +0000 (22:35 -0400)]
2761: minor updates to diagnostics test config explanation.
Tim Pierce [Wed, 17 Sep 2014 02:34:20 +0000 (22:34 -0400)]
3705: use %v to format interface types
Peter Amstutz [Wed, 17 Sep 2014 02:30:21 +0000 (22:30 -0400)]
Fix arv-run-pipeline-instance to not crash when template is null. no issue #
Tim Pierce [Wed, 17 Sep 2014 02:09:34 +0000 (22:09 -0400)]
3705: drop unnecessary 'items' from BlockWorkList
Tim Pierce [Wed, 17 Sep 2014 01:56:55 +0000 (21:56 -0400)]
3705: use helper functions in tests
radhika [Tue, 16 Sep 2014 22:40:57 +0000 (18:40 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
radhika [Tue, 16 Sep 2014 22:40:43 +0000 (18:40 -0400)]
2761: update config
Tim Pierce [Tue, 16 Sep 2014 21:54:40 +0000 (17:54 -0400)]
3705: drop unnecessary current_list pointer
radhika [Tue, 16 Sep 2014 21:27:33 +0000 (17:27 -0400)]
no issue # remove pipeline instance fixture to address failing test.
Merge branch '2875-pipeline-description'
radhika [Tue, 16 Sep 2014 21:26:13 +0000 (17:26 -0400)]
2875: remove pipeline instance fixture and use an existing one.
Tom Clegg [Tue, 16 Sep 2014 21:04:10 +0000 (17:04 -0400)]
Merge branch '3877-log-memory-leak' closes #3877
radhika [Tue, 16 Sep 2014 20:55:22 +0000 (16:55 -0400)]
2761: add diagnostics section to config
mishaz [Tue, 16 Sep 2014 20:52:40 +0000 (20:52 +0000)]
Combined all examples into one big, runable source file with syntax coloring.
Found and fixed some bugs in example code.
Added example of requesting manifest text.
Turned references to source directories into links.
syntax-colored import statemtns.
Tim Pierce [Tue, 16 Sep 2014 20:49:37 +0000 (16:49 -0400)]
3411: code review
Feedback from code review:
* Dropped unnecessary lambda from Collection.default_scope.
* Set owner_uuid of new collection test fixtures to user 'active',
removed unnecessary permission link test fixtures.
* Removed permit_unsigned_manifests from unit tests
* Added tests for :show and :update to expired and unexpired
collections.
* Added rake config:check test to make sure default_trash_lifetime is at
least 24 hours.
Ward Vandewege [Tue, 16 Sep 2014 20:36:03 +0000 (16:36 -0400)]
Make sure to run apt-get update before trying to install
openjdk-7-jre-headless into the java-bwa-samtools arvados docker image.
no issue #
Peter Amstutz [Tue, 16 Sep 2014 20:05:18 +0000 (16:05 -0400)]
Merge branch '3878-arv-mount-block-cache' closes #3878
Peter Amstutz [Tue, 16 Sep 2014 20:04:37 +0000 (16:04 -0400)]
3878: Remove raise debugging exception.
mishaz [Tue, 16 Sep 2014 20:01:56 +0000 (20:01 +0000)]
Moved file.
Tom Clegg [Tue, 16 Sep 2014 20:00:11 +0000 (16:00 -0400)]
3550: Fix crash when --template loaded from local JSON file has no uuid.
Tom Clegg [Tue, 16 Sep 2014 19:59:04 +0000 (15:59 -0400)]
3550: Remove extraneous "to" in usage message.
Tim Pierce [Tue, 16 Sep 2014 04:57:44 +0000 (00:57 -0400)]
3411: set default collection expiration policy
* Added default_scope to Collections restricting them to collections that
have not yet expired
* Added a default_trash_lifetime setting in application.default.yml,
exposed in the discovery doc setting 'defaultTrashLifetime' (default:
2 weeks)
* Added test fixtures to exercise fetching expired collections and
collections that expire in the future.
Peter Amstutz [Tue, 16 Sep 2014 18:49:38 +0000 (14:49 -0400)]
3878: Fix block cache sharing across threads so arv-mount uses a bounded amount
of memory to store block. Also fixes bug in cache management code and cleans
some exception handler error reporting.
radhika [Tue, 16 Sep 2014 17:01:26 +0000 (13:01 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
radhika [Tue, 16 Sep 2014 15:28:53 +0000 (11:28 -0400)]
closes #2875
Merge branch '2875-pipeline-description'
radhika [Tue, 16 Sep 2014 15:27:30 +0000 (11:27 -0400)]
2875: minor text update
radhika [Tue, 16 Sep 2014 15:22:02 +0000 (11:22 -0400)]
2875: collection description is now textile and also the display is updated.
radhika [Tue, 16 Sep 2014 14:54:53 +0000 (10:54 -0400)]
2875: remove junk migration lines
Tom Clegg [Tue, 16 Sep 2014 14:51:27 +0000 (10:51 -0400)]
3877: Fix memory leak after "log truncated" decision. Clean up code.
Tim Pierce [Tue, 16 Sep 2014 06:15:13 +0000 (02:15 -0400)]
3705: update for code review
* Changed the type of the NextItem channel from *list.Element to
interface{} (i.e. a list.Element.Value)
* Better comments
* Cleaner testing framework
* TestBlockWorkListReaderBlocks to exercise the case where readers block
when the list is exhausted, and resume when new data is supplied.
Tim Pierce [Mon, 15 Sep 2014 22:19:40 +0000 (18:19 -0400)]
3705: describe BlockWorkList flow more explicitly
Updated file comments to describe the overall data flow for a
BlockWorkList manager and worker more explicitly.
Tom Clegg [Mon, 15 Sep 2014 16:20:15 +0000 (12:20 -0400)]
3550: Update docs to match new flag name. Add note about job re-use.
radhika [Mon, 15 Sep 2014 16:01:58 +0000 (12:01 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
Conflicts:
apps/workbench/config/application.default.yml
radhika [Mon, 15 Sep 2014 15:27:45 +0000 (11:27 -0400)]
no issue # fix failing test to use selenium driver
radhika [Mon, 15 Sep 2014 14:54:10 +0000 (10:54 -0400)]
2875: integration tests to verify description on pipeline templates, instances, and jobs.
Tom Clegg [Mon, 15 Sep 2014 13:55:22 +0000 (09:55 -0400)]
3550: Merge branch 'master' into 3550-local-pipeline
Tom Clegg [Mon, 15 Sep 2014 13:55:14 +0000 (09:55 -0400)]
3550: Clarify help message, mention that there are limitations.
Peter Amstutz [Mon, 15 Sep 2014 13:46:54 +0000 (09:46 -0400)]
Updated Gemfile to pull in changes from commit:
ac594f1 refs #3187
radhika [Mon, 15 Sep 2014 12:18:37 +0000 (08:18 -0400)]
2875: render template description as textile attribte in show recent page
radhika [Mon, 15 Sep 2014 12:10:29 +0000 (08:10 -0400)]
2875: add description option
radhika [Fri, 12 Sep 2014 22:15:21 +0000 (18:15 -0400)]
2875: add initial description to pipeline instance when created using arv-run-pipeline-instance script
radhika [Fri, 12 Sep 2014 20:49:57 +0000 (16:49 -0400)]
Merge branch 'master' into 2875-pipeline-description
radhika [Fri, 12 Sep 2014 20:46:51 +0000 (16:46 -0400)]
closes #3654
Merge branch '3654-combine-selections'
radhika [Fri, 12 Sep 2014 20:43:28 +0000 (16:43 -0400)]
Merge branch 'master' into 3654-combine-selections
radhika [Fri, 12 Sep 2014 20:41:48 +0000 (16:41 -0400)]
2875: initial description on pipeline instance when the template has no name.
radhika [Fri, 12 Sep 2014 19:48:45 +0000 (15:48 -0400)]
Merge branch 'master' into 2875-pipeline-description
radhika [Fri, 12 Sep 2014 19:46:05 +0000 (15:46 -0400)]
2875: set initial description on the new pipeline instance created by running a template.
Tim Pierce [Fri, 12 Sep 2014 19:18:15 +0000 (15:18 -0400)]
Bug fix: manifests with extra spaces
Extend the regular expression to match manifest_text to permit more than
a single space in manifest entries (seen in e.g.
91534558193f42a2f7f8aca872e5a78d+15723)
No issue #
radhika [Fri, 12 Sep 2014 18:19:44 +0000 (14:19 -0400)]
3654: disable search icon collection show page rather than hide it when it is not applicable.
radhika [Fri, 12 Sep 2014 17:26:37 +0000 (13:26 -0400)]
Merge branch 'master' into 3654-combine-selections
radhika [Fri, 12 Sep 2014 17:23:06 +0000 (13:23 -0400)]
Merge branch 'master' into 2875-pipeline-description
Conflicts:
services/api/app/models/pipeline_instance.rb
services/api/db/structure.sql
radhika [Fri, 12 Sep 2014 17:17:14 +0000 (13:17 -0400)]
2875: add new partial to display name and description.
Peter Amstutz [Fri, 12 Sep 2014 14:25:55 +0000 (10:25 -0400)]
3605: Provide "info" field to all requesters. Filters out any keys with text
"secret" to non-admin users. Also fix fiddlesticks on workbench viewing
details for node.
Peter Amstutz [Fri, 12 Sep 2014 13:43:34 +0000 (09:43 -0400)]
Merge branch '3187-start-finish-timestamps-tasks-pipelines' refs #3187
Peter Amstutz [Fri, 12 Sep 2014 13:39:09 +0000 (09:39 -0400)]
Fixed typo Y% -> %Y
radhika [Thu, 11 Sep 2014 23:37:39 +0000 (19:37 -0400)]
3654: update tests to match the selection dropdown text changes.
radhika [Thu, 11 Sep 2014 23:20:04 +0000 (19:20 -0400)]
2875: add description to jobs and pipeline_instances.
mishaz [Thu, 11 Sep 2014 22:30:46 +0000 (22:30 +0000)]
Included included file.
mishaz [Thu, 11 Sep 2014 22:29:27 +0000 (22:29 +0000)]
Moved code to seperate file for syntax coloring.
Switched to using arv.List instead of arv.Call.
radhika [Thu, 11 Sep 2014 20:19:52 +0000 (16:19 -0400)]
Merge branch 'master' into 3654-combine-selections
radhika [Thu, 11 Sep 2014 20:18:07 +0000 (16:18 -0400)]
3654: move the checkbox to the left of the row in collection show page. also, fixed a bug where the newly added selection dropdown shows up in the collection file chooser popup.
Peter Amstutz [Thu, 11 Sep 2014 19:54:50 +0000 (15:54 -0400)]
3187: Update the task start time when the task actually starts.
Ward Vandewege [Thu, 11 Sep 2014 19:01:41 +0000 (15:01 -0400)]
Fallout from #3036: the test for the checkbox value on acceptance of the
user agreement was expecting a keep hash, rather than an Arvados UUID.
This fixes accepting the user agreement (if one or more are present).
refs #3036
radhika [Thu, 11 Sep 2014 19:01:07 +0000 (15:01 -0400)]
3654: add a default name to newly created combined collection
Tim Pierce [Thu, 11 Sep 2014 18:44:48 +0000 (14:44 -0400)]
3705: replace pullmgr with a BlockWorkList
radhika [Thu, 11 Sep 2014 17:38:00 +0000 (13:38 -0400)]
Merge branch 'master' into 3654-combine-selections
Brett Smith [Thu, 11 Sep 2014 15:21:36 +0000 (11:21 -0400)]
Clean up manifest whitespace in split-fastq.
The previous code was generating two spaces between the stream name
and block list, because it had the space from as_manifest() as well as
its own join. This yielded an invalid manifest.
No issue #.
radhika [Thu, 11 Sep 2014 14:33:41 +0000 (10:33 -0400)]
2761: update comment
projects / arvados.git / log