Tom Clegg [Wed, 17 Sep 2014 14:57:41 +0000 (10:57 -0400)]
3550: Fix running local job repeatedly on subsequent loop iterations.
Phil Hodgson [Wed, 17 Sep 2014 14:51:06 +0000 (10:51 -0400)]
3661: proposed change of the selection javascript to use the new copies_to_projects? class method on Group
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
Tim Pierce [Wed, 17 Sep 2014 13:44:05 +0000 (09:44 -0400)]
3699: bugfix (renamed repository_map -> local_repo_dir)
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 13:13:52 +0000 (09:13 -0400)]
Merge branch 'master' into 3605-improved-dashboard
Conflicts:
apps/workbench/app/models/job.rb
services/api/app/models/job.rb
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
Peter Amstutz [Wed, 17 Sep 2014 01:00:14 +0000 (21:00 -0400)]
Fix test
Phil Hodgson [Tue, 16 Sep 2014 23:09:32 +0000 (19:09 -0400)]
3338: move the user_is_manager and shared items to the already-overridden #find_object_by_uuid method so that these are available to all the same actions
Phil Hodgson [Tue, 16 Sep 2014 23:05:45 +0000 (19:05 -0400)]
3338: fix the integration test so that it checks the on-screen collection count
rather than trying to use the fixtures which doesn't work anyway
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 #
Phil Hodgson [Tue, 16 Sep 2014 20:23:08 +0000 (16:23 -0400)]
3661: add centralized method for defining whether an object can be copied to a project
Phil Hodgson [Tue, 16 Sep 2014 20:22:14 +0000 (16:22 -0400)]
3661: removed useless method to wrong project
(fix from last commit)
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.
Tim Pierce [Tue, 16 Sep 2014 20:03:01 +0000 (16:03 -0400)]
3699: update script_version and supplied_script_version
When copying git repositories, any script_version or
supplied_script_version in the components or jobs should be renamed to
their commit hashes, to ensure that they can be resolved on the
destination (which will not have any of the symbolic names from the
source repository)
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.
Peter Amstutz [Tue, 16 Sep 2014 19:23:14 +0000 (15:23 -0400)]
3605: Automatically reload the dashboard using ajax.
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.
Tim Pierce [Tue, 16 Sep 2014 17:30:53 +0000 (13:30 -0400)]
3699: document required options --src and --dst
Tim Pierce [Tue, 16 Sep 2014 17:28:12 +0000 (13:28 -0400)]
3699: more help text for --src and --dst options
Tim Pierce [Tue, 16 Sep 2014 17:21:29 +0000 (13:21 -0400)]
3699: update --src, --dst, --dst-git-repo args
Per code review:
* Use mandatory --src and --dst flags to specify source and destination
Arvados. Each one can specify either a pathname to a config file or a
bareword which identifies a file in
$HOME/.arvados/config/instance.conf.
* --dst-git-repo is only required when copying a pipeline recursively;
not for non-recursive copies or collections.
Phil Hodgson [Tue, 16 Sep 2014 17:05:28 +0000 (13:05 -0400)]
3634: add gem that handles Bootstrap tab state automagically
radhika [Tue, 16 Sep 2014 17:01:26 +0000 (13:01 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
Tim Pierce [Tue, 16 Sep 2014 15:31:17 +0000 (11:31 -0400)]
3699: code review
* Issue helpful error message when config file cannot be opened
* Require --dst_git_repo argument
* Allow collections without owner_uuid (i.e. when retrieved by data hash
rather than uuid)
* Corrected "source"/"destination" error message in copy_git_repo
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.
Peter Amstutz [Tue, 16 Sep 2014 00:41:26 +0000 (20:41 -0400)]
3605: Getting jobs/queue_size from API server works. Fixed server-side
sorting. Date rendering improvements.
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.
Peter Amstutz [Mon, 15 Sep 2014 19:08:19 +0000 (15:08 -0400)]
Merge remote-tracking branch 'origin/master' into 3605-improved-dashboard
Peter Amstutz [Mon, 15 Sep 2014 19:08:08 +0000 (15:08 -0400)]
3605: Finally settled on a layout. Adding in remaining information and fixing bugs.
Tim Pierce [Mon, 15 Sep 2014 18:43:32 +0000 (14:43 -0400)]
3699: copy collection properties, name, etc.
copy_collection now copies the original collection object from src to dst,
changing uuid/owner_uuid/ensure_unique_name appropriately.
Tim Pierce [Mon, 15 Sep 2014 18:20:00 +0000 (14:20 -0400)]
3699: report success/failure unambiguously
Tim Pierce [Mon, 15 Sep 2014 17:58:44 +0000 (13:58 -0400)]
3699: back out attempts to change tempfile.tempdir
Too many error conditions -- if the disk is full, have the user change
it manually with TMPDIR=/scratch
Tim Pierce [Mon, 15 Sep 2014 17:30:52 +0000 (13:30 -0400)]
3699: typo fix
Tim Pierce [Mon, 15 Sep 2014 17:28:42 +0000 (13:28 -0400)]
3699: use /scratch instead of /tmp for git copies
Tim Pierce [Mon, 15 Sep 2014 17:13:45 +0000 (13:13 -0400)]
3699: ensure unique names for new pipelines
Tim Pierce [Mon, 15 Sep 2014 17:11:21 +0000 (13:11 -0400)]
Merge branch 'master' into 3699-arv-copy
Tim Pierce [Mon, 15 Sep 2014 17:06:45 +0000 (13:06 -0400)]
3699: delete pi['uuid'] before committing
Tim Pierce [Mon, 15 Sep 2014 17:03:28 +0000 (13:03 -0400)]
3699: copy_pipeline_template requires dst_git_repo
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
Tim Pierce [Mon, 15 Sep 2014 15:39:25 +0000 (11:39 -0400)]
3699: allow pipeline instances without templates
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.
Tim Pierce [Mon, 15 Sep 2014 14:48:59 +0000 (10:48 -0400)]
3699: fix inconsistent function parameters
All copy methods/functions now start with (object_to_copy, src_client,
dst_client).
Tim Pierce [Mon, 15 Sep 2014 14:40:45 +0000 (10:40 -0400)]
3699: bug fix (return value for copy_git_repo)
Tim Pierce [Mon, 15 Sep 2014 14:30:47 +0000 (10:30 -0400)]
3699: use a consistent destination branch for copy_git_repo
copy_git_repo copies commits from the source repository to a branch in
the destination named for the source repository URL. Thus, if the same
source repository is copied several times to the same destination, it
will not add redundant branches.
Tim Pierce [Mon, 15 Sep 2014 14:10:45 +0000 (10:10 -0400)]
3699: fix copy_git_repo
Need to specify destination branch explicitly when pushing.
Tim Pierce [Mon, 15 Sep 2014 13:56:12 +0000 (09:56 -0400)]
3699: bug fixes
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
Peter Amstutz [Mon, 15 Sep 2014 13:44:57 +0000 (09:44 -0400)]
Remove projects panels from dashboard
Peter Amstutz [Mon, 15 Sep 2014 13:41:46 +0000 (09:41 -0400)]
Merge branch '3187-pipeline-instance-page' into 3605-improved-dashboard
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
Tim Pierce [Fri, 12 Sep 2014 21:30:29 +0000 (17:30 -0400)]
3699: bug fixes and feedback
* added 'arv copy' front end to sdk/cli/bin/arv
* can supply --recursive for pipeline templates as well as pipeline
instance
* collections and git repositories are now properly renamed in the
pipeline template and instance when copying recursively
* copy_collection skips copying blocks if the collection already exists
at the destination
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.
Peter Amstutz [Fri, 12 Sep 2014 20:32:01 +0000 (16:32 -0400)]
Working on recent pipelines/collections tables
Peter Amstutz [Fri, 12 Sep 2014 19:52:30 +0000 (15:52 -0400)]
Merge branch 'master' into 3605-improved-dashboard
Peter Amstutz [Fri, 12 Sep 2014 19:52:03 +0000 (15:52 -0400)]
3605: Dashboard compute node and pipeline status work in progress
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