Tom Clegg [Sun, 17 Mar 2013 22:24:20 +0000 (15:24 -0700)]
restart dispatch_jobs service on deploy
Tom Clegg [Sun, 17 Mar 2013 22:10:02 +0000 (15:10 -0700)]
upcase job command parameters when passing to whjobmanager
Tom Clegg [Sat, 16 Mar 2013 21:39:49 +0000 (14:39 -0700)]
add script/dispatch_jobs.rb and related Job features
Tom Clegg [Wed, 13 Mar 2013 23:25:27 +0000 (16:25 -0700)]
rename Project to Group
Tom Clegg [Wed, 13 Mar 2013 22:34:00 +0000 (15:34 -0700)]
rename Project to Group
Tom Clegg [Wed, 13 Mar 2013 17:32:22 +0000 (10:32 -0700)]
refuse to change ec2_instance_id once an EC2 instance has claimed a Node
Tom Clegg [Wed, 13 Mar 2013 16:10:40 +0000 (09:10 -0700)]
use spot instances for compute nodes
Tom Clegg [Tue, 12 Mar 2013 17:04:45 +0000 (10:04 -0700)]
ignore Keep hints when verifying collection uuid == md5sum
Tom Clegg [Tue, 5 Mar 2013 18:08:25 +0000 (10:08 -0800)]
prepare pipeline summary CSV and save in specimen->result link. refs #1239
Tom Clegg [Mon, 4 Mar 2013 22:58:16 +0000 (14:58 -0800)]
add chromosome_calls and inferred_sex to factory job summary
Tom Clegg [Mon, 4 Mar 2013 22:31:08 +0000 (14:31 -0800)]
add picard-casm statistics to factory job summary
Tom Clegg [Mon, 4 Mar 2013 21:23:07 +0000 (13:23 -0800)]
add fill_ftp_accounts script
Ward Vandewege [Tue, 26 Feb 2013 22:04:26 +0000 (17:04 -0500)]
Remove superfluous fields from the Link object.
Tom Clegg [Tue, 26 Feb 2013 21:58:21 +0000 (13:58 -0800)]
add a Link from specimen to collection when pipeline finishes (instead of storing summary info in the pipeline_invocation)
Ward Vandewege [Tue, 26 Feb 2013 21:56:18 +0000 (16:56 -0500)]
Weed out (most of) the unnecessary leftover bits in our rest discovery file.
Tom Clegg [Tue, 26 Feb 2013 08:14:16 +0000 (00:14 -0800)]
add region_padding=10
Tom Clegg [Mon, 25 Feb 2013 20:26:38 +0000 (12:26 -0800)]
add pipelines#show
Tom Clegg [Fri, 22 Feb 2013 23:17:12 +0000 (15:17 -0800)]
show "sinfo" results on /nodes page
Tom Clegg [Tue, 19 Feb 2013 07:52:38 +0000 (23:52 -0800)]
tweak factory_jobs display
Tom Clegg [Tue, 19 Feb 2013 06:43:33 +0000 (22:43 -0800)]
move vcf pipeline stats code to a helper, generate stats when pipeline finishes, cache in #properties
Tom Clegg [Mon, 18 Feb 2013 21:05:54 +0000 (13:05 -0800)]
add first,last,[] methods
Tom Clegg [Mon, 18 Feb 2013 21:05:15 +0000 (13:05 -0800)]
show raw components json on pipeline_invocations#show
Tom Clegg [Mon, 18 Feb 2013 18:16:13 +0000 (10:16 -0800)]
add PipelineInvocation#properties
Tom Clegg [Mon, 18 Feb 2013 00:00:31 +0000 (16:00 -0800)]
set exome regions
Tom Clegg [Sun, 17 Feb 2013 23:38:55 +0000 (15:38 -0800)]
Rearrange pipeline_invocation handling
* move whpipeline bits into a separate cron job (just 1 proc per site)
* use native code instead of whpipeline to set pipeline job parameters
* add "reset pipeline" buttons to /factory_jobs table
Tom Clegg [Sun, 17 Feb 2013 21:33:30 +0000 (13:33 -0800)]
let pipeline_invocation#active be a regular attribute
Tom Clegg [Sun, 17 Feb 2013 21:22:34 +0000 (13:22 -0800)]
accept json-encoded pipeline[components] param
Tom Clegg [Tue, 12 Feb 2013 21:11:30 +0000 (14:11 -0700)]
do not delete uuid if provided in new object (notably collection)
Tom Clegg [Tue, 12 Feb 2013 21:10:20 +0000 (14:10 -0700)]
allow re-saving an existing collection without complaint
Tom Clegg [Tue, 12 Feb 2013 20:38:26 +0000 (13:38 -0700)]
fix broken orvos_model#initialize
Tom Clegg [Sun, 10 Feb 2013 17:16:10 +0000 (12:16 -0500)]
be more selective about invoking array-of-strings display on generic object#show page
Tom Clegg [Sun, 10 Feb 2013 17:14:10 +0000 (12:14 -0500)]
emphasize local part of uuid
Tom Clegg [Sun, 10 Feb 2013 06:51:40 +0000 (01:51 -0500)]
render pipeline_invocation components as job/progress table
Tom Clegg [Sun, 10 Feb 2013 06:31:50 +0000 (01:31 -0500)]
check serialized attribute types during create/update
Tom Clegg [Sat, 9 Feb 2013 08:16:07 +0000 (03:16 -0500)]
set modified_by_user=nil instead of breaking if no user is logged in
Tom Clegg [Sat, 9 Feb 2013 08:06:42 +0000 (03:06 -0500)]
do not require user login for node#ping
Tom Clegg [Fri, 8 Feb 2013 00:24:45 +0000 (19:24 -0500)]
do not hyperlink collections that do not have corresponding objects to look up
Tom Clegg [Fri, 8 Feb 2013 00:24:01 +0000 (19:24 -0500)]
use Enumerable and to_ary for implicit conversion to array instead of forcing caller to use where()
Tom Clegg [Thu, 7 Feb 2013 23:40:06 +0000 (18:40 -0500)]
use generic orvos link helper in collections#index
Tom Clegg [Thu, 7 Feb 2013 20:09:57 +0000 (15:09 -0500)]
sort lists on modified_at by default
Tom Clegg [Thu, 7 Feb 2013 19:57:44 +0000 (14:57 -0500)]
use old owner, not new owner, when checking permission to change attributes
Tom Clegg [Thu, 7 Feb 2013 19:45:47 +0000 (14:45 -0500)]
add links to generic specimen and project #show
Tom Clegg [Thu, 7 Feb 2013 19:03:40 +0000 (14:03 -0500)]
link to pipeline invocations from factory_jobs page
Tom Clegg [Thu, 7 Feb 2013 19:03:26 +0000 (14:03 -0500)]
fix double render
Tom Clegg [Thu, 7 Feb 2013 18:01:53 +0000 (13:01 -0500)]
fix misleading label
Tom Clegg [Thu, 7 Feb 2013 17:56:55 +0000 (12:56 -0500)]
make resource_class_for_uuid more convenient and robust
Tom Clegg [Thu, 7 Feb 2013 17:52:28 +0000 (12:52 -0500)]
add generic #show page for orvos objects and use it for Log and User
Tom Clegg [Thu, 7 Feb 2013 16:14:15 +0000 (11:14 -0500)]
show log#event_type
Tom Clegg [Thu, 7 Feb 2013 16:13:26 +0000 (11:13 -0500)]
update server-assigned attributes after saving objects
Tom Clegg [Thu, 7 Feb 2013 02:24:54 +0000 (21:24 -0500)]
add logs#show
Tom Clegg [Wed, 6 Feb 2013 21:35:27 +0000 (16:35 -0500)]
use JSON.dump so timestamps load back as Time, and Oj.load for fast loading
Tom Clegg [Wed, 6 Feb 2013 21:31:28 +0000 (16:31 -0500)]
add orvos_resource_list#to_hash
Tom Clegg [Tue, 5 Feb 2013 20:20:36 +0000 (15:20 -0500)]
fix storage=cache pill coloron Source data tab
Tom Clegg [Tue, 5 Feb 2013 20:09:37 +0000 (15:09 -0500)]
add Files pane on Collections#show
Tom Clegg [Tue, 5 Feb 2013 20:00:51 +0000 (15:00 -0500)]
split jobs into provenance chart and job list
Tom Clegg [Tue, 5 Feb 2013 16:58:13 +0000 (11:58 -0500)]
abandon "bold megabytes" feature
Tom Clegg [Tue, 5 Feb 2013 16:57:45 +0000 (11:57 -0500)]
use real instead of test data size
Tom Clegg [Tue, 5 Feb 2013 15:22:08 +0000 (10:22 -0500)]
default to data page instead of factory_jobs
Tom Clegg [Tue, 5 Feb 2013 15:21:43 +0000 (10:21 -0500)]
obey eager() and limit() in all()
Tom Clegg [Tue, 5 Feb 2013 15:20:22 +0000 (10:20 -0500)]
limit 100 instead of 1000
Tom Clegg [Tue, 5 Feb 2013 13:47:58 +0000 (08:47 -0500)]
human readable data size
Tom Clegg [Tue, 5 Feb 2013 07:44:15 +0000 (02:44 -0500)]
make bootstrap tabs really work
Tom Clegg [Tue, 5 Feb 2013 07:00:49 +0000 (02:00 -0500)]
fix commit-id -> redmine link
Tom Clegg [Tue, 5 Feb 2013 03:31:43 +0000 (22:31 -0500)]
include data_size and files list in Collection api response
Tom Clegg [Tue, 5 Feb 2013 03:35:08 +0000 (22:35 -0500)]
add Collections#show page
Ward Vandewege [Tue, 5 Feb 2013 01:45:52 +0000 (20:45 -0500)]
Support
where={"any":["contains","hu34"]}
style parameter. For now, 'any' just means a field called 'name'
Ward Vandewege [Tue, 5 Feb 2013 01:44:19 +0000 (20:44 -0500)]
When no limit is supplied, limit number of index results to 100.
Tom Clegg [Tue, 5 Feb 2013 00:09:03 +0000 (16:09 -0800)]
limit data page to 1-3000 collections
Tom Clegg [Tue, 5 Feb 2013 00:07:17 +0000 (16:07 -0800)]
support limit parameter in #index
Tom Clegg [Mon, 4 Feb 2013 10:04:53 +0000 (02:04 -0800)]
add Job#dependencies
Ward Vandewege [Mon, 4 Feb 2013 16:54:11 +0000 (11:54 -0500)]
Back out upgrade to MultiJson for now until we upgrade to rails 3.2. See
comment in Gemfile.
Ward Vandewege [Mon, 4 Feb 2013 16:25:30 +0000 (11:25 -0500)]
Switch to MultiJson which uses Oj under the hood (since it is available).
Ward Vandewege [Mon, 4 Feb 2013 15:45:01 +0000 (10:45 -0500)]
Switch to MultiJson which uses Oj under the hood (since it is available).
Ward Vandewege [Mon, 4 Feb 2013 14:53:48 +0000 (09:53 -0500)]
Switch to Oj for faster JSON handling.
Ward Vandewege [Mon, 4 Feb 2013 14:51:11 +0000 (09:51 -0500)]
Merge branch 'master' of git.clinicalfuture.com:orvos-server
Ward Vandewege [Mon, 4 Feb 2013 14:50:57 +0000 (09:50 -0500)]
Switch to Oj for JSON parsing.
Tom Clegg [Mon, 4 Feb 2013 06:57:40 +0000 (22:57 -0800)]
add some nil checks
Ward Vandewege [Mon, 4 Feb 2013 03:29:23 +0000 (22:29 -0500)]
Be careful with the shovel (<<) operator. It modifies the object on the
left hand side. And if that object is just a copy (i.e. reference to) of
another object, bad things like on-the-fly modification of the
orvos_login_base configuration value occur...
This fixes the multiplication of return_to parameters on every call to
the login url.
Ward Vandewege [Mon, 4 Feb 2013 02:06:45 +0000 (21:06 -0500)]
Do not show a 'Log out' link when the user is not logged in.
Tom Clegg [Sun, 3 Feb 2013 21:48:02 +0000 (13:48 -0800)]
fix "home" link
Ward Vandewege [Sun, 3 Feb 2013 20:43:13 +0000 (15:43 -0500)]
Fix test for :orvos_api_token in Thread.current, and log errors if it is
not there.
Ward Vandewege [Sun, 3 Feb 2013 20:00:54 +0000 (15:00 -0500)]
Throw an error when the uuid used for find() is invalid.
Tom Clegg [Sun, 3 Feb 2013 19:48:04 +0000 (11:48 -0800)]
add permission logging
Ward Vandewege [Sun, 3 Feb 2013 19:07:24 +0000 (14:07 -0500)]
Do not assume uuid_or_hash is a string when using it in string
concatenation.
Ward Vandewege [Sun, 3 Feb 2013 16:12:21 +0000 (11:12 -0500)]
Remove some unneeded stuff from the ant deploy file.
Tom Clegg [Sun, 3 Feb 2013 11:56:40 +0000 (03:56 -0800)]
add jobs and jobsteps
Tom Clegg [Sun, 3 Feb 2013 11:53:57 +0000 (03:53 -0800)]
add Job#priority
Tom Clegg [Sun, 3 Feb 2013 11:31:17 +0000 (03:31 -0800)]
fix setting modified_* and default owner when creating objects
Tom Clegg [Sun, 3 Feb 2013 11:30:33 +0000 (03:30 -0800)]
add Job and JobStep resources
Tom Clegg [Sun, 3 Feb 2013 09:32:57 +0000 (01:32 -0800)]
add deploy files for ant install
Tom Clegg [Sun, 3 Feb 2013 08:57:45 +0000 (00:57 -0800)]
support user and API client using different URIs for same API endpoint
Tom Clegg [Sun, 3 Feb 2013 08:56:45 +0000 (00:56 -0800)]
allow current_user => nil for pages that do not require login
Ward Vandewege [Fri, 1 Feb 2013 21:09:01 +0000 (16:09 -0500)]
Add deploy scripts for the Orvos instance on Ant.
Tom Clegg [Fri, 1 Feb 2013 17:41:38 +0000 (09:41 -0800)]
move logout link to right
Tom Clegg [Fri, 1 Feb 2013 07:13:08 +0000 (23:13 -0800)]
add table/graph nav pills
Tom Clegg [Fri, 1 Feb 2013 06:52:20 +0000 (22:52 -0800)]
add tabular /collections
Tom Clegg [Fri, 1 Feb 2013 06:20:00 +0000 (22:20 -0800)]
add Log out button, hide admin-only nav links if not admin
Tom Clegg [Fri, 1 Feb 2013 06:09:22 +0000 (22:09 -0800)]
fix login bug
Tom Clegg [Fri, 1 Feb 2013 05:57:31 +0000 (21:57 -0800)]
support return_to after logout
Tom Clegg [Fri, 1 Feb 2013 01:51:58 +0000 (17:51 -0800)]
add bootstrap