Ward Vandewege [Wed, 10 Apr 2013 15:26:58 +0000 (11:26 -0400)]
moved api server code into new directory structure
Tom Clegg [Wed, 10 Apr 2013 02:07:08 +0000 (19:07 -0700)]
add a bunch of API pages
Tom Clegg [Wed, 10 Apr 2013 01:10:56 +0000 (18:10 -0700)]
highlight active side nav
Tom Clegg [Wed, 10 Apr 2013 00:09:12 +0000 (17:09 -0700)]
use arvados.org favicon
Tom Clegg [Tue, 9 Apr 2013 22:17:13 +0000 (15:17 -0700)]
add provenance, using git, using keep pages
Tom Clegg [Tue, 9 Apr 2013 21:44:00 +0000 (14:44 -0700)]
rename ssh keys -> ssh access
Tom Clegg [Tue, 9 Apr 2013 21:30:46 +0000 (14:30 -0700)]
tweak front page of doc
Tom Clegg [Tue, 9 Apr 2013 21:27:25 +0000 (14:27 -0700)]
add ssh keys page
Tom Clegg [Tue, 9 Apr 2013 20:45:37 +0000 (13:45 -0700)]
fix "active section" style
Tom Clegg [Tue, 9 Apr 2013 19:15:30 +0000 (12:15 -0700)]
add jekyll doc tree
Samuel Shapiro [Fri, 29 Mar 2013 17:32:53 +0000 (13:32 -0400)]
added initial python wh file
Tom Clegg [Wed, 27 Mar 2013 19:26:45 +0000 (12:26 -0700)]
set instance.success when finished. refs #1424
Tom Clegg [Wed, 27 Mar 2013 00:14:59 +0000 (17:14 -0700)]
add --create-only and --instance arguments. refs #1448
Tom Clegg [Wed, 27 Mar 2013 00:43:23 +0000 (17:43 -0700)]
tweak serialized attribute search. refs #1447
Tom Clegg [Tue, 26 Mar 2013 23:39:19 +0000 (16:39 -0700)]
pass component[:script_parameters] to server when searching for jobs. refs #1447
Tom Clegg [Tue, 26 Mar 2013 23:38:07 +0000 (16:38 -0700)]
hack search on serialized fields. refs #1447
Tom Clegg [Tue, 26 Mar 2013 23:37:29 +0000 (16:37 -0700)]
fix crash on non-string job#script_parameters
Tom Clegg [Tue, 26 Mar 2013 23:10:04 +0000 (16:10 -0700)]
pass component[:script_version_descends_from] to server when searching for jobs. refs #1445
Tom Clegg [Tue, 26 Mar 2013 22:47:52 +0000 (15:47 -0700)]
Tweak git commit lookup. refs #1445
Tom Clegg [Tue, 26 Mar 2013 22:24:37 +0000 (15:24 -0700)]
Support searching jobs by script_version_descends_from. refs #1445
Tom Clegg [Mon, 25 Mar 2013 18:51:47 +0000 (11:51 -0700)]
add config.git_repositories_dir. refs #1445
Tom Clegg [Mon, 25 Mar 2013 18:50:53 +0000 (11:50 -0700)]
do not include ApiClient* in discovery document. refs #1405 refs #1406
Tom Clegg [Mon, 25 Mar 2013 21:20:29 +0000 (14:20 -0700)]
show pipeline instance uuid in plain text status. refs #1440
Ward Vandewege [Mon, 25 Mar 2013 21:18:14 +0000 (17:18 -0400)]
Merge branch 'master' of git.clinicalfuture.com:clients
Ward Vandewege [Mon, 25 Mar 2013 21:17:25 +0000 (17:17 -0400)]
Make subcommands singular. Slight layout improvement, too.
Tom Clegg [Mon, 25 Mar 2013 19:59:24 +0000 (12:59 -0700)]
create/update PipelineInstance while working. some code cleanup. refs #1440
Tom Clegg [Mon, 25 Mar 2013 21:13:16 +0000 (14:13 -0700)]
add pipeline_instances#index, fix #show to work with new-school pipelines. refs #1421 refs #1422
Ward Vandewege [Mon, 25 Mar 2013 20:47:36 +0000 (16:47 -0400)]
Fix up the discovery document - make sure we define 'items' in the the
various ObjectList definitions.
Also really fix up the issue with ObjectList vs ObjectsList.
This makes the Python SDK happy.
Ward Vandewege [Mon, 25 Mar 2013 19:50:34 +0000 (15:50 -0400)]
Make sure to pluralized object names in the List method as listed in the
REST discovery document.
This makes the Python SDK happy.
Tom Clegg [Mon, 25 Mar 2013 19:34:46 +0000 (12:34 -0700)]
accept pipeline template uuid in --template argument, improve docs. refs #1424
Tom Clegg [Mon, 25 Mar 2013 19:10:58 +0000 (12:10 -0700)]
rename wh-pipeline to wh-run-pipeline-instance. refs #1424
Tom Clegg [Mon, 25 Mar 2013 18:44:06 +0000 (11:44 -0700)]
tweak generic object display
Tom Clegg [Mon, 25 Mar 2013 18:21:43 +0000 (11:21 -0700)]
add /pipeline_templates index page. refs #1420
Tom Clegg [Mon, 25 Mar 2013 07:24:54 +0000 (00:24 -0700)]
fix rdoc. refs #1424
Tom Clegg [Fri, 22 Mar 2013 21:42:09 +0000 (14:42 -0700)]
add wh-pipeline. refs #1424
Tom Clegg [Fri, 22 Mar 2013 06:50:44 +0000 (23:50 -0700)]
show PGP huID tags. refs #1408 refs #1419
Tom Clegg [Fri, 22 Mar 2013 05:40:41 +0000 (22:40 -0700)]
tweak table border
Tom Clegg [Fri, 22 Mar 2013 04:18:08 +0000 (21:18 -0700)]
add names and keep flags to groups -> collections list. refs #1408
Tom Clegg [Thu, 21 Mar 2013 18:52:00 +0000 (11:52 -0700)]
use label instead of btn for labels on collections#show
Tom Clegg [Thu, 21 Mar 2013 17:14:34 +0000 (10:14 -0700)]
add Collections tab to groups#show page
Tom Clegg [Thu, 21 Mar 2013 17:14:02 +0000 (10:14 -0700)]
add "usual orvos object details" tab on collections#show page
Tom Clegg [Thu, 21 Mar 2013 17:13:20 +0000 (10:13 -0700)]
use ORVOS_API_TOKEN environment variable in rails console
Tom Clegg [Thu, 21 Mar 2013 15:59:14 +0000 (08:59 -0700)]
add Link to known-types list
Ward Vandewege [Wed, 20 Mar 2013 19:52:14 +0000 (15:52 -0400)]
Do not assume
session[:api_client_authorization_id]
exists when session[:user_id] is set.
Tom Clegg [Wed, 20 Mar 2013 02:56:17 +0000 (19:56 -0700)]
fix list logic. refs #1405 refs #1406
Tom Clegg [Wed, 20 Mar 2013 02:50:10 +0000 (19:50 -0700)]
add delete method. refs #1406
Tom Clegg [Wed, 20 Mar 2013 02:46:11 +0000 (19:46 -0700)]
add update method. refs #1406
Tom Clegg [Wed, 20 Mar 2013 02:42:55 +0000 (19:42 -0700)]
generalize output logic. refs #1405 refs #1406
Tom Clegg [Wed, 20 Mar 2013 02:34:56 +0000 (19:34 -0700)]
add create method. refs #1406
Tom Clegg [Wed, 20 Mar 2013 02:34:37 +0000 (19:34 -0700)]
improve error checking
Tom Clegg [Wed, 20 Mar 2013 02:34:01 +0000 (19:34 -0700)]
handle parameter types :object, :datetime, :text. refs #1405 refs #1406
Ward Vandewege [Wed, 20 Mar 2013 01:38:48 +0000 (21:38 -0400)]
Handle errors more gracefully.
Ward Vandewege [Wed, 20 Mar 2013 01:25:28 +0000 (21:25 -0400)]
Do not blow up when a default value for an argument is a boolean.
Ward Vandewege [Wed, 20 Mar 2013 01:23:49 +0000 (21:23 -0400)]
Now make sure we are really using the new rest file. refs #1406
Tom Clegg [Wed, 20 Mar 2013 01:08:26 +0000 (18:08 -0700)]
fix call to api_client.uuid when api_client is nil
Ward Vandewege [Wed, 20 Mar 2013 01:07:24 +0000 (21:07 -0400)]
Merge branch 'master' of git.clinicalfuture.com:orvos-server
Ward Vandewege [Wed, 20 Mar 2013 01:06:44 +0000 (21:06 -0400)]
Move auto-generated REST discovery document to the right path.
refs #1406
Tom Clegg [Wed, 20 Mar 2013 00:38:35 +0000 (17:38 -0700)]
use new permission methods to check model transactions. refs #1415
Tom Clegg [Wed, 20 Mar 2013 00:18:03 +0000 (17:18 -0700)]
add per-user and per-session default_owner. refs #1415
Tom Clegg [Tue, 19 Mar 2013 21:07:10 +0000 (14:07 -0700)]
fix exception when tasks_summary[:running] == nil
Tom Clegg [Tue, 19 Mar 2013 20:30:10 +0000 (13:30 -0700)]
rename job steps to job tasks. refs #1416
Tom Clegg [Tue, 19 Mar 2013 20:22:08 +0000 (13:22 -0700)]
rename job steps to job tasks. refs #1416
Tom Clegg [Tue, 19 Mar 2013 20:05:17 +0000 (13:05 -0700)]
rename pipeline to pipeline template. refs #1416
Tom Clegg [Tue, 19 Mar 2013 19:53:08 +0000 (12:53 -0700)]
rename pipeline to pipeline template. refs #1416
Tom Clegg [Tue, 19 Mar 2013 18:47:53 +0000 (11:47 -0700)]
rename pipeline invocation to pipeline instance. refs #1416
Tom Clegg [Tue, 19 Mar 2013 18:18:15 +0000 (11:18 -0700)]
rename pipeline invocation to pipeline instance. refs #1416
Tom Clegg [Tue, 19 Mar 2013 17:12:04 +0000 (10:12 -0700)]
rename job command to script. refs #1416
Tom Clegg [Tue, 19 Mar 2013 19:19:37 +0000 (12:19 -0700)]
fix cache keys
Tom Clegg [Tue, 19 Mar 2013 17:11:41 +0000 (10:11 -0700)]
rename job command to script. refs #1416
Ward Vandewege [Tue, 19 Mar 2013 16:19:34 +0000 (12:19 -0400)]
Initial version of the cli client.
Tom Clegg [Tue, 19 Mar 2013 08:06:30 +0000 (01:06 -0700)]
generate discovery document at /orvos/v1/rest. refs #1406
Tom Clegg [Tue, 19 Mar 2013 06:24:35 +0000 (23:24 -0700)]
add group#index and group#show pages. refs #1415
Tom Clegg [Mon, 18 Mar 2013 23:32:52 +0000 (16:32 -0700)]
add Job#show template. refs #1417
Tom Clegg [Mon, 18 Mar 2013 23:20:01 +0000 (16:20 -0700)]
relocate permissions code, use resulting :read permissions in #index. refs #1415
Tom Clegg [Mon, 18 Mar 2013 22:28:27 +0000 (15:28 -0700)]
current_group_permissions, groups_i_can(:read). refs #1415
amends
cf70bb6f00f0ded0624bac59a909a1cf8602dbff
Tom Clegg [Mon, 18 Mar 2013 22:25:37 +0000 (15:25 -0700)]
show progress bar and tasks summary on /jobs page. refs #1417
Ward Vandewege [Mon, 18 Mar 2013 20:01:17 +0000 (16:01 -0400)]
maxResults is really called limit, update the discovery document accordingly
Tom Clegg [Mon, 18 Mar 2013 19:50:22 +0000 (12:50 -0700)]
add helpers: current_group_permissions, groups_i_can(:read). refs #1415
Tom Clegg [Mon, 18 Mar 2013 16:21:08 +0000 (09:21 -0700)]
clean up /jobs page. refs #1417
Tom Clegg [Mon, 18 Mar 2013 16:20:47 +0000 (09:20 -0700)]
enable auto job links
Tom Clegg [Mon, 18 Mar 2013 03:02:03 +0000 (20:02 -0700)]
add /jobs page. refs #1417
Tom Clegg [Mon, 18 Mar 2013 02:57:39 +0000 (19:57 -0700)]
Add Job#resource_limits to API response. refs #1417
Tom Clegg [Mon, 18 Mar 2013 02:44:37 +0000 (19:44 -0700)]
record started_at, and command_version reported by whjobmanager. refs #1417
Tom Clegg [Mon, 18 Mar 2013 02:27:38 +0000 (19:27 -0700)]
add output to Job api response. refs #1417
Tom Clegg [Mon, 18 Mar 2013 02:03:05 +0000 (19:03 -0700)]
Tom Clegg [Mon, 18 Mar 2013 02:02:41 +0000 (19:02 -0700)]
Fix slurm node counting, and pass along min_nodes to salloc. refs #1417
Tom Clegg [Mon, 18 Mar 2013 01:46:36 +0000 (18:46 -0700)]
Do not try to start a job when too few slurm nodes are idle. refs #1417
Tom Clegg [Mon, 18 Mar 2013 00:48:25 +0000 (17:48 -0700)]
add Jobs#resource_limits attribute. refs #1417
Tom Clegg [Sun, 17 Mar 2013 22:29:18 +0000 (15:29 -0700)]
fix no-tasks-todo -> success logic
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
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