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Author SHA1 Message Date
Dannon Baker 4dc04e1472 Fix a few instances of incorrect (deprecated) use of value instead of identity testing in xml parsing. 2015-02-08 11:16:14 -05:00
John Chilton 0e582719fe Fix running tool tests for recent control reworking. 2015-02-07 19:32:16 -05:00
John Chilton 9e0d530c0c Rework control queue setup to work in non-web contexts. 
Namely in the new lib/galaxy/main.py. I think this break down of the code makes more sense also since control queues aren't inheriently something web-y so lib/galaxy/app.py makes more sense for configuring them. Dannon feel free to reorganize if you dislike this particular organization - I just wanted to make sure lib/galaxy/main.py could share in the new stuff.
 2015-02-07 19:32:16 -05:00
Aysam Guerler 05787784c2 Ui: Use placeholder title 2015-02-06 23:32:58 -05:00
Aysam Guerler 0718fca13f ToolForm: Update repeat blocks 2015-02-06 23:23:26 -05:00
Aysam Guerler 3dd4207f03 ToolForm: More style adjustments 2015-02-06 22:03:33 -05:00
John Chilton 7f5f15b4f3 Merged in JenCabral/galaxy-central/tool_shed_test_fix-DB_initialization (pull request #662) 
Fix tool shed tests - create database directory
 2015-02-06 21:33:49 -05:00
Aysam Guerler 57b9fefb07 Ui: Repack styles 2015-02-06 20:49:58 -05:00
Aysam Guerler 1750027b57 Ui: Add tooltip to options 2015-02-06 20:47:28 -05:00
Aysam Guerler aca45c1b36 ToolForm: Try new data selector style 2015-02-06 19:09:53 -05:00
Aysam Guerler 50c0ce8228 Ui: Fix slider value element 2015-02-06 16:38:11 -05:00
Carl Eberhard 0547725d03 Fix to 8c71422: add the file 2015-02-06 13:56:31 -05:00
Carl Eberhard 242f2634cf API, configuration: expand exposed settings to include those needed by the masthead in galaxy.masthead.mako, add serializers for config 2015-02-06 13:38:53 -05:00
JenCabral d0dedc8404 adding a comment and moving out of else statement 2015-02-06 11:05:04 -06:00
JenCabral ee3fe10503 checks to see if directory for database exists if not creates the directory 2015-02-06 10:59:53 -06:00
Daniel Blankenberg 1155ead7ff Fix for SelectToolParameters that utilize dynamic options and that make use of __trans__ failing at get_legal_values(). 2015-02-06 11:56:54 -05:00
Jennifer Cabral 940bfc48a2 Created new branch tool_shed_test_fix-DB_initialization 2015-02-06 16:51:03 +00:00
Dannon Baker f4ec978d9e Relocate uwsgi test to the beginning of config, since this might affect other config options down the road. 2015-02-06 11:40:47 -05:00
Dannon Baker c6cda49498 Merge. 2015-02-06 11:33:45 -05:00
Dannon Baker f457c09f07 Adjust generated queue names to match with new postfork manipulation of config.server_name 2015-02-06 11:33:33 -05:00
Aysam Guerler 68d9ea0fad Ui: Fix class name 2015-02-06 11:23:19 -05:00
Aysam Guerler 928f558b08 Merge 2015-02-06 11:06:29 -05:00
Aysam Guerler 836b3bb913 Ui: Revise portlet margins 2015-02-06 11:05:23 -05:00
Dannon Baker 7adff59c5f Force postfork unique servername on uwsgi workers in the format of 'servername.workername'. Use this for correctly routing messages. 2015-02-06 11:05:06 -05:00
Dannon Baker 5eff5db70d Minor formatting of routes in buildapp.py 2015-02-06 10:55:15 -05:00
Dannon Baker 2fed958e86 The other half of d89864b9f5daaec89dfda0ad5772a13aed72536b. 2015-02-06 09:00:12 -05:00
Dannon Baker 9f826acff7 Merge. 2015-02-06 08:56:03 -05:00
Dannon Baker c973726bb1 Postfork (under uwsgi at least -- otherwise just the last bit before webapp returns) magic for kicking off workers (and potentially other things) 2015-02-06 08:55:50 -05:00
Aysam Guerler 7053352ab2 ToolForm: Increase padding 2015-02-06 00:19:28 -05:00
Aysam Guerler 72c725bb22 ToolForm: Update style 2015-02-06 00:07:21 -05:00
Aysam Guerler 6c9fe7f735 ToolForm: Log conversion warning 2015-02-05 22:56:46 -05:00
Aysam Guerler c8aece99eb Workflow: Add style for workflow tool form 2015-02-05 22:25:22 -05:00
John Chilton ba825fc553 Fix reports webapp for MySQL. 
Big thanks for Eric Enns and Fernandez Edgar for contributing patches to the galaxy-dev list.
 2015-02-05 21:27:53 -05:00
John Chilton 09c88b119c PEP-8 fixes for reports controllers and app. 2015-02-05 21:27:53 -05:00
Dannon Baker 17d3311f3a Minor pep8'ing in lib/galaxy/config.py 2015-02-05 19:16:19 -05:00
Dannon Baker 269cab275f Remove TODO about moving uwsgi test since I did it. 2015-02-05 19:15:10 -05:00
Dannon Baker c3004f7af1 Relocate is_uwsgi to app.config (determined at configuration time via import). 2015-02-05 19:13:59 -05:00
Dannon Baker 7b8dac532e Merge. 2015-02-05 18:55:20 -05:00
Dannon Baker d3fac05f1d Fix lunr availability for tool form. Turns out javascript define needs a target. Oops. 2015-02-05 18:55:15 -05:00
Dannon Baker a5c151ead8 Add reference to the webapp to galaxy.app 2015-02-05 18:35:43 -05:00
Carl Eberhard d31335fbcf Fix to 3abf1c3: pass app to super 2015-02-05 17:36:26 -05:00
Carl Eberhard 23991f5e1b Managers, users: add filters for later admin use, quota serializers, and a fallback anonymous user serialization; DatasetAssociations & HDAs: add filters 2015-02-05 16:55:23 -05:00
Aysam Guerler a251de996a ToolForm: Update version selection, use underscores for internal parameters 2015-02-05 13:34:51 -05:00
John Chilton ab2bfa88b8 Bugfix for bugfix d3b1f6b. 
d3b1f6b fix the GUI (in an obsecure use) but broke fairly typical uses of the API.
 2015-02-05 13:32:56 -05:00
John Chilton 5956c42d2c Improved error message if things don't match up when recovering workflows. 
Ideally this shouldn't really happen - but this should help if it does.
 2015-02-05 12:27:46 -05:00
John Chilton afed259b39 Fix scheduling_manager.py for unknown attribute reference. 
Not sure if this was a poor rebasing or a copy and paste error.
 2015-02-05 12:27:46 -05:00
John Chilton 5a1336f7de Workflow scheduling delay fix. 
There were problems if all three of these conditions were met - 1) workflow from GUI, 2) workflow evaluation delayed, and 3) a delayed step was connected to a input dataset. This fixes these workflows.
 2015-02-05 12:27:46 -05:00
John Chilton 85eb1fed9f Fix workflow schedulers to fallback onto sample like other config files. 2015-02-05 12:27:46 -05:00
Aysam Guerler 840176e543 Workflow: Fix text and boolean parameter handling, simplify module update 2015-02-05 10:08:45 -05:00
Dannon Baker 2de2e340a2 pep8, cleanup in galaxy/buildapp 2015-02-05 09:45:15 -05:00