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Author SHA1 Message Date
Aysam Guerler 9efc2a16f8 Upload: Use nginx_upload_path setting 2013-11-19 14:56:07 -05:00
Jeremy Goecks feb126b4c2 Make viz_filter_cols metadata attribute optional. 2013-11-19 14:23:32 -05:00
Dannon Baker f06cf661f3 Merged in kellrott/galaxy-central/search (pull request #261) 
Adding history_id selection to hda search
 2013-11-19 11:20:33 -08:00
Nicola Soranzo 79a7fb9339 Fix API workflow show for workflows created with history Extract Workflow. 
To reproduce:
1) for an existing history, select "Extract Workflow" from the history menu
2) find the id of the new workflow, e.g. by opening /api/workflows/
3) open /api/workflows/$workflow_id

Result is an Internal Server Error.
In Galaxy log:

galaxy.web.framework ERROR 2013-11-19 12:44:17,367 Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/srv/galaxy/lib/galaxy/web/framework/__init__.py", line 197, in decorator
    rval = func( self, trans, *args, **kwargs)
  File "/srv/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 77, in show
    inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""}
TypeError: 'NoneType' object has no attribute '__getitem__'

Reported-by: Simone Leo <simone.leo@crs4.it>
 2013-11-19 19:36:17 +01:00
Carl Eberhard be7439e601 Remove print from f166a09 2013-11-19 10:29:38 -05:00
Carl Eberhard a8607736cd Visualizations Registry: propery default to str eqv test for test_type, properly call getattr_lambda 2013-11-19 10:26:48 -05:00
Carl Eberhard f62746c58a Visualizations API: fix create/update validation 2013-11-19 10:24:35 -05:00
Carl Eberhard 018f5187e8 Scatterplot (plugin version): small fixes, move dataset out of config, namespace hbrs templates 2013-11-19 10:19:22 -05:00
Dave Bouvier b2cffd410c Log more information about tool dependency and repository installation status when installing and testing. 2013-11-19 09:51:30 -05:00
Greg Von Kuster 2831fda269 Fix for populating the missing tool dependencies container in certain special cases in Tool Shed repositories. 2013-11-19 08:55:23 -05:00
Greg Von Kuster 0aa3b2bc32 Fix for populating and unpopulating complex repository dependency tags sets in tool dependency definitions contained in tool shed repositories. 2013-11-19 08:52:20 -05:00
John Chilton fd77149823 Re-fix tool API for uploads coming through nginx. 
Give tools.get_incoming_value a chance to mangle all keys and see if they appear in some other format. Thanks to @natefoo for detecting the problem, determining the source of the error, and describing the exact path through the code - i.e.  doing all the work.
 2013-11-18 21:26:29 -06:00
Aysam Guerler 7ab6e8f41a Toolshed: Fix grids 2013-11-18 16:02:41 -05:00
Jeremy Goecks d1c091fa11 Trackster: more improvements for drawing deletions in read and variant track. 2013-11-18 15:57:15 -05:00
Jeremy Goecks d3041bd82e Trackster painters: rename y_center variable to y_start to reflect real position. 2013-11-18 14:18:10 -05:00
Jeremy Goecks e5621a9485 Trackster: add support for detecting and drawing deletions in VCF datasets. Create shared read painter utils that are used by multiple painters. 2013-11-18 13:55:43 -05:00
Carl Eberhard 17f642019c History panel: ensure tooltip deletion on hda view removal, add class selectors for primary action buttons; pack scripts 2013-11-18 12:39:52 -05:00
John Chilton 2b6bbac874 Refactor smaller methods out of tool output test parsing. 2013-11-18 00:51:54 -06:00
John Chilton 467ea7ff57 Make formerly public methods in ToolTestBuilder private now that it does its own construction. 2013-11-18 00:51:54 -06:00
John Chilton 37714b3f2a Refactor tool test parsing logic out of Tool and into ToolTestBuilder. 2013-11-18 00:51:54 -06:00
John Chilton ef3e5e9fd5 PEP-8 fixes related to tool test parsing. 2013-11-18 00:51:54 -06:00
John Chilton 5142dbe44d Redo fix from 8b65e61 so it works when no Twill clicking at all occurs (e.g. all default params used). 2013-11-18 00:51:54 -06:00
Aysam Guerler 11824714b4 Grids: Remove console output 2013-11-17 05:37:57 -05:00
Aysam Guerler a6accba94c Grids: Remove console output 2013-11-17 05:16:54 -05:00
Aysam Guerler 51e7a2935a Grids: Reduce mako templating to json generation, introduce GridsView, bug fixes 
iG: changed templates/webapps/galaxy/tracks/history_select_grid.mako
 2013-11-17 05:08:25 -05:00
John Chilton f05eacf362 Functional tool test fix. 
No tests with a repeat and min=1 were ever going to past.
 2013-11-17 02:03:28 -06:00
John Chilton 4cba87cc16 PEP-8 and style adjustments for lib/galaxy/webapps/galaxy/api/provenance.py. 2013-11-17 00:53:00 -06:00
John Chilton ddab3d2239 Consolidate duplicated code for loading HDAs from the API. 2013-11-17 00:47:26 -06:00
John Chilton fcaa566e60 Fix logic in tool's populate_state logic to handle multiple uploads. 
Enables composite uploads through API.
 2013-11-17 00:47:26 -06:00
John Chilton 6ef8fc7181 Do not reference values before use when GALAXY_TEST_EXTERNAL used. 
GALAXY_TEST_EXTERNAL still quite broken.
 2013-11-17 00:47:26 -06:00
Nate Coraor c014405099 Merged in nsoranzo/galaxy-central (pull request #262) 
Convert other 3 tools to $GALAXY_SLOTS
 2013-11-15 19:05:06 -05:00
Nicola Soranzo 3e528ae02b Enhance bowtie2 to utilize GALAXY_SLOTS configuration when available. 2013-11-16 00:53:52 +01:00
Nicola Soranzo c4e9999a33 Enhance mosaik to utilize GALAXY_SLOTS configuration when available. 2013-11-16 00:53:35 +01:00
Nicola Soranzo a481327ab3 Enhance trinity to utilize GALAXY_SLOTS configuration when available. 2013-11-16 00:52:36 +01:00
Kyle Ellrott a9b85f345d Adding 'copied_from_hda_id' field to hda view. 2013-11-15 15:26:24 -08:00
Carl Eberhard dd315841b2 History panel: fix disabled class on icon buttons 2013-11-15 15:53:59 -05:00
Carl Eberhard d06f88455e Update jquery.form.js to 3.45 and fix chrome upload bug; pack scripts 2013-11-15 15:18:18 -05:00
Kyle Ellrott 8471e4aa0f Adding in history_id selection to hda view, so hda elements can be selected by their parent history 2013-11-15 11:46:52 -08:00
Kyle Ellrott 46c2df2ba9 Default merge 2013-11-15 11:29:10 -08:00
Nate Coraor 3f11b97087 Merge stable. 2013-11-15 14:19:09 -05:00
Kyle Ellrott a9f56c7c15 Merged galaxy/galaxy-central into default 2013-11-15 11:18:26 -08:00
Nate Coraor ce31bc4742 Properly handle PBS' -q argument. 2013-11-15 14:18:09 -05:00
Nate Coraor b9b735a7f7 Detect nginx upload injected params in the API tool runner. 2013-11-15 14:15:00 -05:00
Dave Bouvier 44d7f92352 Fix for exporting a repository with a complex repository dependency. 2013-11-15 11:14:26 -05:00
Dave Bouvier 92998fb377 Fix for exporting a repository capsule. 2013-11-15 10:50:49 -05:00
John Chilton 3fe4ea3d52 Merge latest stable. 2013-11-15 08:20:36 -06:00
John Chilton 553efe99d3 Fix small typo in 9ce5afd (tool shed autoconf action). 2013-11-15 08:20:06 -06:00
John Chilton 7f9712c48c Fix bug in 4f7e715 that actually allows multiple repeat values to be specified via API. 2013-11-14 23:39:52 -06:00
John Chilton 3d03f12e0a PEP-8 fixes for test/base/twilltestcase.py. 
Still hundreds of lines to fix.
 2013-11-14 17:49:58 -06:00
Dave Bouvier 249082d983 Remove reference to undefined variable. 2013-11-14 18:43:58 -05:00