Dannon Baker
78a4042517
Fixes for Search API.
2013-04-10 13:59:33 -04:00
Dannon Baker
f1317d6a51
Merge pull request 137: Galaxy Search Engine.
2013-04-10 12:56:00 -04:00
Carl Eberhard
b1c3cb55ff
Edit attributes: HDA name, info, annotation: display 'None' values in inputs as empty strings; History panel: remove last modal/alert
2013-04-10 12:22:11 -04:00
Carl Eberhard
73a4e9ded6
History panel: hack to show expanded HDA bodies in chrome; pack scripts
2013-04-10 11:30:37 -04:00
Jeremy Goecks
4ce073f25a
Trackster: Implement and use reference-based read drawing when genome reference is available. This reduces the data transfer for read tracks by ~50%. Fix bugs in reference-based data provider code and remove client-side debugging statements.
2013-04-10 10:34:30 -04:00
Carl Eberhard
f799e0fded
history panel: handle errors better on the client side, remove alerts, continue update attempts if error is 'Bad Gateway'
2013-04-09 19:17:51 -04:00
Jeremy Goecks
e2e4448c3c
Custom build bug fix to indicate availability of reference data during conversion. Parameter cleanup via Pylint as well.
2013-04-09 16:48:08 -04:00
Carl Eberhard
be0a279497
remove debugging
2013-04-09 16:42:08 -04:00
Carl Eberhard
551cf6b971
history panel: better error-handling
2013-04-09 16:39:43 -04:00
Aysam Guerler
6cc810345b
Enhance button for trackster visualization in data display viewer
2013-04-09 13:59:56 -04:00
Dannon Baker
53e5eb371d
Add missing imports to tool shed repository API. Add NERD_tree_2fixme for variable used out of context
2013-04-09 13:42:27 -04:00
Dannon Baker
a02919c0b0
Fix string templating mismatch in tool shed repository API. Similar to 9328:b2a5169daea4
2013-04-09 13:36:18 -04:00
Dannon Baker
924d0a0896
Add Parsley egg prior to merging search API.
2013-04-09 13:20:29 -04:00
Daniel Blankenberg
73843b539d
Change database logging of stderr and stdout to take text from start and end of the string (instead of just the start) when the size exceeds the set character limit (32k).
2013-04-09 13:00:47 -04:00
Daniel Blankenberg
0b17de996b
Fix for generating stderr/stdout links in hda show_params.
2013-04-09 12:26:05 -04:00
James Taylor
d02155ad7b
Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5
2013-04-09 11:57:38 -04:00
Carl Eberhard
e9797bacee
history panel: move alternate_history.mako to history.mako
2013-04-09 10:58:38 -04:00
Dannon Baker
ccaf1865ed
Merged in BjoernGruening/galaxy-central-bgruening/error-message-fix (pull request #150 )
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change error message
2013-04-09 09:56:12 -04:00
Dannon Baker
3651f2b74e
Import cleanup, space methods, strip trailing whitespace.
2013-04-09 09:36:23 -04:00
Dannon Baker
440cd89c74
Fix bug from 8333 which prevented ToolDataTable loading .loc files from directories other than the default galaxy tool_data_path.
2013-04-09 09:34:24 -04:00
Kyle Ellrott
75d343930e
Merge and check to see if hda.history is not null before adding history id in get_api_value
2013-04-08 22:33:01 -07:00
Kyle Ellrott
9e49883204
Adding ldda parent_library_id field to search.
2013-04-08 22:25:02 -07:00
Jeremy Goecks
2e1f98d430
Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #140 )
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Improvements to Tool XML Macroing System
2013-04-08 17:10:21 -04:00
Nate Coraor
505f4409ef
Merged stable.
2013-04-08 12:30:08 -04:00
Nate Coraor
9d2d364f82
Added tag security_2013.04.08 for changeset 2cc8d10988e0
2013-04-08 12:28:46 -04:00
Dannon Baker
d008db0e06
Add Reports runtime files to .hgignore
2013-04-08 10:56:26 -04:00
Aysam Guerler
1633386bfc
Inserted a button for trackster visualization into the BED-file data display viewer.
2013-04-08 10:19:37 -04:00
Bjoern Gruening
dadda8f1e0
change error message
2013-04-06 15:00:37 +02:00
Nate Coraor
08986d7cb2
Merged in jmchilton/galaxy-central-multi-input-tool-fixes-2 (pull request #143 )
2013-04-05 17:05:41 -04:00
Carl Eberhard
16ea5d52d0
controllers/root.default: have default return the same message as a 404 (HTTPNotFound)
2013-04-05 17:02:07 -04:00
Dannon Baker
4e18f06a29
Relocate TracksterConfig import in tools package to avoid circular import w/ visual_analytics that was preventing the reports app from functioning.
2013-04-05 15:58:31 -04:00
Carl Eberhard
4477aeab85
history panel: do not fetch display apps if there are no hdas yet
2013-04-05 14:01:59 -04:00
Carl Eberhard
b02f3851e9
history panel: fix test for partial/full render of hdas to prevent 'blinking'2
2013-04-05 13:50:24 -04:00
Carl Eberhard
0cc21367d2
merge to stable
2013-04-05 13:09:11 -04:00
Carl Eberhard
2475ede3de
controllers/history: use get_history in switch_to_history
2013-04-05 13:07:50 -04:00
Dave Bouvier
9dbf1f4abb
Tool shed functional test enhancements. Tests for 8-bit ASCII characters displayed in repository files. Tests for using the mercurial API to simulate a command line push. Tests for deleting tool dependencies.
2013-04-05 11:18:39 -04:00
Jeremy Goecks
501195c101
Implement a reference-based compression approach for encoding aligned reads' sequence and cigar. Move cigar functions into own file.
2013-04-05 09:39:05 -04:00
Carl Eberhard
581f726e87
controllers/root: remove methods my_data, dataset_state, dataset_code; add documentation; clean imports
2013-04-04 20:08:58 -04:00
Carl Eberhard
a391e6c3e2
Remove history.mako; old history panel from root.history; remove from root: user_get_usage, history_item_updates, history_get_disk_size
2013-04-04 18:16:46 -04:00
Kyle Ellrott
3f63c32202
Mainline merge
2013-04-04 14:50:01 -07:00
Carl Eberhard
7d5a318dff
add missing select2 image to css and images
2013-04-04 16:14:52 -04:00
Dannon Baker
f23c39f4d4
Fix for incorrect template inheritance causing the tool shed base_panels to be displayed in the galaxy app upon logout.
...
Mako's inherit directives are processed *before* non-global logic, so you need a built-in switch (as implemented, now) or, ideally, refactor into different templates for each webapp that inherit correctly.
2013-04-04 15:34:43 -04:00
Dannon Baker
d27381fddd
Fix for incorrect template inheritance causing the tool shed base_panels to be displayed in the galaxy app upon logout.
...
Mako's inherit directives are processed *before* non-global logic, so you need a built-in switch (as implemented, now) or, ideally, refactor into different templates for each webapp that inherit correctly.
2013-04-04 15:34:43 -04:00
Greg Von Kuster
0db2c70d14
Use styles when displaying tool functional test results in the tool shed.
2013-04-04 14:23:19 -04:00
Daniel Blankenberg
f16854a723
Fix for preview flag in Dataset display.
2013-04-04 13:01:39 -04:00
Daniel Blankenberg
3b30904f8e
Fix for preview flag in Dataset display.
2013-04-04 13:01:39 -04:00
Greg Von Kuster
b85d7ce6c0
Better handling for mercurial command line pushes to tool shed repositories when invalid credentials are sent.
2013-04-04 11:59:18 -04:00
Jeremy Goecks
b935651558
Fixes for commit 4317a15.
2013-04-04 11:39:32 -04:00
Dannon Baker
c829a8b736
Fixes logout with remote_user=True (almost, logout.mako still uses the wrong template -- bug introduced in 56de0ee7932f)
2013-04-04 10:19:17 -04:00
Dannon Baker
f2b496ef35
Relocate TracksterConfig import in tools package to avoid circular import w/ visual_analytics that was preventing the reports app from functioning.
2013-04-05 15:58:31 -04:00
Dannon Baker