Martin Cech
4dbb249ca6
removed bug with missing return
2014-09-16 13:15:32 -04:00
Martin Cech
3cc0b971d1
trying to merge
2014-09-16 11:56:13 -04:00
Martin Cech
2b0cda6bbe
Merge
2014-09-16 11:40:08 -04:00
Martin Cech
7b67fe13db
allow admins to paste paths, pack scripts
2014-09-16 11:39:17 -04:00
Dannon Baker
d869a18c5e
Merged in natefoo/galaxy-central (pull request #495 )
...
Clean up the root directory and rename universe_wsgi.ini
2014-09-16 09:08:35 -04:00
Aysam Guerler
1a307de0b6
Ui: Add packed script, fix attributes
2014-09-16 02:42:09 -04:00
Aysam Guerler
ce679acf89
Ui: Unify checkboxes and radio buttons, extend functionality, Upload: Fix code style, ToolForm: Extend dataset filtering
2014-09-16 01:46:17 -04:00
Nate Coraor
8fadc6392b
Rename universe_wsgi.ini -> galaxy.ini everywhere.
2014-09-15 16:43:51 -04:00
Dannon Baker
48dbd1f4a5
Pack scripts.
2014-09-12 19:47:00 -04:00
Dannon Baker
7ac2ae2f6d
Prevent double submission of workflow.
2014-09-12 19:45:06 -04:00
Carl Eberhard
373093aa93
Fix to 618b02d13329: remove console, add documentation
2014-09-11 14:11:37 -04:00
Carl Eberhard
e1ec150da7
History panels: allow foldout display of collections in display_by_slug, pages, and /view
2014-09-11 12:23:00 -04:00
Aysam Guerler
b692c0ebf3
ToolForm: Implements error handling, applies fixes to styles and structure, UI: Fixes code style for frames
2014-09-11 12:02:21 -04:00
Carl Eberhard
04b72d65f8
Cleanup b0c8da2
2014-09-08 16:56:07 -04:00
Aysam Guerler
8420169b7e
ToolForm: Generate json for tools api, improve ui-tabs
2014-09-08 16:52:28 -04:00
Carl Eberhard
33dc9c283e
History panel: make search input shown by default, remove toggle; List panel: make collection-panel and history-panel inherit from list-panel, move list-panel and base-mvc.list-item to mvc/list; general history and collection panel refactoring
2014-09-08 16:49:30 -04:00
Carl Eberhard
1d32e43a37
Fix to 419ca68: re-add ability to re-size right and left panels using mouse events
2014-09-08 15:10:49 -04:00
Martin Cech
5934a68685
adding compressed version of jstree jquery plugin
2014-09-08 14:45:37 -04:00
Martin Cech
3bddbcf11f
initial implementation of UI, API and flow for importing from Galaxy user directories, introduces jstree browser into the project, includes refactoring of some library API methods into common managers
2014-09-08 14:27:49 -04:00
Aysam Guerler
25fd90792e
ToolForm: Add jobs module, fix minor issues and revise tool form style
2014-09-06 16:08:35 -04:00
Aysam Guerler
38d5ac8f90
ToolForm: Additional buttons, fixes and improvements, genome build selector, first commit for multiple dataset and collection selector
2014-09-05 11:24:55 -04:00
Aysam Guerler
aaa5a810ab
ToolForm: Fix multi-select field
2014-09-03 23:33:30 -04:00
Aysam Guerler
d9f008af7f
ToolForm: Adjust textarea element
2014-09-03 16:47:14 -04:00
Aysam Guerler
5f7aff8553
ToolForm: Adjustments and refactoring
2014-09-03 15:30:50 -04:00
John Chilton
6d727ce454
Merge stable.
2014-09-02 16:41:48 -04:00
Aysam Guerler
7dfb30354e
ToolForm: Add sliders, radio buttons for boolean and integer fields, Ui: Update frames
2014-09-02 16:06:35 -04:00
Carl Eberhard
cabe8ed425
History API: remove set_as_current, api/histories/current, and POST api/histories with current == True (create new current history), replace with controllers/history/set_as_current, current_history_json, and create_new_current (respectively) - all returning json; add exceptions.DeprecatedMethod; pack scripts
2014-09-02 13:26:47 -04:00
John Chilton
9978e26dce
Pack scripts.
2014-09-02 11:21:08 -04:00
John Chilton
24e914f57b
Fix workflow editor bug related state updates for collections attached to multiple input data parameters.
...
Detail bug report from Michael Crusoe here : https://trello.com/c/0mdGCx4P .
This also fixes a test case added in 289e48b which was both attempting to assert something wrong and was incorrectly implemented. Augmenting the workflow editor test suite with some actually valid test cases that assert the correct behaviors.
For a longer explaination - workflow input terminals have two related concepts 'canAccept' and 'attachable'. An output terminal is 'attachable' if in the abstract it could be attached to the input regardless of whether the input is already filled or not. 'canAccept' is more stateful in that an output terminal is 'canAccept'able if the input terminal is not filled ('_inputFilled') and it is 'attachable'.
So - the problem was 'attachable' was not correctly defined for a multiple input data parameters. 'attachable' was asserting that any connected input terminal could not be 'attachable' by an collection output terminal - so on these asynchronous node state changes collections attached to multiple input data parameters were being wiped out. The more percise/correct distinction is that if a multiple input data parameter has single inputs connected to it - it cannot also have a collection connected to it (yet anyway). This fixes the mentioned bug.
The problematic test case was conflating 'attachable' and 'canAccept'able - I have fixed the test case to verify the correct 'attachable' logic and added newer, higher level test cases to test the canAccept logic and the actual behavior the end user would observe (of the connector being destroy).
2014-09-02 11:20:44 -04:00
Dannon Baker
fd53ed075d
Pack scripts.
2014-09-02 09:29:50 -04:00
John Chilton
e8b7272aa8
Merge latest stable changes.
2014-09-02 08:54:56 -04:00
Jeremy Goecks
0c75a102d0
HDA/LDDA models: synchronize them with 'data_type' and 'file_ext', properly fill data_type with Galaxy data types, and use file_ext in place of data_type throughput client code.
2014-08-29 17:17:44 -04:00
Carl Eberhard
b8b1c4e36f
History contents: allow copying accessible datasets into this history
2014-08-29 10:43:51 -04:00
John Chilton
b78d059f4c
Pack scripts.
2014-08-29 00:31:59 -04:00
John Chilton
d80d1b1a8f
Fix for at workflow editor glitch.
2014-08-29 00:30:30 -04:00
Carl Eberhard
8b1af7ece5
Fix to history: remove prev. loading indicator before showing another
2014-08-28 16:51:28 -04:00
Aysam Guerler
34e146b33d
ToolForm: Adds limits for repeat blocks and fixes
2014-08-28 16:35:59 -04:00
Aysam Guerler
5980c1e467
ToolForm: Enables hierarchical references and conversion of the tool form into a json/xml tree structure
2014-08-28 14:03:35 -04:00
Carl Eberhard
17a6595b5c
Fix: remove 'jquery.event.drag.js' from base_panels.mako; Paired collection creator: allow single/multiple pairs to be re-ordered by drag and drop
2014-08-28 12:19:16 -04:00
Carl Eberhard
fb5a6afa97
UI, Paired collection creator: fixes and refactoring, allow pairs to be selected
2014-08-27 14:47:54 -04:00
Carl Eberhard
0baf3bfee3
UI, Paired collection creator: refactoring of paired HTML and fixes to draggable partition, add brush selection to unpaired
2014-08-26 16:30:46 -04:00
Carl Eberhard
da5513f038
(add packed scripts)
2014-08-26 12:59:59 -04:00
Carl Eberhard
8a9b24dcd4
UI, Dataset choice control: add DatasetChoiceModal for choosing single or multiple datasets, add DatasetChoice and MultiDatasetChoice for displaying and activating selection modal from within a page; correct lookup of galaxy_config in dataset-model; add ListPanel for displaying collections of ListViews; add DatasetListPanel for displaying collections of generic datasets; add default no-op localizer (_l) to ui.js until that file is AMD; factor out icon-btn.less from history.less; remove make_popup_menus in default expandable behaviors
2014-08-26 12:59:15 -04:00
John Chilton
62f0d9da61
Merge latest stable.
2014-08-25 15:35:45 -04:00
Aysam Guerler
6173935263
ToolForm: Add repeat blocks, refactor conditionals, fix styles, pack scripts
2014-08-25 12:27:18 -04:00
Aysam Guerler
707f180cdc
ToolForm: Implements conditionals
2014-08-22 14:32:07 -04:00
Dannon Baker
0da37adb13
Strip trailing whitespace from galaxy.menu.js
2014-08-20 12:56:01 -04:00
Dannon Baker
930fe2fa61
Swap remote user logout to actually follow galaxy internal logout procedure and then redirect. Also fix logic for user dropdown -- it was preventing users from seeing stuff that was actually available before.
2014-08-20 12:55:32 -04:00
Aysam Guerler
d995301098
ToolForm: Add data selector, dynamic column selector and checkboxes, extends json content for basic parameters
2014-08-19 15:01:57 -04:00
Dannon Baker
09f2a6967d
Update to jquery1.11.1. This resolves at least one issue related to submit listeners not being attached in iframes, causing tool form failures for tools using conditional parameters like single/paired end reads, default/advanced parameter sets, and so on.
2014-08-19 12:47:34 -04:00
Martin Cech