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Commit Graph
3297 Commits
Author SHA1 Message Date
Dannon Baker 0f099b75b6 Merge branch 'release_16.01' into dev 2016-03-24 17:30:00 -04:00
Dannon Baker b51bdd06b1 Basepanels don't have Galaxy object, causing failures in views like published tracks, etc., when resource urls are generated incorrectly 2016-03-23 16:55:38 -04:00
Dannon Baker 033241c99f Merge 16.01, rebuild. 2016-03-23 12:39:06 -04:00
Martin Cech 21e71a9b46 Merge pull request #1905 from dannon/library_errors 
[16.01] Encoding in libraries
 2016-03-23 12:04:27 -04:00
Dannon Baker 9a0f971596 Merge branch 'release_16.01' into dev 2016-03-15 16:24:17 -04:00
Eric Rasche 90fcd8c668 Handle sections in view workflow 
Fixes 1723
 2016-03-14 14:47:21 +00:00
Dannon Baker 0c225bec2e Update library_info.mako escaping. This allows use of non-ascii characters like 'This is Ă data library' 2016-03-10 20:11:51 -05:00
Brad Langhorst 7955a2b769 Update run.mako 2016-03-09 01:43:45 +00:00
Brad Langhorst 079d645beb typo fix 2016-03-08 13:33:10 -05:00
Brad Langhorst 9b251e567b Tones down the warning message about tool changes 
This looked like an error to people here. I think this proposed language is a bit softer, but still conveys the message that users can proceed  but should review the changes first to make sure their results will not be affected.
 2016-03-08 11:41:42 -05:00
John Chilton 36d85e81ee Merge pull request #1843 from dannon/click_workflow_overview 
Workflow editor overview click navigation
 2016-03-08 09:04:27 -05:00
John Chilton 57c2573149 Merge pull request #1838 from guerler/remove_decoding_000 
Remove decryption/encryption of tool states
 2016-03-08 05:18:37 -05:00
John Chilton 3aa1023434 Merge remote-tracking branch 'jmchilton/release_16.01' into dev 2016-03-05 22:31:32 +00:00
guerler 96b1274b12 Remove encode_runtime_state 2016-03-05 13:00:02 -05:00
guerler 9f5b7a5f66 Revise tool state encryption, remove copy/paste hacks 2016-03-05 12:34:14 -05:00
Dannon Baker 5561c8c2ea Remove stray debug statement (I think) 2016-03-02 18:10:02 -05:00
Martin Cech f67cbe72d5 revert escaping added in a24e206ff7 
that prevented line endings and spaces to be rendered properly
 2016-03-01 14:09:22 -05:00
John Chilton eb2005e7a2 Merge pull request #1764 from guerler/fix_check_and_update_000 
Use visit inputs for check_and_update_param_values
 2016-03-01 12:40:16 -05:00
Dannon Baker 9f590b8a0e Merge branch 'release_16.01' into dev 2016-03-01 09:57:34 -05:00
Martin Cech 281f5b7346 Merge branch 'release_16.01' of https://github.com/galaxyproject/galaxy into release_16.01 2016-02-29 15:08:22 -05:00
guerler 5bc55f9fa2 Add js for mako based masthead 2016-02-29 15:08:00 -05:00
guerler 02187afb57 Handle missing parameters 2016-02-27 02:43:07 -05:00
Marius van den Beek 1aa1d6164a Fix workflow parameters not rendered when tool parameter wrapped in conditional. 2016-02-25 18:35:34 +01:00
guerler d32c6b9021 Move job resource parameter xml to job config 2016-02-24 21:26:30 -05:00
Nate Coraor 9e6afea498 Security fixes for tool shed repository browsing 2016-02-24 11:18:24 -05:00
Nate Coraor ffcd4fe192 Remove sample tracking manual external service transfer due to security concerns 2016-02-24 11:18:24 -05:00
Nate Coraor e4a1d57278 Security fixes for tool shed repository browsing 2016-02-24 11:18:23 -05:00
Nate Coraor cd8b96553f Remove sample tracking manual external service transfer due to security concerns 2016-02-24 11:18:23 -05:00
guerler 7b8f675172 Place logo into config, add masthead test cases 2016-02-18 17:40:28 -05:00
Nicola Soranzo a0537762f2 Merge branch 'release_16.01' into dev 
Conflicts:
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
 2016-02-18 19:52:23 +00:00
carlfeberhard 84de6b4ed3 Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change 2016-02-17 14:41:08 -05:00
Dannon Baker 6a5d2653a7 Merge pull request #1670 from jmchilton/input_param_walking_fix 
Modify show_param input walking to account for multiple data parameters.
 2016-02-10 11:07:19 -05:00
John Chilton 7a60f669fa Merge pull request #1632 from zipho/resolver_dependencies 
added resolver dependency display to the tool view page
 2016-02-08 13:42:03 -05:00
John Chilton 167eb50dd3 Modify show_param input walking to account for multiple data parmaeters. 
xref https://github.com/galaxyproject/galaxy/pull/1561
fixes https://github.com/galaxyproject/galaxy/issues/1660
 2016-02-03 14:12:34 +00:00
Zipho Mashologu 0a440f60ae fixed variable names and making user feedback friendlier 2016-02-02 22:53:06 +02:00
Zipho Mashologu 95cb53a2fb Merge branch 'dev' into resolver_dependencies 2016-02-02 22:41:44 +02:00
Nicola Soranzo a8be2222eb Merge branch 'release_16.01' into dev 
Conflicts:
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
	static/style/blue/base.css
 2016-02-02 19:42:42 +00:00
John Chilton 85eccba791 Public name is mandatory not optional, update help text. 2016-02-02 14:06:53 +00:00
Zipho Mashologu 20f18793cd added resolver dependency display to the tool view page 2016-02-01 15:57:30 +02:00
guerler b3f3f81a7d Remove unused to_html helper 2016-01-27 01:50:05 -05:00
carlfeberhard 4a61a4cb47 UI, Histories: use links for file inputs shown in show_params (the 'i' button in the datasets of histories) that, when clicked, 1) scroll the history to the dataset shown and 2) open *that* datasets info/show_params in the center panel 2016-01-21 16:18:28 -05:00
Martin Cech fe6d22e1a7 Merge pull request #1537 from carlfeberhard/handlebars.removal 
Remove handlebars and rely solely on underscore templates
 2016-01-19 18:24:01 -05:00
carlfeberhard bf459c8d55 UI: (cleaning up) remove handlebars compiled/map and remaining references 2016-01-19 14:12:28 -05:00
carlfeberhard ea304e2f58 UI, Tools: remove handlebars path alias for requirejs from mako templates 2016-01-19 12:43:04 -05:00
guerler 27ee036c69 Add js for mako based masthead 2016-01-19 12:37:52 -05:00
Dannon Baker f939c4eab5 Merge from release to dev. 2016-01-12 14:58:57 -05:00
carlfeberhard 9b4ff63a16 Clean up: remove print statements in templates 2016-01-08 13:56:46 -05:00
John Chilton f8a7ac0820 Merge release_15.10 into release_16.01. 
Conflicts:
	eggs.ini
	lib/galaxy/tools/__init__.py
	lib/galaxy/tools/actions/__init__.py
	lib/galaxy/tools/toolbox/base.py
	static/maps/mvc/collection/list-collection-creator.js.map
	static/maps/mvc/library/library-foldertoolbar-view.js.map
	static/maps/utils/uploadbox.js.map
	static/scripts/mvc/collection/list-collection-creator.js
	static/scripts/mvc/library/library-foldertoolbar-view.js
	static/scripts/utils/uploadbox.js
	test/base/twilltestcase.py
	test/functional/tools/samples_tool_conf.xml
 2016-01-08 18:06:28 +00:00
Dannon Baker da8b943f53 Merge. 2016-01-04 19:23:06 -05:00
Björn Grüning 34bb21c411 Merge pull request #1407 from guerler/revise_masthead_000 
Masthead/Scratchbook revision and test cases
 2016-01-04 01:31:44 +01:00