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Author SHA1 Message Date
Carl Eberhard fe523237c6 Fix display_structure by using serializer; fix structure by removing extra decode_id 2015-02-27 10:03:47 -05:00
guerler d4b6df5330 ToolForm/Ui: Restrict available option requirement to single select fields 2015-02-27 04:36:20 -05:00
guerler e0ad2d78e1 Parameters: Set hidden attribute for hidden dataset parameter 2015-02-27 04:26:15 -05:00
guerler d58d2abf57 Parameters: Fix deleted datasets validation message 2015-02-27 01:59:43 -05:00
guerler 5a78162f6f ToolForm/Ui: Limit selection to available options 2015-02-27 01:57:39 -05:00
guerler 0207fc1035 Parameters: Prevent uncaught exception on unavailable datasets in column validation 2015-02-27 01:49:53 -05:00
guerler c7943f33b5 ToolForm/Collections: Re-introduce parameter expansion 2015-02-27 01:35:38 -05:00
guerler a3b1e604a7 ToolForm: Show initial validation errors on re-run 2015-02-27 01:30:48 -05:00
Daniel Blankenberg 1b362331da Allow TabularToolDataTable to be loaded from a url instead of a path. 2015-02-26 17:16:55 -05:00
Carl Eberhard a34695d07c Fix visualization controller to use security.decode_id in grids 2015-02-26 14:15:47 -05:00
Dannon Baker 057a9c9f16 Attempt at a fix for get('') in tools/params/basic.py 2015-02-26 14:07:35 -05:00
John Chilton f0903932cc Bugfix: serializing "None" for UUIDs for older workflows. 
Prevents workflows from being saved :(.
 2015-02-26 12:50:08 -05:00
Dannon Baker 64485fe551 Merge branch 'fix_cache_bust' into release_15.03 2015-02-26 12:48:08 -05:00
Dannon Baker 3e6090c7e4 Move server_starttime to base universe application so shared templates between galaxy/shed/etc don't break. 2015-02-26 12:47:50 -05:00
Dannon Baker 44c8eb5ffb Merge branch 'fix_cache_bust' into release_15.03 2015-02-26 12:40:49 -05:00
Dannon Baker 721c6ad71c Fix cache-busting under require.js. 2015-02-26 12:40:26 -05:00
guerler a39796dfe0 Remove collection expansion 2015-02-26 11:12:45 -05:00
guerler ab25fe16ef Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 2015-02-26 01:10:11 -05:00
guerler e8dc95670b Collections: Enable the batch mode execution for nested collections (without adding a new button) 2015-02-26 01:05:27 -05:00
Dannon Baker 8cea3c0b0e Fix returning encoded None library folder parent ids in library_contents API; thanks to nsoranzo 2015-02-25 15:09:39 -05:00
Daniel Blankenberg b89a5be319 Fix for ToolShed not having config.shed_tool_data_path 2015-02-25 12:07:39 -05:00
John Chilton 09a65cfcd4 Expand out meta parameters when validating for tool.to_json(). 
Bring this code closer inline with what handle_input() does and should solve the problem with column validation of parameters that are being 'batched'.

See https://trello.com/c/8NweTvLh and comment on https://github.com/galaxyproject/galaxy/commit/d57088409c7b23e55ead4c9f2fad38b2600eb8b7.
 2015-02-25 09:14:06 -05:00
John Chilton 0b2a8b7b0f Improved tool diagnostics API. 2015-02-25 08:01:05 -05:00
John Chilton 0ca4068dbc Tool diagnostic API endpoints. 
It is easy to get Galaxy's database and shed tool files out of sync and the results are bad. I don't think this is new but I may have made it worse this cycle by trying to slowly walk back Galaxy's use of the database to track lineages (e.g. https://bitbucket.org/galaxy/galaxy-central/commits/08f8850853d004bf8a456a147436a6694d0a1a11).

New API endpoints include:

  /api/configuration/dynamic_tool_confs
  /api/configuration/tool_lineages
  /api/<tool_id>/diagnostics
 2015-02-25 08:00:53 -05:00
guerler e6971e191d ToolForm: Enable collection for multiple data parameter 2015-02-24 20:31:43 -05:00
guerler e6399874e8 Charts: Fix missing data message 2015-02-24 19:41:30 -05:00
guerler e2f5e9e326 Charts: Rebuild and update charts 2015-02-24 19:08:36 -05:00
Dannon Baker 59c788a2b6 More tweaks to mutable capabilities, adding back in a copy and stripping pickle from MutationList 2015-02-24 18:55:50 -05:00
guerler 475fcf6f2d Show error message on server error 2015-02-24 18:37:52 -05:00
guerler af79513e51 Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 2015-02-24 18:14:13 -05:00
Carl Eberhard 86035ed64a Merge remote-tracking branch 'upstream/release_15.03' into release_15.03 2015-02-24 17:34:47 -05:00
Carl Eberhard c59980b7b1 Fix to layering of dropdown buttons and menus 2015-02-24 17:20:10 -05:00
guerler 3c0275ae52 Fix job ids in success message 2015-02-24 15:52:51 -05:00
guerler fc23aee3a6 Allow text selection in tool form 2015-02-24 15:52:17 -05:00
Dannon Baker 2fb5d0cd02 Apply custom_types bugfixes from dev branch to release. 2015-02-24 14:50:02 -05:00
Daniel Blankenberg ca41396d2a Fix for installing .loc files from the toolshed to respect shed_tool_data_path. Mention shed_tool_data_path in galaxy.ini.sample. 2015-02-24 12:02:42 -05:00
John Chilton 77b167bbd1 Comment out broken liftOver tests. 
liftOver loc file handling is problematic (https://trello.com/c/A6I6zQvF). If it weren't this wouldn't be a problem. I could fix the API functional test framework to mimic the older form driven approach but it would take a week and would be rendered moot by fixing liftOver. Unfortunately, fixing liftOver would likely break a lot of existing workflows and tool reruns so I am not fixing that either.

Only option left, admittedly a crappy one, is to comment out the tests.
 2015-02-23 23:09:19 -05:00
John Chilton 2bcc9e202e Fix for watching tools on some more interesting file systems. 2015-02-23 19:58:12 -05:00
Carl Eberhard 7a256045bb UI, history panel: correctly default clearMessages target when no event is given 2015-02-23 17:14:37 -05:00
Dannon Baker 23179f3b48 Verify and apply @jmchilton's fix from https://github.com/jmchilton/galaxy-central/commit/306a86558a7ee7be1bc2d68cd939b16b5f1863d4 to next-stable. Should be refactored into using the same galaxy.menu.js objects -- I'm assuming that's why things like PopupMenu.fromExistingDom exist and are otherwise unused. 2015-02-23 16:28:01 -05:00
Dannon Baker d54b3b08c7 Merge branch 'cancelfix' into release_15.03 2015-02-23 15:08:31 -05:00
Dannon Baker 74336019ff Bugfix for clicking cancel in a menu and having the action happen anyway. 2015-02-23 15:07:58 -05:00
Martin Cech c6237def42 fix error preventing change of username in TS 2015-02-23 13:53:13 -05:00
guerler cec5854398 Select2 fix 2015-02-23 12:50:27 -05:00
Dannon Baker a6b13a28a0 Clone .gitignore 2015-02-23 11:28:07 -05:00
Daniel Blankenberg cebd5f8b77 Fixes for handling Data Managers that use undeclared data tables. 2015-02-21 13:29:58 -05:00
Dannon Baker f2771f77fb Merge back from next-stable. 2015-02-17 15:20:40 -05:00
Dannon Baker 815b3a271f Merge. 2015-02-17 15:19:40 -05:00
Dannon Baker 3a8b2bf93a Merge. 2015-02-17 15:19:00 -05:00
Dannon Baker 5c94d23d2d Merge bugfix from next-stable. 2015-02-17 15:18:45 -05:00