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8895 Commits
Author SHA1 Message Date
guerler f515e29504 Enable remap condition 2015-03-06 15:28:22 -05:00
guerler 949b785fac Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 2015-03-06 15:26:24 -05:00
guerler d079ad8f8c Add resume option for job dependencies 2015-03-06 15:24:31 -05:00
Daniel Blankenberg 18d77b008f Make api/config /version usable as sessionless in addition to anonymous. 2015-03-06 14:18:48 -05:00
guerler f0bebc997f Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 2015-03-05 22:16:54 -05:00
guerler 1a1f5a33c9 Fix dataset and collection mapping for re-run in imported histories 2015-03-05 22:15:21 -05:00
Dannon Baker 6db6b7e93b Tweaks to the password reset email template to help email clients not mangle it, and when they do, to suggest copying and pasting. 2015-03-05 13:27:22 -05:00
Dannon Baker 826f69fb62 Python 2.6 has a bug in deepcopy that causes an error when attempting to copy datasets between users (which uses deepcopy). Py2.7 worked fine. Now they both should. 2015-03-04 18:04:00 -05:00
John Chilton 9364b9d3c5 API fixes for tools and datatypes. 
By replacing _future_expose_api_anonymous with _future_expose_api_anonymous_and_sessionless.
 2015-03-04 14:51:43 -05:00
Daniel Blankenberg 2e3bebbfe2 Fix for reports app not running mysql. 2015-03-03 11:55:47 -05:00
Daniel Blankenberg 853f5156c0 When loading Dynamic Display application links, allow the application to load even if one set of links does not. 2015-03-03 10:49:12 -05:00
Daniel Blankenberg 05ff2aa6ce Add a 10 second timeout to loading data URLs for Tool Data Tables. 2015-03-03 10:24:58 -05:00
guerler 0d62ee6960 Parameters: Fix collection selection for multiple dataset input field 2015-03-02 18:25:46 -05:00
guerler 434aa056a2 Parameters: Cover additional case for multiple hdas 2015-03-02 18:12:34 -05:00
Martin Cech 8e6fbe34ca tweak toolbox search to provide better (and more) results 
with the inclusion of toolhelp in index and with more versions
of the same tools being massively installed the search results were
inconsistent and inaccurate and incomplete.
addresses https://trello.com/c/6Bvbduci/2486-toolbox-search-is-behaving-wrongly-differently
 2015-03-02 16:33:43 -05:00
Dannon Baker 1b23706b8f Rearranging the layers of middleware to allow sentry and debug to coexist without exploding (but you probably don't want to use both at once anyway) 2015-03-02 14:54:29 -05:00
Carl Eberhard ebda6ac03d Fix to remove validation of genome builds since some data source tools will assign invalid genome builds and later validation makes these hdas un-updatable 2015-03-02 14:22:00 -05:00
John Chilton 589b3fb226 Update basic.py to allow collection reduction with new tool form. 2015-03-02 13:53:17 -05:00
Daniel Blankenberg 9f68fe0792 Allow External display applications to use Tool Data Tables. 2015-02-27 15:50:13 -05:00
Dannon Baker 10f8b6e21f Merge branch 'release_15.03' of github.com:galaxyproject/galaxy into release_15.03 2015-02-27 15:19:32 -05:00
dannon f73467f19d Fix server_starttime being in app for reports, toolshed. I will be refactoring this shortly to have a base UniverseApplication from which things inherit. 2015-02-27 15:19:17 -05:00
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 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 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
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
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
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 2bcc9e202e Fix for watching tools on some more interesting file systems. 2015-02-23 19:58:12 -05:00
guerler cec5854398 Select2 fix 2015-02-23 12:50:27 -05:00
Daniel Blankenberg cebd5f8b77 Fixes for handling Data Managers that use undeclared data tables. 2015-02-21 13:29:58 -05:00
Daniel Blankenberg 8d48f1753d For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed. 2015-02-17 15:17:17 -05:00
Dannon Baker 0afbfdefc7 Fix another identity vs value test error in xml handling. 2015-02-17 15:08:45 -05:00