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Author SHA1 Message Date
Carl Eberhard b224959469 Fix to replace get_dataset in visualization registry ResourceParser with hda_manager.get_accessible 2015-01-23 12:44:46 -05:00
John Chilton 2d227d2daf Merged in BjoernGruening/galaxy-central-1/snpeff_datatype (pull request #640) 
Add SnpEff datatypes
 2015-01-23 12:12:43 -05:00
John Chilton c64c1bac0c Merged in BjoernGruening/galaxy-central-1/toolshed_blacklist_additions (pull request #627) 
Add planemo test file to tool shed upoad blacklist.
 2015-01-23 12:11:03 -05:00
Aysam Guerler 178666baeb ToolForm: Fix optional dataset parameters, fix inconsistencies in parameter handling 2015-01-23 12:04:50 -05:00
Dannon Baker 426b093da7 Pack scripts 2015-01-23 11:10:17 -05:00
Dannon Baker b191d891a5 Copy changes from PR644 to client. 2015-01-23 11:08:05 -05:00
Dannon Baker 91318fafab Merge Upload UI Enhancements from JCabral 2015-01-23 10:59:45 -05:00
JenCabral 532ef29e07 fixing compatibility issues in IE and Firefox 2015-01-23 09:13:13 -06:00
JenCabral 0a60d7801f adding packed files and changing fcn name for addToUpBox to updateUpBox 2015-01-23 08:19:25 -06:00
Dannon Baker 664f92a0ea Merge. 2015-01-23 08:14:02 -05:00
Dannon Baker cdabbe2af8 Add missing parameter in provenance controller. 2015-01-23 08:13:45 -05:00
Carl Eberhard 0ff2c2139d Fix bootstrapped user data to use proper escaping (crap...) and allow history/hda tag to autocomplete again 2015-01-22 18:55:37 -05:00
Dannon Baker 51043f8130 Resolve scope issues in visualization controller, add missing imports and organize. 2015-01-22 18:24:25 -05:00
Dannon Baker e6d877196a Remove a trailing semicolon in the page controller. 2015-01-22 18:19:08 -05:00
Dannon Baker 2bf6763dc6 misc cleanup, pep8 in page controller 2015-01-22 18:18:14 -05:00
Dannon Baker 91bc856cf5 Remove cruft in history controller. 2015-01-22 18:07:19 -05:00
Dannon Baker cd585d91c9 Import cleanup in history controller. 2015-01-22 18:05:11 -05:00
Dannon Baker f869d82fb4 Merge. 2015-01-22 17:57:15 -05:00
Dannon Baker b0774dafc3 Cleanup/pep8 in imp_exp. 2015-01-22 17:57:04 -05:00
Carl Eberhard 1a48c1953e Fix: remove debugging statement 2015-01-22 17:55:14 -05:00
Dannon Baker dafc96e135 Import cleanup in visualizations manager. 2015-01-22 17:46:00 -05:00
Dannon Baker a2e6b4504a Fix set_slug method in sharable manager / scope issues. 2015-01-22 17:34:40 -05:00
Carl Eberhard fe8bb01b78 Sharable managers: Generate slug on user share only if needed 2015-01-22 17:33:02 -05:00
Dannon Baker 421462bc76 pep8 lddamanager 2015-01-22 17:31:20 -05:00
Dannon Baker 950a67d7ed Remove unused imports from pages manager, minor formatting. 2015-01-22 17:28:43 -05:00
Dannon Baker e11ceb615e Fix missing required import in ldda manager. 2015-01-22 17:22:39 -05:00
Dannon Baker 396c491d96 Fix several bugs in histories manager. 2015-01-22 17:14:20 -05:00
Dannon Baker aeb22db5ba Fix import error of collections_util in histories manager. 2015-01-22 17:03:06 -05:00
Dannon Baker d688cc208f Prevent redefinition of role in datasets manager. Harmless now, but dangerous laterhg st 2015-01-22 16:57:45 -05:00
Dannon Baker 8cf4fe4314 Log was undefined here in hda manager, would have blown up. 2015-01-22 16:54:53 -05:00
Dannon Baker 00f3876619 Import cleanup, organization in collections manager. 2015-01-22 16:52:27 -05:00
Dannon Baker ad4cd862ec Prevent redefinition of model, cleanup/pep8 in annotatable manager. 2015-01-22 16:51:14 -05:00
Dannon Baker 89abb15e05 cleanup, pep8 base manager 2015-01-22 16:48:26 -05:00
Dannon Baker ed47dfc605 Pep8 api/datasets. 2015-01-22 16:34:19 -05:00
Dannon Baker c3385a26d8 Fix error in datasets API/serializer 2015-01-22 16:29:45 -05:00
Dannon Baker 03a67d52ba Fix error in managers collections_util. 2015-01-22 15:39:56 -05:00
Carl Eberhard e4e79f6b84 Merge 2015-01-22 14:51:09 -05:00
Carl Eberhard 8d844b16ec Fix to annotatable: setting/deserializing the annotation to None deletes the annotation for the current user 2015-01-22 14:47:38 -05:00
Dannon Baker 587a488724 Correctly pass flush through to the hdamanager's purge method. 2015-01-22 14:45:50 -05:00
Dannon Baker 2ec1808cc5 Add two missing orm imports for history import/export. 2015-01-22 14:44:19 -05:00
Dannon Baker 2bfeae7077 Slightly more comprehensive fix for default_order_by; there's no reason to have two methods for setting ordering here. 2015-01-22 12:23:05 -05:00
Daniel Blankenberg d50eb6a69e Fix for ModelManager._apply_order_by when using default_order_by. 2015-01-22 12:00:08 -05:00
Carl Eberhard 87e2718c93 UI: update Raven.js to 1.1.16 (463f68f) 2015-01-22 11:29:07 -05:00
Dannon Baker 4a7d2e7ad7 Fix workflow step tracking migration downgrade -- previously blew up because there are no TABLES 2015-01-21 18:22:58 -05:00
Dannon Baker c9ad647c98 Merge. 2015-01-21 16:38:00 -05:00
Dannon Baker 46faa14448 Merged in carlfeberhard/galaxy-central-api-v2 (pull request #637) 
Expand on Base, History, and HDA managers
 2015-01-21 16:32:27 -05:00
Carl Eberhard 71aa5ebd71 UI: update tracekit to latest (github.com/occ/TraceKit) 2015-01-21 16:29:35 -05:00
Carl Eberhard 4a52254587 UI: update jQuery to 1.11.2 2015-01-21 16:13:39 -05:00
Nate Coraor 21409d676c Update tag latest_2015.01.13 for changeset 4039bfd5584a 2015-01-21 16:00:24 -05:00
Carl Eberhard e7a7d98a9b Client build: add webpack and bower-install-simple to dev dependencies, add bower.json listing our external libraries (in most cases with most current version), add grunt task 'install-libs' which will fetch external libraries and move the files we use into scripts/libs 2015-01-21 15:23:44 -05:00