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Author SHA1 Message Date
Jeremy Goecks 1bf74a256b Client-side visualization framework: remove extend aliasing. 2014-07-24 14:34:53 -04:00
Jeremy Goecks e8ab0f78fe Trackster: variable clean up for read track painter, preventing features from being cutoff at the bottom. 2014-07-24 13:54:50 -04:00
Jeremy Goecks f5fef7a8c9 Trackster: resolve name collision due to refactoring. 2014-07-24 09:26:39 -04:00
Greg Von Kuster 36a9b802f5 Fix missing import in the Tool Shed's ToolValidator. 2014-07-23 16:31:59 -04:00
Dannon Baker 9335a84155 Merge. 2014-07-23 16:27:42 -04:00
Greg Von Kuster 6ea01799c3 Fix for exporting repositories that contain package recipes that define additional packages needed only for compiling the dependent package. 2014-07-23 16:19:39 -04:00
Dannon Baker e713d62c56 Fix another variable definition issue in user address deletion. 2014-07-23 15:42:23 -04:00
Dannon Baker 401b913fe7 Fix 'decod_id' invocation to use the correct function when deleting user addresses. 2014-07-23 15:41:14 -04:00
Greg Von Kuster 0d935b1483 Strip repository names when creating in the Tool Shed. 2014-07-23 13:40:23 -04:00
Carl Eberhard de12ab8aa9 History/Collection/HDA MVC: refactoring; Base MVC: create mixin shortcut to extend, use with HistoryContentMixin; Pages: allow display of collections; HDAs: fix annotation default overwriting existing when only partial model is saved; Style: begin separation of collections styles and prep for DOM class renaming; pack scripts 2014-07-23 12:59:04 -04:00
Greg Von Kuster adca85401e Add a CustomDatatypeLoader for Galaxy installs, eliminate the use of the tool shed's datatyps_util module. 2014-07-23 11:26:49 -04:00
John Chilton 65f47df4db More standardized (if still terse) exception handling in AuthenticationController. 2014-07-23 09:16:08 -05:00
Greg Von Kuster c2f089dcb0 Fixes in exception handlers in the Tool Shed's create_categories and create_users API modules. 2014-07-23 09:47:21 -04:00
Greg Von Kuster 59066ff1d5 Move some functions out of the Tool Shed's shed_util_common module. 2014-07-22 16:46:30 -04:00
Greg Von Kuster e584e1dc9a Rename the Tool Shed's repository_maintenance_util module to be repository_util. 2014-07-22 15:38:59 -04:00
Greg Von Kuster 0760ab25ea Add a ToolDataTableManager for managing tool data tables in the Tool Shed. 2014-07-22 15:12:40 -04:00
Greg Von Kuster 493827e891 Add a DataManagerHandler for Galaxy installs from the Tool Shed, eliminating the use of the data_manager_util.py module. 2014-07-22 13:46:40 -04:00
Greg Von Kuster a008302925 Add a ToolVersionManager to manage tool versions in the Tool Shed and Galaxy installs. 2014-07-22 11:33:35 -04:00
Dave Bouvier 48f20e428a Delete images for tools that are no longer in the distribution. 2014-07-22 11:01:23 -04:00
Greg Von Kuster 947af70db7 Move some functions out of the tool shed's shed_util_common module into appropriate classes. 2014-07-21 16:44:32 -04:00
Jeremy Goecks 3ea21ff715 Automated merge 2014-07-21 13:42:14 -04:00
Greg Von Kuster b5137f31ec Some code cleanup for setting metadata on tool shed repositories. 2014-07-21 13:38:43 -04:00
Jeremy Goecks 6a3344ea24 Trackster: do not reset overview when changing chromosome. 2014-07-21 13:23:41 -04:00
Greg Von Kuster 76d0960467 Add a ToolPanelManager for Galaxy installs from the Tool Shed. 2014-07-21 11:36:29 -04:00
Jeremy Goecks 7e506617d9 Trackster: some fixes for vertical position element. 2014-07-21 10:27:44 -04:00
Jeremy Goecks e7f68902ab Trackster: remove bottom label track because it is redundant. 2014-07-21 10:26:18 -04:00
Jeremy Goecks 8f4e28a3b9 Use jquery to remove event handler. 2014-07-21 10:19:14 -04:00
Greg Von Kuster 6d4cce5afe Add a missing function to the ToolValidator. 2014-07-18 16:44:54 -04:00
Greg Von Kuster fd6da0659b Add a ToolValidator to validate tools contained in tool shed repositories. 2014-07-18 16:38:57 -04:00
Greg Von Kuster 26da936f27 As much as possible, eliminate the use of trans in the tool shed's tool_util.py module. 2014-07-18 14:41:44 -04:00
Greg Von Kuster 76703030bd Fix for bug introduced when I eliminated the use of trans from the tool shed's review_util.py module. 2014-07-18 06:50:16 -04:00
Jeremy Goecks b752a6a065 Update embedded visualizations to work with recent refactoring. 2014-07-17 16:53:04 -04:00
Jeremy Goecks 674eba1ca0 Remove duplicated function definition. 2014-07-17 16:34:20 -04:00
Jeremy Goecks a004dd6d9c Automated merge. 2014-07-17 16:23:33 -04:00
Jeremy Goecks 19edf28795 Trackster: merge all top-level UI code into the same file for simplicity. 2014-07-17 16:23:17 -04:00
Greg Von Kuster 8cc9558aba Eliminate the use of trans in the tool shed's tool_dependency_util.py module. 2014-07-17 15:49:48 -04:00
Greg Von Kuster 6ee8b83fbb Eliminate the use of trans in the tool shed's search_util.py module. 2014-07-17 15:46:42 -04:00
Jeremy Goecks a433287dbe Trackster: remove unused requirements. 2014-07-17 15:44:45 -04:00
Greg Von Kuster ed47c5242b Eliminate the use of trans in the tool shed's review_util.py module. 2014-07-17 15:41:56 -04:00
Greg Von Kuster 97820f0465 Eliminate the use of trans in functions within the hg_util.py module. 2014-07-17 15:22:51 -04:00
Greg Von Kuster a580d9a4ac Make sure dir is not None when used to create a path - than Nicolas Lapalu. 2014-07-17 13:38:53 -04:00
Greg Von Kuster 802f7f3945 Add classes for managing tool shed repository metadata. 2014-07-17 13:20:49 -04:00
Greg Von Kuster ecece2807f Add a DependencyDisplayer class for Galaxy installs from the Tool Shed. 2014-07-16 14:30:36 -04:00
Dave Bouvier a44672251b Make the tool shed's database migrations compatible with MySQL. 2014-07-16 12:50:15 -04:00
Greg Von Kuster 48544b2e34 Rename the ~/tool_shed/dependencies/dependency_manager.py module to be attribute_handlers.py 2014-07-16 09:16:35 -04:00
Jeremy Goecks 7a618fcf6d Visualization framework: fix bug in searching interval features. 2014-07-15 17:04:33 -04:00
Greg Von Kuster 598ae476c4 Eliminate the use of trans in all remaining functions in the metadata_util.py tool shed module. 2014-07-15 16:44:02 -04:00
Dave Bouvier 2e893a17eb Fix display of job stdio when using the twill interactor. 2014-07-15 16:30:35 -04:00
Dave Bouvier 0fd3b0743c Fix rare scenario where installing a set of repositories that depend on each other would result in one of them being installed twice. 2014-07-15 16:13:28 -04:00
Jeremy Goecks 3d8862608d Visualization framework bug fixes + remove debugging statement. 2014-07-15 15:41:38 -04:00