| f4d7bd7 | Nate Coraor | 01 April 2013, 17:16:02 UTC | Merge next-stable to stable for release. | 01 April 2013, 17:16:02 UTC |
| 599e009 | Nate Coraor | 01 April 2013, 16:35:49 UTC | Close the next-stable branch. | 01 April 2013, 16:35:49 UTC |
| cfcb8a9 | Greg Von Kuster | 29 March 2013, 17:02:18 UTC | Fix missing import in tool shed's hg middleware controller. | 29 March 2013, 17:02:18 UTC |
| c4989ef | Greg Von Kuster | 29 March 2013, 13:46:19 UTC | Be less restrictive when loacting tool image help files for tools contained in repositories. | 29 March 2013, 13:46:19 UTC |
| eb89ce8 | Dave Bouvier | 29 March 2013, 13:30:36 UTC | Fix for server error when logging out of the tool shed. | 29 March 2013, 13:30:36 UTC |
| 586e56c | Greg Von Kuster | 28 March 2013, 20:32:59 UTC | merging from next-stable | 28 March 2013, 20:32:59 UTC |
| 011e72a | Greg Von Kuster | 28 March 2013, 20:32:32 UTC | Fix for displaying tool shep images in for tools contained in repositories either in the tool shed or in Galaxy. | 28 March 2013, 20:32:32 UTC |
| 02190d6 | Carl Eberhard | 28 March 2013, 20:24:16 UTC | merge stable | 28 March 2013, 20:24:16 UTC |
| 81b5ff4 | Carl Eberhard | 28 March 2013, 20:23:51 UTC | history: remove job subquery | 28 March 2013, 20:23:51 UTC |
| fb6a186 | James Taylor | 28 March 2013, 16:40:44 UTC | biostar: do not fill in question title | 28 March 2013, 16:40:44 UTC |
| 65950ca | James Taylor | 28 March 2013, 16:38:35 UTC | biostar: open tool question link in new window/tab | 28 March 2013, 16:38:35 UTC |
| b4827ce | Carl Eberhard | 28 March 2013, 15:21:56 UTC | merge next-stable | 28 March 2013, 15:21:56 UTC |
| 1f13e10 | Carl Eberhard | 28 March 2013, 15:21:23 UTC | UsesHDA: fix new-style display apps; documentation | 28 March 2013, 15:21:23 UTC |
| 44eb87b | James Taylor | 27 March 2013, 19:36:07 UTC | biostar: send encoded unique ID for user as username | 27 March 2013, 19:36:07 UTC |
| fe9b340 | Carl Eberhard | 27 March 2013, 19:32:19 UTC | merge next-stable | 27 March 2013, 19:32:19 UTC |
| 2c70f8c | Carl Eberhard | 27 March 2013, 19:31:41 UTC | history panel: only fetch force_history_refresh for running/queued HDAs | 27 March 2013, 19:31:41 UTC |
| 1c2ffbd | Dannon Baker | 27 March 2013, 18:27:14 UTC | Strip whitespace in jobs/__init__.py | 27 March 2013, 18:27:14 UTC |
| fd46d14 | Dannon Baker | 27 March 2013, 18:26:38 UTC | Jobs: Fix job finish() to only set state after reconciling all outputs. This will allow us to eliminate force_history_refresh in the new history panel. Slight import cleanup. | 27 March 2013, 18:26:38 UTC |
| 8a747d1 | Dannon Baker | 27 March 2013, 15:53:18 UTC | Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #136) select2 fixes for workflow running. | 27 March 2013, 15:53:18 UTC |
| a1e6b1e | Dave Bouvier | 27 March 2013, 15:20:39 UTC | Change install and test script to never set do_not_test = True. | 27 March 2013, 15:20:39 UTC |
| cd6ab96 | Dave Bouvier | 27 March 2013, 14:10:26 UTC | Merged correctly this time. | 27 March 2013, 14:10:26 UTC |
| 2ede098 | Dave Bouvier | 27 March 2013, 13:53:55 UTC | Merge next-stable. | 27 March 2013, 13:53:55 UTC |
| f8e83f9 | Dave Bouvier | 27 March 2013, 13:52:55 UTC | Apply changes from pull request 146 by Roy Storey. Manually committed to exclude .hgflow mercurial extension configuration file. | 27 March 2013, 13:52:55 UTC |
| 3d4db30 | Dave Bouvier | 27 March 2013, 13:50:32 UTC | Apply changes from pull request 145 by Roy Storey. Manually committed to exclude .hgflow mercurial extension configuration file. | 27 March 2013, 13:50:32 UTC |
| cf11722 | Nate Coraor | 26 March 2013, 19:40:59 UTC | merge next-stable. | 26 March 2013, 19:40:59 UTC |
| 4a132fb | Nate Coraor | 26 March 2013, 19:40:36 UTC | Fix setting of external metadata broken by refactoring job preparation. | 26 March 2013, 19:40:36 UTC |
| 64f2bcc | Carl Eberhard | 26 March 2013, 19:11:34 UTC | merge next-stable | 26 March 2013, 19:11:34 UTC |
| 1f75046 | Carl Eberhard | 26 March 2013, 19:10:42 UTC | fix for exception handling in root.history | 26 March 2013, 19:10:42 UTC |
| 620263d | James Taylor | 26 March 2013, 17:04:36 UTC | biostar: pass slugified version of tool name as tag when sending to question form | 26 March 2013, 17:04:36 UTC |
| fa3b669 | Greg Von Kuster | 26 March 2013, 15:41:49 UTC | Fix tool shed utility file imports and withe space to follow new Galaxy dev team coding standards. | 26 March 2013, 15:41:49 UTC |
| 701c0da | Dave Bouvier | 26 March 2013, 14:02:17 UTC | Set do_not_test = True if the repository fails functional tests. Set do_not_test = False if the repository passes functional tests, so that the repository will always be re-tested against the most recent code. | 26 March 2013, 14:02:17 UTC |
| 5d50290 | Greg Von Kuster | 26 March 2013, 13:29:02 UTC | Enhance and correct documentation in the new tool_shed_repositories Galaxy API controller as well as the documentation in the example API install scripts. Fix discovery of the tool_path setting in the selected shed-related tool panel config file in the tool_shed_repositories controller's install_repository_revision method. | 26 March 2013, 13:29:02 UTC |
| 86faef9 | Dave Bouvier | 26 March 2013, 13:27:39 UTC | More explicit specification of return codes, documentation of same. | 26 March 2013, 13:27:39 UTC |
| 6b28ae9 | Carl Eberhard | 25 March 2013, 23:05:30 UTC | merge next-stable | 25 March 2013, 23:05:30 UTC |
| 9103d2e | Carl Eberhard | 25 March 2013, 23:04:37 UTC | history panel: better bootstrapped history and hda data; UsesHistoryDatasetAssociationMixin: don't try to provide full data for deleted, purged, or non-accessible hda | 25 March 2013, 23:04:37 UTC |
| ed0ee2c | Nate Coraor | 25 March 2013, 22:22:25 UTC | merge next-stable | 25 March 2013, 22:22:25 UTC |
| 355c511 | Nate Coraor | 25 March 2013, 22:22:11 UTC | Don't misuse PBS parameters in the sample job config. | 25 March 2013, 22:22:11 UTC |
| ed7248a | Greg Von Kuster | 25 March 2013, 21:18:17 UTC | Fix a few typos in my last commit. | 25 March 2013, 21:18:17 UTC |
| b9c6df9 | Greg Von Kuster | 25 March 2013, 21:05:14 UTC | Add baseline cupport for installing tool shed repositories from a specified tool shed into Galaxy via a combination of the tool shed API and the now enhanced Galaxy API. There are 3 new example scripts in ~/scripts/api that demonstrate how this works. The are named like: install_repository... In this implementation, all tools contained in repositories will be loaded into the Galaxy tool panel. The user can specify the following when sending a POST to the new Galaxy API URL: /api/tool_shed_repositories/new/install_repository_revision 1) an existing tool panel section id for loading tools or a new tool panel section label in which case a new ToolPanelSection will be created for containing the tools. 2) if they want tool dependencies installed along with the repository. 3) if they want repository dependencies installed along with the repository 4) which defined shed-related tool panel config file to use for installed tools | 25 March 2013, 21:05:14 UTC |
| 7621c97 | James Taylor | 25 March 2013, 20:30:16 UTC | biostar: bugfix for encoding data | 25 March 2013, 20:30:16 UTC |
| 8cc8cc7 | Carl Eberhard | 25 March 2013, 17:34:27 UTC | merge next-stable | 25 March 2013, 17:34:27 UTC |
| a011b48 | Carl Eberhard | 25 March 2013, 17:33:30 UTC | api/histories, show: capture job states | 25 March 2013, 17:33:30 UTC |
| 13fec82 | Dave Bouvier | 25 March 2013, 16:05:17 UTC | Specify return codes so the automated framework will more correctly report success/failure. | 25 March 2013, 16:05:17 UTC |
| 4e054ce | Jeremy Goecks | 25 March 2013, 13:37:48 UTC | Automated merge. | 25 March 2013, 13:37:48 UTC |
| ade0bca | Jeremy Goecks | 25 March 2013, 13:37:17 UTC | Trackster: more flexible parsing of location string. | 25 March 2013, 13:37:17 UTC |
| d297d28 | Dave Bouvier | 25 March 2013, 13:36:02 UTC | Update tests to reflect new default for component review approval status. | 25 March 2013, 13:36:02 UTC |
| 6267972 | Greg Von Kuster | 23 March 2013, 14:44:46 UTC | Refactor several methods in Galaxy's admin_toolshed controller in preparation for supporting installing tool shed repositories via the tool shed and Galaxy APIs. | 23 March 2013, 14:44:46 UTC |
| d53f76c | Nate Coraor | 22 March 2013, 22:09:33 UTC | Merge next-stable. | 22 March 2013, 22:09:33 UTC |
| f1f9c35 | Nate Coraor | 22 March 2013, 22:08:45 UTC | Merge. | 22 March 2013, 22:08:45 UTC |
| e3752aa | Nate Coraor | 22 March 2013, 22:07:40 UTC | Additional examples for the job configuration sample. | 22 March 2013, 22:07:40 UTC |
| 00d1c7b | Nate Coraor | 22 March 2013, 22:04:52 UTC | Don't finish jobs that are deleted. | 22 March 2013, 22:04:52 UTC |
| 20342de | Nate Coraor | 22 March 2013, 21:58:55 UTC | Additional CLI runner fixes for destinations. | 22 March 2013, 21:58:55 UTC |
| f762868 | Greg Von Kuster | 22 March 2013, 20:26:07 UTC | Add an expose_api_anonymous decorator to the Galaxy web framework to enable exposing API methods without requiring an API key or a Galaxy or Tool Shed user session. | 22 March 2013, 20:26:07 UTC |
| fe410b4 | Greg Von Kuster | 22 March 2013, 18:38:01 UTC | Extract several methods from Galaxy's admin_toolshed controller and the tool shed's repository controller and move them to ~/tool_shed/galaxy_install/repository_util in preparation for enhancing the Galaxy api to enable installing a repository from the tool shed. | 22 March 2013, 18:38:01 UTC |
| 0bbe5c0 | Daniel Blankenberg | 22 March 2013, 18:23:24 UTC | Fix for average_rating in repository_review. | 22 March 2013, 18:23:24 UTC |
| 9a48465 | Daniel Blankenberg | 22 March 2013, 18:23:24 UTC | Fix for average_rating in repository_review. | 22 March 2013, 18:23:24 UTC |
| ccc5581 | Nate Coraor | 22 March 2013, 17:14:50 UTC | Convert condor runner from URLs to destinations. | 22 March 2013, 17:14:50 UTC |
| db08c7e | Nate Coraor | 22 March 2013, 17:14:25 UTC | Convert drmaa runner from URLs to destinations. | 22 March 2013, 17:14:25 UTC |
| 7d63682 | Nate Coraor | 22 March 2013, 17:13:05 UTC | Refactor common operations in to AsynchronousJobSate/AsynchronousJobRunner. | 22 March 2013, 17:13:05 UTC |
| b7f3935 | Nate Coraor | 22 March 2013, 17:11:57 UTC | Fix URL->destination conversion of jobs running prior to upgrade to destinations. | 22 March 2013, 17:11:57 UTC |
| 0224858 | Daniel Blankenberg | 22 March 2013, 16:33:10 UTC | Add some comments to the new-style display applications module. | 22 March 2013, 16:33:10 UTC |
| 81a246e | Daniel Blankenberg | 22 March 2013, 16:26:03 UTC | Do not display old-style display links in client-side history when they are disabled. | 22 March 2013, 16:26:03 UTC |
| e97a6f2 | Daniel Blankenberg | 22 March 2013, 16:26:03 UTC | Do not display old-style display links in client-side history when they are disabled. | 22 March 2013, 16:26:03 UTC |
| 09c7682 | Daniel Blankenberg | 22 March 2013, 16:23:05 UTC | Do not display old-style display links in server-side history when they are disabled. | 22 March 2013, 16:23:05 UTC |
| b7c256d | Daniel Blankenberg | 22 March 2013, 16:23:05 UTC | Do not display old-style display links in server-side history when they are disabled. | 22 March 2013, 16:23:05 UTC |
| e277697 | Daniel Blankenberg | 22 March 2013, 16:23:05 UTC | Do not display old-style display links in server-side history when they are disabled. | 22 March 2013, 16:23:05 UTC |
| 88238a1 | Daniel Blankenberg | 22 March 2013, 15:43:42 UTC | Allow old-style display applications to be disabled. | 22 March 2013, 15:43:42 UTC |
| 98a5147 | Daniel Blankenberg | 22 March 2013, 15:43:42 UTC | Allow old-style display applications to be disabled. | 22 March 2013, 15:43:42 UTC |
| f59c2e7 | Daniel Blankenberg | 22 March 2013, 15:43:42 UTC | Allow old-style display applications to be disabled. | 22 March 2013, 15:43:42 UTC |
| 9dee845 | Greg Von Kuster | 22 March 2013, 14:43:58 UTC | Eliminate unnecessary resource mappers and api classes in the tool shed api, clean up the remaining tool shed api classes, and enhance the tool shed api by adding the ability to retrieve information about a specified repository and repository revision. | 22 March 2013, 14:43:58 UTC |
| f3868d1 | Dave Bouvier | 21 March 2013, 23:23:43 UTC | Update install and test script to correctly load tool data tables. | 21 March 2013, 23:23:43 UTC |
| dfcebf4 | Dave Bouvier | 21 March 2013, 18:54:42 UTC | Merge in bugfix from next-stable. | 21 March 2013, 18:54:42 UTC |
| 56f985c | Nate Coraor | 21 March 2013, 17:59:21 UTC | Convert the CLI runner to use job destinations. | 21 March 2013, 17:59:21 UTC |
| 9790cf5 | Nate Coraor | 21 March 2013, 17:58:32 UTC | Standardize some job state properties common to asynchronous runners in AsynchronousJobState. | 21 March 2013, 17:58:32 UTC |
| f97fd4d | Carl Eberhard | 21 March 2013, 17:56:18 UTC | merge stable | 21 March 2013, 17:56:18 UTC |
| eab606b | Carl Eberhard | 21 March 2013, 17:55:36 UTC | history, view: fix show_deleted/hide_deleted | 21 March 2013, 17:55:36 UTC |
| 3a2e877 | Dannon Baker | 21 March 2013, 17:45:12 UTC | Fix broken tool_dependency_util -- was missing galaxy's 'util' import as well as 'shutil'. | 21 March 2013, 17:45:12 UTC |
| c316195 | Dannon Baker | 21 March 2013, 17:45:12 UTC | Fix broken tool_dependency_util -- was missing galaxy's 'util' import as well as 'shutil'. | 21 March 2013, 17:45:12 UTC |
| 6a69ebc | Jeremy Goecks | 21 March 2013, 16:19:45 UTC | Merge in next-stable | 21 March 2013, 16:19:45 UTC |
| bacf200 | Jeremy Goecks | 21 March 2013, 16:19:14 UTC | Add support for column ranges to Cut tool. Thank to John Chilton for this code. | 21 March 2013, 16:19:14 UTC |
| d791d11 | Greg Von Kuster | 21 March 2013, 14:58:11 UTC | Move the tool_shed_repository_revision_update.py api example script to ~/lib/tool_shed/scripts/api | 21 March 2013, 14:58:11 UTC |
| 1f975df | Dave Bouvier | 21 March 2013, 14:02:13 UTC | Merged in changes from next-stable. | 21 March 2013, 14:02:13 UTC |
| a7095dd | Dave Bouvier | 21 March 2013, 14:01:49 UTC | Make approved column blank if None. | 21 March 2013, 14:01:49 UTC |
| bbf2658 | Dave Bouvier | 21 March 2013, 13:52:57 UTC | Merge in changes from next-stable | 21 March 2013, 13:52:57 UTC |
| d0943fc | Dave Bouvier | 21 March 2013, 13:51:51 UTC | Add columns for rating and approval status to repositories with reviews grid. | 21 March 2013, 13:51:51 UTC |
| f1b56a7 | Jeremy Goecks | 21 March 2013, 12:51:10 UTC | Merge in next-stable | 21 March 2013, 12:51:10 UTC |
| 18b5747 | Jeremy Goecks | 21 March 2013, 12:50:38 UTC | Update Cuffdiff wrapper to use working directory rather than a temporary directory. | 21 March 2013, 12:50:38 UTC |
| 04e9baf | Greg Von Kuster | 20 March 2013, 19:09:43 UTC | Clean up the tool shed api methods. | 20 March 2013, 19:09:43 UTC |
| abdfdbf | Jeremy Goecks | 20 March 2013, 17:22:43 UTC | Merge in next-stable. | 20 March 2013, 17:22:43 UTC |
| e08e2f5 | Jeremy Goecks | 20 March 2013, 17:18:13 UTC | Simplify help text for eye icon. | 20 March 2013, 17:18:13 UTC |
| da4f17b | Nate Coraor | 20 March 2013, 17:11:45 UTC | Have the PBS runner use the superclass convenience method for pre-queueing sanity checks. | 20 March 2013, 17:11:45 UTC |
| df5f075 | Nate Coraor | 20 March 2013, 17:11:18 UTC | Add cleanup when skipping a queued job that was deleted. | 20 March 2013, 17:11:18 UTC |
| 3325448 | Nate Coraor | 20 March 2013, 16:56:13 UTC | Bugfixes for the pbs job runner and the move to job destinations. | 20 March 2013, 16:56:13 UTC |
| febd14f | Nate Coraor | 20 March 2013, 16:55:52 UTC | Fix for processing Torque's 'E' state in the CLI runner. | 20 March 2013, 16:55:52 UTC |
| a7374bc | Jeremy Goecks | 20 March 2013, 14:55:46 UTC | Merge in next-stable | 20 March 2013, 14:55:46 UTC |
| e45a787 | Jeremy Goecks | 20 March 2013, 14:55:24 UTC | Trackster fixes: (a) render bases/colors in Firefox; (b) make deletions black to avoid color conflicts with colored bases; (c) use group name for composite track. Modal fix: set maximum body height so that it does not overflow the bottom of the page. Pack scripts. | 20 March 2013, 14:55:24 UTC |
| 628b18e | Dave Bouvier | 20 March 2013, 13:33:34 UTC | Display an error message when cookies are blocked between the tool shed and galaxy. | 20 March 2013, 13:33:34 UTC |
| feddffd | Dave Bouvier | 20 March 2013, 13:33:34 UTC | Display an error message when cookies are blocked between the tool shed and galaxy. | 20 March 2013, 13:33:34 UTC |
| b5a3953 | Dave Bouvier | 19 March 2013, 20:59:27 UTC | Add option to specify extra tool data for the automated install and test framework. | 19 March 2013, 20:59:27 UTC |
| bd56365 | Dave Bouvier | 19 March 2013, 16:26:33 UTC | Add missing import in upload controller. | 19 March 2013, 16:26:33 UTC |
