| e3b9e64 | Dannon Baker | 23 February 2015, 16:24:53 UTC | Clone .gitignore | 23 February 2015, 16:24:53 UTC |
| e2a5756 | Daniel Blankenberg | 13 January 2015, 15:26:27 UTC | Fix a critical security vulnerability where unsanitized user-modifiable values could be included in a command line template. | 13 January 2015, 15:26:27 UTC |
| 7313176 | Nate Coraor | 30 July 2014, 14:53:01 UTC | Apply 2014.07.30 security fix to release_2013.04.01 | 30 July 2014, 14:53:01 UTC |
| 4425904 | Nate Coraor | 30 July 2014, 14:44:55 UTC | Added tag latest_2013.02.08 for changeset 3e62060b14b9 | 30 July 2014, 14:44:55 UTC |
| e2cf60e | Nate Coraor | 30 July 2014, 14:44:41 UTC | Apply 2014.07.30 security fix to release_2013.02.08 | 30 July 2014, 14:44:41 UTC |
| 4cc2067 | Nate Coraor | 30 July 2014, 14:40:27 UTC | Added tag latest_2013.01.13 for changeset 6b0bd93038a8 | 30 July 2014, 14:40:27 UTC |
| 926c1b1 | Nate Coraor | 30 July 2014, 14:40:05 UTC | Fix a critical security vulnerability with handling pickled data. Thanks to Inge Alexander Raknes for reporting the isssue. | 30 July 2014, 14:40:05 UTC |
| 8a15acb | Daniel Blankenberg | 23 May 2013, 15:11:37 UTC | Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name. | 23 May 2013, 15:11:37 UTC |
| 1f09118 | Daniel Blankenberg | 15 May 2013, 15:09:32 UTC | Unicode fixes for workflow names in Tool Menu. | 15 May 2013, 15:09:32 UTC |
| bdadb7a | Daniel Blankenberg | 14 May 2013, 17:13:21 UTC | Use util.unicodify when generating dataset peeks. | 14 May 2013, 17:13:21 UTC |
| 97fb2b5 | Daniel Blankenberg | 14 May 2013, 17:13:21 UTC | Have datatypes.checkers.check_binary call util.is_binary. Fixes unicode file upload under certain conditions. | 14 May 2013, 17:13:21 UTC |
| 7ba8819 | Daniel Blankenberg | 10 May 2013, 15:55:40 UTC | use_panels fix for login.mako in toolshed. | 10 May 2013, 15:55:40 UTC |
| 1b793df | Daniel Blankenberg | 10 May 2013, 15:49:16 UTC | use_panels fix for login.mako. | 10 May 2013, 15:49:16 UTC |
| 08ed30b | Dave Bouvier | 09 May 2013, 18:25:51 UTC | Only look for and process tool help image definitions if the tool XML defines a help block. | 09 May 2013, 18:25:51 UTC |
| befe50f | Daniel Blankenberg | 09 May 2013, 14:49:02 UTC | Unicode fixes for previewing large datasets. | 09 May 2013, 14:49:02 UTC |
| cfe579e | Daniel Blankenberg | 08 May 2013, 18:37:33 UTC | Fix for incorrect template inheritance causing the tool shed base_panels to be displayed in the galaxy app when logging in after logout. | 08 May 2013, 18:37:33 UTC |
| 742d06f | Dannon Baker | 17 April 2013, 12:40:24 UTC | Fix more broken tooltips from the tipsy->bootstrap.tooltip() swap | 17 April 2013, 12:40:24 UTC |
| 98d0605 | Dannon Baker | 17 April 2013, 02:27:07 UTC | Add tooltips for (un)linking icon on run workflow page. | 17 April 2013, 02:27:07 UTC |
| 2f033f9 | Dannon Baker | 17 April 2013, 01:47:17 UTC | Update multiselect tooltip, now functional. Was still using tipsy's 'original-title' attribute. | 17 April 2013, 01:47:17 UTC |
| 7ad17fc | Dannon Baker | 17 April 2013, 01:38:38 UTC | Disable select2 for Input Dataset steps on the run workflow page. | 17 April 2013, 01:38:38 UTC |
| ac74123 | Nate Coraor | 01 May 2013, 13:50:31 UTC | Use Galaxy's ErrorMiddleware since Paste's doesn't return start_response. Fixes downloading tarballs from the Tool Shed when use_debug = false. | 01 May 2013, 13:50:31 UTC |
| 7a76d80 | Daniel Blankenberg | 30 April 2013, 21:19:11 UTC | Update GenomeSpace serverurl.properties file location. Should resolve network issues experienced with Jumbo Frames and the Broad. | 30 April 2013, 21:19:11 UTC |
| 662d8f5 | Dave Bouvier | 24 April 2013, 13:52:40 UTC | Fix functional test issue with forms having refresh_on_change. | 24 April 2013, 13:52:40 UTC |
| 8773004 | Dave Bouvier | 17 April 2013, 20:11:20 UTC | Account for condition where output filename is not defined. | 17 April 2013, 20:11:20 UTC |
| d487769 | Dave Bouvier | 17 April 2013, 18:31:27 UTC | Improve recording of invalid tests. Check for the existence each file required by functional tests. | 17 April 2013, 18:31:27 UTC |
| ba1f390 | Daniel Blankenberg | 09 April 2013, 16:26:05 UTC | Fix for generating stderr/stdout links in hda show_params. | 09 April 2013, 16:26:05 UTC |
| de1a836 | Jeremy Goecks | 12 April 2013, 20:12:01 UTC | Fixes for running tools in Trackster. | 12 April 2013, 20:12:01 UTC |
| 44f55ec | Jeremy Goecks | 11 April 2013, 17:16:36 UTC | Do not escape backslashes in sweepster config. | 11 April 2013, 17:16:36 UTC |
| 9d2d364 | Nate Coraor | 08 April 2013, 16:28:46 UTC | Added tag security_2013.04.08 for changeset 2cc8d10988e0 | 08 April 2013, 16:28:46 UTC |
| c829a8b | Dannon Baker | 04 April 2013, 14:19:17 UTC | Fixes logout with remote_user=True (almost, logout.mako still uses the wrong template -- bug introduced in 56de0ee7932f) | 04 April 2013, 14:19:17 UTC |
| f2b496e | Dannon Baker | 05 April 2013, 19:58:31 UTC | Relocate TracksterConfig import in tools package to avoid circular import w/ visual_analytics that was preventing the reports app from functioning. | 05 April 2013, 19:58:31 UTC |
| 2475ede | Carl Eberhard | 05 April 2013, 17:07:50 UTC | controllers/history: use get_history in switch_to_history | 05 April 2013, 17:07:50 UTC |
| f23c39f | Dannon Baker | 04 April 2013, 19:34:43 UTC | Fix for incorrect template inheritance causing the tool shed base_panels to be displayed in the galaxy app upon logout. Mako's inherit directives are processed *before* non-global logic, so you need a built-in switch (as implemented, now) or, ideally, refactor into different templates for each webapp that inherit correctly. | 04 April 2013, 19:34:43 UTC |
| f16854a | Daniel Blankenberg | 04 April 2013, 17:01:39 UTC | Fix for preview flag in Dataset display. | 04 April 2013, 17:01:39 UTC |
| d886bb7 | Nate Coraor | 04 April 2013, 12:20:46 UTC | Fix bug in the sample advanced job configuration noticed by Anthonius deBoer. | 04 April 2013, 12:20:46 UTC |
| ddb0f8a | Dave Bouvier | 03 April 2013, 13:27:44 UTC | Fix for errors encountered during installation of complex repository dependencies, courtesy of Björn Grüning. | 03 April 2013, 13:27:44 UTC |
| 28487f8 | Dave Bouvier | 02 April 2013, 17:34:25 UTC | Enable scrolling for the left panel in the tool shed. Fix for determining if a repository dependency can be added to a container. | 02 April 2013, 17:34:25 UTC |
| 3008447 | Nate Coraor | 01 April 2013, 17:16:32 UTC | Added tag release_2013.04.01 for changeset 75f09617abaa | 01 April 2013, 17:16:32 UTC |
| 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 |
