| 438db6b | Dannon Baker | 23 February 2015, 16:25:23 UTC | Clone .gitignore | 23 February 2015, 16:25:23 UTC |
| 4cd434b | John Chilton | 15 January 2015, 21:01:03 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:03 UTC |
| bb3a003 | Daniel Blankenberg | 13 January 2015, 15:26:40 UTC | Fix a critical security vulnerability where unsanitized user-modifiable values could be included in a command line template. | 13 January 2015, 15:26:40 UTC |
| 653b73b | Nate Coraor | 30 July 2014, 14:55:57 UTC | Apply 2014.07.30 security fix to release_2013.06.03 | 30 July 2014, 14:55:57 UTC |
| 35cf1e3 | Nate Coraor | 30 July 2014, 14:53:14 UTC | Added tag latest_2013.04.01 for changeset 425009b3ff4d | 30 July 2014, 14:53:14 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 |
| a34b360 | Daniel Blankenberg | 19 July 2013, 17:40:39 UTC | Fix server error when an invalid locale is provided by a clients browser. Better handling of locales provided with surrounding whitespace. | 19 July 2013, 17:40:39 UTC |
| 4de7530 | Carl Eberhard | 17 July 2013, 22:42:46 UTC | Saved histories (and grids in gen.): fix busted query in grids when using log_actions=True | 17 July 2013, 22:42:46 UTC |
| 6e3e918 | Dannon Baker | 02 July 2013, 14:48:31 UTC | Fix two more downgrade invocations to accept the migrate_engine parameter | 02 July 2013, 14:48:31 UTC |
| f2f51f4 | Brad Chapman | 02 July 2013, 00:24:07 UTC | Add new engine parameter to downgrade function for 0112 | 02 July 2013, 00:24:07 UTC |
| 7bf8e86 | Dannon Baker | 30 June 2013, 05:26:31 UTC | Make default ami configurable via universe | 30 June 2013, 05:26:31 UTC |
| 08790d3 | Dannon Baker | 31 May 2013, 15:55:46 UTC | Add bucket_default userData (param-based only) to cloudlaunch. | 31 May 2013, 15:55:46 UTC |
| 0312016 | Dannon Baker | 30 May 2013, 15:23:29 UTC | Add specific ami functionality (via GET param) to cloudlaunch. Prevent existing instance selection when using a share string. | 30 May 2013, 15:23:29 UTC |
| 85918b7 | Jeremy Goecks | 28 June 2013, 19:26:27 UTC | Enhance multi-value select parsing to split on all whitespace; this fixes a bug that prevents multi-value selects from being used in workflows due to web browsers using \r\n for newline designation. | 28 June 2013, 19:26:27 UTC |
| 56557f7 | Jeremy Goecks | 27 June 2013, 16:11:21 UTC | Fix unicode issues in page editor. | 27 June 2013, 16:11:21 UTC |
| 5458590 | Daniel Blankenberg | 26 June 2013, 15:57:51 UTC | Change EBI SRA tool to use auto detect for format determination now that they are providing additional formats. Fixes issue seen when sending SFF files. | 26 June 2013, 15:57:51 UTC |
| 56e5bcc | Daniel Blankenberg | 26 June 2013, 15:44:09 UTC | Fix for sniff.handle_uploaded_dataset_file broken in 7605:8bccff9db86973c924b17a4251573e25af7618a4 affects handling of data_source binary files. | 26 June 2013, 15:44:09 UTC |
| ef98fb9 | Daniel Blankenberg | 20 June 2013, 20:24:33 UTC | Fix for GenomeSpace Export root directory listing. | 20 June 2013, 20:24:33 UTC |
| 0c35ab0 | Dave Bouvier | 19 June 2013, 19:03:26 UTC | Fix for tool dependency installation when tarballs raise non-fatal errors, for example if the tarball contains a symlink to a file that does not exist on the local syste. | 19 June 2013, 19:03:26 UTC |
| 98aaf2d | Daniel Blankenberg | 19 June 2013, 18:53:43 UTC | Fix for loading workflows with complex ToolShed Repositories dependencies. | 19 June 2013, 18:53:43 UTC |
| 3677b7e | Greg Von Kuster | 18 June 2013, 13:44:13 UTC | Fix for handing comments as the last element in a set_environment tag set in tool dependency definitions. Contributed by Adam Novak. | 18 June 2013, 13:44:13 UTC |
| 784cbce | Dannon Baker | 15 June 2013, 13:08:09 UTC | Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e4b3/943 | 15 June 2013, 13:08:09 UTC |
| 2aa2143 | Carl Eberhard | 14 June 2013, 19:06:56 UTC | Remove print statements from api/search, ctrl/visualization, ctrl/workflow | 14 June 2013, 19:06:56 UTC |
| 1fafd43 | Dannon Baker | 13 June 2013, 23:08:16 UTC | Fix toolshed migration 0017 to work with both postgres, postgresql dialect names | 13 June 2013, 23:08:16 UTC |
| 241ae73 | Dannon Baker | 13 June 2013, 19:29:57 UTC | Refactor logic in migration 0032, fix sqlite duplicate index. | 13 June 2013, 19:29:57 UTC |
| 75356c7 | Dannon Baker | 13 June 2013, 17:06:22 UTC | Merge | 13 June 2013, 17:06:22 UTC |
| 61f2ac3 | Dannon Baker | 13 June 2013, 16:56:19 UTC | Create indexes in migration 0035 manually to supply mysql_length. After this changeset, mysql instances can migrate from scratch though there are still a few more issues w/ column dropping. | 13 June 2013, 16:56:19 UTC |
| 979c041 | Jeremy Goecks | 12 June 2013, 20:02:19 UTC | Trackster performance fix: extend Cache to support any object that can be converted to a String. Use this enhancement to avoid creating Backbone objects, which can be slow. | 12 June 2013, 20:02:19 UTC |
| 98c3b7c | Dannon Baker | 12 June 2013, 14:39:09 UTC | For user impersonation, fully log the admin out prior to assuming user persona to avoid any history/session corruption. | 12 June 2013, 14:39:09 UTC |
| e039fb9 | Greg Von Kuster | 12 June 2013, 13:50:21 UTC | Fix for getting potential readme files included (or not) in repositories being installed or reinstalled. | 12 June 2013, 13:50:21 UTC |
| cdde7ac | Greg Von Kuster | 12 June 2013, 13:09:33 UTC | Make sure custom datatypes contained in newly installed tool shed repositories are loaded into the upload form's File Format select list. Also, when an installed repository is uninstalled, remove the appropriate datatype extensions from the upload form's select list. | 12 June 2013, 13:09:33 UTC |
| f55a314 | Jeremy Goecks | 11 June 2013, 21:34:26 UTC | Use len_file_path config option rather than hardcoded path for chromInfo tool parameter. | 11 June 2013, 21:34:26 UTC |
| d6e949b | Jeremy Goecks | 11 June 2013, 20:25:27 UTC | Trackster: fix config fallback to defaults. | 11 June 2013, 20:25:27 UTC |
| d602daf | Dannon Baker | 11 June 2013, 15:39:40 UTC | Fix index creation for mysql in 0054 | 11 June 2013, 15:39:40 UTC |
| 4008329 | Dave Bouvier | 11 June 2013, 13:37:55 UTC | Fix server error when renaming a tool shed category. | 11 June 2013, 13:37:55 UTC |
| e842edf | Dannon Baker | 10 June 2013, 20:39:56 UTC | Fix migration 0032 for mysql -- specify index length | 10 June 2013, 20:39:56 UTC |
| 0269bc0 | Dannon Baker | 10 June 2013, 20:20:50 UTC | Fix migration 0030 for mysql, slug index length | 10 June 2013, 20:20:50 UTC |
| d703cc0 | Dannon Baker | 10 June 2013, 20:19:21 UTC | Add mysql_length to TEXT index in to migrate 0017 | 10 June 2013, 20:19:21 UTC |
| 22d4b6b | Dannon Baker | 10 June 2013, 20:18:36 UTC | Fix mysql index length in migrate 0014. | 10 June 2013, 20:18:36 UTC |
| fd0b0fe | Jeremy Goecks | 07 June 2013, 17:05:01 UTC | Trackster: enable feature track post-draw actions to handle display of both coverage and interval data. | 07 June 2013, 17:05:01 UTC |
| c0f9478 | Dannon Baker | 07 June 2013, 16:11:58 UTC | Remove select2 from all standard edit permissions forms -- this fixes library permission page (and others). | 07 June 2013, 16:11:58 UTC |
| b08a15a | Greg Von Kuster | 06 June 2013, 19:05:10 UTC | A slight variation on Nick Soranzo's pull request # 176 for fixing large file downloades using download_by_url. | 06 June 2013, 19:05:10 UTC |
| 5333a09 | Nate Coraor | 05 June 2013, 19:25:19 UTC | Fix a couple bugs in job recovery in the Condor runner found by Branden Timm. | 05 June 2013, 19:25:19 UTC |
| 82bb377 | Dannon Baker | 05 June 2013, 15:24:55 UTC | Require decorator in manage_db.py -- resolves decorator not found for particular deployments | 05 June 2013, 15:24:55 UTC |
| 2fd2b09 | Dannon Baker | 05 June 2013, 14:13:40 UTC | Strip select2 behavior from quota, role, and group creation in the admin panel | 05 June 2013, 14:13:40 UTC |
| bf6ad2c | Greg Von Kuster | 05 June 2013, 13:58:11 UTC | Fix for handling multiple repository installations simultaneously when handle repository dependencies is checked and at least 1 selected repository for installation has no repository dependencies while at least one selected repository for installation does. This scenario occurs only when searching the tool shed for tools rather than browssing it for repositories. | 05 June 2013, 13:58:11 UTC |
| 10a01ff | Dave Bouvier | 04 June 2013, 16:02:55 UTC | Fix missing import. | 04 June 2013, 16:02:55 UTC |
| 6334bd0 | Dave Bouvier | 04 June 2013, 15:05:17 UTC | Fix server error when displaying a tool dependency installation status when the tool dependency contains certain unicode characters in the displayed error message. | 04 June 2013, 15:05:17 UTC |
| 64f08d4 | Nate Coraor | 03 June 2013, 20:17:31 UTC | Update tag for stable_2013.06.03 | 03 June 2013, 20:17:31 UTC |
| 7ff56bf | Dave Bouvier | 03 June 2013, 20:12:24 UTC | Cleanup after merge conflict. | 03 June 2013, 20:12:24 UTC |
| b8ed2c1 | Nate Coraor | 03 June 2013, 19:45:31 UTC | Added tag release_2013.06.03 for changeset 58811a78af8a | 03 June 2013, 19:45:31 UTC |
| 0bc8e9f | Nate Coraor | 03 June 2013, 19:44:31 UTC | Merge changes from next-stable to stable. | 03 June 2013, 19:44:31 UTC |
| c04ccc3 | Nate Coraor | 03 June 2013, 19:43:31 UTC | Close the next-stable branch. | 03 June 2013, 19:43:31 UTC |
| f4106af | Greg Von Kuster | 03 June 2013, 19:40:37 UTC | Fix for rendering xml elements that were not loaded using normal parsing methods. | 03 June 2013, 19:40:37 UTC |
| 485add5 | Dave Bouvier | 03 June 2013, 16:33:02 UTC | Fix for installing a tool dependencies when set_environment actions are distributed between multiple action tag groups. | 03 June 2013, 16:33:02 UTC |
| 950c146 | Greg Von Kuster | 03 June 2013, 16:05:24 UTC | Fix for handling tool panel section selection when installting tool shed repositories. | 03 June 2013, 16:05:24 UTC |
| f1e572b | Jeremy Goecks | 03 June 2013, 13:43:42 UTC | Remove documentation for Tophat -F option because it is no longer supported. | 03 June 2013, 13:43:42 UTC |
| 84a2fd3 | Greg Von Kuster | 01 June 2013, 21:22:27 UTC | Fix for resetting all metadata on writable repositories in the tool shed when the user is not an admin. | 01 June 2013, 21:22:27 UTC |
| 12b1cfc | Greg Von Kuster | 01 June 2013, 18:29:31 UTC | Strip traling / from tool shed url when using it's value to search the Galaxy database. | 01 June 2013, 18:29:31 UTC |
| 1d320bd | Dave Bouvier | 31 May 2013, 20:19:21 UTC | Fix for populating environment variables referenced with the $ENV[] syntax when installing repositories with complex repository dependencies. | 31 May 2013, 20:19:21 UTC |
| 232afae | Dave Bouvier | 31 May 2013, 16:53:56 UTC | Fix for redundant environment settings in env.sh when set_environment actions are distributed across multiple action sections. | 31 May 2013, 16:53:56 UTC |
| 97e8dc4 | Jeremy Goecks | 30 May 2013, 21:38:57 UTC | During workflow export, update workflow modules before visiting inputs to avoid errors resulting from parameter changes. | 30 May 2013, 21:38:57 UTC |
| 4ef01c2 | Jeremy Goecks | 30 May 2013, 21:17:23 UTC | Enhance unicodify to correctly handle non-string input. | 30 May 2013, 21:17:23 UTC |
| 758189c | Jeremy Goecks | 30 May 2013, 20:57:03 UTC | Remove manual JSON parsing because it is not needed. | 30 May 2013, 20:57:03 UTC |
| 51f8c4b | Greg Von Kuster | 30 May 2013, 19:32:25 UTC | Add the ability for a user to reset metadata on a selected list of repositories in the tool shed for those repositories for which they are authorized to change. | 30 May 2013, 19:32:25 UTC |
| 80bf94e | Dave Bouvier | 30 May 2013, 17:23:16 UTC | Fix for incorrect changeset revision being selected on the preview page when installing a repository from the tool shed. Fix for exception being raised when resetting metadata on a repository that does not contain tools. | 30 May 2013, 17:23:16 UTC |
| 36fec6c | Dave Bouvier | 30 May 2013, 14:36:40 UTC | Fix error reporting in the tool dependency installation process. | 30 May 2013, 14:36:40 UTC |
| 8eebd20 | Carl Eberhard | 29 May 2013, 20:25:01 UTC | HDA.get_api_value: remove history_id as tuple | 29 May 2013, 20:25:01 UTC |
| 4f7d717 | Greg Von Kuster | 29 May 2013, 20:18:27 UTC | Fix styles for automated tool test results containers in the tool shed. | 29 May 2013, 20:18:27 UTC |
| c1fb32d | Nate Coraor | 29 May 2013, 20:16:11 UTC | Update pgcleanup.py for dialect name change. | 29 May 2013, 20:16:11 UTC |
| 25c9866 | Dave Bouvier | 29 May 2013, 19:24:52 UTC | Make the functional test results RSS feed output properly formatted data. | 29 May 2013, 19:24:52 UTC |
| c9ca524 | Nate Coraor | 29 May 2013, 17:55:08 UTC | Make PBKDF2 password hashing conditional, enable by default. | 29 May 2013, 17:55:08 UTC |
| 795dfde | Dave Bouvier | 29 May 2013, 17:26:38 UTC | Fix for set_environment appearing in multiple action sections. Fix for interpolating multiple environment variables in set_environment actions. | 29 May 2013, 17:26:38 UTC |
| c2afb99 | Dannon Baker | 28 May 2013, 21:23:17 UTC | Bugfix for standard dataset upload | 28 May 2013, 21:23:17 UTC |
| d477295 | Dave Bouvier | 28 May 2013, 18:49:19 UTC | Explicitly filter by tag name actions when building the actions dict for tool dependency installation. | 28 May 2013, 18:49:19 UTC |
| b65685f | John Chilton | 26 May 2013, 20:15:19 UTC | Fix job splitting to rewrite references in config files in addition to command-line. | 26 May 2013, 20:15:19 UTC |
| 8999130 | John Chilton | 26 May 2013, 20:10:43 UTC | Fix API uploads (must have broken with API/Web transaction unification). | 26 May 2013, 20:10:43 UTC |
| 8eb3e7d | Greg Von Kuster | 28 May 2013, 16:24:52 UTC | Eliminate the use of Galaxy's elementree egg within the tool shed. | 28 May 2013, 16:24:52 UTC |
| 5e912d4 | Dave Bouvier | 28 May 2013, 13:53:36 UTC | Fixes for backward compatibility with 2012-12-20 release of Galaxy. | 28 May 2013, 13:53:36 UTC |
| f5432bd | Dave Bouvier | 24 May 2013, 18:02:14 UTC | Fix for missing_test_components always being present, causing misleading test result display on repository pages. | 24 May 2013, 18:02:14 UTC |
| 43863a3 | Daniel Blankenberg | 24 May 2013, 17:59:26 UTC | Unicode fixes for tool parameters | 24 May 2013, 17:59:26 UTC |
| 6a5b539 | Daniel Blankenberg | 24 May 2013, 17:56:42 UTC | Fix for displaying unicode characters in TextField in form_builder. | 24 May 2013, 17:56:42 UTC |
| 9b7cb64 | Daniel Blankenberg | 24 May 2013, 17:43:25 UTC | Fix for displaying unicode characters in select checkboxes in form_builder. | 24 May 2013, 17:43:25 UTC |
| 54298b3 | Daniel Blankenberg | 24 May 2013, 17:36:17 UTC | Fix for displaying unicode characters in select menus in form_builder. | 24 May 2013, 17:36:17 UTC |
| 1a362aa | Daniel Blankenberg | 24 May 2013, 17:04:32 UTC | Fix for MetadataInDataTableColumnValidator becoming stale when a tool data table is updated during Galaxy runtime. | 24 May 2013, 17:04:32 UTC |
| 6bda99e | Dave Bouvier | 23 May 2013, 19:49:46 UTC | Fix of environment variables being set in set_environment_for_install, but not being propagated to set_environment actions. | 23 May 2013, 19:49:46 UTC |
| ba34c92 | Carl Eberhard | 23 May 2013, 19:44:17 UTC | Remove access check from get_hda_dict; Add profiler version of same | 23 May 2013, 19:44:17 UTC |
| 98948dd | Greg Von Kuster | 23 May 2013, 18:57:12 UTC | Fixes for xml handling in the tol shed. | 23 May 2013, 18:57:12 UTC |
| d21bf21 | Carl Eberhard | 23 May 2013, 17:47:03 UTC | Controllers.dataset: add exception string to log msg in _delete | 23 May 2013, 17:47:03 UTC |
| e7945c8 | Greg Von Kuster | 23 May 2013, 15:49:52 UTC | Keep all contents of dependency definition files when re-writing them to include missing toolshed and changeset_revision attributes. | 23 May 2013, 15:49:52 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 |
| e8c57e2 | 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 |
| 6547215 | Dave Bouvier | 23 May 2013, 13:45:24 UTC | Fix for missing tool test results display on manage repository page. | 23 May 2013, 13:45:24 UTC |
| ce76fce | Greg Von Kuster | 22 May 2013, 20:11:55 UTC | Populate the toolshed attribute when it is missing from the repository tag in dependency definitions with the current tool shed url. | 22 May 2013, 20:11:55 UTC |
| 755256a | Jeremy Goecks | 22 May 2013, 19:23:15 UTC | Trackster: for variant track painter, only draw loci in viewing region. | 22 May 2013, 19:23:15 UTC |
| d618359 | Jeremy Goecks | 22 May 2013, 18:47:37 UTC | Trackster: fix for subsetting variant tracks. | 22 May 2013, 18:47:37 UTC |
