| c78b7b6 | guerler | 09 March 2015, 17:55:47 UTC | Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 | 09 March 2015, 17:55:47 UTC |
| 4d347dc | guerler | 09 March 2015, 17:55:18 UTC | Fix select2 field arrow style | 09 March 2015, 17:55:18 UTC |
| dd5b765 | Dannon Baker | 19 February 2015, 19:45:44 UTC | Cherry-pick e01310e3f82e67ea9048e547205fdbe5748d60ac over to release_15.03 | 09 March 2015, 15:56:29 UTC |
| d0c9794 | Dannon Baker | 06 March 2015, 21:04:43 UTC | Ensure path was well constructed (has value) before trying to determine whether or not it exists. | 06 March 2015, 21:04:43 UTC |
| eb9d3a9 | Dannon Baker | 06 March 2015, 20:49:14 UTC | Minor wording tweaks. | 06 March 2015, 20:49:14 UTC |
| f515e29 | guerler | 06 March 2015, 20:28:22 UTC | Enable remap condition | 06 March 2015, 20:28:22 UTC |
| 949b785 | guerler | 06 March 2015, 20:26:24 UTC | Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 | 06 March 2015, 20:26:24 UTC |
| d079ad8 | guerler | 06 March 2015, 20:24:31 UTC | Add resume option for job dependencies | 06 March 2015, 20:24:31 UTC |
| 18d77b0 | Daniel Blankenberg | 06 March 2015, 19:18:48 UTC | Make api/config /version usable as sessionless in addition to anonymous. | 06 March 2015, 19:18:48 UTC |
| f0bebc9 | guerler | 06 March 2015, 03:16:54 UTC | Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 | 06 March 2015, 03:16:54 UTC |
| 1a1f5a3 | guerler | 06 March 2015, 03:15:21 UTC | Fix dataset and collection mapping for re-run in imported histories | 06 March 2015, 03:15:21 UTC |
| 9316ccc | Daniel Blankenberg | 05 March 2015, 22:02:45 UTC | Fix for displaying Tools in ToolShed that use Dynamically Generated multiple selects as checkboxes and for displaying select lists using old-style dynamic options. | 05 March 2015, 22:02:45 UTC |
| 6db6b7e | Dannon Baker | 05 March 2015, 18:27:22 UTC | Tweaks to the password reset email template to help email clients not mangle it, and when they do, to suggest copying and pasting. | 05 March 2015, 18:27:22 UTC |
| 826f69f | Dannon Baker | 04 March 2015, 23:04:00 UTC | Python 2.6 has a bug in deepcopy that causes an error when attempting to copy datasets between users (which uses deepcopy). Py2.7 worked fine. Now they both should. | 04 March 2015, 23:04:00 UTC |
| 9364b9d | John Chilton | 04 March 2015, 16:09:29 UTC | API fixes for tools and datatypes. By replacing _future_expose_api_anonymous with _future_expose_api_anonymous_and_sessionless. | 04 March 2015, 19:51:43 UTC |
| aa9c7e6 | Carl Eberhard | 04 March 2015, 18:13:29 UTC | Fix: in multi-history order properly instantiate Dates for comparison and handle variadic better | 04 March 2015, 18:13:29 UTC |
| 5cba388 | Dannon Baker | 04 March 2015, 14:23:38 UTC | Update .gitignore to include run_api_tests.html | 04 March 2015, 14:27:23 UTC |
| d0b9664 | Carl Eberhard | 04 March 2015, 14:23:19 UTC | UI, multi-history: swap 'done' and 'create' buttons for better rtl intuition | 04 March 2015, 14:23:19 UTC |
| d390ef2 | Carl Eberhard | 03 March 2015, 18:13:26 UTC | Fix to safari that still uses prefixed flexbox attributes | 03 March 2015, 18:13:26 UTC |
| 2e3bebb | Daniel Blankenberg | 03 March 2015, 16:55:47 UTC | Fix for reports app not running mysql. | 03 March 2015, 16:55:47 UTC |
| 853f515 | Daniel Blankenberg | 03 March 2015, 15:49:12 UTC | When loading Dynamic Display application links, allow the application to load even if one set of links does not. | 03 March 2015, 15:49:12 UTC |
| 05ff2aa | Daniel Blankenberg | 03 March 2015, 15:24:58 UTC | Add a 10 second timeout to loading data URLs for Tool Data Tables. | 03 March 2015, 15:24:58 UTC |
| f823278 | John Chilton | 03 March 2015, 14:37:30 UTC | Fix bug in workflows test for implicit connections between steps. It would fail when being run with the rest of the suite and not on its own - because it was using the same id for the workflow id and invocation id - which is obviously wrong unless it is a completely fresh database :). | 03 March 2015, 14:37:30 UTC |
| fc0a6d8 | John Chilton | 03 March 2015, 14:30:55 UTC | Fix intermittently failing test test_workflow_run_dynamic_output_collections. Love it when the bugs correspond to actual TODOs I left in the code. | 03 March 2015, 14:30:55 UTC |
| 391abd5 | John Chilton | 03 March 2015, 03:34:40 UTC | Remove assert False from test/api/test_workflows_from_yaml.py. These aren't ideal tests - but it is some indication that things are working that the API will import the workflow and produce a representation. Should follow up at some point and verify the representation is in fact the correct one. | 03 March 2015, 03:39:58 UTC |
| f8bfe89 | John Chilton | 03 March 2015, 03:33:07 UTC | Clarify failing test test_tools.py. | 03 March 2015, 03:39:58 UTC |
| a20938f | John Chilton | 03 March 2015, 03:31:32 UTC | Attempt to fix intermittently failing jobs API test. Retry check several times in case there is some sort of timing problem where a history turns okay - before a job. Improve assertion error message. | 03 March 2015, 03:39:50 UTC |
| b1f3654 | John Chilton | 03 March 2015, 02:32:30 UTC | Tool data API testing fixes. - Add files I didn't commit previously in test/functional/tool-data/. - Comment out test for tool data table deletion since Dan fixed the problem of regular users running data managers through the API (https://github.com/galaxyproject/galaxy/commit/48f77dc742acf01ddbafafcc4634e69378f1f020) that I previously exploited to write the test. | 03 March 2015, 03:36:24 UTC |
| 0d62ee6 | guerler | 02 March 2015, 23:25:46 UTC | Parameters: Fix collection selection for multiple dataset input field | 02 March 2015, 23:25:46 UTC |
| 434aa05 | guerler | 02 March 2015, 23:12:34 UTC | Parameters: Cover additional case for multiple hdas | 02 March 2015, 23:12:34 UTC |
| 8e6fbe3 | Martin Cech | 02 March 2015, 21:33:43 UTC | tweak toolbox search to provide better (and more) results with the inclusion of toolhelp in index and with more versions of the same tools being massively installed the search results were inconsistent and inaccurate and incomplete. addresses https://trello.com/c/6Bvbduci/2486-toolbox-search-is-behaving-wrongly-differently | 02 March 2015, 21:33:43 UTC |
| 1b23706 | Dannon Baker | 02 March 2015, 19:54:29 UTC | Rearranging the layers of middleware to allow sentry and debug to coexist without exploding (but you probably don't want to use both at once anyway) | 02 March 2015, 19:54:29 UTC |
| ebda6ac | Carl Eberhard | 02 March 2015, 19:22:00 UTC | Fix to remove validation of genome builds since some data source tools will assign invalid genome builds and later validation makes these hdas un-updatable | 02 March 2015, 19:22:00 UTC |
| 589b3fb | John Chilton | 02 March 2015, 18:45:12 UTC | Update basic.py to allow collection reduction with new tool form. | 02 March 2015, 18:53:17 UTC |
| 5bee11d | guerler | 28 February 2015, 17:12:10 UTC | Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful) | 28 February 2015, 17:12:10 UTC |
| 76a337b | guerler | 28 February 2015, 09:37:37 UTC | ToolForm: Use default closing behaviour for progress modal | 28 February 2015, 09:37:37 UTC |
| 1bf37af | guerler | 28 February 2015, 09:30:14 UTC | ToolForm: Do not show submission error if user closes progress modal | 28 February 2015, 09:30:14 UTC |
| 54eba77 | guerler | 28 February 2015, 06:36:21 UTC | Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 | 28 February 2015, 06:36:21 UTC |
| 772f08d | guerler | 28 February 2015, 06:33:15 UTC | ToolForm: Update biostar url for tool search | 28 February 2015, 06:33:15 UTC |
| 1260d07 | Daniel Blankenberg | 27 February 2015, 20:50:28 UTC | Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37). | 27 February 2015, 20:50:28 UTC |
| 9f68fe0 | Daniel Blankenberg | 27 February 2015, 20:50:13 UTC | Allow External display applications to use Tool Data Tables. | 27 February 2015, 20:50:13 UTC |
| 10f8b6e | Dannon Baker | 27 February 2015, 20:19:32 UTC | Merge branch 'release_15.03' of github.com:galaxyproject/galaxy into release_15.03 | 27 February 2015, 20:19:32 UTC |
| f73467f | dannon | 27 February 2015, 00:59:26 UTC | Fix server_starttime being in app for reports, toolshed. I will be refactoring this shortly to have a base UniverseApplication from which things inherit. | 27 February 2015, 20:19:17 UTC |
| 002fef9 | Nate Coraor | 27 February 2015, 19:21:22 UTC | Fix a typo in datatypes_conf.xml.sample | 27 February 2015, 19:21:22 UTC |
| f6afc9b | guerler | 27 February 2015, 18:43:39 UTC | ToolForm: Make deep copy of current state in order to be on the safe side | 27 February 2015, 18:43:39 UTC |
| 6080ff9 | guerler | 27 February 2015, 15:17:05 UTC | Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 | 27 February 2015, 15:17:05 UTC |
| 3c11c85 | guerler | 27 February 2015, 15:12:13 UTC | ToolForm: Fix dataset order for multi select run | 27 February 2015, 15:12:13 UTC |
| fe52323 | Carl Eberhard | 27 February 2015, 15:03:47 UTC | Fix display_structure by using serializer; fix structure by removing extra decode_id | 27 February 2015, 15:03:47 UTC |
| d4b6df5 | guerler | 27 February 2015, 09:36:20 UTC | ToolForm/Ui: Restrict available option requirement to single select fields | 27 February 2015, 09:36:20 UTC |
| e0ad2d7 | guerler | 27 February 2015, 09:26:15 UTC | Parameters: Set hidden attribute for hidden dataset parameter | 27 February 2015, 09:26:15 UTC |
| d58d2ab | guerler | 27 February 2015, 06:59:43 UTC | Parameters: Fix deleted datasets validation message | 27 February 2015, 06:59:43 UTC |
| 5a78162 | guerler | 27 February 2015, 06:57:39 UTC | ToolForm/Ui: Limit selection to available options | 27 February 2015, 06:57:39 UTC |
| 0207fc1 | guerler | 27 February 2015, 06:49:53 UTC | Parameters: Prevent uncaught exception on unavailable datasets in column validation | 27 February 2015, 06:49:53 UTC |
| c7943f3 | guerler | 27 February 2015, 06:35:38 UTC | ToolForm/Collections: Re-introduce parameter expansion | 27 February 2015, 06:35:38 UTC |
| a3b1e60 | guerler | 27 February 2015, 06:30:48 UTC | ToolForm: Show initial validation errors on re-run | 27 February 2015, 06:30:48 UTC |
| 1b36233 | Daniel Blankenberg | 26 February 2015, 22:16:55 UTC | Allow TabularToolDataTable to be loaded from a url instead of a path. | 26 February 2015, 22:16:55 UTC |
| a34695d | Carl Eberhard | 26 February 2015, 19:15:47 UTC | Fix visualization controller to use security.decode_id in grids | 26 February 2015, 19:15:47 UTC |
| 057a9c9 | Dannon Baker | 26 February 2015, 19:07:35 UTC | Attempt at a fix for get('') in tools/params/basic.py | 26 February 2015, 19:07:35 UTC |
| f090393 | John Chilton | 26 February 2015, 17:48:28 UTC | Bugfix: serializing "None" for UUIDs for older workflows. Prevents workflows from being saved :(. | 26 February 2015, 17:50:08 UTC |
| 64485fe | Dannon Baker | 26 February 2015, 17:48:08 UTC | Merge branch 'fix_cache_bust' into release_15.03 | 26 February 2015, 17:48:08 UTC |
| 3e6090c | Dannon Baker | 26 February 2015, 17:47:50 UTC | Move server_starttime to base universe application so shared templates between galaxy/shed/etc don't break. | 26 February 2015, 17:47:50 UTC |
| 44c8eb5 | Dannon Baker | 26 February 2015, 17:40:49 UTC | Merge branch 'fix_cache_bust' into release_15.03 | 26 February 2015, 17:40:49 UTC |
| 721c6ad | Dannon Baker | 26 February 2015, 17:40:26 UTC | Fix cache-busting under require.js. | 26 February 2015, 17:40:26 UTC |
| a39796d | guerler | 26 February 2015, 16:12:45 UTC | Remove collection expansion | 26 February 2015, 16:12:45 UTC |
| ab25fe1 | guerler | 26 February 2015, 06:10:11 UTC | Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 | 26 February 2015, 06:10:11 UTC |
| e8dc956 | guerler | 26 February 2015, 06:05:27 UTC | Collections: Enable the batch mode execution for nested collections (without adding a new button) | 26 February 2015, 06:05:27 UTC |
| 8cea3c0 | Dannon Baker | 25 February 2015, 14:14:59 UTC | Fix returning encoded None library folder parent ids in library_contents API; thanks to nsoranzo | 25 February 2015, 20:09:39 UTC |
| b89a5be | Daniel Blankenberg | 25 February 2015, 17:07:39 UTC | Fix for ToolShed not having config.shed_tool_data_path | 25 February 2015, 17:07:39 UTC |
| 09a65cf | John Chilton | 25 February 2015, 14:10:17 UTC | Expand out meta parameters when validating for tool.to_json(). Bring this code closer inline with what handle_input() does and should solve the problem with column validation of parameters that are being 'batched'. See https://trello.com/c/8NweTvLh and comment on https://github.com/galaxyproject/galaxy/commit/d57088409c7b23e55ead4c9f2fad38b2600eb8b7. | 25 February 2015, 14:14:06 UTC |
| 0b2a8b7 | John Chilton | 24 February 2015, 00:52:17 UTC | Improved tool diagnostics API. | 25 February 2015, 13:01:05 UTC |
| 0ca4068 | John Chilton | 18 February 2015, 16:34:23 UTC | Tool diagnostic API endpoints. It is easy to get Galaxy's database and shed tool files out of sync and the results are bad. I don't think this is new but I may have made it worse this cycle by trying to slowly walk back Galaxy's use of the database to track lineages (e.g. https://bitbucket.org/galaxy/galaxy-central/commits/08f8850853d004bf8a456a147436a6694d0a1a11). New API endpoints include: /api/configuration/dynamic_tool_confs /api/configuration/tool_lineages /api/<tool_id>/diagnostics | 25 February 2015, 13:00:53 UTC |
| e6971e1 | guerler | 25 February 2015, 01:31:43 UTC | ToolForm: Enable collection for multiple data parameter | 25 February 2015, 01:31:43 UTC |
| e639987 | guerler | 25 February 2015, 00:41:30 UTC | Charts: Fix missing data message | 25 February 2015, 00:41:30 UTC |
| e2f5e9e | guerler | 25 February 2015, 00:08:36 UTC | Charts: Rebuild and update charts | 25 February 2015, 00:08:36 UTC |
| 59c788a | Dannon Baker | 24 February 2015, 23:55:50 UTC | More tweaks to mutable capabilities, adding back in a copy and stripping pickle from MutationList | 24 February 2015, 23:55:50 UTC |
| 475fcf6 | guerler | 24 February 2015, 23:37:52 UTC | Show error message on server error | 24 February 2015, 23:37:52 UTC |
| af79513 | guerler | 24 February 2015, 23:14:13 UTC | Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03 | 24 February 2015, 23:14:13 UTC |
| 86035ed | Carl Eberhard | 24 February 2015, 22:34:47 UTC | Merge remote-tracking branch 'upstream/release_15.03' into release_15.03 | 24 February 2015, 22:34:47 UTC |
| c59980b | Carl Eberhard | 24 February 2015, 22:20:10 UTC | Fix to layering of dropdown buttons and menus | 24 February 2015, 22:20:10 UTC |
| 3c0275a | guerler | 23 February 2015, 23:04:02 UTC | Fix job ids in success message | 24 February 2015, 20:52:51 UTC |
| fc23aee | guerler | 23 February 2015, 22:56:38 UTC | Allow text selection in tool form | 24 February 2015, 20:52:17 UTC |
| 2fb5d0c | Dannon Baker | 24 February 2015, 19:50:02 UTC | Apply custom_types bugfixes from dev branch to release. | 24 February 2015, 19:50:02 UTC |
| ca41396 | Daniel Blankenberg | 24 February 2015, 17:02:42 UTC | Fix for installing .loc files from the toolshed to respect shed_tool_data_path. Mention shed_tool_data_path in galaxy.ini.sample. | 24 February 2015, 17:02:42 UTC |
| 77b167b | John Chilton | 24 February 2015, 04:09:19 UTC | Comment out broken liftOver tests. liftOver loc file handling is problematic (https://trello.com/c/A6I6zQvF). If it weren't this wouldn't be a problem. I could fix the API functional test framework to mimic the older form driven approach but it would take a week and would be rendered moot by fixing liftOver. Unfortunately, fixing liftOver would likely break a lot of existing workflows and tool reruns so I am not fixing that either. Only option left, admittedly a crappy one, is to comment out the tests. | 24 February 2015, 04:09:19 UTC |
| 2bcc9e2 | John Chilton | 22 February 2015, 05:32:46 UTC | Fix for watching tools on some more interesting file systems. | 24 February 2015, 00:58:12 UTC |
| 7a25604 | Carl Eberhard | 23 February 2015, 22:14:37 UTC | UI, history panel: correctly default clearMessages target when no event is given | 23 February 2015, 22:14:37 UTC |
| 23179f3 | Dannon Baker | 23 February 2015, 21:28:01 UTC | Verify and apply @jmchilton's fix from https://github.com/jmchilton/galaxy-central/commit/306a86558a7ee7be1bc2d68cd939b16b5f1863d4 to next-stable. Should be refactored into using the same galaxy.menu.js objects -- I'm assuming that's why things like PopupMenu.fromExistingDom exist and are otherwise unused. | 23 February 2015, 21:28:01 UTC |
| d54b3b0 | Dannon Baker | 23 February 2015, 20:08:31 UTC | Merge branch 'cancelfix' into release_15.03 | 23 February 2015, 20:08:31 UTC |
| 7433601 | Dannon Baker | 23 February 2015, 20:07:58 UTC | Bugfix for clicking cancel in a menu and having the action happen anyway. | 23 February 2015, 20:07:58 UTC |
| c6237de | Martin Cech | 23 February 2015, 18:53:13 UTC | fix error preventing change of username in TS | 23 February 2015, 18:53:13 UTC |
| cec5854 | guerler | 23 February 2015, 17:50:27 UTC | Select2 fix | 23 February 2015, 17:50:27 UTC |
| a6b13a2 | Dannon Baker | 23 February 2015, 16:28:07 UTC | Clone .gitignore | 23 February 2015, 16:28:07 UTC |
| cebd5f8 | Daniel Blankenberg | 18 February 2015, 19:39:07 UTC | Fixes for handling Data Managers that use undeclared data tables. | 21 February 2015, 18:29:58 UTC |
| f2771f7 | Dannon Baker | 17 February 2015, 20:20:40 UTC | Merge back from next-stable. | 17 February 2015, 20:20:40 UTC |
| 815b3a2 | Dannon Baker | 17 February 2015, 20:19:40 UTC | Merge. | 17 February 2015, 20:19:40 UTC |
| 3a8b2bf | Dannon Baker | 17 February 2015, 20:19:00 UTC | Merge. | 17 February 2015, 20:19:00 UTC |
| 5c94d23 | Dannon Baker | 17 February 2015, 20:18:45 UTC | Merge bugfix from next-stable. | 17 February 2015, 20:18:45 UTC |
| f22ef12 | Dannon Baker | 17 February 2015, 20:18:08 UTC | Fix xml.etree relative import error happening in test/asserts/xml.py | 17 February 2015, 20:18:08 UTC |
| 8d48f17 | Daniel Blankenberg | 17 February 2015, 20:17:17 UTC | For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed. | 17 February 2015, 20:17:17 UTC |
| fb2c305 | Daniel Blankenberg | 17 February 2015, 20:17:17 UTC | For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed. | 17 February 2015, 20:17:17 UTC |
