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Author SHA1 Message Date
Nicola Soranzo 2f650b8866 Fix file extension determination 
Extension was determined uncorrectly for filenames with more than 1 dot
 2013-03-06 12:37:08 +01:00
Greg Von Kuster de3cff9379 Enhance the display of functional test results in the tol shed for tests run against contained tools when the repository is installed into Galaxy. 2013-03-05 16:37:51 -05:00
Dannon Baker 2bdaadeb4f Workflow modules: Adjust spacing to new guidelines. 2013-03-05 16:18:16 -05:00
Dannon Baker 9ecb567516 Fix workflow modules imports. 2013-03-05 16:15:54 -05:00
Dannon Baker 32b14762f4 Remove import *, fix a docstring in actions/admin 2013-03-05 16:10:45 -05:00
Dannon Baker 5e297f3b67 Strip dead test code (that actually threw an exception when enabled due to undefined variables). 2013-03-05 16:07:35 -05:00
Dannon Baker 9a4d211a9a Strip whitespace. 2013-03-05 15:59:30 -05:00
Dannon Baker 4b4ef8f301 Fix incorrect addition of child_dataset to sa_session. 2013-03-05 15:59:06 -05:00
Dannon Baker 0204f04ae2 Tools module import cleanup, removal of dead code. 2013-03-05 15:58:13 -05:00
Dannon Baker 4062e869c5 Fix spacing between methods in base controller. 2013-03-05 15:52:09 -05:00
Dannon Baker 8e9bb76611 Trim whitespace. 2013-03-05 15:44:03 -05:00
Dannon Baker 4ca14e3dea Kill unused step error dict - this is handled elsewhere. 2013-03-05 15:43:40 -05:00
Dannon Baker e29f450cf2 Fix bug introduced in 6028 -- encoded_id should be just 'id' 2013-03-05 15:41:22 -05:00
Dannon Baker d6903c2d86 Base controller import cleanup, remove unused variables. 2013-03-05 15:39:22 -05:00
Carl Eberhard 29143f0eb2 Browser testing: add tests (and conv. fns) for working with the history options, history panel 2013-03-05 15:35:59 -05:00
Greg Von Kuster 06e435db24 Add baseline support for reviewing functional test results for installing repositories and executing functional tests on the contained tool inside a Galaxy instance for tools included in repositories in the tool shed. 2013-03-05 12:36:58 -05:00
Dave Bouvier 6bc5251965 Removed the must_include_tools filter from the repository revisions API controller, since repository_metadata now has a flag includes_tools. 2013-03-05 10:23:55 -05:00
Dave Bouvier 4dc0ae6cc8 Script to check repositories and determine whether functional tests are defined for all tools, and set the do_not_test flag accordingly. Cleaned up the install and test framework and functional test common methods. 2013-03-05 10:23:21 -05:00
Greg Von Kuster 21b6a1d7a3 Add white space to the tool shed's admin and repository_review controllers per new Galaxy dev team standards and factor out grid utility methods. 2013-03-05 09:27:50 -05:00
Dannon Baker 9786b8c451 Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #133) 
Add `file_ext` attribute to image classes. Whitespace fixes for same classes.
 2013-03-05 08:18:39 -05:00
Greg Von Kuster 810efdefcb Add links for set_environment tool dependency type in the Tool dependency definitions Galaxy Utilities grid. 2013-03-04 19:47:23 -05:00
Greg Von Kuster 84d382ee14 Better aggangement of Galaxy utility grid columns in the tool shed, and fix for the Repository Dependency link in the Valid repository dependency definitions Galaxy Utilities grid. 2013-03-04 19:39:23 -05:00
Greg Von Kuster dba5a62a5c Speed up the searches for tools and workflows contained in repositories in the tool shed. 2013-03-04 17:21:46 -05:00
Dannon Baker eef0490fc6 Update migrate_tools to the correct path. 2013-03-04 14:43:41 -05:00
Greg Von Kuster cc0c717cff Fix links in the tool shed's Galaxy utilities grids. 2013-03-04 14:29:23 -05:00
John Chilton 062fb48398 Add file_ext attribute to image classes. Whitespace fixes for same classes. 2013-03-04 13:14:08 -06:00
Carl Eberhard 1d0ab0969a call_hook: Fix to handle exception.args more gracefully when modifying 2013-03-04 13:51:52 -05:00
Greg Von Kuster 3a7fe470f2 Clean up recently introduced tool shed repository Galaxy utilities grids. 2013-03-04 13:01:33 -05:00
Dannon Baker d08546152a Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #131) 
Implement equivalent of dataset display through the API.
 2013-03-04 12:06:15 -05:00
John Chilton 466db569a2 Per Jeremy's request I have moved the API history contents dataset display functionality to the dataset controller - https://bitbucket.org/galaxy/galaxy-central/pull-request/131/implement-equivalent-of-dataset-display/diff. 2013-03-04 10:32:32 -06:00
Greg Von Kuster 9a0fcad321 Move the tool shed's repository review grid classes out of the repository_review controller and into ~/tool_shed/grids. 2013-03-04 10:07:31 -05:00
Greg Von Kuster c8e0514c81 Move the tool shed's administrative grids out of the admin controller and into ~/tool_shed/grids. 2013-03-04 09:47:37 -05:00
Greg Von Kuster fe69136e4a Move the many Grid classes out of the tool shed's repository controller into the new location for tool shed grids: ~/tool_shed/grids. 2013-03-04 09:26:59 -05:00
Jeremy Goecks e84d447d07 Trackster: (a) handle corner case when feature starts at tile boundary and (b) remove poor tile index usage. Pack script. 2013-03-01 16:18:23 -05:00
Greg Von Kuster d12a90fea6 Be conservative when displaying custom datatypes in the tool shed. 2013-03-01 16:13:29 -05:00
Greg Von Kuster 821a475eeb Implement more granular grids for valid Galaxy utilities in the tool shed - custom datatypes, tools, tool dependencies and repository dependencies are now accessible. 2013-03-01 16:08:25 -05:00
Dave Bouvier 8d2655503b Improved documentation for automated repository installation and testing. Handle cases where a repository is missing test data. Limit the list of repositories to test to those that have tools. Update the parse_tool_panel_config method to return a flag specifying whether test data was found for the specified tool panel entry. 2013-03-01 15:13:20 -05:00
Carl Eberhard 2337695990 fix server_env saved output dir name; clean up prev. debugging statements 2013-03-01 12:49:08 -05:00
Greg Von Kuster ee10eed481 Add RepositoryMetadata attributes that enable improved query abilities for tool shed repository revisions that contain Galaxy utilities. 2013-03-01 11:13:15 -05:00
Greg Von Kuster 9096f96b22 Fix the level 16 database migration script for the tool shed. 2013-03-01 10:52:13 -05:00
Greg Von Kuster 9565587d6c Fix for starting up Galaxy after community webapp was renamed to be tool_shed. 2013-03-01 10:16:20 -05:00
Greg Von Kuster f5962529a6 Add the method for displaying tool functional test errors for a repository in the tool shed to the repository controller in preparation for the upcoming install and test framework. 2013-03-01 09:14:38 -05:00
Nate Coraor 9b74b4665d Merged in jmchilton/galaxy-central-lwr (pull request #132) 
Updates required to target LWR servers configured to point to a toolbox.
 2013-03-01 08:23:58 -05:00
Dannon Baker ad5e8296b1 Bugfix: Missing paste import in data.py, log being used before definition. 2013-03-01 08:07:56 -05:00
John Chilton 9d31f3499d Update LWR client to pass along tool id and version, required if LWR server is configured to point to a toolbox. The LWR server uses this information to match the job up with a tool and uses the tool to validate inputs. 
For more information see:
https://lwr.readthedocs.org/en/latest/#setting-up-a-public-lwr-server
https://bitbucket.org/jmchilton/lwr/src/tip/test/validator_test.py

Updates the LWR client to revision 8a249f4254eb6aa1eed8669f738c5a9764caccdb of the LWR.
https://bitbucket.org/jmchilton/lwr/commits/8a249f4254eb6aa1eed8669f738c5a9764caccdb
 2013-02-28 23:56:56 -06:00
Jeremy Goecks 5be04ef7b9 Trackster: standardize start and end of regions to fall between bases. 2013-02-28 22:54:11 -05:00
Jeremy Goecks 15ca057151 Pack scripts. 2013-02-28 16:55:33 -05:00
Jeremy Goecks 9c97ac4854 Trackster enhancements: (a) rename reference data manager to more appropriate name; (b) fetch reference data more readily so that variants can be drawn even when not zoomed way in; and (c) use base letters to denote variants only when there is sufficient room. 2013-02-28 16:54:26 -05:00
Jeremy Goecks b7543d7120 Trackster: (a) color reference bases and (b) color variants when reference data is available. 2013-02-28 16:27:31 -05:00
Dave Bouvier 080eee90d9 Removed unneeded log data from functional test error reports, use url_join to generate api URLs. 2013-02-28 14:41:53 -05:00