Greg Von Kuster
04ef9af929
Provide more useful details when logging the results of the prep script for the Tool Shed's install and test framework.
2013-11-28 08:41:23 -05:00
Greg Von Kuster
a5fd026149
Moinor fixes and adjustments to the tool shed's install and test framework.
2013-11-27 21:10:52 -05:00
Dave Bouvier
af88ddf8ff
Fix imports.
2013-11-27 15:37:02 -05:00
Greg Von Kuster
f96fdc565f
Fixes for the tool shed's install and test framework and enhancements to allow a configurable number of test runs to be stored and displayed.
2013-11-27 15:28:03 -05:00
Greg Von Kuster
9bc4c4a237
More code cleanup and fixes for the tool shed's install and test framework. The test environment information for both the tool shed and Galaxy should now be stored correctly in the Tool test results container on the view or manage repository page in the tool shed.
2013-11-26 11:40:25 -05:00
Greg Von Kuster
b928152268
Minor fixes for the prep script for installing and testing tool shed repositories of type tool_dependency_definition.
2013-11-25 16:43:01 -05:00
Greg Von Kuster
6968b7f016
More fixes for the tool shed's install and test framework - the test environment including time last tested should now display correctly again (among other fixes).
2013-11-25 15:09:50 -05:00
Greg Von Kuster
0a99ad6519
More code cleanup, fixes and additional exception handling for the tool shed's install and test framework.
2013-11-22 16:19:18 -05:00
Greg Von Kuster
dd35b2602b
Refactor the tool shed's install and test framework to enable restriction of bugs introduced into the Galaxy framework that result in server exceptions to specific repository tests rather than the entire framework.
2013-11-22 13:49:30 -05:00
Greg Von Kuster
7ccddceb66
Code cleanup and minor fixes in prep scripts for tool shed nightly test runs and its functional test framework.
2013-11-21 10:28:22 -05:00
Dave Bouvier
fd942b5339
Fix string interpolation in a log message.
2013-11-20 16:51:02 -05:00
Greg Von Kuster
0659e43b41
Add a script to check repositories of type tool dependency definition in the tool shed to prep for installation testing.
2013-11-20 16:41:33 -05:00
Greg Von Kuster
1fd87b557d
Enhance the tool shed repository's tool test inspection components to categorize empty <tests> or <test> tag sets defined in tool configs as "tool missing tests" instead of testing the tools with resulting test failures.
2013-11-20 13:20:14 -05:00
Dave Bouvier
5f5e9f90ce
Script to check the contents of an S3 bucket for tool dependency installation paths that have no contents, or that contain only the installation log. Optionally delete any found paths.
2013-11-19 16:37:11 -05:00
Greg Von Kuster
6b431f44fc
Enhance the Tool Shed API to enable importing a repository capsule.
2013-11-08 16:51:25 -05:00
Greg Von Kuster
ba857229c9
Restrict diff file size to something reasonable when browsing changesets in the Tool shed, and add some additional logging and error handling when setting metadata on repositories in the tool shed and Galaxy.
2013-10-18 13:07:37 -04:00
Greg Von Kuster
8f2bdd7816
Allow for skipping specified repositories when setting metadata in the tool shed.
2013-10-17 11:18:05 -04:00
Greg Von Kuster
c90c0e503b
Enhance the Tool Shed API feature supporting resetting metadata on certain repositories to allow for individual repositories per request.
2013-10-16 16:29:00 -04:00
Greg Von Kuster
a610d0d458
Enhance the Tool Shed and Galaxy APIs to support resetting metadata on repositories in the Tool Shed or installed into Galaxy respectively. When resetting repository metadata in the Tool Shed, if the API key is associated with an admin user, then setting the my_writable param value to True will restrict resetting metadata to only repositories that are writable by the user in addition to those repositories of type tool_dependency_definition. This param is ignored if the current user is not an admin user, in which case this same restriction is automatic. Also, when resetting metadata in the Tool Shed, repositories of type tool_dependency_definition are reset before repositories of type unrestricted. When setting metadata for installed repositories in Galaxy, neither repository types nor order are considered since these concepts are irrelevant in that environment.
2013-10-16 14:19:26 -04:00
Dannon Baker
0f120bd92c
Strip trailing whitespace (and windows line endings) from all python files in lib
2013-08-29 23:39:52 -04:00
Greg Von Kuster
ba17fe567b
Enhance the generated name of the archive file created when exporting a tool shed repository.
2013-08-05 15:59:49 -04:00
Greg Von Kuster
cf96dccddb
Add the ability to export a specified repository revision from the tool shed to a gzip compressed archive saved locally. The ability to import this archive to the same or another tool shed is not yet implemented, but coming soon. All of the repository's repository dependencies can optionally be exported into the same archive. The archive includes a manifest.xml file that contains the order in whcih the repositories in the archive must be imported.
...
This feature is now available for any installable revision of a repository using the new "Export this revision" option in the Repository actions menu in the browser. It is also available via the Tool Shed API using a command like the following:
export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
2013-08-02 19:30:03 -04:00
Dave Bouvier
a4313a37f3
When checking tool shed repositories for functional tests and test data, explicitly filter out metadata records that have been specified not to be tested by the repository owner.
2013-07-29 13:50:55 -04:00
Daniel Blankenberg
4ee293dae8
Add traceable prefixes to various tempfile creation.
2013-06-03 16:30:51 -04:00
Dave Bouvier
f5432bdc6c
Fix for missing_test_components always being present, causing misleading test result display on repository pages.
2013-05-24 14:02:14 -04:00
Dave Bouvier
a2de4b4fc5
Update repository metadata generation to provide the file path for tool functional test output files. Update script that checks for tool functional tests and test data to use the updated metadata structure.
2013-05-01 10:23:13 -04:00
Dave Bouvier
4fb04e43a9
Update tool_test_results dict's attribute names for consistency. Only flag a changeset revision not to be tested if there no valid tests found in that revision.
2013-04-25 11:13:53 -04:00
Greg Von Kuster
97ec214602
Tool shed database migration script to alter the repository_metadata table by dropping the tool_test_errors column and adding columns tool_test_results, missing_test_components.
2013-04-25 09:36:52 -04:00
Dave Bouvier
02fca8974f
Account for condition where output filename is not defined.
2013-04-17 16:11:20 -04:00
Dave Bouvier
8221d1024b
Improve recording of invalid tests. Check for the existence each file required by functional tests.
2013-04-17 14:31:27 -04:00
Greg Von Kuster
6267972180
Refactor several methods in Galaxy's admin_toolshed controller in preparation for supporting installing tool shed repositories via the tool shed and Galaxy APIs.
2013-03-23 10:44:46 -04:00
Greg Von Kuster
d791d11683
Move the tool_shed_repository_revision_update.py api example script to ~/lib/tool_shed/scripts/api
2013-03-21 10:58:11 -04:00
Dave Bouvier
2c0a9cbbab
Automated script to mark repositories as deprecated if no metadata records are associated with the repository, and the repository is older than the specified cutoff date.
2013-03-12 11:29:12 -04:00
Dave Bouvier
e2477b7bd2
Fix issue where the check script was unsetting the galaxy environment information.
2013-03-12 09:36:56 -04:00
Dave Bouvier
8ca6594306
Improve structure of invalid tools dict. Clarify summary and detailed log output. Add check for required environment variables.
2013-03-11 13:49:12 -04:00
Dave Bouvier
75ecb4759e
Enhance the script that checks repositories for functional tests, adding support for multiple web frontends.
2013-03-08 14:44:57 -05:00
Dave Bouvier
b84b45e7d0
Added even more information to the tool_test_errors dict. Separated failed and passed tests in the metadata record. Added documentation.
2013-03-08 14:25:06 -05:00
Dave Bouvier
fb0eea6c80
Added more information to the tool test environment dict. Restrict when do_not_test flag is set. Made test logging format more structured. Moved some utility code to the util module.
2013-03-06 16:07:32 -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