Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Greg Von Kuster
8bce650dda
Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.
2014-04-10 17:11:01 -04:00
Greg Von Kuster
27e60943bf
The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.
2014-04-09 10:11:48 -04:00
Greg Von Kuster
e01cc26dd1
Fixes and code cleanup for the tool shed's install and test framework.
2014-01-20 11:48:05 -05:00
Dannon Baker
c1558e8205
One more simplejson/json fix that slipped through the merge.
2014-01-10 07:42:58 -05:00
Dannon Baker
a40457ab09
Merge.
2014-01-10 07:40:02 -05:00
Dannon Baker
559ecb4ec8
Remove dependency on simplejson; convert everything over to using the json module in the python standard library.
2014-01-10 07:29:05 -05:00
Greg Von Kuster
3014265a07
Tool Shed API fixes and code cleanup.
2014-01-09 15:59:18 -05:00
Greg Von Kuster
b4147910a4
Fix imports in the tool shed install and test framework.
2013-12-21 19:07:38 -05:00
Greg Von Kuster
af0525adcb
Refactor and fix prep scripts for the tool shed's install and test frameowrk.
2013-12-21 08:07:11 -05:00
Greg Von Kuster
b177363064
Make the tool shed's install and test exclude list locally accessible rather than stored in cfengine.
2013-12-20 09:50:03 -05:00
Greg Von Kuster
dfc8083fb2
Corrections to statistics for the tool shed's install and test runs and successful installation results for repositories of type tool_dependency_definition now reported to the tool shed.
2013-12-18 16:20:36 -05:00
Dave Bouvier
20425d57a2
Another bugfix to the tool dependency cleaning script.
2013-12-18 13:14:24 -05:00
Dave Bouvier
43ec159fbd
Fix error when attempting to remove a file.
2013-12-18 13:11:37 -05:00
Dave Bouvier
4de9c13127
Clean up maintenance scripts for the EC2 environment.
2013-12-18 12:07:49 -05:00
Dave Bouvier
4fc15cc185
Add script to clean up or display the contents of a tool dependency path.
2013-12-17 12:20:08 -05:00
Greg Von Kuster
2f38da8025
Enhance the tool shed's install and test framework to uninstall repositories in an ordered fashion so that repositories are not uninstalled when they are dependencies of other installed repositories.
2013-12-16 15:52:29 -05:00
Greg Von Kuster
1b17f9482b
Allow storage of multiple test runs in the prep script for install and testing tool dependencies and restrict creation of new entries in the tool test results dictionary when running the prep script for install and test repositories.
2013-12-13 15:44:39 -05:00
Dave Bouvier
731edf31e3
Add script to check the filesystem for empty tool dependency installation paths and optionally delete them.
2013-12-11 09:53:11 -05:00
Greg Von Kuster
0ebb57196c
Further restrict when the tool_functionally_correct column will be set to False in the Tool Shed's repository_metadata table.
2013-12-10 09:48:50 -05:00
Greg Von Kuster
340762bbf1
Correctly use the initialized test_environment dict when running the tool shed's install and test framework and additional code cleanup for the framework.
2013-12-04 15:07:39 -05:00
Greg Von Kuster
24ee75b05c
Actually skip inspection of repository revisions that have the skip_tool_test set in the Tool Shed instead of just stating we're going to...
2013-12-04 11:01:32 -05:00
Greg Von Kuster
00857760f0
Fixes for filtering repository revision to be tested by the Tool Shed's install and test framework, and a new Tool Shed API script to enable analyzing the the Tool Shed's install and test framework.
2013-12-03 15:16:14 -05:00
Greg Von Kuster
b5e5b5bb69
Additional code cleanup, better logging and more minor fixes for the tool shed's install and test framework.
2013-11-29 14:34:35 -05:00
Greg Von Kuster
444b304d96
Set a repository revision as missing test components only if test components are missing for all tools in the revision.
2013-11-28 17:38:38 -05:00
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