This directory is required to exist but usually unneeded because Galaxy creates this directory on startup. However, when setting metadata remotely with the LWR that remote Galaxy instance may have never been started and this directory may not exist.
-framework will still cause just a small set of non-default, non-user facing tools to be tested and exerise various aspects of the tool and test frameworks, but now an argument can be passed in -with_framework_test_tools to allow these tools to be used as part of the normal test framework (i.e. when not using -framework). This serves two purposes - to ensure the feature coverage of existing tests remains high as the tests are migrated out of the distribution and to allow a set of tests to be available for functional (e.g. API tests) that users don't need to see.
Enable task splitting in functional tests to test this. Specify tool_dir in samples tool_conf.xml so it doesn't need to be explicitly set in scripts/functional_tests.py.
... if you can call 1 new class a framework. Includes a few test cases to exercise/drive it. These examples include a histories API test (a typical API test) and a general test of the API framework itself (mostly just the run_as functionality).
This includes changes to interactor.py to make it more useful outside the context of tool/workflow testing as well as a tweak to test Galaxy that gets started to allow testing of the run_as feature.
Pull logic for how master and user API keys are determinined for testing out of functional_tests.py for reuse elsewhere.
This refactoring will help the creation of an API test framework.
To obtain the behavior (assigning all groups for a given user for each job submission) change the property - 'drmaa_external_runjob_script' from 'scripts/drmaa_external_runner.py' to 'scripts/drmaa_external_runner.py --assign_all_groups'.
Making this optional because my concern is that this could be an expensive operation on some clusters.
create_db and manage_db should now work with install as well.
Migrations are symbolic links into lib/galaxy/model/migrate/versions of migrations affecting these tables. All future migrations to these tables should created in one place like this and linked in the other.
Shared across Tool Shed and Galaxy to reduce code duplication. Previously this was just a bunch, making it a real class allows placing some shared logic in there.
This refactoring also eliminates some global variables galaxy.model.mapping.Session, galaxy.model.mapping.context, and same for tool shed. This may break things, but these are things that should probably be fixed anyway.
In particular small changes to db_shell.py and a unit test that depended on these global variables have been updated. The functional test frameworks likewise needed to be updated to not depend on these - these changes were more substantial.
To fix these functional tests, I essentially replace old references to global variables in Galaxy with references to global variables just defined in the test framework in test/functional/database_contexts.py (a slight improvement).
Dave Bouvier