Implemented a while ago to aid debugging but disabled by default because it can cause sqlite locking errors. It can now be enabled as needed using GALAXY_TEST_VERBOSE_ERRORS.
Fix bug in buildbot related to differences between local handling of list/tuple parameters and requests handling (I mostly use requests locally, but buildbot doesn't have it available). Add test that fails without @kellrott's pull request #314 (and in turn verifies it fixes a problem).
Previous run_as method has some potential limitations, seems testing permission/security things is more correct if actually using normal alternative user key.
... tweaked styling of several functional tests (the non-toolbox,datamanager,workflow,api functional tests) along the way - mostly PEP-8 fixes and eliminating * imports. Did not modify tests which do not pass - but did not in the source where they fail inside a TODO.
... 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.
Lessens the need to import things in a specific order - as long as database context is run before interactor methods everything should be fine now. TODO: Eliminate rest of dependencies on this variable.
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.
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).
E.g. composite data types. API should probably return the original output name since that is the purpose of the parameter but I am not sure how much work that would be.
- Report formatted standard error and standard output of tools like Twill interactor.
- Respect testdef.maxseconds to timeout test cases.
- Check history item - like Twill interactor do not verify 'error' datasets.
- Properly raise exceptions with reported API error messages when running tools.
... from verify_dataset_correctness. Introduce simple, extensible abstraction for fetching outputs for verification in twilltestcase.py. Will want to reuse the core verification of the displayed dataset in the API driven case and will not need or be able to use the extra cruft related to checking UI, job state, etc...
Also small twilltestcase code structure updates for Python 2.6+.
And pass an encoded id to display action in root controller.
Would definitely like to simplify or better yet remove root.display if not used anywhere else, it should be coming in through dataset controller.
Dave Bouvier