- Add another test to demonstrate referencing entries in galaxy.json for datasets by dataset path basename instead of ID.
- Add a bit more documentation to test tools.
- Redo the structure of galaxy.json for profile >= 17.09 tools with two new test tools to demonstrate the new structure - for both output dataset metadata and discovered dataset metadata.
- Improved abstractions for interaction between tools and jobs to enable different tool provided metadata collection depending on tool profile version.
Seems like a race condition but I can't determine why there would be one here - this check should help determine if it is a race condition or something else.
I call explicit outputs galaxy.json entries of type="dataset" (as opposed to type="new_primary_dataset" - which I call discovered datasets). Previously galaxy.json could set the name and extension of these datasets. I've added a test case to verify this and a small tweak to the tool test framework to allow easy testing of such metadata setting.
In order to bring explicit output metadata setting closer to parity with discovered dataset metadata setting, I've added the ability to define 'dbkey' and 'info' entries in galaxy.json for these outputs.
John Chilton