Implement default locations for data and collection parameters.

[jmchilton]

Works for both files and collections. Workflow defaults override tool defaults.

This is not strictly better or worse than #14938 / #13110, but to my eyes this is both cleaner than that approach and brings in more CWL (the raw_to_galaxy here is a cleanup and generalization of a CWL-branch-ism). Both approaches commit Galaxy to doing some long term, difficult things - I think by not adding a new tool form type, not adding new models, not adding new ways users can have data associated with their account, etc... this approach is a bit more conservative. Both approaches do some things with workflow state that make me uncomfortable and this approach adds some tool features - but I feel good about the tool features (they are useful, tested, and feel both cohesive and 'galaxy').

TODO:

• Fix up the UI
• Unit test case to ensure this only works for non-default, non-multi data parameters.
• Implement XSD once syntax is finalized.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[jmchilton]

Initial rebase for the 2023 biohackathon done... next step is I think synchronizing this with the conditionals work. They both brought in similar code from the CWL branch in different ways.

[jmchilton]

XSD needs some progress made also - luckily test failures caught this.

not ok 27 test/functional/tools/collection_nested_default.xml
    -:10: element collection: Schemas validity error : Element 'collection': This element is not expected. Expected is one of ( change_format, filter, discover_datasets, actions ).
    - fails to validate
test/functional/tools/collection_nested_test.xml
ok 28
test/functional/tools/collection_optional_param.xml
ok 29
test/functional/tools/collection_paired_conditional_structured_like.xml
ok 30
test/functional/tools/collection_paired_default.xml
not ok 31 test/functional/tools/collection_paired_default.xml
    -:8: element element: Schemas validity error : Element 'element', attribute 'location': The attribute 'location' is not allowed.
    -:9: element element: Schemas validity error : Element 'element', attribute 'location': The attribute 'location' is not allowed.
    - fails to validate
test/functional/tools/collection_paired_structured_like.xml

[jmchilton]

Test tools now validate and I fixed the typing issue I discovered in the conditional branch of the code. I'd be interesting to see how this works the CWL branch now.

[mvdbeek]

Thanks a lot @jmchilton!

[mvdbeek]

That seems like a perfectly legitimate case, just like default values on optional parameters. It's a UI thing that we can't reset them to None/null/undefined (didn't check, it might actually be possible now) ... but let's get this in, this is a slightly off-topic discussion.

[jmchilton]

I don't disagree in principle but perhaps better to add explicitly after the fact with a lot of intentionality and with explicit tests - UI + API + Cheetah Tests.