Fixes for output discovery

[bernt-matthias]

Fixes: #17263 .. guess both bugs are there forever (>10 years)

1. primary_output_assigned needs to be reset for each output

   lets say there are two outputs: datasets (a normal dataset)
   and discovered (discovered datasets). if datasets is
   processed after discovered then primary_output_assigned
   is still true from the first loop (where discovered was precessed).
   this leads to overwriting of info (e.g. name) of the dataset output
   (in the if primary_output_assigned branch at the end of the outer
   loop).

2. assign_primary_output must be obeyed for all outputs (not just the
   first).

   sticking to the above example, assign_primary_output would
   work only if dataset is processed after discovered

I added a test case for the 2nd part. No idea how to test the first (I manually tested it with planemo serve).

#16203 is still broken

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]

This looks right to me. I wonder if this was meant as a niche feature that should have just not been documented and only worked with one output - but given the investment we've put into it, I think this looks really good.

[bernt-matthias]

Thanks for the review. Any suggestions regarding backporting?

[mvdbeek]

First check that this didn't cause any regressions ? And then I'd say not far, since there can't really be any tools relying on this. 23.1 ?

[bernt-matthias]

To me 23.2 would be sufficient. Most important to me is that galaxyproject/tools-iuc#5699 can continue. Wondering if discover_datasets or from_workdir is prefered to cover the case where a single file is to be discovered via a some pattern.

[mvdbeek]

discover_datasets is always inferior to something static like from_workdir or mv thing*.txt $output