[24.1] Fix possible CircularDependencyError when importing collections

[davelopez]

Fixes #18927

Making copied HistoryDatasetCollectionAssociation relationships view-only as an attempt to avoid potential circular dependency errors.

In practice, this gets rid of the error when importing but I'm not 100% sure this is the correct solution if copied_from_history_dataset_collection_association and/or copied_to_history_dataset_collection_association are meant to be used for persistency and not just for querying at any point.

How to test the changes?

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  • Try to import any exported invocation provided in Cannot import RO-Crate of an Invocation using Collection as input #18927
  • Observe there is no CircularDependencyError during the import

License

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

[davelopez]

Nope, other tests will fail if set those relationships to view-only. Out of ideas then...

@jdavcs do you know how to get rid of the circular dependency here?

[mvdbeek]

Which tests are that ?

[davelopez]

At least these 2:

galaxy/test/unit/app/tools/test_history_imp_exp.py

Line 502 in 4e56b47

def test_export_copied_collection():

galaxy/lib/galaxy_test/api/test_workflow_extraction.py

Line 99 in 4e56b47

def test_extract_copied_mapping_from_history(self, history_id):

[mvdbeek]

I would ignore the unit test, that's fairly artificial. Do you have a link to the CI results ?

[davelopez]

Here from the API tests: https://github.com/galaxyproject/galaxy/actions/runs/11364836955

[mvdbeek]

https://github.com/galaxyproject/galaxy/actions/runs/11364836955/job/31611696527#step:10:1167:

galaxy.web.framework.decorators ERROR 2024-10-16 12:46:10,011 [pN:main,p:2686,tN:WSGI_0] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/web/framework/decorators.py", line 346, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/webapps/galaxy/api/workflows.py", line 293, in create
    stored_workflow = extract_workflow(
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/workflow/extract.py", line 48, in extract_workflow
    steps = extract_steps(
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/workflow/extract.py", line 142, in extract_steps
    raise AssertionError("Attempt to create workflow with job not connected to current history")

this might be good and I wouldn't necessarily say you're on the wrong track ?

[davelopez]

this might be good and I wouldn't necessarily say you're on the wrong track ?

Alright, I'll reopen and investigate the test.

Update: GitHub doesn't let me reopen it because I force-pushed it while it was closed. I'll have to open a new one.