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ENSCORESW-3453: do not add linkage_annotation for MIM xrefs

Marek Szuba requested to merge bugfix/mim2gene_dependent into master

Created by: magaliruffier

Requirements

  • Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
  • Review the contributing guidelines for this repository; remember in particular:
    • do not modify code without testing for regression
    • provide simple unit tests to test the changes
    • if you change the schema you must patch the test databases as well, see Updating the schema
    • the PR must not fail unit testing

Description

Using one or more sentences, describe in detail the proposed changes. MIM2Gene parser uses wrong argument in xref creation linkage_annotation is added to the dependent_xref, causing it to be treated as a GO xref later in the mapping stage

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. when the MIM2Gene xrefs are processed during the DirectXrefs stage, it will throw an error the presence of a value in the linkage_annotation column leads to it being processed like a go_xref, but the expected data for a go_xref is missing

Benefits

If applicable, describe the advantages the changes will have. the pipeline does not fail for human

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes.

Testing

Have you added/modified unit tests to test the changes? NA

If so, do the tests pass/fail?

Have you run the entire test suite and no regression was detected? the whole xref pipeline was run on human and does not fail

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