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Feature/xref config cleanup

Marek Szuba requested to merge feature/xref_config_cleanup 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. Massive cleanup of the xref configuration file. Deprecated sources have been removed, so have duplicated sources (no species-specific RefSeq sources but everything from the same file). Configuration for all vertebrate species has been removed as they inherit directly from the vertebrates configuration, only species-specific (HGNC, MGI...) configuration remains. Unfortunately, git does not understand large removal of lines, so it looks like more has been removed than is actually the case

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. The current configuration file is hard to maintain. It is also not clear what needs to be added where when sources or species get added. This is the first attempt at removing some of the clutter.

Benefits

If applicable, describe the advantages the changes will have. The file has been simplified, hopefully making it easier to maintain in the future.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes. The history will be difficult to disentangle as git does not like removing a large number of lines

Testing

Have you added/modified unit tests to test the changes? The pipeline was run on all vertebrate species with the complete set of changes. Results were compared with those from a previous run to ensure all sources are still correctly added for all species.

If so, do the tests pass/fail? The results are comparable to previous run.

Have you run the entire test suite and no regression was detected? xref_config2sql.pl runs without errors

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