Feature/xref config

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. Xref configuration file cleaned up by removing deprecated sources and using default settings for each division

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 second pass at cleaning it up, mostly focusing on duplicated sources for non-vertebrates.

Benefits

If applicable, describe the advantages the changes will have. The file has been simplified, hopefully making it easier to maintain in the future. There are default settings for most divisions, meaning there is no need to update the file when a new species is included.

Possible Drawbacks

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

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