backport ENSCORESW-2767: multi-species support for protein feature

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.

In e!92 ProteinFeatureAdaptor.pm was updated to be a BaseAlignFeatureAdaptor rather than a BaseAdaptor to support GIFTS import, with a side effect of failing for collection databases. There is already a hack in place for feature types that needs to be restricted to species_id (in coord_system table), which helps the UnmappedObjectAdaptor to get around it. Similar workaround is implemented for BaseAlignFeatureAdaptor.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place.

The production pipeline (VEP cache creation pipeline on EG collection databases) and the transcript pages for species that are in collection db failed with similar error messages ( 'Unknown column 'pf.seq_region_id' in 'where clause' at BaseAdaptor.pm).

Benefits

If applicable, describe the advantages the changes will have.

Both the above use cases works with the changes in place.

Possible Drawbacks

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

We might be missing some scenarios where this could still fail.

Testing

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

If so, do the tests pass/fail? Pass

Have you run the entire test suite and no regression was detected? Yes