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Bugfix/default aln method

Marek Szuba requested to merge bugfix/default_aln_method 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

Ensure there is a default align_type for protein_feature and it is ensembl

Use case

The align_type column in the protein_feature table is an enum. Existing scripts and pipeline that do not use this column should not have to worry about assigning it, hence it is useful to have a default value that makes sense. This is set to 'ensembl' by default. Other

Benefits

When new entries are added, the align_type will not be set to an empty string.

Possible Drawbacks

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

This will be updating the protein_feature table in all existing core databases, so this might take a while to run

Testing

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

No additional tests required.

If so, do the tests pass/fail?

All tests pass, in particular schemaPatches, that ensures the patch file is in sync with table.sql

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

Yes.

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