Skip to content

Bugfix/default aln method

Marek Szuba requested to merge bugfix/default_aln_method into master

Created by: magaliruffier


  • 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


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


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


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?


Merge request reports