Source code for bioregistry.align.obofoundry

# -*- coding: utf-8 -*-

"""Align the OBO Foundry with the Bioregistry."""

from typing import Mapping

from bioregistry.align.utils import Aligner
from bioregistry.external.obofoundry import SKIP, get_obofoundry, get_obofoundry_example

__all__ = [

[docs]class OBOFoundryAligner(Aligner): """Aligner for the OBO Foundry.""" key = "obofoundry" getter = get_obofoundry curation_header = ("deprecated", "name", "description") include_new = True normalize_invmap = True
[docs] def get_skip(self) -> Mapping[str, str]: """Get the prefixes in the OBO Foundry that should be skipped.""" return SKIP
def _align_action(self, bioregistry_id, external_id, external_entry): super()._align_action(bioregistry_id, external_id, external_entry) if ( self.manager.get_example(bioregistry_id) or self.manager.has_no_terms(bioregistry_id) or self.manager.is_deprecated(bioregistry_id) ): return example = get_obofoundry_example(external_id) if example: self.internal_registry[bioregistry_id]["example"] = example
if __name__ == "__main__": OBOFoundryAligner.cli()