Source code for bioregistry.align.wikidata

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

"""Align Wikidata with the Bioregistry."""

from typing import Sequence

from bioregistry.align.utils import Aligner
from bioregistry.external.wikidata import get_wikidata

__all__ = [

# Unlike the other aligners, the wikidata one doesn't really do the job of making the alignment.
# It's more of a stand-in and curation sheet generator right now.

[docs]class WikidataAligner(Aligner): """Aligner for Wikidata properties.""" key = "wikidata" getter = get_wikidata curation_header = ("miriam", "databaseMiriam", "name", "database", "databaseLabel")
[docs] def get_curation_row(self, external_id, external_entry) -> Sequence[str]: """Prepare curation rows for unaligned Wikidata properties.""" return [ external_entry.get("miriam"), external_entry.get("database.miriam"), external_entry["name"], external_entry["database"], external_entry["database.label"], ]
[docs] def prepare_external(self, external_id, external_entry): """Prepare the external Wikidata data dictionary for alignment.""" # If it's already aligned, we don't need these extra MIRIAM annotations external_entry.pop("miriam", None) external_entry.pop("database.miriam", None) return external_entry
if __name__ == "__main__": WikidataAligner.align()