Source code for bioregistry.align.biocontext

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

"""Align the BioContext with the Bioregistry."""

from typing import Any, Dict, Mapping, Sequence

from bioregistry.align.utils import Aligner
from bioregistry.constants import URI_FORMAT_KEY
from bioregistry.external.biocontext import get_biocontext

__all__ = [

SKIP_PARTS = {"", ""}

[docs]class BioContextAligner(Aligner): """Aligner for BioContext.""" key = "biocontext" getter = get_biocontext curation_header = [URI_FORMAT_KEY]
[docs] def get_skip(self) -> Mapping[str, str]: """Get entries for BioContext that should be skipped.""" return { "fbql": "not a real resource, as far as I can tell", }
[docs] def prepare_external(self, external_id, external_entry) -> Dict[str, Any]: """Prepare BioContext data to be added to the BioContext for each BioPortal registry entry.""" uri_format = external_entry[URI_FORMAT_KEY] if any(p in uri_format for p in SKIP_PARTS): return {} return {URI_FORMAT_KEY: uri_format}
[docs] def get_curation_row(self, external_id, external_entry) -> Sequence[str]: """Prepare curation rows for unaligned BioContext registry entries.""" formatter = external_entry[URI_FORMAT_KEY] return [formatter]
if __name__ == "__main__": BioContextAligner.cli()