Source code for bioregistry.align.biolink

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

"""Align the Biolink with the Bioregistry."""

import json
from typing import Any, Dict, Mapping, Sequence

from bioregistry.align.utils import Aligner
from bioregistry.constants import DATA_DIRECTORY, URI_FORMAT_KEY
from bioregistry.external.biolink import get_biolink

__all__ = [

PROCESSING_BIOLINK_PATH = DATA_DIRECTORY / "processing_biolink.json"

[docs]class BiolinkAligner(Aligner): """Aligner for Biolink.""" key = "biolink" getter = get_biolink curation_header = [URI_FORMAT_KEY, "identifiers", "purl"]
[docs] def get_skip(self) -> Mapping[str, str]: """Get the skipped Biolink identifiers.""" with as file: j = json.load(file) return {entry["prefix"]: entry["reason"] for entry in j["skip"]}
[docs] def prepare_external(self, external_id, external_entry) -> Dict[str, Any]: """Prepare Biolink data to be added to the Biolink for each BioPortal registry entry.""" uri_format = external_entry[URI_FORMAT_KEY] return { URI_FORMAT_KEY: uri_format, "is_identifiers": uri_format.startswith(""), "is_obo": uri_format.startswith(""), }
[docs] def get_curation_row(self, external_id, external_entry) -> Sequence[str]: """Prepare curation rows for unaligned Biolink registry entries.""" uri_format = external_entry[URI_FORMAT_KEY] return [ uri_format, uri_format.startswith(""), uri_format.startswith(""), ]
if __name__ == "__main__": BiolinkAligner.cli()