Source code for bioregistry.external.bartoc

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

"""Download the BARTOC registry."""

import json
from typing import Any, Mapping

import requests
from tqdm import tqdm

from bioregistry.constants import EXTERNAL
from bioregistry.license_standardizer import standardize_license

DIRECTORY.mkdir(exist_ok=True, parents=True)
PROCESSED_PATH = DIRECTORY / "processed.json"
URL = ""

[docs]def get_bartoc(force_download: bool = True) -> Mapping[str, Mapping[str, Any]]: """Get the BARTOC registry. :param force_download: If true, forces download. If false and the file is already cached, reuses it. :returns: The BARTOC registry .. seealso:: """ if PROCESSED_PATH.is_file() and not force_download: return json.loads(PROCESSED_PATH.read_text()) rv = {} for line in requests.get(URL).iter_lines(): record = json.loads(line) record = _process_bartoc_record(record) rv[record["prefix"]] = record PROCESSED_PATH.write_text(json.dumps(rv, indent=2, ensure_ascii=False, sort_keys=True)) return rv
def _process_bartoc_record(record): prefix = record["uri"][len("") :] rv = { "prefix": prefix, "description": record.get("definition", {}).get("en", [""])[0].strip('"').strip(), "homepage": record.get("url", "").strip(), "name": record.get("prefLabel", {}).get("en", "").strip(), } pattern = record.get("notationPattern") if pattern: rv["pattern"] = "^" + pattern.strip().lstrip("^").rstrip("$") + "$" for identifier in record.get("identifier", []): if identifier.startswith(""): rv["wikidata_database"] = identifier[len("") :] abbreviations = record.get("notation") if abbreviations: if len(abbreviations) > 1: tqdm.write(f"[bartoc:{prefix}] got multiple abbr.: {abbreviations}") abbreviation = abbreviations[0].strip() if " " in abbreviation: tqdm.write(f"[bartoc:{prefix}] space in abbr.: {abbreviation}") rv["abbreviation"] = abbreviation for license_dict in record.get("license", []): license_key = standardize_license(license_dict["uri"].strip()) if license_key: rv["license"] = license_key return {k: v for k, v in rv.items() if k and v} if __name__ == "__main__": get_bartoc()