"""Download the BARTOC registry."""
import json
from collections.abc import Sequence
from pathlib import Path
from typing import Any, ClassVar
import requests
from tqdm import tqdm
from bioregistry.constants import URI_FORMAT_KEY
from bioregistry.external.alignment_utils import Aligner, load_processed
from bioregistry.license_standardizer import standardize_license
__all__ = [
"BartocAligner",
"get_bartoc",
]
HERE = Path(__file__).parent.resolve()
PROCESSED_PATH = HERE / "processed.json"
URL = "https://bartoc.org/data/dumps/latest.ndjson"
[docs]
def get_bartoc(*, force_download: bool = True) -> dict[str, dict[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::
https://bartoc.org/
"""
if PROCESSED_PATH.is_file() and not force_download:
return load_processed(PROCESSED_PATH)
rv = {}
for line in requests.get(URL, timeout=15).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
URI_FORMAT_SKIPS: dict[str, str] = {}
def _process_bartoc_record(record: dict[str, Any]) -> dict[str, Any]:
prefix = record["uri"][len("http://bartoc.org/en/node/") :]
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("http://www.wikidata.org/entity/"):
rv["wikidata_database"] = identifier[len("http://www.wikidata.org/entity/") :]
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
if prefix in URI_FORMAT_SKIPS:
pass
elif uri_prefix := record.pop("namespace", None):
rv[URI_FORMAT_KEY] = uri_prefix.strip() + "$1"
elif uri_pattern := record.get("uriPattern"):
if "(" not in uri_pattern and ")" not in uri_pattern:
tqdm.write(f"bad URI pattern: {uri_pattern}, assuming is URI prefix")
rv[URI_FORMAT_KEY] = uri_pattern.strip() + "$1"
else:
left_pos = uri_pattern.find("(")
right_pos = uri_pattern.find(")")
rv[URI_FORMAT_KEY] = uri_pattern[:left_pos] + "$1" + uri_pattern[1 + right_pos :]
if examples := record.pop("EXAMPLES", []):
rv["example"] = examples[0].strip()
return {k: v for k, v in rv.items() if k and v}
class BartocAligner(Aligner):
"""Aligner for BARTOC."""
key = "bartoc"
getter = get_bartoc
alt_key_match = "abbreviation"
curation_header: ClassVar[Sequence[str]] = ["name", "homepage", "description"]
if __name__ == "__main__":
BartocAligner.cli()