"""Download registry information from OntoBee."""
import json
import textwrap
from collections.abc import Sequence
from pathlib import Path
from typing import Any, ClassVar
from bs4 import BeautifulSoup
from pystow.utils import download
from bioregistry.constants import RAW_DIRECTORY
from bioregistry.external.alignment_utils import Aligner, load_processed
__all__ = [
"OntobeeAligner",
"get_ontobee",
]
DIRECTORY = Path(__file__).parent.resolve()
RAW_PATH = RAW_DIRECTORY / "ontobee.html"
PROCESSED_PATH = DIRECTORY / "processed.json"
URL = "http://www.ontobee.org/"
LEGEND = {
"F": "Foundry",
"L": "Library",
"N": "Not Specified/No",
}
[docs]
def get_ontobee(force_download: bool = False) -> dict[str, dict[str, Any]]:
"""Get the OntoBee registry."""
if PROCESSED_PATH.exists() and not force_download:
return load_processed(PROCESSED_PATH)
download(url=URL, path=RAW_PATH, force=True)
with RAW_PATH.open() as f:
soup = BeautifulSoup(f, "html.parser")
ontology_list = soup.find(id="ontologyList")
if ontology_list is None:
raise ValueError
table_body = ontology_list.find("tbody")
if table_body is None:
raise ValueError
rv = {}
for row in table_body.find_all("tr"): # type:ignore
cells = row.find_all("td")
prefix = cells[1].text
rv[prefix] = {
"name": cells[2].text,
"library": LEGEND[cells[3].text.upper()],
# "link": cells[1].find("a").attrs["href"],
}
with PROCESSED_PATH.open("w") as file:
json.dump(rv, file, indent=2, sort_keys=True)
return rv
class OntobeeAligner(Aligner):
"""Aligner for OntoBee xref registry."""
key = "ontobee"
getter = get_ontobee
curation_header: ClassVar[Sequence[str]] = ("name", "url")
def get_curation_row(self, external_id: str, external_entry: dict[str, Any]) -> Sequence[str]:
"""Return the relevant fields from an OntoBee entry for pretty-printing."""
return [
textwrap.shorten(external_entry["name"], 50),
external_entry.get("url", ""),
]
if __name__ == "__main__":
OntobeeAligner.cli()