Source code for bioregistry.external.cellosaurus

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

"""Download the Cellosaurus registry."""

import itertools as itt
import json

from pystow.utils import download

from bioregistry.constants import EXTERNAL, URI_FORMAT_KEY

URL = ""

DIRECTORY = EXTERNAL / "cellosaurus"
DIRECTORY.mkdir(exist_ok=True, parents=True)
RAW_PATH = DIRECTORY / "raw.txt"
PROCESSED_PATH = DIRECTORY / "processed.json"
    "Abbrev": "prefix",
    "Cat": "category",
    "Name": "name",
    "Server": "homepage",

[docs]def get_cellosaurus(force_download: bool = False, keep_missing_uri: bool = True): """Get the Cellosaurus registry.""" if PROCESSED_PATH.exists() and not force_download: with as file: return json.load(file) download(url=URL, path=RAW_PATH, force=True) with"ISO8859-1") as file: lines = [line.rstrip() for line in file] # Get up until the third big line break and chomp two extra lines # for the line break break_line_idxs = [i for i, line in enumerate(lines) if line.startswith("------")] lines = lines[break_line_idxs[3] + 2 :] rv = {} for cond, slines in itt.groupby(lines, lambda line: line == "//"): if cond: continue d = {} for line in slines: if line[6] != ":": # strip notes out continue key, value = (s.strip() for s in line.split(":", 1)) mapped_key = KEYMAP.get(key) if mapped_key is None: continue if mapped_key == URI_FORMAT_KEY: value = _process_db_url(value) if value is None: continue d[mapped_key] = value if not keep_missing_uri and URI_FORMAT_KEY not in d: continue rv[d.pop("prefix")] = d with"w") as file: json.dump(rv, file, indent=2, sort_keys=True) return rv
def _process_db_url(value): if value in {"https://%s", "None"}: return return value.rstrip("/").replace("%s", "$1") if __name__ == "__main__": print(len(get_cellosaurus(force_download=True))) # noqa:T201