#!/usr/bin/env python # -*- coding: utf-8 -*- """ Collect the measles dataset See the README file for more information. Author: G.J.J. van den Burg License: This file is part of TCPD, see the top-level LICENSE file. Copyright: 2019, The Alan Turing Institute """ import argparse import clevercsv import hashlib import json import os from functools import wraps from urllib.request import urlretrieve DAT_URL = "https://web.archive.org/web/20191128124615if_/https://ms.mcmaster.ca/~bolker/measdata/ewmeas.dat" MD5_DAT = "143d1dacd791df963674468c8b005bf9" MD5_JSON = "e42afd03be893fc7deb98514c94fa4c7" NAME_DAT = "ewmeas.dat" NAME_JSON = "measles.json" class ValidationError(Exception): def __init__(self, filename): message = ( "Validating the file '%s' failed. \n" "Please raise an issue on the GitHub page for this project " "if the error persists." % filename ) super().__init__(message) def check_md5sum(filename, checksum): with open(filename, "rb") as fp: data = fp.read() h = hashlib.md5(data).hexdigest() return h == checksum def validate(checksum): """Decorator that validates the target file.""" def validate_decorator(func): @wraps(func) def wrapper(*args, **kwargs): target = kwargs.get("target_path", None) if os.path.exists(target) and check_md5sum(target, checksum): return out = func(*args, **kwargs) if not os.path.exists(target): raise FileNotFoundError("Target file expected at: %s" % target) if not check_md5sum(target, checksum): raise ValidationError(target) return out return wrapper return validate_decorator @validate(MD5_DAT) def download_zip(target_path=None): urlretrieve(DAT_URL, target_path) @validate(MD5_JSON) def write_json(dat_path, target_path=None): with open(dat_path, "r", newline="", encoding="ascii") as fp: reader = clevercsv.reader( fp, delimiter=" ", quotechar="", escapechar="" ) rows = list(reader) as_dicts = {t: int(x) for t, x in rows} time = sorted(as_dicts.keys()) values = [as_dicts[t] for t in time] series = [{"label": "V1", "type": "int", "raw": values}] data = { "name": "measles", "longname": "Measles cases (England & Wales)", "n_obs": len(time), "n_dim": len(series), "time": { "type": "string", "format": "%Y-%F", "index": list(range(len(time))), "raw": time, }, "series": series, } with open(target_path, "w") as fp: json.dump(data, fp, indent="\t") def collect(output_dir="."): dat_path = os.path.join(output_dir, NAME_DAT) json_path = os.path.join(output_dir, NAME_JSON) download_zip(target_path=dat_path) write_json(dat_path, target_path=json_path) def clean(output_dir="."): dat_path = os.path.join(output_dir, NAME_DAT) json_path = os.path.join(output_dir, NAME_JSON) if os.path.exists(dat_path): os.unlink(dat_path) if os.path.exists(json_path): os.unlink(json_path) def parse_args(): parser = argparse.ArgumentParser() parser.add_argument( "-o", "--output-dir", help="output directory to use", default="." ) parser.add_argument( "action", choices=["collect", "clean"], help="Action to perform", default="collect", nargs="?", ) return parser.parse_args() def main(output_dir="."): args = parse_args() if args.action == "collect": collect(output_dir=args.output_dir) elif args.action == "clean": clean(output_dir=args.output_dir) if __name__ == "__main__": main()