#!/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 import sys import time from functools import wraps from urllib.request import urlretrieve from urllib.error import URLError 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): count = 0 while count < 5: count += 1 try: urlretrieve(DAT_URL, target_path) return except URLError as err: print( "Error occurred (%r) when trying to download zip. Retrying in 5 seconds" % err, sys.stderr, ) time.sleep(5) @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()