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1 files changed, 150 insertions, 0 deletions

diff --git a/datasets/measles/get_measles.py b/datasets/measles/get_measles.py
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+++ b/datasets/measles/get_measles.py
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+#!/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/20191128124615/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("ewmeas.dat", "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()