A simple GIST to easily download all of the MIMIC III data from PhysioNet

get_mimic.py

import requests
from requests.auth import HTTPBasicAuth
import lxml.html
import requests, zipfile, io
user_name = "Replace this with your MIMIC username"
your_password = "Replace this with your MIMIC password"
headers = {'User-Agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_1) AppleWebKit/537.36 
           (KHTML, like Gecko) Chrome/39.0.2171.95 Safari/537.36'}
response = requests.get("https://physionet.org/works/MIMICIIIClinicalDatabase/files/", 
                        auth=HTTPBasicAuth(user_name, your_password), headers=headers)
def download_file(url):
    """Function to download the file"""
    local_filename = url.split('/')[-1]
    # NOTE the stream=True parameter
    r = requests.get(url, stream=True, auth=HTTPBasicAuth(user_name, your_password))
    with open(local_filename, 'wb') as f:
        for chunk in r.iter_content(chunk_size=1024):
            if chunk: # filter out keep-alive new chunks
                f.write(chunk)
                #f.flush() commented by recommendation from J.F.Sebastian
    return local_filename

html = lxml.html.fromstring(response.content)
urls = html.xpath('//ol//li//a/@href')

for url in urls:
    download_file("https://physionet.org/works/MIMICIIIClinicalDatabase/files/" + url)