jherskovic

medication_parser = re.compile(r"""^\s*(?P<name>.*?)
                                  \s+(?P<dose>[0-9\.\/]+)
                                  \s*(?P<units>([mck]|mc)g|[md]l)
                                  \s*(?P<formulation>.*?)
                                  ;
                                  \s*?(?P<instructions>.*)""",
    re.IGNORECASE | re.VERBOSE)

jherskovic

import glob
import xmltodict
import sys
import os
import logging
import hashlib
from gzip import GzipFile
from pprint import pprint

try:

jherskovic

# Parse each article. Create dictionary journal->MeSH terms
# Accumulate MeSH terms by journal
# Put every article output in a QUEUE, PICK IT UP with a single process
# This way, we can process multiple PubMed files in parallel
from read_medline import *

import multiprocessing
import cPickle as pickle
import traceback
import sys