def run_matchengine():
"""
Computes matches between all trials in the database and the given subset list of patient MRNs
:param mrns: List of patient MRNs
:return: database collection of trial matches
"""
db = database.get_db()
me = MatchEngine(db)
me.find_trial_matches()
def run_matchengine():
"""
Computes matches between all trials in the database and the given subset list of patient MRNs
:param mrns: List of patient MRNs
:return: database collection of trial matches
"""
db = database.get_db()
me = MatchEngine(db)
me.find_trial_matches()
def match(args):
"""
Matches all trials in database to patients
:param daemon: Boolean flag; when true, runs the matchengine once per 24 hours.
"""
db = get_db(args.mongo_uri)
while True:
me = MatchEngine(db)
me.find_trial_matches()
# exit if it is not set to run as a nightly automated daemon, otherwise sleep for a day
if not args.daemon:
# choose output file format
if args.json_format:
file_format = 'json'
elif args.outpath and len(args.outpath.split('.')) > 1:
file_format = args.outpath.split('.')[-1]
if file_format not in ['json', 'csv']:
file_format = 'csv'
else:
file_format = 'csv'
# choose output path
if args.outpath:
outpath = args.outpath.split('.')[0]
else:
outpath = './results'
# export results
export_results(args.mongo_uri, file_format, outpath)
break
else:
time.sleep(86400) # sleep for 24 hours