trials.py

#!/usr/bin/python

import argparse
import ctrials.db as db
import ctrials.charts as charts
import ctrials.updater as updater
import os

def main():
	# Handle the arguments
	args = parseArguments()
	dbPath = None

	# Create the database if requested
	if args.createDB:
		if args.xmlFilesPath is None:
			print "If you're going to create a database, you must pass in the path to the XML files directory"
			return 0
		else:
			dbPath =  db.create(args.dbPath, args.xmlFilesPath, args.startNumber, args.limit)

	if args.update:
		update(args.dbPath)

	# Create the charts
	charts.create(args.chartsPath, args.dbPath, args.force)


def update(dbPath):
	update = updater.Updater(dbPath)
	update.update


def parseArguments():
	parser = argparse.ArgumentParser(description='Manage and data mine a clinical trials database')
	parser.add_argument('--createDB', dest='createDB', action='store_true', default=False,
						help='Create and initalize the DB file using the path provided')
	parser.add_argument('--xmlFilesPath', dest='xmlFilesPath',
						help='A directory of trials in ClinicalTrials.gov\'s XML format')
	parser.add_argument('--chartsPath', dest='chartsPath', default="web/js/charts.json",
						help='Choose a destination for the JSON file describing the charts; defaults to "web/js/charts.json"')
	parser.add_argument('--limit', dest='limit', type=int,
						help='Set a limit on the number of files from the XML path to be included')
	parser.add_argument('--start', dest='startNumber', type=int, default=0,
						help='Choose an NCT ID number to start from; eg 500 for NCT00000500. Need not actually exist')
	parser.add_argument('dbPath', default='trialsDB.sqlite3',
						help='The path to the trials database file, either to be created or already there')
	parser.add_argument('--force', dest='force', action='store_true', default=False,
						help='Ignore database version mismatch')
	parser.add_argument('--update', dest='update', action='store_true', default=False,
						help='Update database with trials added since the most recent one')

	return parser.parse_args()



# Default function is main()
if __name__ == '__main__':
	main()