xnat_scan_info

#!/usr/bin/env python

# Copyright (c) 2016 Washington University
# Author(s) Timothy B. Brown (tbbrown at wustl.edu)

PROCESSING_SESSION_TYPE = 'xnat:mrSessionData'

import argparse # For parsing command line arguments
import csv      # Comma Separated Value (csv) reading
import StringIO # Read string buffers as if they were files (i.e. read in-memory files)

from xnat_access import XnatAccess # The XnatAccess class allows us to interact with an XNAT instance

def create_resource_file_name_to_scan_number_map(xnat_access):
	"""
	create a map/dict which when given a file name will return the scan number that corresponds
	to that file name
	"""

	scan_number_mapping_file_name = 'filescans.csv'
	
	file_name_to_scan_number = dict()
	file_name_list = xnat_access.get_resource_file_name_list()
	if scan_number_mapping_file_name in file_name_list:
		scan_mapping_str = xnat_access.get_named_resource_file_content(scan_number_mapping_file_name)
		f = StringIO.StringIO(scan_mapping_str)
		reader = csv.reader(f, delimiter=',')
		for row in reader:
			key = row[1].replace("'", "")
			val = row[0].replace("'", "")
			if val != 'Scan':
				file_name_to_scan_number[key] = val
				
	return file_name_to_scan_number

def check_resource_exists(args):

	# Establish connection to XNAT
	if args.debug:
		print("\nxnat_scan_info.check_resource_exists: Connecting to: " + args.server)

	xnat_access = XnatAccess(args.server, args.username, args.password)

	# Establish project
	if args.debug:
		print("xnat_scan_info.check_resource_exists: Establishing project: " + args.project)

	xnat_access.project=args.project

	# Establish subject
	if args.debug:
		print("xnat_scan_info.check_resource_exists: Establishing subject: " + args.subject)

	xnat_access.subject=args.subject

	# Validate appropriate MR session exists and establish session
	if args.debug:
		print("xnat_scan_info.check_resource_exists: Validating session: " + args.session)

	session_type = xnat_access.get_session_type(args.session)
	if args.debug:
		print("xnat_scan_info.check_resource_exists: Session Type: " + session_type)

	if session_type != PROCESSING_SESSION_TYPE:
		print("xnat_scan_info.check_resource_exists: Session: " + args.session + " is not of correct session type.")
		sys.exit(1)

	if args.debug:
		print("xnat_scan_info.check_resource_exists: Establishing session: " + args.session)
		
	xnat_access.session = args.session

	# Determine if resource exists
	if (xnat_access.does_resource_exist(args.resource)) :
		print("TRUE")
	else:
		print("FALSE")
	
def get_data(args):

	# Establish connection to XNAT
	if args.debug:
		print("\nxnat_scan_info.get_data: Connecting to: " + args.server)

	xnat_access = XnatAccess(args.server, args.username, args.password)

	# Establish project
	if args.debug:
		print("xnat_scan_info.get_data: Establishing project: " + args.project)

	xnat_access.project=args.project

	# Establish subject
	if args.debug:
		print("xnat_scan_info.get_data: Establishing subject: " + args.subject)

	xnat_access.subject=args.subject

	# Validate appropriate MR session exists and establish session
	if args.debug:
		print("xnat_scan_info.get_data: Validating session: " + args.session)
		
	session_type = xnat_access.get_session_type(args.session)
	if args.debug:
		print("xnat_scan_info.get_data: Session Type: " + session_type)

	if session_type != PROCESSING_SESSION_TYPE:
		print("xnat_scan_info.get_data: Session: " + args.session + " is not of correct session type.")
		sys.exit(1)

	if args.debug:
		print("xnat_scan_info.get_data: Establishing session: " + args.session)
		
	xnat_access.session = args.session

	# Determine if resource exists
	if (xnat_access.does_resource_exist(args.resource)) :
		if args.debug:
			print("xnat_scan_info.get_data: Establishing resource: " + args.resource)
			
		xnat_access.resource = args.resource
		file_name_to_scan_number = create_resource_file_name_to_scan_number_map(xnat_access)

		scan_number = file_name_to_scan_number[args.filename]
		if args.debug:
			print("xnat_scan_info.get_data: scan_number: " + scan_number);
		
		item_value = xnat_access.get_scan_data_field_value(scan_number, args.item)

		print(item_value)

def main():
	parser = argparse.ArgumentParser(prog="xnat_scan_info",
									description="Script to get XNAT scan info")

	parser.add_argument("-d", "--debug", dest="debug", action='store_true')
	parser.add_argument("-s", "--server", dest="server", default="db.humanconnectome.org", type=str)
	parser.add_argument("-u", "--username", dest="username", required=True, type=str)
	parser.add_argument("-p", "--password", dest="password", required=True, type=str)
	parser.add_argument("-pr", "--project", dest="project", required=True, type=str,
						help="e.g. PipelineTest, HCP_Staging, HCP_Staging_RT, etc.")
	parser.add_argument("-su", "--subject", dest="subject", required=True, type=str)
	parser.add_argument("-se", "--session", dest="session", required=True, type=str)
	parser.add_argument("-r", "--resource", dest="resource", required=True, type=str)

	subparsers = parser.add_subparsers(help='xnat_scan_info sub-commands')

	# setup the exists sub-command
	parser_check_resource_exists = subparsers.add_parser('check_resource_exists', help='determine whether the scan exists')
	parser_check_resource_exists.set_defaults(func=check_resource_exists)
	
	# setup the get_data sub-command
	parser_get_data = subparsers.add_parser('get_data', help='get_data about a scan')
	parser_get_data.add_argument("-f", "--filename", dest="filename", required=True, type=str)
	parser_get_data.add_argument("-i", "--item", dest="item", required=True, type=str)
	parser_get_data.set_defaults(func=get_data)

	# parse the arguments and dispatch the call
	args = parser.parse_args()
	args.func(args)
	
if __name__ == '__main__':
	main()