dcm4chee-connector.py

from helpers.connector import dcm4cheeConnector
from argparse import ArgumentParser
import os
import csv
# from dotenv import load_dotenv
from helpers import config
from datetime import datetime

def read_csv(file):
    parameters = {}
    
    try:
        reader = csv.reader(open(file, 'r'))
    except FileNotFoundError:
        print('Query CSV file not found.')
        return
    
    for row in reader:
        if len(row) == 2:
            parameters[row[0]] = row[1]
    return parameters

def main():


    
    parser = ArgumentParser(description='DCM4Chee Connector toolKIT')

    parser.add_argument('-q', '--query', action="store_true", help='Query to send to DCM4CHEE')
    parser.add_argument('-d', '--download', action='store_true', help='Download data from DCM4CHEE')
    parser.add_argument('-o', '--out', action='store_true', help='Output CSV file for query results')
    parser.add_argument('--aet', type=str, help='AET of the DCM4CHEE server')
    parser.add_argument('--clientId', type=str, help='Client ID of the DCM4CHEE server')
    parser.add_argument('--query-csv', type=str, help='CSV file containing query parameters')
    parser.add_argument('--dicom-destination', type=str, help='Destination folder for downloaded data')
    
    args = parser.parse_args()


    aet = args.aet if args.aet else os.getenv('AET')
    clientId = args.clientId if args.clientId else os.getenv('CLIENT_ID')

    username = os.getenv('USERNAME') if os.getenv('USERNAME') else None
    password = os.getenv('PASSWORD') if os.getenv('PASSWORD') else None
    
    if username is None:
        username = str(input('Enter username: '))
        if username is None:
            print('Username is required.')
            return
    if password is None:
        password = str(input('Enter password: '))
        if password is None:
            print('Password is required.')
            return



    query_csv = args.query_csv if args.query_csv else None

    connector = dcm4cheeConnector(clientId, aet, username, password)
    authentication = connector.authenticate()
    if authentication['status'] != 200:
        print('Authentication failed. Please check your credentials.')
        return
    else:
        print(f'Authentication successful. {authentication["msg"]}')
    if args.query:
        
        if query_csv is None and os.getenv('QUERY_CSV') is not None:
            query_csv = os.getenv('QUERY_CSV')
        else:
            print('CSV file with query parameters is required.')
            return
        if not os.path.exists(query_csv):
            print('Query CSV file not found.')
            return
        query_params = read_csv(query_csv)

        if args.out:
            output_csvfile = f"{datetime.now().strftime('%Y%m%d')}_output.csv"
        else:
            output_csvfile = None
        
        clause = connector.getQueryParams(query_params)
        result = connector.query(clause)
        print(result['msg'])
        export_result = ""
        if result['status'] == True and output_csvfile is not None:
            export_result = connector.exportQueryAsCSV(output_csvfile)
        elif result['status'] == True:
            export_result = connector.exportQueryAsTable()
        print(export_result)

    if args.download:
         
        if query_csv is None and os.getenv('QUERY_CSV') is not None:
            query_csv = os.getenv('QUERY_CSV')
        else:
            print('CSV file with query parameters is required.')
            return
        
        if not os.path.exists(query_csv):
            print('Query CSV file not found.')
            return
        
        
    
        if args.dicom_destination:
            dicom_destination = args.dicom_destination
        elif os.getenv('DESTINATION') is not None:
            dicom_destination = os.getenv('DESTINATION')
        else:
            print('Destination folder is required to download data.')
            return

        if not os.path.exists(dicom_destination):
            os.makedirs(dicom_destination)
        
        # Query Data
        query_params = read_csv(query_csv)
        clause = connector.getQueryParams(query_params)
        result = connector.query(clause)

        print(result['msg'])
        export_result = ""
        if result['status'] == True :
            export_result = connector.exportQueryAsDicom(destination=dicom_destination)
        print(export_result)

        

if __name__ == "__main__":
    main()