run.py

#!/usr/bin/env python3
"""Main script for dicom-send gear."""

import logging
import os

import flywheel
import flywheel_gear_toolkit

from utils import parse_config
from utils import dicom_send
from utils import report_generator


def main(gear_context):
    """Orchestrate dicom-send gear."""
    log.info("Starting dicom-send gear.")

    # Prepare gear arguments by parsing the gear configuration
    gear_args, download = parse_config.generate_gear_args(gear_context)


    # Run dicom-send
    if download is True:
        DICOMS_PRESENT, DICOMS_SENT = dicom_send.download_and_send(**gear_args)
        session_id = gear_args['session_id']

    elif download is False:
        session_id = gear_args.pop('session_id')
        DICOMS_PRESENT, DICOMS_SENT = dicom_send.run(**gear_args)

    report_generator.upload_report(gear_args['api_key'], session_id, gear_args.get('parent_acq'))

    # Log number of DICOM files transmitted and exit accordingly
    if DICOMS_SENT == 0:
        log.error("No DICOM files were transmitted. Exiting.")
        os.sys.exit(1)
    elif DICOMS_SENT < DICOMS_PRESENT:
        log.error("Not all DICOMS were successfully transmitted. Please check report.")
        os.sys.exit(1)
    else:
        log.info(f"!!! TOTAL -- There were {DICOMS_SENT} DICOM files transmitted.")
        exit_status = 0
        return exit_status


if __name__ == "__main__":

    with flywheel_gear_toolkit.GearToolkitContext() as gear_context:
        gear_context.init_logging()
        log = gear_context.log
        exit_status = main(gear_context)

    log.info(f"Successful dicom-send gear execution with exit status {exit_status}.")