runner.py

import argparse
from typing import Tuple, cast

from lab_share_lib.config_readers import get_config

from crawler import main
from crawler.config.centres import get_centres_config
from crawler.constants import CENTRE_KEY_PREFIX
from crawler.types import Config


def centre_prefix_choices():
    config, _ = cast(Tuple[Config, str], get_config(""))
    centres = get_centres_config(config, "SFTP")

    return [centre[CENTRE_KEY_PREFIX] for centre in centres]


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Parse CSV files from the Lighthouse Labs and store the sample information in MongoDB"
    )

    parser.add_argument(
        "--sftp",
        dest="sftp",
        action="store_true",
        help="use SFTP to download CSV files, defaults to using local files",
    )
    parser.add_argument(
        "--keep-files",
        dest="keep_files",
        action="store_true",
        help="keeps the CSV files after the runner has been executed",
    )
    parser.add_argument(
        "--add-to-dart",
        dest="add_to_dart",
        action="store_true",
        help="on processing samples, also add them to DART",
    )
    parser.add_argument(
        "--centre-prefix",
        dest="centre_prefix",
        choices=centre_prefix_choices(),
        help="process only this centre's plate map files",
    )

    parser.set_defaults(sftp=False)
    parser.set_defaults(keep_files=False)
    parser.set_defaults(add_to_dart=False)

    args = parser.parse_args()

    main.run(sftp=args.sftp, keep_files=args.keep_files, add_to_dart=args.add_to_dart, centre_prefix=args.centre_prefix)