loader.py

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# regarding copyright ownership.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
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import argparse as ap
from app import orm
import sys
from app import create_app
from loader import parse_fasta


def run():
    app = create_app()
    with app.app_context():
        args = parse_args()
        rg = orm.Refget()
        fasta = args.fasta
        parse_fasta(fasta, args, rg)


def parse_args():
    p = ap.ArgumentParser(description="FASTA loader for refget")
    required = p.add_argument_group("required named arguments")
    required.add_argument(
        "-f",
        "--fasta",
        help="Input FASTA file to load. Supports compressed and uncompressed",
        type=str,
        required=True,
    )
    required.add_argument(
        "-t", "--type", help="Sequence type to add", type=str, required=True
    )
    p.add_argument(
        "-a",
        "--authority",
        help="Identifier authority to use. If FASTA sequence IDs are already formatted as CURIEs then do not specify",
        type=str,
    )
    p.add_argument(
        "-c",
        "--commit",
        help="Number of records to commit after. Defaults to 1000",
        nargs="?",
        const=1000,
        default=1000,
        type=int,
    )
    return p.parse_args()


if __name__ == "__main__":
    run()