annotate data_manager/data_manager_fetch_pharokka_db.py @ 1:50caca83e7c9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31

#!/usr/bin/env python

import argparse
import json
import os
import subprocess
import sys
from datetime import datetime


def main():
    # Parse Command Line
    parser = argparse.ArgumentParser(description="Create data manager JSON.")
    parser.add_argument("--out", dest="output", action="store", help="JSON filename")
    parser.add_argument("--version", dest="version", action="store", help="Version of the DB")
    parser.add_argument(
        "--test",
        action="store_true",
        help="option to test the script with an lighted database",
    )

    args = parser.parse_args()

    # the output file of a DM is a json containing args that can be used by the DM
    # most tools mainly use these args to find the extra_files_path for the DM, which can be used
    # to store the DB data
    with open(args.output) as fh:
        params = json.load(fh)

    workdir = params["output_data"][0]["extra_files_path"]
    os.mkdir(workdir)

    time = datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
    db_value = "db_from_{0}".format(time)
    db_path = os.path.join(workdir, db_value)

    # create DB
    if args.test:  # the test only checks that the pharokka download script is available and copies the test DB

        # check if install_databases.py is there
        command_args = ["install_databases.py", "-h"]
        proc = subprocess.Popen(args=command_args, shell=False)
        return_code = proc.wait()
        if return_code:
            print("Error downloading Pharokka database.", file=sys.stderr)
            sys.exit(return_code)

        # copy the test DB
        test_db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "subset_pharokka_db")
        command_args = ["cp", "-r", test_db_path, db_path]
    else:
        command_args = ["install_databases.py", "-o", db_path]

    proc = subprocess.Popen(args=command_args, shell=False)
    return_code = proc.wait()
    if return_code:
        print("Error downloading Pharokka database.", file=sys.stderr)
        sys.exit(return_code)

    # Update Data Manager JSON and write to file
    data_manager_entry = {
        "data_tables": {
            "pharokka_db_versioned": {
                "value": db_value,
                "dbkey": db_value,
                "version": args.version,
                "name": f"Pharokka DB version {args.version} downloaded at {datetime.now()}",
                "path": db_path,
            }
        }
    }

    with open(os.path.join(args.output), "w+") as fh:
        json.dump(data_manager_entry, fh, sort_keys=True)


if __name__ == "__main__":
    main()