annotate data_manager/make_json.py @ 6:889a857303e0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

import argparse
import json
import os
import shutil


def main(args):
    data_manager_entry = {}
    data_manager_entry['value'] = args.database.lower()
    data_manager_entry['name'] = args.database
    data_manager_entry['path'] = '.'
    data_manager_json = dict(data_tables=dict(kraken_databases=data_manager_entry))
    with open(args.output) as fh:
        params = json.load(fh)
    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    output_path = os.path.join(os.getcwd(), 'kraken-database')
    for filename in os.listdir(output_path):
        shutil.move(os.path.join(output_path, filename), target_directory)
    with open(args.output, 'w') as fh:
        json.dump(data_manager_json, fh, sort_keys=True)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Create data manager json.')
    parser.add_argument('--db', dest='database', action='store', help='Database name')
    parser.add_argument('--out', dest='output', action='store', help='JSON filename')
    args = parser.parse_args()
    main(args)