view data_manager/make_json.py @ 1:cf0fe3793f6c draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit ae0b6f9da114f0889a8d31411d2f2c9bbf0c2004

import json
import argparse
import os
import shutil

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()

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))
    params = json.loads(open(args.output).read())
    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)
    file(args.output, 'w').write(json.dumps(data_manager_json))

if __name__ == '__main__':
    main(args)