annotate data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.py @ 0:715bc9aeef69 draft

planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188

import argparse
import datetime
import json
import os
import shutil
import sys
import tarfile
import urllib.request, urllib.error, urllib.parse
import zipfile
from import_data import run, _main

parser = argparse.ArgumentParser(description='Create data manager json.')
parser.add_argument('--url', dest='url', action='store', help='Url for CARD data')
parser.add_argument('--out', dest='output', action='store', help='JSON filename')
parser.add_argument('--name', dest='name', action='store', default='CARD_data-' + str(datetime.datetime.now().strftime('%Y-%B-%d-%H:%M:%S')), help='Data table database name')
args = parser.parse_args()

print('[rgi_database_builder] Importing...')

_main(args)

def main(args):
    print('[rgi_database_builder] Building......')

    data_manager_entry = {}
    data_manager_entry['value'] = args.name.lower()
    data_manager_entry['name'] = args.name
    data_manager_entry['path'] = '.'

    data_manager_json = dict(data_tables = dict(rgi_databases=data_manager_entry))

    params = json.loads(open(args.output,'r').read())

    target_directory = params['output_data'][0]['extra_files_path']
    os.mkdir(target_directory)
    output_path = os.path.join(os.getcwd(), 'rgi-database')

    for filename in os.listdir(output_path):
        print('[rgi_database_builder] move file: {} from {} to {}'.format(filename, output_path, target_directory))
        shutil.move(os.path.join(output_path, filename), target_directory)

    print(args.output)
    print('[rgi_database_builder] write file: {}'.format(args.output))
    open(args.output, 'w').write(json.dumps(data_manager_json))

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