Mercurial > repos > card > rgi
comparison 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
author | card |
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date | Wed, 27 Feb 2019 09:08:21 -0500 |
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-1:000000000000 | 0:715bc9aeef69 |
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1 import argparse | |
2 import datetime | |
3 import json | |
4 import os | |
5 import shutil | |
6 import sys | |
7 import tarfile | |
8 import urllib.request, urllib.error, urllib.parse | |
9 import zipfile | |
10 from import_data import run, _main | |
11 | |
12 parser = argparse.ArgumentParser(description='Create data manager json.') | |
13 parser.add_argument('--url', dest='url', action='store', help='Url for CARD data') | |
14 parser.add_argument('--out', dest='output', action='store', help='JSON filename') | |
15 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') | |
16 args = parser.parse_args() | |
17 | |
18 print('[rgi_database_builder] Importing...') | |
19 | |
20 _main(args) | |
21 | |
22 def main(args): | |
23 print('[rgi_database_builder] Building......') | |
24 | |
25 data_manager_entry = {} | |
26 data_manager_entry['value'] = args.name.lower() | |
27 data_manager_entry['name'] = args.name | |
28 data_manager_entry['path'] = '.' | |
29 | |
30 data_manager_json = dict(data_tables = dict(rgi_databases=data_manager_entry)) | |
31 | |
32 params = json.loads(open(args.output,'r').read()) | |
33 | |
34 target_directory = params['output_data'][0]['extra_files_path'] | |
35 os.mkdir(target_directory) | |
36 output_path = os.path.join(os.getcwd(), 'rgi-database') | |
37 | |
38 for filename in os.listdir(output_path): | |
39 print('[rgi_database_builder] move file: {} from {} to {}'.format(filename, output_path, target_directory)) | |
40 shutil.move(os.path.join(output_path, filename), target_directory) | |
41 | |
42 print(args.output) | |
43 print('[rgi_database_builder] write file: {}'.format(args.output)) | |
44 open(args.output, 'w').write(json.dumps(data_manager_json)) | |
45 | |
46 if __name__ == '__main__': | |
47 main(args) |