|
0
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 import argparse
|
|
|
4 import json
|
|
|
5 import os
|
|
|
6 import sys
|
|
|
7 import tarfile
|
|
|
8 from urllib.request import Request, urlopen
|
|
|
9 from urllib.parse import urlparse
|
|
|
10
|
|
|
11
|
|
1
|
12 def url_download(url, target_directory):
|
|
0
|
13 url_parts = urlparse(url)
|
|
1
|
14 tarball = os.path.abspath(os.path.join(target_directory, os.path.basename(url_parts.path)))
|
|
0
|
15 src = None
|
|
|
16 dst = None
|
|
|
17 try:
|
|
|
18 req = Request(url)
|
|
|
19 src = urlopen(req)
|
|
1
|
20 with open(tarball, 'wb') as dst:
|
|
0
|
21 while True:
|
|
|
22 chunk = src.read(2**10)
|
|
|
23 if chunk:
|
|
|
24 dst.write(chunk)
|
|
|
25 else:
|
|
|
26 break
|
|
|
27 except Exception as e:
|
|
|
28 sys.exit(str(e))
|
|
|
29 finally:
|
|
1
|
30 if src is not None:
|
|
0
|
31 src.close()
|
|
1
|
32 if tarfile.is_tarfile(tarball):
|
|
|
33 fh = tarfile.open(tarball, 'r:*')
|
|
0
|
34 else:
|
|
1
|
35 return tarball
|
|
|
36 fh.extractall(target_directory)
|
|
|
37 fh.close()
|
|
|
38 os.remove(tarball)
|
|
|
39 return target_directory
|
|
0
|
40
|
|
|
41
|
|
|
42 def download(database_id, database_name, url, out_file):
|
|
|
43
|
|
|
44 with open(out_file) as fh:
|
|
|
45 params = json.load(fh)
|
|
|
46
|
|
1
|
47 target_directory = params['output_data'][0]['extra_files_path']
|
|
|
48 os.makedirs(target_directory)
|
|
|
49 file_path = url_download(url, target_directory)
|
|
0
|
50
|
|
|
51 data_manager_json = {"data_tables": {}}
|
|
|
52 data_manager_entry = {}
|
|
|
53 data_manager_entry['value'] = database_id
|
|
|
54 data_manager_entry['name'] = database_name
|
|
2
|
55 data_manager_entry['path'] = file_path
|
|
0
|
56 data_manager_json["data_tables"]["gtdbtk_database"] = data_manager_entry
|
|
|
57
|
|
|
58 with open(out_file, 'w') as fh:
|
|
|
59 json.dump(data_manager_json, fh, sort_keys=True)
|
|
|
60
|
|
|
61
|
|
|
62 parser = argparse.ArgumentParser()
|
|
|
63
|
|
|
64 parser.add_argument('--database_name', dest='database_name', help='GTDB-Tk database display name')
|
|
|
65 parser.add_argument('--database_id', dest='database_id', help='Unique GTDB-Tk database id')
|
|
|
66 parser.add_argument('--url', dest='url', help='URL to download GTDB-Tk databse version')
|
|
|
67 parser.add_argument('--out_file', dest='out_file', help='JSON output file')
|
|
|
68
|
|
|
69 args = parser.parse_args()
|
|
|
70
|
|
|
71 download(args.database_id, args.database_name, args.url, args.out_file)
|
