Mercurial > repos > greg > data_manager_pima_pv_downloader

comparison data_manager/pima_pv_downloader.py @ 0:53652e89e415 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Tue, 18 Oct 2022 20:37:28 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:53652e89e415
1 import argparse
2 import datetime
3 import json
4 import os
5 import sys
6
7 from urllib.request import Request, urlopen
8
9
10 def url_download(url, workdir):
11 file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
12 src = None
13 dst = None
14 try:
15 req = Request(url)
16 src = urlopen(req)
17 with open(file_path, 'wb') as dst:
18 while True:
19 chunk = src.read(2**10)
20 if chunk:
21 dst.write(chunk)
22 else:
23 break
24 except Exception as e:
25 sys.exit(str(e))
26 finally:
27 if src:
28 src.close()
29 return file_path
30
31
32 def download(url, out_file):
33 today = datetime.datetime.utcnow().strftime("%Y-%m-%d")
34
35 with open(out_file) as fh:
36 params = json.load(fh)
37
38 workdir = params['output_data'][0]['extra_files_path']
39 os.makedirs(workdir)
40 file_path = url_download(url, workdir)
41 value = '%s_pima_plasmids_and_values' % today
42 name = '%s %s' % (today, os.path.basename(file_path))
43
44 data_manager_json = {"data_tables": {}}
45 data_manager_entry = {}
46 data_manager_entry['value'] = value
47 data_manager_entry['name'] = name
48 data_manager_entry['path'] = file_path
49 data_manager_json["data_tables"]["vsnp_genbank"] = data_manager_entry
50
51 with open(out_file, 'w') as fh:
52 json.dump(data_manager_json, fh, sort_keys=True)
53
54
55 parser = argparse.ArgumentParser()
56
57 parser.add_argument('--url', dest='url', help='URL to download plasmids_and_vectors.fasta file')
58 parser.add_argument('--out_file', dest='out_file', help='JSON output file')
59
60 args = parser.parse_args()
61
62 download(args.url, args.out_file)