Mercurial > repos > greg > data_manager_vsnp_dnaprints

comparison data_manager/vsnp_dnaprints_fetcher.py @ 0:f58178a5eebc draft

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author greg
date Fri, 14 Feb 2020 13:41:36 -0500
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-1:000000000000 0:f58178a5eebc
1 import argparse
2 import json
3 import os
4 import sys
5 try:
6 # For Python 3.0 and later
7 from urllib.request import Request, urlopen
8 except ImportError:
9 # Fall back to Python 2 imports
10 from urllib2 import Request, urlopen
11
12
13 def url_download(url, workdir):
14 file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
15 src = None
16 dst = None
17 try:
18 req = Request(url)
19 src = urlopen(req)
20 with open(file_path, 'wb') as dst:
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:
30 if src:
31 src.close()
32 return file_path
33
34
35 def download(dbkey, name, url, out_file):
36
37 with open(out_file) as fh:
38 params = json.loads(fh.read())
39
40 workdir = params['output_data'][0]['extra_files_path']
41 os.makedirs(workdir)
42 file_path = url_download(url, workdir)
43 entry_name = os.path.basename(file_path)
44
45 data_manager_json = {"data_tables": {}}
46 data_manager_entry = {}
47 data_manager_entry['value'] = dbkey
48 data_manager_entry['name'] = entry_name
49 data_manager_entry['path'] = file_path
50 data_manager_entry['description'] = "DNAprints file for %s" % name
51 data_manager_json["data_tables"]["vsnp_dnaprints"] = data_manager_entry
52
53 with open(out_file, 'w') as fh:
54 fh.write(json.dumps(data_manager_json, sort_keys=True))
55
56
57 parser = argparse.ArgumentParser()
58
59 parser.add_argument('--dbkey', dest='dbkey', help='Genome reference dbkey')
60 parser.add_argument('--name', dest='name', help='Reference display name')
61 parser.add_argument('--url', dest='url', help='URL to download DNAprints file')
62 parser.add_argument('--out_file', dest='out_file', help='JSON output file')
63
64 args = parser.parse_args()
65
66 download(args.dbkey, args.name, args.url, args.out_file)