Mercurial > repos > greg > vsnp_excel_filter
comparison data_manager/vsnp_excel_filter_fetcher.py @ 0:3fbd172e4055 draft default tip
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author | greg |
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date | Mon, 09 Mar 2020 13:42:19 -0400 |
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-1:000000000000 | 0:3fbd172e4055 |
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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'] = "Excel Filter file for %s" % name | |
51 data_manager_json["data_tables"]["vsnp_excel_filter"] = 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 Excel 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) |