annotate data_manager/data_manager.py @ 39:2ab076cf69df draft

planemo upload for repository https://[e-mail]/repos/scottx611x/data_manager_fetch_gene_annotation

1 import os
2 import sys
3 import uuid
4 import json
5 import argparse
6 import requests
7 from requests.exceptions import ContentDecodingError
8 
9 
10 def url_download(url):
11     """Attempt to download gene annotation file from a given url
12     :param url: full url to gene annotation file
13     :type url: str.
14     :returns: name of downloaded gene annotation file
15     :raises: ContentDecodingError, IOError
16     """
17     response = requests.get(url=url, stream=True)
18 
19     # Generate file_name
20     file_name = response.url.split("/")[-1]
21 
22     block_size = 10 * 1024 * 1024  # 10MB chunked download
23     with open(file_name, 'w+') as f:
24         try:
25             # Good to note here that requests' iter_content() will
26             # automatically handle decoding "gzip" and "deflate" encoding
27             # formats
28             for buf in response.iter_content(block_size):
29                 f.write(buf)
30         except (ContentDecodingError, IOError) as e:
31             sys.stderr.write("Error occured downloading reference file: %s"
32                              % e)
33             os.remove(file_name)
34 
35     return file_name
36 
37 
38 def main():
39 
40     # Generate and parse command line args
41     parser = argparse.ArgumentParser(description='Create data manager JSON.')
42     parser.add_argument('--out', dest='output', action='store',
43                         help='JSON filename')
44     parser.add_argument('--name', dest='name', action='store',
45                         default=uuid.uuid4(), help='Data table entry unique ID'
46                         )
47     parser.add_argument('--url', dest='url', action='store',
48                         help='Url to download gtf file from')
49 
50     args = parser.parse_args()
51 
52     work_dir = os.getcwd()
53 
54     # Attempt to download gene annotation file from given url
55     gene_annotation_file_name = url_download(args.url)
56 
57     # Update Data Manager JSON and write to file
58     data_manager_entry = {
59         'data_tables': {
60             'gene_annotation': {
61                 'value': str(args.name),
62                 'dbkey': str(args.name),
63                 'name': gene_annotation_file_name,
64                 'path': os.path.join(work_dir, gene_annotation_file_name)
65             }
66         }
67     }
68 
69     with open(os.path.join(args.output), "w+") as f:
70         f.write(json.dumps(data_manager_entry))
71 
72 if __name__ == '__main__':
73     main()