Mercurial > repos > pjbriggs > ceas

comparison data_manager/data_manager_ceas_fetch_annotations.py @ 1:d9032bb158b9 draft

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Add in data manager for CEAS annotation databases.
author pjbriggs
date Wed, 28 Jan 2015 05:04:46 -0500
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children 4e2883bb058d
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0:8b25779ee261 1:d9032bb158b9
1 #!/usr/bin/env python
2 #
3
4 import sys
5 import os
6 import optparse
7 import urllib2
8 import gzip
9
10 from galaxy.util.json import from_json_string, to_json_string
11
12 # Download file from specified URL and put into local subdir
13
14 if __name__ == '__main__':
15 #Parse Command Line
16 parser = optparse.OptionParser()
17 parser.add_option('--download',dest='url',action='store',
18 type="string",default=None,help='URL to download')
19 options,args = parser.parse_args()
20 print "options: %s" % options
21 print "args : %s" % args
22 if len(args) != 2:
23 p.error("Need to supply JSON file name and description text")
24
25 # Read the JSON supplied from the data manager tool
26 # Results from this program will be returned via the
27 # same file
28 jsonfile = args[0]
29 params = from_json_string(open(jsonfile).read() )
30 print "%s" % params
31
32 # Extract the data from the input JSON
33 # See https://wiki.galaxyproject.org/Admin/Tools/DataManagers/HowTo/Define?highlight=%28\bAdmin%2FTools%2FDataManagers\b%29
34 # for example of JSON
35 #
36 # We want the values set in the data manager XML
37 dbkey = params['param_dict']['dbkey']
38 description = params['param_dict']['description']
39 # Where to put the output file
40 # Nb we have to make this ourselves, it doesn't exist by default
41 target_dir = params['output_data'][0]['extra_files_path']
42 os.mkdir(target_dir)
43
44 # Dictionary for returning to data manager
45 data_manager_dict = {}
46
47 # Download from URL
48 if options.url is not None:
49 print "Downloading: %s" % options.url
50 annotation_file_name = os.path.basename(options.url)
51 annotation_file_path = os.path.join(target_dir,annotation_file_name)
52 print "Annotation file name: %s" % annotation_file_name
53 print "Annotation file path: %s" % annotation_file_path
54 open(annotation_file_path,'wb').write(urllib2.urlopen(options.url).read())
55 if annotation_file_name.endswith('.gz'):
56 # Uncompress
57 uncompressed_file = annotation_file_path[:-3]
58 open(uncompressed_file,'wb').write(gzip.open(annotation_file_path,'rb').read())
59 # Remove gzipped file
60 os.remove(annotation_file_path)
61 annotation_file_name = os.path.basename(uncompressed_file)
62 annotation_file_path = uncompressed_file
63 # Update the output dictionary
64 data_manager_dict['data_tables'] = dict()
65 data_manager_dict['data_tables']['ceas_annotations'] = {
66 'dbkey': dbkey,
67 'name': description,
68 'value': annotation_file_name,
69 }
70 else:
71 raise NotImplementedError("Non-download options not implemented")
72
73 #save info to json file
74 open(jsonfile,'wb').write(to_json_string(data_manager_dict))
75