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