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6
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1 #!/usr/bin/env python
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2 import json
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3 import optparse
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4 import urllib
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5 import os.path
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6 import os
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7 from operator import itemgetter
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8 import tarfile
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9
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10 __version__ = "1.0.0"
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11 CHUNK_SIZE = 2**20 #1mb
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12 VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
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13
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14
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15 def splitext(path):
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16 for ext in ['.tar.gz', '.tar.bz2']:
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17 if path.endswith(ext):
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18 path, ext = path[:-len(ext)], path[-len(ext):]
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19 break
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20 else:
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21 path, ext = os.path.splitext(path)
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22 return path, ext[1:]
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23
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24
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25 def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ):
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26 source_method = getattr( source_stream, source_method )
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27 target_method = getattr( target_stream, target_method )
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28 while True:
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29 chunk = source_method( CHUNK_SIZE )
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30 if chunk:
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31 target_method( chunk )
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32 else:
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33 break
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34
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35
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36 def deconstruct_multi_filename( multi_filename ):
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37 keys = [ 'primary', 'id', 'name', 'visible', 'file_type' ]
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38 return ( dict( zip( keys, multi_filename.split('_') ) ) )
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39
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40
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41 def construct_multi_filename( id, name, file_type ):
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42 """ Implementation of *Number of Output datasets cannot be determined until tool run* from documentation_.
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43 .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
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44 """
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45 filename = "%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type )
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46 return filename
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47
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48
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49 def download_from_query( query_data, target_output_filename ):
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50 """ Download file from the json data and write it to target_output_filename.
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51 """
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52 query_url = query_data.get( 'url' )
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53 query_file_type = query_data.get( 'extension' )
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54 query_stream = urllib.urlopen( query_url )
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55 output_stream = open( target_output_filename, 'wb' )
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56 chunk_write( query_stream, output_stream )
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57 query_stream.close()
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58 output_stream.close()
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59
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60 def store_file_from_archive( file_object, target_output_filename ):
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61 """ Store file after extracting from archive and organize them as a collection using the structure
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62 (collection-name)_(file-name).ext as file name
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63 """
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64 output_stream = open( target_output_filename, 'wb' )
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65 chunk_write( file_object.read(), output_stream )
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66 output_stream.close()
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67
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68
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69 def download_extra_data( query_ext_data, base_path ):
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70 """ Download any extra data defined in the JSON.
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71 NOTE: the "path" value is a relative path to the file on our
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72 file system. This is slightly dangerous and we should make every effort
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73 to avoid a malicious absolute path to write the file elsewhere on the
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74 filesystem.
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75 """
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76 for ext_data in query_ext_data:
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77 if not os.path.exists( base_path ):
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78 os.mkdir( base_path )
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79 query_stream = urllib.urlopen( ext_data.get( 'url' ) )
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80 ext_path = ext_data.get( 'path' )
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81 os.makedirs( os.path.normpath( '/'.join( [ base_path, os.path.dirname( ext_path ) ] ) ) )
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82 output_stream = open( os.path.normpath( '/'.join( [ base_path, ext_path ] ) ), 'wb' )
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83 chunk_write( query_stream, output_stream )
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84 query_stream.close()
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85 output_stream.close()
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86
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87
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88 def metadata_to_json_for_archive_entry( dataset_id, extension, metaname, filename, ds_type='dataset', primary=False ):
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89 """ Return line separated JSON """
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90 meta_dict = dict( type = ds_type,
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91 ext = extension,
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92 filename = filename,
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93 name = metaname,
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94 metadata = {} )
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95 if primary:
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96 meta_dict[ 'base_dataset_id' ] = dataset_id
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97 else:
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98 meta_dict[ 'dataset_id' ] = dataset_id
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99 return "%s\n" % json.dumps( meta_dict )
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100
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101
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102 def metadata_to_json( dataset_id, metadata, filename, ds_type='dataset', primary=False):
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103 """ Return line separated JSON """
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104 meta_dict = dict( type = ds_type,
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105 ext = metadata.get( 'extension' ),
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106 filename = filename,
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107 name = metadata.get( 'name' ),
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108 metadata = metadata.get( 'metadata', {} ) )
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109 if metadata.get( 'extra_data', None ):
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110 meta_dict[ 'extra_files' ] = '_'.join( [ filename, 'files' ] )
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111 if primary:
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112 meta_dict[ 'base_dataset_id' ] = dataset_id
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113 else:
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114 meta_dict[ 'dataset_id' ] = dataset_id
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115 return "%s\n" % json.dumps( meta_dict )
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116
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117
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118 def download_files_and_write_metadata(query_item, json_params, output_base_path, metadata_parameter_file, primary, appdata_path):
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119 """ Main work function that operates on the JSON representation of
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120 one dataset and its metadata. Returns True.
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121 """
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122 dataset_url, output_filename, \
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123 extra_files_path, file_name, \
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124 ext, out_data_name, \
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125 hda_id, dataset_id = set_up_config_values(json_params)
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126 extension = query_item.get( 'extension' )
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127 filename = query_item.get( 'url' )
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128 extra_data = query_item.get( 'extra_data', None )
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129 if primary:
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130 filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
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131 name = construct_multi_filename( hda_id, filename, extension )
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132 target_output_filename = os.path.normpath( '/'.join( [ output_base_path, name ] ) )
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133 metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
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134 target_output_filename,
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135 ds_type='new_primary_dataset',
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136 primary=primary) )
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137 else:
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138 target_output_filename = output_filename
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139 metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
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140 target_output_filename,
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141 ds_type='dataset',
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142 primary=primary) )
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143 download_from_query( query_item, target_output_filename )
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144 if extra_data:
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145 extra_files_path = ''.join( [ target_output_filename, 'files' ] )
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146 download_extra_data( extra_data, extra_files_path )
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147
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10
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148 """ the following code handles archives and decompress them in a collection """
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6
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149 check_ext = ""
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150 if ( fname.endswith( "gz" ) ):
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151 check_ext = "r:gz"
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152 elif ( fname.endswith( "bz2" ) ):
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153 check_ext = "r:bz2"
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154 elif ( fname.endswith( "tar" ) ):
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155 check_ext = "r:"
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156 if ( bool( check_ext and check_ext.strip() ) ):
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157 with tarfile.open( target_output_filename, check_ext ) as tf:
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158 for entry in tf:
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159 fileobj = tf.extractfile( entry )
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160 if entry.isfile():
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10
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161
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162 #dataset_url, output_filename, \
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163 # extra_files_path, file_name, \
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164 # ext, out_data_name, \
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165 # hda_id, dataset_id = set_up_config_values(json_params)
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166
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6
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167 filename = os.path.basename( entry.name )
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168 extension = splitext( filename )
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169 extra_data = None
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170 #target_output_filename = output_filename
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10
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171 # (?P<archive_name>.*)_(?P<file_name>.*)\..*
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172 filename_with_collection_prefix = query_item.get( 'name' ) + "_" + filename
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173 target_output_filename = os.path.join(appdata_path, filename_with_collection_prefix)
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10
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174
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175 #metadata_parameter_file.write( metadata_to_json_for_archive_entry( dataset_id, extension,
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176 # filename, target_output_filename,
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177 # ds_type='dataset',
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178 # primary=primary) )
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179
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6
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180 store_file_from_archive( fileobj, target_output_filename )
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181
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182 return True
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183
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184
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185 def set_up_config_values():
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186 extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \
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187 itemgetter('extra_files_path', 'file_name', 'ext', 'out_data_name', 'hda_id', 'dataset_id')(output_data[0])
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188
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189 def set_up_config_values(json_params):
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190 """ Parse json_params file and return a tuple of necessary configuration
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191 values.
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192 """
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193 datasource_params = json_params.get( 'param_dict' )
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194 dataset_url = datasource_params.get( 'URL' )
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195 output_filename = datasource_params.get( 'output1', None )
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196 output_data = json_params.get( 'output_data' )
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197 extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \
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198 itemgetter('extra_files_path', 'file_name', 'ext', 'out_data_name', 'hda_id', 'dataset_id')(output_data[0])
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199 return (dataset_url, output_filename,
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200 extra_files_path, file_name,
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201 ext, out_data_name,
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202 hda_id, dataset_id)
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203
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204
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205 def download_from_json_data( options, args ):
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206 """ Parse the returned JSON data and download files. Write metadata
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207 to flat JSON file.
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208 """
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209 output_base_path = options.path
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210 appdata_path = options.appdata
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211 if not os.path.exists(appdata_path):
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212 os.makedirs(appdata_path)
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213
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214 # read tool job configuration file and parse parameters we need
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215 json_params = json.loads( open( options.json_param_file, 'r' ).read() )
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216 dataset_url, output_filename, \
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217 extra_files_path, file_name, \
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218 ext, out_data_name, \
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219 hda_id, dataset_id = set_up_config_values(json_params)
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220 # line separated JSON file to contain all dataset metadata
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221 metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' )
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222
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223 # get JSON response from data source
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224 # TODO: make sure response is not enormous
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225 query_params = json.loads(urllib.urlopen( dataset_url ).read())
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226 # download and write files
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227 primary = False
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228 # query_item, hda_id, output_base_path, dataset_id
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229 for query_item in query_params:
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230 if isinstance( query_item, list ):
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231 # TODO: do something with the nested list as a collection
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232 for query_subitem in query_item:
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233 primary = download_files_and_write_metadata(query_subitem, json_params, output_base_path,
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234 metadata_parameter_file, primary, appdata_path)
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235
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236 elif isinstance( query_item, dict ):
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237 primary = download_files_and_write_metadata(query_item, json_params, output_base_path,
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238 metadata_parameter_file, primary, appdata_path)
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239 metadata_parameter_file.close()
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240
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241 def __main__():
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242 """ Read the JSON return from a data source. Parse each line and request
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243 the data, download to "newfilepath", and write metadata.
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244
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245 Schema
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246 ------
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247
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248 [ {"url":"http://url_of_file",
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249 "name":"encode WigData",
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250 "extension":"wig",
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251 "metadata":{"db_key":"hg19"},
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252 "extra_data":[ {"url":"http://url_of_ext_file",
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253 "path":"rel/path/to/ext_file"}
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254 ]
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255 }
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256 ]
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257
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258 """
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259 # Parse the command line options
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260 usage = "Usage: json_data_source_mod.py max_size --json_param_file filename [options]"
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261 parser = optparse.OptionParser(usage = usage)
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262 parser.add_option("-j", "--json_param_file", type="string",
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263 action="store", dest="json_param_file", help="json schema return data")
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264 parser.add_option("-p", "--path", type="string",
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265 action="store", dest="path", help="new file path")
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266 parser.add_option("-a", "--appdata", type="string",
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267 action="store", dest="appdata", help="appdata folder name")
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268 parser.add_option("-v", "--version", action="store_true", dest="version",
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269 default=False, help="display version and exit")
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270
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271 (options, args) = parser.parse_args()
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272 if options.version:
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273 print __version__
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274 else:
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275 download_from_json_data( options, args )
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276
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277
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278 if __name__ == "__main__": __main__()
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