Mercurial > repos > fabio > gdcwebapp

comparison json_data_source_mod.py @ 10:c0be9583df97 draft

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Uploaded 20170525
author fabio
date Thu, 25 May 2017 17:58:15 -0400
parents 7815152f70c6
children 80593f75d74a
comparison
equal deleted inserted replaced
9:61989e353d24 10:c0be9583df97
143 download_from_query( query_item, target_output_filename ) 143 download_from_query( query_item, target_output_filename )
144 if extra_data: 144 if extra_data:
145 extra_files_path = ''.join( [ target_output_filename, 'files' ] ) 145 extra_files_path = ''.join( [ target_output_filename, 'files' ] )
146 download_extra_data( extra_data, extra_files_path ) 146 download_extra_data( extra_data, extra_files_path )
147 147
148 """ the following code handles archives and decompress them in a collection """
148 check_ext = "" 149 check_ext = ""
149 if ( fname.endswith( "gz" ) ): 150 if ( fname.endswith( "gz" ) ):
150 check_ext = "r:gz" 151 check_ext = "r:gz"
151 elif ( fname.endswith( "bz2" ) ): 152 elif ( fname.endswith( "bz2" ) ):
152 check_ext = "r:bz2" 153 check_ext = "r:bz2"
155 if ( bool( check_ext and check_ext.strip() ) ): 156 if ( bool( check_ext and check_ext.strip() ) ):
156 with tarfile.open( target_output_filename, check_ext ) as tf: 157 with tarfile.open( target_output_filename, check_ext ) as tf:
157 for entry in tf: 158 for entry in tf:
158 fileobj = tf.extractfile( entry ) 159 fileobj = tf.extractfile( entry )
159 if entry.isfile(): 160 if entry.isfile():
160 """ 161
161 dataset_url, output_filename, \ 162 #dataset_url, output_filename, \
162 extra_files_path, file_name, \ 163 # extra_files_path, file_name, \
163 ext, out_data_name, \ 164 # ext, out_data_name, \
164 hda_id, dataset_id = set_up_config_values(json_params) 165 # hda_id, dataset_id = set_up_config_values(json_params)
165 """ 166
166 filename = os.path.basename( entry.name ) 167 filename = os.path.basename( entry.name )
167 extension = splitext( filename ) 168 extension = splitext( filename )
168 extra_data = None 169 extra_data = None
169 #target_output_filename = output_filename 170 #target_output_filename = output_filename
170 """ (?P<archive_name>.*)_(?P<file_name>.*)\..* """ 171 # (?P<archive_name>.*)_(?P<file_name>.*)\..*
171 filename_with_collection_prefix = query_item.get( 'name' ) + "_" + filename 172 filename_with_collection_prefix = query_item.get( 'name' ) + "_" + filename
172 target_output_filename = os.path.join(appdata_path, filename_with_collection_prefix) 173 target_output_filename = os.path.join(appdata_path, filename_with_collection_prefix)
173 """ 174
174 metadata_parameter_file.write( metadata_to_json_for_archive_entry( dataset_id, extension, 175 #metadata_parameter_file.write( metadata_to_json_for_archive_entry( dataset_id, extension,
175 filename, target_output_filename, 176 # filename, target_output_filename,
176 ds_type='dataset', 177 # ds_type='dataset',
177 primary=primary) ) 178 # primary=primary) )
178 """ 179
179 store_file_from_archive( fileobj, target_output_filename ) 180 store_file_from_archive( fileobj, target_output_filename )
180 181
181 return True 182 return True
182 183
183 184