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comparison json_data_source.py @ 5:33fa019735a4

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Save extra files path as extra_files, not extra_data. Changed type of dataset for new primary datasets. db_key becomes dbkey. Added example json files.
author Matt Shirley <mdshw5@gmail.com>
date Thu, 10 Jul 2014 11:41:54 -0400
parents 96103d66b7af
children 46b589e9747a
comparison
equal deleted inserted replaced
4:96103d66b7af 5:33fa019735a4
71 ext = metadata.get( 'extension' ), 71 ext = metadata.get( 'extension' ),
72 filename = filename, 72 filename = filename,
73 name = metadata.get( 'name' ), 73 name = metadata.get( 'name' ),
74 metadata = metadata.get( 'metadata' ) ) 74 metadata = metadata.get( 'metadata' ) )
75 if metadata.get( 'extra_data', None ): 75 if metadata.get( 'extra_data', None ):
76 meta_dict[ 'extra_data' ] = '_'.join( [ filename, 'files' ] ) 76 meta_dict[ 'extra_files' ] = '_'.join( [ filename, 'files' ] )
77 if primary: 77 if primary:
78 meta_dict[ 'base_dataset_id' ] = dataset_id 78 meta_dict[ 'base_dataset_id' ] = dataset_id
79 else: 79 else:
80 meta_dict[ 'dataset_id' ] = dataset_id 80 meta_dict[ 'dataset_id' ] = dataset_id
81 return "%s\n" % json.dumps( meta_dict ) 81 return "%s\n" % json.dumps( meta_dict )
94 extra_data = query_item.get( 'extra_data', None ) 94 extra_data = query_item.get( 'extra_data', None )
95 if primary: 95 if primary:
96 filename = ''.join( c in VALID_CHARS and c or '-' for c in filename ) 96 filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
97 name = construct_multi_filename( hda_id, filename, extension ) 97 name = construct_multi_filename( hda_id, filename, extension )
98 target_output_filename = os.path.normpath( '/'.join( [ output_base_path, name ] ) ) 98 target_output_filename = os.path.normpath( '/'.join( [ output_base_path, name ] ) )
99 metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
100 target_output_filename,
101 ds_type='new_primary_dataset'
102 primary=primary) )
99 else: 103 else:
100 target_output_filename = output_filename 104 target_output_filename = output_filename
105 metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
106 target_output_filename,
107 ds_type='dataset'
108 primary=primary) )
101 download_from_query( query_item, target_output_filename ) 109 download_from_query( query_item, target_output_filename )
102 if extra_data: 110 if extra_data:
103 download_extra_data( extra_data, '_'.join( [ target_output_filename, 'files' ] ) ) 111 download_extra_data( extra_data, '_'.join( [ target_output_filename, 'files' ] ) )
104 metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
105 target_output_filename,
106 primary=primary) )
107 return True 112 return True
108 113
109 114
110 def set_up_config_values(json_params): 115 def set_up_config_values(json_params):
111 """ Parse json_params file and return a tuple of necessary configuration 116 """ Parse json_params file and return a tuple of necessary configuration