1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/a28faa6ac188/ Changeset: a28faa6ac188 User: dan Date: 2013-06-04 20:05:20 Summary: Data Managers: allow multiple value translations to be specifed per column and also allow multiple types of value translations. Affected #: 1 file

diff -r df488dbd5bdb22dc78549118834788992e5cabcb -r a28faa6ac188594a60cd495327661a15efd37ea5 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -16,6 +16,8 @@ log = logging.getLogger( __name__ )

SUPPORTED_DATA_TABLE_TYPES = ( TabularToolDataTable ) +VALUE_TRANSLATION_FUNCTIONS = dict( abspath=os.path.abspath ) +DEFAULT_VALUE_TRANSLATION_TYPE = 'template'

class DataManagers( object ): def __init__( self, app, xml_filename=None ): @@ -160,15 +162,24 @@ if data_table_name not in self.output_ref_by_data_table: self.output_ref_by_data_table[ data_table_name ] = {} self.output_ref_by_data_table[ data_table_name ][ data_table_coumn_name ] = output_ref - value_translation_elem = column_elem.find( 'value_translation' ) - if value_translation_elem is not None: - value_translation = value_translation_elem.text - else: - value_translation = None - if value_translation is not None: - if data_table_name not in self.value_translation_by_data_table_column: - self.value_translation_by_data_table_column[ data_table_name ] = {} - self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = value_translation + value_translation_elems = column_elem.findall( 'value_translation' ) + if value_translation_elems is not None: + for value_translation_elem in value_translation_elems: + value_translation = value_translation_elem.text + if value_translation is not None: + value_translation_type = value_translation_elem.get( 'type', DEFAULT_VALUE_TRANSLATION_TYPE ) + if data_table_name not in self.value_translation_by_data_table_column: + self.value_translation_by_data_table_column[ data_table_name ] = {} + if data_table_coumn_name not in self.value_translation_by_data_table_column[ data_table_name ]: + self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = [] + if value_translation_type == 'function': + if value_translation in VALUE_TRANSLATION_FUNCTIONS: + value_translation = VALUE_TRANSLATION_FUNCTIONS[ value_translation ] + else: + raise ValueError( "Unsupported value translation function: '%s'" % ( value_translation ) ) + else: + assert value_translation_type == DEFAULT_VALUE_TRANSLATION_TYPE, ValueError( "Unsupported value translation type: '%s'" % ( value_translation_type ) ) + self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ].append( value_translation )

for move_elem in column_elem.findall( 'move' ): move_type = move_elem.get( 'type', 'directory' ) @@ -290,8 +301,11 @@ def process_value_translation( self, data_table_name, column_name, **kwd ): value = kwd.get( column_name ) if data_table_name in self.value_translation_by_data_table_column and column_name in self.value_translation_by_data_table_column[ data_table_name ]: - value_translation = self.value_translation_by_data_table_column[ data_table_name ][ column_name ] - value = fill_template( value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd ) + for value_translation in self.value_translation_by_data_table_column[ data_table_name ][ column_name ]: + if isinstance( value_translation, basestring ): + value = fill_template( value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd ) + else: + value = value_translation( value ) return value

def get_tool_shed_repository_info_dict( self ):

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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