# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan@bx.psu.edu> # Date 1283439625 14400 # Node ID fa1d4be027649ad4d745c62a053e024fe2db35e9 # Parent 04c59f0a5202a89731f76b33525a4e753e0cfa42 Add 'NullToolOutputActionOption' to tool output dataset actions. This action option is used implicitly when no ToolOutputActionOption's have been defined. This will allow e.g. setting a metadata value to a static value on a per ToolOutput basis. Example which sets the strand assignment of an interval dataset to column 10: <outputs> <data format="interval" name="output1"> <actions> <action type="metadata" name="strandCol" default="10"/> </actions> </data> </outputs> --- a/lib/galaxy/tools/parameters/output.py +++ b/lib/galaxy/tools/parameters/output.py @@ -104,7 +104,6 @@ class ToolOutputAction( object ): self.parent = parent self.default = elem.get( 'default', None ) option_elem = elem.find( 'option' ) - assert option_elem is not None, "Required 'option' element missing from ToolOutputAction" self.option = ToolOutputActionOption.from_elem( self, option_elem ) def apply_action( self, output_dataset, other_values ): raise TypeError( "Not implemented" ) @@ -117,20 +116,29 @@ class ToolOutputActionOption( object ): @classmethod def from_elem( cls, parent, elem ): """Loads the proper action by the type attribute of elem""" - option_type = elem.get( 'type', None ) + if elem is None: + option_type = NullToolOutputActionOption.tag # no ToolOutputActionOption's have been defined, use implicit NullToolOutputActionOption + else: + option_type = elem.get( 'type', None ) assert option_type is not None, "Required 'type' attribute missing from ToolOutputActionOption" return option_types[ option_type ]( parent, elem ) def __init__( self, parent, elem ): self.parent = parent self.filters = [] - for filter_elem in elem.findall( 'filter' ): - self.filters.append( ToolOutputActionOptionFilter.from_elem( self, filter_elem ) ) + if elem is not None: + for filter_elem in elem.findall( 'filter' ): + self.filters.append( ToolOutputActionOptionFilter.from_elem( self, filter_elem ) ) def get_value( self, other_values ): raise TypeError( "Not implemented" ) @property def tool( self ): return self.parent.tool +class NullToolOutputActionOption( ToolOutputActionOption ): + tag = "null_option" + def get_value( self, other_values ): + return None + class FromFileToolOutputActionOption( ToolOutputActionOption ): tag = "from_file" def __init__( self, parent, elem ): @@ -454,7 +462,7 @@ for action_type in [ MetadataToolOutputA action_types[ action_type.tag ] = action_type option_types = {} -for option_type in [ FromFileToolOutputActionOption, FromParamToolOutputActionOption, FromDataTableOutputActionOption ]: +for option_type in [ NullToolOutputActionOption, FromFileToolOutputActionOption, FromParamToolOutputActionOption, FromDataTableOutputActionOption ]: option_types[ option_type.tag ] = option_type filter_types = {}