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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.

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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>
This commit is contained in:
Daniel Blankenberg
2010-09-02 11:00:25 -04:00
parent 44b0b1ca4d
commit ea9a6bbbe4
1 changed files with 13 additions and 5 deletions
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lib/galaxy/tools/parameters/output.py
+13 -5
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@@ -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 [ MetadataToolOutputAction, FormatToolOutputAction ]:
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 = {}