Workflow modules: Adjust spacing to new guidelines.

lib/galaxy/workflow/modules.py

@@ -15,9 +15,9 @@ from galaxy.tools.parameters import check_param, DataToolParameter, DummyDataset
 from galaxy.util.bunch import Bunch
 from galaxy.util.json import from_json_string, to_json_string
 
-
 log = logging.getLogger( __name__ )
 
+
 class WorkflowModule( object ):
 
     def __init__( self, trans ):
@@ -31,6 +31,7 @@ class WorkflowModule( object ):
         Create a new instance of the module with default state
         """
         return Class( trans )
+
     @classmethod
     def from_dict( Class, trans, d ):
         """
@@ -38,6 +39,7 @@ class WorkflowModule( object ):
         dictionary `d`.
         """
         return Class( trans )
+
     @classmethod
     def from_workflow_step( Class, trans, step ):
         return Class( trans )
@@ -51,10 +53,13 @@ class WorkflowModule( object ):
 
     def get_type( self ):
         return self.type
+
     def get_name( self ):
         return self.name
+
     def get_tool_id( self ):
         return None
+
     def get_tooltip( self, static_path='' ):
         return None
 
@@ -62,14 +67,19 @@ class WorkflowModule( object ):
 
     def get_state( self ):
         return None
+
     def get_errors( self ):
         return None
+
     def get_data_inputs( self ):
         return []
+
     def get_data_outputs( self ):
         return []
+
     def update_state( self ):
         pass
+
     def get_config_form( self ):
         raise TypeError( "Abstract method" )
 
@@ -84,18 +94,23 @@ class WorkflowModule( object ):
 
     def get_runtime_inputs( self ):
         raise TypeError( "Abstract method" )
+
     def get_runtime_state( self ):
         raise TypeError( "Abstract method" )
+
     def encode_runtime_state( self, trans, state ):
         raise TypeError( "Abstract method" )
+
     def decode_runtime_state( self, trans, string ):
         raise TypeError( "Abstract method" )
+
     def update_runtime_state( self, trans, state, values ):
         raise TypeError( "Abstract method" )
 
     def execute( self, trans, state ):
         raise TypeError( "Abstract method" )
 
+
 class InputDataModule( WorkflowModule ):
     type = "data_input"
     name = "Input dataset"
@@ -105,12 +120,14 @@ class InputDataModule( WorkflowModule ):
         module = Class( trans )
         module.state = dict( name="Input Dataset" )
         return module
+
     @classmethod
     def from_dict( Class, trans, d, secure=True ):
         module = Class( trans )
         state = from_json_string( d["tool_state"] )
         module.state = dict( name=state.get( "name", "Input Dataset" ) )
         return module
+
     @classmethod
     def from_workflow_step( Class, trans, step ):
         module = Class( trans )
@@ -172,6 +189,7 @@ class InputDataModule( WorkflowModule ):
     def execute( self, trans, state ):
         return None, dict( output=state.inputs['input'])
 
+
 class ToolModule( WorkflowModule ):
 
     type = "tool"
@@ -286,6 +304,7 @@ class ToolModule( WorkflowModule ):
 
     def get_data_inputs( self ):
         data_inputs = []
+
         def callback( input, value, prefixed_name, prefixed_label ):
             if isinstance( input, DataToolParameter ):
                 data_inputs.append( dict(
@@ -293,6 +312,7 @@ class ToolModule( WorkflowModule ):
                     label=prefixed_label,
                     multiple=input.multiple,
                     extensions=input.extensions ) )
+
         visit_input_values( self.tool.inputs, self.state.inputs, callback )
         return data_inputs
 
@@ -338,6 +358,7 @@ class ToolModule( WorkflowModule ):
 
         make_runtime_key = incoming.get( 'make_runtime', None )
         make_buildtime_key = incoming.get( 'make_buildtime', None )
+
         def item_callback( trans, key, input, value, error, old_value, context ):
             # Dummy value for Data parameters
             if isinstance( input, DataToolParameter ):
@@ -354,6 +375,7 @@ class ToolModule( WorkflowModule ):
                 return value, None
             else:
                 return value, error
+
         # Update state using incoming values
         errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback )
         self.errors = errors or None
@@ -370,6 +392,7 @@ class ToolModule( WorkflowModule ):
             input_connections_by_name = {}
         # Any connected input needs to have value DummyDataset (these
         # are not persisted so we need to do it every time)
+
         def callback( input, value, prefixed_name, prefixed_label ):
             replacement = None
             if isinstance( input, DataToolParameter ):
@@ -379,9 +402,12 @@ class ToolModule( WorkflowModule ):
                     else:
                         replacement = DummyDataset()
             return replacement
+
         visit_input_values( self.tool.inputs, self.state.inputs, callback )
 
+
 class WorkflowModuleFactory( object ):
+
     def __init__( self, module_types ):
         self.module_types = module_types