Remove DummyDataset

client/galaxy/scripts/mvc/tool/tool-form-workflow.js

@@ -50,7 +50,7 @@ define(['utils/utils', 'mvc/tool/tool-form-base'],
                     if ( [ 'data', 'data_collection' ].indexOf( input.type ) != -1 ) {
                         input.type = 'hidden';
                         input.info = 'Data input \'' + input.name + '\' (' + Utils.textify( input.extensions && input.extensions.toString() ) + ')';
-                        input.value = null;
+                        input.value = {'__class__': 'RuntimeValue'};
                     } else {
                         input.collapsible_value = {'__class__': 'RuntimeValue'};
                         input.is_workflow = ( input.options && input.options.length == 0 ) ||

lib/galaxy/tools/parameters/__init__.py

@@ -2,7 +2,7 @@
 Classes encapsulating Galaxy tool parameters.
 """
 import re
-from basic import DummyDataset, RuntimeValue
+from basic import RuntimeValue
 from grouping import Conditional, Repeat, Section, UploadDataset
 from galaxy.util import string_as_bool
 from galaxy.util.json import dumps, json_fix, loads
@@ -67,8 +67,6 @@ def check_param( trans, param, incoming_value, param_values ):
     error = None
     try:
         if trans.workflow_building_mode:
-            if isinstance( value, DummyDataset ):
-                return [ None, None ]
             if isinstance( value, RuntimeValue ):
                 return [ { '__class__' : 'RuntimeValue' }, None ]
             if isinstance( value, dict ):

lib/galaxy/tools/parameters/basic.py

@@ -1640,10 +1640,6 @@ def to_dict( self, trans, view='collection', value_mapper=None, other_values={}
         return d
 
 
-class DummyDataset( object ):
-    pass
-
-
 class BaseDataToolParameter( ToolParameter ):
 
     def __init__( self, tool, input_source, trans ):
@@ -1899,7 +1895,7 @@ def get_initial_value_from_history_prevent_repeats( self, trans, other_values, a
         """
         # Can't look at history in workflow mode. Tool shed has no histories.
         if trans.workflow_building_mode or trans.app.name == 'tool_shed':
-            return DummyDataset()
+            return RuntimeValue()
         history = self._get_history( trans )
         dataset_matcher = DatasetMatcher( trans, self, None, other_values )
         if self.optional:
@@ -2003,9 +1999,9 @@ def to_string( self, value, app ):
             return value
         elif isinstance( value, int ):
             return str( value )
-        elif isinstance( value, DummyDataset ):
+        elif isinstance( value, RuntimeValue ):
             return None
-        elif isinstance( value, list) and len(value) > 0 and isinstance( value[0], DummyDataset):
+        elif isinstance( value, list) and len(value) > 0 and isinstance( value[0], RuntimeValue):
             return None
         elif isinstance( value, list ):
             return ",".join( [ str( self.to_string( val, app ) ) for val in value ] )
@@ -2325,7 +2321,7 @@ def from_html( self, value, trans, other_values={} ):
     def to_string( self, value, app ):
         if value is None or isinstance( value, basestring ):
             return value
-        elif isinstance( value, DummyDataset ):
+        elif isinstance( value, RuntimeValue ):
             return None
         try:
             if isinstance( value, galaxy.model.DatasetCollectionElement ):

lib/galaxy/workflow/modules.py

@@ -21,7 +21,6 @@
     parameter_types,
     DataCollectionToolParameter,
     DataToolParameter,
-    DummyDataset,
     RuntimeValue,
 )
 from galaxy.tools.parameters.wrapped import make_dict_copy
@@ -1049,11 +1048,9 @@ def encode_runtime_state( self, trans, state ):
         return encoded
 
     def update_state( self, incoming ):
-        """ Update the current state of the module against the user supplied
-        parameters in the dict-like object `incoming`.
-        """
         self.label = incoming.get( 'label' )
         self.state.inputs = copy.deepcopy( incoming )
+        print self.state.inputs
 
     def check_and_update_state( self ):
         inputs = self.state.inputs
@@ -1065,14 +1062,8 @@ def compute_runtime_state( self, trans, step_updates=None ):
         state = self.state
         self.runtime_post_job_actions = {}
         if step_updates:
-            # Get the tool
-            tool = self.tool
-            # Get old errors
-            old_errors = state.inputs.pop( "__errors__", {} )
-            # Update the state
             self.runtime_post_job_actions = step_updates.get(RUNTIME_POST_JOB_ACTIONS_KEY, {})
-            step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates,
-                                             update_only=True, old_errors=old_errors )
+            self.tool.populate_state( trans, self.tool.inputs, state.inputs, step_updates, step_errors )
             step_metadata_runtime_state = self.__step_meta_runtime_state()
             if step_metadata_runtime_state:
                 state.inputs[ RUNTIME_STEP_META_STATE_KEY ] = step_metadata_runtime_state
@@ -1211,20 +1202,20 @@ def add_dummy_datasets( self, connections=None):
                 dict( ( conn.input_name, conn ) for conn in connections )
         else:
             input_connections_by_name = {}
-        # Any connected input needs to have value DummyDataset (these
+        # Any connected input needs to have value RuntimeValue (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 ):
                 if connections is None or prefixed_name in input_connections_by_name:
                     if input.multiple:
-                        replacement = [] if not connections else [DummyDataset() for conn in connections]
+                        replacement = [] if not connections else [RuntimeValue() for conn in connections]
                     else:
-                        replacement = DummyDataset()
+                        replacement = RuntimeValue()
             elif isinstance( input, DataCollectionToolParameter ):
                 if connections is None or prefixed_name in input_connections_by_name:
-                    replacement = DummyDataset()
+                    replacement = RuntimeValue()
             return replacement
 
         visit_input_values( self.tool.inputs, self.state.inputs, callback )