Inject data module values in connected steps on initialization

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

@@ -56,7 +56,9 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                     errors                  : step.messages,
                     initial_errors          : true,
                     cls                     : 'ui-portlet-narrow',
-                    hide_operations         : true
+                    hide_operations         : true,
+                    needs_refresh           : false,
+                    always_refresh          : step.step_type != 'tool'
                 }, step );
                 self.steps[ i ] = step;
                 self.links[ i ] = [];
@@ -205,9 +207,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
             if ( !_.isEmpty( this.wp_inputs ) ) {
                 this.wp_form = new Form({ title: '<b>Workflow Parameters</b>', inputs: this.wp_inputs, cls: 'ui-portlet-narrow', onchange: function() {
                         _.each( self.wp_form.input_list, function( input_def, i ) {
-                            _.each( input_def.links, function( step ) {
-                                self._refreshStep( step );
-                            });
+                            _.each( input_def.links, function( step ) { self._refreshStep( step ) } );
                         });
                     }
                 });
@@ -276,7 +276,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                     self._append( self.$steps, form.$el );
                 }
                 self.forms[ i ] = form;
-                self._refreshStep( step );
+                step.needs_refresh && self._refreshStep( step );
                 self._resolve( form.deferred, promise );
                 self.execute_btn.model.set( 'percentage', ( i + 1 ) * 100.0 / self.steps.length );
                 Galaxy.emit.debug( 'tool-form-composite::initialize()', i + ' : Workflow step state ready.', step );
@@ -327,6 +327,8 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                     }
                 });
                 form.trigger( 'change' );
+            } else {
+                step.needs_refresh = true;
             }
         },
 

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -1135,7 +1135,7 @@ def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ):
                 trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
                 for step in workflow.steps:
                     try:
-                        module_injector.inject( step )
+                        module_injector.inject( step, steps=workflow.steps )
                     except MissingToolException:
                         if step.tool_id not in missing_tools:
                             missing_tools.append(step.tool_id)

lib/galaxy/workflow/modules.py

@@ -132,7 +132,7 @@ def check_and_update_state( self ):
         """
         pass
 
-    def add_dummy_datasets( self, connections=None):
+    def add_dummy_datasets( self, connections=None, steps=None ):
         # Replaced connected inputs with DummyDataset values.
         pass
 
@@ -417,7 +417,7 @@ def check_and_update_state( self ):
         """
         return None
 
-    def add_dummy_datasets( self, connections=None):
+    def add_dummy_datasets( self, connections=None, steps=None ):
         # Replaced connected inputs with DummyDataset values.
         return None
 
@@ -1139,22 +1139,30 @@ def _handle_post_job_actions( self, step, job, replacement_dict ):
         if flush_required:
             self.trans.sa_session.flush()
 
-    def add_dummy_datasets( self, connections=None):
+    def add_dummy_datasets( self, connections=None, steps=None ):
         if connections:
             # Store onnections by input name
-            input_connections_by_name = \
-                dict( ( conn.input_name, conn ) for conn in connections )
+            input_connections_by_name = dict( ( conn.input_name, conn ) for conn in connections )
         else:
             input_connections_by_name = {}
 
         # Any connected input needs to have value RuntimeValue (these
         # are not persisted so we need to do it every time)
         def callback( input, prefixed_name, context, **kwargs ):
             if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ):
-                if connections is None or prefixed_name in input_connections_by_name:
+                if self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY:
+                    if connections is None or prefixed_name in input_connections_by_name:
+                        if steps:
+                            connection = input_connections_by_name[ prefixed_name ]
+                            output_step = next( output_step for output_step in steps if connection.output_step_id == output_step.id )
+                            if output_step.type.startswith( 'data' ):
+                                output_inputs = output_step.module.get_runtime_inputs()
+                                return output_inputs[ 'input' ].get_initial_value( self.trans, context )
+                        return RuntimeValue()
+                    else:
+                        return input.get_initial_value( self.trans, context )
+                elif connections is None or prefixed_name in input_connections_by_name:
                     return RuntimeValue()
-                elif self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY:
-                    return input.get_initial_value( self.trans, context )
 
         visit_input_values( self.tool.inputs, self.state.inputs, callback )
 
@@ -1289,7 +1297,7 @@ def __init__( self, trans, allow_tool_state_corrections=False ):
         self.trans = trans
         self.allow_tool_state_corrections = allow_tool_state_corrections
 
-    def inject( self, step, step_args=None ):
+    def inject( self, step, step_args=None, steps=None ):
         """ Pre-condition: `step` is an ORM object coming from the database, if
         supplied `step_args` is the representation of the inputs for that step
         supplied via web form.
@@ -1319,7 +1327,7 @@ def inject( self, step, step_args=None ):
 
         # Any connected input needs to have value DummyDataset (these
         # are not persisted so we need to do it every time)
-        module.add_dummy_datasets( connections=step.input_connections )
+        module.add_dummy_datasets( connections=step.input_connections, steps=steps )
         state, step_errors = module.compute_runtime_state( self.trans, step_args )
         step.state = state
         if step.type == "subworkflow":