Merge pull request #2632 from guerler/fix_workflow_data_on_load

Properly initialize datasets when workflow is loaded for execution

lib/galaxy/tools/parameters/basic.py

@@ -1838,7 +1838,7 @@ class DataToolParameter( BaseDataToolParameter ):
               happens twice (here and when generating HTML).
         """
         # Can't look at history in workflow mode. Tool shed has no histories.
-        if trans.workflow_building_mode or trans.app.name == 'tool_shed':
+        if trans.workflow_building_mode is workflow_building_modes.ENABLED or trans.app.name == 'tool_shed':
             return RuntimeValue()
         history = self._get_history( trans )
         dataset_matcher = DatasetMatcher( trans, self, None, other_values )

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

@@ -32,6 +32,7 @@ from galaxy.workflow.modules import WorkflowModuleInjector
 from galaxy.workflow.render import WorkflowCanvas
 from galaxy.workflow.run import invoke
 from galaxy.workflow.run import WorkflowRunConfig
+from galaxy.tools.parameters.basic import workflow_building_modes
 
 log = logging.getLogger( __name__ )
 
@@ -1130,6 +1131,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
             else:
                 # Prepare each step
                 missing_tools = []
+                trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
                 for step in workflow.steps:
                     try:
                         module_injector.inject( step )

lib/galaxy/workflow/modules.py

@@ -16,6 +16,7 @@ from galaxy.tools.parameters.basic import (
     DataCollectionToolParameter,
     DataToolParameter,
     RuntimeValue,
+    workflow_building_modes
 )
 from galaxy.tools.parameters.wrapped import make_dict_copy
 from galaxy.tools import DefaultToolState
@@ -1148,10 +1149,12 @@ class ToolModule( WorkflowModule ):
 
         # 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, **kwargs ):
+        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:
                     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 )