Rebase into sub workflows.

lib/galaxy/managers/workflows.py

@@ -249,8 +249,16 @@ def update_workflow_from_dict(self, trans, stored_workflow, workflow_data, from_
             steps.append( step )
             steps_by_external_id[ step_dict['id' ] ] = step
             if 'workflow_outputs' in step_dict:
-                for output_name in step_dict['workflow_outputs']:
+                workflow_outputs = step_dict['workflow_outputs']
+                for output_name in workflow_outputs:
                     m = model.WorkflowOutput(workflow_step=step, output_name=output_name)
+                    if isinstance(workflow_outputs, dict):
+                        uuid = workflow_outputs.get("uuid", None)
+                        label = workflow_outputs.get("label", None)
+                        if uuid is not None:
+                            m.uuid = uuid
+                        if label is not None:
+                            m.label = label
                     trans.sa_session.add(m)
             if step.tool_errors:
                 # DBTODO Check for conditional inputs here.
@@ -628,6 +636,9 @@ def __walk_step_dicts( self, data ):
         discovered_labels = set()
         discovered_uuids = set()
 
+        discovered_output_labels = set()
+        discovered_output_uuids = set()
+
         # First pass to build step objects and populate basic values
         for step_index in step_indices:
             step_dict = supplied_steps[ step_index ]
@@ -642,6 +653,25 @@ def __walk_step_dicts( self, data ):
                     raise exceptions.DuplicatedIdentifierException("Duplicated step label in request.")
                 discovered_labels.add(label)
 
+            if 'workflow_outputs' in step_dict:
+                outputs = step_dict['workflow_outputs']
+                # outputs may be list of name (deprecated legacy behavior)
+                # or dictionary of names to {uuid: <uuid>, label: <label>}
+                if isinstance(outputs, dict):
+                    for output_name in outputs:
+                        output_dict = outputs[output_name]
+                        output_label = output_dict.get("label", None)
+                        if output_label:
+                            if label in discovered_output_labels:
+                                raise exceptions.DuplicatedIdentifierException("Duplicated workflow output label in request.")
+                            discovered_output_labels.add(label)
+
+                        output_uuid = step_dict.get("output_uuid", None)
+                        if output_uuid:
+                            if output_uuid in discovered_output_uuids:
+                                raise exceptions.DuplicatedIdentifierException("Duplicate workflow output UUID in request.")
+                            discovered_output_uuids.add(uuid)
+
             yield step_dict
 
     def __module_from_dict( self, trans, step_dict, secure ):

lib/galaxy/model/__init__.py

@@ -3538,9 +3538,13 @@ def non_data_connection(self):
 
 class WorkflowOutput(object):
 
-    def __init__( self, workflow_step, output_name):
+    def __init__( self, workflow_step, output_name, uuid=None):
         self.workflow_step = workflow_step
         self.output_name = output_name
+        if uuid is None:
+            self.uuid = uuid4()
+        else:
+            self.uuid = UUID(str(uuid))
 
 
 class StoredWorkflowUserShareAssociation( object ):

lib/galaxy/model/mapping.py

@@ -872,7 +872,10 @@
     "workflow_output", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False ),
-    Column( "output_name", String(255), nullable=True ) )
+    Column( "output_name", String(255), nullable=True ),
+    Column( "label", Unicode(255) ),
+    Column( "uuid", UUIDType ),
+)
 
 model.WorkflowInvocation.table = Table(
     "workflow_invocation", metadata,

lib/galaxy/model/migrate/versions/0132_subworkflows.py

@@ -6,6 +6,8 @@
 
 from sqlalchemy import Column, Integer, ForeignKey, MetaData, Table
 
+from galaxy.model.custom_types import TrimmedString, UUIDType
+
 now = datetime.datetime.utcnow
 log = logging.getLogger( __name__ )
 metadata = MetaData()
@@ -22,6 +24,13 @@ def upgrade(migrate_engine):
     parent_workflow_id_column = Column( "parent_workflow_id", Integer, ForeignKey("workflow.id"), nullable=True )
     __add_column( parent_workflow_id_column, "workflow", metadata )
 
+    workflow_output_label_column = Column( "label", TrimmedString(255) )
+    workflow_output_uuid_column = Column( "uuid", UUIDType, nullable=True )
+    __add_column( workflow_output_label_column, "workflow_output", metadata )
+    __add_column( workflow_output_uuid_column, "workflow_output", metadata )
+
+    # Make stored_workflow_id nullable, since now workflows can belong to either
+    # a stored workflow or a parent workflow.
     __alter_column("workflow", "stored_workflow_id", metadata, nullable=True)
 
 
@@ -32,6 +41,9 @@ def downgrade(migrate_engine):
     __drop_column( "subworkflow_id", "workflow_step", metadata )
     __drop_column( "parent_workflow_id", "workflow_step", metadata )
 
+    __drop_column( "label", "workflow_output", metadata )
+    __drop_column( "uuid", "workflow_output", metadata )
+
     __alter_column("workflow", "stored_workflow_id", metadata, nullable=False)