Fix for the creation of workflows from shared histories.

Added a column 'copied_from_history_dataset_association' to history_dataset_association. This requires a db change.

lib/galaxy/model/__init__.py

@@ -104,7 +104,7 @@ class JobToOutputDatasetAssociation( object ):
 class HistoryDatasetAssociation( object ):
     def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, 
                   dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None,
-                  parent_id=None, validation_errors=None, visible=True, create_dataset = False ):
+                  parent_id=None, copied_from_history_dataset_association = None, validation_errors=None, visible=True, create_dataset = False ):
         self.name = name or "Unnamed dataset"
         self.id = id
         self.hid = hid
@@ -125,6 +125,7 @@ class HistoryDatasetAssociation( object ):
         self.dataset = dataset
         self.parent_id = parent_id
         self.validation_errors = validation_errors
+        self.copied_from_history_dataset_association = copied_from_history_dataset_association
     
     @property
     def ext( self ):
@@ -252,7 +253,7 @@ class HistoryDatasetAssociation( object ):
         return self.datatype.get_converter_types( self, datatypes_registry)
     
     def copy( self, copy_children = False, parent_id = None ):
-        des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id )
+        des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self )
         des.flush()
         if copy_children:
             for child in self.children:

lib/galaxy/model/mapping.py

@@ -72,6 +72,7 @@ HistoryDatasetAssociation.table = Table( "history_dataset_association", metadata
     Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ),
     Column( "hid", Integer ),
     Column( "name", TrimmedString( 255 ) ),
     Column( "info", TrimmedString( 255 ) ),
@@ -250,13 +251,17 @@ assign_mapper( context, HistoryDatasetAssociation, HistoryDatasetAssociation.tab
         history=relation( 
             History, 
             primaryjoin=( History.table.c.id == HistoryDatasetAssociation.table.c.history_id ) ),
+        copied_to_history_dataset_associations=relation( 
+            HistoryDatasetAssociation, 
+            primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ),
+            backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id] ) ),
         implicitly_converted_datasets=relation( 
             ImplicitlyConvertedDatasetAssociation, 
             primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ),
         children=relation( 
             HistoryDatasetAssociation, 
             primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ),
-            backref=backref( "parent", remote_side=[HistoryDatasetAssociation.table.c.id] ) )
+            backref=backref( "parent", primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id] ) )
             ) )
 
 assign_mapper( context, Dataset, Dataset.table,

lib/galaxy/web/controllers/workflow.py

@@ -676,9 +676,16 @@ def get_job_dict( trans ):
         if dataset.state in ( 'new', 'running', 'queued' ):
             warnings.add( "Some datasets still queued or running were ignored" )
             continue
-        if not dataset.creating_job_associations:
-            jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]        
-        for assoc in dataset.creating_job_associations:
+        
+        #if this hda was copied from another, we need to find the job that created the origial hda
+        job_hda = dataset
+        while job_hda.copied_from_history_dataset_association:
+            job_hda = job_hda.copied_from_history_dataset_association
+        
+        if not job_hda.creating_job_associations:
+            jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
+        
+        for assoc in job_hda.creating_job_associations:
             job = assoc.job
             if job in jobs:
                 jobs[ job ].append( ( assoc.name, dataset ) )