diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 1bc9eed01cc..57617478c3e 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -199,7 +199,7 @@ class JobQueue( object ):
             try:
                 # Clear the session for each job so we get fresh states for
                 # job and all datasets
-                self.sa_session.clear()
+                self.sa_session.expunge_all()
                 # Get the real job entity corresponding to the wrapper (if we
                 # are tracking in the database this is probably cached in
                 # the session from the origianl query above)
@@ -346,7 +346,7 @@ class JobWrapper( object ):
         Prepare the job to run by creating the working directory and the
         config files.
         """
-        self.sa_session.clear() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner
+        self.sa_session.expunge_all() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner
         if not os.path.exists( self.working_directory ):
             os.mkdir( self.working_directory )
         # Restore parameters from the database
@@ -477,7 +477,7 @@ class JobWrapper( object ):
         the contents of the output files. 
         """
         # default post job setup
-        self.sa_session.clear()
+        self.sa_session.expunge_all()
         job = self.sa_session.query( model.Job ).get( self.job_id )
         # if the job was deleted, don't finish it
         if job.state == job.states.DELETED:
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 1093c39c5f4..6fbebc8161e 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -817,7 +817,7 @@ assign_mapper( context, UserRoleAssociation, UserRoleAssociation.table,
         user=relation( User, backref="roles" ),
         non_private_roles=relation( User, 
                                     backref="non_private_roles",
-                                    primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email & Role.table.c.type == 'private' ) ) ),
+                                    primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email ) ) ),
         role=relation( Role )
     )
 )
@@ -1134,7 +1134,7 @@ def init( file_path, url, engine_options={}, create_tables=False ):
     # Pack everything into a bunch
     result = Bunch( **globals() )
     result.engine = engine
-    result.flush = lambda *args, **kwargs: Session.flush( *args, **kwargs )
+    # model.flush() has been removed.
     result.session = Session
     # For backward compatibility with "model.context.current"
     result.context = Session
diff --git a/lib/galaxy/model/mapping_tests.py b/lib/galaxy/model/mapping_tests.py
index a7a4bc9bd53..c06f3815acc 100644
--- a/lib/galaxy/model/mapping_tests.py
+++ b/lib/galaxy/model/mapping_tests.py
@@ -19,16 +19,17 @@ class MappingTests( unittest.TestCase ):
         d1 = model.HistoryDatasetAssociation( extension="interval", metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True )
         #h2.queries.append( q1 )
         #h2.queries.append( model.Query( "h2->q2" ) )
-        model.context.current.flush()
-        model.context.current.clear()
+        model.session.add_all( ( u, h1, h2, d1 ) )
+        model.session.flush()
+        model.session.expunge_all()
         # Check
-        users = model.context.current.query( model.User ).all()
+        users = model.session.query( model.User ).all()
         assert len( users ) == 1
         assert users[0].email == "james@foo.bar.baz"
         assert users[0].password == "password"
         assert len( users[0].histories ) == 1
         assert users[0].histories[0].name == "History 1"    
-        hists = model.context.current.query( model.History ).all()
+        hists = model.session.query( model.History ).all()
         assert hists[0].name == "History 1"
         assert hists[1].name == ( "H" * 255 )
         assert hists[0].user == users[0]
@@ -38,9 +39,9 @@ class MappingTests( unittest.TestCase ):
         assert hists[1].datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id )
         # Do an update and check
         hists[1].name = "History 2b"
-        model.context.current.flush()
-        model.context.current.clear()
-        hists = model.context.current.query( model.History ).all()
+        model.session.flush()
+        model.session.expunge_all()
+        hists = model.session.query( model.History ).all()
         assert hists[0].name == "History 1"
         assert hists[1].name == "History 2b"
         # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like.
diff --git a/lib/galaxy/model/migrate/versions/0025_user_info.py b/lib/galaxy/model/migrate/versions/0025_user_info.py
index 566c2e6d24d..7ed147c80a5 100644
--- a/lib/galaxy/model/migrate/versions/0025_user_info.py
+++ b/lib/galaxy/model/migrate/versions/0025_user_info.py
@@ -21,7 +21,7 @@ handler.setFormatter( formatter )
 log.addHandler( handler )
 
 metadata = MetaData( migrate_engine )
-db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
 
 def display_migration_details():
     print "========================================"
@@ -59,4 +59,4 @@ def upgrade():
             except Exception, e:
                 log.debug( "Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: %s" % ( str( e ) ) )
 def downgrade():
-    pass
\ No newline at end of file
+    pass
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index a85b4651a20..d8e957ed7db 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -235,7 +235,7 @@ class DefaultToolAction( object ):
                 # Store output 
                 out_data[ name ] = data
                 # Store all changes to database
-                trans.app.model.flush()
+                trans.sa_session.flush()
         # Add all the top-level (non-child) datasets to the history
         for name in out_data.keys():
             if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created
@@ -248,7 +248,7 @@ class DefaultToolAction( object ):
             child_dataset = out_data[ child_name ]
             parent_dataset.children.append( child_dataset )
         # Store data after custom code runs 
-        trans.app.model.flush()
+        trans.sa_session.flush()
         # Create the job object
         job = trans.app.model.Job()
         job.session_id = trans.get_galaxy_session().id
@@ -274,7 +274,8 @@ class DefaultToolAction( object ):
                 job.add_input_dataset( name, None )
         for name, dataset in out_data.iteritems():
             job.add_output_dataset( name, dataset )
-        trans.app.model.flush()
+        trans.sa_session.add( job )
+        trans.sa_session.flush()
         # Some tools are not really executable, but jobs are still created for them ( for record keeping ).
         # Examples include tools that redirect to other applications ( epigraph ).  These special tools must
         # include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job
diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py
index 55203ac8f7e..7cbb6a1705a 100644
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -26,7 +26,8 @@ class SetMetadataToolAction( ToolAction ):
             job.tool_version = tool.version
         except:
             job.tool_version = "1.0.0"
-        job.flush() #ensure job.id is available
+        trans.sa_session.add( job )
+        trans.sa_session.flush() #ensure job.id is available
         
         #add parameters to job_parameter table
         # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)? 
@@ -49,7 +50,7 @@ class SetMetadataToolAction( ToolAction ):
         #Need a special state here to show that metadata is being set and also allow the job to run
         #   i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state
         dataset.state = dataset.states.SETTING_METADATA
-        trans.app.model.flush()
+        trans.sa_session.flush()
         
         # Queue the job for execution
         trans.app.job_queue.put( job.id, tool )
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index b55f125e12a..6db570b1ca9 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -121,6 +121,7 @@ def new_history_upload( trans, uploaded_dataset, state=None ):
     trans.history.add_dataset( hda, genome_build = uploaded_dataset.dbkey )
     permissions = trans.app.security_agent.history_get_default_permissions( trans.history )
     trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions )
+    trans.sa_session.flush()
     return hda
 
 def new_library_upload( trans, uploaded_dataset, library_bunch, state=None ):
@@ -291,7 +292,8 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None ):
         for i, dataset in enumerate( data_list ):
             job.add_output_dataset( 'output%i' % i, dataset )
     job.state = job.states.NEW
-    trans.app.model.flush()
+    trans.sa_session.add( job )
+    trans.sa_session.flush()
 
     # Queue the job for execution
     trans.app.job_queue.put( job.id, tool )
diff --git a/lib/galaxy/web/controllers/async.py b/lib/galaxy/web/controllers/async.py
index 1dcb5677343..3631e1a148a 100644
--- a/lib/galaxy/web/controllers/async.py
+++ b/lib/galaxy/web/controllers/async.py
@@ -77,7 +77,7 @@ class ASync( BaseController ):
                 data.state = data.blurb = jobs.JOB_ERROR
                 data.info  = "Error -> %s" % STATUS
             
-            trans.model.flush()
+            trans.sa_session.flush()
             
             return "Data %s with status %s received. OK" % (data_id, STATUS)
    
@@ -112,7 +112,7 @@ class ASync( BaseController ):
             data.flush()
             open( data.file_name, 'wb' ).close() #create the file
             trans.history.add_dataset( data, genome_build=GALAXY_BUILD )
-            trans.model.flush()
+            trans.sa_session.flush()
             trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id )
 
             try:
@@ -132,6 +132,6 @@ class ASync( BaseController ):
                 data.info  = str(e)
                 data.state = data.blurb = data.states.ERROR
             
-            trans.model.flush()
+            trans.sa_session.flush()
 
         return trans.fill_template('tool_executed.tmpl', out_data={}, tool=tool, config=self.app.config )
diff --git a/lib/galaxy/web/controllers/dataset.py b/lib/galaxy/web/controllers/dataset.py
index d2e1325aeea..95afcc3119b 100644
--- a/lib/galaxy/web/controllers/dataset.py
+++ b/lib/galaxy/web/controllers/dataset.py
@@ -335,7 +335,7 @@ class DatasetInterface( BaseController ):
             assert topmost_parent in history.datasets, "Data does not belong to current history"
             # Mark undeleted
             data.mark_undeleted()
-            self.app.model.flush()
+            trans.sa_session.flush()
             trans.log_event( "Dataset id %s has been undeleted" % str(id) )
             return True
         return False
@@ -407,7 +407,7 @@ class DatasetInterface( BaseController ):
                             hist.add_dataset( data.copy( copy_children = True ) )
                 if history in target_histories:
                     refresh_frames = ['history']
-                trans.app.model.flush()
+                trans.sa_session.flush()
                 done_msg = "%i datasets copied to %i histories." % ( len( source_dataset_ids ) - invalid_datasets, len( target_histories ) )
                 trans.sa_session.refresh( history )
         elif create_new_history:
diff --git a/lib/galaxy/web/controllers/library.py b/lib/galaxy/web/controllers/library.py
index 7a374d7a814..384e3718ec5 100644
--- a/lib/galaxy/web/controllers/library.py
+++ b/lib/galaxy/web/controllers/library.py
@@ -421,7 +421,7 @@ class Library( BaseController ):
             if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
                 if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
                     trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
-                    trans.app.model.flush()
+                    trans.sa_session.flush()
                     msg = "Data type changed for library dataset '%s'" % ldda.name
                     messagetype = 'done'
                 else:
@@ -463,7 +463,7 @@ class Library( BaseController ):
                             setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) )
                     ldda.metadata.dbkey = dbkey
                     ldda.datatype.after_edit( ldda )
-                    trans.app.model.flush()
+                    trans.sa_session.flush()
                     msg = 'Attributes updated for library dataset %s' % ldda.name
                     messagetype = 'done'
             else:
@@ -486,7 +486,7 @@ class Library( BaseController ):
                             setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) )
                 ldda.datatype.set_meta( ldda )
                 ldda.datatype.after_edit( ldda )
-                trans.app.model.flush()
+                trans.sa_session.flush()
                 msg = 'Attributes updated for library dataset %s' % ldda.name
                 messagetype = 'done'
             else:
diff --git a/lib/galaxy/web/controllers/library_admin.py b/lib/galaxy/web/controllers/library_admin.py
index 89f359c1798..0f424ff6f7b 100644
--- a/lib/galaxy/web/controllers/library_admin.py
+++ b/lib/galaxy/web/controllers/library_admin.py
@@ -432,7 +432,7 @@ class LibraryAdmin( BaseController ):
             # The user clicked the Save button on the 'Change data type' form
             if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
                 trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
-                trans.app.model.flush()
+                trans.sa_session.flush()
                 msg = "Data type changed for library dataset '%s'" % ldda.name
                 return trans.fill_template( "/admin/library/ldda_edit_info.mako", 
                                             ldda=ldda,
@@ -469,7 +469,7 @@ class LibraryAdmin( BaseController ):
                         setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) )
                 ldda.metadata.dbkey = dbkey
                 ldda.datatype.after_edit( ldda )
-                trans.app.model.flush()
+                trans.sa_session.flush()
                 msg = 'Attributes updated for library dataset %s' % ldda.name
                 messagetype = 'done'
             return trans.fill_template( "/admin/library/ldda_edit_info.mako", 
@@ -488,7 +488,7 @@ class LibraryAdmin( BaseController ):
                         setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) )
             ldda.datatype.set_meta( ldda )
             ldda.datatype.after_edit( ldda )
-            trans.app.model.flush()
+            trans.sa_session.flush()
             msg = 'Attributes updated for library dataset %s' % ldda.name
             return trans.fill_template( "/admin/library/ldda_edit_info.mako", 
                                         ldda=ldda,
@@ -674,6 +674,10 @@ class LibraryAdmin( BaseController ):
         replace_id = params.get( 'replace_id', None )
         if replace_id not in [ None, 'None' ]:
             replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( int( replace_id ) )
+            # The name is separately - by the time the new ldda is created,
+            # replace_dataset.name will point to the new ldda, not the one it's
+            # replacing.
+            replace_dataset_name = replace_dataset.name
             if not last_used_build:
                 last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
             # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
@@ -701,7 +705,7 @@ class LibraryAdmin( BaseController ):
             if created_outputs:
                 total_added = len( created_outputs.values() )
                 if replace_dataset:
-                    msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name )
+                    msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name )
                 else:
                     if not folder.parent:
                         # Libraries have the same name as their root_folder
diff --git a/lib/galaxy/web/controllers/requests.py b/lib/galaxy/web/controllers/requests.py
index 2b19d23d21d..e01d9e76c57 100644
--- a/lib/galaxy/web/controllers/requests.py
+++ b/lib/galaxy/web/controllers/requests.py
@@ -294,7 +294,7 @@ class Requests( BaseController ):
             # save all the new/unsaved samples entered by the user
             if edit_mode == 'False':
                 for index in range(len(current_samples)-len(request.samples)):
-                    sample_index = index + len(request.samples)
+                    sample_index = len(request.samples)
                     sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
                     sample_values = []
                     for field_index in range(len(request.type.sample_form.fields)):
diff --git a/lib/galaxy/web/controllers/root.py b/lib/galaxy/web/controllers/root.py
index 3cd8b1c0948..ce1c434fcb9 100644
--- a/lib/galaxy/web/controllers/root.py
+++ b/lib/galaxy/web/controllers/root.py
@@ -277,7 +277,7 @@ class RootController( BaseController ):
                     if not __ok_to_edit_metadata( data.id ):
                         return trans.show_error_message( "This dataset is currently being used as input or output.  You cannot change datatype until the jobs have completed or you have canceled them." )
                     trans.app.datatypes_registry.change_datatype( data, params.datatype )
-                    trans.app.model.flush()
+                    trans.sa_session.flush()
                 else:
                     return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) )
             elif params.save:
@@ -303,7 +303,7 @@ class RootController( BaseController ):
                     data.datatype.after_edit( data )
                 else:
                     msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)'
-                trans.app.model.flush()
+                trans.sa_session.flush()
                 return trans.show_ok_message( "Attributes updated%s" % msg, refresh_frames=['history'] )
             elif params.detect:
                 # The user clicked the Auto-detect button on the 'Edit Attributes' form
@@ -322,7 +322,7 @@ class RootController( BaseController ):
                     msg = 'Attributes updated'
                     data.set_meta()
                     data.datatype.after_edit( data )
-                trans.app.model.flush()
+                trans.sa_session.flush()
                 return trans.show_ok_message( msg, refresh_frames=['history'] )
             elif params.convert_data:
                 target_type = kwd.get("target_type", None)
@@ -383,7 +383,7 @@ class RootController( BaseController ):
                     if job.check_if_output_datasets_deleted():
                         job.mark_deleted()                
                         self.app.job_manager.job_stop_queue.put( job.id )
-            self.app.model.flush()
+            trans.sa_session.flush()
 
     @web.expose
     def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd):
@@ -432,7 +432,7 @@ class RootController( BaseController ):
         for dataset in history.datasets:
             dataset.deleted = True
             dataset.clear_associated_files()
-        self.app.model.flush()
+        trans.sa_session.flush()
         trans.log_event( "History id %s cleared" % (str(history.id)) )
         trans.response.send_redirect( url_for("/index" ) )
     @web.expose
diff --git a/lib/galaxy/web/controllers/tool_runner.py b/lib/galaxy/web/controllers/tool_runner.py
index 38b7a1654f8..03db15b879a 100644
--- a/lib/galaxy/web/controllers/tool_runner.py
+++ b/lib/galaxy/web/controllers/tool_runner.py
@@ -198,8 +198,6 @@ class ToolRunner( BaseController ):
                                 # pasted data
                                 datasets.append( create_dataset( 'Pasted Entry' ) )
                                 break
-        if datasets:
-            trans.model.flush()
         return [ d.id for d in datasets ]
 
     @web.expose
diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py
index d8745428075..b2320248b02 100644
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -139,7 +139,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         self.__galaxy_session = NOT_SET
         base.DefaultWebTransaction.__init__( self, environ )
         self.setup_i18n()
-        self.sa_session.clear()
+        self.sa_session.expunge_all()
         self.debug = asbool( self.app.config.get( 'debug', False ) )
         # Flag indicating whether we are in workflow building mode (means
         # that the current history should not be used for parameter values
@@ -302,12 +302,12 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
             self.galaxy_session = galaxy_session
         # Do we need to flush the session?
         if galaxy_session_requires_flush:
-            objects_to_flush = [ galaxy_session ]
+            sa_session.add( galaxy_session )
             # FIXME: If prev_session is a proper relation this would not
             #        be needed.
             if prev_galaxy_session:
-                objects_to_flush.append( prev_galaxy_session )            
-            sa_session.flush( objects_to_flush )
+                sa_session.add( prev_galaxy_session )            
+            sa_session.flush()
         # If the old session was invalid, get a new history with our new session
         if invalidate_existing_session:
             self.new_history()
@@ -427,7 +427,8 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         if not last_accessed:
             # Only set default history permissions if current history is not from a previous session
             self.app.security_agent.history_set_default_permissions( history, dataset=True, bypass_manage_permission=True )
-        self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session, history ] )
+        self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session, history ) )
+        self.sa_session.flush()
         # This method is not called from the Galaxy reports, so the cookie will always be galaxysession
         self.__update_session_cookie( name='galaxysession' )
     def handle_user_logout( self ):
@@ -439,7 +440,8 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         prev_galaxy_session = self.galaxy_session
         prev_galaxy_session.is_valid = False
         self.galaxy_session = self.__create_new_session( prev_galaxy_session )
-        self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] )
+        self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session ) )
+        self.sa_session.flush()
         # This method is not called from the Galaxy reports, so the cookie will always be galaxysession
         self.__update_session_cookie( name='galaxysession' )
         
@@ -466,7 +468,8 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
     def set_history( self, history ):
         if history and not history.deleted:
             self.galaxy_session.current_history = history
-        self.sa_session.flush( [ self.galaxy_session ] )
+        self.sa_session.add( self.galaxy_session )
+        self.sa_session.flush()
     history = property( get_history, set_history )
     def new_history( self, name=None ):
         """
@@ -489,7 +492,8 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         # Set the user's default history permissions
         self.app.security_agent.history_set_default_permissions( history )
         # Save
-        self.sa_session.flush( [ self.galaxy_session, history ] )
+        self.sa_session.add_all( ( self.galaxy_session, history ) )
+        self.sa_session.flush()
         return history
 
     def get_user( self ):
@@ -498,7 +502,8 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
     def set_user( self, user ):
         """Set the current user."""
         self.galaxy_session.user = user
-        self.sa_session.flush( [ self.galaxy_session ] )
+        self.sa_session.add( self.galaxy_session )
+        self.sa_session.flush()
     user = property( get_user, set_user )
 
     def get_user_and_roles( self ):
diff --git a/test/functional/test_forms_and_requests.py b/test/functional/test_forms_and_requests.py
index 827f59cb528..76d13884671 100644
--- a/test/functional/test_forms_and_requests.py
+++ b/test/functional/test_forms_and_requests.py
@@ -29,6 +29,7 @@ def get_latest_form(form_name):
                          .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \
                          .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() )
     for fdc in fdc_list:
+        sa_session.refresh( fdc.latest_form )
         if form_name == fdc.latest_form.name:
             return fdc.latest_form
     return None
diff --git a/test/functional/test_security_and_libraries.py b/test/functional/test_security_and_libraries.py
index d3a75a6aa08..745a942fe28 100644
--- a/test/functional/test_security_and_libraries.py
+++ b/test/functional/test_security_and_libraries.py
@@ -156,7 +156,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
                 raise AssertionError( '%s not in history id %d default_permissions after they were changed' % ( value.action, latest_history.id ) )
         # Add a dataset to the history
         self.upload_file( '1.bed' )
-        latest_dataset = galaxy.model.Dataset.query().order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first()
+        latest_dataset = sa_session.query( galaxy.model.Dataset ).order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first()
         # Make sure DatasetPermissionss are correct
         if len( latest_dataset.actions ) != len( latest_history.default_permissions ):
             raise AssertionError( '%d DatasetPermissionss were created for dataset id %d when it was created ( should have been %d )' % \
diff --git a/test/functional/test_user_info.py b/test/functional/test_user_info.py
index 915a3aef014..e57f129fe69 100644
--- a/test/functional/test_user_info.py
+++ b/test/functional/test_user_info.py
@@ -14,6 +14,7 @@ def get_latest_form(form_name):
                          .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \
                          .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() )
     for fdc in fdc_list:
+        sa_session.refresh( fdc.latest_form )
         if form_name == fdc.latest_form.name:
             return fdc.latest_form
     return None
@@ -146,4 +147,4 @@ class TestUserInfo( TwillTestCase ):
         self.visit_page('forms/manage?show_filter=Deleted')
         self.check_page_for_string(form_one_latest.name)
         self.logout()
-        
\ No newline at end of file
+        
diff --git a/tools/data_source/microbial_import_code.py b/tools/data_source/microbial_import_code.py
index 08c74f0e6d8..5c927691e01 100644
--- a/tools/data_source/microbial_import_code.py
+++ b/tools/data_source/microbial_import_code.py
@@ -123,7 +123,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             data = app.datatypes_registry.change_datatype( data, file_type )
             data.init_meta()
             data.set_peek()
-            app.model.flush()
+            data.flush()
         elif fields[0] == "#NewFile":
             description = fields[1]
             chr = fields[2]
@@ -137,7 +137,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             newdata.flush()
             app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset )
             history.add_dataset( newdata )
-            app.model.flush()
+            history.flush()
             try:
                 copyfile(filepath,newdata.file_name)
                 newdata.info = newdata.name
@@ -148,4 +148,4 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             newdata.dbkey = dbkey
             newdata.init_meta()
             newdata.set_peek()
-            app.model.flush()
+            newdata.flush()
diff --git a/tools/filters/lav_to_bed_code.py b/tools/filters/lav_to_bed_code.py
index e90ab05faa1..19a8f8b6b82 100644
--- a/tools/filters/lav_to_bed_code.py
+++ b/tools/filters/lav_to_bed_code.py
@@ -16,4 +16,3 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             data.flush()
         except:
             continue
-    app.model.flush()
\ No newline at end of file
diff --git a/tools/maf/maf_to_bed_code.py b/tools/maf/maf_to_bed_code.py
index be2c5521aba..b83aef8b2a6 100644
--- a/tools/maf/maf_to_bed_code.py
+++ b/tools/maf/maf_to_bed_code.py
@@ -21,7 +21,6 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             output_data.dbkey = dbkey
             output_data.name = basic_name + " (" + dbkey + ")"
             output_data.flush()
-            app.model.flush()
             output_data_list.append(output_data)
         elif line.startswith("#FILE"):
             fields = line.split("\t")
@@ -36,7 +35,6 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset )
             newdata.flush()
             history.flush()
-            app.model.flush()
             try:
                 move(filepath,newdata.file_name)
                 newdata.info = newdata.name
@@ -47,7 +45,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             newdata.dbkey = dbkey
             newdata.init_meta()
             newdata.set_peek()
-            app.model.flush()
+            newdata.flush()
             output_data_list.append(newdata)
         else:
             new_stdout = new_stdout + line