diff --git a/eggs.ini b/eggs.ini
index a462166cf65..8aac2d67857 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -28,6 +28,7 @@ PSI = 0.3b1.1
 [eggs:noplatform]
 amqplib = 0.6.1
 Beaker = 1.4
+decorator = 3.1.2
 docutils = 0.4
 elementtree = 1.2.6_20050316
 lrucache = 0.2
@@ -41,8 +42,8 @@ PasteDeploy = 1.3.1
 PasteScript = 1.3.6
 Routes = 1.6.3
 simplejson = 1.5
-SQLAlchemy = 0.4.7p1
-sqlalchemy_migrate = 0.4.5
+SQLAlchemy = 0.5.6
+sqlalchemy_migrate = 0.5.4
 Tempita = 0.1
 twill = 0.9
 WebError = 0.8a
@@ -77,6 +78,7 @@ threadframe = http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz
 guppy = http://pypi.python.org/packages/source/g/guppy/guppy-0.1.8.tar.gz
 amqplib = http://py-amqplib.googlecode.com/files/amqplib-0.6.1.tgz
 Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-1.4.tar.gz
+decorator = http://pypi.python.org/packages/source/d/decorator/decorator-3.1.2.tar.gz
 docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz
 elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz
 lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz
@@ -90,8 +92,8 @@ PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteSc
 PSI = http://pypi.python.org/packages/source/P/PSI/PSI-0.3b1.1.tar.gz
 Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz
 simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.tar.gz
-SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.4.7p1.tar.gz
-sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migrate-0.4.5.tar.gz
+SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.5.6.tar.gz
+sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migrate-0.5.4.tar.gz
 Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz
 twill = http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz
 WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index e9dbf4f3e11..1093c39c5f4 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -18,7 +18,7 @@ from sqlalchemy.orm.collections import attribute_mapped_collection
 from sqlalchemy.ext.associationproxy import association_proxy
 
 metadata = MetaData()
-context = Session = scoped_session( sessionmaker( autoflush=False, transactional=False ) )
+context = Session = scoped_session( sessionmaker( autoflush=False, autocommit=True ) )
 
 # For backward compatibility with "context.current"
 context.current = Session
diff --git a/lib/galaxy/model/migrate/check.py b/lib/galaxy/model/migrate/check.py
index a240e2d69b5..3ca81a319a9 100644
--- a/lib/galaxy/model/migrate/check.py
+++ b/lib/galaxy/model/migrate/check.py
@@ -7,7 +7,7 @@ pkg_resources.require( "sqlalchemy-migrate" )
 
 from migrate.versioning import repository, schema
 from sqlalchemy import *
-from sqlalchemy.exceptions import NoSuchTableError
+from sqlalchemy.exc import NoSuchTableError
 
 log = logging.getLogger( __name__ )
 
diff --git a/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py b/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
index b33b7038529..2146f37404d 100644
--- a/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
+++ b/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
@@ -1,6 +1,6 @@
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 
@@ -20,7 +20,7 @@ log.addHandler( handler )
 from galaxy.model.custom_types import *
 
 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 ) )
 
 if migrate_engine.name == 'postgres':
     # http://blog.pythonisito.com/2008/01/cascading-drop-table-with-sqlalchemy.html
diff --git a/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
index 6efa10af143..fd5c290134a 100644
--- a/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
+++ b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
@@ -12,7 +12,7 @@ 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 ) )
 User_table = Table( "galaxy_user", metadata, autoload=True )
 HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True )
 
diff --git a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
index ac12d06411e..f05a3c85098 100644
--- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
+++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
@@ -23,7 +23,7 @@ from galaxy.util.bunch import Bunch
 
 
 metadata = MetaData( migrate_engine )
-context = scoped_session( sessionmaker( autoflush=False, transactional=False ) )
+context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) )
 
 
 ## classes
@@ -662,7 +662,7 @@ def upgrade():
     log.debug( "Fixing a discrepancy concerning deleted shared history items." )
     affected_items = 0
     start_time = time.time()
-    for dataset in context.query( Dataset ).filter( and_( Dataset.c.deleted == True, Dataset.c.purged == False ) ):
+    for dataset in context.query( Dataset ).filter( and_( Dataset.deleted == True, Dataset.purged == False ) ):
         for dataset_instance in dataset.history_associations + dataset.library_associations:
             if not dataset_instance.deleted:
                 dataset.deleted = False
diff --git a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
index bfeddbff592..ef327b6b34b 100644
--- a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
+++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
@@ -16,7 +16,7 @@ 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 "========================================"
diff --git a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
index e1f79051a9a..fd62c795448 100644
--- a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
+++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
@@ -11,7 +11,7 @@ This migration script adds the following new tables for supporting Galaxy forms:
 """
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 
@@ -31,7 +31,7 @@ log.addHandler( handler )
 from galaxy.model.custom_types import *
 
 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 "========================================"
diff --git a/lib/galaxy/model/migrate/versions/0009_request_table.py b/lib/galaxy/model/migrate/versions/0009_request_table.py
index 218aa824e22..793ae12e638 100644
--- a/lib/galaxy/model/migrate/versions/0009_request_table.py
+++ b/lib/galaxy/model/migrate/versions/0009_request_table.py
@@ -9,7 +9,7 @@ from migrate import *
 from migrate.changeset import *
 import sys, logging
 from galaxy.model.custom_types import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 
 log = logging.getLogger( __name__ )
 log.setLevel(logging.DEBUG)
diff --git a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
index 12926283578..7a0efa7ba8f 100644
--- a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
+++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
@@ -10,7 +10,7 @@ is too long
 """
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 
@@ -30,7 +30,7 @@ log.addHandler( handler )
 from galaxy.model.custom_types import *
 
 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 "========================================"
diff --git a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
index f3907a371e9..8f96aa8eef1 100644
--- a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
+++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
@@ -5,7 +5,7 @@ manually created.
 """
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 
@@ -25,7 +25,7 @@ log.addHandler( handler )
 from galaxy.model.custom_types import *
 
 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 "========================================"
diff --git a/lib/galaxy/model/migrate/versions/0012_user_address.py b/lib/galaxy/model/migrate/versions/0012_user_address.py
index 8f541a57eaa..9c8f7cddea3 100644
--- a/lib/galaxy/model/migrate/versions/0012_user_address.py
+++ b/lib/galaxy/model/migrate/versions/0012_user_address.py
@@ -6,7 +6,7 @@ which is a string, allowing for more flexibility with request states.
 """
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 import datetime
@@ -24,7 +24,7 @@ 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 "========================================"
diff --git a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
index 98a73e55141..55db4aa0d23 100644
--- a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
+++ b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
@@ -17,7 +17,7 @@ with a shortened name.
 """
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 import sys, logging
diff --git a/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py b/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
index 159b36a7a6d..6d0e2104c89 100644
--- a/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
+++ b/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
@@ -16,7 +16,7 @@ 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 ) )
 LibraryFolder_table = Table( "library_folder", metadata, autoload=True )
 LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True )
 LibraryDataset_table = Table( "library_dataset", metadata, autoload=True )
diff --git a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
index 6260845934d..1df905318dc 100644
--- a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
+++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
@@ -5,7 +5,7 @@ This migration script provides support for (a) ordering tags by recency and
 
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 import migrate.changeset
 
diff --git a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py
index 5f438b2afba..e2772c00953 100644
--- a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py
+++ b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py
@@ -1,6 +1,6 @@
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 import datetime
@@ -18,7 +18,7 @@ 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 "========================================"
diff --git a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py
index 461fd7610e1..dd2395f2d4d 100644
--- a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py
+++ b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py
@@ -1,6 +1,6 @@
 from sqlalchemy import *
 from sqlalchemy.orm import *
-from sqlalchemy.exceptions import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 import datetime
@@ -18,7 +18,7 @@ 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 ""
diff --git a/lib/galaxy/model/orm/ext/assignmapper.py b/lib/galaxy/model/orm/ext/assignmapper.py
index 08bf1dd7c32..8b7cc27751a 100644
--- a/lib/galaxy/model/orm/ext/assignmapper.py
+++ b/lib/galaxy/model/orm/ext/assignmapper.py
@@ -15,22 +15,36 @@ __all__ = [ 'assign_mapper' ]
 
 from sqlalchemy import util, exceptions
 import types
-from sqlalchemy.orm import mapper, Query
+from sqlalchemy.orm import Query
+from sqlalchemy.orm import mapper as sqla_mapper
 
-def _monkeypatch_session_method(name, session, class_, make_list=False):
-    def do(self, *args, **kwargs):
-        if make_list:
-            self = [ self ]
-        return getattr(session, name)( self, *args, **kwargs )
+def _monkeypatch_session_method( name, session, class_ ):
+    # TODO: eliminate this method by fixing the session flushes
+    def do( self, *args, **kwargs ):
+        if self not in session.deleted:
+            session.add( self )
+        return session.flush() 
     try:
         do.__name__ = name
     except:
         pass
-    if not hasattr(class_, name):
-        setattr(class_, name, do)
-
+    if not hasattr( class_, name ):
+        setattr( class_, name, do )
+def session_mapper( scoped_session, class_, *args, **kwargs ):
+    def mapper( cls, *arg, **kw ):
+        validate = kw.pop( 'validate', False )
+        if cls.__init__ is object.__init__:
+            def __init__( self, **kwargs ):
+                for key, value in kwargs.items():
+                    if validate:
+                        if not cls_mapper.has_property( key ):
+                            raise TypeError( "Invalid __init__ argument: '%s'" % key )
+                    setattr( self, key, value )
+            cls.__init__ = __init__
+        cls.query = scoped_session.query_property()
+        _monkeypatch_session_method( 'flush', scoped_session, cls )
+        return sqla_mapper( cls, *arg, **kw )
+    return mapper( class_, *args, **kwargs )
 def assign_mapper( session, class_, *args, **kwargs ):
-    m = class_.mapper = session.mapper( class_, *args, **kwargs )
-    for name in ( 'flush', ):
-        _monkeypatch_session_method( name, session, class_, make_list=True )
+    m = class_.mapper = session_mapper( session, class_, *args, **kwargs )
     return m
diff --git a/lib/galaxy/web/controllers/forms.py b/lib/galaxy/web/controllers/forms.py
index be48d993319..30515b238a5 100644
--- a/lib/galaxy/web/controllers/forms.py
+++ b/lib/galaxy/web/controllers/forms.py
@@ -450,7 +450,7 @@ class Forms( BaseController ):
         # create corresponding row in the form_definition_current table
         fd.form_definition_current = fdc
         fdc.latest_form = fd
-        trans.sa_session.save_or_update( fdc )
+        trans.sa_session.add( fdc )
         trans.sa_session.flush()
         msg = "The new form named '%s' has been created. " % (fd.name)
         return fd, msg
diff --git a/lib/galaxy/web/controllers/history.py b/lib/galaxy/web/controllers/history.py
index fe3f3e36187..ca539603be2 100644
--- a/lib/galaxy/web/controllers/history.py
+++ b/lib/galaxy/web/controllers/history.py
@@ -726,7 +726,7 @@ class HistoryController( BaseController ):
                     share.history = history
                     share.user = send_to_user
                     session = trans.sa_session
-                    session.save_or_update( share )
+                    session.add( share )
                     session.flush()
                     if history not in shared_histories:
                         shared_histories.append( history )
diff --git a/lib/galaxy/web/controllers/page.py b/lib/galaxy/web/controllers/page.py
index 09a0771bf55..1cca24b74f8 100644
--- a/lib/galaxy/web/controllers/page.py
+++ b/lib/galaxy/web/controllers/page.py
@@ -135,7 +135,7 @@ class PageController( BaseController ):
                 page_revision.content = ""
                 # Persist
                 session = trans.sa_session
-                session.save_or_update( page )
+                session.add( page )
                 session.flush()
                 # Display the management page
                 ## trans.set_message( "Page '%s' created" % page.title )
@@ -240,4 +240,4 @@ class PageController( BaseController ):
             raise web.httpexceptions.HTTPNotFound()
         return trans.fill_template( "page/display.mako", page=page )
     
-    
\ No newline at end of file
+    
diff --git a/lib/galaxy/web/controllers/workflow.py b/lib/galaxy/web/controllers/workflow.py
index 7b06b997f67..1d80915e369 100644
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -30,7 +30,7 @@ class WorkflowController( BaseController ):
         user = trans.get_user()
         workflows = trans.sa_session.query( model.StoredWorkflow ) \
             .filter_by( user=user, deleted=False ) \
-            .order_by( desc( model.StoredWorkflow.c.update_time ) ) \
+            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
             .all()
         shared_by_others = trans.sa_session \
             .query( model.StoredWorkflowUserShareAssociation ) \
@@ -53,13 +53,13 @@ class WorkflowController( BaseController ):
         user = trans.get_user()
         workflows = trans.sa_session.query( model.StoredWorkflow ) \
             .filter_by( user=user, deleted=False ) \
-            .order_by( desc( model.StoredWorkflow.c.update_time ) ) \
+            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
             .all()
         shared_by_others = trans.sa_session \
             .query( model.StoredWorkflowUserShareAssociation ) \
             .filter_by( user=user ) \
-            .filter( model.StoredWorkflow.c.deleted == False ) \
-            .order_by( desc( model.StoredWorkflow.c.update_time ) ) \
+            .filter( model.StoredWorkflow.deleted == False ) \
+            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
             .all()
         return trans.fill_template( "workflow/list_for_run.mako",
                                     workflows = workflows,
@@ -91,7 +91,7 @@ class WorkflowController( BaseController ):
                 share.stored_workflow = stored
                 share.user = other
                 session = trans.sa_session
-                session.save_or_update( share )
+                session.add( share )
                 session.flush()
                 trans.set_message( "Workflow '%s' shared with user '%s'" % ( stored.name, other.email ) )
                 return trans.response.send_redirect( url_for( controller='workflow', action='sharing', id=id ) )
@@ -142,7 +142,7 @@ class WorkflowController( BaseController ):
             share.stored_workflow = stored
             share.user = trans.user
             session = trans.sa_session
-            session.save_or_update( share )
+            session.add( share )
             session.flush()
             # Redirect to load galaxy frames.
             return trans.response.send_redirect( url_for( controller='workflow' ) )
@@ -180,7 +180,7 @@ class WorkflowController( BaseController ):
         new_stored.user = user
         # Persist
         session = trans.sa_session
-        session.save_or_update( new_stored )
+        session.add( new_stored )
         session.flush()
         # Display the management page
         trans.set_message( 'Clone created with name "%s"' % new_stored.name )
@@ -205,7 +205,7 @@ class WorkflowController( BaseController ):
             stored_workflow.latest_workflow = workflow
             # Persist
             session = trans.sa_session
-            session.save_or_update( stored_workflow )
+            session.add( stored_workflow )
             session.flush()
             # Display the management page
             trans.set_message( "Workflow '%s' created" % stored_workflow.name )
@@ -514,7 +514,7 @@ class WorkflowController( BaseController ):
             stored.name = workflow_name
             workflow.stored_workflow = stored
             stored.latest_workflow = workflow
-            trans.sa_session.save_or_update( stored )
+            trans.sa_session.add( stored )
             trans.sa_session.flush()
             # Index page with message
             return trans.show_message( "Workflow '%s' created from current history." % workflow_name )
@@ -656,12 +656,12 @@ class WorkflowController( BaseController ):
             ids_in_menu = set( [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ] )
             workflows = trans.sa_session.query( model.StoredWorkflow ) \
                 .filter_by( user=user, deleted=False ) \
-                .order_by( desc( model.StoredWorkflow.c.update_time ) ) \
+                .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
                 .all()
             shared_by_others = trans.sa_session \
                 .query( model.StoredWorkflowUserShareAssociation ) \
                 .filter_by( user=user ) \
-                .filter( model.StoredWorkflow.c.deleted == False ) \
+                .filter( model.StoredWorkflow.deleted == False ) \
                 .all()
             return trans.fill_template( "workflow/configure_menu.mako",
                                         workflows=workflows,
diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py
index b364b613a24..3f4f6040e53 100644
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -111,10 +111,10 @@ class Grid( object ):
             if sort_key.startswith( "-" ):
                 sort_key = sort_key[1:]
                 sort_order = 'desc'
-                query = query.order_by( self.model_class.c.get( sort_key ).desc() )
+                query = query.order_by( self.model_class.table.c.get( sort_key ).desc() )
             else:
                 sort_order = 'asc'
-                query = query.order_by( self.model_class.c.get( sort_key ).asc() )
+                query = query.order_by( self.model_class.table.c.get( sort_key ).asc() )
         extra_url_args['sort'] = encoded_sort_key
         
         # There might be a current row