[galaxy-dev] [hg] galaxy 2909: Make sqlalchemy queries use sa_session.query( ...

27 Oct 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/2c4ed83f76ef
changeset: 2909:2c4ed83f76ef
user:      Greg Von Kuster <greg@bx.psu.edu>
date:      Thu Oct 22 23:02:28 2009 -0400
description:
Make sqlalchemy queries use sa_session.query( object ) rather than object.query().  This eliminates the need for the _monkeypatch_query_method() in assignmapper.py.  Also eliminate the need for the _monkeypatch_session_method() for everything except object.flush() - I just ran out of time and will handle flush() asap.  I also eliminated the .all() call on several queries where it was not necessary - should improve performance.  I fixed several bugs I found as well.

62 file(s) affected in this change:

lib/galaxy/datatypes/metadata.py
lib/galaxy/jobs/__init__.py
lib/galaxy/model/__init__.py
lib/galaxy/model/mapping_tests.py
lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
lib/galaxy/model/orm/ext/assignmapper.py
lib/galaxy/security/__init__.py
lib/galaxy/tags/tag_handler.py
lib/galaxy/tools/__init__.py
lib/galaxy/tools/actions/__init__.py
lib/galaxy/tools/actions/metadata.py
lib/galaxy/tools/actions/upload_common.py
lib/galaxy/tools/parameters/basic.py
lib/galaxy/web/controllers/admin.py
lib/galaxy/web/controllers/async.py
lib/galaxy/web/controllers/dataset.py
lib/galaxy/web/controllers/forms.py
lib/galaxy/web/controllers/genetrack.py
lib/galaxy/web/controllers/history.py
lib/galaxy/web/controllers/library.py
lib/galaxy/web/controllers/library_admin.py
lib/galaxy/web/controllers/library_common.py
lib/galaxy/web/controllers/mobile.py
lib/galaxy/web/controllers/page.py
lib/galaxy/web/controllers/requests.py
lib/galaxy/web/controllers/requests_admin.py
lib/galaxy/web/controllers/root.py
lib/galaxy/web/controllers/tag.py
lib/galaxy/web/controllers/tool_runner.py
lib/galaxy/web/controllers/tracks.py
lib/galaxy/web/controllers/user.py
lib/galaxy/web/controllers/workflow.py
lib/galaxy/web/framework/__init__.py
lib/galaxy/webapps/reports/controllers/users.py
scripts/cleanup_datasets/cleanup_datasets.py
templates/admin/dataset_security/deleted_groups.mako
templates/admin/dataset_security/deleted_roles.mako
templates/admin/dataset_security/groups.mako
templates/admin/dataset_security/roles.mako
templates/admin/library/folder_permissions.mako
templates/admin/library/ldda_info.mako
templates/admin/library/ldda_permissions.mako
templates/admin/library/library_dataset_permissions.mako
templates/admin/library/library_info.mako
templates/admin/library/library_permissions.mako
templates/admin/requests/grid.mako
templates/admin/requests/show_request.mako
templates/library/ldda_permissions.mako
templates/library/library_dataset_permissions.mako
templates/library/library_permissions.mako
templates/mobile/manage_library.mako
templates/requests/show_request.mako
templates/user/address.mako
test/base/twilltestcase.py
test/functional/test_DNAse_flanked_genes.py
test/functional/test_forms_and_requests.py
test/functional/test_get_data.py
test/functional/test_history_functions.py
test/functional/test_metadata_editing.py
test/functional/test_security_and_libraries.py
test/functional/test_sniffing_and_metadata_settings.py
test/functional/test_toolbox.py

diffs (truncated from 6168 to 3000 lines):

diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/datatypes/metadata.py

--- a/lib/galaxy/datatypes/metadata.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/datatypes/metadata.py	Thu Oct 22 23:02:28 2009 -0400
@@ -489,15 +489,22 @@
     #We will use JSON as the medium of exchange of information, except for the DatasetInstance object which will use pickle (in the future this could be JSONified as well)
     def __init__( self, job ):
         self.job_id = job.id
-    def get_output_filenames_by_dataset( self, dataset ):
+    def get_output_filenames_by_dataset( self, dataset, sa_session ):
         if isinstance( dataset, galaxy.model.HistoryDatasetAssociation ):
-            return galaxy.model.JobExternalOutputMetadata.filter_by( job_id = self.job_id, history_dataset_association_id = dataset.id ).first() #there should only be one or None
+            return sa_session.query( galaxy.model.JobExternalOutputMetadata ) \
+                             .filter_by( job_id = self.job_id, history_dataset_association_id = dataset.id ) \
+                             .first() #there should only be one or None
         elif isinstance( dataset, galaxy.model.LibraryDatasetDatasetAssociation ):
-            return galaxy.model.JobExternalOutputMetadata.filter_by( job_id = self.job_id, library_dataset_dataset_association_id = dataset.id ).first() #there should only be one or None
+            return sa_session.query( galaxy.model.JobExternalOutputMetadata ) \
+                             .filter_by( job_id = self.job_id, library_dataset_dataset_association_id = dataset.id ) \
+                             .first() #there should only be one or None
         return None
     def get_dataset_metadata_key( self, dataset ):
-        return "%s_%d" % ( dataset.__class__.__name__, dataset.id ) #set meta can be called on library items and history items, need to make different keys for them, since ids can overlap
-    def setup_external_metadata( self, datasets, exec_dir = None, tmp_dir = None, dataset_files_path = None, output_fnames = None, config_root = None, datatypes_config = None, kwds = {} ):
+         # Set meta can be called on library items and history items, 
+         # need to make different keys for them, since ids can overlap
+        return "%s_%d" % ( dataset.__class__.__name__, dataset.id )
+    def setup_external_metadata( self, datasets, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, 
+                                 output_fnames=None, config_root=None, datatypes_config=None, kwds={} ):
         #fill in metadata_files_dict and return the command with args required to set metadata
         def __metadata_files_list_to_cmd_line( metadata_files ):
             def __get_filename_override():
@@ -527,7 +534,7 @@
             #when setting metadata externally, via 'auto-detect' button in edit attributes, etc., 
             #we don't want to overwrite (losing the ability to cleanup) our existing dataset keys and files, 
             #so we will only populate the dictionary once
-            metadata_files = self.get_output_filenames_by_dataset( dataset )
+            metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )
             if not metadata_files:
                 metadata_files = galaxy.model.JobExternalOutputMetadata( dataset = dataset)
                 metadata_files.job_id = self.job_id
@@ -553,8 +560,8 @@
         #return command required to build
         return "%s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, config_root, datatypes_config, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) )
     
-    def external_metadata_set_successfully( self, dataset ):
-        metadata_files = self.get_output_filenames_by_dataset( dataset )
+    def external_metadata_set_successfully( self, dataset, sa_session ):
+        metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )
         if not metadata_files:
             return False # this file doesn't exist
         rval, rstring = simplejson.load( open( metadata_files.filename_results_code ) )
@@ -578,4 +585,3 @@
         for metadata_files in galaxy.model.Job.get( self.job_id ).external_output_metadata:
             metadata_files.job_runner_external_pid = pid
             metadata_files.flush()
-        
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/jobs/__init__.py	Thu Oct 22 23:02:28 2009 -0400
@@ -1,7 +1,6 @@
 import logging, threading, sys, os, time, subprocess, string, tempfile, re, traceback, shutil
 
 from galaxy import util, model
-from galaxy.model import mapping
 from galaxy.model.orm import lazyload
 from galaxy.datatypes.tabular import *
 from galaxy.datatypes.interval import *
@@ -73,6 +72,7 @@
     def __init__( self, app, dispatcher ):
         """Start the job manager"""
         self.app = app
+        self.sa_session = app.model.context
         # Should we read jobs form the database, or use an in memory queue
         self.track_jobs_in_database = app.config.get_bool( 'track_jobs_in_database', False )
         # Check if any special scheduling policy should be used. If not, default is FIFO.
@@ -126,14 +126,14 @@
         job manager starts.
         """
         model = self.app.model
-        for job in model.Job.filter( model.Job.c.state==model.Job.states.NEW ).all():
+        for job in self.sa_session.query( model.Job ).filter( model.Job.state == model.Job.states.NEW ):
             if job.tool_id not in self.app.toolbox.tools_by_id:
                 log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) )
                 JobWrapper( job, None, self ).fail( 'This tool was disabled before the job completed.  Please contact your Galaxy administrator, or' )
             else:
                 log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id )
                 self.queue.put( ( job.id, job.tool_id ) )
-        for job in model.Job.filter( (model.Job.c.state == model.Job.states.RUNNING) | (model.Job.c.state == model.Job.states.QUEUED) ).all():
+        for job in self.sa_session.query( model.Job ).filter( ( model.Job.state == model.Job.states.RUNNING ) | ( model.Job.state == model.Job.states.QUEUED ) ):
             if job.tool_id not in self.app.toolbox.tools_by_id:
                 log.warning( "Tool '%s' removed from tool config, unable to recover job: %s" % ( job.tool_id, job.id ) )
                 JobWrapper( job, None, self ).fail( 'This tool was disabled before the job completed.  Please contact your Galaxy administrator, or' )
@@ -169,12 +169,12 @@
         it is marked as having errors and removed from the queue. Otherwise,
         the job is dispatched.
         """
-        # Get an orm session
-        session = mapping.Session()
         # Pull all new jobs from the queue at once
         new_jobs = []
         if self.track_jobs_in_database:
-            for j in session.query( model.Job ).options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ).filter( model.Job.c.state == model.Job.states.NEW ).all():
+            for j in session.query( model.Job ) \
+                            .options( lazyload( "external_output_metadata" ), lazyload( "parameters" ) ) \
+                            .filter( model.Job.c.state == model.Job.states.NEW ):
                 job = JobWrapper( j, self.app.toolbox.tools_by_id[ j.tool_id ], self )
                 new_jobs.append( job )
         else:
@@ -186,7 +186,7 @@
                     # Unpack the message
                     job_id, tool_id = message
                     # Create a job wrapper from it
-                    job_entity = session.query( model.Job ).get( job_id )
+                    job_entity = self.sa_session.query( model.Job ).get( job_id )
                     job = JobWrapper( job_entity, self.app.toolbox.tools_by_id[ tool_id ], self )
                     # Append to watch queue
                     new_jobs.append( job )
@@ -199,11 +199,11 @@
             try:
                 # Clear the session for each job so we get fresh states for
                 # job and all datasets
-                session.clear()
+                self.sa_session.clear()
                 # 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)
-                job_entity = session.query( model.Job ).get( job.job_id )
+                job_entity = self.sa_session.query( model.Job ).get( job.job_id )
                 # Check the job's dependencies, requeue if they're not done                    
                 job_state = self.__check_if_ready_to_run( job, job_entity )
                 if job_state == JOB_WAIT: 
@@ -254,7 +254,7 @@
                     job.fail( "failure running job %d: %s" % ( sjob.job_id, str( e ) ) )
                     log.exception( "failure running job %d" % sjob.job_id )
         # Done with the session
-        mapping.Session.remove()
+        self.sa_session.remove()
         
     def __check_if_ready_to_run( self, job_wrapper, job ):
         """
@@ -319,6 +319,7 @@
         self.tool = tool
         self.queue = queue
         self.app = queue.app
+        self.sa_session = self.app.model.context
         self.extra_filenames = []
         self.command_line = None
         self.galaxy_lib_dir = None
@@ -335,7 +336,7 @@
         """
         Restore the dictionary of parameters from the database.
         """
-        job = model.Job.get( self.job_id )
+        job = self.sa_session.query( model.Job ).get( self.job_id )
         param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         param_dict = self.tool.params_from_strings( param_dict, self.app )
         return param_dict
@@ -345,11 +346,11 @@
         Prepare the job to run by creating the working directory and the
         config files.
         """
-        mapping.context.current.clear() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner
+        self.sa_session.clear() #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
-        job = model.Job.get( self.job_id )
+        job = self.sa_session.query( model.Job ).get( self.job_id )
         incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] )
         incoming = self.tool.params_from_strings( incoming, self.app )
         # Do any validation that could not be done at job creation
@@ -376,7 +377,7 @@
         # Run the before queue ("exec_before_job") hook
         self.tool.call_hook( 'exec_before_job', self.queue.app, inp_data=inp_data, 
                              out_data=out_data, tool=self.tool, param_dict=incoming)
-        mapping.context.current.flush()
+        self.sa_session.flush()
         # Build any required config files
         config_filenames = self.tool.build_config_files( param_dict, self.working_directory )
         # FIXME: Build the param file (might return None, DEPRECATED)
@@ -403,8 +404,8 @@
         Indicate job failure by setting state and message on all output 
         datasets.
         """
-        job = model.Job.get( self.job_id )
-        job.refresh()
+        job = self.sa_session.query( model.Job ).get( self.job_id )
+        self.sa_session.refresh( job )
         # if the job was deleted, don't fail it
         if not job.state == model.Job.states.DELETED:
             # Check if the failure is due to an exception
@@ -427,7 +428,7 @@
                         log.error( "fail(): Missing output file in working directory: %s" % e )
             for dataset_assoc in job.output_datasets + job.output_library_datasets:
                 dataset = dataset_assoc.dataset
-                dataset.refresh()
+                self.sa_session.refresh( dataset )
                 dataset.state = dataset.states.ERROR
                 dataset.blurb = 'tool error'
                 dataset.info = message
@@ -443,11 +444,11 @@
         self.cleanup()
         
     def change_state( self, state, info = False ):
-        job = model.Job.get( self.job_id )
-        job.refresh()
+        job = self.sa_session.query( model.Job ).get( self.job_id )
+        self.sa_session.refresh( job )
         for dataset_assoc in job.output_datasets + job.output_library_datasets:
             dataset = dataset_assoc.dataset
-            dataset.refresh()
+            self.sa_session.refresh( dataset )
             dataset.state = state
             if info:
                 dataset.info = info
@@ -458,13 +459,13 @@
         job.flush()
 
     def get_state( self ):
-        job = model.Job.get( self.job_id )
-        job.refresh()
+        job = self.sa_session.query( model.Job ).get( self.job_id )
+        self.sa_session.refresh( job )
         return job.state
 
     def set_runner( self, runner_url, external_id ):
-        job = model.Job.get( self.job_id )
-        job.refresh()
+        job = self.sa_session.query( model.Job ).get( self.job_id )
+        self.sa_session.refresh( job )
         job.job_runner_name = runner_url
         job.job_runner_external_id = external_id
         job.flush()
@@ -476,8 +477,8 @@
         the contents of the output files. 
         """
         # default post job setup
-        mapping.context.current.clear()
-        job = model.Job.get( self.job_id )
+        self.sa_session.clear()
+        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:
             self.cleanup()
@@ -523,7 +524,7 @@
                     #either use the metadata from originating output dataset, or call set_meta on the copies
                     #it would be quicker to just copy the metadata from the originating output dataset, 
                     #but somewhat trickier (need to recurse up the copied_from tree), for now we'll call set_meta()
-                    if not self.external_output_metadata.external_metadata_set_successfully( dataset ):
+                    if not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ):
                         # Only set metadata values if they are missing...
                         dataset.set_meta( overwrite = False )
                     else:
@@ -563,7 +564,7 @@
             # ERROR.  The user will never see that the datasets are in error if
             # they were flushed as OK here, since upon doing so, the history
             # panel stops checking for updates.  So allow the
-            # mapping.context.current.flush() at the bottom of this method set
+            # self.sa_session.flush() at the bottom of this method set
             # the state instead.
             #dataset_assoc.dataset.dataset.flush()
         
@@ -596,7 +597,7 @@
         # TODO
         # validate output datasets
         job.command_line = self.command_line
-        mapping.context.current.flush()
+        self.sa_session.flush()
         log.debug( 'job %d ended' % self.job_id )
         self.cleanup()
         
@@ -619,7 +620,7 @@
         return self.session_id
 
     def get_input_fnames( self ):
-        job = model.Job.get( self.job_id )
+        job = self.sa_session.query( model.Job ).get( self.job_id )
         filenames = []
         for da in job.input_datasets: #da is JobToInputDatasetAssociation object
             if da.dataset:
@@ -646,7 +647,7 @@
                 else:
                     return self.false_path
 
-        job = model.Job.get( self.job_id )
+        job = self.sa_session.query( model.Job ).get( self.job_id )
         if self.app.config.outputs_to_working_directory:
             self.output_paths = []
             for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]:
@@ -709,12 +710,12 @@
         return sizes
     def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, **kwds ):
         # extension could still be 'auto' if this is the upload tool.
-        job = model.Job.get( self.job_id )
+        job = self.sa_session.query( model.Job ).get( self.job_id )
         for output_dataset_assoc in job.output_datasets:
             if output_dataset_assoc.dataset.ext == 'auto':
                 context = self.get_dataset_finish_context( dict(), output_dataset_assoc.dataset.dataset )
                 output_dataset_assoc.dataset.extension = context.get( 'ext', 'data' )
-        mapping.context.current.flush()
+        self.sa_session.flush()
         if tmp_dir is None:
             #this dir should should relative to the exec_dir
             tmp_dir = self.app.config.new_file_path
@@ -724,7 +725,14 @@
             config_root = self.app.config.root
         if datatypes_config is None:
             datatypes_config = self.app.config.datatypes_config
-        return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, config_root = config_root, datatypes_config = datatypes_config, **kwds )
+        return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ],
+                                                                      self.sa_session,
+                                                                      exec_dir = exec_dir,
+                                                                      tmp_dir = tmp_dir,
+                                                                      dataset_files_path = dataset_files_path,
+                                                                      config_root = config_root,
+                                                                      datatypes_config = datatypes_config,
+                                                                      **kwds )
 
 class DefaultJobDispatcher( object ):
     def __init__( self, app ):
@@ -772,6 +780,7 @@
     STOP_SIGNAL = object()
     def __init__( self, app, dispatcher ):
         self.app = app
+        self.sa_session = app.model.context
         self.dispatcher = dispatcher
 
         # Keep track of the pid that started the job manager, only it
@@ -821,8 +830,8 @@
             pass  
 
         for job_id, error_msg in jobs:
-            job = model.Job.get( job_id )
-            job.refresh()
+            job = self.sa_session.query( model.Job ).get( job_id )
+            self.sa_session.refresh( job )
             # if desired, error the job so we can inform the user.
             if error_msg is not None:
                 job.state = job.states.ERROR
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/model/__init__.py	Thu Oct 22 23:02:28 2009 -0400
@@ -1292,8 +1292,7 @@
         if self.phone:
             html = html + '<br/>' + 'Phone: ' + self.phone
         return html
-
-                
+    
 class Page( object ):
     def __init__( self ):
         self.id = None
@@ -1330,8 +1329,7 @@
         
     def __str__ ( self ):
         return "%s(item_id=%s, item_tag=%s, user_tname=%s, value=%s, user_value=%s)" % (self.__class__.__name__, self.item_id, self.tag_id, self.user_tname, self.value. self.user_value )  
-    
-    
+
 class HistoryTagAssociation ( ItemTagAssociation ):
     pass
 
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/model/mapping_tests.py
--- a/lib/galaxy/model/mapping_tests.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/model/mapping_tests.py	Thu Oct 22 23:02:28 2009 -0400
@@ -22,13 +22,13 @@
         model.context.current.flush()
         model.context.current.clear()
         # Check
-        users = model.User.query().all()
+        users = model.context.current.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.History.query().all()
+        hists = model.context.current.query( model.History ).all()
         assert hists[0].name == "History 1"
         assert hists[1].name == ( "H" * 255 )
         assert hists[0].user == users[0]
@@ -40,7 +40,7 @@
         hists[1].name = "History 2b"
         model.context.current.flush()
         model.context.current.clear()
-        hists = model.History.query().all()
+        hists = model.context.current.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 -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
--- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py	Thu Oct 22 23:02:28 2009 -0400
@@ -662,7 +662,7 @@
     log.debug( "Fixing a discrepancy concerning deleted shared history items." )
     affected_items = 0
     start_time = time.time()
-    for dataset in Dataset.filter( and_( Dataset.c.deleted == True, Dataset.c.purged == False ) ).all():
+    for dataset in context.query( Dataset ).filter( and_( Dataset.c.deleted == True, Dataset.c.purged == False ) ):
         for dataset_instance in dataset.history_associations + dataset.library_associations:
             if not dataset_instance.deleted:
                 dataset.deleted = False
@@ -679,7 +679,7 @@
     dataset_by_filename = {}
     changed_associations = 0
     start_time = time.time()
-    for dataset in Dataset.filter( Dataset.external_filename.like( '%dataset_%.dat' ) ).all():
+    for dataset in context.query( Dataset ).filter( Dataset.external_filename.like( '%dataset_%.dat' ) ):
         if dataset.file_name in dataset_by_filename:
             guessed_dataset = dataset_by_filename[ dataset.file_name ]
         else:
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/model/orm/ext/assignmapper.py
--- a/lib/galaxy/model/orm/ext/assignmapper.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/model/orm/ext/assignmapper.py	Thu Oct 22 23:02:28 2009 -0400
@@ -3,20 +3,12 @@
 with some compatibility fixes. It assumes that the session is a ScopedSession,
 and thus has the "mapper" method to attach contextual mappers to a class. It
 adds additional query and session methods to the class to support the
-SQLAlchemy 0.3 style of access. The following methods which would normally be
-accessed through "Object.query().method()" are available directly through the
-object:
+SQLAlchemy 0.3 style of access.
 
-    'get', 'filter', 'filter_by', 'select', 'select_by',
-    'selectfirst', 'selectfirst_by', 'selectone', 'selectone_by',
-    'get_by', 'join_to', 'join_via', 'count', 'count_by',
-    'options', 'instances'
-
-Additionally, the following Session methods, which normally accept an instance
+The following Session methods, which normally accept an instance
 or list of instances, are available directly through the objects, e.g.
 "Session.flush( [instance] )" can be performed as "instance.flush()":
 
-    'refresh', 'expire', 'delete', 'expunge', 'update'
 """
 
 __all__ = [ 'assign_mapper' ]
@@ -24,17 +16,6 @@
 from sqlalchemy import util, exceptions
 import types
 from sqlalchemy.orm import mapper, Query
-
-def _monkeypatch_query_method( name, session, class_ ):
-    def do(self, *args, **kwargs):
-        ## util.warn_deprecated('Query methods on the class are deprecated; use %s.query.%s instead' % (class_.__name__, name))
-        return getattr( class_.query, name)(*args, **kwargs)
-    try:
-        do.__name__ = name
-    except:
-        pass
-    if not hasattr(class_, name):
-        setattr(class_, name, classmethod(do))
 
 def _monkeypatch_session_method(name, session, class_, make_list=False):
     def do(self, *args, **kwargs):
@@ -50,13 +31,6 @@
 
 def assign_mapper( session, class_, *args, **kwargs ):
     m = class_.mapper = session.mapper( class_, *args, **kwargs )
-    for name in ('get', 'filter', 'filter_by', 'select', 'select_by',
-                 'selectfirst', 'selectfirst_by', 'selectone', 'selectone_by',
-                 'get_by', 'join_to', 'join_via', 'count', 'count_by',
-                 'options', 'instances'):
-        _monkeypatch_query_method(name, session, class_)
-    for name in ('refresh', 'expire', 'delete', 'expunge', 'update'):
-        _monkeypatch_session_method(name, session, class_)
     for name in ( 'flush', ):
         _monkeypatch_session_method( name, session, class_, make_list=True )
     return m
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/security/__init__.py
--- a/lib/galaxy/security/__init__.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/security/__init__.py	Thu Oct 22 23:02:28 2009 -0400
@@ -205,8 +205,10 @@
         self.associate_components( role=role, user=user )
         return role
     def get_private_user_role( self, user, auto_create=False ):
-        role = self.model.Role.filter( and_( self.model.Role.table.c.name == user.email, 
-                                             self.model.Role.table.c.type == self.model.Role.types.PRIVATE ) ).first()
+        role = self.sa_session.query( self.model.Role ) \
+                              .filter( and_( self.model.Role.table.c.name == user.email, 
+                                             self.model.Role.table.c.type == self.model.Role.types.PRIVATE ) ) \
+                              .first()
         if not role:
             if auto_create:
                 return self.create_private_user_role( user )
@@ -225,7 +227,7 @@
                 permissions[ self.permitted_actions.DATASET_ACCESS ] = permissions.values()[ 0 ]
         # Delete all of the current default permissions for the user
         for dup in user.default_permissions:
-            dup.delete()
+            self.sa_session.delete( dup )
             dup.flush()
         # Add the new default permissions for the user
         for action, roles in permissions.items():
@@ -255,7 +257,7 @@
             permissions = self.user_get_default_permissions( user )
         # Delete all of the current default permission for the history
         for dhp in history.default_permissions:
-            dhp.delete()
+            self.sa_session.delete( dhp )
             dhp.flush()
         # Add the new default permissions for the history
         for action, roles in permissions.items():
@@ -293,7 +295,7 @@
         # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset,
         # or the dataset is inaccessible.  See admin/library_dataset_dataset_association()
         for dp in dataset.actions:
-            dp.delete()
+            self.sa_session.delete( dp )
             dp.flush()
         # Add the new permissions on the dataset
         for action, roles in permissions.items():
@@ -314,7 +316,7 @@
             # Delete the current specific permission on the dataset if one exists
             for dp in dataset.actions:
                 if dp.action == action:
-                    dp.delete()
+                    self.sa_session.delete( dp )
                     dp.flush()
             # Add the new specific permission on the dataset
             for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]:
@@ -328,7 +330,7 @@
         # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant.
         for dp in dataset.actions:
             if dp.action == self.permitted_actions.DATASET_ACCESS.action:
-                dp.delete()
+                self.sa_session.delete( dp )
                 dp.flush()
     def get_dataset_permissions( self, dataset ):
         """
@@ -379,7 +381,7 @@
     def set_all_library_permissions( self, library_item, permissions={} ):
         # Set new permissions on library_item, eliminating all current permissions
         for role_assoc in library_item.actions:
-            role_assoc.delete()
+            self.sa_session.delete( role_assoc )
             role_assoc.flush()
         # Add the new permissions on library_item
         for item_class, permission_class in self.library_item_assocs:
@@ -472,9 +474,9 @@
         for user in users:
             if delete_existing_assocs:
                 for a in user.non_private_roles + user.groups:
-                    a.delete()
+                    self.sa_session.delete( a )
                     a.flush()
-            user.refresh()
+            self.sa_session.refresh( user )
             for role in roles:
                 # Make sure we are not creating an additional association with a PRIVATE role
                 if role not in user.roles:
@@ -485,7 +487,7 @@
         for group in groups:
             if delete_existing_assocs:
                 for a in group.roles + group.users:
-                    a.delete()
+                    self.sa_session.delete( a )
                     a.flush()
             for role in roles:
                 self.associate_components( group=group, role=role )
@@ -495,7 +497,7 @@
         for role in roles:
             if delete_existing_assocs:
                 for a in role.users + role.groups:
-                    a.delete()
+                    self.sa_session.delete( a )
                     a.flush()
             for user in users:
                 self.associate_components( user=user, role=role )
@@ -505,15 +507,15 @@
         assert len( kwd ) == 2, 'You must specify exactly 2 Galaxy security components to check for associations.'
         if 'dataset' in kwd:
             if 'action' in kwd:
-                return self.model.DatasetPermissions.filter_by( action = kwd['action'].action, dataset_id = kwd['dataset'].id ).first()
+                return self.sa_session.query( self.model.DatasetPermissions ).filter_by( action = kwd['action'].action, dataset_id = kwd['dataset'].id ).first()
         elif 'user' in kwd:
             if 'group' in kwd:
-                return self.model.UserGroupAssociation.filter_by( group_id = kwd['group'].id, user_id = kwd['user'].id ).first()
+                return self.sa_session.query( self.model.UserGroupAssociation ).filter_by( group_id = kwd['group'].id, user_id = kwd['user'].id ).first()
             elif 'role' in kwd:
-                return self.model.UserRoleAssociation.filter_by( role_id = kwd['role'].id, user_id = kwd['user'].id ).first()
+                return self.sa_session.query( self.model.UserRoleAssociation ).filter_by( role_id = kwd['role'].id, user_id = kwd['user'].id ).first()
         elif 'group' in kwd:
             if 'role' in kwd:
-                return self.model.GroupRoleAssociation.filter_by( role_id = kwd['role'].id, group_id = kwd['group'].id ).first()
+                return self.sa_session.query( self.model.GroupRoleAssociation ).filter_by( role_id = kwd['role'].id, group_id = kwd['group'].id ).first()
         raise 'No valid method of associating provided components: %s' % kwd
     def check_folder_contents( self, user, roles, folder, hidden_folder_ids='' ):
         """
@@ -526,11 +528,11 @@
         """
         action = self.permitted_actions.DATASET_ACCESS
         lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \
-            .join( "library_dataset" ) \
-            .filter( self.model.LibraryDataset.folder == folder ) \
-            .join( "dataset" ) \
-            .options( eagerload_all( "dataset.actions" ) ) \
-            .all()
+                               .join( "library_dataset" ) \
+                               .filter( self.model.LibraryDataset.folder == folder ) \
+                               .join( "dataset" ) \
+                               .options( eagerload_all( "dataset.actions" ) ) \
+                               .all()
         for ldda in lddas:
             ldda_access_permissions = self.get_item_actions( action, ldda.dataset )
             if not ldda_access_permissions:
@@ -573,7 +575,8 @@
             if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in hda.dataset.actions ]:
                 log.debug( 'Allowing access to public dataset with hda: %i.' % hda.id )
                 return True # dataset has no roles associated with the access permission, thus is already public
-            hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization.filter_by( history_dataset_association_id = hda.id ).first()
+            hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \
+                                    .filter_by( history_dataset_association_id = hda.id ).first()
             if not hdadaa:
                 log.debug( 'Denying access to private dataset with hda: %i.  No hdadaa record for this dataset.' % hda.id )
                 return False # no auth
@@ -602,7 +605,8 @@
         else:
             raise 'The dataset access permission is the only valid permission in the host security agent.'
     def set_dataset_permissions( self, hda, user, site ):
-        hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization.filter_by( history_dataset_association_id = hda.id ).first()
+        hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \
+                                .filter_by( history_dataset_association_id = hda.id ).first()
         if hdadaa:
             hdadaa.update_time = datetime.utcnow()
         else:
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/tags/tag_handler.py
--- a/lib/galaxy/tags/tag_handler.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/tags/tag_handler.py	Thu Oct 22 23:02:28 2009 -0400
@@ -21,7 +21,7 @@
     def get_tag_assoc_class(self, entity_class):
         return self.tag_assoc_classes[entity_class]
         
-    def remove_item_tag(self, item, tag_name):
+    def remove_item_tag( self, trans, item, tag_name ):
         """Remove a tag from an item."""
         # Get item tag association.
         item_tag_assoc = self._get_item_tag_assoc(item, tag_name)
@@ -29,17 +29,17 @@
         # Remove association.
         if item_tag_assoc:
             # Delete association.
-            item_tag_assoc.delete()
+            trans.sa_session.delete( item_tag_assoc )
             item.tags.remove(item_tag_assoc)
             return True
         
         return False
     
-    def delete_item_tags(self, item):
+    def delete_item_tags( self, trans, item ):
         """Delete tags from an item."""
         # Delete item-tag associations.
         for tag in item.tags:
-            tag.delete()
+            trans.sa_ession.delete( tag )
             
         # Delete tags from item.
         del item.tags[:]
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/tools/__init__.py	Thu Oct 22 23:02:28 2009 -0400
@@ -167,7 +167,7 @@
         which is encoded in the tool panel.
         """
         id = self.app.security.decode_id( workflow_id )
-        stored = self.app.model.StoredWorkflow.get( id )
+        stored = self.app.model.context.query( self.app.model.StoredWorkflow ).get( id )
         return stored.latest_workflow
 
 class ToolSection( object ):
@@ -863,7 +863,7 @@
         if 'async_datasets' in inputs and inputs['async_datasets'] not in [ 'None', '', None ]:
             for id in inputs['async_datasets'].split(','):
                 try:
-                    data = trans.model.HistoryDatasetAssociation.get( int( id ) )
+                    data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( int( id ) )
                 except:
                     log.exception( 'Unable to load precreated dataset (%s) sent in upload form' % id )
                     continue
@@ -1567,7 +1567,7 @@
     def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ):
         for name, dataset in inp_data.iteritems():
             external_metadata = galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper( job )
-            if external_metadata.external_metadata_set_successfully( dataset ):
+            if external_metadata.external_metadata_set_successfully( dataset, app.model.context ):
                 dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset ).filename_out )    
             # If setting external metadata has failed, how can we inform the user?
             # For now, we'll leave the default metadata and set the state back to its original.
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/tools/actions/__init__.py	Thu Oct 22 23:02:28 2009 -0400
@@ -32,7 +32,8 @@
         def visitor( prefix, input, value, parent = None ):
             def process_dataset( data ):
                 if data and not isinstance( data.datatype, input.formats ):
-                    data.refresh() #need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion
+                    # Need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion
+                    trans.sa_session.refresh( data )
                     target_ext, converted_dataset = data.find_conversion_destination( input.formats, converter_safe = input.converter_safe( param_values, trans ) )
                     if target_ext:
                         if converted_dataset:
@@ -172,7 +173,7 @@
                 #      this happens i.e. as a result of the async controller
                 if name in incoming:
                     dataid = incoming[name]
-                    data = trans.app.model.HistoryDatasetAssociation.get( dataid )
+                    data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataid )
                     assert data != None
                     out_data[name] = data
                 else:
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/tools/actions/metadata.py
--- a/lib/galaxy/tools/actions/metadata.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/tools/actions/metadata.py	Thu Oct 22 23:02:28 2009 -0400
@@ -29,9 +29,18 @@
         job.flush() #ensure job.id is available
         
         #add parameters to job_parameter table
-        incoming[ '__ORIGINAL_DATASET_STATE__' ] = dataset.state #store original dataset state, so we can restore it. A seperate table might be better (no chance of 'loosing' the original state)? 
+        # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)? 
+        incoming[ '__ORIGINAL_DATASET_STATE__' ] = dataset.state
         external_metadata_wrapper = JobExternalOutputMetadataWrapper( job )
-        cmd_line = external_metadata_wrapper.setup_external_metadata( dataset, exec_dir = None, tmp_dir = trans.app.config.new_file_path, dataset_files_path = trans.app.model.Dataset.file_path, output_fnames = None, config_root = None, datatypes_config = None, kwds = { 'overwrite' : True } )
+        cmd_line = external_metadata_wrapper.setup_external_metadata( dataset,
+                                                                      trans.sa_session,
+                                                                      exec_dir = None,
+                                                                      tmp_dir = trans.app.config.new_file_path,
+                                                                      dataset_files_path = trans.app.model.Dataset.file_path,
+                                                                      output_fnames = None,
+                                                                      config_root = None,
+                                                                      datatypes_config = None,
+                                                                      kwds = { 'overwrite' : True } )
         incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line
         for name, value in tool.params_to_strings( incoming, trans.app ).iteritems():
             job.add_parameter( name, value )
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/tools/actions/upload_common.py
--- a/lib/galaxy/tools/actions/upload_common.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/tools/actions/upload_common.py	Thu Oct 22 23:02:28 2009 -0400
@@ -41,12 +41,12 @@
     # See if we have any template field contents
     library_bunch.template_field_contents = []
     template_id = params.get( 'template_id', None )
-    library_bunch.folder = trans.app.model.LibraryFolder.get( folder_id )
+    library_bunch.folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder_id )
     # We are inheriting the folder's info_association, so we did not
     # receive any inherited contents, but we may have redirected here
     # after the user entered template contents ( due to errors ).
     if template_id not in [ None, 'None' ]:
-        library_bunch.template = trans.app.model.FormDefinition.get( template_id )
+        library_bunch.template = trans.sa_session.query( trans.app.model.FormDefinition ).get( template_id )
         for field_index in range( len( library_bunch.template.fields ) ):
             field_name = 'field_%i' % field_index
             if params.get( field_name, False ):
@@ -56,7 +56,8 @@
         library_bunch.template = None
     library_bunch.roles = []
     for role_id in util.listify( params.get( 'roles', [] ) ):
-            library_bunch.roles.append( trans.app.model.Role.get( role_id ) )
+        role = trans.sa_session.query( trans.app.model.Role ).get( role_id )
+        library_bunch.roles.append( role )
     return library_bunch
 
 def get_precreated_datasets( trans, params, data_obj, controller='root' ):
@@ -132,7 +133,7 @@
     if uploaded_dataset.get( 'in_folder', False ):
         # Create subfolders if desired
         for name in uploaded_dataset.in_folder.split( os.path.sep ):
-            folder.refresh()
+            trans.sa_session.refresh( folder )
             matches = filter( lambda x: x.name == name, active_folders( trans, folder ) )
             if matches:
                 folder = matches[0]
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/tools/parameters/basic.py	Thu Oct 22 23:02:28 2009 -0400
@@ -1239,7 +1239,7 @@
         elif isinstance( value, trans.app.model.HistoryDatasetAssociation ):
             return value
         else:
-            return trans.app.model.HistoryDatasetAssociation.get( value )
+            return trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value )
 
     def to_string( self, value, app ):
         if value is None or isinstance( value, str ):
@@ -1253,7 +1253,7 @@
         # indicates that the dataset is optional, while '' indicates that it is not.
         if value is None or value == '' or value == 'None':
             return value
-        return app.model.HistoryDatasetAssociation.get( int( value ) )
+        return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) )
 
     def to_param_dict_string( self, value, other_values={} ):
         if value is None: return "None"
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/admin.py	Thu Oct 22 23:02:28 2009 -0400
@@ -119,9 +119,9 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        roles = trans.app.model.Role.filter( and_( trans.app.model.Role.table.c.deleted==False,
-                                                   trans.app.model.Role.table.c.type != trans.app.model.Role.types.PRIVATE ) ) \
-                                    .order_by( trans.app.model.Role.table.c.name ).all()
+        roles = trans.sa_session.query( trans.app.model.Role ).filter( and_( trans.app.model.Role.table.c.deleted==False,
+                                                                             trans.app.model.Role.table.c.type != trans.app.model.Role.types.PRIVATE ) ) \
+                                                              .order_by( trans.app.model.Role.table.c.name )
         return trans.fill_template( '/admin/dataset_security/roles.mako',
                                     roles=roles,
                                     msg=msg,
@@ -140,18 +140,18 @@
             create_group_for_role = params.get( 'create_group_for_role', 'no' )
             if not name or not description:
                 msg = "Enter a valid name and a description"
-            elif trans.app.model.Role.filter( trans.app.model.Role.table.c.name==name ).first():
+            elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==name ).first():
                 msg = "A role with that name already exists"
             else:
                 # Create the role
                 role = trans.app.model.Role( name=name, description=description, type=trans.app.model.Role.types.ADMIN )
                 role.flush()
                 # Create the UserRoleAssociations
-                for user in [ trans.app.model.User.get( x ) for x in in_users ]:
+                for user in [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in in_users ]:
                     ura = trans.app.model.UserRoleAssociation( user, role )
                     ura.flush()
                 # Create the GroupRoleAssociations
-                for group in [ trans.app.model.Group.get( x ) for x in in_groups ]:
+                for group in [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in in_groups ]:
                     gra = trans.app.model.GroupRoleAssociation( group, role )
                     gra.flush()
                 if create_group_for_role == 'yes':
@@ -165,10 +165,14 @@
                 trans.response.send_redirect( web.url_for( controller='admin', action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) )
             trans.response.send_redirect( web.url_for( controller='admin', action='create_role', msg=util.sanitize_text( msg ), messagetype='error' ) )
         out_users = []
-        for user in trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all():
+        for user in trans.sa_session.query( trans.app.model.User ) \
+                                    .filter( trans.app.model.User.table.c.deleted==False ) \
+                                    .order_by( trans.app.model.User.table.c.email ):
             out_users.append( ( user.id, user.email ) )
         out_groups = []
-        for group in trans.app.model.Group.filter( trans.app.model.Group.table.c.deleted==False ).order_by( trans.app.model.Group.table.c.name ).all():
+        for group in trans.sa_session.query( trans.app.model.Group ) \
+                                     .filter( trans.app.model.Group.table.c.deleted==False ) \
+                                     .order_by( trans.app.model.Group.table.c.name ):
             out_groups.append( ( group.id, group.name ) )
         return trans.fill_template( '/admin/dataset_security/role_create.mako',
                                     in_users=[],
@@ -183,26 +187,26 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        role = trans.app.model.Role.get( int( params.role_id ) )
+        role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) )
         if params.get( 'role_members_edit_button', False ):
-            in_users = [ trans.app.model.User.get( x ) for x in util.listify( params.in_users ) ]
+            in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ]
             for ura in role.users:
-                user = trans.app.model.User.get( ura.user_id )
+                user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id )
                 if user not in in_users:
                     # Delete DefaultUserPermissions for previously associated users that have been removed from the role
                     for dup in user.default_permissions:
                         if role == dup.role:
-                            dup.delete()
+                            trans.sa_session.delete( dup )
                             dup.flush()
                     # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role
                     for history in user.histories:
                         for dhp in history.default_permissions:
                             if role == dhp.role:
-                                dhp.delete()
+                                trans.sa_session.delete( dhp )
                                 dhp.flush()
-            in_groups = [ trans.app.model.Group.get( x ) for x in util.listify( params.in_groups ) ]
+            in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ]
             trans.app.security_agent.set_entity_role_associations( roles=[ role ], users=in_users, groups=in_groups )
-            role.refresh()
+            trans.sa_session.refresh( role )
             msg = "Role '%s' has been updated with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) )
             trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype=messagetype ) )
         elif params.get( 'rename', False ):
@@ -213,7 +217,7 @@
                 if not new_name:
                     msg = 'Enter a valid name'
                     return trans.fill_template( '/admin/dataset_security/role_rename.mako', role=role, msg=msg, messagetype='error' )
-                elif trans.app.model.Role.filter( trans.app.model.Role.table.c.name==new_name ).first():
+                elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==new_name ).first():
                     msg = 'A role with that name already exists'
                     return trans.fill_template( '/admin/dataset_security/role_rename.mako', role=role, msg=msg, messagetype='error' )
                 else:
@@ -227,12 +231,16 @@
         out_users = []
         in_groups = []
         out_groups = []
-        for user in trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all():
+        for user in trans.sa_session.query( trans.app.model.User ) \
+                                    .filter( trans.app.model.User.table.c.deleted==False ) \
+                                    .order_by( trans.app.model.User.table.c.email ):
             if user in [ x.user for x in role.users ]:
                 in_users.append( ( user.id, user.email ) )
             else:
                 out_users.append( ( user.id, user.email ) )
-        for group in trans.app.model.Group.filter( trans.app.model.Group.table.c.deleted==False ).order_by( trans.app.model.Group.table.c.name ).all():
+        for group in trans.sa_session.query( trans.app.model.Group ) \
+                                     .filter( trans.app.model.Group.table.c.deleted==False ) \
+                                     .order_by( trans.app.model.Group.table.c.name ):
             if group in [ x.group for x in role.groups ]:
                 in_groups.append( ( group.id, group.name ) )
             else:
@@ -242,9 +250,8 @@
         # [ ( LibraryDatasetDatasetAssociation [ action, action ] ) ]
         library_dataset_actions = {}
         for dp in role.dataset_actions:
-            for ldda in trans.app.model.LibraryDatasetDatasetAssociation \
-                            .filter( trans.app.model.LibraryDatasetDatasetAssociation.dataset_id==dp.dataset_id ) \
-                            .all():
+            for ldda in trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
+                                        .filter( trans.app.model.LibraryDatasetDatasetAssociation.dataset_id==dp.dataset_id ):
                 root_found = False
                 folder_path = ''
                 folder = ldda.library_dataset.folder
@@ -255,7 +262,9 @@
                     else:
                         folder = folder.parent
                 folder_path = '%s %s' % ( folder_path, ldda.name )
-                library = trans.app.model.Library.filter( trans.app.model.Library.table.c.root_folder_id == folder.id ).first()
+                library = trans.sa_session.query( trans.app.model.Library ) \
+                                          .filter( trans.app.model.Library.table.c.root_folder_id == folder.id ) \
+                                          .first()
                 if library not in library_dataset_actions:
                     library_dataset_actions[ library ] = {}
                 try:
@@ -275,7 +284,7 @@
     @web.require_admin
     def mark_role_deleted( self, trans, **kwd ):
         params = util.Params( kwd )
-        role = trans.app.model.Role.get( int( params.role_id ) )
+        role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) )
         role.deleted = True
         role.flush()
         msg = "Role '%s' has been marked as deleted." % role.name
@@ -286,10 +295,9 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        roles = trans.app.model.Role.query() \
-            .filter( trans.app.model.Role.table.c.deleted==True ) \
-            .order_by( trans.app.model.Role.table.c.name ) \
-            .all()
+        roles = trans.sa_session.query( trans.app.model.Role ) \
+                                .filter( trans.app.model.Role.table.c.deleted==True ) \
+                                .order_by( trans.app.model.Role.table.c.name )
         return trans.fill_template( '/admin/dataset_security/deleted_roles.mako', 
                                     roles=roles, 
                                     msg=msg,
@@ -298,7 +306,7 @@
     @web.require_admin
     def undelete_role( self, trans, **kwd ):
         params = util.Params( kwd )
-        role = trans.app.model.Role.get( int( params.role_id ) )
+        role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) )
         role.deleted = False
         role.flush()
         msg = "Role '%s' has been marked as not deleted." % role.name
@@ -314,34 +322,34 @@
         # - GroupRoleAssociations where role_id == Role.id
         # - DatasetPermissionss where role_id == Role.id
         params = util.Params( kwd )
-        role = trans.app.model.Role.get( int( params.role_id ) )
+        role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) )
         if not role.deleted:
             # We should never reach here, but just in case there is a bug somewhere...
             msg = "Role '%s' has not been deleted, so it cannot be purged." % role.name
             trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='error' ) )
         # Delete UserRoleAssociations
         for ura in role.users:
-            user = trans.app.model.User.get( ura.user_id )
+            user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id )
             # Delete DefaultUserPermissions for associated users
             for dup in user.default_permissions:
                 if role == dup.role:
-                    dup.delete()
+                    trans.sa_session.delete( dup )
                     dup.flush()
             # Delete DefaultHistoryPermissions for associated users
             for history in user.histories:
                 for dhp in history.default_permissions:
                     if role == dhp.role:
-                        dhp.delete()
+                        trans.sa_session.delete( dhp )
                         dhp.flush()
-            ura.delete()
+            trans.sa_session.delete( ura )
             ura.flush()
         # Delete GroupRoleAssociations
         for gra in role.groups:
-            gra.delete()
+            trans.sa_session.delete( gra )
             gra.flush()
         # Delete DatasetPermissionss
         for dp in role.dataset_actions:
-            dp.delete()
+            trans.sa_session.delete( dp )
             dp.flush()
         msg = "The following have been purged from the database for role '%s': " % role.name
         msg += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, DatasetPermissionss."
@@ -354,10 +362,9 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        groups = trans.app.model.Group.query() \
-            .filter( trans.app.model.Group.table.c.deleted==False ) \
-            .order_by( trans.app.model.Group.table.c.name ) \
-            .all()
+        groups = trans.sa_session.query( trans.app.model.Group ) \
+                                 .filter( trans.app.model.Group.table.c.deleted==False ) \
+                                 .order_by( trans.app.model.Group.table.c.name )
         return trans.fill_template( '/admin/dataset_security/groups.mako', 
                                     groups=groups, 
                                     msg=msg,
@@ -368,12 +375,12 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        group = trans.app.model.Group.get( int( params.group_id ) )
+        group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) )
         if params.get( 'group_roles_users_edit_button', False ):
-            in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.in_roles ) ]
-            in_users = [ trans.app.model.User.get( x ) for x in util.listify( params.in_users ) ]
+            in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.in_roles ) ]
+            in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ]
             trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=in_roles, users=in_users )
-            group.refresh()
+            trans.sa_session.refresh( group )
             msg += "Group '%s' has been updated with %d associated roles and %d associated users" % ( group.name, len( in_roles ), len( in_users ) )
             trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype=messagetype ) )
         if params.get( 'rename', False ):
@@ -383,7 +390,7 @@
                 if not new_name:
                     msg = 'Enter a valid name'
                     return trans.fill_template( '/admin/dataset_security/group_rename.mako', group=group, msg=msg, messagetype='error' )
-                elif trans.app.model.Group.filter( trans.app.model.Group.table.c.name==new_name ).first():
+                elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==new_name ).first():
                     msg = 'A group with that name already exists'
                     return trans.fill_template( '/admin/dataset_security/group_rename.mako', group=group, msg=msg, messagetype='error' )
                 else:
@@ -396,12 +403,16 @@
         out_roles = []
         in_users = []
         out_users = []
-        for role in trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all():
+        for role in trans.sa_session.query(trans.app.model.Role ) \
+                                    .filter( trans.app.model.Role.table.c.deleted==False ) \
+                                    .order_by( trans.app.model.Role.table.c.name ):
             if role in [ x.role for x in group.roles ]:
                 in_roles.append( ( role.id, role.name ) )
             else:
                 out_roles.append( ( role.id, role.name ) )
-        for user in trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all():
+        for user in trans.sa_session.query( trans.app.model.User ) \
+                                    .filter( trans.app.model.User.table.c.deleted==False ) \
+                                    .order_by( trans.app.model.User.table.c.email ):
             if user in [ x.user for x in group.users ]:
                 in_users.append( ( user.id, user.email ) )
             else:
@@ -427,28 +438,32 @@
             in_roles = util.listify( params.get( 'in_roles', [] ) )
             if not name:
                 msg = "Enter a valid name"
-            elif trans.app.model.Group.filter( trans.app.model.Group.table.c.name==name ).first():
+            elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first():
                 msg = "A group with that name already exists"
             else:
                 # Create the group
                 group = trans.app.model.Group( name=name )
                 group.flush()
                 # Create the UserRoleAssociations
-                for user in [ trans.app.model.User.get( x ) for x in in_users ]:
+                for user in [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in in_users ]:
                     uga = trans.app.model.UserGroupAssociation( user, group )
                     uga.flush()
                 # Create the GroupRoleAssociations
-                for role in [ trans.app.model.Role.get( x ) for x in in_roles ]:
+                for role in [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in in_roles ]:
                     gra = trans.app.model.GroupRoleAssociation( group, role )
                     gra.flush()
                 msg = "Group '%s' has been created with %d associated users and %d associated roles" % ( name, len( in_users ), len( in_roles ) )
                 trans.response.send_redirect( web.url_for( controller='admin', action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) )
             trans.response.send_redirect( web.url_for( controller='admin', action='create_group', msg=util.sanitize_text( msg ), messagetype='error' ) )
         out_users = []
-        for user in trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all():
+        for user in trans.sa_session.query( trans.app.model.User ) \
+                                    .filter( trans.app.model.User.table.c.deleted==False ) \
+                                    .order_by( trans.app.model.User.table.c.email ):
             out_users.append( ( user.id, user.email ) )
         out_roles = []
-        for role in trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all():
+        for role in trans.sa_session.query( trans.app.model.Role ) \
+                                    .filter( trans.app.model.Role.table.c.deleted==False ) \
+                                    .order_by( trans.app.model.Role.table.c.name ):
             out_roles.append( ( role.id, role.name ) )
         return trans.fill_template( '/admin/dataset_security/group_create.mako',
                                     in_users=[],
@@ -461,7 +476,7 @@
     @web.require_admin
     def mark_group_deleted( self, trans, **kwd ):
         params = util.Params( kwd )
-        group = trans.app.model.Group.get( int( params.group_id ) )
+        group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) )
         group.deleted = True
         group.flush()
         msg = "Group '%s' has been marked as deleted." % group.name
@@ -472,10 +487,9 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        groups = trans.app.model.Group.query() \
-            .filter( trans.app.model.Group.table.c.deleted==True ) \
-            .order_by( trans.app.model.Group.table.c.name ) \
-            .all()
+        groups = trans.sa_session.query( trans.app.model.Group ) \
+                                 .filter( trans.app.model.Group.table.c.deleted==True ) \
+                                 .order_by( trans.app.model.Group.table.c.name )
         return trans.fill_template( '/admin/dataset_security/deleted_groups.mako', 
                                     groups=groups, 
                                     msg=msg,
@@ -484,7 +498,7 @@
     @web.require_admin
     def undelete_group( self, trans, **kwd ):
         params = util.Params( kwd )
-        group = trans.app.model.Group.get( int( params.group_id ) )
+        group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) )
         group.deleted = False
         group.flush()
         msg = "Group '%s' has been marked as not deleted." % group.name
@@ -495,18 +509,18 @@
         # This method should only be called for a Group that has previously been deleted.
         # Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations.
         params = util.Params( kwd )
-        group = trans.app.model.Group.get( int( params.group_id ) )
+        group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) )
         if not group.deleted:
             # We should never reach here, but just in case there is a bug somewhere...
             msg = "Group '%s' has not been deleted, so it cannot be purged." % group.name
             trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='error' ) )
         # Delete UserGroupAssociations
         for uga in group.users:
-            uga.delete()
+            trans.sa_session.delete( uga )
             uga.flush()
         # Delete GroupRoleAssociations
         for gra in group.roles:
-            gra.delete()
+            trans.sa_session.delete( gra )
             gra.flush()
         # Delete the Group
         msg = "The following have been purged from the database for group '%s': UserGroupAssociations, GroupRoleAssociations." % group.name
@@ -538,7 +552,7 @@
                 message = 'Enter a real email address'
             elif len( email) > 255:
                 message = 'Email address exceeds maximum allowable length'
-            elif trans.app.model.User.filter_by( email=email ).all():
+            elif trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first():
                 message = 'User with that email already exists'
             elif len( password ) < 6:
                 message = 'Use a password of at least 6 characters'
@@ -683,10 +697,10 @@
             private_role = trans.app.security_agent.get_private_user_role( user )
             # Delete History
             for h in user.active_histories:
-                h.refresh()
+                trans.sa_session.refresh( h )
                 for hda in h.active_datasets:
                     # Delete HistoryDatasetAssociation
-                    d = trans.app.model.Dataset.get( hda.dataset_id )
+                    d = trans.sa_session.query( trans.app.model.Dataset ).get( hda.dataset_id )
                     # Delete Dataset
                     if not d.deleted:
                         d.deleted = True
@@ -697,12 +711,12 @@
                 h.flush()
             # Delete UserGroupAssociations
             for uga in user.groups:
-                uga.delete()
+                trans.sa_session.delete( uga )
                 uga.flush()
             # Delete UserRoleAssociations EXCEPT FOR THE PRIVATE ROLE
             for ura in user.roles:
                 if ura.role_id != private_role.id:
-                    ura.delete()
+                    trans.sa_session.delete( ura )
                     ura.flush()
             # Purge the user
             user.purged = True
@@ -749,22 +763,22 @@
             # Make sure the user is not dis-associating himself from his private role
             out_roles = kwd.get( 'out_roles', [] )
             if out_roles:
-                out_roles = [ trans.app.model.Role.get( x ) for x in util.listify( out_roles ) ]
+                out_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( out_roles ) ]
             if private_role in out_roles:
                 message += "You cannot eliminate a user's private role association.  "
                 status = 'error'
             in_roles = kwd.get( 'in_roles', [] )
             if in_roles:
-                in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( in_roles ) ]
+                in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( in_roles ) ]
             out_groups = kwd.get( 'out_groups', [] )
             if out_groups:
-                out_groups = [ trans.app.model.Group.get( x ) for x in util.listify( out_groups ) ]
+                out_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( out_groups ) ]
             in_groups = kwd.get( 'in_groups', [] )
             if in_groups:
-                in_groups = [ trans.app.model.Group.get( x ) for x in util.listify( in_groups ) ]
+                in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( in_groups ) ]
             if in_roles:
                 trans.app.security_agent.set_entity_user_associations( users=[ user ], roles=in_roles, groups=in_groups )
-                user.refresh()
+                trans.sa_session.refresh( user )
                 message += "User '%s' has been updated with %d associated roles and %d associated groups (private roles are not displayed)" % \
                     ( user.email, len( in_roles ), len( in_groups ) )
                 trans.response.send_redirect( web.url_for( action='users',
@@ -774,8 +788,8 @@
         out_roles = []
         in_groups = []
         out_groups = []
-        for role in trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ) \
-                                        .order_by( trans.app.model.Role.table.c.name ).all():
+        for role in trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.deleted==False ) \
+                                                                  .order_by( trans.app.model.Role.table.c.name ):
             if role in [ x.role for x in user.roles ]:
                 in_roles.append( ( role.id, role.name ) )
             elif role.type != trans.app.model.Role.types.PRIVATE:
@@ -784,8 +798,8 @@
                 # role, which should always be in in_roles.  The check above is added as an additional
                 # precaution, since for a period of time we were including private roles in the form fields.
                 out_roles.append( ( role.id, role.name ) )
-        for group in trans.app.model.Group.filter( trans.app.model.Group.table.c.deleted==False ) \
-                                          .order_by( trans.app.model.Group.table.c.name ).all():
+        for group in trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.deleted==False ) \
+                                                                    .order_by( trans.app.model.Group.table.c.name ):
             if group in [ x.group for x in user.groups ]:
                 in_groups.append( ( group.id, group.name ) )
             else:
@@ -867,15 +881,13 @@
             msg += ', '.join( deleted )
             messagetype = 'done'
         cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) )
-        jobs = trans.app.model.Job.filter(
-            and_( trans.app.model.Job.table.c.update_time < cutoff_time,
-                or_( trans.app.model.Job.c.state == trans.app.model.Job.states.NEW,
-                     trans.app.model.Job.c.state == trans.app.model.Job.states.QUEUED,
-                     trans.app.model.Job.c.state == trans.app.model.Job.states.RUNNING,
-                     trans.app.model.Job.c.state == trans.app.model.Job.states.UPLOAD,
-                )
-            )
-        ).order_by(trans.app.model.Job.c.update_time.desc()).all()
+        jobs = trans.sa_session.query( trans.app.model.Job ) \
+                               .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time,
+                                              or_( trans.app.model.Job.state == trans.app.model.Job.states.NEW,
+                                                   trans.app.model.Job.state == trans.app.model.Job.states.QUEUED,
+                                                   trans.app.model.Job.state == trans.app.model.Job.states.RUNNING,
+                                                   trans.app.model.Job.state == trans.app.model.Job.states.UPLOAD ) ) ) \
+                               .order_by( trans.app.model.Job.table.c.update_time.desc() )
         last_updated = {}
         for job in jobs:
             delta = datetime.utcnow() - job.update_time
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/async.py
--- a/lib/galaxy/web/controllers/async.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/async.py	Thu Oct 22 23:02:28 2009 -0400
@@ -52,7 +52,7 @@
         if data_id:
             if not URL:
                 return "No URL parameter was submitted for data %s" % data_id
-            data = trans.model.HistoryDatasetAssociation.get( data_id )
+            data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( data_id )
            
             if not data:
                 return "Data %s does not exist or has already been deleted" % data_id
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/dataset.py
--- a/lib/galaxy/web/controllers/dataset.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/dataset.py	Thu Oct 22 23:02:28 2009 -0400
@@ -138,12 +138,12 @@
 
     @web.expose
     def errors( self, trans, id ):
-        dataset = model.HistoryDatasetAssociation.get( id )
+        dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
         return trans.fill_template( "dataset/errors.mako", dataset=dataset )
     
     @web.expose
     def stderr( self, trans, id ):
-        dataset = model.HistoryDatasetAssociation.get( id )
+        dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
         job = dataset.creating_job_associations[0].job
         trans.response.set_content_type( 'text/plain' )
         return job.stderr
@@ -157,7 +157,7 @@
         if to_address is None:
             return trans.show_error_message( "Sorry, error reporting has been disabled for this galaxy instance" )
         # Get the dataset and associated job
-        dataset = model.HistoryDatasetAssociation.get( id )
+        dataset = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id )
         job = dataset.creating_job_associations[0].job
         # Get the name of the server hosting the Galaxy instance from which this report originated
         host = trans.request.host
@@ -207,7 +207,7 @@
             dataset_id = int( dataset_id )
         except ValueError:
             dataset_id = trans.security.decode_id( dataset_id )
-        data = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
+        data = data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
         if not data:
             raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
         user, roles = trans.get_user_and_roles()
@@ -305,7 +305,7 @@
     def display_at( self, trans, dataset_id, filename=None, **kwd ):
         """Sets up a dataset permissions so it is viewable at an external site"""
         site = filename
-        data = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
+        data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
         if not data:
             raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
         if 'display_url' not in kwd or 'redirect_url' not in kwd:
@@ -326,7 +326,7 @@
         except ValueError, e:
             return False
         history = trans.get_history()
-        data = self.app.model.HistoryDatasetAssociation.get( id )
+        data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
         if data and data.undeletable:
             # Walk up parent datasets to find the containing history
             topmost_parent = data
@@ -390,12 +390,12 @@
                     new_history.flush()
                     target_history_ids.append( new_history.id )
                 if user:
-                    target_histories = [ hist for hist in map( trans.app.model.History.get, target_history_ids ) if ( hist is not None and hist.user == user )]
+                    target_histories = [ hist for hist in map( trans.sa_session.query( trans.app.model.History ).get, target_history_ids ) if ( hist is not None and hist.user == user )]
                 else:
                     target_histories = [ history ]
                 if len( target_histories ) != len( target_history_ids ):
                     error_msg = error_msg + "You do not have permission to add datasets to %i requested histories.  " % ( len( target_history_ids ) - len( target_histories ) )
-                for data in map( trans.app.model.HistoryDatasetAssociation.get, source_dataset_ids ):
+                for data in map( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get, source_dataset_ids ):
                     if data is None:
                         error_msg = error_msg + "You tried to copy a dataset that does not exist.  "
                         invalid_datasets += 1
@@ -409,7 +409,7 @@
                     refresh_frames = ['history']
                 trans.app.model.flush()
                 done_msg = "%i datasets copied to %i histories." % ( len( source_dataset_ids ) - invalid_datasets, len( target_histories ) )
-                history.refresh()
+                trans.sa_session.refresh( history )
         elif create_new_history:
             target_history_ids.append( "create_new_history" )
         source_datasets = history.active_datasets
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/forms.py
--- a/lib/galaxy/web/controllers/forms.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/forms.py	Thu Oct 22 23:02:28 2009 -0400
@@ -39,7 +39,7 @@
         show_filter = params.get( 'show_filter', 'Active' )
         return self._show_forms_list(trans, msg, messagetype, show_filter)
     def _show_forms_list(self, trans, msg, messagetype, show_filter='Active'):
-        all_forms = trans.app.model.FormDefinitionCurrent.query().all()
+        all_forms = trans.sa_session.query( trans.app.model.FormDefinitionCurrent )
         if show_filter == 'All':
             forms_list = all_forms
         elif show_filter == 'Deleted':
@@ -109,7 +109,7 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        fd = trans.app.model.FormDefinition.get(int(util.restore_text( params.form_id )))
+        fd = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( util.restore_text( params.form_id ) ) )
         fd.form_definition_current.deleted = True
         fd.form_definition_current.flush()
         return self._show_forms_list(trans, 
@@ -121,7 +121,7 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        fd = trans.app.model.FormDefinition.get(int(util.restore_text( params.form_id )))
+        fd = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( util.restore_text( params.form_id ) ) )
         fd.form_definition_current.deleted = False
         fd.form_definition_current.flush()
         return self._show_forms_list(trans, 
@@ -138,7 +138,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            fd = trans.app.model.FormDefinition.get( int( params.get( 'form_id', None ) ) )
+            fd = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.get( 'form_id', None ) ) )
         except:
             return trans.response.send_redirect( web.url_for( controller='forms',
                                                               action='manage',
@@ -444,7 +444,7 @@
         if fdc_id: # save changes to the existing form    
             # change the pointer in the form_definition_current table to point 
             # to this new record
-            fdc = trans.app.model.FormDefinitionCurrent.get(fdc_id)
+            fdc = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ).get( fdc_id )
         else: # create a new form
             fdc = trans.app.model.FormDefinitionCurrent()
         # create corresponding row in the form_definition_current table
@@ -578,11 +578,11 @@
     of all the forms from the form_definition table.
     '''
     if all_versions:
-        return trans.app.model.FormDefinition.query().all()
+        return trans.sa_session.query( trans.app.model.FormDefinition )
     if filter:
-        fdc_list = trans.app.model.FormDefinitionCurrent.query().filter_by(**filter)
+        fdc_list = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ).filter_by( **filter )
     else:
-        fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
+        fdc_list = trans.sa_session.query( trans.app.model.FormDefinitionCurrent )
     if form_type == 'All':
         return [ fdc.latest_form for fdc in fdc_list ]
     else:
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/genetrack.py
--- a/lib/galaxy/web/controllers/genetrack.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/genetrack.py	Thu Oct 22 23:02:28 2009 -0400
@@ -154,7 +154,7 @@
         """
         Default search page
         """
-        data = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
+        data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
         if not data:
             raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
         # the main configuration file
@@ -202,7 +202,7 @@
         Main request handler
         """
         color = cycle( [LIGHT, WHITE] )
-        data = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
+        data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
         if not data:
             raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
         # the main configuration file
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/history.py	Thu Oct 22 23:02:28 2009 -0400
@@ -233,9 +233,9 @@
                     status, message = self._list_undelete( trans, histories )
                 elif operation == "unshare":
                     for history in histories:
-                        husas = trans.app.model.HistoryUserShareAssociation.filter_by( history=history ).all()
-                        for husa in husas:
-                            husa.delete()
+                        for husa in trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
+                                                    .filter_by( history=history ):
+                            trans.sa_session.delete( husa )
                 elif operation == "enable import via link":
                     for history in histories:
                         if not history.importable:
@@ -306,8 +306,9 @@
         new_history = histories[0]
         galaxy_session = trans.get_galaxy_session()
         try:
-            association = trans.app.model.GalaxySessionToHistoryAssociation \
-                .filter_by( session_id=galaxy_session.id, history_id=trans.security.decode_id( new_history.id ) ).first()
+            association = trans.sa_session.query( trans.app.model.GalaxySessionToHistoryAssociation ) \
+                                          .filter_by( session_id=galaxy_session.id, history_id=trans.security.decode_id( new_history.id ) ) \
+                                          .first()
         except:
             association = None
         new_history.add_galaxy_session( galaxy_session, association=association )
@@ -338,8 +339,8 @@
                 histories = [ get_history( trans, history_id ) for history_id in ids ]
                 for history in histories:
                     # Current user is the user with which the histories were shared
-                    association = trans.app.model.HistoryUserShareAssociation.filter_by( user=trans.user, history=history ).one()
-                    association.delete()
+                    association = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=trans.user, history=history ).one()
+                    trans.sa_session.delete( association )
                     association.flush()
                 message = "Unshared %d shared histories" % len( ids )
                 status = 'done'
@@ -360,7 +361,7 @@
         return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] )
     @web.expose
     def rename_async( self, trans, id=None, new_name=None ):
-        history = model.History.get( id )
+        history = trans.sa_session.query( model.History ).get( id )
         # Check that the history exists, and is either owned by the current
         # user (if logged in) or the current history
         assert history is not None
@@ -393,8 +394,9 @@
             new_history.user_id = user.id
             galaxy_session = trans.get_galaxy_session()
             try:
-                association = trans.app.model.GalaxySessionToHistoryAssociation \
-                    .filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first()
+                association = trans.sa_session.query( trans.app.model.GalaxySessionToHistoryAssociation ) \
+                                              .filter_by( session_id=galaxy_session.id, history_id=new_history.id ) \
+                                              .first()
             except:
                 association = None
             new_history.add_galaxy_session( galaxy_session, association=association )
@@ -410,8 +412,9 @@
             new_history.user_id = None
             galaxy_session = trans.get_galaxy_session()
             try:
-                association = trans.app.model.GalaxySessionToHistoryAssociation \
-                    .filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first()
+                association = trans.sa_session.query( trans.app.model.GalaxySessionToHistoryAssociation ) \
+                                              .filter_by( session_id=galaxy_session.id, history_id=new_history.id ) \
+                                              .first()
             except:
                 association = None
             new_history.add_galaxy_session( galaxy_session, association=association )
@@ -443,10 +446,10 @@
 
         # View history.
         query = trans.sa_session.query( model.HistoryDatasetAssociation ) \
-            .filter( model.HistoryDatasetAssociation.history == history_to_view ) \
-            .options( eagerload( "children" ) ) \
-            .join( "dataset" ).filter( model.Dataset.purged == False ) \
-            .options( eagerload_all( "dataset.actions" ) )
+                                .filter( model.HistoryDatasetAssociation.history == history_to_view ) \
+                                .options( eagerload( "children" ) ) \
+                                .join( "dataset" ).filter( model.Dataset.purged == False ) \
+                                .options( eagerload_all( "dataset.actions" ) )
         # Do not show deleted datasets.
         query = query.filter( model.HistoryDatasetAssociation.deleted == False )
         user_owns_history = ( trans.get_user() == history_to_view.user )
@@ -547,10 +550,10 @@
         for send_to_user, history_dict in can_change.items():
             for history in history_dict:                  
                 # Make sure the current history has not already been shared with the current send_to_user
-                if trans.app.model.HistoryUserShareAssociation \
-                    .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, 
-                                  trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
-                    .count() > 0:
+                if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
+                                   .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, 
+                                                  trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
+                                   .count() > 0:
                     send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
                 else:
                     # Only deal with datasets that have not been purged
@@ -590,8 +593,10 @@
                 if email_address == user.email:
                     send_to_err += "You cannot send histories to yourself.  "
                 else:
-                    send_to_user = trans.app.model.User.filter( and_( trans.app.model.User.table.c.email==email_address,
-                                                                      trans.app.model.User.table.c.deleted==False ) ).first()                                                                      
+                    send_to_user = trans.sa_session.query( trans.app.model.User ) \
+                                                   .filter( and_( trans.app.model.User.table.c.email==email_address,
+                                                                  trans.app.model.User.table.c.deleted==False ) ) \
+                                                   .first()                                                                      
                     if send_to_user:
                         send_to_users.append( send_to_user )
                     else:
@@ -608,10 +613,10 @@
         for send_to_user, history_dict in other.items():
             for history in history_dict:
                 # Make sure the current history has not already been shared with the current send_to_user
-                if trans.app.model.HistoryUserShareAssociation \
-                    .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, 
-                                  trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
-                    .count() > 0:
+                if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
+                                   .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, 
+                                                  trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
+                                   .count() > 0:
                     send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
                 else:
                     # Build the dict that will be used for sharing
@@ -640,10 +645,10 @@
         for history in histories:
             for send_to_user in send_to_users:
                 # Make sure the current history has not already been shared with the current send_to_user
-                if trans.app.model.HistoryUserShareAssociation \
-                    .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, 
-                                  trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
-                    .count() > 0:
+                if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
+                                   .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id, 
+                                                  trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
+                                   .count() > 0:
                     send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
                 else:
                     # Only deal with datasets that have not been purged
@@ -748,14 +753,14 @@
                 history.importable = False
                 history.flush()
             elif params.get( 'unshare_user', False ):
-                user = trans.app.model.User.get( trans.security.decode_id( kwd[ 'unshare_user' ] ) )
+                user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( kwd[ 'unshare_user' ] ) )
                 if not user:
                     msg = 'History (%s) does not seem to be shared with user (%s)' % ( history.name, user.email )
                     return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='error' )
-                husas = trans.app.model.HistoryUserShareAssociation.filter_by( user=user, history=history ).all()
+                husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=user, history=history ).all()
                 if husas:
                     for husa in husas:
-                        husa.delete()
+                        trans.sa_session.delete( husa )
                         husa.flush()
         histories = []
         # Get all histories that have been shared with others
@@ -763,8 +768,7 @@
                                 .join( "history" ) \
                                 .filter( and_( trans.app.model.History.user == trans.user,
                                                trans.app.model.History.deleted == False ) ) \
-                                .order_by( trans.app.model.History.table.c.name ) \
-                                .all()
+                                .order_by( trans.app.model.History.table.c.name )
         for husa in husas:
             history = husa.history
             if history not in histories:
@@ -772,8 +776,7 @@
         # Get all histories that are importable
         importables = trans.sa_session.query( trans.app.model.History ) \
                                       .filter_by( user=trans.user, importable=True, deleted=False ) \
-                                      .order_by( trans.app.model.History.table.c.name ) \
-                                      .all()
+                                      .order_by( trans.app.model.History.table.c.name )
         for importable in importables:
             if importable not in histories:
                 histories.append( importable )
@@ -843,7 +846,8 @@
                 owner = True
             else:
                 if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
-                        .filter_by( user=user, history=history ).count() == 0:
+                                   .filter_by( user=user, history=history ) \
+                                   .count() == 0:
                     return trans.show_error_message( "The history you are attempting to clone is not owned by you or shared with you.  " )
                 owner = False
             name = "Clone of '%s'" % history.name
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/library.py
--- a/lib/galaxy/web/controllers/library.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/library.py	Thu Oct 22 23:02:28 2009 -0400
@@ -63,8 +63,9 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         user, roles = trans.get_user_and_roles()
-        all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted==False ) \
-                                               .order_by( trans.app.model.Library.name ).all()
+        all_libraries = trans.sa_session.query( trans.app.model.Library ) \
+                                        .filter( trans.app.model.Library.table.c.deleted==False ) \
+                                        .order_by( trans.app.model.Library.name )
         library_actions = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD,
                             trans.app.security_agent.permitted_actions.LIBRARY_MODIFY,
                             trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ]
@@ -102,7 +103,7 @@
                                                               default_action=params.get( 'default_action', None ),
                                                               msg=util.sanitize_text( msg ),
                                                               messagetype='error' ) )
-        library = library=trans.app.model.Library.get( library_id )
+        library = trans.sa_session.query( trans.app.model.Library ).get( library_id )
         if not library:
             # To handle bots
             msg = "Invalid library id ( %s )." % str( library_id )
@@ -144,7 +145,7 @@
                                                               action='browse_libraries',
                                                               msg=util.sanitize_text( msg ),
                                                               messagetype='error' ) )
-        library = trans.app.model.Library.get( int( library_id ) )
+        library = trans.sa_session.query( trans.app.model.Library ).get( int( library_id ) )
         if not library:
             msg = "Invalid library id ( %s ) specified." % str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='library',
@@ -190,10 +191,10 @@
                 # The user clicked the Save button on the 'Associate With Roles' form
                 permissions = {}
                 for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
                     permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
                 trans.app.security_agent.set_all_library_permissions( library, permissions )
-                library.refresh()
+                trans.sa_session.refresh( library )
                 # Copy the permissions to the root folder
                 trans.app.security_agent.copy_library_permissions( library, library.root_folder )
                 msg = "Permissions updated for library '%s'" % library.name
@@ -221,7 +222,7 @@
         else:
             # 'information' will be the default
             action = 'information'
-        folder = trans.app.model.LibraryFolder.get( int( obj_id ) )
+        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( obj_id ) )
         if not folder:
             msg = "Invalid folder specified, id: %s" % str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='library',
@@ -301,10 +302,10 @@
                 if trans.app.security_agent.can_manage_library_item( user, roles, folder ):
                     permissions = {}
                     for k, v in trans.app.model.Library.permitted_actions.items():
-                        in_roles = [ trans.app.model.Role.get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
+                        in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
                         permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
                     trans.app.security_agent.set_all_library_permissions( folder, permissions )
-                    folder.refresh()
+                    trans.sa_session.refresh( folder )
                     msg = 'Permissions updated for folder %s' % folder.name
                     return trans.response.send_redirect( web.url_for( controller='library',
                                                                       action='folder',
@@ -336,7 +337,7 @@
             action = 'permissions'
         else:
             action = 'information'
-        library_dataset = trans.app.model.LibraryDataset.get( obj_id )
+        library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( obj_id )
         if not library_dataset:
             msg = "Invalid library dataset specified, id: %s" %str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='library',
@@ -375,15 +376,15 @@
                     # The user clicked the Save button on the 'Associate With Roles' form
                     permissions = {}
                     for k, v in trans.app.model.Library.permitted_actions.items():
-                        in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
+                        in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
                         permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
                     # Set the LIBRARY permissions on the LibraryDataset
                     # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
                     trans.app.security_agent.set_all_library_permissions( library_dataset, permissions )
-                    library_dataset.refresh()
+                    trans.sa_session.refresh( library_dataset )
                     # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
                     trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions )
-                    library_dataset.library_dataset_dataset_association.refresh()
+                    trans.sa_session.refresh( library_dataset.library_dataset_dataset_association )
                     msg = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name
                     messagetype = 'done'
                 else:
@@ -399,7 +400,7 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
+        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
         if not ldda:
             msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='library',
@@ -535,7 +536,7 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
+        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
         if not ldda:
             msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='admin',
@@ -560,7 +561,7 @@
         # Display permission form, permissions will be updated for all lddas simultaneously.
         lddas = []
         for obj_id in [ int( obj_id ) for obj_id in obj_ids ]:
-            ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
+            ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
             if ldda is None:
                 msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( obj_id )
                 trans.response.send_redirect( web.url_for( controller='library',
@@ -574,24 +575,24 @@
                 trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
                 permissions = {}
                 for k, v in trans.app.model.Dataset.permitted_actions.items():
-                    in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
                     permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
                 for ldda in lddas:
                     # Set the DATASET permissions on the Dataset
                     trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions )
-                    ldda.dataset.refresh()
+                    trans.sa_session.refresh( ldda.dataset )
                 permissions = {}
                 for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
                     permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
                 for ldda in lddas:
                     # Set the LIBRARY permissions on the LibraryDataset
                     # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
                     trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions )
-                    ldda.library_dataset.refresh()
+                    trans.sa_session.refresh( ldda.library_dataset )
                     # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
                     trans.app.security_agent.set_all_library_permissions( ldda, permissions )
-                    ldda.refresh()
+                    trans.sa_session.refresh( ldda )
                 msg = 'Permissions and roles have been updated on %d datasets' % len( lddas )
                 messagetype = 'done'
             else:
@@ -645,12 +646,12 @@
             last_used_build = dbkey[0]
         else:
             last_used_build = dbkey
-        folder = trans.app.model.LibraryFolder.get( folder_id )
+        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder_id )
         if folder and last_used_build in [ 'None', None, '?' ]:
             last_used_build = folder.genome_build
         replace_id = params.get( 'replace_id', None )
         if replace_id not in [ None, 'None' ]:
-            replace_dataset = trans.app.model.LibraryDataset.get( params.get( 'replace_id', None ) )
+            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( replace_id )
             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
@@ -691,7 +692,7 @@
                             msg = "Added %d datasets to the folder '%s' ( each is selected ).  " % ( total_added, folder.name )
                     # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
                     # to check one of them to see if the current user can manage permissions on them.
-                    check_ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id_list[0] )
+                    check_ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id_list[0] )
                     if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ):
                         if replace_dataset:
                             default_action = ''
@@ -728,10 +729,12 @@
                 yield build_name, dbkey, ( dbkey==last_used_build )
         dbkeys = get_dbkey_options( last_used_build )
         # Send list of roles to the form so the dataset can be associated with 1 or more of them.
-        roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all()
+        roles = trans.sa_session.query( trans.app.model.Role ) \
+                                .filter( trans.app.model.Role.table.c.deleted==False ) \
+                                .order_by( trans.app.model.Role.table.c.name )
         # Send the current history to the form to enable importing datasets from history to library
         history = trans.get_history()
-        history.refresh()
+        trans.sa_session.refresh( history )
         # If we're using nginx upload, override the form action
         action = web.url_for( controller='library', action='upload_library_dataset' )
         if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
@@ -756,7 +759,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            folder = trans.app.model.LibraryFolder.get( int( folder_id ) )
+            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( folder_id ) )
         except:
             msg = "Invalid folder id: %s" % str( folder_id )
             return trans.response.send_redirect( web.url_for( controller='library',
@@ -766,12 +769,12 @@
                                                               messagetype='error' ) )
         replace_id = params.get( 'replace_id', None )
         if replace_id:
-            replace_dataset = trans.app.model.LibraryDataset.get( replace_id )
+            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( replace_id )
         else:
             replace_dataset = None
         # See if the current history is empty
         history = trans.get_history()
-        history.refresh()
+        trans.sa_session.refresh( history )
         if not history.active_datasets:
             msg = 'Your current history is empty'
             return trans.response.send_redirect( web.url_for( controller='library',
@@ -785,7 +788,7 @@
                 dataset_names = []
                 created_ldda_ids = ''
                 for hda_id in hda_ids:
-                    hda = trans.app.model.HistoryDatasetAssociation.get( hda_id )
+                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( hda_id )
                     if hda:
                         ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset )
                         created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
@@ -818,7 +821,7 @@
                             msg = "Added %d datasets to the folder '%s' ( each is selected ).  " % ( total_added, folder.name )
                     # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
                     # to check one of them to see if the current user can manage permissions on them.
-                    check_ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id_list[0] )
+                    check_ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id_list[0] )
                     user, roles = trans.get_user_and_roles()
                     if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ):
                         if replace_dataset:
@@ -848,7 +851,9 @@
                         yield build_name, dbkey, ( dbkey==last_used_build )
                 dbkeys = get_dbkey_options( last_used_build )
                 # Send list of roles to the form so the dataset can be associated with 1 or more of them.
-                roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all()
+                roles = trans.sa_session.query( trans.app.model.Role ) \
+                                        .filter( trans.app.model.Role.table.c.deleted==False ) \
+                                        .order_by( trans.app.model.Role.table.c.name )
                 return trans.fill_template( "/library/upload.mako",
                                             upload_option=upload_option,
                                             library_id=library_id,
@@ -887,7 +892,7 @@
         if params.do_action == 'add':
             history = trans.get_history()
             for ldda_id in ldda_ids:
-                ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id )
+                ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id )
                 hda = ldda.to_history_dataset_association( target_history=history, add_to_history = True )
             history.flush()
             msg = "%i dataset(s) have been imported into your history" % len( ldda_ids )
@@ -898,7 +903,7 @@
                                                               messagetype='done' ) )
         elif params.do_action == 'manage_permissions':
             # We need the folder containing the LibraryDatasetDatasetAssociation(s)
-            ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_ids[0] )
+            ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_ids[0] )
             trans.response.send_redirect( web.url_for( controller='library',
                                                        action='upload_library_dataset',
                                                        library_id=library_id,
@@ -933,7 +938,7 @@
             seen = []
             user, roles = trans.get_user_and_roles()
             for ldda_id in ldda_ids:
-                ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id )
+                ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id )
                 if not ldda or not trans.app.security_agent.can_access_dataset( roles, ldda.dataset ):
                     continue
                 path = ""
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/library_admin.py
--- a/lib/galaxy/web/controllers/library_admin.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/library_admin.py	Thu Oct 22 23:02:28 2009 -0400
@@ -19,8 +19,9 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         return trans.fill_template( '/admin/library/browse_libraries.mako', 
-                                    libraries=trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted==False ) \
-                                                                     .order_by( trans.app.model.Library.name ).all(),
+                                    libraries=trans.sa_session.query( trans.app.model.Library ) \
+                                                               .filter( trans.app.model.Library.table.c.deleted==False ) \
+                                                               .order_by( trans.app.model.Library.name ),
                                     deleted=False,
                                     show_deleted=False,
                                     msg=msg,
@@ -41,7 +42,7 @@
                                                               messagetype='error' ) )
         deleted = util.string_as_bool( params.get( 'deleted', False ) )
         show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
-        library = library=trans.app.model.Library.get( library_id )
+        library = trans.sa_session.query( trans.app.model.Library ).get( library_id )
         if not library:
             msg = "Invalid library id ( %s )." % str( library_id )
             return trans.response.send_redirect( web.url_for( controller='library_admin',
@@ -82,7 +83,7 @@
                                                               msg=util.sanitize_text( msg ),
                                                               messagetype='error' ) )
         if not action == 'new':
-            library = trans.app.model.Library.get( int( library_id ) )
+            library = trans.sa_session.query( trans.app.model.Library ).get( int( library_id ) )
         if action == 'new':
             if params.new == 'submitted':
                 library = trans.app.model.Library( name = util.restore_text( params.name ), 
@@ -134,14 +135,14 @@
                                         messagetype=messagetype )
         elif action == 'delete':
             def delete_folder( library_folder ):
-                library_folder.refresh()
+                trans.sa_session.refresh( library_folder )
                 for folder in library_folder.folders:
                     delete_folder( folder )
                 for library_dataset in library_folder.datasets:
-                    library_dataset.refresh()
+                    trans.sa_session.refresh( library_dataset )
                     ldda = library_dataset.library_dataset_dataset_association
                     if ldda:
-                        ldda.refresh()
+                        trans.sa_session.refresh( ldda )
                         # We don't set ldda.dataset.deleted to True here because the cleanup_dataset script
                         # will eventually remove it from disk.  The purge_library method below sets the dataset
                         # to deleted.  This allows for the library to be undeleted ( before it is purged ), 
@@ -152,7 +153,7 @@
                     library_dataset.flush()
                 library_folder.deleted = True
                 library_folder.flush()
-            library.refresh()
+            trans.sa_session.refresh( library )
             delete_folder( library.root_folder )
             library.deleted = True
             library.flush()
@@ -163,10 +164,10 @@
                 # The user clicked the Save button on the 'Associate With Roles' form
                 permissions = {}
                 for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
                     permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
                 trans.app.security_agent.set_all_library_permissions( library, permissions )
-                library.refresh()
+                trans.sa_session.refresh( library )
                 # Copy the permissions to the root folder
                 trans.app.security_agent.copy_library_permissions( library, library.root_folder )
                 msg = "Permissions updated for library '%s'" % library.name
@@ -186,9 +187,10 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        libraries=trans.app.model.Library.filter( and_( trans.app.model.Library.table.c.deleted==True,
-                                                        trans.app.model.Library.table.c.purged==False ) ) \
-                                         .order_by( trans.app.model.Library.table.c.name ).all()
+        libraries = trans.sa_session.query( trans.app.model.Library ) \
+                                    .filter( and_( trans.app.model.Library.table.c.deleted==True,
+                                                   trans.app.model.Library.table.c.purged==False ) ) \
+                                    .order_by( trans.app.model.Library.table.c.name )
         return trans.fill_template( '/admin/library/browse_libraries.mako', 
                                     libraries=libraries,
                                     deleted=True,
@@ -199,18 +201,18 @@
     @web.require_admin
     def purge_library( self, trans, **kwd ):
         params = util.Params( kwd )
-        library = trans.app.model.Library.get( int( params.obj_id ) )
+        library = trans.sa_session.query( trans.app.model.Library ).get( int( params.obj_id ) )
         def purge_folder( library_folder ):
             for lf in library_folder.folders:
                 purge_folder( lf )
-            library_folder.refresh()
+            trans.sa_session.refresh( library_folder )
             for library_dataset in library_folder.datasets:
-                library_dataset.refresh()
+                trans.sa_session.refresh( library_dataset )
                 ldda = library_dataset.library_dataset_dataset_association
                 if ldda:
-                    ldda.refresh()
+                    trans.sa_session.refresh( ldda )
                     dataset = ldda.dataset
-                    dataset.refresh()
+                    trans.sa_session.refresh( dataset )
                     # If the dataset is not associated with any additional undeleted folders, then we can delete it.
                     # We don't set dataset.purged to True here because the cleanup_datasets script will do that for
                     # us, as well as removing the file from disk.
@@ -254,7 +256,7 @@
         else:
             # 'information' will be the default
             action = 'information'
-        folder = trans.app.model.LibraryFolder.get( int( obj_id ) )
+        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( obj_id ) )
         if not folder:
             msg = "Invalid folder specified, id: %s" % str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='library_admin',
@@ -331,10 +333,10 @@
                 # The user clicked the Save button on the 'Associate With Roles' form
                 permissions = {}
                 for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.app.model.Role.get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
                     permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
                 trans.app.security_agent.set_all_library_permissions( folder, permissions )
-                folder.refresh()
+                trans.sa_session.refresh( folder )
                 msg = "Permissions updated for folder '%s'" % folder.name
                 return trans.response.send_redirect( web.url_for( controller='library_admin',
                                                                   action='folder',
@@ -358,7 +360,7 @@
             action = 'permissions'
         else:
             action = 'information'
-        library_dataset = trans.app.model.LibraryDataset.get( obj_id )
+        library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( obj_id )
         if not library_dataset:
             msg = "Invalid library dataset specified, id: %s" %str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='library_admin',
@@ -390,15 +392,15 @@
                 # The user clicked the Save button on the 'Edit permissions and role associations' form
                 permissions = {}
                 for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
                     permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
                 # Set the LIBRARY permissions on the LibraryDataset
                 # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
                 trans.app.security_agent.set_all_library_permissions( library_dataset, permissions )
-                library_dataset.refresh()
+                trans.sa_session.refresh( library_dataset )
                 # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
                 trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions )
-                library_dataset.library_dataset_dataset_association.refresh()
+                trans.sa_session.refresh( library_dataset.library_dataset_dataset_association )
                 msg = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name
             return trans.fill_template( '/admin/library/library_dataset_permissions.mako',
                                         library_dataset=library_dataset,
@@ -411,7 +413,7 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
+        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
         if not ldda:
             msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='library_admin',
@@ -528,7 +530,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
-        ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
+        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
         if not ldda:
             msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id )
             return trans.response.send_redirect( web.url_for( controller='library_admin',
@@ -555,7 +557,7 @@
         # Display permission form, permissions will be updated for all lddas simultaneously.
         lddas = []
         for obj_id in [ int( obj_id ) for obj_id in obj_ids ]:
-            ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
+            ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
             if ldda is None:
                 msg = 'You specified an invalid LibraryDatasetDatasetAssociation obj_id: %s' %str( obj_id )
                 trans.response.send_redirect( web.url_for( controller='library_admin',
@@ -568,7 +570,7 @@
             permissions = {}
             accessible = False
             for k, v in trans.app.model.Dataset.permitted_actions.items():
-                in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
+                in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
                 # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible
                 if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
                     if len( in_roles ) > 1:
@@ -599,19 +601,19 @@
             for ldda in lddas:
                 # Set the DATASET permissions on the Dataset
                 trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions )
-                ldda.dataset.refresh()
+                trans.sa_session.refresh( ldda.dataset )
             permissions = {}
             for k, v in trans.app.model.Library.permitted_actions.items():
-                in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
+                in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
                 permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
             for ldda in lddas:
                 # Set the LIBRARY permissions on the LibraryDataset
                 # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
                 trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions )
-                ldda.library_dataset.refresh()
+                trans.sa_session.refresh( ldda.library_dataset )
                 # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
                 trans.app.security_agent.set_all_library_permissions( ldda, permissions )
-                ldda.refresh()
+                trans.sa_session.refresh( ldda )
             if not accessible:
                 msg = "At least 1 user must have every role associated with accessing these %d datasets. " % len( lddas )
                 msg += "The roles you attempted to associate for access would make these datasets inaccessible by everyone, "
@@ -666,12 +668,12 @@
             last_used_build = dbkey[0]
         else:
             last_used_build = dbkey
-        folder = trans.app.model.LibraryFolder.get( folder_id )
+        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder_id )
         if folder and last_used_build in [ 'None', None, '?' ]:
             last_used_build = folder.genome_build
         replace_id = params.get( 'replace_id', None )
         if replace_id not in [ None, 'None' ]:
-            replace_dataset = trans.app.model.LibraryDataset.get( int( replace_id ) )
+            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( int( replace_id ) )
             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
@@ -729,10 +731,12 @@
                 yield build_name, dbkey, ( dbkey==last_used_build )
         dbkeys = get_dbkey_options( last_used_build )
         # Send list of roles to the form so the dataset can be associated with 1 or more of them.
-        roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all()
+        roles = trans.sa_session.query( trans.app.model.Role ) \
+                                .filter( trans.app.model.Role.table.c.deleted==False ) \
+                                .order_by( trans.app.model.Role.table.c.name )
         # Send the current history to the form to enable importing datasets from history to library
         history = trans.get_history()
-        history.refresh()
+        trans.sa_session.refresh( history )
         # If we're using nginx upload, override the form action
         action = web.url_for( controller='library_admin', action='upload_library_dataset' )
         if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
@@ -758,7 +762,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            folder = trans.app.model.LibraryFolder.get( int( folder_id ) )
+            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( folder_id ) )
         except:
             msg = "Invalid folder id: %s" % str( folder_id )
             return trans.response.send_redirect( web.url_for( controller='library_admin',
@@ -768,12 +772,12 @@
                                                               messagetype='error' ) )
         replace_id = params.get( 'replace_id', None )
         if replace_id:
-            replace_dataset = trans.app.model.LibraryDataset.get( replace_id )
+            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( replace_id )
         else:
             replace_dataset = None
         # See if the current history is empty
         history = trans.get_history()
-        history.refresh()
+        trans.sa_session.refresh( history )
         if not history.active_datasets:
             msg = 'Your current history is empty'
             return trans.response.send_redirect( web.url_for( controller='library_admin',
@@ -787,7 +791,7 @@
                 dataset_names = []
                 created_ldda_ids = ''
                 for hda_id in hda_ids:
-                    hda = trans.app.model.HistoryDatasetAssociation.get( hda_id )
+                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( hda_id )
                     if hda:
                         ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset )
                         created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
@@ -838,7 +842,9 @@
                         yield build_name, dbkey, ( dbkey==last_used_build )
                 dbkeys = get_dbkey_options( last_used_build )
                 # Send list of roles to the form so the dataset can be associated with 1 or more of them.
-                roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all()
+                roles = trans.sa_session.query( trans.app.model.Role ) \
+                                        .filter( trans.app.model.Role.table.c.deleted==False ) \
+                                        .order_by( trans.app.model.Role.table.c.name )
                 return trans.fill_template( "/admin/library/upload.mako",
                                             upload_option=upload_option,
                                             library_id=library_id,
@@ -871,7 +877,7 @@
                                                            messagetype='error' ) )
             if params.action == 'manage_permissions':
                 # We need the folder containing the LibraryDatasetDatasetAssociation(s)
-                ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_ids[0] ) )
+                ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( int( ldda_ids[0] ) )
                 trans.response.send_redirect( web.url_for( controller='library_admin',
                                                            action='ldda_manage_permissions',
                                                            library_id=library_id,
@@ -881,7 +887,7 @@
                                                            messagetype=messagetype ) )
             elif params.action == 'delete':
                 for ldda_id in ldda_ids:
-                    ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id )
+                    ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id )
                     ldda.deleted = True
                     ldda.flush()
                 msg = "The selected datasets have been removed from this data library"
@@ -918,7 +924,7 @@
                 library_item_desc = 'Dataset'
             else:
                 library_item_desc = library_item_type.capitalize()
-            library_item = library_item_types[ library_item_type ].get( int( library_item_id ) )
+            library_item = trans.sa_session.query( library_item_types[ library_item_type ] ).get( int( library_item_id ) )
             library_item.deleted = True
             library_item.flush()
             msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( library_item_desc, library_item.name ) )
@@ -945,7 +951,7 @@
                 library_item_desc = 'Dataset'
             else:
                 library_item_desc = library_item_type.capitalize()
-            library_item = library_item_types[ library_item_type ].get( int( library_item_id ) )
+            library_item = trans.sa_session.query( library_item_types[ library_item_type ] ).get( int( library_item_id ) )
             if library_item.purged:
                 msg = '%s %s has been purged, so it cannot be undeleted' % ( library_item_desc, library_item.name )
                 messagetype = 'error'
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/library_common.py
--- a/lib/galaxy/web/controllers/library_common.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/library_common.py	Thu Oct 22 23:02:28 2009 -0400
@@ -22,7 +22,7 @@
             ids = map( int, ids.split( "," ) )
             states = states.split( "," )
             for id, state in zip( ids, states ):
-                data = self.app.model.LibraryDatasetDatasetAssociation.get( id )
+                data = trans.sa_session.query( self.app.model.LibraryDatasetDatasetAssociation ).get( id )
                 if data.state != state:
                     job_ldda = data
                     while job_ldda.copied_from_library_dataset_dataset_association:
@@ -184,7 +184,7 @@
     def download_dataset_from_folder( self, trans, cntrller, obj_id, library_id=None, **kwd ):
         """Catches the dataset id and displays file contents as directed"""
         # id must refer to a LibraryDatasetDatasetAssociation object
-        ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id )
+        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
         if not ldda.dataset:
             msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id )
             return trans.response.send_redirect( web.url_for( controller=cntrller,
@@ -218,19 +218,19 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         if obj_id:
-            library_item = trans.app.model.FormDefinition.get( int( obj_id ) )
+            library_item = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( obj_id ) )
             library_item_desc = 'information template'
             response_id = obj_id
         elif folder_id:
-            library_item = trans.app.model.LibraryFolder.get( int( folder_id ) )
+            library_item = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( folder_id ) )
             library_item_desc = 'folder'
             response_id = folder_id
         elif ldda_id:
-            library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_id ) )
+            library_item = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( int( ldda_id ) )
             library_item_desc = 'library dataset'
             response_id = ldda_id
         else:
-            library_item = trans.app.model.Library.get( int( library_id ) )
+            library_item = trans.sa_session.query( trans.app.model.Library ).get( int( library_id ) )
             library_item_desc = 'library'
             response_id = library_id
         forms = get_all_forms( trans,
@@ -244,7 +244,7 @@
                                                        msg=msg,
                                                        messagetype='done' ) )
         if params.get( 'add_info_template_button', False ):
-            form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) )
+            form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( kwd[ 'form_id' ] ) )
             #fields = list( copy.deepcopy( form.fields ) )
             form_values = trans.app.model.FormValues( form, [] )
             form_values.flush()
@@ -280,13 +280,13 @@
         messagetype = params.get( 'messagetype', 'done' )
         folder_id = None
         if library_item_type == 'library':
-            library_item = trans.app.model.Library.get( library_item_id )
+            library_item = trans.sa_session.query( trans.app.model.Library ).get( library_item_id )
         elif library_item_type == 'library_dataset':
-            library_item = trans.app.model.LibraryDataset.get( library_item_id )
+            library_item = trans.sa_session.query( trans.app.model.LibraryDataset ).get( library_item_id )
         elif library_item_type == 'folder':
-            library_item = trans.app.model.LibraryFolder.get( library_item_id )
+            library_item = trans.sa_session.query( trans.app.model.LibraryFolder ).get( library_item_id )
         elif library_item_type == 'library_dataset_dataset_association':
-            library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id )
+            library_item = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( library_item_id )
             # This response_action method requires a folder_id
             folder_id = library_item.library_dataset.folder.id
         else:
@@ -310,7 +310,7 @@
             if info_association:
                 template = info_association.template
                 info = info_association.info
-                form_values = trans.app.model.FormValues.get( info.id )
+                form_values = trans.sa_session.query( trans.app.model.FormValues ).get( info.id )
                 # Update existing content only if it has changed
                 if form_values.content != field_contents:
                     form_values.content = field_contents
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/mobile.py
--- a/lib/galaxy/web/controllers/mobile.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/mobile.py	Thu Oct 22 23:02:28 2009 -0400
@@ -11,19 +11,19 @@
         
     @web.expose
     def history_detail( self, trans, id ):
-        history = trans.app.model.History.get( id )
+        history = trans.sa_session.query( trans.app.model.History ).get( id )
         assert history.user == trans.user
         return trans.fill_template( "mobile/history/detail.mako", history=history )
 
     @web.expose
     def dataset_detail( self, trans, id ):
-        dataset = trans.app.model.HistoryDatasetAssociation.get( id )
+        dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id )
         assert dataset.history.user == trans.user
         return trans.fill_template( "mobile/dataset/detail.mako", dataset=dataset )
 
     @web.expose
     def dataset_peek( self, trans, id ):
-        dataset = trans.app.model.HistoryDatasetAssociation.get( id )
+        dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id )
         assert dataset.history.user == trans.user
         return trans.fill_template( "mobile/dataset/peek.mako", dataset=dataset )
         
@@ -45,7 +45,7 @@
 
     def __login( self, trans, email="", password="" ):
         error = password_error = None
-        user = model.User.filter( model.User.table.c.email==email ).first()
+        user = trans.sa_session.query( model.User ).filter_by( email = email ).first()
         if not user:
             error = "No such user"
         elif user.deleted:
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/page.py
--- a/lib/galaxy/web/controllers/page.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/page.py	Thu Oct 22 23:02:28 2009 -0400
@@ -65,7 +65,7 @@
                 page_slug_err = "Page id is required"
             elif not VALID_SLUG_RE.match( page_slug ):
                 page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
-            elif model.Page.filter_by( user=user, slug=page_slug ).first():
+            elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug ).first():
                 page_slug_err = "Page id must be unique"
             else:
                 # Create the new stored workflow
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/requests.py
--- a/lib/galaxy/web/controllers/requests.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/requests.py	Thu Oct 22 23:02:28 2009 -0400
@@ -108,7 +108,7 @@
     
     def __show_request(self, trans, id, add_sample=False):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             return trans.response.send_redirect( web.url_for( controller='requests',
                                                               action='list',
@@ -130,7 +130,7 @@
         '''
         Shows the request details
         '''
-        request = trans.app.model.Request.get(id)
+        request = trans.sa_session.query( trans.app.model.Request ).get( id )
         # list of widgets to be rendered on the request form
         request_details = []
         # main details
@@ -171,7 +171,7 @@
             if field['type'] == 'AddressField':
                 if request.values.content[index]:
                     request_details.append(dict(label=field['label'],
-                                                value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(),
+                                                value=trans.sa_session.query( trans.app.model.UserAddress ).get( int( request.values.content[index] ) ).get_html(),
                                                 helptext=field['helptext']+' ('+req+')'))
                 else:
                     request_details.append(dict(label=field['label'],
@@ -220,7 +220,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            request = trans.app.model.Request.get(int(params.get('request_id', None)))
+            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
         except:
             return trans.response.send_redirect( web.url_for( controller='requests',
                                                               action='list',
@@ -313,7 +313,7 @@
                         sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
                     sample = request.has_sample(sample_name)
                     if sample:
-                        form_values = trans.app.model.FormValues.get(sample.values.id)
+                        form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
                         form_values.content = sample_values
                         form_values.flush()
                         sample.name = new_sample_name
@@ -344,13 +344,13 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        request = trans.app.model.Request.get(int(params.get('request_id', 0)))
+        request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
         current_samples, details, edit_mode = self.__update_samples( request, **kwd )
         sample_index = int(params.get('sample_id', 0))
         sample_name = current_samples[sample_index][0]
         s = request.has_sample(sample_name)
         if s:
-            s.delete()
+            trans.sa_session.delete( s )
             s.flush()
             request.flush()
         del current_samples[sample_index]  
@@ -368,7 +368,8 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        request = trans.app.model.Request.get(int(params.get('request_id', 0)))
+        # TODO: Fix the following - can we get a Request.id == 0???
+        request = trans.sa_session.query( trans.app.model.Request ).get(int(params.get('request_id', 0)))
         current_samples, details, edit_mode = self.__update_samples( request, **kwd )
         return trans.fill_template( '/requests/show_request.mako',
                                     request=request,
@@ -379,7 +380,7 @@
                                     edit_mode=edit_mode)
     def __select_request_type(self, trans, rtid):
         rt_ids = ['none']
-        for rt in trans.app.model.RequestType.query().all():
+        for rt in trans.sa_session.query( trans.app.model.RequestType ):
             if not rt.deleted:
                 rt_ids.append(str(rt.id))
         select_reqtype = SelectField('select_request_type', 
@@ -389,7 +390,7 @@
             select_reqtype.add_option('Select one', 'none', selected=True)
         else:
             select_reqtype.add_option('Select one', 'none')
-        for rt in trans.app.model.RequestType.query().all():
+        for rt in trans.sa_session.query( trans.app.model.RequestType ):
             if not rt.deleted:
                 if rtid == rt.id:
                     select_reqtype.add_option(rt.name, rt.id, selected=True)
@@ -411,7 +412,7 @@
         elif params.get('create', False) == 'True':
             if params.get('create_request_button', False) == 'Save' \
                or params.get('create_request_samples_button', False) == 'Add samples':
-                request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
                 if not util.restore_text(params.get('name', '')):
                     msg = 'Please enter the <b>Name</b> of the request'
                     kwd['create'] = 'True'
@@ -448,7 +449,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+            request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
         except:
             return trans.fill_template( '/requests/new_request.mako',
                                         select_request_type=self.__select_request_type(trans, 'none'),                                 
@@ -496,8 +497,9 @@
                 lib_id = str(request.library.id)
                 selected_lib = request.library
         # get all permitted libraries for this user
-        all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \
-                                               .order_by( trans.app.model.Library.name ).all()
+        all_libraries = trans.sa_session.query( trans.app.model.Library ) \
+                                        .filter( trans.app.model.Library.table.c.deleted == False ) \
+                                        .order_by( trans.app.model.Library.name )
         user, roles = trans.get_user_and_roles()
         actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ]
         libraries = odict()
@@ -600,16 +602,16 @@
         This method saves a new request if request_id is None. 
         '''
         params = util.Params( kwd )
-        request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+        request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
         name = util.restore_text(params.get('name', ''))
         desc = util.restore_text(params.get('desc', ''))
         # library
         try:
-            library = trans.app.model.Library.get(int(params.get('library_id', None)))
+            library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'library_id', None ) ) )
         except:
             library = None
         try:
-            folder = trans.app.model.LibraryFolder.get(int(params.get('folder_id', None)))
+            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'folder_id', None ) ) )
         except:
             if library:
                 folder = library.root_folder
@@ -633,7 +635,7 @@
                     user_address.country = util.restore_text(params.get('field_%i_country' % index, ''))
                     user_address.phone = util.restore_text(params.get('field_%i_phone' % index, ''))
                     user_address.flush()
-                    trans.user.refresh()
+                    trans.sa_session.refresh( trans.user )
                     values.append(int(user_address.id))
                 elif value == unicode('none'):
                     values.append('')
@@ -667,7 +669,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            request = trans.app.model.Request.get(int(params.get('request_id', None)))
+            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
         except:
             return trans.response.send_redirect( web.url_for( controller='requests',
                                                               action='list',
@@ -678,7 +680,7 @@
             return self.__edit_request(trans, request.id, **kwd)
         elif params.get('save_changes_request_button', False) == 'Save changes' \
              or params.get('edit_samples_button', False) == 'Edit samples':
-                request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
                 if not util.restore_text(params.get('name', '')):
                     msg = 'Please enter the <b>Name</b> of the request'
                     kwd['messagetype'] = 'error'
@@ -708,7 +710,7 @@
             
     def __edit_request(self, trans, id, **kwd):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -750,7 +752,7 @@
         return self.__show_request_form(trans)
     def __delete_request(self, trans, id):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -777,7 +779,7 @@
                                                           **kwd) )
     def __undelete_request(self, trans, id):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -798,7 +800,7 @@
                                                           **kwd) )
     def __submit(self, trans, id):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -837,7 +839,7 @@
         params = util.Params( kwd )
         try:
             id = int(params.get('id', False))
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -876,7 +878,7 @@
         params = util.Params( kwd )
         try:
             sample_id = int(params.get('sample_id', False))
-            sample = trans.app.model.Sample.get(sample_id)
+            sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
         except:
             msg = "Invalid sample ID"
             return trans.response.send_redirect( web.url_for( controller='requests',
@@ -897,7 +899,3 @@
                                     events_list=events_list,
                                     sample_name=sample.name,
                                     request=sample.request)
-
-            
-    
-    
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/requests_admin.py	Thu Oct 22 23:02:28 2009 -0400
@@ -50,11 +50,11 @@
         grids.GridColumnFilter( "All", args=dict( deleted=False ) )
     ]
     def get_user(self, trans, request):
-        return trans.app.model.User.get(request.user_id).email
+        return trans.sa_session.query( trans.app.model.User ).get( request.user_id ).email
     def get_current_item( self, trans ):
         return None
     def get_request_type(self, trans, request):
-        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        request_type = trans.sa_session.query( trans.app.model.RequestType ).get( request.request_type_id )
         return request_type.name
     def number_of_samples(self, trans, request):
         return str(len(request.samples))
@@ -116,7 +116,7 @@
         return self.request_grid( trans, **kwargs )
     def __show_request(self, trans, id, messagetype, msg):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='list',
@@ -136,7 +136,7 @@
 
     def __edit_request(self, trans, id, **kwd):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -178,7 +178,7 @@
         return self.__show_request_form(trans)
     def __delete_request(self, trans, id):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -206,7 +206,7 @@
                                                           **kwd) )
     def __undelete_request(self, trans, id):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -228,7 +228,7 @@
                                                           **kwd) )
     def __submit(self, trans, id):
         try:
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -267,7 +267,7 @@
 #    
     def __select_request_type(self, trans, rtid):
         rt_ids = ['none']
-        for rt in trans.app.model.RequestType.query().all():
+        for rt in trans.sa_session.query( trans.app.model.RequestType ):
             if not rt.deleted:
                 rt_ids.append(str(rt.id))
         select_reqtype = SelectField('select_request_type', 
@@ -277,7 +277,7 @@
             select_reqtype.add_option('Select one', 'none', selected=True)
         else:
             select_reqtype.add_option('Select one', 'none')
-        for rt in trans.app.model.RequestType.query().all():
+        for rt in trans.sa_session.query( trans.app.model.RequestType ):
             if not rt.deleted:
                 if rtid == rt.id:
                     select_reqtype.add_option(rt.name, rt.id, selected=True)
@@ -299,7 +299,7 @@
         elif params.get('create', False) == 'True':
             if params.get('create_request_button', False) == 'Save' \
                or params.get('create_request_samples_button', False) == 'Add samples':
-                request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
                 if not util.restore_text(params.get('name', '')) \
                     or util.restore_text(params.get('select_user', '')) == unicode('none'):
                     msg = 'Please enter the <b>Name</b> of the request and the <b>user</b> on behalf of whom this request will be submitted before saving this request'
@@ -338,7 +338,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+            request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
         except:
             return trans.fill_template( '/admin/requests/new_request.mako',
                                         select_request_type=self.__select_request_type(trans, 'none'),                                 
@@ -350,7 +350,7 @@
         # user
         user_id = params.get( 'select_user', 'none' )
         try:
-            user = trans.app.model.User.get(int(user_id))
+            user = trans.sa_session.query( trans.app.model.User ).get( int( user_id ) )
         except:
             user = None
         # list of widgets to be rendered on the request form
@@ -378,7 +378,7 @@
                                     messagetype=messagetype)
     def __select_user(self, trans, userid):
         user_ids = ['none']
-        for user in trans.app.model.User.query().all():
+        for user in trans.sa_session.query( trans.app.model.User ):
             if not user.deleted:
                 user_ids.append(str(user.id))
         select_user = SelectField('select_user', 
@@ -390,7 +390,7 @@
             select_user.add_option('Select one', 'none')
         def __get_email(user):
             return user.email
-        user_list = trans.app.model.User.query().all()
+        user_list = trans.sa_session.query( trans.app.model.User )
         user_list.sort(key=__get_email)
         for user in user_list:
             if not user.deleted:
@@ -423,8 +423,9 @@
             libraries = {}
         else:
             # get all permitted libraries for this user
-            all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \
-                                                   .order_by( trans.app.model.Library.name ).all()
+            all_libraries = trans.sa_session.query( trans.app.model.Library ) \
+                                            .filter( trans.app.model.Library.table.c.deleted == False ) \
+                                            .order_by( trans.app.model.Library.name )
             roles = user.all_roles()
             actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ]
             # The libraries dictionary looks like: { library : '1,2' }, library : '3' }
@@ -539,20 +540,20 @@
         This method saves a new request if request_id is None. 
         '''
         params = util.Params( kwd )
-        request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+        request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
         if request:
             user = request.user
         else:
-            user = trans.app.model.User.get(int(params.get('select_user', '')))
+            user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'select_user', '' ) ) )
         name = util.restore_text(params.get('name', ''))
         desc = util.restore_text(params.get('desc', ''))
         # library
         try:
-            library = trans.app.model.Library.get(int(params.get('library_id', None)))
+            library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'library_id', None ) ) )
         except:
             library = None
         try:
-            folder = trans.app.model.LibraryFolder.get(int(params.get('folder_id', None)))
+            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'folder_id', None ) ) )
         except:
             if library:
                 folder = library.root_folder
@@ -576,7 +577,7 @@
                     user_address.country = util.restore_text(params.get('field_%i_country' % index, ''))
                     user_address.phone = util.restore_text(params.get('field_%i_phone' % index, ''))
                     user_address.flush()
-                    trans.user.refresh()
+                    trans.sa_session.refresh( trans.user )
                     values.append(int(user_address.id))
                 elif value == unicode('none'):
                     values.append('')
@@ -614,7 +615,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            request = trans.app.model.Request.get(int(params.get('request_id', None)))
+            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
         except:
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='list',
@@ -625,7 +626,7 @@
             return self.__edit_request(trans, request.id, **kwd)
         elif params.get('save_changes_request_button', False) == 'Save changes' \
              or params.get('edit_samples_button', False) == 'Edit samples':
-                request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+                request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
                 if not util.restore_text(params.get('name', '')):
                     msg = 'Please enter the <b>Name</b> of the request'
                     kwd['messagetype'] = 'error'
@@ -658,7 +659,7 @@
         params = util.Params( kwd )
         try:
             id = int(params.get('id', False))
-            request = trans.app.model.Request.get(id)
+            request = trans.sa_session.query( trans.app.model.Request ).get( id )
         except:
             msg = "Invalid request ID"
             log.warn( msg )
@@ -727,7 +728,7 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         try:
-            request = trans.app.model.Request.get(int(params.get('request_id', None)))
+            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
         except:
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='list',
@@ -820,7 +821,7 @@
                         sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
                     sample = request.has_sample(sample_name)
                     if sample:
-                        form_values = trans.app.model.FormValues.get(sample.values.id)
+                        form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
                         form_values.content = sample_values
                         form_values.flush()
                         sample.name = new_sample_name
@@ -851,13 +852,13 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        request = trans.app.model.Request.get(int(params.get('request_id', 0)))
+        request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
         current_samples, details, edit_mode = self.__update_samples( request, **kwd )
         sample_index = int(params.get('sample_id', 0))
         sample_name = current_samples[sample_index][0]
         s = request.has_sample(sample_name)
         if s:
-            s.delete()
+            trans.sa_session.delete( s )
             s.flush()
             request.flush()
         del current_samples[sample_index]  
@@ -875,7 +876,7 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        request = trans.app.model.Request.get(int(params.get('request_id', 0)))
+        request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
         current_samples, details, edit_mode = self.__update_samples( request, **kwd )
         return trans.fill_template( '/admin/requests/show_request.mako',
                                     request=request,
@@ -890,7 +891,7 @@
         '''
         Shows the request details
         '''
-        request = trans.app.model.Request.get(id)
+        request = trans.sa_session.query( trans.app.model.Request ).get( id )
         # list of widgets to be rendered on the request form
         request_details = []
         # main details
@@ -935,7 +936,7 @@
             if field['type'] == 'AddressField':
                 if request.values.content[index]:
                     request_details.append(dict(label=field['label'],
-                                                value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(),
+                                                value=trans.sa_session.query( trans.app.model.UserAddress ).get( int( request.values.content[index] ) ).get_html(),
                                                 helptext=field['helptext']+' ('+req+')'))
                 else:
                     request_details.append(dict(label=field['label'],
@@ -954,7 +955,7 @@
         messagetype = params.get( 'messagetype', 'done' )
         request_id = params.get( 'request_id', None )
         if request_id:
-            request = trans.app.model.Request.get( int( request_id ))
+            request = trans.sa_session.query( trans.app.model.Request ).get( int( request_id ))
         if not request:
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='list',
@@ -980,7 +981,7 @@
     def save_bar_codes(self, trans, **kwd):
         params = util.Params( kwd )
         try:
-            request = trans.app.model.Request.get(int(params.get('request_id', None)))
+            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
         except:
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='list',
@@ -1008,7 +1009,7 @@
                          (bar_code, request.samples[index].name)
                 break
             # check all the saved bar codes
-            all_samples = trans.app.model.Sample.query.all()
+            all_samples = trans.sa_session.query( trans.app.model.Sample )
             for sample in all_samples:
                 if bar_code == sample.bar_code:
                     msg = '''The bar code <b>%s</b> of sample <b>%s</b> already 
@@ -1077,7 +1078,7 @@
         params = util.Params( kwd )
         try:
             sample_id = int(params.get('sample_id', False))
-            sample = trans.app.model.Sample.get(sample_id)
+            sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
         except:
             msg = "Invalid sample ID"
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
@@ -1087,8 +1088,10 @@
                                                               **kwd) )
         comments = util.restore_text( params.comment )
         selected_state = int( params.select_state )
-        new_state = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == sample.request.type.id 
-                                                        and trans.app.model.SampleState.table.c.id == selected_state)[0]
+        new_state = trans.sa_session.query( trans.app.model.SampleState ) \
+                                    .filter( and_( trans.app.model.SampleState.table.c.request_type_id == sample.request.type.id,
+                                                   trans.app.model.SampleState.table.c.id == selected_state ) ) \
+                                    .first()
         event = trans.app.model.SampleEvent(sample, new_state, comments)
         event.flush()
         self.__set_request_state(sample.request)
@@ -1101,7 +1104,7 @@
         params = util.Params( kwd )
         try:
             sample_id = int(params.get('sample_id', False))
-            sample = trans.app.model.Sample.get(sample_id)
+            sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
         except:
             msg = "Invalid sample ID"
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
@@ -1134,7 +1137,7 @@
         messagetype = params.get( 'messagetype', 'done' )
         show_filter = util.restore_text( params.get( 'show_filter', 'Active'  ) )
         forms = get_all_forms(trans, all_versions=True)
-        request_types_list = trans.app.model.RequestType.query().all()
+        request_types_list = trans.sa_session.query( trans.app.model.RequestType )
         if show_filter == 'All':
             request_types = request_types_list
         elif show_filter == 'Deleted':
@@ -1184,8 +1187,8 @@
                                                               msg='Request type <b>%s</b> has been created' % st.name,
                                                               messagetype='done') )
         elif params.get('view', False):
-            rt = trans.app.model.RequestType.get(int(util.restore_text( params.id )))
-            ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all()
+            rt = trans.sa_session.query( trans.app.model.RequestType ).get( int( util.restore_text( params.id ) ) )
+            ss_list = trans.sa_session.query( trans.app.model.SampleState ).filter( trans.app.model.SampleState.table.c.request_type_id == rt.id )
             return trans.fill_template( '/admin/requests/view_request_type.mako', 
                                         request_type=rt,
                                         forms=get_all_forms( trans ),
@@ -1208,13 +1211,13 @@
         rt = trans.app.model.RequestType() 
         rt.name = util.restore_text( params.name ) 
         rt.desc = util.restore_text( params.description ) or ""
-        rt.request_form = trans.app.model.FormDefinition.get(int( params.request_form_id ))
-        rt.sample_form = trans.app.model.FormDefinition.get(int( params.sample_form_id ))
+        rt.request_form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.request_form_id ) )
+        rt.sample_form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.sample_form_id ) )
         rt.flush()
         # set sample states
-        ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all()
+        ss_list = trans.sa_session.query( trans.app.model.SampleState ).filter( trans.app.model.SampleState.table.c.request_type_id == rt.id )
         for ss in ss_list:
-            ss.delete()
+            trans.sa_session.delete( ss )
             ss.flush()
         for i in range( num_states ):
             name = util.restore_text( params.get( 'state_name_%i' % i, None ))
@@ -1229,7 +1232,7 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        rt = trans.app.model.RequestType.get(int(util.restore_text( params.request_type_id )))
+        rt = trans.sa_session.query( trans.app.model.RequestType ).get( int( util.restore_text( params.request_type_id ) ) )
         rt.deleted = True
         rt.flush()
         return trans.response.send_redirect( web.url_for( controller='requests_admin',
@@ -1242,7 +1245,7 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        rt = trans.app.model.RequestType.get(int(util.restore_text( params.request_type_id )))
+        rt = trans.sa_session.query( trans.app.model.RequestType ).get( int( util.restore_text( params.request_type_id ) ) )
         rt.deleted = False
         rt.flush()
         return trans.response.send_redirect( web.url_for( controller='requests_admin',
diff -r 20b319780138 -r 2c4ed83f76ef lib/galaxy/web/controllers/root.py
--- a/lib/galaxy/web/controllers/root.py	Wed Oct 21 23:15:22 2009 -0400
+++ b/lib/galaxy/web/controllers/root.py	Thu Oct 22 23:02:28 2009 -0400
@@ -85,7 +85,7 @@
     def dataset_state ( self, trans, id=None, stamp=None ):
         if id is not None:
             try: 
-                data = self.app.model.HistoryDatasetAssociation.get( id )
+                data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
             except: 
                 return trans.show_error_message( "Unable to check dataset %s." %str( id ) )
             trans.response.headers['X-Dataset-State'] = data.state
@@ -99,7 +99,7 @@
     def dataset_code( self, trans, id=None, hid=None, stamp=None ):
         if id is not None:
             try: 
-                data = self.app.model.HistoryDatasetAssociation.get( id )
+                data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
             except: 
                 return trans.show_error_message( "Unable to check dataset %s." %str( id ) )
             trans.response.headers['Pragma'] = 'no-cache'
@@ -119,7 +119,7 @@
             ids = map( int, ids.split( "," ) )
             states = states.split( "," )
             for id, state in zip( ids, states ):
-                data = self.app.model.HistoryDatasetAssociation.get( id )
+                data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id )
                 if data.state != state:
                     job_hda = data
                     while job_hda.copied_from_history_dataset_association:

    