details: http://www.bx.psu.edu/hg/galaxy/rev/d872c1e16afb changeset: 2950:d872c1e16afb user: Nate Coraor nate@bx.psu.edu date: Tue Nov 03 12:52:01 2009 -0500 description: imported patch alchemy05_fixes_02
diffstat:
lib/galaxy/jobs/__init__.py | 6 +++--- lib/galaxy/model/mapping.py | 4 ++-- lib/galaxy/model/mapping_tests.py | 15 ++++++++------- lib/galaxy/model/migrate/versions/0025_user_info.py | 4 ++-- lib/galaxy/tools/actions/__init__.py | 7 ++++--- lib/galaxy/tools/actions/metadata.py | 5 +++-- lib/galaxy/tools/actions/upload_common.py | 4 +++- lib/galaxy/web/controllers/async.py | 6 +++--- lib/galaxy/web/controllers/dataset.py | 4 ++-- lib/galaxy/web/controllers/library.py | 6 +++--- lib/galaxy/web/controllers/library_admin.py | 12 ++++++++---- lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/root.py | 10 +++++----- lib/galaxy/web/controllers/tool_runner.py | 2 -- lib/galaxy/web/framework/__init__.py | 23 ++++++++++++++--------- test/functional/test_forms_and_requests.py | 1 + test/functional/test_security_and_libraries.py | 2 +- test/functional/test_user_info.py | 3 ++- tools/data_source/microbial_import_code.py | 6 +++--- tools/filters/lav_to_bed_code.py | 1 - tools/maf/maf_to_bed_code.py | 4 +--- 21 files changed, 69 insertions(+), 58 deletions(-)
diffs (567 lines):
diff -r 133252175425 -r d872c1e16afb lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -199,7 +199,7 @@ try: # Clear the session for each job so we get fresh states for # job and all datasets - self.sa_session.clear() + self.sa_session.expunge_all() # Get the real job entity corresponding to the wrapper (if we # are tracking in the database this is probably cached in # the session from the origianl query above) @@ -346,7 +346,7 @@ Prepare the job to run by creating the working directory and the config files. """ - self.sa_session.clear() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner + self.sa_session.expunge_all() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner if not os.path.exists( self.working_directory ): os.mkdir( self.working_directory ) # Restore parameters from the database @@ -477,7 +477,7 @@ the contents of the output files. """ # default post job setup - self.sa_session.clear() + self.sa_session.expunge_all() job = self.sa_session.query( model.Job ).get( self.job_id ) # if the job was deleted, don't finish it if job.state == job.states.DELETED: diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/mapping.py Tue Nov 03 12:52:01 2009 -0500 @@ -817,7 +817,7 @@ user=relation( User, backref="roles" ), non_private_roles=relation( User, backref="non_private_roles", - primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email & Role.table.c.type == 'private' ) ) ), + primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email ) ) ), role=relation( Role ) ) ) @@ -1134,7 +1134,7 @@ # Pack everything into a bunch result = Bunch( **globals() ) result.engine = engine - result.flush = lambda *args, **kwargs: Session.flush( *args, **kwargs ) + # model.flush() has been removed. result.session = Session # For backward compatibility with "model.context.current" result.context = Session diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/mapping_tests.py --- a/lib/galaxy/model/mapping_tests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/mapping_tests.py Tue Nov 03 12:52:01 2009 -0500 @@ -19,16 +19,17 @@ d1 = model.HistoryDatasetAssociation( extension="interval", metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True ) #h2.queries.append( q1 ) #h2.queries.append( model.Query( "h2->q2" ) ) - model.context.current.flush() - model.context.current.clear() + model.session.add_all( ( u, h1, h2, d1 ) ) + model.session.flush() + model.session.expunge_all() # Check - users = model.context.current.query( model.User ).all() + users = model.session.query( model.User ).all() assert len( users ) == 1 assert users[0].email == "james@foo.bar.baz" assert users[0].password == "password" assert len( users[0].histories ) == 1 assert users[0].histories[0].name == "History 1" - hists = model.context.current.query( model.History ).all() + hists = model.session.query( model.History ).all() assert hists[0].name == "History 1" assert hists[1].name == ( "H" * 255 ) assert hists[0].user == users[0] @@ -38,9 +39,9 @@ assert hists[1].datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id ) # Do an update and check hists[1].name = "History 2b" - model.context.current.flush() - model.context.current.clear() - hists = model.context.current.query( model.History ).all() + model.session.flush() + model.session.expunge_all() + hists = model.session.query( model.History ).all() assert hists[0].name == "History 1" assert hists[1].name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/migrate/versions/0025_user_info.py --- a/lib/galaxy/model/migrate/versions/0025_user_info.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0025_user_info.py Tue Nov 03 12:52:01 2009 -0500 @@ -21,7 +21,7 @@ log.addHandler( handler )
metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
def display_migration_details(): print "========================================" @@ -59,4 +59,4 @@ except Exception, e: log.debug( "Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: %s" % ( str( e ) ) ) def downgrade(): - pass \ No newline at end of file + pass diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -235,7 +235,7 @@ # Store output out_data[ name ] = data # Store all changes to database - trans.app.model.flush() + trans.sa_session.flush() # Add all the top-level (non-child) datasets to the history for name in out_data.keys(): if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created @@ -248,7 +248,7 @@ child_dataset = out_data[ child_name ] parent_dataset.children.append( child_dataset ) # Store data after custom code runs - trans.app.model.flush() + trans.sa_session.flush() # Create the job object job = trans.app.model.Job() job.session_id = trans.get_galaxy_session().id @@ -274,7 +274,8 @@ job.add_input_dataset( name, None ) for name, dataset in out_data.iteritems(): job.add_output_dataset( name, dataset ) - trans.app.model.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() # Some tools are not really executable, but jobs are still created for them ( for record keeping ). # Examples include tools that redirect to other applications ( epigraph ). These special tools must # include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/metadata.py Tue Nov 03 12:52:01 2009 -0500 @@ -26,7 +26,8 @@ job.tool_version = tool.version except: job.tool_version = "1.0.0" - job.flush() #ensure job.id is available + trans.sa_session.add( job ) + trans.sa_session.flush() #ensure job.id is available
#add parameters to job_parameter table # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)? @@ -49,7 +50,7 @@ #Need a special state here to show that metadata is being set and also allow the job to run # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state dataset.state = dataset.states.SETTING_METADATA - trans.app.model.flush() + trans.sa_session.flush()
# Queue the job for execution trans.app.job_queue.put( job.id, tool ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Nov 03 12:52:01 2009 -0500 @@ -121,6 +121,7 @@ trans.history.add_dataset( hda, genome_build = uploaded_dataset.dbkey ) permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) + trans.sa_session.flush() return hda
def new_library_upload( trans, uploaded_dataset, library_bunch, state=None ): @@ -291,7 +292,8 @@ for i, dataset in enumerate( data_list ): job.add_output_dataset( 'output%i' % i, dataset ) job.state = job.states.NEW - trans.app.model.flush() + trans.sa_session.add( job ) + trans.sa_session.flush()
# Queue the job for execution trans.app.job_queue.put( job.id, tool ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/async.py Tue Nov 03 12:52:01 2009 -0500 @@ -77,7 +77,7 @@ data.state = data.blurb = jobs.JOB_ERROR data.info = "Error -> %s" % STATUS
- trans.model.flush() + trans.sa_session.flush()
return "Data %s with status %s received. OK" % (data_id, STATUS)
@@ -112,7 +112,7 @@ data.flush() open( data.file_name, 'wb' ).close() #create the file trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) - trans.model.flush() + trans.sa_session.flush() trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id )
try: @@ -132,6 +132,6 @@ data.info = str(e) data.state = data.blurb = data.states.ERROR
- trans.model.flush() + trans.sa_session.flush()
return trans.fill_template('tool_executed.tmpl', out_data={}, tool=tool, config=self.app.config ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Nov 03 12:52:01 2009 -0500 @@ -335,7 +335,7 @@ assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark undeleted data.mark_undeleted() - self.app.model.flush() + trans.sa_session.flush() trans.log_event( "Dataset id %s has been undeleted" % str(id) ) return True return False @@ -407,7 +407,7 @@ hist.add_dataset( data.copy( copy_children = True ) ) if history in target_histories: refresh_frames = ['history'] - trans.app.model.flush() + trans.sa_session.flush() done_msg = "%i datasets copied to %i histories." % ( len( source_dataset_ids ) - invalid_datasets, len( target_histories ) ) trans.sa_session.refresh( history ) elif create_new_history: diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/library.py Tue Nov 03 12:52:01 2009 -0500 @@ -421,7 +421,7 @@ if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() msg = "Data type changed for library dataset '%s'" % ldda.name messagetype = 'done' else: @@ -463,7 +463,7 @@ setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' else: @@ -486,7 +486,7 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) ldda.datatype.set_meta( ldda ) ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' else: diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Tue Nov 03 12:52:01 2009 -0500 @@ -432,7 +432,7 @@ # The user clicked the Save button on the 'Change data type' form if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() msg = "Data type changed for library dataset '%s'" % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -469,7 +469,7 @@ setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' return trans.fill_template( "/admin/library/ldda_edit_info.mako", @@ -488,7 +488,7 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) ldda.datatype.set_meta( ldda ) ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -674,6 +674,10 @@ replace_id = params.get( 'replace_id', None ) if replace_id not in [ None, 'None' ]: replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( int( replace_id ) ) + # The name is separately - by the time the new ldda is created, + # replace_dataset.name will point to the new ldda, not the one it's + # replacing. + replace_dataset_name = replace_dataset.name if not last_used_build: last_used_build = replace_dataset.library_dataset_dataset_association.dbkey # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version @@ -701,7 +705,7 @@ if created_outputs: total_added = len( created_outputs.values() ) if replace_dataset: - msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) + msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) else: if not folder.parent: # Libraries have the same name as their root_folder diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Tue Nov 03 12:52:01 2009 -0500 @@ -294,7 +294,7 @@ # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): - sample_index = index + len(request.samples) + sample_index = len(request.samples) sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] for field_index in range(len(request.type.sample_form.fields)): diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Nov 03 12:52:01 2009 -0500 @@ -277,7 +277,7 @@ if not __ok_to_edit_metadata( data.id ): return trans.show_error_message( "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." ) trans.app.datatypes_registry.change_datatype( data, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() else: return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) ) elif params.save: @@ -303,7 +303,7 @@ data.datatype.after_edit( data ) else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' - trans.app.model.flush() + trans.sa_session.flush() return trans.show_ok_message( "Attributes updated%s" % msg, refresh_frames=['history'] ) elif params.detect: # The user clicked the Auto-detect button on the 'Edit Attributes' form @@ -322,7 +322,7 @@ msg = 'Attributes updated' data.set_meta() data.datatype.after_edit( data ) - trans.app.model.flush() + trans.sa_session.flush() return trans.show_ok_message( msg, refresh_frames=['history'] ) elif params.convert_data: target_type = kwd.get("target_type", None) @@ -383,7 +383,7 @@ if job.check_if_output_datasets_deleted(): job.mark_deleted() self.app.job_manager.job_stop_queue.put( job.id ) - self.app.model.flush() + trans.sa_session.flush()
@web.expose def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd): @@ -432,7 +432,7 @@ for dataset in history.datasets: dataset.deleted = True dataset.clear_associated_files() - self.app.model.flush() + trans.sa_session.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) @web.expose diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/tool_runner.py Tue Nov 03 12:52:01 2009 -0500 @@ -198,8 +198,6 @@ # pasted data datasets.append( create_dataset( 'Pasted Entry' ) ) break - if datasets: - trans.model.flush() return [ d.id for d in datasets ]
@web.expose diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -139,7 +139,7 @@ self.__galaxy_session = NOT_SET base.DefaultWebTransaction.__init__( self, environ ) self.setup_i18n() - self.sa_session.clear() + self.sa_session.expunge_all() self.debug = asbool( self.app.config.get( 'debug', False ) ) # Flag indicating whether we are in workflow building mode (means # that the current history should not be used for parameter values @@ -302,12 +302,12 @@ self.galaxy_session = galaxy_session # Do we need to flush the session? if galaxy_session_requires_flush: - objects_to_flush = [ galaxy_session ] + sa_session.add( galaxy_session ) # FIXME: If prev_session is a proper relation this would not # be needed. if prev_galaxy_session: - objects_to_flush.append( prev_galaxy_session ) - sa_session.flush( objects_to_flush ) + sa_session.add( prev_galaxy_session ) + sa_session.flush() # If the old session was invalid, get a new history with our new session if invalidate_existing_session: self.new_history() @@ -427,7 +427,8 @@ if not last_accessed: # Only set default history permissions if current history is not from a previous session self.app.security_agent.history_set_default_permissions( history, dataset=True, bypass_manage_permission=True ) - self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session, history ] ) + self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session, history ) ) + self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' ) def handle_user_logout( self ): @@ -439,7 +440,8 @@ prev_galaxy_session = self.galaxy_session prev_galaxy_session.is_valid = False self.galaxy_session = self.__create_new_session( prev_galaxy_session ) - self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] ) + self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session ) ) + self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' )
@@ -466,7 +468,8 @@ def set_history( self, history ): if history and not history.deleted: self.galaxy_session.current_history = history - self.sa_session.flush( [ self.galaxy_session ] ) + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() history = property( get_history, set_history ) def new_history( self, name=None ): """ @@ -489,7 +492,8 @@ # Set the user's default history permissions self.app.security_agent.history_set_default_permissions( history ) # Save - self.sa_session.flush( [ self.galaxy_session, history ] ) + self.sa_session.add_all( ( self.galaxy_session, history ) ) + self.sa_session.flush() return history
def get_user( self ): @@ -498,7 +502,8 @@ def set_user( self, user ): """Set the current user.""" self.galaxy_session.user = user - self.sa_session.flush( [ self.galaxy_session ] ) + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() user = property( get_user, set_user )
def get_user_and_roles( self ): diff -r 133252175425 -r d872c1e16afb test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Tue Nov 03 12:52:01 2009 -0500 @@ -29,6 +29,7 @@ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: + sa_session.refresh( fdc.latest_form ) if form_name == fdc.latest_form.name: return fdc.latest_form return None diff -r 133252175425 -r d872c1e16afb test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_security_and_libraries.py Tue Nov 03 12:52:01 2009 -0500 @@ -156,7 +156,7 @@ raise AssertionError( '%s not in history id %d default_permissions after they were changed' % ( value.action, latest_history.id ) ) # Add a dataset to the history self.upload_file( '1.bed' ) - latest_dataset = galaxy.model.Dataset.query().order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() + latest_dataset = sa_session.query( galaxy.model.Dataset ).order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() # Make sure DatasetPermissionss are correct if len( latest_dataset.actions ) != len( latest_history.default_permissions ): raise AssertionError( '%d DatasetPermissionss were created for dataset id %d when it was created ( should have been %d )' % \ diff -r 133252175425 -r d872c1e16afb test/functional/test_user_info.py --- a/test/functional/test_user_info.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_user_info.py Tue Nov 03 12:52:01 2009 -0500 @@ -14,6 +14,7 @@ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: + sa_session.refresh( fdc.latest_form ) if form_name == fdc.latest_form.name: return fdc.latest_form return None @@ -146,4 +147,4 @@ self.visit_page('forms/manage?show_filter=Deleted') self.check_page_for_string(form_one_latest.name) self.logout() - \ No newline at end of file + diff -r 133252175425 -r d872c1e16afb tools/data_source/microbial_import_code.py --- a/tools/data_source/microbial_import_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/data_source/microbial_import_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -123,7 +123,7 @@ data = app.datatypes_registry.change_datatype( data, file_type ) data.init_meta() data.set_peek() - app.model.flush() + data.flush() elif fields[0] == "#NewFile": description = fields[1] chr = fields[2] @@ -137,7 +137,7 @@ newdata.flush() app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) history.add_dataset( newdata ) - app.model.flush() + history.flush() try: copyfile(filepath,newdata.file_name) newdata.info = newdata.name @@ -148,4 +148,4 @@ newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() - app.model.flush() + newdata.flush() diff -r 133252175425 -r d872c1e16afb tools/filters/lav_to_bed_code.py --- a/tools/filters/lav_to_bed_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/filters/lav_to_bed_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -16,4 +16,3 @@ data.flush() except: continue - app.model.flush() \ No newline at end of file diff -r 133252175425 -r d872c1e16afb tools/maf/maf_to_bed_code.py --- a/tools/maf/maf_to_bed_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/maf/maf_to_bed_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -21,7 +21,6 @@ output_data.dbkey = dbkey output_data.name = basic_name + " (" + dbkey + ")" output_data.flush() - app.model.flush() output_data_list.append(output_data) elif line.startswith("#FILE"): fields = line.split("\t") @@ -36,7 +35,6 @@ app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset ) newdata.flush() history.flush() - app.model.flush() try: move(filepath,newdata.file_name) newdata.info = newdata.name @@ -47,7 +45,7 @@ newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() - app.model.flush() + newdata.flush() output_data_list.append(newdata) else: new_stdout = new_stdout + line