details: http://www.bx.psu.edu/hg/galaxy/rev/04fa6cbeb28c changeset: 3395:04fa6cbeb28c user: Greg Von Kuster greg@bx.psu.edu date: Mon Feb 15 16:56:02 2010 -0500 description: Sort the datasets by name when browsing a library from the Data Libraries view. Add a cleanup method to the functional test script for forms and requests - functional tests for libraries should now pass.
diffstat:
lib/galaxy/model/__init__.py | 20 ++++++++++++++++++-- lib/galaxy/web/controllers/library_admin.py | 11 +++++++---- lib/galaxy/web/controllers/library_common.py | 8 +++++--- test/functional/test_forms_and_requests.py | 17 +++++++++++++++++ test/functional/test_security_and_libraries.py | 5 +++-- 5 files changed, 50 insertions(+), 11 deletions(-)
diffs (120 lines):
diff -r eeff3f4f9b81 -r 04fa6cbeb28c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Feb 15 12:49:23 2010 -0500 +++ b/lib/galaxy/model/__init__.py Mon Feb 15 16:56:02 2010 -0500 @@ -5,7 +5,7 @@ the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """
-import os.path, os, errno, sys, codecs +import os.path, os, errno, sys, codecs, operator import galaxy.datatypes from galaxy.util.bunch import Bunch from galaxy import util @@ -848,8 +848,24 @@ return [] @property def active_library_datasets( self ): + def sort_by_attr( seq, attr ): + """ + Sort the sequence of objects by object's attribute + Arguments: + seq - the list or any sequence (including immutable one) of objects to sort. + attr - the name of attribute to sort by + """ + # Use the "Schwartzian transform" + # Create the auxiliary list of tuples where every i-th tuple has form + # (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not + # only to provide stable sorting, but mainly to eliminate comparison of objects + # (which can be expensive or prohibited) in case of equal attribute values. + intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) + intermed.sort() + return map( operator.getitem, intermed, ( -1, ) * len( intermed ) ) # This needs to be a list - return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ] + active_library_datasets = [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ] + return sort_by_attr( [ ld for ld in active_library_datasets ], 'name' ) @property def activatable_library_datasets( self ): # This needs to be a list diff -r eeff3f4f9b81 -r 04fa6cbeb28c lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Mon Feb 15 12:49:23 2010 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Mon Feb 15 16:56:02 2010 -0500 @@ -98,10 +98,13 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) if params.get( 'create_library_button', False ): - library = trans.app.model.Library( name = util.restore_text( params.name ), - description = util.restore_text( params.description ), - synopsis = util.restore_text( params.synopsis ) ) - root_folder = trans.app.model.LibraryFolder( name = util.restore_text( params.name ), description = "" ) + name = util.restore_text( params.get( 'name', 'No name' ) ) + description = util.restore_text( params.get( 'description', '' ) ) + synopsis = util.restore_text( params.get( 'synopsis', '' ) ) + if synopsis in [ 'None', None ]: + synopsis = '' + library = trans.app.model.Library( name=name, description=description, synopsis=synopsis ) + root_folder = trans.app.model.LibraryFolder( name=name, description='' ) library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() diff -r eeff3f4f9b81 -r 04fa6cbeb28c lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Feb 15 12:49:23 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Mon Feb 15 16:56:02 2010 -0500 @@ -137,13 +137,15 @@ show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) if params.get( 'rename_library_button', False ): old_name = library.name - new_name = util.restore_text( params.name ) - new_description = util.restore_text( params.description ) - new_synopsis = util.restore_text( params.synopsis ) + new_name = util.restore_text( params.get( 'name', 'No name' ) ) if not new_name: msg = 'Enter a valid name' messagetype='error' else: + new_description = util.restore_text( params.get( 'description', '' ) ) + new_synopsis = util.restore_text( params.get( 'synopsis', '' ) ) + if new_synopsis in [ None, 'None' ]: + new_synopsis = '' library.name = new_name library.description = new_description library.synopsis = new_synopsis diff -r eeff3f4f9b81 -r 04fa6cbeb28c test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Mon Feb 15 12:49:23 2010 -0500 +++ b/test/functional/test_forms_and_requests.py Mon Feb 15 16:56:02 2010 -0500 @@ -312,3 +312,20 @@ # check if the request's state is now set to 'submitted' assert request_two.state is not request_two.states.REJECTED, "The state of the request '%s' should be set to '%s'" \ % ( request_two.name, request_two.states.REJECTED ) + def test_050_reset_data_for_later_test_runs( self ): + """Reseting data to enable later test runs to pass""" + # TODO: RC: add whatever is missing from this method that should be marked + # deleted or purged so that later test runs will correctly test features if the + # database has not be purged. + # + # Logged in as admin_user + ################## + # Eliminate all non-private roles + ################## + for role in [ role_one ]: + self.mark_role_deleted( self.security.encode_id( role.id ), role.name ) + self.purge_role( self.security.encode_id( role.id ), role.name ) + # Manually delete the role from the database + sa_session.refresh( role ) + sa_session.delete( role ) + sa_session.flush() diff -r eeff3f4f9b81 -r 04fa6cbeb28c test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Mon Feb 15 12:49:23 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Mon Feb 15 16:56:02 2010 -0500 @@ -113,8 +113,9 @@ .first() # Make sure DatasetPermissions is correct - default is 'manage permissions' if len( latest_dataset.actions ) > 1: - raise AssertionError( '%d DatasetPermissions were created for dataset id %d when it was created ( should have been 1 )' \ - % ( len( latest_dataset.actions ), latest_dataset.id ) ) + actions = [ a.action for a in latest_dataset.actions ] + raise AssertionError( '%d DatasetPermissions (%s) were created for dataset id %d when it was created ( should have been 1 )' \ + % ( len( latest_dataset.actions ), str( actions ), latest_dataset.id ) ) dp = sa_session.query( galaxy.model.DatasetPermissions ) \ .filter( galaxy.model.DatasetPermissions.table.c.dataset_id==latest_dataset.id ) \ .first()