[galaxy-commits] commit/galaxy-central: davebgx: Fix most of the failing functional tests in test_sample_tracking.py.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31eee538eb21/ Changeset: 31eee538eb21 User: davebgx Date: 2014-04-17 21:16:57 Summary: Fix most of the failing functional tests in test_sample_tracking.py. Affected #: 4 files diff -r 76ad26875b62c8ff3257b845df86a5864f0d1c91 -r 31eee538eb2161a378425d9190e600b42a0d32e3 lib/galaxy/webapps/galaxy/controllers/requests_common.py --- a/lib/galaxy/webapps/galaxy/controllers/requests_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_common.py @@ -888,7 +888,7 @@ field_values = {} if copy_sample_index != -1: # The user has selected a sample to copy. - library_id = displayable_sample_widgets[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) + library_id = displayable_sample_widgets[ copy_sample_index ][ 'library_select_field' ].get_selected( return_value=True ) folder_id = displayable_sample_widgets[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) name = displayable_sample_widgets[ copy_sample_index ][ 'name' ] + '_%i' % ( len( displayable_sample_widgets ) + 1 ) history_id = displayable_sample_widgets[ copy_sample_index ][ 'history_select_field' ].get_selected( return_value=True ) @@ -1347,7 +1347,7 @@ if not sample.bar_code: # If the sample's associated SampleState is still the initial state # configured by the admin for the request's RequestType, this must be - # the first time a bar code was added to the sample, so change it's state + # the first time a bar code was added to the sample, so change its state # to the next associated SampleState. if sample.state.id == request.type.states[0].id: # Change the sample state only if its request_type @@ -1659,7 +1659,7 @@ return build_select_field( trans, active_users, 'email', 'user_id', selected_value=selected_value, refresh_on_change=True ) def __build_sample_operation_select_field( self, trans, is_admin, request, selected_value ): # The sample_operation SelectField is displayed only after the request has been submitted. - # It's label is "For selected samples" + # its label is "For selected samples" if is_admin: if request.is_complete: bulk_operations = [ trans.model.Sample.bulk_operations.CHANGE_STATE ] diff -r 76ad26875b62c8ff3257b845df86a5864f0d1c91 -r 31eee538eb2161a378425d9190e600b42a0d32e3 templates/webapps/galaxy/requests/common/common.mako --- a/templates/webapps/galaxy/requests/common/common.mako +++ b/templates/webapps/galaxy/requests/common/common.mako @@ -728,7 +728,7 @@ %endif %if is_admin and is_submitted and request.samples_without_library_destinations: <div class='infomessage'> - Select a target data library and folder for a sample before selecting it's datasets to transfer from the external service. + Select a target data library and folder for a sample before selecting its datasets to transfer from the external service. </div><br/> %endif %if message: diff -r 76ad26875b62c8ff3257b845df86a5864f0d1c91 -r 31eee538eb2161a378425d9190e600b42a0d32e3 templates/webapps/galaxy/requests/common/create_request.mako --- a/templates/webapps/galaxy/requests/common/create_request.mako +++ b/templates/webapps/galaxy/requests/common/create_request.mako @@ -22,7 +22,7 @@ <div class="toolForm"><div class="toolFormTitle">Create a new sequencing request</div> - %if len( request_type_select_field.options ) == 1: + %if len( request_type_select_field.options ) < 1: There are no request types available for ${trans.user.email} to create sequencing requests. %else: <div class="toolFormBody"> diff -r 76ad26875b62c8ff3257b845df86a5864f0d1c91 -r 31eee538eb2161a378425d9190e600b42a0d32e3 test/functional/test_sample_tracking.py --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -4,10 +4,10 @@ from base.test_db_util import * -# TODO: Functional tests start failing at 025, fix or eliminate rest of tests. class TestFormsAndSampleTracking( TwillTestCase ): # ====== Setup Users, Groups & Roles required for this test suite ========= - def test_000_initiate_users( self ): + + def test_0000_initiate_users( self ): """Ensuring all required user accounts exist""" self.logout() self.login( email='test1@bx.psu.edu', username='regular-user1' ) @@ -37,7 +37,8 @@ assert admin_user is not None, 'Problem retrieving user with email "test@bx.psu.edu" from the database' global admin_user_private_role admin_user_private_role = get_private_role( admin_user ) - def test_005_create_required_groups_and_roles( self ): + + def test_0005_create_required_groups_and_roles( self ): """Testing creating all required groups and roles for this script""" # Logged in as admin_user # Create role1 @@ -80,7 +81,8 @@ global role2 role2 = get_role_by_name( name ) assert role2 is not None, 'Problem retrieving role named "Role2" from the database' - def test_006_create_library_and_folder( self ): + + def test_0010_create_library( self ): """Testing creating the target data library and folder""" # Logged in as admin_user for index in range( 0, 2 ): @@ -108,6 +110,8 @@ str( role1.id ), permissions_in, permissions_out ) + + def test_0015_create_folders( self ): # adding a folder for library in [ library1, library2 ]: name = "%s_folder1" % library.name @@ -161,7 +165,8 @@ # # ====== Form definition test methods ================================================ # - def test_010_create_request_form_definition( self ): + + def test_0020_create_request_form_definition( self ): """Testing creating a sequencing request form definition, editing the name and description and adding fields""" # Logged in as admin_user # Create a form definition @@ -175,10 +180,15 @@ field_name='1_field_name', strings_displayed=[ 'Create a new form definition' ], strings_displayed_after_submit=[ tmp_name, tmp_desc, form_type ] ) + + def test_0025_edit_request_form_fields( self ): + # field names + tmp_name = "Temp form" tmp_form = get_form( tmp_name ) # Edit the name and description of the form definition, and add 3 fields. new_name = "Request Form" new_desc = "Request Form description" + form_type = galaxy.model.FormDefinition.types.REQUEST # labels global request_field_label1 request_field_label1 = 'Request form field1' @@ -186,7 +196,6 @@ request_field_label2 = 'Request form field2' global request_field_label3 request_field_label3 = 'Request form field3' - # field names global request_form_field_name1 request_form_field_name1 = 'request_form_field1' global request_form_field_name2 @@ -227,7 +236,8 @@ form_desc=new_desc, form_type=form_type, field_dicts=field_dicts ) - def test_015_create_sample_form_definition( self ): + + def test_0030_create_sample_form_definition( self ): """Testing creating sequencing sample form definition and adding fields""" name = "Sample Form" desc = "This is Sample Form's description" @@ -242,8 +252,13 @@ field_name='1_field_name', strings_displayed=[ 'Create a new form definition' ], strings_displayed_after_submit=[ "The form '%s' has been updated with the changes." % name ] ) + + def test_0035_add_fields_to_sample_form( self ): + # now add fields to the sample form definition + name = "Sample Form" + desc = "This is Sample Form's description" + form_type = galaxy.model.FormDefinition.types.SAMPLE tmp_form = get_form( name ) - # now add fields to the sample form definition global sample_field_label1 sample_field_label1 = 'Sample form field1' global sample_field_label2 @@ -284,7 +299,8 @@ form_type=form_type, form_layout_name=sample_form_layout_grid_name, field_dicts=field_dicts ) - def test_020_create_request_type( self ): + + def test_0040_create_request_type( self ): """Testing creating a request_type""" name = 'Request type1' sample_states = [ ( 'New', 'Sample entered into the system' ), @@ -308,11 +324,12 @@ strings_displayed=[ request_form_definition1.name, sample_form_definition1.name ], sample_states=sample_states) - # Set permissions + + def test_0045_set_request_type_permissions( self ): + # Role1 members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for + # REQUEST_TYPE_ACCESS on this request_type permissions_in = [ k for k, v in galaxy.model.RequestType.permitted_actions.items() ] permissions_out = [] - # Role1 members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for - # REQUEST_TYPE_ACCESS on this request_type self.request_type_permissions( self.security.encode_id( request_type1.id ), request_type1.name, str( role1.id ), @@ -330,7 +347,8 @@ self.logout() self.login( email=admin_user.email ) # ====== Sequencing request test methods - regular user perspective ================ - def test_025_create_request( self ): + + def test_0050_create_request( self ): """Testing creating a sequencing request as a regular user""" # logged in as admin_user # Create a user_address @@ -369,7 +387,9 @@ strings_displayed_after_submit=[ 'The sequencing request has been created.', name, desc ] ) global request1 - request1 = get_request_by_name( name ) + request1 = get_request_by_name( name ) + + def test_0055_verify_request_details( self ): # Make sure the request's state is now set to NEW assert request1.state is not request1.states.NEW, "The state of the request '%s' should be set to '%s'" \ % ( request1.name, request1.states.NEW ) @@ -394,7 +414,8 @@ strings_not_displayed=[ request1.states.SUBMITTED, request1.states.COMPLETE, request1.states.REJECTED ] ) - def test_030_edit_basic_request_info( self ): + + def test_0060_edit_basic_request_info( self ): """Testing editing the basic information and email settings of a sequencing request""" # logged in as regular_user1 fields = [ ( request_form_field_name1, 'option2' ), @@ -443,7 +464,8 @@ request_id=self.security.encode_id( request1.id ), strings_displayed=strings_displayed, strings_not_displayed=[] ) - def test_035_add_samples_to_request( self ): + + def test_0065_add_samples_to_request( self ): """Testing adding samples to request""" # logged in as regular_user1 # Sample fields - the tuple represents a sample name and a list of sample form field values @@ -481,7 +503,8 @@ request_id=self.security.encode_id( request1.id ), strings_displayed=strings_displayed, strings_displayed_count=strings_displayed_count ) - def test_040_edit_samples_of_new_request( self ): + + def test_0070_edit_samples_of_new_request( self ): """Testing editing the sample information of new request1""" # logged in as regular_user1 # target data library - change it to library1 @@ -519,7 +542,8 @@ request_id=self.security.encode_id( request1.id ), strings_displayed=strings_displayed, strings_displayed_count=strings_displayed_count ) - def test_045_submit_request( self ): + + def test_0075_submit_request( self ): """Testing submitting a sequencing request""" # logged in as regular_user1 self.submit_request( cntrller='requests', @@ -555,7 +579,8 @@ strings_not_displayed=[ request1.states.COMPLETE, request1.states.REJECTED ] ) # ====== Sequencing request test methods - Admin perspective ================ - def test_050_receive_request_as_admin( self ): + + def test_0080_receive_request_as_admin( self ): """Testing receiving a sequencing request and assigning it barcodes""" # logged in as regular_user1 self.logout() @@ -571,6 +596,8 @@ self.view_request( cntrller='requests_admin', request_id=self.security.encode_id( request1.id ), strings_displayed=strings_displayed ) + + def test_0085_add_bar_codes( self ): # Set bar codes for the samples bar_codes = [ '10001', '10002', '10003' ] strings_displayed_after_submit = [ 'Changes made to the samples have been saved.' ] @@ -604,7 +631,8 @@ sample_id=self.security.encode_id( sample.id ), strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) - def test_055_request_lifecycle( self ): + + def test_0090_request_lifecycle( self ): """Testing request life-cycle as it goes through all the states""" # logged in as admin_user self.check_request_grid( cntrller='requests_admin', @@ -645,7 +673,8 @@ strings_displayed=[ request1.name ] ) assert request1.state is not request1.states.COMPLETE, "The state of the sequencing request '%s' should be set to '%s'" \ % ( request1.name, request1.states.COMPLETE ) - def test_060_admin_create_request_on_behalf_of_regular_user( self ): + + def test_0095_admin_create_request_on_behalf_of_regular_user( self ): """Testing creating and submitting a request as an admin on behalf of a regular user""" # Logged in as regular_user1 self.logout() @@ -691,7 +720,9 @@ # Make sure the request's state is now set to 'new' assert request2.state is not request2.states.NEW, "The state of the request '%s' should be set to '%s'" \ % ( request2.name, request2.states.NEW ) - target_library_info = dict(library='none', folder='none' ) + + def test_0100_add_samples_to_request( self ): + target_library_info = dict( library='none', folder='none' ) # Sample fields - the tuple represents a sample name and a list of sample form field values sample_value_tuples = \ [ ( 'Sample1', target_library_info, [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ), @@ -710,7 +741,7 @@ '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # Submit the request - select_target_library_message = "Select a target data library and folder for a sample before selecting it's datasets to transfer from the external service" + select_target_library_message = "Select a target data library and folder for a sample before selecting its datasets to transfer from the external service" self.submit_request( cntrller='requests_admin', request_id=self.security.encode_id( request2.id ), request_name=request2.name, @@ -728,6 +759,8 @@ self.check_request_grid( cntrller='requests_admin', state='All', strings_displayed=[ request1.name, request2.name ] ) + + def test_0105_set_request_target_library( self ): # list folders that populates folder selectfield when a data library is selected folder_options = [ library2_folder1.name, library2_folder2.name, library2_folder3.name, library2_folder4.name ] # set the target data library to library2 using sample operation user interface @@ -749,7 +782,8 @@ strings_displayed=strings_displayed, strings_not_displayed=[ select_target_library_message ], strings_displayed_count=strings_displayed_count ) - def test_065_reject_request( self ): + + def test_0110_reject_request( self ): """Testing rejecting a request""" # Logged in as admin_user rejection_reason="This is why the sequencing request was rejected." @@ -790,7 +824,8 @@ strings_not_displayed=[ request1.states.SUBMITTED, request1.states.COMPLETE, request1.states.NEW] ) - def __test_070_select_datasets_for_transfer( self ): + + def __test_0115_select_datasets_for_transfer( self ): """Testing selecting datasets for data transfer""" # Logged in as admin_user self.logout() @@ -820,7 +855,8 @@ sample1_dataset.transfer_status.NOT_STARTED ] self.view_sample_dataset( sample_dataset_id=self.security.encode_id( sample1_dataset.id ), strings_displayed=strings_displayed ) - def __test_075_manage_sample_datasets( self ): + + def __test_0120_manage_sample_datasets( self ): """Testing renaming, deleting and initiating transfer of sample datasets""" # Logged in as admin_user # Check renaming datasets @@ -873,6 +909,7 @@ sample1_dataset.transfer_status.NOT_STARTED ] self.view_sample_dataset( sample_dataset_id=self.security.encode_id( sample1_dataset.id ), strings_displayed=strings_displayed ) + def test_999_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as admin_user @@ -887,8 +924,7 @@ self.security.encode_id( library.id ), library.name, item_type='library' ) - self.purge_library( self.security.encode_id( library.id ), library.name ) - + self.purge_library( self.security.encode_id( library.id ), library.name ) ################## # Mark all requests deleted and delete all their samples ################## Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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