- added the change data library sample operation functional test.

- renaming dataset now checks for incorrect filename characters
- fixed bugs

lib/galaxy/web/controllers/forms.py

@@ -635,8 +635,8 @@ class Forms( BaseController ):
             if form_type == trans.model.FormDefinition.types.SAMPLE:
                 for ft in trans.model.Sample.supported_field_types:
                     if ft.__name__ == field[ 'type' ]:
-                        self.fieldtype.add_option( ft.__name__, ft__name__, selected=True )
-                        if ft == 'SelectField':
+                        self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True )
+                        if ft.__name__ == 'SelectField':
                             self.selectbox_ui( field )
                     else:
                         self.fieldtype.add_option( ft.__name__, ft.__name__ )
@@ -644,7 +644,7 @@ class Forms( BaseController ):
                 for ft in trans.model.FormDefinition.supported_field_types:
                     if ft.__name__ == field[ 'type' ]:
                         self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True )
-                        if ft == 'SelectField':
+                        if ft.__name__ == 'SelectField':
                             self.selectbox_ui( field )
                     else:
                         self.fieldtype.add_option( ft.__name__, ft.__name__ )

lib/galaxy/web/controllers/requests_admin.py

@@ -361,17 +361,29 @@ class RequestsAdmin( BaseController, UsesFormDefinitionWidgets ):
             sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) )
             sample_datasets.append( sample_dataset )
         if params.get( 'rename_datasets_button', False ):
+            incorrect_dataset_names = []
             for sample_dataset in sample_datasets:
                 encoded_id = trans.security.encode_id( sample_dataset.id )
                 selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) )
                 new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) )
+                if not new_name:
+                    incorrect_dataset_names.append( sample_dataset.name )
+                    continue
+                new_name = util.sanitize_for_filename( new_name )
                 if selected_option == 'none':
                     sample_dataset.name = new_name
                 else: 
                     sample_dataset.name = '%s_%s' % ( selected_option, new_name )
                 trans.sa_session.add( sample_dataset )
                 trans.sa_session.flush()
-            message = 'Changes saved successfully.'
+            if len( sample_datasets ) == len( incorrect_dataset_names ):
+                status = 'error'
+                message = 'All datasets renamed incorrectly.'
+            elif len( incorrect_dataset_names ):
+                status = 'done'
+                message = 'Changes saved successfully. The following datasets were renamed incorrectly: %s.' % str( incorrect_dataset_names )
+            else:
+                message = 'Changes saved successfully.'
             return trans.fill_template( '/admin/requests/rename_datasets.mako', 
                                         sample=sample,
                                         id_list=id_list,

lib/galaxy/web/controllers/requests_common.py

@@ -1079,7 +1079,7 @@ class RequestsCommon( BaseController, UsesFormDefinitionWidgets ):
                                                                   cntrller=cntrller, 
                                                                   action='update_request_state',
                                                                   request_id=trans.security.encode_id( request.id ) ) )
-            elif sample_operation == trans.model.sample.bulk_operations.SELECT_LIBRARY:
+            elif sample_operation == trans.model.Sample.bulk_operations.SELECT_LIBRARY:
                 # TODO: fix the code so that the sample_operation_select_field does not use
                 # sample_0_library_id as it's name.  it should use something like sample_operation_library_id
                 # and sample_operation_folder_id because the name sample_0_library_id should belong to the

scripts/galaxy_messaging/server/setup_rabbitmq.py

@@ -24,7 +24,7 @@ def main( config_file ):
         
     cmd_list = [
                 'add_user %s %s' % ( username, password ),
-                'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ),
+                'add_vhost %s' % virtual_host,
                 'set_permissions -p %s %s ".*" ".*" ".*"' % ( virtual_host, username )
                ]
     

templates/admin/requests/rename_datasets.mako

@@ -16,6 +16,7 @@
 
 <div class="toolForm">
 	<form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" >
+
 	    <table class="grid">
 	        <thead>
 	            <tr>
@@ -43,9 +44,16 @@
 	        </tbody>
 	    </table>
 	    <br/>
+        <div class="form-row">
+	        <div class="toolParamHelp" style="clear: both;">
+	            A dataset name should only contain the alphanumeric characters or underscore(_).
+	            If a dataset name contains any other character, it would be replaced by an underscore(_).
+	        </div>
+        </div>
 	    <div class="form-row">
 		    <input type="submit" name="rename_datasets_button" value="Save"/>
 		    <input type="submit" name="cancel_rename_datasets_button" value="Close"/>
 	    </div>
 	</form>
+
 </div>

test/base/twilltestcase.py

@@ -1638,6 +1638,23 @@ class TwillTestCase( unittest.TestCase ):
         tc.submit( "save_samples_button" )
         for check_str in strings_displayed_after_submit:
             self.check_page_for_string( check_str )
+    def change_sample_target_data_library( self, cntrller, request_id, sample_ids, new_library_id, new_folder_id, comment='', strings_displayed=[], strings_displayed_after_submit=[] ):
+        url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id )
+        self.visit_url( url )
+        for check_str in strings_displayed:
+            self.check_page_for_string( check_str )
+        for sample_id in sample_ids:
+            tc.fv( "1", "select_sample_%i" % sample_id, True )
+        tc.fv( "1", "sample_operation", 'Select data library and folder' )
+        self.refresh_form( "sample_operation", 'Select data library and folder' )
+        self.check_page_for_string( "Select data library:" )
+        tc.fv( "1", "sample_0_library_id", new_library_id )
+        self.refresh_form( "sample_0_library_id", new_library_id )
+        self.check_page_for_string( "Select folder:" )
+        tc.fv( "1", "sample_0_folder_id", new_folder_id )
+        tc.submit( "save_samples_button" )
+        for check_str in strings_displayed_after_submit:
+            self.check_page_for_string( check_str )
     def add_user_address( self, user_id, address_dict ):
         self.home()
         self.visit_url( "%s/user/new_address?admin_view=False&user_id=%i" % ( self.url, user_id ) )

test/functional/test_sample_tracking.py

@@ -430,8 +430,8 @@ class TestFormsAndRequests( TwillTestCase ):
         """Testing editing the sample information of new request1"""
         # logged in as regular_user1
         # target data library - change it to library1
-        target_library_info = dict(library=self.security.encode_id(library1.id), 
-                                   folder=self.security.encode_id(library1_folder1.id) )
+        target_library_info = dict(library=self.security.encode_id( library1.id ), 
+                                   folder=self.security.encode_id( library1_folder1.id ) )
         new_sample_value_tuples = \
         [ ( 'Sample1_renamed', target_library_info, [ 'option2', 'sample1 field2 value edited', 'sample1 field3 value edited' ] ),
           ( 'Sample2_renamed', target_library_info, [ 'option1', 'sample2 field2 value edited', 'sample2 field3 value edited' ] ),
@@ -494,6 +494,23 @@ class TestFormsAndRequests( TwillTestCase ):
                                    strings_displayed_count=strings_displayed_count,
                                    strings_not_displayed=[ request1.states.COMPLETE,
                                                            request1.states.REJECTED ] )
+        # change the target data library back to library2 using sample operation user interface
+        self.change_sample_target_data_library( cntrller='requests',
+                                                request_id=self.security.encode_id( request1.id ),
+                                                sample_ids=[ sample.id for sample in request1.samples ],
+                                                new_library_id=self.security.encode_id( library2.id ), 
+                                                new_folder_id=self.security.encode_id( library2_folder1.id ),
+                                                strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name ],
+                                                strings_displayed_after_submit=[ 'Changes made to the samples have been saved.' ] )
+        # check the changed target data library & folder on the request page
+        strings_displayed_count = []
+        strings_displayed_count.append( ( library2.name, len( request1.samples ) ) )
+        strings_displayed_count.append( ( library2_folder1.name, len( request1.samples ) ) )
+        self.view_request( cntrller='requests',
+                           request_id=self.security.encode_id( request1.id ),
+                           strings_displayed=[],
+                           strings_displayed_count=strings_displayed_count )
+
     #
     # ====== Sequencing request test methods - Admin perspective ================ 
     #
@@ -537,7 +554,7 @@ class TestFormsAndRequests( TwillTestCase ):
                                 request1.type.states[4].desc ]
         # check history of each sample
         for sample in request1.samples:
-            strings_displayed = [ 'Events for Sample "%s"' % sample.name,
+            strings_displayed = [ 'History of sample "%s"' % sample.name,
                                   'Sequencing request submitted and sample state set to %s' % request1.type.states[0].name,
                                    request1.type.states[0].name,
                                    request1.type.states[1].name ]