fixed request_type permissions bug & code cleanup

lib/galaxy/security/__init__.py

@@ -26,7 +26,7 @@ class RBACAgent:
         LIBRARY_MODIFY = Action( "modify library item", "Users having associated role can modify this library item", "grant" ),
         LIBRARY_MANAGE = Action( "manage library permissions", "Users having associated role can manage roles associated with permissions on this library item", "grant" ),
         # Request type permissions
-        REQUEST_TYPE_ACCESS = Action( "access request_type", "Restrict access to only users having associated role", "restrict" )
+        REQUEST_TYPE_ACCESS = Action( "access request_type", "Users having associated role can access this sequencer configuration", "grant" )
         
     )
     def get_action( self, name, default=None ):
@@ -917,12 +917,12 @@ class GalaxyRBACAgent( RBACAgent ):
         request_type_actions = []
         for permission in request_type.actions:
             if permission.action == action.action:
-                request_type_actions.append(permission)
+                request_type_actions.append( permission )
         if not request_type_actions:
-            return action.model == 'restrict'
+            return False
         ret_val = False
-        for item_action in item_actions:
-            if item_action.role in roles:
+        for request_type_action in request_type_actions:
+            if request_type_action.role in roles:
                 ret_val = True
                 break
         return ret_val

lib/galaxy/web/controllers/requests_common.py

@@ -170,6 +170,11 @@ class RequestsCommon( BaseController, UsesFormDefinitionWidgets ):
             elif user is None:
                 message = 'Invalid user ID (%s)' % str(user_id)
                 status = 'error'
+            # when creating a request from the user perspective, check if the 
+            # user has access permission to this request_type 
+            elif cntrller == 'requests' and not trans.app.security_agent.can_access_request_type( user.all_roles(), request_type ):
+                message = '%s does not have access permission to the "%s" sequencer configuration.' % ( user.email, request_type.name )
+                status = 'error'
             elif not name:
                 message = 'Enter the name of the request.'
                 status = 'error'

test/functional/test_sample_tracking.py

@@ -444,12 +444,7 @@ class TestFormsAndSampleTracking( TwillTestCase ):
             for values in field_values:
                 strings_displayed_after_submit.append( values )
         # list folders that populates folder selectfield when a data library is selected
-        folder_options = []
-        folder_options.append( library2_folder1.name )
-        folder_options.append( library2_folder2.name )
-        folder_options.append( library2_folder3.name )
-        folder_options.append( library2_folder4.name )
-        # Add samples to the request
+        folder_options = [ library2_folder1.name, library2_folder2.name, library2_folder3.name, library2_folder4.name ]        # Add samples to the request
         self.add_samples( cntrller='requests',
                           request_id=self.security.encode_id( request1.id ),
                           sample_value_tuples=sample_value_tuples,
@@ -485,12 +480,11 @@ class TestFormsAndSampleTracking( TwillTestCase ):
             for values in field_values:
                 strings_displayed_after_submit.append( values )
         strings_displayed = [ 'Edit Current Samples of Sequencing Request "%s"' % request1.name,
-                              '<input type="text" name="sample_0_name" value="Sample1" size="10"/>' ] # sample name input field
-        # all the folders in library2 should show up in the folder selectlist
-        strings_displayed.append( library2_folder1.name )
-        strings_displayed.append( library2_folder2.name )
-        strings_displayed.append( library2_folder3.name )
-        strings_displayed.append( library2_folder4.name )
+                              '<input type="text" name="sample_0_name" value="Sample1" size="10"/>', # sample name input field
+                              library2_folder1.name, # all the folders in library2 should show up in the folder selectlist 
+                              library2_folder2.name, 
+                              library2_folder3.name, 
+                              library2_folder4.name ]
         # Add samples to the request
         self.edit_samples( cntrller='requests',
                            request_id=self.security.encode_id( request1.id ),
@@ -716,11 +710,7 @@ class TestFormsAndSampleTracking( TwillTestCase ):
                                  state='All',
                                  strings_displayed=[ request1.name, request2.name ] )
         # list folders that populates folder selectfield when a data library is selected
-        folder_options = []
-        folder_options.append( library2_folder1.name )
-        folder_options.append( library2_folder2.name )
-        folder_options.append( library2_folder3.name )
-        folder_options.append( library2_folder4.name )
+        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
         self.change_sample_target_data_library( cntrller='requests',
                                                 request_id=self.security.encode_id( request2.id ),