Merge pull request #168 from galaxyproject/make_resource_reqs_trump_defaults

Prioritize resource requirements over defaults

Author: nuwang

tests/test_mapper_resource_requirements.py

@@ -161,7 +161,7 @@ def test_default_entity_creation_overrides_resource_requirements(self):
         destination = self._map_to_destination(tool, user, datasets)
 
         self.assertIsNotNone(destination)
-        assert destination.params["native_spec"] == "--mem 8 --cores 2 --gpus 2"
+        assert destination.params["native_spec"] == "--mem 8 --cores 3 --gpus 2"
 
     def test_user_defined_tool_correctly_routed(self):
         tool = mock_galaxy.Tool("user_defined", mock_galaxy.DynamicTool("08175037-030a-44c5-8468-c9d36cc29067"))

tpv/core/mapper.py

@@ -65,12 +65,12 @@ def _find_entities_matching_id(
         entity_type: type[EntityType],
     ) -> List[EntityType]:
         matches: List[EntityType] = []
-        env_inherits = self.__get_environment_inherits(entity_type, context)
-        if env_inherits:
-            matches += [env_inherits]
         default_inherits = self.__get_default_inherits(entity_list)
         if default_inherits:
             matches += [default_inherits]
+        env_inherits = self.__get_environment_inherits(entity_type, context)
+        if env_inherits:
+            matches += [env_inherits]
         for key in entity_list.keys():
             if self.lookup_tool_regex(key).match(entity_name):
                 match = entity_list[key]