Add test to ensure default inheritance can be overridden

tests/fixtures/mapping-inheritance-override-default-inherits.yml

@@ -0,0 +1,34 @@
+global:
+  default_inherits: _default
+
+tools:
+  _default:
+    abstract: true
+    cores: 1
+    mem: cores * 2.7
+    context:
+      roundup_large_partition: multi
+      time: "36:00:00"
+  hisat:
+    cores: 4
+    scheduling:
+      require:
+        - hisat
+
+destinations:
+  _roundup_common:
+    abstract: true
+    runner: slurm
+    params:
+      tmp_dir: true
+  roundup:
+    inherits: _roundup_common
+    min_accepted_cores: 2
+    min_accepted_mem: 8
+    max_accepted_cores: 16
+    max_accepted_mem: 64
+    params:
+      native_spec: "--nodes=1 --ntasks={cores} --mem={round(mem*1024)} --time={time} --partition={roundup_large_partition}"
+    scheduling:
+      prefer:
+        - hisat

tests/test_mapper_inheritance.py

@@ -114,3 +114,16 @@ def test_general_destination_inheritance(self):
         self.assertTrue('ABC' in [e.get('name') for e in destination.env])
         self.assertEqual('extra-args', destination.params.get('docker_extra'))
         self.assertEqual('k8s', destination.runner)
+
+    def test_override_default_inherits(self):
+        user = mock_galaxy.User('majikthise', 'majikthise@vortex.org')
+        tool = mock_galaxy.Tool('hisat')
+        tpv_config_files = [
+            os.path.join(os.path.dirname(__file__), 'fixtures/mapping-inheritance.yml'),
+            os.path.join(os.path.dirname(__file__), 'fixtures/mapping-inheritance-override-default-inherits.yml'),
+        ]
+        destination = self._map_to_destination(tool, user, datasets=[], tpv_config_files=tpv_config_files)
+        self.assertEqual('roundup', destination.id)
+        self.assertEqual('--nodes=1 --ntasks=4 --mem=16384 --time=36:00:00 --partition=multi', destination.params.get('native_spec'))
+        # Job slots should not be in env since default inheritance was overridden
+        self.assertTrue('TEST_JOB_SLOTS' not in [e['name'] for e in destination.env])

tpv/core/mapper.py

@@ -86,8 +86,9 @@ def rank(self, entity, destinations, context):
     def match_and_rank_destinations(self, entity, destinations, context):
         # At this point, the resource requirements (cores, mem, gpus) are unevaluated.
         # So temporarily evaluate them so we can match up with a destination.
+        evaluated_entity = entity.evaluate_resources(context)
         matches = [dest for dest in self.__apply_default_destination_inheritance(destinations)
-                   if dest.matches(entity.evaluate_resources(context), context)]
+                   if dest.matches(evaluated_entity, context)]
         return self.rank(entity, matches, context)
 
     def to_galaxy_destination(self, destination):

tpv/rules/gateway.py

@@ -28,7 +28,7 @@ def setup_destination_mapper(app, tpv_config_files):
     mapper = load_destination_mapper(tpv_config_files)
 
     def reload_destination_mapper(path=None):
-        # reload all config files when one file changes to preserve order of loading the files
+        # reload all config files when one file changes to preserve the order of loading files
         global ACTIVE_DESTINATION_MAPPER
         ACTIVE_DESTINATION_MAPPER = load_destination_mapper(tpv_config_files, reload=True)