Add a test that a tool with id kraken2000 will not inherit parameters for kraken2

tests/fixtures/mapping-inheritance.yml

@@ -48,6 +48,14 @@ tools:
     inherits: ~
     gpus: 5
   kraken2:
+    env:
+      this_is_kraken2: yes
+    scheduling:
+      require:
+        - custom-indices
+  kraken2000:
+    env:
+      this_is_kraken2000: yes
     scheduling:
       require:
         - custom-indices

tests/fixtures/mapping-invalid-regex.yml

@@ -20,7 +20,7 @@ tools:
     abstract: true
   my_concrete_tool:
     inherits: default
-  bwa\:
+  bwa[:
     scheduling:
       require:
         - pulsar

tests/test_mapper_basic.py

@@ -51,7 +51,7 @@ def test_map_tool_by_regex_mismatch(self):
     def test_map_tool_with_invalid_regex(self):
         tool = mock_galaxy.Tool('sometool')
         config = os.path.join(os.path.dirname(__file__), 'fixtures/mapping-invalid-regex.yml')
-        with self.assertRaisesRegex(re.error, "bad escape"):
+        with self.assertRaisesRegex(re.error, "unterminated character set"):
             self._map_to_destination(tool, tpv_config_path=config)
 
     def test_map_abstract_tool_should_fail(self):

tests/test_mapper_inheritance.py

@@ -114,3 +114,12 @@ 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_noninheritance_of_tool_with_substring_id(self):
+        tool_id = 'kraken2000'
+        user = mock_galaxy.User('benjy', '[email protected]')
+        tool = mock_galaxy.Tool(tool_id)
+        datasets = [mock_galaxy.DatasetAssociation("test", mock_galaxy.Dataset("test.txt", file_size=5*1024**3))]
+        destination = self._map_to_destination(tool, user, datasets)
+        self.assertEqual(len([e for e in destination.env if e['name'] == 'this_is_kraken2000']), 1)
+        self.assertEqual(len([e for e in destination.env if e['name'] == 'this_is_kraken2']), 0)

tpv/core/mapper.py

@@ -23,10 +23,13 @@ def __init__(self, loader: TPVConfigLoader):
         self.destinations = loader.destinations
         self.default_inherits = loader.global_settings.get('default_inherits')
         self.global_context = loader.global_settings.get('context')
-        self.lookup_tool_regex = functools.lru_cache(maxsize=None)(self.__compile_tool_regex)
+        self.lookup_entity_regex = functools.lru_cache(maxsize=None)(self.__compile_entity_regex)
         self.inherit_matching_entities = functools.lru_cache(maxsize=None)(self.__inherit_matching_entities)
 
-    def __compile_tool_regex(self, key):
+    def __compile_entity_regex(self, key):
+        # append an EOL anchor so that it's an exact match
+        if not key.endswith("$"):
+            key += "$"
         try:
             return re.compile(key)
         except re.error:
@@ -40,7 +43,7 @@ def _find_entities_matching_id(self, entity_list, entity_name):
         else:
             matches = []
         for key in entity_list.keys():
-            if self.lookup_tool_regex(key).match(entity_name):
+            if self.lookup_entity_regex(key).match(entity_name):
                 match = entity_list[key]
                 if match.abstract:
                     from galaxy.jobs.mapper import JobMappingException