Merge branch 'main' into colinmegill/geneset-prototype

server/common/annotations/annotations.py

@@ -33,10 +33,10 @@ class Annotations(metaclass=ABCMeta):
             raise OntologyLoadFailure("Unable to find OBO ontology path") from e
 
         except SyntaxError as e:
-            raise OntologyLoadFailure("Syntax error loading OBO ontology") from e
+            raise OntologyLoadFailure(f"{path}:{e.lineno}:{e.offset} OBO syntax error, unable to read ontology") from e
 
         except Exception as e:
-            raise OntologyLoadFailure("Error loading OBO file") from e
+            raise OntologyLoadFailure(f"{path}:Error loading OBO file") from e
 
     def get_schema(self, data_adaptor):
         schema = []

server/common/config/server_config.py

@@ -42,6 +42,9 @@ class ServerConfig(BaseConfig):
             self.app__web_base_url = default_config["app"]["web_base_url"]
 
             self.authentication__type = default_config["authentication"]["type"]
+            self.authentication__insecure_test_environment = default_config["authentication"][
+                "insecure_test_environment"
+            ]
             self.authentication__params_oauth__oauth_api_base_url = default_config["authentication"]["params_oauth"][
                 "oauth_api_base_url"
             ]
@@ -168,6 +171,10 @@ class ServerConfig(BaseConfig):
 
     def handle_authentication(self):
         self.validate_correct_type_of_configuration_attribute("authentication__type", (type(None), str))
+        self.validate_correct_type_of_configuration_attribute("authentication__insecure_test_environment", bool)
+
+        if self.authentication__type == "test" and not self.authentication__insecure_test_environment:
+            raise ConfigurationError("Test auth can only be used in an insecure test environment")
 
         # oauth
         ptypes = str if self.authentication__type == "oauth" else (type(None), str)

server/common/utils/type_conversion_utils.py

@@ -44,7 +44,7 @@ def get_dtype_from_dtype(dtype, array_values=None):
     if dtype_name == "bool":
         return np.uint8
     if dtype_name == "object" and dtype_kind == "O":
-        return np.unicode
+        return str
     if dtype_name == "category":
         return get_dtype_from_dtype(dtype.categories.dtype, array_values)