Fix eva config update bug (#393)

* Fix eva config update bug

Updating the yaml file was appending to instead of rewriting file

* Fix configuration test bug

Mode field was being reset to the value of datasets_dir instead of the
old value of mode.

eva/configuration/bootstrap_environment.py

@@ -89,7 +89,9 @@ def bootstrap_environment(eva_config_dir: Path, eva_installation_dir: Path):
         config_obj["core"]["catalog_database_uri"] = DB_DEFAULT_URI
         config_obj["storage"]["upload_dir"] = str(upload_dir.resolve())
 
+        yml_file.seek(0)
         yml_file.write(yaml.dump(config_obj))
+        yml_file.truncate()
 
     # set logger to appropriate level (debug or release)
     level = logging.WARN if mode == "release" else logging.DEBUG

eva/configuration/configuration_manager.py

@@ -60,7 +60,9 @@ def _update(cls, category: str, key: str, value: str):
                 raise ValueError(f"Invalid yml file at {cls._yml_path}")
 
             config_obj[category][key] = value
+            yml_file.seek(0)
             yml_file.write(yaml.dump(config_obj))
+            yml_file.truncate()
 
     @classmethod
     def get_value(cls, category: str, key: str) -> Any:

test/configuration/test_configuration_manager.py

@@ -37,7 +37,7 @@ def test_configuration_manager_read_invalid_key(self):
             _ = self.config.get_value("core", "invalid")
 
     def test_configuration_manager_update_valid_key(self):
-        value = self.config.get_value("core", "datasets_dir")
+        value = self.config.get_value("core", "mode")
 
         updated = "debug2"
         self.config.update_value("core", "mode", updated)