Source code for immuneML.dsl.ObjectParser

import inspect

from immuneML.dsl.DefaultParamsLoader import DefaultParamsLoader
from immuneML.util.ParameterValidator import ParameterValidator
from immuneML.util.ReflectionHandler import ReflectionHandler


[docs] class ObjectParser:
[docs] @staticmethod def get_class_name(specs, valid_class_names, class_name_ending, location, key): if isinstance(specs, str): class_name = specs elif isinstance(specs, dict): assert len(specs) == 1, \ f"{location}: More than one parameter passed to {class_name_ending.lower()} under key {key}. " \ f"Only one value can be specified here. Valid options are: {str(valid_class_names)[1:-1]}" class_name = list(specs.keys())[0] else: raise AssertionError(f"{location}: Incorrect specification under key {key}.\n" f"Please choose one of the following:\n" f"(1) To specify an analysis component without parameters, simply specify the component as a single value, e.g;\n" f"my_component: ComponentName\n" f"\n" f"(2) To specify an analysis component with parameter values, specify it as a key containing " f"key-value pairs, e.g;\n" f"my_component: ComponentName\n" f" parameter: value\n" f"\nMake sure the indentation is correct. Valid options are: {str(valid_class_names)[1:-1]}. \n" f"For more information and details on how to specify parameters, please refer to the documentation.") return class_name
[docs] @staticmethod def get_params(specs, class_name): params = {} if isinstance(specs, dict): params = specs[class_name] return params
[docs] @staticmethod def get_class(specs, valid_class_names, class_name_ending, class_path, location, key): class_name = ObjectParser.get_class_name(specs, valid_class_names, class_name_ending, location, key) cls = ReflectionHandler.get_class_by_name(f"{class_name}{class_name_ending}", class_path) return cls
[docs] @staticmethod def get_all_params(specs, class_path, short_class_name, key: str = None): default_params = DefaultParamsLoader.load(class_path, short_class_name) specified_params = ObjectParser.get_params(specs, short_class_name) params = {**default_params, **specified_params, "name": key} return params
[docs] @staticmethod def parse_object(specs, valid_class_names: list, class_name_ending: str, class_path: str, location: str, key: str, builder: bool = False, return_params_dict: bool = False): class_name = ObjectParser.get_class_name(specs, valid_class_names, class_name_ending, location, key) ParameterValidator.assert_in_valid_list(class_name, valid_class_names, location, key) cls = ReflectionHandler.get_class_by_name(f"{class_name}{class_name_ending}", class_path) params = ObjectParser.get_all_params(specs, class_path, class_name, key) try: if "name" not in inspect.signature(cls.__init__).parameters.keys(): del params["name"] obj = cls.build_object(**params) if builder and hasattr(cls, "build_object") else cls(**params) except TypeError as err: raise AssertionError(f"{location}: invalid parameter {err.args[0]} when specifying parameters in {specs} " f"under key {key}. Valid parameter names are: " f"{[name for name in inspect.signature(cls.__init__).parameters.keys()]}") return (obj, {class_name: params}) if return_params_dict else obj