diff --git a/golem/core/optimisers/genetic/gp_optimizer.py b/golem/core/optimisers/genetic/gp_optimizer.py index c661b8b4..2c8d602b 100644 --- a/golem/core/optimisers/genetic/gp_optimizer.py +++ b/golem/core/optimisers/genetic/gp_optimizer.py @@ -86,10 +86,11 @@ def _extend_population(self, pop: PopulationT, target_pop_size: int) -> Populati if len(extended_pop) == target_pop_size: break new_ind = self.mutation(choice(pop)) - new_graph = new_ind.graph - if new_graph not in pop_graphs and verifier(new_graph): - extended_pop.append(new_ind) - pop_graphs.append(new_graph) + if new_ind: + new_graph = new_ind.graph + if new_graph not in pop_graphs and verifier(new_graph): + extended_pop.append(new_ind) + pop_graphs.append(new_graph) else: self.log.warning(f'Exceeded max number of attempts for extending initial graphs, stopping.' f'Current size {len(pop)}, required {target_pop_size} graphs.') diff --git a/golem/serializers/coders/graph_serialization.py b/golem/serializers/coders/graph_serialization.py index 112048e2..c032c649 100644 --- a/golem/serializers/coders/graph_serialization.py +++ b/golem/serializers/coders/graph_serialization.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, Type, Sequence +from typing import Any, Dict, Type, Sequence, Union from golem.core.dag.graph import Graph from golem.core.dag.graph_delegate import GraphDelegate @@ -20,13 +20,21 @@ def graph_from_json(cls: Type[Graph], json_obj: Dict[str, Any]) -> Graph: return obj -def _reassign_edges_by_node_ids(nodes: Sequence[LinkedGraphNode]): +def _reassign_edges_by_node_ids(nodes: Sequence[Union[LinkedGraphNode, dict]]): """ Assigns each from "nodes_from" to equal from "nodes" (cause each node from "nodes_from" in fact should point to the same node from "nodes") """ - lookup_dict = {node.uid: node for node in nodes} + lookup_dict = {} for node in nodes: - if node.nodes_from: - for parent_node_idx, parent_node_uid in enumerate(node.nodes_from): - node.nodes_from[parent_node_idx] = lookup_dict.get(parent_node_uid, None) + if isinstance(node, dict): + lookup_dict[node['uid']] = node + else: + lookup_dict[node.uid] = node + + for node in nodes: + nodes_from = node['_nodes_from'] if isinstance(node, dict) else node.nodes_from + if not nodes_from: + continue + for parent_node_idx, parent_node_uid in enumerate(nodes_from): + nodes_from[parent_node_idx] = lookup_dict.get(parent_node_uid, None) diff --git a/golem/serializers/serializer.py b/golem/serializers/serializer.py index aff8d83e..4504f528 100644 --- a/golem/serializers/serializer.py +++ b/golem/serializers/serializer.py @@ -5,13 +5,16 @@ from json import JSONDecoder, JSONEncoder from typing import Any, Callable, Dict, Optional, Type, TypeVar, Union +from golem.core.dag.linked_graph import LinkedGraph +from golem.core.dag.linked_graph_node import LinkedGraphNode +from golem.core.log import default_log + # NB: at the end of module init happens registration of default class coders INSTANCE_OR_CALLABLE = TypeVar('INSTANCE_OR_CALLABLE', object, Callable) EncodeCallable = Callable[[INSTANCE_OR_CALLABLE], Dict[str, Any]] DecodeCallable = Callable[[Type[INSTANCE_OR_CALLABLE], Dict[str, Any]], INSTANCE_OR_CALLABLE] - MODULE_X_NAME_DELIMITER = '/' CLASS_PATH_KEY = '_class_path' @@ -56,7 +59,6 @@ class Serializer(JSONEncoder, JSONDecoder): - _to_json = 'to_json' _from_json = 'from_json' @@ -222,7 +224,7 @@ def default(self, obj: INSTANCE_OR_CALLABLE) -> Dict[str, Any]: return JSONEncoder.default(self, obj) @staticmethod - def _get_class(class_path: str) -> Type[INSTANCE_OR_CALLABLE]: + def _get_class(json_obj: dict) -> Optional[Type[INSTANCE_OR_CALLABLE]]: """ Gets the object type from the class_path @@ -230,11 +232,25 @@ def _get_class(class_path: str) -> Type[INSTANCE_OR_CALLABLE]: :return: class, function or method type """ + class_path = json_obj[CLASS_PATH_KEY] class_path = LEGACY_CLASS_PATHS.get(class_path, class_path) module_name, class_name = class_path.split(MODULE_X_NAME_DELIMITER) module_name = Serializer._legacy_module_map(module_name) - obj_cls = import_module(module_name) + try: + obj_cls = import_module(module_name) + except ImportError as ex: + obj_cls = Serializer._import_as_base_class(json_obj) + if not obj_cls: + default_log('Serializer').info( + f'Object was not decoded and will be stored as a dict ' + f'because of an ImportError: {ex}.') + else: + default_log('Serializer').info( + f'Object was decoded as {obj_cls} and not as an original class ' + f'because of an ImportError: {ex}.') + return obj_cls + for sub in class_name.split('.'): obj_cls = getattr(obj_cls, sub) return obj_cls @@ -250,6 +266,18 @@ def _legacy_module_map(module_path: str) -> str: def _is_bound_method(method: Callable) -> bool: return hasattr(method, '__self__') + @staticmethod + def _import_as_base_class(json_obj: dict) \ + -> Optional[Union[Type[LinkedGraph], Type[LinkedGraphNode]]]: + linked_graph_keys = {'_nodes', '_postprocess_nodes'} + linked_node_keys = {'content', '_nodes_from', 'uid'} + if linked_graph_keys.issubset(json_obj.keys()): + return LinkedGraph + elif linked_node_keys.issubset(json_obj.keys()): + return LinkedGraphNode + else: + return None + @staticmethod def object_hook(json_obj: Dict[str, Any]) -> Union[INSTANCE_OR_CALLABLE, dict]: """ @@ -261,7 +289,7 @@ def object_hook(json_obj: Dict[str, Any]) -> Union[INSTANCE_OR_CALLABLE, dict]: :return: Python class, function or method object OR input if it's just a regular dict """ if CLASS_PATH_KEY in json_obj: - obj_cls = Serializer._get_class(json_obj[CLASS_PATH_KEY]) + obj_cls = Serializer._get_class(json_obj) del json_obj[CLASS_PATH_KEY] base_type = Serializer._get_base_type(obj_cls) if isclass(obj_cls) and base_type is not None: @@ -273,7 +301,8 @@ def object_hook(json_obj: Dict[str, Any]) -> Union[INSTANCE_OR_CALLABLE, dict]: return coder(obj_cls, json_obj) elif isfunction(obj_cls) or ismethod(obj_cls): return obj_cls - raise TypeError(f'Parsed obj_cls={obj_cls} is not serializable, but should be') + else: + return json_obj return json_obj @@ -288,6 +317,7 @@ def default_save(obj: Any, json_file_path: Optional[Union[str, os.PathLike]] = N def default_load(json_str_or_file_path: Union[str, os.PathLike]) -> Any: """ Default load from json using Serializer """ + def load_as_file_path(): with open(json_str_or_file_path, mode='r') as json_file: return json.load(json_file, cls=Serializer) diff --git a/test/data/history_composite_bn_healthcare.json b/test/data/history_composite_bn_healthcare.json new file mode 100644 index 00000000..43825afa --- /dev/null +++ b/test/data/history_composite_bn_healthcare.json @@ -0,0 +1,42570 @@ +{ + "_default_save_dir": "C:\\Users\\anaxa\\AppData\\Local\\Temp\\GOLEM", + "_objective": { + "is_multi_objective": false, + "metric_names": [ + "custom" + ], + "_class_path": "golem.core.optimisers.objective.objective/ObjectiveInfo" + }, + "_tuning_result": null, + "archive_history": [ + [ + 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+ "uid": "0bddaab1-cea8-4ab6-a0a3-5547b5a06403", + "_class_path": "golem.core.dag.linked_graph_node/LinkedGraphNode" + }, + { + "_nodes_from": [ + "eec45543-74f7-4ed2-adcc-88f38cfae9b3" + ], + "content": { + "name": "O", + "type": "cont", + "parent_model": "SGDRegressor" + }, + "uid": "613a7e4b-8730-4236-bdcb-1357626b111a", + "_class_path": "golem.core.dag.linked_graph_node/LinkedGraphNode" + }, + { + "_nodes_from": [], + "content": { + "name": "T", + "type": "cont", + "parent_model": null + }, + "uid": "21a36c2b-3a43-4669-9803-0f62f1595e7d", + "_class_path": "golem.core.dag.linked_graph_node/LinkedGraphNode" + } + ], + "_postprocess_nodes": { + "_class_path": "golem.core.dag.linked_graph/LinkedGraph._empty_postprocess" + }, + "_class_path": "golem.core.dag.linked_graph/LinkedGraph" + }, + "unique_pipeline_id": 1, + "_class_path": "golem.core.dag.graph_delegate/GraphDelegate" + }, + "metadata": { + "use_input_preprocessing": true, + "computation_time_in_seconds": 0.6961173999999914, + "evaluation_time_iso": "2023-05-30T15:38:12.810813" + }, + "native_generation": 50, + "parent_operator": { + "operators": [ + { + "_class_path": "composite_bn_genetic_operators/custom_mutation_reverse_structure" + } + ], + "parent_individuals": [ + "6284b1d3-c990-411b-8f21-dd430d6ab9eb" + ], + "type_": "mutation", + "uid": "bfa5ed55-5224-4e0e-8d54-4dd39068890b", + "_class_path": "golem.core.optimisers.opt_history_objects.parent_operator/ParentOperator" + }, + "uid": "c59bf9cc-c83e-4659-8a30-f35466b5c297", + "_class_path": "golem.core.optimisers.opt_history_objects.individual/Individual" + } + ], + "_class_path": "golem.core.optimisers.opt_history_objects.opt_history/OptHistory" +} \ No newline at end of file diff --git a/test/integration/test_external_history_visualize.py b/test/integration/test_external_history_visualize.py new file mode 100644 index 00000000..e4550ec7 --- /dev/null +++ b/test/integration/test_external_history_visualize.py @@ -0,0 +1,24 @@ +from pathlib import Path + +import pytest + +from golem.core.optimisers.opt_history_objects.opt_history import OptHistory +from golem.core.paths import project_root +from golem.visualisation.opt_viz import PlotTypesEnum, OptHistoryVisualizer + + +@pytest.mark.parametrize('history_path', [ + 'test/data/history_composite_bn_healthcare.json', +]) +@pytest.mark.parametrize('plot_type', PlotTypesEnum) +def test_visualizations_for_external_history(tmp_path, history_path, plot_type): + history_path = project_root() / history_path + history = OptHistory.load(history_path) + save_path = Path(tmp_path, plot_type.name) + save_path = save_path.with_suffix('.gif') if plot_type is PlotTypesEnum.operations_animated_bar \ + else save_path.with_suffix('.png') + visualizer = OptHistoryVisualizer(history) + visualization = plot_type.value(visualizer.history, visualizer.visuals_params) + visualization.visualize(save_path=str(save_path), best_fraction=0.1, dpi=100) + if plot_type is not PlotTypesEnum.fitness_line_interactive: + assert save_path.exists() diff --git a/test/unit/serialization/conftest.py b/test/unit/serialization/conftest.py index ec15f6d2..d49f32fc 100644 --- a/test/unit/serialization/conftest.py +++ b/test/unit/serialization/conftest.py @@ -1,7 +1,7 @@ from uuid import UUID import pytest -from golem.serializers import Serializer, any_to_json, any_from_json +from golem.serializers import Serializer, any_to_json, any_from_json, CLASS_PATH_KEY from golem.serializers.coders import ( enum_from_json, enum_to_json, @@ -17,8 +17,8 @@ @pytest.fixture def get_class_fixture(monkeypatch): - def mock_get_class(obj_type: type): - return obj_type + def mock_get_class(json_obj: dict): + return json_obj[CLASS_PATH_KEY] monkeypatch.setattr( f'{Serializer._get_class.__module__}.{Serializer._get_class.__qualname__}', diff --git a/test/unit/serialization/dataclasses/__init__.py b/test/unit/serialization/dataclasses/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/test/unit/serialization/dataclasses/serialization_dataclasses.py b/test/unit/serialization/serialization_dataclasses.py similarity index 94% rename from test/unit/serialization/dataclasses/serialization_dataclasses.py rename to test/unit/serialization/serialization_dataclasses.py index f74d6a01..0725e3af 100644 --- a/test/unit/serialization/dataclasses/serialization_dataclasses.py +++ b/test/unit/serialization/serialization_dataclasses.py @@ -18,7 +18,7 @@ class EncoderTestCase: @dataclass class GetClassCase: - test_input: str + test_input: Dict[str, Any] test_answer: INSTANCE_OR_CALLABLE diff --git a/test/unit/serialization/test_decoder.py b/test/unit/serialization/test_decoder.py index a77278d2..8bb9e019 100644 --- a/test/unit/serialization/test_decoder.py +++ b/test/unit/serialization/test_decoder.py @@ -2,7 +2,7 @@ import pytest from golem.serializers import CLASS_PATH_KEY, Serializer -from .dataclasses.serialization_dataclasses import DecoderTestCase +from test.unit.serialization.serialization_dataclasses import DecoderTestCase from test.unit.mocks.serialization_mocks import MockGraph, MockNode, MockOperation from .shared_data import ( @@ -127,4 +127,4 @@ def test_decoder(case: DecoderTestCase, get_class_fixture, mock_classes_fixture) else: decoded = deserializer.object_hook(case.test_input) assert isinstance(decoded, type(case.test_answer)), 'Decoded object has wrong type' - assert decoded == case.test_answer, f'Object was decoded incorrectly' + assert decoded == case.test_answer, 'Object was decoded incorrectly' diff --git a/test/unit/serialization/test_encoder.py b/test/unit/serialization/test_encoder.py index 98d03404..448fe9e9 100644 --- a/test/unit/serialization/test_encoder.py +++ b/test/unit/serialization/test_encoder.py @@ -4,7 +4,7 @@ import pytest from golem.serializers import CLASS_PATH_KEY, Serializer -from .dataclasses.serialization_dataclasses import EncoderTestCase +from test.unit.serialization.serialization_dataclasses import EncoderTestCase from test.unit.mocks.serialization_mocks import MockGraph, MockOperation from .shared_data import ( MOCK_NODE_1, diff --git a/test/unit/serialization/test_external_serialize.py b/test/unit/serialization/test_external_serialize.py new file mode 100644 index 00000000..9d611dc3 --- /dev/null +++ b/test/unit/serialization/test_external_serialize.py @@ -0,0 +1,58 @@ +import os.path +from itertools import chain + +import pytest + +from golem.core.dag.graph import Graph +from golem.core.dag.graph_node import GraphNode +from golem.core.optimisers.fitness import Fitness +from golem.core.optimisers.opt_history_objects.individual import Individual +from golem.core.optimisers.opt_history_objects.opt_history import OptHistory +from golem.core.paths import project_root + + +@pytest.mark.parametrize('history_path', [ + 'test/data/history_composite_bn_healthcare.json', +]) +def test_external_history_load(history_path): + """The idea is that external histories must be loadable by GOLEM. + External histories are those by projects that depend on GOLEM, e.g. BAMT. + + This is needed so that GOLEM could be used as a stand-alone + analytic tool for external histories. Or, or example, external histories + could be used in FEDOT.Web that depends only on GOLEM. + """ + history_path = project_root() / history_path + + assert os.path.exists(history_path) + + # Expect load without errors + history: OptHistory = OptHistory.load(history_path) + + assert history is not None + history_plausible(history) + assert len(history.individuals) > 0 + + +def history_plausible(history: OptHistory): + def individual_plausible(individual: Individual): + graph_correct = isinstance(individual.graph, (Graph, dict)) + nodes_are_correct = True + if not isinstance(individual.graph, dict): + nodes_are_correct = all(isinstance(node, (GraphNode, dict)) for node in individual.graph.nodes) + fitness_correct = isinstance(individual.fitness, Fitness) + parent_operator = individual.parent_operator + operations_correct = True + if parent_operator: + type_correct = parent_operator.type_ in ['mutation', 'crossover', 'selection'] + parent_inds_correct = all(isinstance(ind, Individual) for ind in parent_operator.parent_individuals) + operations_correct = type_correct and parent_inds_correct + assert graph_correct + assert nodes_are_correct + assert fitness_correct + assert operations_correct + + all_historical_fitness_correct = all(isinstance(value, float) for value in history.all_historical_fitness) + assert all_historical_fitness_correct + for individual in chain(*history.generations): + individual_plausible(individual) diff --git a/test/unit/serialization/test_get_class.py b/test/unit/serialization/test_get_class.py index 6e43f0a0..2ff28a6d 100644 --- a/test/unit/serialization/test_get_class.py +++ b/test/unit/serialization/test_get_class.py @@ -1,43 +1,51 @@ from uuid import UUID import pytest -from golem.serializers import MODULE_X_NAME_DELIMITER, Serializer +from golem.serializers import MODULE_X_NAME_DELIMITER, Serializer, CLASS_PATH_KEY -from .dataclasses.serialization_dataclasses import GetClassCase +from test.unit.serialization.serialization_dataclasses import GetClassCase from test.unit.mocks.serialization_mocks import MockGraph, MockNode, MockOperation from .shared_data import TestClass, TestEnum, TestSerializableClass, test_func GET_CLASS_CASES = [ GetClassCase( - test_input=f'{UUID.__module__}{MODULE_X_NAME_DELIMITER}{UUID.__qualname__}', + test_input={CLASS_PATH_KEY: + f'{UUID.__module__}{MODULE_X_NAME_DELIMITER}{UUID.__qualname__}'}, test_answer=UUID ), GetClassCase( - test_input=f'{TestEnum.__module__}{MODULE_X_NAME_DELIMITER}{TestEnum.__qualname__}', + test_input={CLASS_PATH_KEY: + f'{TestEnum.__module__}{MODULE_X_NAME_DELIMITER}{TestEnum.__qualname__}'}, test_answer=TestEnum ), GetClassCase( - test_input=f'{test_func.__module__}{MODULE_X_NAME_DELIMITER}{test_func.__qualname__}', + test_input={CLASS_PATH_KEY: + f'{test_func.__module__}{MODULE_X_NAME_DELIMITER}{test_func.__qualname__}'}, test_answer=test_func ), GetClassCase( - test_input=f'{TestClass().test_func.__module__}{MODULE_X_NAME_DELIMITER}{TestClass().test_func.__qualname__}', + test_input={CLASS_PATH_KEY: + f'{TestClass().test_func.__module__}{MODULE_X_NAME_DELIMITER}{TestClass().test_func.__qualname__}'}, test_answer=TestClass.test_func ), GetClassCase( - test_input=f'{TestSerializableClass.__module__}{MODULE_X_NAME_DELIMITER}{TestSerializableClass.__qualname__}', + test_input={CLASS_PATH_KEY: + f'{TestSerializableClass.__module__}{MODULE_X_NAME_DELIMITER}{TestSerializableClass.__qualname__}'}, test_answer=TestSerializableClass ), GetClassCase( - test_input=f'{MockOperation.__module__}{MODULE_X_NAME_DELIMITER}{MockOperation.__qualname__}', + test_input={CLASS_PATH_KEY: + f'{MockOperation.__module__}{MODULE_X_NAME_DELIMITER}{MockOperation.__qualname__}'}, test_answer=MockOperation ), GetClassCase( - test_input=f'{MockNode.__module__}{MODULE_X_NAME_DELIMITER}{MockNode.__qualname__}', + test_input={CLASS_PATH_KEY: + f'{MockNode.__module__}{MODULE_X_NAME_DELIMITER}{MockNode.__qualname__}'}, test_answer=MockNode ), GetClassCase( - test_input=f'{MockGraph.__module__}{MODULE_X_NAME_DELIMITER}{MockGraph.__qualname__}', + test_input={CLASS_PATH_KEY: + f'{MockGraph.__module__}{MODULE_X_NAME_DELIMITER}{MockGraph.__qualname__}'}, test_answer=MockGraph ) ] diff --git a/test/unit/serialization/test_object_path_dumping.py b/test/unit/serialization/test_object_path_dumping.py index 468f7044..94cd1ae9 100644 --- a/test/unit/serialization/test_object_path_dumping.py +++ b/test/unit/serialization/test_object_path_dumping.py @@ -3,7 +3,7 @@ import pytest from golem.serializers import CLASS_PATH_KEY, MODULE_X_NAME_DELIMITER, Serializer -from .dataclasses.serialization_dataclasses import DumpObjectTestCase +from test.unit.serialization.serialization_dataclasses import DumpObjectTestCase from .shared_data import TEST_MODULE_PATH, TEST_UUID, TestClass, TestEnum, TestSerializableClass, test_func DUMPING_CASES = [ @@ -43,4 +43,4 @@ @pytest.mark.parametrize('case', DUMPING_CASES) def test_dumping(case: DumpObjectTestCase): dumped = Serializer.dump_path_to_obj(case.test_input) - assert dumped == case.test_answer, f'Object dumping works incorrectly!' + assert dumped == case.test_answer, 'Object dumping works incorrectly!'