import os
import shutil
from pathlib import Path
from typing import Tuple
from immuneML.IO.ml_method.MLImport import MLImport
from immuneML.dsl.symbol_table.SymbolTable import SymbolTable
from immuneML.dsl.symbol_table.SymbolType import SymbolType
from immuneML.environment.Label import Label
from immuneML.environment.LabelConfiguration import LabelConfiguration
from immuneML.hyperparameter_optimization.HPSetting import HPSetting
from immuneML.util.ParameterValidator import ParameterValidator
from immuneML.util.PathBuilder import PathBuilder
from immuneML.workflows.instructions.ml_model_application.MLApplicationInstruction import MLApplicationInstruction
[docs]class MLApplicationParser:
"""
Specification example for the MLApplication instruction:
.. highlight:: yaml
.. code-block:: yaml
instruction_name:
type: MLApplication
dataset: d1
config_path: ./config.zip
number_of_processes: 4
label: CD
"""
[docs] def parse(self, key: str, instruction: dict, symbol_table: SymbolTable, path: Path) -> MLApplicationInstruction:
location = MLApplicationParser.__name__
ParameterValidator.assert_keys(instruction.keys(), ['type', 'dataset', 'number_of_processes', 'config_path'], location, key)
ParameterValidator.assert_in_valid_list(instruction['dataset'], symbol_table.get_keys_by_type(SymbolType.DATASET), location, f"{key}: dataset")
ParameterValidator.assert_type_and_value(instruction['number_of_processes'], int, location, f"{key}: number_of_processes", min_inclusive=1)
ParameterValidator.assert_type_and_value(instruction['config_path'], str, location, f'{key}: config_path')
hp_setting, label = self._parse_hp_setting(instruction, path, key)
instruction = MLApplicationInstruction(dataset=symbol_table.get(instruction['dataset']), name=key, number_of_processes=instruction['number_of_processes'],
label_configuration=LabelConfiguration([label]), hp_setting=hp_setting)
return instruction
def _parse_hp_setting(self, instruction: dict, path: Path, key: str) -> Tuple[HPSetting, Label]:
assert os.path.isfile(instruction['config_path']), f'MLApplicationParser: {instruction["config_path"]} is not file path.'
assert '.zip' in instruction['config_path'], f'MLApplicationParser: {instruction["config_path"]} is not a zip file.'
config_dir = PathBuilder.build(path / f"unpacked_{key}/")
shutil.unpack_archive(instruction['config_path'], config_dir, 'zip')
hp_setting, label = MLImport.import_hp_setting(config_dir)
return hp_setting, label