Source code for immuneML.api.galaxy.ApplyGenModelTool

import os
from pathlib import Path

import yaml

from immuneML.IO.dataset_export.AIRRExporter import AIRRExporter
from immuneML.api.galaxy.GalaxyTool import GalaxyTool
from immuneML.api.galaxy.Util import Util
from immuneML.app.ImmuneMLApp import ImmuneMLApp
from immuneML.util.Logger import print_log
from immuneML.util.ParameterValidator import ParameterValidator
from immuneML.util.PathBuilder import PathBuilder
from immuneML.workflows.instructions.apply_gen_model.ApplyGenModelInstruction import ApplyGenModelInstruction


[docs] class ApplyGenModelTool(GalaxyTool): def __init__(self, specification_path: Path, result_path: Path, **kwargs): Util.check_parameters(specification_path, result_path, kwargs, ApplyGenModelTool.__name__) super().__init__(specification_path, result_path, **kwargs) def _run(self): PathBuilder.build(self.result_path) self._check_specs() state = ImmuneMLApp(self.yaml_path, self.result_path).run()[0] Util.export_galaxy_dataset(state.generated_dataset, self.result_path) print_log("Run the generative model, the resulting dataset is exported.") def _check_specs(self): with open(self.yaml_path, "r") as file: specs = yaml.safe_load(file) instruction_name = Util.check_instruction_type(specs, ApplyGenModelTool.__name__, ApplyGenModelInstruction.__name__[:-11]) ParameterValidator.assert_keys_present(list(specs['instructions'][instruction_name].keys()), ["ml_config_path", 'gen_examples_count'], ApplyGenModelTool.__name__, instruction_name) assert os.path.isfile(specs['instructions'][instruction_name]['ml_config_path']), \ f"{ApplyGenModelTool.__name__}: file specified under 'ml_config_path' parameter " \ f"({specs['instructions'][instruction_name]['ml_config_path']}) is not available. Please check if it was " \ f"correctly uploaded or if the file name is correct."