Source code for immuneML.api.galaxy.GalaxyMLApplicationTool

import os
import shutil
from pathlib import Path

import yaml

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.ml_model_application.MLApplicationInstruction import MLApplicationInstruction




class GalaxyMLApplicationTool(GalaxyTool):

    def __init__(self, specification_path: Path, result_path: Path, **kwargs):
        Util.check_parameters(specification_path, result_path, kwargs, GalaxyMLApplicationTool.__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]
        if os.path.relpath(state.predictions_path) != os.path.relpath(self.result_path / "predictions.csv"):
            shutil.copy(state.predictions_path, self.result_path / "predictions.csv")
        print_log("Applied ML model to the dataset, predictions are available.")

    def _check_specs(self):
        with open(self.yaml_path, "r") as file:
            specs = yaml.safe_load(file)

        instruction_name = Util.check_instruction_type(specs, GalaxyMLApplicationTool.__name__, MLApplicationInstruction.__name__[:-11])

        ParameterValidator.assert_keys_present(list(specs['instructions'][instruction_name].keys()), ["dataset", "config_path"],
                                               GalaxyMLApplicationTool.__name__, instruction_name)

        assert os.path.isfile(specs['instructions'][instruction_name]['config_path']), \
            f"{GalaxyMLApplicationTool.__name__}: file specified under 'config_path' parameter " \
            f"({specs['instructions'][instruction_name]['config_path']}) is not available. Please check if it was correctly uploaded or if the file" \
            f" name is correct."