Source code for immuneML.api.galaxy.GalaxyYamlTool

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.PathBuilder import PathBuilder


class GalaxyYamlTool(GalaxyTool):

    def __init__(self, specification_path: Path, result_path: Path, **kwargs):
        Util.check_parameters(specification_path, result_path, kwargs, "GalaxyYamlTool")
        super().__init__(specification_path, result_path, **kwargs)

    def _run(self):
        PathBuilder.build(self.result_path)
        self.update_specs()

        app = ImmuneMLApp(self.yaml_path, self.result_path)
        output_file_path = app.run()

        return output_file_path

    def update_specs(self):
        with self.yaml_path.open("r") as file:
            specs_dict = yaml.safe_load(file)

        Util.check_paths(specs_dict, 'GalaxyYamlTool')
        Util.update_result_paths(specs_dict, self.result_path, self.yaml_path)