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


[docs] 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
[docs] def update_specs(self): with self.yaml_path.open("r") as file: specs_dict = yaml.safe_load(file) Util.update_dataset_key(specs_dict, GalaxyYamlTool.__name__) Util.check_paths(specs_dict, 'GalaxyYamlTool') Util.update_result_paths(specs_dict, self.result_path, self.yaml_path)