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."