def prepare_specs(self):
with self.yaml_path.open("r") as file:
specs = yaml.safe_load(file)
instruction_name = Util.check_instruction_type(
specs, GalaxySimulationTool.__name__,
SimulationInstruction.__name__[:-11])
Util.check_export_format(specs, GalaxySimulationTool.__name__,
instruction_name)
Util.update_dataset_key(specs, GalaxySimulationTool.__name__)
Util.check_paths(specs, "GalaxySimulationTool")
Util.update_result_paths(specs, self.result_path, self.yaml_path)
def _update_specs(self):
with self.yaml_path.open('r') as file:
specs = yaml.safe_load(file)
ParameterValidator.assert_keys_present(specs.keys(),
["definitions", "instructions"],
DatasetGenerationTool.__name__,
"YAML specification")
ParameterValidator.assert_all_in_valid_list(
specs.keys(), ["definitions", "instructions", "output"],
DatasetGenerationTool.__name__, "YAML specification")
self._check_dataset(specs)
self._check_instruction(specs)
Util.update_dataset_key(specs, DatasetGenerationTool.__name__)
Util.check_paths(specs, DatasetGenerationTool.__name__)
Util.update_result_paths(specs, self.result_path, self.yaml_path)
def prepare_specs(self):
with self.yaml_path.open("r") as file:
specs = yaml.safe_load(file)
self.instruction_name = Util.check_instruction_type(
specs, DataSimulationTool.__name__, self.expected_instruction)
self.export_format = Util.check_export_format(
specs, DataSimulationTool.__name__, self.instruction_name)
ParameterValidator.assert_keys_present(specs["definitions"],
["datasets"],
DataSimulationTool.__name__,
"definitions/datasets")
ParameterValidator.assert_type_and_value(
specs['definitions']['datasets'], dict,
DataSimulationTool.__name__, "definitions/datasets")
self.dataset_name = "dataset"
Util.update_dataset_key(specs, DataSimulationTool.__name__,
self.dataset_name)
Util.check_paths(specs, DataSimulationTool.__name__)
Util.update_result_paths(specs, self.result_path, self.yaml_path)