from pathlib import Path
from typing import Tuple
from immuneML.IO.dataset_import.DataImport import DataImport
from immuneML.IO.dataset_import.IReceptorImport import IReceptorImport
from immuneML.data_model.receptor.ChainPair import ChainPair
from immuneML.dsl.DefaultParamsLoader import DefaultParamsLoader
from immuneML.dsl.symbol_table.SymbolTable import SymbolTable
from immuneML.dsl.symbol_table.SymbolType import SymbolType
from immuneML.util.Logger import log
from immuneML.util.ParameterValidator import ParameterValidator
from immuneML.util.ReflectionHandler import ReflectionHandler
[docs]class ImportParser:
keyword = "datasets"
valid_keys = ["format", "params"]
[docs] @staticmethod
def parse(workflow_specification: dict, symbol_table: SymbolTable, result_path: Path) -> Tuple[SymbolTable, dict]:
assert ImportParser.keyword in workflow_specification and isinstance(workflow_specification[ImportParser.keyword], dict), \
"ImmuneMLParser: datasets are not defined."
for key in workflow_specification[ImportParser.keyword].keys():
symbol_table = ImportParser._parse_dataset(key, workflow_specification[ImportParser.keyword][key], symbol_table, result_path)
return symbol_table, workflow_specification[ImportParser.keyword]
@staticmethod
@log
def _parse_dataset(key: str, dataset_specs: dict, symbol_table: SymbolTable, result_path: Path) -> SymbolTable:
location = "ImportParser"
ParameterValidator.assert_keys(list(dataset_specs.keys()), ImportParser.valid_keys, location, f"datasets:{key}", False)
valid_formats = ReflectionHandler.all_nonabstract_subclass_basic_names(DataImport, "Import", "IO/dataset_import/")
ParameterValidator.assert_in_valid_list(dataset_specs["format"], valid_formats, location, "format")
import_cls = ReflectionHandler.get_class_by_name("{}Import".format(dataset_specs["format"]))
params = ImportParser._prepare_params(dataset_specs, result_path, key)
if "is_repertoire" in params:
ParameterValidator.assert_type_and_value(params["is_repertoire"], bool, location, "is_repertoire")
if params["is_repertoire"] == True:
if import_cls != IReceptorImport:
assert "metadata_file" in params, f"{location}: Missing parameter: metadata_file under {key}/params/"
ParameterValidator.assert_type_and_value(params["metadata_file"], Path, location, "metadata_file")
if params["is_repertoire"] == False:
assert "paired" in params, f"{location}: Missing parameter: paired under {key}/params/"
ParameterValidator.assert_type_and_value(params["paired"], bool, location, "paired")
if params["paired"] == True:
assert "receptor_chains" in params, f"{location}: Missing parameter: receptor_chains under {key}/params/"
ParameterValidator.assert_in_valid_list(params["receptor_chains"], ["_".join(cp.value) for cp in ChainPair], location, "receptor_chains")
try:
dataset = import_cls.import_dataset(params, key)
dataset.name = key
symbol_table.add(key, SymbolType.DATASET, dataset)
except KeyError as key_error:
raise KeyError(f"{key_error}\n\nAn error occurred during parsing of dataset {key}. "
f"The keyword {key_error.args[0]} was missing. This either means this argument was "
f"not defined under definitions/datasets/{key}/params, or this column was missing from "
f"an input data file. ")
except Exception as ex:
raise Exception(f"{ex}\n\nAn error occurred while parsing the dataset {key}. See the log above for more details.")
return symbol_table
@staticmethod
def _prepare_params(dataset_specs: dict, result_path: Path, dataset_name: str):
params = DefaultParamsLoader.load(ImportParser.keyword, dataset_specs["format"])
if "params" in dataset_specs.keys():
params = {**params, **dataset_specs["params"]}
if "result_path" not in params or params["result_path"] is None:
params["result_path"] = Path(result_path) / "datasets" / dataset_name
else:
params["result_path"] = Path(params["result_path"])
if "path" in params:
params["path"] = Path(params["path"])
if "metadata_file" in params:
params["metadata_file"] = Path(params["metadata_file"])
dataset_specs["params"] = params
return params