from pathlib import Path
import pandas as pd
from immuneML.data_model.SequenceParams import RegionType
from immuneML.environment.SequenceType import SequenceType
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class ParameterValidator:
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@staticmethod
def assert_any_value_present(values: list, expected_values: list, location: str, parameter_name: str):
assert any(exp_val in values for exp_val in
expected_values), f"{location}: expected at least one of values {expected_values} for " \
f"parameter {parameter_name} to be set, but none were found in {values}."
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@staticmethod
def assert_keys_present(values: list, expected_values: list, location: str, parameter_name: str):
for value in expected_values:
assert value in values, f"{location}: expected {value} to be set for {parameter_name}, but got {str(values)[1:-1]} instead."
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@staticmethod
def assert_all_in_valid_list(values: list, valid_values: list, location: str, parameter_name: str):
for value in values:
ParameterValidator.assert_in_valid_list(value, valid_values, location, parameter_name)
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@staticmethod
def assert_in_valid_list(value, valid_values: list, location: str, parameter_name: str):
assert value in valid_values, \
f"{location}: {value} is not a valid value for parameter {parameter_name}. Valid values are {str(valid_values)[1:-1]}."
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@staticmethod
def assert_all_type_and_value(values, parameter_type, location: str, parameter_name: str, min_inclusive=None,
max_inclusive=None):
for value in values:
ParameterValidator.assert_type_and_value(value, parameter_type, location, parameter_name, min_inclusive,
max_inclusive)
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@staticmethod
def assert_type_and_value(value, parameter_type, location: str, parameter_name: str,
min_inclusive=None, max_inclusive=None,
min_exclusive=None, max_exclusive=None, exact_value=None):
type_name = " or ".join([t.__name__ for t in parameter_type]) if type(
parameter_type) is tuple else parameter_type.__name__
base_mssg = f"{location}: {value} is not a valid value for parameter {parameter_name}. "
assert isinstance(value,
parameter_type), f"{base_mssg}It has to be of type {type_name}, but is now of type {type(value).__name__}."
if min_inclusive is not None:
assert value >= min_inclusive, base_mssg + f"It has to be greater or equal to {min_inclusive}."
if max_inclusive is not None:
assert value <= max_inclusive, base_mssg + f"It has to be less or equal to {max_inclusive}."
if min_exclusive is not None:
assert value > min_exclusive, base_mssg + f"It has to be greater than {min_inclusive}."
if max_exclusive is not None:
assert value < max_exclusive, base_mssg + f"It has to be less than {max_inclusive}."
if exact_value is not None:
assert value == exact_value, base_mssg + f"It has to be equal to {exact_value}."
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@staticmethod
def assert_keys(keys, valid_keys, location: str, parameter_name: str, exclusive: bool = True):
for key in keys:
assert key in valid_keys, f"{location}: {key} is not a valid parameter under {parameter_name}. " \
f"Valid parameters are: {str(valid_keys)[1:-1]}."
if exclusive:
if len(keys) > len(valid_keys):
raise AssertionError(
f"{location}: {str(list(set(keys) - set(valid_keys)))[1:-1]} are not valid parameters "
f" under {parameter_name}. Valid parameters are: {str(valid_keys)[1:-1]}. "
f"Remove invalid parameters.")
elif len(keys) < len(valid_keys):
raise AssertionError(f"{location}: Missing parameters: {str(list(set(valid_keys) - set(keys)))[1:-1]} "
f"under {parameter_name}. Valid parameters are: {str(valid_keys)[1:-1]}. "
f"Please add missing parameters.")
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@staticmethod
def assert_valid_tabular_file(file_path, location: str, parameter_name: str, sep="\t",
expected_columns: list = None):
assert Path(file_path).is_file(), f"{location}: {parameter_name} {str(file_path)} is not an existing file."
if expected_columns is not None:
columns = pd.read_csv(file_path, index_col=0, nrows=0, sep=sep).columns.tolist()
assert set(columns) == set(
expected_columns), f"{location}: columns for {parameter_name} are not as expected.\n" \
f"Expected: {expected_columns}\n" \
f"Found: {columns}"
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@staticmethod
def assert_sequence_type(params, location: str = ""):
assert "sequence_type" in params, f"{location}: 'sequence_type' is missing: {params}."
if not isinstance(params['sequence_type'], SequenceType):
assert params['sequence_type'].upper() in [st.name for st in SequenceType], \
(f"{location}: {params['sequence_type']} is not a valid sequence type. "
f"Valid sequence types are: {[st.name for st in SequenceType]}.")
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@staticmethod
def assert_region_type(params, location: str = ""):
assert "region_type" in params, f"{location}: 'region_type' is missing: {params}."
if not isinstance(params['region_type'], RegionType):
assert params['region_type'].upper() in [rt.name for rt in RegionType], \
(f"{location}: {params['region_type']} is not a valid region type. Valid sequence types "
f"are: {[rt.name for rt in RegionType]}.")