"""Validation of data using schema."""
import logging
import os
import re
from pathlib import Path
import numpy as np
from astropy import units as u
from astropy.table import Column, Table, unique
from astropy.utils.diff import report_diff_values
import simtools.utils.general as gen
__all__ = ["DataValidator"]
[docs]
class DataValidator:
"""
Validate data for type and units following a describing schema; converts or transform data.
Data can be of table or dict format (internally, all data is converted to astropy tables).
Parameters
----------
schema_file: Path
Schema file describing input data and transformations.
data_file: Path
Input data file.
data_table: astropy.table
Input data table.
data_dict: dict
Input data dict.
check_exact_data_type: bool
Check for exact data type (default: True).
"""
def __init__(
self,
schema_file=None,
data_file=None,
data_table=None,
data_dict=None,
check_exact_data_type=True,
):
"""Initialize validation class and read required reference data columns."""
self._logger = logging.getLogger(__name__)
self.data_file_name = data_file
self.schema_file_name = schema_file
self._data_description = None
self.data_dict = data_dict
self.data_table = data_table
self.check_exact_data_type = check_exact_data_type
[docs]
def validate_data_file(self):
"""
Open data file and read data from file.
Doing this successfully is understood as file validation.
"""
try:
if Path(self.data_file_name).suffix in (".yml", ".yaml", ".json"):
self.data_dict = gen.collect_data_from_file_or_dict(self.data_file_name, None)
self._logger.info(f"Validating data from: {self.data_file_name}")
else:
self.data_table = Table.read(self.data_file_name, guess=True, delimiter=r"\s")
self._logger.info(f"Validating tabled data from: {self.data_file_name}")
except (AttributeError, TypeError):
pass
[docs]
def validate_parameter_and_file_name(self):
"""Validate that file name and key 'parameter_name' in data dict are the same."""
if self.data_dict.get("parameter") != Path(self.data_file_name).stem:
raise ValueError(
f"Parameter name in data dict {self.data_dict.get('parameter')} and "
f"file name {Path(self.data_file_name).stem} do not match."
)
def _validate_data_dict(self):
"""
Validate values in a dictionary.
Handles different types of naming in data dicts (using 'name' or 'parameter'
keys for name fields).
Raises
------
KeyError
if data dict does not contain a 'name' or 'parameter' key.
"""
if not (_name := self.data_dict.get("name") or self.data_dict.get("parameter")):
raise KeyError("Data dict does not contain a 'name' or 'parameter' key.")
self._data_description = self._read_validation_schema(self.schema_file_name, _name)
# validation assumes lists for values and units - convert to list if required
value_as_list = (
self.data_dict.get("value")
if isinstance(self.data_dict["value"], list | np.ndarray)
else [self.data_dict["value"]]
)
unit_as_list = (
self.data_dict.get("unit")
if isinstance(self.data_dict["unit"], list | np.ndarray)
else [self.data_dict["unit"]]
)
unit_as_list = [None if unit == "null" else unit for unit in unit_as_list]
for index, (value, unit) in enumerate(zip(value_as_list, unit_as_list)):
if self._get_data_description(index).get("type", None) == "dict":
self._logger.debug(f"Skipping validation of dict type for entry {index}")
else:
self._check_data_type(np.array(value).dtype, index)
if self.data_dict.get("type") != "string":
self._check_for_not_a_number(value, index)
value_as_list[index], unit_as_list[index] = self._check_and_convert_units(
value, unit, index
)
for range_type in ("allowed_range", "required_range"):
self._check_range(index, np.nanmin(value), np.nanmax(value), range_type)
if len(value_as_list) == 1:
self.data_dict["value"], self.data_dict["unit"] = value_as_list[0], unit_as_list[0]
self._check_version_string(self.data_dict.get("version"))
def _validate_data_table(self):
"""Validate tabulated data."""
try:
self._data_description = self._read_validation_schema(self.schema_file_name)[0].get(
"table_columns", None
)
except IndexError:
self._logger.error(f"Error reading validation schema from {self.schema_file_name}")
raise
if self._data_description is not None:
self._validate_data_columns()
self._check_data_for_duplicates()
self._sort_data()
def _validate_data_columns(self):
"""
Validate that data columns.
This includes:
- required data columns are available
- columns are in the correct units (if necessary apply a unit conversion)
- ranges (minimum, maximum) are correct.
This is not applied to columns of type 'string'.
"""
self._check_required_columns()
for col_name in self.data_table.colnames:
col = self.data_table[col_name]
if not self._get_data_description(col_name, status_test=True):
continue
if not np.issubdtype(col.dtype, np.number):
continue
self._check_for_not_a_number(col.data, col_name)
self._check_data_type(col.dtype, col_name)
self.data_table[col_name] = col.to(u.Unit(self._get_reference_unit(col_name)))
self._check_range(col_name, np.nanmin(col.data), np.nanmax(col.data), "allowed_range")
self._check_range(col_name, np.nanmin(col.data), np.nanmax(col.data), "required_range")
def _check_required_columns(self):
"""
Check that all required data columns are available in the input data table.
Raises
------
KeyError
if a required data column is missing
"""
for entry in self._data_description:
if entry.get("required", False):
if entry["name"] in self.data_table.columns:
self._logger.debug(f"Found required data column {entry['name']}")
else:
raise KeyError(f"Missing required column {entry['name']}")
def _sort_data(self):
"""
Sort data according to one data column (if required by any column attribute).
Data is either sorted or reverse sorted.
Raises
------
AttributeError
if no table is defined for sorting
"""
_columns_by_which_to_sort = []
_columns_by_which_to_reverse_sort = []
for entry in self._data_description:
if "input_processing" in entry:
if "sort" in entry["input_processing"]:
_columns_by_which_to_sort.append(entry["name"])
elif "reversesort" in entry["input_processing"]:
_columns_by_which_to_reverse_sort.append(entry["name"])
if len(_columns_by_which_to_sort) > 0:
self._logger.debug(f"Sorting data columns: {_columns_by_which_to_sort}")
try:
self.data_table.sort(_columns_by_which_to_sort)
except AttributeError:
self._logger.error("No data table defined for sorting")
raise
elif len(_columns_by_which_to_reverse_sort) > 0:
self._logger.debug(f"Reverse sorting data columns: {_columns_by_which_to_reverse_sort}")
try:
self.data_table.sort(_columns_by_which_to_reverse_sort, reverse=True)
except AttributeError:
self._logger.error("No data table defined for reverse sorting")
raise
def _check_data_for_duplicates(self):
"""
Remove duplicates from data columns as defined in the data columns description.
Raises
------
if row values are different for those rows with duplications in the data columns to be
checked for unique values.
"""
_column_with_unique_requirement = self._get_unique_column_requirement()
if len(_column_with_unique_requirement) == 0:
self._logger.debug("No data columns with unique value requirement")
return
_data_table_unique_for_key_column = unique(
self.data_table, keys=_column_with_unique_requirement
)
_data_table_unique_for_all_columns = unique(self.data_table, keys=None)
with open(os.devnull, "w", encoding="utf-8") as devnull:
if report_diff_values(
_data_table_unique_for_key_column,
_data_table_unique_for_all_columns,
fileobj=devnull,
):
self.data_table = unique(self.data_table)
else:
raise ValueError(
"Failed removal of duplication for column "
f"{_column_with_unique_requirement}, values are not unique"
)
def _get_unique_column_requirement(self):
"""
Return data column name with unique value requirement.
Returns
-------
list
list of data column with unique value requirement
"""
_unique_required_column = []
for entry in self._data_description:
if "input_processing" in entry and "remove_duplicates" in entry["input_processing"]:
self._logger.debug(f"Removing duplicates for column {entry['name']}")
_unique_required_column.append(entry["name"])
self._logger.debug(f"Unique required columns: {_unique_required_column}")
return _unique_required_column
def _get_reference_unit(self, column_name):
"""
Return reference column unit. Includes correct treatment of dimensionless units.
Parameters
----------
column_name: str
column name of reference data column
Returns
-------
astro.unit
unit for reference column
Raises
------
KeyError
if column name is not found in reference data columns
"""
reference_unit = self._get_data_description(column_name).get("unit", None)
if reference_unit in ("dimensionless", None, ""):
return u.dimensionless_unscaled
return u.Unit(reference_unit)
def _check_data_type(self, dtype, column_name):
"""
Check column data type.
Parameters
----------
dtype: numpy.dtype
data type
column_name: str
column name
Raises
------
TypeError
if data type is not correct
"""
reference_dtype = self._get_data_description(column_name).get("type", None)
if not gen.validate_data_type(
reference_dtype=reference_dtype,
value=None,
dtype=dtype,
allow_subtypes=(not self.check_exact_data_type),
):
self._logger.error(
f"Invalid data type in column '{column_name}'. "
f"Expected type '{reference_dtype}', found '{dtype}' "
f"(exact type: {self.check_exact_data_type})"
)
raise TypeError
def _check_for_not_a_number(self, data, col_name):
"""
Check that column values are finite and not NaN.
Parameters
----------
data: value or numpy.ndarray
data to be tested
col_name: str
column name
Returns
-------
bool
if at least one column value is NaN or Inf.
Raises
------
ValueError
if at least one column value is NaN or Inf.
"""
if isinstance(data, str):
return True
if not isinstance(data, np.ndarray):
data = np.array(data)
if np.isnan(data).any():
self._logger.info(f"Column {col_name} contains NaN.")
if np.isinf(data).any():
self._logger.info(f"Column {col_name} contains infinite value.")
entry = self._get_data_description(col_name)
if "allow_nan" in entry.get("input_processing", {}):
return np.isnan(data).any() or np.isinf(data).any()
if np.isnan(data).any() or np.isinf(data).any():
raise ValueError("NaN or Inf values found in data")
return False
@staticmethod
def _is_dimensionless(unit):
"""
Check if unit is dimensionless, None, or empty.
Parameters
----------
unit: str
unit of data column
Returns
-------
bool
True if unit is dimensionless, None, or empty
"""
return unit in ("dimensionless", None, "")
def _check_and_convert_units(self, data, unit, col_name):
"""
Check that input data have an allowed unit.
Convert to reference unit (e.g., Angstrom to nm).
Note on dimensionless columns:
- should be given in unit descriptor as unit: ''
- be forgiving and assume that in cases no unit is given in the data files
means that it should be dimensionless (e.g., for a efficiency)
Parameters
----------
data: astropy.column, Quantity, list, value
data to be converted
unit: str
unit of data column (read from column or Quantity if possible)
col_name: str
column name
Returns
-------
data: astropy.column, Quantity, list, value
unit-converted data
Raises
------
u.core.UnitConversionError
If unit conversions fails
"""
self._logger.debug(f"Checking data column '{col_name}'")
reference_unit = self._get_reference_unit(col_name)
try:
column_unit = data.unit
except AttributeError:
column_unit = unit
if self._is_dimensionless(column_unit) and self._is_dimensionless(reference_unit):
return data, u.dimensionless_unscaled
self._logger.debug(
f"Data column '{col_name}' with reference unit "
f"'{reference_unit}' and data unit '{column_unit}'"
)
try:
if isinstance(data, u.Quantity | Column):
return data.to(reference_unit), reference_unit
if isinstance(data, list | np.ndarray):
return self._check_and_convert_units_for_list(data, column_unit, reference_unit)
# ensure that the data type is preserved (e.g., integers)
return (type(data)(u.Unit(column_unit).to(reference_unit) * data), reference_unit)
except (u.core.UnitConversionError, ValueError) as exc:
self._logger.error(
f"Invalid unit in data column '{col_name}'. "
f"Expected type '{reference_unit}', found '{column_unit}'"
)
raise u.core.UnitConversionError from exc
def _check_and_convert_units_for_list(self, data, column_unit, reference_unit):
"""
Check and convert units data in a list or or numpy array.
Takes into account that data can be dimensionless (with unit 'None', 'dimensionless'
or '').
Parameters
----------
data: list
list of data
column_unit: str
unit of data column
reference_unit: str
reference unit
Returns
-------
list
converted data
"""
return [
(
u.Unit(_to_unit).to(reference_unit) * d
if _to_unit not in (None, "dimensionless", "")
else d
)
for d, _to_unit in zip(data, column_unit)
], reference_unit
def _check_range(self, col_name, col_min, col_max, range_type="allowed_range"):
"""
Check that column data is within allowed range or required range.
Assumes that column and ranges have the same units.
Parameters
----------
col_name: string
column name
col_min: float
minimum value of data column
col_max: float
maximum value of data column
range_type: string
column range type (either 'allowed_range' or 'required_range')
Raises
------
ValueError
if columns are not in the required range
KeyError
if requested columns cannot be found or
if there is now defined of required or allowed
range columns
"""
self._logger.debug(f"Checking data in column '{col_name}' for '{range_type}' ")
if range_type not in ("allowed_range", "required_range"):
raise KeyError("Allowed range types are 'allowed_range', 'required_range'")
_entry = self._get_data_description(col_name)
if range_type not in _entry:
return
if not self._interval_check(
(col_min, col_max),
(_entry[range_type].get("min", -np.inf), _entry[range_type].get("max", np.inf)),
range_type,
):
raise ValueError(
f"Value for column '{col_name}' out of range. "
f"([{col_min}, {col_max}], {range_type}: "
f"[{_entry[range_type].get('min', -np.inf)}, "
f"{_entry[range_type].get('max', np.inf)}])"
)
@staticmethod
def _interval_check(data, axis_range, range_type):
"""
Range checking for a given set of data.
Check that values are inside allowed range or interval. This(range_type='allowed_range')
or span at least the given interval (range_type='required_range').
Parameters
----------
data: tuple
min and max of data
axis_range: tuple
allowed or required min max
range_type: string
column range type (either 'allowed_range' or 'required_range')
Returns
-------
boolean
True if range test is passed
"""
if range_type == "allowed_range":
if data[0] >= axis_range[0] and data[1] <= axis_range[1]:
return True
if range_type == "required_range":
if data[0] <= axis_range[0] and data[1] >= axis_range[1]:
return True
return False
def _read_validation_schema(self, schema_file, parameter=None):
"""
Read validation schema from file.
Parameters
----------
schema_file: Path
Schema file describing input data.
If this is a directory, a filename of
'<par>.schema.yml' is assumed.
parameter: str
Parameter name of required schema
(if None, return first schema in file)
Returns
-------
dict
validation schema
Raises
------
KeyError
if 'data' can not be read from dict in schema file
"""
try:
if Path(schema_file).is_dir():
return gen.collect_data_from_file_or_dict(
file_name=Path(schema_file) / (parameter + ".schema.yml"),
in_dict=None,
)["data"]
return gen.collect_data_from_file_or_dict(file_name=schema_file, in_dict=None)["data"]
except KeyError:
self._logger.error(f"Error reading validation schema from {schema_file}")
raise
def _get_data_description(self, column_name=None, status_test=False):
"""
Return data description as provided by the schema file.
For tables (type: 'data_table'), return the description of
the column named 'column_name'. For other types, return
all data descriptions.
For columns named 'colX' return the Xth column in the reference data.
Parameters
----------
column_name: str
Column name.
status_test: bool
Test if reference column exists.
Returns
-------
dict
Reference schema column (for status_test==False).
bool
True if reference column exists (for status_test==True).
Raises
------
IndexError
If data column is not found.
"""
self._logger.debug(
f"Getting reference data column {column_name} from schema {self._data_description}"
)
try:
return (
self._data_description[column_name]
if not status_test
else (
self._data_description[column_name] is not None
and len(self._data_description) > 0
)
)
except IndexError as exc:
self._logger.error(
f"Data column '{column_name}' not found in reference column definition"
)
raise exc
except TypeError:
pass # column_name is not an integer
_index = 0
if bool(re.match(r"^col\d$", column_name)):
_index = int(column_name[3:])
_entry = self._data_description
else:
_entry = [item for item in self._data_description if item["name"] == column_name]
if status_test:
return len(_entry) > 0
try:
return _entry[_index]
except IndexError:
self._logger.error(
f"Data column '{column_name}' not found in reference column definition"
)
raise
def _prepare_model_parameter(self):
"""Apply data preparation for model parameters."""
if isinstance(self.data_dict["value"], str):
try:
_is_float = self.data_dict.get("type").startswith("float") | self.data_dict.get(
"type"
).startswith("double")
except AttributeError:
_is_float = True
self.data_dict["value"] = gen.convert_string_to_list(
self.data_dict["value"], is_float=_is_float
)
self.data_dict["unit"] = (
None
if self.data_dict["unit"] is None
else gen.convert_string_to_list(self.data_dict["unit"])
)
def _check_version_string(self, version):
"""
Check that version string follows semantic versioning.
Parameters
----------
version: str
version string
Raises
------
ValueError
if version string does not follow semantic versioning
"""
if version is None:
return
semver_regex = r"^\d+\.\d+\.\d+(-[0-9A-Za-z.-]+)?(\+[0-9A-Za-z.-]+)?$"
if not re.match(semver_regex, version):
raise ValueError(f"Invalid version string '{version}'")
self._logger.debug(f"Valid version string '{version}'")
