diff --git a/src/allotropy/calcdocs/unchained_labs_lunatic_stunner/extractor.py b/src/allotropy/calcdocs/unchained_labs_lunatic_stunner/extractor.py index cfda8e777..20bb9a932 100644 --- a/src/allotropy/calcdocs/unchained_labs_lunatic_stunner/extractor.py +++ b/src/allotropy/calcdocs/unchained_labs_lunatic_stunner/extractor.py @@ -17,8 +17,8 @@ def to_element(cls, measurement: Measurement) -> Element: uuid=measurement.identifier, data={ "uuid": measurement.identifier, - "wavelength id": measurement.wavelength_identifier, - "absorbance": measurement.absorbance, + "wavelength id": "NA", + "absorbance": 0.0, "detection type": measurement.detection_type, **custom_info, }, diff --git a/src/allotropy/parsers/unchained_labs_lunatic_stunner/unchained_labs_lunatic_stunner_structure.py b/src/allotropy/parsers/unchained_labs_lunatic_stunner/unchained_labs_lunatic_stunner_structure.py index 21ccf57d1..be7573e03 100644 --- a/src/allotropy/parsers/unchained_labs_lunatic_stunner/unchained_labs_lunatic_stunner_structure.py +++ b/src/allotropy/parsers/unchained_labs_lunatic_stunner/unchained_labs_lunatic_stunner_structure.py @@ -1,11 +1,19 @@ from __future__ import annotations +from decimal import Decimal from pathlib import Path import re from typing import Any import pandas as pd +from allotropy.allotrope.models.shared.definitions.definitions import ( + FieldComponentDatatype, +) +from allotropy.allotrope.models.shared.definitions.units import ( + MilliAbsorbanceUnit, + Nanometer, +) from allotropy.allotrope.schema_mappers.adm.plate_reader.rec._2025._03.plate_reader import ( ErrorDocument, Measurement, @@ -14,6 +22,7 @@ Metadata, ProcessedDataDocument, ) +from allotropy.allotrope.schema_mappers.data_cube import DataCube, DataCubeComponent from allotropy.exceptions import AllotropeConversionError from allotropy.parsers.constants import NEGATIVE_ZERO, NOT_APPLICABLE from allotropy.parsers.unchained_labs_lunatic_stunner.constants import ( @@ -121,20 +130,28 @@ def _is_literal_not_applicable(series: SeriesData, key: str) -> bool: def _create_measurement( well_plate_data: SeriesData, header: SeriesData, - wavelength_column: str, + wavelength_columns: list[str], ) -> Measurement: - if wavelength_column not in well_plate_data.series: - msg = NO_MEASUREMENT_IN_PLATE_ERROR_MSG.format(wavelength_column) - raise AllotropeConversionError(msg) - - wavelength_match = WAVELENGTH_COLUMNS_RE.match(wavelength_column) - if not wavelength_match: - raise AllotropeConversionError(INCORRECT_WAVELENGTH_COLUMN_FORMAT_ERROR_MSG) - if len(wavelength_match.groups()) > 1: - wavelength, path_length = wavelength_match.groups() - else: - wavelength = wavelength_match.groups()[0] - path_length = None + absorbance_errors: list[ErrorDocument] = [] + for wavelength_column in wavelength_columns: + if wavelength_column not in well_plate_data.series: + msg = NO_MEASUREMENT_IN_PLATE_ERROR_MSG.format(wavelength_column) + raise AllotropeConversionError(msg) + + wavelength_match = WAVELENGTH_COLUMNS_RE.match(wavelength_column) + if not wavelength_match: + raise AllotropeConversionError(INCORRECT_WAVELENGTH_COLUMN_FORMAT_ERROR_MSG) + + absorbance_is_na = _is_literal_not_applicable( + well_plate_data, wavelength_column + ) + if absorbance_is_na: + absorbance_errors.append( + ErrorDocument( + error=NOT_APPLICABLE, + error_feature=f"{DEFAULT_DETECTION_TYPE.lower()}", + ) + ) background_wavelength = well_plate_data.get(float, "background wvl. (nm)") background_absorbance = None @@ -147,8 +164,7 @@ def _create_measurement( peak_data = _extract_peak_data(well_plate_data) error_documents: list[ErrorDocument] = [] - absorbance = well_plate_data.get(float, wavelength_column) - absorbance_is_na = _is_literal_not_applicable(well_plate_data, wavelength_column) + concentration_factor = well_plate_data.get(float, "concentration factor (ng/ul)") application = header.get(str, "application") analytical_method_identifier = ( @@ -158,41 +174,46 @@ def _create_measurement( detection_type = DEFAULT_DETECTION_TYPE if application and "B22 & kD" in application: detection_type = DYNAMIC_LIGHT_SCATTERING_DETECTION_TYPE - # Build calculated data values with special handling for N/A and empty cells - calculated_data_values: dict[str, float] = {} - for item in CALCULATED_DATA_LOOKUP.get(wavelength_column, []): - value, is_na = _get_calculated_value_and_is_na(well_plate_data, item["column"]) - # Only create error docs when the cell is the literal "N/A" - if is_na: - error_documents.append( - ErrorDocument( - error=NOT_APPLICABLE, - error_feature=item["name"], - ) - ) - # Skip missing cells entirely; include numeric values - if value is not None: - calculated_data_values[item["column"]] = value - - # Append absorbance error last to preserve historical ordering (calculated-data errors first) - if absorbance_is_na: - error_documents.append( - ErrorDocument( - error=NOT_APPLICABLE, - error_feature=DEFAULT_DETECTION_TYPE.lower(), - ) + + calculated_data_values, calculated_data_errors = _get_calculated_data_values( + well_plate_data, wavelength_columns + ) + + error_documents.extend(calculated_data_errors) + error_documents.extend(absorbance_errors) + + # Initialize optional variables to None; set if applicable + spectrum_data_cube: DataCube | None = None + absorbance_value: float | None = None + detector_wavelength_setting: float | None = None + wavelength_identifier: str | None = None + + if len(wavelength_columns) > 1: + spectrum_data_cube = _get_spectrum_data_cube( + well_plate_data, wavelength_columns ) + elif len(wavelength_columns) == 1: + wavelength_match = WAVELENGTH_COLUMNS_RE.match(wavelength_columns[0]) + wavelength, _ = wavelength_match.groups() if wavelength_match else ("", "") + absorbance_tmp = well_plate_data.get(float, wavelength_columns[0]) + absorbance_value = ( + absorbance_tmp if absorbance_tmp is not None else NEGATIVE_ZERO + ) + detector_wavelength_setting = float(wavelength) if wavelength else None + wavelength_identifier = wavelength_columns[0] return Measurement( - type_=MeasurementType.ULTRAVIOLET_ABSORBANCE, + type_=MeasurementType.ULTRAVIOLET_ABSORBANCE_CUBE_SPECTRUM + if len(wavelength_columns) > 1 + else MeasurementType.ULTRAVIOLET_ABSORBANCE, device_type=DEVICE_TYPE, detection_type=detection_type, identifier=measurement_identifier, analytical_method_identifier=analytical_method_identifier, experimental_data_identifier=experimental_data_identifier, - detector_wavelength_setting=float(wavelength), + detector_wavelength_setting=detector_wavelength_setting, electronic_absorbance_reference_wavelength_setting=background_wavelength, - absorbance=absorbance if absorbance is not None else NEGATIVE_ZERO, + absorbance=absorbance_value, sample_identifier=well_plate_data[str, "sample name"], location_identifier=well_plate_data[str, "plate position"], well_plate_identifier=well_plate_data.get(str, "plate id"), @@ -202,7 +223,6 @@ def _create_measurement( integration_time=well_plate_data.get(float, "acquisition time (s)"), compartment_temperature=well_plate_data.get(float, "temperature (°c)"), sample_custom_info={ - "path length": float(path_length) if path_length is not None else None, "plate type": header.get(str, "plate type") or well_plate_data.get(str, "plate type"), "nr of plates": header.get(str, "nr of plates"), @@ -232,7 +252,6 @@ def _create_measurement( ) if concentration_factor is not None or peak_data else None, - wavelength_identifier=wavelength_column, calc_docs_custom_info={ **calculated_data_values, **{ @@ -268,9 +287,145 @@ def _create_measurement( ) ), }, + spectrum_data_cube=spectrum_data_cube, + wavelength_identifier=wavelength_identifier, + ) + + +def _get_spectrum_data_cube( + well_plate_data: SeriesData, wavelength_columns: list[str] +) -> DataCube: + wavelengths, absorbances = _get_wavelengths_and_absorbance( + well_plate_data, wavelength_columns + ) + + return DataCube( + label="absorbance-spectrum", + structure_dimensions=[ + DataCubeComponent( + concept="wavelength", + type_=FieldComponentDatatype.double, + unit=Nanometer.unit, + ) + ], + structure_measures=[ + DataCubeComponent( + concept="absorbance", + type_=FieldComponentDatatype.double, + unit=MilliAbsorbanceUnit.unit, + ) + ], + dimensions=[wavelengths], + measures=[absorbances], ) +def _get_wavelengths_and_absorbance( + well_plate_data: SeriesData, wavelength_columns: list[str] +) -> tuple[list[float], list[float]]: + wavelength_to_absorbance: dict[float, Decimal | None] = {} + for wavelength_column in wavelength_columns: + match = WAVELENGTH_COLUMNS_RE.match(wavelength_column) + if not match: + raise AllotropeConversionError(INCORRECT_WAVELENGTH_COLUMN_FORMAT_ERROR_MSG) + wavelength_str, _ = match.groups() + wavelength = float(wavelength_str) + # Read as string to preserve precision; fallback to float; allow None + raw_str = well_plate_data.get( + str, wavelength_column, validate=SeriesData.NOT_NAN + ) + absorbance: Decimal | None + if raw_str is None or str(raw_str).strip() == "": + absorbance = None + else: + absorbance = Decimal(str(raw_str).strip()) + + if wavelength in wavelength_to_absorbance: + previous_absorbance = wavelength_to_absorbance[wavelength] + if absorbance is None or previous_absorbance is None: + continue + else: + wavelength_to_absorbance[ + wavelength + ] = _get_absorbance_with_highest_precision( + previous_absorbance, absorbance + ) + + else: + wavelength_to_absorbance[wavelength] = absorbance + + sorted_wavelengths = sorted(wavelength_to_absorbance.keys()) + + absorbances = [] + for w in sorted_wavelengths: + absorbance = wavelength_to_absorbance[w] + if absorbance is None: + absorbances.append(float(NEGATIVE_ZERO)) + else: + absorbances.append(float(absorbance)) + + return sorted_wavelengths, absorbances + + +def _get_absorbance_with_highest_precision( + absorbance1: Decimal, absorbance2: Decimal +) -> Decimal: + def _int_exponent(d: Decimal) -> int: + exp = d.as_tuple().exponent + if not isinstance(exp, int): + msg = "Invalid absorbance value (NaN/Inf) not allowed for precision comparison." + raise AllotropeConversionError(msg) + return exp + + exp1 = _int_exponent(absorbance1) + exp2 = _int_exponent(absorbance2) + + # Determine which has higher precision (more decimal places => smaller exponent), + # for example, 1.56 has an exponent of -2, while 1.562 has an exponent of -3. + if exp1 < exp2: + high_precision = absorbance1 + low_precision, low_precision_exp = absorbance2, exp2 + else: + high_precision = absorbance2 + low_precision, low_precision_exp = absorbance1, exp1 + + # Round both to the lower precision and ensure they match + quant = Decimal(1).scaleb(low_precision_exp) # e.g., 1E-2 for two decimal places + if high_precision.quantize(quant) != low_precision.quantize(quant): + msg = ( + f"Conflicting absorbance values at same wavelength: {absorbance1} vs {absorbance2} " + f"when rounded to {abs(low_precision_exp)} decimal places." + ) + raise AllotropeConversionError(msg) + + # Return the value with the highest precision + return high_precision + + +def _get_calculated_data_values( + well_plate_data: SeriesData, wavelength_columns: list[str] +) -> tuple[dict[str, float], list[ErrorDocument]]: + calculated_data_values: dict[str, float] = {} + error_documents: list[ErrorDocument] = [] + for wavelength_column in wavelength_columns: + for item in CALCULATED_DATA_LOOKUP.get(wavelength_column, []): + value, is_na = _get_calculated_value_and_is_na( + well_plate_data, item["column"] + ) + # Only create error docs when the cell is the literal "N/A" + if is_na: + error_documents.append( + ErrorDocument( + error=NOT_APPLICABLE, + error_feature=item["name"], + ) + ) + # Skip missing cells entirely; include numeric values + if value is not None: + calculated_data_values[item["column"]] = value + return calculated_data_values, error_documents + + def _create_measurement_group( data: SeriesData, wavelength_columns: list[str], @@ -287,10 +442,7 @@ def _create_measurement_group( measurement_time=assert_not_none(timestamp, msg=NO_DATE_OR_TIME_ERROR_MSG), analyst=header.get(str, "test performed by"), plate_well_count=96, - measurements=[ - _create_measurement(data, header, wavelength_column) - for wavelength_column in wavelength_columns - ], + measurements=[_create_measurement(data, header, wavelength_columns)], ) diff --git a/tests/parsers/unchained_labs_lunatic_stunner/testdata/spectrum_measurement.json b/tests/parsers/unchained_labs_lunatic_stunner/testdata/spectrum_measurement.json index 600811299..24a929af7 100644 --- a/tests/parsers/unchained_labs_lunatic_stunner/testdata/spectrum_measurement.json +++ b/tests/parsers/unchained_labs_lunatic_stunner/testdata/spectrum_measurement.json @@ -11,15114 +11,6 @@ { "device type": "plate reader", "detection type": "Absorbance", - "detector wavelength setting": { - "value": 230.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_0", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.728, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 231.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_1", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.696, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 232.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_2", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.668, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 233.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_3", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.64, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 234.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_4", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.617, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 235.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_5", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.599, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 236.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_6", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.588, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 237.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_7", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.579, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 238.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_8", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.573, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 239.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_9", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.571, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 240.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_10", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.569, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 241.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" - } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_11", - "sample document": { - "location identifier": "A1", - "sample identifier": "sample_A1", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.569, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.16 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0.091, 0.087, 0.082, 0.079, 0.077, 0.074, 0.073, 0.072, 0.07, 0.068, 0.066, 0.063, 0.06, 0.058, 0.056, 0.053, 0.05, 0.048, 0.046, 0.044, 0.04, 0.036, 0.034, 0.031, 0.029, 0.028, 0.026, 0.024, 0.022, 0.021, 0.02, 0.019, 0.018, 0.016, 0.015, 0.012, 0.008, 0.003, 0.0, + -0.002, + -0.002, + -0.001, 0.0, 0.002, 0.002, 0.003, 0.001, + -0.001, + -0.005 + ] + ] } - }, - "absorbance": { - "value": 0.0, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.0 } - }, + } + ], + "measurement time": "2024-03-09T14:37:50+00:00", + "plate well count": { + "value": 96, + "unit": "#" + }, + "container type": "well plate" + } + }, + { + "measurement aggregate document": { + "measurement document": [ { "device control aggregate document": { "device control document": [ { "device type": "plate reader", "detection type": "Absorbance", - "detector wavelength setting": { - "value": 348.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, "custom information document": { "path length mode": "single", "pump": "0", @@ -15253,124 +90,63 @@ } ] }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_362", + "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_1", "sample document": { - "location identifier": "B3", - "sample identifier": "blank_B3", + "location identifier": "A3", + "sample identifier": "reference_A3", "batch identifier": "Sample Group", "well plate identifier": "Plate 1", "custom information document": { - "path length": 10.0, "plate type": "Lunatic Plate" } }, - "absorbance": { - "value": 0.0, - "unit": "mAU" - }, "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.0 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 349.0, + "absorption spectrum data cube": { + "label": "absorbance-spectrum", + "cube-structure": { + "dimensions": [ + { + "@componentDatatype": "double", + "concept": "wavelength", "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_363", - "sample document": { - "location identifier": "B3", - "sample identifier": "blank_B3", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" - } - }, - "absorbance": { - "value": 0.0, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.0 - } - }, - { - "device control aggregate document": { - "device control document": [ - { - "device type": "plate reader", - "detection type": "Absorbance", - "detector wavelength setting": { - "value": 350.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, - "custom information document": { - "path length mode": "single", - "pump": "0", - "column": "1" + ], + "measures": [ + { + "@componentDatatype": "double", + "concept": "absorbance", + "unit": "mAU" } - } - ] - }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_364", - "sample document": { - "location identifier": "B3", - "sample identifier": "blank_B3", - "batch identifier": "Sample Group", - "well plate identifier": "Plate 1", - "custom information document": { - "path length": 10.0, - "plate type": "Lunatic Plate" + ] + }, + "data": { + "dimensions": [ + [230.0, 231.0, 232.0, 233.0, 234.0, 235.0, 236.0, 237.0, 238.0, 239.0, 240.0, 241.0, 242.0, 243.0, 244.0, 245.0, 246.0, 247.0, 248.0, 249.0, 250.0, 251.0, 252.0, 253.0, 254.0, 255.0, 256.0, 257.0, 258.0, 259.0, 260.0, 261.0, 262.0, 263.0, 264.0, 265.0, 266.0, 267.0, 268.0, 269.0, 270.0, 271.0, 272.0, 273.0, 274.0, 275.0, 276.0, 277.0, 278.0, 279.0, 280.0, 281.0, 282.0, 283.0, 284.0, 285.0, 286.0, 287.0, 288.0, 289.0, 290.0, 291.0, 292.0, 293.0, 294.0, 295.0, 296.0, 297.0, 298.0, 299.0, 300.0, 301.0, 302.0, 303.0, 304.0, 305.0, 306.0, 307.0, 308.0, 309.0, 310.0, 311.0, 312.0, 313.0, 314.0, 315.0, 316.0, 317.0, 318.0, 319.0, 320.0, 321.0, 322.0, 323.0, 324.0, 325.0, 326.0, 327.0, 328.0, 329.0, 330.0, 331.0, 332.0, 333.0, 334.0, 335.0, 336.0, 337.0, 338.0, 339.0, 340.0, 341.0, 342.0, 343.0, 344.0, 345.0, 346.0, 347.0, 348.0, 349.0, 350.0] + ], + "measures": [ + [0.005, 0.002, 0.001, 0.001, 0.004, 0.005, 0.008, 0.011, 0.012, 0.012, 0.009, 0.008, 0.007, 0.006, 0.006, 0.007, 0.009, 0.01, 0.01, 0.01, 0.008, 0.005, 0.001, 0.002, 0.005, 0.009, 0.012, 0.015, 0.017, 0.017, 0.014, 0.009, 0.006, 0.007, 0.009, 0.013, 0.017, 0.018, 0.018, 0.016, 0.012, 0.01, 0.009, 0.008, 0.007, 0.007, 0.009, 0.01, 0.012, 0.013, 0.011, 0.011, 0.01, 0.008, 0.005, 0.004, 0.003, 0.004, 0.005, 0.005, 0.006, 0.008, 0.011, 0.013, 0.014, 0.013, 0.013, 0.013, 0.012, 0.01, 0.009, 0.009, 0.01, 0.01, 0.011, 0.012, 0.013, 0.013, 0.012, 0.011, 0.011, 0.011, 0.01, 0.011, 0.011, 0.011, 0.011, 0.009, 0.008, 0.009, 0.009, 0.009, 0.007, 0.006, 0.005, 0.003, 0.003, 0.004, 0.004, 0.005, 0.004, 0.004, 0.004, 0.004, 0.004, 0.003, 0.004, 0.003, 0.002, 0.001, 0.0, 0.0, 0.002, 0.004, 0.007, 0.009, 0.01, 0.011, 0.013, 0.012, 0.01] + ] } - }, - "absorbance": { - "value": 0.0, - "unit": "mAU" - }, - "analytical method identifier": "dsDNA (Single point)", - "custom information document": { - "electronic absorbance reference absorbance": 0.0 } - }, + } + ], + "measurement time": "2024-03-09T14:37:50+00:00", + "plate well count": { + "value": 96, + "unit": "#" + }, + "container type": "well plate" + } + }, + { + "measurement aggregate document": { + "measurement document": [ { "device control aggregate document": { "device control document": [ { "device type": "plate reader", "detection type": "Absorbance", - "detector wavelength setting": { - "value": 260.0, - "unit": "nm" - }, - "electronic absorbance reference wavelength setting": { - "value": 340.0, - "unit": "nm" - }, "custom information document": { "path length mode": "single", "pump": "0", @@ -15379,7 +155,7 @@ } ] }, - "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_365", + "measurement identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_2", "sample document": { "location identifier": "B3", "sample identifier": "blank_B3", @@ -15389,10 +165,6 @@ "plate type": "Lunatic Plate" } }, - "absorbance": { - "value": 0.0, - "unit": "mAU" - }, "analytical method identifier": "dsDNA (Single point)", "error aggregate document": { "error document": [ @@ -15406,8 +178,32 @@ } ] }, - "custom information document": { - "electronic absorbance reference absorbance": 0.0 + "absorption spectrum data cube": { + "label": "absorbance-spectrum", + "cube-structure": { + "dimensions": [ + { + "@componentDatatype": "double", + "concept": "wavelength", + "unit": "nm" + } + ], + "measures": [ + { + "@componentDatatype": "double", + "concept": "absorbance", + "unit": "mAU" + } + ] + }, + "data": { + "dimensions": [ + [230.0, 231.0, 232.0, 233.0, 234.0, 235.0, 236.0, 237.0, 238.0, 239.0, 240.0, 241.0, 242.0, 243.0, 244.0, 245.0, 246.0, 247.0, 248.0, 249.0, 250.0, 251.0, 252.0, 253.0, 254.0, 255.0, 256.0, 257.0, 258.0, 259.0, 260.0, 261.0, 262.0, 263.0, 264.0, 265.0, 266.0, 267.0, 268.0, 269.0, 270.0, 271.0, 272.0, 273.0, 274.0, 275.0, 276.0, 277.0, 278.0, 279.0, 280.0, 281.0, 282.0, 283.0, 284.0, 285.0, 286.0, 287.0, 288.0, 289.0, 290.0, 291.0, 292.0, 293.0, 294.0, 295.0, 296.0, 297.0, 298.0, 299.0, 300.0, 301.0, 302.0, 303.0, 304.0, 305.0, 306.0, 307.0, 308.0, 309.0, 310.0, 311.0, 312.0, 313.0, 314.0, 315.0, 316.0, 317.0, 318.0, 319.0, 320.0, 321.0, 322.0, 323.0, 324.0, 325.0, 326.0, 327.0, 328.0, 329.0, 330.0, 331.0, 332.0, 333.0, 334.0, 335.0, 336.0, 337.0, 338.0, 339.0, 340.0, 341.0, 342.0, 343.0, 344.0, 345.0, 346.0, 347.0, 348.0, 349.0, 350.0] + ], + "measures": [ + [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] + ] + } } } ], @@ -15428,11 +224,11 @@ "unit": "ng/µL", "value": 29.2 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_366", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_3", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_121", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_0", "data source feature": "absorbance" } ] @@ -15444,11 +240,11 @@ "unit": "ng/µL", "value": 0.7 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_367", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_4", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_243", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_1", "data source feature": "absorbance" } ] @@ -15460,11 +256,11 @@ "unit": "ng/µL", "value": 0.0 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_368", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_5", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_365", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_2", "data source feature": "absorbance" } ] @@ -15476,11 +272,11 @@ "unit": "(unitless)", "value": 0.8 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_369", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_6", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_121", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_0", "data source feature": "absorbance" } ] @@ -15492,11 +288,11 @@ "unit": "(unitless)", "value": 2.63 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_370", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_7", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_243", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_1", "data source feature": "absorbance" } ] @@ -15508,11 +304,11 @@ "unit": "(unitless)", "value": -0.0 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_371", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_8", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_365", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_2", "data source feature": "absorbance" } ] @@ -15524,11 +320,11 @@ "unit": "(unitless)", "value": 1.65 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_372", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_9", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_121", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_0", "data source feature": "absorbance" } ] @@ -15540,11 +336,11 @@ "unit": "(unitless)", "value": 1.28 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_373", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_10", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_243", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_1", "data source feature": "absorbance" } ] @@ -15556,11 +352,11 @@ "unit": "(unitless)", "value": -0.0 }, - "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_374", + "calculated data identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_11", "data source aggregate document": { "data source document": [ { - "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_365", + "data source identifier": "UNCHAINED_LABS_LUNATIC_TEST_ID_2", "data source feature": "absorbance" } ] @@ -15574,7 +370,7 @@ "UNC path": "tests/parsers/unchained_labs_lunatic_stunner/testdata/spectrum_measurement.csv", "file name": "spectrum_measurement.csv", "ASM converter name": "allotropy_unchained_labs_lunatic_&_stunner", - "ASM converter version": "0.1.102", + "ASM converter version": "0.1.105", "software name": "Lunatic and Stunner Analysis" }, "device system document": { diff --git a/tests/parsers/unchained_labs_lunatic_stunner/unchained_labs_lunatic_structure_test.py b/tests/parsers/unchained_labs_lunatic_stunner/unchained_labs_lunatic_structure_test.py index e42a8d2c4..26ba4b24c 100644 --- a/tests/parsers/unchained_labs_lunatic_stunner/unchained_labs_lunatic_structure_test.py +++ b/tests/parsers/unchained_labs_lunatic_stunner/unchained_labs_lunatic_structure_test.py @@ -1,3 +1,4 @@ +from decimal import Decimal from io import StringIO import re @@ -24,6 +25,8 @@ from allotropy.parsers.unchained_labs_lunatic_stunner.unchained_labs_lunatic_stunner_structure import ( _create_measurement, _create_measurement_group, + _get_absorbance_with_highest_precision, + _get_wavelengths_and_absorbance, create_measurement_groups, create_metadata, ) @@ -54,7 +57,7 @@ def test__create_measurement( } header = SeriesData(pd.Series()) measurement = _create_measurement( - SeriesData(pd.Series(well_plate_data)), header, wavelength_column + SeriesData(pd.Series(well_plate_data)), header, [wavelength_column] ) assert measurement.detector_wavelength_setting == wavelength @@ -78,7 +81,7 @@ def test__create_measurement_with_no_wavelength_column() -> None: wavelength_column = "a250" msg = NO_MEASUREMENT_IN_PLATE_ERROR_MSG.format(wavelength_column) with pytest.raises(AllotropeConversionError, match=msg): - _create_measurement(well_plate_data, header, wavelength_column) + _create_measurement(well_plate_data, header, [wavelength_column]) def test__create_measurement_with_incorrect_wavelength_column_format() -> None: @@ -86,7 +89,7 @@ def test__create_measurement_with_incorrect_wavelength_column_format() -> None: well_plate_data = SeriesData(pd.Series({"sample name": "dummy name"})) header = SeriesData(pd.Series()) with pytest.raises(AllotropeConversionError, match=re.escape(msg)): - _create_measurement(well_plate_data, header, "sample name") + _create_measurement(well_plate_data, header, ["sample name"]) def test__get_calculated_data_from_measurement_for_unknown_wavelength() -> None: @@ -101,7 +104,7 @@ def test__get_calculated_data_from_measurement_for_unknown_wavelength() -> None: } header = SeriesData(pd.Series()) measurement = _create_measurement( - SeriesData(pd.Series(well_plate_data)), header, "a240" + SeriesData(pd.Series(well_plate_data)), header, ["a240"] ) measurement_group = MeasurementGroup( @@ -127,7 +130,7 @@ def test__get_calculated_data_from_measurement_for_A260() -> None: # noqa: N802 header = SeriesData(pd.Series()) wavelength = "a260" measurement = _create_measurement( - SeriesData(pd.Series(well_plate_data)), header, wavelength + SeriesData(pd.Series(well_plate_data)), header, [wavelength] ) measurement_group = MeasurementGroup( @@ -181,7 +184,7 @@ def test_create_well_plate_with_two_measurements() -> None: SeriesData(pd.Series(plate_data)), ["a452", "a280"], SeriesData(pd.Series()) ) - assert len(well_plate.measurements) == 2 + assert len(well_plate.measurements) == 1 def test_create_well_plate_use_datetime_from_data_over_header() -> None: @@ -244,6 +247,7 @@ def test_get_calculated_data_items_from_data_with_the_right_values() -> None: ) reader = UnchainedLabsLunaticReader(NamedFileContents(contents, "filename.csv")) _, calculated_data = create_measurement_groups(reader.header, reader.data) + assert calculated_data calculated_data_item = calculated_data[0] @@ -322,3 +326,60 @@ def test_create_data() -> None: assert metadata.device_identifier == "14" assert len(measurement_groups) == 3 + + +def test__get_wavelength_and_absorbance_unique() -> None: + series = SeriesData( + pd.Series( + { + "A280": "2.34", + "A260": "1.23", + } + ) + ) + wavelengths, absorbances = _get_wavelengths_and_absorbance(series, ["A280", "A260"]) + assert wavelengths == [260.0, 280.0] + assert absorbances == pytest.approx([1.23, 2.34], rel=1e-12) + + +def test__get_wavelength_and_absorbance_duplicates_keep_high_precision() -> None: + series = SeriesData( + pd.Series( + { + "A260": "1.57", + "A260 (10mm)": "1.5678", + } + ) + ) + wavelengths, absorbances = _get_wavelengths_and_absorbance( + series, ["A260", "A260 (10mm)"] + ) + assert wavelengths == [260.0] + assert absorbances == pytest.approx([1.5678], rel=1e-12) + + +def test__get_wavelength_and_absorbance_duplicates_mismatch_raises() -> None: + series = SeriesData( + pd.Series( + { + "A260": "1.57", + "A260 (10mm)": "1.564", + } + ) + ) + with pytest.raises(AllotropeConversionError): + _get_wavelengths_and_absorbance(series, ["A260", "A260 (10mm)"]) + + +def test__get_absorbance_with_highest_precision_keeps_high_precision() -> None: + high = Decimal("1.5678") + low = Decimal("1.57") + result = _get_absorbance_with_highest_precision(high, low) + assert result == high + + +def test__get_absorbance_with_highest_precision_raises_on_mismatch() -> None: + a = Decimal("1.564") + b = Decimal("1.57") + with pytest.raises(AllotropeConversionError): + _get_absorbance_with_highest_precision(a, b)