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Feat: luminex xponent adapter (#255)
Add Luminex Xponent support.
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src/allotropy/parsers/luminex_xponent/luminex_xponent_parser.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,160 @@ | ||
| from allotropy.allotrope.models.multi_analyte_profiling_benchling_2024_01_multi_analyte_profiling import ( | ||
| AnalyteAggregateDocument, | ||
| AnalyteDocumentItem, | ||
| CalibrationAggregateDocument, | ||
| CalibrationDocumentItem, | ||
| DataSystemDocument, | ||
| DeviceControlAggregateDocument, | ||
| DeviceControlDocumentItem, | ||
| DeviceSystemDocument, | ||
| ErrorAggregateDocument, | ||
| ErrorDocumentItem, | ||
| MeasurementAggregateDocument, | ||
| MeasurementDocumentItem, | ||
| Model, | ||
| MultiAnalyteProfilingAggregateDocument, | ||
| MultiAnalyteProfilingDocumentItem, | ||
| SampleDocument, | ||
| ) | ||
| from allotropy.allotrope.models.shared.definitions.custom import ( | ||
| TQuantityValueMicroliter, | ||
| TQuantityValueNumber, | ||
| TQuantityValueRelativeFluorescenceUnit, | ||
| TQuantityValueUnitless, | ||
| ) | ||
| from allotropy.allotrope.models.shared.definitions.definitions import ( | ||
| TStatisticDatumRole, | ||
| ) | ||
| from allotropy.constants import ASM_CONVERTER_NAME, ASM_CONVERTER_VERSION | ||
| from allotropy.named_file_contents import NamedFileContents | ||
| from allotropy.parsers.lines_reader import CsvReader, read_to_lines | ||
| from allotropy.parsers.luminex_xponent.luminex_xponent_structure import ( | ||
| Data, | ||
| Header, | ||
| Measurement, | ||
| ) | ||
| from allotropy.parsers.utils.uuids import random_uuid_str | ||
| from allotropy.parsers.vendor_parser import VendorParser | ||
|
|
||
| DEFAULT_SOFTWARE_NAME = "xPONENT" | ||
| DEFAULT_CONTAINER_TYPE = "well plate" | ||
| DEFAULT_DEVICE_TYPE = "multi analyte profiling analyzer" | ||
|
|
||
|
|
||
| class LuminexXponentParser(VendorParser): | ||
| def to_allotrope(self, named_file_contents: NamedFileContents) -> Model: | ||
| lines = read_to_lines(named_file_contents.contents) | ||
| reader = CsvReader(lines) | ||
| data = Data.create(reader, self.timestamp_parser) | ||
| return self._get_model(named_file_contents.original_file_name, data) | ||
|
|
||
| def _get_model(self, file_name: str, data: Data) -> Model: | ||
| header = data.header | ||
| return Model( | ||
| field_asm_manifest="http://purl.allotrope.org/manifests/multi-analyte-profiling/BENCHLING/2024/01/multi-analyte-profiling.manifest", | ||
| multi_analyte_profiling_aggregate_document=MultiAnalyteProfilingAggregateDocument( | ||
| device_system_document=DeviceSystemDocument( | ||
| model_number=header.model_number, | ||
| equipment_serial_number=header.equipment_serial_number, | ||
| calibration_aggregate_document=CalibrationAggregateDocument( | ||
| calibration_document=[ | ||
| CalibrationDocumentItem( | ||
| calibration_name=calibration_item.name, | ||
| calibration_report=calibration_item.report, | ||
| calibration_time=calibration_item.time, | ||
| ) | ||
| for calibration_item in data.calibration_data | ||
| ] | ||
| ), | ||
| ), | ||
| data_system_document=DataSystemDocument( | ||
| data_system_instance_identifier=header.data_system_instance_identifier, | ||
| file_name=file_name, | ||
| software_name=DEFAULT_SOFTWARE_NAME, | ||
| software_version=header.software_version, | ||
| ASM_converter_name=ASM_CONVERTER_NAME, | ||
| ASM_converter_version=ASM_CONVERTER_VERSION, | ||
| ), | ||
| multi_analyte_profiling_document=[ | ||
| MultiAnalyteProfilingDocumentItem( | ||
| analyst=header.analyst, | ||
| measurement_aggregate_document=MeasurementAggregateDocument( | ||
| analytical_method_identifier=header.analytical_method_identifier, | ||
| method_version=header.method_version, | ||
| experimental_data_identifier=header.experimental_data_identifier, | ||
| container_type=DEFAULT_CONTAINER_TYPE, | ||
| plate_well_count=TQuantityValueNumber( | ||
| value=header.plate_well_count | ||
| ), | ||
| measurement_document=[ | ||
| self._get_measurement_document_item( | ||
| measurement, | ||
| header, | ||
| data.minimum_bead_count_setting, | ||
| ) | ||
| for measurement in data.measurement_list.measurements | ||
| ], | ||
| ), | ||
| ) | ||
| ], | ||
| ), | ||
| ) | ||
|
|
||
| def _get_measurement_document_item( | ||
| self, | ||
| measurement: Measurement, | ||
| header_data: Header, | ||
| minimum_bead_count_setting: float, | ||
| ) -> MeasurementDocumentItem: | ||
| error_aggregate_document = None | ||
| if measurement.errors: | ||
| error_aggregate_document = ErrorAggregateDocument( | ||
| error_document=[ | ||
| ErrorDocumentItem(error=error) for error in measurement.errors | ||
| ] | ||
| ) | ||
|
|
||
| return MeasurementDocumentItem( | ||
| measurement_identifier=random_uuid_str(), | ||
| measurement_time=header_data.measurement_time, | ||
| sample_document=SampleDocument( | ||
| sample_identifier=measurement.sample_identifier, | ||
| location_identifier=measurement.location_identifier, | ||
| ), | ||
| device_control_aggregate_document=DeviceControlAggregateDocument( | ||
| device_control_document=[ | ||
| DeviceControlDocumentItem( | ||
| device_type=DEFAULT_DEVICE_TYPE, | ||
| sample_volume_setting=TQuantityValueMicroliter( | ||
| value=header_data.sample_volume_setting | ||
| ), | ||
| dilution_factor_setting=TQuantityValueUnitless( | ||
| value=measurement.dilution_factor_setting | ||
| ), | ||
| detector_gain_setting=header_data.detector_gain_setting, | ||
| minimum_assay_bead_count_setting=TQuantityValueUnitless( | ||
| value=minimum_bead_count_setting | ||
| ), | ||
| ) | ||
| ] | ||
| ), | ||
| assay_bead_count=TQuantityValueNumber(value=measurement.assay_bead_count), | ||
| analyte_aggregate_document=AnalyteAggregateDocument( | ||
| analyte_document=[ | ||
| AnalyteDocumentItem( | ||
| analyte_identifier=random_uuid_str(), | ||
| analyte_name=analyte.analyte_name, | ||
| assay_bead_identifier=analyte.assay_bead_identifier, | ||
| assay_bead_count=TQuantityValueNumber( | ||
| value=analyte.assay_bead_count | ||
| ), | ||
| fluorescence=TQuantityValueRelativeFluorescenceUnit( | ||
| value=analyte.fluorescence, | ||
| has_statistic_datum_role=TStatisticDatumRole.median_role, | ||
| ), | ||
| ) | ||
| for analyte in measurement.analytes | ||
| ] | ||
| ), | ||
| error_aggregate_document=error_aggregate_document, | ||
| ) |
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