diff --git a/SUPPORTED_INSTRUMENT_SOFTWARE.adoc b/SUPPORTED_INSTRUMENT_SOFTWARE.adoc index 73f35276a3..a42db7d4f9 100644 --- a/SUPPORTED_INSTRUMENT_SOFTWARE.adoc +++ b/SUPPORTED_INSTRUMENT_SOFTWARE.adoc @@ -15,7 +15,8 @@ The parsers follow maturation levels of: Recommended, Candidate Release, Working [cols="4*^.^"] |=== |Instrument Category|Instrument Software|Release Status|Exported ASM Schema -.1+|Binding Affinity Analyzer|Cytiva Biacore T200 Control|Recommended|WD/2024/12 +.2+|Binding Affinity Analyzer|Cytiva Biacore Insight|Recommended|WD/2024/12 +|Cytiva Biacore T200 Control|Recommended|WD/2024/12 .6+|Cell Counting|Beckman Coulter Vi-Cell BLU|Recommended|REC/2024/09 |Beckman Coulter Vi-Cell XR|Recommended|REC/2024/09 |ChemoMetec NC View|Recommended|REC/2024/09 diff --git a/src/allotropy/allotrope/models/adm/binding_affinity_analyzer/wd/_2024/_12/binding_affinity_analyzer.py b/src/allotropy/allotrope/models/adm/binding_affinity_analyzer/wd/_2024/_12/binding_affinity_analyzer.py index 686d0bd867..13be70f6ab 100644 --- a/src/allotropy/allotrope/models/adm/binding_affinity_analyzer/wd/_2024/_12/binding_affinity_analyzer.py +++ b/src/allotropy/allotrope/models/adm/binding_affinity_analyzer/wd/_2024/_12/binding_affinity_analyzer.py @@ -1,6 +1,6 @@ # generated by datamodel-codegen: # filename: binding-affinity-analyzer.schema.json -# timestamp: 2025-02-26T19:19:58+00:00 +# timestamp: 2025-08-29T17:23:20+00:00 from __future__ import annotations @@ -14,10 +14,10 @@ TQuantityValueMolar, TQuantityValueNanomolar, TQuantityValuePercent, + TQuantityValuePerMolarPerSecond, TQuantityValuePerSecond, TQuantityValueResonanceUnits, TQuantityValueSecondTime, - TQuantityValueTODO, ) from allotropy.allotrope.models.shared.definitions.definitions import ( TBooleanValue, @@ -268,10 +268,12 @@ class ProcessedDataDocumentItem: field_index: int | None = None POSIX_path: TStringValue | None = None identifier: TStringValue | None = None - binding_on_rate_measurement_datum__kon_: TQuantityValueTODO | None = None + binding_on_rate_measurement_datum__kon_: TQuantityValuePerMolarPerSecond | None = ( + None + ) binding_off_rate_measurement_datum__koff_: TQuantityValuePerSecond | None = None equilibrium_dissociation_constant__KD_: TQuantityValueMolar | None = None - maximum_binding_capacity__Rmax_: TQuantityValueTODO | None = None + maximum_binding_capacity__Rmax_: TQuantityValueResonanceUnits | None = None report_point_aggregate_document: ReportPointAggregateDocument | None = None diff --git a/src/allotropy/allotrope/models/shared/definitions/custom.py b/src/allotropy/allotrope/models/shared/definitions/custom.py index 84eb93e147..19bd9c4468 100644 --- a/src/allotropy/allotrope/models/shared/definitions/custom.py +++ b/src/allotropy/allotrope/models/shared/definitions/custom.py @@ -71,6 +71,7 @@ SeimensPerMeter, SquareCentimetersPerGram, SquareCentimetersPerMole, + SquareResonanceUnits, TODO, Unitless, UnitPerLiter, @@ -807,6 +808,18 @@ class TNullableQuantityValueSquareCentimetersPerMole( pass +@dataclass(frozen=True, kw_only=True) +class TQuantityValueSquareResonanceUnits(SquareResonanceUnits, TQuantityValue): + pass + + +@dataclass(frozen=True, kw_only=True) +class TNullableQuantityValueSquareResonanceUnits( + SquareResonanceUnits, TNullableQuantityValue +): + pass + + @dataclass(frozen=True, kw_only=True) class TQuantityValueTODO(TODO, TQuantityValue): pass diff --git a/src/allotropy/allotrope/models/shared/definitions/units.py b/src/allotropy/allotrope/models/shared/definitions/units.py index 9f5cc1d9a7..58767bb482 100644 --- a/src/allotropy/allotrope/models/shared/definitions/units.py +++ b/src/allotropy/allotrope/models/shared/definitions/units.py @@ -334,6 +334,11 @@ class SquareCentimetersPerMole(HasUnit): unit: str = "cm^2/mol" +@dataclass(frozen=True, kw_only=True) +class SquareResonanceUnits(HasUnit): + unit: str = "RU^2" + + @dataclass(frozen=True, kw_only=True) class TODO(HasUnit): unit: str = "TODO" diff --git a/src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py b/src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py index 58d05bb015..ee3b7e203b 100644 --- a/src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py +++ b/src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py @@ -28,8 +28,11 @@ from allotropy.allotrope.models.shared.definitions.custom import ( TQuantityValueDegreeCelsius, TQuantityValueMicroliterPerMinute, + TQuantityValueMolar, TQuantityValueNanomolar, TQuantityValuePercent, + TQuantityValuePerMolarPerSecond, + TQuantityValuePerSecond, TQuantityValueResonanceUnits, TQuantityValueSecondTime, ) @@ -41,7 +44,7 @@ from allotropy.parsers.utils.calculated_data_documents.definition import ( CalculatedDocument, ) -from allotropy.parsers.utils.values import assert_not_none, quantity_or_none +from allotropy.parsers.utils.values import assert_not_none, has_value, quantity_or_none from allotropy.types import DictType @@ -87,12 +90,24 @@ class ReportPoint: custom_info: DictType | None = None +@dataclass(frozen=True) +class DeviceControlDocument: + device_type: str + flow_cell_identifier: str | None = None + flow_path: str | None = None + flow_rate: float | None = None + contact_time: float | None = None + dilution: float | None = None + sample_temperature_setting: float | None = None + device_control_custom_info: DictType | None = None + + @dataclass(frozen=True) class Measurement: identifier: str sample_identifier: str - device_type: str type_: MeasurementType + device_control_document: list[DeviceControlDocument] location_identifier: str | None = None batch_identifier: str | None = None well_plate_identifier: str | None = None @@ -100,20 +115,24 @@ class Measurement: concentration: float | None = None method_name: str | None = None ligand_identifier: str | None = None - flow_cell_identifier: str | None = None - flow_path: str | None = None - flow_rate: float | None = None - contact_time: float | None = None - dilution: float | None = None - device_control_custom_info: DictType | None = None sample_custom_info: DictType | None = None # Sensorgram sensorgram_data_cube: DataCube | None = None + # Processed Data + binding_on_rate_measurement_datum__kon_: float | None = None + binding_off_rate_measurement_datum__koff_: float | None = None + equilibrium_dissociation_constant__kd_: float | None = None + maximum_binding_capacity__rmax_: float | None = None + processed_data_custom_info: DictType | None = None + # Report point report_point_data: list[ReportPoint] | None = None + # Data processing + data_processing_document: DictType | None = None + @dataclass(frozen=True) class MeasurementGroup: @@ -153,6 +172,7 @@ def map_model(self, data: Data) -> Model: model_number=data.metadata.model_number, brand_name=data.metadata.brand_name, product_manufacturer=data.metadata.product_manufacturer, + equipment_serial_number=data.metadata.equipment_serial_number, device_document=( [ DeviceDocumentItem( @@ -213,6 +233,60 @@ def _get_measurement_document_item( def _get_surface_plasmon_resonance_measurement_document( self, measurement: Measurement, metadata: Metadata ) -> MeasurementDocument: + processed_data_document = ProcessedDataDocumentItem( + data_processing_document=( + { + key: value + for key, value in measurement.data_processing_document.items() + if value is not None + } + if measurement.data_processing_document + else None + ), + binding_on_rate_measurement_datum__kon_=quantity_or_none( + TQuantityValuePerMolarPerSecond, + measurement.binding_on_rate_measurement_datum__kon_, + ), + binding_off_rate_measurement_datum__koff_=quantity_or_none( + TQuantityValuePerSecond, + measurement.binding_off_rate_measurement_datum__koff_, + ), + equilibrium_dissociation_constant__KD_=quantity_or_none( + TQuantityValueMolar, + measurement.equilibrium_dissociation_constant__kd_, + ), + maximum_binding_capacity__Rmax_=quantity_or_none( + TQuantityValueResonanceUnits, + measurement.maximum_binding_capacity__rmax_, + ), + report_point_aggregate_document=( + ReportPointAggregateDocument( + report_point_document=[ + add_custom_information_document( + ReportPointDocumentItem( + report_point_identifier=report_point.identifier, + identifier_role=report_point.identifier_role, + absolute_resonance=TQuantityValueResonanceUnits( + value=report_point.absolute_resonance + ), + relative_resonance=quantity_or_none( + TQuantityValueResonanceUnits, + report_point.relative_resonance, + ), + time_setting=TQuantityValueSecondTime( + value=report_point.time_setting + ), + ), + custom_info_doc=report_point.custom_info, + ) + for report_point in measurement.report_point_data + ] + ) + if measurement.report_point_data + else None + ), + ) + return MeasurementDocument( measurement_identifier=measurement.identifier, sample_document=add_custom_information_document( @@ -245,55 +319,39 @@ def _get_surface_plasmon_resonance_measurement_document( device_control_document=[ add_custom_information_document( DeviceControlDocumentItem( - flow_cell_identifier=measurement.flow_cell_identifier, - flow_path=measurement.flow_path, + sample_temperature_setting=quantity_or_none( + TQuantityValueDegreeCelsius, + device_control.sample_temperature_setting, + ), + flow_cell_identifier=device_control.flow_cell_identifier, + flow_path=device_control.flow_path, flow_rate=quantity_or_none( TQuantityValueMicroliterPerMinute, - measurement.flow_rate, + device_control.flow_rate, ), contact_time=quantity_or_none( - TQuantityValueSecondTime, measurement.contact_time + TQuantityValueSecondTime, device_control.contact_time ), dilution_factor=quantity_or_none( - TQuantityValuePercent, measurement.dilution + TQuantityValuePercent, device_control.dilution ), - device_type=measurement.device_type, + device_type=device_control.device_type, ), - custom_info_doc=measurement.device_control_custom_info, + custom_info_doc=device_control.device_control_custom_info, ) + for device_control in measurement.device_control_document ] ), processed_data_aggregate_document=( ProcessedDataAggregateDocument( processed_data_document=[ - ProcessedDataDocumentItem( - report_point_aggregate_document=ReportPointAggregateDocument( - report_point_document=[ - add_custom_information_document( - ReportPointDocumentItem( - report_point_identifier=report_point.identifier, - identifier_role=report_point.identifier_role, - absolute_resonance=TQuantityValueResonanceUnits( - value=report_point.absolute_resonance - ), - relative_resonance=quantity_or_none( - TQuantityValueResonanceUnits, - report_point.relative_resonance, - ), - time_setting=TQuantityValueSecondTime( - value=report_point.time_setting - ), - ), - # TODO: probably this should be at the processed document level. - custom_info_doc=report_point.custom_info, - ) - for report_point in measurement.report_point_data - ] - ) - ), + add_custom_information_document( + processed_data_document, + custom_info_doc=measurement.processed_data_custom_info, + ) ] ) - if measurement.report_point_data + if has_value(processed_data_document) else None ), ) diff --git a/src/allotropy/allotrope/schemas/adm/binding-affinity-analyzer/WD/2024/12/binding-affinity-analyzer.schema.json b/src/allotropy/allotrope/schemas/adm/binding-affinity-analyzer/WD/2024/12/binding-affinity-analyzer.schema.json index 6b7610f476..c6854073bf 100644 --- a/src/allotropy/allotrope/schemas/adm/binding-affinity-analyzer/WD/2024/12/binding-affinity-analyzer.schema.json +++ b/src/allotropy/allotrope/schemas/adm/binding-affinity-analyzer/WD/2024/12/binding-affinity-analyzer.schema.json @@ -180,7 +180,7 @@ "$ref": "http://purl.allotrope.org/json-schemas/adm/core/REC/2024/09/core.schema#/$defs/tQuantityValue" }, { - "$ref": "TODO" + "$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/PerMolarPerSecond" } ] }, @@ -216,7 +216,7 @@ "$ref": "http://purl.allotrope.org/json-schemas/adm/core/REC/2024/09/core.schema#/$defs/tQuantityValue" }, { - "$ref": "TODO" + "$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/ResonanceUnits" } ] } @@ -4521,6 +4521,18 @@ "unit" ] }, + "M-1s-1": { + "properties": { + "unit": { + "$asm.unit-iri": "http://purl.allotrope.org/ontology/qudt-ext/unit#PerMolarPerSecond", + "const": "M-1s-1", + "type": "string" + } + }, + "required": [ + "unit" + ] + }, "MHz": { "properties": { "unit": { diff --git a/src/allotropy/allotrope/schemas/shared/definitions/custom.json b/src/allotropy/allotrope/schemas/shared/definitions/custom.json index f40308e307..abe47993b4 100644 --- a/src/allotropy/allotrope/schemas/shared/definitions/custom.json +++ b/src/allotropy/allotrope/schemas/shared/definitions/custom.json @@ -1299,6 +1299,26 @@ } ] }, + "tQuantityValueSquareResonanceUnits": { + "allOf": [ + { + "$ref": "#/$defs/tQuantityValue" + }, + { + "$ref": "#/$defs/SquareResonanceUnits" + } + ] + }, + "tNullableQuantityValueSquareResonanceUnits": { + "allOf": [ + { + "$ref": "#/$defs/tNullableQuantityValue" + }, + { + "$ref": "#/$defs/SquareResonanceUnits" + } + ] + }, "tQuantityValueTODO": { "allOf": [ { diff --git a/src/allotropy/allotrope/schemas/shared/definitions/units.json b/src/allotropy/allotrope/schemas/shared/definitions/units.json index dd50198f60..ee95d3401d 100644 --- a/src/allotropy/allotrope/schemas/shared/definitions/units.json +++ b/src/allotropy/allotrope/schemas/shared/definitions/units.json @@ -779,6 +779,18 @@ "unit" ] }, + "SquareResonanceUnits": { + "properties": { + "unit": { + "type": "string", + "const": "RU^2", + "$asm.unit-iri": "TODO" + } + }, + "required": [ + "unit" + ] + }, "TODO": { "properties": { "unit": { diff --git a/src/allotropy/parser_factory.py b/src/allotropy/parser_factory.py index af41b2632f..b1118a84c6 100644 --- a/src/allotropy/parser_factory.py +++ b/src/allotropy/parser_factory.py @@ -57,6 +57,9 @@ ChemometecNucleoviewParser, ) from allotropy.parsers.ctl_immunospot.ctl_immunospot_parser import CtlImmunospotParser +from allotropy.parsers.cytiva_biacore_insight.cytiva_biacore_insight_parser import ( + CytivaBiacoreInsightParser, +) from allotropy.parsers.cytiva_biacore_t200_control.cytiva_biacore_t200_control_parser import ( CytivaBiacoreT200ControlParser, ) @@ -148,6 +151,7 @@ class Vendor(Enum): CHEMOMETEC_NC_VIEW = "CHEMOMETEC_NC_VIEW" CHEMOMETEC_NUCLEOVIEW = "CHEMOMETEC_NUCLEOVIEW" CTL_IMMUNOSPOT = "CTL_IMMUNOSPOT" + CYTIVA_BIACORE_INSIGHT = "CYTIVA_BIACORE_INSIGHT" CYTIVA_BIACORE_T200_CONTROL = "CYTIVA_BIACORE_T200_CONTROL" CYTIVA_UNICORN = "CYTIVA_UNICORN" EXAMPLE_WEYLAND_YUTANI = "EXAMPLE_WEYLAND_YUTANI" @@ -244,6 +248,7 @@ def get_parser( Vendor.CHEMOMETEC_NC_VIEW: ChemometecNcViewParser, Vendor.CHEMOMETEC_NUCLEOVIEW: ChemometecNucleoviewParser, Vendor.CTL_IMMUNOSPOT: CtlImmunospotParser, + Vendor.CYTIVA_BIACORE_INSIGHT: CytivaBiacoreInsightParser, Vendor.CYTIVA_BIACORE_T200_CONTROL: CytivaBiacoreT200ControlParser, Vendor.CYTIVA_UNICORN: CytivaUnicornParser, Vendor.EXAMPLE_WEYLAND_YUTANI: ExampleWeylandYutaniParser, diff --git a/src/allotropy/parsers/cytiva_biacore_insight/__init__.py b/src/allotropy/parsers/cytiva_biacore_insight/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/src/allotropy/parsers/cytiva_biacore_insight/constants.py b/src/allotropy/parsers/cytiva_biacore_insight/constants.py new file mode 100644 index 0000000000..a42dcf09af --- /dev/null +++ b/src/allotropy/parsers/cytiva_biacore_insight/constants.py @@ -0,0 +1,7 @@ +DISPLAY_NAME = "Cytiva Biacore Insight" +DEVICE_IDENTIFIER = "Biacore" +DEVICE_TYPE = "Binding Affinity Analyzer" +DETECTION_TYPE = "Surface Plasmon Resonance" +PRODUCT_MANUFACTURER = "Cytiva" + +COMPARTMENT_TEMP_REGEX = r"Sample compartment temperature (\d+),.*" diff --git a/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py new file mode 100644 index 0000000000..d7a1f32a91 --- /dev/null +++ b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py @@ -0,0 +1,190 @@ +from pathlib import Path + +from allotropy.allotrope.models.shared.definitions.custom import ( + TQuantityValueHertz, + TQuantityValueNumber, + TQuantityValueSecondTime, + TQuantityValueSquareResonanceUnits, + TQuantityValueUnitless, +) +from allotropy.allotrope.models.shared.definitions.units import Unitless +from allotropy.allotrope.schema_mappers.adm.binding_affinity_analyzer.benchling._2024._12.binding_affinity_analyzer import ( + Measurement, + MeasurementGroup, + MeasurementType, + Metadata, + ReportPoint, +) +from allotropy.parsers.constants import NOT_APPLICABLE +from allotropy.parsers.cytiva_biacore_insight import constants +from allotropy.parsers.cytiva_biacore_insight.cytiva_biacore_insight_structure import ( + BiacoreInsightMetadata, + Data, + MeasurementData, + ReportPointData, +) +from allotropy.parsers.utils.calculated_data_documents.definition import ( + CalculatedDocument, + DataSource, + Referenceable, +) +from allotropy.parsers.utils.uuids import random_uuid_str +from allotropy.parsers.utils.values import quantity_or_none + + +def create_metadata(metadata: BiacoreInsightMetadata, file_path: str) -> Metadata: + path = Path(file_path) + run_metadata = metadata.runs[0] + return Metadata( + device_identifier=constants.DEVICE_IDENTIFIER, + asm_file_identifier=path.with_suffix(".json").name, + data_system_instance_identifier=NOT_APPLICABLE, + model_number=run_metadata.model_number, + sensor_chip_identifier=run_metadata.sensor_chip_id, + product_manufacturer=constants.PRODUCT_MANUFACTURER, + software_name=metadata.software_name, + software_version=metadata.software_version, + file_name=metadata.file_name, + unc_path=metadata.unc_path, + detection_type=constants.DETECTION_TYPE, + equipment_serial_number=run_metadata.equipment_serial_number, + compartment_temperature=run_metadata.compartment_temperature, + sensor_chip_type=run_metadata.sensor_chip_type, + lot_number=run_metadata.lot_number, + ) + + +def create_measurement_groups(data: Data) -> list[MeasurementGroup]: + # Here we assume that the first run contains the relevant metadata for the measurement group. + run_metadata = data.metadata.runs[0] + return [ + MeasurementGroup( + measurement_time=run_metadata.measurement_time, + analytical_method_identifier=data.metadata.analytical_method_id, + analyst=data.metadata.analyst, + measurement_aggregate_custom_info={ + "number_of_cycles": TQuantityValueNumber( + value=run_metadata.number_of_cycles + ), + "data_collection_rate": TQuantityValueHertz( + value=run_metadata.data_collection_rate + ), + "running_buffer": run_metadata.running_buffer, + "measurement_end_time": run_metadata.measurement_end_time, + }, + measurements=_get_measurements(cycle_measurements, data.metadata), + ) + for cycle_measurements in data.cycles.values() + ] + + +def _get_measurements( + measurement_data: list[MeasurementData], metadata: BiacoreInsightMetadata +) -> list[Measurement]: + data_processing_document = dict(metadata.data_processing_document or {}) + + return [ + Measurement( + identifier=measurement.identifier, + sample_identifier=measurement.sample_identifier, + type_=MeasurementType.SURFACE_PLASMON_RESONANCE, + method_name=measurement.method_name, + ligand_identifier=measurement.ligand_identifier, + device_control_document=measurement.device_control_document, + sample_custom_info=measurement.sample_custom_info, + binding_on_rate_measurement_datum__kon_=( + measurement.kinetics.binding_on_rate_measurement_datum + ), + binding_off_rate_measurement_datum__koff_=( + measurement.kinetics.binding_off_rate_measurement_datum + ), + equilibrium_dissociation_constant__kd_=( + measurement.kinetics.equilibrium_dissociation_constant + ), + maximum_binding_capacity__rmax_=( + measurement.kinetics.maximum_binding_capacity + ), + processed_data_custom_info=( + { + "Kinetics Chi squared": quantity_or_none( + TQuantityValueSquareResonanceUnits, + measurement.kinetics.kinetics_chi_squared, + ), + "tc": quantity_or_none( + TQuantityValueUnitless, measurement.kinetics.tc + ), + } + ), + report_point_data=[ + ReportPoint( + identifier=rp.identifier, + identifier_role=rp.identifier_role, + absolute_resonance=rp.absolute_resonance, + time_setting=rp.time_setting, + relative_resonance=rp.relative_resonance, + custom_info={ + "Step name": rp.step_name, + "Step purpose": rp.step_purpose, + "Window": quantity_or_none(TQuantityValueSecondTime, rp.window), + "Baseline": rp.baseline, + }, + ) + for rp in measurement.report_point_data + ], + data_processing_document={ + **data_processing_document, + "Acceptance State": measurement.kinetics.acceptance_state, + "Curve Markers": measurement.kinetics.curve_markers, + "Kinetics Model": measurement.kinetics.kinetics_model, + }, + ) + for measurement in measurement_data + ] + + +def create_calculated_data(data: Data) -> list[CalculatedDocument]: + calculated_data = [] + for cycle_measurements in data.cycles.values(): + for measurement in cycle_measurements: + for rp in measurement.report_point_data: + calculated_data.extend(_get_report_point_calc_data(rp)) + + return calculated_data + + +def _get_report_point_calc_data(rp: ReportPointData) -> list[CalculatedDocument]: + calc_data = [] + data_source = DataSource( + feature="Absolute Response", reference=Referenceable(rp.identifier) + ) + if rp.lrsd is not None: + calc_data.append( + CalculatedDocument( + uuid=random_uuid_str(), + name="LRSD", + value=rp.lrsd, + data_sources=[data_source], + unit=Unitless.unit, + ) + ) + if rp.slope is not None: + calc_data.append( + CalculatedDocument( + uuid=random_uuid_str(), + name="Slope", + value=rp.slope, + data_sources=[data_source], + unit=Unitless.unit, + ) + ) + if rp.standard_deviation is not None: + calc_data.append( + CalculatedDocument( + uuid=random_uuid_str(), + name="Standard deviation", + value=rp.standard_deviation, + data_sources=[data_source], + unit=Unitless.unit, + ) + ) + return calc_data diff --git a/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_parser.py b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_parser.py new file mode 100644 index 0000000000..c5c449b9d5 --- /dev/null +++ b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_parser.py @@ -0,0 +1,38 @@ +from allotropy.allotrope.models.adm.binding_affinity_analyzer.wd._2024._12.binding_affinity_analyzer import ( + Model, +) +from allotropy.allotrope.schema_mappers.adm.binding_affinity_analyzer.benchling._2024._12.binding_affinity_analyzer import ( + Data as MapperData, + Mapper, +) +from allotropy.named_file_contents import NamedFileContents +from allotropy.parsers.cytiva_biacore_insight.constants import DISPLAY_NAME +from allotropy.parsers.cytiva_biacore_insight.cytiva_biacore_insight_data_creator import ( + create_calculated_data, + create_measurement_groups, + create_metadata, +) +from allotropy.parsers.cytiva_biacore_insight.cytiva_biacore_insight_reader import ( + CytivaBiacoreInsightReader, +) +from allotropy.parsers.cytiva_biacore_insight.cytiva_biacore_insight_structure import ( + Data, +) +from allotropy.parsers.release_state import ReleaseState +from allotropy.parsers.vendor_parser import VendorParser + + +class CytivaBiacoreInsightParser(VendorParser[MapperData, Model]): + DISPLAY_NAME = DISPLAY_NAME + RELEASE_STATE = ReleaseState.RECOMMENDED + SUPPORTED_EXTENSIONS = CytivaBiacoreInsightReader.SUPPORTED_EXTENSIONS + SCHEMA_MAPPER = Mapper + + def create_data(self, named_file_contents: NamedFileContents) -> MapperData: + reader = CytivaBiacoreInsightReader.create(named_file_contents) + data = Data.create(reader) + return MapperData( + create_metadata(data.metadata, named_file_contents.original_file_path), + create_measurement_groups(data), + create_calculated_data(data), + ) diff --git a/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_reader.py b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_reader.py new file mode 100644 index 0000000000..f5301ef960 --- /dev/null +++ b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_reader.py @@ -0,0 +1,30 @@ +from __future__ import annotations + +import pandas as pd + +from allotropy.exceptions import AllotropeConversionError +from allotropy.named_file_contents import NamedFileContents +from allotropy.parsers.utils.pandas import read_multisheet_excel + +REQUIRED_SHEETS = ("Properties", "Report point table", "Evaluation - Kinetics") + + +class CytivaBiacoreInsightReader: + SUPPORTED_EXTENSIONS = "xlsx, xlsm" + data: dict[str, pd.DataFrame] + + @staticmethod + def create(named_file_contents: NamedFileContents) -> CytivaBiacoreInsightReader: + data = read_multisheet_excel( + named_file_contents.contents, + header=None, + engine="calamine", + ) + if missing_sheets := [sheet for sheet in REQUIRED_SHEETS if sheet not in data]: + msg = f"Missing required sheets: {', '.join(missing_sheets)}" + raise AllotropeConversionError(msg) + + return CytivaBiacoreInsightReader(data) + + def __init__(self, data: dict[str, pd.DataFrame]) -> None: + self.data = data diff --git a/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_structure.py b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_structure.py new file mode 100644 index 0000000000..6553531f72 --- /dev/null +++ b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_structure.py @@ -0,0 +1,471 @@ +from __future__ import annotations + +import re +from typing import Any + +from attr import dataclass +import numpy as np +import pandas as pd + +from allotropy.allotrope.models.shared.definitions.custom import ( + TQuantityValueDalton, + TQuantityValueMicroliterPerMinute, + TQuantityValueNanomolar, + TQuantityValueResonanceUnits, + TQuantityValueSecondTime, +) +from allotropy.allotrope.schema_mappers.adm.binding_affinity_analyzer.benchling._2024._12.binding_affinity_analyzer import ( + DeviceControlDocument, +) +from allotropy.exceptions import AllotropeConversionError +from allotropy.parsers.cytiva_biacore_insight import constants +from allotropy.parsers.cytiva_biacore_insight.cytiva_biacore_insight_reader import ( + CytivaBiacoreInsightReader, +) +from allotropy.parsers.utils.pandas import ( + df_to_series_data, + drop_df_rows_while, + map_rows, + parse_header_row, + SeriesData, + split_dataframe, +) +from allotropy.parsers.utils.uuids import random_uuid_str +from allotropy.parsers.utils.values import ( + assert_not_none, + quantity_or_none, +) +from allotropy.types import DictType + + +def _get_table_from_dataframe(df: pd.DataFrame, split_on: str) -> pd.DataFrame: + data_table = drop_df_rows_while(df, lambda row: row[0] != split_on) + return parse_header_row( + assert_not_none(data_table).replace(np.nan, None) + ).reset_index(drop=True) + + +def _first_not_null_or_none(series: pd.Series[Any]) -> str | None: + """Get the first non-null value from a Series or None.""" + return str(series[idx]) if (idx := series.first_valid_index()) is not None else None + + +@dataclass(frozen=True) +class RunMetadata: + sensor_chip_id: str + sensor_chip_type: str + lot_number: str + model_number: str + equipment_serial_number: str + measurement_time: str + number_of_cycles: float + data_collection_rate: float + running_buffer: str + measurement_end_time: str + method_name: str + compartment_temperature: float | None + run_table: pd.DataFrame + + @staticmethod + def create_runs(runs_data: pd.DataFrame) -> list[RunMetadata]: + runs_data = runs_data.reset_index(drop=True) + run, rest = split_dataframe( + runs_data, lambda row: str(row[0]).startswith("Run") + ) + runs = [run] + while rest is not None: + run, rest = split_dataframe(rest, lambda row: str(row[0]).startswith("Run")) + runs.append(run) + if len(runs) > 1: + msg = "Instrument file contains multiple runs. Only single runs are supported at the moment." + raise AllotropeConversionError(msg) + return [RunMetadata.create(run) for run in runs if not run.empty] + + @staticmethod + def create(run_data: pd.DataFrame) -> RunMetadata: + def get_run_information(idx: int) -> SeriesData: + idx1, idx2 = idx + 1, idx + 4 + rd1 = run_data.loc[idx1:idx2][[3, 4]].rename(columns={3: "n", 4: "v"}) + rd2 = run_data.loc[idx1:idx2][[6, 7]].rename(columns={6: "n", 7: "v"}) + rd3 = run_data.loc[idx1:idx2][[10, 11]].rename(columns={10: "n", 11: "v"}) + return df_to_series_data(parse_header_row(pd.concat((rd1, rd2, rd3)).T)) + + run_table_start = 0 + chip_data = SeriesData() + run_information = SeriesData() + run_table = pd.DataFrame() + compartment_temperature = None + for index, row in run_data.iterrows(): + idx = int(str(index)) + if row[0] == "Chip information": + chip_data = df_to_series_data( + parse_header_row(run_data.loc[idx + 1 : idx + 4][[0, 1]].T) + ) + run_information = get_run_information(idx) + elif row[0] == "Flow cell": + run_table_start = idx + elif row[0] == "Method summary": + run_table = ( + parse_header_row(run_data.loc[run_table_start : idx - 1]) + .dropna(how="all") + .reset_index(drop=True) + ) + run_table = run_table.loc[:, ~run_table.columns.str.contains("^nan$")] + elif row[0] == "Set temperatures 1": + if match := re.match(constants.COMPARTMENT_TEMP_REGEX, row[1]): + compartment_temperature = float(match.group(1)) + + return RunMetadata( + sensor_chip_id=chip_data[str, "Chip id"], + sensor_chip_type=chip_data[str, "Chip type"], + lot_number=chip_data[str, "Lot number"], + model_number=run_information[str, "Instrument type"], + equipment_serial_number=run_information[str, "Instrument id"], + measurement_time=run_information[str, "Start"], + number_of_cycles=run_information[float, "Cycles"], + data_collection_rate=run_information[float, "Data collection rate"], + running_buffer=run_information[str, "Running buffer"], + measurement_end_time=run_information[str, "End"], + method_name=run_information[str, "Method"], + compartment_temperature=compartment_temperature, + run_table=run_table, + ) + + +@dataclass(frozen=True) +class BiacoreInsightMetadata: + file_name: str + unc_path: str + software_name: str + software_version: str + analyst: str + analytical_method_id: str + runs: list[RunMetadata] + data_processing_document: DictType | None = None + + @staticmethod + def create(reader: CytivaBiacoreInsightReader) -> BiacoreInsightMetadata: + + properties = reader.data["Properties"] + properties, runs_data = split_dataframe( + properties, lambda row: str(row[0]).startswith("Run") + ) + if runs_data is None or runs_data.empty: + msg = "No run data found in the properties section of instrument file." + raise AllotropeConversionError(msg) + for index, row in properties.iterrows(): + idx = int(str(index)) + if row[0] == "Evaluation": + evaluation_data = df_to_series_data( + parse_header_row(properties.loc[idx + 1 : idx + 4][[0, 1]].T) + ) + elif row[0] == "Software": + software_data = df_to_series_data( + parse_header_row(properties.loc[idx + 1 : idx + 2][[0, 1]].T) + ) + + data_processing_doc = BiacoreInsightMetadata.get_data_processing_doc(reader) + + return BiacoreInsightMetadata( + file_name=evaluation_data[str, "Name"], + unc_path=evaluation_data[str, "Path"], + software_name=software_data[str, "Name"], + software_version=software_data[str, "Version"], + analyst=evaluation_data[str, "Modified by"], + analytical_method_id=evaluation_data[str, "Name"], + runs=RunMetadata.create_runs(runs_data), + data_processing_document=data_processing_doc, + ) + + @staticmethod + def get_data_processing_doc(reader: CytivaBiacoreInsightReader) -> DictType | None: + table_names = [ + "QC - Capture baseline", + "QC - Capture level", + "QC - Binding to reference", + ] + qc_tables = [table for table in table_names if table in reader.data] + qc_df = None + while qc_df is None and qc_tables: + qc_table = qc_tables.pop(0) + _, qc_df = split_dataframe( + reader.data[qc_table], + lambda row: row[0] == "Blank subtraction", + include_split_row=True, + ) + + if qc_df is None or qc_df.empty: + return None + + qc_metadata = df_to_series_data( + parse_header_row(qc_df.dropna(how="all", axis=0).T[0:2]) + ) + metadata_keys = [ + "Blank subtraction", + "Molecular weight adjustment", + "Capture/ligand adjustment", + "Adjustment for controls", + "Curve analysis", + ] + return {key: qc_metadata.get(str, key) for key in metadata_keys} + + +@dataclass(frozen=True) +class KineticsData: + acceptance_state: str | None = None + curve_markers: str | None = None + kinetics_model: str | None = None + binding_on_rate_measurement_datum: float | None = None + binding_off_rate_measurement_datum: float | None = None + equilibrium_dissociation_constant: float | None = None + maximum_binding_capacity: float | None = None + kinetics_chi_squared: float | None = None + tc: float | None = None + + @staticmethod + def create(kinetics_data: SeriesData) -> KineticsData: + return KineticsData( + acceptance_state=kinetics_data.get(str, "Acceptance state"), + curve_markers=kinetics_data.get(str, "Curve markers"), + kinetics_model=kinetics_data.get(str, "Kinetics model"), + binding_on_rate_measurement_datum=kinetics_data.get(float, "ka (1/Ms)"), + binding_off_rate_measurement_datum=kinetics_data.get(float, "kd (1/s)"), + equilibrium_dissociation_constant=kinetics_data.get(float, "KD (M)"), + maximum_binding_capacity=kinetics_data.get(float, "Rmax (RU)"), + kinetics_chi_squared=kinetics_data.get(float, "Kinetics Chi² (RU²)"), + tc=kinetics_data.get(float, "tc"), + ) + + +class EvaluationKinetics: + _data: dict[str, KineticsData] + + def __init__(self, kinetics_table: pd.DataFrame) -> None: + def _get_key(row: pd.Series[Any]) -> str: + return f'{row["Channel"]} {row["Capture 1 Solution"]} {row["Analyte 1 Solution"]}' + + self._data = { + _get_key(row): KineticsData.create(SeriesData(row)) + for _, row in kinetics_table.iterrows() + } + + def get_data( + self, + channel: int, + capture_solution: str | None, + analyte_solution: str | None, + ) -> KineticsData: + empty = KineticsData() + if capture_solution is None or analyte_solution is None: + return empty + return self._data.get(f"{channel} {capture_solution} {analyte_solution}", empty) + + +@dataclass(frozen=True) +class ReportPointData: + identifier: str + identifier_role: str + absolute_resonance: float + time_setting: float + relative_resonance: float | None + step_name: str | None + step_purpose: str | None + window: float | None + baseline: str | None + lrsd: float | None + slope: float | None + standard_deviation: float | None + + @staticmethod + def create(row: SeriesData) -> ReportPointData: + return ReportPointData( + identifier=random_uuid_str(), + identifier_role=row[str, "Name"], + absolute_resonance=row[float, "Absolute response (RU)"], + time_setting=row[float, "Time (s)"], + relative_resonance=row.get(float, "Relative response (RU)"), + step_name=row.get(str, "Name"), + step_purpose=row.get(str, "Step purpose"), + window=row.get(float, "Window (s)"), + baseline=row.get(str, "Baseline"), + lrsd=row.get(float, "LRSD"), + slope=row.get(float, "Slope (RU/s)"), + standard_deviation=row.get(float, "Standard deviation"), + ) + + +@dataclass(frozen=True) +class MeasurementData: + identifier: str + sample_identifier: str + method_name: str + ligand_identifier: str | None + device_control_document: list[DeviceControlDocument] + sample_custom_info: dict[str, Any | None] + kinetics: KineticsData + report_point_data: list[ReportPointData] + + @staticmethod + def create( + channel_data: pd.DataFrame, + metadata: BiacoreInsightMetadata, + evaluation_kinetics: EvaluationKinetics, + ) -> MeasurementData: + identifier = random_uuid_str() + run_metadata = metadata.runs[0] + first_row_data = SeriesData(channel_data.iloc[0]) + run = first_row_data[int, "Run"] + cycle_number = first_row_data[int, "Cycle"] + channel = first_row_data[int, "Channel"] + + run_table = run_metadata.run_table + device_control_document = [] + for flow_cell, flow_cell_data in channel_data.groupby("Flow cell"): + run_data = run_table[ + (run_table["Flow cell"].astype(str) == str(flow_cell)) + & (run_table["Channel"] == channel) + ] + run_info = SeriesData() if run_data.empty else df_to_series_data(run_data) + # All the info needed in the device control document is the same for all flow cell data + flow_cell_info = SeriesData(flow_cell_data.iloc[0]) + device_control_document.append( + DeviceControlDocument( + device_type=constants.DEVICE_TYPE, + flow_cell_identifier=str(flow_cell), + sample_temperature_setting=flow_cell_info.get( + float, "Temperature (°C)" + ), + device_control_custom_info={ + "Analyte 1 Contact time": quantity_or_none( + TQuantityValueSecondTime, + flow_cell_info.get(float, "Analyte 1 Contact time (s)"), + ), + "Analyte 1 Dissociation time": quantity_or_none( + TQuantityValueSecondTime, + flow_cell_info.get( + float, "Analyte 1 Dissociation time (s)" + ), + ), + "Analyte 1 Flow rate": quantity_or_none( + TQuantityValueMicroliterPerMinute, + flow_cell_info.get(float, "Analyte 1 Flow rate (µl/min)"), + ), + "Regeneration 1 Contact time": quantity_or_none( + TQuantityValueSecondTime, + flow_cell_info.get( + float, "Regeneration 1 Contact time (s)" + ), + ), + "Regeneration 1 Flow rate": quantity_or_none( + TQuantityValueMicroliterPerMinute, + flow_cell_info.get( + float, "Regeneration 1 Flow rate (µl/min)" + ), + ), + "Included": run_info.get(str, "Included"), + "Sensorgram type": flow_cell_info.get( + str, "Sensorgram type", run_info.get(str, "Sensorgram type") + ), + "Level": quantity_or_none( + TQuantityValueResonanceUnits, + run_info.get(float, "Level (RU)"), + ), + }, + ) + ) + + capture_solution = _first_not_null_or_none(channel_data["Capture 1 Solution"]) + analyte_solution = first_row_data.get(str, "Analyte 1 Solution") + + return MeasurementData( + identifier=identifier, + sample_identifier=f"Run{run}_Cycle{cycle_number}", + method_name=run_metadata.method_name, + ligand_identifier=run_info.get(str, "Ligand"), + device_control_document=device_control_document, + sample_custom_info={ + "Run": run, + "Cycle": cycle_number, + "Channel": channel, + "Analyte 1 Solution": analyte_solution, + "Analyte 1 Plate id": first_row_data.get(str, "Analyte 1 Plate id"), + "Analyte 1 Position": first_row_data.get(str, "Analyte 1 Position"), + "Analyte 1 Control type": first_row_data.get( + str, "Analyte 1 Control type" + ), + "Regeneration 1 Solution": first_row_data.get( + str, "Regeneration 1 Solution" + ), + "Regeneration 1 Plate id": first_row_data.get( + str, "Regeneration 1 Plate id" + ), + "Regeneration 1 Position": first_row_data.get( + str, "Regeneration 1 Position" + ), + "Regeneration 1 Control type": first_row_data.get( + str, "Regeneration 1 Control type" + ), + # Capture data is not reported for the Reference flow cell, + # so we have to look for the first non-null value + "Capture 1 Solution": capture_solution, + "Capture 1 Plate id": _first_not_null_or_none( + channel_data["Capture 1 Plate id"] + ), + "Capture 1 Position": _first_not_null_or_none( + channel_data["Capture 1 Position"] + ), + "Capture 1 Control type": _first_not_null_or_none( + channel_data["Capture 1 Control type"] + ), + "Analyte 1 Concentration": quantity_or_none( + TQuantityValueNanomolar, + first_row_data.get(float, "Analyte 1 Concentration (nM)"), + ), + "Analyte 1 Molecular weight": quantity_or_none( + TQuantityValueDalton, + first_row_data.get(float, "Analyte 1 Molecular weight (Da)"), + ), + }, + kinetics=evaluation_kinetics.get_data( + channel, capture_solution, analyte_solution + ), + report_point_data=map_rows(channel_data, ReportPointData.create), + ) + + +@dataclass(frozen=True) +class Data: + metadata: BiacoreInsightMetadata + cycles: dict[int, list[MeasurementData]] + + @staticmethod + def create(reader: CytivaBiacoreInsightReader) -> Data: + metadata = BiacoreInsightMetadata.create(reader) + return Data( + metadata=metadata, + cycles={ + cycle: Data.create_measurements_for_cycle(cycle, metadata, reader) + for cycle in range(1, int(metadata.runs[0].number_of_cycles) + 1) + }, + ) + + @staticmethod + def create_measurements_for_cycle( + cycle_number: int, + metadata: BiacoreInsightMetadata, + reader: CytivaBiacoreInsightReader, + ) -> list[MeasurementData]: + # Report point table is the entry point + report_point_table = _get_table_from_dataframe( + reader.data["Report point table"], split_on="Run" + ) + cycle_data = report_point_table[report_point_table["Cycle"] == cycle_number] + evaluation_kinetics_table = _get_table_from_dataframe( + reader.data["Evaluation - Kinetics"], split_on="Group" + ) + evaluation_kinetics = EvaluationKinetics(evaluation_kinetics_table) + + return [ + MeasurementData.create(channel_data, metadata, evaluation_kinetics) + for _, channel_data in cycle_data.groupby("Channel") + ] diff --git a/src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py b/src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py index d836b1e2d8..cc0ab6ac16 100644 --- a/src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py +++ b/src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py @@ -16,6 +16,7 @@ ) from allotropy.allotrope.models.shared.definitions.units import ResonanceUnits, Unitless from allotropy.allotrope.schema_mappers.adm.binding_affinity_analyzer.benchling._2024._12.binding_affinity_analyzer import ( + DeviceControlDocument, DeviceDocument, Measurement, MeasurementGroup, @@ -112,13 +113,21 @@ def create_measurements( Measurement( identifier=measurement.identifier, type_=measurement.type_, - device_type=measurement.device_type, sample_identifier=measurement.sample_identifier, location_identifier=measurement.location_identifier, sample_role_type=measurement.sample_role_type, concentration=measurement.concentration, - flow_cell_identifier=measurement.flow_cell_identifier, - device_control_custom_info=device_control_custom_info, + device_control_document=[ + DeviceControlDocument( + device_type=measurement.device_type, + flow_cell_identifier=measurement.flow_cell_identifier, + flow_path=measurement.flow_path, + flow_rate=measurement.flow_rate, + contact_time=measurement.contact_time, + dilution=measurement.dilution, + device_control_custom_info=device_control_custom_info, + ) + ], sample_custom_info={ "molecular weight": quantity_or_none( TQuantityValueDalton, measurement.molecular_weight @@ -143,10 +152,6 @@ def create_measurements( # for Mobilization experiments method_name=measurement.method_name, ligand_identifier=measurement.ligand_identifier, - flow_path=measurement.flow_path, - flow_rate=measurement.flow_rate, - contact_time=measurement.contact_time, - dilution=measurement.dilution, ) for measurement in measurements_data ] diff --git a/src/allotropy/parsers/utils/values.py b/src/allotropy/parsers/utils/values.py index da28878be1..4552825e03 100644 --- a/src/allotropy/parsers/utils/values.py +++ b/src/allotropy/parsers/utils/values.py @@ -175,3 +175,8 @@ def num_to_chars(n: int) -> str: def str_or_none(value: Any) -> str | None: return None if value is None else str(value) + + +def has_value(model: object) -> bool: + # For models with all optional attributes, returns whether any attribute has a value. + return any(value is not None for value in model.__dict__.values()) diff --git a/tests/parsers/cytiva_biacore_insight/__init__.py b/tests/parsers/cytiva_biacore_insight/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json b/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json new file mode 100644 index 0000000000..bf60c3e4f3 --- /dev/null +++ b/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json @@ -0,0 +1,38763 @@ +{ + "$asm.manifest": "http://purl.allotrope.org/manifests/binding-affinity-analyzer/WD/2024/12/binding-affinity-analyzer.manifest", + "binding affinity analyzer aggregate document": { + "binding affinity analyzer document": [ + { + "measurement aggregate document": { + "measurement document": [ + { + "device control aggregate document": { + "device control document": [ + { + "device type": "Binding Affinity Analyzer", + "sample temperature setting": { + "value": 25.0, + "unit": "degC" + }, + "flow cell identifier": "1", + "custom information document": { + "Analyte 1 Contact time": { + "value": 200.0, + "unit": "s" + }, + "Analyte 1 Dissociation time": { + "value": 300.0, + "unit": "s" + }, + "Analyte 1 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Regeneration 1 Contact time": { + "value": 10.0, + "unit": "s" + }, + "Regeneration 1 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Included": "Yes", + "Sensorgram type": "Reference", + "Level": { + "value": 1.0, + "unit": "RU" + } + } + }, + { + "device type": "Binding Affinity Analyzer", + "sample temperature setting": { + "value": 25.0, + "unit": "degC" + }, + "flow cell identifier": "2", + "custom information document": { + "Analyte 1 Contact time": { + "value": 200.0, + "unit": "s" + }, + "Analyte 1 Dissociation time": { + "value": 300.0, + "unit": "s" + }, + "Analyte 1 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Regeneration 1 Contact time": { + "value": 10.0, + "unit": "s" + }, + "Regeneration 1 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Included": "Yes", + "Sensorgram type": "Active", + "Level": { + "value": 9.0, + "unit": "RU" + } + } + }, + { + "device type": "Binding Affinity Analyzer", + "sample temperature setting": { + "value": 25.0, + "unit": "degC" + }, + "flow cell identifier": "2-1", + "custom information document": { + "Analyte 1 Contact time": { + "value": 200.0, + "unit": "s" + }, + "Analyte 1 Dissociation time": { + "value": 300.0, + "unit": "s" + }, + "Analyte 1 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Regeneration 1 Contact time": { + "value": 10.0, + "unit": "s" + }, + "Regeneration 1 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Sensorgram type": "Reference subtracted" + } + } + ] + }, + "measurement identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_0", + "sample document": { + "sample identifier": "Run1_Cycle1", + "custom information document": { + "Run": 1, + "Cycle": 1, + "Channel": 1, + "Analyte 1 Solution": "Buffer", + "Analyte 1 Plate id": "Plate 1", + "Analyte 1 Position": "A7", + "Analyte 1 Control type": "Blank control", + "Regeneration 1 Solution": "Regeneration_Buffer", + "Regeneration 1 Plate id": "Plate 1", + "Regeneration 1 Position": "A12", + "Regeneration 1 Control type": "Not a control", + "Capture 1 Solution": "Buffer", + 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"(unitless)" + }, + "calculated data identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_1998", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_511", + "data source feature": "Absolute Response" + } + ] + } + }, + { + "calculated data name": "Standard deviation", + "calculated result": { + "value": 0.629019301502167, + "unit": "(unitless)" + }, + "calculated data identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_1999", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_511", + "data source feature": "Absolute Response" + } + ] + } + } + ] + }, + "data system document": { + "ASM file identifier": "Cytiva_Biacore_Insight_Example01.json", + "data system instance identifier": "N/A", + "file name": "evaluation_name", + "UNC path": "my_evaluation_path", + "ASM converter name": "allotropy_cytiva_biacore_insight", + "ASM converter version": "0.1.105", + "software name": "Biacore Insight Evaluation", + "software version": "6.0.0.0000" + }, + "device system document": { + "device identifier": "Biacore", + "model number": "Biacore 8K+", + "equipment serial number": "123456", + "product manufacturer": "Cytiva" + } + } +} diff --git a/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.xlsx b/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.xlsx new file mode 100644 index 0000000000..a160f5b17f Binary files /dev/null and b/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.xlsx differ diff --git a/tests/parsers/cytiva_biacore_insight/to_allotrope_test.py b/tests/parsers/cytiva_biacore_insight/to_allotrope_test.py new file mode 100644 index 0000000000..ad5139e406 --- /dev/null +++ b/tests/parsers/cytiva_biacore_insight/to_allotrope_test.py @@ -0,0 +1,10 @@ +from allotropy.parser_factory import Vendor +from allotropy.testing.utils import get_testdata_dir +from tests.to_allotrope_test import ParserTest + +VENDOR_TYPE = Vendor.CYTIVA_BIACORE_INSIGHT +TESTDATA = get_testdata_dir(__file__) + + +class TestParser(ParserTest): + VENDOR = VENDOR_TYPE