feat: Cytiva Biacore Insight - initial implementation

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

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
 
 

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

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"

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
 
 
@@ -87,33 +90,49 @@ 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
     sample_role_type: str | None = None
     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
             ),
         )

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": {

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": [
       {

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": {