feat: Cytiva Biacore Insight - Add support for Affinity and Concentration analysis files

src/allotropy/parsers/cytiva_biacore_insight/constants.py

@@ -3,5 +3,6 @@
 DEVICE_TYPE = "Binding Affinity Analyzer"
 DETECTION_TYPE = "Surface Plasmon Resonance"
 PRODUCT_MANUFACTURER = "Cytiva"
+REQUIRED_SHEETS = ("Properties", "Report point table")
 
 COMPARTMENT_TEMP_REGEX = r"Sample compartment temperature (\d+),.*"

src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py

@@ -1,8 +1,12 @@
 from pathlib import Path
+from typing import Any
+
+import numpy as np
 
 from allotropy.allotrope.models.shared.definitions.custom import (
     TQuantityValueHertz,
     TQuantityValueNumber,
+    TQuantityValueResponseUnit,
     TQuantityValueSecondTime,
     TQuantityValueSquareResponseUnit,
     TQuantityValueUnitless,
@@ -35,6 +39,29 @@
 from allotropy.parsers.utils.values import quantity_or_none
 
 
+def _clean_custom_info(custom_info: dict[str, Any]) -> dict[str, Any]:
+    """Remove None and NaN values from custom_info dictionaries."""
+
+    def is_valid_value(value: Any) -> bool:
+        if value is None:
+            return False
+        # Check for NaN in plain float values
+        if isinstance(value, float) and np.isnan(value):
+            return False
+        # Check for NaN in quantity objects (objects with 'value' attribute or dicts with 'value' key)
+        if hasattr(value, "value"):
+            val = value.value
+            if isinstance(val, float) and np.isnan(val):
+                return False
+        elif isinstance(value, dict) and "value" in value:
+            val = value["value"]
+            if isinstance(val, float) and np.isnan(val):
+                return False
+        return True
+
+    return {key: value for key, value in custom_info.items() if is_valid_value(value)}
+
+
 def create_metadata(metadata: BiacoreInsightMetadata, file_path: str) -> Metadata:
     path = Path(file_path)
     run_metadata = metadata.runs[0]
@@ -107,15 +134,23 @@ def _get_measurements(
             maximum_binding_capacity__rmax_=(
                 measurement.kinetics.maximum_binding_capacity
             ),
-            processed_data_custom_info=(
+            processed_data_custom_info=_clean_custom_info(
                 {
-                    "Kinetics Chi squared": quantity_or_none(
+                    (
+                        "Affinity Chi squared"
+                        if measurement.kinetics.is_affinity_measurement
+                        else "Kinetics Chi squared"
+                    ): quantity_or_none(
                         TQuantityValueSquareResponseUnit,
                         measurement.kinetics.kinetics_chi_squared,
                     ),
                     "tc": quantity_or_none(
                         TQuantityValueUnitless, measurement.kinetics.tc
                     ),
+                    "offset": quantity_or_none(
+                        TQuantityValueResponseUnit,
+                        measurement.kinetics.offset,
+                    ),
                 }
             ),
             report_point_data=[
@@ -125,21 +160,26 @@ def _get_measurements(
                     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,
-                    },
+                    custom_info=_clean_custom_info(
+                        {
+                            "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,
-            },
+            data_processing_document=_clean_custom_info(
+                {
+                    **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
     ]

src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_reader.py

@@ -4,10 +4,9 @@
 
 from allotropy.exceptions import AllotropeConversionError
 from allotropy.named_file_contents import NamedFileContents
+from allotropy.parsers.cytiva_biacore_insight.constants import REQUIRED_SHEETS
 from allotropy.parsers.utils.pandas import read_multisheet_excel
 
-REQUIRED_SHEETS = ("Properties", "Report point table", "Evaluation - Kinetics")
-
 
 class CytivaBiacoreInsightReader:
     SUPPORTED_EXTENSIONS = "xlsx, xlsm"