fix: Molecular Devices SoftMax Pro - fix duplicate data source documents in spectrum measurements (#1033)

Author: nathan-stender

src/allotropy/allotrope/schema_mappers/adm/plate_reader/rec/_2025/_03/plate_reader.py

@@ -99,6 +99,16 @@ class MeasurementType(Enum):
     EMISSION_LUMINESCENCE_CUBE_SPECTRUM = "EMISSION_LUMINESCENCE_CUBE_SPECTRUM"
     EXCITATION_LUMINESCENCE_CUBE_SPECTRUM = "EXCITATION_LUMINESCENCE_CUBE_SPECTRUM"
 
+    @property
+    def is_spectrum(self) -> bool:
+        return self in (
+            MeasurementType.ULTRAVIOLET_ABSORBANCE_CUBE_SPECTRUM,
+            MeasurementType.EMISSION_FLUORESCENCE_CUBE_SPECTRUM,
+            MeasurementType.EXCITATION_FLUORESCENCE_CUBE_SPECTRUM,
+            MeasurementType.EMISSION_LUMINESCENCE_CUBE_SPECTRUM,
+            MeasurementType.EXCITATION_LUMINESCENCE_CUBE_SPECTRUM,
+        )
+
 
 @dataclass(frozen=True)
 class ErrorDocument:

src/allotropy/parsers/moldev_softmax_pro/softmax_pro_data_creator.py

@@ -170,34 +170,27 @@ def _create_spectrum_measurement(
 
 
 def _create_measurements(plate_block: PlateBlock, position: str) -> list[Measurement]:
-
-    measurement_type = plate_block.measurement_type
     data_elements = list(plate_block.iter_data_elements(position))
 
     # Handle spectrum measurements - create single measurement with spectrum_data_cube
-    if measurement_type in (
-        MeasurementType.ULTRAVIOLET_ABSORBANCE_CUBE_SPECTRUM,
-        MeasurementType.EMISSION_FLUORESCENCE_CUBE_SPECTRUM,
-        MeasurementType.EXCITATION_FLUORESCENCE_CUBE_SPECTRUM,
-        MeasurementType.EMISSION_LUMINESCENCE_CUBE_SPECTRUM,
-        MeasurementType.EXCITATION_LUMINESCENCE_CUBE_SPECTRUM,
-    ):
+    if plate_block.measurement_type.is_spectrum:
         measurement = _create_spectrum_measurement(plate_block, data_elements)
         if not measurement:
             return []
         return [measurement]
 
     return [
         Measurement(
-            type_=measurement_type,
+            type_=plate_block.measurement_type,
             identifier=data_element.uuid,
             absorbance=(
                 (
                     data_element.value
                     if data_element.value is not None
                     else NEGATIVE_ZERO
                 )
-                if measurement_type == MeasurementType.ULTRAVIOLET_ABSORBANCE
+                if plate_block.measurement_type
+                is MeasurementType.ULTRAVIOLET_ABSORBANCE
                 else None
             ),
             fluorescence=(
@@ -206,7 +199,7 @@ def _create_measurements(plate_block: PlateBlock, position: str) -> list[Measure
                     if data_element.value is not None
                     else NEGATIVE_ZERO
                 )
-                if measurement_type == MeasurementType.FLUORESCENCE
+                if plate_block.measurement_type is MeasurementType.FLUORESCENCE
                 else None
             ),
             luminescence=(
@@ -215,7 +208,7 @@ def _create_measurements(plate_block: PlateBlock, position: str) -> list[Measure
                     if data_element.value is not None
                     else NEGATIVE_ZERO
                 )
-                if measurement_type == MeasurementType.LUMINESCENCE
+                if plate_block.measurement_type is MeasurementType.LUMINESCENCE
                 else None
             ),
             profile_data_cube=_get_data_cube(plate_block, data_element),
@@ -299,12 +292,22 @@ def create_calculated_data(data: StructureData) -> list[CalculatedDocument]:
 def _get_calc_docs_data_sources(
     plate_block: PlateBlock, position: str
 ) -> list[DataSource]:
+    data_elements = list(plate_block.iter_data_elements(position))
+
+    if plate_block.measurement_type.is_spectrum:
+        return [
+            DataSource(
+                reference=Referenceable(data_elements[0].uuid),
+                feature=plate_block.header.read_mode,
+            )
+        ]
+
     return [
         DataSource(
             reference=Referenceable(data_source.uuid),
             feature=plate_block.header.read_mode,
         )
-        for data_source in plate_block.iter_data_elements(position)
+        for data_source in data_elements
     ]