feat: Molecular Devices SoftMax Pro - Enable Reduced-only file parsing

pyproject.toml

@@ -34,6 +34,7 @@ authors = [
   { name = "Stephen Worlow", email = "stephen.worlow@benchling.com" },
   { name = "Brian Worth", email = "brian@benchling.com" },
   { name = "Alex Reis", email = "alex@manifold.bio" },
+  { name = "Jane Dance", email = "jane.dance@abcellera.com" },
 ]
 classifiers = [
   "License :: OSI Approved :: MIT License",

src/allotropy/parsers/moldev_softmax_pro/softmax_pro_structure.py

@@ -726,6 +726,7 @@ def create(
             msg="unable to find raw data from time block.",
         )
         set_columns(data, columns)
+
         return TimeWavelengthData(
             wavelength=wavelength,
             measurement_data=[
@@ -798,15 +799,72 @@ def create(
         reader: CsvReader,
         header: PlateHeader,
     ) -> TimeData:
+        raw_data = None
+        reduced_data = None
+
+        # Read raw data if data_type is RAW or BOTH
+        if header.data_type in (DataType.RAW.value, DataType.BOTH.value):
+            raw_data = TimeRawData.create(reader, header)
+        # For REDUCED only, create synthetic raw data with error message
+        else:
+            raw_data = TimeData._create_synthetic_raw_data(header)
+
+        # Read reduced data if available, regardless of data_type (RAW can have reduced data!)
+        if reader.current_line_exists():
+            reduced_data = TimeReducedData.create(reader, header)
+
         return TimeData(
-            raw_data=TimeRawData.create(reader, header),
-            reduced_data=(
-                TimeReducedData.create(reader, header)
-                if reader.current_line_exists()
-                else None
-            ),
+            raw_data=raw_data,
+            reduced_data=reduced_data,
         )
 
+    @staticmethod
+    def _create_synthetic_raw_data(header: PlateHeader) -> TimeRawData:
+        """Create synthetic raw data with error messages when only reduced data is available."""
+        synthetic_wavelength_data = []
+
+        for wavelength in header.wavelengths:
+            # For each position in the plate, create a data element with an error document
+            num_cols = header.num_columns
+            num_rows = header.num_rows
+
+            # Create synthetic data elements for all well positions
+            data_elements = {}
+            for row in range(1, num_rows + 1):
+                for col in range(1, num_cols + 1):
+                    position = f"{num_to_chars(row-1)}{col}"
+                    data_elements[position] = DataElement(
+                        uuid=random_uuid_str(),
+                        plate=header.name,
+                        temperature=None,
+                        wavelength=wavelength,
+                        position=position,
+                        value=NEGATIVE_ZERO,
+                        error_document=[
+                            ErrorDocument("Not reported", header.read_mode)
+                        ],
+                        elapsed_time=[
+                            0.0
+                        ],  # Add a dummy value to ensure array is not empty
+                        kinetic_measures=[
+                            NEGATIVE_ZERO
+                        ],  # Add a dummy value to ensure array is not empty
+                    )
+
+            # Create a single TimeMeasurementData with all positions
+            measurement_data = [TimeMeasurementData(data_elements=data_elements)]
+
+            # Add this wavelength data to our list
+            synthetic_wavelength_data.append(
+                TimeWavelengthData(
+                    wavelength=wavelength,
+                    measurement_data=measurement_data,
+                )
+            )
+
+        # Create TimeRawData with our synthetic wavelength data
+        return TimeRawData(wavelength_data=synthetic_wavelength_data)
+
     def iter_data_elements(self, position: str) -> Iterator[DataElement]:
         for time_wavelength_data in self.raw_data.wavelength_data:
             for measurement_data in time_wavelength_data.measurement_data:
@@ -892,8 +950,12 @@ def get_read_mode(cls, read_type: str, read_mode_raw: str) -> str:
 
     @classmethod
     def check_data_type(cls, data_type: str) -> None:
-        if data_type not in (DataType.RAW.value, DataType.BOTH.value):
-            msg = f"The SoftMax Pro file is required to include either 'Raw' or 'Both' (Raw and Reduced) data for all plates, got {data_type}."
+        if data_type not in (
+            DataType.RAW.value,
+            DataType.BOTH.value,
+            DataType.REDUCED.value,
+        ):
+            msg = f"Unexpected data type: {data_type}, supported values are RAW, REDUCED, or BOTH."
             raise AllotropeConversionError(msg)
 
     @classmethod