fix: Molecular Devices SoftMax Pro - handle reduced data blocks with empty rows correctly (#1110)

Raw data blocks are read using plate dimensions, but reduced data blocks
were being parsed with `pop_csv_block_as_df` which ends at an empty
line.

This does not always work for reduced blocks either, which may have
empty rows (row a row of wells with no measurements). So use plate
dimensions for reduced blocks as well.

The function to read using plate dimensions is factored out to allow for
code reuse.

Author: nathan-stender

src/allotropy/parsers/moldev_softmax_pro/softmax_pro_structure.py

@@ -467,37 +467,48 @@ def update_kinetic_data_elements(
             self.data_elements[position].kinetic_measures.append(value)
 
 
-@dataclass(frozen=True)
-class RawData:
-    wavelength_data: list[PlateWavelengthData]
+def get_plate_dataframe(
+    reader: CsvReader, header: PlateHeader, columns: pd.Series[str] | None = None
+) -> pd.DataFrame:
+    if columns is None:
+        columns = assert_not_none(
+            reader.pop_as_series(sep="\t"),
+            msg="unable to find data columns for plate block raw data.",
+        )
+    dimensions = assert_not_none(
+        NUM_WELLS_TO_PLATE_DIMENSIONS.get(header.num_wells),
+        msg="unable to determine plate dimensions",
+    )
+    rows = dimensions[1]
 
-    @staticmethod
-    def get_measurement_section(
-        reader: CsvReader, columns: pd.Series[str], rows: int
-    ) -> pd.DataFrame:
-        lines = []
-        # read number of rows in plate section
-        for i in range(rows):
-            if not (line := reader.pop()):
-                msg = f"Expected {rows} rows in measurement table, got {i}."
-                raise AllotropeConversionError(msg)
-            lines.append(line)
-        reader.drop_empty()
+    lines = []
+    # read number of rows in plate section
+    for i in range(rows):
+        if not (line := reader.pop()):
+            msg = f"Expected {rows} rows in measurement table, got {i}."
+            raise AllotropeConversionError(msg)
+        lines.append(line)
+    reader.drop_empty()
 
-        # convert rows to df
-        data = assert_not_none(
-            reader.lines_as_df(lines=lines, sep="\t"),
-            msg="unable to find data from plate block.",
-        )
+    # convert rows to df
+    data = assert_not_none(
+        reader.lines_as_df(lines=lines, sep="\t"),
+        msg="unable to find data from plate block.",
+    )
 
-        # Truncate columns Series to match the actual number of data columns
-        if len(columns) >= data.shape[1]:
-            columns = columns.iloc[: data.shape[1]]
-        elif len(columns) < data.shape[1]:
-            data = data.loc[:, : len(columns) - 1]
+    # Truncate columns Series to match the actual number of data columns
+    if len(columns) >= data.shape[1]:
+        columns = columns.iloc[: data.shape[1]]
+    elif len(columns) < data.shape[1]:
+        data = data.loc[:, : len(columns) - 1]
 
-        set_columns(data, columns)
-        return data
+    set_columns(data, columns)
+    return data
+
+
+@dataclass(frozen=True)
+class RawData:
+    wavelength_data: list[PlateWavelengthData]
 
 
 @dataclass(frozen=True)
@@ -508,13 +519,7 @@ def create(reader: CsvReader, header: PlateHeader) -> PlateRawData:
             reader.pop_as_series(sep="\t"),
             msg="unable to find data columns for plate block raw data.",
         )
-        # use plate dimensions to determine how many rows of plate block to read
-        dimensions = assert_not_none(
-            NUM_WELLS_TO_PLATE_DIMENSIONS.get(header.num_wells),
-            msg="unable to determine plate dimensions",
-        )
-        rows = dimensions[1]
-        data = RawData.get_measurement_section(reader, columns, rows)
+        data = get_plate_dataframe(reader, header, columns=columns)
 
         # get temperature and elapsed time (kinetic) from the first column of the first row with value
         first_row_idx = int(pd.to_numeric(data.first_valid_index()))
@@ -534,7 +539,7 @@ def create(reader: CsvReader, header: PlateHeader) -> PlateRawData:
 
         if elapsed_time is not None and header.kinetic_points > 1:
             for _ in range(header.kinetic_points - 1):
-                data = RawData.get_measurement_section(reader, columns, rows)
+                data = get_plate_dataframe(reader, header, columns=columns)
 
                 elapsed_time = time_to_seconds(str(data.iloc[0, 0]))
                 plate_raw_data._update_kinetic_data(
@@ -584,15 +589,9 @@ def create(reader: CsvReader, header: PlateHeader) -> SpectrumPlateRawData:
             reader.pop_as_series(sep="\t"),
             msg="unable to find data columns for plate block raw data.",
         )
-        dimensions = assert_not_none(
-            NUM_WELLS_TO_PLATE_DIMENSIONS.get(header.num_wells),
-            msg="unable to determine plate dimensions",
-        )
-        rows = dimensions[1]
         wavelength_data: list[PlateWavelengthData] = []
-
         for wavelength in header.wavelengths:
-            data = RawData.get_measurement_section(reader, columns, rows)
+            data = get_plate_dataframe(reader, header, columns=columns)
             first_row_idx = int(pd.to_numeric(data.first_valid_index()))
             temperature = try_non_nan_float_or_none(str(data.iloc[first_row_idx, 1]))
             wavelength_data.append(
@@ -615,15 +614,10 @@ class PlateReducedData:
 
     @staticmethod
     def create(reader: CsvReader, header: PlateHeader) -> PlateReducedData:
-
-        raw_data = assert_not_none(
-            reader.pop_csv_block_as_df(sep="\t", header=0),
-            msg="Unable to find reduced data for plate block.",
-        )
-
+        raw_data: pd.DataFrame = get_plate_dataframe(reader, header)
+        # Reduced data has 2 empty columns where
         start = 2
         df_data = raw_data.iloc[:, start : (start + header.num_columns)]
-
         reduced_data_elements = []
         for row, *data in df_data.itertuples():
             for col, str_value in zip(df_data.columns, data, strict=True):