Added well count and removed errors from missing assay bed ids

Author: felipenarv

src/allotropy/parsers/luminex_xponent/luminex_xponent_reader.py

@@ -8,6 +8,7 @@
 
 from allotropy.exceptions import AllotropeConversionError, AllotropeParsingError
 from allotropy.named_file_contents import NamedFileContents
+from allotropy.parsers.constants import round_to_nearest_well_count
 from allotropy.parsers.lines_reader import CsvReader, read_to_lines
 from allotropy.parsers.luminex_xponent import constants
 from allotropy.parsers.utils.pandas import read_csv
@@ -222,6 +223,17 @@ def add_mandatory_columns(
             )
             results["Units"] = units_df
 
+    @staticmethod
+    def _get_well_count(df: pd.DataFrame) -> int:
+        # Count unique values in WELL LOCATION matching Excel-like cell ids: Letter(s) + Number(s)
+        # Example matches: A1, B12, AA3
+        pattern = r"^[A-Za-z]+\d+$"
+        values = df["WELL LOCATION"].astype(str).str.strip()
+        matching = values[values.str.match(pattern)]
+        unique_count = int(matching.str.upper().nunique())
+        nearest = round_to_nearest_well_count(unique_count)
+        return int(nearest or 0)
+
     @classmethod
     def parse(
         cls, lines: list[str]
@@ -295,7 +307,7 @@ def parse(
                     ],
                     2: ["", "", "", "", "", "", ""],
                     3: ["", "", "", "", "", "", ""],
-                    4: ["", "", "", "", "", "", ""],
+                    4: ["", "", "", "", cls._get_well_count(df), "", ""],
                     5: ["", "", "", "", "", "", ""],
                 }
             )

src/allotropy/parsers/luminex_xponent/luminex_xponent_structure.py

@@ -138,8 +138,7 @@ def _get_plate_well_count(cls, header_data: pd.DataFrame) -> float:
             msg = "Unable to find plate well count in ProtocolPlate row, expected value at index 3."
             raise AllotropeConversionError(msg) from e
 
-        plate_well_count = try_non_nan_float_or_none(str(plate_well_count))
-        return plate_well_count or -0.0
+        return try_float(str(plate_well_count), "plate well count")
 
 
 def create_calibration(calibration_data: SeriesData) -> Calibration:
@@ -274,13 +273,7 @@ def get_statistic_dimensions(analyte: str) -> list[StatisticDimension]:
             key for key in count_data.series.index if key not in metadata_keys
         ]
         for analyte in analyte_keys:
-            assay_bead_identifier = bead_ids_data.get(str, analyte, "")
-            if not assay_bead_identifier:
-                errors.append(
-                    Error(
-                        error="Not reported", feature=f"{analyte} assay bead identifier"
-                    )
-                )
+            assay_bead_identifier = bead_ids_data.get(str, analyte, "N/A")
             analytes.append(
                 Analyte(
                     identifier=(analyte_identifier := random_uuid_str()),