fix: Luminex xponent - handle case for missing calibration report field (#1039)

Author: joshua-benchling

src/allotropy/allotrope/schema_mappers/adm/multi_analyte_profiling/benchling/_2024/_09/multi_analyte_profiling.py

@@ -117,8 +117,8 @@ class MeasurementGroup:
 @dataclass(frozen=True)
 class Calibration:
     name: str
-    report: str
     time: str
+    report: str | None = None
 
 
 @dataclass(frozen=True)

src/allotropy/parsers/luminex_xponent/luminex_xponent_structure.py

@@ -129,22 +129,39 @@ def _get_plate_well_count(cls, header_data: pd.DataFrame) -> float:
 def create_calibration(calibration_data: SeriesData) -> Calibration:
     """Create a CalibrationItem from a calibration line.
 
-    Each line should follow the pattern "Last <calibration_name>,<calibration_report> <calibration_time><,,,,"
-    example: "Last F3DeCAL1 Calibration,Passed 05/17/2023 09:25:11,,,,,,"
+    Each line should follow one of these patterns:
+    - "Last <calibration_name>,<calibration_report> <calibration_time><,,,,"
+    - "Last <calibration_name>,<calibration_time><,,,,"
     """
     if len(calibration_data.series.index) < MINIMUM_CALIBRATION_LINE_COLS:
         msg = f"Expected at least two columns on the calibration line, got:\n{calibration_data.series}."
         raise AllotropeConversionError(msg)
 
-    calibration_result = calibration_data.series.iloc[1].split(maxsplit=1)
-    if len(calibration_result) != EXPECTED_CALIBRATION_RESULT_LEN:
-        msg = f"Invalid calibration result format, expected to split into two values, got: {calibration_result}."
+    calibration_info = calibration_data.series.iloc[1].strip()
+
+    # Check if the calibration info starts with a known status value
+    status_values = ["Passed", "Failed", "Calibrated", "Verified"]
+    first_word = calibration_info.split()[0] if calibration_info.split() else ""
+
+    report = None
+    time = None
+
+    if first_word in status_values:
+        calibration_result = calibration_info.split(maxsplit=1)
+        if len(calibration_result) == EXPECTED_CALIBRATION_RESULT_LEN:
+            report = calibration_result[0]
+            time = calibration_result[1]
+    elif calibration_info and any(char.isdigit() for char in calibration_info):
+        time = calibration_info
+
+    if not time:
+        msg = f"Invalid calibration result format, got: ['{calibration_info}']."
         raise AllotropeConversionError(msg)
 
     return Calibration(
         name=calibration_data.series.iloc[0].replace("Last", "").strip(),
-        report=calibration_result[0],
-        time=calibration_result[1],
+        time=time,
+        report=report,
     )
 
 

tests/parsers/luminex_xponent/luminex_xponent_structure_test.py

@@ -138,7 +138,7 @@ def test_create_calibration_item() -> None:
 
     assert create_calibration(
         SeriesData(pd.Series([name, f"{report} {time}"]))
-    ) == Calibration(name, report, time)
+    ) == Calibration(name, time, report)
 
 
 def test_create_calibration_item_invalid_line_format() -> None:
@@ -153,7 +153,7 @@ def test_create_calibration_item_invalid_line_format() -> None:
 
 def test_create_calibration_item_invalid_calibration_result() -> None:
     bad_result = "bad_result"
-    error = f"Invalid calibration result format, expected to split into two values, got: ['{bad_result}']"
+    error = f"Invalid calibration result format, got: ['{bad_result}']"
     with pytest.raises(AllotropeConversionError, match=re.escape(error)):
         create_calibration(SeriesData(pd.Series(["Last CalReport", bad_result])))
 

tests/parsers/luminex_xponent/testdata/luminex_xPONENT_NaN_and_not_reported_values.json

@@ -20553,7 +20553,7 @@
             "file name": "luminex_xPONENT_NaN_and_not_reported_values.csv",
             "UNC path": "tests/parsers/luminex_xponent/testdata/luminex_xPONENT_NaN_and_not_reported_values.csv",
             "ASM converter name": "allotropy_luminex_xponent",
-            "ASM converter version": "0.1.98",
+            "ASM converter version": "0.1.99",
             "software name": "xPONENT",
             "software version": "4.3.309.1"
         },
@@ -20564,33 +20564,27 @@
                 "calibration document": [
                     {
                         "calibration name": "F3DeCAL1 Calibration",
-                        "calibration time": "2025-07-17T01:00:00+00:00",
-                        "calibration report": "1/1/2025"
+                        "calibration time": "2025-01-01T01:00:00+00:00"
                     },
                     {
                         "calibration name": "F3DCAL2 Calibration",
-                        "calibration time": "2025-07-17T01:00:00+00:00",
-                        "calibration report": "1/1/2025"
+                        "calibration time": "2025-01-01T01:00:00+00:00"
                     },
                     {
                         "calibration name": "F3DCAL3 Calibration",
-                        "calibration time": "2025-07-17T01:00:00+00:00",
-                        "calibration report": "1/1/2025"
+                        "calibration time": "2025-01-01T01:00:00+00:00"
                     },
                     {
                         "calibration name": "F3DeVER1 Verification",
-                        "calibration time": "2025-07-17T01:00:00+00:00",
-                        "calibration report": "1/1/2025"
+                        "calibration time": "2025-01-01T01:00:00+00:00"
                     },
                     {
                         "calibration name": "F3DVER2 Verification",
-                        "calibration time": "2025-07-17T01:00:00+00:00",
-                        "calibration report": "1/1/2025"
+                        "calibration time": "2025-01-01T01:00:00+00:00"
                     },
                     {
                         "calibration name": "Fluidics Test",
-                        "calibration time": "2025-07-17T01:00:00+00:00",
-                        "calibration report": "1/1/2025"
+                        "calibration time": "2025-01-01T01:00:00+00:00"
                     }
                 ]
             }