feat: Roche Cedex Bioht - use get_unread (#1084)

Co-authored-by: james-leinas <157071641+james-leinas@users.noreply.github.com>

Author: felipenarv

src/allotropy/parsers/roche_cedex_bioht/roche_cedex_bioht_structure.py

@@ -39,6 +39,7 @@ class Title:
 
     @staticmethod
     def create(title_data: SeriesData) -> Title:
+        title_data.get_unread()
         return Title(
             title_data[str, "data processing time"],
             title_data[str, "analyst"],
@@ -69,28 +70,53 @@ def create(data: SeriesData) -> RawMeasurement:
             concentration_value, data[str, "concentration unit"]
         )
 
-        custom_info = data.get_custom_keys({"detection kit", "detection kit range"})
-
-        if error:
-            custom_info["flag"] = error
-
-        custom_info_sorted = dict(sorted(custom_info.items()))
-
         # Instead of reporting '< TEST RNG' as the error, we report the original concentration value,
         # as the error, which comes as a string like '< 8.706'
         if error == BELOW_TEST_RANGE:
             error = data.get(str, "original concentration value", error)
 
-        return RawMeasurement(
+        custom_info = data.get_custom_keys(
+            {"detection kit", "detection kit range", "analyte code"}
+        )
+        custom_info["record type"] = data.get(str, "row type", None)
+        data.mark_read(
+            {
+                "sample identifier",
+                "batch identifier",
+                "col4",
+                "col5",
+                "col6",
+                "col8",
+                "col10",
+                "col11",
+                "col12",
+                "col13",
+                "original concentration value",
+                "sample role type",
+            }
+        )
+
+        if error:
+            custom_info["flag"] = error
+
+        measurement = RawMeasurement(
             data[str, "analyte name"],
             data[str, "measurement time"],
             value,
             unit,
             data[str, "analyte code"],
             error,
-            custom_info_sorted,
+            {},
         )
 
+        if isinstance(measurement.custom_info, dict):
+            custom_info.update(data.get_unread())
+            custom_info_sorted = dict(sorted(custom_info.items()))
+
+            measurement.custom_info.update(custom_info_sorted)
+
+        return measurement
+
     @staticmethod
     def _get_value_and_unit(value: JsonFloat, unit: str) -> tuple[JsonFloat, str]:
         multiplier = 1.0

tests/parsers/roche_cedex_bioht/roche_cedex_bioht_structure_test.py

@@ -107,7 +107,13 @@ def test_create_measurements() -> None:
     assert measurements == {
         "2021-05-20T16:55:51+00:00": {
             "lactate_LAC2B": RawMeasurement(
-                "lactate", "2021-05-20T16:55:51+00:00", 2.45, "g/L", "LAC2B", None, {}
+                "lactate",
+                "2021-05-20T16:55:51+00:00",
+                2.45,
+                "g/L",
+                "LAC2B",
+                None,
+                {"analyte code": "LAC2B", "record type": None},
             ),
             "glutamine_GLN2B": RawMeasurement(
                 "glutamine",
@@ -116,7 +122,7 @@ def test_create_measurements() -> None:
                 "mmol/L",
                 "GLN2B",
                 None,
-                {},
+                {"analyte code": "GLN2B", "record type": None},
             ),
             "osmolality_OSM2B": RawMeasurement(
                 "osmolality",
@@ -125,7 +131,7 @@ def test_create_measurements() -> None:
                 "mosm/kg",
                 "OSM2B",
                 None,
-                {},
+                {"analyte code": "OSM2B", "record type": None},
             ),
         }
     }
@@ -150,7 +156,13 @@ def test_create_measurements_more_than_one_measurement_docs() -> None:
     assert measurements == {
         "2021-05-20T16:55:51+00:00": {
             "lactate_LAC2B": RawMeasurement(
-                "lactate", "2021-05-20T16:55:51+00:00", 2.45, "g/L", "LAC2B", None, {}
+                "lactate",
+                "2021-05-20T16:55:51+00:00",
+                2.45,
+                "g/L",
+                "LAC2B",
+                None,
+                {"analyte code": "LAC2B", "record type": None},
             ),
             "glutamine_GLN2B": RawMeasurement(
                 "glutamine",
@@ -159,7 +171,7 @@ def test_create_measurements_more_than_one_measurement_docs() -> None:
                 "mmol/L",
                 "GLN2B",
                 None,
-                {},
+                {"analyte code": "GLN2B", "record type": None},
             ),
         },
         "2021-05-21T16:57:51+00:00": {
@@ -170,7 +182,7 @@ def test_create_measurements_more_than_one_measurement_docs() -> None:
                 "mmol/L",
                 "GLN2B",
                 None,
-                {},
+                {"analyte code": "GLN2B", "record type": None},
             ),
         },
     }
@@ -224,10 +236,22 @@ def test_create_sample() -> None:
     assert sample.measurements == {
         "2021-05-20 16:55:51": {
             "lactate_LAC2B": RawMeasurement(
-                "lactate", "2021-05-20 16:55:51", 2.45, "g/L", "LAC2B", None, {}
+                "lactate",
+                "2021-05-20 16:55:51",
+                2.45,
+                "g/L",
+                "LAC2B",
+                None,
+                {"analyte code": "LAC2B", "record type": None},
             ),
             "glutamine_GLN2B": RawMeasurement(
-                "glutamine", "2021-05-20 16:56:51", 4.35, "mmol/L", "GLN2B", None, {}
+                "glutamine",
+                "2021-05-20 16:56:51",
+                4.35,
+                "mmol/L",
+                "GLN2B",
+                None,
+                {"analyte code": "GLN2B", "record type": None},
             ),
         }
     }