Add first test

adtl/__init__.py

@@ -745,13 +745,18 @@ def update_table(self, table: str, row: StrDict):
                                     existing_value + value
                                 )
                         elif combined_type == "firstNonNull":
+                            # only use the first value found
                             pass
                         else:
                             raise ValueError(
-                                f"Could not return value for {combined_type}"
+                                f"Unrecognised combined type: {combined_type}"
                             )
                     else:
                         # otherwise overwrite?
+                        logging.debug(
+                            f"Multiple rows of data found for {attr} without a"
+                            " combinedType listed. Data being overwritten."
+                        )
                         self.data[table][group_key][attr] = value
         elif kind == "oneToMany":
             for match in self.spec[table]:

tests/parsers/stop-overwriting.toml

@@ -0,0 +1,40 @@
+[adtl]
+  name = "overwrite"
+  description = "Example using groupBy on data with multiple rows per subject"
+
+[adtl.tables.visit]
+  kind = "groupBy"
+  groupBy = "subject_id"
+  aggregation = "lastNotNull"
+
+[visit]
+
+  [visit.subject_id]
+    field = "subjid"
+    description = "Subject ID"
+
+  [visit.earliest_admission]
+    combinedType = "min"
+    fields = [
+      { field = "first_admit" },
+    ]
+
+  [visit.start_date]
+    combinedType = "firstNonNull"
+    fields = [
+      { field = "first_admit" },
+      { field = "enrolment" },
+    ]
+
+  [visit.treatment_antiviral_type]
+    combinedType = "set"
+    excludeWhen = "none"
+    fields = [
+      { field = "daily_antiviral_type___1", values = { 1 = "Ribavirin" } },
+      { field = "daily_antiviral_type___2", values = { 1 = "Lopinavir" } },
+      { field = "daily_antiviral_type___3", values = { 1 = "Interferon" } },
+      { field = "overall_antiviral_dc___1", values = { 1 = "Ribavirin" } },
+      { field = "overall_antiviral_dc___2", values = { 1 = "Lopinavir" } },
+      { field = "overall_antiviral_dc___3", values = { 1 = "Interferon" } },
+      ]
+

tests/sources/stop-overwriting.csv

@@ -0,0 +1,11 @@
+subjid,redcap,first_admit,enrolment,daily_antiviral_type___1,daily_antiviral_type___2,daily_antiviral_type___3,overall_antiviral_dc___1,overall_antiviral_dc___2,overall_antiviral_dc___3
+1,admit,2023-11-20,2023-11-23,0,0,0,0,0,0
+1,discharge,,,0,0,0,1,0,1
+1,day1,2023-11-19,,1,0,0,0,0,0
+1,day2,,,1,0,0,0,0,0
+2,admit,,2022-11-23,0,0,0,0,0,0
+2,discharge,,2020-11-23,0,0,0,0,0,0
+2,day1,,,0,1,0,0,0,0
+3,admit,,2020-02-20,0,0,0,0,0,0
+3,discharge,,,0,0,0,0,1,1
+3,day1,,,1,0,0,0,0,0

tests/test_parser.py

@@ -1316,3 +1316,32 @@ def test_combinedtype_wordsubstituteset(test_row, test_combination, expected):
     }
 
     assert parser.get_combined_type(test_row, test_rule) == unordered(expected)
+
+
+OVERWRITE_OUTPUT = [
+    {
+        "subject_id": 1,
+        "earliest_admission": "2023-11-19",
+        "start_date": "2023-11-20",
+        "treatment_antiviral_type": unordered(["Ribavirin", "Interferon"]),
+    },
+    {
+        "subject_id": 2,
+        "start_date": "2022-11-23",
+        "treatment_antiviral_type": ["Lopinavir"],
+    },
+    {
+        "subject_id": 3,
+        "start_date": "2020-02-20",
+        "treatment_antiviral_type": unordered(["Ribavirin", "Lopinavir", "Interferon"]),
+    },
+]
+
+
+def test_no_overwriting():
+    overwriting_output = list(
+        parser.Parser(TEST_PARSERS_PATH / "stop-overwriting.toml")
+        .parse(TEST_SOURCES_PATH / "stop-overwriting.csv")
+        .read_table("visit")
+    )
+    assert overwriting_output == OVERWRITE_OUTPUT