Increase coverage

globaldothealth · Nov 23, 2023 · 5cd4ab7 · 5cd4ab7
1 parent f08df25
commit 5cd4ab7
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Showing 4 changed files with 52 additions and 48 deletions.
diff --git a/adtl/__init__.py b/adtl/__init__.py
@@ -718,46 +718,42 @@ def update_table(self, table: str, row: StrDict):
             for attr in self.spec[table]:
                 value = get_value(row, self.spec[table][attr], self.ctx(attr))
                 # Check against all null elements, for combinedType=set/list, null is []
-                if (
-                    value is not None
-                    and value != []
-                    and attr not in self.data[table][group_key].keys()
-                ):
-                    # if data for this field hasn't already been captured
-                    self.data[table][group_key][attr] = value
-                elif value is not None and value != []:
-                    if "combinedType" in self.spec[table][attr]:
-                        combined_type = self.spec[table][attr]["combinedType"]
-                        existing_value = self.data[table][group_key][attr]
-                        if combined_type in ["all", "any", "min", "max"]:
-                            values = [existing_value, value]
-                            # normally calling eval() is a bad idea, but here values are restricted, so okay
-                            self.data[table][group_key][attr] = eval(combined_type)(
-                                values
-                            )
-                        elif combined_type in ["list", "set"]:
-                            if combined_type == "set":
-                                self.data[table][group_key][attr] = list(
-                                    set(existing_value + value)
-                                )
-                            else:
-                                self.data[table][group_key][attr] = (
-                                    existing_value + value
+                if value is not None and value != []:
+                    if attr not in self.data[table][group_key].keys():
+                        # if data for this field hasn't already been captured
+                        self.data[table][group_key][attr] = value
+
+                    else:
+                        if "combinedType" in self.spec[table][attr]:
+                            combined_type = self.spec[table][attr]["combinedType"]
+                            existing_value = self.data[table][group_key][attr]
+
+                            if combined_type in ["all", "any", "min", "max"]:
+                                values = [existing_value, value]
+                                # normally calling eval() is a bad idea, but here values are restricted, so okay
+                                self.data[table][group_key][attr] = eval(combined_type)(
+                                    values
                                 )
-                        elif combined_type == "firstNonNull":
-                            # only use the first value found
-                            pass
+                            elif combined_type in ["list", "set"]:
+                                if combined_type == "set":
+                                    self.data[table][group_key][attr] = list(
+                                        set(existing_value + value)
+                                    )
+                                else:
+                                    self.data[table][group_key][attr] = (
+                                        existing_value + value
+                                    )
+                            elif combined_type == "firstNonNull":
+                                # only use the first value found
+                                pass
                         else:
-                            raise ValueError(
-                                f"Unrecognised combined type: {combined_type}"
+                            # otherwise overwrite?
+                            logging.debug(
+                                f"Multiple rows of data found for {attr} without a"
+                                " combinedType listed. Data being overwritten."
                             )
-                    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
+                            self.data[table][group_key][attr] = value
+
         elif kind == "oneToMany":
             for match in self.spec[table]:
                 if "if" not in match:

diff --git a/tests/parsers/stop-overwriting.toml b/tests/parsers/stop-overwriting.toml
@@ -26,6 +26,13 @@
       { field = "enrolment" },
     ]
 
+  [visit.icu_admission_date]
+    combinedType = "list"
+    excludeWhen = "none"
+    fields = [
+      {field = "icu_admission_date"}
+    ]
+
   [visit.treatment_antiviral_type]
     combinedType = "set"
     excludeWhen = "none"

diff --git a/tests/sources/stop-overwriting.csv b/tests/sources/stop-overwriting.csv
@@ -1,11 +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
+subjid,redcap,first_admit,enrolment,icu_admission_date,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,,2020-11-23,2020-11-25,0,0,0,0,0,0
+2,day1,,,2020-11-30,0,1,0,0,0,0
+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
diff --git a/tests/test_parser.py b/tests/test_parser.py
@@ -1328,6 +1328,7 @@ def test_combinedtype_wordsubstituteset(test_row, test_combination, expected):
     {
         "subject_id": 2,
         "start_date": "2022-11-23",
+        "icu_admission_date": unordered(["2020-11-25", "2020-11-30"]),
         "treatment_antiviral_type": ["Lopinavir"],
     },
     {