functioning score phenotype tests with casting to int

Bayer-Group · Nov 14, 2024 · a92777c · a92777c
1 parent f02fe75
commit a92777c
Show file tree

Hide file tree

Showing 3 changed files with 23 additions and 10 deletions.
diff --git a/phenex/phenotypes/computation_graph_phenotypes.py b/phenex/phenotypes/computation_graph_phenotypes.py
@@ -72,6 +72,12 @@ def _execute(self, tables: Dict[str, Table]) -> PhenotypeTable:
             PhenotypeTable: The resulting phenotype table containing the required columns.
         """
         joined_table = hstack(self.children, tables['PERSON'].select('PERSON_ID'))
+
+        if self._populate == 'value' and self._operate_on == 'boolean':
+            for child in self.children:
+                column_name = f"{child.name}_BOOLEAN"
+                joined_table = joined_table.mutate(**{column_name: joined_table[column_name].cast(float)})
+
         if self._populate == "value":
             _expression = self.computation_graph.get_value_expression(
                 joined_table, operate_on=self._operate_on

diff --git a/phenex/phenotypes/phenotype.py b/phenex/phenotypes/phenotype.py
@@ -256,7 +256,7 @@ def manage_node(node):
             elif isinstance(node, Phenotype):
                 if operate_on == "boolean":
                     return table[f"{node.name}_BOOLEAN"]
-                return table[f"{node.name}_vALUE"]
+                return table[f"{node.name}_VALUE"]
             return node
 
         left = manage_node(self.left)

diff --git a/phenex/test/phenotypes/test_score_phenotype.py b/phenex/test/phenotypes/test_score_phenotype.py
@@ -23,10 +23,17 @@ def define_input_tables(self):
             code_type_columnname="CODE_TYPE",
             event_date_columnname="EVENT_DATE",
         )
+
+        df_person = pd.DataFrame()
+        df_person['PERSON_ID'] = df['PERSON_ID'].unique()
         return [
             {
                 "name": "CONDITION_OCCURRENCE",
                 "df": df,
+            },
+            {
+                "name": "PERSON",
+                "df": df_person
             }
         ]
 
@@ -64,24 +71,24 @@ def define_phenotype_tests(self):
 
         score1 = {
             "name": "score1",
-            "persons": [f"P{x}" for x in range(1, 7)],
-            "values": [2, 2, 1, 1, 1, 1],
+            "persons": [f"P{x}" for x in range(1, 8)],
+            "values": [2, 2, 1, 1, 1, 1,0],
             "phenotype": ScorePhenotype(expression=(c1["phenotype"] + c2["phenotype"])),
         }
 
         score2 = {
             "name": "score2",
-            "persons": [f"P{x}" for x in range(1, 7)],
-            "values": [3, 3, 2, 2, 1, 1],
+            "persons": [f"P{x}" for x in range(1, 8)],
+            "values": [3, 3, 2, 2, 1, 1,0],
             "phenotype": ScorePhenotype(
                 expression=(c1["phenotype"] * 2 + c2["phenotype"])
             ),
         }
 
         score3 = {
             "name": "score3",
-            "persons": [f"P{x}" for x in range(1, 7)],
-            "values": [3, 3, 1, 1, 2, 2],
+            "persons": [f"P{x}" for x in range(1, 8)],
+            "values": [3, 3, 1, 1, 2, 2,0],
             "phenotype": ScorePhenotype(
                 expression=(c1["phenotype"] + c2["phenotype"] * 2)
             ),
@@ -107,8 +114,8 @@ def define_phenotype_tests(self):
 
         score6 = {
             "name": "score6",
-            "persons": [f"P{x}" for x in range(1, 7)],
-            "values": [3, 3, 1, 1, 2, 2],
+            "persons": [f"P{x}" for x in range(1, 8)],
+            "values": [3, 3, 1, 1, 2, 2,0],
             "phenotype": ScorePhenotype(expression=(c1["phenotype"] * c2["phenotype"])),
         }
 
@@ -122,7 +129,7 @@ def define_phenotype_tests(self):
 
 def test_score_phenotype():
     tg = ScorePhenotypeTestGenerator()
-    # tg.run_tests()
+    tg.run_tests()
 
 
 if __name__ == "__main__":