tests

Author: sprivite

phenex/phenotypes/continuous_coverage_phenotype.py

@@ -24,7 +24,7 @@ class SexPhenotype(Phenotype):
     def __init__(
         self,
         name: str = "sex",
-        allowed_values: List[str] = ["male", "female"],
+        allowed_values: Optional[List[str]] = None,
         domain: str = "PERSON",
     ):
         self.name = name
@@ -37,7 +37,8 @@ def _execute(self, tables: Dict[str, Table]) -> PhenotypeTable:
         person_table = tables[self.domain]
         assert is_phenex_person_table(person_table)
 
-        sex_filter = CategoricalFilter(column_name="SEX", allowed_values=self.allowed_values)
-        filtered_table = sex_filter._filter(person_table)
+        if self.allowed_values is not None:
+            sex_filter = CategoricalFilter(column_name="SEX", allowed_values=self.allowed_values)
+            person_table = sex_filter._filter(person_table)
 
-        return filtered_table.mutate(VALUE=filtered_table.SEX, EVENT_DATE= ibis.null())
+        return person_table.mutate(VALUE=person_table.SEX, EVENT_DATE= ibis.null())

phenex/phenotypes/sex_phenotype.py

@@ -139,7 +139,7 @@ def df_from_test_info(test_info):
                 if "date" in col.lower():
                     schema[col] = datetime.date
                 elif "value" in col.lower():
-                    schema[col] = float
+                    schema[col] = str if isinstance(df[col].iloc[0], str) else float
                 elif "boolean" in col.lower():
                     schema[col] = bool
                 else:

phenex/test/phenotype_test_generator.py

@@ -29,7 +29,7 @@ def define_input_tables(self):
 
         column_types_person = {}
         input_info_person = {
-            "name": "person",
+            "name": "PERSON",
             "df": df_person,
             "column_types": column_types_person,
         }