black

phenex/filters/filter.py

@@ -28,7 +28,7 @@ def filter(self, table: Table) -> Table:
             raise ValueError(f"Filter must not remove columns.")
 
         return type(table)(filtered_table.select(input_columns))
-    
+
     def _filter(self, table: Table) -> Table:
         """
         Returns the logical condition that the filter is applying.
@@ -43,7 +43,7 @@ def __or__(self, other):
 
     def __invert__(self):
         return NotFilter(self)
-    
+
 
 class AndFilter(Filter):
     """
@@ -56,7 +56,7 @@ def __init__(self, filter1, filter2):
 
     def _get_predicate(self, table: Table) -> Table:
         return self.filter1._get_predicate(table) & self.filter2._get_predicate(table)
-    
+
     def filter(self, table: Table) -> Table:
         table = self.filter1.filter(table)
         return self.filter2.filter(table)
@@ -77,7 +77,7 @@ def __init__(self, filter1, filter2):
 
     def _get_predicate(self, table: Table) -> Table:
         return self.filter1._get_predicate(table) | self.filter2._get_predicate(table)
-    
+
     def filter(self, table: Table) -> Table:
         table1 = self.filter1.filter(table).table
         table2 = self.filter2.filter(table).table
@@ -87,7 +87,7 @@ def autojoin_filter(self, table: "PhenexTable", tables: dict = None):
         table1 = self.filter1.autojoin_filter(table, tables).table
         table2 = self.filter2.autojoin_filter(table, tables).table
         return type(table)(table1.union(table2, distinct=True))
-    
+
 
 class NotFilter(Filter):
     """
@@ -103,7 +103,7 @@ def _get_predicate(self, table: Table) -> Table:
     def filter(self, table: Table) -> Table:
         filtered_table = self.filter.filter(table).table
         return type(table)(table.difference(filtered_table))
-    
+
     def autojoin_filter(self, table: "PhenexTable", tables: dict = None):
         filtered_table = self.filter.autojoin_filter(table, tables).table
-        return type(table)(table.difference(filtered_table))
+        return type(table)(table.difference(filtered_table))

phenex/phenotypes/phenotype.py

@@ -9,6 +9,7 @@
 
 logger = create_logger(__name__)
 
+
 class Phenotype:
     """
     All Phenotype's in PhenEx derive from the Phenotype class. Phenotype's take in the complete specification of what the Phenotype
@@ -55,10 +56,14 @@ def execute(self, tables: Dict[str, Table]) -> PhenotypeTable:
         logger.info(f"Phenotype '{self.name}': executing...")
         for child in self.children:
             if child.table is None:
-                logger.debug(f"Phenotype {self.name}: executing child phenotype '{child.name}'...")
+                logger.debug(
+                    f"Phenotype {self.name}: executing child phenotype '{child.name}'..."
+                )
                 child.execute(tables)
             else:
-                logger.debug(f"Phenotype {self.name}: skipping already computed child phenotype '{child.name}'.")
+                logger.debug(
+                    f"Phenotype {self.name}: skipping already computed child phenotype '{child.name}'."
+                )
 
         table = self._execute(tables).mutate(BOOLEAN=True)
 

phenex/test/phenotypes/test_codelist_phenotype.py

@@ -12,8 +12,10 @@
 from phenex.filters.value import *
 from phenex.filters.categorical_filter import CategoricalFilter
 
-import ibis 
-ibis.options.interactive =True
+import ibis
+
+ibis.options.interactive = True
+
 
 class CodelistPhenotypeTestGenerator(PhenotypeTestGenerator):
     name_space = "clpt"
@@ -664,7 +666,9 @@ def define_phenotype_tests(self):
         return test_infos
 
 
-class CodelistPhenotypeCategoricalFilterLogicalCombinationsTestGenerator(PhenotypeTestGenerator):
+class CodelistPhenotypeCategoricalFilterLogicalCombinationsTestGenerator(
+    PhenotypeTestGenerator
+):
     name_space = "clpt_categorical_filter_logic"
 
     def define_input_tables(self):
@@ -755,7 +759,7 @@ def define_phenotype_tests(self):
             "phenotype": CodelistPhenotype(
                 codelist=codelist_factory.get_codelist("c1"),
                 domain="condition_occurrence",
-                categorical_filter= ~CategoricalFilter(
+                categorical_filter=~CategoricalFilter(
                     allowed_values=["z1"], column_name="z"
                 ),
             ),
@@ -828,7 +832,9 @@ def define_phenotype_tests(self):
         return [test1, test2, test3]
 
 
-class CodelistPhenotypeCategoricalFilterLogicalCombinationsAutojoinTestGenerator(PhenotypeTestGenerator):
+class CodelistPhenotypeCategoricalFilterLogicalCombinationsAutojoinTestGenerator(
+    PhenotypeTestGenerator
+):
     name_space = "clpt_categorical_filter_autojoin"
 
     def define_input_tables(self):
@@ -839,7 +845,7 @@ def define_input_tables(self):
         df["CODE"] = "c1"
         df["CODE_TYPE"] = "ICD10CM"
         df["DATE"] = datetime.datetime.strptime("10-10-2021", "%m-%d-%Y")
-        df['DX_POS'] = ['first'] * 5 + ['second'] * 5
+        df["DX_POS"] = ["first"] * 5 + ["second"] * 5
 
         df2 = pd.DataFrame()
         df2["PERSON_ID"] = [f"P{i}" for i in range(N)]
@@ -880,20 +886,22 @@ def define_phenotype_tests(self):
             "phenotype": CodelistPhenotype(
                 codelist=codelist_factory.get_codelist("c1"),
                 domain="condition_occurrence",
-                categorical_filter= a_cat_filter | b_cat_filter
+                categorical_filter=a_cat_filter | b_cat_filter,
             ),
         }
 
-        primary_pos =  CategoricalFilter(
-            allowed_values=["first"], column_name="DX_POS", domain="condition_occurrence"
+        primary_pos = CategoricalFilter(
+            allowed_values=["first"],
+            column_name="DX_POS",
+            domain="condition_occurrence",
         )
         c2 = {
             "name": "a_and_primary_pos_autojoin_table",
             "persons": [f"P{i}" for i in range(2)],
             "phenotype": CodelistPhenotype(
                 codelist=codelist_factory.get_codelist("c1"),
                 domain="condition_occurrence",
-                categorical_filter= a_cat_filter & primary_pos
+                categorical_filter=a_cat_filter & primary_pos,
             ),
         }
 
@@ -903,21 +911,20 @@ def define_phenotype_tests(self):
             "phenotype": CodelistPhenotype(
                 codelist=codelist_factory.get_codelist("c1"),
                 domain="condition_occurrence",
-                categorical_filter= (a_cat_filter & primary_pos) | b_cat_filter
+                categorical_filter=(a_cat_filter & primary_pos) | b_cat_filter,
             ),
         }
 
-
         c_cat_filter = CategoricalFilter(
             allowed_values=["c"], column_name="flag1", domain="encounter"
         )
         c4 = {
             "name": "a_and_not_primary_pos_or_b_autojoin_table",
-            "persons": [f"P{i}" for i in range(2, 4)] +  [f"P{i}" for i in range(5, 10)],
+            "persons": [f"P{i}" for i in range(2, 4)] + [f"P{i}" for i in range(5, 10)],
             "phenotype": CodelistPhenotype(
                 codelist=codelist_factory.get_codelist("c1"),
                 domain="condition_occurrence",
-                categorical_filter= (c_cat_filter & ~primary_pos) | b_cat_filter
+                categorical_filter=(c_cat_filter & ~primary_pos) | b_cat_filter,
             ),
         }
 
@@ -932,10 +939,12 @@ def test_categorical_filter_logic():
     tg = CodelistPhenotypeCategoricalFilterLogicalCombinationsTestGenerator()
     tg.run_tests()
 
+
 def test_categorical_filter_logic_autojoin():
     tg = CodelistPhenotypeCategoricalFilterLogicalCombinationsAutojoinTestGenerator()
     tg.run_tests()
 
+
 def test_fuzzy_match():
     tg = CodelistPhenotypeFuzzyMatchTestGenerator()
     tg.run_tests()