update to released 0.5.19 of oaklib, update model, format

backend/pyproject.toml

@@ -30,7 +30,7 @@ pystow = ">=0.5.0"
 loguru = "*"
 ### Optional API dependencies
 fastapi ={ version = "^0.87.0", optional = true }
-oaklib = "0.5.19rc-1"
+oaklib = "0.5.19"
 
 
 [tool.poetry.group.dev.dependencies]

backend/src/monarch_py/api/semsim.py

@@ -58,7 +58,7 @@ def _post_compare(
 def _search(
     subjects: str = Query(...),
     target_group: SemsimSearchCategory = Query(...),
-    limit: int = Query(default=10, ge=1, le=500)
+    limit: int = Query(default=10, ge=1, le=500),
 ):
     """
     Search for genes or diseases by phenotype similarity<br>

backend/src/monarch_py/implementations/oak/oak_implementation.py

@@ -42,9 +42,9 @@ def init_semsim(self, phenio_path: str = None, force_update: bool = False):
                 self.semsim = get_adapter(f"semsimian:sqlite:{phenio_path}")
             else:
                 monarchstow = pystow.module("monarch")
-                with monarchstow.ensure_gunzip("phenio",
-                                               url=self.default_phenio_db_url,
-                                               force=force_update) as stowed_phenio_path:
+                with monarchstow.ensure_gunzip(
+                    "phenio", url=self.default_phenio_db_url, force=force_update
+                ) as stowed_phenio_path:
                     self.semsim = get_adapter(f"semsimian:sqlite:{stowed_phenio_path}")
 
             # run a query to get the adapter to initialize properly
@@ -76,11 +76,13 @@ def compare(
         response_dict = self.json_dumper.to_dict(response)
         return TermSetPairwiseSimilarity(**response_dict)
 
-    def search(self,
-               objects: List[str],
-               target_groups: List[SemsimSearchCategory] = None,
-               predicates: List[str] = None,
-               limit: int = 10):
+    def search(
+        self,
+        objects: List[str],
+        target_groups: List[SemsimSearchCategory] = None,
+        predicates: List[str] = None,
+        limit: int = 10,
+    ):
         predicates = predicates or self.default_predicates
         return self.semsim.associations_subject_search(
             predicates={"biolink:has_phenotype"},