lint

tests/test_transformer/test_biolink_subsetting.py

@@ -1,16 +1,20 @@
 from pathlib import Path
+from pprint import pprint
 from typing import List
 
+from linkml_runtime.dumpers import yaml_dumper
+from linkml_runtime.utils.formatutils import camelcase, underscore
+from linkml_runtime.utils.schemaview import SchemaView
 from pytest import fixture
 
-from linkml_runtime.dumpers import yaml_dumper
-from linkml_map.datamodel.transformer_model import TransformationSpecification, ClassDerivation, SlotDerivation
+from linkml_map.datamodel.transformer_model import (
+    ClassDerivation,
+    SlotDerivation,
+    TransformationSpecification,
+)
 from linkml_map.inference.schema_mapper import SchemaMapper
 from linkml_map.session import Session
-from linkml_runtime.utils.schemaview import SchemaView
 from src.linkml_map.utils.loaders import load_specification
-from linkml_runtime.utils.formatutils import camelcase, underscore
-from pprint import pprint
 
 REPO_ROOT = Path(__file__).resolve().parent.parent
 
@@ -25,10 +29,9 @@ def get_biolink_class_derivations(sv, subset_classes) -> dict:
     """
     # Example implementation to fetch class definitions
     # This should be replaced with the actual implementation
-    class_derivations ={}
+    class_derivations = {}
     for class_name in subset_classes:
-        class_derivation = ClassDerivation(populated_from=class_name,
-                                           name=camelcase(class_name))
+        class_derivation = ClassDerivation(populated_from=class_name, name=camelcase(class_name))
         induced_slots = sv.class_induced_slots(class_name)
         for slot in induced_slots:
             slot_derivation = SlotDerivation(populated_from=slot.name, name=underscore(slot.name))
@@ -49,13 +52,16 @@ def biolink_schema():
     sv = SchemaView(schema_url)
     return sv
 
+
 def test_biolink_subsetting_manual(biolink_schema):
     """
     Test to subset the Biolink schema manually
 
     :param biolink_schema: Fixture to load Biolink schema
     """
-    transform_file = REPO_ROOT / "input/examples/biolink/transform/biolink-example-profile.transform.yaml"
+    transform_file = (
+        REPO_ROOT / "input/examples/biolink/transform/biolink-example-profile.transform.yaml"
+    )
     # Initialize Session and SchemaBuilder
     session = Session()
 
@@ -66,10 +72,11 @@ def test_biolink_subsetting_manual(biolink_schema):
     mapper = SchemaMapper()
     mapper.source_schemaview = biolink_schema
 
-    target_schema_obj = mapper.derive_schema(specification=tr_spec,
-                                             target_schema_id="biolink-profile",
-                                             target_schema_name="BiolinkProfile")
-
+    target_schema_obj = mapper.derive_schema(
+        specification=tr_spec,
+        target_schema_id="biolink-profile",
+        target_schema_name="BiolinkProfile",
+    )
 
     yaml_dumper.dump(target_schema_obj, str("biolink-profile.yaml"))
 
@@ -95,14 +102,15 @@ def test_biolink_subset_auto(biolink_schema):
     # Set the source schema in the session
     session.set_source_schema(biolink_schema)
 
-    SUBSET_CLASSES = ["gene",
-                      "disease",
-                      "case to phenotypic feature association",
-                      "gene to disease association",
-                      "gene to phenotypic feature association",
-                      "case",
-                      "phenotypic feature",
-                      ]
+    SUBSET_CLASSES = [
+        "gene",
+        "disease",
+        "case to phenotypic feature association",
+        "gene to disease association",
+        "gene to phenotypic feature association",
+        "case",
+        "phenotypic feature",
+    ]
 
     class_derivations = get_biolink_class_derivations(biolink_schema, SUBSET_CLASSES)
 
@@ -111,9 +119,9 @@ def test_biolink_subset_auto(biolink_schema):
     mapper = SchemaMapper()
     mapper.source_schemaview = biolink_schema
 
-    target_schema_obj = mapper.derive_schema(specification=ts,
-                                             target_schema_id="biolink-profile",
-                                             target_schema_name="BiolinkProfile")
+    target_schema_obj = mapper.derive_schema(
+        specification=ts, target_schema_id="biolink-profile", target_schema_name="BiolinkProfile"
+    )
 
     yaml_dumper.dump(target_schema_obj, str("biolink-subset.yaml"))
 
@@ -124,5 +132,3 @@ def test_biolink_subset_auto(biolink_schema):
     print()
     for slot_name in transformed_sv.all_slots():
         print(slot_name)
-
-