Merge pull request #362 from vincentkelleher/fix_different_types_with_same_name

Fix SchemaView metadata injection and get URI

Author: amc-corey-cox

linkml_runtime/utils/schemaview.py

@@ -324,7 +324,16 @@ def imports_closure(self, imports: bool = True, traverse: Optional[bool] = None,
 
         if inject_metadata:
             for s in self.schema_map.values():
-                for x in {**s.classes, **s.enums, **s.slots, **s.subsets, **s.types}.values():
+                # It is important to merge element definitions as a list as multiple elements of different kinds can
+                # have the same name which means they have the same dict key.
+                elements = []
+                elements.extend(s.classes.values())
+                elements.extend(s.enums.values())
+                elements.extend(s.slots.values())
+                elements.extend(s.subsets.values())
+                elements.extend(s.types.values())
+
+                for x in elements:
                     x.from_schema = s.id
                 for c in s.classes.values():
                     for a in c.attributes.values():
@@ -1070,14 +1079,14 @@ def get_uri(self, element: Union[ElementName, Element], imports=True, expand=Fal
         Return the CURIE or URI for a schema element. If the schema defines a specific URI, this is
         used, otherwise this is constructed from the default prefix combined with the element name
 
-        :param element_name: name of schema element
+        :param element: name of schema element
         :param imports: include imports closure
         :param native: return the native CURIE or URI rather than what is declared in the uri slot
         :param expand: expand the CURIE to a URI; defaults to False
         :return: URI or CURIE as a string
         """
         e = self.get_element(element, imports=imports)
-        e_name = e.name
+
         if isinstance(e, ClassDefinition):
             uri = e.class_uri
             e_name = camelcase(e.name)
@@ -1091,8 +1100,8 @@ def get_uri(self, element: Union[ElementName, Element], imports=True, expand=Fal
             raise ValueError(f'Must be class or slot or type: {e}')
         if uri is None or native:
             if e.from_schema is not None:
-                schema = next(sc for sc in self.schema_map.values() if sc.id == e.from_schema)
-                if schema == None:
+                schema = next((sc for sc in self.schema_map.values() if sc.id == e.from_schema), None)
+                if schema is None:
                     raise ValueError(f'Cannot find {e.from_schema} in schema_map')
             else:
                 schema = self.schema_map[self.in_schema(e.name)]

tests/test_utils/test_schemaview.py

@@ -6,8 +6,9 @@
 from jsonasobj2 import JsonObj
 
 from linkml_runtime.dumpers import yaml_dumper
-from linkml_runtime.linkml_model.meta import Example, SchemaDefinition, ClassDefinition, SlotDefinitionName, SlotDefinition, \
-    ClassDefinitionName, Prefix
+from linkml_runtime.linkml_model.meta import Example, SchemaDefinition, ClassDefinition, SlotDefinitionName, \
+    SlotDefinition, \
+    ClassDefinitionName, Prefix, TypeDefinition
 from linkml_runtime.loaders.yaml_loader import YAMLLoader
 from linkml_runtime.utils.introspection import package_schemaview
 from linkml_runtime.utils.schemaview import SchemaView, SchemaUsage, OrderedBy
@@ -896,4 +897,18 @@ def test_materialize_nonscalar_slot_usage():
     assert cls.attributes["tempo"].annotations.expected_value.value == "a number between 0 and 200"
     assert cls.attributes["tempo"].annotations.preferred_unit.value == "BPM"
     assert cls.attributes["tempo"].domain_of == ["DJController"]
-    assert cls.slot_usage["tempo"].domain_of == []
+    assert cls.slot_usage["tempo"].domain_of == []
+
+
+def test_type_and_slot_with_same_name():
+    """
+    Test that checks the case where a URI needs to be resolved and a name is ambiguously used for a slot and a
+    type
+    """
+    schema_definition = SchemaDefinition(id="https://example.org/test#", name="test_schema", default_prefix="ex")
+
+    view = SchemaView(schema_definition)
+    view.add_slot(SlotDefinition(name="test", from_schema="https://example.org/another#"))
+    view.add_type(TypeDefinition(name="test", from_schema="https://example.org/imported#"))
+
+    assert view.get_uri("test", imports=True) == "ex:test"