raise an error when two classes have the same ambiguous attribute

Closes linkml/linkml#2403

Signed-off-by: Vincent Kelleher <[email protected]>

Author: Vincent Kelleher

linkml_runtime/exceptions.py

@@ -1,2 +1,10 @@
 class OrderingError(RuntimeError):
-    """Exception raised when there is a problem with SchemaView ordering"""
+    """Exception raised when there is a problem with SchemaView ordering"""
+
+
+class AmbiguousNameError(RuntimeError):
+    """Exception raised in the case of an ambiguous element name"""
+
+
+class MissingElementError(RuntimeError):
+    """Exception raised when an element is missing"""

linkml_runtime/utils/schemaview.py

@@ -15,7 +15,7 @@
 from linkml_runtime.utils.formatutils import is_empty
 from linkml_runtime.utils.pattern import PatternResolver
 from linkml_runtime.linkml_model.meta import *
-from linkml_runtime.exceptions import OrderingError
+from linkml_runtime.exceptions import OrderingError, AmbiguousNameError, MissingElementError
 from enum import Enum
 
 logger = logging.getLogger(__name__)
@@ -148,7 +148,6 @@ class SchemaView(object):
     # cached hash
     _hash: Optional[int] = None
 
-
     def __init__(self, schema: Union[str, Path, SchemaDefinition],
                  importmap: Optional[Dict[str, str]] = None, merge_imports: bool = False, base_dir: str = None):
         if isinstance(schema, Path):
@@ -631,13 +630,16 @@ def get_slot(self, slot_name: SLOT_NAME, imports=True, attributes=True, strict=F
             for c in self.all_classes(imports=imports).values():
                 if slot_name in c.attributes:
                     if slot is not None:
-                        # slot name is ambiguous: return a stub slot
-                        return SlotDefinition(slot_name)
+                        raise AmbiguousNameError(
+                            f'Attribute "{slot_name}" is already defined in another class, these attributes will be '
+                            f'ambiguous in RDF generators and you may need to rename them or restructure your schema. '
+                            f'Furthermore, you can use the induced_slot method with the slot name and its containing '
+                            f'class as arguments.')
                     slot = copy(c.attributes[slot_name])
                     slot.from_schema = c.from_schema
                     slot.owner = c.name
         if strict and slot is None:
-            raise ValueError(f'No such slot as "{slot_name}"')
+            raise MissingElementError(f'No such slot as "{slot_name}"')
         return slot
 
     @lru_cache(None)

tests/test_utils/input/get_slot_with_ambiguous_attributes.yaml

@@ -0,0 +1,36 @@
+id: https://examples.org/get-slot-with-attribute#
+name: get-slot-with-attribute
+
+prefixes:
+  test: https://examples.org/get-slot-with-attribute#
+
+default_prefix: test
+default_range: string
+
+slots:
+  uniqueSlot:
+    description: "A unique slot just to test that get_slot still works when attributes are ignored in this schema"
+    range: string
+
+classes:
+  ClassWithAttributes:
+    slots:
+      - uniquesSlot
+    attributes:
+      randomAttribute:
+        description: "A random attribute for testing purposes"
+        range: integer
+        minimum_value: 0
+        maximum_value: 999
+
+  ImportantSecondClass:
+    description: "Important class to reproduce the error I got as the class loop needs to have at least a 
+              second iteration"
+    slots:
+      - uniqueSlot
+    attributes:
+      randomAttribute:
+        description: "Now you see the ambiguity intensifying ?"
+        range: integer
+        minimum_value: 0
+        maximum_value: 111

tests/test_utils/test_schemaview.py

@@ -6,6 +6,7 @@
 from jsonasobj2 import JsonObj
 
 from linkml_runtime.dumpers import yaml_dumper
+from linkml_runtime.exceptions import AmbiguousNameError, MissingElementError
 from linkml_runtime.linkml_model.meta import Example, SchemaDefinition, ClassDefinition, SlotDefinitionName, SlotDefinition, \
     ClassDefinitionName, Prefix
 from linkml_runtime.loaders.yaml_loader import YAMLLoader
@@ -701,7 +702,7 @@ def test_slot_inheritance():
 
     # Test dangling
     view.add_slot(SlotDefinition('s5', is_a='does-not-exist'))
-    with pytest.raises(ValueError):
+    with pytest.raises(MissingElementError):
         view.slot_ancestors('s5')
 
 def test_attribute_inheritance():
@@ -744,9 +745,6 @@ def test_ambiguous_attributes():
     a2x = SlotDefinition('a2', range='BarEnum')
     view.add_class(ClassDefinition('C2', attributes={a1x.name: a1x, a2x.name: a2x}))
 
-    assert view.get_slot(a1.name).range is None
-    assert view.get_slot(a2.name).range is None
-    assert view.get_slot(a3.name).range is not None
     assert len(view.all_slots(attributes=True)) == 3
     assert len(view.all_slots(attributes=False)) == 0
     assert len(view.all_slots()) == 3
@@ -757,6 +755,21 @@ def test_ambiguous_attributes():
     assert view.induced_slot(a2x.name, 'C2').range == a2x.range
 
 
+def test_ambiguous_attribute_through_get_slot():
+    schema_path = os.path.join(INPUT_DIR, "get_slot_with_ambiguous_attributes.yaml")
+    sv = SchemaView(schema_path)
+
+    assert sv.get_slot("uniqueSlot") is not None
+    assert sv.get_slot("randomAttribute", attributes=False) is None
+    assert sv.induced_slot("uniqueSlot", "ImportantSecondClass") is not None
+
+    with pytest.raises(AmbiguousNameError) as exception:
+        sv.get_slot("randomAttribute")
+    assert str(exception.value) == ('Attribute "randomAttribute" is already defined in another class, '
+                                    'these attributes will be ambiguous in RDF generators and you may need to rename '
+                                    'them or restructure your schema. Furthermore, you can use the induced_slot '
+                                    'method with the slot name and its containing class as arguments.')
+
 def test_metamodel_in_schemaview():
     view = package_schemaview('linkml_runtime.linkml_model.meta')
     assert 'meta' in view.imports_closure()