Corrected get_by_label to use only labels in the ontology

ontopy/ontology.py

@@ -49,7 +49,7 @@
 )
 
 if TYPE_CHECKING:
     from typing import List, Sequence
 
 
 # Default annotations to look up
@@ -100,8 +100,9 @@
                 this Ontology subclass.  Defaults to `ontopy.Ontology`.
             label_annotations: Sequence of label IRIs used for accessing
                 entities in the ontology given that they are in the ontology.
-                Label IRIs not in the ontology will simply be ignored.
-                Detault to DEFAULT_LABEL_ANNOTATIONS module variable.
+                Label IRIs not in the ontology will need to be added to
+                ontologies in order to be accessible.
+                Default is None.
         """
         base_iri = base_iri.as_uri() if isinstance(base_iri, Path) else base_iri
 
@@ -526,24 +527,24 @@
             stacklevel=2,
         )
         if hasattr(iri, "iri"):
             iri = iri.iri
         if iri not in self.label_annotations:
             self.label_annotations.append(iri)
 
     def remove_label_annotation(self, iri):
         """Removes label annotation used by get_by_label()."""
         warnings.warn(
-            "Ontology.add_label_annotations() is deprecated. "
+            "Ontology.remove_label_annotations() is deprecated. "
             "Direct modify the `label_annotations` attribute instead.",
             DeprecationWarning,
             stacklevel=2,
         )
         if hasattr(iri, "iri"):
             iri = iri.iri
         try:
             self.label_annotations.remove(iri)
         except ValueError:
             pass
 
     def set_common_prefix(
         self,

tests/ontopy_tests/test_deprecation_warnings.py

@@ -0,0 +1,23 @@
+from typing import TYPE_CHECKING
+import pytest
+from owlready2.entity import ThingClass
+from owlready2.prop import ObjectPropertyClass, DataPropertyClass
+from owlready2 import AnnotationPropertyClass
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+
+@pytest.mark.filterwarnings(
+    "ignore:Ontology.add_label_annotations() is deprecated. Direct modify the `label_annotations` attribute instead."
+)
+def test_deprecation_warnings() -> None:
+    """Test functionalities will be removed and currently have depracation warnings"""
+    from ontopy import get_ontology
+    from ontopy.ontology import DEFAULT_LABEL_ANNOTATIONS
+
+    testonto = get_ontology("http://domain_ontology/new_ontology")
+
+    testonto.add_label_annotation(DEFAULT_LABEL_ANNOTATIONS[0])
+
+    testonto.remove_label_annotation(DEFAULT_LABEL_ANNOTATIONS[0])

tests/ontopy_tests/test_new_entity.py

@@ -33,6 +33,14 @@ def test_new_entity(testonto: "Ontology") -> None:
     testonto.new_entity(
         "AnotherClass", testonto.TestClass, entitytype=ThingClass
     )
+
+    testonto.new_entity(
+        "YetAnotherClass",
+        testonto.TestClass,
+        entitytype=ThingClass,
+        preflabel="YetAnotherClass",
+    )
+
     testonto.new_entity(
         "hasSubObjectProperty",
         testonto.hasObjectProperty,
@@ -100,3 +108,14 @@ def test_new_entity(testonto: "Ontology") -> None:
     testonto.new_annotation_property(
         "hasSubAnnotationProperty3", testonto.hasAnnotationProperty
     )
+
+    from ontopy import get_ontology
+    from ontopy.ontology import DEFAULT_LABEL_ANNOTATIONS
+
+    testonto2 = get_ontology("http://domain_ontology/new_ontology")
+    testonto2.new_entity(
+        "NewClass",
+        testonto.TestClass,
+        entitytype=ThingClass,
+        preflabel="NewClass",
+    )

tests/ontopy_tests/test_ontology_helper_functions.py

@@ -0,0 +1,18 @@
+from typing import TYPE_CHECKING
+import pytest
+from owlready2.entity import ThingClass
+from owlready2.prop import ObjectPropertyClass, DataPropertyClass
+from owlready2 import AnnotationPropertyClass
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+
+def test_ontology_to_storids(testonto: "Ontology") -> None:
+    """Test adding helper functions in ontopy.ontology"""
+    from ontopy.ontology import DEFAULT_LABEL_ANNOTATIONS
+
+    label_annotations = DEFAULT_LABEL_ANNOTATIONS
+    assert len(testonto._to_storids(label_annotations)) == 3
+    assert testonto._to_storids(None) == []
+    assert testonto._to_storids([testonto.TestClass])

tests/test_get_by_label.py

@@ -82,6 +82,23 @@ def test_get_by_label_onto(repo_dir) -> None:
         testonto.Class,
     }
 
+    # Test with label annotations given directly when creating the ontology
+    testonto2 = get_ontology(
+        "http://domain_ontology/new_ontology",
+        label_annotations=[
+            "http://www.w3.org/2004/02/skos/core#prefLabel",
+            "http://www.w3.org/2004/02/skos/core#altLabel",
+        ],
+    )
+
+    testonto2.new_annotation_property(
+        "prefLabel",
+        parent=[owlready2.AnnotationProperty],
+    )
+    testonto2.new_entity("Class", owlready2.Thing, preflabel="Klasse")
+
+    assert testonto2.get_by_label("Klasse") == testonto2.Class
+
 
 def test_get_by_label_emmo(emmo: "Ontology") -> None:
     # Loading emmo-inferred where everything is sqashed into one ontology