Update to comply with owlready2>0.41 (#639)

* Update to comply with owlready2>0.41 which returns a owlready2.locstr
instead of str


* Updated excelparser to use emmo1.0.0-beta4, patch and excelparser OK.

* _getattr monkey patch so that ThingClass annotations can be directly accessed.

* Added some get_by_albel_tests that codecov is complaining about.

* Added wu-palmer test in test_generations

ontopy/excelparser.py

@@ -319,12 +319,10 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
         # Set given or default base_iri if base_iri_from_metadata is False.
         if not base_iri_from_metadata:
             onto.base_iri = base_iri
-
-    onto.sync_python_names()
+    # onto.sync_python_names()
     # prefLabel, label, and altLabel
     # are default label annotations
     onto.set_default_label_annotations()
-
     # Add object properties
     if objectproperties is not None:
         objectproperties = _clean_dataframe(objectproperties)
@@ -367,7 +365,6 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     onto.sync_attributes(
         name_policy="uuid", name_prefix="EMMO_", class_docstring="elucidation"
     )
-
     # Clean up data frame with new concepts
     data = _clean_dataframe(data)
     # Add entities
@@ -562,7 +559,6 @@ def get_metadata_from_dataframe(  # pylint: disable=too-many-locals,too-many-bra
             )
         except AttributeError:
             pass
-
     return onto, catalog
 
 

ontopy/graph.py

@@ -720,11 +720,11 @@ def _relation_styles(
         """
         for relation in entity.mro():
             if relation in rels:
-                if get_label(relation) in relations:
-                    rattrs = relations[get_label(relation)]
+                if str(get_label(relation)) in relations:
+                    rattrs = relations[str(get_label(relation))]
                 else:
                     for alt_label in relation.get_annotations()["altLabel"]:
-                        rattrs = relations[alt_label]
+                        rattrs = relations[str(alt_label)]
 
                 break
         else:

ontopy/ontology.py

@@ -904,7 +904,6 @@ def save(
             )
 
         revmap = {value: key for key, value in FMAP.items()}
-
         if filename is None:
             if format:
                 fmt = revmap.get(format, format)

ontopy/patch.py

@@ -6,6 +6,7 @@
 from owlready2 import AnnotationPropertyClass, ThingClass, PropertyClass
 from owlready2 import Metadata, Thing, Restriction, Namespace
 from ontopy.utils import EMMOntoPyException
+from ontopy.ontology import Ontology as OntopyOntology
 
 
 def render_func(entity):
@@ -27,6 +28,10 @@ def render_func(entity):
 #
 # Extending ThingClass (classes)
 # ==============================
+
+save_getattr = ThingClass.__getattr__
+
+
 def get_preferred_label(self):
     """Returns the preferred label as a string (not list).
 
@@ -69,7 +74,7 @@ def get_parents(self, strict=False):
 def _dir(self):
     """Extend dir() listing of ontology classes."""
     set_dir = set(object.__dir__(self))
-    props = self.namespace.world._props.keys()
+    props = [str(key) for key in self.namespace.world._props.keys()]
     set_dir.update(props)
     return sorted(set_dir)
 
@@ -91,14 +96,16 @@ def _setitem(self, name, value):
 
     Example:
     >>> from emmopy import get_emmo
+    >>> from owlready2 import locstr
     >>> emmo = get_emmo()
     >>> emmo.Atom['altLabel']
-    ['ChemicalElement']
+    [locstr('ChemicalElement', 'en')]
     >>> emmo.Atom['altLabel'] = 'Element'
+    >>> emmo.Atom['altLabel'] = locstr('Atomo', 'it')
     >>> emmo.Atom['altLabel']
-    ['ChemicalElement', 'Element']
-
+    [locstr('ChemicalElement', 'en'), 'Element', locstr('Atomo', 'it')]
     """
+
     item = _getitem(self, name)
     item.append(value)
 
@@ -112,6 +119,24 @@ def _delitem(self, name):
     item.clear()
 
 
+def _getattr(self, name):
+    """Provide attribute access to annotation properties.
+
+    This upates __getattr__ in owlready2. If name is not found as
+    attribute it tries using the iriname of the annotation property.
+    """
+    try:
+        return save_getattr(self, name)
+    except AttributeError as err:
+        # make sure we are using and ontopy Ontology which has get_by_label
+        if isinstance(self.namespace.ontology, OntopyOntology):
+            entity = self.namespace.ontology.get_by_label(name)
+            # add annotation property to world._props for faster access later
+            self.namespace.world._props[name] = entity
+            return save_getattr(self, entity.name)
+        raise err
+
+
 def get_annotations(
     self, all=False, imported=True
 ):  # pylint: disable=redefined-builtin
@@ -125,7 +150,7 @@ def get_annotations(
     onto = self.namespace.ontology
 
     annotations = {
-        get_preferred_label(_): _._get_values_for_class(self)
+        str(get_preferred_label(_)): _._get_values_for_class(self)
         for _ in onto.annotation_properties(imported=imported)
     }
     if all:
@@ -197,6 +222,7 @@ def get_indirect_is_a(self, skip_classes=True):
 setattr(ThingClass, "__getitem__", _getitem)
 setattr(ThingClass, "__setitem__", _setitem)
 setattr(ThingClass, "__delitem__", _delitem)
+setattr(ThingClass, "__getattr__", _getattr)
 setattr(ThingClass, "get_preferred_label", get_preferred_label)
 setattr(ThingClass, "get_parents", get_parents)
 setattr(ThingClass, "get_annotations", get_annotations)
@@ -252,7 +278,7 @@ def namespace_init(self, world_or_ontology, base_iri, name=None):
 # Extending Metadata
 # ==================
 def keys(self):
-    """Return a generator over annotation property names associates
+    """Return a generator over annotation property names associated
     with this ontology."""
     namespace = self.namespace
     for annotation in namespace.annotation_properties():

requirements.txt

@@ -4,7 +4,7 @@ defusedxml>=0.7.1,<1
 graphviz>=0.16,<0.21
 numpy>=1.19.5,<2
 openpyxl>=3.0.9,<3.2
-Owlready2>=0.28,!=0.32,!=0.34,<0.42
+Owlready2>=0.28,!=0.32,!=0.34,<0.44
 packaging>=21.0,<24
 pandas>=1.2,<2.1
 Pygments>=2.7.4,<3

tests/conftest.py

@@ -6,6 +6,11 @@
 
 if TYPE_CHECKING:
     from ontopy.ontology import Ontology
+    from typing import Sequence
+import sys, os
+
+# Add test-specific utilities to path
+sys.path.append(os.path.join(os.path.dirname(__file__), "utilities"))
 
 
 @pytest.fixture(scope="session")
@@ -16,7 +21,14 @@ def repo_dir() -> Path:
 
 @pytest.fixture
 def emmo() -> "Ontology":
-    """Load and return EMMO."""
+    """Load and return EMMO.
+
+    Note that this loads the version of EMMO that is
+    the current defailt in ontopy.
+
+    When updating the defeault EMMO for ontopy,
+    tests might need to be updated.
+    """
     from emmopy import get_emmo
 
     emmo = get_emmo()

tests/ontopy_tests/conftest.py

@@ -5,43 +5,3 @@
 
 # Files to skip
 collect_ignore = ["interactive_test.py"]
-
-
-# Utilities
-def abbreviate(onto, iri, must_exist=True):
-    """Returns existing Owlready2 storid for `iri`."""
-    if iri is None:
-        return None
-    abbreviater = getattr(onto, "_abbreviate")
-    storid = abbreviater(iri, create_if_missing=False)
-    if storid is None and must_exist:
-        raise ValueError(f"no such IRI in ontology: {iri}")
-    return storid
-
-
-def get_triples(onto, s=None, p=None, o=None) -> list:
-    """Returns a list of triples matching spo."""
-    return [
-        (
-            onto._unabbreviate(s_) if isinstance(s_, int) and s_ > 0 else s_,
-            onto._unabbreviate(p_) if isinstance(p_, int) and p_ > 0 else p_,
-            onto._unabbreviate(o_) if isinstance(o_, int) and o_ > 0 else o_,
-        )
-        for s_, p_, o_, d in onto._get_triples_spod_spod(
-            abbreviate(onto, s),
-            abbreviate(onto, p),
-            abbreviate(onto, o, False) or o,
-            None,
-        )
-    ]
-
-
-def has_triple(onto, s=None, p=None, o=None) -> bool:
-    """Returns true if ontology `onto` contains the given triple.
-
-    None may be used as a wildcard for of `s`, `p` or `o`.
-    """
-    try:
-        return bool(get_triples(onto, s, p, o))
-    except ValueError:
-        return False

tests/ontopy_tests/test_patch.py

@@ -1,48 +1,91 @@
 """Tests Owlready2 patches implemented in ontopy/patch.py
 
-Implemented as a script, such that it easy to understand and use for debugging.
 """
+
 import pytest
 
 from ontopy import get_ontology
 
 from owlready2 import owl, Inverse
 
+from utilities import setassert
+
+
+def test_get_by_label_onto(emmo: "Ontology") -> None:
+    # Test some ThingClass extensions implemented in patch.py
+    assert str(emmo.Atom.get_preferred_label()) == "Atom"
+
+    assert emmo.Atom.get_parents() == {emmo.MolecularEntity}
+
+    setassert(
+        emmo.Atom.get_annotations().keys(),
+        {
+            "prefLabel",
+            "altLabel",
+            "elucidation",
+            "comment",
+        },
+    )
+    setassert(
+        emmo.Atom.get_annotations(all=True).keys(),
+        {
+            "qualifiedCardinality",
+            "minQualifiedCardinality",
+            "prefLabel",
+            "abstract",
+            "hiddenLabel",
+            "etymology",
+            "altLabel",
+            "example",
+            "elucidation",
+            "OWLDLRestrictedAxiom",
+            "wikipediaReference",
+            "conceptualisation",
+            "logo",
+            "comment",
+            "dbpediaReference",
+            "definition",
+            "VIMTerm",
+            "creator",
+            "iupacReference",
+            "contact",
+            "omReference",
+            "ISO9000Reference",
+            "ISO80000Reference",
+            "qudtReference",
+            "contributor",
+            "license",
+            "ISO14040Reference",
+            "figure",
+            "title",
+            "publisher",
+        },
+    )
+
+    # Test item access/assignment/deletion for classes
+    setassert(emmo.Atom["altLabel"], {"ChemicalElement"})
+
+    with pytest.raises(KeyError):
+        emmo.Atom["hasPart"]
+
+    emmo.Atom["altLabel"] = "Element"
+    setassert(emmo.Atom["altLabel"], {"ChemicalElement", "Element"})
+
+    del emmo.Atom["altLabel"]
+    assert emmo.Atom["altLabel"] == []
+
+    emmo.Atom.altLabel = "ChemicalElement"
+    assert emmo.Atom["altLabel"] == ["ChemicalElement"]
+
+    assert emmo.Atom.is_defined == False
+    assert emmo.Holistic.is_defined == True
+    assert (
+        emmo.wikipediaReference
+    )  # Check that wikipediaReference is in ontology
+    assert (
+        emmo.Atom.wikipediaReference == []
+    )  # Check that wikipediaReference can be acceses as attribute
 
-emmo = get_ontology().load()
-
-
-# Test some ThingClass extensions implemented in patch.py
-assert emmo.Atom.get_preferred_label() == "Atom"
-
-assert emmo.Atom.get_parents() == {emmo.MolecularEntity}
-
-assert set(emmo.Atom.get_annotations().keys()) == {
-    "prefLabel",
-    "altLabel",
-    "elucidation",
-    "comment",
-}
-
-
-# Test item access/assignment/deletion for classes
-assert set(emmo.Atom["altLabel"]) == {"ChemicalElement"}
-
-with pytest.raises(KeyError):
-    emmo.Atom["hasPart"]
-
-emmo.Atom["altLabel"] = "Element"
-assert set(emmo.Atom["altLabel"]) == {"ChemicalElement", "Element"}
-
-del emmo.Atom["altLabel"]
-assert emmo.Atom["altLabel"] == []
-
-emmo.Atom["altLabel"] = "ChemicalElement"
-assert emmo.Atom["altLabel"] == ["ChemicalElement"]
-
-
-assert emmo.Atom.is_defined == False
-assert emmo.Holistic.is_defined == True
 
 # TODO: Fix disjoint_with().
 # It seems not to take into account disjoint unions.

tests/ontopy_tests/test_prefix.py

@@ -1,6 +1,7 @@
 from typing import TYPE_CHECKING
 import pytest
 from ontopy.utils import NoSuchLabelError
+import warnings
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -37,6 +38,12 @@ def test_prefix(testonto: "Ontology", emmo: "Ontology") -> None:
         "TestClass", prefix="models"
     )
 
+    with pytest.raises(ValueError):
+        testonto.get_by_label_all(" ")
+
+    with pytest.raises(TypeError):
+        testonto.get_by_label(1)
+
 
 def test_prefix_emmo(emmo: "Ontology") -> None:
     """Test prefix in ontology"""

tests/ontopy_tests/test_utils.py

@@ -1,5 +1,5 @@
 import ontopy.utils as utils
-from testutils import get_triples, has_triple
+from utilities import get_triples, has_triple
 
 
 def test_annotate_source(testonto: "Ontology"):

tests/test_dir.py

@@ -2,7 +2,6 @@
 
 from ontopy import get_ontology
 
-
 thisdir = Path(__file__).resolve().parent
 
 onto = get_ontology(