default_annotations no longer forced in get_by_label

ontopy/excelparser.py

@@ -20,7 +20,8 @@
 import ontopy
 from ontopy import get_ontology
 from ontopy.utils import EMMOntoPyException, NoSuchLabelError
-from ontopy.utils import ReadCatalogError, read_catalog
+from ontopy.utils import ReadCatalogError
+from ontopy.utils import read_catalog, english
 from ontopy.ontology import LabelDefinitionError
 from ontopy.manchester import evaluate
 import owlready2  # pylint: disable=C0411
@@ -30,11 +31,6 @@ class ExcelError(EMMOntoPyException):
     """Raised on errors in Excel file."""
 
 
-def english(string):
-    """Returns `string` as an English location string."""
-    return owlready2.locstr(string, lang="en")
-
-
 def create_ontology_from_excel(  # pylint: disable=too-many-arguments, too-many-locals
     excelpath: str,
     concept_sheet_name: str = "Concepts",
@@ -325,6 +321,9 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
             onto.base_iri = base_iri
 
     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:
@@ -365,7 +364,6 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
             entitytype=owlready2.DataPropertyClass,
             force=force,
         )
-
     onto.sync_attributes(
         name_policy="uuid", name_prefix="EMMO_", class_docstring="elucidation"
     )

ontopy/ontology.py

@@ -6,6 +6,7 @@
 # pylint: disable=too-many-lines,fixme,arguments-differ,protected-access
 from typing import TYPE_CHECKING, Optional, Union
 import os
+import fnmatch
 import itertools
 import inspect
 import warnings
@@ -28,6 +29,7 @@
 
 from ontopy.factpluspluswrapper.sync_factpp import sync_reasoner_factpp
 from ontopy.utils import (
+    english,
     asstring,
     read_catalog,
     write_catalog,
@@ -266,7 +268,8 @@ def get_unabbreviated_triples(
             self, subject=subject, predicate=predicate, obj=obj, blank=blank
         )
 
-    def _set_label_annotations(self):
+    def set_default_label_annotations(self):
+        """Sets the default label annotations."""
         if self._label_annotations is None:
             for iri in DEFAULT_LABEL_ANNOTATIONS:
                 try:
@@ -315,8 +318,6 @@ def get_by_label(
                 f"Invalid label definition, must be a string: {label!r}"
             )
 
-        self._set_label_annotations()
-
         if colon_in_label is None:
             colon_in_label = self._colon_in_label
         if colon_in_label:
@@ -332,7 +333,7 @@ def get_by_label(
                     warnings.warn(
                         f"Prefix given both as argument ({prefix}) "
                         f"and in label ({splitlabel[0]}). "
-                        "Prefix given in argument takes presendence "
+                        "Prefix given in argument takes precedence. "
                     )
                 if not prefix:
                     prefix = splitlabel[0]
@@ -343,12 +344,13 @@ def get_by_label(
                 label_annotations=label_annotations,
                 prefix=prefix,
             )
-            if len(entitylist) > 0:
-                return entitylist[0]
+            if len(entitylist) == 1:
+                return next(iter(entitylist))
 
             raise NoSuchLabelError(
-                f"No label annotations matches {label!r} with prefix "
-                f"{prefix!r}"
+                f"Either no label annotations matches for {label!r} "
+                f"with prefix {prefix!r} or several entities have "
+                "the same label and prefix."
             )
 
         # Label is a full IRI
@@ -357,19 +359,25 @@ def get_by_label(
             return entity
 
         # First entity with matching label annotation
-        annotation_ids = (
-            (self._abbreviate(ann, False) for ann in label_annotations)
-            if label_annotations
-            else (ann.storid for ann in self.label_annotations)
-        )
+
+        if label_annotations:
+            annotation_ids = (
+                self._abbreviate(ann, False) for ann in label_annotations
+            )
+        elif self._label_annotations:
+            annotation_ids = (ann.storid for ann in self._label_annotations)
+        else:
+            annotation_ids = None
+
         get_triples = (
             self.world._get_data_triples_spod_spod
             if imported
             else self._get_data_triples_spod_spod
         )
-        for annotation_id in annotation_ids:
-            for s, _, _, _ in get_triples(None, annotation_id, label, None):
-                return self.world[self._unabbreviate(s)]
+        if annotation_ids:
+            for annotation_id in annotation_ids:
+                for s, _, _, _ in get_triples(None, annotation_id, label, None):
+                    return self.world[self._unabbreviate(s)]
 
         # Special labels
         if self._special_labels and label in self._special_labels:
@@ -398,7 +406,6 @@ def get_by_label_all(self, label, label_annotations=None, prefix=None):
         The current implementation also supports "*" as a wildcard
         matching any number of characters. This may change in the future.
         """
-        self._set_label_annotations()
 
         if not isinstance(label, str):
             raise TypeError(
@@ -409,26 +416,38 @@ def get_by_label_all(self, label, label_annotations=None, prefix=None):
                 f"Invalid label definition, {label!r} contains spaces."
             )
 
-        if label_annotations is None:
-            annotations = (_.name for _ in self.label_annotations)
-        else:
+        if label_annotations:
             annotations = (
                 _.name if hasattr(_, "storid") else _ for _ in label_annotations
             )
-        entity = self.world.search(**{next(annotations): label})
-        for key in annotations:
-            entity.extend(self.world.search(**{key: label}))
+        elif self._label_annotations:
+            annotations = (_.name for _ in self.label_annotations)
+
+        else:
+            annotations = None
+        entities = set()
+        if annotations:
+            # entity = self.world.search(**{next(annotations): label})
+            for key in annotations:
+                entities.update(self.world.search(**{key: label}))
 
         if self._special_labels and label in self._special_labels:
-            entity.append(self._special_labels[label])
+            entities.update(self._special_labels[label])
+
+        # Find existence in get_entities
+        matches = fnmatch.filter(
+            (ent.name for ent in self.get_entities()), label
+        )
 
-        entity_accessed_directly = self.world[self.base_iri + label]
-        if entity_accessed_directly and entity_accessed_directly not in entity:
-            entity.append(entity_accessed_directly)
+        entities.update(
+            ent for ent in self.get_entities() if ent.name in matches
+        )
 
         if prefix:
-            return [_ for _ in entity if _.namespace.ontology.prefix == prefix]
-        return entity
+            return set(
+                _ for _ in entities if _.namespace.ontology.prefix == prefix
+            )
+        return entities
 
     def add_label_annotation(self, iri):
         """Adds label annotation used by get_by_label().
@@ -1717,6 +1736,12 @@ def new_entity(
 
         with self:
             entity = types.new_class(name, parents)
+            # Set prefLabel to name if label_annotations is set
+            # and prefLabel is one of the annotations
+            if self.label_annotations and "prefLabel" in [
+                ann.name for ann in self.label_annotations
+            ]:
+                entity.prefLabel = english(name)
         return entity
 
     # Method that creates new ThingClass using new_entity

ontopy/utils.py

@@ -74,6 +74,11 @@ class EntityClassDefinitionError(EMMOntoPyException):
     """Error in ThingClass definition."""
 
 
+def english(string):
+    """Returns `string` as an English location string."""
+    return owlready2.locstr(string, lang="en")
+
+
 def isinteractive():
     """Returns true if we are running from an interactive interpreater,
     false otherwise."""

tests/ontopy_tests/test_new_entity.py

@@ -21,11 +21,12 @@ def test_new_entity(testonto: "Ontology") -> None:
 
     # Test that new entity is found by both version of get_by_label
     assert testonto.get_by_label("FantasyClass") == testonto.FantasyClass
-    assert testonto.get_by_label_all("FantasyClass") == [testonto.FantasyClass]
+    print(testonto.get_by_label_all("*"))
+    assert testonto.get_by_label_all("FantasyClass") == {testonto.FantasyClass}
 
     testonto.sync_attributes()
     # Test that after sync_attributes, the entity is not counted more than once
-    assert testonto.get_by_label_all("FantasyClass") == [testonto.FantasyClass]
+    assert testonto.get_by_label_all("FantasyClass") == {testonto.FantasyClass}
 
     with pytest.raises(LabelDefinitionError):
         testonto.new_entity("Fantasy Class", testonto.TestClass)

tests/ontopy_tests/test_prefix.py

@@ -9,7 +9,7 @@
 def test_prefix(testonto: "Ontology", emmo: "Ontology") -> None:
     """Test prefix in ontology"""
 
-    assert len(testonto.get_by_label_all("*")) == 6
+    assert len(testonto.get_by_label_all("*")) == 7
     assert set(testonto.get_by_label_all("*", prefix="testonto")) == set(
         [
             testonto.hasObjectProperty,

tests/test_basic.py

@@ -21,11 +21,11 @@ def test_basic(emmo: "Ontology") -> None:
 
     # Test that new entity is found by both version of get_by_label
     assert onto.get_by_label("Hydrogen") == onto.Hydrogen
-    assert onto.get_by_label_all("Hydrogen") == [onto.Hydrogen]
+    assert onto.get_by_label_all("Hydrogen") == {onto.Hydrogen}
 
     onto.sync_attributes()
     # Test that after sync_attributes, the entity is not counted more than once
-    assert onto.get_by_label_all("Hydrogen") == [onto.Hydrogen]
+    assert onto.get_by_label_all("Hydrogen") == {onto.Hydrogen}
 
     with pytest.raises(LabelDefinitionError):
         onto.new_entity("Hydr ogen", emmo.Atom)

tests/test_excelparser/test_excelparser.py

@@ -32,6 +32,7 @@ def test_excelparser(repo_dir: "Path") -> None:
         repo_dir / "tests" / "test_excelparser" / "onto_update.xlsx"
     )
     ontology, catalog, errors = create_ontology_from_excel(xlspath, force=True)
+    ontology.save("test.ttl")
     assert onto == ontology
     assert errors.keys() == {
         "already_defined",

tests/test_get_by_label.py

@@ -4,6 +4,78 @@
 from ontopy.ontology import NoSuchLabelError
 
 
+def test_get_by_label_onto() -> None:
+    """Test that label annotations are added correctly if they are not added before
+    using get_by_label
+    """
+    import owlready2
+
+    testonto = get_ontology("http://domain_ontology/new_ontology")
+    testonto.new_entity("Class", owlready2.Thing)
+    assert testonto._label_annotations == None
+    assert testonto.get_by_label("Class") == testonto.Class
+
+
+def test_get_by_label_all_onto() -> None:
+    """Test that label annotations are added correctly if they are not added before
+    using get_by_label_all
+    """
+    import owlready2
+
+    testonto = get_ontology("http://domain_ontology/new_ontology")
+    testonto.new_entity("Class", owlready2.Thing)
+    assert testonto._label_annotations == None
+    assert testonto.get_by_label_all("*") == {testonto.Class}
+    testonto.new_annotation_property(
+        "SpecialAnnotation", owlready2.AnnotationProperty
+    )
+    testonto.Class.SpecialAnnotation.append("This is a comment")
+    testonto.set_default_label_annotations()
+
+    testonto.new_entity("Klasse", testonto.Class)
+
+    assert testonto.Klasse.prefLabel == ["Klasse"]
+
+    testonto.Klasse.altLabel = "Class2"
+    assert testonto.get_by_label_all("*") == {
+        testonto.prefLabel,
+        testonto.altLabel,
+        testonto.Class,
+        testonto.SpecialAnnotation,
+        testonto.Klasse,
+    }
+    assert testonto.get_by_label_all("Class*") == {
+        testonto.Class,
+        testonto.Klasse,
+    }
+
+
+def test_get_by_label_emmo(emmo: "Ontology") -> None:
+    # Loading emmo-inferred where everything is sqashed into one ontology
+    emmo = get_ontology().load()
+    assert emmo[emmo.Atom.name] == emmo.Atom
+    assert emmo[emmo.Atom.iri] == emmo.Atom
+
+    # Load an ontology with imported sub-ontologies
+    onto = get_ontology(
+        "https://raw.githubusercontent.com/BIG-MAP/BattINFO/master/battinfo.ttl"
+    ).load()
+    assert onto.Electrolyte.prefLabel.first() == "Electrolyte"
+
+    # Check colon_in_name argument
+    onto.Atom.altLabel.append("Element:X")
+    with pytest.raises(NoSuchLabelError):
+        onto.get_by_label("Element:X")
+
+    assert onto.get_by_label("Element:X", colon_in_label=True) == onto.Atom
+
+
+import pytest
+
+from ontopy import get_ontology
+from ontopy.ontology import NoSuchLabelError
+
+
 # Loading emmo-inferred where everything is sqashed into one ontology
 emmo = get_ontology().load()
 assert emmo[emmo.Atom.name] == emmo.Atom