Update Metadata so that all metadata-items can be accessed (#845)

# Description
closes  #841 

## Type of change
<!-- Put an `x` in the box that applies. -->
- [x] Bug fix.
- [ ] New feature.
- [ ] Documentation update.
- [x] Test update.

## Checklist
<!-- Put an `x` in the boxes that apply. You can also fill these out
after creating the PR. -->

This checklist can be used as a help for the reviewer.

- [ ] Is the code easy to read and understand?
- [ ] Are comments for humans to read, not computers to disregard?
- [ ] Does a new feature has an accompanying new test (in the CI or unit
testing schemes)?
- [ ] Has the documentation been updated as necessary?
- [ ] Does this close the issue?
- [ ] Is the change limited to the issue?
- [ ] Are errors handled for all outcomes?
- [ ] Does the new feature provide new restrictions on dependencies, and
if so is this documented?

## Comments
<!-- Additional comments here, including clarifications on checklist if
applicable. -->

Author: francescalb

ontopy/ontology.py

@@ -2190,6 +2190,7 @@ def new_data_property(
             parent: parent(s) of the data property
             iri: IRI of the new data property.  If None, a new IRI will be
                 based on the ontology base IRI and the entity name.
+
         Returns:
             the new data property.
         """

ontopy/patch.py

@@ -2,15 +2,24 @@
 
 # pylint: disable=protected-access
 import types
+from typing import TYPE_CHECKING
 
 import owlready2
 from owlready2 import AnnotationPropertyClass, ThingClass, PropertyClass
 from owlready2 import Metadata, Thing, Restriction, Namespace
-from ontopy.utils import EMMOntoPyException  # pylint: disable=cyclic-import
+
+# pylint: disable=wrong-import-order
+from ontopy.utils import (  # pylint: disable=cyclic-import
+    EMMOntoPyException,
+    NoSuchLabelError,
+)
 from ontopy.ontology import (  # pylint: disable=cyclic-import
     Ontology as OntopyOntology,
 )
 
+if TYPE_CHECKING:
+    from typing import Any, Generator, Tuple
+
 
 def render_func(entity):
     """Improve default rendering of entities."""
@@ -298,30 +307,45 @@ def namespace_init(self, world_or_ontology, base_iri, name=None):
 #
 # Extending Metadata
 # ==================
-def keys(self):
+def keys(self) -> "Generator[str, None, None]":
     """Return a generator over annotation property names associated
-    with this ontology."""
+    with this ontology, i.e. metadata keys."""
+
     namespace = self.namespace
-    for annotation in namespace.annotation_properties():
-        if namespace._has_data_triple_spod(
-            s=namespace.storid, p=annotation.storid
-        ):
-            yield annotation
+    predicates = set(x[1] for x in namespace.get_triples(s=self.storid))
+    for pred in predicates:
+        try:
+            pred = namespace[namespace._unabbreviate(pred)].iri
+        except NoSuchLabelError:
+            pred = namespace._unabbreviate(pred)
 
+        yield pred
 
-def items(self):
-    """Return a generator over annotation property (name, value_list)
-    pairs associates with this ontology."""
+
+def items(self) -> "Generator[Tuple[str, Any], None, None]":
+    """Return a dict of annotation properties as (name, value_list)
+    pairs associated with this ontology, i.e. the metadata."""
     namespace = self.namespace
-    for annotation in namespace.annotation_properties():
-        if namespace._has_data_triple_spod(
-            s=namespace.storid, p=annotation.storid
-        ):
-            yield annotation, getattr(self, annotation.name)
 
+    for key in self.keys():
+        triples = namespace._get_triples_spod_spod(
+            s=self.storid, p=namespace._abbreviate(key), o=None
+        )
+
+        obj = []
+        for triple in triples:
+            if isinstance(triple[2], str):
+                obj.append(triple[2])
+            else:
+                try:
+                    obj.append(namespace[namespace._unabbreviate(triple[2])])
+                except NoSuchLabelError:
+                    obj.append(namespace._unabbreviate(triple[2]))
+        yield key, obj
 
-def has(self, name):
-    """Returns true if `name`"""
+
+def has(self, name) -> bool:
+    """Returns true if name"""
     return name in set(self.keys())
 
 
@@ -359,23 +383,33 @@ def __setattr__(self, attr, values):
 
 
 def __repr__(self):
-    result = ["Metadata("]
-    for annotation, values in self.items():
-        sep = f"\n{' ' * (len(annotation.name) + 4)}"
-        result.append(
-            f"  {annotation.name}=[{sep.join(repr(_) for _ in values)}],"
-        )
-    result.append(")")
-    return "\n".join(result)
+    return f"Metadata({dict(self.items())})"
+
+
+def _getname(iri):
+    label_startpos = iri.rfind("#") if iri.rfind("#") != -1 else iri.rfind("/")
+    return iri[label_startpos + 1 :] if label_startpos != -1 else iri
+
+
+def __metadata_getattr__(self, attr):
+    try:
+        return metadata__getattr__save(self, attr)
+    except AttributeError:
+        if attr in self.keys():
+            return dict(self.items())[attr]
+        d = {_getname(key): val for key, val in self.items()}
+        return d[attr]
 
 
 metadata__setattr__save = Metadata.__setattr__
+metadata__getattr__save = Metadata.__getattr__
 setattr(Metadata, "keys", keys)
 setattr(Metadata, "items", items)
 setattr(Metadata, "has", has)
 setattr(Metadata, "__contains__", __contains__)
 setattr(Metadata, "__iter__", __iter__)
 setattr(Metadata, "__setattr__", __setattr__)
 setattr(Metadata, "__repr__", __repr__)
+setattr(Metadata, "__getattr__", __metadata_getattr__)
 Metadata.__getitem__ = Metadata.__getattr__
 Metadata.__setitem__ = Metadata.__setattr__

tests/ontopy_tests/test_get_version.py

@@ -11,9 +11,9 @@ def test_get_version(repo_dir: "Path", testonto: "Ontology") -> None:
 
     ontopath = repo_dir / "tests" / "testonto"
     assert (
-        testonto.get_version(as_iri=True) == "http://emmo.info/testonto/0.1.0"
+        testonto.get_version(as_iri=True) == "http://emmo.info/testonto/0.2.0"
     )
-    assert testonto.get_version() == "0.1.0"
+    assert testonto.get_version() == "0.2.0"
 
     testonto_noVersionIRI = get_ontology(
         str(ontopath) + "/testonto_noVersionIRI.ttl"

tests/ontopy_tests/test_prefix.py

@@ -10,9 +10,17 @@
 def test_prefix(testonto: "Ontology", emmo: "Ontology") -> None:
     """Test prefix in ontology"""
 
-    assert len(testonto.get_by_label_all("*")) == 7
+    print(testonto.get_by_label_all("*"))
+    assert len(testonto.get_by_label_all("*")) == 14
     assert set(testonto.get_by_label_all("*", prefix="testonto")) == set(
         [
+            testonto.alternative,
+            testonto.homepage,
+            testonto.status,
+            testonto.preferredNamespacePrefix,
+            testonto.preferredNamespaceUri,
+            testonto.created,
+            testonto.hasFormat,
             testonto.hasObjectProperty,
             testonto.TestClass,
             testonto.hasAnnotationProperty,

tests/test_classes.py

@@ -44,6 +44,13 @@ def test_classes(repo_dir) -> None:
     assert set(testonto.object_properties(imported=False)) == set()
 
     assert set(testonto.annotation_properties(imported=True)) == {
+        testonto.preferredNamespaceUri,
+        testonto.alternative,
+        testonto.homepage,
+        testonto.preferredNamespacePrefix,
+        testonto.hasFormat,
+        testonto.created,
+        testonto.status,
         testonto.prefLabel,
         testonto.altLabel,
         testonto.hasAnnotationProperty,

tests/test_metadata.py

@@ -0,0 +1,61 @@
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+from pathlib import Path
+
+
+def test_metadata() -> None:
+    from pathlib import Path
+    from ontopy import get_ontology
+
+    repo_dir = Path(__file__).resolve().parent.parent
+    testonto = get_ontology(
+        str(repo_dir / "tests" / "testonto" / "testonto.ttl")
+    ).load()
+
+    expected_keys = set(
+        [
+            "http://purl.org/vocab/vann/preferredNamespacePrefix",
+            "http://purl.org/vocab/vann/preferredNamespaceUri",
+            "http://purl.org/dc/terms/created",
+            "http://purl.org/dc/terms/alternative",
+            "http://purl.org/ontology/bibo/status",
+            "http://www.w3.org/1999/02/22-rdf-syntax-ns#type",
+            "http://www.w3.org/2000/01/rdf-schema#comment",
+            "http://purl.org/dc/terms/abstract",
+            "http://purl.org/dc/terms/license",
+            "http://purl.org/dc/terms/title",
+            "http://emmo.info/testonto#EMMO_1246b120_abbe_4840_b0f8_3e4348b24a17",
+            "http://www.w3.org/2002/07/owl#versionIRI",
+            "http://www.w3.org/2002/07/owl#imports",
+            "http://purl.org/dc/terms/contributor",
+            "http://www.w3.org/2002/07/owl#versionInfo",
+            "http://purl.org/dc/terms/creator",
+            "http://purl.org/dc/terms/hasFormat",
+            "http://xmlns.com/foaf/0.1/homepage",
+        ]
+    )
+
+    # versionInfo and comment are not defined in the ontology
+    # but are still available predefined in owlready2
+    assert set(testonto.metadata.keys()) == expected_keys
+
+    items_dict = dict(testonto.metadata.items())
+
+    assert set(items_dict.keys()) == set(testonto.metadata.keys())
+
+    assert testonto.metadata["http://purl.org/dc/terms/title"] == [
+        "The test ontology (TESTONTO)"
+    ]
+    assert testonto.metadata.title == ["The test ontology (TESTONTO)"]
+
+    assert testonto.metadata.creator == [
+        "https://orcid.org/0000-0001-8869-3718",
+        "http://emmo.info/testonto#JesperFriis",
+    ]
+
+    assert testonto.metadata.versionInfo == ["0.2.0"]
+
+    assert str(testonto.metadata).startswith("Metadata({")

tests/testonto/testonto.ttl

@@ -5,12 +5,58 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix bibo: <http://purl.org/ontology/bibo/> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+@prefix vann: <http://purl.org/vocab/vann/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
 @base <http://emmo.info/testonto> .
 
 <http://emmo.info/testonto> rdf:type owl:Ontology ;
-                             owl:versionIRI <http://emmo.info/testonto/0.1.0> ;
-                             owl:imports <http://emmo.info/testonto/0.1.0/models> ;
-			     owl:versionInfo "0.1.0" .
+    owl:versionIRI <http://emmo.info/testonto/0.2.0> ;
+    owl:imports <http://emmo.info/testonto/0.1.0/models> ;
+	owl:versionInfo "0.2.0" ;
+    dcterms:abstract "This is the abstract of the testonto."@en ;
+	dcterms:alternative "Testonto_alternative"@en ;
+    dcterms:contributor :SimonClark ;
+    dcterms:created "2024-03" ;
+    dcterms:creator <https://orcid.org/0000-0001-8869-3718> ,
+                    :JesperFriis ;
+    dcterms:hasFormat <https://www.w3.org/TR/turtle/> ;
+    dcterms:license "https://creativecommons.org/licenses/by/4.0/legalcode" ;
+    dcterms:title "The test ontology (TESTONTO)"@en ;
+    bibo:status "test ontology ." ;
+    vann:preferredNamespacePrefix "testonto" ;
+    vann:preferredNamespaceUri "http://emmo.info/testonto" ;
+    rdfs:comment "This ontology contains metadata that matches the metadat of EMMOv1.0.0."@en ;
+    foaf:homepage <https://github.com/emmo-repo/EMMOntoPy> ;
+    :EMMO_1246b120_abbe_4840_b0f8_3e4348b24a17 "[email protected]" .
+
+###  http://purl.org/dc/terms/alternative
+dcterms:alternative rdf:type owl:AnnotationProperty .
+
+
+###  http://purl.org/dc/terms/created
+dcterms:created rdf:type owl:AnnotationProperty .
+
+
+###  http://purl.org/dc/terms/hasFormat
+dcterms:hasFormat rdf:type owl:AnnotationProperty .
+
+
+###  http://purl.org/ontology/bibo/status
+bibo:status rdf:type owl:AnnotationProperty .
+
+
+###  http://purl.org/vocab/vann/preferredNamespacePrefix
+vann:preferredNamespacePrefix rdf:type owl:AnnotationProperty .
+
+
+###  http://purl.org/vocab/vann/preferredNamespaceUri
+vann:preferredNamespaceUri rdf:type owl:AnnotationProperty .
+
+
+###  http://xmlns.com/foaf/0.1/homepage
+foaf:homepage rdf:type owl:AnnotationProperty .
 
 
 :testclass rdf:type owl:Class ;