Merge branch 'ci/dependabot-updates' into dependabot/pip/ci/dependabot-updates/pytest-cov-approx-eq-5.0

Author: francescalb

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
   - id: check-symlinks
   - id: check-xml
@@ -17,7 +17,7 @@ repos:
     args: [--markdown-linebreak-ext=md]
 
 - repo: https://github.com/ambv/black
-  rev: 24.2.0
+  rev: 24.3.0
   hooks:
   - id: black
     name: Blacken

emmopy/emmocheck.py

@@ -73,17 +73,30 @@ def test_number_of_labels(self):
         """
         exceptions = set(
             (
-                "terms.license",
+                "0.1.homepage",  # foaf:homepage
+                "0.1.logo",
+                "0.1.page",
+                "0.1.name",
+                "bibo:doi",
+                "core.altLabel",
+                "core.hiddenLabel",
+                "core.prefLabel",
                 "terms.abstract",
+                "terms.alternative",
+                "terms:bibliographicCitation",
                 "terms.contributor",
+                "terms.created",
                 "terms.creator",
+                "terms.hasFormat",
+                "terms.identifier",
+                "terms.issued",
+                "terms.license",
+                "terms.modified",
                 "terms.publisher",
+                "terms.source",
                 "terms.title",
-                "core.prefLabel",
-                "core.altLabel",
-                "core.hiddenLabel",
-                "foaf.logo",
-                "0.1.logo",  # foaf.logo
+                "vann:preferredNamespacePrefix",
+                "vann:preferredNamespaceUri",
             )
         )
         exceptions.update(

ontopy/ontology.py

@@ -1004,15 +1004,19 @@ def save(
             # Make a copy of the owlready2 graph object to not mess with
             # owlready2 internals
             graph = rdflib.Graph()
-            graph_owlready2 = self.world.as_rdflib_graph()
-            for triple in graph_owlready2.triples((None, None, None)):
+            for triple in self.world.as_rdflib_graph():
                 graph.add(triple)
 
-            # Add namespaces
-            graph.namespace_manager.bind("", rdflib.Namespace(self.base_iri))
-            graph.namespace_manager.bind(
-                "swrl", rdflib.Namespace("http://www.w3.org/2003/11/swrl#")
-            )
+            # Add common namespaces unknown to rdflib
+            extra_namespaces = [
+                ("", self.base_iri),
+                ("swrl", "http://www.w3.org/2003/11/swrl#"),
+                ("bibo", "http://purl.org/ontology/bibo/"),
+            ]
+            for prefix, iri in extra_namespaces:
+                graph.namespace_manager.bind(
+                    prefix, rdflib.Namespace(iri), override=False
+                )
 
             # Remove all ontology-declarations in the graph that are
             # not the current ontology.

ontopy/utils.py

@@ -835,3 +835,38 @@ def recur(o):
                     )
 
     return layout
+
+
+def copy_annotation(onto, src, dst):
+    """In all classes and properties in `onto`, copy annotation `src` to `dst`.
+
+    Arguments:
+        onto: Ontology to work on.
+        src: Name of source annotation.
+        dst: Name or IRI of destination annotation.  Use IRI if the
+            destination annotation is not already in the ontology.
+    """
+    if onto.world[src]:
+        src = onto.world[src]
+    else:
+        src = onto[src]
+
+    if onto.world[dst]:
+        dst = onto.world[dst]
+    elif dst in onto:
+        dst = onto[dst]
+    else:
+        if "://" not in dst:
+            raise ValueError(
+                "new destination annotation property must be provided as "
+                "a full IRI"
+            )
+        name = min(dst.rsplit("#")[-1], dst.rsplit("/")[-1], key=len)
+        iri = dst
+        dst = onto.new_annotation_property(name, owlready2.AnnotationProperty)
+        dst.iri = iri
+
+    for e in onto.get_entities():
+        new = getattr(e, src.name).first()
+        if new and new not in getattr(e, dst.name):
+            getattr(e, dst.name).append(new)

tests/test_get_by_label.py

@@ -109,8 +109,11 @@ def test_get_by_label_emmo(emmo: "Ontology") -> None:
     assert emmo[emmo.Atom.iri] == emmo.Atom
 
     # Load an ontology with imported sub-ontologies
+    # Note that this test also includes testing of loading
+    # ontology with catalog file directly from the web
+    # It is therefore not duplicated in test_load.
     onto = get_ontology(
-        "https://raw.githubusercontent.com/BIG-MAP/BattINFO/master/battinfo.ttl"
+        "https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl"
     ).load()
     assert onto.Electrolyte.prefLabel.en.first() == "Electrolyte"
 

tests/test_load.py

@@ -35,11 +35,8 @@ def test_load(repo_dir: "Path", testonto: "Ontology") -> None:
     assert str(testonto.TestClass.prefLabel.first()) == "TestClass"
 
     # Use catalog file when downloading from web
-    onto = get_ontology(
-        "https://raw.githubusercontent.com/BIG-MAP/BattINFO/master/"
-        "battinfo.ttl"
-    ).load()
-    assert str(onto.Electrolyte.prefLabel.first()) == "Electrolyte"
+    # This is tested in test_get_by_label in which some additional tests
+    # are performed on labels.
 
     with pytest.raises(
         EMMOntoPyException,

tests/testonto/domainonto.ttl

@@ -0,0 +1,51 @@
+@prefix : <https://w3id.org/emmo/domain-onto#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@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 dcterms: <http://purl.org/dc/terms/> .
+@prefix emmo: <https://www.w3.org/emmo#> .
+
+
+<https://w3id/org/emmo/domain-onto> rdf:type owl:Ontology ;
+    owl:versionIRI <https://w3id/org/emmo/domain-onto/0.1.0> ;
+    owl:versionInfo "0.1.0" ;
+    dcterms:abstract "Test for an EMMO-based domain ontolgoy."@en .
+
+
+:testclass rdf:type owl:Class ;
+    rdfs:subClassOf owl:Thing ;
+    skos:prefLabel "TestClass"@en ;
+    emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "A test class."@en .
+
+:testobjectproperty rdf:type owl:ObjectProperty ;
+    rdfs:domain :testclass ;
+    rdfs:range :testclass ;
+    skos:prefLabel "hasObjectProperty"@en .
+
+:testannotationproperty rdf:type owl:AnnotationProperty ;
+    rdfs:domain :testclass ;
+    rdfs:range rdfs:Literal ;
+    skos:prefLabel "hasAnnotationProperty"@en .
+
+:testdatatypeproperty rdf:type owl:DatatypeProperty ;
+    rdfs:domain :testclass ;
+    rdfs:range xsd:string ;
+    skos:prefLabel "hasDataProperty"@en .
+
+
+# Declare skos:prefLabel, emmo:elucidation and emmo:definition here
+# since we are not importing these ontologies
+emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 a owl:AnnotationProperty ;
+    rdfs:subPropertyOf rdfs:comment ;
+    skos:prefLabel "elucidation"@en ;
+    rdfs:comment "Short enlightening explanation aimed to facilitate the user in drawing the connection (interpretation) between a OWL entity and the real world object(s) for which it stands."@en .
+
+:EMMO_70fe84ff_99b6_4206_a9fc_9a8931836d84 a owl:AnnotationProperty ;
+    rdfs:subPropertyOf rdfs:comment ;
+    skos:prefLabel "definition"@en ;
+    rdfs:comment "Precise and univocal description of an ontological entity in the framework of an axiomatic system."@en .
+
+skos:prefLabel a owl:AnnotationProperty .

tests/tools/test_ontoconvert.py

@@ -39,3 +39,39 @@ def test_run() -> None:
     assert re.search("@prefix : <https://w3id.org/ex/testonto#>", output2)
     assert re.search("<https://w3id.org/ex/testonto> .* owl:Ontology", output2)
     assert re.search("testclass .* owl:Class", output2)
+
+    # Test 3 - copy-emmo-annotations
+    infile3 = ontodir / "domainonto.ttl"
+    outfile3 = outdir / "test_ontoconvert3.ttl"
+    ontoconvert.main(
+        [
+            "--copy-emmo-annotations",
+            "--iri=https://w3id.org/ex/testonto",
+            "--base-iri=https://w3id.org/ex/testonto#",
+            str(infile3),
+            str(outfile3),
+        ]
+    )
+    input3 = infile3.read_text()
+    output3 = outfile3.read_text()
+    assert 'rdfs:label "hasAnnotationProperty"@en' not in input3
+    assert 'rdfs:label "hasAnnotationProperty"@en' in output3
+    assert 'rdfs:comment "A test class."@en' not in input3
+    assert 'rdfs:comment "A test class."@en' in output3
+
+    # Test 4 - copy-annotation with source as annotation label
+    infile4 = ontodir / "testonto.ttl"
+    outfile4 = outdir / "test_ontoconvert3.ttl"
+    ontoconvert.main(
+        [
+            "-c prefLabel-->http://www.w3.org/2004/02/skos/core#hiddenLabel",
+            "--iri=https://w3id.org/ex/testonto",
+            "--base-iri=https://w3id.org/ex/testonto#",
+            str(infile4),
+            str(outfile4),
+        ]
+    )
+    input4 = infile4.read_text()
+    output4 = outfile4.read_text()
+    assert not re.search('skos:hiddenLabel "hasAnnotationProperty"@en', input4)
+    assert re.search('skos:hiddenLabel "hasAnnotationProperty"@en', output4)

tools/ontoconvert

@@ -7,7 +7,7 @@ import warnings
 from rdflib.util import guess_format
 
 from ontopy import get_ontology
-from ontopy.utils import annotate_source, rename_iris
+from ontopy.utils import annotate_source, rename_iris, copy_annotation
 
 
 def main(argv: list = None):
@@ -59,6 +59,36 @@ def main(argv: list = None):
             "The default is to append to it."
         ),
     )
+    parser.add_argument(
+        "--copy-annotation",
+        "-c",
+        action="append",
+        default=[],
+        metavar="FROM-->TO",
+        help=(
+            "Copy annotation FROM to annotation TO in each class and "
+            "property in the ontology.  FROM and TO may be given as "
+            "full IRIs or (if they already exists as annotations in the "
+            "ontology) as entity names.  "
+            "This option be given multiple times."
+        ),
+    )
+    parser.add_argument(
+        "--copy-emmo-annotations",
+        "-e",
+        action="store_true",
+        help=(
+            "Make a copy of EMMO annotations to plain RDFS for increased "
+            "interoperability. "
+            "Alias for: `--copy-annotation="
+            "http://www.w3.org/2004/02/skos/core#prefLabel"
+            "-->http://www.w3.org/2000/01/rdf-schema#label "
+            "--copy-annotation=elucidation"
+            "-->http://www.w3.org/2000/01/rdf-schema#comment`"
+            "--copy-annotation=definition"
+            "-->http://www.w3.org/2000/01/rdf-schema#comment`"
+        ),
+    )
     parser.add_argument(
         "--no-catalog",
         "-n",
@@ -72,7 +102,7 @@ def main(argv: list = None):
         "--infer",
         "-i",
         nargs="?",
-        const="FaCT++",
+        const="HermiT",
         choices=["HermiT", "Pellet", "FaCT++"],
         metavar="NAME",
         help=(
@@ -188,6 +218,17 @@ def main(argv: list = None):
     if not output_format:
         output_format = "xml"
 
+    # Annotations to copy with --copy-emmo-annotations
+    if args.copy_emmo_annotations:
+        args.copy_annotation.extend(
+            [
+                "http://www.w3.org/2004/02/skos/core#prefLabel"
+                "-->http://www.w3.org/2000/01/rdf-schema#label",
+                "elucidation-->http://www.w3.org/2000/01/rdf-schema#comment",
+                "definition-->http://www.w3.org/2000/01/rdf-schema#comment",
+            ]
+        )
+
     # Perform conversion
     with warnings.catch_warnings(record=True) as warnings_handle:
         warnings.simplefilter("always")
@@ -218,6 +259,10 @@ def main(argv: list = None):
                 debug=verbose,
             )
 
+        for cpy in args.copy_annotation:
+            src, dst = cpy.split("-->", 1)
+            copy_annotation(onto, src.strip(), dst.strip())
+
         onto.save(
             args.output,
             format=output_format,