Add --copy-annotation option to ontoconvert (#732)

# Description
This option is needed to automatically rdfs:label annotations to classes
and properties when publishing EMMO to increase the FAIRness or the
ontology.

## Type of change
- [ ] Bug fix.
- [x] New feature.
- [ ] Documentation update.
- [ ] Test update.

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/tools/test_ontoconvert.py

@@ -39,3 +39,33 @@ 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-annotation
+    ontoconvert.main(
+        [
+            "-p",
+            "--iri=https://w3id.org/ex/testonto",
+            "--base-iri=https://w3id.org/ex/testonto#",
+            str(ontodir / "testonto.ttl"),
+            str(outdir / "test_ontoconvert3.ttl"),
+        ]
+    )
+    input3 = (ontodir / "testonto.ttl").read_text()
+    output3 = (outdir / "test_ontoconvert3.ttl").read_text()
+    assert not re.search('rdfs:label "hasAnnotationProperty"@en', input3)
+    assert re.search('rdfs:label "hasAnnotationProperty"@en', output3)
+
+    # Test 4 - copy-annotation with source as annotation label
+    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(ontodir / "testonto.ttl"),
+            str(outdir / "test_ontoconvert4.ttl"),
+        ]
+    )
+    input4 = (ontodir / "testonto.ttl").read_text()
+    output4 = (outdir / "test_ontoconvert4.ttl").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 +59,29 @@ 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-preflabel",
+        "-p",
+        action="store_true",
+        help=(
+            "Alias for: `--copy-annotation=http://www.w3.org/2004/02/skos/"
+            "core#prefLabel-->http://www.w3.org/2000/01/rdf-schema#label`"
+        ),
+    )
     parser.add_argument(
         "--no-catalog",
         "-n",
@@ -72,7 +95,7 @@ def main(argv: list = None):
         "--infer",
         "-i",
         nargs="?",
-        const="FaCT++",
+        const="HermiT",
         choices=["HermiT", "Pellet", "FaCT++"],
         metavar="NAME",
         help=(
@@ -188,6 +211,14 @@ def main(argv: list = None):
     if not output_format:
         output_format = "xml"
 
+    if args.copy_annotation is None:
+        args.copy_annotation = []
+    if args.copy_preflabel:
+        args.copy_annotation.append(
+            "http://www.w3.org/2004/02/skos/core#prefLabel-->"
+            "http://www.w3.org/2000/01/rdf-schema#label"
+        )
+
     # Perform conversion
     with warnings.catch_warnings(record=True) as warnings_handle:
         warnings.simplefilter("always")
@@ -218,6 +249,10 @@ 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,