Added test for descriptions (#766)

# Description
Added test for that entities should be described. We require that a
entities should have at least a *elucidation*, *definition* or
*conceptualisation*. In addition we require that each of them can max be
provided once.

Also update ontoconvert to include conceptualisations the
`--copy-emmo-annotations` option.

Tested against EMMO during development, but no additional EMMO-dependent
test has been added to the EMMOntoPy repo.

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

---------

Co-authored-by: Francesca L. Bleken <[email protected]>

emmopy/emmocheck.py

@@ -185,6 +185,91 @@ def test_object_property_label(self):
 class TestFunctionalEMMOConventions(TestEMMOConventions):
     """Test functional EMMO conventions."""
 
+    def test_description(self):
+        """Check that all entities have a description.
+
+        A description is either an emmo:elucidation, an
+        emmo:definition or an emmo:conceptualisation.
+
+        Exceptions include entities from standard w3c vocabularies.
+
+        """
+        exceptions = set()
+        exceptions.update(self.get_config("test_description.exceptions", ()))
+        props = self.onto.world._props  # pylint: disable=protected-access
+        if (
+            "EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9" not in props
+            or "EMMO_31252f35_c767_4b97_a877_1235076c3e13" not in props
+            or "EMMO_70fe84ff_99b6_4206_a9fc_9a8931836d84" not in props
+        ):
+            self.fail(
+                "ontology has no description (emmo:elucidation, "
+                "emmo:definition or emmo:conceptualisation)"
+            )
+        for entity in self.onto.classes(self.check_imported):
+
+            # Skip concepts from exceptions and common w3c vocabularies
+            vocabs = "owl.", "0.1.", "bibo.", "core.", "terms.", "vann."
+            r = repr(entity)
+            if r in exceptions or any(r.startswith(v) for v in vocabs):
+                continue
+
+            label = str(get_label(entity))
+            with self.subTest(entity=entity, label=label):
+                self.assertTrue(
+                    hasattr(entity, "elucidation"),
+                    msg=f"{label} has no emmo:elucidation",
+                )
+                self.assertTrue(
+                    hasattr(entity, "definition"),
+                    msg=f"{label} has no emmo:definition",
+                )
+                self.assertTrue(
+                    hasattr(entity, "conceptualisation"),
+                    msg=f"{label} has no emmo:conceptualisation",
+                )
+                self.assertTrue(
+                    len(entity.elucidation)
+                    + len(entity.definition)
+                    + len(entity.conceptualisation)
+                    >= 1,
+                    msg="missing description (emmo:elucidation, "
+                    f"emmo:deinition and/or emmo:conceptualidation): {label}",
+                )
+                self.assertTrue(
+                    len(
+                        [
+                            s
+                            for s in entity.elucidation
+                            if not hasattr(s, "lang") or s.lang == "en"
+                        ]
+                    )
+                    < 2,
+                    msg=f"more than one emmo:elucidation for {label}",
+                )
+                self.assertTrue(
+                    len(
+                        [
+                            s
+                            for s in entity.definition
+                            if not hasattr(s, "lang") or s.lang == "en"
+                        ]
+                    )
+                    < 2,
+                    msg=f"more than one emmo:definition for {label}",
+                )
+                self.assertTrue(
+                    len(
+                        [
+                            s
+                            for s in entity.conceptualisation
+                            if not hasattr(s, "lang") or s.lang == "en"
+                        ]
+                    )
+                    < 2,
+                    msg=f"more than one emmo:conceptualisation for {label}",
+                )
+
     def test_unit_dimension(self):
         """Check that all measurement units have a physical dimension.
 

ontopy/utils.py

@@ -888,8 +888,11 @@ def copy_annotation(onto, src, dst):
     """
     if onto.world[src]:
         src = onto.world[src]
-    else:
+    elif src in onto:
         src = onto[src]
+    else:
+        warnings.warn(f"no such annotation: '{src}' Skip copy annotation...")
+        return
 
     if onto.world[dst]:
         dst = onto.world[dst]

tests/tools/test_emmocheck.py

@@ -15,4 +15,9 @@ def test_run() -> None:
     test_file = ontodir / "models.ttl"
     emmocheck = get_tool_module("emmocheck")
 
+    # The main() method will raise an exception on error, so it is
+    # sufficient to just call it here
+
+    emmocheck.main(["--skip=test_description", str(test_file)])
+
     emmocheck.main([str(test_file)])

tools/ontoconvert

@@ -244,6 +244,8 @@ def main(argv: list = None):
                 "-->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",
+                "conceptualisation"
+                "-->http://www.w3.org/2000/01/rdf-schema#comment",
                 "comment-->http://www.w3.org/2000/01/rdf-schema#comment",
             ]
         )