Update test_unit_dimension in emmocheck to EMMO 1.0.0-beta5 (#678)

# Description
Update test_unit_dimension in emmocheck to EMMO 1.0.0-beta5.

A test for this PR is added in PR #679.

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

@@ -126,7 +126,7 @@ def test_class_label(self):
 
         for cls in self.onto.classes(self.check_imported):
             for label in cls.label + getattr(cls, "prefLabel", []):
-                if label not in exceptions:
+                if str(label) not in exceptions:
                     with self.subTest(entity=cls, label=label):
                         self.assertTrue(label.isidentifier())
                         self.assertTrue(label[0].isupper())
@@ -206,6 +206,7 @@ def test_unit_dimension(self):
                 "emmo.DerivedUnit",
                 "emmo.BaseUnit",
                 "emmo.UnitSymbol",
+                "emmo.SIAccepted",
                 "emmo.SICoherentDerivedUnit",
                 "emmo.SINonCoherentDerivedUnit",
                 "emmo.SISpecialUnit",
@@ -219,9 +220,7 @@ def test_unit_dimension(self):
         if not hasattr(self.onto, "MeasurementUnit"):
             return
         exceptions.update(self.get_config("test_unit_dimension.exceptions", ()))
-        regex = re.compile(
-            r"^(emmo|metrology).hasPhysicalDimension.some\(.*\)$"
-        )
+        regex = re.compile(r"^(emmo|metrology).hasDimensionString.value\(.*\)$")
         classes = set(self.onto.classes(self.check_imported))
         for cls in self.onto.MeasurementUnit.descendants():
             if not self.check_imported and cls not in classes:

ontopy/ontology.py

@@ -118,7 +118,7 @@ def get_ontology(
             )
         elif base_iri == "emmo-development":
             base_iri = (
-                "https://emmo-repo.github.io/versions/1.0.0-beta4/"
+                "https://emmo-repo.github.io/versions/1.0.0-beta5/"
                 "emmo-inferred.ttl"
             )
 

ontopy/patch.py

@@ -187,15 +187,18 @@ def get_indirect_is_a(self, skip_classes=True):
     """
     subclass_relations = set()
     for entity in reversed(self.mro()):
-        if hasattr(entity, "is_a"):
-            if skip_classes:
-                subclass_relations.update(
-                    _
-                    for _ in entity.is_a
-                    if not isinstance(_, owlready2.ThingClass)
-                )
-            else:
-                subclass_relations.update(entity.is_a)
+        for attr in "is_a", "equivalent_to":
+            if hasattr(entity, attr):
+                lst = getattr(entity, attr)
+                if skip_classes:
+                    subclass_relations.update(
+                        r
+                        for r in lst
+                        if not isinstance(r, owlready2.ThingClass)
+                    )
+                else:
+                    subclass_relations.update(lst)
+
     subclass_relations.update(self.is_a)
     return subclass_relations
 

tests/ontopy_tests/test_patch.py

@@ -1,11 +1,11 @@
 """Tests Owlready2 patches implemented in ontopy/patch.py
 
 """
+import re
 
 import pytest
 
 from ontopy import get_ontology
-
 from owlready2 import owl, Inverse
 
 from utilities import setassert
@@ -87,6 +87,25 @@ def test_get_by_label_onto(emmo: "Ontology") -> None:
     )  # Check that wikipediaReference can be acceses as attribute
 
 
+def test_get_indirect_is_a() -> None:
+    import re
+    from ontopy import get_ontology
+
+    emmo = get_ontology("emmo-development").load()
+    assert any(
+        re.match("^emmo.*\.hasDimensionString.value(.*)$", str(e))
+        for e in emmo.MicroPascal.get_indirect_is_a()
+    )
+    assert all(
+        re.match("^emmo.*\.Item$", str(e)) is None
+        for e in emmo.MicroPascal.get_indirect_is_a()
+    )
+    assert any(
+        re.match("^emmo.*\.Item$", str(e))
+        for e in emmo.MicroPascal.get_indirect_is_a(skip_classes=False)
+    )
+
+
 # TODO: Fix disjoint_with().
 # It seems not to take into account disjoint unions.
 # assert set(emmo.Collection.disjoint_with()) == {emmo.Item}

tests/test_emmocheck_module.py

@@ -1,11 +1,13 @@
 from emmopy.emmocheck import main
 
 
-main(
+status = main(
     argv=[
         "--url-from-catalog",
         "--check-imported",
         # Test against a specific commit of EMMO 1.0.0-beta5
-        "https://raw.githubusercontent.com/emmo-repo/EMMO/3b93e2c9c45ab8d9882d2d6385276ff905095798/emmo.ttl",
+        "https://raw.githubusercontent.com/emmo-repo/EMMO/f282769978af9fda7e1c55d1adeeb0ef9e24fc48/emmo.ttl",
     ]
 )
+
+assert status == 0

tools/ontoconvert

@@ -203,6 +203,7 @@ def main(argv: list = None):
                 include_imported=include_imported,
                 debug=verbose,
             )
+
         onto.save(
             args.output,
             format=output_format,