New concepts allowed even if name alrady exists in imported ontologies

ontopy/excelparser.py

@@ -82,12 +82,12 @@ def create_ontology_from_excel(  # pylint: disable=too-many-arguments
               following keys:
 
                 - "already_defined": These are concepts that are already in the
-                    ontology, either because they were already added in a
+                    ontology, because they were already added in a
                     previous line of the excelfile/pandas dataframe, or because
-                    it is already defined in the imported ontologies.
+                    it is already defined in an imported ontology with the same
+                    base_iri as the newly created ontology.
                 - "in_imported_ontologies": Concepts that are defined in the
                     excel, but already exist in the imported ontologies.
-                    This is a subset of the 'already_defined'.
                 - "wrongly_defined": Concepts that are given an invalid
                     prefLabel (e.g. with a space in the name).
                 - "missing_parents": Concepts that are missing parents.
@@ -170,10 +170,6 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     onto, catalog = get_metadata_from_dataframe(
         metadata, base_iri, imports=imports
     )
-    # Get a set of imported concepts
-    imported_concepts = {
-        concept.prefLabel.first() for concept in onto.get_entities()
-    }
 
     # Set given or default base_iri if base_iri_from_metadata is False.
     if not base_iri_from_metadata:
@@ -206,20 +202,18 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
                 name = row["prefLabel"]
                 try:
                     onto.get_by_label(name)
-                    if not force:
-                        raise ExcelError(
-                            f'Concept "{name}" already in ontology'
+                    if onto.world[onto.base_iri + name]:
+                        if not force:
+                            raise ExcelError(
+                                f'Concept "{name}" already in ontology'
+                            )
+                        warnings.warn(
+                            f'Ignoring concept "{name}" since it is already in '
+                            "the ontology."
                         )
-                    warnings.warn(
-                        f'Ignoring concept "{name}" since it is already in '
-                        "the ontology."
-                    )
-                    concepts_with_errors["already_defined"].append(name)
-                    # What to do if we want to add info to this concept?
-                    # Should that be not allowed?
-                    # If it should be allowed the index has to be added to
-                    # added_rows
-                    continue
+                        concepts_with_errors["already_defined"].append(name)
+                        continue
+                    concepts_with_errors["in_imported_ontologies"].append(name)
                 except (ValueError, TypeError) as err:
                     warnings.warn(
                         f'Ignoring concept "{name}". '
@@ -389,9 +383,6 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     concepts_with_errors = {
         key: set(value) for key, value in concepts_with_errors.items()
     }
-    concepts_with_errors["in_imported_ontologies"] = concepts_with_errors[
-        "already_defined"
-    ].intersection(imported_concepts)
 
     return onto, catalog, concepts_with_errors
 

tests/test_excelparser/fromexcelonto.ttl

@@ -77,7 +77,7 @@
     rdfs:comment "Used for our own special purpose"@en ;
     rdfs:subClassOf [ a owl:Restriction ;
             owl:onProperty emmo:EMMO_17e27c22_37e1_468c_9dd7_95e137f73e7f ;
-            owl:someValuesFrom emmo:EMMO_eb77076b_a104_42ac_a065_798b2d2809ad ],
+            owl:someValuesFrom :EMMO_8b758694-7dd3-547a-8589-a835c15a0fb2 ],
         emmo:EMMO_3397f270_dfc1_4500_8f6f_4d0d85ac5f71 ;
     core:prefLabel "SpecialMolecule"@en .
 
@@ -104,6 +104,10 @@
     rdfs:subClassOf :EMMO_9fa9ca88-2891-538a-a8dd-ccb8a08b9890 ;
     core:prefLabel "SpatialPattern"@en .
 
+:EMMO_8b758694-7dd3-547a-8589-a835c15a0fb2 a owl:Class ;
+    rdfs:subClassOf emmo:EMMO_eb77076b_a104_42ac_a065_798b2d2809ad ;
+    core:prefLabel "Atom"@en .
+
 :EMMO_1b2bfe71-5da9-5c46-b137-be45c3e3f9c3 a owl:Class ;
     emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "NEED elucidation"@en ;
     rdfs:subClassOf emmo:EMMO_649bf97b_4397_4005_90d9_219755d92e34 ;

tests/test_excelparser/test_excelparser.py

@@ -15,9 +15,10 @@ def test_excelparser(repo_dir: "Path") -> None:
     onto = get_ontology(str(ontopath)).load()
     xlspath = repo_dir / "tests" / "test_excelparser" / "onto.xlsx"
     ontology, catalog, errors = create_ontology_from_excel(xlspath, force=True)
+
     assert onto == ontology
 
-    assert errors["already_defined"] == {"Atom", "Pattern"}
+    assert errors["already_defined"] == {"Pattern"}
     assert errors["in_imported_ontologies"] == {"Atom"}
     assert errors["wrongly_defined"] == {"Temporal Boundary"}
     assert errors["missing_parents"] == {"SpatioTemporalBoundary"}
@@ -27,7 +28,8 @@ def test_excelparser(repo_dir: "Path") -> None:
         "SubgrainBoundary",
     }
     assert errors["nonadded_concepts"] == {
-        "Atom",
         "Pattern",
         "Temporal Boundary",
     }
+
+    assert len(ontology.get_by_label_all("Atom")) == 2