From d3f8e88243a86c422f66653415e1fc662bc12b1b Mon Sep 17 00:00:00 2001
From: "Francesca L. Bleken" <48128015+francescalb@users.noreply.github.com>
Date: Tue, 29 Oct 2024 14:33:58 +0100
Subject: [PATCH] Handle owlready2:python_names in genated triples in
 excelparser (#795)

# Description
EMMOntoPy tests fail with owlready0.45 and higher.
I want to fix one owlready release at a time, since there seem to be
different things that are
incompatible going up to v0.48.

In v 0.45 owlready2 introduced the python names defined with the
predicate
"http://www.lesfleursdunormal.fr/static/_downloads/owlready_ontology.owl#python_name"
in the ontology. These should not be part of the generated ontology and
have therefore been removed
in the ontology generated with the excelparser.
---
 ontopy/excelparser.py                      | 24 ++++++++++++++++
 requirements.txt                           |  2 +-
 tests/test_excelparser/test_excelparser.py | 33 ++++++++++++++++++++++
 3 files changed, 58 insertions(+), 1 deletion(-)

diff --git a/ontopy/excelparser.py b/ontopy/excelparser.py
index a537a286e..cb22ea59e 100755
--- a/ontopy/excelparser.py
+++ b/ontopy/excelparser.py
@@ -313,6 +313,15 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     if input_ontology:
         onto = input_ontology
         catalog = {}
+        # Since we will remove newly created python_name added
+        # by owlready2 in the triples, we keep track of those
+        # that come from the input ontology
+        pyname_triples_to_keep = list(
+            onto.get_unabbreviated_triples(
+                predicate="http://www.lesfleursdunormal.fr/static/_downloads/"
+                "owlready_ontology.owl#python_name"
+            )
+        )
     else:  # Create new ontology
         onto, catalog = get_metadata_from_dataframe(
             metadata, base_iri, imports=imports
@@ -456,6 +465,21 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     entities_with_errors = {
         key: set(value) for key, value in entities_with_errors.items()
     }
+
+    # Remove triples with predicate 'python_name' added by owlready2
+    onto._del_data_triple_spod(  # pylint: disable=protected-access
+        p=onto._abbreviate(  # pylint: disable=protected-access
+            "http://www.lesfleursdunormal.fr/static/_downloads/"
+            "owlready_ontology.owl#python_name"
+        )
+    )
+    # Add back the triples python name triples that were in the input_ontology.
+    if input_ontology:
+        for triple in pyname_triples_to_keep:
+            onto._add_data_triple_spod(  # pylint: disable=protected-access
+                s=triple[0], p=triple[1], o=triple[2]
+            )
+
     return onto, catalog, entities_with_errors
 
 
diff --git a/requirements.txt b/requirements.txt
index 8576bf3d4..77559d07d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,7 +4,7 @@ defusedxml>=0.7.1,<1
 graphviz>=0.16,<0.21
 numpy>=1.19.5,<3
 openpyxl>=3.0.9,<3.2
-Owlready2>=0.28,!=0.32,!=0.34,<0.45
+Owlready2>=0.28,!=0.32,!=0.34,<0.46
 packaging>=21.0,<25
 pandas>=1.2,<2.3
 Pygments>=2.7.4,<3
diff --git a/tests/test_excelparser/test_excelparser.py b/tests/test_excelparser/test_excelparser.py
index 58d6da30a..571b00d9b 100644
--- a/tests/test_excelparser/test_excelparser.py
+++ b/tests/test_excelparser/test_excelparser.py
@@ -95,6 +95,39 @@ def test_excelparser(repo_dir: "Path") -> None:
     assert updated_onto.FinitePattern.iri == onto.FinitePattern.iri
     assert len(list(onto.classes())) + 1 == len(list(updated_onto.classes()))
 
+    # check that the owlready2 generated python names are not in the triples
+    assert (
+        list(
+            ontology.get_unabbreviated_triples(
+                predicate="http://www.lesfleursdunormal.fr/static/_downloads/"
+                "owlready_ontology.owl#python_name"
+            )
+        )
+        == []
+    )
+    # check that the owlready2 generated python names are not in the triples
+    assert (
+        list(
+            updated_onto.get_unabbreviated_triples(
+                predicate="http://www.lesfleursdunormal.fr/static/_downloads/"
+                "owlready_ontology.owl#python_name"
+            )
+        )
+        == []
+    )
+
+    # Just to be sure that the method of getting the correct triples is OK
+    assert (
+        len(
+            list(
+                ontology.get_unabbreviated_triples(
+                    predicate="http://www.w3.org/2000/01/rdf-schema#subClassOf"
+                )
+            )
+        )
+        > 1
+    )
+
 
 def test_excelparser_only_classes(repo_dir: "Path") -> None:
     """This loads the excelfile used and tests that the resulting ontology prior