Avoid dropping axioms or misplacing annotations when malformed axiom annotations are present

contract/src/test/java/org/semanticweb/owlapi/rio/TestRDFParsingAmongMalformedAxiomAnnotations.java

@@ -0,0 +1,33 @@
+package org.semanticweb.owlapi.rio;
+
+
+import org.junit.jupiter.api.Test;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Optional;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+
+public class TestRDFParsingAmongMalformedAxiomAnnotations {
+
+    @Test
+    public void testAxiomParsing() throws OWLOntologyCreationException, IOException {
+        try (InputStream ttlStream = this.getClass().getResourceAsStream("/rdfParserReservedPropertiesAnnotations.ttl")) {
+            OWLOntology ontTTL = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(ttlStream);
+            assertEquals(14, ontTTL.getAxiomCount(), "Test file should have 14 axioms");
+            Optional<OWLAnnotation> annotationOpt = ontTTL.getAxioms().stream()
+                    .flatMap(ax -> ax.getAnnotations().stream())
+                    .filter(ann -> ann.getValue().isLiteral())
+                    .filter(ann -> ann.getValue().asLiteral().get().getLiteral().equals("This assertion is annotated"))
+                    .findAny();
+            assertFalse(annotationOpt.isPresent(), "Annotation should not have been added to any axiom.");
+        }
+    }
+
+}

contract/src/test/resources/rdfParserReservedPropertiesAnnotations.ttl

@@ -0,0 +1,115 @@
+@prefix : <http://example.org/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@base <http://example.org/> .
+
+<http://example.org/> rdf:type owl:Ontology .
+
+#################################################################
+#    Object Properties
+#################################################################
+
+###  http://example.org/contains
+:contains rdf:type owl:ObjectProperty .
+
+
+###  http://example.org/has_book
+:has_book rdf:type owl:ObjectProperty ;
+          owl:propertyChainAxiom ( :has_books
+                                   :contains
+                                 ) .
+
+
+###  http://example.org/has_books
+:has_books rdf:type owl:ObjectProperty .
+
+
+#################################################################
+#    Classes
+#################################################################
+
+###  http://example.org/Book
+:Book rdf:type owl:Class .
+
+
+###  http://example.org/BookOrLibrary
+:BookOrLibrary rdf:type owl:Class ;
+               owl:equivalentClass [ rdf:type owl:Class ;
+                                     owl:unionOf ( :Book
+                                                   :Library
+                                                 )
+                                   ] .
+
+[ rdf:type owl:Axiom ;
+   owl:annotatedSource :BookOrLibrary ;
+   owl:annotatedProperty owl:equivalentClass ;
+   owl:annotatedTarget [ rdf:type owl:Class ;
+                         owl:unionOf ( :Book
+                                       :Library
+                                     )
+                       ] ;
+   rdfs:comment "This equivalence axiom is annotated."
+ ] .
+
+
+###  http://example.org/Library
+:Library rdf:type owl:Class ;
+         rdfs:subClassOf [ rdf:type owl:Restriction ;
+                           owl:onProperty :has_books ;
+                           owl:allValuesFrom [ rdf:type owl:Restriction ;
+                                               owl:onProperty :contains ;
+                                               owl:allValuesFrom :Book
+                                             ]
+                         ] .
+
+
+#################################################################
+#    Individuals
+#################################################################
+
+###  http://example.org/moby_dick
+:moby_dick rdf:type owl:NamedIndividual .
+
+
+###  http://example.org/the_library
+:the_library rdf:type owl:NamedIndividual ,
+                      :Library .
+
+[ rdf:type owl:Axiom ;
+   owl:annotatedSource :the_library ;
+   owl:annotatedProperty rdf:type ;
+   owl:annotatedTarget :Library ;
+   rdfs:comment "This class assertion is annotated."
+ ] .
+
+
+###  http://example.org/the_republic
+:the_republic rdf:type owl:NamedIndividual .
+
+_:genid42 rdf:type owl:Axiom ;
+   owl:annotatedSource _:genid8 ;
+   owl:annotatedProperty rdf:first ;
+   owl:annotatedTarget :moby_dick ;
+   rdfs:comment "This assertion is annotated" .
+
+# These triples should be ignored
+_:genid43 rdf:type owl:Axiom ;
+   owl:annotatedSource _:genid8 ;
+   owl:annotatedProperty rdfs:first ; #Not a real property but triggers bug
+   owl:annotatedTarget :moby_dick ;
+   rdfs:comment "This assertion is annotated" .
+
+# These triples should be ignored
+_:genid44 rdf:type owl:Axiom ;
+   owl:annotatedSource _:genid8 ;
+   owl:annotatedProperty rdf:subject ;
+   owl:annotatedTarget :moby_dick ;
+   rdfs:comment "This assertion is annotated" .
+
+_:genid8 :contains :moby_dick .
+
+
+###  Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi

parsers/src/main/java/org/semanticweb/owlapi/rdf/rdfxml/parser/TripleHandlers.java

@@ -436,6 +436,10 @@ protected void handle(IRI s, IRI p, IRI o) {
                     }
                 }
             }
+            // Clears pending annotations; if this triple represents an annotated axiom, then if an axiom was created to annotate,
+            // pending will already be cleared. However, if an axiom was not created (e.g. invalid triple such as misuse of reserved
+            // vocabulary) if annotations are left they will be placed on an incorrect axiom.
+            consumer.getPendingAnnotations();
         }
 
         protected void handle(IRI s, IRI p, OWLLiteral o) {
@@ -2385,8 +2389,10 @@ public void handleTriple(IRI s, IRI p, IRI o) {
                 }
                 if (!annotations.isEmpty()) {
                     OWLAxiom ax = consumer.getLastAddedAxiom();
-                    consumer.removeAxiom(verifyNotNull(ax, "no axiom added yet by the consumer")
-                        .getAxiomWithoutAnnotations());
+                    // Only remove unannotated axiom if it received annotations
+                    if (!verifyNotNull(ax, "no axiom added yet by the consumer").getAnnotations().isEmpty()) {
+                        consumer.removeAxiom(ax.getAxiomWithoutAnnotations());
+                    }
                 }
                 consume(s, p, o);
             }