Fix Annotations on DifferentIndividualsAxioms lost #816

Errors and missing rendering/parsing for annotations on three-argument different/same individuals. Missng roundtrip tests.
owlcs · May 20, 2022 · a7e81ef · a7e81ef
1 parent 5c031b5
commit a7e81ef
Show file tree

Hide file tree

Showing 6 changed files with 307 additions and 107 deletions.
diff --git a/apibinding/src/main/java/org/semanticweb/owlapi/apibinding/OWLFunctionalSyntaxFactory.java b/apibinding/src/main/java/org/semanticweb/owlapi/apibinding/OWLFunctionalSyntaxFactory.java
diff --git a/...test/java/org/semanticweb/owlapi/api/test/baseclasses/AnnotatedAxiomRountripTestCase.java b/...test/java/org/semanticweb/owlapi/api/test/baseclasses/AnnotatedAxiomRountripTestCase.java
@@ -24,11 +24,13 @@
 import static org.semanticweb.owlapi.api.test.TestEntities.P;
 import static org.semanticweb.owlapi.api.test.TestEntities.Q;
 import static org.semanticweb.owlapi.api.test.TestEntities.R;
+import static org.semanticweb.owlapi.api.test.TestEntities.i;
 import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.AsymmetricObjectProperty;
 import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.ClassAssertion;
 import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.DataPropertyAssertion;
 import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.DataPropertyDomain;
 import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.DataPropertyRange;
+import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.DifferentIndividuals;
 import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.DisjointClasses;
 import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.DisjointDataProperties;
 import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.DisjointObjectProperties;
@@ -91,6 +93,8 @@ public static List<Function<List<OWLAnnotation>, OWLAxiom>> getData() {
             a -> ObjectPropertyDomain(P, A, a), a -> ObjectPropertyRange(P, A, a), a -> ReflexiveObjectProperty(P, a),
             a -> df.getOWLSubClassOfAxiom(A, B, a), a -> SubDataPropertyOf(DP, DQ, a),
             a -> SubObjectPropertyOf(P, Q, a), a -> SymmetricObjectProperty(P, a), a -> TransitiveObjectProperty(P, a),
-            a -> SubPropertyChainOf(Arrays.asList(P, Q), R, a));
+            a -> SubPropertyChainOf(Arrays.asList(P, Q), R, a), a -> DifferentIndividuals(Arrays.asList(i, I, J), a),
+            a -> DifferentIndividuals(Arrays.asList(I, J), a), a -> DifferentIndividuals(Arrays.asList(i, I, J), a),
+            a -> DifferentIndividuals(Arrays.asList(I, J), a));
     }
 }
diff --git a/...in/java/org/semanticweb/owlapi/manchestersyntax/parser/ManchesterOWLSyntaxParserImpl.java b/...in/java/org/semanticweb/owlapi/manchestersyntax/parser/ManchesterOWLSyntaxParserImpl.java
@@ -392,8 +392,6 @@ private void initialiseIndividualFrameSections() {
         initialiseSection(new AnnAxiom<>(this::parseFact, FACTS, (s, o, anns) -> o.getAnnotatedAxiom(anns)), individualFrames);
         initialiseSection(new AnnAxiom<OWLIndividual, OWLIndividual>(x -> parseIndividual(), SAME_AS, (s, o, anns) -> df.getOWLSameIndividualAxiom(s, o, anns)), individualFrames);
         initialiseSection(new AnnAxiom<OWLIndividual, OWLIndividual>(x -> parseIndividual(), DIFFERENT_FROM, (s, o, anns) -> df.getOWLDifferentIndividualsAxiom(s, o, anns)), individualFrames);
-        // Extensions
-        initialiseSection(new AnnAxiom<OWLIndividual, Set<OWLIndividual>>(x -> parseIndividualList(), DIFFERENT_INDIVIDUALS, (s, o, anns) -> create(df, s, o, anns)), individualFrames);
       //@formatter:on
     }
 
@@ -1762,9 +1760,9 @@ private Set<OntologyAxiomPair> parseSameIndividual() {
         if (!SAME_INDIVIDUAL.matches(section)) {
             throw new ExceptionBuilder().withKeyword(SAME_INDIVIDUAL).build();
         }
-        Set<OWLIndividual> individuals = parseIndividualList();
         Set<OWLOntology> ontologies = getOntologies();
         Set<OWLAnnotation> annotations = parseAnnotations();
+        Set<OWLIndividual> individuals = parseIndividualList();
         Set<OntologyAxiomPair> pairs = new HashSet<>();
         for (OWLOntology ont : ontologies) {
             pairs.add(new OntologyAxiomPair(ont, df.getOWLSameIndividualAxiom(individuals, annotations)));

diff --git a/...va/org/semanticweb/owlapi/manchestersyntax/renderer/ManchesterOWLSyntaxFrameRenderer.java b/...va/org/semanticweb/owlapi/manchestersyntax/renderer/ManchesterOWLSyntaxFrameRenderer.java
@@ -47,6 +47,7 @@
 import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntax.REFLEXIVE;
 import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntax.RULE;
 import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntax.SAME_AS;
+import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntax.SAME_INDIVIDUAL;
 import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntax.SUBCLASS_OF;
 import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntax.SUB_PROPERTY_CHAIN;
 import static org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntax.SUB_PROPERTY_OF;
@@ -294,12 +295,25 @@ public void writeOntology() throws OWLOntologyStorageException {
             .forEach(ax -> writeMoreThanTwo(ax, ax.getOperandsAsList(), EQUIVALENT_PROPERTIES));
         // Nary different individuals
         o.axioms(AxiomType.DIFFERENT_INDIVIDUALS).sorted(ooc)
-            .forEach(ax -> writeMoreThanTwo(ax, ax.getOperandsAsList(), DIFFERENT_INDIVIDUALS));
+            .forEach(ax -> writeMoreThanTwo(ax, ax.getOperandsAsList(), DIFFERENT_INDIVIDUALS, true));
+        // Nary same individuals
+        o.axioms(AxiomType.SAME_INDIVIDUAL).sorted(ooc)
+            .forEach(ax -> writeMoreThanTwo(ax, ax.getOperandsAsList(), SAME_INDIVIDUAL, true));
         o.axioms(AxiomType.SWRL_RULE).sorted(ooc)
             .forEach(rule -> writeSection(RULE, Collections.singleton(rule).iterator(), ", ", false));
         flush();
     }
 
+    protected <T> void writeMoreThanTwo(OWLAxiom ax, List<T> individuals, ManchesterOWLSyntax section,
+        boolean writeTwoIfAnnotated) {
+        if (individuals.size() > 2
+            || writeTwoIfAnnotated && individuals.size() == 2 && !ax.annotationsAsList().isEmpty()) {
+            SectionMap<Object, OWLAxiom> map = new SectionMap<>();
+            map.put(individuals, ax);
+            writeSection(section, map, ",", false);
+        }
+    }
+
     protected <T> void writeMoreThanTwo(OWLAxiom ax, List<T> individuals, ManchesterOWLSyntax section) {
         if (individuals.size() > 2) {
             SectionMap<Object, OWLAxiom> map = new SectionMap<>();
@@ -764,8 +778,10 @@ public Collection<OWLAxiom> write(OWLIndividual individual) {
         if (!isFiltered(AxiomType.SAME_INDIVIDUAL)) {
             Collection<OWLIndividual> inds = sortedCollection();
             filtersort(o.sameIndividualAxioms(individual)).forEach(ax -> {
-                add(inds, ax.individuals());
-                axioms.add(ax);
+                if (ax.getOperandsAsList().size() == 2 && ax.annotationsAsList().isEmpty()) {
+                    add(inds, ax.individuals());
+                    axioms.add(ax);
+                }
             });
             inds.remove(individual);
             writeSection(SAME_AS, inds.iterator(), ",", true);
@@ -774,7 +790,7 @@ public Collection<OWLAxiom> write(OWLIndividual individual) {
             Collection<OWLIndividual> inds = sortedCollection();
             Collection<OWLDifferentIndividualsAxiom> nary = sortedCollection();
             filtersort(o.differentIndividualAxioms(individual)).forEach(ax -> {
-                if (ax.getOperandsAsList().size() == 2) {
+                if (ax.getOperandsAsList().size() == 2 && ax.annotationsAsList().isEmpty()) {
                     add(inds, ax.individuals());
                     axioms.add(ax);
                 } else {

diff --git a/rdfformats/src/main/java/org/semanticweb/owlapi/rdf/model/AbstractTranslator.java b/rdfformats/src/main/java/org/semanticweb/owlapi/rdf/model/AbstractTranslator.java
@@ -662,7 +662,8 @@ public void visit(OWLHasKeyAxiom axiom) {
 
     @Override
     public void visit(OWLSameIndividualAxiom axiom) {
-        addPairwise(axiom, axiom.individuals(), OWL_SAME_AS.getIRI());
+        axiom.splitToAnnotatedPairs().forEach(a -> addSingleTripleAxiom(a, a.getOperandsAsList().get(0),
+            OWL_SAME_AS.getIRI(), a.getOperandsAsList().get(1)));
         processIfAnonymous(axiom.individuals(), axiom);
     }
 
@@ -671,6 +672,7 @@ public void visit(OWLDifferentIndividualsAxiom axiom) {
         translateAnonymousNode(axiom);
         addTriple(axiom, RDF_TYPE.getIRI(), OWL_ALL_DIFFERENT.getIRI());
         addListTriples(axiom, OWL_DISTINCT_MEMBERS.getIRI(), axiom.individuals());
+        translateAnnotations(axiom);
         processIfAnonymous(axiom.individuals(), axiom);
     }
 

diff --git a/rdfformats/src/main/java/org/semanticweb/owlapi/rdf/rdfxml/parser/OWLRDFConsumer.java b/rdfformats/src/main/java/org/semanticweb/owlapi/rdf/rdfxml/parser/OWLRDFConsumer.java
@@ -1339,6 +1339,8 @@ protected boolean canHandleAllDifferent(IRI s) {
     protected boolean handleAllDifferentTriple(IRI s, IRI p, IRI o) {
         IRI listNode = object(s, OWL_MEMBERS, OWL_DISTINCT_MEMBERS);
         if (listNode != null) {
+            List<OWLAnnotation> annotations = pendingAnns(s);
+            pendingAnnotations.addAll(annotations);
             add(df.getOWLDifferentIndividualsAxiom(individuals(listNode), pendingAnns()));
             return tripleIndex.consumeTriple(s, p, o);
         }