Fix Annotations on DifferentIndividualsAxioms lost #816

Errors and missing rendering/parsing for annotations on three-argument
different/same individuals. Missng roundtrip tests.

contract/src/test/java/org/semanticweb/owlapi/api/test/classexpressions/DifferentIndividualsAxiomAnnotatedTestCase.java

@@ -0,0 +1,41 @@
+/* This file is part of the OWL API.
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ * Copyright 2014, The University of Manchester
+ * 
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+ * You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+ *
+ * Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0 in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */
+package org.semanticweb.owlapi.api.test.classexpressions;
+
+import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.NamedIndividual;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Nonnull;
+
+import org.semanticweb.owlapi.api.test.baseclasses.AbstractAnnotatedAxiomRoundTrippingTestCase;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+
+/**
+ * @author Matthew Horridge, The University of Manchester, Information Management Group
+ * @since 3.0.0
+ */
+public class DifferentIndividualsAxiomAnnotatedTestCase
+    extends AbstractAnnotatedAxiomRoundTrippingTestCase {
+
+    @Override
+    protected OWLAxiom getMainAxiom(@Nonnull Set<OWLAnnotation> annos) {
+        Set<OWLNamedIndividual> asList =
+            new HashSet<>(Arrays.asList(NamedIndividual(iri("A")), NamedIndividual(iri("B"))));
+        return df.getOWLDifferentIndividualsAxiom(asList, annos);
+    }
+}

contract/src/test/java/org/semanticweb/owlapi/api/test/classexpressions/DifferentIndividualsThreeElementsAxiomAnnotatedTestCase.java

@@ -0,0 +1,41 @@
+/* This file is part of the OWL API.
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ * Copyright 2014, The University of Manchester
+ * 
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+ * You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+ *
+ * Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0 in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */
+package org.semanticweb.owlapi.api.test.classexpressions;
+
+import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.NamedIndividual;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Nonnull;
+
+import org.semanticweb.owlapi.api.test.baseclasses.AbstractAnnotatedAxiomRoundTrippingTestCase;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+
+/**
+ * @author Matthew Horridge, The University of Manchester, Information Management Group
+ * @since 3.0.0
+ */
+public class DifferentIndividualsThreeElementsAxiomAnnotatedTestCase
+    extends AbstractAnnotatedAxiomRoundTrippingTestCase {
+
+    @Override
+    protected OWLAxiom getMainAxiom(@Nonnull Set<OWLAnnotation> annos) {
+        Set<OWLNamedIndividual> asList = new HashSet<>(Arrays.asList(NamedIndividual(iri("A")),
+            NamedIndividual(iri("B")), NamedIndividual(iri("C"))));
+        return df.getOWLDifferentIndividualsAxiom(asList, annos);
+    }
+}

contract/src/test/java/org/semanticweb/owlapi/api/test/classexpressions/SameIndividualsAxiomAnnotatedTestCase.java

@@ -0,0 +1,41 @@
+/* This file is part of the OWL API.
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ * Copyright 2014, The University of Manchester
+ * 
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+ * You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+ *
+ * Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0 in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */
+package org.semanticweb.owlapi.api.test.classexpressions;
+
+import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.NamedIndividual;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Nonnull;
+
+import org.semanticweb.owlapi.api.test.baseclasses.AbstractAnnotatedAxiomRoundTrippingTestCase;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+
+/**
+ * @author Matthew Horridge, The University of Manchester, Information Management Group
+ * @since 3.0.0
+ */
+public class SameIndividualsAxiomAnnotatedTestCase
+    extends AbstractAnnotatedAxiomRoundTrippingTestCase {
+
+    @Override
+    protected OWLAxiom getMainAxiom(@Nonnull Set<OWLAnnotation> annos) {
+        Set<OWLNamedIndividual> asList =
+            new HashSet<>(Arrays.asList(NamedIndividual(iri("A")), NamedIndividual(iri("B"))));
+        return df.getOWLSameIndividualAxiom(asList, annos);
+    }
+}

contract/src/test/java/org/semanticweb/owlapi/api/test/classexpressions/SameIndividualsThreeElementsAxiomAnnotatedTestCase.java

@@ -0,0 +1,113 @@
+/* This file is part of the OWL API.
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ * Copyright 2014, The University of Manchester
+ * 
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+ * You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+ *
+ * Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0 in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */
+package org.semanticweb.owlapi.api.test.classexpressions;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.semanticweb.owlapi.apibinding.OWLFunctionalSyntaxFactory.NamedIndividual;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Nonnull;
+
+import org.semanticweb.owlapi.api.test.baseclasses.AbstractAnnotatedAxiomRoundTrippingTestCase;
+import org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory;
+import org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory;
+import org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory;
+import org.semanticweb.owlapi.formats.RDFXMLDocumentFormatFactory;
+import org.semanticweb.owlapi.formats.TrigDocumentFormatFactory;
+import org.semanticweb.owlapi.formats.TurtleDocumentFormatFactory;
+import org.semanticweb.owlapi.model.AxiomType;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLDocumentFormatFactory;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.OWLSameIndividualAxiom;
+
+/**
+ * @author Matthew Horridge, The University of Manchester, Information Management Group
+ * @since 3.0.0
+ */
+public class SameIndividualsThreeElementsAxiomAnnotatedTestCase
+    extends AbstractAnnotatedAxiomRoundTrippingTestCase {
+
+    @Override
+    protected OWLAxiom getMainAxiom(@Nonnull Set<OWLAnnotation> annos) {
+        Set<OWLNamedIndividual> asList = new HashSet<>(Arrays.asList(NamedIndividual(iri("A")),
+            NamedIndividual(iri("B")), NamedIndividual(iri("C"))));
+        return df.getOWLSameIndividualAxiom(asList, annos);
+    }
+
+    @Override
+    public void testRDFXML() throws Exception {
+        // axioms with three or more elements cannot be represented as one axiom in this syntax
+        sameIndividualAssertion(getOnt(), new RDFXMLDocumentFormatFactory());
+    }
+
+    @Override
+    public void testTrig() throws Exception {
+        // axioms with three or more elements cannot be represented as one axiom in this syntax
+        sameIndividualAssertion(getOnt(), new TrigDocumentFormatFactory());
+    }
+
+    @Override
+    public void testRDFJSON() throws Exception {
+        // axioms with three or more elements cannot be represented as one axiom in this syntax
+        sameIndividualAssertion(getOnt(), new RDFJsonDocumentFormatFactory());
+    }
+
+    @Override
+    public void testNTriples() throws Exception {
+        // axioms with three or more elements cannot be represented as one axiom in this syntax
+        sameIndividualAssertion(getOnt(), new NTriplesDocumentFormatFactory());
+    }
+
+    @Override
+    public void roundTripRDFXMLAndFunctionalShouldBeSame() {
+        // axioms with three or more elements cannot be represented as one axiom in this syntax
+        // super.roundTripRDFXMLAndFunctionalShouldBeSame();
+    }
+
+    @Override
+    public void testJSONLD() throws Exception {
+        // axioms with three or more elements cannot be represented as one axiom in this syntax
+        sameIndividualAssertion(getOnt(), new RDFJsonDocumentFormatFactory());
+    }
+
+    @Override
+    public void testNQuads() throws Exception {
+        // axioms with three or more elements cannot be represented as one axiom in this syntax
+        sameIndividualAssertion(getOnt(), new NQuadsDocumentFormatFactory());
+    }
+
+    @Override
+    public void testTurtle() throws Exception {
+        // axioms with three or more elements cannot be represented as one axiom in this syntax
+        sameIndividualAssertion(getOnt(), new TurtleDocumentFormatFactory());
+    }
+
+    protected void sameIndividualAssertion(OWLOntology ont, OWLDocumentFormatFactory f)
+        throws OWLOntologyCreationException, OWLOntologyStorageException {
+        OWLOntology o =
+            loadOntologyFromString(saveOntology(ont, f.createFormat()), f.createFormat());
+        assertEquals(2, o.getAxiomCount(AxiomType.SAME_INDIVIDUAL));
+        Set<OWLSameIndividualAxiom> axioms = ont.getAxioms(AxiomType.SAME_INDIVIDUAL);
+        axioms.stream().map(OWLSameIndividualAxiom::splitToAnnotatedPairs)
+            .forEach(axs -> axs.forEach(a -> assertTrue(o.containsAxiom(a))));
+    }
+}

parsers/src/main/java/org/semanticweb/owlapi/manchestersyntax/parser/ManchesterOWLSyntaxParserImpl.java

@@ -405,8 +405,6 @@ private void initialiseIndividualFrameSections() {
         initialiseSection(new IndividualFactsItemParser(), individualFrameSections);
         initialiseSection(new IndividualSameAsItemParser(), individualFrameSections);
         initialiseSection(new IndividualDifferentFromItemParser(), individualFrameSections);
-        // Extensions
-        initialiseSection(new IndividualDifferentIndividualsItemParser(), individualFrameSections);
     }
 
     @Override
@@ -1889,9 +1887,9 @@ 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) {
             assert ont != null;
@@ -3451,29 +3449,6 @@ public ManchesterOWLSyntax getFrameSectionKeyword() {
         }
     }
 
-    class IndividualDifferentIndividualsItemParser
-        implements AnnotatedListItemParser<OWLIndividual, Set<OWLIndividual>> {
-
-        @Override
-        public Set<OWLIndividual> parseItem(OWLIndividual s) {
-            return parseIndividualList();
-        }
-
-        @Override
-        public OWLAxiom createAxiom(OWLIndividual s, Set<OWLIndividual> o,
-            Set<OWLAnnotation> anns) {
-            Set<OWLIndividual> individuals = new HashSet<>();
-            individuals.add(s);
-            individuals.addAll(o);
-            return dataFactory.getOWLDifferentIndividualsAxiom(individuals, anns);
-        }
-
-        @Override
-        public ManchesterOWLSyntax getFrameSectionKeyword() {
-            return DIFFERENT_INDIVIDUALS;
-        }
-    }
-
     class IndividualAnnotationItemParser
         implements AnnotatedListItemParser<OWLIndividual, OWLAnnotation> {
 

parsers/src/main/java/org/semanticweb/owlapi/manchestersyntax/renderer/ManchesterOWLSyntaxFrameRenderer.java

@@ -46,6 +46,7 @@
 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;
@@ -424,12 +425,23 @@ public void writeOntology() throws OWLRendererException {
         // Nary different individuals
         for (OWLDifferentIndividualsAxiom ax : sortedCollection(
             ontology.getAxioms(AxiomType.DIFFERENT_INDIVIDUALS))) {
-            if (ax.getIndividuals().size() > 2) {
+            if (ax.getIndividuals().size() > 2
+                || ax.getIndividuals().size() == 2 && !ax.getAnnotations().isEmpty()) {
                 SectionMap<Object, OWLAxiom> map = new SectionMap<>();
                 map.put(ax.getIndividuals(), ax);
                 writeSection(DIFFERENT_INDIVIDUALS, map, ",", false, ontology);
             }
         }
+        // Nary same individuals
+        for (OWLSameIndividualAxiom ax : sortedCollection(
+            ontology.getAxioms(AxiomType.SAME_INDIVIDUAL))) {
+            if (ax.getIndividuals().size() > 2
+                || ax.getIndividuals().size() == 2 && !ax.getAnnotations().isEmpty()) {
+                SectionMap<Object, OWLAxiom> map = new SectionMap<>();
+                map.put(ax.getIndividuals(), ax);
+                writeSection(SAME_INDIVIDUAL, map, ",", false, ontology);
+            }
+        }
         for (SWRLRule rule : sortedCollection(ontology.getAxioms(AxiomType.SWRL_RULE))) {
             @Nonnull
             Set<SWRLRule> singleton = Collections.singleton(rule);
@@ -1097,8 +1109,10 @@ public Collection<OWLAxiom> write(@Nonnull OWLIndividual individual) {
                 Collection<OWLIndividual> inds = sortedCollection();
                 for (OWLSameIndividualAxiom ax : ontology.getSameIndividualAxioms(individual)) {
                     if (isDisplayed(ax)) {
-                        inds.addAll(ax.getIndividuals());
-                        axioms.add(ax);
+                        if (ax.getIndividuals().size() == 2 && ax.getAnnotations().isEmpty()) {
+                            inds.addAll(ax.getIndividuals());
+                            axioms.add(ax);
+                        }
                     }
                 }
                 inds.remove(individual);
@@ -1111,11 +1125,13 @@ public Collection<OWLAxiom> write(@Nonnull OWLIndividual individual) {
                 Collection<OWLDifferentIndividualsAxiom> nary = sortedCollection();
                 for (OWLDifferentIndividualsAxiom ax : ontology
                     .getDifferentIndividualAxioms(individual)) {
-                    if (ax.getIndividuals().size() == 2 && isDisplayed(ax)) {
-                        inds.addAll(ax.getIndividuals());
-                        axioms.add(ax);
-                    } else {
-                        nary.add(ax);
+                    if (isDisplayed(ax)) {
+                        if (ax.getIndividuals().size() == 2 && ax.getAnnotations().isEmpty()) {
+                            inds.addAll(ax.getIndividuals());
+                            axioms.add(ax);
+                        } else {
+                            nary.add(ax);
+                        }
                     }
                 }
                 inds.remove(individual);