[VIVO-1394] Make AboxRecomputer deal with inferred types correctly

api/src/main/java/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java

@@ -218,15 +218,11 @@ public class ABoxRecomputer {
         Model assertions = getAssertions(individualURI);
         log.debug((System.currentTimeMillis() - start) + " ms to get assertions.");
         long prevRebuildSize = (simpleReasoner.getSameAsEnabled()) ? rebuildModel.size() : 0;
-        Model additionalInferences = recomputeIndividual(
-                individualURI, null, assertions, rebuildModel, caches, RUN_PLUGINS);
         if (simpleReasoner.getSameAsEnabled()) {
             Set<String> sameAsInds = getSameAsIndividuals(individualURI);
             for (String sameAsInd : sameAsInds) {
                 // sameAs for plugins is handled by the SimpleReasoner
                 Model sameAsIndAssertions = getAssertions(sameAsInd);
-                recomputeIndividual(
-                        sameAsInd, individualURI, sameAsIndAssertions, rebuildModel, caches, SKIP_PLUGINS);
                 rebuildModel.add(
                         rewriteInferences(getAssertions(sameAsInd), individualURI));
                 Resource indRes = ResourceFactory.createResource(individualURI);
@@ -242,6 +238,8 @@ public class ABoxRecomputer {
                 individualQueue.addAll(sameAsInds);
             }
         }
+        Model additionalInferences = recomputeIndividual(
+                individualURI, null, assertions, rebuildModel, caches, RUN_PLUGINS);
         return additionalInferences;
     }
 
@@ -262,6 +260,7 @@ public class ABoxRecomputer {
         long start = System.currentTimeMillis();
         Model types = ModelFactory.createDefaultModel();
         types.add(assertions.listStatements(null, RDF.type, (RDFNode) null));
+        types.add(rebuildModel.listStatements(null, RDF.type, (RDFNode) null));
         Model inferredTypes = rewriteInferences(getInferredTypes(individual, types, caches), aliasURI);
         rebuildModel.add(inferredTypes);
         log.trace((System.currentTimeMillis() - start) + " to infer " + inferredTypes.size() + " types");

api/src/test/java/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerSameAsTest.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.reasoner;
 import org.apache.log4j.Level;
 import org.junit.Assert;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 
 import org.apache.jena.ontology.AnnotationProperty;
@@ -454,7 +455,7 @@ public class SimpleReasonerSameAsTest extends SimpleReasonerTBoxHelper {
 	 * adding and removing a type assertion for an individual who has
 	 * a sameAs individual.
 	 */
-	//@Test
+	@Test
 	public void tBoxTypeAssertion1() {
 		// Create a Tbox with a simple class hierarchy. B is a subclass of A.
 		OntModel tBox = createTBoxModel(); 
@@ -493,7 +494,7 @@ public class SimpleReasonerSameAsTest extends SimpleReasonerTBoxHelper {
 	 * adding and removing subclass assertion when there is an 
 	 * individual member who has a sameAs individual.
 	 */
-	//@Test
+	@Test
 	public void tBoxSubclassAssertion1() throws InterruptedException {
 		// Create a Tbox with a simple class hierarchy. B is a subclass of A.
 		OntModel tBox = createTBoxModel(); 
@@ -596,14 +597,16 @@ public class SimpleReasonerSameAsTest extends SimpleReasonerTBoxHelper {
 	 * test that mostSpecificType inferences propagate to sameAs 
 	 * individuals
 	 */
-	//@Test
+	@Test
 	public void mostSpecificTypeTest1() {
 		// Create a Tbox with a simple class hierarchy. B is a subclass of A.
 		OntModel tBox = createTBoxModel(); 
 		OntClass classA = createClass(tBox, "http://test.vivo/A", "class A"); 
-		OntClass classC = createClass(tBox, "http://test.vivo/B", "class C"); 
+		OntClass classC = createClass(tBox, "http://test.vivo/C", "class C");
-		OntClass classD = createClass(tBox, "http://test.vivo/B", "class D"); 
+		OntClass classD = createClass(tBox, "http://test.vivo/D", "class D");
-		OntClass classE = createClass(tBox, "http://test.vivo/B", "class E");
+		OntClass classE = createClass(tBox, "http://test.vivo/E", "class E");
+
+		// A is superclass of C, C is superclass of D and E
 		addSubclass(classA, classC);
 		addSubclass(classC, classD);
 		addSubclass(classC, classE);
@@ -627,21 +630,27 @@ public class SimpleReasonerSameAsTest extends SimpleReasonerTBoxHelper {
 		Resource c = aBox.createResource("http://test.vivo/c");
 		Resource d = aBox.createResource("http://test.vivo/d");
 
+		// Assert a, b, c and d are the same
 		aBox.add(a, OWL.sameAs, b);
 		aBox.add(c, OWL.sameAs, b);
 		aBox.add(d, OWL.sameAs, a);		
 
+		// Assert a is D, and d ic C
+		// All resources will therefore be C and D
 		aBox.add(a, RDF.type, classD);	
 		aBox.add(d, RDF.type, classC);
-		Assert.assertFalse(inf.contains(a,RDF.type,classD));
+
+		// All resources should be inferred as C and D, except a and d which have direct assertions
+		Assert.assertFalse(inf.contains(a,RDF.type,classD));	// D is asserted for a
 		Assert.assertTrue(inf.contains(a,RDF.type,classC));
 		Assert.assertTrue(inf.contains(b,RDF.type, classD));
 		Assert.assertTrue(inf.contains(b,RDF.type, classC));
 		Assert.assertTrue(inf.contains(c,RDF.type, classD));
 		Assert.assertTrue(inf.contains(c,RDF.type, classC));
 		Assert.assertTrue(inf.contains(d,RDF.type, classD));
-		Assert.assertFalse(inf.contains(d,RDF.type, classC));
+		Assert.assertFalse(inf.contains(d,RDF.type, classC));	// C is asserted for d
 
+		// In all cases, mostSpecificType should be D, not C
 		Assert.assertTrue(inf.contains(a, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
 		Assert.assertTrue(inf.contains(b, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
 		Assert.assertTrue(inf.contains(c, mostSpecificType, ResourceFactory.createResource(classD.getURI())));