From 66b12eb4be79bdb68adfe3212d8d600be12ca7b2 Mon Sep 17 00:00:00 2001
From: stellamit <stellamit@440791e1-c2bf-4c1e-ad7c-caf3f8b0ebe8>
Date: Mon, 11 Jun 2012 00:19:54 +0000
Subject: [PATCH] NIHVIVO-3697 sameAs support in SimpleReasoner

---
 .../vitro/webapp/reasoner/SimpleReasoner.java | 52 ++++++++++---------
 .../reasoner/SimpleReasonerSameAsTest.java    | 32 +++++-------
 2 files changed, 40 insertions(+), 44 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
index d32851ec5..b23e67017 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
@@ -890,31 +890,35 @@ public class SimpleReasoner extends StatementListener {
 	// subject is of type cls; otherwise returns false.
 	protected boolean entailedType(Resource subject, OntClass cls) {
 
+		List<Resource> sameIndividuals = getSameIndividuals(subject,inferenceModel);
+		sameIndividuals.add(subject);
+				
 		tboxModel.enterCriticalSection(Lock.READ);
-		aboxModel.enterCriticalSection(Lock.READ);
-		
-		try {			
-			List<OntClass> subclasses = null;
-			subclasses = (cls.listSubClasses(false)).toList();		
-			subclasses.addAll((cls.listEquivalentClasses()).toList());
-			
-			Iterator<OntClass> iter = subclasses.iterator();
-						
-			while (iter.hasNext()) {		
-				OntClass childClass = iter.next();
-				if (childClass.equals(cls)) continue;
-				Statement stmt = ResourceFactory.createStatement(subject, RDF.type, childClass);
-				if (aboxModel.contains(stmt)) return true;
-			}
-			
-			return false;
-		} catch (Exception e) {
-			log.debug("exception in method entailedType: " + e.getMessage());
-			return false;
-		} finally { 
-			aboxModel.leaveCriticalSection();
-			tboxModel.leaveCriticalSection();
-		}	
+		try {
+			aboxModel.enterCriticalSection(Lock.READ);
+			try {			
+				List<OntClass> subclasses = null;
+				subclasses = (cls.listSubClasses(false)).toList();		
+				subclasses.addAll((cls.listEquivalentClasses()).toList());
+				
+				Iterator<OntClass> iter = subclasses.iterator();
+				while (iter.hasNext()) {		
+					OntClass childClass = iter.next();
+					if (childClass.equals(cls)) continue;  // TODO - determine whether this is needed
+					Iterator<Resource> sameIter = sameIndividuals.iterator();
+					while (sameIter.hasNext()) {
+						Statement stmt = ResourceFactory.createStatement(sameIter.next(), RDF.type, childClass);
+						if (aboxModel.contains(stmt)) 
+						   return true;						
+					}
+				}
+				return false;
+			} finally { 
+				aboxModel.leaveCriticalSection();
+			}	
+		} finally {
+			tboxModel.leaveCriticalSection();			
+		}
 	}
 		
 	// Returns true if the triple is entailed by inverse property
diff --git a/webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerSameAsTest.java b/webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerSameAsTest.java
index b7b3574d4..7f1b083c0 100644
--- a/webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerSameAsTest.java
+++ b/webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerSameAsTest.java
@@ -555,21 +555,9 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
 	 */
 	//@Test
 	public void mostSpecificTypeTest1() throws InterruptedException {
-		// Create TBox, ABox and Inference models and register
-		// the ABox reasoner listeners with the ABox and TBox
-		// Pellet will compute TBox inferences
+
+		// set up tbox. Pellet is reasoning; SimpleReasonerTBoxListener is not being used.
 		OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); 
-		OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); 
-        Model inf = ModelFactory.createDefaultModel();
-		
-        SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
-		aBox.register(simpleReasoner);
-		SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
-		tBox.register(simpleReasonerTBoxListener);
-		
-		// Set up the Tbox with a class hierarchy. C is a
-		// subclass of A. D and E are subclasses C.
-		// Pellet will compute TBox inferences.
 		AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
 		
 		OntClass classA = tBox.createClass("http://test.vivo/A");
@@ -584,10 +572,16 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
 	    classA.addSubClass(classC);	   	    
 	    classC.addSubClass(classD);
 	    classC.addSubClass(classE);
-	    
-	    while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
-	    	Thread.sleep(delay);
-	    }
+
+		// this will receive the abox inferences
+        Model inf = ModelFactory.createDefaultModel();
+        
+        // abox
+		OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); 
+
+        // set up SimpleReasoner and register it with abox		
+        SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
+		aBox.register(simpleReasoner);
 	    
         // add & remove ABox type statements and verify inferences
 		Resource a = aBox.createResource("http://test.vivo/a");
@@ -636,8 +630,6 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
 		Assert.assertFalse(inf.contains(b, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
 		Assert.assertFalse(inf.contains(c, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
 		Assert.assertFalse(inf.contains(d, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
-		
-		simpleReasonerTBoxListener.setStopRequested();		
 	}	
 
 	/*