Merge branch 'maint-rel-1.6' into develop

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

@@ -107,6 +107,9 @@ public class ABoxRecomputer {
 	    }
 	}
 
+	// don't check for existing inferences in the rebuild model
+	private boolean DO_CHECK = true;
+	
 	/*
 	 * Recompute the entire ABox inference graph. The new 
 	 * inference graph is built in a separate model and
@@ -132,11 +135,13 @@ public class ABoxRecomputer {
 			
 			log.info("Recomputing inferences for " + individuals.size() + " individuals");
 			
+            long start = System.currentTimeMillis();
+			
 			for (String individualURI : individuals) {			
 				Resource individual = ResourceFactory.createResource(individualURI);
 				
 				try {
-					addedABoxTypeAssertion(individual, inferenceRebuildModel, unknownTypes);
+					addedABoxTypeAssertion(individual, inferenceRebuildModel, unknownTypes, DO_CHECK);
 					simpleReasoner.setMostSpecificTypes(individual, inferenceRebuildModel, unknownTypes);
 					List<ReasonerPlugin> pluginList = simpleReasoner.getPluginList();
 					if (pluginList.size() > 0) {
@@ -165,8 +170,11 @@ public class ABoxRecomputer {
 				}
 				
 				numStmts++;
-	            if ((numStmts % 10000) == 0) {
+	            if ((numStmts % 1000) == 0) {
-	                log.info("Still computing class subsumption ABox inferences...");
+	                log.info("Still computing class subsumption ABox inferences (" 
+	                        + numStmts + "/" + individuals.size() + " individuals)");
+	                log.info((System.currentTimeMillis() - start) / 1000 + " ms per individual");
+	                start = System.currentTimeMillis();
 	            }
 	            
 	            if (stopRequested) {
@@ -275,7 +283,7 @@ public class ABoxRecomputer {
 			log.info("Finished computing sameAs ABox inferences");	
 			
 			try {
-				if (updateInferenceModel(inferenceRebuildModel)) {
+				if (updateInferenceModel(inferenceRebuildModel, individuals)) {
 		        	log.info("a stopRequested signal was received during updateInferenceModel. Halting Processing.");
 		        	return;
 				}
@@ -366,7 +374,13 @@ public class ABoxRecomputer {
 				
 	}
 	
-	protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
+   protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel,
+           HashSet<String> unknownTypes) {
+       addedABoxTypeAssertion(individual, inferenceModel, unknownTypes, true);
+   }
+	   
+	protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel, 
+	        HashSet<String> unknownTypes, boolean checkRedundancy) {
 
 		StmtIterator iter = null;
 		
@@ -376,7 +390,8 @@ public class ABoxRecomputer {
 			
 			while (iter.hasNext()) {	
 				Statement stmt = iter.next();
-				simpleReasoner.addedABoxTypeAssertion(stmt, inferenceModel, unknownTypes);
+				simpleReasoner.addedABoxTypeAssertion(
+				        stmt, inferenceModel, unknownTypes, checkRedundancy);
 			}
 		} finally {
 		    if (iter != null) {
@@ -388,121 +403,68 @@ public class ABoxRecomputer {
 	/*
 	 * reconcile a set of inferences into the application inference model
 	 */
-	protected boolean updateInferenceModel(Model inferenceRebuildModel) {
+	protected boolean updateInferenceModel(Model inferenceRebuildModel, 
+	        Collection<String> individuals) {
 
 	    log.info("Updating ABox inference model");
-	Iterator<Statement> iter = null;
 
 	    // Remove everything from the current inference model that is not
 	    // in the recomputed inference model	
 	    int num = 0;
 	    scratchpadModel.enterCriticalSection(Lock.WRITE);
 	    scratchpadModel.removeAll();	
-	log.info("Updating ABox inference model (checking for outdated inferences)");
+	    Model rebuild = ModelFactory.createDefaultModel();
-	try {
+	    Model existing = ModelFactory.createDefaultModel();
-		inferenceModel.enterCriticalSection(Lock.READ);
 	    
+	    long start = System.currentTimeMillis();
+	    
+	    for (String individualURI : individuals) {
+	        rebuild.removeAll();
+	        existing.removeAll();
+	        Resource subjInd = ResourceFactory.createResource(individualURI); 
+	        inferenceModel.enterCriticalSection(Lock.READ);		
 	        try {
-			iter = listModelStatements(inferenceModel, JenaDataSourceSetupBase.JENA_INF_MODEL);
+	            existing.add(inferenceModel.listStatements(subjInd, null, (RDFNode) null));
-			while (iter.hasNext()) {				
+	        } finally {
-				Statement stmt = iter.next();
+	            inferenceModel.leaveCriticalSection();
-				if (!inferenceRebuildModel.contains(stmt)) {
+	        }
-				   scratchpadModel.add(stmt);  
+	        inferenceRebuildModel.enterCriticalSection(Lock.READ);        
+            try {
+                rebuild.add(inferenceRebuildModel.listStatements(subjInd, null, (RDFNode) null));
+            } finally {
+                inferenceRebuildModel.leaveCriticalSection();
+            }
+            
+            Model retractions = existing.difference(rebuild);
+	        Model additions = rebuild.difference(existing);
+
+	        inferenceModel.enterCriticalSection(Lock.WRITE);
+	        try {
+	            inferenceModel.remove(retractions);
+	            inferenceModel.add(additions);
+	        } finally {
+	            inferenceModel.leaveCriticalSection();
+	        }
+	        
+	        inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
+            try {
+                inferenceRebuildModel.remove(rebuild);
+            } finally {
+                inferenceRebuildModel.leaveCriticalSection();
             }
 
 	        num++;
-                if ((num % 10000) == 0) {
+	        if ((num % 1000) == 0) {
-                    log.info("Still updating ABox inference model (checking for outdated inferences)...");
+	            log.info("Still updating ABox inference model (" + 
+                        + num + "/" + individuals.size() + " individuals)");
+                log.info((System.currentTimeMillis() - start) / 1000 + " ms per individual");
+                start = System.currentTimeMillis();
 	        }
 
 	        if (stopRequested) {
 	            return true;
-                }
-			}
-		} finally {
-//		    if (iter != null) {
-//			    iter.close();
-//		    }
-            inferenceModel.leaveCriticalSection();
 	        }
 
-		try {
-			iter = listModelStatements(scratchpadModel, SimpleReasonerSetup.JENA_INF_MODEL_SCRATCHPAD);
-			while (iter.hasNext()) {
-				Statement stmt = iter.next();
-				
-				// skip statements with blank nodes to avoid excessive deletion
-				if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
-				    continue;
-				}
-				
-				inferenceModel.enterCriticalSection(Lock.WRITE);
-				try {
-					inferenceModel.remove(stmt);
-				} finally {
-					inferenceModel.leaveCriticalSection();
-				}
-			}
-		} finally {
-//		    if (iter != null) {
-//		        iter.close();    
-//		    }
-		}
-					
-		// Add everything from the recomputed inference model that is not already
-		// in the current inference model to the current inference model.	
-		try {
-			scratchpadModel.removeAll();
-			log.info("Updating ABox inference model (adding any new inferences)");
-			iter = listModelStatements(inferenceRebuildModel, SimpleReasonerSetup.JENA_INF_MODEL_REBUILD); 
-			
-			while (iter.hasNext()) {				
-				Statement stmt = iter.next();
-				
-				inferenceModel.enterCriticalSection(Lock.READ);
-				try {
-					if (!inferenceModel.contains(stmt)) {
-						 scratchpadModel.add(stmt);
-					}
-				} finally {
-				     inferenceModel.leaveCriticalSection();	
-				}
-									
-				num++;
-                if ((num % 10000) == 0) {
-                    log.info("Still updating ABox inference model (adding any new inferences)...");
-                }
-                
-                if (stopRequested) {
-                	return true;
-                }
-			}
-		} finally {
-//		    if (iter != null) {
-//			    iter.close();	
-//		    }
-		}
-					
-		iter = listModelStatements(scratchpadModel, SimpleReasonerSetup.JENA_INF_MODEL_SCRATCHPAD);
-		try {
-    		while (iter.hasNext()) {
-    			Statement stmt = iter.next();
-    			
-    			inferenceModel.enterCriticalSection(Lock.WRITE);
-    			try {
-    				inferenceModel.add(stmt);
-    			} finally {
-    				inferenceModel.leaveCriticalSection();
-    			}
-    		}
-		} finally {
-//		    if (iter != null) {
-//		        iter.close();
-//		    }
-		}
-	} finally {
-		scratchpadModel.removeAll();
-		scratchpadModel.leaveCriticalSection();			
 	    }
 
     	log.info("ABox inference model updated");

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ReasonerPlugin.java

@@ -12,6 +12,8 @@ public interface ReasonerPlugin {
 	
 	public boolean isInterestedInRemovedStatement(Statement stmt);
 	
+	public boolean isConfigurationOnlyPlugin();
+	
 	public void addedABoxStatement(Statement stmt, 
 			                       Model aboxAssertionsModel, 
 			                       Model aboxInferencesModel, 

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java

@@ -162,6 +162,10 @@ public class SimpleReasoner extends StatementListener {
         this.doSameAs = tf;
     }
     
+    public boolean getSameAsEnabled() {
+        return this.doSameAs;
+    }
+
 	/*
 	 * Performs incremental ABox reasoning based
 	 * on the addition of a new statement
@@ -343,6 +347,12 @@ public class SimpleReasoner extends StatementListener {
         changedTBoxStatement(stmt, false);
 	}
 
+	protected void addedABoxTypeAssertion(Statement stmt, 
+	        Model inferenceModel, 
+	        HashSet<String> unknownTypes) {
+	    addedABoxTypeAssertion(stmt, inferenceModel, unknownTypes, true);
+	}
+	
 	/**
 	 * Performs incremental reasoning based on a new type assertion
 	 * added to the ABox (assertion that an individual is of a certain
@@ -353,7 +363,8 @@ public class SimpleReasoner extends StatementListener {
 	 */
 	protected void addedABoxTypeAssertion(Statement stmt, 
                                           Model inferenceModel, 
-                                          HashSet<String> unknownTypes) {
+                                          HashSet<String> unknownTypes,
+                                          boolean checkRedundancy) {
 				
 	    tboxModel.enterCriticalSection(Lock.READ);
 		try {
@@ -379,7 +390,7 @@ public class SimpleReasoner extends StatementListener {
 							Statement infStmt = 
                                 ResourceFactory.createStatement(stmt.getSubject(), 
                                                                 RDF.type, parentClass);
-							addInference(infStmt,inferenceModel,true);
+							addInference(infStmt, inferenceModel, true, checkRedundancy);
 						}						
 					}					
 				} else {
@@ -1189,13 +1200,20 @@ public class SimpleReasoner extends StatementListener {
         addInference(infStmt,inferenceModel,true);
 	}
 	
-	protected void addInference(Statement infStmt, Model inferenceModel, boolean handleSameAs) {
+	protected void addInference(Statement infStmt, Model inferenceModel, 
+	        boolean handleSameAs) {
+	    addInference(infStmt, inferenceModel, handleSameAs, true);
+	}
+	
+	protected void addInference(Statement infStmt, Model inferenceModel, 
+	        boolean handleSameAs, boolean checkRedundancy) {
 		
 		aboxModel.enterCriticalSection(Lock.READ);
 		try {
 			inferenceModel.enterCriticalSection(Lock.WRITE);
 			try {
-				if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt))  {
+				if (!checkRedundancy 
+				        || (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt)))  {
 					inferenceModel.add(infStmt);
 			    }
 		
@@ -1732,8 +1750,6 @@ public class SimpleReasoner extends StatementListener {
         }        
     } 
 
-
-
 	/**
 	 * Utility method for logging
 	 */

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/plugin/DisableSameAs.java

@@ -15,7 +15,7 @@ import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
 /**
  * Disables sameAs in associated SimpleReasoner.
  */
-public abstract class DisableSameAs implements ReasonerPlugin {
+public class DisableSameAs implements ReasonerPlugin {
 	
     private static final Log log = LogFactory.getLog(DisableSameAs.class);
     	
@@ -27,6 +27,10 @@ public abstract class DisableSameAs implements ReasonerPlugin {
         log.info("owl:sameAs disabled in SimpleReasoner.");
     }	
 	
+    public boolean isConfigurationOnlyPlugin() {
+        return true;
+    }
+    
     public SimpleReasoner getSimpleReasoner() {
     	return this.simpleReasoner;
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/plugin/SimpleBridgingRule.java

@@ -62,6 +62,10 @@ public abstract class SimpleBridgingRule implements ReasonerPlugin {
         
 	}
 	
+	public boolean isConfigurationOnlyPlugin() {
+	    return false;
+	}
+	
 	public boolean isInterestedInAddedStatement(Statement stmt) {
 		return isRelevantPredicate(stmt);
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/plugin/SimplePropertyAndTypeRule.java

@@ -36,6 +36,10 @@ public abstract class SimplePropertyAndTypeRule implements ReasonerPlugin {
         INFERRED_PROP = ResourceFactory.createProperty(inferredProp);
 	}
 	
+	public boolean isConfigurationOnlyPlugin() {
+        return false;
+    }
+	
 	public boolean isInterestedInAddedStatement(Statement stmt) {
 		return (RDF.type.equals(stmt.getPredicate()) || isRelevantPredicate(stmt));
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java

@@ -104,7 +104,10 @@ public class SimpleReasonerSetup implements ServletContextListener {
                     ReasonerPlugin plugin = (ReasonerPlugin) Class.forName(
                             classname).getConstructors()[0].newInstance();
                     plugin.setSimpleReasoner(simpleReasoner);
+                    if (!plugin.isConfigurationOnlyPlugin()) {
                         pluginList.add(plugin);
+                        log.info("adding reasoner plugin " + plugin.getClass().getName());
+                    }
                 } catch(Throwable t) {              
                     ss.info(this, "Could not instantiate reasoner plugin " + classname);
                 }

webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerInversePropertyTest.java

@@ -14,6 +14,7 @@ import com.hp.hpl.jena.ontology.OntProperty;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
@@ -431,10 +432,10 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
 		tBox.register(simpleReasonerTBoxListener);
 
         // add abox data
-		Resource a = aBox.createResource("http://test.vivo/a");
+		Resource a = aBox.createIndividual("http://test.vivo/a", OWL.Thing);
-		Resource b = aBox.createResource("http://test.vivo/b");
+		Resource b = aBox.createIndividual("http://test.vivo/b", OWL.Thing);
-		Resource c = aBox.createResource("http://test.vivo/c");
+		Resource c = aBox.createIndividual("http://test.vivo/c", OWL.Thing);
-		Resource d = aBox.createResource("http://test.vivo/d");
+		Resource d = aBox.createIndividual("http://test.vivo/d", OWL.Thing);
 				
 		aBox.add(a,P,b);	
 	    aBox.add(c,P,d);
@@ -496,8 +497,8 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
 		tBox.register(simpleReasonerTBoxListener);	    
 		
         // add statements to the abox and verify inference
-		Resource c = aBox.createResource("http://test.vivo/c");
+		Resource c = aBox.createIndividual("http://test.vivo/c", OWL.Thing);
-		Resource d = aBox.createResource("http://test.vivo/d");
+		Resource d = aBox.createIndividual("http://test.vivo/d", OWL.Thing);
 	    aBox.add(c,P,d);
 		Assert.assertTrue(inf.contains(d,Q,c));
 		
@@ -555,10 +556,10 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
 		aBox.register(simpleReasoner);
 		
         // abox statements
-		Resource a = aBox.createResource("http://test.vivo/a");
+		Resource a = aBox.createIndividual("http://test.vivo/a", OWL.Thing);
-		Resource b = aBox.createResource("http://test.vivo/b");
+		Resource b = aBox.createIndividual("http://test.vivo/b", OWL.Thing);
-		Resource c = aBox.createResource("http://test.vivo/c");
+		Resource c = aBox.createIndividual("http://test.vivo/c", OWL.Thing);
-		Resource d = aBox.createResource("http://test.vivo/d");
+		Resource d = aBox.createIndividual("http://test.vivo/d", OWL.Thing);
 
 	    aBox.add(a,P,b);
         aBox.add(c,X,d);

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

@@ -782,10 +782,10 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
 		aBox.register(simpleReasoner);
 		
         // Individuals a, b, c and d
-		Resource a = aBox.createResource("http://test.vivo/a");
+		Resource a = aBox.createIndividual("http://test.vivo/a", OWL.Thing);
-		Resource b = aBox.createResource("http://test.vivo/b");
+		Resource b = aBox.createIndividual("http://test.vivo/b", OWL.Thing);
-		Resource c = aBox.createResource("http://test.vivo/c");
+		Resource c = aBox.createIndividual("http://test.vivo/c", OWL.Thing);
-		Resource d = aBox.createResource("http://test.vivo/d");
+		Resource d = aBox.createIndividual("http://test.vivo/d", OWL.Thing);
 		
 		aBox.add(a,P,c);
 		aBox.add(a,S,literal1);