incremental development for nihvivo-3206

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java

@@ -95,7 +95,7 @@ public class ABoxUpdater {
 			      break;
 			   case DELETE:
 				  if ("Delete".equals(change.getNotes())) {
-				     deleteClass(change);
+				     deleteIndividualsOfType(change);
 				  } else {
 					 renameClassToParent(change);
 				  }
@@ -325,13 +325,13 @@ public class ABoxUpdater {
 	
 	/**
 	 * 
-	 * Remove all instances of and references to a class in the abox of the knowledge base.
+	 * Remove all instances of the given class from the abox of the knowledge base.
 	 * 
 	 * @param   change - an AtomicOntologyChange object representing a class
 	 *                   delete operation.
 	 *                    
 	 */
-	public void deleteClass(AtomicOntologyChange change) throws IOException {
+	public void deleteIndividualsOfType(AtomicOntologyChange change) throws IOException {
 
 		//logger.log("Processing a class deletion of class " + change.getSourceURI());
 		
@@ -348,17 +348,32 @@ public class ABoxUpdater {
 		aboxModel.enterCriticalSection(Lock.WRITE);
 	    try {
 	       int count = 0;
+	       int refCount = 0;
 	       StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass);
 
     	   while (iter.hasNext()) {
 			   count++;
 			   Statement typeStmt = iter.next();
-			   retractions.add(typeStmt);
+			   
+			   StmtIterator iter2 = aboxModel.listStatements(typeStmt.getSubject(), (Property) null, (RDFNode) null);
+			   
+			   while (iter2.hasNext()) {
+				  Statement subjstmt = iter2.next();
+			      retractions.add(subjstmt);
+			   }
+			   
+			   StmtIterator iter3 = aboxModel.listStatements((Resource) null, (Property) null, typeStmt.getSubject());
+			   
+			   while (iter3.hasNext()) {
+				  Statement objstmt = iter3.next();
+			      retractions.add(objstmt);
+			      refCount++;
+			   }
 		   }   
 		   
 		   //log summary of changes
 		   if (count > 0) {
-			   logger.log("Removed " + count + " " + deletedClass.getURI() + " type assertion" + ((count > 1) ? "s" : ""));
+			   logger.log("Removed " + count + " individual " + ((count > 1) ? "s" : "" + " of type " + deletedClass.getURI()) + " (refs = " + refCount + ")");
 		   }
 		   
 		   aboxModel.remove(retractions);

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java

@@ -32,11 +32,8 @@ import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
 
 /**
- * Performs knowledge base updates if necessary to align with a
+ * Performs knowledge base updates necessary to align with a
  * new ontology version.
- * 
- * @author bjl23
- *
  */
 public class KnowledgeBaseUpdater {
 
@@ -90,9 +87,9 @@ public class KnowledgeBaseUpdater {
 	private void performUpdate() throws IOException {
 		
 		log.info("\tperforming SPARQL construct additions (abox)");
-		performSparqlConstructAdditions(settings.getSparqlConstructAdditionsDir(), settings.getAssertionOntModelSelector().getABoxModel());
+		performSparqlConstructAdditions(settings.getSparqlConstructAdditionsDir(), settings.getUnionOntModelSelector().getABoxModel() , settings.getAssertionOntModelSelector().getABoxModel());
 		log.info("\tperforming SPARQL construct deletions (inferences)");
-		performSparqlConstructRetractions(settings.getSparqlConstructDeletionsDir(), settings.getInferenceOntModelSelector().getABoxModel());
+		performSparqlConstructRetractions(settings.getSparqlConstructDeletionsDir(), settings.getUnionOntModelSelector().getABoxModel() , settings.getAssertionOntModelSelector().getABoxModel());
 		
 		List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
 		
@@ -107,51 +104,50 @@ public class KnowledgeBaseUpdater {
     	updateABox(changes);
 	}
 	
-	private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel aboxModel) throws IOException {
+	private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
 		
-		Model anonModel = performSparqlConstructs(sparqlConstructDir, aboxModel, true);
+		Model anonModel = performSparqlConstructs(sparqlConstructDir, readModel, true);
 		
 		if (anonModel == null) {
 			return;
 		}
 		
-		aboxModel.enterCriticalSection(Lock.WRITE);
+		writeModel.enterCriticalSection(Lock.WRITE);
 		try {
 			JenaIngestUtils jiu = new JenaIngestUtils();
-			Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", aboxModel);
+			Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", writeModel);
 			Model actualAdditions = ModelFactory.createDefaultModel();
 			StmtIterator stmtIt = additions.listStatements();
 			
 			while (stmtIt.hasNext()) {
 				Statement stmt = stmtIt.nextStatement();
-				if (!aboxModel.contains(stmt)) {
+				if (!writeModel.contains(stmt)) {
 					actualAdditions.add(stmt);
 				}
 			}
 			
-			aboxModel.add(actualAdditions);
+			writeModel.add(actualAdditions);
 			record.recordAdditions(actualAdditions);
 		} finally {
-			aboxModel.leaveCriticalSection();
+			writeModel.leaveCriticalSection();
 		}	
-		
 	}
 	
-	private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel model) throws IOException {
+	private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
 		
-		Model retractions = performSparqlConstructs(sparqlConstructDir, model, false);
+		Model retractions = performSparqlConstructs(sparqlConstructDir, readModel, false);
 		
 		if (retractions == null) {
 			return;
 		}
 		
-		model.enterCriticalSection(Lock.WRITE);
+		writeModel.enterCriticalSection(Lock.WRITE);
 		
 		try {
-			model.remove(retractions);
+			writeModel.remove(retractions);
 			record.recordRetractions(retractions);
 		} finally {
-			model.leaveCriticalSection();
+			writeModel.leaveCriticalSection();
 		}
 		
 	}
@@ -165,7 +161,8 @@ public class KnowledgeBaseUpdater {
 	 * @param aboxModel
 	 */
 	private Model performSparqlConstructs(String sparqlConstructDir, 
-			                              OntModel aboxModel, boolean add) throws IOException {
+			                              OntModel readModel,
+			                              boolean add)   throws IOException {
 		
 		Model anonModel = ModelFactory.createDefaultModel();
 		File sparqlConstructDirectory = new File(sparqlConstructDir);
@@ -182,32 +179,33 @@ public class KnowledgeBaseUpdater {
 		for (int i = 0; i < sparqlFiles.length; i ++) {
 			File sparqlFile = sparqlFiles[i];			
 			try {
-				BufferedReader reader = 
+				BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
-					new BufferedReader(new FileReader(sparqlFile));
 				StringBuffer fileContents = new StringBuffer();
 				String ln;
+				
 				while ( (ln = reader.readLine()) != null) {
 					fileContents.append(ln).append('\n');
 				}
+				
 				try {
 					log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFiles[i].getName());
 					Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
-					aboxModel.enterCriticalSection(Lock.WRITE);
+					readModel.enterCriticalSection(Lock.READ);
 					try {
-						QueryExecution qe = QueryExecutionFactory.create(q,	aboxModel);
+						QueryExecution qe = QueryExecutionFactory.create(q,	readModel);
 						long numBefore = anonModel.size();
 						qe.execConstruct(anonModel);
 						long numAfter = anonModel.size();
                         long num = numAfter - numBefore;
                         
                         if (num > 0) {
-						   logger.log((add ? "Added " : "Removed ") + num + (add ? "" : " inferred") +
+						   logger.log((add ? "Added " : "Removed ") + num + 
 								   " statement"  + ((num > 1) ? "s" : "") + 
 								   " using the SPARQL construct query from file " + sparqlFiles[i].getName());
                         }
                         qe.close();
 					} finally {
-						aboxModel.leaveCriticalSection();
+						readModel.leaveCriticalSection();
 					}
 				} catch (Exception e) {
 					logger.logError(this.getClass().getName() + 

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/UpdateSettings.java

@@ -23,6 +23,7 @@ public class UpdateSettings {
 	private String defaultNamespace;
 	private OntModelSelector assertionOntModelSelector;
 	private OntModelSelector inferenceOntModelSelector;
+	private OntModelSelector unionOntModelSelector;
 	private OntModel oldTBoxModel;
 	private OntModel newTBoxModel;
 	private OntModel oldTBoxAnnotationsModel;
@@ -82,6 +83,9 @@ public class UpdateSettings {
 	public OntModelSelector getInferenceOntModelSelector() {
 		return inferenceOntModelSelector;
 	}
+	public OntModelSelector getUnionOntModelSelector() {
+		return unionOntModelSelector;
+	}
 	public String getLogFile() {
 		return logFile;
 	}
@@ -118,6 +122,9 @@ public class UpdateSettings {
 	public void setInferenceOntModelSelector(OntModelSelector ontModelSelector) {
 		this.inferenceOntModelSelector = ontModelSelector;
 	}
+	public void setUnionOntModelSelector(OntModelSelector ontModelSelector) {
+		this.unionOntModelSelector = ontModelSelector;
+	}
 	public OntModel getOldTBoxModel() {
 		return oldTBoxModel;
 	}

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

@@ -90,6 +90,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			settings.setDefaultNamespace(wadf.getDefaultNamespace());
 			settings.setAssertionOntModelSelector(ModelContext.getBaseOntModelSelector(ctx));
 			settings.setInferenceOntModelSelector(ModelContext.getInferenceOntModelSelector(ctx));
+			settings.setUnionOntModelSelector(ModelContext.getUnionOntModelSelector(ctx));
 			
 			try {
 				OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));