merging in 1.1 branch changes

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

@@ -267,7 +267,7 @@ public class ABoxUpdater {
 					
 					if (count > 0) {
 						//TODO - take out the detailed logging after our internal testing is completed.
-				        logger.log("There " + ((count > 1) ? "are" : "is") + " " + count + " individuals in the model that are of type " + parentOfAddedClass.getURI() + "," +
+				        logger.log("There " + ((count > 1) ? "are" : "is") + " " + count + " individual" + ((count > 1) ? "s" : "")  + " in the model that " + ((count > 1) ? "are" : "is") + " of type " + parentOfAddedClass.getURI() + "," +
 				        		    " and a new subclass of that class has been added: " + addedClass.getURI() + ". " +
 				        		    "Please review " + ((count > 1) ? "these" : "this") + " individual" + ((count > 1) ? "s" : "") + " to see whether " + ((count > 1) ? "they" : "it") + " should be of type: " +  addedClass.getURI() );
 					}

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

@@ -81,6 +81,7 @@ public class OntologyUpdater {
 	private void performUpdate() throws IOException {
 		
 		performSparqlConstructAdditions(settings.getSparqlConstructAdditionsDir(), settings.getOntModelSelector().getABoxModel());
+		performSparqlConstructRetractions(settings.getSparqlConstructDeletionsDir(), settings.getOntModelSelector().getABoxModel());
 		
 		List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
 		
@@ -128,9 +129,38 @@ public class OntologyUpdater {
 			aboxModel.leaveCriticalSection();
 		}
 		
-
 	}
 	
+	private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel aboxModel) throws IOException {
+		
+		Model retractions = performSparqlConstructs(sparqlConstructDir, aboxModel);
+		
+		if (retractions == null) {
+			return;
+		}
+		
+		aboxModel.enterCriticalSection(Lock.WRITE);
+		try {
+			Model actualRetractions = ModelFactory.createDefaultModel();
+			StmtIterator stmtIt = retractions.listStatements();
+			while (stmtIt.hasNext()) {
+				Statement stmt = stmtIt.nextStatement();
+				if (aboxModel.contains(stmt)) {
+					actualRetractions.add(stmt);
+				}
+			}
+			aboxModel.remove(actualRetractions);
+			if (actualRetractions.size() > 0) {
+				logger.log("Removed " + actualRetractions.size() + " statement" 
+						   + ((actualRetractions.size() > 1) ? "s" : "") + 
+						   " using SPARQL CONSTRUCT queries.");
+			}
+			record.recordRetractions(actualRetractions);
+		} finally {
+			aboxModel.leaveCriticalSection();
+		}
+		
+	}
 	
 	/**
 	 * Performs a set of arbitrary SPARQL CONSTRUCT queries on the 

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

@@ -31,6 +31,7 @@ public class TBoxUpdater {
 	private OntModel siteModel;
 	private OntologyChangeLogger logger;  
 	private OntologyChangeRecord record;
+	private boolean detailLogs = false;
 
 	/**
 	 * 
@@ -160,31 +161,53 @@ public class TBoxUpdater {
 				 continue; 
 			 }
 			 
+			 // If a subject-property pair occurs in the old annotation TBox and the new annotations 
+			 // TBox, but not in the site model, then it is considered an erroneous deletion and
+			 // the value from the new TBox is added into the site model.
+			 // sjm: 7-16-2010. We want this here now to add back in annotations mistakenly dropped
+			 // in the .9 to 1.0 migration, but I'm not sure we would want this here permanently.
+			 // Shouldn't a site be allowed to delete annotations if they want to?
+			 
+			 NodeIterator siteObjects = siteModel.listObjectsOfProperty(subject,predicate);
+			 
+			 if (siteObjects == null || !siteObjects.hasNext()) {
+	        	    try {
+	    				additions.add(subject, predicate, newObject);
+	    			
+						if (detailLogs) {
+							   logger.log( "adding Statement: subject = " + subject.getURI() +
+								           " property = " + predicate.getURI() +
+				                           " object = " + (newObject.isLiteral() ?  ((Literal)newObject).getLexicalForm() 
+				                		                                          : ((Resource)newObject).getURI()));	
+							}
+					} catch (Exception e) {
+						logger.logError("Error trying to add statement with property " + predicate.getURI() +
+								" of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
+					}				 
+				 
+				   continue;
+			 }
+			 
+			 			 			 
 			 if (!newObject.equals(oldObject)) {
-				 NodeIterator siteObjects = siteModel.listObjectsOfProperty(subject,predicate);
 
-				 RDFNode siteObject = null;
+				 RDFNode siteObject = siteObjects.next();
 
-				 if (siteObjects != null && siteObjects.hasNext()) {
+		         i = 1;
-			
+				 while (siteObjects.hasNext()) {
-					 siteObject = siteObjects.next();
+					 i++; 
-	
+					 siteObjects.next();
-			         i = 1;
-					 while (siteObjects.hasNext()) {
-						 i++; 
-						 siteObjects.next();
-					 } 
-	
-					 if (i > 1) {
-						 logger.log("WARNING: found " + i +
-								 " statements with subject = " + subject.getURI() + 
-								 " and property = " + predicate.getURI() +
-								 " in the site annotations model. (maximum of one is expected). "); 
-						 continue; 
-					 }
 				 } 
 
-				 if (siteObject == null || siteObject.equals(oldObject)) {
+				 if (i > 1) {
+					 logger.log("WARNING: found " + i +
+							 " statements with subject = " + subject.getURI() + 
+							 " and property = " + predicate.getURI() +
+							 " in the site annotations model. (maximum of one is expected). "); 
+					 continue; 
+				 }
+				 	 
+				 if (siteObject.equals(oldObject)) {
 	        	    try {
 	        	    	StmtIterator it = siteModel.listStatements(subject, predicate, (RDFNode)null);
 	        	    	while (it.hasNext()) {
@@ -199,13 +222,15 @@ public class TBoxUpdater {
 	        	    try {
 	    				additions.add(subject, predicate, newObject);
 	    				
-						logger.log("Changed the value of property "  + predicate.getURI() +
+	    				if (detailLogs) {
+						   logger.log("Changed the value of property "  + predicate.getURI() +
 								" of subject = " + subject.getURI() + 
 								" from " +
 								 (oldObject.isResource() ? ((Resource)oldObject).getURI() : ((Literal)oldObject).getLexicalForm()) +								
 								" to " + 
 								 (newObject.isResource() ? ((Resource)newObject).getURI() : ((Literal)newObject).getLexicalForm()) +
 								 " in the knowledge base:\n");
+	    				}
 					} catch (Exception e) {
 						logger.logError("Error trying to change the value of property " + predicate.getURI() +
 								" of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
@@ -230,7 +255,7 @@ public class TBoxUpdater {
            long numRemoved = actualRetractions.size() - actualAdditions.size();
            if (numRemoved > 0) {
 	           logger.log("Removed " + numRemoved +
-	        		      " superfluous vitro annotation property setting" + ((numRemoved > 1) ? "s" : "") + " from the knowledge base.");
+	        		      " outdated vitro annotation property setting" + ((numRemoved > 1) ? "s" : "") + " from the knowledge base.");
            }
            
 		    //	   Copy annotation property settings that were introduced in the new ontology
@@ -245,19 +270,19 @@ public class TBoxUpdater {
 				if (!siteModel.contains(stmt)) {
 					newAnnotationSettingsToAdd.add(stmt);
 				
-					// TODO remove this for production
+					if (detailLogs) {
-					logger.log( "adding Statement: subject = " + stmt.getSubject().getURI() +
+					   logger.log( "adding Statement: subject = " + stmt.getSubject().getURI() +
-						    " property = " + stmt.getPredicate().getURI() +
+						           " property = " + stmt.getPredicate().getURI() +
-		                    " object = " + (stmt.getObject().isLiteral() ?  ((Literal)stmt.getObject()).getLexicalForm() 
+		                           " object = " + (stmt.getObject().isLiteral() ?  ((Literal)stmt.getObject()).getLexicalForm() 
 		                		                                          : ((Resource)stmt.getObject()).getURI()));	
+					}
 				}
 			}
 			
 			siteModel.add(newAnnotationSettingsToAdd);
 			record.recordAdditions(newAnnotationSettingsToAdd);
             
-			// log the additions
+			// log the additions - summary
-            //summary
 			if (newAnnotationSettingsToAdd.size() > 0) {
 				boolean plural = (newAnnotationSettingsToAdd.size() > 1);
 	            logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property setting" + (plural ? "s" : "") + " to the knowledge base. This includes " +