NIHVIVO-2804 individuals deleted in error during kb migration

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

@@ -344,46 +344,21 @@ public class ABoxUpdater {
 
 	    Model retractions = ModelFactory.createDefaultModel();
 		
-		// Remove statements where the deleted class is the subject  (e.g. statements with vitro annotation properties as the predicate)
-		aboxModel.enterCriticalSection(Lock.WRITE);
-	    try {
-	       int count = 0;
-		   StmtIterator iter = aboxModel.listStatements(deletedClass, (Property) null, (RDFNode) null);
-		   
-		   while (iter.hasNext()) {
-			   Statement oldStatement = iter.next();
-			   count++;
-			   retractions.add(oldStatement);
-			   //logChange(oldStatement, false);
-		   }
-		   
-		   if (count > 0) {
-			   logger.log("Removed " + count + " subject reference" + ((count > 1) ? "s" : "") + " to the "  + deletedClass.getURI() + " class");
-		   }
-		} finally {
-			aboxModel.leaveCriticalSection();
-		}
-
 		// Remove instances of the deleted class
 		aboxModel.enterCriticalSection(Lock.WRITE);
 	    try {
-	    	int count = 0;
+	       int count = 0;
-	    	StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass);
+	       StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, deletedClass);
 
-    		while (iter.hasNext()) {
+    	   while (iter.hasNext()) {
 			   count++;
 			   Statement typeStmt = iter.next();
 			   retractions.add(typeStmt);
-
+		   }   
-			   StmtIterator iter2 = aboxModel.listStatements(typeStmt.getSubject(), (Property) null, (RDFNode) null);
-			   while (iter2.hasNext()) {
-				   retractions.add(iter2.next());
-			   }   
-		   }
 		   
 		   //log summary of changes
 		   if (count > 0) {
-			   logger.log("Removed " + count + " instance" + ((count > 1) ? "s" : "") + " of the "  + deletedClass.getURI() + " class");
+			   logger.log("Removed " + count + " " + deletedClass.getURI() + " type assertion" + ((count > 1) ? "s" : ""));
 		   }
 		   
 		   aboxModel.remove(retractions);
@@ -392,30 +367,6 @@ public class ABoxUpdater {
 		} finally {
 			aboxModel.leaveCriticalSection();
 		}
-
-	    // Remove other object references to the deleted class - what would these be? nothing, I think.
-		aboxModel.enterCriticalSection(Lock.WRITE);
-	    try {
-	       int count = 0;
-	       StmtIterator iter = aboxModel.listStatements((Resource) null, (Property) null, deletedClass);
-   
-		   while (iter.hasNext()) {
-			   count++;
-			   Statement oldStatement = iter.next();
-			   retractions.add(oldStatement);
-			   //logChange(oldStatement, false);
-		   }
-		   
-		   //log summary of changes
-		   if (count > 0) {
-			   logger.log("Removed " + count + " object reference" + ((count > 1) ? "s" : "") + " to the "  + deletedClass.getURI() + " class");
-		   }
-
-		   aboxModel.remove(retractions);
-		   record.recordRetractions(retractions);		   
-		} finally {
-			aboxModel.leaveCriticalSection();
-		}
 	}
 	
 	public void processPropertyChanges(List<AtomicOntologyChange> changes) throws IOException {

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

@@ -91,7 +91,7 @@ public class KnowledgeBaseUpdater {
 		
 		log.info("\tperforming SPARQL construct additions (abox)");
 		performSparqlConstructAdditions(settings.getSparqlConstructAdditionsDir(), settings.getAssertionOntModelSelector().getABoxModel());
-		log.info("\tperforming SPARQL construct deletions (infenences)");
+		log.info("\tperforming SPARQL construct deletions (inferences)");
 		performSparqlConstructRetractions(settings.getSparqlConstructDeletionsDir(), settings.getInferenceOntModelSelector().getABoxModel());
 		
 		List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();

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

@@ -933,6 +933,7 @@ public class SimpleReasoner extends StatementListener {
 				setMostSpecificTypes(stmt.getSubject(), inferenceRebuildModel);
 			}
 			
+ /*			
 			log.info("Computing property-based ABox inferences");			
 			iter = tboxModel.listStatements((Resource) null, RDFS.subPropertyOf, (RDFNode) null);
 			int numStmts = 0;
@@ -974,6 +975,7 @@ public class SimpleReasoner extends StatementListener {
                     log.info("Still computing property-based ABox inferences...");
                 }
 			}
+	*/
 		} catch (Exception e) {
 			 log.error("Exception while recomputing ABox inference model", e);
 			 inferenceRebuildModel.removeAll(); // don't do this in the finally, it's needed in the case
@@ -985,6 +987,7 @@ public class SimpleReasoner extends StatementListener {
 			 inferenceRebuildModel.leaveCriticalSection();
 		}			
 		
+			
 		// reflect the recomputed inferences into the application inference
 		// model.
 		inferenceRebuildModel.enterCriticalSection(Lock.WRITE);

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

@@ -245,7 +245,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 	
 	private static String timestampedFileName(String prefix, String suffix) {
 		SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH-mm-sss");
-		return prefix + "." + sdf.format(new Date()) + suffix;
+		return prefix + "." + sdf.format(new Date()) + "." + suffix;
 	}
 	
 	private class ModelDirectoryNotFoundException extends RuntimeException {