improvements and bugfixes for NIHVIVO-205 ontology upgrade

webapp/config/web.xml

@@ -72,18 +72,19 @@
     <listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetup</listener-class>
   </listener>
 
+  <!-- Invokes process to perform updates to align with ontology changes if needed -->
+  <!-- Needs to run before submodels are attached and Pellet is set up -->
+
+  <listener>
+     <listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase</listener-class>
+  </listener>
+
   <!-- Attaching submodels permits extra RDF files to be made visible without storing the data in the DB. -->
 
   <listener>
      <listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.AttachSubmodels</listener-class>
   </listener>
 
-  <!-- Invokes process to perform updates to align with ontology changes if needed -->
-
-  <listener>
-     <listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase</listener-class>
-  </listener>
-
   <!-- Pellet setup enables reasoning.  Inferences are cached in a separate DB graph. -->
   <!-- Changing the class name sets the kindss of inferences that are materialized. -->
   <!-- See documentation for details. -->

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

@@ -84,7 +84,7 @@ public class OntologyUpdater {
 		
 		AtomicOntologyChangeLists changes = 
 				new AtomicOntologyChangeLists(rawChanges, 
-						settings.getOntModelSelector().getTBoxModel(), 
+						settings.getNewTBoxModel(), 
 						settings.getOldTBoxModel());
 		
 		//updateTBox(changes);
@@ -186,7 +186,7 @@ public class OntologyUpdater {
 	private void updateTBoxAnnotations() throws IOException {
 		(new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
 				settings.getNewTBoxAnnotationsModel(),
-		        settings.getOntModelSelector().getTBoxModel(), logger, record))
+		        settings.getOntModelSelector().getABoxModel(), logger, record))
 		        .updateVitroPropertyDefaultValues();
 	}
 	

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

@@ -46,13 +46,17 @@ public class SimpleOntologyChangeRecord implements OntologyChangeRecord {
 	
 	public void recordAdditions(Model incrementalAdditions) {
 		additionsModel.add(incrementalAdditions);
+		if (additionsModel.size() > 0) {
 			write(additionsModel, additionsFile);
 		}
+	}
 
 	public void recordRetractions(Model incrementalRetractions) {
 		retractionsModel.add(incrementalRetractions);
+		if (retractionsModel.size() > 0) {
 			write(retractionsModel, retractionsFile);
 		}
+	}
 	
 	private void write(Model model, File file) {
 		try {

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

@@ -123,6 +123,10 @@ public class TBoxUpdater {
 			 if (!newObject.equals(oldObject)) {
 				 objects = siteModel.listObjectsOfProperty(subject,predicate);
 				 
+				 if (!objects.hasNext()) {
+					 continue;
+				 }
+				 
 				 RDFNode siteObject = objects.next();
 				 if (objects.hasNext()) {
 					 logger.logError("Warning: found " + objects.toList().size() +
@@ -163,18 +167,18 @@ public class TBoxUpdater {
 			 }		  
 		   }
 		  
-		   siteModel.add(additions);
+		   Model actualAdditions = additions.difference(retractions);
-		   record.recordAdditions(additions);
+		   siteModel.add(actualAdditions);
-		   siteModel.remove(retractions);
+		   record.recordAdditions(actualAdditions);
-		   record.recordRetractions(retractions);
+		   Model actualRetractions = retractions.difference(additions);
+		   siteModel.remove(actualRetractions);
+		   record.recordRetractions(actualRetractions);
 		
 		   // log summary of changes
-           StmtIterator addedIter = additions.listStatements();
            logger.log("Updated the default vitro annotation value for " + 
-        		   addedIter.toList().size() + " statments in the knowledge base.");
+        		   actualAdditions.size() + " statments in the knowledge base.");
 		   
-           StmtIterator removedIter = retractions.listStatements();
+           long numRemoved = actualRetractions.size() - actualAdditions.size();
-           int numRemoved = removedIter.toList().size() - addedIter.toList().size();
            logger.log("Removed " + numRemoved +
         		      " superfluous vitro annotation property settings from the knowledge base.");
            
@@ -183,15 +187,21 @@ public class TBoxUpdater {
 		    //		  
 
 			Model newAnnotationSettings = newTboxModel.difference(oldTboxModel);
-			siteModel.add(newAnnotationSettings);
+			Model newAnnotationSettingsToAdd = ModelFactory.createDefaultModel();
-			record.recordAdditions(newAnnotationSettings);
+			StmtIterator newStmtIt = newAnnotationSettings.listStatements();
+			while (newStmtIt.hasNext()) {
+				Statement stmt = newStmtIt.next();
+				if (!siteModel.contains(stmt)) {
+					newAnnotationSettingsToAdd.add(stmt);
+				}
+			}
+			siteModel.add(newAnnotationSettingsToAdd);
+			record.recordAdditions(newAnnotationSettingsToAdd);
             
 			// log the additions
-            iter = newAnnotationSettings.listStatements();
-			  
             //summary
-            logger.log("Added " + iter.toList().size() + " new annotation property settings to the knowledge base. This includes " +
+            logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property settings to the knowledge base. This includes " +
-                         "exsiting annotation properties applied to exsiting classes where they weren't applied before, or existing " +
+                         "existing annotation properties applied to existing classes where they weren't applied before, or existing " +
                          "properties applied to new classes. No new annotation properties have been introduced.");
             //details
             

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

@@ -60,6 +60,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 	private final String SPARQL_CONSTRUCTS_DIR = DATA_DIR + "sparqlConstructs/";
 	private final String MISC_REPLACEMENTS_FILE = DATA_DIR + "miscReplacements.rdf";
 	private final String OLD_TBOX_MODEL_DIR = DATA_DIR + "oldVersion/";
+	private final String NEW_TBOX_MODEL_DIR = "/WEB-INF/submodels/";
 	private final String OLD_TBOX_ANNOTATIONS_DIR = DATA_DIR + "oldAnnotations/";
 	private final String NEW_TBOX_ANNOTATIONS_DIR = "/WEB-INF/ontologies/user";
 	
@@ -91,7 +92,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			settings.setOntModelSelector(oms);
 			OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
 			settings.setOldTBoxModel(oldTBoxModel);
-			settings.setNewTBoxModel(oms.getTBoxModel());
+			OntModel newTBoxModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_MODEL_DIR));
+			settings.setNewTBoxModel(newTBoxModel);
 			OntModel oldTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_ANNOTATIONS_DIR));
 			settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
 			OntModel newTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_ANNOTATIONS_DIR));