various migration improvements

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

@@ -64,7 +64,7 @@ public class KnowledgeBaseUpdater {
 		}
 			
 		long startTime = System.currentTimeMillis();
-        log.info("Migrating the knowledge base");
+        log.info("Performing any necessary data migration");
         logger.log("Started knowledge base migration");
 		
 		try {
@@ -104,12 +104,6 @@ public class KnowledgeBaseUpdater {
     		    log.error(e,e);
     		}
     	    
-    	    try {
-        	    migrateMigrationMetadata(servletContext);
-    		    logger.log("Migrated migration metadata");
-    	    } catch (Exception e) {
-    	    	log.error("unable to migrate migration metadata " + e.getMessage());
-    	    }
 		}
 	        	
 		// update ABox data any time
@@ -264,39 +258,6 @@ public class KnowledgeBaseUpdater {
 		aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
 	}
 	
-	// special for 1.5 - temporary code
-	// migrate past migration indicators to not use blank nodes and move them to app metadata model
-	// changing structure for pre 1.5 ones in the process
-	private void migrateMigrationMetadata(ServletContext servletContext) throws Exception {
-		
-		String baseResourceURI = "http://vitro.mannlib.cornell.edu/ns/vitro/metadata/migration/";
-		String queryFile = "MigrationData.sparql";
-		
-		RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(servletContext).getRDFService();
-
-		String fmQuery = FileUtils.readFileToString(new File(settings.getSparqlConstructDeletionsDir() + "/" + queryFile));
-		Model toRemove = ModelFactory.createDefaultModel();
-		toRemove.read(rdfService.sparqlConstructQuery(fmQuery, RDFService.ModelSerializationFormat.RDFXML), null);
-	
-		String cmQuery = FileUtils.readFileToString(new File(settings.getSparqlConstructAdditionsDir() + "/" + queryFile));
-		Model toAdd = ModelFactory.createDefaultModel();
-		toAdd.read(rdfService.sparqlConstructQuery(cmQuery, RDFService.ModelSerializationFormat.RDFXML), null);
-		
-		ByteArrayOutputStream outAdd = new ByteArrayOutputStream();
-		toAdd.write(outAdd);
-		InputStream inAdd = new ByteArrayInputStream(outAdd.toByteArray());		
-		ChangeSet addChangeSet = rdfService.manufactureChangeSet();		    
-	    addChangeSet.addAddition(inAdd, RDFService.ModelSerializationFormat.RDFXML, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
-		rdfService.changeSetUpdate(addChangeSet);	
-
-		ByteArrayOutputStream outRemove = new ByteArrayOutputStream();
-		toRemove.write(outRemove);
-		InputStream inRemove = new ByteArrayInputStream(outRemove.toByteArray());		
-		ChangeSet removeChangeSet = rdfService.manufactureChangeSet();		    
-	    removeChangeSet.addRemoval(inRemove, RDFService.ModelSerializationFormat.RDFXML, JenaDataSourceSetupBase.JENA_DB_MODEL);
-		rdfService.changeSetUpdate(removeChangeSet);	
-	}
-	
 	private void updateTBoxAnnotations() {
 		TBoxUpdater tboxUpdater = new TBoxUpdater(settings, logger, record);         
 		try {

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

@@ -88,10 +88,6 @@ public class TBoxUpdater {
     public void modifyPropertyQualifications() throws IOException {
  
     }
-
-    private Model mergeConfigurations(Model oldConfig, Model newConfig) {
-        return null;
-    }
     
     public void updateDefaultAnnotationValues() throws IOException {
         updateDefaultAnnotationValues(null);
@@ -528,7 +524,8 @@ public class TBoxUpdater {
                 "    OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
                 "               ?configuration config:propertyGroup ?rgroup } \n" +
                 "    OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
-                "               ?configuration config:displayName ?rlabel } \n " +
+                "               ?configuration config:displayName ?rlabel . \n " +
+                "                   FILTER(?rlabel != ?label) } \n " +
                 "    OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
                 "               ?configuration vitro:displayRantAnnot ?rdisplayRank } \n " +
                 "    OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +

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

@@ -81,6 +81,8 @@ public class SimpleReasonerSetup implements ServletContextListener {
             
             log.info("Pellet reasoner connected for the TBox");
      
+            waitForTBoxReasoning(sce); 
+            
             // set up simple reasoning for the ABox
                                 
             RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService();            
@@ -131,7 +133,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
         int sleeps = 0;
         // sleep at least once to make sure the TBox reasoning gets started
         while ((0 == sleeps) || ((sleeps < 1000) && pelletListener.isReasoning())) {
-            if ((sleeps % 10) == 0) { // print message at 10 second intervals
+            if (((sleeps - 1) % 10) == 0) { // print message at 10 second intervals
                 log.info("Waiting for initial TBox reasoning to complete");
             }
             Thread.sleep(1000);   

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

@@ -141,7 +141,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			if(!JenaDataSourceSetupBase.isFirstStartup()) {
     			try {
     			    ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
-    			    log.info("Data migration required");
     			    migrationChangesMade = ontologyUpdater.update(ctx);
     			    if (tryMigrateDisplay) {
     			        try {
@@ -221,8 +220,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		StartupStatus.getBean(ctx).info(this, "Updating knowledge base: reports are in '" + dataDir + "'");
 
 		Path changedDir = createDirectory(dataDir, "changedData");
-		settings.setAddedDataFile(changedDir.resolve("addedData.n3").toString());
+		settings.setAddedDataFile(changedDir.resolve(timestampedFileName("addedData", "n3")).toString());
-		settings.setRemovedDataFile(changedDir.resolve("removedData.n3").toString());
+		settings.setRemovedDataFile(changedDir.resolve(timestampedFileName("removedData", "n3")).toString());
 		
 		Path logDir = createDirectory(dataDir, "logs");
 		settings.setLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate", "log")).toString());