VIVO-542 fixes bug with restriction deletion and various small improvements

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Classes2ClassesOperationController.java

@@ -57,7 +57,7 @@ public class Classes2ClassesOperationController extends BaseEditController {
             return;
         }
 
-        VClassDao vcDao = request.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = request.getLanguageNeutralWebappDaoFactory().getVClassDao();
         
         String modeStr = request.getParameter("opMode");
         modeStr = (modeStr == null) ? "" : modeStr;

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java

@@ -1048,11 +1048,20 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         try {
             OntResource subclass = getOntClass(ontModel,c2c.getSubclassURI());
             OntResource superclass = getOntClass(ontModel,c2c.getSuperclassURI());
+            if(subclass == null || superclass == null) {
+                log.warn("unable to delete " + c2c.getSubclassURI() + 
+                        " rdfs:subClassOf " + c2c.getSuperclassURI());
+                if (subclass == null) {
+                    log.warn(c2c.getSubclassURI() + " not found in the model.");
+                }
+                if (superclass == null) {
+                    log.warn(c2c.getSuperclassURI() + " not found in the model.");
+                }
+                return;
+            }
             Model removal = ModelFactory.createDefaultModel();
             Model additions = ModelFactory.createDefaultModel(); // to repair any rdf:Lists
-            if ((subclass != null) && (superclass != null)) {
+            removal.add(ontModel.listStatements(subclass, RDFS.subClassOf, superclass));
-                removal.add(ontModel.listStatements(subclass, RDFS.subClassOf, superclass));
-            }
             if (subclass.isAnon()) {
                 Model[] changeSet = getSmartRemoval(subclass, getOntModel());
                 removal.add(changeSet[0]);

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

@@ -207,6 +207,14 @@ public class KnowledgeBaseUpdater {
                 StmtIterator sit = anonModel.listStatements();
                 while (sit.hasNext()) {
                     Statement stmt = sit.nextStatement();
+                    // Skip statements with blank nodes (unsupported) to avoid 
+                    // excessive deletion.  In the future, the whole updater 
+                    // could be modified to change whole graphs at once through
+                    // the RDFService, but right now this whole thing is statement
+                    // based.
+                    if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
+                        continue;
+                    }
                     Iterator<String> graphIt = dataset.listNames();
                     while(graphIt.hasNext()) {
                         String graph = graphIt.next();
@@ -223,8 +231,9 @@ public class KnowledgeBaseUpdater {
                 //log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs");
             } else {
                 Model writeModel = dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL);
+                Model dedupeModel = dataset.getDefaultModel();
                 Model additions = jiu.renameBNodes(
-                        anonModel, settings.getDefaultNamespace() + "n", writeModel);
+                        anonModel, settings.getDefaultNamespace() + "n", dedupeModel);
                 Model actualAdditions = ModelFactory.createDefaultModel();
                 StmtIterator stmtIt = additions.listStatements();      
                 while (stmtIt.hasNext()) {

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java

@@ -217,6 +217,9 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
     private List<Statement> sort(List<Statement> stmts) {
         List<Statement> output = new ArrayList<Statement>();
         int originalSize = stmts.size();
+        if(originalSize == 1) {
+            return stmts;
+        }
         List <Statement> remaining = stmts;
         ConcurrentLinkedQueue<Resource> subjQueue = new ConcurrentLinkedQueue<Resource>();
         for(Statement stmt : remaining) {

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java

@@ -744,6 +744,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
     private List<Statement> sort(List<Statement> stmts) {
         List<Statement> output = new ArrayList<Statement>();
         int originalSize = stmts.size();
+        if (originalSize == 1) 
+            return stmts;
         List <Statement> remaining = stmts;
         ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource> subjQueue = 
                 new ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource>();

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

@@ -410,6 +410,11 @@ public class ABoxRecomputer {
 			while (iter.hasNext()) {
 				Statement stmt = iter.next();
 				
+				// skip statements with blank nodes to avoid excessive deletion
+				if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
+				    continue;
+				}
+				
 				inferenceModel.enterCriticalSection(Lock.WRITE);
 				try {
 					inferenceModel.remove(stmt);

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

@@ -221,7 +221,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
        int[] maxActiveAndIdle = getMaxActiveAndIdle(ctx);
        cpds.setMaxPoolSize(maxActiveAndIdle[0]);
        cpds.setMinPoolSize(maxActiveAndIdle[1]);
-       cpds.setMaxIdleTime(3600); // ms
+       cpds.setMaxIdleTime(43200); // s
        cpds.setMaxIdleTimeExcessConnections(300);
        cpds.setAcquireIncrement(5);
        cpds.setNumHelperThreads(6);