setting the stage for some connection management improvements

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java

@@ -1313,8 +1313,5 @@ private String doRename(String oldNamespace,String newNamespace,HttpServletRespo
 		return result;
 		
     }
-	public void prepareSmush (VitroRequest vreq) {
-		String smushPropURI = vreq.getParameter("smushPropURI");
-	}
 	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java

@@ -10,11 +10,14 @@ import java.util.List;
 import java.util.Map;
 
 import javax.servlet.RequestDispatcher;
+import javax.servlet.ServletContext;
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
+import javax.servlet.http.HttpSession;
 
 import org.apache.commons.fileupload.FileItem;
+import org.apache.commons.fileupload.servlet.ServletFileUpload;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -47,6 +50,7 @@ public class RDFUploadController extends BaseEditController {
 	
 	public void doPost(HttpServletRequest rawRequest,
 			HttpServletResponse response) throws ServletException, IOException {
+	    
 		FileUploadServletRequest req = FileUploadServletRequest.parseRequest(rawRequest,
 				maxFileSizeInBytes);
 		if (req.hasFileUploadException()) {
@@ -85,6 +89,10 @@ public class RDFUploadController extends BaseEditController {
 		
 		boolean makeClassgroups = (request.getParameter("makeClassgroups") != null);
 		
+		// add directly to the ABox model without reading first into 
+		// a temporary in-memory model
+		boolean directRead = ("directAddABox".equals(request.getParameter("mode")));
+		
 		int[] portalArray = null;
 		String individualCheckIn = request.getParameter("checkIndividualsIntoPortal"); 
 		if (individualCheckIn != null) {
@@ -109,13 +117,20 @@ public class RDFUploadController extends BaseEditController {
           
 		String uploadDesc ="";		
 				
-		OntModel tempModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+		OntModel uploadModel = (directRead) 
+		    ? getABoxModel(request.getSession(), getServletContext())
+		    : ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
 		
 		/* ********************* GET RDF by URL ********************** */
 		String RDFUrlStr =  request.getParameter("rdfUrl");
 		if (RDFUrlStr != null && RDFUrlStr.length() > 0) {
 			try {
-				tempModel.read(RDFUrlStr, languageStr); // languageStr may be null and default would be RDF/XML
+			    uploadModel.enterCriticalSection(Lock.WRITE);
+			    try {
+			        uploadModel.read(RDFUrlStr, languageStr); // languageStr may be null and default would be RDF/XML
+			    } finally {
+			        uploadModel.leaveCriticalSection();
+			    }
 				uploadDesc = verb + " RDF from " + RDFUrlStr;				
 			} catch (JenaException ex){
 	                forwardToFileUploadError("Could not parse file to " + languageStr + ": " + ex.getMessage(), req, response);
@@ -129,7 +144,12 @@ public class RDFUploadController extends BaseEditController {
 		    if( fileStreams.get("rdfStream") != null && fileStreams.get("rdfStream").size() > 0 ){
 		        FileItem rdfStream = fileStreams.get("rdfStream").get(0);
 		        try {
-		            tempModel.read( rdfStream.getInputStream(), null, languageStr);
+		            uploadModel.enterCriticalSection(Lock.WRITE);
+		            try {
+		                uploadModel.read( rdfStream.getInputStream(), null, languageStr);
+		            } finally {
+		                uploadModel.leaveCriticalSection();
+		            }
 		            uploadDesc = verb + " RDF from file " + rdfStream.getName();                
 		        } catch (IOException e) {
 		            forwardToFileUploadError("Could not read file: " + e.getLocalizedMessage(), req, response);
@@ -145,43 +165,31 @@ public class RDFUploadController extends BaseEditController {
 		        }
 		    }
 		}
+		
 		/* ********** Do the model changes *********** */
+		if( !directRead && uploadModel != null ){
 		    long tboxstmtCount = 0L;
 		    long aboxstmtCount = 0L;
-		if( tempModel != null ){
+
 			JenaModelUtils xutil = new JenaModelUtils();
-		    OntModel tboxModel=null;
+		    OntModel tboxModel = getTBoxModel(
-		    OntModel aboxModel=null;
+		            request.getSession(), getServletContext());
+		    OntModel aboxModel = getABoxModel(
+		            request.getSession(), getServletContext());
 		    OntModel tboxChangeModel=null;
 		    Model aboxChangeModel=null;
-		    
-		    try {
-		       tboxModel = ((OntModelSelector) request.getSession()
-            			.getAttribute("baseOntModelSelector")).getTBoxModel(); 
-		       aboxModel = ((OntModelSelector) request.getSession()
-           			.getAttribute("baseOntModelSelector")).getABoxModel(); 
-		       
-		    } catch (Exception e) {}
-		    if (tboxModel==null) {
-		        tboxModel = ((OntModelSelector) getServletContext()
-            			.getAttribute("baseOntModelSelector")).getTBoxModel();
-		    }
-		    if (aboxModel==null) {
-		        aboxModel = ((OntModelSelector) getServletContext()
-            			.getAttribute("baseOntModelSelector")).getABoxModel();
-		    }
 		    if (tboxModel != null) {
-		    	tboxChangeModel = xutil.extractTBox(tempModel);
+		    	tboxChangeModel = xutil.extractTBox(uploadModel);
 		        tboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(), tboxModel,tboxChangeModel,remove,makeClassgroups,portalArray,loginBean.getUserURI());
 		    }
 		    if (aboxModel != null) {
-		    	aboxChangeModel = tempModel.remove(tboxChangeModel);
+		    	aboxChangeModel = uploadModel.remove(tboxChangeModel);
 		        aboxstmtCount = operateOnModel(request.getFullWebappDaoFactory(), aboxModel,aboxChangeModel,remove,makeClassgroups,portalArray,loginBean.getUserURI());
 		    }
-		    
-		}
-			
 		    request.setAttribute("uploadDesc", uploadDesc + ". " + verb + " " + (tboxstmtCount + aboxstmtCount) + "  statements.");
+		} else {
+		    request.setAttribute("uploadDesc", "RDF upload successful.");
+		}
 	    
         RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
         request.setAttribute("bodyJsp","/templates/edit/specific/upload_rdf_result.jsp");
@@ -308,5 +316,31 @@ public class RDFUploadController extends BaseEditController {
   		return new VitroJenaSpecialModelMaker(myVjmm, request);
   	 }
      
+     private OntModel getABoxModel(HttpSession session, ServletContext ctx) {   
+         if (session != null 
+                 && session.getAttribute("baseOntModelSelector")
+                         instanceof OntModelSelector) {
+             return ((OntModelSelector) 
+                     session.getAttribute("baseOntModelSelector"))
+                     .getABoxModel();   
+         } else {
+             return ((OntModelSelector) 
+                     ctx.getAttribute("baseOntModelSelector")).getABoxModel();
+         }
+     }    
+
+     private OntModel getTBoxModel(HttpSession session, ServletContext ctx) {   
+         if (session != null 
+                 && session.getAttribute("baseOntModelSelector")
+                         instanceof OntModelSelector) {
+             return ((OntModelSelector) 
+                     session.getAttribute("baseOntModelSelector"))
+                     .getTBoxModel();   
+         } else {
+             return ((OntModelSelector) 
+                     ctx.getAttribute("baseOntModelSelector")).getTBoxModel();
+         }
+     }    
+     
 	private static final Log log = LogFactory.getLog(RDFUploadController.class.getName());
 }

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

@@ -35,11 +35,11 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 public class DataPropertyStatementDaoSDB extends DataPropertyStatementDaoJena
 							implements DataPropertyStatementDao {
 
-	private Dataset dataset;
+	private DatasetWrapperFactory dwf;
 	
-	public DataPropertyStatementDaoSDB(Dataset dataset, WebappDaoFactoryJena wadf) {
+	public DataPropertyStatementDaoSDB(DatasetWrapperFactory datasetWrapperFactory, WebappDaoFactoryJena wadf) {
 		super (wadf);
-		this.dataset = dataset;
+		this.dwf = datasetWrapperFactory;
 	}
 	
 	@Override
@@ -58,7 +58,16 @@ public class DataPropertyStatementDaoSDB extends DataPropertyStatementDaoJena
 			       "   <" + entity.getURI() + "> ?p ?o . \n" +
 			       "   FILTER(isLiteral(?o)) \n" +
 	            "} }" ;
-        	Model results = QueryExecutionFactory.create(QueryFactory.create(query), dataset).execConstruct();
+        	Model results = null;
+        	DatasetWrapper w = dwf.getDatasetWrapper();
+            Dataset dataset = w.getDataset();
+            dataset.getLock().enterCriticalSection(Lock.READ);
+            try { 
+        	    results = QueryExecutionFactory.create(QueryFactory.create(query), dataset).execConstruct();
+            } finally {
+                dataset.getLock().leaveCriticalSection();
+                w.close();
+            }
         	OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, results); 
             ontModel.enterCriticalSection(Lock.READ);
             try {

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

@@ -0,0 +1,34 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.sdb.sql.SDBConnection;
+
+public class DatasetWrapper {
+
+    private SDBConnection conn;
+    private Dataset dataset;
+    private boolean closed = false;
+    
+    public DatasetWrapper(Dataset dataset) {
+        this.dataset = dataset;
+    }
+    
+    public Dataset getDataset() {
+        if (!closed) {
+            return dataset;
+        } else throw new RuntimeException("No operations on a closed dataset");
+    }
+    
+    public void close() {
+        if (!closed) {
+            closed = true;
+            if (conn != null) {
+                dataset.close();
+                conn.close();
+            }
+        }
+    }
+    
+}

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

@@ -0,0 +1,9 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+public interface DatasetWrapperFactory {
+
+    public DatasetWrapper getDatasetWrapper();
+    
+}

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

@@ -41,26 +41,27 @@ import com.hp.hpl.jena.vocabulary.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 
 public class IndividualDaoSDB extends IndividualDaoJena {
 
-	private Dataset dataset;
+	private DatasetWrapperFactory dwf;
 	private WebappDaoFactoryJena wadf;
 	
-    public IndividualDaoSDB(Dataset dataset, WebappDaoFactoryJena wadf) {
+    public IndividualDaoSDB(DatasetWrapperFactory dwf, WebappDaoFactoryJena wadf) {
         super(wadf);
-        this.dataset = dataset;
+        this.dwf = dwf;
     }
     
-    protected Dataset getDataset() {
+    protected DatasetWrapper getDatasetWrapper() {
-    	return this.dataset;
+    	return dwf.getDatasetWrapper();
     }
     
     protected Individual makeIndividual(String individualURI) {
-    	return new IndividualSDB2(individualURI, getDataset(), getWebappDaoFactory());
+    	return new IndividualSDB(individualURI, this.dwf, getWebappDaoFactory());
     }
 
     private static final Log log = LogFactory.getLog(IndividualDaoSDB.class.getName());
@@ -90,7 +91,10 @@ public class IndividualDaoSDB extends IndividualDaoJena {
         		ents.addAll(getIndividualsByVClass(vc));
         	}
         } else {
-        	Model model;
+        	Model model = null;
+        	try {
+        	    DatasetWrapper w = getDatasetWrapper();
+        	    Dataset dataset = w.getDataset();
             	dataset.getLock().enterCriticalSection(Lock.READ);
             	try {
             		String query = 
@@ -108,18 +112,28 @@ public class IndividualDaoSDB extends IndividualDaoJena {
             		model = QueryExecutionFactory.create(QueryFactory.create(query), dataset).execConstruct();
             	} finally {
             		dataset.getLock().leaveCriticalSection();
+            		w.close();
             	}
                 ResIterator resIt = model.listSubjects();
                 try {
                     while (resIt.hasNext()) {
                         Resource ind = resIt.nextResource();
                         if (!ind.isAnon()) {
+                            //Individual indd = new IndividualImpl(ind.getURI());
+                            //indd.setLocalName(ind.getLocalName());
+                            //indd.setName(ind.getLocalName());
+                            //ents.add(indd);
                         	ents.add(new IndividualSDB(ind.getURI(), dataset, getWebappDaoFactory(), model));
                         }
                     }
                 } finally {
                     resIt.close();
                 }
+        	} finally {
+        	    if (model != null && !model.isClosed()) {
+        	        model.close();
+        	    }
+        	}
         }
      
 
@@ -285,6 +299,9 @@ public class IndividualDaoSDB extends IndividualDaoJena {
         
         
 	    Query q = QueryFactory.create(query);
+	    DatasetWrapper w = getDatasetWrapper();
+	    Dataset dataset = w.getDataset();
+	    dataset.getLock().enterCriticalSection(Lock.READ);
 	    QueryExecution qe = QueryExecutionFactory.create(q, dataset);
 	    try {
 	        ResultSet rs = qe.execSelect();
@@ -296,6 +313,8 @@ public class IndividualDaoSDB extends IndividualDaoJena {
 	        }
         } finally {
         	qe.close();
+        	dataset.getLock().leaveCriticalSection();
+        	w.close();
         }
         
 //        getOntModel().enterCriticalSection(Lock.READ);

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

@@ -69,13 +69,13 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     private WebappDaoFactoryJena webappDaoFactory = null;
     private Float _searchBoostJena = null;
     private boolean retreivedNullRdfsLabel = false;
-    private Dataset dataset = null;
+    private DatasetWrapperFactory dwf = null;
     private String individualURI = null; 
     private Model model = null;
     
-    public IndividualSDB(String individualURI, Dataset dataset, WebappDaoFactoryJena wadf, Model initModel) {
+    public IndividualSDB(String individualURI, DatasetWrapperFactory datasetWrapperFactory, WebappDaoFactoryJena wadf, Model initModel) {
     	this.individualURI = individualURI;
-    	this.dataset = dataset;
+    	this.dwf = datasetWrapperFactory;
       
     	try {
 	    	initModel.getLock().enterCriticalSection(Lock.READ);
@@ -113,12 +113,14 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         this.webappDaoFactory = wadf;
     }
     
-    public IndividualSDB(String individualURI, Dataset dataset, WebappDaoFactoryJena wadf) {
+    public IndividualSDB(String individualURI, DatasetWrapperFactory datasetWrapperFactory, WebappDaoFactoryJena wadf) {
     	this.individualURI = individualURI;
-    	this.dataset = dataset;
+    	this.dwf = datasetWrapperFactory;
     	
+    	DatasetWrapper w = getDatasetWrapper();
+    	Dataset dataset = w.getDataset();
     	try {
-	    	this.dataset.getLock().enterCriticalSection(Lock.READ);
+	    	dataset.getLock().enterCriticalSection(Lock.READ);
 	    	String getStatements = 
 	    		"CONSTRUCT " +
 	    		"{ <"+individualURI+">  <" + RDFS.label.getURI() + "> ?ooo. \n" +
@@ -133,7 +135,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
 	    		 "}";
     		model = QueryExecutionFactory.create(QueryFactory.create(getStatements), dataset).execConstruct();
     	} finally {
-    		this.dataset.getLock().leaveCriticalSection();
+    		dataset.getLock().leaveCriticalSection();
+    		w.close();
     	}
     	
     	OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, model);
@@ -155,6 +158,10 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         this.webappDaoFactory = wadf;
     }
 
+    private DatasetWrapper getDatasetWrapper() {
+        return this.dwf.getDatasetWrapper();
+    }
+    
     public String getName() { 
         if (this.name != null) {
             return name;
@@ -250,9 +257,10 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     */
     public boolean doesFlag1Match(int flagBitMask) { 
         Long [] numerics = FlagMathUtils.numeric2numerics(flagBitMask);
-        this.dataset.getLock().enterCriticalSection(Lock.READ);
         String Ask = null;      
-        
+        DatasetWrapper w = getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+        dataset.getLock().enterCriticalSection(Lock.READ);
         try{
             for( Long numericPortal : numerics){
                 int portalid = FlagMathUtils.numeric2Portalid(numericPortal);
@@ -262,19 +270,19 @@ public class IndividualSDB extends IndividualImpl implements Individual {
                 	return false;
             }
         }finally{
-           
+        	dataset.getLock().leaveCriticalSection();
-        	this.dataset.getLock().leaveCriticalSection();
+        	w.close();
         }
         return true;
     }
 
     private void doFlag1() {
-       
     	String getObjects = null;
-    	
-        dataset.getLock().enterCriticalSection(Lock.READ);
         Model tempModel = ModelFactory.createDefaultModel();
         OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+        DatasetWrapper w = getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+        dataset.getLock().enterCriticalSection(Lock.READ);
         try {
         	ClosableIterator typeIt = null;
             int portalNumeric = 0;
@@ -310,16 +318,19 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         } finally {
             tempModel.close();
             ontModel.close();
-        	this.dataset.getLock().leaveCriticalSection();
+            dataset.getLock().leaveCriticalSection();
+        	w.close();
         }
     }
 
     
     private void doFlag2() {
     	String getObjects = null;
-    	dataset.getLock().enterCriticalSection(Lock.READ);
         Model tempModel = ModelFactory.createDefaultModel();
         OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+        DatasetWrapper w = getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+    	dataset.getLock().enterCriticalSection(Lock.READ);
         try {
             ClosableIterator typeIt=null;
             String flagSet = "";
@@ -352,7 +363,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         } finally {
         	tempModel.close();
             ontModel.close();
-        	this.dataset.getLock().leaveCriticalSection();
+        	dataset.getLock().leaveCriticalSection();
+        	w.close();
         }
     }
 
@@ -566,7 +578,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             String getPropertyValue = 
             	"SELECT ?value" +
             	"WHERE { GRAPH ?g { <" + individualURI + ">" + webappDaoFactory.getJenaBaseDao().SEARCH_BOOST_ANNOT + "?value} }";
-            
+            DatasetWrapper w = getDatasetWrapper();
+            Dataset dataset = w.getDataset();
         	dataset.getLock().enterCriticalSection(Lock.READ);
             try{
                 try {
@@ -577,8 +590,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
                 }                
                 return searchBoost;
             }finally{
-               
             	dataset.getLock().leaveCriticalSection();
+            	w.close();
             }
         }
     }    
@@ -646,10 +659,11 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     }
 
     private void doUrlAndAnchor() { 
-        
-    	this.dataset.getLock().enterCriticalSection(Lock.READ);
         Model tempModel = ModelFactory.createDefaultModel();
         OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+        DatasetWrapper w = getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+    	dataset.getLock().enterCriticalSection(Lock.READ);
         try {
             if (webappDaoFactory.getJenaBaseDao().PRIMARY_LINK != null) {
             	String listPropertyValues =
@@ -685,7 +699,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         } finally {
         	tempModel.close();
         	ontModel.close();
-        	this.dataset.getLock().leaveCriticalSection();
+        	dataset.getLock().leaveCriticalSection();
+        	w.close();
         }
     }
 
@@ -767,11 +782,12 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	}
     	List<ObjectPropertyStatement> objectPropertyStatements = new ArrayList<ObjectPropertyStatement>();
     
-    	dataset.getLock().enterCriticalSection(Lock.READ);
 	    Model tempModel = ModelFactory.createDefaultModel();
         OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+        DatasetWrapper w = getDatasetWrapper();
+        Dataset dataset = w.getDataset();
+    	dataset.getLock().enterCriticalSection(Lock.READ);
     	try {
-    		
     		String valuesOfProperty = 
     			"CONSTRUCT{<" + this.individualURI + "> <" + propertyURI + "> ?object}" +
     			"WHERE{ GRAPH ?g { <" + this.individualURI + "> <" + propertyURI + "> ?object} }";
@@ -784,8 +800,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     			if (!s.getSubject().canAs(OntResource.class) || !s.getObject().canAs(OntResource.class)) {
     			    continue;	
     			}
-    			Individual subj = new IndividualSDB(((OntResource) s.getSubject().as(OntResource.class)).getURI(), dataset, webappDaoFactory);
+    			Individual subj = new IndividualSDB(((OntResource) s.getSubject().as(OntResource.class)).getURI(), this.dwf, webappDaoFactory);
-    			Individual obj = new IndividualSDB(((OntResource) s.getObject().as(OntResource.class)).getURI(), dataset, webappDaoFactory);
+    			Individual obj = new IndividualSDB(((OntResource) s.getObject().as(OntResource.class)).getURI(), this.dwf, webappDaoFactory);
     			ObjectProperty op = webappDaoFactory.getObjectPropertyDao().getObjectPropertyByURI(s.getPredicate().getURI());
     			if (subj != null && obj != null && op != null) {
     				ObjectPropertyStatement ops = new ObjectPropertyStatementImpl();
@@ -802,6 +818,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     		tempModel.close();
     		ontModel.close();
      		dataset.getLock().leaveCriticalSection();
+     		w.close();
     	}
      	return objectPropertyStatements;
     }
@@ -813,6 +830,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	}
     	List<Individual> relatedIndividuals = new ArrayList<Individual>();
     	
+    	DatasetWrapper w = getDatasetWrapper();
+    	Dataset dataset = w.getDataset();
     	dataset.getLock().enterCriticalSection(Lock.READ);
     	try {
     		String valuesOfProperty = 
@@ -825,11 +844,12 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	    	RDFNode value = result.get("object");
     	    	if (value.canAs(OntResource.class)) {
         	    	relatedIndividuals.add(
-        	    		new IndividualSDB(((OntResource) value.as(OntResource.class)).getURI(), dataset, webappDaoFactory) );  
+        	    		new IndividualSDB(((OntResource) value.as(OntResource.class)).getURI(), this.dwf, webappDaoFactory) );  
         	    } 
     	    }
     	} finally {
     		dataset.getLock().leaveCriticalSection();
+    		w.close();
     	}
     	return relatedIndividuals;
     }
@@ -839,7 +859,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	if (propertyURI == null) {
     		return null;
     	}
-    	
+    	DatasetWrapper w = getDatasetWrapper();
+    	Dataset dataset = w.getDataset();
     	dataset.getLock().enterCriticalSection(Lock.READ);
     	try {
     		String valueOfProperty = 
@@ -849,12 +870,13 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     		QuerySolution result = results.next();
     		RDFNode value = result.get("object");
     	    if (value != null && value.canAs(OntResource.class)) {
-    	    	return new IndividualSDB(((OntResource) value.as(OntResource.class)).getURI(), dataset, webappDaoFactory);  
+    	    	return new IndividualSDB(((OntResource) value.as(OntResource.class)).getURI(), dwf, webappDaoFactory);  
     	    } else {
     	    	return null;
     	    }
     	} finally {
     		dataset.getLock().leaveCriticalSection();
+    		w.close();
     	}
     }
     

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

@@ -31,11 +31,13 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 public class ObjectPropertyStatementDaoSDB extends
 		ObjectPropertyStatementDaoJena implements ObjectPropertyStatementDao {
 
-	private Dataset dataset;
+	private DatasetWrapperFactory dwf;
 	
-	public ObjectPropertyStatementDaoSDB(Dataset dataset, WebappDaoFactoryJena wadf) {
+	public ObjectPropertyStatementDaoSDB(
+	            DatasetWrapperFactory datasetWrapperFactory, 
+	            WebappDaoFactoryJena wadf) {
 		super (wadf);
-		this.dataset = dataset;
+		this.dwf = datasetWrapperFactory;
 	}
 	
 	@Override
@@ -56,12 +58,15 @@ public class ObjectPropertyStatementDaoSDB extends
         			       "   OPTIONAL { ?o <" + VitroVocabulary.MONIKER + "> ?oMoniker }  \n" +
                            "} }";
         	long startTime = System.currentTimeMillis();
-        	dataset.getLock().enterCriticalSection(Lock.READ);
         	Model m = null;
+        	DatasetWrapper w = dwf.getDatasetWrapper();
+        	Dataset dataset = w.getDataset();
+        	dataset.getLock().enterCriticalSection(Lock.READ);
         	try {
         		m = QueryExecutionFactory.create(QueryFactory.create(query), dataset).execConstruct();
         	} finally {
         		dataset.getLock().leaveCriticalSection();
+        		w.close();
         	}
         	if (log.isDebugEnabled()) {
 	        	log.debug("Time (ms) to query for related individuals: " + (System.currentTimeMillis() - startTime));
@@ -112,12 +117,18 @@ public class ObjectPropertyStatementDaoSDB extends
 	                            	continue;                                                                
 	                            }
 	                            if (objPropertyStmt.getObjectURI() != null) {
-	                                Individual objInd = new IndividualSDB(objPropertyStmt.getObjectURI(), dataset, getWebappDaoFactory(), m);
+	                                Individual objInd = new IndividualSDB(
+	                                        objPropertyStmt.getObjectURI(), 
+	                                        this.dwf, 
+	                                        getWebappDaoFactory(),
+	                                        m);
 	                                objPropertyStmt.setObject(objInd);
 	                            }
 	
 	                            //add object property statement to list for Individual
-	                            if ((objPropertyStmt.getSubjectURI() != null) && (objPropertyStmt.getPropertyURI() != null) && (objPropertyStmt.getObject() != null)){
+	                            if ((objPropertyStmt.getSubjectURI() != null) 
+	                                    && (objPropertyStmt.getPropertyURI() != null) 
+	                                    && (objPropertyStmt.getObject() != null)){
 	                                objPropertyStmtList.add(objPropertyStmt);                           
 	                            } 
 	                        } catch (Throwable t) {

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

@@ -26,16 +26,16 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 
 public class VClassDaoSDB extends VClassDaoJena {
 
-	private Dataset dataset;
+	private DatasetWrapperFactory dwf;
-	private WebappDaoFactoryJena wadf;
 	
-    public VClassDaoSDB(Dataset dataset, WebappDaoFactoryJena wadf) {
+    public VClassDaoSDB(DatasetWrapperFactory datasetWrapperFactory, 
+                WebappDaoFactoryJena wadf) {
         super(wadf);
-        this.dataset = dataset;
+        this.dwf = datasetWrapperFactory;
     }
     
-    protected Dataset getDataset() {
+    protected DatasetWrapper getDatasetWrapper() {
-    	return this.dataset;
+    	return dwf.getDatasetWrapper();
     }
     
     @Deprecated
@@ -63,9 +63,17 @@ public class VClassDaoSDB extends VClassDaoJena {
                                     		String countQueryStr = "SELECT COUNT(*) WHERE \n" +
                                     		                       "{ GRAPH ?g { ?s a <" + cls.getURI() + "> } } \n";
                                     		Query countQuery = QueryFactory.create(countQueryStr, Syntax.syntaxARQ);
-                                    		QueryExecution qe = QueryExecutionFactory.create(countQuery, getDataset());
+                                    		DatasetWrapper w = getDatasetWrapper();
-                                    		ResultSet rs =qe.execSelect();
+                                    		Dataset dataset = w.getDataset();
+                                    		dataset.getLock().enterCriticalSection(Lock.READ);
+                                    		try {
+                                        		QueryExecution qe = QueryExecutionFactory.create(countQuery, dataset);
+                                        		ResultSet rs = qe.execSelect();
                                         		count = Integer.parseInt(((Literal) rs.nextSolution().get(".1")).getLexicalForm());
+                                    		} finally {
+                                    		    dataset.getLock().leaveCriticalSection();
+                                    		    w.close();
+                                    		}
                                     	} finally {
                                     		aboxModel.leaveCriticalSection();
                                     	}

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

@@ -13,16 +13,28 @@ import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
 public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 
-	private Dataset dataset;
+	private DatasetWrapperFactory dwf;
 	
+	/**
+	 * For use when any database connection associated with the Dataset
+	 * is managed externally
+	 * @param ontModelSelector
+	 * @param dataset
+	 */
 	public WebappDaoFactorySDB(OntModelSelector ontModelSelector, Dataset dataset) {
 		super(ontModelSelector);
-		this.dataset = dataset;
+		this.dwf = new StaticDatasetFactory(dataset);
 	}
 	
+    /**
+     * For use when any database connection associated with the Dataset
+     * is managed externally
+     * @param ontModelSelector
+     * @param dataset
+     */
 	public WebappDaoFactorySDB(OntModelSelector ontModelSelector, Dataset dataset, String defaultNamespace, HashSet<String> nonuserNamespaces, String[] preferredLanguages) {
 		super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
-        this.dataset = dataset;
+        this.dwf = new StaticDatasetFactory(dataset);
 	}
 	
 	@Override
@@ -30,7 +42,7 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
         if (entityWebappDao != null)
             return entityWebappDao;
         else
-            return entityWebappDao = new IndividualDaoSDB(dataset, this);
+            return entityWebappDao = new IndividualDaoSDB(dwf, this);
     }
 	
 	@Override
@@ -38,7 +50,7 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 		if (dataPropertyStatementDao != null) 
 			return dataPropertyStatementDao;
 		else
-			return dataPropertyStatementDao = new DataPropertyStatementDaoSDB(dataset, this);
+			return dataPropertyStatementDao = new DataPropertyStatementDaoSDB(dwf, this);
 	}
 	
 	@Override
@@ -46,7 +58,7 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 		if (objectPropertyStatementDao != null) 
 			return objectPropertyStatementDao;
 		else
-			return objectPropertyStatementDao = new ObjectPropertyStatementDaoSDB(dataset, this);
+			return objectPropertyStatementDao = new ObjectPropertyStatementDaoSDB(dwf, this);
 	}
 	
 	@Override
@@ -54,7 +66,21 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 		if (vClassDao != null) 
 			return vClassDao;
 		else
-			return vClassDao = new VClassDaoSDB(dataset, this);
+			return vClassDao = new VClassDaoSDB(dwf, this);
+	}
+	
+	private class StaticDatasetFactory implements DatasetWrapperFactory {
+	 
+	    private Dataset dataset;
+	    
+	    public StaticDatasetFactory (Dataset dataset) {
+	        this.dataset = dataset;
+	    }
+	    
+	    public DatasetWrapper getDatasetWrapper() {
+	        return new DatasetWrapper(dataset);
+	    }
+	    
 	}
 	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/uploadrequest/MultipartHttpServletRequest.java

@@ -137,7 +137,7 @@ class MultipartHttpServletRequest extends FileUploadServletRequest {
 	 */
 	private ServletFileUpload createUploadHandler(int maxFileSize, File tempDir) {
 		DiskFileItemFactory factory = new DiskFileItemFactory();
-		factory.setSizeThreshold(maxFileSize);
+		factory.setSizeThreshold(DiskFileItemFactory.DEFAULT_SIZE_THRESHOLD);
 		factory.setRepository(tempDir);
 
 		ServletFileUpload upload = new ServletFileUpload(factory);

webapp/web/templates/edit/specific/upload_rdf.jsp

@@ -13,13 +13,18 @@
     <p><strong class="warning">${errMsg}</strong></p>
 </c:if>
 
-    <p>Enter Web-accessible URL of RDF document:</p>
+    <p>Enter Web-accessible URL of document containing RDF to add or remove:</p>
     <p><input name="rdfUrl" type="text" style="width:67%;" value="<c:out value='${param.rdfUrl}'/>"/></p>
     
     <p>Or upload a file from your computer: </p>
     <p><input type="file" name="rdfStream"/> </p>
     
-    <p><input type="radio" name="mode" value="add" checked="checked"/>add RDF <input type="radio" name="mode" value="remove"/>remove RDF</p>
+    <ul style="list-style-type:none;">
+        <li><input type="radio" name="mode" value="directAddABox" checked="checked"/>add instance data (supports large data files)</li> 
+        <li><input type="radio" name="mode" value="add"/>add mixed RDF (instances and/or ontology)</li> 
+        <li><input type="radio" name="mode" value="remove"/>remove mixed RDF (instances and/or ontology)</li>
+    </ul>
+
     <select name="language">
         	<option value="RDF/XML">RDF/XML</option>
         	<option value="N3">N3</option>