Closing QueryExecution in some code. Adding EditN3GeneratorTest.

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/OntologyController.java

@@ -18,6 +18,7 @@ import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntResource;
+import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.rdf.model.Model;
@@ -131,27 +132,36 @@ public class OntologyController extends VitroHttpServlet{
 		if( ontModel == null)
 			ontModel = (OntModel)getServletContext().getAttribute("jenaOntModel");
 
+        boolean found = false;
+        Model newModel = ModelFactory.createDefaultModel();			
 		ontModel.enterCriticalSection(Lock.READ);
+        try{
             OntResource ontResource = ontModel.getOntResource(url);
             if(ontResource == null)
                 ontResource = ontModel.getOntResource(url + "/");
-		Model newModel = ModelFactory.createDefaultModel();
             if(ontResource != null){
+                found = true;
                 Resource resource = (Resource)ontResource;
+                QueryExecution qexec = null;
                 try{
                     String queryString = "Describe <" + resource.getURI() + ">"; 
-				newModel = QueryExecutionFactory.create(QueryFactory.create(queryString), ontModel).execDescribe();
+                    qexec = QueryExecutionFactory.create(QueryFactory.create(queryString), ontModel);
+                    newModel = qexec.execDescribe();
+                } finally{
+                    qexec.close();
                 }
-			finally{
+            } else {
+                found = false;
+            }
+        }finally{
             ontModel.leaveCriticalSection();
         }
-		}
-		else{
-			ontModel.leaveCriticalSection();
-			doNotFound(vreq,res);
-			return;
-		}
 
+        if( ! found ){
+            //respond to HTTP outside of critical section
+            doNotFound(req,res);
+            return;
+        } else {		
             res.setContentType(rdfFormat.getMediaType());
             String format = ""; 
             if ( RDFXML_MIMETYPE.equals(rdfFormat.getMediaType()))
@@ -162,6 +172,8 @@ public class OntologyController extends VitroHttpServlet{
                 format ="TTL";
 		
             newModel.write( res.getOutputStream(), format );		
+            return;
+        }
 	}
 	
 	private static Pattern URI_PATTERN = Pattern.compile("^/ontology/([^/]*)/([^/]*)$");

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

@@ -22,6 +22,7 @@ import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntProperty;
 import com.hp.hpl.jena.ontology.OntResource;
 import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.query.QuerySolution;
@@ -217,9 +218,11 @@ public class RefactorOperationController extends BaseEditController {
 		queryStr += " union { GRAPH ?graph { ?subj ?prop <" +  oldURIStr  + ">}}}";
 		Dataset dataset = request.getDataset();
 		
+        QueryExecution qexec = null;
     	dataset.getLock().enterCriticalSection(Lock.READ);        
     	try {
-    		ResultSet resultSet = QueryExecutionFactory.create(QueryFactory.create(queryStr), dataset).execSelect();
+            qexec = QueryExecutionFactory.create(QueryFactory.create(queryStr), dataset);
+    		ResultSet resultSet = qexec.execSelect();
     		
     		while (resultSet.hasNext()) {
     			QuerySolution qs = resultSet.next();
@@ -245,6 +248,7 @@ public class RefactorOperationController extends BaseEditController {
     			renameResourceInModel(model, userURI, oldURIStr, newURIStr, doNotify);
     		}	
     	} finally {
+            if(qexec != null) qexec.close();
     		dataset.getLock().leaveCriticalSection();
     	}
 		

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

@@ -68,9 +68,12 @@ public class DataPropertyStatementDaoSDB extends DataPropertyStatementDaoJena
         	DatasetWrapper w = dwf.getDatasetWrapper();
             Dataset dataset = w.getDataset();
             dataset.getLock().enterCriticalSection(Lock.READ);
+            QueryExecution qexec = null;
             try { 
-        	    results = QueryExecutionFactory.create(QueryFactory.create(query), dataset).execConstruct();
+                qexec = QueryExecutionFactory.create(QueryFactory.create(query), dataset);                
+        	    results = qexec.execConstruct();
             } finally {
+                if(qexec!=null) qexec.close();
                 dataset.getLock().leaveCriticalSection();
                 w.close();
             }

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

@@ -18,6 +18,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.joda.time.DateTime;
 
+import com.clarkparsia.pellet.sparqldl.engine.QueryExec;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.ontology.OntResource;
@@ -509,12 +510,15 @@ public class IndividualSDB extends IndividualImpl implements Individual {
           DatasetWrapper w = getDatasetWrapper();
             Dataset dataset = w.getDataset();
             dataset.getLock().enterCriticalSection(Lock.READ);
+            QueryExecution qexec = null;
             try{            
-                _hasThumb = QueryExecutionFactory.create(QueryFactory.create(ask), dataset).execAsk();                      
+                qexec = QueryExecutionFactory.create(QueryFactory.create(ask), dataset);
+                _hasThumb = qexec.execAsk();
             }catch(Exception ex){
                 _hasThumb = false;
                 log.error(ex,ex);
             }finally{
+                if(qexec!=null) qexec.close();
                 dataset.getLock().leaveCriticalSection();
                 w.close();
             }
@@ -670,11 +674,13 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         DatasetWrapper w = getDatasetWrapper();
         Dataset dataset = w.getDataset();
     	dataset.getLock().enterCriticalSection(Lock.READ);
+        QueryExecution qexec = null;
     	try {
     		String valuesOfProperty = 
     			"CONSTRUCT{ <" + this.individualURI + "> <" + propertyURI + "> ?object }" +
     			"WHERE{ <" + this.individualURI + "> <" + propertyURI + "> ?object } \n";
-    	    tempModel = QueryExecutionFactory.create(QueryFactory.create(valuesOfProperty), dataset).execConstruct();
+            qexec = QueryExecutionFactory.create(QueryFactory.create(valuesOfProperty), dataset);
+    	    tempModel = qexec.execConstruct();
     	    ontModel.add(tempModel.listStatements());
     	    Resource ontRes = ontModel.getResource(this.individualURI);
     	    StmtIterator sit = ontRes.listProperties(ontRes.getModel().getProperty(propertyURI));
@@ -698,6 +704,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     			}
     		}
      	} finally {
+            if(qexec!=null) qexec.close();
     		tempModel.close();
     		ontModel.close();
      		dataset.getLock().leaveCriticalSection();

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/processEdit/EditN3Generator.java

@@ -40,6 +40,15 @@ public class EditN3Generator {
         return Collections.EMPTY_LIST;
     }
 
+    /**
+     * This is the method to use to substitute in URIs into variables of target N3 strings.
+     * This takes into account multiple values that would be returned from a select list.
+     * subInUris should no longer be used.
+     */
+    public static List<String> subInMultiUris(Map<String,List<String>> varsToVals, List<String> n3targets){       
+       return null;
+    }
+    
     public static List<String> subInUris(Map<String,String> varsToVals, List<String> targets){
         if( varsToVals == null || varsToVals.isEmpty() ) return targets;
         ArrayList<String> outv = new ArrayList<String>();
@@ -80,6 +89,15 @@ public class EditN3Generator {
         return outv;
     }
 
+    /**
+     * This is the method to use to substitute in Literals into variables of target N3 strings.
+     * This takes into account multiple values that would be returned from a select list.
+     * subInUris should no longer be used.
+     */
+    public static List<String> subInMultiLiterals(Map<String,List<String>> varsToVals, List<String> n3targets){       
+       return null;
+    }
+    
     public  List<String> subInLiterals(Map<String, Literal> varsToVals, List<String> targets){
         if( varsToVals == null || varsToVals.isEmpty()) return targets;
 

webapp/src/edu/cornell/mannlib/vitro/webapp/search/beans/IndividualProhibitedFromSearchImpl.java

@@ -9,6 +9,7 @@ import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.shared.Lock;
@@ -37,11 +38,14 @@ public class IndividualProhibitedFromSearchImpl implements IndividualProhibitedF
             return true;
         
         boolean prohibited = false;
+        QueryExecution qexec = null;
         try {
             fullModel.getLock().enterCriticalSection(Lock.READ);                               
             Query query = makeAskQueryForUri( uri );
-            prohibited = QueryExecutionFactory.create( query, fullModel).execAsk();            
+            qexec = QueryExecutionFactory.create( query, fullModel);
+            prohibited = qexec.execAsk();            
         } finally {
+            if( qexec != null ) qexec.close();
             fullModel.getLock().leaveCriticalSection();
         }
         if( prohibited )

webapp/test/edu/cornell/mannlib/vitro/webapp/edit/n3editing/processEdit/EditN3GeneratorTest.java

@@ -0,0 +1,41 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.edit.n3editing.processEdit;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class EditN3GeneratorTest {
+
+    @Test
+    public void testSubInMultiUris() {
+//        String n3 = "?subject ?predicate ?multivalue." ;
+//        List<String> strs = new ArrayList<String>();
+//        strs.add(n3);
+//        
+//        Map<String,List<String>> keyToValues = new HashMap<String,List<String>>();
+//        List<String> values = new ArrayList<String>();               
+//        values.add("http://a.com/2");
+//        values.add("http://b.com/ont#2");
+//        values.add("http://c.com/individual/n23431");        
+//        keyToValues.put("multivalue", values);
+//        
+//        List<String> n3results = EditN3Generator.subInMultiLiterals(keyToValues, strs);
+//        
+//        Assert.assertNotNull(n3results);
+//        Assert.assertTrue( n3results.size() == 1 );
+//        String expected ="?subject ?predicate <http://a.com/2>, <http://b.com/ont#2>, <http://c.com/individual/n23431>.";
+//        Assert.assertEquals(expected, n3results);
+//        
+        //make a model,
+        //add statements
+        //prase resultn3
+        //compare
+    }
+
+}