NIHVIVO-2717 fixed graph keyword tokenization bug and switched WebappDaoFactorySDBPrep to set SDB union graph as JenaOntModel

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

@@ -151,18 +151,13 @@ public class SparqlQueryServlet extends BaseEditController {
 		
 		String queryParam = vreq.getParameter("query");
 		boolean graphPresent = false;
-		StringTokenizer tokenizer = new StringTokenizer(queryParam, " ");
+		String[] tokens = queryParam.split("\\s");
-	    while(tokenizer.hasMoreTokens()){
+	    for(int i = 0; i < tokens.length; i++){
-	    	if("graph".equalsIgnoreCase(tokenizer.nextToken())){
+	    	if("graph".equalsIgnoreCase(tokens[i])){
-	    		graphPresent = true;
+	    		return vreq.getDataset();
-	    		break;
 	    	}
 	    }
-		Dataset dataset = vreq.getDataset();
+		
-		if (dataset != null && graphPresent) {
-			return dataset;
-		}
-
 		DataSource dataSource = DatasetFactory.create();
 		dataSource.setDefaultModel(vreq.getJenaOntModel());
 		return dataSource;

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

@@ -70,6 +70,10 @@ public class VitroRequest extends HttpServletRequestWrapper {
     	setAttribute("dataset", dataset);
     }
     
+    public void setJenaOntModel(OntModel ontModel) {
+    	setAttribute("jenaOntModel", ontModel);
+    }
+    
     /** gets assertions + inferences WebappDaoFactory with no filtering **/
     public WebappDaoFactory getFullWebappDaoFactory() {
     	Object webappDaoFactoryAttr = _req.getAttribute("fullWebappDaoFactory");
@@ -106,6 +110,10 @@ public class VitroRequest extends HttpServletRequestWrapper {
     }
     
     public OntModel getJenaOntModel() {
+    	Object ontModel = getAttribute("jenaOntModel");
+    	if (ontModel instanceof OntModel) {
+    		return (OntModel) ontModel;
+    	}
     	OntModel jenaOntModel = (OntModel)_req.getSession().getAttribute( JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME );
     	if ( jenaOntModel == null ) {
     		jenaOntModel = (OntModel)_req.getSession().getServletContext().getAttribute( JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME );

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/IndividualController.java

@@ -334,13 +334,7 @@ public class IndividualController extends FreemarkerHttpServlet {
 	private ResponseValues doRdf(VitroRequest vreq, Individual individual,
 			ContentType rdfFormat) throws IOException, ServletException {    	
 				
-		OntModel ontModel = null;
+		OntModel ontModel = vreq.getJenaOntModel();		
-		HttpSession session = vreq.getSession(false);
-		if( session != null )
-			ontModel = (OntModel)session.getAttribute("jenaOntModel");		
-		if( ontModel == null)
-			ontModel = (OntModel)getServletContext().getAttribute("jenaOntModel");
-		
                 
         String[] includes = vreq.getParameterValues("include");
 		Model newModel = getRDF(individual,ontModel,ModelFactory.createDefaultModel(),0,includes);		

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

@@ -933,21 +933,18 @@ public class IndividualSDB extends IndividualImpl implements Individual {
 		if (ind.getModel().contains((Resource) null, RDF.type, (RDFNode) null)){
 		    tempModel = ind.getModel();
 		} else {
+			String[] graphVars = { "?g" };
     		String getTypes = 
         		"CONSTRUCT{ <" + this.individualURI + "> <" + RDF.type +
         		        "> ?types }\n" +
-        		"WHERE{ GRAPH " + 
+        		"WHERE{ GRAPH ?g"   
-        		((direct) 
+        		+ " { <" + this.individualURI +"> <" +RDF.type+ "> ?types } \n" 
-        		    ? "<http://vitro.mannlib.cornell.edu/default/vitro-kb-2>" 
+   		        + WebappDaoFactorySDB.getFilterBlock(
-        		    : "?g") 
+   		        		graphVars, (direct 
-        		+ " { <" + this.individualURI +"> <" +RDF.type+ "> ?types } \n" ;
+   		        				? WebappDaoFactorySDB.SDBDatasetMode
-    		
+   		        						.ASSERTIONS_ONLY 
-    		    if (!direct) {
+   		        			    : datasetMode)) 
-    		        String[] graphVars = { "?g" };
+        		+ "} \n";        	
-    		        getTypes += WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode);
-    		    }
-    		
-        		getTypes += "} \n";        	
         	DatasetWrapper w = getDatasetWrapper();
         	Dataset dataset = w.getDataset();
         	dataset.getLock().enterCriticalSection(Lock.READ);

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

@@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 	
+	public static final String UNION_GRAPH = "urn:x-arq:UnionGraph"; 
     private SDBDatasetMode datasetMode = SDBDatasetMode.ASSERTIONS_AND_INFERENCES;
     
 	/**

webapp/src/edu/cornell/mannlib/vitro/webapp/filters/WebappDaoFactorySDBPrep.java

@@ -21,7 +21,9 @@ import org.apache.commons.dbcp.BasicDataSource;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.sdb.SDBFactory;
 import com.hp.hpl.jena.sdb.Store;
 import com.hp.hpl.jena.sdb.StoreDesc;
@@ -106,6 +108,9 @@ public class WebappDaoFactorySDBPrep implements Filter {
 				vreq.setWebappDaoFactory(wadf);
 				vreq.setFullWebappDaoFactory(wadf);
 				vreq.setDataset(dataset);
+				vreq.setJenaOntModel(ModelFactory.createOntologyModel(
+						OntModelSpec.OWL_MEM, dataset.getNamedModel(
+								WebappDaoFactorySDB.UNION_GRAPH)));
 			}
 		} catch (Throwable t) {
 			log.error("Unable to filter request to set up SDB connection", t);