NIHVIVO-1734 assertions-only DAO fixes for SDB

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

@@ -31,15 +31,21 @@ import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode;
 
 public class DataPropertyStatementDaoSDB extends DataPropertyStatementDaoJena
 							implements DataPropertyStatementDao {
 
 	private DatasetWrapperFactory dwf;
+	private SDBDatasetMode datasetMode;
 	
-	public DataPropertyStatementDaoSDB(DatasetWrapperFactory datasetWrapperFactory, WebappDaoFactoryJena wadf) {
+	public DataPropertyStatementDaoSDB(
+	        DatasetWrapperFactory datasetWrapperFactory, 
+	        SDBDatasetMode datasetMode, 
+	        WebappDaoFactoryJena wadf) {
 		super (datasetWrapperFactory, wadf);
 		this.dwf = datasetWrapperFactory;
+		this.datasetMode = datasetMode;
 	}
 	
 	@Override
@@ -51,12 +57,14 @@ public class DataPropertyStatementDaoSDB extends DataPropertyStatementDaoJena
         }
         else
         {
+            String[] graphVars = { "?g" };
         	String query = 
 	        	"CONSTRUCT { \n" +
 			       "   <" + entity.getURI() + "> ?p ?o . \n" +
 			       "} WHERE { GRAPH ?g { \n" +
 			       "   <" + entity.getURI() + "> ?p ?o . \n" +
 			       "   FILTER(isLiteral(?o)) \n" +
+			       WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
 	            "} }" ;
         	Model results = null;
         	DatasetWrapper w = dwf.getDatasetWrapper();

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

@@ -45,15 +45,20 @@ 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;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode;
 
 public class IndividualDaoSDB extends IndividualDaoJena {
 
 	private DatasetWrapperFactory dwf;
+    private SDBDatasetMode datasetMode;
 	private WebappDaoFactoryJena wadf;
 	
-    public IndividualDaoSDB(DatasetWrapperFactory dwf, WebappDaoFactoryJena wadf) {
+    public IndividualDaoSDB(DatasetWrapperFactory dwf, 
+                            SDBDatasetMode datasetMode, 
+                            WebappDaoFactoryJena wadf) {
         super(wadf);
         this.dwf = dwf;
+        this.datasetMode = datasetMode;
     }
     
     protected DatasetWrapper getDatasetWrapper() {
@@ -61,7 +66,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     }
     
     protected Individual makeIndividual(String individualURI) {
-    	return new IndividualSDB(individualURI, this.dwf, getWebappDaoFactory());
+    	return new IndividualSDB(individualURI, this.dwf, datasetMode, getWebappDaoFactory());
     }
 
     private static final Log log = LogFactory.getLog(IndividualDaoSDB.class.getName());
@@ -97,6 +102,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     	    Dataset dataset = w.getDataset();
         	dataset.getLock().enterCriticalSection(Lock.READ);
         	try {
+        	    String[] graphVars = {"?g", "?h", "?i"};
         		String query = 
     	    		"SELECT DISTINCT ?ind ?label ?moniker " +
     	    		"WHERE " +
@@ -105,6 +111,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     	    		    "} \n" +
     	    		 	"OPTIONAL { GRAPH ?h { ?ind  <" + RDFS.label.getURI() + "> ?label } }\n" +
     	    		 	"OPTIONAL { GRAPH ?i { ?ind  <" + VitroVocabulary.MONIKER + "> ?moniker } } \n" +
+    	    		 	WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
     	    		 "} ORDER BY ?label";
         		ResultSet rs =QueryExecutionFactory.create(
         		        QueryFactory.create(query), dataset)
@@ -117,7 +124,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
         		            && !currRes.isAnon()) {    		        
         		        res = currRes;
         		        Individual ent = new IndividualSDB(currRes.getURI(), 
-                                this.dwf, getWebappDaoFactory(), 
+                                this.dwf, datasetMode, getWebappDaoFactory(), 
                                 SKIP_INITIALIZATION);
         		        Literal label = sol.getLiteral("label");
         		        if (label != null) {

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

@@ -2,8 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
-import java.io.UnsupportedEncodingException;
-import java.net.URLDecoder;
 import java.sql.Timestamp;
 import java.text.Collator;
 import java.util.ArrayList;
@@ -30,21 +28,16 @@ import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.NodeIterator;
-import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.ResIterator;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
-import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
@@ -60,6 +53,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatementImpl;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode;
 import edu.cornell.mannlib.vitro.webapp.filestorage.model.ImageInfo;
 import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 import edu.cornell.mannlib.vitro.webapp.utils.FlagMathUtils;
@@ -73,12 +67,16 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     private Float _searchBoostJena = null;
     private boolean retreivedNullRdfsLabel = false;
     private DatasetWrapperFactory dwf = null;
+    private SDBDatasetMode datasetMode = 
+                SDBDatasetMode.ASSERTIONS_AND_INFERENCES;
     private String individualURI = null; 
     private Model model = null;
     
     public IndividualSDB(String individualURI, 
-                         DatasetWrapperFactory datasetWrapperFactory, 
+                         DatasetWrapperFactory datasetWrapperFactory,
-                         WebappDaoFactoryJena wadf, Model initModel) {
+                         SDBDatasetMode datasetMode,
+                         WebappDaoFactoryJena wadf,
+                         Model initModel) {
     	this.individualURI = individualURI;
     	this.dwf = datasetWrapperFactory;
       
@@ -115,9 +113,11 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     
     public IndividualSDB(String individualURI, 
             DatasetWrapperFactory datasetWrapperFactory, 
+            SDBDatasetMode datasetMode,
             WebappDaoFactoryJena wadf,
             boolean skipInitialization) {
     	this.individualURI = individualURI;
+    	this.datasetMode = datasetMode;
     	this.dwf = datasetWrapperFactory;
     	
     	if (skipInitialization) {
@@ -129,6 +129,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         	Dataset dataset = w.getDataset();
         	try {
     	    	dataset.getLock().enterCriticalSection(Lock.READ);
+    	    	String[] graphVars = {"?g", "?h", "?i"};
     	    	String getStatements = 
     	    		"CONSTRUCT " +
     	    		"{ <"+individualURI+">  <" + RDFS.label.getURI() + 
@@ -146,6 +147,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	    		 	"} } \n" +
     	    		 	"UNION { GRAPH ?i { <"
     	    		 	    + individualURI + "> a ?type } } \n" +
+    	    		    WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
     	    		 "}";
         		model = QueryExecutionFactory.create(
         		        QueryFactory.create(getStatements), dataset)
@@ -167,9 +169,14 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     private static final boolean SKIP_INITIALIZATION = true;
     
     public IndividualSDB(String individualURI, 
-            DatasetWrapperFactory datasetWrapperFactory, 
+            DatasetWrapperFactory datasetWrapperFactory,
+            SDBDatasetMode datasetMode,
             WebappDaoFactoryJena wadf) {
-        this(individualURI, datasetWrapperFactory, wadf, !SKIP_INITIALIZATION);
+        this(individualURI, 
+             datasetWrapperFactory, 
+             datasetMode, 
+             wadf, 
+             !SKIP_INITIALIZATION);
     }
     
     private void setUpURIParts(OntResource ind) {
@@ -589,10 +596,13 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         Dataset dataset = w.getDataset();
         dataset.getLock().enterCriticalSection(Lock.READ);
         try {
+            String[] graphVars = { "?g" };
             String queryStr = "CONSTRUCT { ?ind <" + 
                     propertyURI + "> ?value } \n" +
                     "WHERE { GRAPH ?g {  ?ind <" +
-                    propertyURI + "> ?value } } \n";
+                    propertyURI + "> ?value } \n" + 
+                    WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
+                    "\n} \n";
             Query query = QueryFactory.create(queryStr);
             QueryExecution qe = QueryExecutionFactory.create(
                     query, dataset);
@@ -607,11 +617,14 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         if( this._searchBoostJena != null ){
             return this._searchBoostJena;
         }else{
+            String[] graphVars = { "?g" };
             String getPropertyValue = 
             	"SELECT ?value" +
             	"WHERE { GRAPH ?g { <" + individualURI + ">" + 
             	        webappDaoFactory.getJenaBaseDao().SEARCH_BOOST_ANNOT + 
-            	        "?value} }";
+            	        "?value} \n" + 
+            	        WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
+            	        "}";
             DatasetWrapper w = getDatasetWrapper();
             Dataset dataset = w.getDataset();
         	dataset.getLock().enterCriticalSection(Lock.READ);
@@ -704,6 +717,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         Dataset dataset = w.getDataset();
     	dataset.getLock().enterCriticalSection(Lock.READ);
         try {
+            String graphVars[] = { "?g" };
         	StringBuffer selectPrimaryLinkQueryBuff = new StringBuffer().append(
         		"SELECT ?url ?anchor \n" ).append(
         		"WHERE{ GRAPH ?g { \n " ).append(
@@ -714,7 +728,9 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         		        ).append(
         		"    ?link <" + VitroVocabulary.LINK_ANCHOR + "> ?anchor . \n" 
         		        ).append(
-        		"} }");
+        		"} \n")
+        		.append(WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode))
+        		.append("}");
         	QueryExecution qexec = QueryExecutionFactory.create(
                     QueryFactory.create(selectPrimaryLinkQueryBuff.toString())
                             , dataset);
@@ -827,9 +843,12 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         Dataset dataset = w.getDataset();
     	dataset.getLock().enterCriticalSection(Lock.READ);
     	try {
+    	    String[] graphVars = { "?g" };
     		String valuesOfProperty = 
     			"CONSTRUCT{<" + this.individualURI + "> <" + propertyURI + "> ?object}" +
-    			"WHERE{ GRAPH ?g { <" + this.individualURI + "> <" + propertyURI + "> ?object} }";
+    			"WHERE{ GRAPH ?g { <" + this.individualURI + "> <" + propertyURI + "> ?object} \n" +
+    			WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
+    			"}";
     	    tempModel = QueryExecutionFactory.create(QueryFactory.create(valuesOfProperty), dataset).execConstruct();
     	    ontModel.add(tempModel.listStatements());
     	    Resource ontRes = ontModel.getResource(this.individualURI);
@@ -839,8 +858,8 @@ 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(), this.dwf, webappDaoFactory);
+    			Individual subj = new IndividualSDB(((OntResource) s.getSubject().as(OntResource.class)).getURI(), this.dwf, datasetMode, webappDaoFactory);
-    			Individual obj = new IndividualSDB(((OntResource) s.getObject().as(OntResource.class)).getURI(), this.dwf, webappDaoFactory);
+    			Individual obj = new IndividualSDB(((OntResource) s.getObject().as(OntResource.class)).getURI(), this.dwf, datasetMode, webappDaoFactory);
     			ObjectProperty op = webappDaoFactory.getObjectPropertyDao().getObjectPropertyByURI(s.getPredicate().getURI());
     			if (subj != null && obj != null && op != null) {
     				ObjectPropertyStatement ops = new ObjectPropertyStatementImpl();
@@ -873,10 +892,13 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	Dataset dataset = w.getDataset();
     	dataset.getLock().enterCriticalSection(Lock.READ);
     	try {
+    	    String[] graphVars = { "?g" };
     		String valuesOfProperty = 
     			"SELECT ?object" +
     			"WHERE{ GRAPH ?g { <" + this.individualURI + "> <" + 
-    			        propertyURI + "> ?object} }";
+    			        propertyURI + "> ?object} \n" +
+    			        WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +       
+    			 "}";
     		ResultSet values = QueryExecutionFactory.create(
     		        QueryFactory.create(valuesOfProperty), dataset)
     		                .execSelect();
@@ -889,7 +911,9 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         	    		new IndividualSDB(
         	    		        ((OntResource) value.as(OntResource.class))
         	    		                .getURI(), 
-        	    		                this.dwf, webappDaoFactory) );  
+        	    		                this.dwf, 
+        	    		                datasetMode, 
+        	    		                webappDaoFactory) );  
         	    } 
     	    }
     	} finally {
@@ -908,10 +932,13 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	Dataset dataset = w.getDataset();
     	dataset.getLock().enterCriticalSection(Lock.READ);
     	try {
+    	    String[] graphVars = { "?g" };
     		String valueOfProperty = 
     			"SELECT ?object" +
     			"WHERE{ GRAPH ?g { <" + this.individualURI + "> <" + 
-    			        propertyURI + "> ?object} }";
+    			        propertyURI + "> ?object} \n" +
+    			        WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
+    			"}";
     		ResultSet results = QueryExecutionFactory.create(
     		        QueryFactory.create(valueOfProperty), dataset).execSelect();
     		QuerySolution result = results.next();
@@ -919,7 +946,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	    if (value != null && value.canAs(OntResource.class)) {
     	    	return new IndividualSDB(
     	    	        ((OntResource) value.as(OntResource.class)).getURI(), 
-    	    	                dwf, webappDaoFactory);  
+    	    	                dwf, datasetMode, webappDaoFactory);  
     	    } else {
     	    	return null;
     	    }
@@ -1088,8 +1115,14 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         		((direct) 
         		    ? "<http://vitro.mannlib.cornell.edu/default/vitro-kb-2>" 
         		    : "?g") 
-        		+ " { <" + this.individualURI +"> <" +RDF.type+ "> ?types \n" +
+        		+ " { <" + this.individualURI +"> <" +RDF.type+ "> ?types } \n" ;
-        				"} } \n";        	
+    		
+    		    if (!direct) {
+    		        String[] graphVars = { "?g" };
+    		        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/ObjectPropertyStatementDaoSDB.java

@@ -27,17 +27,21 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatementImpl;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode;
 
 public class ObjectPropertyStatementDaoSDB extends
 		ObjectPropertyStatementDaoJena implements ObjectPropertyStatementDao {
 
 	private DatasetWrapperFactory dwf;
+	private SDBDatasetMode datasetMode;
 	
 	public ObjectPropertyStatementDaoSDB(
 	            DatasetWrapperFactory dwf, 
+	            SDBDatasetMode datasetMode,
 	            WebappDaoFactoryJena wadf) {
 		super (dwf, wadf);
 		this.dwf = dwf;
+		this.datasetMode = datasetMode;
 	}
 	
 	@Override
@@ -46,6 +50,7 @@ public class ObjectPropertyStatementDaoSDB extends
             return entity;
         else {
         	Map<String, ObjectProperty> uriToObjectProperty = new HashMap<String,ObjectProperty>();
+        	String[] graphVars = { "?g", "?h", "?i", "?j" };
         	String query = "CONSTRUCT { \n" +
         			       "   <" + entity.getURI() + "> ?p ?o . \n" +
         			       "   ?o a ?oType . \n" +
@@ -56,7 +61,9 @@ public class ObjectPropertyStatementDaoSDB extends
         			       "   OPTIONAL { GRAPH ?h { ?o a ?oType } } \n" +
         			       "   OPTIONAL { GRAPH ?i { ?o <" + RDFS.label.getURI() + "> ?oLabel } } \n" +
         			       "   OPTIONAL { GRAPH ?j { ?o <" + VitroVocabulary.MONIKER + "> ?oMoniker } }  \n" +
-                           "} }";
+                           "} \n" +
+                           WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
+        			       "}";
         	long startTime = System.currentTimeMillis();
         	Model m = null;
         	DatasetWrapper w = dwf.getDatasetWrapper();
@@ -119,6 +126,7 @@ public class ObjectPropertyStatementDaoSDB extends
 	                                Individual objInd = new IndividualSDB(
 	                                        objPropertyStmt.getObjectURI(), 
 	                                        this.dwf, 
+	                                        datasetMode,
 	                                        getWebappDaoFactory(),
 	                                        m);
 	                                objPropertyStmt.setObject(objInd);

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

@@ -23,15 +23,19 @@ import com.hp.hpl.jena.vocabulary.RDF;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode;
 
 public class VClassDaoSDB extends VClassDaoJena {
 
 	private DatasetWrapperFactory dwf;
+	private SDBDatasetMode datasetMode;
 	
     public VClassDaoSDB(DatasetWrapperFactory datasetWrapperFactory, 
-                WebappDaoFactoryJena wadf) {
+                        SDBDatasetMode datasetMode,
+                        WebappDaoFactoryJena wadf) {
         super(wadf);
         this.dwf = datasetWrapperFactory;
+        this.datasetMode = datasetMode;
     }
     
     protected DatasetWrapper getDatasetWrapper() {
@@ -60,8 +64,11 @@ public class VClassDaoSDB extends VClassDaoJena {
                                     	aboxModel.enterCriticalSection(Lock.READ);
                                     	int count = 0;
                                     	try {
+                                    	    String[] graphVars = { "?g" };
                                     		String countQueryStr = "SELECT COUNT(*) WHERE \n" +
-                                    		                       "{ GRAPH ?g { ?s a <" + cls.getURI() + "> } } \n";
+                                    		                       "{ GRAPH ?g { ?s a <" + cls.getURI() + "> } \n" +
+                                    		                       WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
+                                    		                       "} \n";
                                     		Query countQuery = QueryFactory.create(countQueryStr, Syntax.syntaxARQ);
                                     		DatasetWrapper w = getDatasetWrapper();
                                     		Dataset dataset = w.getDataset();

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

@@ -19,14 +19,15 @@ import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 	
+    private SDBDatasetMode datasetMode = SDBDatasetMode.ASSERTIONS_AND_INFERENCES;
+    
 	/**
 	 * 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);
@@ -36,8 +37,6 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
     /**
      * For use when any database connection associated with the Dataset
      * is managed externally
-     * @param ontModelSelector
-     * @param dataset
      */
 	public WebappDaoFactorySDB(OntModelSelector ontModelSelector, 
 	                            Dataset dataset, 
@@ -51,8 +50,6 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
     /**
      * For use when any Dataset access should get a temporary DB connection
      * from a pool
-     * @param ontModelSelector
-     * @param dataset
      */
     public WebappDaoFactorySDB(OntModelSelector ontModelSelector, 
                                 BasicDataSource bds,
@@ -64,6 +61,23 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
         this.dwf = new ReconnectingDatasetFactory(bds, storeDesc);
     }
     
+    /**
+     * For use when any Dataset access should get a temporary DB connection
+     * from a pool, and access to the inference graph needs to be specified.
+     */
+    public WebappDaoFactorySDB(OntModelSelector ontModelSelector, 
+                                BasicDataSource bds,
+                                StoreDesc storeDesc,
+                                String defaultNamespace, 
+                                HashSet<String> nonuserNamespaces, 
+                                String[] preferredLanguages,
+                                SDBDatasetMode datasetMode) {
+        super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
+        this.dwf = new ReconnectingDatasetFactory(bds, storeDesc);
+        this.datasetMode = datasetMode;
+    }
+   
+    
     public WebappDaoFactorySDB(WebappDaoFactorySDB base, String userURI) {
         super(base.ontModelSelector);
         this.ontModelSelector = base.ontModelSelector;
@@ -81,7 +95,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
         if (entityWebappDao != null)
             return entityWebappDao;
         else
-            return entityWebappDao = new IndividualDaoSDB(dwf, this);
+            return entityWebappDao = new IndividualDaoSDB(
+                    dwf, datasetMode, this);
     }
 	
 	@Override
@@ -89,7 +104,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 		if (dataPropertyStatementDao != null) 
 			return dataPropertyStatementDao;
 		else
-			return dataPropertyStatementDao = new DataPropertyStatementDaoSDB(dwf, this);
+			return dataPropertyStatementDao = new DataPropertyStatementDaoSDB(
+			        dwf, datasetMode, this);
 	}
 	
 	@Override
@@ -97,7 +113,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 		if (objectPropertyStatementDao != null) 
 			return objectPropertyStatementDao;
 		else
-			return objectPropertyStatementDao = new ObjectPropertyStatementDaoSDB(dwf, this);
+			return objectPropertyStatementDao = 
+			    new ObjectPropertyStatementDaoSDB(dwf, datasetMode, this);
 	}
 	
 	@Override
@@ -105,7 +122,7 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 		if (vClassDao != null) 
 			return vClassDao;
 		else
-			return vClassDao = new VClassDaoSDB(dwf, this);
+			return vClassDao = new VClassDaoSDB(dwf, datasetMode, this);
 	}
 	
 	public WebappDaoFactory getUserAwareDaoFactory(String userURI) {
@@ -113,6 +130,40 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
         return new WebappDaoFactorySDB(this, userURI);
     }
 	
+	public enum SDBDatasetMode {
+	    ASSERTIONS_ONLY, INFERENCES_ONLY, ASSERTIONS_AND_INFERENCES
+	}
+	
+	public static String getFilterBlock(String[] graphVars, 
+	                                    SDBDatasetMode datasetMode) {
+	    StringBuffer filterBlock = new StringBuffer();
+	    for (int i = 0; i < graphVars.length; i++) {
+	        switch (datasetMode) {
+	            case ASSERTIONS_ONLY :  
+	                    filterBlock.append("FILTER (").append(graphVars[i])
+	                        .append(" != <")
+	                        .append(JenaDataSourceSetupBase.JENA_INF_MODEL)
+	                        .append("> && ").append(graphVars[i])
+	                        .append(" != <")
+	                        .append(JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL)
+	                        .append(">) \n");
+	                    break;
+	            case INFERENCES_ONLY :  
+                    filterBlock.append("FILTER (").append(graphVars[i])
+                        .append(" = <")
+                        .append(JenaDataSourceSetupBase.JENA_INF_MODEL)
+                        .append("> || ").append(graphVars[i])
+                        .append(" = <")
+                        .append(JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL)
+                        .append(">) \n");
+                    break;
+	            default:
+	                break;
+	        }
+	    }
+	    return filterBlock.toString();
+	}
+	
 	private class ReconnectingDatasetFactory implements DatasetWrapperFactory {
 	    
 	    private BasicDataSource _bds;

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

@@ -187,16 +187,28 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
                     ModelFactory.createUnion(baseOms.getABoxModel(), baseOms.getTBoxModel()));
             baseOms.setFullModel(baseUnion);
             ModelContext.setBaseOntModel(baseOms.getFullModel(), sce.getServletContext());
-            WebappDaoFactory baseWadf = new WebappDaoFactorySDB(baseOms, bds, storeDesc, defaultNamespace, null, null);
+            WebappDaoFactory baseWadf = new WebappDaoFactorySDB(
-            //WebappDaoFactory baseWadf = new WebappDaoFactorySDB(baseOms, dataset, defaultNamespace, null, null);
+                    baseOms,
+                    bds,
+                    storeDesc, 
+                    defaultNamespace, 
+                    null, 
+                    null, 
+                    WebappDaoFactorySDB.SDBDatasetMode.ASSERTIONS_ONLY);
             sce.getServletContext().setAttribute("assertionsWebappDaoFactory",baseWadf);
             
             OntModel inferenceUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
                     ModelFactory.createUnion(inferenceOms.getABoxModel(), inferenceOms.getTBoxModel()));
             inferenceOms.setFullModel(inferenceUnion);
             ModelContext.setInferenceOntModel(inferenceOms.getFullModel(), sce.getServletContext());
-            WebappDaoFactory infWadf = new WebappDaoFactorySDB(inferenceOms, bds, storeDesc, defaultNamespace, null, null);
+            WebappDaoFactory infWadf = new WebappDaoFactorySDB(
-            //WebappDaoFactory infWadf = new WebappDaoFactorySDB(inferenceOms, dataset, defaultNamespace, null, null);
+                    inferenceOms, 
+                    bds, 
+                    storeDesc, 
+                    defaultNamespace, 
+                    null, 
+                    null, 
+                    WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
             sce.getServletContext().setAttribute("deductionsWebappDaoFactory", infWadf);
             
             OntModel masterUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,