NIHVIVO-3312 cleanup of WebappDaoFactory

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

@@ -28,7 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
-import edu.cornell.mannlib.vitro.webapp.dao.VitroModelProperties;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
 public class VclassEditController extends BaseEditController {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/ClassHierarchyListingController.java

@@ -33,7 +33,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
-import edu.cornell.mannlib.vitro.webapp.dao.VitroModelProperties;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
 

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactoryConfig.java

@@ -5,44 +5,22 @@ package edu.cornell.mannlib.vitro.webapp.dao;
 import java.util.HashSet;
 import java.util.Set;
 
-public class VitroModelProperties {
+public class WebappDaoFactoryConfig {
 	
-	public static final int RDF_ABOX_ONLY = 50;
-	public static final int RDFS = 100;
-	public static final int OWL_FULL = 200;
-	public static final int OWL_DL = 202;
-	public static final int OWL_LITE = 204;
-	
-	private int languageProfile;
 	private String[] preferredLanguages;
 	private String defaultNamespace;
 	private Set<String> nonUserNamespaces;
 	
-	public static boolean isOWL(int languageProfile) {
+	public WebappDaoFactoryConfig() {
-		return ((OWL_FULL <= languageProfile && OWL_LITE >= languageProfile));
+        preferredLanguages = new String[3];
-	}
+        preferredLanguages[0] = "en-US";
-	
+        preferredLanguages[1] = "en";
-	public static boolean isRDFS(int languageProfile) {
+        preferredLanguages[2] = "EN";
-		return (languageProfile==100);
-	}
-	
-	public VitroModelProperties() {
-		languageProfile = 200;
-		preferredLanguages = new String[1];
-		preferredLanguages[0] = null;
 		defaultNamespace = "http://vitro.mannlib.cornell.edu/ns/default#";
 		nonUserNamespaces = new HashSet<String>();
 		nonUserNamespaces.add(VitroVocabulary.vitroURI);
 	}
 	
-	public int getLanguageProfile() {
-		return this.languageProfile;
-	}
-	
-	public void setLanguageProfile(int languageProfile) {
-		this.languageProfile = languageProfile;
-	}
-	
 	public String[] getPreferredLanguages() {
 		return this.preferredLanguages;
 	}

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

@@ -25,11 +25,8 @@ import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
 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.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
@@ -38,6 +35,7 @@ import com.hp.hpl.jena.vocabulary.RDFS;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
 
 public class JenaModelUtils {
 	
@@ -67,7 +65,10 @@ public class JenaModelUtils {
 		SimpleOntModelSelector oms = new SimpleOntModelSelector();
 		oms.setTBoxModel(ontModel);
 		oms.setApplicationMetadataModel(modelForClassgroups);
-		WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena(new SimpleOntModelSelector(ontModel),wadf.getDefaultNamespace(),null,null,null);
+		WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
+		config.setDefaultNamespace(wadf.getDefaultNamespace());
+		WebappDaoFactory myWebappDaoFactory = new WebappDaoFactoryJena(
+				new SimpleOntModelSelector(ontModel), config, null);
 		OntModel tempModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
 	    Resource classGroupClass = ResourceFactory.createResource(VitroVocabulary.CLASSGROUP);
 	    Property inClassGroupProperty = ResourceFactory.createProperty(VitroVocabulary.IN_CLASSGROUP);

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

@@ -54,6 +54,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
@@ -72,17 +73,12 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     
     protected OntModelSelector ontModelSelector;
     
-    protected String defaultNamespace;
+    protected WebappDaoFactoryConfig config;
-    protected HashSet<String> nonuserNamespaces;
-    protected String[] preferredLanguages;
     
     protected PelletListener pelletListener;
 
     protected String userURI;
 	
-	protected boolean INCLUDE_TOP_CONCEPT = false;
-	protected boolean INCLUDE_BOTTOM_CONCEPT = false;
-	
 	private Map<String,String> properties = new HashMap<String,String>();
 	
 	protected DatasetWrapperFactory dwf;
@@ -91,9 +87,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
 
     public WebappDaoFactoryJena(WebappDaoFactoryJena base, String userURI) {
         this.ontModelSelector = base.ontModelSelector;
-        this.defaultNamespace = base.defaultNamespace;
+        this.config = base.config;
-        this.nonuserNamespaces = base.nonuserNamespaces;
-        this.preferredLanguages = base.preferredLanguages;
         this.userURI = userURI;
         this.dwf = base.dwf;
     }
@@ -101,50 +95,12 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
                                 OntModelSelector baseOntModelSelector,
                                 OntModelSelector inferenceOntModelSelector,
-                                String defaultNamespace, 
+                                WebappDaoFactoryConfig config, 
-                                HashSet<String> nonuserNamespaces, 
+                                String userURI) {
-                                String[] preferredLanguages, 
-                                String userURI){
     	
         this.ontModelSelector = ontModelSelector;
-        
+        this.config = config;
-        if (defaultNamespace != null) {
-            this.defaultNamespace = defaultNamespace;
-        } else {
-            initDefaultNamespace();
-        }
-        if (nonuserNamespaces != null) {
-            this.nonuserNamespaces = nonuserNamespaces;
-        } else {
-            initNonuserNamespaces();
-        }
-        if (preferredLanguages != null) {
-            this.preferredLanguages = preferredLanguages;
-        } else {
-            initPreferredLanguages();
-        }
         this.userURI = userURI;
-        Model languageUniversalsModel = ModelFactory.createDefaultModel();
-        if (INCLUDE_TOP_CONCEPT) {
-        	Resource top = getTopConcept();
-        	if (top != null) {
-        		languageUniversalsModel.add(top, RDF.type, 
-        				this.ontModelSelector.getTBoxModel().getProfile()
-        				        .CLASS());
-        	}
-        }
-        if (INCLUDE_BOTTOM_CONCEPT) {
-        	Resource bottom = getBottomConcept();
-        	if (bottom != null) {
-        		languageUniversalsModel.add(bottom, RDF.type, 
-        				this.ontModelSelector.getTBoxModel().getProfile()
-        				        .CLASS());
-        	}
-        }
-        if (languageUniversalsModel.size()>0) {
-        	this.ontModelSelector.getTBoxModel().addSubModel(
-        			languageUniversalsModel);
-        }
         
         Model assertions = (baseOntModelSelector != null) 
                 ? baseOntModelSelector.getFullModel()
@@ -158,6 +114,45 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         
     } 
 
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
+                                WebappDaoFactoryConfig config,
+                                String userURI) {
+        this(ontModelSelector, null, null, config, userURI);
+    }
+
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
+                                WebappDaoFactoryConfig config) {
+        this(ontModelSelector, config, null);
+    }
+    
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
+    		                    OntModelSelector baseOntModelSelector, 
+    		                    OntModelSelector inferenceOntModelSelector, 
+    		                    WebappDaoFactoryConfig config) {
+        this(ontModelSelector, 
+             baseOntModelSelector, 
+             inferenceOntModelSelector, 
+             config,
+             null);
+    }
+
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector) {
+        this(ontModelSelector, new WebappDaoFactoryConfig(), null);
+    }
+    
+    public WebappDaoFactoryJena(OntModel ontModel) {
+    	this(new SimpleOntModelSelector(
+    			ontModel), new WebappDaoFactoryConfig(), null);
+    }
+    
+    public OntModelSelector getOntModelSelector() {
+    	return this.ontModelSelector;
+    }
+    
+    public OntModel getOntModel() {
+    	return this.ontModelSelector.getFullModel();
+    }
+       
     public static Dataset makeInMemoryDataset(Model assertions, 
                                               Model inferences) {
         DataSource dataset = DatasetFactory.create();        
@@ -176,128 +171,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         return dataset;
     }
 
-    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
-            String defaultNamespace, 
-            HashSet<String> nonuserNamespaces, 
-            String[] preferredLanguages, 
-            String userURI){
-        this(ontModelSelector, 
-             null, 
-             null,
-             defaultNamespace,
-             nonuserNamespaces, 
-             preferredLanguages, 
-             userURI);
-    }
-
-    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
-    		                    String defaultNamespace, 
-    		                    HashSet<String> nonuserNamespaces, 
-    		                    String[] preferredLanguages) {
-        this(ontModelSelector, 
-             defaultNamespace, 
-             nonuserNamespaces, 
-             preferredLanguages, 
-             null);
-    }
-    
-    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
-    		                    OntModelSelector baseOntModelSelector, 
-    		                    OntModelSelector inferenceOntModelSelector, 
-    		                    String defaultNamespace, 
-    		                    HashSet<String> nonuserNamespaces, 
-    		                    String[] preferredLanguages){
-        this(ontModelSelector, 
-             baseOntModelSelector, 
-             inferenceOntModelSelector, 
-             defaultNamespace, 
-             nonuserNamespaces, 
-             preferredLanguages, 
-             null);
-    }
-
-    public WebappDaoFactoryJena(OntModelSelector ontModelSelector) {
-        this(ontModelSelector, null, null, null, null, null);
-    }
-
-    public WebappDaoFactoryJena(OntModel ontModel, 
-    		                    String defaultNamespace, 
-    		                    HashSet<String> nonuserNamespaces, 
-    		                    String[] preferredLanguages, 
-    		                    String userURI) {
-    	this(new SimpleOntModelSelector(ontModel), 
-             defaultNamespace, 
-             nonuserNamespaces, 
-             preferredLanguages, 
-             userURI);
-    } 
-
-    public WebappDaoFactoryJena(OntModel ontModel, 
-                                String defaultNamespace, 
-                                HashSet<String> nonuserNamespaces, 
-                                String[] preferredLanguages) {
-        this(new SimpleOntModelSelector(ontModel), 
-             defaultNamespace, 
-             nonuserNamespaces, 
-             preferredLanguages, 
-             null);
-    }
-
-    public WebappDaoFactoryJena(OntModel ontModel) {
-        this(new SimpleOntModelSelector(
-        		ontModel), null, null, null, null, null);
-    }
-    
-    public OntModelSelector getOntModelSelector() {
-    	return this.ontModelSelector;
-    }
-    
-    public OntModel getOntModel() {
-    	return this.ontModelSelector.getFullModel();
-    }
-    
-    /**
-     * Return the current language profile's Top concept as a Jena resource, 
-     * or null if not applicable.  The special case is RDFS, where we use 
-     * rdfs:Resource as the analog of Top, rather than returning null.
-     * @return
-     */
-    public Resource getTopConcept() {
-      	Resource top = null;
-    	if (this.ontModelSelector.getTBoxModel().getProfile().NAMESPACE()
-    			.equals(RDFS.getURI())) {
-    		top = RDFS.Resource;
-    	} else {
-    		top = this.ontModelSelector.getTBoxModel().getProfile().THING();
-    	}
-    	return top;
-    }
-    
-    /**
-     * Return the current language profile's Bottom concept as a Jena resource, 
-     * or null if not applicable.
-     * @return
-     */
-    public Resource getBottomConcept() {
-    	return this.ontModelSelector.getTBoxModel().getProfile().THING();
-    }
-    
-    private void initDefaultNamespace() {
-        defaultNamespace = "http://vivo.library.cornell.edu/ns/0.1#";
-    }
-
-    private void initNonuserNamespaces() {
-        nonuserNamespaces = new HashSet<String>();
-        nonuserNamespaces.add(VitroVocabulary.vitroURI);
-    }
-
-    private void initPreferredLanguages() {
-        preferredLanguages = new String[3];
-        preferredLanguages[0] = "en-US";
-        preferredLanguages[1] = "en";
-        preferredLanguages[2] = "EN";
-    }
-
     /* ******************************************** */
 
 	public Map<String,String> getProperties() {
@@ -366,15 +239,15 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     /* **************** accessors ***************** */
 
     public String getDefaultNamespace() {
-        return defaultNamespace;
+        return config.getDefaultNamespace();
     }
     
     public String[] getPreferredLanguages() {
-    	return this.preferredLanguages;
+    	return config.getPreferredLanguages();
     }
     
     public Set<String> getNonuserNamespaces() {
-    	return nonuserNamespaces;
+    	return config.getNonUserNamespaces();
     }
     
     /**
@@ -595,9 +468,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     		//Not sure what this is but will set to equivalence here
     		this.ontModelSelector = base.ontModelSelector;
     	}   	
-        this.defaultNamespace = base.defaultNamespace;
+        this.config = base.config;
-        this.nonuserNamespaces = base.nonuserNamespaces;
-        this.preferredLanguages = base.preferredLanguages;
         this.userURI = base.userURI;
         this.dwf = base.dwf;
     }

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

@@ -19,6 +19,7 @@ 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.dao.WebappDaoFactoryConfig;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
@@ -30,7 +31,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 	 * For use when any database connection associated with the Dataset
 	 * is managed externally
 	 */
-	public WebappDaoFactorySDB(OntModelSelector ontModelSelector, Dataset dataset) {
+	public WebappDaoFactorySDB(OntModelSelector ontModelSelector, 
+                               Dataset dataset) {
 		super(ontModelSelector);
 		this.dwf = new StaticDatasetFactory(dataset);
 	}
@@ -41,10 +43,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
      */
 	public WebappDaoFactorySDB(OntModelSelector ontModelSelector, 
 	                            Dataset dataset, 
-	                            String defaultNamespace, 
+	                            WebappDaoFactoryConfig config) {
-	                            HashSet<String> nonuserNamespaces, 
+		super(ontModelSelector, config);
-	                            String[] preferredLanguages) {
-		super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
         this.dwf = new StaticDatasetFactory(dataset);
 	}
 	
@@ -55,10 +55,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
     public WebappDaoFactorySDB(OntModelSelector ontModelSelector, 
                                 BasicDataSource bds,
                                 StoreDesc storeDesc,
-                                String defaultNamespace, 
+                                WebappDaoFactoryConfig config) {
-                                HashSet<String> nonuserNamespaces, 
+        super(ontModelSelector, config);
-                                String[] preferredLanguages) {
-        super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
         this.dwf = new ReconnectingDatasetFactory(bds, storeDesc);
     }
     
@@ -69,11 +67,9 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
     public WebappDaoFactorySDB(OntModelSelector ontModelSelector, 
                                 BasicDataSource bds,
                                 StoreDesc storeDesc,
-                                String defaultNamespace, 
+                                WebappDaoFactoryConfig config,
-                                HashSet<String> nonuserNamespaces, 
-                                String[] preferredLanguages,
                                 SDBDatasetMode datasetMode) {
-        super(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages);
+        super(ontModelSelector, config);
         this.dwf = new ReconnectingDatasetFactory(bds, storeDesc);
         this.datasetMode = datasetMode;
     }
@@ -82,9 +78,7 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
     public WebappDaoFactorySDB(WebappDaoFactorySDB base, String userURI) {
         super(base.ontModelSelector);
         this.ontModelSelector = base.ontModelSelector;
-        this.defaultNamespace = base.defaultNamespace;
+        this.config = base.config;
-        this.nonuserNamespaces = base.nonuserNamespaces;
-        this.preferredLanguages = base.preferredLanguages;
         this.userURI = userURI;
         this.dwf = base.dwf;
     }
@@ -125,7 +119,6 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 	}
 	
 	public WebappDaoFactory getUserAwareDaoFactory(String userURI) {
-        // TODO: put the user-aware factories in a hashmap so we don't keep re-creating them
         return new WebappDaoFactorySDB(this, userURI);
     }
 	
@@ -174,7 +167,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 	    private BasicDataSource _bds;
 	    private StoreDesc _storeDesc;
 	    
-	    public ReconnectingDatasetFactory(BasicDataSource bds, StoreDesc storeDesc) {
+	    public ReconnectingDatasetFactory(BasicDataSource bds, 
+                                          StoreDesc storeDesc) {
 	        _bds = bds;
 	        _storeDesc = storeDesc;
 	    }
@@ -187,7 +181,8 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
                 Dataset dataset = SDBFactory.connectDataset(store);
                 return new DatasetWrapper(dataset, conn);
             } catch (SQLException sqe) {
-                throw new RuntimeException("Unable to connect to database", sqe);
+                throw new RuntimeException(
+                		"Unable to connect to database", sqe);
             }
 	    }
 	    

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

@@ -31,6 +31,7 @@ import com.hp.hpl.jena.sdb.sql.SDBConnection;
 
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
@@ -103,8 +104,9 @@ public class WebappDaoFactorySDBPrep implements Filter {
 				store = SDBFactory.connectStore(conn, storeDesc);
 				dataset = SDBFactory.connectDataset(store);
 				VitroRequest vreq = new VitroRequest((HttpServletRequest) request);
-				wadf = 
+				WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
-					new WebappDaoFactorySDB(oms, dataset, defaultNamespace, null, null);
+				config.setDefaultNamespace(defaultNamespace);
+				wadf = new WebappDaoFactorySDB(oms, dataset, config);
 				vreq.setWebappDaoFactory(wadf);
 				vreq.setFullWebappDaoFactory(wadf);
 				vreq.setDataset(dataset);

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

@@ -43,6 +43,7 @@ import com.hp.hpl.jena.vocabulary.RDF;
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
@@ -54,7 +55,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
 
-public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements javax.servlet.ServletContextListener {
+public class JenaDataSourceSetup extends JenaDataSourceSetupBase 
+        implements javax.servlet.ServletContextListener {
     
     private static final Log log = LogFactory.getLog(JenaDataSourceSetup.class);
     
@@ -120,38 +122,57 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
             }
         }
         
-        // The code below, which sets up the OntModelSelectors, controls whether each
+        // The code below, which sets up the OntModelSelectors, controls whether 
-        // model is maintained in memory, in the DB, or both while the application
+        // each model is maintained in memory, in the DB, or both while the 
-        // is running.         
+        // application is running.         
                 
-        // Populate the three OntModelSelectors (BaseOntModel=assertions, InferenceOntModel=inferences
+        // Populate the three OntModelSelectors (BaseOntModel = assertions, 
-        // and JenaOntModel=union of assertions and inferences) with the post-SDB-conversion models.
+        // InferenceOntModel = inferences and JenaOntModel = union of assertions
+        // and inferences) with the post-SDB-conversion models.
 
         // ABox assertions
-        Model aboxAssertions = makeDBModel(bds, JenaDataSourceSetupBase.JENA_DB_MODEL, DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx);
+        Model aboxAssertions = makeDBModel(
-        Model listenableAboxAssertions = ModelFactory.createUnion(aboxAssertions, ModelFactory.createDefaultModel());
+        		bds, JenaDataSourceSetupBase.JENA_DB_MODEL, DB_ONT_MODEL_SPEC, 
-        baseOms.setABoxModel(ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, listenableAboxAssertions));
+        		TripleStoreType.SDB, ctx);
+        Model listenableAboxAssertions = ModelFactory.createUnion(
+        		aboxAssertions, ModelFactory.createDefaultModel());
+        baseOms.setABoxModel(
+        		ModelFactory.createOntologyModel(
+        				OntModelSpec.OWL_MEM, listenableAboxAssertions));
         
         // ABox inferences
-        Model aboxInferences = makeDBModel(bds, JenaDataSourceSetupBase.JENA_INF_MODEL, DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx);
+        Model aboxInferences = makeDBModel(
-        Model listenableAboxInferences = ModelFactory.createUnion(aboxInferences, ModelFactory.createDefaultModel());
+        		bds, JenaDataSourceSetupBase.JENA_INF_MODEL, DB_ONT_MODEL_SPEC, 
-        inferenceOms.setABoxModel(ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, listenableAboxInferences));
+        		TripleStoreType.SDB, ctx);
+        Model listenableAboxInferences = ModelFactory.createUnion(
+        		aboxInferences, ModelFactory.createDefaultModel());
+        inferenceOms.setABoxModel(ModelFactory.createOntologyModel(
+        		OntModelSpec.OWL_MEM, listenableAboxInferences));
+      
+        
+        // Since the TBox models are in memory, they do not have timeout issues 
+        // like the like the ABox models do (and so don't need the extra step 
+        // to make them listenable.)
         
-        // Since the TBox models are in memory, they do not have time out issues like the
-        // ABox models do (and so don't need the extra step to make them listenable).
         // TBox assertions
         try {
-            Model tboxAssertionsDB = makeDBModel(bds, JENA_TBOX_ASSERTIONS_MODEL, DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx);
+            Model tboxAssertionsDB = makeDBModel(
-            OntModel tboxAssertions = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
+            		bds, JENA_TBOX_ASSERTIONS_MODEL, DB_ONT_MODEL_SPEC, 
+            		TripleStoreType.SDB, ctx);
+            OntModel tboxAssertions = ModelFactory.createOntologyModel(
+            		MEM_ONT_MODEL_SPEC);
             
             if (tboxAssertionsDB != null) {
                 long startTime = System.currentTimeMillis();
-                System.out.println("Copying cached tbox assertions into memory");
+                System.out.println(
+                		"Copying cached tbox assertions into memory");
                 tboxAssertions.add(tboxAssertionsDB);
-                System.out.println((System.currentTimeMillis()-startTime)/1000+" seconds to load tbox assertions");
+                System.out.println((System.currentTimeMillis() - startTime)
+                		/ 1000 + " seconds to load tbox assertions");
             }
 
-            tboxAssertions.getBaseModel().register(new ModelSynchronizer(tboxAssertionsDB));
+            tboxAssertions.getBaseModel().register(new ModelSynchronizer(
+            		tboxAssertionsDB));
             baseOms.setTBoxModel(tboxAssertions);
         } catch (Throwable e) {
             log.error("Unable to load tbox assertion cache from DB", e);
@@ -159,56 +180,80 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         
         // TBox inferences
         try {
-            Model tboxInferencesDB = makeDBModel(bds, JENA_TBOX_INF_MODEL, DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx);
+            Model tboxInferencesDB = makeDBModel(
-            OntModel tboxInferences = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
+            		bds, JENA_TBOX_INF_MODEL, DB_ONT_MODEL_SPEC, 
+            		TripleStoreType.SDB, ctx);
+            OntModel tboxInferences = ModelFactory.createOntologyModel(
+            		MEM_ONT_MODEL_SPEC);
             
             if (tboxInferencesDB != null) {
                 long startTime = System.currentTimeMillis();
-                System.out.println("Copying cached tbox inferences into memory");
+                System.out.println(
+                		"Copying cached tbox inferences into memory");
                 tboxInferences.add(tboxInferencesDB);
-                System.out.println((System.currentTimeMillis()-startTime)/1000+" seconds to load tbox inferences");
+                System.out.println((System.currentTimeMillis() - startTime)
+                		/ 1000 + " seconds to load tbox inferences");
             }
             
-            tboxInferences.getBaseModel().register(new ModelSynchronizer(tboxInferencesDB));
+            tboxInferences.getBaseModel().register(new ModelSynchronizer(
+            		tboxInferencesDB));
             inferenceOms.setTBoxModel(tboxInferences);
         } catch (Throwable e) {
             log.error("Unable to load tbox inference cache from DB", e);
         }
                               
         // union ABox
-        OntModel unionABoxModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(baseOms.getABoxModel(), inferenceOms.getABoxModel()));
+        OntModel unionABoxModel = ModelFactory.createOntologyModel(
+        		MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(
+        				baseOms.getABoxModel(), inferenceOms.getABoxModel()));
         unionOms.setABoxModel(unionABoxModel);
         
         // union TBox
-        OntModel unionTBoxModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(baseOms.getTBoxModel(), inferenceOms.getTBoxModel()));       
+        OntModel unionTBoxModel = ModelFactory.createOntologyModel(
+        		MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(
+        				baseOms.getTBoxModel(), inferenceOms.getTBoxModel()));       
         unionOms.setTBoxModel(unionTBoxModel);
                   
         
         // Application metadata model is cached in memory.
         try {
             
-            Model applicationMetadataModelDB = makeDBModel(bds, JENA_APPLICATION_METADATA_MODEL, DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx);
+            Model applicationMetadataModelDB = makeDBModel(
-            OntModel applicationMetadataModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
+            		bds, JENA_APPLICATION_METADATA_MODEL, DB_ONT_MODEL_SPEC, 
+            		TripleStoreType.SDB, ctx);
+            OntModel applicationMetadataModel = 
+                    ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
             
             long startTime = System.currentTimeMillis();
-            System.out.println("Copying cached application metadata model into memory");
+            System.out.println(
+            		"Copying cached application metadata model into memory");
             applicationMetadataModel.add(applicationMetadataModelDB);
-            System.out.println((System.currentTimeMillis()-startTime)/1000+" seconds to load application metadata model assertions of size " + applicationMetadataModel.size());
+            System.out.println((System.currentTimeMillis() - startTime) 
-            applicationMetadataModel.getBaseModel().register(new ModelSynchronizer(applicationMetadataModelDB));
+            		/ 1000 + " seconds to load application metadata model " +
+            		"assertions of size " + applicationMetadataModel.size());
+            applicationMetadataModel.getBaseModel().register(
+            		new ModelSynchronizer(applicationMetadataModelDB));
             
             if (isFirstStartup()) {
-            	applicationMetadataModel.add(InitialJenaModelUtils.loadInitialModel(ctx, getDefaultNamespace(ctx)));
+            	applicationMetadataModel.add(
+            			InitialJenaModelUtils.loadInitialModel(
+            					ctx, getDefaultNamespace(ctx)));
             	
             } else if (applicationMetadataModelDB.size() == 0) {
-                repairAppMetadataModel(applicationMetadataModel, aboxAssertions, aboxInferences);
+                repairAppMetadataModel(
+                		applicationMetadataModel, aboxAssertions, 
+                		aboxInferences);
             }
             
             baseOms.setApplicationMetadataModel(applicationMetadataModel);
-            inferenceOms.setApplicationMetadataModel(baseOms.getApplicationMetadataModel());
+            inferenceOms.setApplicationMetadataModel(
-            unionOms.setApplicationMetadataModel(baseOms.getApplicationMetadataModel());
+            		baseOms.getApplicationMetadataModel());
+            unionOms.setApplicationMetadataModel(
+            		baseOms.getApplicationMetadataModel());
             
         } catch (Throwable e) {
-            log.error("Unable to load application metadata model cache from DB", e);
+            log.error("Unable to load application metadata model cache from DB"
+                    , e);
         }
         
         checkForNamespaceMismatch( baseOms.getApplicationMetadataModel(), ctx );
@@ -220,31 +265,28 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         log.info("Setting up union models and DAO factories");
         
         // create TBox + ABox union models and set up webapp DAO factories
-        OntModel baseUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
+        OntModel baseUnion = ModelFactory.createOntologyModel(
-                ModelFactory.createUnion(baseOms.getABoxModel(), baseOms.getTBoxModel()));
+        		OntModelSpec.OWL_MEM,
+                ModelFactory.createUnion(baseOms.getABoxModel(), 
+                		baseOms.getTBoxModel()));
         baseOms.setFullModel(baseUnion);
         ModelContext.setBaseOntModel(baseOms.getFullModel(), ctx);
+        WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
+        config.setDefaultNamespace(getDefaultNamespace(ctx));
         WebappDaoFactory baseWadf = new WebappDaoFactorySDB(
-                baseOms,
+                baseOms, bds, storeDesc, config,
-                bds,
-                storeDesc, 
-                getDefaultNamespace(ctx), 
-                null, 
-                null, 
                 WebappDaoFactorySDB.SDBDatasetMode.ASSERTIONS_ONLY);
         ctx.setAttribute("assertionsWebappDaoFactory",baseWadf);
         
-        OntModel inferenceUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
+        OntModel inferenceUnion = ModelFactory.createOntologyModel(
-                ModelFactory.createUnion(inferenceOms.getABoxModel(), inferenceOms.getTBoxModel()));
+        		OntModelSpec.OWL_MEM,
+                ModelFactory.createUnion(
+                		inferenceOms.getABoxModel(), 
+                		inferenceOms.getTBoxModel()));
         inferenceOms.setFullModel(inferenceUnion);
         ModelContext.setInferenceOntModel(inferenceOms.getFullModel(), ctx);
         WebappDaoFactory infWadf = new WebappDaoFactorySDB(
-                inferenceOms, 
+                inferenceOms, bds, storeDesc, config, 
-                bds, 
-                storeDesc, 
-                getDefaultNamespace(ctx), 
-                null, 
-                null, 
                 WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
         ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
         
@@ -252,23 +294,19 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         		DB_ONT_MODEL_SPEC, makeDBModel(
         				bds, WebappDaoFactorySDB.UNION_GRAPH,
         						DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx));
-        //OntModel masterUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
-        //        ModelFactory.createUnion(unionABoxModel, unionTBoxModel));
         unionOms.setFullModel(masterUnion);
         ctx.setAttribute("jenaOntModel", masterUnion);  
-        WebappDaoFactory wadf = new WebappDaoFactorySDB(unionOms, bds, storeDesc, getDefaultNamespace(ctx), null, null);
+        WebappDaoFactory wadf = new WebappDaoFactorySDB(
+        		unionOms, bds, storeDesc, config);
         ctx.setAttribute("webappDaoFactory",wadf);
 
         ModelContext.setOntModelSelector(unionOms, ctx);
-        ModelContext.setUnionOntModelSelector(unionOms, ctx);          // assertions and inferences
+        ModelContext.setUnionOntModelSelector(unionOms, ctx);          
-        ModelContext.setBaseOntModelSelector(baseOms, ctx);            // assertions
+                                           // assertions and inferences
-        ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);  // inferences       
+        ModelContext.setBaseOntModelSelector(baseOms, ctx);            
-        
+                                           // assertions
-        //log.info("Setting up namespace mapper");
+        ModelContext.setInferenceOntModelSelector(inferenceOms, ctx);  
-        
+                                           // inferences       
-        //NamespaceMapper namespaceMapper = new NamespaceMapperJena(masterUnion, masterUnion, defaultNamespace);
-        //ctx.setAttribute("NamespaceMapper", namespaceMapper);
-        //unionOms.getFullModel().getBaseModel().register(namespaceMapper);
         
         ctx.setAttribute("defaultNamespace", getDefaultNamespace(ctx));
         
@@ -352,7 +390,7 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
 	}
 	
 
-    /* ====================================================================== */
+    /* ===================================================================== */
     
     
     @Override
@@ -360,7 +398,8 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
     	// Nothing to do.
     }
     
-    private OntModel ontModelFromContextAttribute(ServletContext ctx, String attribute) {
+    private OntModel ontModelFromContextAttribute(ServletContext ctx, 
+    	                                          String attribute) {
         OntModel ontModel;
         Object attributeValue = ctx.getAttribute(attribute);
         if (attributeValue != null && attributeValue instanceof OntModel) {
@@ -387,7 +426,8 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         }
     }
     
-    private void loadDataFromFilesystem(OntModelSelector baseOms, ServletContext ctx) {
+    private void loadDataFromFilesystem(OntModelSelector baseOms, 
+    	                                ServletContext ctx) {
         Long startTime = System.currentTimeMillis();
         log.debug("Initializing models from RDF files");    
         readOntologyFilesInPathSet(USER_ABOX_PATH, ctx, baseOms.getABoxModel());
@@ -398,7 +438,9 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         		+ " seconds to read RDF files ");
     }
 
-    private static void getTBoxModel(Model fullModel, Model submodels, Model tboxModel) {
+    private static void getTBoxModel(Model fullModel, 
+    		                         Model submodels, 
+    		                         Model tboxModel) {
   
         JenaModelUtils modelUtils = new JenaModelUtils();
        
@@ -421,7 +463,9 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
     /* 
      * Copy all statements from model 1 that are not in model 2 to model 3.
      */
-    private static void copyDifference(Model model1, Model model2, Model model3) {
+    private static void copyDifference(Model model1, 
+    	                               Model model2, 
+    	                               Model model3) {
                  
         StmtIterator iter = model1.listStatements();
         
@@ -502,16 +546,17 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         try {
         
             // This is a one-time copy of stored KB data - from a Jena RDB store
-            // to a Jena SDB store. In the process, we will also separate out the
+            // to a Jena SDB store. In the process, we will also separate out 
-            // TBox from the Abox; these are in the same graph in pre 1.2 VIVO 
+        	// the TBox from the Abox; these are in the same graph in pre-1.2 
-            // versions and will now be stored and maintained in separate models
+        	// VIVO versions and will now be stored and maintained in separate 
-            // Access to the Jena RDB data is through the OntModelSelectors that have
+        	// models.  Access to the Jena RDB data is through the 
-            // been set up earlier in the current session by
+        	// OntModelSelectors that have been set up earlier in the current 
-            // JenaPersistentDataSourceSetup.java
+        	// session by JenaPersistentDataSourceSetup.java.  In the code 
-            // In the code below, note that the current getABoxModel() methods on 
+        	// below, note that the current getABoxModel() methods on the 
-            // the OntModelSelectors return a graph with both ABox and TBox data.
+        	// OntModelSelectors return a graph with both ABox and TBox data.
         
-            OntModel submodels = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
+            OntModel submodels = ModelFactory.createOntologyModel(
+            		MEM_ONT_MODEL_SPEC);
             readOntologyFilesInPathSet(SUBMODELS, ctx, submodels);
             
             Model tboxAssertions = SDBFactory.connectNamedModel(
@@ -540,10 +585,12 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
             
             // Set up the application metadata model
             Model applicationMetadataModel = SDBFactory.connectNamedModel(
-                    store, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
+                    store, 
+                    JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
             getAppMetadata(memModel, applicationMetadataModel);
-    	   	log.info("During initial SDB setup, created an application metadata model of size " 
+    	   	log.info("During initial SDB setup, created an application " +
-    	   	        + applicationMetadataModel.size());
+    	   			"metadata model of size " +
+    	   			applicationMetadataModel.size());
     	   	
     	   	// remove application metadata from ABox model
     	   	aboxAssertions.remove(applicationMetadataModel);
@@ -583,7 +630,10 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         // even if the store exists, it may be empty
         
         try {
-            return (SDBFactory.connectNamedModel(store, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL)).size() > 0;    
+            return (SDBFactory.connectNamedModel(
+            		store, 
+            		JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL))
+            		        .size() > 0;    
         } catch (Exception e) { 
             return false;
         }