NIHVIVO-3312 minor cleanup of WebappDaoFactory

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

@@ -50,10 +50,8 @@ public class VclassEditController extends BaseEditController {
         VClass vcl = (VClass)vcwDao.getVClassByURI(request.getParameter("uri"));
         
         if (vcl == null) {
-        	if (VitroModelProperties.isRDFS(request.getFullWebappDaoFactory().getLanguageProfile()) 
+        	vcl = request.getFullWebappDaoFactory()
-        			&& ( (RDF.getURI()+"Resource").equals(request.getParameter("uri")))) {
+        	        .getVClassDao().getTopConcept();
-        		vcl = new VClass(RDF.getURI()+"Resource");
-        	}
         }
 
         request.setAttribute("VClass",vcl);

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

@@ -84,36 +84,15 @@ public class ClassHierarchyListingController extends BaseEditController {
         } else if (startClassUri != null) {
         	roots = new LinkedList<VClass>();
         	roots.add(vcDao.getVClassByURI(startClassUri));
-        } else {
-        	/* TODO: this needs more thinking */
-        	if (false) { // (getWebappDaoFactory() instanceof WebappDaoFactoryJena) {
-        		String topConceptURI = null;
-        		int langProfile = ((WebappDaoFactoryJena) vrequest.getFullWebappDaoFactory()).getLanguageProfile();
-        		if (langProfile==WebappDaoFactoryJena.OWL_CONST) {
-        			topConceptURI = OWL.Thing.getURI();
-        		} else if (langProfile==WebappDaoFactoryJena.RDFS_CONST) {
-        			topConceptURI = RDFS.Resource.getURI();
-        		}
-        		VClass top = vcDao.getVClassByURI(topConceptURI);
-        		if (top != null) {
-        			roots = new LinkedList<VClass>();
-        			roots.add(top);
         } else {    	
        		roots = vcDao.getRootClasses();
         }
-        	} else {
-        		roots = vcDao.getRootClasses();
-        	}
-        }
         
         // DEBUGGING
         if (roots == null) {
         	roots = new LinkedList<VClass>();
-        	if (VitroModelProperties.isOWL(vrequest.getFullWebappDaoFactory().getLanguageProfile())) {
+        	roots.add(vrequest.getFullWebappDaoFactory().getVClassDao()
-        		roots.add(vcDao.getVClassByURI(OWL.Thing.getURI()));
+        			.getTopConcept());
-        	} else if (VitroModelProperties.isRDFS(vrequest.getFullWebappDaoFactory().getLanguageProfile())) {
-        		roots.add(new VClass(RDF.getURI()+"Resource"));
-        	} 
         }
         
         Collections.sort(roots);

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

@@ -1,16 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao;
-
-/**
- * Created by IntelliJ IDEA.
- * User: bdc34
- * Date: Apr 18, 2007
- * Time: 4:32:30 PM
- * To change this template use File | Settings | File Templates.
- */
-public interface FlagDao {
-    String getFlagNames(String table, String field);
-    public String convertNumericFlagToInsertString(int numeric,String column,String table);
-    public String convertNumericFlagToInsertString(int numeric,String flagColumns);
-}

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

@@ -9,26 +9,32 @@ import java.util.Set;
 public interface WebappDaoFactory {
 
     /**
-	 * Retrieves a map containing arbitrary key-value pairs describing this WebappDaoFactory
+     * Free any resources associated with this WebappDaoFactory  
+     */
+    public void close();
+	
+	/**
+	 * Retrieves a map containing arbitrary key-value pairs describing this 
+	 * WebappDaoFactory
 	 */
 	public Map<String,String> getProperties();
 
 	/**
-	 * Checks a URI String for two things: well-formedness and uniqueness in the model.
+	 * Checks a URI String for two things: well-formedness and uniqueness in the
-	 * Ill-formed strings or those matching URIs already in use will cause an error message to be returned.
+	 * model.  Ill-formed strings or those matching URIs already in use will 
+	 * cause an error message to be returned.
 	 * @return error message String if invalid; otherwise null
 	 */
 	public String checkURI(String uriStr);
 	
 	/**
-	 * Checks a URI String for two things: well-formedness and, optionally, uniqueness in the model.
+	 * Checks a URI String for two things: well-formedness and, optionally, 
-	 * Ill-formed strings or those matching URIs already in use will cause an error message to be returned.
+	 * uniqueness in the model.  Ill-formed strings or those matching URIs 
+	 * already in use will cause an error message to be returned.
 	 * @return error message String if invalid; otherwise null
 	 */
 	public String checkURI(String uriStr, boolean checkUniqueness);
 	
-	public int getLanguageProfile();
-	
     public String getDefaultNamespace();
     
     public Set<String> getNonuserNamespaces();
@@ -36,33 +42,37 @@ public interface WebappDaoFactory {
     public String[] getPreferredLanguages();
     
     /**
-     * BJL23 2008-05-20: Putting this here for lack of a more logical place.  We need to build better support for the RDFS vocabulary into our API.
+     * BJL23 2008-05-20: Putting this here for lack of a more logical place.  
-     * Returns a list of the simple lexical form strings of the rdfs:comment values for a resource; empty list if none found.
+     * We need to build better support for the RDFS vocabulary into our API.
+     * Returns a list of the simple lexical form strings of the rdfs:comment 
+     * values for a resource; empty list if none found.
      */
     public List<String> getCommentsForResource(String resourceURI);
 
     /**
-     * Copy this DAO factory to a new object associated with the specified user URI, or return the same factory if a user-aware version cannot be used.
+     * Copy this DAO factory to a new object associated with the specified user 
+     * URI, or return the same factory if a user-aware version cannot be used.
      * @param userURI
      * @return
      */
     public WebappDaoFactory getUserAwareDaoFactory(String userURI);
 
     /**
-     * Return URI of user associated with this WebappDaoFactory, or null if not applicable.
+     * Return URI of user associated with this WebappDaoFactory, 
+     * or null if not applicable.
      * @return
      */
     public String getUserURI();
 
-    /* ======================== DAOs for ontology (TBox) manipulation ======================== */
+    /* =============== DAOs for ontology (TBox) manipulation =============== */
 
     /**
-     * returns a Data Access Object for working with class subsumption axioms in the model
+     * returns a Data Access Object for working with class subsumption axioms 
      */
     public Classes2ClassesDao getClasses2ClassesDao();
 
     /**
-     * returns a Data Access Object for working with DataProperties in the model
+     * returns a Data Access Object for working with DataProperties
      */
     public DataPropertyDao getDataPropertyDao();
 
@@ -72,42 +82,42 @@ public interface WebappDaoFactory {
     public DatatypeDao getDatatypeDao();
 
     /**
-     * returns a Data Access Object for working with ObjectProperties in the model
+     * returns a Data Access Object for working with ObjectProperties
      */
     public ObjectPropertyDao getObjectPropertyDao();
 
     /**
-     * returns a Data Access Object for working with Ontologies in the model
+     * returns a Data Access Object for working with Ontologies
      */
     public OntologyDao getOntologyDao();
 
     /**
-     * returns a Data Access Object for working with ontology class objects in the model
+     * returns a Data Access Object for working with ontology class objects 
      */
     public VClassDao getVClassDao();
 
 
-    /* ======================== DAOs for ABox manipulation ======================== */
+    /* ==================== DAOs for ABox manipulation ===================== */
 
     /**
-     * returns a Data Access Object for working with DatatypePropertyStatements in the model
+     * returns a Data Access Object for working with DatatypePropertyStatements 
      */
     public DataPropertyStatementDao getDataPropertyStatementDao();
 
     /**
-     * returns a Data Access Object for working with Individuals in the model
+     * returns a Data Access Object for working with Individuals 
      */
     public IndividualDao getIndividualDao();
 
     /**
-     * returns a Data Access Object for working with ObjectPropertyStatements in the model
+     * returns a Data Access Object for working with ObjectPropertyStatements 
      */
     public ObjectPropertyStatementDao getObjectPropertyStatementDao();
 
 
     public DisplayModelDao getDisplayModelDao();
     
-    /* ======================== DAOs for other objects ======================== */
+    /* ====================== DAOs for other objects ======================= */
 
     public ApplicationDao getApplicationDao();
 
@@ -125,5 +135,4 @@ public interface WebappDaoFactory {
     
     public MenuDao getMenuDao();    
     
-    public void close();
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/WebappDaoFactoryFiltering.java

@@ -94,10 +94,6 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
         return innerWebappDaoFactory.getUserAwareDaoFactory(userURI);
     }
     
-    public int getLanguageProfile() {
-    	return innerWebappDaoFactory.getLanguageProfile();
-    }
-    
     public String getDefaultNamespace() {
         return innerWebappDaoFactory.getDefaultNamespace();
     }

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

@@ -888,22 +888,6 @@ public class JenaBaseDao extends JenaBaseDaoCon {
         return PREFERRED_LANGUAGES[0];
     }
     
-    protected Map<String,OntClass>getFlag2ValueMap() {
-        try {
-            return ((WebappDaoFactoryJena) this.webappDaoFactory).getFlag2ValueMap();
-        } catch (ClassCastException cce) {
-            return null;
-        }
-    }
-
-    protected Map<Resource,String>getFlag2ClassLabelMap() {
-        try {
-            return ((WebappDaoFactoryJena) this.webappDaoFactory).getFlag2ClassLabelMap();
-        } catch (ClassCastException cce) {
-            return null;
-        }
-    }
-    
     /**
      * Checks a URI for validity.  Jena models can store invalid URIs, but this causes RDF/XML output serialization to fail.
      * @param uri

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

@@ -1,36 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import com.hp.hpl.jena.ontology.OntModel;
-
-import edu.cornell.mannlib.vitro.webapp.dao.VitroModelProperties;
-
-public class VitroJenaModel {
-
-	private String graphURI = null;
-	private OntModel jenaOntModel = null;
-	private VitroModelProperties vitroModelProperties = null;
-	
-	public String getGraphURI() {
-		return graphURI;
-	}
-	public void setGraphURI(String graphURI) {
-		this.graphURI = graphURI;
-	}
-	
-	public OntModel getJenaOntModel() {
-		return this.jenaOntModel;
-	}
-	public void setJenaOntModel(OntModel ontModel) {
-		this.jenaOntModel = ontModel;
-	}
-	
-	public VitroModelProperties getVitroModelProperties() {
-		return this.vitroModelProperties;
-	}
-	public void setVitroModelProperties(VitroModelProperties vitroModelProperties) {
-		this.vitroModelProperties = vitroModelProperties;
-	}
-	
-}

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

@@ -1,19 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-public interface VitroJenaModelSource {
-
-	public abstract VitroJenaModel getVitroJenaModel();
-	
-	public abstract VitroJenaModel getVitroJenaModel(String namespace);
-
-	public abstract VitroJenaModel getMutableVitroJenaModel();
-	
-	public abstract VitroJenaModel getMutableVitroJenaModel(String namespace);
-	
-	public abstract VitroJenaModel getVitroAnnotationsJenaModel();
-	
-	public abstract VitroJenaModel getVitroAnnotationsJenaModel(String namespace);
-	
-}

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

@@ -13,7 +13,6 @@ import java.util.Set;
 import com.hp.hpl.jena.iri.IRI;
 import com.hp.hpl.jena.iri.IRIFactory;
 import com.hp.hpl.jena.iri.Violation;
-import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.ontology.OntResource;
@@ -27,20 +26,18 @@ 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.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;
 
-import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
 import edu.cornell.mannlib.vitro.webapp.dao.ApplicationDao;
 import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DisplayModelDao;
-import edu.cornell.mannlib.vitro.webapp.dao.FlagDao;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.LinksDao;
 import edu.cornell.mannlib.vitro.webapp.dao.LinktypeDao;
@@ -63,7 +60,6 @@ import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 public class WebappDaoFactoryJena implements WebappDaoFactory {
 
     protected IndividualDao entityWebappDao;
-    protected FlagDao flagDao;
     protected LinksDao linksDao;
     protected LinktypeDao linktypeDao;
     protected ApplicationDaoJena applicationDao;
@@ -84,9 +80,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
 
     protected String userURI;
 
-    protected Map<String,OntClass> flag2ValueMap;
-    protected Map<Resource,String> flag2ClassLabelMap;
-    
 	protected boolean INCLUDE_TOP_CONCEPT = false;
 	protected boolean INCLUDE_BOTTOM_CONCEPT = false;
 	
@@ -94,9 +87,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
 	
 	protected DatasetWrapperFactory dwf;
 	
-    // for temporary use to construct URIs for the things that still use integer IDs.
-    // As these objects get changed to support getURI(), this should become unnecessary.
-
     /* **************** constructors **************** */
 
     public WebappDaoFactoryJena(WebappDaoFactoryJena base, String userURI) {
@@ -105,8 +95,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         this.nonuserNamespaces = base.nonuserNamespaces;
         this.preferredLanguages = base.preferredLanguages;
         this.userURI = userURI;
-        this.flag2ValueMap = base.flag2ValueMap;
-        this.flag2ClassLabelMap = base.flag2ClassLabelMap;
         this.dwf = base.dwf;
     }
 
@@ -120,17 +108,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     	
         this.ontModelSelector = ontModelSelector;
         
-        // BJL23 2009-04-27
-        // As I understand it, the the following setting should allow more 
-        // relaxed use of .as() in Jena's polymorphic framework and avoid
-        // ClassCastExceptions deep in Jena when, for example, a resource 
-        // used as a class is not explicitly typed as such.  In reality,
-        // this setting seems to have dangerous consequences and causes
-        // bizarre other exceptions to be thrown in ways that make the model
-        // seem to behave even *more* strictly.  Uncomment at your own risk:
-        
-        // this.ontModel.setStrictMode(false);
-        
         if (defaultNamespace != null) {
             this.defaultNamespace = defaultNamespace;
         } else {
@@ -151,17 +128,22 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         if (INCLUDE_TOP_CONCEPT) {
         	Resource top = getTopConcept();
         	if (top != null) {
-        		languageUniversalsModel.add(top, RDF.type, this.ontModelSelector.getTBoxModel().getProfile().CLASS());
+        		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());
+        		languageUniversalsModel.add(bottom, RDF.type, 
+        				this.ontModelSelector.getTBoxModel().getProfile()
+        				        .CLASS());
         	}
         }
         if (languageUniversalsModel.size()>0) {
-        	this.ontModelSelector.getTBoxModel().addSubModel(languageUniversalsModel);
+        	this.ontModelSelector.getTBoxModel().addSubModel(
+        			languageUniversalsModel);
         }
         
         Model assertions = (baseOntModelSelector != null) 
@@ -176,13 +158,13 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         
     } 
     
-    public static Dataset makeInMemoryDataset(Model assertions, Model inferences) {
+    public static Dataset makeInMemoryDataset(Model assertions, 
+                                              Model inferences) {
         DataSource dataset = DatasetFactory.create();        
-        
         OntModel union = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);        
-        
         if (assertions != null) {
-            dataset.addNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL, assertions);
+            dataset.addNamedModel(
+            		JenaDataSourceSetupBase.JENA_DB_MODEL, assertions);
             union.addSubModel(assertions);
         } 
         if (inferences != null) {
@@ -208,28 +190,62 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
              userURI);
     }
 
-    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, String defaultNamespace, HashSet<String> nonuserNamespaces, String[] preferredLanguages){
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
-        this(ontModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages, null);
+    		                    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){
+    public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 
-        this(ontModelSelector, baseOntModelSelector, inferenceOntModelSelector, defaultNamespace, nonuserNamespaces, preferredLanguages, null);
+    		                    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){
+    public WebappDaoFactoryJena(OntModel ontModel, 
-    	this(new SimpleOntModelSelector(ontModel), defaultNamespace, nonuserNamespaces, preferredLanguages, userURI);
+    		                    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){
+    public WebappDaoFactoryJena(OntModel ontModel, 
-        this(new SimpleOntModelSelector(ontModel), defaultNamespace, nonuserNamespaces, preferredLanguages, null);
+                                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);
+        this(new SimpleOntModelSelector(
+        		ontModel), null, null, null, null, null);
     }
     
     public OntModelSelector getOntModelSelector() {
@@ -241,13 +257,15 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     }
     
     /**
-     * Return the current language profile's Top concept as a Jena resource, or null if not applicable.
+     * Return the current language profile's Top concept as a Jena resource, 
-     * The special case is RDFS, where we use rdfs:Resource as the analog of Top, rather than returning null.
+     * 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())) {
+    	if (this.ontModelSelector.getTBoxModel().getProfile().NAMESPACE()
+    			.equals(RDFS.getURI())) {
     		top = RDFS.Resource;
     	} else {
     		top = this.ontModelSelector.getTBoxModel().getProfile().THING();
@@ -256,7 +274,8 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     }
     
     /**
-     * Return the current language profile's Bottom concept as a Jena resource, or null if not applicable.
+     * Return the current language profile's Bottom concept as a Jena resource, 
+     * or null if not applicable.
      * @return
      */
     public Resource getBottomConcept() {
@@ -269,11 +288,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
 
     private void initNonuserNamespaces() {
         nonuserNamespaces = new HashSet<String>();
-        //nonuserNamespaces.add(VitroVocabulary.RDF);
-        //nonuserNamespaces.add(VitroVocabulary.RDFS);
-        //nonuserNamespaces.add(VitroVocabulary.OWL);
         nonuserNamespaces.add(VitroVocabulary.vitroURI);
-        nonuserNamespaces.add("http://lowe.mannlib.cornell.edu/ns/vitro0.1/vitro.owl#"); // obsolete Vitro URI
     }
 
     private void initPreferredLanguages() {
@@ -297,19 +312,22 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         uriStr = (uriStr == null) ? " " : uriStr;
 		boolean validURI = true;
 		String errorMsg = "";
-		String duplicateMsg = "URI is already in use. Please enter another URI. ";
+		String duplicateMsg = "URI is already in use. " +
+		                      "Please enter another URI. ";
 		IRIFactory factory = IRIFactory.jenaImplementation();
 	    IRI iri = factory.create( uriStr );
 	    if (iri.hasViolation(false) ) {
 	    	validURI = false;
-	    	errorMsg += ((Violation)iri.violations(false).next()).getShortMessage()+" ";
+	    	errorMsg += ((Violation)iri.violations(false).next())
+	    	                    .getShortMessage() + " ";
 	    } else if (checkUniqueness) {
 	    	OntModel ontModel = ontModelSelector.getFullModel(); 
 			ontModel.enterCriticalSection(Lock.READ);
 			try {
 				Resource newURIAsRes = ResourceFactory.createResource(uriStr);
 				Property newURIAsProp = ResourceFactory.createProperty(uriStr);
-				ClosableIterator closeIt = ontModel.listStatements(newURIAsRes, null, (RDFNode)null);
+				StmtIterator closeIt = ontModel.listStatements(
+						newURIAsRes, null, (RDFNode)null);
 				if (closeIt.hasNext()) {
 					validURI = false;
 					errorMsg+="Not a valid URI.  Please enter another URI. ";
@@ -323,7 +341,8 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
 					}
 				}
 				if (validURI) {
-					closeIt = ontModel.listStatements(null, newURIAsProp, (RDFNode)null);
+					closeIt = ontModel.listStatements(
+							null, newURIAsProp, (RDFNode)null);
 					if (closeIt.hasNext()) {
 						validURI = false;
 						errorMsg+=duplicateMsg;
@@ -337,7 +356,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     }
     
     public WebappDaoFactory getUserAwareDaoFactory(String userURI) {
-        // TODO: put the user-aware factories in a hashmap so we don't keep re-creating them
         return new WebappDaoFactoryJena(this, userURI);
     }
 
@@ -351,20 +369,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         return defaultNamespace;
     }
     
-    public static int OWL_CONST = 202;
-    public static int RDFS_CONST = 100;
-    
-    public int getLanguageProfile() {
-    	OntModel ontModel = ontModelSelector.getTBoxModel();
-    	if (ontModel.getProfile().NAMESPACE().equals(OWL.NAMESPACE.getURI())) {
-    		return OWL_CONST;
-    	} else if (ontModel.getProfile().NAMESPACE().equals(RDFS.getURI())) {
-    		return RDFS_CONST;
-    	} else {
-    		return -1;
-    	}
-    }
-    
     public String[] getPreferredLanguages() {
     	return this.preferredLanguages;
     }
@@ -392,9 +396,9 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     	try {
     		OntResource res = ontModel.getOntResource(resourceURI);
     		if (res != null) {
-    			ClosableIterator closeIt = res.listComments(null);
+    			ClosableIterator<RDFNode> closeIt = res.listComments(null);
     			try {
-    				for (Iterator commIt = closeIt; commIt.hasNext();) {
+    				for(Iterator<RDFNode> commIt = closeIt; commIt.hasNext();) {
     					Literal lit = (Literal) commIt.next();
     					commentList.add(lit.getLexicalForm());
     				}
@@ -532,14 +536,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         return jenaBaseDao;
     }
 
-    public Map<String,OntClass> getFlag2ValueMap() {
-        return this.flag2ValueMap;
-    }
-
-    public Map<Resource,String> getFlag2ClassLabelMap() {
-        return this.flag2ClassLabelMap;
-    }
-
     @Override
     public PageDao getPageDao() {
         if( pageDao == null )
@@ -566,62 +562,58 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         }   
     }
     
-    //Method for creating a copy - does not pass the same object
+    /**
+     * Method for creating a copy - does not pass the same object
+     * @param base
+     */
     public WebappDaoFactoryJena (WebappDaoFactoryJena base) {
-    	//Not sure if selector somehow has greater longevity so making a copy instead of reference
+    	// Not sure if selector somehow has greater longevity so 
-    	
+    	// making a copy instead of reference.    	
     	if(base.ontModelSelector instanceof OntModelSelectorImpl) {
     		OntModelSelectorImpl selector = new OntModelSelectorImpl();
     		selector.setABoxModel(base.ontModelSelector.getABoxModel());
-    		selector.setApplicationMetadataModel(base.ontModelSelector.getApplicationMetadataModel());
+    		selector.setApplicationMetadataModel(
+    				base.ontModelSelector.getApplicationMetadataModel());
     		selector.setDisplayModel(base.ontModelSelector.getDisplayModel());
     		selector.setFullModel(base.ontModelSelector.getFullModel());
     		selector.setTBoxModel(base.ontModelSelector.getTBoxModel());
-    		selector.setUserAccountsModel(base.ontModelSelector.getUserAccountsModel());
+    		selector.setUserAccountsModel(
+    				base.ontModelSelector.getUserAccountsModel());
     		this.ontModelSelector = selector;
     	} else if(base.ontModelSelector instanceof SimpleOntModelSelector) {
     		SimpleOntModelSelector selector = new SimpleOntModelSelector();
     		selector.setABoxModel(base.ontModelSelector.getABoxModel());
-    		selector.setApplicationMetadataModel(base.ontModelSelector.getApplicationMetadataModel());
+    		selector.setApplicationMetadataModel(
+    				base.ontModelSelector.getApplicationMetadataModel());
     		selector.setDisplayModel(base.ontModelSelector.getDisplayModel());
     		selector.setFullModel(base.ontModelSelector.getFullModel());
     		selector.setTBoxModel(base.ontModelSelector.getTBoxModel());
-    		selector.setUserAccountsModel(base.ontModelSelector.getUserAccountsModel());
+    		selector.setUserAccountsModel(
+    				base.ontModelSelector.getUserAccountsModel());
     		this.ontModelSelector = selector;
     	} else {
     		//Not sure what this is but will set to equivalence here
     		this.ontModelSelector = base.ontModelSelector;
     	}   	
-    	
         this.defaultNamespace = base.defaultNamespace;
         this.nonuserNamespaces = base.nonuserNamespaces;
         this.preferredLanguages = base.preferredLanguages;
         this.userURI = base.userURI;
-        if(base.flag2ValueMap != null) {
-	        this.flag2ValueMap = new HashMap<String,OntClass>();
-	        this.flag2ValueMap.putAll(base.flag2ValueMap);
-        } else {
-        	this.flag2ValueMap = null;
-        }
-        if(base.flag2ClassLabelMap != null) {
-	        this.flag2ClassLabelMap = new HashMap<Resource, String>();
-	        this.flag2ClassLabelMap.putAll(base.flag2ClassLabelMap);
-        } else {
-        	this.flag2ClassLabelMap = null;
-        }
         this.dwf = base.dwf;
     }
     
     /**
-     * Method for using special model for webapp dao factory, such as display model.  
+     * Method for using a special model, such as the display model, with the 
-     * The goal here is to modify this WebappDaoFactory so that it is using the
+     * WebappDaoFactory.  The goal here is to modify this WebappDaoFactory so 
-     * specialModel, specialTboxModel and the specialDisplayModel for individual 
+     * that it is using specialModel, specialTboxModel and specialDisplayModel 
-     * editing. 
+     * for individual editing. 
      * 
-     * DAOs related to the application configuration, user accounts, and namespaces
+     * DAOs related to the application configuration and user accounts
      * should remain unchanged.
      */    
-    public void setSpecialDataModel(OntModel specialModel, OntModel specialTboxModel, OntModel specialDisplayModel) {
+    public void setSpecialDataModel(OntModel specialModel, 
+                                    OntModel specialTboxModel, 
+                                    OntModel specialDisplayModel) {
         if( specialModel == null )
             throw new IllegalStateException("specialModel must not be null");
         
@@ -629,22 +621,26 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     	OntModelSelector originalSelector = this.getOntModelSelector();
     	
     	// Set up model selector for this special WDF
-    	//The selector is used by the object property DAO, therefore should be set up even though we 
+    	// The selector is used by the object property DAO, therefore should be
-    	//use the new webapp dao factory object to generate portions to overwrite the regular webapp dao factory
+    	// set up even though we use the new webapp dao factory object to 
+    	// generate portions to overwrite the regular webapp dao factory.
     	
     	//The WDF expects the full model in the OntModelSelect that has 
     	//both the ABox and TBox.  This is used to run SPARQL queries against.    	
-    	OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+    	OntModel unionModel = ModelFactory.createOntologyModel(
+    			OntModelSpec.OWL_MEM);
         unionModel.addSubModel(specialModel);
         
     	OntModelSelectorImpl specialSelector = new OntModelSelectorImpl();
     	specialSelector.setFullModel(unionModel);
-    	//Keeping original application metadata model and adding special model
+    	// Keeping original application metadata model and adding special model.
-    	//adding both allows us to prevent errors in ApplicationDao which may depend on 
+    	// Adding both  allows us to prevent errors in  ApplicationDao which may 
-    	//a specific individual from the regular application metadata model to pick theme
+    	// depend on a specific individual from the regular application metadata 
-    	//Adding the new model would take care of special situations where the switch model may
+    	// model to  pick the theme.   Adding the new  model would  take care of 
-    	//contain important information
+    	// special  situations  where  the switch  model  may  contain important 
-    	OntModel newApplicationModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+    	// information.
+    	OntModel newApplicationModel = ModelFactory.createOntologyModel(
+    			OntModelSpec.OWL_MEM);
     	newApplicationModel.add(specialModel);
     	newApplicationModel.add(originalSelector.getApplicationMetadataModel());
     	specialSelector.setApplicationMetadataModel(newApplicationModel);    	
@@ -655,7 +651,8 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     	} else {
     		OntModel selectorDisplayModel = originalSelector.getDisplayModel();
     		if(selectorDisplayModel != null) {
-    			specialSelector.setDisplayModel(originalSelector.getDisplayModel());
+    			specialSelector.setDisplayModel(
+    					originalSelector.getDisplayModel());
     		}
     	}
     	if(specialTboxModel != null) {
@@ -670,16 +667,19 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     	
     	specialSelector.setABoxModel(specialModel);
     	specialSelector.setUserAccountsModel(specialModel);
-    	//although we're only use part of the new wadf and copy over below, the object property dao
+    	// Although we're only using part of the new wadf and copy over below, 
-    	//utilizes methods that will employ the display model returned from the simple ontmodel selector
+    	// the object property dao utilizes methods that will employ the display 
-    	//so if the object property dao is to be copied over we need to ensure we have the correct display model
+    	// model returned from the simple ontmodel selector, so if the object 
-    	//and tbox model
+    	// property dao is to be copied over we need to ensure we have the 
-    	WebappDaoFactoryJena specialWadfj = new WebappDaoFactoryJena(specialSelector);
+    	// correct display model and tbox model.
+    	WebappDaoFactoryJena specialWadfj = new WebappDaoFactoryJena(
+    			specialSelector);
     	entityWebappDao = specialWadfj.getIndividualDao();
     	vClassGroupDao = specialWadfj.getVClassGroupDao();
     	// To allow for testing, add a property group, this will allow
-    	//the unassigned group method section to be executed and main Image to be assigned to that group
+    	// the unassigned group method section to be executed and main Image to 
-    	//otherwise the dummy group does not allow for the unassigned group to be executed
+    	// be assigned to that group.  Otherwise, the dummy group does not allow 
+    	// for the unassigned group to be executed.
     	propertyGroupDao = specialWadfj.getPropertyGroupDao();
     	objectPropertyDao = specialWadfj.getObjectPropertyDao();
     	objectPropertyStatementDao = specialWadfj.getObjectPropertyStatementDao();

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

@@ -86,8 +86,6 @@ public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
         this.nonuserNamespaces = base.nonuserNamespaces;
         this.preferredLanguages = base.preferredLanguages;
         this.userURI = userURI;
-        this.flag2ValueMap = base.flag2ValueMap;
-        this.flag2ClassLabelMap = base.flag2ClassLabelMap;
         this.dwf = base.dwf;
     }
 	

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactoryStub.java

@@ -104,12 +104,6 @@ public class WebappDaoFactoryStub implements WebappDaoFactory {
 				"WebappDaoFactory.checkURI() not implemented.");
 	}
 
-	@Override
-	public int getLanguageProfile() {
-		throw new RuntimeException(
-				"WebappDaoFactory.getLanguageProfile() not implemented.");
-	}
-
 	@Override
 	public String getDefaultNamespace() {
 		throw new RuntimeException(