Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop

Conflicts:
	webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsForIndividualGenerator.java

webapp/src/edu/cornell/mannlib/vedit/validator/impl/UrlValidator.java

@@ -2,28 +2,37 @@
 
 package edu.cornell.mannlib.vedit.validator.impl;
 
-import edu.cornell.mannlib.vedit.validator.Validator;
+import java.util.Iterator;
+
+import com.hp.hpl.jena.iri.IRI;
+import com.hp.hpl.jena.iri.IRIFactory;
+import com.hp.hpl.jena.iri.Violation;
+
 import edu.cornell.mannlib.vedit.validator.ValidationObject;
-import java.util.regex.*;
+import edu.cornell.mannlib.vedit.validator.Validator;
 
 public class UrlValidator implements Validator {
 
     public ValidationObject validate (Object obj) throws IllegalArgumentException {
 
         ValidationObject vo = new ValidationObject();
-        String theString = null;
 
         if (!(obj instanceof String)){
             throw new IllegalArgumentException("Expected instance of String");
         }
 
-        Pattern pat = Pattern.compile("[a-z]{3,5}*://.*\\.[a-z]{2,4}");
+        IRIFactory factory = IRIFactory.jenaImplementation();
-        Matcher mat = pat.matcher(theString);
+        IRI iri = factory.create((String) obj);
-        if (mat.matches()){
+        if (iri.hasViolation(false) ) {
-            vo.setValid(true);
+            String errorStr = "";
-        } else {
+            Iterator<Violation> violIt = iri.violations(false);
+            while(violIt.hasNext()) {
+                errorStr += violIt.next().getShortMessage() + "  ";
+            }
             vo.setValid(false);
-            vo.setMessage("Please enter a valid URL");
+            vo.setMessage("Please enter a valid URL.  " + errorStr);
+        } else {
+            vo.setValid(true);
         }
 
         vo.setValidatedObject(obj);

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/DisplayByRolePermission.java

@@ -16,6 +16,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAct
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Is the user authorized to display properties that are marked as restricted to
@@ -82,7 +83,7 @@ public class DisplayByRolePermission extends Permission {
 	 */
 	private boolean isAuthorized(DisplayDataProperty action) {
 		String predicateUri = action.getDataProperty().getURI();
-		return canDisplayPredicate(predicateUri);
+		return canDisplayPredicate(new Property(predicateUri));
 	}
 
 	/**
@@ -90,8 +91,7 @@ public class DisplayByRolePermission extends Permission {
 	 * predicate.
 	 */
 	private boolean isAuthorized(DisplayObjectProperty action) {
-		String predicateUri = action.getObjectProperty().getURI();
+		return canDisplayPredicate(action.getObjectProperty());
-		return canDisplayPredicate(predicateUri);
 	}
 
 	/**
@@ -103,7 +103,7 @@ public class DisplayByRolePermission extends Permission {
 		String subjectUri = stmt.getIndividualURI();
 		String predicateUri = stmt.getDatapropURI();
 		return canDisplayResource(subjectUri)
-				&& canDisplayPredicate(predicateUri);
+				&& canDisplayPredicate(new Property(predicateUri));
 	}
 
 	/**
@@ -113,12 +113,10 @@ public class DisplayByRolePermission extends Permission {
 	private boolean isAuthorized(DisplayObjectPropertyStatement action) {
 		ObjectPropertyStatement stmt = action.getObjectPropertyStatement();
 		String subjectUri = stmt.getSubjectURI();
-		String predicateUri = stmt.getPropertyURI();
+		Property predicate = stmt.getProperty(); 
-		String rangeUri = (stmt.getProperty() == null) ? null 
-		        : stmt.getProperty().getRangeVClassURI();
 		String objectUri = stmt.getObjectURI();
 		return canDisplayResource(subjectUri)
-				&& canDisplayPredicate(predicateUri, rangeUri)
+				&& canDisplayPredicate(predicate)
 				&& canDisplayResource(objectUri);
 	}
 
@@ -127,13 +125,9 @@ public class DisplayByRolePermission extends Permission {
 				resourceUri, this.roleLevel);
 	}
 
-	private boolean canDisplayPredicate(String predicateUri) {
+	private boolean canDisplayPredicate(Property predicate) {
-	    return canDisplayPredicate(predicateUri, null);
-	}
-
-	private boolean canDisplayPredicate(String predicateUri, String rangeUri) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx)
-				.canDisplayPredicate(predicateUri, rangeUri, this.roleLevel);
+				.canDisplayPredicate(predicate, this.roleLevel);
 	}
 
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/EditByRolePermission.java

@@ -12,6 +12,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAct
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractDataPropertyStatementAction;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractObjectPropertyStatementAction;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Is the user authorized to edit properties that are marked as restricted to a
@@ -78,9 +79,9 @@ public class EditByRolePermission extends Permission {
 	 */
 	private boolean isAuthorized(AbstractDataPropertyStatementAction action) {
 		String subjectUri = action.getSubjectUri();
-		String predicateUri = action.getPredicateUri();
+		Property predicate = action.getPredicate();
 		return canModifyResource(subjectUri)
-				&& canModifyPredicate(predicateUri);
+				&& canModifyPredicate(predicate);
 	}
 
 	/**
@@ -89,10 +90,10 @@ public class EditByRolePermission extends Permission {
 	 */
 	private boolean isAuthorized(AbstractObjectPropertyStatementAction action) {
 		String subjectUri = action.getSubjectUri();
-		String predicateUri = action.getPredicateUri();
+		Property predicate = action.getPredicate();
 		String objectUri = action.getObjectUri();
 		return canModifyResource(subjectUri)
-				&& canModifyPredicate(predicateUri)
+				&& canModifyPredicate(predicate)
 				&& canModifyResource(objectUri);
 	}
 
@@ -101,9 +102,9 @@ public class EditByRolePermission extends Permission {
 				resourceUri, roleLevel);
 	}
 
-	private boolean canModifyPredicate(String predicateUri) {
+	private boolean canModifyPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx).canModifyPredicate(
-				predicateUri, roleLevel);
+				predicate, roleLevel);
 	}
 
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/BaseSelfEditingPolicy.java

@@ -8,6 +8,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.policy.bean.PropertyRestrictionPoli
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.Authorization;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.PolicyDecision;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A base class with utility methods for policies involving self-editing.
@@ -26,9 +27,9 @@ public abstract class BaseSelfEditingPolicy {
 				uri, roleLevel);
 	}
 
-	protected boolean canModifyPredicate(String uri) {
+	protected boolean canModifyPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx).canModifyPredicate(
-				uri, roleLevel);
+				predicate, roleLevel);
 	}
 
 	protected PolicyDecision cantModifyResource(String uri) {
@@ -36,9 +37,9 @@ public abstract class BaseSelfEditingPolicy {
 				+ uri);
 	}
 
-	protected PolicyDecision cantModifyPredicate(String uri) {
+	protected PolicyDecision cantModifyPredicate(Property predicate) {
 		return inconclusiveDecision("No access to admin predicates; cannot modify "
-				+ uri);
+				+ predicate.getURI());
 	}
 
 	protected PolicyDecision userNotAuthorizedToStatement() {

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/DisplayRestrictedDataToSelfPolicy.java

@@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAct
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Permit display of various data if it relates to the user's associated
@@ -92,14 +93,14 @@ public class DisplayRestrictedDataToSelfPolicy implements PolicyIface {
 			Collection<String> individuals) {
 		DataPropertyStatement stmt = action.getDataPropertyStatement();
 		String subjectUri = stmt.getIndividualURI();
-		String predicateUri = stmt.getDatapropURI();
+		Property predicate = new Property(stmt.getDatapropURI());
-		if (canDisplayResource(subjectUri) && canDisplayPredicate(predicateUri)
+		if (canDisplayResource(subjectUri) && canDisplayPredicate(predicate)
 				&& isAboutAssociatedIndividual(individuals, stmt)) {
 			return authorized("user may view DataPropertyStatement "
-					+ subjectUri + " ==> " + predicateUri);
+					+ subjectUri + " ==> " + predicate.getURI());
 		} else {
 			return defaultDecision("user may not view DataPropertyStatement "
-					+ subjectUri + " ==> " + predicateUri);
+					+ subjectUri + " ==> " + predicate.getURI());
 		}
 	}
 
@@ -115,7 +116,8 @@ public class DisplayRestrictedDataToSelfPolicy implements PolicyIface {
 		String subjectUri = stmt.getSubjectURI();
 		String predicateUri = stmt.getPropertyURI();
 		String objectUri = stmt.getObjectURI();
-		if (canDisplayResource(subjectUri) && canDisplayPredicate(predicateUri)
+		if (canDisplayResource(subjectUri) && canDisplayPredicate(new Property
+		                (predicateUri))
 				&& canDisplayResource(objectUri)
 				&& isAboutAssociatedIndividual(individuals, stmt)) {
 			return authorized("user may view ObjectPropertyStatement "
@@ -143,9 +145,9 @@ public class DisplayRestrictedDataToSelfPolicy implements PolicyIface {
 				uri, RoleLevel.SELF);
 	}
 
-	private boolean canDisplayPredicate(String uri) {
+	private boolean canDisplayPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx)
-				.canDisplayPredicate(uri, RoleLevel.SELF);
+				.canDisplayPredicate(predicate, RoleLevel.SELF);
 	}
 
 	private boolean isAboutAssociatedIndividual(Collection<String> selves,

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/PermissionsPolicy.java

@@ -35,6 +35,8 @@ public class PermissionsPolicy implements PolicyIface {
 				log.debug("Permission " + p + " approves request " + whatToAuth);
 				return new BasicPolicyDecision(Authorization.AUTHORIZED,
 						"PermissionsPolicy: approved by " + p);
+			} else {
+			    log.trace("Permission " + p + " denies request " + whatToAuth);
 			}
 		}
 		log.debug("No permission will approve " + whatToAuth);

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/PolicyHelper.java

@@ -122,7 +122,8 @@ public class PolicyHelper {
 		}
 
 		Resource subject = stmt.getSubject();
-		Property predicate = stmt.getPredicate();
+		edu.cornell.mannlib.vitro.webapp.beans.Property predicate = 
+		        new edu.cornell.mannlib.vitro.webapp.beans.Property(stmt.getPredicate().getURI());
 		RDFNode objectNode = stmt.getObject();
 		if ((subject == null) || (predicate == null) || (objectNode == null)) {
 			return false;
@@ -131,7 +132,7 @@ public class PolicyHelper {
 		RequestedAction action;
 		if (objectNode.isResource()) {
 			action = new AddObjectPropertyStatement(modelToBeModified,
-					subject.getURI(), predicate.getURI(), objectNode
+					subject.getURI(), predicate, objectNode
 							.asResource().getURI());
 		} else {
 			action = new AddDataPropertyStatement(modelToBeModified,
@@ -153,7 +154,9 @@ public class PolicyHelper {
 		}
 
 		Resource subject = stmt.getSubject();
-		Property predicate = stmt.getPredicate();
+		edu.cornell.mannlib.vitro.webapp.beans.Property predicate = 
+		        new edu.cornell.mannlib.vitro.webapp.beans.Property();
+		predicate.setURI(stmt.getPredicate().getURI());
 		RDFNode objectNode = stmt.getObject();
 		if ((subject == null) || (predicate == null) || (objectNode == null)) {
 			return false;
@@ -162,7 +165,7 @@ public class PolicyHelper {
 		RequestedAction action;
 		if (objectNode.isResource()) {
 			action = new DropObjectPropertyStatement(modelToBeModified,
-					subject.getURI(), predicate.getURI(), objectNode
+					subject.getURI(), predicate, objectNode
 							.asResource().getURI());
 		} else {
 			action = new DropDataPropertyStatement(modelToBeModified,

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/SelfEditingPolicy.java

@@ -16,6 +16,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractDa
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AbstractObjectPropertyStatementAction;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.resource.AbstractResourceAction;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Policy to use for Vivo Self-Editing based on NetId for use at Cornell. All
@@ -69,7 +70,7 @@ public class SelfEditingPolicy extends BaseSelfEditingPolicy implements
 	private PolicyDecision isAuthorizedForObjectPropertyAction(
 			List<String> userUris, AbstractObjectPropertyStatementAction action) {
 		String subject = action.getSubjectUri();
-		String predicate = action.getPredicateUri();
+		Property predicate = action.getPredicate();
 		String object = action.getObjectUri();
 
 		if (!canModifyResource(subject)) {
@@ -96,7 +97,7 @@ public class SelfEditingPolicy extends BaseSelfEditingPolicy implements
 	private PolicyDecision isAuthorizedForDataPropertyAction(
 			List<String> userUris, AbstractDataPropertyStatementAction action) {
 		String subject = action.getSubjectUri();
-		String predicate = action.getPredicateUri();
+		Property predicate = action.getPredicate();
 
 		if (!canModifyResource(subject)) {
 			return cantModifyResource(subject);

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelper.java

@@ -7,6 +7,7 @@ import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 
 import javax.servlet.ServletContext;
@@ -17,6 +18,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -24,18 +26,23 @@ 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.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.rdf.model.impl.Util;
+import com.hp.hpl.jena.sdb.util.Pair;
 import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
+import edu.cornell.mannlib.vitro.webapp.utils.ApplicationConfigurationOntologyUtils;
 
 /**
  * Assists the role-based policies in determining whether a property or resource
@@ -108,17 +115,22 @@ public class PropertyRestrictionPolicyHelper {
 	                                                         Model displayModel) {
 	    
 	    
-		Map<String, RoleLevel> displayThresholdMap = new HashMap<String, RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> displayThresholdMap = 
-		Map<String, RoleLevel> modifyThresholdMap = new HashMap<String, RoleLevel>();
+		        new HashMap<Pair<String, Pair<String,String>>, RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> modifyThresholdMap = 
+		        new HashMap<Pair<String, Pair<String,String>>, RoleLevel>();
 		
-		if (model != null) {
+		OntModel union = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
-			populateThresholdMap(model, displayThresholdMap,
+		        ModelFactory.createUnion(displayModel, model));
+
+
+		populateThresholdMap(union, displayThresholdMap,
 				VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT);
 		populateThresholdMap(
-					model,
+				union,
 				modifyThresholdMap,
 				VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT);
-		}
+
 
 		PropertyRestrictionPolicyHelper bean = new PropertyRestrictionPolicyHelper(
 				PROHIBITED_NAMESPACES, PERMITTED_EXCEPTIONS,
@@ -127,17 +139,50 @@ public class PropertyRestrictionPolicyHelper {
 		return bean;
 	}
 
+	private RoleLevel getModifyThreshold(Property property) {
+	    return getThreshold(property, modifyThresholdMap);
+	}
+	
+	private RoleLevel getThreshold(Property property, 
+	                               Map<Pair<String, Pair<String,String>>, RoleLevel> 
+	                                       thresholdMap) {
+	    if (property.getURI() == null) {
+	        return RoleLevel.NOBODY;
+	    }
+	    RoleLevel roleLevel = getRoleLevelFromMap(
+	            property.getDomainVClassURI(), property.getURI(), 
+	                    property.getRangeVClassURI(), thresholdMap);
+	    if (roleLevel == null) {
+	        roleLevel = getRoleLevelFromMap(
+	                OWL.Thing.getURI(), property.getURI(), OWL.Thing.getURI(),
+	                        thresholdMap);
+	    }
+	    return roleLevel;
+	}
+	
+	private RoleLevel getRoleLevelFromMap(String domainURI, 
+	                                      String predicateURI, 
+	                                      String rangeURI,
+	                                      Map<Pair<String, Pair<String,String>>, 
+	                                              RoleLevel> map) {
+	    return map.get(
+                new Pair<String, Pair<String,String>>(
+                        domainURI, new Pair<String,String>(
+                                predicateURI, rangeURI)));
+	}
+	
 	/**
 	 * Find all the resources that possess this property, and map the resource
 	 * URI to the required RoleLevel.
 	 */
 	private static void populateThresholdMap(OntModel model,
-			Map<String, RoleLevel> map, String propertyUri) {
+			Map<Pair<String,Pair<String,String>>, RoleLevel> map, String propertyUri) {
 		model.enterCriticalSection(Lock.READ);
 		try {
-			Property property = model.getProperty(propertyUri);
+		    com.hp.hpl.jena.rdf.model.Property property = model.getProperty(propertyUri);
 			StmtIterator stmts = model.listStatements((Resource) null,
 					property, (Resource) null);
+			try {
     			while (stmts.hasNext()) {
     				Statement stmt = stmts.next();
     				Resource subject = stmt.getSubject();
@@ -147,9 +192,32 @@ public class PropertyRestrictionPolicyHelper {
     				}
     				Resource object = (Resource) objectNode;
     				RoleLevel role = RoleLevel.getRoleByUri(object.getURI());
-				map.put(subject.getURI(), role);
+    				map.put(new Pair<String,Pair<String,String>>(
+    				        OWL.Thing.getURI(), new Pair<String,String>(
+    				                subject.getURI(), OWL.Thing.getURI())), role);
     			} 
+			} finally {
 	            stmts.close();			    
+			}
+            List<ObjectProperty> fauxOps = ApplicationConfigurationOntologyUtils
+                    .getAdditionalFauxSubproperties(null, null, model, model);
+            for (ObjectProperty faux : fauxOps) {
+                RoleLevel role = null;
+                if(VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT
+                        .equals(propertyUri)) {
+                    role = faux.getProhibitedFromUpdateBelowRoleLevel();
+                } else if (VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT
+                        .equals(propertyUri)) {
+                    role = faux.getHiddenFromDisplayBelowRoleLevel();
+                }
+                if (role != null) {
+                    log.debug("Putting D:" + faux.getDomainVClassURI() + " P:" + faux.getURI() + " R:" + faux.getRangeVClassURI() + " ==> L:" + role);
+                    map.put(new Pair<String,Pair<String,String>>(
+                            faux.getDomainVClassURI(), new Pair<String,String>(
+                                    faux.getURI(), faux.getRangeVClassURI())), role);
+                }
+            }
+
 		} finally {
 			model.leaveCriticalSection();
 		}
@@ -175,15 +243,14 @@ public class PropertyRestrictionPolicyHelper {
 	 * These URIs can be displayed only if the user's role is at least as high
 	 * as the threshold role.
 	 */
-	private final Map<String, RoleLevel> displayThresholdMap;
+	private final Map<Pair<String, Pair<String,String>>, RoleLevel> displayThresholdMap;
 
 	/**
 	 * These URIs can be modified only if the user's role is at least as high as
 	 * the threshold role.
 	 */
-	private final Map<String, RoleLevel> modifyThresholdMap;
+	private final Map<Pair<String, Pair<String,String>>, RoleLevel> modifyThresholdMap;
 	
-	private final Model displayModel;
 
 	/**
 	 * Store unmodifiable versions of the inputs.
@@ -194,14 +261,15 @@ public class PropertyRestrictionPolicyHelper {
 	protected PropertyRestrictionPolicyHelper(
 			Collection<String> modifyProhibitedNamespaces,
 			Collection<String> modifyExceptionsAllowedUris,
-			Map<String, RoleLevel> displayThresholdMap,
+			Map<Pair<String, Pair<String,String>>, RoleLevel> displayThresholdMap,
-			Map<String, RoleLevel> modifyThresholdMap,
+			Map<Pair<String, Pair<String,String>>, RoleLevel> modifyThresholdMap,
 			Model displayModel) {
 		this.modifyProhibitedNamespaces = unmodifiable(modifyProhibitedNamespaces);
 		this.modifyExceptionsAllowedUris = unmodifiable(modifyExceptionsAllowedUris);
-		this.displayThresholdMap = unmodifiable(displayThresholdMap);
+		this.displayThresholdMap = displayThresholdMap;
-		this.modifyThresholdMap = unmodifiable(modifyThresholdMap);
+		this.modifyThresholdMap = modifyThresholdMap;
-		this.displayModel = displayModel;
+//	    this.displayThresholdMap = unmodifiable(displayThresholdMap);
+//	    this.modifyThresholdMap = unmodifiable(modifyThresholdMap);
 
 		if (log.isDebugEnabled()) {
 			log.debug("prohibited: " + this.modifyProhibitedNamespaces);
@@ -219,6 +287,7 @@ public class PropertyRestrictionPolicyHelper {
 		}
 	}
 
+	@SuppressWarnings("unused")
 	private Map<String, RoleLevel> unmodifiable(Map<String, RoleLevel> raw) {
 		if (raw == null) {
 			return Collections.emptyMap();
@@ -272,82 +341,33 @@ public class PropertyRestrictionPolicyHelper {
 		return true;
 	}
 
-	public boolean canDisplayPredicate(String predicateUri, RoleLevel userRole) {
-	    return canDisplayPredicate(predicateUri, null, userRole);
-	}
-
 	/**
 	 * If display of a predicate is restricted, the user's role must be at least
 	 * as high as the restriction level.
 	 */
-	public boolean canDisplayPredicate(String predicateUri, String rangeUri, RoleLevel userRole) {
+	public boolean canDisplayPredicate(Property predicate, RoleLevel userRole) {	    
-		if (predicateUri == null) {
+		if (predicate == null) {
-			log.debug("can't display predicate: predicateUri was null");
+			log.debug("can't display predicate: predicate was null");
 			return false;
 		}
 		
-		RoleLevel displayThreshold = RoleLevel.NOBODY;
+		RoleLevel displayThreshold = getThreshold(predicate, displayThresholdMap);		
-		if (rangeUri == null) {
-		    displayThreshold = displayThresholdMap.get(predicateUri); 
-		} else {
-		    log.debug("Getting display threshold for " + predicateUri + " " + rangeUri);
-		    displayThreshold = getDisplayThreshold(predicateUri, rangeUri);
-		    if (displayThreshold == null) {
-		        displayThreshold = displayThresholdMap.get(predicateUri);
-		    }
-		    log.debug(displayThreshold);
-		}
 		       	        
 		if (isAuthorized(userRole, displayThreshold)) {
-			log.debug("can display predicate: '" + predicateUri
+            log.debug("can display predicate: '" + predicate.getURI() + "', domain=" 
-					+ "', userRole=" + userRole + ", thresholdRole="
+                    + predicate.getDomainVClassURI() + ", range=" 
-					+ displayThreshold);
+                    + predicate.getRangeVClassURI() + ", userRole="
+                    + userRole + ", thresholdRole=" + displayThreshold);
 			return true;
 		}
 
-		log.debug("can't display predicate: '" + predicateUri + "', userRole="
+        log.debug("can't display predicate: '" + predicate.getURI() + "', domain=" 
+                + predicate.getDomainVClassURI() + ", range=" 
+                + predicate.getRangeVClassURI() + ", userRole="
                 + userRole + ", thresholdRole=" + displayThreshold);
 		return false;
 	}
 	
-	/**
-	 * Gets the role level threshold for displaying a predicate with a particular
-	 * object class
-	 * @param predicateUri
-	 * @param rangeUri
-	 * @return RoleLevel threshold
-	 */
-	private RoleLevel getDisplayThreshold(String predicateUri, String rangeUri) {
-	    String query = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
-                "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
-	            "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
-                "SELECT ?level WHERE { \n" +
-//                "    ?p rdfs:subPropertyOf ?property . \n" +
-                "    ?context config:configContextFor ?p . \n" +
-                "    ?context config:qualifiedBy ?range . \n" +
-                "    ?context config:hasConfiguration ?configuration . \n" +
-                "    ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?level \n" +
-                "}";
-	    Query q = QueryFactory.create(query);
-	    QueryExecution qe = QueryExecutionFactory.create(q, displayModel);
-	    try {
-	        ResultSet rs = qe.execSelect();
-	        if (!rs.hasNext()) {
-	            return null;
-	        } 
-	        while(rs.hasNext()) {
-	          QuerySolution qsoln = rs.nextSolution();
-	          Resource levelRes = qsoln.getResource("level");
-	          if (levelRes != null) {
-	              return RoleLevel.getRoleByUri(levelRes.getURI());
-	          }
-	        }
-	    } finally {
-	        qe.close();
-	    }
-	    return null;
-	}
-	
 	/**
 	 * A predicate cannot be modified if its namespace is in the prohibited list
 	 * (some exceptions are allowed).
@@ -355,31 +375,35 @@ public class PropertyRestrictionPolicyHelper {
 	 * If modification of a predicate is restricted, the user's role must be at
 	 * least as high as the restriction level.
 	 */
-	public boolean canModifyPredicate(String predicateUri, RoleLevel userRole) {
+	public boolean canModifyPredicate(Property predicate, RoleLevel userRole) {
-		if (predicateUri == null) {
+		if (predicate == null || predicate.getURI() == null) {
-			log.debug("can't modify predicate: predicateUri was null");
+			log.debug("can't modify predicate: predicate was null");
 			return false;
 		}
 
-		if (modifyProhibitedNamespaces.contains(namespace(predicateUri))) {
+		if (modifyProhibitedNamespaces.contains(namespace(predicate.getURI()))) {
-			if (modifyExceptionsAllowedUris.contains(predicateUri)) {
+			if (modifyExceptionsAllowedUris.contains(predicate.getURI())) {
-				log.debug("'" + predicateUri + "' is a permitted exception");
+				log.debug("'" + predicate.getURI() + "' is a permitted exception");
 			} else {
-				log.debug("can't modify resource '" + predicateUri
+				log.debug("can't modify resource '" + predicate.getURI()
 						+ "': prohibited namespace: '"
-						+ namespace(predicateUri) + "'");
+						+ namespace(predicate.getURI()) + "'");
 				return false;
 			}
 		}
 
-		RoleLevel modifyThreshold = modifyThresholdMap.get(predicateUri);
+		RoleLevel modifyThreshold = getModifyThreshold(predicate);
 		if (isAuthorized(userRole, modifyThreshold)) {
-			log.debug("can modify predicate: '" + predicateUri + "', userRole="
+			log.debug("can modify predicate: '" + predicate.getURI() + "', domain=" 
+		            + predicate.getDomainVClassURI() + ", range=" 
+			        + predicate.getRangeVClassURI() + ", userRole="
 					+ userRole + ", thresholdRole=" + modifyThreshold);
 			return true;
 		}
 
-		log.debug("can't modify predicate: '" + predicateUri + "', userRole="
+        log.debug("can't modify predicate: '" + predicate.getURI() + "', domain=" 
+                + predicate.getDomainVClassURI() + ", range=" 
+                + predicate.getRangeVClassURI() + ", userRole="
                 + userRole + ", thresholdRole=" + modifyThreshold);
 		return false;
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/specialrelationships/AbstractRelationshipPolicy.java

@@ -13,6 +13,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.Authorization;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.PolicyDecision;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ifaces.PolicyIface;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A collection of building-block methods so we can code a policy based on the
@@ -34,9 +35,9 @@ public abstract class AbstractRelationshipPolicy implements PolicyIface {
 				uri, RoleLevel.SELF);
 	}
 
-	protected boolean canModifyPredicate(String uri) {
+	protected boolean canModifyPredicate(Property predicate) {
 		return PropertyRestrictionPolicyHelper.getBean(ctx).canModifyPredicate(
-				uri, RoleLevel.SELF);
+				predicate, RoleLevel.SELF);
 	}
 
 	protected PolicyDecision cantModifyResource(String uri) {

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/ifaces/RequestActionConstants.java

@@ -2,9 +2,12 @@
 
 package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces;
 
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
+
 public class RequestActionConstants {
     public static String actionNamespace = "java:";
     
     public static String SOME_URI = "?SOME_URI";
+    public static Property SOME_PREDICATE = new Property(SOME_URI);
     public static String SOME_LITERAL = "?SOME_LITERAL";
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/AbstractDataPropertyStatementAction.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A base class for requested actions that involve adding, editing, or dropping
@@ -14,12 +15,16 @@ public abstract class AbstractDataPropertyStatementAction extends
 		AbstractPropertyStatementAction {
 	private final String subjectUri;
 	private final String predicateUri;
+	private final Property predicate;
 
 	public AbstractDataPropertyStatementAction(OntModel ontModel,
 			String subjectUri, String predicateUri) {
 		super(ontModel);
 		this.subjectUri = subjectUri;
 		this.predicateUri = predicateUri;
+		Property dataProperty = new Property();
+		dataProperty.setURI(predicateUri);
+		this.predicate = dataProperty;
 	}
 
 	public AbstractDataPropertyStatementAction(OntModel ontModel,
@@ -28,12 +33,19 @@ public abstract class AbstractDataPropertyStatementAction extends
 		this.subjectUri = (dps.getIndividual() == null) ? dps
 				.getIndividualURI() : dps.getIndividual().getURI();
 		this.predicateUri = dps.getDatapropURI();
+	    Property dataProperty = new Property();
+	    dataProperty.setURI(predicateUri);
+	    this.predicate = dataProperty;
 	}
 
 	public String getSubjectUri() {
 		return subjectUri;
 	}
 
+	public Property getPredicate() {
+	    return predicate;
+	}
+	
 	@Override
 	public String getPredicateUri() {
 		return predicateUri;

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/AbstractObjectPropertyStatementAction.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A base class for requested actions that involve adding, editing, or deleting
@@ -13,14 +14,14 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 public abstract class AbstractObjectPropertyStatementAction extends
 		AbstractPropertyStatementAction {
 	private final String subjectUri;
-	private final String predicateUri;
+	private final Property predicate;
 	private final String objectUri;
 
 	public AbstractObjectPropertyStatementAction(OntModel ontModel, String subjectUri,
-			String predicateUri, String objectUri) {
+			Property predicate, String objectUri) {
 		super(ontModel);
 		this.subjectUri = subjectUri;
-		this.predicateUri = predicateUri;
+		this.predicate = predicate;
 		this.objectUri = objectUri;
 	}
 
@@ -28,8 +29,7 @@ public abstract class AbstractObjectPropertyStatementAction extends
 		super(ontModel);
 		this.subjectUri = (ops.getSubject() == null) ? ops.getSubjectURI()
 				: ops.getSubject().getURI();
-		this.predicateUri = (ops.getProperty() == null) ? ops.getPropertyURI()
+		this.predicate = (ops.getProperty());
-				: ops.getProperty().getURI();
 		this.objectUri = (ops.getObject() == null) ? ops.getObjectURI() : ops
 				.getObject().getURI();
 	}
@@ -42,9 +42,13 @@ public abstract class AbstractObjectPropertyStatementAction extends
 		return objectUri;
 	}
 	
+	public Property getPredicate() {
+	    return predicate;
+	}
+	
 	@Override
 	public String getPredicateUri() {
-		return predicateUri;
+		return predicate.getURI();
 	}
 
 	@Override
@@ -55,6 +59,6 @@ public abstract class AbstractObjectPropertyStatementAction extends
 	@Override
 	public String toString() {
 		return this.getClass().getSimpleName() + ": <" + subjectUri + "> <"
-				+ predicateUri + "> <" + objectUri + ">";
+				+ predicate.getURI() + "> <" + objectUri + ">";
 	}
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/AbstractPropertyStatementAction.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAction;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * A base class for requested actions that involve adding, editing, or deleting
@@ -27,5 +28,7 @@ public abstract class AbstractPropertyStatementAction extends RequestedAction {
 	 */
 	public abstract String[] getResourceUris();
 
+	public abstract Property getPredicate();
+	
 	public abstract String getPredicateUri();
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/AddObjectPropertyStatement.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Should we allow the user to add this ObjectPropertyStatement to this model?
@@ -12,8 +13,8 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 public class AddObjectPropertyStatement extends
 		AbstractObjectPropertyStatementAction {
 	public AddObjectPropertyStatement(OntModel ontModel, String uriOfSub,
-			String uriOfPred, String uriOfObj) {
+			Property predicate, String uriOfObj) {
-		super(ontModel, uriOfSub, uriOfPred, uriOfObj);
+		super(ontModel, uriOfSub, predicate, uriOfObj);
 	}
 
 	public AddObjectPropertyStatement(OntModel ontModel,

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/DropObjectPropertyStatement.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Should we allow the user to delete this ObjectPropertyStatement from this
@@ -13,7 +14,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 public class DropObjectPropertyStatement extends
 		AbstractObjectPropertyStatementAction {
 	public DropObjectPropertyStatement(OntModel ontModel, String sub,
-			String pred, String obj) {
+			Property pred, String obj) {
 		super(ontModel, sub, pred, obj);
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/requestedAction/propstmt/EditObjectPropertyStatement.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 
 /**
  * Should we allow the user to edit this ObjectPropertyStatement in this model?
@@ -12,8 +13,8 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 public class EditObjectPropertyStatement extends
 		AbstractObjectPropertyStatementAction {
 	public EditObjectPropertyStatement(OntModel ontModel, String subjectUri,
-			String keywordPredUri, String objectUri) {
+			Property keywordPred, String objectUri) {
-		super(ontModel, subjectUri, keywordPredUri, objectUri);
+		super(ontModel, subjectUri, keywordPred, objectUri);
 	}
 
 	public EditObjectPropertyStatement(OntModel ontModel,

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/ObjectProperty.java

@@ -78,10 +78,12 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
         e.writeObject(this);
     }
 
-
+    @Override
     public String getDomainVClassURI() {
         return domainVClassURI;
     }
+    
+    @Override
     public void setDomainVClassURI(String domainClassURI) {
         this.domainVClassURI = domainClassURI;
     }
@@ -111,9 +113,13 @@ public class ObjectProperty extends Property implements Comparable<ObjectPropert
     public void setParentURI(String parentURI) {
         this.parentURI = parentURI;
     }
+    
+    @Override
     public String getRangeVClassURI() {
         return rangeVClassURI;
     }
+    
+    @Override
     public void setRangeVClassURI(String rangeClassURI) {
         this.rangeVClassURI = rangeClassURI;
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/Property.java

@@ -15,12 +15,21 @@ public class Property extends BaseResourceBean {
     private String  groupURI              = null;
     private String  label                 = null; // keep so can set in a context-specific way
     private final boolean subjectSide     = true; // only relevant to ObjectProperty
+    private String domainVClassURI        = null;
+    private String rangeVClassURI         = null;
+    private boolean editLinkSuppressed    = false;
+    private boolean addLinkSuppressed     = false;
+    private boolean deleteLinkSuppressed  = false;
     
     public Property() {
         this.groupURI = null;
         this.label = null;
     }
     
+    public Property(String URI) {
+        this.setURI(URI);
+    }
+
     public String getCustomEntryForm() {
         return customEntryForm;
     }
@@ -43,10 +52,53 @@ public class Property extends BaseResourceBean {
         this.label = label;
     }
     
+    public String getDomainVClassURI() {
+        return this.domainVClassURI;
+    }
+    
+    public void setDomainVClassURI(String domainVClassURI) {
+        this.domainVClassURI = domainVClassURI;
+    }
+    
+    public String getRangeVClassURI() {
+        return this.rangeVClassURI;
+    }
+    
+    public void setRangeVClassURI(String rangeVClassURI) {
+        this.rangeVClassURI = rangeVClassURI;
+    }
+    
     public boolean isSubjectSide() {
         return subjectSide;
     }
     
+    public boolean isEditLinkSuppressed() {
+        return editLinkSuppressed;
+    }
+    
+    public boolean isAddLinkSuppressed() {
+        return addLinkSuppressed;
+    }
+    
+    public boolean isDeleteLinkSuppressed() {
+        return deleteLinkSuppressed;
+    }
+    
+    public void setEditLinkSuppressed(boolean editLinkSuppressed) {
+        this.editLinkSuppressed = editLinkSuppressed;
+    }
+    
+    public void setAddLinkSuppressed(boolean addLinkSuppressed) {
+        if (this.addLinkSuppressed) {
+            throw new RuntimeException("addLinkSuppressed already true");
+        }
+        this.addLinkSuppressed = addLinkSuppressed;
+    }
+    
+    public void setDeleteLinkSuppressed(boolean deleteLinkSuppressed) {
+        this.deleteLinkSuppressed = deleteLinkSuppressed;
+    }
+    
     /**
      * Sorts Property objects, by property rank, then alphanumeric.
      * @author bdc34

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/VClass.java

@@ -3,6 +3,8 @@
 package edu.cornell.mannlib.vitro.webapp.beans;
 
 import java.text.Collator;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.openrdf.model.impl.URIImpl;
 
@@ -91,6 +93,9 @@ public class VClass extends BaseResourceBean implements Comparable<VClass>
     public Float getSearchBoost() { return searchBoost; }
     public void setSearchBoost( Float boost ){ searchBoost = boost;}
     
+    public boolean isUnion() { return false; }
+    public List<VClass> getUnionComponents() { return new ArrayList<VClass>(); }
+    
     /**
      * Default constructor
      */

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

@@ -9,9 +9,11 @@ import java.io.PrintWriter;
 import java.io.Writer;
 import java.net.URLDecoder;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 import javax.servlet.RequestDispatcher;
 import javax.servlet.ServletException;
@@ -40,6 +42,7 @@ import com.hp.hpl.jena.vocabulary.XSD;
 import edu.cornell.mannlib.vedit.controller.BaseEditController;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
+import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualController;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
@@ -47,44 +50,36 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ResultFormat;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.web.ContentType;
 
 
 /**
- * Services a sparql query.  This will return a simple error message and a 501 if
+ * Services a SPARQL query.  This will return a simple error message and a 501 if
  * there is no Model.
  *
+ *
  * @author bdc34
  *
  */
 public class SparqlQueryServlet extends BaseEditController {
     private static final Log log = LogFactory.getLog(SparqlQueryServlet.class.getName());
     
-    private final static boolean CONVERT = true;
-    
     /**
      * format configurations for SELECT queries.
      */
     protected static HashMap<String,RSFormatConfig> rsFormats = new HashMap<String,RSFormatConfig>();
    
-    private static RSFormatConfig[] rsfs = {
-        new RSFormatConfig( "RS_XML", !CONVERT, ResultFormat.XML, null, "text/xml"),
-        new RSFormatConfig( "RS_TEXT", !CONVERT, ResultFormat.TEXT, null, "text/plain"),
-        new RSFormatConfig( "vitro:csv", !CONVERT, ResultFormat.CSV, null, "text/csv"),
-        new RSFormatConfig( "RS_JSON", !CONVERT, ResultFormat.JSON, null, "application/javascript") };        
-    
     /**
      * format configurations for CONSTRUCT/DESCRIBE queries.
      */
     protected static HashMap<String,ModelFormatConfig> modelFormats = 
         new HashMap<String,ModelFormatConfig>();
 
-    private static ModelFormatConfig[] fmts = {
+    /**
-        new ModelFormatConfig("RDF/XML", !CONVERT, ModelSerializationFormat.RDFXML, null, "application/rdf+xml" ),
+     * Use this map to decide which MIME type is suited for the "accept" header.
-        new ModelFormatConfig("RDF/XML-ABBREV", CONVERT, ModelSerializationFormat.N3, "RDF/XML-ABBREV", "application/rdf+xml" ),
+     */
-        new ModelFormatConfig("N3", !CONVERT, ModelSerializationFormat.N3, null, "text/n3" ),
+    public static final Map<String, Float> ACCEPTED_CONTENT_TYPES;
-        new ModelFormatConfig("N-TRIPLE", !CONVERT, ModelSerializationFormat.NTRIPLE, null, "text/plain" ),
+
-        new ModelFormatConfig("TTL", CONVERT, ModelSerializationFormat.N3, "TTL", "application/x-turtle" ),
-        new ModelFormatConfig("JSON-LD", CONVERT, ModelSerializationFormat.N3, "JSON-LD", "application/javascript" ) };
    
     @Override
     protected void doPost(HttpServletRequest request, HttpServletResponse response)
@@ -113,100 +108,85 @@ public class SparqlQueryServlet extends BaseEditController {
         String queryParam = vreq.getParameter("query");
         log.debug("queryParam was : " + queryParam);
 
-        String resultFormatParam = vreq.getParameter("resultFormat");
+        if( queryParam == null || "".equals(queryParam) ){
-        log.debug("resultFormat was: " + resultFormatParam);
-        
-        String rdfResultFormatParam = vreq.getParameter("rdfResultFormat");
-        if (rdfResultFormatParam == null) {
-        	rdfResultFormatParam = "RDF/XML-ABBREV";
-        }
-        log.debug("rdfResultFormat was: " + rdfResultFormatParam);
-
-        if( queryParam == null || "".equals(queryParam) ||
-            resultFormatParam == null || "".equals(resultFormatParam) ||
-            !rsFormats.containsKey( resultFormatParam ) || 
-            rdfResultFormatParam == null || "".equals(rdfResultFormatParam) ||
-            !modelFormats.containsKey( rdfResultFormatParam ) ) {
             doHelp(request,response);
             return;
         }
         
-        executeQuery(response, resultFormatParam, rdfResultFormatParam, 
+        String contentType = checkForContentType(vreq.getHeader("Accept"));        
-                queryParam, vreq.getUnfilteredRDFService()); 
+        
+        Query query = SparqlQueryUtils.create(queryParam);
+        if( query.isSelectType() ){            
+            String format =  contentType!=null ? contentType:vreq.getParameter("resultFormat");            
+            RSFormatConfig formatConf = rsFormats.get(format);                    
+            doSelect(response, queryParam, formatConf, vreq.getRDFService());            
+        }else if( query.isAskType()){
+            doAsk( queryParam, vreq.getRDFService(), response ); 
+        }else if( query.isConstructType() ){
+            String format = contentType != null ? contentType : vreq.getParameter("rdfResultFormat");                        
+            if (format== null) {
+                format= "RDF/XML-ABBREV";
+            }            
+            ModelFormatConfig formatConf = modelFormats.get(format);
+            doConstruct(response, query, formatConf, vreq.getRDFService());
+        }else{
+            doHelp(request,response);            
+        }
         return;
     }
     
-    private void executeQuery(HttpServletResponse response, 
-                              String resultFormatParam, 
-                              String rdfResultFormatParam, 
-                              String queryParam, 
-                              RDFService rdfService ) throws IOException {        
-    	/* BJL23 2008-11-06
-    	 * modified to support CSV output.
-    	 * Unfortunately, ARQ doesn't make it easy to
-    	 * do this by implementing a new ResultSetFormat, because 
-    	 * ResultSetFormatter is hardwired with expected values.
-    	 * This slightly ugly approach will have to do for now.
-    	 */            	
-//        if ( !("vitro:csv").equals(resultFormatParam) ) {
-//        	rsf = selectFormatSymbols.get(resultFormatParam);
-//        }                       
-//        String mimeType = rdfFormatToMimeType.get(resultFormatParam);
 
-        try{
+    private void doAsk(String queryParam, RDFService rdfService,
-            Query query = SparqlQueryUtils.create(queryParam);
+            HttpServletResponse response) throws ServletException, IOException {
-            if( query.isSelectType() ){
+        
-                doSelectQuery( queryParam, rdfService, resultFormatParam, response);
-            } else if(query.isAskType()){
         // Irrespective of the ResultFormatParam, 
         // this always prints a boolean to the default OutputStream.
-                String result = (rdfService.sparqlAskQuery(queryParam) == true) 
+        String result;
+        try {
+            result = (rdfService.sparqlAskQuery(queryParam) == true) 
                 ? "true" 
                 : "false";
+        } catch (RDFServiceException e) {
+            throw new ServletException( "Could not execute ask query ", e );
+        }
         PrintWriter p = response.getWriter();
         p.write(result);
         return;
-            } else {                
-                doModelResultQuery( query, rdfService, rdfResultFormatParam, response);
-            }
-        } catch (RDFServiceException e) {
-                throw new RuntimeException(e);
-        }
     }
     
     /**
      * Execute the query and send the result to out. Attempt to
      * send the RDFService the same format as the rdfResultFormatParam
      * so that the results from the RDFService can be directly piped to the client.
-     * @param rdfService 
-     * @throws IOException 
-     * @throws RDFServiceException 
      */
-    private void doSelectQuery( String queryParam,
+    private void doSelect(HttpServletResponse response,
-                                RDFService rdfService, String resultFormatParam,
+                                String queryParam,
-                                HttpServletResponse response) throws IOException, RDFServiceException{                
+                                RSFormatConfig formatConf, 
-        RSFormatConfig config = rsFormats.get( resultFormatParam );
+                                RDFService rdfService 
-                
+                                ) throws ServletException {
-        if( ! config.converstionFromWireFormat ){
+        try {
-            response.setContentType( config.responseMimeType );
+            if( ! formatConf.converstionFromWireFormat ){
-            InputStream results = rdfService.sparqlSelectQuery(queryParam, config.wireFormat );                        
+                response.setContentType( formatConf.responseMimeType );
+                InputStream results;                
+                results = rdfService.sparqlSelectQuery(queryParam, formatConf.wireFormat );
                 pipe( results, response.getOutputStream() );
             }else{                        
                 //always use JSON when conversion is needed.
                 InputStream results = rdfService.sparqlSelectQuery(queryParam, ResultFormat.JSON );
                 
-            response.setContentType( config.responseMimeType );
+                response.setContentType( formatConf.responseMimeType );
                             
                 ResultSet rs = ResultSetFactory.fromJSON( results );            
                 OutputStream out = response.getOutputStream();
-            ResultSetFormatter.output(out, rs, config.jenaResponseFormat);
+                ResultSetFormatter.output(out, rs, formatConf.jenaResponseFormat);                
+            }
+        } catch (RDFServiceException e) {
+            throw new ServletException("Cannot get result from the RDFService",e);
+        } catch (IOException e) {
+            throw new ServletException("Cannot perform SPARQL SELECT",e);
+        }
+    }
     
-            // } else {
-            //     Writer out = response.getWriter();
-            //     toCsv(out, results);
-            //}
-        }
-    }
 
     /**
      * Execute the query and send the result to out. Attempt to
@@ -217,25 +197,24 @@ public class SparqlQueryServlet extends BaseEditController {
      * @throws RDFServiceException 
      * @throws  
      */
-    private void doModelResultQuery( Query query, 
+    private void doConstruct( HttpServletResponse response, 
-                                      RDFService rdfService, String rdfResultFormatParam, 
+                               Query query, 
-                                      HttpServletResponse response) throws IOException, RDFServiceException{
+                               ModelFormatConfig formatConfig,
-
+                               RDFService rdfService 
-        //config drives what formats and conversions to use 
+                               ) throws ServletException{
-        ModelFormatConfig config = modelFormats.get( rdfResultFormatParam );
+        try{
-
             InputStream rawResult = null;        
             if( query.isConstructType() ){                    
-            rawResult= rdfService.sparqlConstructQuery( query.toString(), config.wireFormat );
+                rawResult= rdfService.sparqlConstructQuery( query.toString(), formatConfig.wireFormat );
             }else if ( query.isDescribeType() ){
-            rawResult = rdfService.sparqlDescribeQuery( query.toString(), config.wireFormat );
+                rawResult = rdfService.sparqlDescribeQuery( query.toString(), formatConfig.wireFormat );
             }
     
-        response.setContentType(  config.responseMimeType );
+            response.setContentType(  formatConfig.responseMimeType );
             
-        if( config.converstionFromWireFormat ){
+            if( formatConfig.converstionFromWireFormat ){
-            Model resultModel = RDFServiceUtils.parseModel( rawResult, config.wireFormat );                        
+                Model resultModel = RDFServiceUtils.parseModel( rawResult, formatConfig.wireFormat );                        
-            if( "JSON-LD".equals( config.jenaResponseFormat )){
+                if( "JSON-LD".equals( formatConfig.jenaResponseFormat )){
                     //since jena 2.6.4 doesn't support JSON-LD we do it                                                                   
                     try {
                         JenaRDFParser parser = new JenaRDFParser();
@@ -246,12 +225,17 @@ public class SparqlQueryServlet extends BaseEditController {
                     }
                 }else{
                     OutputStream out = response.getOutputStream();
-                resultModel.write(out, config.jenaResponseFormat );
+                    resultModel.write(out, formatConfig.jenaResponseFormat );
                 }
             }else{
                 OutputStream out = response.getOutputStream();
                 pipe( rawResult, out );
             }
+        }catch( IOException ex){
+            throw new ServletException("could not run SPARQL CONSTRUCT",ex);
+        } catch (RDFServiceException ex) {
+            throw new ServletException("could not run SPARQL CONSTRUCT",ex);
+        }
     }
 
     private void pipe( InputStream in, OutputStream out) throws IOException{
@@ -362,13 +346,35 @@ public class SparqlQueryServlet extends BaseEditController {
             rd.forward(req,res);
     }
 
+    /** Simple boolean vaule to improve the legibility of confiugrations. */
+    private final static boolean CONVERT = true;
 
-    public static class ModelFormatConfig{
+    /** Simple vaule to improve the legibility of confiugrations. */
+    private final static String NO_CONVERSION = null;
+
+    public static class FormatConfig{
         public String valueFromForm;
         public boolean converstionFromWireFormat;
+        public String responseMimeType;
+    }
+    
+    private static ModelFormatConfig[] fmts = {
+        new ModelFormatConfig("RDF/XML", 
+                              !CONVERT, ModelSerializationFormat.RDFXML,  NO_CONVERSION,    "application/rdf+xml" ),
+        new ModelFormatConfig("RDF/XML-ABBREV", 
+                              CONVERT,  ModelSerializationFormat.N3,      "RDF/XML-ABBREV", "application/rdf+xml" ),
+        new ModelFormatConfig("N3", 
+                              !CONVERT, ModelSerializationFormat.N3,      NO_CONVERSION,    "text/n3" ),
+        new ModelFormatConfig("N-TRIPLE", 
+                              !CONVERT, ModelSerializationFormat.NTRIPLE, NO_CONVERSION,    "text/plain" ),
+        new ModelFormatConfig("TTL", 
+                              CONVERT,  ModelSerializationFormat.N3,      "TTL",            "application/x-turtle" ),
+        new ModelFormatConfig("JSON-LD", 
+                              CONVERT,  ModelSerializationFormat.N3,      "JSON-LD",        "application/javascript" ) };
+
+    public static class ModelFormatConfig extends FormatConfig{                
         public RDFService.ModelSerializationFormat wireFormat;
         public String jenaResponseFormat;        
-        public String responseMimeType;
         
         public ModelFormatConfig( String valueFromForm,
                                   boolean converstionFromWireFormat, 
@@ -383,12 +389,20 @@ public class SparqlQueryServlet extends BaseEditController {
         }
     }
 
-    public static class RSFormatConfig{
+
-        public String valueFromForm;
+    private static RSFormatConfig[] rsfs = {
-        public boolean converstionFromWireFormat;
+        new RSFormatConfig( "RS_XML", 
+                            !CONVERT, ResultFormat.XML,  null, "text/xml"),
+        new RSFormatConfig( "RS_TEXT", 
+                            !CONVERT, ResultFormat.TEXT, null, "text/plain"),
+        new RSFormatConfig( "vitro:csv", 
+                            !CONVERT, ResultFormat.CSV,  null, "text/csv"),
+        new RSFormatConfig( "RS_JSON", 
+                            !CONVERT, ResultFormat.JSON, null, "application/javascript") }; 
+
+    public static class RSFormatConfig extends FormatConfig{        
         public ResultFormat wireFormat;
         public ResultSetFormat jenaResponseFormat;
-        public String responseMimeType;
         
         public RSFormatConfig( String valueFromForm,
                                boolean converstionFromWireFormat,
@@ -404,13 +418,47 @@ public class SparqlQueryServlet extends BaseEditController {
     }
 
     static{
-        /* move the lists of configs into maps for easy lookup */
+        HashMap<String, Float> map = new HashMap<String, Float>();
+        
+        /* move the lists of configurations into maps for easy lookup
+         * by both MIME content type and the parameters from the form */
         for( RSFormatConfig rsfc : rsfs ){
             rsFormats.put( rsfc.valueFromForm, rsfc );
+            rsFormats.put( rsfc.responseMimeType, rsfc);
+            map.put(rsfc.responseMimeType, 1.0f);
         }
         for( ModelFormatConfig mfc : fmts ){
             modelFormats.put( mfc.valueFromForm, mfc);
-        }        
+            modelFormats.put(mfc.responseMimeType, mfc);
+            map.put(mfc.responseMimeType, 1.0f);
         }
         
+        ACCEPTED_CONTENT_TYPES = Collections.unmodifiableMap(map);
+    }
+
+
+    /**
+     * Get the content type based on content negotiation.
+     * Returns null of no content type can be agreed on or
+     * if there is no accept header.   
+     */
+    protected String checkForContentType( String acceptHeader ) {        
+        if (acceptHeader == null) 
+            return null;        
+    
+        try {
+            Map<String, Float> typesAndQ = ContentType
+                    .getTypesAndQ(acceptHeader);
+            
+            String ctStr = ContentType
+                    .getBestContentType(typesAndQ,ACCEPTED_CONTENT_TYPES); 
+                    
+            if( ACCEPTED_CONTENT_TYPES.containsKey( ctStr )){
+                return ctStr;
+            }
+        } catch (Throwable th) {
+            log.error("Problem while checking accept header ", th);
+        }
+        return null;
+    }
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/admin/ShowAuthController.java

@@ -91,7 +91,7 @@ public class ShowAuthController extends FreemarkerHttpServlet {
 	private boolean mayEditIndividual(VitroRequest vreq, String individualUri) {
 		RequestedAction action = new EditObjectPropertyStatement(
 				vreq.getJenaOntModel(), individualUri,
-				RequestActionConstants.SOME_URI,
+				RequestActionConstants.SOME_PREDICATE,
 				RequestActionConstants.SOME_URI);
 		return PolicyHelper.isAuthorizedForActions(vreq, action);
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Classes2ClassesRetryController.java

@@ -19,6 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
 public class Classes2ClassesRetryController extends BaseEditController {
@@ -43,7 +44,7 @@ public class Classes2ClassesRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        VClassDao vcDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = ModelAccess.on(getServletContext()).getWebappDaoFactory().getVClassDao();
         epo.setDataAccessObject(vcDao);
         Classes2Classes objectForEditing = new Classes2Classes();
 

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

@@ -22,6 +22,7 @@ import edu.cornell.mannlib.vedit.forwarder.impl.UrlForwarder;
 import edu.cornell.mannlib.vedit.util.FormUtils;
 import edu.cornell.mannlib.vedit.validator.Validator;
 import edu.cornell.mannlib.vedit.validator.impl.RequiredFieldValidator;
+import edu.cornell.mannlib.vedit.validator.impl.UrlValidator;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
@@ -47,7 +48,13 @@ public class OntologyRetryController extends BaseEditController {
         epo.setBeanClass(Ontology.class);
         epo.setBeanMask(testMask);
 
-        String action = "insert";
+        String action = null;
+        if (epo.getAction() == null) {
+            action = "insert";
+            epo.setAction("insert");
+        } else {
+            action = epo.getAction();
+        }
 
         OntologyDao oDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
         epo.setDataAccessObject(oDao);
@@ -67,13 +74,12 @@ public class OntologyRetryController extends BaseEditController {
             epo.setOriginalBean(ontologyForEditing);
         } else {
             ontologyForEditing = (Ontology) epo.getNewBean();
-            action = "update";
-            log.error("using newBean");
         }
         
         //validators
         List<Validator> validatorList = new ArrayList<Validator>();
         validatorList.add(new RequiredFieldValidator());
+        validatorList.add(new UrlValidator());
         epo.getValidatorMap().put("URI", validatorList);
 
         //make a simple mask for the class's id

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

@@ -37,6 +37,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.edit.utils.RoleLevelOptionsSetup;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
@@ -69,7 +70,8 @@ public class PropertyRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        ObjectPropertyDao propDao = request.getUnfilteredWebappDaoFactory().getObjectPropertyDao();
+        ObjectPropertyDao propDao = ModelAccess.on(getServletContext()).getWebappDaoFactory().getObjectPropertyDao();
+                //getUnfilteredWebappDaoFactory().getObjectPropertyDao();
         epo.setDataAccessObject(propDao);
         OntologyDao ontDao = request.getUnfilteredWebappDaoFactory().getOntologyDao();
         VClassDao vclassDao = request.getUnfilteredWebappDaoFactory().getVClassDao();

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

@@ -24,6 +24,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
@@ -44,7 +45,7 @@ public class VclassEditController extends BaseEditController {
         EditProcessObject epo = super.createEpo(request, FORCE_NEW);
         request.setAttribute("epoKey", epo.getKey());
 
-        VClassDao vcwDao = request.getUnfilteredWebappDaoFactory().getVClassDao();
+        VClassDao vcwDao = ModelAccess.on(getServletContext()).getBaseWebappDaoFactory().getVClassDao();
         VClass vcl = (VClass)vcwDao.getVClassByURI(request.getParameter("uri"));
         
         if (vcl == null) {
@@ -140,8 +141,8 @@ public class VclassEditController extends BaseEditController {
         HashMap formSelect = new HashMap(); // tells the JSP what select lists are populated, and thus should be displayed
         request.setAttribute("formSelect",formSelect);
 
-        // if supported, we want to show only the asserted superclasses and subclasses.  Don't want to see anonymous classes, restrictions, etc.
+        // if supported, we want to show only the asserted superclasses and subclasses.
-        VClassDao vcDao = request.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
+        VClassDao vcDao = ModelAccess.on(getServletContext()).getBaseWebappDaoFactory().getVClassDao();
         List superURIs = vcDao.getSuperClassURIs(vcl.getURI(),false);
         List superVClasses = new ArrayList();
         Iterator superURIit = superURIs.iterator();

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

@@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AddObjectP
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.DropObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
@@ -147,19 +148,22 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 			Individual entity = validateEntityUri(vreq);
 			String imageUri = entity.getMainImageUri();
 			
+			Property indMainImage = new Property();
+			indMainImage.setURI(VitroVocabulary.IND_MAIN_IMAGE);
+
 			RequestedAction ra;
 			if (ACTION_DELETE.equals(action)
 					|| ACTION_DELETE_EDIT.equals(action)) {
 				ra = new DropObjectPropertyStatement(vreq.getJenaOntModel(),
-						entity.getURI(), VitroVocabulary.IND_MAIN_IMAGE,
+						entity.getURI(), indMainImage,
 						imageUri);
 			} else if (imageUri != null) {
 				ra = new EditObjectPropertyStatement(vreq.getJenaOntModel(),
-						entity.getURI(), VitroVocabulary.IND_MAIN_IMAGE,
+						entity.getURI(), indMainImage,
 						imageUri);
 			} else {
 				ra = new AddObjectPropertyStatement(vreq.getJenaOntModel(),
-						entity.getURI(), VitroVocabulary.IND_MAIN_IMAGE,
+						entity.getURI(), indMainImage,
 						RequestActionConstants.SOME_URI);
 			}
 			return new Actions(ra);

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzer.java

@@ -132,10 +132,11 @@ public class IndividualRequestAnalyzer {
 	 * only provide a set of bytes.
 	 */
 	protected ContentType checkAcceptHeaderForLinkedDataRequest() {
-		String acceptHeader = vreq.getHeader("accept");
+		String acceptHeader = vreq.getHeader("Accept");
-		if (acceptHeader == null) {
+		if (acceptHeader == null) 
+		    acceptHeader = vreq.getHeader("accept");		   
+		if (acceptHeader == null)
 			return null;		
-		}
 	
 		try {
 			Map<String, Float> typesAndQ = ContentType

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java

@@ -77,11 +77,16 @@ public class RDFUploadController extends JenaIngestController {
         VitroRequest request = new VitroRequest(req);        
         LoginStatusBean loginBean = LoginStatusBean.getBean(request);
         
+        try {
             String modelName = req.getParameter("modelName");
             if(modelName!=null){
                 loadRDF(req,request,response);
                 return;
             }    
+        } catch (Exception e) {
+            log.error(e,e);
+            throw new RuntimeException(e);
+        }
                        
         boolean remove = "remove".equals(request.getParameter("mode"));
         String verb = remove?"Removed":"Added";

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

@@ -15,7 +15,7 @@ public interface ObjectPropertyDao extends PropertyDao {
 
     public ObjectProperty getObjectPropertyByURI(String objectPropertyURI);
     
-    public ObjectProperty getObjectPropertyByURIAndRangeURI(String objectPropertyURI, String rangeURI);
+    public ObjectProperty getObjectPropertyByURIs(String objectPropertyURI, String domainURI, String rangeURI);
 
     public List <ObjectProperty> getObjectPropertiesForObjectPropertyStatements(List /*of ObjectPropertyStatement */ objectPropertyStatements);
 

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

@@ -41,8 +41,8 @@ public interface ObjectPropertyStatementDao {
     public Map<String, String> getMostSpecificTypesInClassgroupsForIndividual(String subjectUri);
 
 	List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
-			String subjectUri, String propertyUri, String objectKey, String rangeUri,
+			String subjectUri, String propertyUri, String objectKey, String domainUri, 
-			String queryString, Set<String> constructQueryStrings,
+			String rangeUri, String queryString, Set<String> constructQueryStrings,
 			String sortDirection);
 
 	

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

@@ -7,10 +7,13 @@ public class VitroVocabulary {
 
 	
     public static final String vitroURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#";
+    public static final String configURI= "http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#";
     
     public static final String VITRO_AUTH = "http://vitro.mannlib.cornell.edu/ns/vitro/authorization#";
     public static final String VITRO_PUBLIC = "http://vitro.mannlib.cornell.edu/ns/vitro/public#";
     public static final String VITRO_PUBLIC_ONTOLOGY = "http://vitro.mannlib.cornell.edu/ns/vitro/public";
+    // TODO change the following before 1.6 release
+    public static final String PROPERTY_CONFIG_DATA = "http://example.org/appConfig/";
     
     
     /** BJL23 2008-02-25:
@@ -95,6 +98,9 @@ public class VitroVocabulary {
     public static final String PROPERTY_CUSTOM_LIST_VIEW_ANNOT = vitroURI + "customListViewAnnot";
     public static final String PROPERTY_SELECTFROMEXISTINGANNOT = vitroURI+"selectFromExistingAnnot";
     public static final String PROPERTY_OFFERCREATENEWOPTIONANNOT = vitroURI+"offerCreateNewOptionAnnot";
+    public static final String PROPERTY_EDITLINKSUPPRESSED = configURI + "editLinkSuppressed";
+    public static final String PROPERTY_ADDLINKSUPPRESSED = configURI + "addLinkSuppressed";
+    public static final String PROPERTY_DELETELINKSUPPRESSED = configURI + "deleteLinkSuppressed";
     public static final String PROPERTY_INPROPERTYGROUPANNOT = vitroURI+"inPropertyGroupAnnot";
     public static final String PROPERTYGROUP = vitroURI + "PropertyGroup";
     public static final String MASKS_PROPERTY = vitroURI + "masksProperty";

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

@@ -49,8 +49,8 @@ class ObjectPropertyDaoFiltering extends BaseFiltering implements ObjectProperty
         return (newOprop == null) ? null : new ObjectPropertyFiltering(newOprop, filters);
     }
     
-    public ObjectProperty getObjectPropertyByURIAndRangeURI(String objectPropertyURI, String rangeURI) {
+    public ObjectProperty getObjectPropertyByURIs(String objectPropertyURI, String domainURI, String rangeURI) {
-        ObjectProperty newOprop=innerObjectPropertyDao.getObjectPropertyByURIAndRangeURI(objectPropertyURI, rangeURI);
+        ObjectProperty newOprop=innerObjectPropertyDao.getObjectPropertyByURIs(objectPropertyURI, domainURI, rangeURI);
         return (newOprop == null) ? null : new ObjectPropertyFiltering(newOprop, filters);
     }
 

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

@@ -524,5 +524,35 @@ public class ObjectPropertyFiltering extends ObjectProperty {
 		innerObjectProperty.setCollateBySubclass(collate);
 	}
 	
+	@Override
+	public boolean isEditLinkSuppressed() {
+	    return innerObjectProperty.isEditLinkSuppressed();
+	}
+	
+	@Override 
+	public boolean isAddLinkSuppressed() {
+	    return innerObjectProperty.isAddLinkSuppressed();
+	}
+	
+	@Override 
+	public boolean isDeleteLinkSuppressed() {
+	    return innerObjectProperty.isDeleteLinkSuppressed();
+	}
+	
+	@Override
+    public void setEditLinkSuppressed(boolean editLinkSuppressed) {
+        innerObjectProperty.setEditLinkSuppressed(editLinkSuppressed);
+    }
+    
+    @Override 
+    public void setAddLinkSuppressed(boolean addLinkSuppressed) {
+        innerObjectProperty.setAddLinkSuppressed(addLinkSuppressed);
+    }
+    
+    @Override 
+    public void setDeleteLinkSuppressed(boolean deleteLinkSuppressed) {
+        innerObjectProperty.setDeleteLinkSuppressed(deleteLinkSuppressed);
+    }
+
     
 }

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

@@ -86,12 +86,13 @@ class ObjectPropertyStatementDaoFiltering extends BaseFiltering implements Objec
 	
     @Override
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
-            String subjectUri, String propertyUri, String objectKey, String rangeUri,
+            String subjectUri, String propertyUri, String objectKey, String domainUri, 
-            String query, Set<String> queryStrings, String sortDirection) {
+            String rangeUri, String query, Set<String> queryStrings, String sortDirection) {
         
         List<Map<String, String>> data = 
         	innerObjectPropertyStatementDao.getObjectPropertyStatementsForIndividualByProperty(
-        			subjectUri, propertyUri, objectKey, rangeUri, query, queryStrings,sortDirection);
+        			subjectUri, propertyUri, objectKey, domainUri, rangeUri, query, 
+        			        queryStrings,sortDirection);
         
         /* Filter the data
          * 
@@ -107,6 +108,7 @@ class ObjectPropertyStatementDaoFiltering extends BaseFiltering implements Objec
             ObjectPropertyStatement statement = new ObjectPropertyStatementImpl(subjectUri, propertyUri, objectUri);
             ObjectProperty op = new ObjectProperty();
             op.setURI(propertyUri);
+            op.setDomainVClassURI(domainUri);
             op.setRangeVClassURI(rangeUri);
             statement.setProperty(op);
             stmtsToData.put(statement, map);

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

@@ -834,7 +834,11 @@ public class JenaBaseDao extends JenaBaseDaoCon {
         try {                       
             String localName = r.getLocalName();
             if (localName != null) {
+                if(localName.trim().length() > 0) {
                     label = localName;
+                } else {
+                    label = r.getURI();
+                }
             } else if (r.isAnon()) {
                 label = r.getId().toString();
             } else {
@@ -925,8 +929,10 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     			return null;
     		if (vitroURIStr.indexOf(PSEUDO_BNODE_NS)==0) {
     			String idStr = vitroURIStr.split("#")[1];
+    			log.debug("Trying to get bnode " + idStr);
     			RDFNode rdfNode = ontModel.getRDFNode(Node.createAnon(AnonId.create(idStr)));
     			if ( (rdfNode != null) && (rdfNode.canAs(OntClass.class)) ) {
+    			    log.debug("found it");
     				cls = rdfNode.as(OntClass.class);
     			}
 			} else {

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

@@ -75,6 +75,9 @@ public class JenaBaseDaoCon {
     protected AnnotationProperty PROPERTY_INPROPERTYGROUPANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_INPROPERTYGROUPANNOT);
     protected AnnotationProperty PROPERTY_COLLATEBYSUBCLASSANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_COLLATEBYSUBCLASSANNOT);
     protected AnnotationProperty PROPERTY_STUBOBJECTPROPERTYANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_STUBOBJECTPROPERTYANNOT);
+    protected AnnotationProperty PROPERTY_EDITLINKSUPPRESSED = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_EDITLINKSUPPRESSED);
+    protected AnnotationProperty PROPERTY_ADDLINKSUPPRESSED = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_ADDLINKSUPPRESSED);
+    protected AnnotationProperty PROPERTY_DELETELINKSUPPRESSED = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_DELETELINKSUPPRESSED);
     
     protected OntClass 		     PROPERTYGROUP = _constModel.createClass(VitroVocabulary.PROPERTYGROUP);
 

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

@@ -37,6 +37,7 @@ 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.sparql.expr.NodeValue;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
@@ -224,6 +225,13 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
             Boolean collateBySubclass = getPropertyBooleanValue(op,PROPERTY_COLLATEBYSUBCLASSANNOT);
             p.setCollateBySubclass(collateBySubclass==null ? false : collateBySubclass);
             
+            Boolean editLinkSuppressed = getPropertyBooleanValue(op, PROPERTY_EDITLINKSUPPRESSED);
+            p.setEditLinkSuppressed(editLinkSuppressed == null ? false : editLinkSuppressed);
+            Boolean addLinkSuppressed = getPropertyBooleanValue(op, PROPERTY_ADDLINKSUPPRESSED);
+            p.setAddLinkSuppressed(addLinkSuppressed == null ? false : addLinkSuppressed);
+            Boolean deleteLinkSuppressed = getPropertyBooleanValue(op, PROPERTY_DELETELINKSUPPRESSED);
+            p.setDeleteLinkSuppressed(deleteLinkSuppressed == null ? false : deleteLinkSuppressed);
+            
             Resource groupRes = (Resource) op.getPropertyValue(PROPERTY_INPROPERTYGROUPANNOT);
             if (groupRes != null) {
                 p.setGroupURI(groupRes.getURI());
@@ -284,21 +292,39 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         }
     }
     
-    public ObjectProperty getObjectPropertyByURIAndRangeURI(String propertyURI, String rangeURI) {
+    public ObjectProperty getObjectPropertyByURIs(String propertyURI, String domainURI, String rangeURI) {
+        if(log.isDebugEnabled()) {
+            log.debug("Getting " + propertyURI + " with domain " + domainURI + " and range " + rangeURI);
+        }
         ObjectProperty op = getObjectPropertyByURI(propertyURI);
-        if (op == null) {
+        if (op == null || rangeURI == null) {
             return op;
         }
+        op.setDomainVClassURI(domainURI);
         op.setRangeVClassURI(rangeURI);
         String propQuery = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
                 "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
                 "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
-                "SELECT ?range ?label ?group ?customForm ?displayLevel ?updateLevel WHERE { \n" +
+                "SELECT ?range ?label ?group ?customForm ?displayRank ?displayLevel " +
-                "    ?context config:configContextFor <" + propertyURI + "> . \n" +
+                "    ?updateLevel ?editLinkSuppressed ?addLinkSuppressed ?deleteLinkSuppressed \n" +
-                "    ?context config:qualifiedBy <" + rangeURI + "> . \n" +
+                " WHERE { \n" +
-                "    ?context config:hasConfiguration ?configuration . \n" +
+                "    ?context config:configContextFor <" + propertyURI + "> . \n";
+        if (domainURI != null) {
+                propQuery += "    ?context config:qualifiedByDomain <" + domainURI + "> . \n";
+        } else {
+                propQuery += "   FILTER NOT EXISTS { ?context config:qualifiedByDomain ?domainURI } \n";
+        }
+        if (rangeURI != null) {
+            propQuery += "    ?context config:qualifiedBy <" + rangeURI + "> . \n";
+        };
+                propQuery += "    ?context config:hasConfiguration ?configuration . \n" +
+                "    ?configuration a config:ObjectPropertyDisplayConfig . \n" +
                 "    OPTIONAL { ?configuration config:propertyGroup ?group } \n" +
                 "    OPTIONAL { ?configuration config:displayName ?label } \n" +
+                "    OPTIONAL { ?configuration config:editLinkSuppressed ?editLinkSuppressed } \n" +
+                "    OPTIONAL { ?configuration config:addLinkSuppressed ?addLinkSuppressed } \n" +
+                "    OPTIONAL { ?configuration config:deleteLinkSuppressed ?deleteLinkSuppressed } \n" +
+                "    OPTIONAL { ?configuration vitro:displayRankAnnot ?displayRank } \n" +
                 "    OPTIONAL { ?configuration vitro:customEntryFormAnnot ?customForm } \n" +
                 "    OPTIONAL { ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
                 "    OPTIONAL { ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n" +
@@ -314,6 +340,11 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 if (groupRes != null) {
                     op.setGroupURI(groupRes.getURI());
                 } 
+                Literal displayRankLit = qsoln.getLiteral("displayRank");
+                if(displayRankLit != null) {
+                    op.setDomainDisplayTier(
+                            Integer.parseInt(displayRankLit.getLexicalForm()));
+                } 
                 Resource displayLevelRes = qsoln.getResource("displayLevel");
                 if (displayLevelRes != null) {
                     op.setHiddenFromDisplayBelowRoleLevel(
@@ -334,6 +365,18 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 if (customFormLit != null) {
                     op.setCustomEntryForm(customFormLit.getLexicalForm());
                 } 
+                Literal editLinkSuppressedLit = qsoln.getLiteral("editLinkSuppressed");
+                if (editLinkSuppressedLit != null ) {
+                    op.setEditLinkSuppressed(editLinkSuppressedLit.getBoolean());
+                }
+                Literal addLinkSuppressedLit = qsoln.getLiteral("addLinkSuppressed");
+                if (addLinkSuppressedLit != null ) {
+                    op.setAddLinkSuppressed(addLinkSuppressedLit.getBoolean());
+                }
+                Literal deleteLinkSuppressedLit = qsoln.getLiteral("deleteLinkSuppressed");
+                if (deleteLinkSuppressedLit != null ) {
+                    op.setDeleteLinkSuppressed(deleteLinkSuppressedLit.getBoolean());
+                }
             }  
         } finally {
             qe.close();
@@ -902,14 +945,14 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     protected static final String LIST_VIEW_CONFIG_FILE_QUERY_STRING =
         "PREFIX display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> \n" +
         "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
-        "SELECT ?property ?range ?filename WHERE { \n" +
+        "SELECT ?property ?range ?domain ?filename WHERE { \n" +
         "    { ?property display:listViewConfigFile ?filename \n" +
         "    } UNION { \n" +
-        "        ?lv config:listViewConfigFile ?filename . \n " +
+        "        ?configuration config:listViewConfigFile ?filename . \n " +
-        "        ?configuration config:hasListView ?lv . " +
         "        ?context config:hasConfiguration ?configuration . \n" +
         "        ?context config:configContextFor ?property . \n" +
         "        ?context config:qualifiedBy ?range . \n" +
+        "        OPTIONAL { ?context config:qualifiedByDomain ?domain } \n" +
         "    } \n" +
         "}";
         
@@ -925,14 +968,15 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     
     //TODO private void addPropertyClassCombinationsToListViewMap(HashMap)    
     
-    // Map key is pair of object property and range class URI
+    // Map key is inner pair of object property and range class URI,
-    // If range is unspecified, OWL.Thing.getURI() is used in the key.
+    // with first member of outer pair being a domain class URI.
-    Map<Pair<ObjectProperty, String>, String> customListViewConfigFileMap = null;
+    // If domain or range is unspecified, OWL.Thing.getURI() is used in the key.
+    Map<Pair<String,Pair<ObjectProperty, String>>, String> customListViewConfigFileMap = null;
     
     @Override
     public String getCustomListViewConfigFileName(ObjectProperty op) {
         if (customListViewConfigFileMap == null) {
-            customListViewConfigFileMap = new HashMap<Pair<ObjectProperty, String>, String>();
+            customListViewConfigFileMap = new HashMap<Pair<String,Pair<ObjectProperty, String>>, String>();
             OntModel displayModel = getOntModelSelector().getDisplayModel();
             //Get all property to list view config file mappings in the system
             QueryExecution qexec = QueryExecutionFactory.create(listViewConfigFileQuery, displayModel); 
@@ -945,6 +989,10 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 String rangeUri = (rangeNode != null)
                         ? ((Resource) rangeNode).getURI()
                         : OWL.Thing.getURI();
+                RDFNode domainNode = soln.get("domain");
+                String domainUri = (domainNode != null)
+                        ? ((Resource) domainNode).getURI()
+                        : OWL.Thing.getURI();
                 ObjectProperty prop = getObjectPropertyByURI(propertyUri);
                 if (prop == null) {
                 	//This is a warning only if this property is the one for which we're searching
@@ -955,15 +1003,24 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 	}
                 } else {
                     String filename = soln.getLiteral("filename").getLexicalForm();
-                    customListViewConfigFileMap.put(new Pair<ObjectProperty, String>(prop, rangeUri), filename);     
+                    log.debug("putting " + domainUri + " " + prop.getURI() + " " + rangeUri + " " + filename + " into list view map");
+                    customListViewConfigFileMap.put(
+                            new Pair<String,Pair<ObjectProperty,String>>(
+                                    domainUri, new Pair<ObjectProperty, String>(
+                                            prop, rangeUri)), filename);     
                 }
             }       
             qexec.close();
         }      
         
-        String customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, op.getRangeVClassURI()));
+        String customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<String, Pair<ObjectProperty, String>>(op.getDomainVClassURI(), new Pair<ObjectProperty,String>(op, op.getRangeVClassURI())));
         if (customListViewConfigFileName == null) {
-            customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, OWL.Thing.getURI()));
+            log.debug("no list view found for " + op.getURI() + " qualified by range " + op.getRangeVClassURI() + " and domain " + op.getDomainVClassURI());
+            customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<String, Pair<ObjectProperty, String>>(OWL.Thing.getURI(), new Pair<ObjectProperty,String>(op, op.getRangeVClassURI())));
+        }
+        if (customListViewConfigFileName == null) {
+            log.debug("no list view found for " + op.getURI() + " qualified by range " + op.getRangeVClassURI());
+            customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<String, Pair<ObjectProperty, String>>(OWL.Thing.getURI(), new Pair<ObjectProperty,String>(op, OWL.Thing.getURI())));
         }
         
         return customListViewConfigFileName;

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

@@ -273,8 +273,7 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
             String subjectUri, 
             String propertyUri,             
-            String objectKey, 
+            String objectKey, String domainUri, String rangeUri,
-            String rangeUri,
             String queryString, 
             Set<String> constructQueryStrings,
             String sortDirection) {    	        
@@ -282,12 +281,14 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         Model constructedModel = constructModelForSelectQueries(
                 subjectUri, propertyUri, constructQueryStrings);
                     
+        if(log.isDebugEnabled()) {
+            log.debug("Constructed model has " + constructedModel.size() + " statements.");
+        }
+        
     	if("desc".equalsIgnoreCase( sortDirection ) ){
     		queryString = queryString.replaceAll(" ASC\\(", " DESC(");
     	}
         
-        log.debug("Query string for object property " + propertyUri + ": " + queryString);
-        
         Query query = null;
         try {
             query = QueryFactory.create(queryString, Syntax.syntaxARQ);
@@ -300,10 +301,15 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         QuerySolutionMap initialBindings = new QuerySolutionMap();
         initialBindings.add("subject", ResourceFactory.createResource(subjectUri));
         initialBindings.add("property", ResourceFactory.createResource(propertyUri));
-        if (rangeUri != null) {
+        if (domainUri != null && !domainUri.startsWith(VitroVocabulary.PSEUDO_BNODE_NS)) {
+            initialBindings.add("subjectType", ResourceFactory.createResource(domainUri));
+        }
+        if (rangeUri != null && !rangeUri.startsWith(VitroVocabulary.PSEUDO_BNODE_NS)) {
             initialBindings.add("objectType", ResourceFactory.createResource(rangeUri));
         }
         
+        log.debug("Query string for object property " + propertyUri + ": " + queryString);
+        
         // Run the SPARQL query to get the properties
         List<Map<String, String>> list = new ArrayList<Map<String, String>>();
         DatasetWrapper w = dwf.getDatasetWrapper();
@@ -354,12 +360,12 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         
         for (String queryString : constructQueries) {
                      
-            log.debug("CONSTRUCT query string for object property " + 
-                    propertyUri + ": " + queryString);
-            
             queryString = queryString.replace("?subject", "<" + subjectUri + ">");
             queryString = queryString.replace("?property", "<" + propertyUri + ">");
          
+            log.debug("CONSTRUCT query string for object property " + 
+                    propertyUri + ": " + queryString);
+            
             // we no longer need this query object, but we might want to do this
             // query parse step to improve debugging, depending on the error returned
             // through the RDF API

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

@@ -16,6 +16,7 @@ import java.util.Set;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.ontology.IntersectionClass;
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntProperty;
@@ -33,6 +34,7 @@ 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.sdb.util.Pair;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
 import com.hp.hpl.jena.vocabulary.OWL;
@@ -51,6 +53,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	
 	protected static final Log log = LogFactory.getLog(PropertyDaoJena.class.getName());
+	protected static final String FAUX_PROPERTY_FLAG = "FAUX";
 	
     private static final Map<String, String> NAMESPACES = new HashMap<String, String>() {{
         put("afn", VitroVocabulary.AFN);
@@ -328,7 +331,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
     public List <VClass> getClassesWithRestrictionOnProperty(String propertyURI) {
     	
     	if (propertyURI == null) {
-    		log.info("getClassesWithRestrictionOnProperty: called with null propertyURI");
+    		log.warn("getClassesWithRestrictionOnProperty: called with null propertyURI");
     		return null;
     	}
     	    	
@@ -348,7 +351,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 				   Statement statement = stmtIter.next();
 				   
 				   if ( statement.getSubject().canAs(OntClass.class) ) {
-					   classURISet.addAll(getRelatedClasses(statement.getSubject().as(OntClass.class)));
+					   classURISet.addAll(getRestrictedClasses(statement.getSubject().as(OntClass.class)));
 				   } else {
 					   log.warn("getClassesWithRestrictionOnProperty: Unexpected use of onProperty: it is not applied to a class");
 				   }
@@ -381,9 +384,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
     }
 
 	/**
-	 * Finds all named superclasses, subclasses and equivalent classes of
+	 * Find named classes to which a restriction "applies"
-	 * the given class.
-	 *
 	 * @param   resourceURI  identifier of a class
 	 * @return  set of class URIs
 	 * 
@@ -391,13 +392,12 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	 * the ontology model.
 	 */
 
-    public HashSet<String> getRelatedClasses(OntClass ontClass) {
+    public HashSet<String> getRestrictedClasses(OntClass ontClass) {
     	
         HashSet<String> classSet = new HashSet<String>();
   
         List<OntClass> classList = ontClass.listEquivalentClasses().toList();
         classList.addAll(ontClass.listSubClasses().toList());
-        classList.addAll(ontClass.listSuperClasses().toList());
         
         Iterator<OntClass> it = classList.iterator();
 		         
@@ -406,6 +406,8 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         	
         	if (!oc.isAnon()) {
         		classSet.add(oc.getURI());
+        	} else {
+        	    classSet.addAll(getRestrictedClasses(oc));
         	}
         }
         		
@@ -524,15 +526,8 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
             }
         }
     	
-    	List<PropertyInstance> piList = getAllPropInstByVClasses(vclasses);
+    	return getAllPropInstByVClasses(vclasses);
     	
-    	for (PropertyInstance pi : piList) {
-    		pi.setDomainClassURI(ind.getVClassURI());
-    		// TODO: improve.  This is so the DWR property editing passes the 
-    		// individual's VClass to get the right restrictions
-    	}
-
-		return piList;
     }
     
     /*
@@ -621,6 +616,42 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         return classes;
     }
     
+    private static final int DEPTH_LIMIT = 20;
+    
+    private List<Restriction> getRelatedRestrictions(OntClass ontClass) {
+        return getRelatedRestrictions(ontClass, new ArrayList<Restriction>(), DEPTH_LIMIT);
+    }
+    
+    private List<Restriction> getRelatedRestrictions(OntClass ontClass, 
+            List<Restriction> relatedRestrictions, int limit) {
+        limit--;
+        if (ontClass.isRestriction()) {
+            relatedRestrictions.add(ontClass.as(Restriction.class));
+        } else if (ontClass.isIntersectionClass()) {
+            IntersectionClass inter = ontClass.as(IntersectionClass.class);
+            Iterator<? extends OntClass> operIt = inter.listOperands();
+            while (operIt.hasNext()) {
+                OntClass operand = operIt.next();
+                if (!relatedRestrictions.contains(operand) && limit > 0) {
+                    relatedRestrictions.addAll(
+                            getRelatedRestrictions(
+                                    operand, relatedRestrictions, limit));
+                }
+            }   
+        } else {
+            List<OntClass> superClasses = listSuperClasses(ontClass);
+            superClasses.addAll(listEquivalentClasses(ontClass));
+            for (OntClass sup : superClasses) {
+                if (sup.isAnon() && !sup.equals(ontClass) 
+                        && !relatedRestrictions.contains(ontClass) && limit > 0) {
+                    relatedRestrictions.addAll(
+                            getRelatedRestrictions(sup, relatedRestrictions, limit));
+                }
+            }
+        }
+        return relatedRestrictions;
+    }
+    
     public List<PropertyInstance> getAllPropInstByVClasses(List<VClass> vclasses) {
         
         List<PropertyInstance> propInsts = new ArrayList<PropertyInstance>();
@@ -651,17 +682,15 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 		            String VClassURI = vclass.getURI();
 		            
 		        	OntClass ontClass = getOntClass(ontModel,VClassURI);
-		        	if (ontClass != null) {
+		        	if (ontClass == null) {
-		        	    List<OntClass> relatedClasses = new ArrayList<OntClass>();
+		        	    continue;  
-		        	    relatedClasses.addAll(listEquivalentClasses(ontClass));		        	    
+		        	}
-		        	    relatedClasses.addAll(listSuperClasses(ontClass));
+	        	    List<Restriction> relatedRestrictions = getRelatedRestrictions(ontClass);
-		        	    for (OntClass relatedClass : relatedClasses) {
+	        	    for (Restriction rest : relatedRestrictions) {
 		        	    // find properties in restrictions
-    		        		if (relatedClass.isRestriction() && relatedClass.canAs(Restriction.class)) {
 	        			// TODO: check if restriction is something like
 	        			// maxCardinality 0 or allValuesFrom owl:Nothing,
 	        			// in which case the property is NOT applicable!
-    		        			Restriction rest = relatedClass.as(Restriction.class);
 	        			OntProperty onProperty = rest.getOnProperty();
 	        			if (onProperty != null) {
 	        			    Resource[] ranges = new Resource[2];
@@ -673,7 +702,6 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	        				updatePropertyRangeMap(applicableProperties, onProperty.getURI(), ranges);
 		        		}
 	        	    }
-		        	    }
 	        		
 	        	    List<Resource> propertyList = 
 	        	    	    getPropertiesWithAppropriateDomainFor(VClassURI);
@@ -699,7 +727,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	        		}
 	        		
 	        	}
-		        }       
+		             
         	} catch (Exception e) {
         		log.error("Unable to get applicable properties " +
         		          "by examining property restrictions and domains", e);
@@ -718,12 +746,36 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 	                            : (op.getRange() == null && foundRanges[1] != null)
 	                            ? foundRanges[1]
 	                                    : op.getRange();
-	                            propInsts.add(getPropInstForPropertyAndRange(op, rangeRes, applicableProperties));
+	            Resource domainRes = op.getDomain();
-	            List<String> additionalFauxSubpropertyRangeURIs = getAdditionalFauxSubpropertyRangeURIsForPropertyURI(propertyURI);
+	                            propInsts.add(getPropInst(
-	            for (String rangeURI : additionalFauxSubpropertyRangeURIs) {
+	                                    op, domainRes, rangeRes, applicableProperties));
-	                if (getWebappDaoFactory().getVClassDao().isSubClassOf(rangeURI, rangeRes.getURI())) {
+	            List<Pair<String,String>> additionalFauxSubpropertyDomainAndRangeURIs = 
-	                    propInsts.add(getPropInstForPropertyAndRange(
+	                    getAdditionalFauxSubpropertyDomainAndRangeURIsForPropertyURI(
-	                            op, ResourceFactory.createResource(rangeURI), applicableProperties));
+	                            propertyURI);
+	            for (Pair<String,String> domainAndRangeURIs : 
+	                    additionalFauxSubpropertyDomainAndRangeURIs) {
+	                boolean applicablePropInst = false;
+	                if (rangeRes == null ||  
+	                        !getWebappDaoFactory().getVClassDao().isSubClassOf(
+	                            rangeRes.getURI(), domainAndRangeURIs.getRight())) { 
+	                    if (domainAndRangeURIs.getLeft() == null) {
+	                        applicablePropInst = true;
+	                    } else {
+    	                    for(VClass vclass : vclasses) {
+    	                        if (vclass.getURI() != null && vclass.getURI().equals(
+    	                                domainAndRangeURIs.getLeft())) {
+    	                            applicablePropInst = true;
+    	                            break;
+    	                        }
+    	                    }
+	                    }
+	                    if (applicablePropInst) {
+    	                    propInsts.add(getPropInst(
+                                    op,
+                                    ResourceFactory.createResource(domainAndRangeURIs.getLeft()),
+                                    ResourceFactory.createResource(domainAndRangeURIs.getRight()), 
+                                    applicableProperties));
+	                    }
 	                }
 	            }
 	        }
@@ -736,11 +788,19 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         
     }
     
-    private PropertyInstance getPropInstForPropertyAndRange(OntProperty op, Resource rangeRes, 
+    private PropertyInstance getPropInst(OntProperty op, Resource domainRes, Resource rangeRes, 
                                                               Map<String, Resource[]> applicableProperties) {  
+        if (log.isDebugEnabled() && domainRes != null && rangeRes != null) {
+            log.debug("getPropInst() op: " + op.getURI() + " domain: " + 
+                domainRes.getURI() + " range: " + rangeRes.getURI());
+        }
         PropertyInstance pi = new PropertyInstance();
-        String domainURIStr = getURIStr(op.getDomain());
+        String domainURIStr = (domainRes != null && !domainRes.isAnon()) ? 
-        if (rangeRes != null) {
+                domainURIStr = domainRes.getURI()
+                : null;
+        if (rangeRes == null) {
+            pi.setRangeClassURI(OWL.Thing.getURI()); // TODO see above
+        } else {
             String rangeClassURI;
             if (rangeRes.isAnon()) {
                 rangeClassURI = PSEUDO_BNODE_NS + rangeRes.getId()
@@ -757,10 +817,9 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
                 range.setName(range.getLocalName());
             }
             pi.setRangeClassName(range.getName());
-        } else {
-            pi.setRangeClassURI(OWL.Thing.getURI()); // TODO see above
         }
         pi.setDomainClassURI(domainURIStr);
+        if (domainURIStr != null) {
             VClass domain = getWebappDaoFactory().getVClassDao()
                     .getVClassByURI(domainURIStr);
             if (domain == null) {
@@ -769,6 +828,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
                 domain.setName(domain.getLocalName());
             }
             pi.setDomainClassName(domain.getName());
+        }
         pi.setSubjectSide(true);
         pi.setPropertyURI(op.getURI());
         pi.setPropertyName(getLabelOrId(op)); // TODO
@@ -777,14 +837,15 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         return pi;
     }
     
-    private List<String> getAdditionalFauxSubpropertyRangeURIsForPropertyURI(String propertyURI) {
+    private List<Pair<String,String>> getAdditionalFauxSubpropertyDomainAndRangeURIsForPropertyURI(String propertyURI) {
-        List<String> rangeURIs = new ArrayList<String>();
+        List<Pair<String,String>> domainAndRangeURIs = new ArrayList<Pair<String,String>>();
         String propQuery = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
                 "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
                 "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
-                "SELECT ?range WHERE { \n" +
+                "SELECT ?domain ?range WHERE { \n" +
                 "    ?context config:configContextFor <" + propertyURI + "> . \n" +
                 "    ?context config:qualifiedBy ?range . \n" +
+                "    OPTIONAL { ?context config:qualifiedByDomain ?domain } \n" +
                 "}"; 
 
         Query q = QueryFactory.create(propQuery);
@@ -794,12 +855,18 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
             while (rs.hasNext()) {
                 QuerySolution qsoln = rs.nextSolution();
                 Resource rangeRes = qsoln.getResource("range");
-                rangeURIs.add(rangeRes.getURI());
+                String rangeURI = rangeRes.getURI();
+                Resource domainRes = qsoln.getResource("domain");
+                String domainURI = null;
+                if (domainRes != null && !domainRes.isAnon()) {
+                    domainURI = domainRes.getURI();
+                } 
+                domainAndRangeURIs.add(new Pair<String,String>(domainURI, rangeURI));
             }  
         } finally {
             qe.close();
         }
-        return rangeURIs;
+        return domainAndRangeURIs;
     }
 
     private String getURIStr(Resource res) {

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

@@ -462,10 +462,12 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                 while (classIt.hasNext()) {
                     try {
                         Individual classInd = classIt.next();
+                        if(classInd.canAs(OntClass.class)) {
                             OntClass cls = classInd.as(OntClass.class);
                             if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) {
                                 classes.add(new VClassJena(cls,getWebappDaoFactory()));
                             }
+                        }
                     } catch (ClassCastException cce) {
                         log.error(cce, cce);
                     }
@@ -1091,11 +1093,8 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
         OntModel ontModel = getOntModel();
         try {
             ontModel.enterCriticalSection(Lock.READ);
-            OntClass oc1 = getOntClass(ontModel, vclassURI1);
+            Resource oc1 = ontModel.getResource(vclassURI1);
-            OntClass oc2 = getOntClass(ontModel, vclassURI2);
+            Resource oc2 = ontModel.getResource(vclassURI2);
-            if (oc1 == null || oc2 == null) {
-                return false;
-            } 
             return ontModel.contains(oc1, RDFS.subClassOf, oc2);
         } finally {
             ontModel.leaveCriticalSection();

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

@@ -2,10 +2,15 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.UnionClass;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.Statement;
@@ -376,4 +381,27 @@ public class VClassJena extends VClass {
             }
         }		 	                      
     }
+    
+    @Override
+    public boolean isUnion() {
+        return this.cls.isUnionClass();
+    }
+    
+    //TODO consider anonymous components
+    @Override
+    public List<VClass> getUnionComponents() {
+        List<VClass> unionComponents = new ArrayList<VClass>();
+        if (isUnion()) {
+            UnionClass union = this.cls.as(UnionClass.class);
+            Iterator<? extends OntClass> opIt = union.listOperands();
+            while(opIt.hasNext()) {
+                OntClass component = opIt.next();
+                if (!component.isAnon()) {
+                    unionComponents.add(new VClassJena(component, this.webappDaoFactory));  
+                }
+            }
+        }
+        return unionComponents;
+    }
+    
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/pellet/PelletListener.java

@@ -624,8 +624,10 @@ public class PelletListener implements ModelChangedListener {
 				if ( (additionModel.size() > 0) || (removalModel.size()>0) ) {
 					if (!isSynchronizing) {
 						if (foreground) {
+                            log.debug("Running Pellet in foreground.");
 							(new PelletSynchronizer()).run();
 						} else {
+                            log.debug("Running Pellet in background.");
 							new Thread(new PelletSynchronizer(), "PelletListener.PelletSynchronizer").start();
 						}
 					}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/pellet/ReasonerConfiguration.java

@@ -31,7 +31,6 @@ public class ReasonerConfiguration {
 	 * The default reasoner configuration is designed to provide acceptable performance on larger knowledge bases.
 	 * It will classify and realize, and add inferred disjointWith statements.
 	 * It ignores domain and range "axioms," on the assumption that they are not truly axioms but editing constraints.  
-	 * It also ignores "owl:inverseOf."  
 	 */
 	public static ReasonerConfiguration DEFAULT;
 	
@@ -78,6 +77,7 @@ public class ReasonerConfiguration {
         defaultInferenceDrivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,RDF.first,null));
         defaultInferenceDrivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,RDF.rest,null));
         defaultInferenceDrivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,OWL.disjointWith,null));
+        defaultInferenceDrivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,OWL.inverseOf,null));
         DEFAULT.setInferenceDrivingPatternAllowSet(defaultInferenceDrivingPatternAllowSet);
         Set<ObjectPropertyStatementPattern> defaultInferenceReceivingPatternAllowSet = new HashSet<ObjectPropertyStatementPattern>();
         defaultInferenceReceivingPatternAllowSet.add(ObjectPropertyStatementPatternFactory.getPattern(null,RDF.type,null));

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/EditConfigurationUtils.java

@@ -53,12 +53,22 @@ public class EditConfigurationUtils {
     	return vreq.getParameter("objectUri");
     }
     
+    public static String getDomainUri(VitroRequest vreq) {
+        return vreq.getParameter("domainUri");
+    }
+    
     public static String getRangeUri(VitroRequest vreq) {
         return vreq.getParameter("rangeUri");
     }
     
     public static VClass getRangeVClass(VitroRequest vreq) {
-        return vreq.getWebappDaoFactory().getVClassDao().getVClassByURI(getRangeUri(vreq));
+        // This needs a WebappDaoFactory with no filtering/RDFService
+        // funny business because it needs to be able to retrieve anonymous union
+        // classes by their "pseudo-bnode URIs".
+        // Someday we'll need to figure out a different way of doing this.
+        WebappDaoFactory ctxDaoFact = ModelAccess.on(
+                vreq.getSession().getServletContext()).getWebappDaoFactory();
+        return ctxDaoFact.getVClassDao().getVClassByURI(getRangeUri(vreq));
     }
     
     //get individual

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/fields/IndividualsViaObjectPropetyOptions.java

@@ -27,13 +27,13 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
     private static final String LEFT_BLANK = "";
     private String subjectUri;
     private String predicateUri;    
-    private String rangeUri;
+    private List<VClass> rangeTypes;
     private String objectUri;
     
     private String defaultOptionLabel;
     
     public IndividualsViaObjectPropetyOptions(String subjectUri,
-            String predicateUri, String rangeUri, String objectUri) throws Exception {
+            String predicateUri, List<VClass> rangeTypes, String objectUri) throws Exception {
         super();
         
         if (subjectUri == null || subjectUri.equals("")) {
@@ -45,7 +45,7 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
 
         this.subjectUri = subjectUri;
         this.predicateUri = predicateUri;
-        this.rangeUri = rangeUri;
+        this.rangeTypes = rangeTypes;
         this.objectUri = objectUri;
     }
     
@@ -78,8 +78,8 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
         //get all vclasses applicable to the individual subject
         HashSet<String> vclassesURIs = getApplicableVClassURIs(subject, wDaoFact);
         
-        if (rangeUri != null) {
+        if (!rangeTypes.isEmpty()) {
-            vclassesURIs = filterToSubclassesOfRange(vclassesURIs, rangeUri, wDaoFact);
+            vclassesURIs = filterToSubclassesOfRange(vclassesURIs, rangeTypes, wDaoFact);
         }
                 
         if (vclassesURIs.size() == 0) {           
@@ -117,9 +117,13 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
 
     private HashSet<String> getApplicableVClassURIs(Individual subject, WebappDaoFactory wDaoFact) {
         HashSet<String> vclassesURIs = new HashSet<String>();
-        if (rangeUri != null) {
+        if (!rangeTypes.isEmpty()) {
-            log.debug("individualsViaObjectProperty using rangeUri " + rangeUri);
+            StringBuffer rangeBuff = new StringBuffer();
-            vclassesURIs.add(rangeUri);
+            for (VClass rangeType : rangeTypes) {
+                vclassesURIs.add(rangeType.getURI());
+                rangeBuff.append(rangeType.getURI()).append(", ");
+            }
+            log.debug("individualsViaObjectProperty using rangeUri " + rangeBuff.toString());            
             return vclassesURIs;
         } 
         
@@ -144,15 +148,17 @@ public class IndividualsViaObjectPropetyOptions implements FieldOptions {
     }
     
     private HashSet<String> filterToSubclassesOfRange(HashSet<String> vclassesURIs, 
-                                              String rangeUri, 
+                                              List<VClass> rangeTypes, 
                                               WebappDaoFactory wDaoFact) {
         HashSet<String> filteredVClassesURIs = new HashSet<String>();
         VClassDao vcDao = wDaoFact.getVClassDao();
         for (String vclass : vclassesURIs) {
-            if (vclass.equals(rangeUri) || vcDao.isSubClassOf(vclass, rangeUri)) {
+            for (VClass rangeType : rangeTypes) {
+                if (vclass.equals(rangeType.getURI()) || vcDao.isSubClassOf(vclass, rangeType.getURI())) {
                     filteredVClassesURIs.add(vclass);
                 }
             }
+        }
         return filteredVClassesURIs;
     }
     

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DefaultObjectPropertyFormGenerator.java

@@ -99,40 +99,59 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
     	return getDefaultObjectEditConfiguration(vreq, session);
     }
 	
-    protected List<String> getRangeTypes(VitroRequest vreq) {
+    protected List<VClass> getRangeTypes(VitroRequest vreq) {
-        WebappDaoFactory wDaoFact = vreq.getWebappDaoFactory();
+        // This first part needs a WebappDaoFactory with no filtering/RDFService
-        List<String> types = new ArrayList<String>();
+        // funny business because it needs to be able to retrieve anonymous union
+        // classes by their "pseudo-bnode URIs".
+        // Someday we'll need to figure out a different way of doing this.
+        WebappDaoFactory ctxDaoFact = ModelAccess.on(
+                vreq.getSession().getServletContext()).getWebappDaoFactory();
+        List<VClass> types = new ArrayList<VClass>();
     	Individual subject = EditConfigurationUtils.getSubjectIndividual(vreq);
    		String predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
    		String rangeUri = EditConfigurationUtils.getRangeUri(vreq);
    		if (rangeUri != null) {
-   		    types.add(rangeUri);
+   		    VClass rangeVClass = ctxDaoFact.getVClassDao().getVClassByURI(rangeUri);
+   		    if (!rangeVClass.isUnion()) {
+   		        types.add(rangeVClass);    
+   		    } else {
+   		        for (VClass unionComponent : rangeVClass.getUnionComponents()) {
+   		            types.add(unionComponent);
+   		        }
+   		    }
 	        return types;
    		}
+   		WebappDaoFactory wDaoFact = vreq.getWebappDaoFactory();
 		//Get all vclasses applicable to subject
 		List<VClass> vClasses = subject.getVClasses();
-		HashSet<String> typesHash = new HashSet<String>();
+		HashMap<String, VClass> typesHash = new HashMap<String, VClass>();
 		for(VClass vclass: vClasses) {
 			 List<VClass> rangeVclasses = wDaoFact.getVClassDao().getVClassesForProperty(vclass.getURI(),predicateUri);
 			 if(rangeVclasses !=  null) {
 				 for(VClass range: rangeVclasses) {
 					 //a hash will keep a unique list of types and so prevent duplicates
-					 typesHash.add(range.getURI());
+					 typesHash.put(range.getURI(), range);
 				 }
 			 }
 		}
-		types.addAll(typesHash);
+		types.addAll(typesHash.values());
         return types;
 	}	
 	
     private boolean tooManyRangeOptions(VitroRequest vreq, HttpSession session ) throws SolrServerException {
-    	List<String> types = getRangeTypes(vreq);
+    	List<VClass> rangeTypes = getRangeTypes(vreq);
     	SolrServer solrServer = SolrSetup.getSolrServer(session.getServletContext());
     	
+    	List<String> types = new ArrayList<String>();
     	//empty list means the range is not set to anything, force Thing
         if(types.size() == 0 ){
-    		types = new ArrayList<String>();
             types.add(VitroVocabulary.OWL_THING);
+        } else { 
+        	for (VClass vclass : rangeTypes) {
+        	    if (vclass.getURI() != null) {
+        	        types.add(vclass.getURI());
+        	    }
+        	}
         }
     	
     	long count = 0;    		   
@@ -184,7 +203,7 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
     	this.setSparqlQueries(editConfiguration);
     	
     	//set fields
-    	setFields(editConfiguration, vreq, EditConfigurationUtils.getPredicateUri(vreq), EditConfigurationUtils.getRangeUri(vreq));
+    	setFields(editConfiguration, vreq, EditConfigurationUtils.getPredicateUri(vreq), getRangeTypes(vreq));
     	
     //	No need to put in session here b/c put in session within edit request dispatch controller instead
     	//placing in session depends on having edit key which is handled in edit request dispatch controller
@@ -358,7 +377,7 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
         setFields(editConfiguration, vreq, predicateUri, null);
     }
     
-    protected void setFields(EditConfigurationVTwo editConfiguration, VitroRequest vreq, String predicateUri, String rangeUri) throws Exception {
+    protected void setFields(EditConfigurationVTwo editConfiguration, VitroRequest vreq, String predicateUri, List<VClass> rangeTypes) throws Exception {
 		FieldVTwo field = new FieldVTwo();
     	field.setName("objectVar");    	
     	
@@ -370,7 +389,7 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
     		field.setOptions( new IndividualsViaObjectPropetyOptions(
     	        subjectUri, 
     	        predicateUri,
-    	        rangeUri,
+    	        rangeTypes,
     	        objectUri));
     	}else{
     		field.setOptions(null);
@@ -441,14 +460,22 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
 		formSpecificData.put("editMode", getEditMode(vreq).toString().toLowerCase());
 		
 		//We also need the type of the object itself
-		List<String> types = getRangeTypes(vreq);
+		List<VClass> types = getRangeTypes(vreq);
         //if types array contains only owl:Thing, the search will not return any results
         //In this case, set an empty array
-        if(types.size() == 1 && types.get(0).equals(VitroVocabulary.OWL_THING) ){
+        if(types.size() == 1 && types.get(0).getURI().equals(VitroVocabulary.OWL_THING) ){
-        	types = new ArrayList<String>();
+        	types = new ArrayList<VClass>();
         }
 		
-		formSpecificData.put("objectTypes", StringUtils.join(types, ","));
+        StringBuffer typesBuff = new StringBuffer();
+        for (VClass type : types) {
+            if (type.getURI() != null) {
+                typesBuff.append(type.getURI()).append(",");
+            }
+        }
+        
+		formSpecificData.put("objectTypes", typesBuff.toString());
+		log.debug("autocomplete object types : "  + formSpecificData.get("objectTypes"));
 		
 		//Get label for individual if it exists
 		if(EditConfigurationUtils.getObjectIndividual(vreq) != null) {
@@ -464,15 +491,15 @@ public class DefaultObjectPropertyFormGenerator implements EditConfigurationGene
 		editConfiguration.setFormSpecificData(formSpecificData);
 	}
 	
-	private Object rangeIndividualsExist(HttpSession session, List<String> types) throws SolrServerException {		
+	private Object rangeIndividualsExist(HttpSession session, List<VClass> types) throws SolrServerException {		
     	SolrServer solrServer = SolrSetup.getSolrServer(session.getServletContext());
     	
     	boolean rangeIndividualsFound = false;
-    	for( String type:types){
+    	for( VClass type:types){
     		//solr for type count.
     		SolrQuery query = new SolrQuery();   
     		
-    		query.setQuery( VitroSearchTermNames.RDFTYPE + ":" + type);
+    		query.setQuery( VitroSearchTermNames.RDFTYPE + ":" + type.getURI());
     		query.setRows(0);
     		
     		QueryResponse rsp = solrServer.query(query);

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsForIndividualGenerator.java

@@ -28,8 +28,10 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestActio
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AddDataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.AddObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@@ -272,7 +274,7 @@ public class ManageLabelsForIndividualGenerator extends BaseEditConfigurationGen
 				RequestActionConstants.SOME_URI);
 		AddObjectPropertyStatement aops = new AddObjectPropertyStatement(
 				vreq.getJenaOntModel(), individual.getURI(),
-				RequestActionConstants.SOME_URI,
+				RequestActionConstants.SOME_PREDICATE,
 				RequestActionConstants.SOME_URI);
     	return PolicyHelper.isAuthorizedForActions(vreq, new Actions(adps).or(aops));
 	}
@@ -317,8 +319,8 @@ public class ManageLabelsForIndividualGenerator extends BaseEditConfigurationGen
 				//This should put the label in the list
 				//Create label information instance with the required information
 				//To generate link
-				DataPropertyStatementTemplateModel dpstm = new DataPropertyStatementTemplateModel(subjectUri, propertyUri, l,
+				DataPropertyStatementTemplateModel dpstm = new DataPropertyStatementTemplateModel(
-			            template, vreq);
+				        subjectUri, new Property(propertyUri), l, template, vreq);
 				labelsList.add(new LabelInformation(
 						l, dpstm.getEditUrl(), dpstm.getDeleteUrl(), languageTag, languageName));
 			}

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/controller/EditRequestDispatchController.java

@@ -171,6 +171,9 @@ public class EditRequestDispatchController extends FreemarkerHttpServlet {
     	    	    makeEditConfigurationVTwo( editConfGeneratorName, vreq, session);
     	}
     	 
+    	if(editConfig == null) {
+    	    log.error("editConfig is null! How did this happen?");
+    	}
     	String editKey = EditConfigurationUtils.getEditKey(vreq); 
     	editConfig.setEditKey(editKey);        
         
@@ -199,6 +202,7 @@ public class EditRequestDispatchController extends FreemarkerHttpServlet {
 	    String editConfGeneratorName = null;
 	    
 	    String predicateUri =  getPredicateUri(vreq);
+	    String domainUri = EditConfigurationUtils.getDomainUri(vreq);
 	    String rangeUri = EditConfigurationUtils.getRangeUri(vreq);
 	    
         // *** handle the case where the form is specified as a request parameter ***	    
@@ -215,9 +219,9 @@ public class EditRequestDispatchController extends FreemarkerHttpServlet {
 
       	// *** check for a predicate URI in the request        	
         }else if( predicateUri != null && !predicateUri.isEmpty() ){                      
-            Property prop = getProperty( predicateUri, vreq);
+            Property prop = getProperty( predicateUri, domainUri, rangeUri, vreq);
             if (prop != null && rangeUri != null) {
-                editConfGeneratorName = getCustomEntryFormForPropertyAndRange(prop, rangeUri);
+                editConfGeneratorName = getCustomEntryForm(prop);
             } else if( prop != null && prop.getCustomEntryForm() != null ){
                 //there is a custom form, great! let's use it.
                 editConfGeneratorName = prop.getCustomEntryForm();
@@ -247,25 +251,19 @@ public class EditRequestDispatchController extends FreemarkerHttpServlet {
         return editConfGeneratorName;
 	}
 
-	private String getCustomEntryFormForPropertyAndRange(Property prop, String rangeUri){
+	private String getCustomEntryForm(Property prop){
-	    String entryFormName = null;
+	    if (prop.getCustomEntryForm() == null) {
-	    // = ApplicationConfigurationOntologyUtils.getEntryForm(prop.getURI(), rangeUri);
-	    if (entryFormName == null) {
-	        if (prop.getCustomEntryForm() != null) {
-	            return prop.getCustomEntryForm();
-	        } else {
 	        return DEFAULT_OBJ_FORM;
-	        }
 	    } else {
-	        prop.setCustomEntryForm(entryFormName);
+	        return prop.getCustomEntryForm();
-	        return entryFormName;
 	    }
 	}
 	
-	private Property getProperty(String predicateUri, VitroRequest vreq) {	   
+	private Property getProperty(String predicateUri, String domainUri, String rangeUri, VitroRequest vreq) {	   
 		Property p = null;
 		try{
-    		p = vreq.getWebappDaoFactory().getObjectPropertyDao().getObjectPropertyByURI(predicateUri);
+    		p = vreq.getWebappDaoFactory().getObjectPropertyDao().getObjectPropertyByURIs(
+    		        predicateUri, domainUri, rangeUri);
     		if(p == null) {
     			p = vreq.getWebappDaoFactory().getDataPropertyDao().getDataPropertyByURI(predicateUri);
     		}

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java

@@ -4,14 +4,17 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 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.OntProperty;
+import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -24,9 +27,10 @@ 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;
-import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 
 /**  
 * Performs knowledge base updates to the abox to align with a new ontology version
@@ -34,10 +38,13 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
 */ 
 public class ABoxUpdater {
 
+    private final Log log = LogFactory.getLog(ABoxUpdater.class);
 	private OntModel oldTboxModel;
 	private OntModel newTboxModel;
-	private OntModel aboxModel;
+	private Dataset dataset;
+	private RDFService rdfService;
 	private OntModel newTBoxAnnotationsModel;
+	private TBoxUpdater tboxUpdater;
 	private ChangeLogger logger;  
 	private ChangeRecord record;
 	private OntClass OWL_THING = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createClass(OWL.Thing.getURI());
@@ -55,19 +62,19 @@ public class ABoxUpdater {
 	 *                         and the retractions model.
 	 *                    
 	 */
-	public ABoxUpdater(OntModel oldTboxModel,
+	public ABoxUpdater(UpdateSettings settings,
-			           OntModel newTboxModel,
-			           OntModel aboxModel,
-			           OntModel newAnnotationsModel,
 		               ChangeLogger logger,
 		               ChangeRecord record) {
 		
-		this.oldTboxModel = oldTboxModel;
+	    this.oldTboxModel = settings.getOldTBoxModel();
-		this.newTboxModel = newTboxModel;
+        this.newTboxModel = settings.getNewTBoxModel();
-		this.aboxModel = aboxModel;
+        RDFService rdfService = settings.getRDFService();
-		this.newTBoxAnnotationsModel = newAnnotationsModel;
+		this.dataset = new RDFServiceDataset(rdfService);
+		this.rdfService = rdfService;
+		this.newTBoxAnnotationsModel = settings.getNewTBoxAnnotationsModel();
 		this.logger = logger;
 		this.record = record;
+		this.tboxUpdater = new TBoxUpdater(settings, logger, record);
 	}
 	
 	/**
@@ -124,8 +131,15 @@ public class ABoxUpdater {
 	public void renameClass(AtomicOntologyChange change) throws IOException {
 		
 		//logger.log("Processing a class rename from: " + change.getSourceURI() + " to " + change.getDestinationURI());
-		aboxModel.enterCriticalSection(Lock.WRITE);
 	    
+	    Iterator<String> graphIt = dataset.listNames();
+	    while(graphIt.hasNext()) {
+	        String graph = graphIt.next();
+	        if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+	            continue;
+	        }
+	        Model aboxModel = dataset.getNamedModel(graph);
+	        aboxModel.enterCriticalSection(Lock.WRITE);
     		try {
     			
     	       Model additions = ModelFactory.createDefaultModel();
@@ -185,7 +199,7 @@ public class ABoxUpdater {
     		} finally {
     			aboxModel.leaveCriticalSection();
     		}
-		
+	    }
 	}
 
 	/**
@@ -231,16 +245,17 @@ public class ABoxUpdater {
 
 			if (!parentOfAddedClass.equals(OWL.Thing)) {
 				
+			    Iterator<String> graphIt = dataset.listNames();
+	            while(graphIt.hasNext()) {
+	                String graph = graphIt.next();
+	                if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+	                    continue;
+	                }
+			        Model aboxModel = dataset.getNamedModel(graph);
+			            
     				StmtIterator stmtIter = aboxModel.listStatements(null, RDF.type, parentOfAddedClass);
     				
     				int count = stmtIter.toList().size();
-				if (count > 0) {
-					
-					String indList = "";
-					while (stmtIter.hasNext()) {
-						Statement stmt = stmtIter.next();
-						indList += "\n\t" + stmt.getSubject().getURI(); 
-					}
     					
 					if (count > 0) {
 						//TODO - take out the detailed logging after our internal testing is completed.
@@ -248,6 +263,7 @@ public class ABoxUpdater {
 				        		    " and a new subclass of that class has been added: " + addedClass.getURI() + ". " +
 				        		    "Please review " + ((count > 1) ? "these" : "this") + " individual" + ((count > 1) ? "s" : "") + " to see whether " + ((count > 1) ? "they" : "it") + " should be of type: " +  addedClass.getURI() );
 					}
+				
 	            }
 			}			
 		}
@@ -330,6 +346,13 @@ public class ABoxUpdater {
 		}
 		
 		// Remove instances of the deleted class
+        Iterator<String> graphIt = dataset.listNames();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
     		aboxModel.enterCriticalSection(Lock.WRITE);
     	    try {
     	       int count = 0;
@@ -350,12 +373,20 @@ public class ABoxUpdater {
     			aboxModel.leaveCriticalSection();
     		}
         }
+	}
 	
 	protected int deleteIndividual(Resource individual) throws IOException {
 
 	    Model retractions = ModelFactory.createDefaultModel();
 	    int refCount = 0;
 	    
+        Iterator<String> graphIt = dataset.listNames();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
     		aboxModel.enterCriticalSection(Lock.WRITE);
     	    try {			   
     		   StmtIterator iter = aboxModel.listStatements(individual, (Property) null, (RDFNode) null);
@@ -379,6 +410,7 @@ public class ABoxUpdater {
     		} finally {
     			aboxModel.leaveCriticalSection();
     		}
+        }
 		
 		return refCount;
 	}
@@ -388,20 +420,33 @@ public class ABoxUpdater {
 		Iterator<AtomicOntologyChange> propItr = changes.iterator();
 		while(propItr.hasNext()){
 			AtomicOntologyChange propChangeObj = propItr.next();
+			log.debug("processing " + propChangeObj);
+			try {
+			    if (propChangeObj.getAtomicChangeType() == null) {
+			        log.error("Missing change type; skipping " + propChangeObj);
+			        continue;
+			    }
     			switch (propChangeObj.getAtomicChangeType()){
     			  case ADD: 
+    			   log.debug("add");
     			   addProperty(propChangeObj);
     			   break;
     			case DELETE: 
+    			   log.debug("delete");
     			   deleteProperty(propChangeObj);
     			   break;
     			case RENAME: 
+    			   log.debug("rename");
     			   renameProperty(propChangeObj);
     			   break;
     			default: 
+    			   log.debug("unknown");
     			   logger.logError("unexpected change type indicator: " + propChangeObj.getAtomicChangeType());
     			   break;
     		    }	
+			} catch (Exception e) {
+			    log.error(e,e);
+			}
 		}
 	}
 	
@@ -424,6 +469,13 @@ public class ABoxUpdater {
 		
 		if (inverseOfAddedProperty != null) {
 			Model additions = ModelFactory.createDefaultModel();
+            Iterator<String> graphIt = dataset.listNames();
+            while(graphIt.hasNext()) {
+                String graph = graphIt.next();
+                if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                    continue;
+                }
+                Model aboxModel = dataset.getNamedModel(graph);
     			aboxModel.enterCriticalSection(Lock.WRITE);
     			
     			try {
@@ -457,6 +509,7 @@ public class ABoxUpdater {
     			}
             }
 		}
+	}
 	
 	private void deleteProperty(AtomicOntologyChange propObj) throws IOException{
 		
@@ -492,6 +545,13 @@ public class ABoxUpdater {
 			}
 		}
 		
+        Iterator<String> graphIt = dataset.listNames();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
     		Model deletePropModel = ModelFactory.createDefaultModel();
     		
     		if (replacementProperty == null) {
@@ -513,12 +573,13 @@ public class ABoxUpdater {
     			AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes());
     			renameProperty(chg);
     		}		
+        }
 		
 	}
 	
 	private void renameProperty(AtomicOntologyChange propObj) throws IOException {
 		
-		//logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
+		logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
 		
 		OntProperty oldProperty = oldTboxModel.getOntProperty(propObj.getSourceURI());
 		OntProperty newProperty = newTboxModel.getOntProperty(propObj.getDestinationURI());
@@ -533,6 +594,14 @@ public class ABoxUpdater {
 			return;
 		}
 		
+        Iterator<String> graphIt = dataset.listNames();
+        while(graphIt.hasNext()) {
+            String graph = graphIt.next();
+            if(!KnowledgeBaseUpdater.isUpdatableABoxGraph(graph)){
+                continue;
+            }
+            Model aboxModel = dataset.getNamedModel(graph);
+		
     		Model renamePropAddModel = ModelFactory.createDefaultModel();
     		Model renamePropRetractModel = 	ModelFactory.createDefaultModel();
     		
@@ -564,6 +633,9 @@ public class ABoxUpdater {
     		}
         }
         
+        tboxUpdater.renameProperty(propObj);
+	}
+	
 	public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {
        logChange(oldStatement,false);
        logChange(newStatement,true);

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/AtomicOntologyChange.java

@@ -30,6 +30,11 @@ public class AtomicOntologyChange {
 		this.notes = notes;
     }
 
+	@Override
+	public String toString() {
+	    return "Source: " + sourceURI + "; Destination: " + destinationURI +
+	            "; Type: " + atomicChangeType + "; Notes:" + notes;
+	}
 	
 	/**
 	 * Contains the URI of a class or property in the previous version of

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ChangeRecord.java

@@ -12,4 +12,6 @@ public interface ChangeRecord {
 	
 	public void writeChanges();
 	
+	public boolean hasRecordedChanges();
+	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java

@@ -11,6 +11,8 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -22,19 +24,16 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.Syntax;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.shared.Lock;
 
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
@@ -58,14 +57,13 @@ public class KnowledgeBaseUpdater {
 		this.record = new SimpleChangeRecord(settings.getAddedDataFile(), settings.getRemovedDataFile());
 	}
 	
-	public void update(ServletContext servletContext) throws IOException {	
+	public boolean update(ServletContext servletContext) throws IOException {	
 					
 		if (this.logger == null) {
 			this.logger = new SimpleChangeLogger(settings.getLogFile(),	settings.getErrorLogFile());
 		}
 			
 		long startTime = System.currentTimeMillis();
-        System.out.println("Migrating the knowledge base");
         log.info("Migrating the knowledge base");
         logger.log("Started knowledge base migration");
 		
@@ -73,7 +71,7 @@ public class KnowledgeBaseUpdater {
 		     performUpdate(servletContext);
 		} catch (Exception e) {
 			 logger.logError(e.getMessage());
-			 e.printStackTrace();
+			 log.error(e,e);
 		}
 
 		if (!logger.errorsWritten()) {
@@ -85,10 +83,9 @@ public class KnowledgeBaseUpdater {
 		logger.closeLogs();
 
 		long elapsedSecs = (System.currentTimeMillis() - startTime)/1000;		
-		System.out.println("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
 		log.info("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
 		
-		return;
+		return record.hasRecordedChanges();
 	}
 	
 	private void performUpdate(ServletContext servletContext) throws Exception {
@@ -98,135 +95,152 @@ public class KnowledgeBaseUpdater {
 		AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
 		
         //process the TBox before the ABox
-		log.info("\tupdating tbox annotations");
+		try {
+		    log.debug("\tupdating tbox annotations");
 	        updateTBoxAnnotations();
+		} catch (Exception e) {
+		    log.error(e,e);
+		}
 	    
 	    try {
     	    migrateMigrationMetadata(servletContext);
 		    logger.log("Migrated migration metadata");
 	    } catch (Exception e) {
-	    	log.debug("unable to migrate migration metadata " + e.getMessage());
+	    	log.error("unable to migrate migration metadata " + e.getMessage());
 	    }
 	        	
+    	log.info("performing SPARQL CONSTRUCT additions");
+    	performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
+    	
+        log.info("performing SPARQL CONSTRUCT retractions");
+        performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), settings.getRDFService(), RETRACT);
+        
         log.info("\tupdating the abox");
         updateABox(changes);
-	}
         
-	private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
+        log.info("performing post-processing SPARQL CONSTRUCT additions");
+        performSparqlConstructs(settings.getSparqlConstructAdditionsDir() + "/post/", 
+                settings.getRDFService(), ADD);
         
-		Model anonModel = performSparqlConstructs(sparqlConstructDir, readModel, true);
+        log.info("performing post-processing SPARQL CONSTRUCT retractions");
+        performSparqlConstructs(settings.getSparqlConstructDeletionsDir() + "/post/", 
+                settings.getRDFService(), RETRACT);
         
-		if (anonModel == null) {
-			return;
-		}
-		
-		writeModel.enterCriticalSection(Lock.WRITE);
-		try {
-			JenaIngestUtils jiu = new JenaIngestUtils();
-			Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", writeModel);
-			Model actualAdditions = ModelFactory.createDefaultModel();
-			StmtIterator stmtIt = additions.listStatements();
-			
-			while (stmtIt.hasNext()) {
-				Statement stmt = stmtIt.nextStatement();
-				if (!writeModel.contains(stmt)) {
-					actualAdditions.add(stmt);
-				}
-			}
-			
-			writeModel.add(actualAdditions);
-			record.recordAdditions(actualAdditions);
-		} finally {
-			writeModel.leaveCriticalSection();
-		}	
-	}
-	
-	private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
-		
-		Model retractions = performSparqlConstructs(sparqlConstructDir, readModel, false);
-		
-		if (retractions == null) {
-			return;
-		}
-		
-		writeModel.enterCriticalSection(Lock.WRITE);
-		
-		try {
-			writeModel.remove(retractions);
-			record.recordRetractions(retractions);
-		} finally {
-			writeModel.leaveCriticalSection();
-		}
 
 	}
 	
+    private static final boolean ADD = true;
+    private static final boolean RETRACT = !ADD;
+	
     /**
      * Performs a set of arbitrary SPARQL CONSTRUCT queries on the 
      * data, for changes that cannot be expressed as simple property
      * or class additions, deletions, or renamings.
      * Blank nodes created by the queries are given random URIs.
      * @param sparqlConstructDir
-	 * @param aboxModel
+     * @param readModel
+     * @param writeModel
+     * @param add (add = true; retract = false)
      */
-	private Model performSparqlConstructs(String sparqlConstructDir, 
+    private void performSparqlConstructs(String sparqlConstructDir, 
-			                              OntModel readModel,
+            RDFService rdfService,
             boolean add)   throws IOException {
-		
+        Dataset dataset = new RDFServiceDataset(rdfService);
-		Model anonModel = ModelFactory.createDefaultModel();
         File sparqlConstructDirectory = new File(sparqlConstructDir);
-		
+        log.info("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
         if (!sparqlConstructDirectory.isDirectory()) {
-			logger.logError(this.getClass().getName() + 
+            String logMsg = this.getClass().getName() + 
                     "performSparqlConstructs() expected to find a directory " +
                     " at " + sparqlConstructDir + ". Unable to execute " +
-					" SPARQL CONSTRUCTS.");
+                    " SPARQL CONSTRUCTS.";
-			return null;
+            logger.logError(logMsg);
+            log.error(logMsg);
+            return;
         }
-		
+        List<File> sparqlFiles = Arrays.asList(sparqlConstructDirectory.listFiles());
-		File[] sparqlFiles = sparqlConstructDirectory.listFiles();
+        Collections.sort(sparqlFiles); // queries may depend on being run in a certain order
-		for (int i = 0; i < sparqlFiles.length; i ++) {
+        JenaIngestUtils jiu = new JenaIngestUtils();
-			File sparqlFile = sparqlFiles[i];			
+        for (File sparqlFile : sparqlFiles) {	
+            if(sparqlFile.isDirectory()) {
+                continue;
+            }
+            StringBuffer fileContents = new StringBuffer();
             try {
                 BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
-				StringBuffer fileContents = new StringBuffer();
                 String ln;
-				
                 while ( (ln = reader.readLine()) != null) {
                     fileContents.append(ln).append('\n');
                 }
-				
+            } catch (FileNotFoundException fnfe) {
+                String logMsg = "WARNING: performSparqlConstructs() could not find " +
+                        " SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.";
+                logger.log(logMsg);
+                log.info(logMsg);
+                continue;
+            }   
+            Model anonModel = ModelFactory.createDefaultModel();
             try {
-					log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFiles[i].getName());
+                log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
-					Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
-					readModel.enterCriticalSection(Lock.READ);
-					try {
-						QueryExecution qe = QueryExecutionFactory.create(q,	readModel);
-						long numBefore = anonModel.size();
-						qe.execConstruct(anonModel);
-						long numAfter = anonModel.size();
-                        long num = numAfter - numBefore;
                 
+                anonModel = RDFServiceUtils.parseModel(
+                        rdfService.sparqlConstructQuery(fileContents.toString(), 
+                                RDFService.ModelSerializationFormat.NTRIPLE), 
+                                ModelSerializationFormat.NTRIPLE);
+
+                long num = anonModel.size();
                 if (num > 0) {
-						   logger.log((add ? "Added " : "Removed ") + num + 
+                    String logMsg = (add ? "Added " : "Removed ") + num + 
                             " statement"  + ((num > 1) ? "s" : "") + 
-								   " using the SPARQL construct query from file " + sparqlFiles[i].getParentFile().getName() + "/" + sparqlFiles[i].getName());
+                            " using the SPARQL construct query from file " + 
-                        }
+                            sparqlFile.getParentFile().getName() +
-                        qe.close();
+                            "/" + sparqlFile.getName();
-					} finally {
+                    logger.log(logMsg);
-						readModel.leaveCriticalSection();
+                    log.info(logMsg);
                 }
+        
             } catch (Exception e) {
                 logger.logError(this.getClass().getName() + 
                         ".performSparqlConstructs() unable to execute " +
                         "query at " + sparqlFile + ". Error message is: " + e.getMessage());
-				}
+                log.error(e,e);
-			} catch (FileNotFoundException fnfe) {
-				logger.log("WARNING: performSparqlConstructs() could not find " +
-						   " SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.");
-			}	
             }
         
-        return anonModel;
+            if(!add) {
+                StmtIterator sit = anonModel.listStatements();
+                while (sit.hasNext()) {
+                    Statement stmt = sit.nextStatement();
+                    Iterator<String> graphIt = dataset.listNames();
+                    while(graphIt.hasNext()) {
+                        String graph = graphIt.next();
+                        if(!isUpdatableABoxGraph(graph)) {
+                            continue;
+                        }
+                        Model writeModel = dataset.getNamedModel(graph);
+                        if (writeModel.contains(stmt)) {
+                            writeModel.remove(stmt);
+                        }
+                    }
+                }            
+                record.recordRetractions(anonModel);
+                //log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs");
+            } else {
+                Model writeModel = dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL);
+                Model additions = jiu.renameBNodes(
+                        anonModel, settings.getDefaultNamespace() + "n", writeModel);
+                Model actualAdditions = ModelFactory.createDefaultModel();
+                StmtIterator stmtIt = additions.listStatements();      
+                while (stmtIt.hasNext()) {
+                    Statement stmt = stmtIt.nextStatement();
+                    if (!writeModel.contains(stmt)) {
+                        actualAdditions.add(stmt);
+                    }
+                }      
+                writeModel.add(actualAdditions);
+                //log.info("added " + actualAdditions.size() + " statements from SPARQL CONSTRUCTs");
+                record.recordAdditions(actualAdditions);
+            }
+            
+        }
     }
 	
 	
@@ -240,10 +254,8 @@ public class KnowledgeBaseUpdater {
 	private void updateABox(AtomicOntologyChangeLists changes) 
 			throws IOException {
 		
-		OntModel oldTBoxModel = settings.getOldTBoxModel();
+	
-		OntModel newTBoxModel = settings.getNewTBoxModel();
+		ABoxUpdater aboxUpdater = new ABoxUpdater(settings, logger, record);
-		OntModel ABoxModel = settings.getAssertionOntModelSelector().getABoxModel();
-		ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, ABoxModel,settings.getNewTBoxAnnotationsModel(), logger, record);
 		aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
 		aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
 	}
@@ -281,14 +293,18 @@ public class KnowledgeBaseUpdater {
 		rdfService.changeSetUpdate(removeChangeSet);	
 	}
 	
-	private void updateTBoxAnnotations() throws IOException {
+	private void updateTBoxAnnotations() {
-		
+		TBoxUpdater tboxUpdater = new TBoxUpdater(settings, logger, record);         
-		TBoxUpdater tboxUpdater = new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
+		try {
-		                                          settings.getNewTBoxAnnotationsModel(),
+		    tboxUpdater.modifyPropertyQualifications();
-                                                  settings.getAssertionOntModelSelector().getTBoxModel(), logger, record);
+		} catch (Exception e) {
-                                                  
+		    log.error("Unable to modify qualified property config file ", e);
+		}
+		try {
             tboxUpdater.updateDefaultAnnotationValues();
-        //tboxUpdater.updateAnnotationModel();
+		} catch (Exception e) {
+		    log.error("Unable to update default annotation values ", e);
+		}
 	}
 	
 	/**
@@ -296,7 +312,7 @@ public class KnowledgeBaseUpdater {
 	 * needs to be updated to conform to a new ontology version
 	 */
 	public boolean updateRequired(ServletContext servletContext) throws IOException {
-		boolean required = false;
+		boolean required = true;
 		
 		String sparqlQueryStr = loadSparqlQuery(settings.getAskUpdatedQueryFile());
 		if (sparqlQueryStr == null) {
@@ -338,7 +354,7 @@ public class KnowledgeBaseUpdater {
 		
 		File file = new File(filePath);	
 		if (!file.exists()) {
-			return null;
+			throw new RuntimeException("SPARQL file not found at " + filePath);
 		}
 		BufferedReader reader = new BufferedReader(new FileReader(file));
 		StringBuffer fileContents = new StringBuffer();
@@ -364,7 +380,9 @@ public class KnowledgeBaseUpdater {
 		}		
 	}
 	
-
+	public static boolean isUpdatableABoxGraph(String graphName) {
+	    return (!graphName.contains("tbox") && !graphName.contains("filegraph"));
+	}
 
 	/**
 	 * A class that allows to access two different ontology change lists,
@@ -390,11 +408,13 @@ public class KnowledgeBaseUpdater {
 			while(listItr.hasNext()) {
 				AtomicOntologyChange changeObj = listItr.next();
 				if (changeObj.getSourceURI() != null){
-			
+			        log.debug("triaging " + changeObj);
 					if (oldTboxModel.getOntProperty(changeObj.getSourceURI()) != null){
 						 atomicPropertyChanges.add(changeObj);
+						 log.debug("added to property changes");
 					} else if (oldTboxModel.getOntClass(changeObj.getSourceURI()) != null) {
 						 atomicClassChanges.add(changeObj);
+						 log.debug("added to class changes");
 					} else if ("Prop".equals(changeObj.getNotes())) {
 						 atomicPropertyChanges.add(changeObj);
 					} else if ("Class".equals(changeObj.getNotes())) {
@@ -429,5 +449,6 @@ public class KnowledgeBaseUpdater {
 		public List<AtomicOntologyChange> getAtomicPropertyChanges() {
 			return atomicPropertyChanges;
 		}		
+		
 	}	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyChangeParser.java

@@ -9,6 +9,8 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.skife.csv.CSVReader;
 import org.skife.csv.SimpleReader;
 
@@ -23,6 +25,8 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
 
 public class OntologyChangeParser {
 
+    private final Log log = LogFactory.getLog(OntologyChangeParser.class);
+    
 	private ChangeLogger logger;
 	
 	public OntologyChangeParser(ChangeLogger logger) {
@@ -85,6 +89,8 @@ public class OntologyChangeParser {
 				}
 				
 				
+			    log.debug(changeObj);
+				
 				changeObjects.add(changeObj);
 					
 			}

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/SimpleChangeRecord.java

@@ -26,6 +26,9 @@ public class SimpleChangeRecord implements ChangeRecord {
 	private File additionsFile;
 	private File retractionsFile;
 	
+	private int additionsCount = 0;
+	private int retractionsCount = 0;
+	
 	public SimpleChangeRecord(
 			String additionsFile, String retractionsFile) {
 		this.additionsFile = new File(additionsFile);
@@ -46,11 +49,12 @@ public class SimpleChangeRecord implements ChangeRecord {
 	
 	public void recordAdditions(Model incrementalAdditions) {
 		additionsModel.add(incrementalAdditions);
-	
+	    additionsCount += incrementalAdditions.size();
 	}
 
 	public void recordRetractions(Model incrementalRetractions) {
 		retractionsModel.add(incrementalRetractions);
+		retractionsCount += incrementalRetractions.size();
 	}
 	
 	private void write(Model model, File file) {
@@ -72,4 +76,8 @@ public class SimpleChangeRecord implements ChangeRecord {
 		}
 	}
 	
+	public boolean hasRecordedChanges() {
+	    return additionsCount > 0 || retractionsCount > 0;
+	}
+
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java

@@ -2,11 +2,22 @@
 
 package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.List;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -14,6 +25,7 @@ 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.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;
@@ -21,6 +33,8 @@ import com.hp.hpl.jena.vocabulary.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 /**  
  * Performs knowledge base updates to the tbox to align with a new ontology version
@@ -28,6 +42,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
  */ 
 public class TBoxUpdater {
 
+    private static final Log log = LogFactory.getLog(TBoxUpdater.class);
+
+    private UpdateSettings settings;
     private OntModel oldTboxAnnotationsModel;
     private OntModel newTboxAnnotationsModel;
     private OntModel siteModel;
@@ -53,19 +70,33 @@ public class TBoxUpdater {
      *                         and the retractions model.
      *                    
      */
-	public TBoxUpdater(OntModel oldTboxAnnotationsModel,
+    public TBoxUpdater(UpdateSettings settings,
-			           OntModel newTboxAnnotationsModel,
-			           OntModel siteModel,
             ChangeLogger logger,
             ChangeRecord record) {
-		
+        this.settings = settings;
-		this.oldTboxAnnotationsModel = oldTboxAnnotationsModel;
+        this.oldTboxAnnotationsModel = settings.getOldTBoxAnnotationsModel();
-		this.newTboxAnnotationsModel = newTboxAnnotationsModel;
+        this.newTboxAnnotationsModel = settings.getNewTBoxAnnotationsModel();
-		this.siteModel = siteModel;
+        this.siteModel = settings.getAssertionOntModelSelector().getTBoxModel();
         this.logger = logger;
         this.record = record;
     }
 
+    /**
+     * Update application ontology data for domain and range-qualified properties
+     * to use any applicable settings from obsolete subproperties
+     */
+    public void modifyPropertyQualifications() throws IOException {
+ 
+    }
+
+    private Model mergeConfigurations(Model oldConfig, Model newConfig) {
+        return null;
+    }
+    
+    public void updateDefaultAnnotationValues() throws IOException {
+        updateDefaultAnnotationValues(null);
+    }
+
     /**
      * 
      * Update a knowledge base to align with changes to vitro annotation property default 
@@ -91,7 +122,7 @@ public class TBoxUpdater {
      *  Note: as specified, this method for now assumes that no new vitro annotation
      *  properties have been introduced. This should be updated for future versions.
      */
-	public void updateDefaultAnnotationValues() throws IOException {
+    public void updateDefaultAnnotationValues(String subjectURI) throws IOException {
 
         siteModel.enterCriticalSection(Lock.WRITE);
 
@@ -104,7 +135,14 @@ public class TBoxUpdater {
             //  if the default has changed in the new version of the ontology AND if 
             //  the site hasn't overidden the previous default in their knowledge base.
 
-		  StmtIterator iter = oldTboxAnnotationsModel.listStatements();
+            if(oldTboxAnnotationsModel == null) {
+                logger.log("oldTboxAnnotationModel is null; aborting update of annotation values");
+                return;
+            }
+            
+            Resource subj = (subjectURI == null) ? null : ResourceFactory.createResource(subjectURI);
+
+            StmtIterator iter = oldTboxAnnotationsModel.listStatements(subj, null, (RDFNode) null);
 
             while (iter.hasNext()) {
 
@@ -415,4 +453,122 @@ public void removeObsoleteAnnotations() throws IOException {
         }
     }
     
+    public void renameProperty(AtomicOntologyChange changeObj) throws IOException {
+        Dataset dataset = new RDFServiceDataset(settings.getRDFService());
+        Model userAnnotationsModel = dataset.getNamedModel(
+                JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
+        if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) {
+            mergePropertyAnnotationsToPropertyConfig(changeObj, userAnnotationsModel);
+        }        
+        Resource renamedProperty = userAnnotationsModel.getResource(changeObj.getSourceURI());
+        userAnnotationsModel.removeAll(renamedProperty, null, (RDFNode) null);
+        userAnnotationsModel.removeAll(null, null, renamedProperty);
+    }
+    
+    private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj,
+            Model userAnnotationsModel) throws IOException {
+        String contextURI = VitroVocabulary.PROPERTY_CONFIG_DATA + changeObj.getNotes().substring(3);
+        String oldPropertyURI = changeObj.getSourceURI();
+        
+        Model oldAnnotationsModel = settings.getOldTBoxAnnotationsModel();
+        
+        String propertyAnnotationsQuery = 
+                "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                "CONSTRUCT { \n" +
+                "    <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
+                "    <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
+                "    <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
+                "    <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
+                "    <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                "    <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
+                "} WHERE { \n" +
+                "    { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
+                "    UNION { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
+                "} \n" ; 
+        
+        Model userChangesModel = construct(
+                propertyAnnotationsQuery, userAnnotationsModel).difference(
+                        construct(propertyAnnotationsQuery, oldAnnotationsModel));
+        
+        String addQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                          "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                          "CONSTRUCT { \n" +
+                          "    ?configuration config:propertyGroup ?group . \n" +
+                          "    ?configuration config:displayName ?label . \n" +
+                          "    ?configuration vitro:displayRankAnnot ?displayRank . \n" +
+                          "    ?configuration vitro:customEntryFormAnnot ?customForm . \n" +
+                          "    ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                          "    ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +                              
+                          "} WHERE { \n" +
+                          "    <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
+                          "} \n" ;
+        
+        String retractQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                "CONSTRUCT { \n" +
+                "    <" + oldPropertyURI + "> config:propertyGroup ?rgroup . \n" +
+                "    ?configuration config:displayName ?rlabel . \n" +
+                "    ?configuration vitro:displayRankAnnot ?rdisplayRank . \n" +
+                "    ?configuration vitro:customEntryFormAnnot ?rcustomForm . \n" +
+                "    ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel . \n" +
+                "    ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?rupdateLevel . \n " +                              
+                "} WHERE { \n" +
+                "    <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
+                "               ?configuration config:propertyGroup ?rgroup } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
+                "               ?configuration config:displayName ?rlabel } \n " +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
+                "               ?configuration vitro:displayRantAnnot ?rdisplayRank } \n " +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
+                "               ?configuration vitro:customEntryFormAnnot ?rcustomForm } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                "               ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
+                "               ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } " +
+                "} \n" ;
+        
+        Model configModel = ModelFactory.createDefaultModel();
+        String configFileName = settings.getQualifiedPropertyConfigFile();
+        File file = new File(configFileName);
+        FileInputStream fis = new FileInputStream(file);
+        configModel.read(fis, null, "N3");
+
+        Model union = ModelFactory.createUnion(configModel, 
+                userChangesModel);
+
+        Model additions = construct(addQuery, union);
+        Model retractions = construct(retractQuery, union);
+        
+        if (additions.size() > 0 || retractions.size() > 0) {
+            configModel.remove(retractions);
+            log.info("Removing " + retractions.size() + " statements from " + contextURI);
+            configModel.add(additions);
+            log.info("Adding " + additions.size() + " statements from " + contextURI);
+            FileOutputStream fos = new FileOutputStream(file);
+            configModel.write(fos, "N3");
+        }
+    }
+    
+    private Model construct(String queryStr, Model model) {    
+        Query query = QueryFactory.create(queryStr);
+        QueryExecution qe = QueryExecutionFactory.create(query, model);
+        try {
+            return qe.execConstruct();
+        } finally {
+            qe.close();
+        }
+    }
+
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/UpdateSettings.java

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 
 public class UpdateSettings {
 
@@ -20,6 +21,7 @@ public class UpdateSettings {
 	private String errorLogFile;
 	private String addedDataFile;
 	private String removedDataFile;
+	private String qualifiedPropertyConfigFile;
 	private String defaultNamespace;
 	private OntModelSelector assertionOntModelSelector;
 	private OntModelSelector inferenceOntModelSelector;
@@ -37,6 +39,8 @@ public class UpdateSettings {
 	private OntModel newDisplayModelFromFile;
 	private OntModel loadedAtStartupDisplayModel;
 	private OntModel oldDisplayModelVivoListViewConfig;
+	private RDFService rdfService;
+	
 	public String getDataDir() {
 		return dataDir;
 	}
@@ -118,6 +122,12 @@ public class UpdateSettings {
 	public void setRemovedDataFile(String removedDataFile) {
 		this.removedDataFile = removedDataFile;
 	}
+	public String getQualifiedPropertyConfigFile() {
+	    return qualifiedPropertyConfigFile;
+	}
+	public void setQualifiedPropertyConfigFile(String qualifiedPropertyConfigFile) {
+	    this.qualifiedPropertyConfigFile = qualifiedPropertyConfigFile;
+	}
  	public String getDefaultNamespace() {
 		return defaultNamespace;
 	}
@@ -223,6 +233,13 @@ public class UpdateSettings {
 		return this.oldDisplayModelVivoListViewConfig;
 	}
 	
+	public RDFService getRDFService() {
+	    return this.rdfService;
+	}
+	
+	public void setRDFService(RDFService rdfService) {
+	    this.rdfService = rdfService;
+	}
 	
 	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java

@@ -6,13 +6,16 @@ import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
 import java.util.ArrayList;
-import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
+import java.util.concurrent.ConcurrentLinkedQueue;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.graph.Node;
 import com.hp.hpl.jena.graph.Triple;
 import com.hp.hpl.jena.query.DataSource;
 import com.hp.hpl.jena.query.Dataset;
@@ -21,11 +24,9 @@ import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.QueryParseException;
 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.query.Syntax;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.RDFNode;
@@ -129,6 +130,7 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
                                 Resource s2 = (Resource) n;
                                 // now run yet another describe query
                                 String smallerTree = makeDescribe(s2);
+                                log.debug(smallerTree);
                                 Query smallerTreeQuery = QueryFactory.create(smallerTree);
                                 QueryExecution qe3 = QueryExecutionFactory.create(
                                         smallerTreeQuery, tree);
@@ -172,13 +174,17 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
         
         StringBuffer queryBuff = new StringBuffer();
         queryBuff.append("CONSTRUCT { \n");
-        addStatementPatterns(stmtIt, queryBuff, !WHERE_CLAUSE);
+        List<Statement> stmts = stmtIt.toList();
+        stmts = sort(stmts);
+        addStatementPatterns(stmts, queryBuff, !WHERE_CLAUSE);
         queryBuff.append("} WHERE { \n");
         if (graphURI != null) {
             queryBuff.append("    GRAPH <" + graphURI + "> { \n");
         }
         stmtIt = model.listStatements();
-        addStatementPatterns(stmtIt, queryBuff, WHERE_CLAUSE);
+        stmts = stmtIt.toList();
+        stmts = sort(stmts);
+        addStatementPatterns(stmts, queryBuff, WHERE_CLAUSE);
         if (graphURI != null) {
             queryBuff.append("    } \n");
         }
@@ -208,11 +214,61 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
         }       
     }
     
+    private List<Statement> sort(List<Statement> stmts) {
+        List<Statement> output = new ArrayList<Statement>();
+        int originalSize = stmts.size();
+        List <Statement> remaining = stmts;
+        ConcurrentLinkedQueue<Resource> subjQueue = new ConcurrentLinkedQueue<Resource>();
+        for(Statement stmt : remaining) {
+            if(stmt.getSubject().isURIResource()) {
+                subjQueue.add(stmt.getSubject());
+                break;
+            }
+        }
+        if (subjQueue.isEmpty()) {
+            throw new RuntimeException("No named subject in statement patterns");
+        }
+        while(remaining.size() > 0) {
+            if(subjQueue.isEmpty()) {
+                subjQueue.add(remaining.get(0).getSubject());
+            }
+            while(!subjQueue.isEmpty()) {
+                Resource subj = subjQueue.poll();
+                List<Statement> temp = new ArrayList<Statement>();
+                for (Statement stmt : remaining) {
+                    if(stmt.getSubject().equals(subj)) {
+                        output.add(stmt);
+                        if (stmt.getObject().isResource()) {
+                            subjQueue.add((Resource) stmt.getObject()); 
+                        }
+                    } else {
+                        temp.add(stmt);
+                    }
+                }
+                remaining = temp;
+            }
+        }
+        if(output.size() != originalSize) {
+            throw new RuntimeException("original list size was " + originalSize + 
+                    " but sorted size is " + output.size());      
+        }
+        return output;
+    }
+    
+    private String getHexString(Node node) {
+        String label = node.getBlankNodeLabel().replaceAll("\\W", "").toUpperCase();
+        if (label.length() > 7) {
+            return label.substring(label.length() - 7);
+        } else {
+            return label;
+        }
+    }
+    
     private static final boolean WHERE_CLAUSE = true;
     
-    private void addStatementPatterns(StmtIterator stmtIt, StringBuffer patternBuff, boolean whereClause) {
+    private void addStatementPatterns(List<Statement> stmts, StringBuffer patternBuff, boolean whereClause) {
-        while(stmtIt.hasNext()) {
+        for(Statement stmt : stmts) {
-            Triple t = stmtIt.next().asTriple();
+            Triple t = stmt.asTriple();
             patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
             patternBuff.append(" ");
             patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java

@@ -9,6 +9,7 @@ import java.io.StringWriter;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.concurrent.ConcurrentLinkedQueue;
 
 import org.apache.commons.httpclient.HttpClient;
 import org.apache.commons.httpclient.MultiThreadedHttpConnectionManager;
@@ -715,7 +716,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
         if (graphURI != null) {
             queryBuff.append("    GRAPH <" + graphURI + "> { \n");
         }
-        addStatementPatterns(stmtIt, queryBuff, !WHERE_CLAUSE);
+        List<Statement> stmts = stmtIt.toList();
+        sort(stmts);
+        addStatementPatterns(stmts, queryBuff, !WHERE_CLAUSE);
         if (graphURI != null) {
             queryBuff.append("    } \n");
         }
@@ -724,7 +727,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
             queryBuff.append("    GRAPH <" + graphURI + "> { \n");
         }
         stmtIt = model.listStatements();
-        addStatementPatterns(stmtIt, queryBuff, WHERE_CLAUSE);
+        stmts = stmtIt.toList();
+        sort(stmts);
+        addStatementPatterns(stmts, queryBuff, WHERE_CLAUSE);
         if (graphURI != null) {
             queryBuff.append("    } \n");
         }
@@ -736,11 +741,53 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
         executeUpdate(queryBuff.toString());
     }
     
+    private List<Statement> sort(List<Statement> stmts) {
+        List<Statement> output = new ArrayList<Statement>();
+        int originalSize = stmts.size();
+        List <Statement> remaining = stmts;
+        ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource> subjQueue = 
+                new ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource>();
+        for(Statement stmt : remaining) {
+            if(stmt.getSubject().isURIResource()) {
+                subjQueue.add(stmt.getSubject());
+                break;
+            }
+        }
+        if (subjQueue.isEmpty()) {
+            throw new RuntimeException("No named subject in statement patterns");
+        }
+        while(remaining.size() > 0) {
+            if(subjQueue.isEmpty()) {
+                subjQueue.add(remaining.get(0).getSubject());
+            }
+            while(!subjQueue.isEmpty()) {
+                com.hp.hpl.jena.rdf.model.Resource subj = subjQueue.poll();
+                List<Statement> temp = new ArrayList<Statement>();
+                for (Statement stmt : remaining) {
+                    if(stmt.getSubject().equals(subj)) {
+                        output.add(stmt);
+                        if (stmt.getObject().isResource()) {
+                            subjQueue.add((com.hp.hpl.jena.rdf.model.Resource) stmt.getObject()); 
+                        }
+                    } else {
+                        temp.add(stmt);
+                    }
+                }
+                remaining = temp;
+            }
+        }
+        if(output.size() != originalSize) {
+            throw new RuntimeException("original list size was " + originalSize + 
+                    " but sorted size is " + output.size());      
+        }
+        return output;
+    }
+    
     private static final boolean WHERE_CLAUSE = true;
     
-    private void addStatementPatterns(StmtIterator stmtIt, StringBuffer patternBuff, boolean whereClause) {
+    private void addStatementPatterns(List<Statement> stmts, StringBuffer patternBuff, boolean whereClause) {
-        while(stmtIt.hasNext()) {
+        for(Statement stmt : stmts) {
-            Triple t = stmtIt.next().asTriple();
+            Triple t = stmt.asTriple();
             patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
             patternBuff.append(" ");
             patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java

@@ -251,19 +251,25 @@ public class SimpleReasoner extends StatementListener {
 				    return;
 				}
 			
-				OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
+				OntClass subject, object;
+				tboxModel.enterCriticalSection(Lock.READ);
+				try {
+    				subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
     				if (subject == null) {
     					log.debug("didn't find subject class in the tbox: " 
                                   + (stmt.getSubject()).getURI());
     					return;
     				}
     				
-				OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); 
+    				object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); 
     				if (object == null) {
     					log.debug("didn't find object class in the tbox: " 
                                   + ((Resource)stmt.getObject()).getURI());
     					return;
     				}
+				} finally {
+				    tboxModel.leaveCriticalSection();
+				}
 				
 				if (stmt.getPredicate().equals(RDFS.subClassOf)) {
                     if( add ){
@@ -1672,6 +1678,10 @@ public class SimpleReasoner extends StatementListener {
                                             typeURIs = getRemainingAssertedTypeURIs(stmt.getSubject());
                                         }
                                         removedABoxTypeAssertion(stmt, inferenceModel, typeURIs);
+                                    } else if (doSameAs && stmt.getPredicate().equals(OWL.sameAs)) {
+                                        removedABoxSameAsAssertion(stmt, inferenceModel);   
+                                    } else {
+                                        removedABoxAssertion(stmt, inferenceModel);
                                     }
                                     doPlugins(ModelUpdate.Operation.RETRACT,stmt);
                                 } catch (NullPointerException npe) {

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

@@ -1,85 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.servlet.setup;
-
-import java.io.InputStream;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Set;
-
-import javax.servlet.ServletContextEvent;
-import javax.servlet.ServletContextListener;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.assembler.Assembler;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-import com.hp.hpl.jena.util.iterator.ExtendedIterator;
-import com.hp.hpl.jena.vocabulary.RDF;
-
-import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
-
-/**
- * This is the beginning of a more sane and flexible model management system,
- * especially necessary for DataStaR.
- * Don't use it yet; it's going to change.
- * (That part is still insane, I know.)
- * @author bjl23
- */
-public class AssembleModelsSetup implements ServletContextListener {
-
-	private static final Log log = LogFactory.getLog(AssembleModelsSetup.class);
-	
-	private List<Model> assembledModels = new LinkedList<Model>();
-	
-	private String ASSEMBLERS_DIR_PATH = "/WEB-INF/assemblers/";
-	private Resource ASSEMBLER_OBJECT = ResourceFactory.createProperty("http://jena.hpl.hp.com/2005/11/Assembler#Object");
-	private String SYNTAX = "N3";
-	
-	public void contextInitialized(ServletContextEvent sce) {
-		OntModel jenaOntModel = ModelAccess.on(sce.getServletContext()).getBaseOntModel();
-		// read assemblers out of assemblers directory
-		Set pathSet = sce.getServletContext().getResourcePaths(ASSEMBLERS_DIR_PATH);
-		for (String path : (Set<String>)pathSet) {
-			InputStream assemblerInputStream = sce.getServletContext().getResourceAsStream(path);
-			Model assemblerModel = ModelFactory.createDefaultModel();
-			try {
-				assemblerModel.read(assemblerInputStream, null, SYNTAX);
-				ExtendedIterator assemblerIt = assemblerModel.listResourcesWithProperty(RDF.type,ASSEMBLER_OBJECT);
-				while (assemblerIt.hasNext()) {
-					Resource assemblerObj = (Resource) assemblerIt.next();
-					Model assembledModel = Assembler.general.openModel(assemblerObj);
-					/* special stuff here */
-					Model memModel = ModelFactory.createDefaultModel();
-					memModel.add(assembledModel);
-					memModel.register(new ModelSynchronizer(assembledModel));
-					/* end special stuff */
-					if (assembledModel != null) {
-						jenaOntModel.addSubModel(memModel);
-					}
-				}
-				if (assemblerIt != null) {
-					assemblerIt.close();
-				}
-			} catch (Exception e) {
-				log.error("Unable to use assembler at "+path);
-			}
-		}
-		System.out.println("ContextListener AssembleModelsSetup done");
-	}
-	
-	public void contextDestroyed(ServletContextEvent sce) {
-		for (Model model : assembledModels) {
-			if (model != null) {
-				model.close();
-			}
-		}
-	}
-
-}

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

@@ -56,7 +56,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
             OntModelSelector inferencesOms = ModelAccess.on(ctx).getInferenceOntModelSelector();
             OntModelSelector unionOms = ModelAccess.on(ctx).getUnionOntModelSelector();
 
-			WebappDaoFactoryJena wadf = (WebappDaoFactoryJena) ModelAccess.on(ctx).getWebappDaoFactory();
+			WebappDaoFactory wadf = ModelAccess.on(ctx).getWebappDaoFactory();
             
             if (!assertionsOms.getTBoxModel().getProfile().NAMESPACE().equals(OWL.NAMESPACE.getNameSpace())) {        
                 log.error("Not connecting Pellet reasoner - the TBox assertions model is not an OWL model");
@@ -75,28 +75,24 @@ public class SimpleReasonerSetup implements ServletContextListener {
             sce.getServletContext().setAttribute("pelletListener",pelletListener);
             sce.getServletContext().setAttribute("pelletOntModel", pelletListener.getPelletModel());
             
-            if (wadf != null) {
+            if (wadf instanceof WebappDaoFactoryJena) {
-                wadf.setPelletListener(pelletListener);
+                ((WebappDaoFactoryJena) wadf).setPelletListener(pelletListener);
             }
             
             log.info("Pellet reasoner connected for the TBox");
      
             // set up simple reasoning for the ABox
                                 
-            DataSource bds = JenaDataSourceSetupBase
-                                    .getApplicationDataSource(ctx);
-            String dbType = ConfigurationProperties.getBean(ctx).getProperty( // database type
-                    "VitroConnection.DataSource.dbtype","MySQL");
-            
             RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService();            
             Dataset dataset = new RDFServiceDataset(rdfService);
             
             Model rebuildModel = dataset.getNamedModel(JENA_INF_MODEL_REBUILD); 
             Model scratchModel = dataset.getNamedModel(JENA_INF_MODEL_SCRATCHPAD);
+            Model inferenceModel = dataset.getNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL);
 
             // the simple reasoner will register itself as a listener to the ABox assertions
             SimpleReasoner simpleReasoner = new SimpleReasoner(
-                    unionOms.getTBoxModel(), rdfService, inferencesOms.getABoxModel(), rebuildModel, scratchModel);
+                    unionOms.getTBoxModel(), rdfService, inferenceModel, rebuildModel, scratchModel);
             sce.getServletContext().setAttribute(SimpleReasoner.class.getName(),simpleReasoner);
             
             StartupStatus ss = StartupStatus.getBean(ctx);
@@ -114,19 +110,6 @@ public class SimpleReasonerSetup implements ServletContextListener {
             }
             simpleReasoner.setPluginList(pluginList);
             
-            
-            if (isRecomputeRequired(sce.getServletContext())) {   
-                log.info("ABox inference recompute required.");
-                waitForTBoxReasoning(pelletListener);  
-                if (JenaDataSourceSetupBase.isFirstStartup()) {
-                    simpleReasoner.recompute();
-                } else {
-                    log.info("starting ABox inference recompute in a separate thread.");
-                    new Thread(new ABoxRecomputer(simpleReasoner),"ABoxRecomputer").start();
-                }
-                
-            } 
-
             SimpleReasonerTBoxListener simpleReasonerTBoxListener = new SimpleReasonerTBoxListener(simpleReasoner);
             sce.getServletContext().setAttribute(SimpleReasonerTBoxListener.class.getName(),simpleReasonerTBoxListener);
             assertionsOms.getTBoxModel().register(simpleReasonerTBoxListener);
@@ -139,10 +122,15 @@ public class SimpleReasonerSetup implements ServletContextListener {
         }        
     }
     
-    private void waitForTBoxReasoning(PelletListener pelletListener) 
+    public static void waitForTBoxReasoning(ServletContextEvent sce) 
         throws InterruptedException {
+        PelletListener pelletListener = (PelletListener) sce.getServletContext().getAttribute("pelletListener");
+        if (pelletListener == null) {
+            return ;
+        }
         int sleeps = 0;
-      while (sleeps < 1000 && pelletListener.isReasoning()) {
+        // sleep at least once to make sure the TBox reasoning gets started
+        while ((0 == sleeps) || ((sleeps < 1000) && pelletListener.isReasoning())) {
             if ((sleeps % 10) == 0) { // print message at 10 second intervals
                 log.info("Waiting for initial TBox reasoning to complete");
             }
@@ -196,7 +184,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
         ctx.setAttribute(RECOMPUTE_REQUIRED_ATTR, true);
     }
     
-    private static boolean isRecomputeRequired(ServletContext ctx) {
+    public static boolean isRecomputeRequired(ServletContext ctx) {
         return (ctx.getAttribute(RECOMPUTE_REQUIRED_ATTR) != null);
     }
   
@@ -211,19 +199,6 @@ public class SimpleReasonerSetup implements ServletContextListener {
         return (ctx.getAttribute(MSTCOMPUTE_REQUIRED_ATTR) != null);
     }
         
-    private class ABoxRecomputer implements Runnable {
-        
-        private SimpleReasoner simpleReasoner;
-        
-        public ABoxRecomputer(SimpleReasoner simpleReasoner) {
-            this.simpleReasoner = simpleReasoner;
-        }
-        
-        public void run() {
-            simpleReasoner.recompute();
-        }
-    }
-        
     /**
      * Read the names of the plugin classes classes.
      * 

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

@@ -41,6 +41,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.UpdateSettings;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
+import edu.cornell.mannlib.vitro.webapp.reasoner.ABoxRecomputer;
+import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 /**
@@ -54,10 +57,11 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 	private final static Log log = LogFactory.getLog(UpdateKnowledgeBase.class);
 	
 	private static final String DATA_DIR = "/WEB-INF/ontologies/update/";
+	private static final String DIFF_FILE = DATA_DIR + "diff.tab.txt";
+	private static final String ASK_QUERY_FILE = DATA_DIR + "askUpdated.sparql";
+	private static final String SUCCESS_ASSERTIONS_FILE = DATA_DIR + "success.n3";
 	private static final String OLD_TBOX_MODEL_DIR = DATA_DIR + "oldVersion/";
-	private static final String NEW_TBOX_MODEL_DIR = "/WEB-INF/filegraph/tbox/";
 	private static final String OLD_TBOX_ANNOTATIONS_DIR = DATA_DIR + "oldAnnotations/";
-	private static final String NEW_TBOX_ANNOTATIONS_DIR = "/WEB-INF/ontologies/user/tbox/";
 	//For display model migration
 	private static final String OLD_DISPLAYMODEL_TBOX_PATH = DATA_DIR + "oldDisplayModel/displayTBOX.n3";
 	private static final String NEW_DISPLAYMODEL_TBOX_PATH = "/WEB-INF/ontologies/app/menuload/displayTBOX.n3";
@@ -72,26 +76,36 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		ServletContext ctx = sce.getServletContext();
 		StartupStatus ss = StartupStatus.getBean(ctx);
 
+        boolean migrationChangesMade = false;
+		
 		try {
 			UpdateSettings settings = new UpdateSettings();
 			putReportingPathsIntoSettings(ctx, settings);
+			putNonReportingPathsIntoSettings(ctx, settings);
+
+            SimpleReasonerSetup.waitForTBoxReasoning(sce); 
 			
 			WebappDaoFactory wadf = ModelAccess.on(ctx).getWebappDaoFactory();
 			settings.setDefaultNamespace(wadf.getDefaultNamespace());
 			settings.setAssertionOntModelSelector(ModelAccess.on(ctx).getBaseOntModelSelector());
 			settings.setInferenceOntModelSelector(ModelAccess.on(ctx).getInferenceOntModelSelector());
 			settings.setUnionOntModelSelector(ModelAccess.on(ctx).getUnionOntModelSelector());
-			boolean tryMigrateDisplay = true;
+			
-			try {
+		    ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
+		    Path homeDir = Paths.get(props.getProperty("vitro.home"));
 			settings.setDisplayModel(ModelAccess.on(ctx).getDisplayModel());
 			OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
 			settings.setOldTBoxModel(oldTBoxModel);
-				OntModel newTBoxModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_MODEL_DIR));
+			OntModel newTBoxModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "filegraph").toString());
 			settings.setNewTBoxModel(newTBoxModel);
 			OntModel oldTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_ANNOTATIONS_DIR));
 			settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
-				OntModel newTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_ANNOTATIONS_DIR));
+			OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "firsttime").toString());
 			settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
+			settings.setRDFService(RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService());
+
+			boolean tryMigrateDisplay = true;
+			try {
 			    //Display model tbox and display metadata 
 			    //old display model tbox model
 			    OntModel oldDisplayModelTboxModel = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_TBOX_PATH));
@@ -112,18 +126,22 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			    settings.setLoadedAtStartupDisplayModel(loadedAtStartupFiles);
 			    OntModel oldDisplayModelVivoListView = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_VIVOLISTVIEW_PATH));
 			    settings.setVivoListViewConfigDisplayModel(oldDisplayModelVivoListView);
+			} catch (ModelFileNotFoundException e) {
+			    // expected if no display migration was intended
+			    tryMigrateDisplay = false;
 			} catch (Exception e) {
-				log.info("unable to read display model migration files, display model not migrated. " + e.getMessage());
+			    log.info("Unable to read display model migration files. ", e);
 			    tryMigrateDisplay = false;
 			}
 
-			try {		
+
 			KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
+			boolean requiredUpdate = ontologyUpdater.updateRequired(ctx);
 
 			try {
-				  if (ontologyUpdater.updateRequired(ctx)) {
 			    ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
-					  ontologyUpdater.update(ctx);
+			    log.info("Data migration required");
+			    migrationChangesMade = ontologyUpdater.update(ctx);
 			    if (tryMigrateDisplay) {
 			        try {
 			            migrateDisplayModel(settings);
@@ -132,16 +150,60 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			            log.warn("unable to successfully update display model: " + e.getMessage());
 			        }
 			    }
-				  }
+			    // reload the display model since the TBoxUpdater may have 
+			    // modified it
+			    new ApplicationModelSetup().contextInitialized(sce);				  
 			} catch (Exception ioe) {
 			    ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
 			}	
+
+		    SimpleReasoner simpleReasoner = (SimpleReasoner) sce.getServletContext()
+		            .getAttribute(SimpleReasoner.class.getName());
+		    if (simpleReasoner != null) {
+		        if ( (requiredUpdate && migrationChangesMade) 
+		                || JenaDataSourceSetupBase.isFirstStartup()) {
+		            log.info("ABox inference recompute required.");
+		            simpleReasoner.recompute();
+		        } else if (SimpleReasonerSetup.isRecomputeRequired(sce.getServletContext()) || migrationChangesMade) {
+		            log.info("starting ABox inference recompute in a separate thread.");
+		            new Thread(
+		                    new ABoxRecomputer(
+		                            simpleReasoner),"ABoxRecomputer").start();
+		        }
+		    }			
+			
 		} catch (Throwable t){
 		    ss.fatal(this, "Exception updating knowledge base for ontology changes: ", t);
 		}
-		} catch (Throwable t) {
+        
-			ss.fatal(this, "Exception updating knowledge base for ontology changes: ", t);
+
+		
 	}	
+
+	private class ABoxRecomputer implements Runnable {
+
+	    private SimpleReasoner simpleReasoner;
+
+	    public ABoxRecomputer(SimpleReasoner simpleReasoner) {
+	        this.simpleReasoner = simpleReasoner;
+	    }
+
+	    public void run() {
+	        simpleReasoner.recompute();
+	    }
+	}
+
+	
+	/**
+	 * Set the paths for the files that specify how to perform the update
+	 */
+	private void putNonReportingPathsIntoSettings(ServletContext ctx, UpdateSettings settings) {
+        settings.setAskUpdatedQueryFile(ctx.getRealPath(ASK_QUERY_FILE));
+        settings.setDiffFile(ctx.getRealPath(DIFF_FILE));
+        settings.setSparqlConstructAdditionsDir(ctx.getRealPath(DATA_DIR + "sparqlConstructs/additions"));
+        settings.setSparqlConstructDeletionsDir(ctx.getRealPath(DATA_DIR + "sparqlConstructs/deletions"));
+        settings.setSuccessAssertionsFile(ctx.getRealPath(SUCCESS_ASSERTIONS_FILE));
+        settings.setSuccessRDFFormat("N3");
 	}
 	
 	/**
@@ -156,14 +218,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		settings.setDataDir(dataDir.toString());
 		StartupStatus.getBean(ctx).info(this, "Updating knowledge base: reports are in '" + dataDir + "'");
 
-		settings.setAskUpdatedQueryFile(dataDir.resolve("askUpdated.sparql").toString());
-		settings.setDiffFile(dataDir.resolve("diff.tab.txt").toString());
-		settings.setSuccessAssertionsFile(dataDir.resolve("success.n3").toString());
-		settings.setSuccessRDFFormat("N3");
-
-		settings.setSparqlConstructAdditionsDir(createDirectory(dataDir, "sparqlConstructs", "additions").toString());
-		settings.setSparqlConstructDeletionsDir(createDirectory(dataDir, "sparqlConstructs", "deletions").toString());
-		
 		Path changedDir = createDirectory(dataDir, "changedData");
 		settings.setAddedDataFile(changedDir.resolve("addedData.n3").toString());
 		settings.setRemovedDataFile(changedDir.resolve("removedData.n3").toString());
@@ -171,6 +225,17 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		Path logDir = createDirectory(dataDir, "logs");
 		settings.setLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate", "log")).toString());
 		settings.setErrorLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate.error", "log")).toString());
+		
+		Path qualifiedPropertyConfigFile = getFilePath(homeDir, "rdf", "display", "everytime", "PropertyConfig.n3");
+		settings.setQualifiedPropertyConfigFile(qualifiedPropertyConfigFile.toString());
+	}
+
+	private Path getFilePath(Path parent, String... children) throws IOException {
+        Path path = parent;
+        for (String child : children) {
+            path = path.resolve(child);
+        }
+        return path;	    
 	}
 	
 	private Path createDirectory(Path parent, String... children) throws IOException {

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/ApplicationConfigurationOntologyUtils.java

@@ -10,100 +10,119 @@ import javax.servlet.ServletContext;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
-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.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess.ModelID;
+import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
 
 public class ApplicationConfigurationOntologyUtils {
 
     private static final Log log = LogFactory.getLog(ApplicationConfigurationOntologyUtils.class);
     
-    public static List<ObjectProperty> getAdditionalFauxSubpropertiesForList(List<ObjectProperty> propList, VitroRequest vreq) {
+    public static List<ObjectProperty> getAdditionalFauxSubpropertiesForList(List<ObjectProperty> propList, Individual subject, VitroRequest vreq) {
         ServletContext ctx = vreq.getSession().getServletContext();
 		Model displayModel = ModelAccess.on(ctx).getDisplayModel();
         Model tboxModel = ModelAccess.on(ctx).getOntModel(ModelID.UNION_TBOX);
-        return getAdditionalFauxSubpropertiesForList(propList, displayModel, tboxModel);
+        return getAdditionalFauxSubpropertiesForList(propList, subject, displayModel, tboxModel);
     }
     
+    public static List<ObjectProperty> getAdditionalFauxSubproperties(ObjectProperty prop, 
+                                                                         Individual subject,
+                                                                         Model tboxModel,
+                                                                         Model union) {
 
-    
-    public static List<ObjectProperty> getAdditionalFauxSubpropertiesForList(List<ObjectProperty> propList, 
-                                                                         Model displayModel, 
-                                                                         Model tboxModel) {
         List<ObjectProperty> additionalProps = new ArrayList<ObjectProperty>();
-        Model union = ModelFactory.createUnion(displayModel, tboxModel);
+        String queryStr = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
-        String propQuery = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" +
                 "PREFIX config: <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#> \n" +
                 "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" +
-                "SELECT ?range ?label ?group ?customForm WHERE { \n" +
+                "SELECT DISTINCT ?range ?domain ?property WHERE { \n" +
-        		"    ?p rdfs:subPropertyOf ?property . \n" +
+                "    ?context config:configContextFor ?property . \n" +
-                "    ?context config:configContextFor ?p . \n" +
                 "    ?context config:qualifiedBy ?range . \n" +
                 "    ?context config:hasConfiguration ?configuration . \n" +
-        		"    OPTIONAL { ?configuration config:propertyGroup ?group } \n" +
+                "    ?configuration a config:ObjectPropertyDisplayConfig . \n" +
-                "    OPTIONAL { ?configuration config:displayName ?label } \n" +
+                "    OPTIONAL { ?context config:qualifiedByDomain ?domain } \n" +
-                "    OPTIONAL { ?configuration vitro:customEntryFormAnnot ?customForm } \n" +
                 "}"; 
       
-        for (ObjectProperty op : propList) {
+        if(prop != null) {
-            log.debug("Checking " + op.getURI() + " for additional properties");
+            log.debug("Checking " + prop.getURI() + " for additional properties");
-            String queryStr = propQuery.replaceAll("\\?property", "<" + op.getURI() + ">");
+            queryStr = queryStr.replaceAll("For \\?property", "For <" + prop.getURI() + ">");
+        }
         log.debug(queryStr);
         Query q = QueryFactory.create(queryStr);
         QueryExecution qe = QueryExecutionFactory.create(q, union);
+        WebappDaoFactory wadf = new WebappDaoFactoryJena(
+                ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, union));
+        ObjectPropertyDao opDao = wadf.getObjectPropertyDao();
         try {
             ResultSet rs = qe.execSelect();
             while (rs.hasNext()) {
-                    ObjectProperty newProp = new ObjectProperty();
-                    newProp.setURI(op.getURI());
                 QuerySolution qsoln = rs.nextSolution();
                 log.debug(qsoln);
-                    Resource rangeRes = qsoln.getResource("range");
+                String opURI = (prop != null) ? prop.getURI() : qsoln.getResource(
-                    if (rangeRes != null) {
+                        "property").getURI();
-                        newProp.setRangeVClassURI(rangeRes.getURI());
+                Resource domainRes = qsoln.getResource("domain");
-                    } else {
+                String domainURI = (domainRes != null) ? domainRes.getURI() : null;
-                        newProp.setRangeVClassURI(op.getRangeVClassURI());
+                String rangeURI = qsoln.getResource("range").getURI();
+                if (appropriateDomain(domainRes, subject, tboxModel)) {
+                    additionalProps.add(opDao.getObjectPropertyByURIs(
+                        opURI, domainURI, rangeURI));              
                 }
-                    Resource groupRes = qsoln.getResource("group");
-                    if (groupRes != null) {
-                        newProp.setGroupURI(groupRes.getURI());
-                    } else {
-                        newProp.setGroupURI(op.getURI());
-                    }
-                    Literal labelLit = qsoln.getLiteral("label");
-                    if (labelLit != null) {
-                        newProp.setDomainPublic(labelLit.getLexicalForm());
-                    } else {
-                        newProp.setDomainPublic(op.getDomainPublic());
-                    }
-                    Literal customFormLit = qsoln.getLiteral("customForm");
-                    if (customFormLit != null) {
-                        newProp.setCustomEntryForm(customFormLit.getLexicalForm());
-                    } else {
-                        newProp.setCustomEntryForm(op.getCustomEntryForm());
-                    }
-                    additionalProps.add(newProp);
             }  
         } finally {
             qe.close();
         }
-        }
-        
         return additionalProps;
     }   
     
     
     
+    public static List<ObjectProperty> getAdditionalFauxSubpropertiesForList(List<ObjectProperty> propList, 
+                                                                         Individual subject, 
+                                                                         Model displayModel, 
+                                                                         Model tboxModel) {
+        
+        List<ObjectProperty> additionalProps = new ArrayList<ObjectProperty>();
+        Model union = ModelFactory.createUnion(displayModel, tboxModel);
+        
+        for (ObjectProperty op : propList) {
+            additionalProps.addAll(getAdditionalFauxSubproperties(op, subject, tboxModel, union));
+        }    
+
+        return additionalProps;
+    }
+    
+    private static boolean appropriateDomain(Resource domainRes, Individual subject, Model tboxModel) {
+        if (subject == null || domainRes == null) {
+            return true;
+        }
+        for (VClass vclass : subject.getVClasses()) {
+            if ((vclass.getURI() != null) &&
+                    ((vclass.getURI().equals(domainRes.getURI()) ||
+                    (tboxModel.contains(
+                            ResourceFactory.createResource(
+                                    vclass.getURI()), RDFS.subClassOf, domainRes))))) {
+                return true;
+            }
+        }
+        return false;
+    }
+    
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/edit/EditConfigurationTemplateModel.java

@@ -453,10 +453,13 @@ public class EditConfigurationTemplateModel extends BaseTemplateModel {
 		String objectKey = vreq.getParameter("objectKey");
 		statementDisplay.put(objectKey, objectUri);
 		
+		ObjectProperty predicate = new ObjectProperty();
+		predicate.setURI(predicateUri);
+		
 		//Using object property statement template model here
 		ObjectPropertyStatementTemplateModel osm = new ObjectPropertyStatementTemplateModel(
 				subjectUri, 
-				predicateUri, 
+				predicate, 
 				objectKey, 
 		        statementDisplay, 
 		        null, vreq);
@@ -524,15 +527,23 @@ public class EditConfigurationTemplateModel extends BaseTemplateModel {
     	if( subjectVClasses == null ) {
     		vclasses = wdf.getVClassDao().getAllVclasses();
     	} else if (rangeClass != null) {
+    	    List<VClass> rangeVClasses = new ArrayList<VClass>();
     	    vclasses = new ArrayList<VClass>();
-    	    vclasses.add(rangeClass);
+    	    if (!rangeClass.isUnion()) {    	        
-    	    List<String> subURIs = wdf.getVClassDao().getSubClassURIs(rangeClass.getURI());
+    	        rangeVClasses.add(rangeClass);
+    	    } else {
+    	        rangeVClasses.addAll(rangeClass.getUnionComponents());
+    	    }
+            for(VClass rangeVClass : rangeVClasses) {	
+                vclasses.add(rangeVClass);
+        	    List<String> subURIs = wdf.getVClassDao().getSubClassURIs(rangeVClass.getURI());
         	    for (String subClassURI : subURIs) {
         	        VClass subClass = wdf.getVClassDao().getVClassByURI(subClassURI);
         	        if (subClass != null) {
         	            vclasses.add(subClass);
         	        }
         	    }
+            }
     	} else {
     		//this hash is used to make sure there are no duplicates in the vclasses
     		//a more elegant method may look at overriding equals/hashcode to enable a single hashset of VClass objects

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/BaseIndividualTemplateModel.java

@@ -117,7 +117,7 @@ public abstract class BaseIndividualTemplateModel extends BaseTemplateModel {
 				RequestActionConstants.SOME_URI);
 		AddObjectPropertyStatement aops = new AddObjectPropertyStatement(
 				vreq.getJenaOntModel(), individual.getURI(),
-				RequestActionConstants.SOME_URI,
+				RequestActionConstants.SOME_PREDICATE,
 				RequestActionConstants.SOME_URI);
     	return PolicyHelper.isAuthorizedForActions(vreq, new Actions(adps).or(aops));
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/CollatedObjectPropertyTemplateModel.java

@@ -18,6 +18,7 @@ import org.apache.commons.logging.LogFactory;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
@@ -58,7 +59,7 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
             postprocess(statementData);
             
             /* Collate the data */
-           subclasses = collate(subjectUri, propertyUri, statementData, editing);
+           subclasses = collate(subjectUri, op, statementData, editing);
             
            for (SubclassTemplateModel subclass : subclasses) {
                List<ObjectPropertyStatementTemplateModel> list = subclass.getStatements();
@@ -188,7 +189,7 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
     }
     
     // Collate the statements by subclass. 
-    private List<SubclassTemplateModel> collate(String subjectUri, String propertyUri,
+    private List<SubclassTemplateModel> collate(String subjectUri, ObjectProperty property,
             List<Map<String, String>> statementData, boolean editing) {
   
         String objectKey = getObjectKey();
@@ -218,7 +219,7 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
             }
 
             listForThisSubclass.add(new ObjectPropertyStatementTemplateModel(subjectUri, 
-                    propertyUri, objectKey, map, getTemplateName(), vreq));
+                    property, objectKey, map, getTemplateName(), vreq));
 
         } 
         

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/DataPropertyStatementTemplateModel.java

@@ -13,12 +13,14 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.DropDataPr
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.RdfLiteralHash;
 
+
 public class DataPropertyStatementTemplateModel extends PropertyStatementTemplateModel {
     private static final Log log = LogFactory.getLog(DataPropertyStatementTemplateModel.class); 
     
@@ -28,9 +30,10 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
     private final String templateName;
 
     //Extended to include vitro request to check for special parameters
-    public DataPropertyStatementTemplateModel(String subjectUri, String propertyUri, Literal literal,
+    public DataPropertyStatementTemplateModel(String subjectUri, Property property, Literal literal,
             String templateName, VitroRequest vreq) {
-        super(subjectUri, propertyUri, vreq);
+        
+        super(subjectUri, property, vreq);
         
         this.literalValue = literal;
         this.templateName = templateName;
@@ -50,7 +53,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
         
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "datapropKey", makeHash(dps),
                 "cmd", "delete");
         
@@ -63,7 +66,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
 	private String makeEditUrl() {
         // vitro:moniker is deprecated. We display existing data values so editors can 
         // move them to other properties and delete, but don't allow editing.
-        if ( propertyUri.equals(VitroVocabulary.MONIKER) ) {
+        if ( VitroVocabulary.MONIKER.equals(property.getURI()) ) {
             return "";           
         }
         
@@ -76,7 +79,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
         
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "datapropKey", makeHash(dps));
         
         if ( deleteUrl.isEmpty() ) {
@@ -89,7 +92,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
 	}
         
 	private DataPropertyStatement makeStatement() {
-		DataPropertyStatement dps = new DataPropertyStatementImpl(subjectUri, propertyUri, literalValue.getLexicalForm());
+		DataPropertyStatement dps = new DataPropertyStatementImpl(subjectUri, property.getURI(), literalValue.getLexicalForm());
 		// Language and datatype are needed to get the correct hash value
 		dps.setLanguage(literalValue.getLanguage());
 		dps.setDatatypeURI(literalValue.getDatatypeURI());

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/DataPropertyTemplateModel.java

@@ -88,7 +88,7 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
             DataPropertyStatementDao dpDao = vreq.getWebappDaoFactory().getDataPropertyStatementDao();
             List<Literal> values = dpDao.getDataPropertyValuesForIndividualByProperty(subject, dp, queryString, constructQueries);            
             for (Literal value : values) {
-                statements.add(new DataPropertyStatementTemplateModel(subjectUri, propertyUri, value, getTemplateName(), vreq));
+                statements.add(new DataPropertyStatementTemplateModel(subjectUri, dp, value, getTemplateName(), vreq));
             }
         } else {
             log.debug("Data property " + getUri() + " is unpopulated.");

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/EditLinkSuppressor.java

@@ -1,94 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
-
-import java.util.Arrays;
-import java.util.List;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-
-/**
- * Sometimes we don't want to show an Add, Edit, or Delete link for a particular
- * property, no matter who the user is.
- * 
- * TODO These are hard-coded while we wait for the Application Ontology to be
- * implemented.
- */
-public class EditLinkSuppressor {
-	private static final Log log = LogFactory.getLog(EditLinkSuppressor.class);
-
-	private static final String CORE = "http://vivoweb.org/ontology/core#";
-	private static final String PUB_TO_AUTHORSHIP = core("informationResourceInAuthorship");
-	private static final String PERSON_TO_AUTHORSHIP = core("authorInAuthorship");
-	private static final String AUTHORSHIP_TO_PERSON = core("linkedAuthor");
-	private static final String AUTHORSHIP_TO_PUB = core("linkedInformationResource");
-	private static final String INDIVIDUAL_TO_WEBPAGE = core("webpage");
-	private static final String WEBPAGE_TO_INDIVIDUAL = core("webpageOf");
-	private static final String HAS_RESEARCH_AREA = core("hasResearchArea");
-	private static final String HAS_SUBJECT_AREA = core("hasSubjectArea");
-	private static final String RESEARCH_AREA_OF = core("researchAreaOf");
-	private static final String SUBJECT_AREA_FOR = core("subjectAreaFor");
-
-	private static String core(String localName) {
-		return CORE + localName;
-	}
-
-	private static final List<String> suppressAddLinksForThese = Arrays
-			.asList(new String[] { AUTHORSHIP_TO_PERSON, AUTHORSHIP_TO_PUB,
-					WEBPAGE_TO_INDIVIDUAL });
-
-	private static final List<String> suppressEditLinksForThese = Arrays
-			.asList(new String[] { WEBPAGE_TO_INDIVIDUAL });
-
-	private static final List<String> suppressDeleteLinksForThese = Arrays
-			.asList(new String[] { PUB_TO_AUTHORSHIP, PERSON_TO_AUTHORSHIP,
-					AUTHORSHIP_TO_PERSON, AUTHORSHIP_TO_PUB,
-					INDIVIDUAL_TO_WEBPAGE, WEBPAGE_TO_INDIVIDUAL,
-					HAS_RESEARCH_AREA, RESEARCH_AREA_OF, HAS_SUBJECT_AREA,
-					SUBJECT_AREA_FOR });
-
-	// TODO When we remove the hard-coding, vreq will allow us to find the
-	// application ontology model.
-	@SuppressWarnings("unused")
-	private final VitroRequest vreq;
-
-	public EditLinkSuppressor(VitroRequest vreq) {
-		this.vreq = vreq;
-	}
-
-	/**
-	 * Should we suppress the Add link on this property?
-	 */
-	public boolean isAddLinkSuppressed(String propertyUri) {
-		if (propertyUri == null) {
-			log.error("Suppressing the add link on a null property.");
-			return true;
-		}
-		return suppressAddLinksForThese.contains(propertyUri);
-	}
-
-	/**
-	 * Should we suppress the Edit link on this property?
-	 */
-	public boolean isEditLinkSuppressed(String propertyUri) {
-		if (propertyUri == null) {
-			log.error("Suppressing the edit link on a null property.");
-			return true;
-		}
-		return suppressEditLinksForThese.contains(propertyUri);
-	}
-
-	/**
-	 * Should we suppress the Delete link on this property?
-	 */
-	public boolean isDeleteLinkSuppressed(String propertyUri) {
-		if (propertyUri == null) {
-			log.error("Suppressing the delete link on a null property.");
-			return true;
-		}
-		return suppressDeleteLinksForThese.contains(propertyUri);
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/GroupedPropertyList.java

@@ -20,6 +20,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
+import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
@@ -74,12 +75,12 @@ public class GroupedPropertyList extends BaseTemplateModel {
         List<ObjectProperty> populatedObjectPropertyList = subject
                 .getPopulatedObjectPropertyList();
         
-        List<ObjectProperty> additions = ApplicationConfigurationOntologyUtils
+        Collection<ObjectProperty> additions = ApplicationConfigurationOntologyUtils
                 .getAdditionalFauxSubpropertiesForList(
-                        populatedObjectPropertyList, vreq);
+                        populatedObjectPropertyList, subject, vreq);
         if (log.isDebugEnabled()) {
             for (ObjectProperty t : additions) {
-                log.debug(t.getDomainPublic() + " " + t.getGroupURI());
+                log.debug(t.getDomainPublic() + " " + t.getGroupURI() + " domain " + t.getDomainVClassURI());
             }
             log.debug("Added " + additions.size() + 
                     " properties due to application configuration ontology");
@@ -175,7 +176,13 @@ public class GroupedPropertyList extends BaseTemplateModel {
         // There is no ObjectPropertyDao.getAllPossibleObjectPropertiesForIndividual() parallel to 
         // DataPropertyDao.getAllPossibleDatapropsForIndividual(). The comparable method for object properties
         // is defined using PropertyInstance rather than ObjectProperty.
-        PropertyInstanceDao piDao = wdf.getPropertyInstanceDao();
+        
+        // Getting WebappDaoFactory from the session because we can't have the filtering
+        // that gets applied to the request.  This breaks blank node structures in the
+        // restrictions that determine applicable properties.
+        WebappDaoFactory wadf = ModelAccess.on(vreq.getSession().getServletContext()).getWebappDaoFactory();
+        PropertyInstanceDao piDao = wadf.getPropertyInstanceDao();
+        
         Collection<PropertyInstance> allPropInstColl = piDao
                 .getAllPossiblePropInstForIndividual(subject.getURI());
         if (allPropInstColl != null) {
@@ -183,7 +190,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
                 if (pi != null) {
                     if (!alreadyOnObjectPropertyList(
                             populatedObjectPropertyList, pi)) {
-                        addObjectPropertyToPropertyList(pi.getPropertyURI(), pi.getRangeClassURI(),
+                        addObjectPropertyToPropertyList(pi.getPropertyURI(), pi.getDomainClassURI(), pi.getRangeClassURI(),
                                 propertyList);
                     }
                 } else {
@@ -199,7 +206,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
         // constitute a special case (i.e., included in piDao.getAllPossiblePropInstForIndividual()).
         for (String propertyUri : VITRO_PROPS_TO_ADD_TO_LIST) {
             if (!alreadyOnPropertyList(propertyList, propertyUri)) {
-                addObjectPropertyToPropertyList(propertyUri, null, propertyList);
+                addObjectPropertyToPropertyList(propertyUri, null, null, propertyList);
             }
         }
     }
@@ -211,16 +218,29 @@ public class GroupedPropertyList extends BaseTemplateModel {
         }
         for (ObjectProperty op : opList) {
             if (op.getURI() != null && op.getURI().equals(pi.getPropertyURI())) {
+                if(op.getDomainVClassURI() == null) {
+                    if(pi.getDomainClassURI() == null) {
                         return true;   
                     }
+                } else if (op.getDomainVClassURI().equals(pi.getDomainClassURI())) {
+                    return true;
+                }
+                if(op.getRangeVClassURI() == null) {
+                    if (pi.getDomainClassURI() == null) {
+                        return true;
+                    }
+                } else if (op.getRangeVClassURI().equals(pi.getRangeClassURI())) {
+                    return true;
+                }
+            }
         }
         return false;
     }
 
-    private void addObjectPropertyToPropertyList(String propertyUri, String rangeUri,
+    private void addObjectPropertyToPropertyList(String propertyUri, String domainUri, String rangeUri,
             List<Property> propertyList) {
         ObjectPropertyDao opDao = wdf.getObjectPropertyDao();
-        ObjectProperty op = opDao.getObjectPropertyByURIAndRangeURI(propertyUri, rangeUri);
+        ObjectProperty op = opDao.getObjectPropertyByURIs(propertyUri, domainUri, rangeUri);
         if (op == null) {
             log.error("ObjectProperty op returned null from opDao.getObjectPropertyByURI(" + propertyUri + ")");
         } else if (op.getURI() == null) {
@@ -457,11 +477,16 @@ public class GroupedPropertyList extends BaseTemplateModel {
     }
 
     public PropertyTemplateModel pullProperty(String propertyUri) {
+        return pullProperty(propertyUri, null);
+    }
+    
+    public PropertyTemplateModel pullProperty(String propertyUri, String rangeUri) {
 
         for (PropertyGroupTemplateModel pgtm : groups) {
             List<PropertyTemplateModel> properties = pgtm.getProperties();
             for (PropertyTemplateModel ptm : properties) {
-                if (propertyUri.equals(ptm.getUri())) {
+                if (propertyUri.equals(ptm.getUri()) && 
+                        (rangeUri == null || rangeUri.equals(ptm.getRangeUri()))) {
                     // Remove the property from the group.
                     // NB Works with a for-each loop instead of an iterator,
                     // since iteration doesn't continue after the remove.

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/NameStatementTemplateModel.java

@@ -14,6 +14,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAct
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
@@ -37,7 +38,7 @@ public class NameStatementTemplateModel extends PropertyStatementTemplateModel {
     private final String editUrl;
 
     NameStatementTemplateModel(String subjectUri, VitroRequest vreq) {
-        super(subjectUri, VitroVocabulary.LABEL, vreq);
+        super(subjectUri, new Property(VitroVocabulary.LABEL), vreq);
 
         // NIHVIVO-2466 Use the same methods to get the label that are used elsewhere in the 
         // application, to guarantee consistent results for individuals with multiple labels
@@ -69,7 +70,7 @@ public class NameStatementTemplateModel extends PropertyStatementTemplateModel {
         
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "datapropKey", makeHash(dps),
                 "deleteProhibited", "prohibited");
         
@@ -80,7 +81,7 @@ public class NameStatementTemplateModel extends PropertyStatementTemplateModel {
         
 	private DataPropertyStatement makeStatement(Literal literalValue) {
 		DataPropertyStatement dps = new DataPropertyStatementImpl(subjectUri,
-				propertyUri, literalValue.getLexicalForm());
+				property.getURI(), literalValue.getLexicalForm());
 		// Language and datatype are needed to get the correct hash value
 		dps.setLanguage(literalValue.getLanguage());
 		dps.setDatatypeURI(literalValue.getDatatypeURI());

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/ObjectPropertyStatementTemplateModel.java

@@ -13,8 +13,10 @@ import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.ifaces.RequestedAction;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.DropObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditObjectPropertyStatement;
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatementImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
@@ -31,9 +33,9 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
     private final String editUrl;
     private final String deleteUrl;
     
-    public ObjectPropertyStatementTemplateModel(String subjectUri, String propertyUri, String objectKey, 
+    public ObjectPropertyStatementTemplateModel(String subjectUri, ObjectProperty predicate, String objectKey, 
             Map<String, String> data, String templateName, VitroRequest vreq) {
-        super(subjectUri, propertyUri, vreq);
+        super(subjectUri, predicate, vreq);
 
         this.data = Collections.unmodifiableMap(new HashMap<String, String>(data));
         this.objectUri = data.get(objectKey);        
@@ -41,7 +43,8 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
         //to keep track of later
         this.objectKey = objectKey;
         
-        ObjectPropertyStatement ops = new ObjectPropertyStatementImpl(subjectUri, propertyUri, objectUri);
+        ObjectPropertyStatement ops = new ObjectPropertyStatementImpl(subjectUri, property.getURI(), objectUri);
+        ops.setProperty(predicate);
         
         // Do delete url first, since it is used in building edit url
         this.deleteUrl = makeDeleteUrl();
@@ -50,24 +53,24 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
 
 	private String makeDeleteUrl() {
     	// Is the delete link suppressed for this property?
-    	if (new EditLinkSuppressor(vreq).isDeleteLinkSuppressed(propertyUri)) {
+    	if (property.isDeleteLinkSuppressed()) {
     		return "";
     	}
         
         // Determine whether the statement can be deleted
 		RequestedAction action = new DropObjectPropertyStatement(
-				vreq.getJenaOntModel(), subjectUri, propertyUri, objectUri);
+				vreq.getJenaOntModel(), subjectUri, property, objectUri);
         if ( ! PolicyHelper.isAuthorizedForActions(vreq, action) ) {
             return "";
         }
         
-        if (propertyUri.equals(VitroVocabulary.IND_MAIN_IMAGE)) {
+        if (VitroVocabulary.IND_MAIN_IMAGE.equals(property.getURI())) {
             return ObjectPropertyTemplateModel.getImageUploadUrl(subjectUri, "delete");
         } 
         
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "objectUri", objectUri,
                 "cmd", "delete",
                 "objectKey", objectKey);
@@ -92,7 +95,7 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
 
 	private String makeEditUrl(ObjectPropertyStatement ops) {
     	// Is the edit link suppressed for this property?
-    	if (new EditLinkSuppressor(vreq).isEditLinkSuppressed(propertyUri)) {
+    	if (property.isEditLinkSuppressed()) {
     		return "";
     	}
         
@@ -102,19 +105,26 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
             return "";
         }
         
-        if (propertyUri.equals(VitroVocabulary.IND_MAIN_IMAGE)) {
+        if (VitroVocabulary.IND_MAIN_IMAGE.equals(property.getURI())) {
             return ObjectPropertyTemplateModel.getImageUploadUrl(subjectUri, "edit");
         } 
 
         ParamMap params = new ParamMap(
                 "subjectUri", subjectUri,
-                "predicateUri", propertyUri,
+                "predicateUri", property.getURI(),
                 "objectUri", objectUri);
         
         if ( deleteUrl.isEmpty() ) {
             params.put("deleteProhibited", "prohibited");
         }
         
+        if (ops.getProperty()!= null && ops.getProperty().getDomainVClassURI() != null) {
+            params.put("domainUri", ops.getProperty().getDomainVClassURI());
+        }
+        if (ops.getProperty()!= null && ops.getProperty().getRangeVClassURI() != null) {
+            params.put("rangeUri", ops.getProperty().getRangeVClassURI());
+        }
+        
         params.putAll(UrlBuilder.getModelParams(vreq));
         
         return UrlBuilder.getUrl(EDIT_PATH, params);

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/ObjectPropertyTemplateModel.java

@@ -80,7 +80,6 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
     private PropertyListConfig config;
     private String objectKey;    
     private String sortDirection;
-    private String rangeURI;
     
     ObjectPropertyTemplateModel(ObjectProperty op, Individual subject, VitroRequest vreq, 
             boolean editing)
@@ -90,7 +89,8 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
         setName(op.getDomainPublic());
         
         sortDirection = op.getDomainEntitySortDirection();
-        rangeURI = op.getRangeVClassURI();
+        domainUri = op.getDomainVClassURI();
+        rangeUri = op.getRangeVClassURI();
         
         // Get the config for this object property
         try {
@@ -110,13 +110,13 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
 
     protected void setAddUrl(Property property) {
     	// Is the add link suppressed for this property?
-    	if (new EditLinkSuppressor(vreq).isAddLinkSuppressed(propertyUri)) {
+    	if (property.isAddLinkSuppressed()) {
     		return;
     	}
         
         // Determine whether a new statement can be added
 		RequestedAction action = new AddObjectPropertyStatement(
-				vreq.getJenaOntModel(), subjectUri, propertyUri,
+				vreq.getJenaOntModel(), subjectUri, property,
 				RequestActionConstants.SOME_URI);
         if ( ! PolicyHelper.isAuthorizedForActions(vreq, action) ) {
             return;
@@ -133,6 +133,9 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
                     "subjectUri", subjectUri,
                     "predicateUri", propertyUri);
             
+            if (domainUri != null) {
+                params.put("domainUri", domainUri);
+            }
             if (rangeUri != null) {
                 params.put("rangeUri", rangeUri);
             }
@@ -157,7 +160,7 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
     
     protected List<Map<String, String>> getStatementData() {
         ObjectPropertyStatementDao opDao = vreq.getWebappDaoFactory().getObjectPropertyStatementDao();
-        return opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, objectKey, rangeURI, getSelectQuery(), getConstructQueries(), sortDirection);
+        return opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, objectKey, domainUri, rangeUri, getSelectQuery(), getConstructQueries(), sortDirection);
     }
     
     protected abstract boolean isEmpty();

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/PropertyGroupTemplateModel.java

@@ -37,7 +37,12 @@ public class PropertyGroupTemplateModel extends BaseTemplateModel {
         for (Property p : propertyList)  {
             if (p instanceof ObjectProperty) {
                 ObjectProperty op = (ObjectProperty) p;
-                properties.add(ObjectPropertyTemplateModel.getObjectPropertyTemplateModel(op, subject, vreq, editing, populatedObjectPropertyList));
+                ObjectPropertyTemplateModel tm = ObjectPropertyTemplateModel.getObjectPropertyTemplateModel(
+                        op, subject, vreq, editing, populatedObjectPropertyList);
+                if (!tm.isEmpty() || (editing && !tm.getAddUrl().isEmpty())) {
+                    properties.add(tm);                    
+                }
+
             } else {
                 properties.add(new DataPropertyTemplateModel((DataProperty)p, subject, vreq, editing, populatedDataPropertyList));
             }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/PropertyStatementTemplateModel.java

@@ -2,6 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.BaseTemplateModel;
 
@@ -10,12 +11,12 @@ public abstract class PropertyStatementTemplateModel extends BaseTemplateModel {
 
     protected final VitroRequest vreq;
     protected final String subjectUri;
-    protected final String propertyUri;
+    protected final Property property;
     
-    PropertyStatementTemplateModel(String subjectUri, String propertyUri, VitroRequest vreq) {
+    PropertyStatementTemplateModel(String subjectUri, Property property, VitroRequest vreq) {
         this.vreq = vreq;        
         this.subjectUri = subjectUri;
-        this.propertyUri = propertyUri;              
+        this.property = property;              
     }
     
     /* Template properties */

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/PropertyTemplateModel.java

@@ -28,7 +28,10 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
     
     protected final VitroRequest vreq;
     protected final String subjectUri;
+    protected final Property property;
     protected final String propertyUri;
+    protected String domainUri;
+    protected String rangeUri;
     private final String localName;
 
     protected Map<String, Object> verboseDisplay;
@@ -41,6 +44,7 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
     PropertyTemplateModel(Property property, Individual subject, VitroRequest vreq) {
         this.vreq = vreq;
         subjectUri = subject.getURI(); 
+        this.property = property;
         propertyUri = property.getURI();
         localName = property.getLocalName();
         setVerboseDisplayValues(property);
@@ -121,6 +125,10 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
         return propertyUri;
     }
     
+    public String getRangeUri() {
+        return rangeUri;
+    }
+    
     public String getAddUrl() {
         //log.info("addUrl=" + addUrl);
         return (addUrl != null) ? addUrl : "";

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/UncollatedObjectPropertyTemplateModel.java

@@ -41,7 +41,7 @@ public class UncollatedObjectPropertyTemplateModel extends ObjectPropertyTemplat
             String objectKey = getObjectKey();
             for (Map<String, String> map : statementData) {
                 statements.add(new ObjectPropertyStatementTemplateModel(subjectUri, 
-                        propertyUri, objectKey, map, getTemplateName(), vreq));
+                        op, objectKey, map, getTemplateName(), vreq));
             }
             
             postprocessStatementList(statements);

webapp/test/edu/cornell/mannlib/vitro/webapp/auth/policy/SelfEditingPolicyTest.java

@@ -42,6 +42,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.DropObject
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 
 public class SelfEditingPolicyTest extends AbstractTestClass {
@@ -55,8 +56,8 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 	private static final String UNSAFE_RESOURCE = UNSAFE_NS
 			+ "otherIndividual99999";
 
-	private static final String SAFE_PREDICATE = SAFE_NS + "hasHairStyle";
+	private static final Property SAFE_PREDICATE = new Property(SAFE_NS + "hasHairStyle");
-	private static final String UNSAFE_PREDICATE = UNSAFE_NS + "hasSuperPowers";
+	private static final Property UNSAFE_PREDICATE = new Property(UNSAFE_NS + "hasSuperPowers");
 
 	private ServletContextStub ctx;
 
@@ -95,19 +96,19 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 		PropertyRestrictionPolicyHelper.setBean(ctx, prph);
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SELFEDITOR_URI,
-				"http://mannlib.cornell.edu/bad#prp234", SAFE_RESOURCE);
+				new Property("http://mannlib.cornell.edu/bad#prp234"), SAFE_RESOURCE);
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SAFE_RESOURCE,
-				"http://mannlib.cornell.edu/bad#prp234", SELFEDITOR_URI);
+				new Property("http://mannlib.cornell.edu/bad#prp234"), SELFEDITOR_URI);
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SELFEDITOR_URI,
-				"http://mannlib.cornell.edu/bad#prp999", SAFE_RESOURCE);
+				new Property("http://mannlib.cornell.edu/bad#prp999"), SAFE_RESOURCE);
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SAFE_RESOURCE,
-				"http://mannlib.cornell.edu/bad#prp999", SELFEDITOR_URI);
+				new Property("http://mannlib.cornell.edu/bad#prp999"), SELFEDITOR_URI);
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddObjectPropertyStatement(ontModel, SAFE_RESOURCE,
@@ -132,11 +133,11 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddDataPropertyStatement(ontModel, SELFEDITOR_URI,
-				SAFE_PREDICATE);
+				SAFE_PREDICATE.getURI());
 		assertDecision(AUTHORIZED, policy.isAuthorized(ids, whatToAuth));
 
 		whatToAuth = new AddDataPropertyStatement(ontModel, SELFEDITOR_URI,
-				UNSAFE_PREDICATE);
+				UNSAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 	}
 
@@ -218,16 +219,16 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 	//
 	@Test
 	public void testVisitIdentifierBundleEditDataPropStmt() {
-		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI,SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI,SAFE_PREDICATE.getURI());
 		assertDecision(AUTHORIZED, policy.isAuthorized(ids, whatToAuth));
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI, UNSAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI, UNSAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, UNSAFE_RESOURCE, SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, UNSAFE_RESOURCE, SAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, SAFE_RESOURCE, SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SAFE_RESOURCE, SAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 	}
 
@@ -287,7 +288,7 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 	public void twoSEIsFindDataPropertySubject() {
 		setUpTwoSEIs();
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI, SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SELFEDITOR_URI, SAFE_PREDICATE.getURI());
 		assertDecision(AUTHORIZED, policy.isAuthorized(ids, whatToAuth));
 	}
 
@@ -295,7 +296,7 @@ public class SelfEditingPolicyTest extends AbstractTestClass {
 	public void twoSEIsDontFindInDataProperty() {
 		setUpTwoSEIs();
 
-		whatToAuth = new EditDataPropertyStatement(ontModel, SAFE_RESOURCE, SAFE_PREDICATE);
+		whatToAuth = new EditDataPropertyStatement(ontModel, SAFE_RESOURCE, SAFE_PREDICATE.getURI());
 		assertDecision(INCONCLUSIVE, policy.isAuthorized(ids, whatToAuth));
 	}
 

webapp/test/edu/cornell/mannlib/vitro/webapp/auth/policy/SelfEditingPolicy_2_Test.java

@@ -32,6 +32,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditDataPr
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.propstmt.EditObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
+import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 
 public class SelfEditingPolicy_2_Test extends AbstractTestClass {
@@ -123,7 +124,7 @@ public class SelfEditingPolicy_2_Test extends AbstractTestClass {
 	@Test
 	public void nullIdentifierBundle() {
 		AddObjectPropertyStatement whatToAuth = new AddObjectPropertyStatement(
-				ontModel, SELFEDITOR_URI, SAFE_PREDICATE, SAFE_RESOURCE);
+				ontModel, SELFEDITOR_URI, new Property(SAFE_PREDICATE), SAFE_RESOURCE);
 		PolicyDecision dec = policy.isAuthorized(null, whatToAuth);
 		Assert.assertNotNull(dec);
 		Assert.assertEquals(Authorization.INCONCLUSIVE, dec.getAuthorized());
@@ -277,7 +278,7 @@ public class SelfEditingPolicy_2_Test extends AbstractTestClass {
 	private void assertAddObjectPropStmt(String uriOfSub, String uriOfPred,
 			String uriOfObj, Authorization expectedAuthorization) {
 		AddObjectPropertyStatement whatToAuth = new AddObjectPropertyStatement(
-				ontModel, uriOfSub, uriOfPred, uriOfObj);
+				ontModel, uriOfSub, new Property(uriOfPred), uriOfObj);
 		PolicyDecision dec = policy.isAuthorized(ids, whatToAuth);
 		log.debug(dec);
 		Assert.assertNotNull(dec);
@@ -291,7 +292,7 @@ public class SelfEditingPolicy_2_Test extends AbstractTestClass {
 	private void assertEditObjPropStmt(String uriOfSub, String uriOfPred,
 			String uriOfObj, Authorization expectedAuthorization) {
 		EditObjectPropertyStatement whatToAuth = new EditObjectPropertyStatement(
-				ontModel, uriOfSub, uriOfPred, uriOfObj);
+				ontModel, uriOfSub, new Property(uriOfPred), uriOfObj);
 		PolicyDecision dec = policy.isAuthorized(ids, whatToAuth);
 		log.debug(dec);
 		Assert.assertNotNull(dec);

webapp/test/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelperTest.java

@@ -18,7 +18,6 @@ import java.util.Map;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.apache.log4j.Level;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -27,6 +26,8 @@ import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.sdb.util.Pair;
+import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean;
@@ -58,17 +59,25 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 //		setLoggerLevel(PropertyRestrictionPolicyHelper.class, Level.DEBUG);
 	}
 
+	private void mapPut(String predicateURI, RoleLevel roleLevel, 
+	                    Map<Pair<String, Pair<String,String>>, RoleLevel> map) { 
+	    map.put(new Pair<String, Pair<String,String>>(
+	            OWL.Thing.getURI(), new Pair<String, String>(
+	                    predicateURI, OWL.Thing.getURI())), roleLevel);
+	}
+	
 	@Before
 	public void createTheBean() {
-		Map<String, RoleLevel> displayLevels = new HashMap<String, BaseResourceBean.RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> displayLevels = 
-		displayLevels.put("http://predicates#display_self", SELF);
+		        new HashMap<Pair<String, Pair<String,String>>, RoleLevel>();
-		displayLevels.put("http://predicates#display_curator", CURATOR);
+		mapPut("http://predicates#display_curator", CURATOR, displayLevels);
-		displayLevels.put("http://predicates#display_hidden", NOBODY);
+		mapPut("http://predicates#display_hidden", NOBODY, displayLevels);
 
-		Map<String, RoleLevel> modifyLevels = new HashMap<String, BaseResourceBean.RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> modifyLevels = 
-		modifyLevels.put("http://predicates#modify_self", SELF);
+		        new HashMap<Pair<String, Pair<String,String>>, RoleLevel>();
-		modifyLevels.put("http://predicates#modify_curator", CURATOR);
+		mapPut("http://predicates#modify_self", SELF, modifyLevels);
-		modifyLevels.put("http://predicates#modify_hidden", NOBODY);
+		mapPut("http://predicates#modify_curator", CURATOR, modifyLevels);
+		mapPut("http://predicates#modify_hidden", NOBODY, modifyLevels);
 
 		bean = new PropertyRestrictionPolicyHelper(
 				Arrays.asList(PROHIBITED_NAMESPACES),
@@ -125,68 +134,75 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 	@Test
 	public void displayPredicateNoRestriction() {
 		assertEquals("displayPredicate: open", true,
-				bean.canDisplayPredicate("http://predicates#open", PUBLIC));
+				bean.canDisplayPredicate(createVitroProperty(
+				        "http://predicates#open"), PUBLIC));
 	}
 
 	@Test
 	public void displayPredicateRestrictionLower() {
 		assertEquals("displayPredicate: lower restriction", true,
-				bean.canDisplayPredicate("http://predicates#display_self",
+				bean.canDisplayPredicate(createVitroProperty(
-						CURATOR));
+				        "http://predicates#display_self"), CURATOR));
 	}
 
 	@Test
 	public void displayPredicateRestrictionEqual() {
 		assertEquals("displayPredicate: equal restriction", true,
-				bean.canDisplayPredicate("http://predicates#display_curator",
+				bean.canDisplayPredicate(createVitroProperty(
-						CURATOR));
+				        "http://predicates#display_curator"), CURATOR));
 	}
 
 	@Test
 	public void displayPredicateRestrictionHigher() {
 		assertEquals("displayPredicate: higher restriction", false,
-				bean.canDisplayPredicate("http://predicates#display_hidden",
+				bean.canDisplayPredicate(createVitroProperty(
-						CURATOR));
+				        "http://predicates#display_hidden"), CURATOR));
 	}
 
 	@Test
 	public void modifyPredicateNoRestriction() {
 		assertEquals("modifyPredicate: open", true,
-				bean.canModifyPredicate("http://predicates#open", PUBLIC));
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        "http://predicates#open"), PUBLIC));
 	}
 
 	@Test
 	public void modifyPredicateRestrictionLower() {
 		assertEquals("modifyPredicate: lower restriction", true,
-				bean.canModifyPredicate("http://predicates#modify_self",
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        "http://predicates#modify_self"),
 						CURATOR));
 	}
 
 	@Test
 	public void modifyPredicateRestrictionEqual() {
 		assertEquals("modifyPredicate: equal restriction", true,
-				bean.canModifyPredicate("http://predicates#modify_curator",
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        "http://predicates#modify_curator"),
 						CURATOR));
 	}
 
 	@Test
 	public void modifyPredicateRestrictionHigher() {
 		assertEquals("modifyPredicate: higher restriction", false,
-				bean.canModifyPredicate("http://predicates#modify_hidden",
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        "http://predicates#modify_hidden"),
 						CURATOR));
 	}
 
 	@Test
 	public void modifyPredicateProhibitedNamespace() {
 		assertEquals("modifyPredicate: prohibited namespace", false,
-				bean.canModifyPredicate(PROHIBITED_NAMESPACES[0] + "randoom",
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        PROHIBITED_NAMESPACES[0] + "randoom"),
 						DB_ADMIN));
 	}
 
 	@Test
 	public void modifyPredicatePermittedException() {
 		assertEquals("modifyPredicate: permitted exception", true,
-				bean.canModifyPredicate(PERMITTED_EXCEPTIONS[0], DB_ADMIN));
+				bean.canModifyPredicate(new edu.cornell.mannlib.vitro.webapp.beans.Property(
+				        PERMITTED_EXCEPTIONS[0]), DB_ADMIN));
 	}
 
 	// ----------------------------------------------------------------------
@@ -195,9 +211,10 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 
 	@Test
 	public void buildDisplayThresholds() {
-		Map<String, RoleLevel> expectedMap = new HashMap<String, BaseResourceBean.RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, BaseResourceBean.RoleLevel> expectedMap = 
-		expectedMap.put("http://thresholds#display_public", PUBLIC);
+		        new HashMap<Pair<String, Pair<String,String>>, BaseResourceBean.RoleLevel>();
-		expectedMap.put("http://thresholds#display_hidden", NOBODY);
+		mapPut("http://thresholds#display_public", PUBLIC, expectedMap);
+		mapPut("http://thresholds#display_hidden", NOBODY, expectedMap);
 
 		Map<String, RoleLevel> actualMap = populateThresholdMap(PROPERTY_DISPLAY_THRESHOLD);
 		assertEquals("display thresholds", expectedMap, actualMap);
@@ -205,9 +222,10 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 
 	@Test
 	public void buildModifyThresholds() {
-		Map<String, RoleLevel> expectedMap = new HashMap<String, BaseResourceBean.RoleLevel>();
+	    Map<Pair<String, Pair<String,String>>, BaseResourceBean.RoleLevel> expectedMap = 
-		expectedMap.put("http://thresholds#modify_editor", EDITOR);
+                new HashMap<Pair<String, Pair<String,String>>, BaseResourceBean.RoleLevel>();
-		expectedMap.put("http://thresholds#modify_curator", CURATOR);
+		mapPut("http://thresholds#modify_editor", EDITOR, expectedMap);
+		mapPut("http://thresholds#modify_curator", CURATOR, expectedMap);
 
 		Map<String, RoleLevel> actualMap = populateThresholdMap(PROPERTY_MODIFY_THRESHOLD);
 		assertEquals("modify thresholds", expectedMap, actualMap);
@@ -244,4 +262,9 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 			model.add(subject, property, object);
 		}
 	}
+	
+	private edu.cornell.mannlib.vitro.webapp.beans.Property createVitroProperty(
+	        String propertyURI) {
+	    return new edu.cornell.mannlib.vitro.webapp.beans.Property(propertyURI);
+	}
 }

webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerInversePropertyTest.java

@@ -82,6 +82,13 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
 		Assert.assertTrue(inf.contains(b,Q,a));				
 		aBox.add(c,Q,d);		
 		Assert.assertTrue(inf.contains(d,P,c));	      
+		
+		// delete assertions and verify that inferences go away
+		aBox.remove(c,Q,d);
+		Assert.assertFalse(inf.contains(d,P,c));
+		aBox.remove(a,P,b);
+		Assert.assertFalse(inf.contains(b,Q,a));
+		
 	}
 
     @Test

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelperStub.java

@@ -10,6 +10,8 @@ import java.util.Set;
 
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.sdb.util.Pair;
+import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.webapp.auth.policy.bean.PropertyRestrictionPolicyHelper;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
@@ -43,10 +45,15 @@ public class PropertyRestrictionPolicyHelperStub extends
 			namespaceSet.addAll(Arrays.asList(restrictedNamespaces));
 		}
 		
-		Map<String, RoleLevel> thresholdMap = new HashMap<String, RoleLevel>();
+		Map<Pair<String, Pair<String,String>>, RoleLevel> thresholdMap = new HashMap<
+		        Pair<String, Pair<String,String>>, RoleLevel>();
 		if (restrictedProperties != null) {
 			for (String prop : restrictedProperties) {
-				thresholdMap.put(prop, RoleLevel.NOBODY);
+				thresholdMap.put(
+				        new Pair<String, Pair<String, String>>(
+				                OWL.Thing.getURI(), new Pair<String, String>(
+				                        prop, OWL.Thing.getURI())), 
+				                                RoleLevel.NOBODY);
 			}
 		}
 		
@@ -57,8 +64,8 @@ public class PropertyRestrictionPolicyHelperStub extends
 	private PropertyRestrictionPolicyHelperStub(
 			Set<String> modifyRestrictedNamespaces,
 			Set<String> modifyPermittedExceptions,
-			Map<String, RoleLevel> displayThresholds,
+			Map<Pair<String, Pair<String,String>>, RoleLevel> displayThresholds,
-			Map<String, RoleLevel> modifyThresholds) {
+			Map<Pair<String, Pair<String,String>>, RoleLevel> modifyThresholds) {
 		super(modifyRestrictedNamespaces, modifyPermittedExceptions,
 				displayThresholds, modifyThresholds, ModelFactory.createDefaultModel());
 	}

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

@@ -67,7 +67,7 @@ public class ObjectPropertyDaoStub implements ObjectPropertyDao {
 	}
 	
     @Override
-    public ObjectProperty getObjectPropertyByURIAndRangeURI(String objectPropertyURI, String rangeURI) {
+    public ObjectProperty getObjectPropertyByURIs(String objectPropertyURI, String domainURI, String rangeURI) {
         return getObjectPropertyByURI(objectPropertyURI);
     }
 

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

@@ -216,7 +216,7 @@ public class ObjectPropertyStatementDaoStub implements
 
 	@Override
 	public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
-			String subjectUri, String propertyUri, String objectKey, String rangeUri,
+			String subjectUri, String propertyUri, String objectKey, String domainUri, String rangeUri,
 			String query, Set<String> constructQueries, String sortDir) {
 		throw new RuntimeException(
 				"ObjectPropertyStatementDaoStub.getObjectPropertyStatementsForIndividualByProperty() not implemented.");

webapp/web/WEB-INF/resources/startup_listeners.txt

@@ -25,8 +25,6 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.UserModelSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ContentModelSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ModelMakerSetup
 
-edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase
-
 edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorageSetup
 
 edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil$Setup
@@ -38,6 +36,8 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup
 
 edu.cornell.mannlib.vitro.webapp.servlet.setup.SimpleReasonerSetup
 
+edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase
+
 # Must run after JenaDataSourceSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ThemeInfoSetup
 

webapp/web/i18n/all.properties

@@ -211,7 +211,6 @@ remove_selection_title = remove selection
 
 external_id_not_provided = Login failed - External ID is not found.
 external_id_already_in_use = User account already exists for ''{0}''
-logins_disabled_for_maintenance = User logins are temporarily disabled while the system is being maintained.
 
 error_no_email = You must supply an email address.
 error_email_already_exists = An account with that email address already exists.
@@ -220,8 +219,6 @@ error_external_auth_already_exists = An account with that external authorization
 error_no_first_name = You must supply a first name.
 error_no_last_name = You must supply a last name.
 error_no_role = You must select a role.
-error_no_password = No password supplied.
-error_password_length = Password must be between {0} and {1} characters.
 error_password_mismatch = Passwords do not match.
 
 logged_in_but_no_profile = You have logged in, but the system contains no profile for you.
@@ -322,7 +319,7 @@ warning = Warning
 warnings_issued = {0} issued warnings during startup.
 startup_trace = Startup trace
 full_list_startup = The full list of startup events and messages.
-startup_status = Startup Status
+startup_status = Startup status
 continue = Continue
 
 #
@@ -479,7 +476,7 @@ hide_show_properties = hide/show properties
 hide_properties = hide properties
 property_hierarchy = Property Hierarchy
 all_x_properties = All {0} Properties
-property_groups = Property Groups
+property_groups = Property groups
 add_new = Add new
 object = object
 data = data
@@ -496,7 +493,7 @@ object_property_hierarchy = Object property hierarchy
 data_property_hierarchy = Data property hierarchy
 
 site_config = Site Configuration
-internal_class = Institutional internal class
+internal_class_i_capped = Institutional internal class
 manage_profile_editing = Manage profile editing
 page_management = Page management
 menu_ordering_mixed_caps = Menu ordering
@@ -504,6 +501,18 @@ restrict_logins_mixed_caps = Restrict logins
 site_information = Site information
 user_accounts = User accounts
 
+#
+# search controller ( PagedSearchController.java )
+#
+error_in_search_request = The search request contained errors.
+enter_search_term = Please enter a search term.
+invalid_search_term = Search term was invalid
+paging_link_more = more...
+no_matching_results = No matching results.
+search_failed = Search failed.
+search_term_error_near = The search term had an error near
+search_for = Search for ''{0}''
+
 #
 # search templates ( /templates/freemarker/body/search )
 #
@@ -520,18 +529,6 @@ previous = Previous
 page_link = page link
 next_capitalized = Next
 
-#
-# search controller ( PagedSearchController.java )
-#
-error_in_search_request = The search request contained errors.
-enter_search_term = Please enter a search term.
-invalid_search_term = Search term was invalid
-paging_link_more = more...
-no_matching_results = No matching results.
-search_failed = Search failed.
-search_term_error_near = The search term had an error near
-search_for = Search for ''{0}''
-
 #
 # shortview templates ( /templates/freemarker/body/partials/shortview )
 #
@@ -668,7 +665,6 @@ account = account
 change_password_to_login = Change Password to Log in
 new_password_capitalized = New Password
 confirm_password_capitalized = Confirm Password
-minimum_password_length = Minimum of {0} characters in length.
 already_logged_in = You are already logged in.
 
 #

webapp/web/templates/freemarker/body/individual/individual-menu.ftl

@@ -18,7 +18,7 @@
     <#-- List the menu items -->
     <ul class="menuItems">
         <#list hasElement.statements as statement>
-            <li class="menuItem"><#include "${hasElement.template}"> <span class="controls"><!--p.editingLinks "hasElement" statement editable /--></span></li>
+            <li class="menuItem"><#include "${hasElement.template}"> <span class="controls"><!--p.editingLinks "hasElement" "" statement editable /--></span></li>
         </#list>
     </ul>
     

webapp/web/templates/freemarker/body/siteAdmin/siteAdmin-siteConfiguration.ftl

@@ -8,7 +8,7 @@
         
         <ul role="navigation">
             <#if siteConfig.internalClass?has_content>
-                <li role="listitem"><a href="${siteConfig.internalClass}" title="${i18n().internal_class}">${i18n().internal_class}</a></li>
+                <li role="listitem"><a href="${siteConfig.internalClass}" title="${i18n().internal_class}">${i18n().internal_class_i_capped}</a></li>
             </#if>     
             
             <#if siteConfig.manageProxies?has_content>

webapp/web/templates/freemarker/edit/forms/js/customFormWithAutocomplete.js

@@ -144,7 +144,7 @@ var customForm = {
         // Put this case first, because in edit mode with
         // validation errors we just want initFormFullView.
 //        if ((!this.supportEdit) && (this.editMode == 'edit' || this.editMode == 'repair')) {
-        if (this.editMode == 'edit' || this.editMode == 'repair') {
+        if (this.editMode == 'edit' || this.editMode == 'repair' || this.editMode == 'error') {
             this.initFormWithValidationErrors();
         }
         else if (this.findValidationErrors()) {
@@ -321,8 +321,12 @@ var customForm = {
                     },
                     complete: function(xhr, status) {
                         // Not sure why, but we need an explicit json parse here. 
-                        var results = $.parseJSON(xhr.responseText),                        
+                        var results = $.parseJSON(xhr.responseText);                        
-                            filteredResults = customForm.filterAcResults(results);
+                        var filteredResults = customForm.filterAcResults(results);
+                        
+                        if ( customForm.acTypes[$(selectedObj).attr('acGroupName')] == "http://www.w3.org/2004/02/skos/core#Concept" ) {
+                            filteredResults = customForm.removeConceptSubclasses(filteredResults);
+                        }
 
                         customForm.acCache[request.term] = filteredResults;
                         response(filteredResults);
@@ -423,6 +427,16 @@ var customForm = {
         
     },
         
+    removeConceptSubclasses: function(array) {
+       $(array).each(function(i) {
+          if(this["msType"] != "http://www.w3.org/2004/02/skos/core#Concept") {
+              //Remove from array
+              array.splice(i, 1);
+          }    
+       });
+       return array;
+    },
+
     showAutocompleteSelection: function(label, uri, selectedObj) {
         // hide the acSelector field and set it's value to the selected ac item
         this.hideFields($(selectedObj).parent());

webapp/web/templates/freemarker/lib/lib-properties.ftl

@@ -108,13 +108,13 @@ name will be used as the label. -->
     <#if editable>
         <#local url = property.addUrl>
         <#if url?has_content>
-            <@showAddLink property.localName label url />
+            <@showAddLink property.localName property.name label url />
         </#if>
     </#if>
 </#macro>
 
-<#macro showAddLink propertyLocalName label url>
+<#macro showAddLink propertyLocalName propertyName label url>
-    <#if propertyLocalName == "informationResourceInAuthorship" || propertyLocalName == "webpage" || propertyLocalName == "hasResearchArea">
+    <#if propertyName == "informationResourceInAuthorship" || propertyName == "webpage" || propertyLocalName == "hasResearchArea">
         <a class="add-${propertyLocalName}" href="${url}" title="${i18n().manage_list_of} ${label?lower_case}">
         <img class="add-individual" src="${urls.images}/individual/manage-icon.png" alt="${i18n().manage}" /></a>
     <#else>
@@ -131,30 +131,42 @@ name will be used as the label. -->
 <#macro propertyListItem property statement editable >
     <li role="listitem">    
         <#nested>       
-        <@editingLinks "${property.localName}" statement editable/>
+        <@editingLinks "${property.localName}" "${property.name}" statement editable/>
     </li>
 </#macro>
 
-<#macro editingLinks propertyLocalName statement editable>
+<#macro editingLinks propertyLocalName propertyName statement editable>
-    <#if editable && (propertyLocalName != "informationResourceInAuthorship" && propertyLocalName != "webpage" && propertyLocalName != "hasResearchArea")>
+    <#if editable && (propertyName != "authors" && propertyName != "webpage" && propertyLocalName != "hasResearchArea")>
-        <@editLink propertyLocalName statement />
+        <@editLink propertyLocalName propertyName statement />
-        <@deleteLink propertyLocalName statement />
+        <@deleteLink propertyLocalName propertyName statement />
      
     </#if>
 </#macro>
-
+<#macro editLink propertyLocalName propertyName statement>
-<#macro editLink propertyLocalName statement>
+<#if propertyLocalName?contains("ARG_2000028")>
+    <#if propertyName?contains("mailing address")>
+        <#local url = statement.editUrl + "&addressUri=" + "${statement.address!}">
+    <#elseif propertyName?contains("phone")>
+        <#local url = statement.editUrl + "&phoneUri=" + "${statement.phone!}">
+    <#elseif propertyName?contains("primary email") || propertyName?contains("additional emails")>
+        <#local url = statement.editUrl + "&emailUri=" + "${statement.email!}">
+    <#elseif propertyName?contains("full name")>
+        <#local url = statement.editUrl + "&fullNameUri=" + "${statement.fullName!}">
+    </#if>
+<#else>
     <#local url = statement.editUrl>
+</#if>
     <#if url?has_content>
         <@showEditLink propertyLocalName url />
     </#if>
+
 </#macro>
 
 <#macro showEditLink propertyLocalName url>
     <a class="edit-${propertyLocalName}" href="${url}" title="${i18n().edit_entry}"><img class="edit-individual" src="${urls.images}/individual/editIcon.gif" alt="${i18n().edit_entry}" /></a>
 </#macro>
 
-<#macro deleteLink propertyLocalName statement> 
+<#macro deleteLink propertyLocalName propertyName statement> 
     <#local url = statement.deleteUrl>
     <#if url?has_content>
         <@showDeleteLink propertyLocalName url />
@@ -197,7 +209,7 @@ name will be used as the label. -->
         <a href="${individual.imageUrl}" title="${i18n().alt_thumbnail_photo}">
         	<img class="individual-photo" src="${thumbUrl}" title="${i18n().click_to_view_larger}" alt="${individual.name}" width="${imageWidth!}" />
         </a>
-        <@editingLinks "${mainImage.localName}" mainImage.first() editable />
+        <@editingLinks "${mainImage.localName}" "" mainImage.first() editable />
     <#else>
         <#local imageLabel><@addLinkWithLabel mainImage editable "${i18n().photo}" /></#local>
         ${imageLabel}
@@ -218,7 +230,7 @@ name will be used as the label. -->
     <#local label = individual.nameStatement>
     ${label.value}
     <#if useEditLink>
-    	<@editingLinks "label" label editable />
+    	<@editingLinks "label" "" label editable />
     <#elseif editable || (labelCount > 1)>
     <#--We display the link even when the user is not logged in case of multiple labels-->
     	<#if editable>