some merges back to the trunk that I forgot to commit earlier

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

@@ -9,7 +9,7 @@ import java.util.Date;
    from the entities, object property statements, properties, and ent2relationships tables
    bundled up in a usable object.
 */
-public class PropertyInstance implements PropertyInstanceIface {
+public class PropertyInstance implements PropertyInstanceIface, Comparable<PropertyInstance> {
 
     private String propertyURI = null;
     private String objectEntURI = null;
@@ -199,4 +199,18 @@ public class PropertyInstance implements PropertyInstanceIface {
         }
         return out;
     }
+    
+    public int compareTo(PropertyInstance pi) {
+
+        try {
+            if (this.getDomainPublic().equals(pi.getDomainPublic())) {
+                return this.getRangeClassName().compareTo(pi.getRangeClassName());
+            } else {
+                return (this.getDomainPublic().compareTo(pi.getDomainPublic()));
+            }
+        } catch (NullPointerException npe) {
+            return -1;
+        }
+
+    }
 }

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

@@ -12,6 +12,7 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 import javax.servlet.RequestDispatcher;
 import javax.servlet.http.HttpServletRequest;
@@ -64,10 +65,28 @@ public class PropertyWebappsListingController extends BaseEditController {
         VClassDao vcDao = vrequest.getFullWebappDaoFactory().getVClassDao();
         PropertyGroupDao pgDao = vrequest.getFullWebappDaoFactory().getPropertyGroupDao();
 
+        String vclassURI = request.getParameter("vclassUri");
+        
         List props = new ArrayList();
         if (request.getParameter("propsForClass") != null) {
             noResultsMsgStr = "There are no properties that apply to this class.";
-            Collection propInsts = piDao.getAllPropInstByVClass(request.getParameter("vclassUri"));
+            
+            // incomplete list of classes to check, but better than before
+            List<String> superclassURIs = vcDao.getAllSuperClassURIs(vclassURI);
+            superclassURIs.add(vclassURI);
+            superclassURIs.addAll(vcDao.getEquivalentClassURIs(vclassURI));
+            
+            Map<String, PropertyInstance> propInstMap = new HashMap<String, PropertyInstance>();
+            for (String classURI : superclassURIs) {
+            	Collection<PropertyInstance> propInsts = piDao.getAllPropInstByVClass(classURI);
+            	for (PropertyInstance propInst : propInsts) {
+            		propInstMap.put(propInst.getPropertyURI(), propInst);
+            	}
+            }
+            List<PropertyInstance> propInsts = new ArrayList<PropertyInstance>();
+            propInsts.addAll(propInstMap.values());
+            Collections.sort(propInsts);
+            
             Iterator propInstIt = propInsts.iterator();
             HashSet propURIs = new HashSet();
             while (propInstIt.hasNext()) {

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

@@ -117,12 +117,14 @@ public class BrowseController extends FreeMarkerHttpServlet {
             // Get all classgroups, each populated with a list of their member vclasses
             List groups = vcgDao.getPublicGroupsWithVClasses(ORDER_BY_DISPLAYRANK, !INCLUDE_UNINSTANTIATED); 
 
+            // remove classes that have been configured to be hidden
+            // from search results
+            removeClassesHiddenFromSearch(groups);
+            
             // now cull out the groups with no populated classes
             //removeUnpopulatedClasses( groups);
             vcgDao.removeUnpopulatedGroups(groups);
             
-            removeClassesHiddenFromSearch(groups);
-
             _groupListMap.put(portalId, groups);
             return groups;
         } else {

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

@@ -45,6 +45,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
 
 public class DataPropertyDaoJena extends PropertyDaoJena implements
@@ -96,6 +97,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
     	// TODO check if used as onProperty of restriction
     	ontModel.enterCriticalSection(Lock.WRITE);
     	try {
+    		getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),true));
 	        DatatypeProperty dp = ontModel.getDatatypeProperty(URI);
 	        if (dp != null) {
 	           	Iterator<Resource> restIt = ontModel.listSubjectsWithProperty(OWL.onProperty, dp);
@@ -109,6 +111,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
             	removeRulesMentioningResource(dp, ontModel);
                 dp.remove();
 	        }
+	        getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),false));
     	} finally {
     		ontModel.leaveCriticalSection();
     	}
@@ -509,6 +512,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
     public String insertDataProperty(DataProperty dtp, OntModel ontModel) throws InsertException {
         ontModel.enterCriticalSection(Lock.WRITE);
         try {
+        	getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),true));
         	String errMsgStr = getWebappDaoFactory().checkURI(dtp.getURI());
         	if (errMsgStr != null) {
         		throw new InsertException(errMsgStr);
@@ -565,6 +569,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
                 log.error("error linking data property "+dtp.getURI()+" to property group");
             }
             addPropertyStringValue(jDataprop,PROPERTY_CUSTOMENTRYFORMANNOT,dtp.getCustomEntryForm(),ontModel);
+            getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),false));
         } finally {
             ontModel.leaveCriticalSection();
         }
@@ -578,6 +583,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
     public void updateDataProperty(DataProperty dtp, OntModel ontModel) {
         ontModel.enterCriticalSection(Lock.WRITE);
         try {
+        	getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),true));
             com.hp.hpl.jena.ontology.DatatypeProperty jDataprop = ontModel.getDatatypeProperty(dtp.getURI());
             
             updateRDFSLabel(jDataprop, dtp.getPublicName());
@@ -614,6 +620,7 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
             }                        
                         
             updatePropertyStringValue(jDataprop,PROPERTY_CUSTOMENTRYFORMANNOT,dtp.getCustomEntryForm(),ontModel);
+            getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),false));
         } finally {
             ontModel.leaveCriticalSection();
         }

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

@@ -379,6 +379,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
 	        doUpdate(prop,p,inv,ontModel);
 	        return 0;
         } finally {
+        	getOntModel().getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),false));
         	ontModel.leaveCriticalSection();
         }
     }

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

@@ -268,6 +268,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
     	getOntModel().enterCriticalSection(Lock.READ);
     	try {
 	    	OntClass ontClass = getOntClass(getOntModel(), classURI);
+	    	System.out.println(classURI);
 	    	ClosableIterator equivalentOntClassIt = ontClass.listEquivalentClasses();
 	    	try {
 	    		for (Iterator eqOntClassIt = equivalentOntClassIt; eqOntClassIt.hasNext(); ) {
@@ -394,7 +395,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 		//if ("true".equalsIgnoreCase(infersTypes)) {
 		
 		PelletListener pl = getWebappDaoFactory().getPelletListener();
-		if (pl != null && pl.isConsistent() && !pl.isInErrorState()) {	
+		if (pl != null && pl.isConsistent() && !pl.isInErrorState() && !pl.isReasoning()) {	
 			superclassURIs = new ArrayList<String>();
 			OntClass cls = getOntClass(getOntModel(),classURI);
 			StmtIterator superClassIt = getOntModel().listStatements(cls,RDFS.subClassOf,(RDFNode)null);
@@ -740,7 +741,9 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 						String isInferencing = getWebappDaoFactory().getProperties().get("infersTypes");
 						// if this model infers types based on the taxonomy, adding the subclasses will only
 						// waste time for no benefit
-						if (isInferencing == null || "false".equalsIgnoreCase(isInferencing)) {
+						PelletListener pl = getWebappDaoFactory().getPelletListener();
+						if (pl == null || !pl.isConsistent() || pl.isInErrorState() || pl.isReasoning() 
+								|| isInferencing == null || "false".equalsIgnoreCase(isInferencing)) {
                         	Iterator classURIs = getAllSubClassURIs(getClassURIStr(superclass)).iterator();
                         	while (classURIs.hasNext()) {
                             	String classURI = (String) classURIs.next();
@@ -748,7 +751,6 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
                             	if (vClass != null)
                             	    vClasses.add(vClass);
                         	}
-						} else {
 						} 
                     }
                 }

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

@@ -80,6 +80,10 @@ public class PelletListener implements ModelChangedListener {
 		return this.inErrorState;
 	}
 	
+	public boolean isReasoning() {
+		return this.isReasoning;
+	}
+	
 	public void closePipe() {
 		pipeOpen = false;
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/SelectListGenerator.java

@@ -30,6 +30,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
+import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
@@ -241,7 +244,28 @@ public class SelectListGenerator {
                         log.error("Cannot find owl:Class " + vclassUri + " in the model" );
                         optionsMap.put("", "Could not find class " + vclassUri);
                     }else{                
-                        List<Individual> individuals = wDaoFact.getIndividualDao().getIndividualsByVClassURI(vclass.getURI(),-1,-1);                                   
+                        Map<String, Individual> individualMap = new HashMap<String, Individual>();
+                		
+                        for (Individual ind : wDaoFact.getIndividualDao().getIndividualsByVClassURI(vclass.getURI(),-1,-1)) {
+                        	if (ind.getURI() != null) {                        		
+                            	individualMap.put(ind.getURI(), ind);
+                        	}
+                        }
+                        
+                        if (!inferenceAvailable) {
+                        	for (String subclassURI : wDaoFact.getVClassDao().getAllSubClassURIs(vclass.getURI())) {
+                        		 for (Individual ind : wDaoFact.getIndividualDao().getIndividualsByVClassURI(subclassURI,-1,-1)) {
+                                 	if (ind.getURI() != null) {
+                                 		individualMap.put(ind.getURI(), ind);
+                                 	}
+                                 }
+                        	}
+                        }
+                        
+                        List<Individual> individuals = new ArrayList<Individual>();
+                        individuals.addAll(individualMap.values());
+                        Collections.sort(individuals);
+                        
                         Map<String, Individual> individualMap = new HashMap<String, Individual>();
                 		
                         for (Individual ind : wDaoFact.getIndividualDao().getIndividualsByVClassURI(vclass.getURI(),-1,-1)) {

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

@@ -163,27 +163,28 @@ public class TBoxUpdater {
 			 if (!newObject.equals(oldObject)) {
 				 NodeIterator siteObjects = siteModel.listObjectsOfProperty(subject,predicate);
 			
-				 if (siteObjects == null || !siteObjects.hasNext()) {
+				 RDFNode siteObject = null;
-					 continue;
+				
+				 if (siteObjects != null && siteObjects.hasNext()) {
+			
+					 siteObject = siteObjects.next();
+	
+			         i = 1;
+					 while (siteObjects.hasNext()) {
+						 i++; 
+						 siteObjects.next();
+					 } 
+	
+					 if (i > 1) {
+						 logger.log("WARNING: found " + i +
+								 " statements with subject = " + subject.getURI() + 
+								 " and property = " + predicate.getURI() +
+								 " in the site annotations model. (maximum of one is expected). "); 
+						 continue; 
+					 }
 				 }
 				 	 
-				 RDFNode siteObject = siteObjects.next();
+				 if (siteObject == null || siteObject.equals(oldObject)) {
-
-		         i = 1;
-				 while (siteObjects.hasNext()) {
-					 i++; 
-					 siteObjects.next();
-				 } 
-
-				 if (i > 1) {
-					 logger.log("WARNING: found " + i +
-							 " statements with subject = " + subject.getURI() + 
-							 " and property = " + predicate.getURI() +
-							 " in the site annotations model. (maximum of one is expected). "); 
-					 continue; 
-				 }
-				 	 
-				 if (siteObject.equals(oldObject)) {
 	        	    try {
 	        	    	StmtIterator it = siteModel.listStatements(subject, predicate, (RDFNode)null);
 	        	    	while (it.hasNext()) {

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

@@ -104,7 +104,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 				  if (ontologyUpdater.updateRequired()) {
 					  ctx.setAttribute(LuceneSetup.INDEX_REBUILD_REQUESTED_AT_STARTUP, Boolean.TRUE);
 					  doMiscAppMetadataReplacements(ctx.getRealPath(MISC_REPLACEMENTS_FILE), oms);
-					  System.out.println(ctx.getRealPath(MISC_REPLACEMENTS_FILE));
 				  }
 			  } catch (Throwable t){
 				  log.error("Unable to perform miscellaneous application metadata replacements", t);