NIHVIVO-1333 Lots of work on display of ontology properties on individual page (nothing visible yet).

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

@@ -46,12 +46,18 @@ public interface Individual extends ResourceBean, VitroTimeWindowedResource, Com
     List<ObjectProperty> getObjectPropertyList();
     void setPropertyList(List<ObjectProperty> propertyList);
 
+    List<ObjectProperty> getPopulatedObjectPropertyList();
+    void setPopulatedObjectPropertyList(List<ObjectProperty> propertyList);
+    
     Map<String,ObjectProperty> getObjectPropertyMap();
     void setObjectPropertyMap(Map<String,ObjectProperty> propertyMap);
     
     List<DataProperty> getDataPropertyList();
     void setDatatypePropertyList(List<DataProperty> datatypePropertyList);
 
+    List<DataProperty> getPopulatedDataPropertyList();
+    void setPopulatedDataPropertyList(List<DataProperty> dataPropertyList);
+    
     Map<String,DataProperty> getDataPropertyMap();
     void setDataPropertyMap(Map<String,DataProperty> propertyMap);
     

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

@@ -36,8 +36,10 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
     protected Date timekey = null;
     protected Timestamp modTime = null;
     protected List <ObjectProperty>propertyList = null;
+    protected List<ObjectProperty> populatedObjectPropertyList = null;
     protected Map <String,ObjectProperty> objectPropertyMap = null;
     protected List <DataProperty>datatypePropertyList = null;
+    protected List<DataProperty> populatedDataPropertyList = null;
     protected Map <String,DataProperty> dataPropertyMap = null;
     protected List <DataPropertyStatement>dataPropertyStatements = null;
     protected List <ObjectPropertyStatement>objectPropertyStatements = null;
@@ -118,6 +120,12 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
     public void setPropertyList(List <ObjectProperty>propertyList) {
         this.propertyList = propertyList;
     }
+    public List<ObjectProperty> getPopulatedObjectPropertyList() {
+        return populatedObjectPropertyList;
+    }
+    public void setPopulatedObjectPropertyList(List<ObjectProperty> propertyList) {
+        populatedObjectPropertyList = propertyList;
+    }
     public Map<String,ObjectProperty> getObjectPropertyMap() {
     	return this.objectPropertyMap;
     }
@@ -130,6 +138,12 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
     public void setDatatypePropertyList(List <DataProperty>datatypePropertyList) {
         this.datatypePropertyList = datatypePropertyList;
     }
+    public List<DataProperty> getPopulatedDataPropertyList() {
+        return populatedDataPropertyList;
+    }
+    public void setPopulatedDataPropertyList(List<DataProperty> propertyList) {
+        populatedDataPropertyList = propertyList;
+    }
     public Map<String,DataProperty> getDataPropertyMap() {
     	return this.dataPropertyMap;
     }

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

@@ -34,5 +34,9 @@ public interface DataPropertyDao extends PropertyDao {
 
     List<DataProperty> getRootDataProperties();
     
-    boolean annotateDataPropertyAsExternalIdentifier(String dataPropertyURI);
+    boolean annotateDataPropertyAsExternalIdentifier(String dataPropertyURI);
+    
+    public List<DataProperty> getDataPropertyList(Individual subject);
+    
+    public List<DataProperty> getDataPropertyList(String subjectUri);
 }

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

@@ -50,5 +50,9 @@ public interface ObjectPropertyDao extends PropertyDao {
 
 //    List /* of ObjectProperty */ getAllObjectProperties();
 
-    List <ObjectProperty> getRootObjectProperties();
+    List <ObjectProperty> getRootObjectProperties();
+    
+    public List<ObjectProperty> getObjectPropertyList(Individual subject);
+    
+    public List<ObjectProperty> getObjectPropertyList(String subjectUri); 
 }

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

@@ -1,15 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao;
-
-import java.util.List;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.Property;
-
-public interface PropertyListDao {
-    
-    public List<Property> getPropertyListForSubject(Individual subject);
-    
-    public List<Property> getPropertyListForSubject(String subjectUri); 
-}

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

@@ -132,6 +132,4 @@ public interface WebappDaoFactory {
     public NamespaceDao getNamespaceDao();
     
     public PropertyInstanceDao getPropertyInstanceDao();    
-    
-    public PropertyListDao getPropertyListDao();
 }

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

@@ -5,6 +5,9 @@ package edu.cornell.mannlib.vitro.webapp.dao.filtering;
 import java.util.Collection;
 import java.util.List;
 
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+
 import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
@@ -188,5 +191,17 @@ class DataPropertyDaoFiltering extends BaseFiltering implements DataPropertyDao{
     public List <VClass> getClassesWithRestrictionOnProperty(String propertyURI) {
     	return innerDataPropertyDao.getClassesWithRestrictionOnProperty(propertyURI);
     }
+    
+    @Override
+    // This may need to be filtered at some point.
+    public List<DataProperty> getDataPropertyList(Individual subject) {
+        return innerDataPropertyDao.getDataPropertyList(subject);
+    }
+    
+    @Override
+    // This may need to be filtered at some point.
+    public List<DataProperty> getDataPropertyList(String subjectUri) {
+        return innerDataPropertyDao.getDataPropertyList(subjectUri);
+    }
 
 }

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

@@ -70,7 +70,27 @@ public class IndividualFiltering implements Individual {
         return outdProps;
     }
 
-
+    public List<DataProperty> getPopulatedDataPropertyList() {
+        List<DataProperty> dprops =  _innerIndividual.getPopulatedDataPropertyList();
+        LinkedList<DataProperty> outdProps = new LinkedList<DataProperty>();
+        Filter.filter(dprops,_filters.getDataPropertyFilter(), outdProps);
+        
+        ListIterator<DataProperty> it = outdProps.listIterator();
+        while(it.hasNext()){
+            DataProperty dp = it.next();
+            List<DataPropertyStatement> filteredStmts = 
+                new LinkedList<DataPropertyStatement>();
+            Filter.filter(dp.getDataPropertyStatements(),
+                    _filters.getDataPropertyStatementFilter(),filteredStmts);
+            if( filteredStmts == null || filteredStmts.size() == 0 ){
+                it.remove();
+            }else{
+                dp.setDataPropertyStatements(filteredStmts);
+            }
+        }
+        return outdProps;
+    }
+    
     public List<DataPropertyStatement> getDataPropertyStatements() {
         List<DataPropertyStatement> dstmts = _innerIndividual.getDataPropertyStatements();
         return filterDataPropertyStatements(dstmts);      
@@ -112,6 +132,13 @@ public class IndividualFiltering implements Individual {
     public List<ObjectProperty> getObjectPropertyList() {
         List <ObjectProperty> oprops = _innerIndividual.getObjectPropertyList();
 //        List<ObjectProperty> outOProps = new LinkedList<ObjectProperty>();
+//        Filter.filter(oprops, _filters.getObjectPropertyFilter(), outOProps);
+        return ObjectPropertyDaoFiltering.filterAndWrap(oprops, _filters);
+    }
+    
+    public List<ObjectProperty> getPopulatedObjectPropertyList() {
+        List <ObjectProperty> oprops = _innerIndividual.getPopulatedObjectPropertyList();
+//        List<ObjectProperty> outOProps = new LinkedList<ObjectProperty>();
 //        Filter.filter(oprops, _filters.getObjectPropertyFilter(), outOProps);
         return ObjectPropertyDaoFiltering.filterAndWrap(oprops, _filters);
     }
@@ -360,6 +387,10 @@ public class IndividualFiltering implements Individual {
         _innerIndividual.setDatatypePropertyList(datatypePropertyList);
     }
 
+    public void setPopulatedDataPropertyList(List<DataProperty> dataPropertyList) {
+        _innerIndividual.setPopulatedDataPropertyList(dataPropertyList);
+    }
+    
     public void setDescription(String in) {
         _innerIndividual.setDescription(in);
     }
@@ -452,6 +483,10 @@ public class IndividualFiltering implements Individual {
         _innerIndividual.setPropertyList(propertyList);
     }
 
+    public void setPopulatedObjectPropertyList(List<ObjectProperty> propertyList) {
+        _innerIndividual.setPopulatedObjectPropertyList(propertyList);
+    }
+    
     public void setStatus(String s) {
         _innerIndividual.setStatus(s);
     }

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

@@ -9,6 +9,7 @@ import java.util.List;
 import net.sf.jga.algorithms.Filter;
 import net.sf.jga.fn.UnaryFunctor;
 import net.sf.jga.fn.adaptor.AndUnary;
+import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
@@ -201,5 +202,16 @@ class ObjectPropertyDaoFiltering extends BaseFiltering implements ObjectProperty
     public List <VClass> getClassesWithRestrictionOnProperty(String propertyURI) {
     	return innerObjectPropertyDao.getClassesWithRestrictionOnProperty(propertyURI);
     }
-	
+
+    @Override
+    // This may need to be filtered at some point.
+    public List<ObjectProperty> getObjectPropertyList(Individual subject) {
+        return innerObjectPropertyDao.getObjectPropertyList(subject);
+    }
+    
+    @Override
+    // This may need to be filtered at some point.
+    public List<ObjectProperty> getObjectPropertyList(String subjectUri) {
+        return innerObjectPropertyDao.getObjectPropertyList(subjectUri);
+    }
 }

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

@@ -24,7 +24,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PortalDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
-import edu.cornell.mannlib.vitro.webapp.dao.PropertyListDao;
 import edu.cornell.mannlib.vitro.webapp.dao.TabDao;
 import edu.cornell.mannlib.vitro.webapp.dao.TabIndividualRelationDao;
 import edu.cornell.mannlib.vitro.webapp.dao.TabVClassRelationDao;
@@ -215,6 +214,11 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
         return innerWebappDaoFactory.getPortalDao();
     }
 
+///////////////////////////////////////////////////////////////////
+
+
+    /* ******************* non-filtering DAOs *************************** */
+
     public Classes2ClassesDao getClasses2ClassesDao() {
         return innerWebappDaoFactory.getClasses2ClassesDao();
     }
@@ -230,11 +234,6 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
     public OntologyDao getOntologyDao() {
         return innerWebappDaoFactory.getOntologyDao();
     }
-    
-    // rjy7 This may actually need to be filtered...
-    public PropertyListDao getPropertyListDao() {
-        return innerWebappDaoFactory.getPropertyListDao();
-    }
   
     /* ******************* filtering DAOs *************************** */
 

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

@@ -22,6 +22,13 @@ import com.hp.hpl.jena.ontology.OntResource;
 import com.hp.hpl.jena.ontology.ProfileException;
 import com.hp.hpl.jena.ontology.Restriction;
 import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
+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.QuerySolutionMap;
+import com.hp.hpl.jena.query.ResultSet;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
@@ -38,6 +45,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean;
 import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
@@ -52,7 +60,28 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
         DataPropertyDao {
     
     protected static final Log log = LogFactory.getLog(DataPropertyDaoJena.class.getName());
-
+    
+    protected static final String dataPropertyQueryString = 
+        PREFIXES + "\n" +
+        "SELECT DISTINCT ?predicate WHERE { \n" +
+        //"   GRAPH ?g {\n" + 
+        "       ?subject ?predicate ?object . \n" +
+        "       ?predicate rdf:type owl:DatatypeProperty . \n" +
+        //"       OPTIONAL { ?predicate vitro:inPropertyGroupAnnot ?group } . \n" +
+        //"   }\n" +
+        "}" +
+        "ORDER BY ?predicate\n";
+    
+    static protected Query dataPropertyQuery;
+    static {
+        try {
+            dataPropertyQuery = QueryFactory.create(dataPropertyQueryString);
+        } catch(Throwable th){
+            log.error("could not create SPARQL query for dataPropertyQueryString " + th.getMessage());
+            log.error(dataPropertyQueryString);
+        }             
+    }
+    
     private class DataPropertyRanker implements Comparator {
         public int compare (Object o1, Object o2) {
             DataProperty dp1 = (DataProperty) o1;
@@ -680,4 +709,30 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
             return rootProperties;
     }
 
+    @Override
+    public List<DataProperty> getDataPropertyList(Individual subject) {
+        return getDataPropertyList(subject.getURI());
+    }
+    
+    @Override
+    public List<DataProperty> getDataPropertyList(String subjectUri) {
+        log.debug("dataPropertyQuery:\n" + dataPropertyQuery);        
+        ResultSet results = getPropertyQueryResults(subjectUri, dataPropertyQuery);
+        List<DataProperty> properties = new ArrayList<DataProperty>();
+        while (results.hasNext()) {
+            QuerySolution sol = results.next();
+            Resource resource = sol.getResource("predicate");
+            // This is a hack to throw out properties in the vitro, rdf, rdfs, and owl namespaces.
+            // It will be implemented in a better way in v1.3 (Editing and Display Configuration).
+            // It must be done here rather than in PropertyList or PropertyListBuilder, because
+            // those properties must be removed for the IndividualFiltering object.
+            if ( ! EXCLUDED_NAMESPACES.contains(resource.getNameSpace())) {
+                String uri = resource.getURI();
+                DataProperty property = getDataPropertyByURI(uri);
+                properties.add(property);
+            }
+        }
+        return properties; 
+    }
+    
 }

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

@@ -43,6 +43,7 @@ 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.VClass;
+import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.filestorage.model.ImageInfo;
@@ -735,6 +736,14 @@ public class IndividualJena extends IndividualImpl implements Individual {
             return this.propertyList;
         }
     }
+
+    @Override 
+    public List<ObjectProperty> getPopulatedObjectPropertyList() {
+        if (populatedObjectPropertyList == null) {
+            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyDao().getObjectPropertyList(this);
+        }
+        return populatedObjectPropertyList;       
+    }
     
     @Override
     public Map<String,ObjectProperty> getObjectPropertyMap() {
@@ -782,6 +791,14 @@ public class IndividualJena extends IndividualImpl implements Individual {
         }
     }
     
+    @Override 
+    public List<DataProperty> getPopulatedDataPropertyList() {
+        if (populatedDataPropertyList == null) {
+            populatedDataPropertyList = webappDaoFactory.getDataPropertyDao().getDataPropertyList(this);
+        }
+        return populatedDataPropertyList;       
+    }
+    
     @Override
     public Map<String,DataProperty> getDataPropertyMap() {
     	if (this.dataPropertyMap != null) {

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

@@ -880,6 +880,14 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             return this.propertyList;
         }
     }
+
+    @Override 
+    public List<ObjectProperty> getPopulatedObjectPropertyList() {
+        if (populatedObjectPropertyList == null) {
+            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyDao().getObjectPropertyList(this);
+        }
+        return populatedObjectPropertyList;       
+    }
     
     @Override
     public Map<String,ObjectProperty> getObjectPropertyMap() { 
@@ -926,6 +934,14 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             return this.datatypePropertyList;
         }
     }
+
+    @Override 
+    public List<DataProperty> getPopulatedDataPropertyList() {
+        if (populatedDataPropertyList == null) {
+            populatedDataPropertyList = webappDaoFactory.getDataPropertyDao().getDataPropertyList(this);
+        }
+        return populatedDataPropertyList;       
+    }
     
     @Override
     public Map<String,DataProperty> getDataPropertyMap() { 

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualSDB2.java

@@ -868,7 +868,15 @@ public class IndividualSDB2 extends IndividualImpl implements Individual {
             return this.propertyList;
         }
     }
-    
+
+    @Override 
+    public List<ObjectProperty> getPopulatedObjectPropertyList() {
+        if (populatedObjectPropertyList == null) {
+            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyDao().getObjectPropertyList(this);
+        }
+        return populatedObjectPropertyList;       
+    }
+
     @Override
     public Map<String,ObjectProperty> getObjectPropertyMap() {
     	if (this.objectPropertyMap != null) {

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

@@ -17,6 +17,11 @@ import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntProperty;
 import com.hp.hpl.jena.ontology.OntResource;
 import com.hp.hpl.jena.ontology.ProfileException;
+import com.hp.hpl.jena.query.Query;
+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.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
@@ -43,6 +48,27 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectPropertyDao {
     private static final Log log = LogFactory.getLog(ObjectPropertyDaoJena.class.getName());
 
+    protected static final String objectPropertyQueryString = 
+        PREFIXES + "\n" +
+        "SELECT DISTINCT ?predicate WHERE { \n" +
+        //"   GRAPH ?g {\n" + 
+        "       ?subject ?predicate ?object . \n" +
+        "       ?predicate rdf:type owl:ObjectProperty . \n" +
+        //"       OPTIONAL { ?predicate vitro:inPropertyGroupAnnot ?group } . \n" +
+        //"   }\n" +
+        "}" +
+        "ORDER BY ?predicate\n";
+
+    static protected Query objectPropertyQuery;
+    static {
+        try {
+            objectPropertyQuery = QueryFactory.create(objectPropertyQueryString);
+        } catch(Throwable th){
+            log.error("could not create SPARQL query for objectPropertyQueryString " + th.getMessage());
+            log.error(objectPropertyQueryString);
+        }           
+    }
+    
     public ObjectPropertyDaoJena(WebappDaoFactoryJena wadf) {
         super(wadf);
     }
@@ -799,4 +825,31 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     	return false;
     }
 
+    @Override
+    public List<ObjectProperty> getObjectPropertyList(Individual subject) {
+        return getObjectPropertyList(subject.getURI());
+    }
+    
+    @Override
+    public List<ObjectProperty> getObjectPropertyList(String subjectUri) {
+        log.debug("objectPropertyQuery:\n" + objectPropertyQuery);
+        ResultSet results = getPropertyQueryResults(subjectUri, objectPropertyQuery);
+        List<ObjectProperty> properties = new ArrayList<ObjectProperty>();
+        while (results.hasNext()) {
+            QuerySolution sol = results.next();
+            Resource resource = sol.getResource("predicate");
+            // This is a hack to throw out properties in the vitro, rdf, rdfs, and owl namespaces.
+            // It will be implemented in a better way in v1.3 (Editing and Display Configuration).
+            // It must be done here rather than in PropertyList or PropertyListBuilder, because
+            // those properties must be removed for the IndividualFiltering object.
+            if ( ! EXCLUDED_NAMESPACES.contains(resource.getNameSpace())) {
+                String uri = resource.getURI();
+                ObjectProperty property = getObjectPropertyByURI(uri);
+                properties.add(property);
+            }
+        }
+        return properties; 
+    }
+
+    
 }

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

@@ -3,6 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.LinkedList;
@@ -14,8 +15,15 @@ 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.OntProperty;
+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.QuerySolution;
+import com.hp.hpl.jena.query.QuerySolutionMap;
+import com.hp.hpl.jena.query.ResultSet;
 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;
@@ -32,7 +40,20 @@ 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 PREFIXES = 
+        "PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
+        "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n" + 
+        "PREFIX owl: <http://www.w3.org/2002/07/owl#> \n";
+
+    protected static final List<String> EXCLUDED_NAMESPACES = Arrays.asList(
+            "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#",
+            "http://vitro.mannlib.cornell.edu/ns/vitro/public#",
+            "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+            "http://www.w3.org/2000/01/rdf-schema#",
+            "http://www.w3.org/2002/07/owl#"            
+        );
+    
     public PropertyDaoJena(WebappDaoFactoryJena wadf) {
         super(wadf);
     }
@@ -369,4 +390,15 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         		
         return classSet;
     }
+     
+    protected ResultSet getPropertyQueryResults(String subjectUri, Query query) {        
+        log.debug("SPARQL query:\n" + query.toString());
+        // Bind the subject's uri to the ?subject query term
+        QuerySolutionMap subjectBinding = new QuerySolutionMap();
+        subjectBinding.add("subject", ResourceFactory.createResource(subjectUri));
+
+        // Run the SPARQL query to get the properties        
+        QueryExecution qexec = QueryExecutionFactory.create(query, getOntModelSelector().getFullModel(), subjectBinding);
+        return qexec.execSelect();        
+    }
 }

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

@@ -1,74 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.util.List;
-
-import com.hp.hpl.jena.ontology.OntModel;
-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.QuerySolutionMap;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.Property;
-import edu.cornell.mannlib.vitro.webapp.dao.PropertyListDao;
-
-public class PropertyListDaoJena extends JenaBaseDao implements PropertyListDao {
-
-    static final protected String propertyQueryString = 
-        "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>\n" +
-        "SELECT ?group ?predicate WHERE {\n" +
-        "   GRAPH ?g {\n" + 
-        "       ?subject ?predicate ?object . \n" +
-        "       OPTIONAL { ?predicate vitro:inPropertyGroupAnnot ?group . \n" +
-        "       }\n" +
-        "   }\n" +
-        "}" +
-        "ORDER BY DESC(?group) ?predicate\n";
-    
-    
-    static protected Query propertyQuery;
-    static {
-        try {
-            propertyQuery = QueryFactory.create(propertyQueryString);
-        } catch(Throwable th){
-            log.error("could not create SPARQL query for propertyQueryString " + th.getMessage());
-            log.error(propertyQueryString);
-        }  
-    }
-    public PropertyListDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-    
-    @Override
-    protected OntModel getOntModel() {
-        return getOntModelSelector().getABoxModel();
-    }
-    
-    @Override
-    public List<Property> getPropertyListForSubject(Individual subject) {
-        return getPropertyListForSubject(subject.getURI());
-    }
-    
-    @Override
-    public List<Property> getPropertyListForSubject(String subjectUri) {
-        
-        // First get all the properties that occur in statements with this subject as subject. We must get these
-        // from a db query because they may include properties that are not defined as "possible properties" 
-        // for a subject of this class.
-        
-        // Bind the subject's uri to the ?subject query term
-        QuerySolutionMap subjectBinding = new QuerySolutionMap();
-        subjectBinding.add("subject", ResourceFactory.createResource(subjectUri));
-
-        // Run the SPARQL query to get the properties        
-        QueryExecution qexec = QueryExecutionFactory.create(propertyQuery, getOntModel());
-        ResultSet results = qexec.execSelect();
-        return null; 
-    }
-
-}

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

@@ -9,6 +9,7 @@ import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.CopyOnWriteArrayList;
 
 import com.hp.hpl.jena.iri.IRI;
 import com.hp.hpl.jena.iri.IRIFactory;
@@ -29,6 +30,7 @@ import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.ApplicationDao;
 import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
@@ -47,7 +49,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PortalDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
-import edu.cornell.mannlib.vitro.webapp.dao.PropertyListDao;
 import edu.cornell.mannlib.vitro.webapp.dao.TabDao;
 import edu.cornell.mannlib.vitro.webapp.dao.TabIndividualRelationDao;
 import edu.cornell.mannlib.vitro.webapp.dao.TabVClassRelationDao;
@@ -547,14 +548,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
             propertyInstanceDao = new PropertyInstanceDaoJena(this);
         return propertyInstanceDao;
     }
-    
-    private PropertyListDao propertyListDao = null;
-    public PropertyListDao getPropertyListDao() {
-        if (propertyListDao == null) {
-            propertyListDao = new PropertyListDaoJena(this);
-        }
-        return propertyListDao;
-    }
 
     protected VClassDao vClassDao = null;
     public VClassDao getVClassDao() {

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

@@ -2,15 +2,18 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
+import java.util.ArrayList;
 import java.util.List;
 
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+
 public class CollatedObjectProperty extends ObjectPropertyTemplateModel {
 
-    private List<SubclassList> subclassList = null;
+    private List<SubclassList> subclassList;
     
-    CollatedObjectProperty(String predicateUri) {
+    CollatedObjectProperty(ObjectProperty property) {
-        super(predicateUri);
+        super(property);
-        // TODO Auto-generated constructor stub
+        subclassList = new ArrayList<SubclassList>();
     }
     
     public List<SubclassList> getSubclassList() {
@@ -20,4 +23,10 @@ public class CollatedObjectProperty extends ObjectPropertyTemplateModel {
     public List<SubclassList> getStatements() {
         return subclassList;
     }
+    
+    /* Access methods for templates */
+    
+    public boolean getIsCollatedBySubtype() {
+        return true;
+    }
 }

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

@@ -2,11 +2,21 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
-public class DataPropertyTemplateModel extends PropertyTemplateModel {
+import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 
-    DataPropertyTemplateModel(String predicateUri) {
+public class DataPropertyTemplateModel extends PropertyTemplateModel {
-        super(predicateUri);
+    
-        // TODO Auto-generated constructor stub
+    private static final String TYPE = "data";
+
+    DataPropertyTemplateModel(DataProperty property) {
+        super(property);
+    }
+
+    
+    /* Access methods for templates */
+    
+    public String getType() {
+        return TYPE;
     }
 
 }

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

@@ -2,25 +2,14 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
 import java.util.List;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import edu.cornell.mannlib.vedit.beans.LoginStatusBean;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.Property;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
-import edu.cornell.mannlib.vitro.webapp.dao.PropertyListDao;
-import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-import edu.cornell.mannlib.vitro.webapp.filters.VitroRequestPrep;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.BaseTemplateModel;
 
 /** The entire grouped property list for the subject.
@@ -32,60 +21,30 @@ import edu.cornell.mannlib.vitro.webapp.web.templatemodels.BaseTemplateModel;
 public class GroupedPropertyList extends BaseTemplateModel {
 
     private static final Log log = LogFactory.getLog(GroupedPropertyList.class);
-    private static final int MAX_GROUP_DISPLAY_RANK = 99;
-    
-    /** Don't include these properties in the list. */
-    private static final Collection<String> SUPPRESSED_OBJECT_PROPERTIES = Collections
-            .unmodifiableCollection(Arrays
-                    .asList(new String[] { VitroVocabulary.IND_MAIN_IMAGE }));
-   
-    // RY Do we really want to store subject and vreq as members? Could just pass around.
-    private Individual subject;
-    private VitroRequest vreq;
     
     private List<PropertyGroupTemplateModel> groups;
 
-    GroupedPropertyList(Individual subject, VitroRequest vreq) {
+    GroupedPropertyList(WebappDaoFactory wdf, PropertyList propertyList) {
-        // RY Do we really want to store these as members? Could just pass around.
-        this.subject = subject;
-        this.vreq = vreq;
         
         // Get the property groups
-        WebappDaoFactory wdf = vreq.getWebappDaoFactory();
+        PropertyGroupDao pgDao = wdf.getPropertyGroupDao(); 
-        PropertyGroupDao pgDao = wdf.getPropertyGroupDao();
         List<PropertyGroup> groupList = pgDao.getPublicGroups(false); // may be returned empty but not null
+//
+//        List<PropertyGroupTemplateModel> groups = new ArrayList<PropertyGroupTemplateModel>(groupList.size());
+//        for (PropertyGroup g : groupList) {
+//            groups.add(new PropertyGroupTemplateModel(g));
+//            // Properties unassigned to any group go in a dummy group with name an empty string. Templates
+//            // must test for <#if ! group.name?has_content> or <#if group.name == ""> or <#if group.name?length == 0>
+//            groups.add(new DummyPropertyGroupTemplateModel(""));
+//        }
+//        // If there are no groups, create a dummy group, so that the template display logic is the same
+//        // in both cases. Name is null. Templates must test for <#if ! group.name??> 
+//        if (groups.isEmpty()) {
+//            groups.add(new DummyPropertyGroupTemplateModel(null));
+//        }
 
-        List<PropertyGroupTemplateModel> groups = new ArrayList<PropertyGroupTemplateModel>(groupList.size());
-        for (PropertyGroup g : groupList) {
-            groups.add(new PropertyGroupTemplateModel(g));
-            // Properties unassigned to any group go in a dummy group with name an empty string. Templates
-            // must test for <#if ! group.name?has_content> or <#if group.name == ""> or <#if group.name?length == 0>
-            groups.add(new DummyPropertyGroupTemplateModel(""));
-        }
-        // If there are no groups, create a dummy group, so that the template display logic is the same
-        // in both cases. Name is null. Templates must test for <#if ! group.name??> 
-        if (groups.isEmpty()) {
-            groups.add(new DummyPropertyGroupTemplateModel(null));
-        }
-        
-        // Create the property list for the subject. The properties will be put into groups later.
-
-        // First get all the properties that occur in statements in the db with this subject as subject.
-        // This may include properties that are not defined as "possible properties" for a subject of this class.
-        PropertyListDao plDao = wdf.getPropertyListDao();
-        List<Property> propertyList = plDao.getPropertyListForSubject(subject);
-    
     }
 
-    /** 
-     * Return true iff the user is editing. 
-     */
-    private boolean getEditingStatus() { 
-        // These tests may change once self-editing issues are straightened out.
-        boolean isSelfEditing = VitroRequestPrep.isSelfEditing(vreq);
-        boolean isCurator = LoginStatusBean.getBean(vreq).isLoggedInAtLeast(LoginStatusBean.CURATOR);
-        return isSelfEditing || isCurator;
-    }
     
     /* 
      * Public getters for templates 

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

@@ -153,9 +153,9 @@ public class IndividualTemplateModel extends BaseTemplateModel {
     }
 
     public GroupedPropertyList getPropertyList() {
-//        PropertyListBuilder propListBuilder = new PropertyListBuilder(individual, vreq);
+        PropertyListBuilder propListBuilder = new PropertyListBuilder(individual, vreq);
-//        return propListBuilder.getPropertyList();
+        return propListBuilder.getPropertyList();
-        return new GroupedPropertyList(individual, vreq);
+        //return new GroupedPropertyList(individual, vreq);
     }
     
     /* These methods simply forward to the methods of the wrapped individual. It would be desirable to 

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

@@ -2,11 +2,23 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
-public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel {
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
 
-    ObjectPropertyTemplateModel(String predicateUri) {
+public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel {
-        super(predicateUri);
+    
-        // TODO Auto-generated constructor stub
+    private static final String TYPE = "object";
+
+    ObjectPropertyTemplateModel(ObjectProperty property) {
+        super(property);
     }
+    
+
+    /* Access methods for templates */
+    
+    public String getType() {
+        return TYPE;
+    }
+    
+    public abstract boolean getIsCollatedBySubtype();
 
 }

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

@@ -0,0 +1,234 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
+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.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.ObjectPropertyDao;
+import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
+import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.web.templatemodels.BaseTemplateModel;
+
+public class PropertyList extends BaseTemplateModel {
+
+    private static final Log log = LogFactory.getLog(PropertyList.class);
+
+    private List<PropertyTemplateModel> propertyList;
+    
+    PropertyList() {
+        propertyList = new ArrayList<PropertyTemplateModel>();
+    }
+
+    protected void addObjectProperties(List<ObjectProperty> propertyList) {
+        for (ObjectProperty op : propertyList) {
+            // This is a hack to throw out properties in the vitro, rdf, rdfs, and owl namespaces.
+            // It will be implemented in a better way in v1.3 (Editing and Display Configuration).
+            //if (! EXCLUDED_NAMESPACES.contains(op.getNamespace())) {            
+                add(op);
+            //} else {
+            //    log.debug("Excluded " + op.getURI() + " from displayed property list on the basis of namespace");
+            //}   
+        }
+    }
+    
+    protected void add(ObjectProperty op) {
+        propertyList.add(op.getCollateBySubclass() ? new CollatedObjectProperty(op) : new UncollatedObjectProperty(op));                   
+    }
+    
+    protected void addDataProperties(List<DataProperty> propertyList) {
+        for (DataProperty dp : propertyList) {       
+                add(dp); 
+        }
+    }
+    
+    protected void add(DataProperty p) {
+        propertyList.add(new DataPropertyTemplateModel(p));
+    }
+    
+    protected boolean contains(Property property) {
+        if (property.getURI() == null) {
+            log.error("Property has no propertyURI in alreadyOnPropertyList()");
+            return true; // don't add to list
+        }
+        for (PropertyTemplateModel ptm : propertyList) {
+            if (ptm.getUri() != null && ptm.getUri().equals(property.getURI())) {
+                return true;
+            }
+        }
+        return false;
+    }
+    
+    private static boolean contains(List<ObjectProperty> list, PropertyInstance pi) {
+        if (pi.getPropertyURI() == null) {
+            return false;
+        }
+        for (ObjectProperty op : list) {
+            if (op.getURI() != null && op.getURI().equals(pi.getPropertyURI())) {
+                return op.isSubjectSide() == pi.getSubjectSide();
+            }
+        }
+        return false;
+    }       
+    
+    protected void mergeAllPossibleObjectProperties(WebappDaoFactory wdf, Individual subject, List<ObjectProperty> objectPropertyList) {
+        PropertyInstanceDao piDao = wdf.getPropertyInstanceDao();
+        // RY *** Does this exclude properties in the excluded namespaces already? If not, need same test as above
+        Collection<PropertyInstance> allPropInstColl = piDao.getAllPossiblePropInstForIndividual(subject.getURI());
+        if (allPropInstColl != null) {
+            for (PropertyInstance pi : allPropInstColl) {
+                if (pi != null) {
+                    // RY Do we need to check this before checking if it's on the property list??
+                    if (! contains(objectPropertyList, pi)) {
+                        ObjectPropertyDao opDao = wdf.getObjectPropertyDao();
+                        ObjectProperty op = opDao.getObjectPropertyByURI(pi.getPropertyURI());
+                        if (op == null) {
+                            log.error("ObjectProperty op returned null from opDao.getObjectPropertyByURI()");
+                        } else if (op.getURI() == null) {
+                            log.error("ObjectProperty op returned with null propertyURI from opDao.getObjectPropertyByURI()");
+                        } else  if (! contains(op)) {
+                            add(op);
+                        }
+                    }
+                } else {
+                    log.error("a property instance in the Collection created by PropertyInstanceDao.getAllPossiblePropInstForIndividual() is unexpectedly null");
+                }
+            }
+        } else {
+            log.error("a null Collection is returned from PropertyInstanceDao.getAllPossiblePropInstForIndividual()");
+        }                    
+    }
+    
+    protected void mergeAllPossibleDataProperties(WebappDaoFactory wdf, Individual subject) {
+        DataPropertyDao dpDao = wdf.getDataPropertyDao();
+        // RY *** Does this exclude properties in the excluded namespaces already? If not, need same test as above
+        Collection <DataProperty> allDatapropColl = dpDao.getAllPossibleDatapropsForIndividual(subject.getURI());
+        if (allDatapropColl != null) {
+            for (DataProperty dp : allDatapropColl ) {
+                if (dp!=null) {
+                    if (dp.getURI() == null) {
+                        log.error("DataProperty dp returned with null propertyURI from dpDao.getAllPossibleDatapropsForIndividual()");
+                    } else if (! contains(dp)) {
+                        add(dp);
+                    }
+                } else {
+                    log.error("a data property in the Collection created in DataPropertyDao.getAllPossibleDatapropsForIndividual() is unexpectedly null)");
+                }
+            }
+        } else {
+            log.error("a null Collection is returned from DataPropertyDao.getAllPossibleDatapropsForIndividual())");
+        }        
+    }
+
+//  private void addUnique(Property p) {
+//      if (! contains(p)) {
+//          add(p);
+//      }
+//  }
+//
+//  protected void add(Property p) {
+//      if (p instanceof ObjectProperty) {
+//          add((ObjectProperty) p);            
+//      } else if (p instanceof DataProperty) {
+//          add((DataProperty) p);
+//      }
+//  }
+
+    @SuppressWarnings("unchecked")
+    protected void sort(VitroRequest vreq) {            
+        try {
+            Collections.sort(propertyList, new PropertyRanker(vreq));
+        } catch (Exception ex) {
+            log.error("Exception sorting merged property list: " + ex.getMessage());
+        }
+    }
+    
+    private class PropertyRanker implements Comparator {
+
+        WebappDaoFactory wdf;
+        PropertyGroupDao pgDao;
+
+        private PropertyRanker(VitroRequest vreq) {
+            this.wdf = vreq.getWebappDaoFactory();
+            this.pgDao = wdf.getPropertyGroupDao();
+        }
+        
+        public int compare (Object o1, Object o2) {
+            Property p1 = (Property) o1;
+            Property p2 = (Property) o2;
+            
+            // sort first by property group rank; if the same, then sort by property rank
+            final int MAX_GROUP_RANK=99;
+            
+            int p1GroupRank=MAX_GROUP_RANK;
+            try {
+                if (p1.getGroupURI()!=null) {
+                    PropertyGroup pg1 = pgDao.getGroupByURI(p1.getGroupURI());
+                    if (pg1!=null) {
+                        p1GroupRank=pg1.getDisplayRank();
+                    }
+                }
+            } catch (Exception ex) {
+                log.error("Cannot retrieve p1GroupRank for group "+p1.getEditLabel());
+            }
+            
+            int p2GroupRank=MAX_GROUP_RANK;
+            try {
+                if (p2.getGroupURI()!=null) {
+                    PropertyGroup pg2 = pgDao.getGroupByURI(p2.getGroupURI());
+                    if (pg2!=null) {
+                        p2GroupRank=pg2.getDisplayRank();
+                    }
+                }
+            } catch (Exception ex) {
+                log.error("Cannot retrieve p2GroupRank for group "+p2.getEditLabel());
+            }
+            
+            // int diff = pgDao.getGroupByURI(p1.getGroupURI()).getDisplayRank() - pgDao.getGroupByURI(p2.getGroupURI()).getDisplayRank();
+            int diff=p1GroupRank - p2GroupRank;
+            if (diff==0) {
+                diff = determineDisplayRank(p1) - determineDisplayRank(p2);
+                if (diff==0) {
+                    return p1.getEditLabel().compareTo(p2.getEditLabel());
+                } else {
+                    return diff;
+                }
+            }
+            return diff;
+        }
+        
+        private int determineDisplayRank(Property p) {
+            if (p instanceof DataProperty) {
+                DataProperty dp = (DataProperty)p;
+                return dp.getDisplayTier();
+            } else if (p instanceof ObjectProperty) {
+                ObjectProperty op = (ObjectProperty)p;
+                String tierStr = op.getDomainDisplayTier(); // no longer used: p.isSubjectSide() ? op.getDomainDisplayTier() : op.getRangeDisplayTier();
+                try {
+                    return Integer.parseInt(tierStr);
+                } catch (NumberFormatException ex) {
+                    log.error("Cannot decode object property display tier value "+tierStr+" as an integer");
+                }
+            } else {
+                log.error("Property is of unknown class in PropertyRanker()");  
+            }
+            return 0;
+        }
+    }
+}

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

@@ -2,9 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 
@@ -12,11 +9,15 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import edu.cornell.mannlib.vedit.beans.LoginStatusBean;
+import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Property;
+import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.filters.VitroRequestPrep;
 
 /**
@@ -32,12 +33,6 @@ public class PropertyListBuilder {
     private static final Log log = LogFactory.getLog(PropertyListBuilder.class);
     private static final int MAX_GROUP_DISPLAY_RANK = 99;
     
-    /** Don't include these properties in the list. */
-    // RY This should perhaps be moved to ObjectPropertyTemplateModel
-    private static final Collection<String> SUPPRESSED_OBJECT_PROPERTIES = Collections
-            .unmodifiableCollection(Arrays
-                    .asList(new String[] { VitroVocabulary.IND_MAIN_IMAGE }));
-    
     protected Individual subject;
     protected VitroRequest vreq;
    
@@ -46,35 +41,169 @@ public class PropertyListBuilder {
         this.vreq = vreq;
     }
     
+    // RY Create the list here first to get it working. Then consider moving to GroupedPropertyList constructor.
     protected GroupedPropertyList getPropertyList() {
         
         // Determine whether we're editing or not.
-        boolean isEditing = getEditingStatus();
+        boolean userCanEditThisProfile = getEditingStatus();
 
-        // Assemble the property list
+    
-        List<Property> mergedPropertyList = new ArrayList<Property>();
-        // First get the properties this entity actually has, presumably populated with statements 
-        List<ObjectProperty> objectPropertyList = subject.getObjectPropertyList();  
 
-        for (ObjectProperty op : objectPropertyList) {
+        
-            if (!SUPPRESSED_OBJECT_PROPERTIES.contains(op)) {
+        // Create the property list for the subject. The properties will be put into groups later.
-                op.setEditLabel(op.getDomainPublic());
+        PropertyList propertyList = new PropertyList();
-                mergedPropertyList.add(op);
+        
-            }else{
+        // First get all the object properties that occur in statements in the db with this subject as subject.
-                log.debug("suppressed " + op.getURI());
+        // This may include properties that are not defined as "possible properties" for a subject of this class,
-            }
+        // so we cannot just rely on getting that list.
+        List<ObjectProperty> objectPropertyList = subject.getPopulatedObjectPropertyList();
+        propertyList.addObjectProperties(objectPropertyList);
+
+        WebappDaoFactory wdf = vreq.getWebappDaoFactory();           
+        
+        // If editing this page, merge in object properties applicable to the individual that are currently
+        // unpopulated, so the properties are displayed to allow statements to be added to these properties.
+        // RY In future, we should limit this to properties that the user CAN add properties to.
+        if (userCanEditThisProfile) {
+            propertyList.mergeAllPossibleObjectProperties(wdf, subject, objectPropertyList);
+        }
+        
+        // Now do much the same with data properties: get the list of populated data properties, then add in placeholders for missing ones
+        List<DataProperty> dataPropertyList = subject.getPopulatedDataPropertyList();
+        propertyList.addDataProperties(dataPropertyList);
+
+        if (userCanEditThisProfile) {
+            propertyList.mergeAllPossibleDataProperties(wdf, subject);           
         }
 
-        return null;        
+        propertyList.sort(vreq);
+
+        // *** ADD collation here *** 
+        // Don't  include custom sorting, since that will be handled from custom short views
+
+        // Put the list into groups
+        
+
+//        if (groupedMode) {
+//            int groupsCount=0;
+//            try {
+//                groupsCount = populateGroupsListWithProperties(pgDao,groupList,propertyList); //,groupForUngroupedProperties);
+//            } catch (Exception ex) {
+//                log.error("Exception on trying to populate groups list with properties: "+ex.getMessage());
+//                ex.printStackTrace();
+//            }
+//            try {
+//                int removedCount = pgDao.removeUnpopulatedGroups(groupList);
+//                if (removedCount == 0) {
+//                    log.warn("Of "+groupsCount+" groups, none removed by removeUnpopulatedGroups");
+//            /*  } else {
+//                    log.warn("Of "+groupsCount+" groups, "+removedCount+" removed by removeUnpopulatedGroups"); */
+//                }
+//                groupsCount -= removedCount;
+//                //req.setAttribute("groupsCount", new Integer(groupsCount));
+//                if (groupsCount > 0) { //still
+//                    for (PropertyGroup g : groupList) {
+//                        int statementCount=0;
+//                        if (g.getPropertyList()!=null && g.getPropertyList().size()>0) {
+//                            for (Property p : g.getPropertyList()) {
+//                                if (p instanceof ObjectProperty) {
+//                                    ObjectProperty op = (ObjectProperty)p;
+//                                    List<ObjectPropertyStatement> opStmts = op.getObjectPropertyStatements();
+//                                    if (op.getObjectPropertyStatements()!=null && opStmts.size()>0) {
+//                                        statementCount += opStmts.size();
+//                                        
+//                                        // If not collated, we need to apply custom sorting now. 
+//                                        //applyCustomSortToUncollatedProperty(op, opStmts);
+//                                    }
+//
+//
+//                                }
+//                            }
+//                        }
+//                        g.setStatementCount(statementCount);
+//                    }
+//                }
+//            } catch (Exception ex) {
+//                log.error("Exception on trying to prune groups list with properties: "+ex.getMessage());
+//            }
+//            propertyList.clear();
+            
+//        } else { // ungrouped mode
+//            for (Property p : mergedPropertyList) {
+//                if (p instanceof ObjectProperty) {
+//                    ObjectProperty op = (ObjectProperty)p;
+//                    applyCustomSortToUncollatedProperty(op, op.getObjectPropertyStatements()); 
+//                }
+//            }        }
+
+        
+        return new GroupedPropertyList(wdf, propertyList);
     }
     
     /** 
      * Return true iff the user is editing. 
+     * These tests may change once self-editing issues are straightened out. What we really need to know
+     * is whether the user can edit this profile, not whether in general they are an editor.
      */
     private boolean getEditingStatus() { 
-        // These tests may change once self-editing issues are straightened out.
         boolean isSelfEditing = VitroRequestPrep.isSelfEditing(vreq);
         boolean isCurator = LoginStatusBean.getBean(vreq).isLoggedInAtLeast(LoginStatusBean.CURATOR);
         return isSelfEditing || isCurator;
     }
+
+//    private int populateGroupsListWithProperties(PropertyGroupDao pgDao, List<PropertyGroup> groupsList, List<Property> mergedPropertyList) {//, String unassignedGroupName) {
+//        int count = groupsList.size();
+//        PropertyGroup tempGroup = null;
+//        String unassignedGroupName = ""; //temp, for compilation
+//        if (unassignedGroupName!=null) {
+//            tempGroup = pgDao.createTempPropertyGroup(unassignedGroupName,MAX_GROUP_DISPLAY_RANK);
+//            log.debug("creating temp property group "+unassignedGroupName+" for any unassigned properties");
+//        }
+//        switch (count) {
+//        case 0: log.warn("groupsList has no groups on entering populateGroupsListWithProperties(); will create a new group \"other\"");
+//                break;
+//        case 1: break;
+//        default: try {
+//                     Collections.sort(groupsList);
+//                 } catch (Exception ex) {
+//                     log.error("Exception on sorting groupsList in populateGroupsListWithProperties()");
+//                 }
+//        }
+//        if (count==0 && unassignedGroupName!=null) {
+//            groupsList.add(tempGroup);
+//        }
+//        for (PropertyGroup pg : groupsList) {
+//             if (pg.getPropertyList().size()>0) {
+//                 pg.getPropertyList().clear();
+//             }
+//             for (Property p : mergedPropertyList) {
+//                 if (p.getURI() == null) {
+//                     log.error("Property p has null URI in populateGroupsListWithProperties()");
+//                 } else if (p.getGroupURI()==null) {
+//                     if (tempGroup!=null) { // not assigned any group yet and are creating a group for unassigned properties
+//                         if (!alreadyOnPropertyList(tempGroup.getPropertyList(),p)) {
+//                             tempGroup.getPropertyList().add(p);
+//                             log.debug("adding property "+p.getEditLabel()+" to members of temp group "+unassignedGroupName);
+//                         }
+//                     } // otherwise don't put that property on the list
+//                 } else if (p.getGroupURI().equals(pg.getURI())) {
+//                     if (!alreadyOnPropertyList(pg.getPropertyList(),p)) {
+//                         pg.getPropertyList().add(p);
+//                     }
+//                 }
+//             }
+//             if (pg.getPropertyList().size()>1) {
+//                 try {
+//                     Collections.sort(pg.getPropertyList(),new Property.DisplayComparatorIgnoringPropertyGroup());
+//                 } catch (Exception ex) {
+//                     log.error("Exception sorting property group "+pg.getName()+" property list: "+ex.getMessage());
+//                 }
+//             }
+//        }
+//        if (count>0 && tempGroup!=null && tempGroup.getPropertyList().size()>0) {
+//            groupsList.add(tempGroup);
+//        }
+//        count = groupsList.size();
+//        return count;
+//    }
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/PropertyTemplateModel.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.web.templatemodels.BaseTemplateModel;
 
 /** 
@@ -9,15 +10,26 @@ import edu.cornell.mannlib.vitro.webapp.web.templatemodels.BaseTemplateModel;
  */
 public abstract class PropertyTemplateModel extends BaseTemplateModel {
     
-    // Not sure whether we need the property or the uri.
+    protected Property property;
-    protected String predicateUri = null; 
     
-    PropertyTemplateModel(String predicateUri) {
+    PropertyTemplateModel(Property propertry) {
-        this.predicateUri = predicateUri;
+        this.property = property;
     }
     
+    protected Property getProperty() {
+        return property;
+    }
+    
+    protected String getUri() {
+        return property.getURI();
+    }
+    
+    /* Access methods for templates */
+    
     public String getAddLink() {
         return null;
     }
+    
+    public abstract String getType();
  
 }

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

@@ -2,19 +2,28 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
+import java.util.ArrayList;
 import java.util.List;
 
+import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
+
 public class UncollatedObjectProperty extends ObjectPropertyTemplateModel {
 
-    private List<ObjectPropertyStatementTemplateModel> statements = null;
+    private List<ObjectPropertyStatementTemplateModel> statements;
     
-    UncollatedObjectProperty(String predicateUri) {
+    UncollatedObjectProperty(ObjectProperty property) {
-        super(predicateUri);
+        super(property);
-        // TODO Auto-generated constructor stub
+        statements = new ArrayList<ObjectPropertyStatementTemplateModel>();
     }
     
     public List<ObjectPropertyStatementTemplateModel> getStatements() {
         return statements;
     }
+    
 
+    /* Access methods for templates */
+    
+    public boolean getIsCollatedBySubtype() {
+        return false;
+    }
 }

webapp/test/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJenaTest.java

@@ -3,7 +3,9 @@
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 
+import org.apache.log4j.Level;
 import org.junit.Assert;
+import org.junit.Before;
 import org.junit.Test;
 
 import com.hp.hpl.jena.ontology.DatatypeProperty;
@@ -11,10 +13,12 @@ import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler;
 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.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 
@@ -23,8 +27,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
  * 
  */
 
-public class DataPropertyDaoJenaTest {
+public class DataPropertyDaoJenaTest extends AbstractTestClass {
-	
+    
 	@Test
 	// Test that the DataPropertyDaoJena::updateDataProperty method will only update the jena model for 
 	// those properties in DataProperty that have a different value from what is already in the

webapp/test/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJenaTest.java

@@ -2,23 +2,27 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
+import org.apache.log4j.Level;
 import org.junit.Assert;
+import org.junit.Before;
 import org.junit.Test;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
 import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
 
-public class ObjectPropertyDaoJenaTest {
+public class ObjectPropertyDaoJenaTest extends AbstractTestClass {  
-
+        
 	@Test
 	public void testCollateBySubclass(){
 		/* Check that we can save collateBySubclass */

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

@@ -71,7 +71,7 @@
                 </ul>
             </div>
         </#if>
-     
+
         <#-- <#include "individual-properties.ftl"> -->
 
         <#-- Keywords -->