NIHVIVO-1333 Revert changes from r6573, and move namespace filtering on properties into the sparql query

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

@@ -46,12 +46,6 @@ public interface Individual extends ResourceBean, VitroTimeWindowedResource, Com
     List<ObjectProperty> getObjectPropertyList();
     void setPropertyList(List<ObjectProperty> propertyList);
 
-    /* 
-     * RY These duplicate the functionality of getObjectPropertyList(),
-     * but get data through a sparql query rather than dao methods. They
-     * use a different field so as not to disrupt any code that depends on 
-     * the propertyList field. The two approaches should be integrated at a later point.
-     */
     List<ObjectProperty> getPopulatedObjectPropertyList();
     void setPopulatedObjectPropertyList(List<ObjectProperty> propertyList);
     
@@ -61,12 +55,6 @@ public interface Individual extends ResourceBean, VitroTimeWindowedResource, Com
     List<DataProperty> getDataPropertyList();
     void setDatatypePropertyList(List<DataProperty> datatypePropertyList);
 
-    /* 
-     * RY These duplicate the functionality of getDataPropertyList(),
-     * but get data through a sparql query rather than dao methods. They
-     * use a different field so as not to disrupt any code that depends on 
-     * the datatypePropertyList field. The two approaches should be integrated at a later point.
-     */
     List<DataProperty> getPopulatedDataPropertyList();
     void setPopulatedDataPropertyList(List<DataProperty> dataPropertyList);
     

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

@@ -35,5 +35,8 @@ public interface DataPropertyDao extends PropertyDao {
     List<DataProperty> getRootDataProperties();
     
     boolean annotateDataPropertyAsExternalIdentifier(String dataPropertyURI);
-
+    
+    public List<DataProperty> getDataPropertyList(Individual subject);
+    
+    public List<DataProperty> getDataPropertyList(String subjectUri);
 }

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

@@ -1,16 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao;
-
-import java.util.List;
-
-import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-
-public interface DataPropertyListDao extends PropertyListDao {
-
-    public List<DataProperty> getDataPropertyList(Individual subject);
-    
-    public List<DataProperty> getDataPropertyList(String subjectUri);
-    
-}

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

@@ -51,5 +51,8 @@ public interface ObjectPropertyDao extends PropertyDao {
 //    List /* of ObjectProperty */ getAllObjectProperties();
 
     List <ObjectProperty> getRootObjectProperties();
-   
+    
+    public List<ObjectProperty> getObjectPropertyList(Individual subject);
+    
+    public List<ObjectProperty> getObjectPropertyList(String subjectUri); 
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/ObjectPropertyListDao.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.ObjectProperty;
-
-public interface ObjectPropertyListDao extends PropertyListDao {
-
-    public List<ObjectProperty> getObjectPropertyList(Individual subject);
-    
-    public List<ObjectProperty> getObjectPropertyList(String subjectUri); 
-}

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

@@ -1,8 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao;
-
-public interface PropertyListDao {
-    
-    // Get rid of this interface if it doesn't declare any methods
-}

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

@@ -132,8 +132,4 @@ public interface WebappDaoFactory {
     public NamespaceDao getNamespaceDao();
     
     public PropertyInstanceDao getPropertyInstanceDao();    
-    
-    public ObjectPropertyListDao getObjectPropertyListDao();
-    
-    public DataPropertyListDao getDataPropertyListDao();
 }

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

@@ -192,4 +192,16 @@ class DataPropertyDaoFiltering extends BaseFiltering implements DataPropertyDao{
     	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

@@ -13,8 +13,6 @@ import java.util.Map;
 
 import net.sf.jga.algorithms.Filter;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 import org.json.JSONException;
 import org.json.JSONObject;
 
@@ -29,7 +27,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean.RoleLevel;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.ObjectPropertyListDaoJena;
 import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 
 /**
@@ -41,9 +38,6 @@ import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
  *
  */
 public class IndividualFiltering implements Individual {
-    
-    protected static final Log log = LogFactory.getLog(IndividualFiltering.class);
-
     private final Individual _innerIndividual;
     private final VitroFilters _filters;
 

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

@@ -203,4 +203,15 @@ class ObjectPropertyDaoFiltering extends BaseFiltering implements ObjectProperty
     	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

@@ -9,7 +9,6 @@ import java.util.Set;
 import edu.cornell.mannlib.vitro.webapp.dao.ApplicationDao;
 import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
-import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyListDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.FlagDao;
@@ -20,7 +19,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.LinksDao;
 import edu.cornell.mannlib.vitro.webapp.dao.LinktypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.NamespaceDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
-import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyListDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PortalDao;
@@ -215,14 +213,6 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
     public PortalDao getPortalDao() {
         return innerWebappDaoFactory.getPortalDao();
     }
-    
-    public ObjectPropertyListDao getObjectPropertyListDao() {
-        return innerWebappDaoFactory.getObjectPropertyListDao();
-    }
-    
-    public DataPropertyListDao getDataPropertyListDao() {
-        return innerWebappDaoFactory.getDataPropertyListDao();
-    }
 
 ///////////////////////////////////////////////////////////////////
 

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

@@ -61,6 +61,26 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
     
     protected static final Log log = LogFactory.getLog(DataPropertyDaoJena.class.getName());
     
+    protected static final String dataPropertyQueryString = 
+        PREFIXES + "\n" +
+        "SELECT DISTINCT ?property WHERE { \n" +
+        //"   GRAPH ?g {\n" + 
+        "       ?subject ?property ?object . \n" +        
+        "       ?property rdf:type owl:DatatypeProperty . \n" +
+        propertyFilters +
+        //"   }\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;
@@ -688,4 +708,32 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
             return rootProperties;
     }
 
+    @Override
+    public List<DataProperty> getDataPropertyList(Individual subject) {
+        return getDataPropertyList(subject.getURI());
+    }
+    
+    @Override
+    /*
+     * SPARQL-based method for getting the individual's data properties.
+     * Ideally this implementation should replace the existing way of getting
+     * the data property list, but the consequences of this may be far-reaching,
+     * so we are implementing a new method now and will merge the old approach
+     * into the new one in a future release.
+     */
+    public List<DataProperty> getDataPropertyList(String subjectUri) {
+        log.debug("dataPropertyQueryString:\n" + dataPropertyQueryString);         
+        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("property");
+            String uri = resource.getURI();
+            DataProperty property = getDataPropertyByURI(uri);
+            properties.add(property);
+        }
+        return properties; 
+    }
+    
 }

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

@@ -1,78 +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.ArrayList;
-import java.util.List;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-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.Resource;
-
-import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
-import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyListDao;
-
-public class DataPropertyListDaoJena extends PropertyListDaoJena implements
-        DataPropertyListDao {
-
-    protected static final Log log = LogFactory.getLog(DataPropertyListDaoJena.class);
-
-    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" +
-        //"   }\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);
-        }             
-    }
-
-    public DataPropertyListDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-    
-    @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();
-                DataPropertyDao dpDao = getWebappDaoFactory().getDataPropertyDao();
-                DataProperty property = dpDao.getDataPropertyByURI(uri);
-                properties.add(property);
-            }
-        }
-        return properties; 
-    }
-    
-}

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

@@ -740,7 +740,7 @@ public class IndividualJena extends IndividualImpl implements Individual {
     @Override 
     public List<ObjectProperty> getPopulatedObjectPropertyList() {
         if (populatedObjectPropertyList == null) {
-            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyListDao().getObjectPropertyList(this);
+            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyDao().getObjectPropertyList(this);
         }
         return populatedObjectPropertyList;       
     }
@@ -794,7 +794,7 @@ public class IndividualJena extends IndividualImpl implements Individual {
     @Override 
     public List<DataProperty> getPopulatedDataPropertyList() {
         if (populatedDataPropertyList == null) {
-            populatedDataPropertyList = webappDaoFactory.getDataPropertyListDao().getDataPropertyList(this);
+            populatedDataPropertyList = webappDaoFactory.getDataPropertyDao().getDataPropertyList(this);
         }
         return populatedDataPropertyList;       
     }

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

@@ -884,7 +884,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     @Override 
     public List<ObjectProperty> getPopulatedObjectPropertyList() {
         if (populatedObjectPropertyList == null) {
-            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyListDao().getObjectPropertyList(this);
+            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyDao().getObjectPropertyList(this);
         }
         return populatedObjectPropertyList;       
     }
@@ -938,7 +938,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     @Override 
     public List<DataProperty> getPopulatedDataPropertyList() {
         if (populatedDataPropertyList == null) {
-            populatedDataPropertyList = webappDaoFactory.getDataPropertyListDao().getDataPropertyList(this);
+            populatedDataPropertyList = webappDaoFactory.getDataPropertyDao().getDataPropertyList(this);
         }
         return populatedDataPropertyList;       
     }

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

@@ -872,7 +872,7 @@ public class IndividualSDB2 extends IndividualImpl implements Individual {
     @Override 
     public List<ObjectProperty> getPopulatedObjectPropertyList() {
         if (populatedObjectPropertyList == null) {
-            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyListDao().getObjectPropertyList(this);
+            populatedObjectPropertyList = webappDaoFactory.getObjectPropertyDao().getObjectPropertyList(this);
         }
         return populatedObjectPropertyList;       
     }
@@ -922,14 +922,6 @@ public class IndividualSDB2 extends IndividualImpl implements Individual {
             return this.datatypePropertyList;
         }
     }
-
-    @Override 
-    public List<DataProperty> getPopulatedDataPropertyList() {
-        if (populatedDataPropertyList == null) {
-            populatedDataPropertyList = webappDaoFactory.getDataPropertyListDao().getDataPropertyList(this);
-        }
-        return populatedDataPropertyList;       
-    }
     
     @Override
     public Map<String,DataProperty> getDataPropertyMap() {

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

@@ -47,6 +47,26 @@ 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 ?property WHERE { \n" +
+        //"   GRAPH ?g {\n" + 
+        "       ?subject ?property ?object . \n" +
+        "       ?property rdf:type owl:ObjectProperty . \n" +
+        propertyFilters +
+        //"   }\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);
@@ -804,4 +824,33 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     	return false;
     }
 
+    @Override
+    public List<ObjectProperty> getObjectPropertyList(Individual subject) {
+        return getObjectPropertyList(subject.getURI());
+    }
+    
+    @Override
+    /*
+     * SPARQL-based method for getting the individual's object properties.
+     * Ideally this implementation should replace the existing way of getting
+     * the object property list, but the consequences of this may be far-reaching,
+     * so we are implementing a new method now and will merge the old approach
+     * into the new one in a future release.
+     */
+    public List<ObjectProperty> getObjectPropertyList(String subjectUri) {
+        log.debug("objectPropertyQueryString:\n" + objectPropertyQueryString);
+        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("property");
+            String uri = resource.getURI();
+            ObjectProperty property = getObjectPropertyByURI(uri);
+            properties.add(property);
+        }
+        return properties; 
+    }
+
+    
 }

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

@@ -1,78 +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.ArrayList;
-import java.util.List;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-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.Resource;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
-import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
-import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyListDao;
-
-public class ObjectPropertyListDaoJena extends PropertyListDaoJena implements
-        ObjectPropertyListDao {
-
-    protected static final Log log = LogFactory.getLog(ObjectPropertyListDaoJena.class);
-    
-    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" +
-        //"   }\n" +
-        "}" +
-        "ORDER BY ?predicate\n";
-
-    protected static 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 ObjectPropertyListDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-    
-    @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();
-                ObjectPropertyDao opDao = getWebappDaoFactory().getObjectPropertyDao();
-                ObjectProperty property = opDao.getObjectPropertyByURI(uri);
-                properties.add(property);
-            }
-        }
-        return properties; 
-    }
-    
-}

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

@@ -40,6 +40,34 @@ 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" +
+        "PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#>";
+
+    /* This may be the intent behind JenaBaseDao.NONUSER_NAMESPACES, but that
+     * value does not contain all of these namespaces.
+     */
+    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#"            
+        ); 
+
+    /*
+     * 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).
+     */
+    protected static String propertyFilters = "";
+    static {
+        for (String s : EXCLUDED_NAMESPACES) {
+            propertyFilters += "FILTER (afn:namespace(?property) != \"" + s + "\") \n";
+        }
+    }
     
     public PropertyDaoJena(WebappDaoFactoryJena wadf) {
         super(wadf);
@@ -377,5 +405,15 @@ 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

@@ -1,67 +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.ArrayList;
-import java.util.Arrays;
-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.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.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-
-import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
-import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
-import edu.cornell.mannlib.vitro.webapp.dao.PropertyListDao;
-
-public class PropertyListDaoJena extends JenaBaseDao implements PropertyListDao {
-
-    protected static final Log log = LogFactory.getLog(PropertyListDaoJena.class);
-    
-    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" +
-        "PREFIX afn: <http://jena.hp1.hp.com/ARQ/function#>";
-
-    /* This may be the intent behind JenaBaseDao.NONUSER_NAMESPACES, but that
-     * value does not contain all of these namespaces.
-     */
-    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 PropertyListDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-    
-    @Override
-    protected OntModel getOntModel() {
-        return getOntModelSelector().getFullModel();
-    }    
-    
-    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/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;
@@ -29,10 +30,10 @@ 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;
-import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyListDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.FlagDao;
@@ -43,7 +44,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.LinksDao;
 import edu.cornell.mannlib.vitro.webapp.dao.LinktypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.NamespaceDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
-import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyListDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PortalDao;
@@ -548,23 +548,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
             propertyInstanceDao = new PropertyInstanceDaoJena(this);
         return propertyInstanceDao;
     }
-    
-    private ObjectPropertyListDao objectPropertyListDao = null;
-    public ObjectPropertyListDao getObjectPropertyListDao() {
-        if (objectPropertyListDao == null) {
-            objectPropertyListDao = new ObjectPropertyListDaoJena(this);
-        }
-        return objectPropertyListDao;
-    }
 
-    private DataPropertyListDao DataPropertyListDao = null;
-    public DataPropertyListDao getDataPropertyListDao() {
-        if (DataPropertyListDao == null) {
-            DataPropertyListDao = new DataPropertyListDaoJena(this);
-        }
-        return DataPropertyListDao;
-    }
-    
     protected VClassDao vClassDao = null;
     public VClassDao getVClassDao() {
         if( vClassDao == null )

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

@@ -35,10 +35,16 @@ public class PropertyList extends BaseTemplateModel {
     PropertyList() {
         propertyList = new ArrayList<PropertyTemplateModel>();
     }
-    
+
     protected void addObjectProperties(List<ObjectProperty> propertyList) {
-        for (ObjectProperty op : propertyList) {       
+        for (ObjectProperty op : propertyList) {
-            add(op); 
+            // 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");
+            //}   
         }
     }
     
@@ -48,7 +54,7 @@ public class PropertyList extends BaseTemplateModel {
     
     protected void addDataProperties(List<DataProperty> propertyList) {
         for (DataProperty dp : propertyList) {       
-            add(dp); 
+                add(dp); 
         }
     }
     
@@ -130,6 +136,20 @@ public class PropertyList extends BaseTemplateModel {
         }        
     }
 
+//  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 {