rewritten list view queries with UNIONs plus various and sundry other bugfixes and improvements; also probably new bugs

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

@@ -15,6 +15,7 @@ import org.openrdf.model.URI;
 import org.openrdf.model.impl.URIImpl;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
 import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
@@ -259,7 +260,7 @@ public class UrlBuilder {
     }
     
     public static String getIndividualProfileUrl(String individualUri, WebappDaoFactory wadf) {
-        Individual individual = wadf.getIndividualDao().getIndividualByURI(individualUri);
+        Individual individual = new IndividualImpl(individualUri);
         return getIndividualProfileUrl(individual, individualUri, wadf);
     }
     

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

@@ -45,6 +45,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.IndividualSDB.IndividualNotFoundException;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB.SDBDatasetMode;
 
 public class IndividualDaoSDB extends IndividualDaoJena {
@@ -66,7 +67,12 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     }
     
     protected Individual makeIndividual(String individualURI) {
+        try {
             return new IndividualSDB(individualURI, this.dwf, datasetMode, getWebappDaoFactory());
+        } catch (IndividualNotFoundException e) {
+            // If the individual does not exist, return null.
+            return null;
+        }
     }
 
     private static final Log log = LogFactory.getLog(IndividualDaoSDB.class.getName());

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

@@ -137,21 +137,21 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	    		"CONSTRUCT " +
     	    		"{ <"+individualURI+">  <" + RDFS.label.getURI() + 
     	    		        "> ?ooo. \n" +
-    	    		   "<"+individualURI+">  a ?type . \n" +
+//    	    		   "<"+individualURI+">  a ?type . \n" +
     	    		   "<"+individualURI+">  <" + VitroVocabulary.MONIKER + 
     	    		           "> ?moniker \n" +
-    	    		 "} WHERE {" +
+    	    		 "} WHERE { GRAPH <urn:x-arq:UnionGraph> {" +
-    	    		 "{ GRAPH ?g { \n" +
+    	    		 "{ \n" +
     	    		 	"{ <"+individualURI+">  <" + RDFS.label.getURI() + 
     	    		 	        "> ?ooo } \n" +
-    	    		 	"UNION { GRAPH ?h { <" +
+    	    		 	"UNION { <" +
     	    		 	    individualURI+">  <" + VitroVocabulary.MONIKER + 
-    	    		 	        "> ?moniker } } \n" +
+    	    		 	        "> ?moniker }  \n" +
-    	    		 	"} } \n" +
+    	    		 	"}  \n" +
-    	    		 	"UNION { GRAPH ?i { <"
+//    	    		 	"UNION { <"
-    	    		 	    + individualURI + "> a ?type } } \n" +
+//    	    		 	    + individualURI + "> a ?type } \n" +
-    	    		    WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
+//    	    		    WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
-    	    		 "}";
+    	    		 "} }";
         		model = QueryExecutionFactory.create(
         		        QueryFactory.create(getStatements), dataset)
         		                .execConstruct();
@@ -163,6 +163,10 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         	OntModel ontModel = ModelFactory.createOntologyModel(
         	        OntModelSpec.OWL_MEM, model);
         	
+        	if (model.isEmpty()) {
+        	    throw new IndividualNotFoundException();
+        	}
+        	
         	this.ind = ontModel.createOntResource(individualURI);  
     	}
     	setUpURIParts(ind);
@@ -182,6 +186,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
              !SKIP_INITIALIZATION);
     }
     
+    public class IndividualNotFoundException extends RuntimeException {}
+    
     private void setUpURIParts(OntResource ind) {
         if (ind != null) {
             if (ind.isAnon()) {
@@ -304,8 +310,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
                 int portalid = FlagMathUtils.numeric2Portalid(numericPortal);
                 String portalTypeUri = VitroVocabulary.vitroURI + 
                         "Flag1Value" + portalid + "Thing";
-                String Ask = "ASK { GRAPH ?g { <" + this.individualURI + 
+                String Ask = "ASK { <" + this.individualURI + 
-                        "> <" +RDF.type+ "> <" + portalTypeUri +">} }"; 
+                        "> <" +RDF.type+ "> <" + portalTypeUri +">} "; 
                 if(!QueryExecutionFactory.create(
                         QueryFactory.create(Ask), dataset).execAsk()) {
                 	return false;
@@ -334,8 +340,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             	getObjects = 
             		"CONSTRUCT{<" + this.individualURI + "> <" + 
             		        RDF.type + "> ?object}" +
-        			"WHERE{ GRAPH ?g { <" + this.individualURI + "> <" + 
+        			"WHERE{ <" + this.individualURI + "> <" + 
-        			        RDF.type + "> ?object} }";
+        			        RDF.type + "> ?object }";
         		tempModel = QueryExecutionFactory.create(
         		        QueryFactory.create(
         		                getObjects), dataset).execConstruct();
@@ -394,8 +400,8 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             	getObjects = 
             		"CONSTRUCT{<" + this.individualURI + "> <" + 
             		        RDF.type + "> ?object}" +
-        			"WHERE{ GRAPH ?g { <" + this.individualURI + "> <" + 
+        			"WHERE{ <" + this.individualURI + "> <" + 
-        			        RDF.type + "> ?object} }";
+        			        RDF.type + "> ?object }";
         		tempModel = QueryExecutionFactory.create(
         		        QueryFactory.create(
         		                getObjects), dataset).execConstruct();

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

@@ -50,19 +50,19 @@ public class ObjectPropertyStatementDaoSDB extends
             return entity;
         else {
         	Map<String, ObjectProperty> uriToObjectProperty = new HashMap<String,ObjectProperty>();
-        	String[] graphVars = { "?g", "?h", "?i", "?j" };
+        	//String[] graphVars = { "?g", "?h", "?i", "?j" };
         	String query = "CONSTRUCT { \n" +
         			       "   <" + entity.getURI() + "> ?p ?o . \n" +
-        			       "   ?o a ?oType . \n" +
+        			      // "   ?o a ?oType . \n" +
         			       "   ?o <" + RDFS.label.getURI() + "> ?oLabel .  \n" +
         			       "   ?o <" + VitroVocabulary.MONIKER + "> ?oMoniker  \n" +
-        			       "} WHERE { GRAPH ?g { \n" +
+        			       "} WHERE { GRAPH <urn:x-arq:UnionGraph> { \n" +
         			       "   <" + entity.getURI() + "> ?p ?o \n" +
-        			       "   OPTIONAL { GRAPH ?h { ?o a ?oType } } \n" +
+        			       //"   OPTIONAL { GRAPH ?h { ?o a ?oType } } \n" +
-        			       "   OPTIONAL { GRAPH ?i { ?o <" + RDFS.label.getURI() + "> ?oLabel } } \n" +
+        			      // "   OPTIONAL {  { ?o <" + RDFS.label.getURI() + "> ?oLabel } } \n" +
-        			       "   OPTIONAL { GRAPH ?j { ?o <" + VitroVocabulary.MONIKER + "> ?oMoniker } }  \n" +
+        			      // "   OPTIONAL {  { ?o <" + VitroVocabulary.MONIKER + "> ?oMoniker } }  \n" +
                            "} \n" +
-                           WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
+                           //WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode) +
         			       "}";
         	long startTime = System.currentTimeMillis();
         	Model m = null;

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

@@ -15,7 +15,9 @@ import org.apache.commons.logging.LogFactory;
 import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
 import com.hp.hpl.jena.ontology.Individual;
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.shared.Lock;
@@ -129,26 +131,44 @@ public class PropertyGroupDaoJena extends JenaBaseDao implements PropertyGroupDa
     	groupInd.setURI(group.getURI());
     	
     	String groupURI = null;
+    	
+        OntModel unionForURIGeneration = ModelFactory.createOntologyModel(
+                OntModelSpec.OWL_MEM, ModelFactory.createUnion(
+                        getOntModelSelector().getApplicationMetadataModel(), 
+                        getOntModelSelector().getFullModel()));
+        
         try {
-    		groupURI = (new WebappDaoFactoryJena(getOntModelSelector().getApplicationMetadataModel())).getIndividualDao().insertNewIndividual(groupInd);
+            groupURI = (new WebappDaoFactoryJena(unionForURIGeneration)).
+                            getIndividualDao().insertNewIndividual(groupInd);
     	} catch (InsertException ie) {
-    		throw new RuntimeException(InsertException.class.getName() + "Unable to insert property group "+groupURI, ie);
+    		throw new RuntimeException(InsertException.class.getName() + 
+    		        "Unable to insert property group " + groupURI, ie);
     	}
     	
     	if (groupURI != null) {
 	        getOntModel().enterCriticalSection(Lock.WRITE);
 	        try {
-	        	com.hp.hpl.jena.ontology.Individual groupJenaInd = getOntModel().getIndividual(groupURI);
+	        	com.hp.hpl.jena.ontology.Individual groupJenaInd = 
+	        	        getOntModel().getIndividual(groupURI);
 	            try {
-	                groupJenaInd.addProperty(DISPLAY_RANK, Integer.toString(group.getDisplayRank()), XSDDatatype.XSDint);
+	                groupJenaInd.addProperty(DISPLAY_RANK, Integer.toString(
+	                        group.getDisplayRank()), XSDDatatype.XSDint);
 	            } catch (Exception e) {
-	                log.error("error setting displayRank for "+groupInd.getURI());
+	                log.error(
+	                        "error setting displayRank for " 
+	                                + groupInd.getURI());
 	            }
-	            if (group.getPublicDescription() != null && group.getPublicDescription().length()>0) {
+	            if (group.getPublicDescription() != null 
+	                    && group.getPublicDescription().length()>0) {
 		            try {   
-		                groupJenaInd.addProperty(PUBLIC_DESCRIPTION_ANNOT, group.getPublicDescription(), XSDDatatype.XSDstring);
+		                groupJenaInd.addProperty(
+		                        PUBLIC_DESCRIPTION_ANNOT, 
+		                        group.getPublicDescription(), 
+		                        XSDDatatype.XSDstring);
 		            } catch (Exception ex) {
-		                log.error("error setting public description for "+groupInd.getURI());
+		                log.error(
+		                        "error setting public description for "
+		                                + groupInd.getURI());
 		            }
 		        }
 	        } finally {

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

@@ -216,8 +216,15 @@ public class VClassGroupDaoJena extends JenaBaseDao implements VClassGroupDao {
     	groupInd.setVClassURI(CLASSGROUP.getURI());
     	
     	String groupURI = null;
+    	
+    	OntModel unionForURIGeneration = ModelFactory.createOntologyModel(
+    	        OntModelSpec.OWL_MEM, ModelFactory.createUnion(
+    	                getOntModelSelector().getApplicationMetadataModel(), 
+    	                getOntModelSelector().getFullModel()));
+    	
     	try {
-    		groupURI = (new WebappDaoFactoryJena(ontModel)).getIndividualDao().insertNewIndividual(groupInd);
+    		groupURI = (new WebappDaoFactoryJena(unionForURIGeneration)).
+                            getIndividualDao().insertNewIndividual(groupInd);
     	} catch (InsertException ie) {
     		throw new RuntimeException(InsertException.class.getName() + "Unable to insert class group "+groupURI, ie);
     	}

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

@@ -15,6 +15,7 @@ import com.hp.hpl.jena.iri.IRIFactory;
 import com.hp.hpl.jena.iri.Violation;
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.ontology.OntResource;
 import com.hp.hpl.jena.query.DataSource;
 import com.hp.hpl.jena.query.Dataset;
@@ -175,20 +176,36 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         if (languageUniversalsModel.size()>0) {
         	this.ontModelSelector.getTBoxModel().addSubModel(languageUniversalsModel);
         }
-        DataSource dataset = DatasetFactory.create();
         
-        dataset.addNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL, 
+        Model assertions = (baseOntModelSelector != null) 
-                (baseOntModelSelector != null) 
                 ? baseOntModelSelector.getFullModel()
-                    : ontModelSelector.getFullModel());
+                : ontModelSelector.getFullModel();
-        if (inferenceOntModelSelector != null) {
+        Model inferences = (inferenceOntModelSelector != null) 
-            dataset.addNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL, 
+                ? inferenceOntModelSelector.getFullModel()
-                    inferenceOntModelSelector.getFullModel());
+                : null;
-        }
+        
+        Dataset dataset = makeInMemoryDataset(assertions, inferences);      
         this.dwf = new StaticDatasetFactory(dataset);
         
+    } 
     
+    public static Dataset makeInMemoryDataset(Model assertions, Model inferences) {
+        DataSource dataset = DatasetFactory.create();
         
+        OntModel union = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+        
+        if (assertions != null) {
+            dataset.addNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL, assertions);
+            union.addSubModel(assertions);
+        } 
+        if (inferences != null) {
+            dataset.addNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL, 
+                    inferences);
+            union.addSubModel(inferences);
+        }
+        dataset.setDefaultModel(union);
+        dataset.addNamedModel("urn:x-arq:UnionGraph", union);
+        return dataset;
     }
     
     public WebappDaoFactoryJena(OntModelSelector ontModelSelector, 

webapp/src/edu/cornell/mannlib/vitro/webapp/filters/VitroRequestPrep.java

@@ -39,6 +39,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.FilterFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.HiddenFromDisplayBelowRoleLevelFilter;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilterUtils;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
 import edu.cornell.mannlib.vitro.webapp.flags.AuthFlag;
 import edu.cornell.mannlib.vitro.webapp.flags.FlagException;
 import edu.cornell.mannlib.vitro.webapp.flags.PortalFlag;
@@ -203,9 +204,8 @@ public class VitroRequestPrep implements Filter {
         
         // support for Dataset interface if using Jena in-memory model
         if (vreq.getDataset() == null) {
-        	DataSource dataset = DatasetFactory.create();
+        	Dataset dataset = WebappDaoFactoryJena.makeInMemoryDataset(
-        	dataset.addNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL, vreq.getAssertionsOntModel());
+        	        vreq.getAssertionsOntModel(), vreq.getInferenceOntModel());
-        	dataset.addNamedModel(JenaDataSourceSetupBase.JENA_INF_MODEL, vreq.getInferenceOntModel());
         	vreq.setDataset(dataset);
         }
         

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

@@ -206,13 +206,16 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
                 log.error("Unable to load application metadata model cache from DB", e);
             }
             
+            log.info("Adding vitro application ontology");
             
-            // add the vitro ontologies to the tbox models
+            // add the vitroontologies to the tbox models
             OntModel vitroTBoxModel = (new JenaBaseDaoCon()).getConstModel();
             baseOms.getTBoxModel().addSubModel(vitroTBoxModel);
             inferenceOms.getTBoxModel().addSubModel(vitroTBoxModel);
             unionOms.getTBoxModel().addSubModel(vitroTBoxModel);
             
+            log.error("Setting up union models and DAO factories");
+            
             // create TBox + ABox union models and set up webapp DAO factories
             OntModel baseUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
                     ModelFactory.createUnion(baseOms.getABoxModel(), baseOms.getTBoxModel()));
@@ -262,6 +265,8 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
             //    loadDataFromFilesystem(unionOms.getFullModel(), sce.getServletContext());
             //}
             
+            log.info("Checking for user account data");
+            
             if (userAccountsModel.size() == 0) {
                 readOntologyFilesInPathSet(AUTHPATH, sce.getServletContext(), userAccountsModel);
                 if (userAccountsModel.size() == 0) {
@@ -269,14 +274,20 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
                 }
             }                        
             
+            log.info("Checking for minimal interface metadata");
+            
             ensureEssentialInterfaceData(unionOms.getApplicationMetadataModel(), sce, wadf);        
             
+            //log.info("Setting up namespace mapper");
+            
             NamespaceMapper namespaceMapper = new NamespaceMapperJena(masterUnion, masterUnion, defaultNamespace);
             sce.getServletContext().setAttribute("NamespaceMapper", namespaceMapper);
             unionOms.getFullModel().getBaseModel().register(namespaceMapper);
             
             sce.getServletContext().setAttribute("defaultNamespace", defaultNamespace);
             
+            log.info("SDB store ready for use");
+            
             makeModelMakerFromConnectionProperties(TripleStoreType.RDB);
             VitroJenaModelMaker vjmm = getVitroJenaModelMaker();
             setVitroJenaModelMaker(vjmm,sce);
@@ -284,6 +295,8 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
             VitroJenaSDBModelMaker vsmm = getVitroJenaSDBModelMaker();
             setVitroJenaSDBModelMaker(vsmm,sce);
             
+            log.info("Model makers set up");
+                     
         } catch (Throwable t) {
             log.error("Throwable in " + this.getClass().getName(), t);
             // printing the error because Tomcat doesn't print context listener
@@ -587,7 +600,9 @@ public class JenaDataSourceSetupSDB extends JenaDataSourceSetupBase implements j
             SimpleReasonerSetup.setRecomputeRequired(ctx);
         
         } finally {
+            log.info("Adding indexes to SDB database tables.");
             store.getTableFormatter().addIndexes();
+            log.info("Indexes created.");
         }
     }
     

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/NamespaceMapperJena.java

@@ -9,6 +9,9 @@ import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.ontology.Individual;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.rdf.listeners.StatementListener;
@@ -26,6 +29,8 @@ import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
 public class NamespaceMapperJena extends StatementListener implements
 		NamespaceMapper {
 	
+    private static final Log log = LogFactory.getLog(NamespaceMapperJena.class);
+    
 	private HashMap<String,String> prefixToNamespaceMap;
 	private HashMap<String,List<String>> namespaceToPrefixMap;
 	
@@ -60,15 +65,23 @@ public class NamespaceMapperJena extends StatementListener implements
 		
 	}
 	
+	private static int LARGE_NS = 200;
+	
 	private void rebuildNamespaceCache() {
 		HashMap<String,String> tempPrefixToNamespaceMap = new HashMap<String,String>();
 		HashMap<String,List<String>> tempNamespaceToPrefixMap = new HashMap<String,List<String>>();
 		metadataModel.enterCriticalSection(Lock.READ);
+		int nsCount = 0;
 		try {	
 			// Iterate through all the namespace objects
 			ClosableIterator closeIt = metadataModel.listIndividuals(metadataModel.getResource(VitroVocabulary.NAMESPACE));
 			try {
 				for (Iterator namespaceIt = closeIt; namespaceIt.hasNext();) {
+				    nsCount++;
+				    if (nsCount == LARGE_NS) {
+				        log.warn("Unusually large number of different namespaces encountered; " +
+				                 "namespace mapper setup may take some time.");
+				    }
 					Individual namespaceInd = (Individual) namespaceIt.next();
 					String namespaceURI = null;
 					RDFNode node = namespaceInd.getPropertyValue(metadataModel.getProperty(VitroVocabulary.NAMESPACE_NAMESPACEURI));

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

@@ -44,6 +44,7 @@ public abstract class BaseObjectPropertyDataPostProcessor implements
     
     /** Postprocessing that applies to the list as a whole - reordering, removing duplicates, etc. */
     protected void processList(List<Map<String, String>> data) {
+        objectPropertyTemplateModel.removeLessSpecificSolutions(data);
         objectPropertyTemplateModel.removeDuplicates(data);
     }
     

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

@@ -9,6 +9,7 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -229,6 +230,67 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
         }        
     }
     
+    /**
+     * For performance reasons, we've had to rewrite SPARQL queries that would
+     * naturally use OPTIONAL blocks to use UNIONs instead.  These UNION queries
+     * return a superset of the solutions returned by the originals.  This 
+     * method filters out the unwanted solutions with extra null values.
+     * 
+     * This operation is polynomial time in the worst case, but should be linear
+     * with the actual queries used for list views.  The ORDER BY clauses
+     * should minimize the seek distance for solution elimination.
+     * 
+     * @param List<Map<String, String>> data
+     */
+    protected void removeLessSpecificSolutions(List<Map<String, String>> data) {
+       List<Map<String, String>> redundantSolns = 
+               new ArrayList<Map<String, String>>();
+       for (int i = 0; i < data.size(); i++) {
+           Map<String,String> soln = data.get(i);
+           boolean redundantSoln = false;
+           // seek forward
+           int j = i + 1;
+           while (!redundantSoln && (j < data.size())) {
+               redundantSoln = isEqualToOrLessSpecificThan(soln, data.get(j));
+               j++;
+           }
+           // loop back around
+           j = 0;
+           while (!redundantSoln && (j < i)) {
+               redundantSoln = isEqualToOrLessSpecificThan(soln, data.get(j));
+               j++;
+           }
+           if (redundantSoln) {
+               redundantSolns.add(soln);
+           }
+       }
+       data.removeAll(redundantSolns);
+    }
+    
+    /**
+     * Returns true if soln1 is equal to or less specific (i.e., has more null
+     * values) than soln2
+     * @param List<Map<String, String>> soln1
+     * @param List<Map<String, String>> soln2
+     */
+    private boolean isEqualToOrLessSpecificThan (Map<String, String> soln1, 
+                                Map<String, String> soln2) {
+        if (soln1.keySet().size() < soln2.keySet().size()) {
+            return true;
+        }
+        for (String key : soln1.keySet()) {
+            String value1 = soln1.get(key);
+            String value2 = soln2.get(key);
+            if (value2 == null && value1 != null) {
+                return false;
+            } 
+            if (value1 != null && value2 != null && !value1.equals(value2)) {
+                return false;
+            }
+        }
+        return true;
+    }
+    
     
     /** The SPARQL query results may contain duplicate rows for a single object, if there are multiple solutions 
      * to the entire query. Remove duplicates here by arbitrarily selecting only the first row returned.

webapp/web/config/listViewConfig-default.xml

@@ -11,9 +11,21 @@
         PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  
           
         SELECT ?object ?name ?moniker {
-            GRAPH ?g1 { ?subject ?property ?object }
+            { 
-            OPTIONAL { GRAPH ?g2 { ?object rdfs:label ?name } }
+                ?subject ?property ?object .
-            OPTIONAL { GRAPH ?g3 { ?object vitro:moniker ?moniker } }
+            }
+            UNION { 
+                ?subject ?property ?object .
+                ?object rdfs:label ?name 
+            }
+            UNION { 
+                ?subject ?property ?object .
+                ?object vitro:moniker ?moniker 
+            } UNION {
+                ?subject ?property ?object .
+                ?object rdfs:label ?name .
+                ?object vitro:moniker ?moniker . 
+            }
         }       
     </query-base>
 
@@ -22,11 +34,28 @@
         PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;  
           
         SELECT ?subclass ?object ?name ?moniker {
-            GRAPH ?g1 { ?subject ?property ?object
+
-                OPTIONAL { ?object a ?subclass } 
+            { 
+                ?subject ?property ?object .
+                ?object a ?subclass .
             }
-            OPTIONAL { GRAPH ?g2 { ?object rdfs:label ?name } }
+            UNION { 
-            OPTIONAL { GRAPH ?g3 { ?object vitro:moniker ?moniker } }           
+                ?subject ?property ?object .
+                ?object a ?subclass .
+                ?object rdfs:label ?name 
+            }
+            UNION { 
+                ?subject ?property ?object .
+                ?object a ?subclass .
+                ?object vitro:moniker ?moniker 
+            } UNION {
+                ?subject ?property ?object .
+                ?object a ?subclass .
+                ?object rdfs:label ?name .
+                ?object vitro:moniker ?moniker . 
+            }
+ 
+
         } ORDER BY ?subclass      
     </query-collated>
     

webapp/web/config/listViewConfig-vitroLink.xml

@@ -14,10 +14,10 @@
                (afn:localname(?link) AS ?linkName) 
                ?anchor 
                ?url WHERE {
-            GRAPH ?g1 { ?subject ?property ?link }
+            ?subject ?property ?link
-            OPTIONAL { GRAPH ?g2 { ?link vitro:linkAnchor ?anchor } }
+            OPTIONAL { ?link vitro:linkAnchor ?anchor }
-            OPTIONAL { GRAPH ?g3 { ?link vitro:linkURL ?url } }
+            OPTIONAL { ?link vitro:linkURL ?url }
-            OPTIONAL { GRAPH ?g4 { ?link vitro:linkDisplayRank ?rank } }
+            OPTIONAL { ?link vitro:linkDisplayRank ?rank }
         } ORDER BY ?rank
     </query-base>