merging picklist optimizations back into trunk

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

@@ -10,6 +10,8 @@ import java.util.Map;
 import org.json.JSONException;
 import org.json.JSONObject;
 
+import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
+
 /**
  * User: bdc34
  * Date: Oct 18, 2007
@@ -71,6 +73,8 @@ public interface Individual extends ResourceBean, VitroTimeWindowedResource, Com
     
     /** Does the individual belong to this class? */
     boolean isVClass(String uri);
+    
+    public boolean isMemberOfClassProhibitedFromSearch(ProhibitedFromSearch pfs);
 
     void setObjectPropertyStatements(List<ObjectPropertyStatement> list);
     List<ObjectPropertyStatement> getObjectPropertyStatements();

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

@@ -6,6 +6,7 @@ import org.json.JSONException;
 import org.json.JSONObject;
 
 import edu.cornell.mannlib.vitro.webapp.filestorage.model.ImageInfo;
+import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 
 import java.lang.reflect.Method;
 import java.sql.Timestamp;
@@ -195,6 +196,11 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
 		}
 		return false;
 	}
+    
+    public boolean isMemberOfClassProhibitedFromSearch(ProhibitedFromSearch pfs) {
+    	throw new UnsupportedOperationException(this.getClass().getName() +
+    		".isMemberOfClassProhibitedFromSearch must be overriden by a subclass");
+    }
 
 	public List<VClass> getVClasses(boolean direct) {
     	if (direct) {

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

@@ -13,6 +13,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.search.beans.ObjectSourceIface;
+import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 
 public interface IndividualDao extends ObjectSourceIface {
 
@@ -105,7 +106,7 @@ public interface IndividualDao extends ObjectSourceIface {
 
         int getCountOfIndividualsInVClass(String vclassURI );
 
-    public boolean isIndividualOfClass(String vclassURI, String indURI);
+    public boolean isIndividualOfClass(String vclassURI, String indURI);
     
     /**
      * Returns a list of individuals with the given value for the given dataProperty.  If

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

@@ -27,6 +27,7 @@ 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.search.beans.ProhibitedFromSearch;
 
 /**
  * A Individual object that will delegate to an inner Individual
@@ -517,7 +518,11 @@ public class IndividualFiltering implements Individual {
     	return _innerIndividual.isVClass(uri);
 	}
 
-
+    @Override
+    public boolean isMemberOfClassProhibitedFromSearch(ProhibitedFromSearch pfs) {
+    	return _innerIndividual.isMemberOfClassProhibitedFromSearch(pfs);
+    }
+    
 	public void setDataPropertyMap(Map<String, DataProperty> propertyMap) {
         _innerIndividual.setDataPropertyMap(propertyMap);
     }

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

@@ -114,17 +114,17 @@ public class VClassDaoFiltering extends BaseFiltering implements VClassDao{
         if(list == null )
             return null;
         filter(list,filters.getClassFilter());
-        correctVClassCounts(list);
+        //correctVClassCounts(list);
         return list;
     }
 
     public List<VClass> getOntologyRootClasses(String ontologyURI) {
-        return (List<VClass>)correctVClassCounts(innerVClassDao.getOntologyRootClasses(ontologyURI));
+        return innerVClassDao.getOntologyRootClasses(ontologyURI);
     }
 
 
     public List <VClass>getRootClasses() {
-        return correctVClassCounts(innerVClassDao.getRootClasses());
+        return innerVClassDao.getRootClasses();
     }
 
 
@@ -142,13 +142,13 @@ public class VClassDaoFiltering extends BaseFiltering implements VClassDao{
 
 
     public List<VClass> getVClassesForProperty(String propertyURI, boolean domainSide) {
-        List<VClass> list = innerVClassDao.getVClassesForProperty(propertyURI, domainSide);
+        return innerVClassDao.getVClassesForProperty(propertyURI, domainSide);
-        return correctVClassCounts(filter(list,filters.getClassFilter()));
+        //return correctVClassCounts(filter(list,filters.getClassFilter()));
     }
     
     public List<VClass> getVClassesForProperty(String vclassURI, String propertyURI) {
-    	List<VClass> list = innerVClassDao.getVClassesForProperty(vclassURI, propertyURI);
+    	return innerVClassDao.getVClassesForProperty(vclassURI, propertyURI);
-    	return correctVClassCounts(filter(list,filters.getClassFilter()));
+    	//return correctVClassCounts(filter(list,filters.getClassFilter()));
     }
 
     public void insertNewVClass(VClass cls) throws InsertException {
@@ -167,7 +167,7 @@ public class VClassDaoFiltering extends BaseFiltering implements VClassDao{
     }
 
     public void addVClassesToGroup(VClassGroup group, boolean includeUninstantiatedClasses) {
-        this.addVClassesToGroup(group, includeUninstantiatedClasses, true);
+        this.addVClassesToGroup(group, includeUninstantiatedClasses, false);
     }
 
     public void addVClassesToGroup(VClassGroup group,

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

@@ -140,54 +140,36 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
     }
 
     public List getIndividualsByVClassURI(String vclassURI, int offset, int quantity ) {
-        if (vclassURI==null) {
+
+    	if (vclassURI==null) {
             return null;
         }
+        
         List ents = new ArrayList();
-        Resource theClass = null;
+        
+        Resource theClass = (vclassURI.indexOf(PSEUDO_BNODE_NS) == 0) 
+            ? getOntModel().createResource(new AnonId(vclassURI.split("#")[1]))
+            : ResourceFactory.createResource(vclassURI);
+    
         getOntModel().enterCriticalSection(Lock.READ);
         try {
-            if (vclassURI.indexOf(PSEUDO_BNODE_NS)==0) {
+            StmtIterator stmtIt = getOntModel().listStatements((Resource) null, RDF.type, theClass);
-                ClosableIterator closeIt = getOntModel().listClasses();
-                try {
-                    for (Iterator clsIt = closeIt ; clsIt.hasNext();) {
-                        OntClass cls = (OntClass) clsIt.next();
-                        if (cls.isAnon() && cls.getId().toString().equals(vclassURI.split("#")[1])) {
-                            theClass = cls;
-                            break;
-                        }
-                    }
-                } finally {
-                    closeIt.close();
-                }
-            } else {
-                theClass = getOntModel().getOntClass(vclassURI);
-            }
-        } finally {
-            getOntModel().leaveCriticalSection();
-        }
-
-        if (theClass == null) {
-            theClass = ResourceFactory.createResource(vclassURI);
-        }
-
-        getOntModel().enterCriticalSection(Lock.READ);
-        try {
-            ClosableIterator indIt = getOntModel().listIndividuals(theClass);
             try {
-                while (indIt.hasNext()) {
+                while (stmtIt.hasNext()) {
-                    com.hp.hpl.jena.ontology.Individual ind = (com.hp.hpl.jena.ontology.Individual) indIt.next();
+                    Statement stmt = stmtIt.nextStatement();
+                    OntResource ind = (OntResource) stmt.getSubject().as(OntResource.class);
                     ents.add(new IndividualJena(ind, (WebappDaoFactoryJena) getWebappDaoFactory()));
                 }
             } finally {
-                indIt.close();
+                stmtIt.close();
             }
         } finally {
             getOntModel().leaveCriticalSection();
         }
-       java.util.Collections.sort(ents);
 
-       return ents;
+        java.util.Collections.sort(ents);
+
+        return ents;
 
     }
 

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

@@ -25,6 +25,7 @@ import com.hp.hpl.jena.rdf.model.Literal;
 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;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.vocabulary.OWL;
@@ -42,6 +43,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 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;
+import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 import edu.cornell.mannlib.vitro.webapp.utils.FlagMathUtils;
 
 public class IndividualJena extends IndividualImpl implements Individual {
@@ -820,6 +822,30 @@ public class IndividualJena extends IndividualImpl implements Individual {
 		}
 		return false;
 	}
+	
+	@Override
+	public boolean isMemberOfClassProhibitedFromSearch(ProhibitedFromSearch pfs) {
+		ind.getModel().enterCriticalSection(Lock.READ);
+		try {
+			StmtIterator stmtIt = ind.listProperties(RDF.type);
+			try {
+				while(stmtIt.hasNext()) {
+					Statement stmt = stmtIt.nextStatement();
+					if (stmt.getObject().isURIResource()) {
+						String typeURI = ((Resource)stmt.getObject()).getURI();
+						if (pfs.isClassProhibited(typeURI)) {
+							return false;
+						}
+					}
+				}
+			} finally {
+				stmtIt.close();
+			}
+			return false;
+		} finally {
+			ind.getModel().leaveCriticalSection();
+		}
+	}
 
     /**
      * Overriding the base method so that we can do the sorting by arbitrary property here.  An

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

@@ -410,7 +410,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
 		            	  p.setInverseOf(inv);
 		            	}
 	            } catch (Exception e) {
-	                   System.out.println("Couldn't set "+prop.getURIInverse()+" as inverse");
+	                   log.debug("Couldn't set "+prop.getURIInverse()+" as inverse");
 				       // BJL: What we really want to do here is create a new property as inverse
 			    }      
 	        }

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

@@ -768,7 +768,7 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
 
         @Deprecated
         public void addVClassesToGroup(VClassGroup group, boolean includeUninstantiatedClasses) {
-            addVClassesToGroup(group, includeUninstantiatedClasses, true);
+            addVClassesToGroup(group, includeUninstantiatedClasses, false);
         }
 
         @Deprecated

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

@@ -172,15 +172,17 @@ public class SelectListGenerator {
                         if( vclasses.size() == 0 )
                             log.error("no owl:Class found for predicate " + predicateUri );
                         
-                        HashMap<String,Individual> indMap = new HashMap<String,Individual>();
+                        List<Individual> individuals = new ArrayList<Individual>();
+                        HashSet<String> uriSet = new HashSet<String>();
+                        long startTime = System.currentTimeMillis();
                         for ( VClass vclass :  vclasses){
                             for( Individual ind : wDaoFact.getIndividualDao().getIndividualsByVClassURI(vclass.getURI(),-1,-1)) {
-                                if( !indMap.containsKey(ind.getURI())) {
+                                if( !uriSet.contains(ind.getURI())) {
-                                    indMap.put(ind.getURI(),ind);
+                                    uriSet.add(ind.getURI());
+                                    individuals.add(ind);
                                 }
                             }
                         }
-                        List<Individual> individuals = new ArrayList<Individual>(indMap.values());
     
                         List<ObjectPropertyStatement> stmts = subject.getObjectPropertyStatements();
                                                         if( stmts == null ) log.error("object properties for subject were null in SelectListGenerator.getOptions()");
@@ -192,24 +194,12 @@ public class SelectListGenerator {
                         
                         for( Individual ind : individuals ){
                             String uri = ind.getURI();
-                            if( uri != null ){   
+                            if( uri != null && (pfs == null || !ind.isMemberOfClassProhibitedFromSearch(pfs)) ){              
-                            	boolean prohibited = false;
+                        		optionsMap.put(uri,ind.getName().trim());                        
-                            	if (pfs != null) {
+                        		++optionsCount;             	
-                            		for (VClass vc : ind.getVClasses()) {
-                            			if (vc.getURI() != null) {
-                            				if (pfs.isClassProhibited(ind.getVClassURI())) {
-                            					prohibited = true;
-                            					break;
-                            				}
-                            			}
-                            		}
-                            	}
-                            	if (!prohibited) {
-                            		optionsMap.put(uri,ind.getName().trim());                        
-                            		++optionsCount;
-                            	}
                             }
                         }
+                        
                     }
                 }
                 break;
@@ -292,23 +282,9 @@ public class SelectListGenerator {
                         	ProhibitedFromSearch pfs = editConfig.getProhibitedFromSearch();
                             for( Individual ind : individuals ) {
                                 String uri = ind.getURI();
-                                if( uri != null ) {       
+                                if( uri != null && (pfs == null || !ind.isMemberOfClassProhibitedFromSearch(pfs)) ) {       
-                                	boolean prohibited = false;
+                                	optionsMap.put(uri,ind.getName().trim());                        
-                                	if (pfs != null) {
+                            		++optionsCount;
-                                		for (VClass vc : ind.getVClasses()) {
-                                			if (vc.getURI() != null) {
-                                				if (pfs.isClassProhibited(ind.getVClassURI())) {
-                                					prohibited = true;
-                                					break;
-                                				}
-                                				
-                                			}
-                                		}
-                                	}
-                                	if(!prohibited) {
-                                		optionsMap.put(uri,ind.getName().trim());                        
-                                		++optionsCount;
-                                	}
                                 }
                             }
                         }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/MiscWebUtils.java

@@ -80,8 +80,7 @@ public class MiscWebUtils {
         return (String) contentObj;
     }
 
-	public static String getCustomShortView(HttpServletRequest request) {
+	public static String getCustomShortView(HttpServletRequest request) {	
-		
 		Individual object = ((ObjectPropertyStatement) request
 				.getAttribute("opStmt")).getObject();
 		return getCustomShortView(object, request);

webapp/src/edu/cornell/mannlib/vitro/webapp/web/jsptags/InputElementFormattingTag.java

@@ -481,7 +481,10 @@ public class InputElementFormattingTag extends TagSupport {
             } else if( getType().equalsIgnoreCase("select")) {
                 String valueStr = doValue(editConfig, editSub);
                 //String sizeStr = getSize(); //"style=\"width:"+getSize()+"%;\"";
-                Map <String,String> optionsMap = SelectListGenerator.getOptions(editConfig,getName(), wdf);
+                Map<String,String> optionsMap = (Map<String,String>) pageContext.getRequest().getAttribute("rangeOptions." + getId());
+                if (optionsMap == null) {
+                	optionsMap = SelectListGenerator.getOptions(editConfig,getName(), wdf);
+                }
                 if (optionsMap==null){
                     log.error("Error in InputElementFormattingTag.doStartTag(): null optionsMap returned from getOptions()");
                 }
@@ -515,7 +518,10 @@ public class InputElementFormattingTag extends TagSupport {
             } else if( getType().equalsIgnoreCase("checkbox")) {
                 String valueStr = doValue(editConfig, editSub);
                 if (definitionTags) { out.print("<dd>"); }
-                Map <String,String> optionsMap = SelectListGenerator.getOptions(editConfig,getName(),wdf);
+                Map<String,String> optionsMap = (Map<String,String>) pageContext.getRequest().getAttribute("rangeOptions." + getId());
+                if (optionsMap == null) {
+                    optionsMap = SelectListGenerator.getOptions(editConfig,getName(),wdf);
+                }
                 if (optionsMap==null){
                     log.error("Error in InputElementFormattingTag.doStartTag(): null optionsMap returned from getOptions()");
                 }
@@ -534,7 +540,10 @@ public class InputElementFormattingTag extends TagSupport {
             } else if( getType().equalsIgnoreCase("radio")) {
                 String valueStr = doValue(editConfig, editSub);
                 if (definitionTags) { out.print("<dd>"); }
-                Map <String,String> optionsMap = SelectListGenerator.getOptions(editConfig,getName(),wdf);
+                Map<String,String> optionsMap = (Map<String,String>) pageContext.getRequest().getAttribute("rangeOptions." + getId());
+                if (optionsMap == null) {
+                    optionsMap = SelectListGenerator.getOptions(editConfig,getName(),wdf);
+                }
                 if (optionsMap==null){
                     log.error("Error in InputElementFormattingTag.doStartTag(): null optionsMap returned from getOptions()");
                 }

webapp/web/edit/forms/defaultObjPropForm.jsp

@@ -24,7 +24,10 @@
 %>
 
 <%@page import="edu.cornell.mannlib.vitro.webapp.edit.n3editing.SelectListGenerator"%>
-<%@page import="java.util.Map"%><v:jsonset var="queryForInverse" >
+<%@page import="java.util.Map"%>
+<%@page import="com.hp.hpl.jena.ontology.OntModel"%>
+<%@page import="edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch"%>
+<%@page import="edu.cornell.mannlib.vitro.webapp.web.DisplayVocabulary"%><v:jsonset var="queryForInverse" >
     PREFIX owl:  <http://www.w3.org/2002/07/owl#>
     SELECT ?inverse_property
     WHERE {
@@ -131,11 +134,24 @@
     }
     
     if( prop.getSelectFromExisting() ){
+    	// set ProhibitedFromSearch object so picklist doesn't show
+        // individuals from classes that should be hidden from list views
+        OntModel displayOntModel = 
+            (OntModel) pageContext.getServletContext()
+                .getAttribute("displayOntModel");
+        if (displayOntModel != null) {
+            ProhibitedFromSearch pfs = new ProhibitedFromSearch(
+                DisplayVocabulary.PRIMARY_LUCENE_INDEX_URI, displayOntModel);
+            if( editConfig != null )
+                editConfig.setProhibitedFromSearch(pfs);
+        }
     	Map<String,String> rangeOptions = SelectListGenerator.getOptions(editConfig, "objectVar" , wdf);    	
-    	if( rangeOptions != null && rangeOptions.size() > 0 )
+    	if( rangeOptions != null && rangeOptions.size() > 0 ) {
     		request.setAttribute("rangeOptionsExist", true);
-    	else 
+    	    request.setAttribute("rangeOptions.objectVar", rangeOptions);
+    	} else { 
     		request.setAttribute("rangeOptionsExist",false);
+    	}
     }
 %>
 <jsp:include page="${preForm}"/>
@@ -150,7 +166,7 @@
 	    </c:if>
 	    <v:input type="select" id="objectVar" size="80" />
 	    <div style="margin-top: 1em">
-	        <v:input type="submit" id="submit" value="<%=submitLabel%>" cancel="true"/>
+ 	        <v:input type="submit" id="submit" value="<%=submitLabel%>" cancel="true"/>
 	    </div>    
     </form>
   </c:if>