Changes for NIHVIVO-2231 and NIHVIVO-2664: setting up menu page editing and retrieval of individuals for class intersections

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

@@ -175,9 +175,28 @@ public class IndividualListController extends FreemarkerHttpServlet {
      public static Map<String,Object> getResultsForVClass(String vclassURI, int page, String alpha, IndividualDao indDao, ServletContext context) 
      throws CorruptIndexException, IOException, ServletException{
     	 Map<String,Object> rvMap = new HashMap<String,Object>();    
-                                  
+    	 try{
 	         //make lucene query for this rdf:type
-         Query query = getQuery(vclassURI, alpha);        
+    		 List<String> classUris = new ArrayList<String>();
+    		 classUris.add(vclassURI);
+	        Query query = getQuery(classUris, alpha);        
+	        rvMap = getResultsForVClassQuery(query, page, alpha, indDao, context);
+	        List<Individual> individuals = (List<Individual>) rvMap.get("entities");
+	        if (individuals == null) 
+	             log.debug("entities list is null for vclass " + vclassURI );                        
+    	 } catch(Throwable th) {
+    		 log.error("An error occurred retrieving results for vclass query", th);
+    	 }
+         return rvMap;
+     }
+     
+     /*
+      * This method includes what was formerly a part of the method above, allowing for refactoring of code
+      * to use for a different number fo classes
+      */
+     public static Map<String,Object> getResultsForVClassQuery(Query query, int page, String alpha, IndividualDao indDao, ServletContext context) 
+     throws CorruptIndexException, IOException, ServletException{
+         Map<String,Object> rvMap = new HashMap<String,Object>();        
          
          //execute lucene query for individuals of the specified type
          IndexSearcher index = LuceneIndexFactory.getIndexSearcher(context);
@@ -237,20 +256,43 @@ public class IndividualListController extends FreemarkerHttpServlet {
          
          rvMap.put("totalCount", size);
          rvMap.put("entities",individuals);                     
-         if (individuals == null) 
-             log.debug("entities list is null for vclass " + vclassURI );                        
          
          return rvMap;
      }
      
-     private static BooleanQuery getQuery(String vclassUri,  String alpha){
+    
+    
+     public static Map<String,Object> getResultsForVClassIntersections(List<String> vclassURIs, int page, String alpha, IndividualDao indDao, ServletContext context) 
+     throws CorruptIndexException, IOException, ServletException{
+         Map<String,Object> rvMap = new HashMap<String,Object>();  
+         try{
+             //make lucene query for multiple rdf types 
+	         Query query = getQuery(vclassURIs, alpha);     
+	         //get results corresponding to this query
+	         rvMap = getResultsForVClassQuery(query, page, alpha, indDao, context);
+	         List<Individual> individuals = (List<Individual>) rvMap.get("entities");
+		     if (individuals == null) 
+		       log.debug("entities list is null for vclass " + vclassURIs.toString() );     
+         } catch(Throwable th) {
+        	 log.error("Error retrieving individuals corresponding to intersection multiple classes." + vclassURIs.toString());
+         }
+         return rvMap;
+     }
+     /*
+      * This method creates a query to search for terms with rdf type corresponding to vclass Uri.
+      * The original version allowed only for one class URI but needed to be extended to enable multiple
+      *  vclass Uris to be passed
+      */
+     
+     private static BooleanQuery getQuery(List<String>vclassUris,  String alpha){
          BooleanQuery query = new BooleanQuery();
          try{      
-            //query term for rdf:type
+            //query term for rdf:type - multiple types possible
+        	for(String vclassUri: vclassUris) {
 	            query.add(
 	                    new TermQuery( new Term(Entity2LuceneDoc.term.RDFTYPE, vclassUri)),
 	                    BooleanClause.Occur.MUST );                          
-                                       
+        	}                           
             //Add alpha filter if it is needed
             Query alphaQuery = null;
             if( alpha != null && !"".equals(alpha) && alpha.length() == 1){      

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

@@ -23,7 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Tem
 import edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.BrowseDataGetter;
 import edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.PageDataGetter;
 import edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.ClassGroupPageData;
-
+import edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.ClassIntersectionDataGetter;
 /**
  * Controller for getting data for pages defined in the display model. 
  * 
@@ -112,7 +112,10 @@ public class PageController extends FreemarkerHttpServlet{
             return Collections.emptyMap();
             
         PageDataGetter getter = getPageDataGetterMap(getServletContext()).get(type);
-        
+        //For now hardcoding, check to see if data getter included within 
+        if((String)page.get("datagetter") != null) {
+        	getter = new ClassIntersectionDataGetter();
+        }
         if( getter != null ){
             try{
                 return getter.getData(getServletContext(), vreq, pageUri, page, type);
@@ -177,6 +180,12 @@ public class PageController extends FreemarkerHttpServlet{
             getPageDataGetterMap(context).put(cgpd.getType(), cgpd);      
             BrowseDataGetter bdg = new BrowseDataGetter();
             getPageDataGetterMap(context).put(bdg.getType(), bdg);
+            //TODO: Check if can include by type here
+            ClassIntersectionDataGetter cidg =  new ClassIntersectionDataGetter();
+            getPageDataGetterMap(context).put(cidg.getType(), cidg);
+            
         }
     }
+    
+    
 }

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

@@ -270,6 +270,12 @@ public class UrlBuilder {
     public static String getPath(Route route, ParamMap params) {
         return getPath(route.path(), params);
     }
+    //Adding method to allow for checking for special parameters
+    public static String getIndividualProfileUrl(String individualUri, VitroRequest vreq) {
+        Individual individual = new IndividualImpl(individualUri);
+        return getIndividualProfileUrl(individual, individualUri, vreq);
+    }
+    
     
     public static String getIndividualProfileUrl(String individualUri, WebappDaoFactory wadf) {
         Individual individual = new IndividualImpl(individualUri);
@@ -281,6 +287,19 @@ public class UrlBuilder {
         return getIndividualProfileUrl(individual, individualUri, wadf);        
     }
     
+    //Trying first with using a form of the method that includes the vitro request
+    private static String getIndividualProfileUrl(Individual individual, String individualUri, VitroRequest vreq) {
+    	WebappDaoFactory wadf = vreq.getWebappDaoFactory();
+    	String profileUrl = getIndividualProfileUrl(individual, individualUri, wadf);
+    	if(profileUrl != null) {
+    		HashMap<String, String> specialParams = getSpecialParams(vreq);
+    		if(specialParams.size() != 0) {
+    			profileUrl = addParams(profileUrl, new ParamMap(specialParams));
+    		}
+    	}
+    	return profileUrl;
+    }
+    
     private static String getIndividualProfileUrl(Individual individual, String individualUri, WebappDaoFactory wadf) {
         String profileUrl = null;
         try {
@@ -346,4 +365,32 @@ public class UrlBuilder {
         return decodedUrl;
     }
     
+    //To be used in different property templates so placing method for reuse here
+    //Check if special params included, specifically for menu management and other models
+    public static HashMap<String,String> getSpecialParams(VitroRequest vreq) {
+    	
+    	HashMap<String,String> specialParams = new HashMap<String, String>();
+    	if(vreq != null) {
+    		//this parameter is sufficient to switch to menu model
+    		String useMenuModelParam = vreq.getParameter("usemenumodel");
+    		//the parameters below allow for using a different model
+	    	String useMainModelUri = vreq.getParameter("usemodel");
+	    	String useTboxModelUri = vreq.getParameter("usetboxmodel");
+	    	String useDisplayModelUri = vreq.getParameter("usedisplaymodel");
+	    	if(useMenuModelParam != null && !useMenuModelParam.isEmpty()) {
+	    		specialParams.put("usemenumodel", useMenuModelParam);
+	    	}
+	    	else if(useMainModelUri != null && !useMainModelUri.isEmpty()) {
+	    		specialParams.put("usemodel", useMainModelUri);
+	    		if(useTboxModelUri != null && !useTboxModelUri.isEmpty()){ 
+	    			specialParams.put("usetboxmodel", useTboxModelUri);
+	    		}
+	    		if(useDisplayModelUri != null && !useDisplayModelUri.isEmpty()) {
+	    			specialParams.put("usedisplaymodel", useDisplayModelUri);
+	    		}
+	    	}
+    	}
+    	return specialParams;
+    }
+
 }

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

@@ -28,10 +28,12 @@ public class DisplayVocabulary {
     public static final String PAGE_TYPE = NS + "Page";
     public static final String HOME_PAGE_TYPE = NS + "HomePage";
     public static final String CLASSGROUP_PAGE_TYPE = NS + "ClassGroupPage";
+    //Including for now, can take out later
+    public static final String 	CLASSINTERSECTION_PAGE_TYPE = NS + "ClassIntersectionPage";
 
     /* Object Properties */
     public static final String FOR_CLASSGROUP = NS + "forClassGroup";
-    
+    public static final String CLASS_INTERSECTION = NS + "intersectsWithClass";
     /* Data Properties */
     public static final DatatypeProperty URL_MAPPING = m_model.createDatatypeProperty(NS + "urlMapping");
     public static final String TITLE = NS + "title";

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

@@ -3,7 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.dao;
 
 import java.util.Map;
-
+import java.util.List;
 public interface PageDao {
 
     Map<String, Object> getPage(String pageUri);
@@ -22,4 +22,6 @@ public interface PageDao {
     String getHomePageUri();
    
     String getClassGroupPage(String pageUri);
+    
+    List<String> getClassIntersections(String pageUri);
 }

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

@@ -38,6 +38,7 @@ public class PageDaoJena extends JenaBaseDao implements PageDao {
     static protected Query pageMappingsQuery;
     static protected Query homePageUriQuery;
     static protected Query classGroupPageQuery;
+    static protected Query classIntersectionPageQuery;
 
     static final String prefixes = 
         "PREFIX rdf:   <" + VitroVocabulary.RDF +"> \n" +
@@ -78,6 +79,10 @@ public class PageDaoJena extends JenaBaseDao implements PageDao {
         prefixes + "\n" +
         "SELECT ?classGroup WHERE { ?pageUri <" + DisplayVocabulary.FOR_CLASSGROUP + "> ?classGroup . }";
     
+    static final protected String classIntersectionPageQueryString = 
+    	prefixes + "\n" + 
+        "SELECT ?classIntersection WHERE { ?pageUri <" + DisplayVocabulary.CLASS_INTERSECTION + "> ?classIntersection . }";
+
     static{
         try{    
             pageQuery=QueryFactory.create(pageQueryString);
@@ -109,6 +114,12 @@ public class PageDaoJena extends JenaBaseDao implements PageDao {
             log.error("could not create SPARQL query for classGroupPageQuery " + th.getMessage());
             log.error(classGroupPageQueryString);
         }
+        try{    
+            classIntersectionPageQuery=QueryFactory.create(classIntersectionPageQueryString);
+        }catch(Throwable th){
+            log.error("could not create SPARQL query for classIntersectionPageQuery " + th.getMessage());
+            log.error(classIntersectionPageQueryString);
+        }  
     }        
     
     public PageDaoJena(WebappDaoFactoryJena wadf) {
@@ -240,6 +251,30 @@ public class PageDaoJena extends JenaBaseDao implements PageDao {
         return classGroupsForPage.get(0);
     }
     
+    /**
+     * Get the names of the classes for class intersection.  Multiple classes possible.
+     */
+    public List<String> getClassIntersections(String pageUri) {
+    	List<String> classIntersections = new ArrayList<String>();
+    	 QuerySolutionMap initialBindings = new QuerySolutionMap();
+         initialBindings.add("pageUri", ResourceFactory.createResource(pageUri));
+         
+         Model displayModel = getOntModelSelector().getDisplayModel();
+         QueryExecution qexec = QueryExecutionFactory.create( classIntersectionPageQuery, displayModel , initialBindings);
+         
+        
+         ResultSet resultSet = qexec.execSelect();        
+         while(resultSet.hasNext()){
+             QuerySolution soln = resultSet.next();
+             classIntersections.add( nodeToString(soln.get("classIntersection")) );        
+         }
+         if( classIntersections.size() == 0 ){
+             log.debug("No class intersections info defined in display model for "+ pageUri);
+             return null;
+         }
+            
+    	return classIntersections;
+    }
     
     /* ****************************************************************************** */
     

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

@@ -635,8 +635,24 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     
     //Method for using special model for webapp dao factory, such as display model
     //This is still in flux, am checking in to allow others to experiment
-    public void setSpecialDataModel(OntModel specialModel, OntModel specialTboxModel) {
+    public boolean isUsingSpecialModel = false;
-    	WebappDaoFactoryJena specialWadfj = new WebappDaoFactoryJena(specialModel);
+    public void setSpecialDataModel(OntModel specialModel, OntModel specialTboxModel, OntModel specialDisplayModel) {
+    	//Set up model selector for the new webapp dao factory object with the input model
+    	//The selector is used by the object property dao, therefore should be set up even though we 
+    	//use the new webapp dao factory object to generate portions to overwrite the regular webapp dao factory
+    	OntModelSelectorImpl specialSelector = new OntModelSelectorImpl();
+    	specialSelector.setFullModel(specialModel);
+    	specialSelector.setApplicationMetadataModel(specialModel);
+    	specialSelector.setDisplayModel(specialDisplayModel);
+    	specialSelector.setTBoxModel(specialTboxModel);
+    	specialSelector.setABoxModel(specialModel);
+    	specialSelector.setUserAccountsModel(specialModel);
+    	//although we're only use part of the new wadf and copy over below, the object property dao
+    	//utilizes methods that will employ the display model returned from the simple ontmodel selector
+    	//so if the object property dao is to be copied over we need to ensure we have the correct display model
+    	//and tbox model
+    	WebappDaoFactoryJena specialWadfj = new WebappDaoFactoryJena(specialSelector);
+    
     	entityWebappDao = specialWadfj.getIndividualDao();
     	keys2EntsDao = specialWadfj.getKeys2EntsDao();
     	keywordDao = specialWadfj.getKeywordDao();
@@ -646,8 +662,11 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     	//To allow for testing, add a property group, this will allow
     	//the unassigned group method section to be executed and main Image to be assigned to that group
     	//otherwise the dummy group does not allow for the unassigned group to be executed
-    	
     	propertyGroupDao = specialWadfj.getPropertyGroupDao();
+    	objectPropertyDao = specialWadfj.getObjectPropertyDao();
+    	objectPropertyStatementDao = specialWadfj.getObjectPropertyStatementDao();
+    	dataPropertyDao = specialWadfj.getDataPropertyDao();
+    	dataPropertyStatementDao = specialWadfj.getDataPropertyStatementDao();
     	PropertyGroup pgtest = new edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup();
     	pgtest.setName("testname");
     	pgtest.setDisplayRank(1);
@@ -657,7 +676,14 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     	if(ontModelSelector instanceof OntModelSelectorImpl) {
     		OntModelSelectorImpl omsImpl = (OntModelSelectorImpl) ontModelSelector;
     		omsImpl.setTBoxModel(specialTboxModel);
+    		omsImpl.setDisplayModel(specialDisplayModel);
     	}
+    	else if(ontModelSelector instanceof SimpleOntModelSelector) {
+    		SimpleOntModelSelector omsImpl = (SimpleOntModelSelector) ontModelSelector;
+    		omsImpl.setTBoxModel(specialTboxModel);
+    		omsImpl.setDisplayModel(specialDisplayModel);
+    	}
+    	isUsingSpecialModel = true;
     }
    
 }

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

@@ -22,6 +22,7 @@ import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Model;
 
 import edu.cornell.mannlib.vitro.webapp.auth.identifier.RequestIdentifiers;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ServletPolicyList;
@@ -36,6 +37,7 @@ 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.servlet.setup.JenaDataSourceSetupBase;
 import org.apache.commons.dbcp.BasicDataSource;
+
 /**
  * This sets up several objects in the Request scope for each
  * incoming HTTP request.  This is done in a Filter so
@@ -199,24 +201,48 @@ public class VitroRequestPrep implements Filter {
     }
 
     //check if special model - this is for enabling the use of a different model for menu management 
+    //Also enables the use of a completely different model and tbox if uris are passed
     private void checkForSpecialWDF(VitroRequest vreq, WebappDaoFactory wadf) {
-    	if(vreq.getParameter("test") != null) {    		
+    	String useMenuModelParam = vreq.getParameter("usemenumodel");
+    	boolean useMenu = (useMenuModelParam != null);
+    	//other parameters to be passed in in case want to use specific models
+    	String useMainModelUri = vreq.getParameter("usemodel");
+    	String useTboxModelUri = vreq.getParameter("usetboxmodel");
+    	String useDisplayModelUri = vreq.getParameter("usedisplaymodel");
+    	if(useMenu || (useMainModelUri != null && !useMainModelUri.isEmpty() && useTboxModelUri != null && !useTboxModelUri.isEmpty())) {    		
     		if(wadf instanceof WebappDaoFactoryJena) {
     			WebappDaoFactoryJena wadfj = (WebappDaoFactoryJena) wadf;
-    			OntModel testDisplayModel = (OntModel) _context.getAttribute("displayOntModel");
+    			OntModel useMainOntModel = null, useTboxOntModel = null, useDisplayOntModel = null;
-        	
+    			Model tboxModel = null, displayModel = null;
-    			//Hardcoding tbox model uri for now
-        		String tboxModelUri =  "http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadataTBOX";
     			BasicDataSource bds = JenaDataSourceSetupBase.getApplicationDataSource(_context);
-        		//Model dbPlainModel = JenaDataSourceSetupBase.makeDBModelFromConfigurationProperties(tboxModelUri, OntModelSpec.OWL_MEM, _context);
 	        	String dbType = ConfigurationProperties.getBean(_context).getProperty( // database type
 	        				"VitroConnection.DataSource.dbtype", "MySQL");
-        		com.hp.hpl.jena.rdf.model.Model displayTboxModel = JenaDataSourceSetupBase.makeDBModel(bds, tboxModelUri, OntModelSpec.OWL_MEM, JenaDataSourceSetupBase.TripleStoreType.RDB, dbType, _context);
+    			if(useMenu) {
-    			System.out.println("Checking what the display tbox model is returning");
+    				//if using special models for menu management, get main menu model from context and set tbox and display uris to be used
-        		displayTboxModel.write(System.out, "N3");
+	    			useMainOntModel = (OntModel) _context.getAttribute("displayOntModel");
-        		OntModel displayTboxOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, displayTboxModel);
+	    			//Hardcoding tbox model uri for now
+	        		useTboxModelUri =  "http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadataTBOX";
+	        		useDisplayModelUri = "http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata-displayModel";
+    			} else {
+    				//If main model uri passed as parameter then retrieve model from parameter
+    				Model mainModel = JenaDataSourceSetupBase.makeDBModel(bds, useMainModelUri, OntModelSpec.OWL_MEM, JenaDataSourceSetupBase.TripleStoreType.RDB, dbType, _context);
+    				//if this uri exists and model exists, then set up ont model version
+    				if(mainModel != null) {
+    					useMainOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, mainModel);
+    				}
+    			}
     			
-        		wadfj.setSpecialDataModel(testDisplayModel, displayTboxOntModel);
+	        	tboxModel = JenaDataSourceSetupBase.makeDBModel(bds, useTboxModelUri, OntModelSpec.OWL_MEM, JenaDataSourceSetupBase.TripleStoreType.RDB, dbType, _context);
+	    		System.out.println("Checking what the display tbox model is returning");
+	        	tboxModel.write(System.out, "N3");
+	        	useTboxOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, tboxModel);
+	    		//Set "display model" for display model
+	        	displayModel = JenaDataSourceSetupBase.makeDBModel(bds, useDisplayModelUri, OntModelSpec.OWL_MEM, JenaDataSourceSetupBase.TripleStoreType.RDB, dbType, _context);
+	        	useDisplayOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, displayModel);
+    			//Set special model for wadfj
+	        	if(useMainOntModel != null) {
+    				wadfj.setSpecialDataModel(useMainOntModel, useTboxOntModel, useDisplayOntModel);
+    			}
     		}
     	}
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/pageDataGetter/ClassIntersectionDataGetter.java

@@ -0,0 +1,126 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.servlet.ServletContext;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.beans.VClass;
+import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.IndividualListController;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.IndividualListController.PageRecord;
+import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.VClassGroupCache;
+import edu.cornell.mannlib.vitro.webapp.web.templatemodels.VClassGroupTemplateModel;
+import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.ListedIndividualTemplateModel;
+import freemarker.ext.beans.BeansWrapper;
+import freemarker.template.TemplateModel;
+
+/**
+ * This will pass these variables to the template:
+ * classGroupUri: uri of the classgroup associated with this page.
+ * vClassGroup: a data structure that is the classgroup associated with this page.     
+ */
+public class ClassIntersectionDataGetter implements PageDataGetter{
+    private static final Log log = LogFactory.getLog(ClassIntersectionDataGetter.class);
+    
+    public Map<String,Object> getData(ServletContext context, VitroRequest vreq, String pageUri, Map<String, Object> page, String type ){
+        HashMap<String, Object> data = new HashMap<String,Object>();
+        List<String> classIntersections = vreq.getWebappDaoFactory().getPageDao().getClassIntersections(pageUri);
+        data.put("classIntersections", classIntersections);
+        //Use Individual List Controller to get all the individuals and related data
+        String alpha = IndividualListController.getAlphaParameter(vreq);
+        int pageParam = IndividualListController.getPageParameter(vreq);
+        try{
+        	Map<String, Object> results = IndividualListController.getResultsForVClassIntersections(classIntersections, pageParam, alpha, vreq.getWebappDaoFactory().getIndividualDao(), context);
+        	data.putAll(results);
+        	//NOTE: Below is copied from Individual List Controller's processing as some of these are used in the template
+        	//below may not be necessary if using a different template
+            List<Individual> inds = (List<Individual>)data.get("entities");
+            List<ListedIndividualTemplateModel> indsTm = new ArrayList<ListedIndividualTemplateModel>();
+            for(Individual ind : inds ){
+                indsTm.add(new ListedIndividualTemplateModel(ind,vreq));
+            }
+            data.put("individuals", indsTm);
+            
+            List<TemplateModel> wpages = new ArrayList<TemplateModel>();
+            List<PageRecord> pages = (List<PageRecord>)data.get("pages");
+            BeansWrapper wrapper = new BeansWrapper();
+            for( PageRecord pr: pages ){
+                wpages.add( wrapper.wrap(pr) );
+            }
+
+           
+            data.put("rdfUrl", vreq.getContextPath()+"/listrdf/");
+        	
+        } catch(Exception ex) {
+        	log.error("An error occurred retrieving Vclass Intersection individuals", ex);
+        }
+        
+
+        
+        
+        //TODO: Check if need class group at all here?
+        //data.put("vClassGroup", group);  //may put null            
+        return data;
+    }        
+    
+    public static VClassGroupTemplateModel getClassGroup(String classGroupUri, ServletContext context, VitroRequest vreq){
+        
+        VClassGroupCache vcgc = VClassGroupCache.getVClassGroupCache(context);
+        List<VClassGroup> vcgList = vcgc.getGroups();
+        VClassGroup group = null;
+        for( VClassGroup vcg : vcgList){
+            if( vcg.getURI() != null && vcg.getURI().equals(classGroupUri)){
+                group = vcg;
+                break;
+            }
+        }
+        
+        if( classGroupUri != null && !classGroupUri.isEmpty() && group == null ){ 
+            /*This could be for two reasons: one is that the classgroup doesn't exist
+             * The other is that there are no individuals in any of the classgroup's classes */
+            group = vreq.getWebappDaoFactory().getVClassGroupDao().getGroupByURI(classGroupUri);
+            if( group != null ){
+                List<VClassGroup> vcgFullList = vreq.getWebappDaoFactory().getVClassGroupDao()
+                    .getPublicGroupsWithVClasses(false, true, false);
+                for( VClassGroup vcg : vcgFullList ){
+                    if( classGroupUri.equals(vcg.getURI()) ){
+                        group = vcg;
+                        break;
+                    }                                
+                }
+                if( group == null ){
+                    log.error("Cannot get classgroup '" + classGroupUri + "'");
+                    return null;
+                }else{
+                    setAllClassCountsToZero(group);
+                }
+            }else{
+                log.error("classgroup " + classGroupUri + " does not exist in the system");
+                return null;
+            }            
+        }
+        
+        return new VClassGroupTemplateModel(group);
+    }
+    
+    public String getType(){
+        return DisplayVocabulary.CLASSINTERSECTION_PAGE_TYPE;
+    } 
+    
+    protected static void setAllClassCountsToZero(VClassGroup vcg){
+        for(VClass vc : vcg){
+            vc.setEntityCount(0);
+        }
+    }
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/web/methods/IndividualProfileUrlMethod.java

@@ -27,7 +27,7 @@ public class IndividualProfileUrlMethod extends BaseTemplateMethodModel {
         Environment env = Environment.getCurrentEnvironment();
         HttpServletRequest request = (HttpServletRequest) env.getCustomAttribute("request");
         VitroRequest vreq = new VitroRequest(request);
-        String url = UrlBuilder.getIndividualProfileUrl(uri, vreq.getWebappDaoFactory());
+        String url = UrlBuilder.getIndividualProfileUrl(uri, vreq);
         return (url == null) ? "" : url; // don't return a null to the template
     }
 

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/BaseTemplateModel.java

@@ -2,11 +2,14 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels;
 
+import java.util.HashMap;
+
 import javax.servlet.ServletContext;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
 

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

@@ -2,6 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
+import java.util.HashMap;
 import java.util.List;
 
 import org.apache.commons.logging.Log;

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

@@ -231,7 +231,7 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
             }
             
             listForThisSubclass.add(new ObjectPropertyStatementTemplateModel(subjectUri, 
-                    propertyUri, objectKey, map, policyHelper, getTemplateName()));
+                    propertyUri, objectKey, map, policyHelper, getTemplateName(), vreq));
         } 
  
         return subclassMap; 

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

@@ -3,7 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
 import java.util.List;
-
+import java.util.HashMap;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -30,12 +30,16 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
     
     // Used for editing
     private String dataPropHash = null;
+    //Useful in case additional params to be retrieved for URL
+    private VitroRequest vitroRequest= null;
    
+    //Extended to include vitro request to check for special parameters
     DataPropertyStatementTemplateModel(String subjectUri, String propertyUri, 
-            Literal literal, EditingPolicyHelper policyHelper) {
+            Literal literal, EditingPolicyHelper policyHelper, VitroRequest vreq) {
         super(subjectUri, propertyUri, policyHelper);
         
         this.value = literal.getLexicalForm();
+        this.vitroRequest = vreq;
         setEditAccess(literal, policyHelper);
        
     }
@@ -48,7 +52,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
      */
     DataPropertyStatementTemplateModel(String subjectUri, String propertyUri, VitroRequest vreq, EditingPolicyHelper policyHelper) {
         super(subjectUri, propertyUri, policyHelper);
-        
+        vitroRequest = vreq;
         DataPropertyStatementDao dpsDao = vreq.getWebappDaoFactory().getDataPropertyStatementDao();
         List<Literal> literals = dpsDao.getDataPropertyValuesForIndividualByProperty(subjectUri, propertyUri);
         
@@ -107,6 +111,12 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
             if (! isDeletable()) {
                 params.put("deleteProhibited", "prohibited");
             }
+            //Check if special parameters being sent
+            
+            HashMap<String, String> specialParams = UrlBuilder.getSpecialParams(vitroRequest);
+            if(specialParams.size() > 0) {
+            	params.putAll(specialParams);
+            }
             editUrl = UrlBuilder.getUrl(EDIT_PATH, params);    
         }
         return editUrl;
@@ -120,6 +130,11 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
                     "predicateUri", propertyUri,
                     "datapropKey", dataPropHash,
                     "cmd", "delete");
+            //Check if special parameters being sent
+            HashMap<String, String> specialParams = UrlBuilder.getSpecialParams(vitroRequest);
+            if(specialParams.size() > 0) {
+            	params.putAll(specialParams);
+            }
             deleteUrl = UrlBuilder.getUrl(EDIT_PATH, params);
         }
         return deleteUrl;

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

@@ -3,6 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 
 import org.apache.commons.logging.Log;
@@ -30,11 +31,12 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
     private static final String EDIT_PATH = "edit/editDatapropStmtRequestDispatch.jsp";  
     
     private List<DataPropertyStatementTemplateModel> statements;
-
+    private VitroRequest vitroRequest = null;
     DataPropertyTemplateModel(DataProperty dp, Individual subject, VitroRequest vreq, 
             EditingPolicyHelper policyHelper, List<DataProperty> populatedDataPropertyList) {
         
         super(dp, subject, policyHelper, vreq);
+        vitroRequest = vreq;
         setName(dp.getPublicName());
 
         statements = new ArrayList<DataPropertyStatementTemplateModel>();
@@ -45,7 +47,7 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
             DataPropertyStatementDao dpDao = vreq.getWebappDaoFactory().getDataPropertyStatementDao();
             List<Literal> values = dpDao.getDataPropertyValuesForIndividualByProperty(subject, dp);            
             for (Literal value : values) {
-                statements.add(new DataPropertyStatementTemplateModel(subjectUri, propertyUri, value, policyHelper));
+                statements.add(new DataPropertyStatementTemplateModel(subjectUri, propertyUri, value, policyHelper, vreq));
             }
         } else {
             log.debug("Data property " + getUri() + " is unpopulated.");
@@ -88,6 +90,12 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
             ParamMap params = new ParamMap(
                     "subjectUri", subjectUri,
                     "predicateUri", propertyUri);
+            //Check if special parameters being sent
+            
+            HashMap<String, String> specialParams = UrlBuilder.getSpecialParams(vitroRequest);
+            if(specialParams.size() > 0) {
+            	params.putAll(specialParams);
+            }
             addUrl = UrlBuilder.getUrl(EDIT_PATH, params);       
         }
         return addUrl;

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

@@ -2,6 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
+import java.util.HashMap;
 import java.util.Map;
 
 import org.apache.commons.logging.Log;
@@ -29,15 +30,16 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
     // Used for editing
     private String objectUri = null;
     private String templateName = null;
-
+    private VitroRequest vitroRequest = null;
+    //Updating to include Vitro Request
     ObjectPropertyStatementTemplateModel(String subjectUri, String propertyUri, String objectKey, 
-            Map<String, String> data, EditingPolicyHelper policyHelper, String templateName) {
+            Map<String, String> data, EditingPolicyHelper policyHelper, String templateName, VitroRequest vreq) {
         super(subjectUri, propertyUri, policyHelper);
         
         this.data = data;
         this.objectUri = data.get(objectKey);
         this.templateName = templateName;
-        
+        this.vitroRequest = vreq;
         setEditAccess(policyHelper);
     }
 
@@ -51,6 +53,7 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
     ObjectPropertyStatementTemplateModel(String subjectUri, String propertyUri, 
             VitroRequest vreq, EditingPolicyHelper policyHelper) {
         super(subjectUri, propertyUri, policyHelper); 
+        vitroRequest = vreq;
     }
 
     private void setEditAccess(EditingPolicyHelper policyHelper) {
@@ -93,6 +96,11 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
             if (! isDeletable()) {
                 params.put("deleteProhibited", "prohibited");
             }
+            //Check if special parameters being sent
+            HashMap<String, String> specialParams = UrlBuilder.getSpecialParams(vitroRequest);
+            if(specialParams.size() > 0) {
+            	params.putAll(specialParams);
+            }
             editUrl = UrlBuilder.getUrl(EDIT_PATH, params);
         }
         
@@ -122,7 +130,11 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
                 }
             }
             params.put("templateName", templateName);
-            
+            //Check if special parameters being sent
+            HashMap<String, String> specialParams = UrlBuilder.getSpecialParams(vitroRequest);
+            if(specialParams.size() > 0) {
+            	params.putAll(specialParams);
+            }
             deleteUrl = UrlBuilder.getUrl(EDIT_PATH, params);
 
         }

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

@@ -6,6 +6,7 @@ import java.io.File;
 import java.io.IOException;
 import java.lang.reflect.Constructor;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
@@ -91,12 +92,14 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
     
     // Used for editing
     private boolean addAccess = false;
-
+    //To allow for checking of special parameters
+    private VitroRequest vitroRequest = null;
     ObjectPropertyTemplateModel(ObjectProperty op, Individual subject, VitroRequest vreq, 
             EditingPolicyHelper policyHelper)
         throws InvalidConfigurationException {
         
         super(op, subject, policyHelper, vreq); 
+        this.vitroRequest = vreq;
         setName(op.getDomainPublic());
         
         // Get the config for this object property
@@ -576,6 +579,12 @@ public abstract class ObjectPropertyTemplateModel extends PropertyTemplateModel
             ParamMap params = new ParamMap(
                     "subjectUri", subjectUri,
                     "predicateUri", propertyUri);  
+            //Check if special parameters being sent
+            
+            HashMap<String, String> specialParams = UrlBuilder.getSpecialParams(vitroRequest);
+            if(specialParams.size() > 0) {
+            	params.putAll(specialParams);
+            }
             addUrl = UrlBuilder.getUrl(EDIT_PATH, params);  
 
         }

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

@@ -3,6 +3,7 @@
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 
 import org.apache.commons.logging.Log;
@@ -71,4 +72,5 @@ public class PropertyGroupTemplateModel extends BaseTemplateModel {
         return properties;
     }
     
+
 }

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

@@ -3,11 +3,13 @@
 package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.BaseTemplateModel;
 
 public abstract class PropertyStatementTemplateModel extends BaseTemplateModel {
@@ -49,4 +51,5 @@ public abstract class PropertyStatementTemplateModel extends BaseTemplateModel {
     protected boolean isDeletable() {
         return editAccessList.contains(EditAccess.DELETE);
     }
+    
 }

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

@@ -42,7 +42,7 @@ public class UncollatedObjectPropertyTemplateModel extends ObjectPropertyTemplat
             String objectKey = getObjectKey();
             for (Map<String, String> map : statementData) {
                 statements.add(new ObjectPropertyStatementTemplateModel(subjectUri, 
-                        propertyUri, objectKey, map, policyHelper, getTemplateName()));
+                        propertyUri, objectKey, map, policyHelper, getTemplateName(), vreq));
             }
             
             postprocessStatementList(statements);

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

@@ -1,7 +1,7 @@
 <#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
 
 <#-- Default individual profile page template -->
-
+<#--@dumpAll /-->
 <section id="individual-intro" class="vcard" role="region">
     <#-- Image -->
     <#assign individualImage>

webapp/web/templates/freemarker/body/menupage/menupage-classintersection.ftl

@@ -0,0 +1,61 @@
+<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+<#-- List individuals in the requested class. -->
+
+<#import "lib-list.ftl" as l>
+
+    <section id="menupage-intro" role="region">
+        <h2>${page.title}</h2>
+	</section>
+${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/browseIndex.css" />')}
+<#assign pageurl = page.urlMapping>
+<section class="individualList">
+    
+    <#if message??>
+        <p>${message}</p>
+    <#else>
+    	
+        <#assign pagination>
+            <#if (pages?size > 1) >
+                pages:
+                <ul class="pagination">
+                    <#list pages as page>
+                     	
+                        <#if page.selected>
+                            <li class="selectedNavPage">${page.text}</li>
+                        <#else>
+                            <#-- RY Ideally the urls would be generated by the controller; see search-pagedResults.ftl -->
+                            <li><a href="${urls.base}${pageurl}?${page.param}">${page.text}</a></li>
+                        </#if>
+                    </#list>
+                    
+                </ul>
+            </#if>
+        </#assign>
+        
+        ${pagination}
+        
+        <ul>
+            <#list individuals as individual>
+                <li>
+                    <#assign moniker = individual.moniker!>
+                    <a href="${individual.profileUrl}">${individual.name}</a><#if moniker?has_content> <span class="moniker">${moniker}</span></#if>
+                    <#assign links = individual.links>
+                    <#if links?has_content>
+                        <ul class="individualData">
+                            <@l.firstLastList>
+                                <#list links as link>
+                                    <li><a class="externalLink" href="${link.url}">${link.anchor}</a></li>
+                                </#list>
+                            </@l.firstLastList>
+                        </ul>
+                    </#if>
+                </li>
+            </#list>
+        </ul>
+        
+        ${pagination}
+    </#if>
+</section> <!-- .individualList -->
+        
+
+    

webapp/web/templates/freemarker/body/partials/individual/lib-properties.ftl

@@ -33,6 +33,7 @@
     </#list> 
 </#macro>
 
+
 <#macro objectProperty property editable template=property.template>
     <#if property.collatedBySubclass> <#-- collated -->
         <@collatedObjectPropertyList property editable template />
@@ -44,6 +45,7 @@
     </#if>
 </#macro>
 
+
 <#macro collatedObjectPropertyList property editable template=property.template >
     <#assign subclasses = property.subclasses>
     <#list subclasses?keys as subclass>
@@ -90,6 +92,7 @@ name will be used as the label. -->
 
 <#macro addLink property editable label="${property.name}" extraParams="">
     <#if editable>
+    	<#--@dump var="property"/-->
         <#local url = property.addUrl>
         <#if url?has_content>
             <@showAddLink property.localName label addParamsToEditUrl(url, extraParams) />
@@ -114,6 +117,7 @@ name will be used as the label. -->
     <h2 id="${property.localName}">${label} <@verboseDisplay property /></h2>     
 </#macro>
 
+
 <#macro propertyListItem property statement editable >
     <li role="listitem">    
         <#nested>        
@@ -217,7 +221,7 @@ name will be used as the label. -->
     <#-- Don't assume that if the mainImage property is populated, there is a thumbnail image (though that is the general case).
          If there's a mainImage statement but no thumbnail image, treat it as if there is no image. -->
     <#if (mainImage.statements)?has_content && thumbUrl?has_content>
-        <a href="${individual.imageUrl}"><img class="individual-photo" src="${thumbUrl}" title="click to view larger image" alt="${individual.name}" width="160" /></a>
+        <a href="${individual.imageUrl}"><img class="individual-photo" src="${tlhumbUrl}" title="click to view larger image" alt="${individual.name}" width="160" /></a>
         <@editingLinks "${mainImage.localName}" mainImage.first editable extraParams />
     <#else>
         <#local imageLabel><@addLinkWithLabel mainImage editable "Photo" extraParams /></#local>
@@ -236,3 +240,5 @@ name will be used as the label. -->
     ${label.value}
     <@editingLinks "label" label editable />
 </#macro>
+
+