updates for page management as well as updates to new URI maker and individual dao jena to handle creation of new URI (old code was returning duplicate when maximum number of attempts was exhausted in NewURIMakerVitro b/c IndividualDaoJena kept returning the same URI since Random instance was set with system time seed and possibly the calls to the method were occurring close together in time and nextInt kept returning the same number).

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

@@ -5,13 +5,18 @@ import java.util.HashSet;
 import java.util.Random;
 import java.util.Set;
 
+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.IndividualImpl;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.IndividualDaoJena;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.NewURIMaker;
 
 public class NewURIMakerVitro implements NewURIMaker {
+    private static final Log log = LogFactory.getLog(NewURIMakerVitro.class.getName());
 
-    private static final int MAX_ATTEMPTS = 10;
+    private static final int MAX_ATTEMPTS = 20;
     WebappDaoFactory wdf;
     Set<String> madeURIs = new HashSet<String>();
     static Random random = new Random();
@@ -27,24 +32,38 @@ public class NewURIMakerVitro implements NewURIMaker {
         String newURI = null;
         int attempts = 0;
         boolean goodNewURI = false;
+        log.debug("Before starting : Made URIs contains " + madeURIs.toString());
+       
         while( ! goodNewURI && attempts < MAX_ATTEMPTS ){
             attempts++;
             
             if( attempts > 2 && prefixURI != null && !prefixURI.isEmpty() ) 
+            {
+            	log.debug("Attempts: " + attempts  + " and prefix not null and prefix not empty " + prefixURI);
                 ind.setURI(prefixURI + random.nextInt() );
-            else
+            }
+            else {
+            	log.debug("Attempts:" + attempts + " and setting uri to " + prefixURI);
                 ind.setURI( prefixURI );
-            
+            }
             newURI = wdf.getIndividualDao().getUnusedURI( ind );
+            log.debug("Created new uri " + newURI + " and does madeURIs contain it?" + madeURIs.contains(newURI));
             if( newURI != null && ! newURI.isEmpty() && ! madeURIs.contains( newURI) ){
+            	log.debug("new URI is not null and new URI is empty and madeURIs does not containt new URI");
                 goodNewURI = true;                
                 madeURIs.add( newURI );                
             } 
+            log.debug("Made URIs contains " + madeURIs.toString());
         }
-        if( newURI != null && !newURI.isEmpty())
+        if(goodNewURI && newURI != null && !newURI.isEmpty()) {
+        	log.debug("Decided on this URI " + newURI);
+        
             return newURI;
-        else
+        }
+        else {
+            log.error("An error occurred and URI could not be created for prefix " + prefixURI);
         	throw new InsertException("Could not get a new URI for the prefix " + prefixURI );
         	}
+    }
 
 }

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

@@ -49,7 +49,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualUpdateEvent;
 import edu.cornell.mannlib.vitro.webapp.edit.EditLiteral;
 
 public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
-
+	//For random number generation, creating it everytime the method is called lead to nextInt being about the same
+	//if calls were made close together in time
+	private Random random = new Random(System.currentTimeMillis());
     public IndividualDaoJena(WebappDaoFactoryJena wadf) {
         super(wadf);
     }
@@ -634,6 +636,9 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
 			//we always want local names like n23423 for the default namespace
 			namespace = DEFAULT_NAMESPACE;
 			uri = null;			
+			log.debug("Setting namespace to default namespace " + DEFAULT_NAMESPACE + " and uri is null");
+			log.debug("Individual : " + individual + " - URI: " + individual.getURI() + " - namespace -" + 
+			individual.getNamespace() + "- ");
 		}else if( individual.getURI() != null ){
 			errMsg = getWebappDaoFactory().checkURI(individual.getURI());
 			if( errMsg == null){
@@ -642,14 +647,16 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
 			}else{
 				throw new InsertException(errMsg);
 			}
+			log.debug("Individual URI not null " + individual.getURI() + " and uriIsGood is true and uri set to individual uri");
 		}else{
 			namespace = individual.getNamespace();
 			if( namespace == null || namespace.length() == 0 )
 				namespace = DEFAULT_NAMESPACE;
 			String localName = individual.getName();
-			
+			log.debug("Namespace " + namespace + " -localname=" + localName);
 			/* try to use the specified namespace and local name */
 			if (localName != null) {
+				log.debug("Local name not equal to null so replacing characters, etc.");
 				localName = localName.replaceAll("\\W", "");
 				localName = localName.replaceAll(":", "");
 				if (localName.length() > 2) {
@@ -662,17 +669,19 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
 						uriIsGood = true;
 					else
 						throw new InsertException(errMsg);		
+					log.debug("uriIsGood is true and uri is " + uri);
 				}
 			}
 			/* else try namespace + n2343 */ 			
 		}
 		
-		Random random = new Random(System.currentTimeMillis());
 		int attempts = 0;
 		
 		while( uriIsGood == false && attempts < 30 ){	
+			log.debug("While loop: Uri is good false, attempt=" + attempts);
 			String localName = "n" + random.nextInt( Math.min(Integer.MAX_VALUE,(int)Math.pow(2,attempts + 13)) );
 			uri = namespace + localName;
+			log.debug("Trying URI " + uri);
 			errMsg = getWebappDaoFactory().checkURI(uri);
 			if(  errMsg != null)
 				uri = null;
@@ -683,7 +692,7 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
 		
 		if( uri == null )
 			throw new InsertException("Could not create URI for individual: " + errMsg);
-								
+		log.debug("Using URI" + uri);						
 		return uri;
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManagePageGenerator.java

@@ -307,6 +307,8 @@ public class ManagePageGenerator extends BaseEditConfigurationGenerator implemen
 	//Takes data getter information, packs within JSON object to send back to the form
 	private void addDataGetterSpecificFormData(String dataGetterURI, ProcessDataGetterN3 pn, OntModel queryModel, JSONArray jsonArray, ServletContext context) {
 		JSONObject jo = pn.getExistingValuesJSON(dataGetterURI, queryModel, context);
+		//Add dataGetterURI to jsonObject
+		jo.element("URI", dataGetterURI);
 		jsonArray.add(jo);
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/ManagePagePreprocessor.java

@@ -85,9 +85,10 @@ public class ManagePagePreprocessor extends
 	
 	private void processExistingValues() {
 		//For all literals that were originally in scope that don't have values on the form
-		//anymore, replace with blank sentinel value
+		//anymore, replace with null value
 		//For those literals, those values will be replaced with form values where overwritten
 		//And will be deleted where not overwritten which is the behavior we desire
+		if(this.editConfiguration.isParamUpdate()) {
 			Map<String, List<Literal>> literalsInScope = this.editConfiguration.getLiteralsInScope();
 			Map<String, List<String>> urisInScope = this.editConfiguration.getUrisInScope();
 			List<String> literalKeys = new ArrayList<String>(literalsInScope.keySet());
@@ -108,9 +109,11 @@ public class ManagePagePreprocessor extends
 				}
 			}
 			
+			
 			for(String uriName: uriKeys) {
 				//these values should never be overwritten or deleted
-			if(uriName != "page" && uriName != "menuItem" && !uriName.startsWith("dataGetter")) {
+				//if(uriName != "page" && uriName != "menuItem" && !uriName.startsWith("dataGetter")) {
+				if(uriName != "page") {
 					boolean hasuv = submission.hasUriValue(uriName);
 					if(!submission.hasUriValue(uriName)) {
 						submission.addUriToForm(editConfiguration, 
@@ -119,7 +122,7 @@ public class ManagePagePreprocessor extends
 					}	
 				}
 			}
-		//Other than data getter itself, also get rid of any of the old URIs if any
+		}
 		
 	}
 	
@@ -236,37 +239,17 @@ public class ManagePagePreprocessor extends
 			 submission.addUriToForm(editConfiguration, submissionUriName, uriValuesSubmission);
 			 
 		 }
-		 //this needs to be different
-		 //Get the literals directly from the processor - which you can get based on counter
-		 //Problem then is we know what the connection is - some way to put that logic within the processor itself?
-		 //It already knows the json object
 		
-		 //--> Get field for this base label, with counter value - that you get from configuration
+		 //To get data getter uris, check if editing an existing set and include those as form inputs
-/*
+		 if(editConfiguration.isParamUpdate()) {
-		 while(jsonObject.keys().hasNext())
+			 String URIValue = jsonObject.getString("URI");
-		 {
+			 if(URIValue != null) {
-			 //Other than class, all other variables considered a submission value corresponding to field
+				 String dataGetterURISubmissionName = pn.getDataGetterVarName(counter);
-			 String key = (String) jsonObject.keys().next();
+				 submission.addUriToForm(editConfiguration, dataGetterURISubmissionName, new String[]{URIValue});
-			 if(key != "dataGetterClass") {
-				 //not expecting multiple values, so will need to either make this array or 
-				 //think about this some more
-				 //TODO: Consider multiple values here
-				 Map<String, String[]> submissionValues = new HashMap<String, String[]>();
-				 submissionValues.put(key, new String[]{jsonObject.getString(key)} );
-				
-				 if(literalLabels.contains(key)) {
-					 submission.addLiteralToForm(editConfiguration.getField(key), field, var, valuesArray)
 			 }
 		 }
 		
 	}
-		 List<String> uris = pn.retrieveUrissOnForm(counter);
-		 for(String l:literals) {
-			 //json object should have 
-			 submissionValues.put(l, new String[]{jsonObject.getString(l)} );
-		 }*/
-		
-	}
 
 	  
 

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessDataGetterAbstract.java

@@ -32,7 +32,12 @@ public abstract class ProcessDataGetterAbstract implements ProcessDataGetterN3 {
 	
     //placeholder so need "?" in front of the variable
     public String getDataGetterVar(int counter) {
-    	return "?dataGetter" + counter;
+    	return "?" + getDataGetterVarName(counter);
+    }
+    
+    //Just the var name, no "?"
+    public String getDataGetterVarName(int counter) {
+    	return "dataGetter" + counter;
     }
     
     public String getPrefixes() {

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessDataGetterN3.java

@@ -28,6 +28,7 @@ public interface ProcessDataGetterN3 {
     public List<String> getUriVarNamesBase();
     public String getVarName(String base, int counter);
     public String getDataGetterVar(int counter);
+    public String getDataGetterVarName(int counter);
     public List<String> getNewResources(int counter);
     
     //Get Existing values to put in scope

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessSparqlDataGetterN3.java

@@ -36,7 +36,6 @@ public  class ProcessSparqlDataGetterN3 extends ProcessDataGetterAbstract {
 	}
 	//Pass in variable that represents the counter 
 
-	//TODO: ensure correct model returned
 	//We shouldn't use the ACTUAL values here but generate the n3 required
     public List<String> retrieveN3Required(int counter) {
     	String dataGetterVar = getDataGetterVar(counter);
@@ -54,14 +53,6 @@ public  class ProcessSparqlDataGetterN3 extends ProcessDataGetterAbstract {
     }
   
     
-    //Need to add method sfor returning the fields, literals on form, and all that
-    /*
-     * addLiteralsAndUrisOnForm(pn, counter);
-			// Add fields
-			addFields(pn, counter);
-			//Add input values to submission
-			addInputsToSubmission(pn, counter);
-     */
     public List<String> retrieveLiteralsOnForm(int counter) {
     	List<String> literalsOnForm = new ArrayList<String>();
     	literalsOnForm.add(getVarName("saveToVar",counter));
@@ -82,15 +73,6 @@ public  class ProcessSparqlDataGetterN3 extends ProcessDataGetterAbstract {
    public List<FieldVTwo> retrieveFields(int counter) {
 	   List<FieldVTwo> fields = new ArrayList<FieldVTwo>();
 	  
-	   //An alternative way of doing this 
-	   /*
-	   List<String> allFieldsBase = new ArrayList<String>();
-	   allFieldsBase.addAll(getLiteralVarNamesBase());
-	   allFieldsBase.addAll(getUriVarNamesBase());
-	   
-	   for(String varName: allFieldsBase) {
-		   fields.add(new FieldVTwo().setName(getVarName(varName, counter)));
-	   } */
 	   //For existing data getters
 	   //fields.add(new FieldVTwo().setName(getVarName("dataGetter", counter)));
 	   fields.add(new FieldVTwo().setName(getVarName("queryModel", counter)));

webapp/test/edu/cornell/mannlib/vitro/webapp/dao/NewURIMakerVitroTest.java

@@ -0,0 +1,111 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+package edu.cornell.mannlib.vitro.webapp.dao;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.junit.Test;
+
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDF;
+
+import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.SimpleOntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
+
+public class NewURIMakerVitroTest extends AbstractTestClass{
+
+	@Test
+	public void testMultipleNewURIs() {
+		//Three items needs new URIs assigned in the default namespace
+		//Var name to namespace, in this case null to denote default namespace
+		Map<String,String> newResources = new HashMap<String, String>();
+		newResources.put("page", null);
+		newResources.put("menuItem", null);
+		newResources.put("dataGetter", null);
+		
+		//Setup webappdaofactory
+		WebappDaoFactoryJena wadf = this.setupWebappDaoFactory();
+		NewURIMakerVitro nv = new NewURIMakerVitro(wadf);
+		
+		//Now test for new URI
+		HashMap<String,String> varToNewURIs = new HashMap<String,String>();       
+		try {
+			for (String key : newResources.keySet()) {
+	           String prefix = newResources.get(key);
+	           String uri = nv.getUnusedNewURI(prefix);                        
+	           varToNewURIs.put(key, uri);  
+			}  
+		} catch(Exception ex) {
+			System.out.println("Error occurred " + ex);
+		}
+		
+		//Ensure that URIs are not included more than once
+		List<String> values = new ArrayList<String>(varToNewURIs.values());
+		Set<String> valuesSet = new HashSet<String>(varToNewURIs.values());
+		assertTrue(valuesSet.size() == values.size());
+
+	}
+	
+	@Test
+	public void testNonNullNamespace() {
+		//Three items needs new URIs assigned in the default namespace
+		//Var name to namespace, in this case null to denote default namespace
+		Map<String,String> newResources = new HashMap<String, String>();
+		newResources.put("page", "http://displayOntology/test/n12");
+	
+		
+		//Setup webappdaofactory
+		WebappDaoFactoryJena wadf = this.setupWebappDaoFactory();
+		NewURIMakerVitro nv = new NewURIMakerVitro(wadf);
+		
+		//Now test for new URI
+		HashMap<String,String> varToNewURIs = new HashMap<String,String>();       
+		try {
+			for (String key : newResources.keySet()) {
+	           String prefix = newResources.get(key);
+	           String uri = nv.getUnusedNewURI(prefix);                        
+	           varToNewURIs.put(key, uri);  
+			}  
+		} catch(Exception ex) {
+			System.out.println("Error occurred " + ex);
+		}
+		
+		//Ensure that URIs are not included more than once
+		List<String> values = new ArrayList<String>(varToNewURIs.values());
+		Set<String> valuesSet = new HashSet<String>(varToNewURIs.values());
+		assertTrue(valuesSet.size() == values.size());
+	}
+	
+	private WebappDaoFactoryJena setupWebappDaoFactory() {
+		String defaultNamespace= "http://vivo.mannlib.cornell.edu/individual/";
+		String testNamespace = "http://displayOntology/test/";
+		OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); 
+		ontModel.add(
+				ontModel.createResource(defaultNamespace + "n234"),
+				RDF.type, 
+				OWL.Thing);
+		ontModel.add(
+				ontModel.createResource(testNamespace + "n234"),
+				RDF.type, 
+				OWL.Thing);
+		OntModelSelector selector = new SimpleOntModelSelector(ontModel);
+		//Set up default namespace somewhere?
+		WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
+        config.setDefaultNamespace(defaultNamespace);
+		//Set up some test uris
+		WebappDaoFactoryJena wadf = new WebappDaoFactoryJena(selector, config);
+		return wadf;
+	}
+
+}

webapp/web/js/menupage/pageManagementUtils.js

@@ -547,6 +547,11 @@ var pageManagementUtils = {
 				var dataGetterProcessor = pageManagementUtils.dataGetterProcessorMap[dataGetterType];
 				//the content type specific processor will create the json object to be returned
 				var jsonObject = dataGetterProcessor.processPageContentSection(pageContentSection);
+				//if data getter uri included, include that as well
+				if(pageContentSection.find("input[name='URI']").length > 0) {
+					var uriValue = pageContentSection.find("input[name='URI']").val();
+					jsonObject["URI"] = uriValue;
+				}
 				return jsonObject;
 			} else {
 				//ERROR handling
@@ -618,6 +623,8 @@ var pageManagementUtils = {
 	    				var $newContentObj = pageManagementUtils.cloneContentAreaForEdit(contentType, contentTypeLabel, additionalLabelText);
 	    				//Populate the section with the values
 	    				dataGetterProcessorObject.populatePageContentSection(JSONContentObject, $newContentObj);
+	    				//Also include a hidden input with data getter URI
+	    				pageManagementUtils.includeDataGetterURI(JSONContentObject, $newContentObj);
 	    			} else {
 	    				//error condition
 	    			}
@@ -627,6 +634,12 @@ var pageManagementUtils = {
     		
     	}
     },
+    includeDataGetterURI:function(JSONContentObject, $newContentObj) {
+    	var uri = JSONContentObject["URI"];
+    	if(uri != null) {
+    		$("<input type='hidden' name='URI' value='" + uri + "'>").appendTo($newContentObj);
+    	}
+    },
     //Get the data getter processor
     getDataGetterProcessorObject:function(pageContentSection) {
     	var dataGetterType = pageManagementUtils.processDataGetterUtils.selectDataGetterType(pageContentSection);