various dev work on language filtering and querying from a generic endpoint

webapp/build.xml

@@ -116,6 +116,16 @@ deploy   - Deploy the application directly into the Tomcat webapps directory.
 			</condition>
 		</fail>
 		
+		<fail message="The vitro.home.directory &quot;${vitro.home.directory}&quot; is not writable.">
+		    <condition>
+		        <not>
+		            <isfileselected file="${vitro.home.directory}" >
+		                <writable/>
+		            </isfileselected>
+		        </not>
+		    </condition>
+		</fail>
+
 		<property name="solr.home.dir" location="${vitro.home.directory}/solr" />
 	</target>
 

webapp/config/licenser/known_exceptions.txt

@@ -133,6 +133,9 @@ webapp/web/WEB-INF/tlds/taglibs-string.tld
 webapp/web/themes/enhanced/css/blueprint/grid.css
 webapp/web/themes/enhanced/css/blueprint/ie.css
 
+# See /doc/3rd-party-licenses.txt for LICENSE file
+webapp/web/css/jquery_plugins/jquery.realperson.css
+
 # PROBLEM: Can't find any info on licensing.
 webapp/web/themes/enhanced/css/blueprint/liquid.css
 

webapp/src/edu/cornell/mannlib/vedit/controller/OperationController.java

@@ -441,14 +441,14 @@ public class OperationController extends BaseEditController {
             } catch (InvocationTargetException e) {
                 log.error(this.getClass().getName()+" encountered exception performing two-stage update");
                 Throwable innerE = e.getTargetException();
-                log.error(innerE);
+                log.error(innerE, innerE);
                 if (innerE.getMessage()!=null) {
-                	log.error(innerE.getMessage());
+                	//log.error(innerE.getMessage());
                 	epo.setAttribute("globalErrorMsg",innerE.getMessage());
                 }
                 return FAILURE;
             } catch (IllegalAccessException iae) {
-            	log.error(iae);
+            	log.error(iae, iae);
             	epo.setAttribute("globalErrorMessage", "Illegal access - see error logs.");
             	return FAILURE;
             }
@@ -459,15 +459,15 @@ public class OperationController extends BaseEditController {
             	log.error(this.getClass().getName()+" encountered exception performing edit action");
                 Throwable innerE = e.getTargetException();
                 //innerE.printStackTrace();
-                log.error(innerE);
+                log.error(innerE, innerE);
                 if (innerE.getMessage()!=null) {
                     //System.out.println(innerE.getMessage());
-                	log.error(innerE.getMessage());
+                	//log.error(innerE.getMessage());
                 	epo.setAttribute("globalErrorMsg",innerE.getMessage());
                 }
                 return FAILURE;
             } catch (IllegalAccessException iae) {
-            	log.error(iae);
+            	log.error(iae, iae);
             	epo.setAttribute("globalErrorMessage", "Illegal access - see error logs.");
             	return FAILURE;
             }

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/SimplePermission.java

@@ -84,6 +84,8 @@ public class SimplePermission extends Permission {
 			"UseMiscellaneousEditorPages");
 	public static final SimplePermission USE_MISCELLANEOUS_PAGES = new SimplePermission(
 			"UseMiscellaneousPages");
+	public static final SimplePermission USE_SPARQL_QUERY_PAGE = new SimplePermission(
+			"UseSparqlQueryPage");
 
 	public static List<SimplePermission> getAllInstances() {
 		return new ArrayList<SimplePermission>(allInstances.values());

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

@@ -7,10 +7,6 @@ public interface ObjectPropertyStatement {
 
     public String toString();
 
-    public boolean isSubjectOriented();
-
-    public void setSubjectOriented(boolean subjectOriented);
-
     public String getSubjectURI();
 
     public void setSubjectURI(String subjectURI);

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

@@ -18,9 +18,7 @@ public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
 
     private String propertyURI = null;
     private ObjectProperty property = null;
-    private String qualifier = null;
     private boolean subjectOriented = true; //is the range the item of interest?  
-    private String description = null;  //generated desc based on subjectOriented during sql query.  
     
    public ObjectPropertyStatementImpl() { }
 
@@ -37,23 +35,7 @@ public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
            String prop = (getProperty()!=null)?getProperty().getDomainPublic():"by propURI"+getPropertyURI();
            String ran = (getObject()!= null)?getObject().getName():"objectURI:"+getObjectURI();
            String dom = (getSubject()!= null)?getSubject().getName():"subjectURI:"+getSubjectURI();
-           String orent = (isSubjectOriented() )?"subject oriented":"object oriented";
+           return "Object Property Statements: "+dom+" "+prop+" to "+ran+" ";
-           return "Object Property Statements: "+dom+" "+prop+" to "+ran+" "+orent;
-    }
-
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#isSubjectOriented()
-     */
-    public boolean isSubjectOriented() {
-        return subjectOriented;
-    }
-
-
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#setSubjectOriented(boolean)
-     */
-    public void setSubjectOriented(boolean subjectOriented) {
-        this.subjectOriented = subjectOriented;
     }
 
     /* (non-Javadoc)
@@ -100,6 +82,11 @@ public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
      */
     public void setSubject(Individual subject) {
         this.subject = subject;
+        if (subject == null || subject.isAnonymous()) {
+            setSubjectURI(null);    
+        } else {
+            setSubjectURI(subject.getURI());
+        }
     }
 
 
@@ -136,6 +123,11 @@ public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
      */
     public void setObject(Individual object) {
         this.object = object;
+        if (object == null || object.isAnonymous()) {
+            setObjectURI(null);    
+        } else {
+            setObjectURI(object.getURI());
+        }
     }
 
 

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

@@ -133,8 +133,14 @@ public class VClass extends BaseResourceBean implements Comparable<VClass>
      * Sorts alphabetically by name
      */
     public int compareTo (VClass o1) {
-        Collator collator = Collator.getInstance();
+        if (this.getName() == null) {
-        return collator.compare(this.getName(),o1.getName());
+            return 1;
+        } else if (o1.getName() == null) {
+            return -1;
+        } else {
+            Collator collator = Collator.getInstance();
+            return collator.compare(this.getName(),o1.getName());
+        }
     }
 
     /**

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/MailUsersServlet.java

@@ -128,8 +128,6 @@ public class MailUsersServlet extends VitroHttpServlet {
         msgBuf.append("</html>" + lineSeparator );
 
         String msgText = msgBuf.toString();
-        // debugging
-        //PrintWriter outFile = new PrintWriter (new FileWriter(request.getSession().getServletContext().getRealPath("/WEB-INF/LatestMessage.html"),true)); //autoflush
 
         Calendar cal = Calendar.getInstance();
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/SparqlQueryServlet.java

@@ -101,7 +101,7 @@ public class SparqlQueryServlet extends BaseEditController {
     throws ServletException, IOException
     {    	    	   	
 		if (!isAuthorizedToDisplayPage(request, response,
-				SimplePermission.USE_ADVANCED_DATA_TOOLS_PAGES.ACTIONS)) {
+				SimplePermission.USE_SPARQL_QUERY_PAGE.ACTIONS)) {
     		return;
     	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/VitroRequest.java

@@ -19,6 +19,7 @@ import com.hp.hpl.jena.query.Dataset;
 import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroModelSource.ModelName;
 
 public class VitroRequest extends HttpServletRequestWrapper {
@@ -78,6 +79,10 @@ public class VitroRequest extends HttpServletRequestWrapper {
     	setAttribute("jenaOntModel", ontModel);
     }
     
+    public void setOntModelSelector(OntModelSelector oms) {
+        setAttribute("ontModelSelector", oms);
+    }
+    
     /** gets assertions + inferences WebappDaoFactory with no filtering **/
     public WebappDaoFactory getFullWebappDaoFactory() {
     	Object webappDaoFactoryAttr = _req.getAttribute("fullWebappDaoFactory");
@@ -97,12 +102,26 @@ public class VitroRequest extends HttpServletRequestWrapper {
     public WebappDaoFactory getAssertionsWebappDaoFactory() {
     	Object webappDaoFactoryAttr = _req.getSession().getAttribute("assertionsWebappDaoFactory");
         if (webappDaoFactoryAttr instanceof WebappDaoFactory) {
+             log.info("Returning assertionsWebappDaoFactory from session");
              return (WebappDaoFactory) webappDaoFactoryAttr;
         } else {
-        	return (WebappDaoFactory) _req.getSession().getServletContext().getAttribute("assertionsWebappDaoFactory");	
+            webappDaoFactoryAttr = getAttribute("assertionsWebappDaoFactory");
+            if (webappDaoFactoryAttr instanceof WebappDaoFactory) {
+                log.info("returning assertionsWebappDaoFactory from request attribute");
+                return (WebappDaoFactory) webappDaoFactoryAttr;     
+            } else {
+                log.info("Returning assertionsWebappDaoFactory from context");
+                return (WebappDaoFactory) _req.getSession().getServletContext().getAttribute("assertionsWebappDaoFactory");
+            }
+        		
         }
     }
     
+    /** gets assertions-only WebappDaoFactory with no filtering */
+    public void setAssertionsWebappDaoFactory(WebappDaoFactory wadf) {
+        setAttribute("assertionsWebappDaoFactory", wadf); 
+    }
+    
     /** gets inferences-only WebappDaoFactory with no filtering */
     public WebappDaoFactory getDeductionsWebappDaoFactory() {
     	Object webappDaoFactoryAttr = _req.getSession().getAttribute("deductionsWebappDaoFactory");
@@ -137,6 +156,16 @@ public class VitroRequest extends HttpServletRequestWrapper {
     	return jenaOntModel;
     }
     
+    public OntModelSelector getOntModelSelector() {
+        Object o = this.getAttribute("ontModelSelector");
+        if (o instanceof OntModelSelector) {
+            return (OntModelSelector) o;
+        } else {
+            return null;
+        }
+    }
+    
+    
     public OntModel getAssertionsOntModel() {
     	OntModel jenaOntModel = (OntModel)_req.getSession().getAttribute( JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME );
     	if ( jenaOntModel == null ) {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/accounts/UserAccountsPage.java

@@ -35,9 +35,6 @@ public abstract class UserAccountsPage extends AbstractPageHandler {
 
 	private static final String PERSON_CLASS_URI = "http://xmlns.com/foaf/0.1/Person";
 
-	private static final String DEFAULT_IMAGE_URL = UrlBuilder
-			.getUrl("/images/placeholders/person.thumbnail.jpg");
-
 	/**
 	 * After the account is created, or the password is reset, the user has this
 	 * many days to repond to the email.
@@ -109,7 +106,6 @@ public abstract class UserAccountsPage extends AbstractPageHandler {
 				UrlBuilder.getUrl("/accounts/firstTimeExternal"));
 		map.put("accountsAjax", UrlBuilder.getUrl("/accountsAjax"));
 		map.put("proxyAjax", UrlBuilder.getUrl("/proxiesAjax"));
-		map.put("defaultImageUrl", DEFAULT_IMAGE_URL);
 
 		return map;
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/accounts/admin/UserAccountsEditPage.java

@@ -237,6 +237,7 @@ public class UserAccountsEditPage extends UserAccountsPage {
 
 		if (!isRootUser()) {
 			body.put("roles", buildListOfSelectableRoles());
+			body.put("externalAuthPermitted", Boolean.TRUE);
 		}
 
 		body.put("profileTypes", buildProfileTypesList());

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ManageProxiesListPage.java

@@ -24,7 +24,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
-import edu.cornell.mannlib.vitro.webapp.utils.ImageUtil;
+import edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil;
 
 /**
  * TODO
@@ -134,8 +134,8 @@ public class ManageProxiesListPage extends AbstractPageHandler {
 	private ProxyItemInfo wrapProxyItem(ProxyItemInfo item) {
 		String imagePath = item.getImageUrl();
 		if (imagePath.isEmpty()) {
-			imagePath = ImageUtil
+			imagePath = PlaceholderUtil.getPlaceholderImagePathForType(vreq,
-					.getPlaceholderImagePathForType(VitroVocabulary.USERACCOUNT);
+					VitroVocabulary.USERACCOUNT);
 		}
 
 		UserAccount ua = userAccountsDao.getUserAccountByUri(item.getUri());
@@ -151,8 +151,8 @@ public class ManageProxiesListPage extends AbstractPageHandler {
 	private ProxyItemInfo wrapProfileItem(ProxyItemInfo item) {
 		String imagePath = item.getImageUrl();
 		if (imagePath.isEmpty()) {
-			imagePath = ImageUtil.getPlaceholderImagePathForIndividual(vreq,
+			imagePath = PlaceholderUtil.getPlaceholderImagePathForIndividual(
-					item.getUri());
+					vreq, item.getUri());
 		}
 
 		return new ProfileItemWrapper(item.getUri(), item.getLabel(),

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ajax/BasicProxiesGetter.java

@@ -24,9 +24,9 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
-import edu.cornell.mannlib.vitro.webapp.utils.ImageUtil;
 import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryRunner;
 import edu.cornell.mannlib.vitro.webapp.utils.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil;
 
 /**
  * Get the basic auto-complete info for the proxy selection.
@@ -64,8 +64,9 @@ public class BasicProxiesGetter extends AbstractAjaxResponder {
 		OntModelSelector oms = ModelContext.getUnionOntModelSelector(ctx);
 		userAccountsModel = oms.getUserAccountsModel();
 
-		placeholderImageUrl = UrlBuilder.getUrl(ImageUtil
+		placeholderImageUrl = UrlBuilder.getUrl(PlaceholderUtil
-				.getPlaceholderImagePathForType(VitroVocabulary.USERACCOUNT));
+				.getPlaceholderImagePathForType(vreq,
+						VitroVocabulary.USERACCOUNT));
 	}
 
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/accounts/manageproxies/ajax/MoreProfileInfo.java

@@ -19,7 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.ajax.AbstractAjaxResponder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
-import edu.cornell.mannlib.vitro.webapp.utils.ImageUtil;
+import edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil;
 
 /**
  * Get more information (class label and image URL) about a selected proxy.
@@ -79,7 +79,7 @@ public class MoreProfileInfo extends AbstractAjaxResponder {
 	private String getFullImageUrl(Individual ind) {
 		String path = ind.getThumbUrl();
 		if ((path == null) || path.isEmpty()) {
-			path = ImageUtil.getPlaceholderImagePathForIndividual(vreq,
+			path = PlaceholderUtil.getPlaceholderImagePathForIndividual(vreq,
 					ind.getURI());
 		}
 		return UrlBuilder.getUrl(path);

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/accounts/user/UserAccountsMyAccountPage.java

@@ -26,6 +26,8 @@ import edu.cornell.mannlib.vitro.webapp.controller.authenticate.Authenticator;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
+import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil;
 
 /**
  * Handle the "My Account" form display and submission.
@@ -268,7 +270,9 @@ public class UserAccountsMyAccountPage extends UserAccountsPage {
 		String userUri = proxyUser.getUri();
 		String label = assembleUserAccountLabel(proxyUser);
 		String classLabel = "";
-		String imageUrl = "";
+		String imageUrl = UrlBuilder.getUrl(PlaceholderUtil
+				.getPlaceholderImagePathForType(vreq,
+						VitroVocabulary.USERACCOUNT));
 
 		// Does this user have a profile? Can we get better info?
 		Individual proxyProfilePage = getProfilePage(proxyUser);

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Classes2ClassesOperationController.java

@@ -16,7 +16,6 @@ import edu.cornell.mannlib.vedit.controller.BaseEditController;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
 public class Classes2ClassesOperationController extends BaseEditController {
@@ -58,7 +57,6 @@ public class Classes2ClassesOperationController extends BaseEditController {
             return;
         }
 
-        Classes2ClassesDao dao = request.getFullWebappDaoFactory().getClasses2ClassesDao();
         VClassDao vcDao = request.getFullWebappDaoFactory().getVClassDao();
         
         String modeStr = request.getParameter("opMode");
@@ -81,7 +79,7 @@ public class Classes2ClassesOperationController extends BaseEditController {
 		                            Classes2Classes c2c = new Classes2Classes();
 		                            c2c.setSubclassURI(subclassURIstrs[i]);
 		                            c2c.setSuperclassURI(superclassURIstr);
-		                            dao.deleteClasses2Classes(c2c);
+		                            vcDao.deleteClasses2Classes(c2c);
 	                        	}
 	                        }
 	                    }
@@ -98,7 +96,7 @@ public class Classes2ClassesOperationController extends BaseEditController {
 		                            Classes2Classes c2c = new Classes2Classes();
 		                            c2c.setSuperclassURI(superclassURIstrs[i]);
 		                            c2c.setSubclassURI(subclassURIstr);
-		                            dao.deleteClasses2Classes(c2c);
+		                            vcDao.deleteClasses2Classes(c2c);
 	                        	}
 	                        }
 	                    }
@@ -112,7 +110,7 @@ public class Classes2ClassesOperationController extends BaseEditController {
 		            	Classes2Classes c2c = new Classes2Classes();
 		                c2c.setSuperclassURI(request.getParameter("SuperclassURI"));
 		                c2c.setSubclassURI(request.getParameter("SubclassURI"));
-		                dao.insertNewClasses2Classes(c2c);
+		                vcDao.insertNewClasses2Classes(c2c);
 	            	}
 	            }
 	        } catch (Exception e) {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Classes2ClassesRetryController.java

@@ -19,7 +19,6 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
 
 public class Classes2ClassesRetryController extends BaseEditController {
@@ -44,9 +43,8 @@ public class Classes2ClassesRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        Classes2ClassesDao c2cDao = request.getFullWebappDaoFactory().getClasses2ClassesDao();
         VClassDao vcDao = request.getFullWebappDaoFactory().getVClassDao();
-        epo.setDataAccessObject(c2cDao);
+        epo.setDataAccessObject(vcDao);
         Classes2Classes objectForEditing = new Classes2Classes();
 
         String superclassURIstr = request.getParameter("SuperclassURI");

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/EntityEditController.java

@@ -48,6 +48,7 @@ public class EntityEditController extends BaseEditController {
         VitroRequest vreq = (new VitroRequest(request));
         ApplicationBean application = vreq.getAppBean();
         
+        //Individual ent = vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(entURI);
         Individual ent = vreq.getAssertionsWebappDaoFactory().getIndividualDao().getIndividualByURI(entURI);
         if (ent == null) {
         	try {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/EntityRetryController.java

@@ -78,7 +78,11 @@ public class EntityRetryController extends BaseEditController {
             action = epo.getAction();
         }
 
-        WebappDaoFactory wadf = (vreq.getAssertionsWebappDaoFactory()!=null) ? vreq.getAssertionsWebappDaoFactory() : vreq.getFullWebappDaoFactory();
+        WebappDaoFactory wadf = vreq.getAssertionsWebappDaoFactory();
+        if (wadf == null) {
+            log.info("Using vreq.getFullWebappDaoFactory()");
+            vreq.getFullWebappDaoFactory();
+        } 
         
         LoginStatusBean loginBean = LoginStatusBean.getBean(request);
         WebappDaoFactory myWebappDaoFactory = wadf.getUserAwareDaoFactory(loginBean.getUserURI());

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/VclassRetryController.java

@@ -197,7 +197,7 @@ public class VclassRetryController extends BaseEditController {
             Classes2Classes c2c = new Classes2Classes();
             c2c.setSubclassURI(((VClass)newObj).getURI());
             c2c.setSuperclassURI(superclassURI);
-            daoFactory.getClasses2ClassesDao().insertNewClasses2Classes(c2c);            
+            daoFactory.getVClassDao().insertNewClasses2Classes(c2c);            
         }
         public void doUpdated(Object oldObj, Object newObj, EditProcessObject epo) {
             // nothing to do

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

@@ -198,9 +198,11 @@ public class BaseSiteAdminController extends FreemarkerHttpServlet {
             urls.put("ingest", UrlBuilder.getUrl("/ingest"));
             urls.put("rdfData", UrlBuilder.getUrl("/uploadRDFForm"));
             urls.put("rdfExport", UrlBuilder.getUrl("/export"));
-            urls.put("sparqlQuery", UrlBuilder.getUrl("/admin/sparqlquery"));
             urls.put("sparqlQueryBuilder", UrlBuilder.getUrl("/admin/sparqlquerybuilder"));
         }
+        if (PolicyHelper.isAuthorizedForActions(vreq, SimplePermission.USE_SPARQL_QUERY_PAGE.ACTIONS)) {            
+        	urls.put("sparqlQuery", UrlBuilder.getUrl("/admin/sparqlquery"));
+        }
         
         return urls;
     }

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

@@ -2,6 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
 
+import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.PrintWriter;
@@ -25,6 +26,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
+import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.TemplateProcessingHelper.TemplateProcessingException;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
@@ -38,7 +40,6 @@ public class ContactMailController extends FreemarkerHttpServlet {
     private static final long serialVersionUID = 1L;
 	
     private final static String SPAM_MESSAGE        = "Your message was flagged as spam.";
-    private final static String EMAIL_BACKUP_FILE_PATH = "/WEB-INF/LatestMessage.html";
     
     private final static String WEB_USERNAME_PARAM  = "webusername";
     private final static String WEB_USEREMAIL_PARAM = "webuseremail";
@@ -48,6 +49,11 @@ public class ContactMailController extends FreemarkerHttpServlet {
     private final static String TEMPLATE_EMAIL = "contactForm-email.ftl";
     private final static String TEMPLATE_BACKUP = "contactForm-backup.ftl";
     private final static String TEMPLATE_ERROR = "contactForm-error.ftl";
+    private final static String TEMPLATE_FORM = "contactForm-form.ftl";
+    
+	private static final String PROPERTY_VITRO_HOME_DIR = "vitro.home.directory";
+	private static final String EMAIL_JOURNAL_FILE_DIR = "emailJournal";
+	private static final String EMAIL_JOURNAL_FILE_NAME = "contactFormEmails.html";
     
 	@Override
     protected String getTitle(String siteName, VitroRequest vreq) {
@@ -70,9 +76,13 @@ public class ContactMailController extends FreemarkerHttpServlet {
 		String webuseremail = nonNullAndTrim(vreq, WEB_USEREMAIL_PARAM);
 		String comments = nonNullAndTrim(vreq, COMMENTS_PARAM);
 	    String formType = nonNullAndTrim(vreq, "DeliveryType");
+	    String captchaInput = nonNullAndTrim(vreq, "defaultReal");
+	    String captchaDisplay = nonNullAndTrim(vreq, "defaultRealHash");
 
-		if (validateInput(webusername, webuseremail, comments) != null) {
+	    String errorMsg = validateInput(webusername, webuseremail, comments, captchaInput, captchaDisplay);
-			return errorParametersNotValid();
+
+		if ( errorMsg != null) {
+			return errorParametersNotValid(errorMsg, webusername, webuseremail, comments);
 		}
 		
 		String spamReason = checkForSpam(comments, formType);
@@ -107,14 +117,14 @@ public class ContactMailController extends FreemarkerHttpServlet {
 	    		deliveryfrom, originalReferer, vreq.getRemoteAddr(), config, vreq);
 	    
 	    try {
-	    	// Write the email to a backup file
+	    	// Write the message to the journal file
-	        FileWriter fw = new FileWriter(getServletContext().getRealPath(EMAIL_BACKUP_FILE_PATH),true);
+	    	FileWriter fw = new FileWriter(locateTheJournalFile(vreq),true);
 	        PrintWriter outFile = new PrintWriter(fw); 
 	        writeBackupCopy(outFile, msgText, config, vreq);
   
-	        Session s = FreemarkerEmailFactory.getEmailSession(vreq);
-
 	        try {
+	        	// Send the message
+	        	Session s = FreemarkerEmailFactory.getEmailSession(vreq);
 	        	sendMessage(s, webuseremail, webusername, recipients, deliveryfrom, msgText);
 	        } catch (AddressException e) {
 	            statusMsg = "Please supply a valid email address.";
@@ -147,6 +157,40 @@ public class ContactMailController extends FreemarkerHttpServlet {
 	    }   
 	}
 
+	/**
+	 * The journal file belongs in a sub-directory of the Vitro home directory.
+	 * If the sub-directory doesn't exist, create it.
+	 */
+	private File locateTheJournalFile(VitroRequest vreq) {
+		String homeDirPath = ConfigurationProperties.getBean(vreq).getProperty(
+				PROPERTY_VITRO_HOME_DIR);
+		if (homeDirPath == null) {
+			throw new IllegalArgumentException(
+					"Configuration properties must contain a value for '"
+							+ PROPERTY_VITRO_HOME_DIR + "'");
+		}
+
+		File homeDir = new File(homeDirPath);
+		if (!homeDir.exists()) {
+			throw new IllegalStateException("Vitro home directory '"
+					+ homeDir.getAbsolutePath() + "' does not exist.");
+		}
+
+		File journalDir = new File(homeDir, EMAIL_JOURNAL_FILE_DIR);
+		if (!journalDir.exists()) {
+			boolean created = journalDir.mkdir();
+			if (!created) {
+				throw new IllegalStateException(
+						"Unable to create email journal directory at '"
+								+ journalDir + "'");
+			}
+		}
+
+		File journalFile = new File(journalDir, EMAIL_JOURNAL_FILE_NAME);
+		return journalFile;
+	}
+
+
 	private String getOriginalRefererFromSession(VitroRequest vreq) {
 		String originalReferer = (String) vreq.getSession().getAttribute("contactFormReferer");        		
 	    if (originalReferer != null) {
@@ -263,20 +307,28 @@ public class ContactMailController extends FreemarkerHttpServlet {
 	}
 
     private String validateInput(String webusername, String webuseremail,
-    							 String comments) {
+    							 String comments, String captchaInput, String captchaDisplay) {
     	
         if( webusername.isEmpty() ){
-            return "A proper webusername field was not found in the form submitted.";
+            return "Please enter a value in the Full name field.";
         } 
 
         if( webuseremail.isEmpty() ){
-            return "A proper webuser email field was not found in the form submitted.";
+            return "Please enter a valid email address.";
         } 
 
         if (comments.isEmpty()) { 
-            return "The proper comments field was not found in the form submitted.";
+            return "Please enter your comments or questions in the space provided.";
         } 
         
+        if (captchaInput.isEmpty()) { 
+            return "Please enter the contents of the gray box in the security field provided.";
+        } 
+        
+		if ( !captchaHash(captchaInput).equals(captchaDisplay) ) {
+			return "The value you entered in the security field did not match the letters displayed in the gray box.";
+		}
+
         return null;
     }
     
@@ -308,6 +360,15 @@ public class ContactMailController extends FreemarkerHttpServlet {
         
     }
     
+	private String captchaHash(String value) {
+		int hash = 5381;
+		value = value.toUpperCase();
+		for(int i = 0; i < value.length(); i++) {
+			hash = ((hash << 5) + hash) + value.charAt(i);
+		}
+		return String.valueOf(hash);
+	}
+
 	private ResponseValues errorNoSmtpServer() {
         Map<String, Object> body = new HashMap<String, Object>();
         body.put("errorMessage", 
@@ -324,11 +385,14 @@ public class ContactMailController extends FreemarkerHttpServlet {
 		return new TemplateResponseValues(TEMPLATE_ERROR, body);
 	}
 	
-	private ResponseValues errorParametersNotValid() {
+	private ResponseValues errorParametersNotValid(String errorMsg, String webusername, String webuseremail, String comments) {
-		// rjy7 We should reload the form, not go to the error page!
         Map<String, Object> body = new HashMap<String, Object>();
-		body.put("errorMessage", "Invalid submission");
+		body.put("errorMessage", errorMsg);
-		return new TemplateResponseValues(TEMPLATE_ERROR, body);
+		body.put("formAction", "submitFeedback");
+		body.put("webusername", webusername);
+		body.put("webuseremail", webuseremail);
+		body.put("comments", comments);
+		return new TemplateResponseValues(TEMPLATE_FORM, body);
 	}
 	
 	private ResponseValues errorSpam() {

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

@@ -19,6 +19,10 @@ import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.config.RevisionInfoBean;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.Route;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfigurationConstants;
+import edu.cornell.mannlib.vitro.webapp.web.methods.IndividualLocalNameMethod;
+import edu.cornell.mannlib.vitro.webapp.web.methods.IndividualPlaceholderImageUrlMethod;
+import edu.cornell.mannlib.vitro.webapp.web.methods.IndividualProfileUrlMethod;
 import freemarker.cache.ClassTemplateLoader;
 import freemarker.cache.FileTemplateLoader;
 import freemarker.cache.MultiTemplateLoader;
@@ -108,6 +112,9 @@ public class FreemarkerConfiguration extends Configuration {
         sharedVariables.putAll(getMethods());
         sharedVariables.put("siteTagline", appBean.getShortHand()); 
         
+        //Put in edit configuration constants - useful for freemarker templates/editing
+        sharedVariables.put("editConfigurationConstants", EditConfigurationConstants.exportConstants());
+        
         for ( Map.Entry<String, Object> variable : sharedVariables.entrySet() ) {
             try {
                 setSharedVariable(variable.getKey(), variable.getValue());
@@ -156,8 +163,9 @@ public class FreemarkerConfiguration extends Configuration {
     
     public static Map<String, Object> getMethods() {
         Map<String, Object> map = new HashMap<String, Object>();
-        map.put("profileUrl", new edu.cornell.mannlib.vitro.webapp.web.methods.IndividualProfileUrlMethod());
+        map.put("profileUrl", new IndividualProfileUrlMethod());
-        map.put("localName", new edu.cornell.mannlib.vitro.webapp.web.methods.IndividualLocalNameMethod());
+        map.put("localName", new IndividualLocalNameMethod());
+        map.put("placeholderImageUrl", new IndividualPlaceholderImageUrlMethod());
         return map;
     }
     

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

@@ -338,42 +338,38 @@ public class FreemarkerHttpServlet extends VitroHttpServlet {
         return appBean.getThemeDir().replaceAll("/$", "");
     }
 
-    /** 
+	/**
-     * Define the request-specific URLs that are accessible to the templates. 
+	 * Define the request-specific URLs that are accessible to the templates.
-     * @param VitroRequest vreq
+	 * Merge it with the context-specific URLs from the configuration, because
-     */
+	 * this map will mask that one.
-    private void setRequestUrls(VitroRequest vreq) {
+	 */
+    private Map<String, Object> buildRequestUrls(VitroRequest vreq) {
+        Map<String, Object> requestUrls = new HashMap<String, Object>();
     	
         FreemarkerConfiguration config = (FreemarkerConfiguration)vreq.getAttribute("freemarkerConfig");
         TemplateModel urlModel = config.getSharedVariable("urls");
         
         try {
             @SuppressWarnings("unchecked")
-            Map<String, Object> urls = (Map<String, Object>) DeepUnwrap.permissiveUnwrap(urlModel);
+			Map<String, Object> configUrls = (Map<String, Object>) DeepUnwrap.permissiveUnwrap(urlModel);
+			requestUrls.putAll(configUrls);
             
             // This is request-specific because email can be configured
             // and de-configured in the application interface. 
             if (FreemarkerEmailFactory.isConfigured(vreq)) {
-                urls.put("contact", UrlBuilder.getUrl(Route.CONTACT));
+                requestUrls.put("contact", UrlBuilder.getUrl(Route.CONTACT));
-            } else {
-                urls.remove("contact"); // clear value from a previous request
             }      
             
-            urls.put("currentPage", getCurrentPageUrl(vreq));
+            requestUrls.put("currentPage", getCurrentPageUrl(vreq));
-            urls.put("referringPage", getReferringPageUrl(vreq));
+            requestUrls.put("referringPage", getReferringPageUrl(vreq));
             
             if (PolicyHelper.isAuthorizedForActions(vreq, SimplePermission.EDIT_OWN_ACCOUNT.ACTIONS)) {
-                urls.put("myAccount", UrlBuilder.getUrl("/accounts/myAccount"));
+            	requestUrls.put("myAccount", UrlBuilder.getUrl("/accounts/myAccount"));
-            } else {
-                urls.remove("myAccount"); // clear value from a previous request
             }
-            
-            config.setSharedVariable("urls", urls);
-
         } catch (TemplateModelException e) {
             log.error(e, e);
         }
-
+        return requestUrls;
     }
     
     private String getCurrentPageUrl(HttpServletRequest request) {
@@ -424,7 +420,7 @@ public class FreemarkerHttpServlet extends VitroHttpServlet {
         // This may be overridden by the body data model received from the subcontroller.
         map.put("title", getTitle(vreq.getAppBean().getApplicationName(), vreq));
         
-        setRequestUrls(vreq);
+        map.put("urls", buildRequestUrls(vreq));
 
         map.put("menu", getDisplayModelMenu(vreq));
         

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

@@ -36,6 +36,7 @@ import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorageSetup;
 import edu.cornell.mannlib.vitro.webapp.filestorage.model.FileInfo;
 import edu.cornell.mannlib.vitro.webapp.filestorage.model.ImageInfo;
 import edu.cornell.mannlib.vitro.webapp.filestorage.uploadrequest.FileUploadServletRequest;
+import edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil;
 
 /**
  * Handle adding, replacing or deleting the main image on an Individual.
@@ -63,12 +64,6 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	/** The form field of the uploaded file; use as a key to the FileItem map. */
 	public static final String PARAMETER_UPLOADED_FILE = "datafile";
 
-	/**
-	 * The image to use as a placeholder when the individual has no image.
-	 * Determined by the template.
-	 */
-	public static final String PARAMETER_PLACEHOLDER_URL = "placeholder";
-
 	/** Here is the main image file. Hold on to it. */
 	public static final String ACTION_UPLOAD = "upload";
 
@@ -141,7 +136,8 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 			String imageUri = entity.getMainImageUri();
 
 			RequestedAction ra;
-			if (ACTION_DELETE.equals(action) || ACTION_DELETE_EDIT.equals(action)) {
+			if (ACTION_DELETE.equals(action)
+					|| ACTION_DELETE_EDIT.equals(action)) {
 				ra = new DropObjectPropStmt(entity.getURI(),
 						VitroVocabulary.IND_MAIN_IMAGE, imageUri);
 			} else if (imageUri != null) {
@@ -405,12 +401,13 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	private TemplateResponseValues showAddImagePage(VitroRequest vreq,
 			Individual entity) {
 
-		String placeholderUrl = vreq.getParameter(PARAMETER_PLACEHOLDER_URL);
-
 		String formAction = (entity == null) ? "" : formAction(entity.getURI(),
-				ACTION_UPLOAD, placeholderUrl);
+				ACTION_UPLOAD);
 		String cancelUrl = (entity == null) ? "" : exitPageUrl(vreq,
 				entity.getURI());
+		String placeholderUrl = (entity == null) ? "" : UrlBuilder
+				.getUrl(PlaceholderUtil.getPlaceholderImagePathForIndividual(
+						vreq, entity.getURI()));
 
 		TemplateResponseValues rv = new TemplateResponseValues(TEMPLATE_NEW);
 
@@ -437,12 +434,11 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	 */
 	private TemplateResponseValues showReplaceImagePage(VitroRequest vreq,
 			Individual entity, ImageInfo imageInfo) {
-		String placeholderUrl = vreq.getParameter(PARAMETER_PLACEHOLDER_URL);
 		TemplateResponseValues rv = new TemplateResponseValues(TEMPLATE_REPLACE);
 		rv.put(BODY_THUMBNAIL_URL, UrlBuilder.getUrl(imageInfo.getThumbnail()
 				.getBytestreamAliasUrl()));
-		rv.put(BODY_DELETE_URL, formAction(entity.getURI(), ACTION_DELETE_EDIT, placeholderUrl));
+		rv.put(BODY_DELETE_URL, formAction(entity.getURI(), ACTION_DELETE_EDIT));
-		rv.put(BODY_FORM_ACTION, formAction(entity.getURI(), ACTION_UPLOAD, placeholderUrl));
+		rv.put(BODY_FORM_ACTION, formAction(entity.getURI(), ACTION_UPLOAD));
 		rv.put(BODY_CANCEL_URL, exitPageUrl(vreq, entity.getURI()));
 		rv.put(BODY_TITLE, "Replace image" + forName(entity));
 		rv.put(BODY_MAX_FILE_SIZE, MAXIMUM_FILE_SIZE / (1024 * 1024));
@@ -468,12 +464,11 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	 */
 	private TemplateResponseValues showCropImagePage(VitroRequest vreq,
 			Individual entity, String imageUrl, Dimensions dimensions) {
-		String placeholderUrl = vreq.getParameter(PARAMETER_PLACEHOLDER_URL);
 		TemplateResponseValues rv = new TemplateResponseValues(TEMPLATE_CROP);
 		rv.put(BODY_MAIN_IMAGE_URL, UrlBuilder.getUrl(imageUrl));
 		rv.put(BODY_MAIN_IMAGE_HEIGHT, dimensions.height);
 		rv.put(BODY_MAIN_IMAGE_WIDTH, dimensions.width);
-		rv.put(BODY_FORM_ACTION, formAction(entity.getURI(), ACTION_SAVE, placeholderUrl));
+		rv.put(BODY_FORM_ACTION, formAction(entity.getURI(), ACTION_SAVE));
 		rv.put(BODY_CANCEL_URL, exitPageUrl(vreq, entity.getURI()));
 		rv.put(BODY_TITLE, "Crop Photo" + forName(entity));
 		return rv;
@@ -518,11 +513,9 @@ public class ImageUploadController extends FreemarkerHttpServlet {
 	 * back to this controller, along with the desired action and the Entity
 	 * URI.
 	 */
-	private String formAction(String entityUri, String action,
+	private String formAction(String entityUri, String action) {
-			String placeholderUrl) {
+		ParamMap params = new ParamMap(PARAMETER_ENTITY_URI, entityUri,
-		ParamMap params = new ParamMap(
+				PARAMETER_ACTION, action);
-				PARAMETER_ENTITY_URI, entityUri, PARAMETER_ACTION, action,
-				PARAMETER_PLACEHOLDER_URL, placeholderUrl);
 		return UrlBuilder.getPath(URL_HERE, params);
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/Classes2ClassesDao.java

@@ -1,13 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
-
-public interface Classes2ClassesDao {
-
-    public abstract void deleteClasses2Classes(Classes2Classes c2c);
-
-    public abstract void insertNewClasses2Classes(Classes2Classes c2c);
-
-}

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

@@ -4,6 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.dao;
 
 import java.util.List;
 
+import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
 
@@ -67,6 +68,10 @@ public interface VClassDao {
 
     void addVClassesToGroup(VClassGroup group);
     
+    void insertNewClasses2Classes(Classes2Classes c2c);
+    
+    void deleteClasses2Classes(Classes2Classes c2c);
+
     @SuppressWarnings("unchecked")
     void addVClassesToGroup(VClassGroup group, boolean includeUninstantiatedClasses);/* (non-Javadoc)
     * @see edu.cornell.mannlib.vitro.webapp.dao.db.VClassDao#addVClassesToGroups(java.util.List)

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

@@ -3,7 +3,6 @@
 package edu.cornell.mannlib.vitro.webapp.dao;
 
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 
 public interface WebappDaoFactory {
@@ -13,12 +12,6 @@ public interface WebappDaoFactory {
      */
     public void close();
 
-	/**
-	 * Retrieves a map containing arbitrary key-value pairs describing this 
-	 * WebappDaoFactory
-	 */
-	public Map<String,String> getProperties();
-
 	/**
 	 * Checks a URI String for two things: well-formedness and uniqueness in the
 	 * model.  Ill-formed strings or those matching URIs already in use will 
@@ -39,7 +32,7 @@ public interface WebappDaoFactory {
     
     public Set<String> getNonuserNamespaces();
     
-    public String[] getPreferredLanguages();
+    public List<String> getPreferredLanguages();
     
     /**
      * BJL23 2008-05-20: Putting this here for lack of a more logical place.  
@@ -66,11 +59,6 @@ public interface WebappDaoFactory {
 
     /* =============== DAOs for ontology (TBox) manipulation =============== */
 
-    /**
-     * returns a Data Access Object for working with class subsumption axioms 
-     */
-    public Classes2ClassesDao getClasses2ClassesDao();
-
     /**
      * returns a Data Access Object for working with DataProperties
      */

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

@@ -2,30 +2,29 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao;
 
+import java.util.Arrays;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 
 public class WebappDaoFactoryConfig {
 	
-	private String[] preferredLanguages;
+	private List<String> preferredLanguages;
 	private String defaultNamespace;
 	private Set<String> nonUserNamespaces;
 	
 	public WebappDaoFactoryConfig() {
-        preferredLanguages = new String[3];
+	    preferredLanguages = Arrays.asList("en-US", "en", "EN");
-        preferredLanguages[0] = "en-US";
-        preferredLanguages[1] = "en";
-        preferredLanguages[2] = "EN";
 		defaultNamespace = "http://vitro.mannlib.cornell.edu/ns/default#";
 		nonUserNamespaces = new HashSet<String>();
 		nonUserNamespaces.add(VitroVocabulary.vitroURI);
 	}
 	
-	public String[] getPreferredLanguages() {
+	public List<String> getPreferredLanguages() {
 		return this.preferredLanguages;
 	}
 	
-	public void setPreferredLanguages(String[] pl) {
+	public void setPreferredLanguages(List<String> pl) {
 		this.preferredLanguages = pl;
 	}
 	

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

@@ -56,10 +56,6 @@ public class ObjectPropertyStatementFiltering implements ObjectPropertyStatement
         return innerStmt.getSubjectURI();
     }
 
-    public boolean isSubjectOriented() {
-        return innerStmt.isSubjectOriented();
-    }
-
     public void setObject(Individual object) {
         innerStmt.setObject(object);
     }
@@ -80,10 +76,6 @@ public class ObjectPropertyStatementFiltering implements ObjectPropertyStatement
         innerStmt.setSubject(subject);
     }
 
-    public void setSubjectOriented(boolean subjectOriented) {
-        innerStmt.setSubjectOriented(subjectOriented);
-    }
-
     public void setSubjectURI(String subjectURI) {
         innerStmt.setSubjectURI(subjectURI);
     }

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

@@ -11,6 +11,7 @@ import java.util.List;
 import net.sf.jga.algorithms.Filter;
 import net.sf.jga.fn.UnaryFunctor;
 import net.sf.jga.fn.property.GetProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
@@ -240,6 +241,14 @@ public class VClassDaoFiltering extends BaseFiltering implements VClassDao{
     	return innerVClassDao.getBottomConcept();
     }
     
+    public void insertNewClasses2Classes(Classes2Classes c2c) {
+        innerVClassDao.insertNewClasses2Classes(c2c);
+    }
+    
+    public void deleteClasses2Classes(Classes2Classes c2c) {
+        innerVClassDao.deleteClasses2Classes(c2c);
+    }
+    
     public boolean isSubClassOf(VClass vc1, VClass vc2) {
 		return innerVClassDao.isSubClassOf(vc1, vc2);
 	}

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

@@ -7,7 +7,6 @@ import java.util.Map;
 import java.util.Set;
 
 import edu.cornell.mannlib.vitro.webapp.dao.ApplicationDao;
-import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
@@ -76,10 +75,6 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
 
     /* ******************* filtering *********************** */
 
-	public Map<String,String> getProperties() {
-		return innerWebappDaoFactory.getProperties();
-	}
-
     public String checkURI(String uriStr) {
     	return innerWebappDaoFactory.checkURI(uriStr);
     }
@@ -101,7 +96,7 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
     	return innerWebappDaoFactory.getNonuserNamespaces();
     }
     
-    public String[] getPreferredLanguages() {
+    public List<String> getPreferredLanguages() {
     	return innerWebappDaoFactory.getPreferredLanguages();
     }
     
@@ -168,10 +163,6 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
 
     /* ******************* non-filtering DAOs *************************** */
 
-    public Classes2ClassesDao getClasses2ClassesDao() {
-        return innerWebappDaoFactory.getClasses2ClassesDao();
-    }
-
     public DatatypeDao getDatatypeDao() {
         return innerWebappDaoFactory.getDatatypeDao();
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/Classes2ClassesDaoJena.java

@@ -1,69 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntResource;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.vocabulary.RDFS;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Classes2Classes;
-import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
-
-/**
- *
- */
-public class Classes2ClassesDaoJena extends JenaBaseDao implements Classes2ClassesDao {
-	
-    public Classes2ClassesDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-
-    public void deleteClasses2Classes( Classes2Classes c2c ) {
-    	deleteClasses2Classes(c2c, getOntModelSelector().getTBoxModel());
-    }
-
-    public void deleteClasses2Classes( Classes2Classes c2c, OntModel ontModel )
-    {
-        ontModel.enterCriticalSection(Lock.WRITE);
-        ontModel.getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),true));
-        try {
-            OntResource subclass = getOntClass(ontModel,c2c.getSubclassURI());
-            OntResource superclass = getOntClass(ontModel,c2c.getSuperclassURI());
-            if ((subclass != null) && (superclass != null)) {
-                ontModel.removeAll(subclass, RDFS.subClassOf, superclass);
-            }
-            if (subclass.isAnon()) {
-            	smartRemove(subclass, getOntModel());
-            }
-            if (superclass.isAnon()) {
-            	smartRemove(superclass, getOntModel());
-            }
-        } finally {
-        	ontModel.getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),false));
-            ontModel.leaveCriticalSection();
-        }
-    }
-
-    public void insertNewClasses2Classes( Classes2Classes c2c ) {
-    	insertNewClasses2Classes(c2c, getOntModelSelector().getTBoxModel());
-    }
-
-    public void insertNewClasses2Classes( Classes2Classes c2c, OntModel ontModel )
-    {
-        ontModel.enterCriticalSection(Lock.WRITE);
-        ontModel.getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),true));
-        try {
-            Resource subclass = ontModel.getResource(c2c.getSubclassURI());
-            Resource superclass = ontModel.getResource(c2c.getSuperclassURI());
-            if ((subclass != null) && (superclass != null)) {
-                ontModel.add(subclass, RDFS.subClassOf, superclass);
-            }
-        } finally {
-        	ontModel.getBaseModel().notifyEvent(new EditEvent(getWebappDaoFactory().getUserURI(),false));
-            ontModel.leaveCriticalSection();
-        }
-    }
-}

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

@@ -43,17 +43,17 @@ public class EmptyReifier implements Reifier {
 
     @Override
     public ExtendedIterator<Triple> find(TripleMatch arg0) {
-        return WrappedIterator.create(Collections.EMPTY_LIST.iterator());
+        return g.find(arg0);
     }
 
     @Override
     public ExtendedIterator<Triple> findEither(TripleMatch arg0, boolean arg1) {
-        return WrappedIterator.create(Collections.EMPTY_LIST.iterator());
+        return find(arg0);
     }
 
     @Override
     public ExtendedIterator<Triple> findExposed(TripleMatch arg0) {
-        return WrappedIterator.create(Collections.EMPTY_LIST.iterator());
+        return find(arg0);
     }
 
     @Override
@@ -68,14 +68,14 @@ public class EmptyReifier implements Reifier {
 
     @Override
     public boolean handledAdd(Triple arg0) {
-        // TODO Auto-generated method stub
+        g.add(arg0);
-        return false;
+        return true;
     }
 
     @Override
     public boolean handledRemove(Triple arg0) {
-        // TODO Auto-generated method stub
+        g.delete(arg0);
-        return false;
+        return true;
     }
 
     @Override
@@ -98,20 +98,17 @@ public class EmptyReifier implements Reifier {
 
     @Override
     public void remove(Triple arg0) {
-        // TODO Auto-generated method stub
+        g.delete(arg0);
-
     }
 
     @Override
     public void remove(Node arg0, Triple arg1) {
-        // TODO Auto-generated method stub
+        g.delete(arg1);
-
     }
 
     @Override
     public int size() {
-        // TODO Auto-generated method stub
+        return g.size();
-        return 0;
     }
 
 }

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

@@ -187,9 +187,10 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     		        continue;
     		    }
     		    if (uri != null && !uri.equals(currRes.getURI())) {
-    		        Individual ent = makeIndividual(uri, label);
+    		        try {
-    		        if (ent != null) {
+    		            ents.add(makeIndividual(uri, label));
-    		            ents.add(ent);
+    		        } catch (IndividualNotFoundException e) {
+    		            // don't add
     		        }
     	            uri = currRes.getURI();
     	            label = null;
@@ -201,9 +202,10 @@ public class IndividualDaoSDB extends IndividualDaoJena {
                     label = labelLit.getLexicalForm();
                 }
                 if (!rs.hasNext()) {
-                    Individual ent = makeIndividual(uri, label);
+                    try {
-                    if (ent != null) {
+                        ents.add(makeIndividual(uri, label));
-                        ents.add(ent);
+                    } catch (IndividualNotFoundException e) {
+                        // don't add   
                     }
                 }
     		}
@@ -237,8 +239,12 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     		    if (currRes.isAnon()) {
     		        continue;
     		    }
-    		    filteredIndividualList.add(
+    		    try {
-    		    		makeIndividual(currRes.getURI(), null));
+    		        filteredIndividualList.add(
+    		    	    	makeIndividual(currRes.getURI(), null));
+    		    } catch (IndividualNotFoundException e) {
+    		        // don't add
+    		    }
     		}
        	} finally {
     		dataset.getLock().leaveCriticalSection();
@@ -247,7 +253,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
        	return filteredIndividualList;
     }
     
-    private Individual makeIndividual(String uri, String label) {
+    private Individual makeIndividual(String uri, String label) throws IndividualNotFoundException {
         Individual ent = new IndividualSDB(uri, 
                 this.dwf, datasetMode, getWebappDaoFactory(), 
                 SKIP_INITIALIZATION);

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

@@ -109,7 +109,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             DatasetWrapperFactory datasetWrapperFactory, 
             SDBDatasetMode datasetMode,
             WebappDaoFactoryJena wadf,
-            boolean skipInitialization) {
+            boolean skipInitialization) throws IndividualNotFoundException {
     	this.individualURI = individualURI;
     	this.datasetMode = datasetMode;
     	this.dwf = datasetWrapperFactory;
@@ -176,7 +176,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     public IndividualSDB(String individualURI, 
             DatasetWrapperFactory datasetWrapperFactory,
             SDBDatasetMode datasetMode,
-            WebappDaoFactoryJena wadf) {
+            WebappDaoFactoryJena wadf) throws IndividualNotFoundException {
         this(individualURI, 
              datasetWrapperFactory, 
              datasetMode, 
@@ -184,7 +184,7 @@ public class IndividualSDB extends IndividualImpl implements Individual {
              !SKIP_INITIALIZATION);
     }
     
-    public class IndividualNotFoundException extends RuntimeException {}
+    public class IndividualNotFoundException extends Exception {}
     
     private void setUpURIParts(OntResource ind) {
         if (ind != null) {
@@ -464,8 +464,24 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     			if (!s.getSubject().canAs(OntResource.class) || !s.getObject().canAs(OntResource.class)) {
     			    continue;	
     			}
-    			Individual subj = new IndividualSDB(((OntResource) s.getSubject().as(OntResource.class)).getURI(), this.dwf, datasetMode, webappDaoFactory);
+    			Individual subj = null;
-    			Individual obj = new IndividualSDB(((OntResource) s.getObject().as(OntResource.class)).getURI(), this.dwf, datasetMode, webappDaoFactory);
+    			try {
+    			    subj = new IndividualSDB(
+    			            ((OntResource) s.getSubject().as(OntResource.class))
+    			                    .getURI(), 
+    			                            this.dwf, datasetMode, webappDaoFactory);
+    			} catch (IndividualNotFoundException e) {
+    			    // leave null subject
+    			}
+    			Individual obj = null;
+    			try {
+    			    obj = new IndividualSDB(
+    			            ((OntResource) s.getObject().as(OntResource.class))
+    			                    .getURI(), 
+    			                            this.dwf, datasetMode, webappDaoFactory);
+    			} catch (IndividualNotFoundException e) {
+    			    // leave null object
+    			}
     			ObjectProperty op = webappDaoFactory.getObjectPropertyDao().getObjectPropertyByURI(s.getPredicate().getURI());
     			// We don't want to filter out statements simply because we 
     			// can't find a type for the property, so we'll just make a 
@@ -517,15 +533,19 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	    while (values.hasNext()) {
     	    	result = values.next();
     	    	RDFNode value = result.get("object");
-    	    	if (value.canAs(OntResource.class)) {
+    	    	try {
-        	    	relatedIndividuals.add(
+        	    	if (value.canAs(OntResource.class)) {
-        	    		new IndividualSDB(
+            	    	relatedIndividuals.add(
-        	    		        ((OntResource) value.as(OntResource.class))
+            	    		new IndividualSDB(
-        	    		                .getURI(), 
+            	    		        ((OntResource) value.as(OntResource.class))
-        	    		                this.dwf, 
+            	    		                .getURI(), 
-        	    		                datasetMode, 
+            	    		                this.dwf, 
-        	    		                webappDaoFactory) );  
+            	    		                datasetMode, 
-        	    } 
+            	    		                webappDaoFactory) );  
+            	    } 
+    	    	} catch (IndividualNotFoundException e) {
+    	    	    // don't add to the list
+    	    	}
     	    }
     	} finally {
     		dataset.getLock().leaveCriticalSection();
@@ -555,9 +575,13 @@ public class IndividualSDB extends IndividualImpl implements Individual {
             		QuerySolution result = results.next();
             		RDFNode value = result.get("object");
             	    if (value != null && value.canAs(OntResource.class)) {
-            	    	return new IndividualSDB(
+            	        try {
-            	    	        ((OntResource) value.as(OntResource.class)).getURI(), 
+                	    	return new IndividualSDB(
-            	    	                dwf, datasetMode, webappDaoFactory);  
+                	    	        ((OntResource) value.as(OntResource.class)).getURI(), 
+                	    	                dwf, datasetMode, webappDaoFactory);
+            	        } catch (IndividualNotFoundException e) {
+            	            return null;
+            	        }
             	    } 
         	    }
         		return null;

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

@@ -80,7 +80,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 
     protected String DEFAULT_NAMESPACE;
     protected Set<String> NONUSER_NAMESPACES;
-    protected String[] PREFERRED_LANGUAGES;
+    protected List<String> PREFERRED_LANGUAGES;
 
     /* ******************* constructor ************************* */
     
@@ -501,7 +501,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
                 }
             }
         } catch (Exception e) {
-            log.error("Error in updatePropertyDateValue");
+            log.error("Error in updatePropertyDateValue", e);
         }
     }
     
@@ -552,8 +552,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
                 }
             }
         } catch (Exception e) {
-            log.error("Error in updatePropertyDateTimeValue");
+            log.error("Error in updatePropertyDateTimeValue", e);
-            log.error(e, e);
         }
     }
 
@@ -767,7 +766,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     		if (label.isLiteral()) {
     			Literal labelLit = ((Literal)label);
     			String labelLanguage = labelLit.getLanguage();
-    			if ( (labelLanguage==null) && (lang==null) ) {
+    			if ( (labelLanguage == null) && (lang == null || lang.isEmpty()) ) {
     				return labelLit;
     			}
     			if ( (lang != null) && (lang.equals(labelLanguage)) ) {
@@ -857,6 +856,10 @@ public class JenaBaseDao extends JenaBaseDaoCon {
     	Literal label = null;
 	    List<RDFNode> labels = r.listPropertyValues(p).toList();
 	    
+	    if (labels.size() == 0) {
+	        return null;
+	    }
+
 	    // Sort by lexical value to guarantee consistent results
 	    Collections.sort(labels, new Comparator<RDFNode>() {
 	        public int compare(RDFNode left, RDFNode right) {
@@ -871,8 +874,7 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 	        }
 	    });
 	    
-	    for (int i=0; i<PREFERRED_LANGUAGES.length; i++) {
+	    for (String lang : PREFERRED_LANGUAGES) {
-	    	String lang = PREFERRED_LANGUAGES[i];
 	    	label = getLabel(lang,labels);
 	    	if (label != null) {
 	    		break;
@@ -880,12 +882,21 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 	    }
         if ( label == null && alsoTryNoLang ) {
         	label = getLabel("", labels);
+        	// accept any label as a last resort
+        	if (label == null) {
+        	    for (RDFNode labelNode : labels) {
+        	      if (labelNode instanceof Literal) {
+        	          label = ((Literal) labelNode);
+        	          break;
+        	      }
+        	    }
+        	}
         }
 	    return label;
     }
 
     protected String getDefaultLanguage() {
-        return PREFERRED_LANGUAGES[0];
+        return PREFERRED_LANGUAGES.get(0);
     }
     
     /**

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

@@ -404,6 +404,17 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
     /** 
      * Finds all mostSpecificTypes of an individual that are members of a classgroup.
      * Returns a list of type labels. 
+     * 
+     * Note that the Map returned is a LinkedHashMap, which means that an iterator 
+     * will return the entries in the order in which the keys were inserted in the map.
+     * Since the SPARQL query included an "ORDER BY ?label" clause, and since an 
+     * iterator through that ResultSet was used to add entries to the map, an iterator
+     * on the map will return entries that are sorted by label (value, not key).
+     * 
+     * While this sorting order is not specified as a requirement (maybe it should be?),
+     * it is certainly useful that the types are returned in some order that is
+     * replicable, so an individual with multiple mostSpecificTypes, will always see
+     * the same list in the same order. (See https://issues.library.cornell.edu/browse/NIHVIVO-568)
      * **/
     public Map<String, String> getMostSpecificTypesInClassgroupsForIndividual(String subjectUri) {
         

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

@@ -132,7 +132,7 @@ public class OntologyDaoJena extends JenaBaseDao implements OntologyDao {
             try {
                 com.hp.hpl.jena.ontology.Ontology o = ontModel.createOntology(adjustOntologyURI(ontology.getURI()));
                 if (ontology.getName() != null && ontology.getName().length()>0) {
-                    o.setLabel(ontology.getName(), PREFERRED_LANGUAGES[0]);
+                    o.setLabel(ontology.getName(), getDefaultLanguage());
                 }
                 if (ontology.getPrefix() != null && ontology.getPrefix().length()>0) {
                     addPropertyStringValue(o,ONTOLOGY_PREFIX_ANNOT,ontology.getPrefix(),ontModel);

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

@@ -3,7 +3,6 @@
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
@@ -35,6 +34,7 @@ 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.sparql.resultset.ResultSetMem;
+import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
@@ -596,6 +596,31 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         }
     }
     
+    private List<OntClass> listSuperClasses(OntClass ontClass) {
+        return relatedClasses(ontClass, RDFS.subClassOf);
+    }
+    
+    private List<OntClass> listEquivalentClasses(OntClass ontClass) {
+        return relatedClasses(ontClass, OWL.equivalentClass);
+    }
+     
+    private List<OntClass> relatedClasses(OntClass ontClass,
+            com.hp.hpl.jena.rdf.model.Property property) {
+        List<OntClass> classes = new ArrayList<OntClass>();
+        StmtIterator closeIt = ontClass.listProperties(property);
+        try {
+            while (closeIt.hasNext()) {
+                Statement stmt = closeIt.nextStatement();
+                if (stmt.getObject().canAs(OntClass.class)) {
+                    classes.add(stmt.getObject().as(OntClass.class));
+                }
+            }
+        } finally {
+            closeIt.close();
+        }
+        return classes;
+    }
+    
     public List<PropertyInstance> getAllPropInstByVClasses(List<VClass> vclasses) {
         
         List<PropertyInstance> propInsts = new ArrayList<PropertyInstance>();
@@ -628,8 +653,8 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
 		        	OntClass ontClass = getOntClass(ontModel,VClassURI);
 		        	if (ontClass != null) {
 		        	    List<OntClass> relatedClasses = new ArrayList<OntClass>();
-		        	    relatedClasses.addAll(ontClass.listEquivalentClasses().toList());
+		        	    relatedClasses.addAll(listEquivalentClasses(ontClass));		        	    
-		        	    relatedClasses.addAll(ontClass.listSuperClasses().toList());
+		        	    relatedClasses.addAll(listSuperClasses(ontClass));
 		        	    for (OntClass relatedClass : relatedClasses) {
     		        	    // find properties in restrictions
     		        		if (relatedClass.isRestriction()) {

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

@@ -14,14 +14,14 @@ import com.hp.hpl.jena.shared.Lock;
  */
 public class SimpleOntModelSelector implements OntModelSelector {
 
-	private OntModel fullModel;
+	protected OntModel fullModel;
-	private OntModel aboxModel;
+	protected OntModel aboxModel;
-	private OntModel applicationMetadataModel;
+	protected OntModel applicationMetadataModel;
-	private OntModel tboxModel;
+	protected OntModel tboxModel;
-	private OntModel userAccountsModel;
+	protected OntModel userAccountsModel;
 	
-	private OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
+	protected OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
-	private OntModel displayModel;
+	protected OntModel displayModel;
 	
 	/**
 	 * Construct an OntModelSelector with a bunch of empty models

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

@@ -0,0 +1,15 @@
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+import com.hp.hpl.jena.ontology.OntModel;
+
+public class SingleContentOntModelSelector extends SimpleOntModelSelector {
+
+    public SingleContentOntModelSelector(OntModel contentModel, 
+                                         OntModel displayModel, 
+                                         OntModel userAccountsModel) {
+        super(contentModel);
+        super.displayModel = displayModel;
+        super.userAccountsModel = userAccountsModel;
+    }
+    
+}

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

@@ -82,11 +82,25 @@ public class SparqlGraph implements GraphWithPerform {
     @Override
     public void performAdd(Triple t) {
         
-        String updateString = "INSERT DATA { " 
+        //log.info("adding " + t);
+        
+        String updateString = "INSERT DATA { GRAPH <junk:junk> { " 
                 + sparqlNode(t.getSubject(), "") + " " 
                 + sparqlNode(t.getPredicate(), "") + " " 
                 + sparqlNode(t.getObject(), "") + 
-                "}";
+                " } }";
+        
+        if (false) {
+            try { 
+            
+                throw new RuntimeException("Breakpoint");
+            } catch (RuntimeException e) {
+                log.error(e, e);
+                //throw(e);
+            }
+        }
+        
+        //log.info(updateString);
         
         try {
             RepositoryConnection conn = getConnection();
@@ -108,11 +122,15 @@ public class SparqlGraph implements GraphWithPerform {
     
     @Override
     public void performDelete(Triple t) {
-        String updateString = "DELETE DATA { " 
+        log.info ("************** DELETE!!!!! ********************");
+        
+        String updateString = "DELETE DATA { GRAPH <junk:junk> { " 
                 + sparqlNode(t.getSubject(), "") + " " 
                 + sparqlNode(t.getPredicate(), "") + " " 
                 + sparqlNode(t.getObject(), "") + 
-                "}";
+                " } }";
+        
+        log.info(updateString);
         
         try {
             RepositoryConnection conn = getConnection();
@@ -158,6 +176,7 @@ public class SparqlGraph implements GraphWithPerform {
 
     @Override
     public void delete(Triple arg0) throws DeleteDeniedException {
+        log.info("********************** DELETE!!!!!! ************************");
         performDelete(arg0);
     }
 
@@ -212,7 +231,7 @@ public class SparqlGraph implements GraphWithPerform {
         .append(sparqlNode(object, "?o"))
         .append("\n}");
         
-        log.info(findQuery.toString());
+        //log.info(findQuery.toString());
         ResultSet rs = execSelect(findQuery.toString());
         //rs = execSelect(findQuery.toString());
         //rs = execSelect(findQuery.toString());
@@ -226,6 +245,7 @@ public class SparqlGraph implements GraphWithPerform {
             //log.info(t);
             triplist.add(t);
         }
+        //log.info(triplist.size() + " results");
         return WrappedIterator.create(triplist.iterator());
     }
 
@@ -236,7 +256,7 @@ public class SparqlGraph implements GraphWithPerform {
     @Override
     public BulkUpdateHandler getBulkUpdateHandler() {
         if (this.bulkUpdateHandler == null) {
-            this.bulkUpdateHandler = new SimpleBulkUpdateHandler(this);
+            this.bulkUpdateHandler = new SparqlGraphBulkUpdater(this);
         }
         return this.bulkUpdateHandler;
     }
@@ -383,7 +403,7 @@ public class SparqlGraph implements GraphWithPerform {
         try {
             return new ResultSetMem(qe.execSelect());
         } finally {
-            log.info((System.currentTimeMillis() - startTime) + " to execute via Jena");
+            //log.info((System.currentTimeMillis() - startTime) + " to execute via Jena");
             qe.close();
         }
     }

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

@@ -0,0 +1,148 @@
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.graph.Triple;
+import com.hp.hpl.jena.graph.TripleMatch;
+import com.hp.hpl.jena.graph.impl.GraphWithPerform;
+import com.hp.hpl.jena.shared.AddDeniedException;
+import com.hp.hpl.jena.sparql.util.NodeFactory;
+import com.hp.hpl.jena.util.iterator.ExtendedIterator;
+import com.hp.hpl.jena.util.iterator.WrappedIterator;
+
+public class SparqlGraphMultilingual extends SparqlGraph implements GraphWithPerform {
+    
+    private static final Log log = LogFactory.getLog(SparqlGraphMultilingual.class);
+    
+    protected List<String> langs;
+    
+    
+    public SparqlGraphMultilingual(String endpointURI, List<String> languages) {
+        super(endpointURI);
+        this.langs = languages;
+    }
+    
+    @Override
+    public void add(Triple arg0) throws AddDeniedException {
+        performAdd(arg0);
+    }
+
+    @Override
+    public void performAdd(Triple t) {
+        if (true) {
+            super.performAdd(t);
+            return;
+        }
+        if (langs == null || langs.size() == 0) {
+            log.info("No language configured - adding original triple " + t);
+            super.performAdd(t);
+        } else if (t.getObject().isLiteral() 
+                && t.getObject().getLiteral().getDatatypeURI() == null) {
+            log.info("adding language tag");
+            super.performAdd(Triple.create(t.getSubject(), 
+                    t.getPredicate(), NodeFactory.createLiteralNode(
+                            t.getObject().getLiteralLexicalForm(), langs.get(0), null)));
+        } else {
+            log.info("adding original triple " + t);
+            super.performAdd(t);
+        }
+    }
+    
+    @Override
+    public ExtendedIterator<Triple> find(TripleMatch arg0) {
+        //log.info("find(TripleMatch) " + arg0);
+        Triple t = arg0.asTriple();
+        return find(t.getSubject(), t.getPredicate(), t.getObject());
+    }
+    
+    @Override
+    public ExtendedIterator<Triple> find(Node subject, Node predicate, Node object) {
+               
+        long startTime = System.currentTimeMillis();
+        
+        ExtendedIterator<Triple> rawResults = super.find(subject, predicate, object);
+        long rawTime = System.currentTimeMillis() - startTime;
+        
+        List<Triple> tripList = new ArrayList<Triple>();
+        while (rawResults.hasNext()) {
+            tripList.add(rawResults.next());
+        }
+        if (tripList.size() == 0) {
+            return WrappedIterator.create(tripList.iterator());
+        }
+        if (subject.isConcrete() && predicate.isConcrete() && !object.isConcrete()) {
+            Collections.sort(tripList, new TripleSortByLang());
+            LinkedList<Triple> tripl = new LinkedList<Triple>();
+            if (!tripList.get(0).getObject().isLiteral()) {
+                tripl.addAll(tripList);
+            } else if (StringUtils.isEmpty(tripList.get(0).getObject().getLiteralLanguage())) {
+                tripl.addAll(tripList); // is this right?
+            } else {
+                String lang = tripList.get(0).getObject().getLiteralLanguage();
+                for (Triple t : tripList) {
+                    if (lang.equals(t.getObject().getLiteralLanguage())) {
+                        tripl.add(t);
+                    } else {
+                        break;
+                    }
+                }
+            }
+            long filterTime = System.currentTimeMillis() - rawTime - startTime;
+            if (filterTime > 1) {
+                log.info("raw time " + rawTime + " ; filter time " + filterTime);
+            }
+            return WrappedIterator.create(tripl.iterator());
+        } else {
+            long filterTime = System.currentTimeMillis() - rawTime - startTime;
+            if (rawTime > 9) {
+                log.info("raw time " + rawTime + " ; filter time " + filterTime);
+                log.info("^ " + subject + " : " + predicate + " : " + object);
+            }
+            return WrappedIterator.create(tripList.iterator());
+        }
+    }
+    
+    private class TripleSortByLang implements Comparator<Triple> {
+        
+        public int compare(Triple t1, Triple t2) {
+            if (t1 == null || t2 == null) {
+                return 0;
+            } else if (!t1.getObject().isLiteral() || !t2.getObject().isLiteral()) {
+                return 0;
+            }
+            
+            String t1lang = t1.getObject().getLiteral().language();
+            String t2lang = t2.getObject().getLiteral().language();
+                    
+            if ( t1lang == null && t2lang == null) {
+                return 0;
+            } else if (t1lang == null) { 
+                return 1;
+            } else if (t2lang == null) {
+                return -1;
+            } else {
+                int t1langPref = langs.indexOf(t1.getObject().getLiteral().language());
+                if (t1langPref == -1) {
+                    t1langPref = Integer.MAX_VALUE; 
+                }
+                int t2langPref = langs.indexOf(t2.getObject().getLiteral().language());
+                if (t2langPref == -1) {
+                    t2langPref = Integer.MAX_VALUE; 
+                }
+                return t1langPref - t2langPref;
+            }           
+        }
+        
+    }
+    
+
+}

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

@@ -30,7 +30,6 @@ import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
 
 import edu.cornell.mannlib.vitro.webapp.dao.ApplicationDao;
-import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
@@ -233,7 +232,7 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
         return config.getDefaultNamespace();
     }
     
-    public String[] getPreferredLanguages() {
+    public List<String> getPreferredLanguages() {
     	return config.getPreferredLanguages();
     }
     
@@ -312,13 +311,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     		return userAccountsDao = new UserAccountsDaoJena(this);
     }
 
-    Classes2ClassesDao classes2ClassesDao = null;
-    public Classes2ClassesDao getClasses2ClassesDao() {
-        if(classes2ClassesDao == null )
-            classes2ClassesDao = new Classes2ClassesDaoJena(this);
-        return classes2ClassesDao;
-    }
-
     DataPropertyStatementDao dataPropertyStatementDao = null;
     public DataPropertyStatementDao getDataPropertyStatementDao() {
         if( dataPropertyStatementDao == null )

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/pellet/PelletListener.java

@@ -163,7 +163,9 @@ public class PelletListener implements ModelChangedListener {
 		this.deletedDataProperties = ModelFactory.createDefaultModel();
 		this.mainModel.enterCriticalSection(Lock.READ);
     	try {
-        	addedStatements(mainModel);
+    	    for (ObjectPropertyStatementPattern pat : this.inferenceDrivingPatternAllowSet) {
+    	        addedStatements(mainModel.listStatements((Resource) null, pat.getPredicate(), (RDFNode) null));    
+    	    }
         	if (!skipReasoningUponInitialization) {
         		this.foreground = foreground;
         		notifyEvent(null,new EditEvent(null,false));

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/ProcessRdfForm.java

@@ -7,6 +7,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Random;
@@ -23,6 +24,7 @@ import com.hp.hpl.jena.shared.Lock;
 import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.DependentResourceDeleteJena;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfigurationConstants;
 import edu.cornell.mannlib.vitro.webapp.edit.n3editing.controller.ProcessRdfFormController.Utilities;
 
 /**
@@ -41,8 +43,7 @@ public class ProcessRdfForm {
     private EditN3GeneratorVTwo populator;
     
     private Map<String,String> urisForNewResources = null; 
-    
+   /**
-    /**
      * Construct the ProcessRdfForm object. 
      */
     public ProcessRdfForm( EditConfigurationVTwo config, NewURIMaker newURIMaker){
@@ -172,6 +173,12 @@ public class ProcessRdfForm {
         //need to substitute into the return to URL becase it may need new resource URIs
         List<String> URLToReturnTo = Arrays.asList(submission.getEntityToReturnTo());
         
+        /* *********** Check if new resource needs to be forcibly created ******** */
+        urisForNewResources = URIsForNewRsources(editConfig, newURIMaker);
+        substituteInForcedNewURIs(urisForNewResources, submission.getUrisFromForm(), requiredAsserts, optionalAsserts, URLToReturnTo);
+        logSubstitue( "Added form URIs that required new URIs", requiredAsserts, optionalAsserts, requiredRetracts, optionalRetracts);
+
+        
         /* ********** Form submission URIs ********* */
         substituteInMultiURIs(submission.getUrisFromForm(), requiredAsserts, optionalAsserts, URLToReturnTo);
         logSubstitue( "Added form URIs", requiredAsserts, optionalAsserts, requiredRetracts, optionalRetracts);
@@ -182,10 +189,13 @@ public class ProcessRdfForm {
         logSubstitue( "Added form Literals", requiredAsserts, optionalAsserts, requiredRetracts, optionalRetracts);
         //Retractions does NOT get values from form.                               
         
+    
+        
         /* *********** Add subject, object and predicate ******** */
         substituteInSubPredObjURIs(editConfig, requiredAsserts, optionalAsserts, requiredRetracts, optionalRetracts, URLToReturnTo);
         logSubstitue( "Added sub, pred and obj URIs", requiredAsserts, optionalAsserts, requiredRetracts, optionalRetracts);
         
+     
         /* ********* Existing URIs and Literals ********** */
         substituteInMultiURIs(editConfig.getUrisInScope(), 
                 requiredAsserts, optionalAsserts, requiredRetracts, optionalRetracts, URLToReturnTo);
@@ -197,7 +207,8 @@ public class ProcessRdfForm {
         //Both Assertions and Retractions get existing values.
         
         /* ************  Edits may need new resources *********** */
-        urisForNewResources = URIsForNewRsources(editConfig, newURIMaker);
+        //moved this up?
+        //urisForNewResources = URIsForNewRsources(editConfig, newURIMaker);
         substituteInURIs( urisForNewResources, requiredAsserts, optionalAsserts, URLToReturnTo);
         logSubstitue( "Added URIs for new Resources", requiredAsserts, optionalAsserts, requiredRetracts, optionalRetracts);
         // Only Assertions get new resources.       
@@ -205,7 +216,9 @@ public class ProcessRdfForm {
         submission.setEntityToReturnTo(URLToReturnTo.get(0));
     }
 
-    //TODO: maybe move this to utils or contorller?
+
+
+	//TODO: maybe move this to utils or contorller?
     public static AdditionsAndRetractions addDependentDeletes( AdditionsAndRetractions changes, Model queryModel){
         //Add retractions for dependent resource delete if that is configured and 
         //if there are any dependent resources.                     
@@ -455,5 +468,35 @@ public class ProcessRdfForm {
        }                
    }    
    
+   /*
+    * In some situations, an object may have an existing URI but be left blank
+    * when the desired behavior is that a new object be created to replace the existing URI
+    * E.g. autocomplete forms that allow editing of autocomplete fields
+    */
+   @SuppressWarnings("unchecked")
+   private void substituteInForcedNewURIs(
+			Map<String, String> urisForNewResources, Map<String, List<String>> urisFromForm,
+			List<String> requiredAsserts, List<String> optionalAsserts,
+			List<String> uRLToReturnTo) {
+	   Map<String, List<String>> newUris = new HashMap<String, List<String>>();
+	   //Check if any values from the submission have the "force new uri" value
+	   //TODO: Check how to handle multiple new resource values
+	   Iterator<String> keyIterator = urisFromForm.keySet().iterator();
+	   while(keyIterator.hasNext()) {
+		   String key = keyIterator.next().toString();
+		   if(urisFromForm.get(key).contains(EditConfigurationConstants.NEW_URI_SENTINEL)) {
+			   String newUri = urisForNewResources.get(key);
+			   List<String> newUrisForKey = new ArrayList<String>();
+			   newUrisForKey.add(newUri);
+			   newUris.put(key, newUrisForKey);
+		   }
+	   }
+	   if(newUris.size() > 0) {
+		   substituteInMultiURIs(newUris, requiredAsserts, optionalAsserts, uRLToReturnTo);
+	   }
+	   
+	}
+   
+      
    private static Log log = LogFactory.getLog(ProcessRdfForm.class);
 }

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

@@ -0,0 +1,38 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration;
+
+import java.lang.reflect.Modifier;
+import java.util.HashMap;
+import java.util.Map;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.ProcessRdfForm;
+
+
+public class EditConfigurationConstants {
+    /** Constants used by edit configuration */
+	//forces creation of new uri if present
+    public static final String NEW_URI_SENTINEL = ">NEW URI REQUIRED<";
+    public static final String BLANK_SENTINEL = ">SUBMITTED VALUE WAS BLANK<";
+
+    //For freemarker configuration
+    public static Map<String, String> exportConstants() {
+    	Map<String, String> constants = new HashMap<String, String>();
+    	java.lang.reflect.Field[] fields = EditConfigurationConstants.class.getDeclaredFields();
+    	for(java.lang.reflect.Field f: fields) {
+    		if(Modifier.isStatic(f.getModifiers()) && 
+    			Modifier.isPublic(f.getModifiers())) {
+    			try {
+    				constants.put(f.getName(), f.get(null).toString());
+    			} catch(Exception ex) {
+    				log.error("An exception occurred in trying to retrieve this field ", ex);
+    			}
+    		}
+    	}
+    	return constants;
+    }
+    private static Log log = LogFactory.getLog(EditConfigurationConstants.class);
+
+}

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

@@ -5,6 +5,9 @@ package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration;
 import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.ontology.OntModel;
 
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@@ -12,6 +15,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
 
 public class StandardModelSelector implements ModelSelector {
 
+    private static final Log log = LogFactory.getLog(StandardModelSelector.class);
+    
     public OntModel getModel(HttpServletRequest request, ServletContext context) {
         VitroRequest vreq = new VitroRequest( request );        
         
@@ -23,11 +28,17 @@ public class StandardModelSelector implements ModelSelector {
             	sessionOntModel = oms.getABoxModel();
             }
         }
-        if(sessionOntModel != null && sessionOntModel instanceof OntModel )
+        if(sessionOntModel != null && sessionOntModel instanceof OntModel ) {
+            log.info("++++++++++ using OntModelSelector from session");
             return (OntModel)sessionOntModel;
-        else 
+        } else if (vreq.getOntModelSelector() != null) {
+            log.info("++++++++++ using OntModelSelector from request");
+            return vreq.getOntModelSelector().getABoxModel();
+        } else {
+            log.info("++++++++++ using OntModelSelector from context");
             return ((OntModelSelector) context
             			.getAttribute("unionOntModelSelector")).getABoxModel();
+        }
     }
     
     public static final ModelSelector selector = new StandardModelSelector();

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

@@ -66,7 +66,7 @@ public abstract class BaseEditConfigurationGenerator implements EditConfiguratio
         //setup the model selectors for query, write and display models on editConfig
         setupModelSelectorsFromVitroRequest(vreq, editConfig);        
         
-        OntModel queryModel = (OntModel)vreq.getAttribute("jenaOntModel");
+        OntModel queryModel = vreq.getJenaOntModel(); // (OntModel)vreq.getAttribute("jenaOntModel");
         
         if( editConfig.getSubjectUri() == null)
             editConfig.setSubjectUri( EditConfigurationUtils.getSubjectUri(vreq));

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/controller/ProcessRdfFormController.java

@@ -50,6 +50,8 @@ public class ProcessRdfFormController extends FreemarkerHttpServlet{
 	
     private Log log = LogFactory.getLog(ProcessRdfFormController.class);
 
+
+    	
     @Override
 	protected Actions requiredActions(VitroRequest vreq) {
     	return SimplePermission.DO_FRONT_END_EDITING.ACTIONS;

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/AllThumbsAdjuster.java

@@ -1,64 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-import java.io.IOException;
-
-import com.hp.hpl.jena.rdf.model.Resource;
-
-/**
- * Adjust any individual that has a thumbnail with no main image.
- */
-public class AllThumbsAdjuster extends FsuScanner {
-	private ImageDirectoryWithBackup imageDirectoryWithBackup;
-
-	public AllThumbsAdjuster(FSUController controller) {
-		super(controller);
-		this.imageDirectoryWithBackup = controller
-				.getImageDirectoryWithBackup();
-	}
-
-	/**
-	 * For every individual with thumbnails but no main images, create a main
-	 * image from the first thumbnail.
-	 */
-	public void adjust() {
-		updateLog.section("Creating main images for thumbnails "
-				+ "that have none.");
-
-		for (Resource resource : ModelWrapper.listResourcesWithProperty(model,
-				thumbProperty)) {
-			if (ResourceWrapper.getProperty(resource, imageProperty) == null) {
-				createMainImageFromThumbnail(resource);
-			}
-		}
-	}
-
-	/**
-	 * This individual has a thumbnail but no main image. Create one.
-	 * <ul>
-	 * <li>Figure a name for the main image.</li>
-	 * <li>Copy the thumbnail image file into the main image file.</li>
-	 * <li>Set that file as an image (old-style) on the individual.</li>
-	 * </ul>
-	 */
-	private void createMainImageFromThumbnail(Resource resource) {
-		String thumbFilename = getValues(resource, thumbProperty).get(0);
-		String mainFilename = addFilenamePrefix("_main_image_", thumbFilename);
-		updateLog.log(resource, "creating a main file at '" + mainFilename
-				+ "' to match the thumbnail at '" + thumbFilename + "'");
-
-		try {
-			File thumbFile = imageDirectoryWithBackup
-					.getExistingFile(thumbFilename);
-			File mainFile = imageDirectoryWithBackup.getNewfile(mainFilename);
-			mainFile = checkNameConflicts(mainFile);
-			FileUtil.copyFile(thumbFile, mainFile);
-			ResourceWrapper.addProperty(resource, imageProperty, mainFilename);
-		} catch (IOException e) {
-			updateLog.error(resource, "failed to create main file '"
-					+ mainFilename + "'", e);
-		}
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/DeadEndPropertyRemover.java

@@ -1,71 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-
-/**
- * Removes any image properties (main or thumbnail) that point to files that
- * don't actually exist.
- */
-public class DeadEndPropertyRemover extends FsuScanner {
-	private ImageDirectoryWithBackup imageDirectoryWithBackup;
-
-	public DeadEndPropertyRemover(FSUController controller) {
-		super(controller);
-		this.imageDirectoryWithBackup = controller
-				.getImageDirectoryWithBackup();
-	}
-
-	/**
-	 * Remove dead end properties for both main images and thumbnails.
-	 */
-	public void remove() {
-		updateLog.section("Removing image properties whose "
-				+ "referenced files do not exist.");
-
-		removeDeadEndProperties(imageProperty, "main image");
-		removeDeadEndProperties(thumbProperty, "thumbnail");
-	}
-
-	/**
-	 * Check all of the individuals that possess this property.
-	 */
-	private void removeDeadEndProperties(Property prop, String label) {
-		for (Resource resource : ModelWrapper.listResourcesWithProperty(model,
-				prop)) {
-			removeDeadEndPropertiesFromResource(resource, prop, label);
-		}
-	}
-
-	/**
-	 * Check these statments on this resource. If any of them does not point to
-	 * an existing file, remove the statement.
-	 */
-	private void removeDeadEndPropertiesFromResource(Resource resource,
-			Property prop, String label) {
-		for (Statement stmt : getStatements(resource, prop)) {
-			RDFNode node = stmt.getObject();
-			if (node.isLiteral()) {
-				String filename = ((Literal) node).getString();
-				File file = imageDirectoryWithBackup.getExistingFile(filename);
-				if (!file.exists()) {
-					updateLog.warn(
-							resource,
-							"removing link to " + label + " '" + filename
-									+ "': file does not exist at '"
-									+ file.getAbsolutePath() + "'.");
-
-					ModelWrapper.removeStatement(model, stmt);
-				}
-			}
-		}
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/FSUController.java

@@ -1,38 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-
-import com.hp.hpl.jena.rdf.model.Model;
-
-import edu.cornell.mannlib.vitro.webapp.filestorage.UploadedFileHelper;
-import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorage;
-
-/**
- * An object that can initialize one of the {@link FsuScanner}s.
- */
-public interface FSUController {
-
-	/** The Jena model. */
-	Model getModel();
-
-	/** The update log. */
-	FSULog getUpdateLog();
-
-	/** The place to find or to create image files. */
-	ImageDirectoryWithBackup getImageDirectoryWithBackup();
-
-	/** A helper with access to the DAO layer and the file storage system. */
-	UploadedFileHelper getUploadedFileHelper();
-
-	/** The file storage system. */
-	FileStorage getFileStorage();
-
-	/** Where to store the files that were translated. */
-	File getTranslatedDirectory();
-
-	/** Where to store the files that weren't in use anyway. */
-	File getUnreferencedDirectory();
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/FSULog.java

@@ -1,181 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-
-import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
-
-/**
- * Writes the log file for the {@link FileStorageUpdater}. Be sure to call
- * {@link #close()} when finished.
- */
-public class FSULog {
-	private final SimpleDateFormat timeStamper = new SimpleDateFormat(
-			"yyyy-MM-dd HH:mm:ss");
-
-	private final File logFile;
-	private final PrintWriter writer;
-	private boolean open;
-
-	FSULog(File logDirectory, String prefix) throws IOException {
-		this.logFile = generateTimestampedFilename(logDirectory, prefix);
-		this.writer = new PrintWriter(this.logFile);
-		open = true;
-	}
-
-	/**
-	 * Create a filename for the log file that contains a timestamp, so if we
-	 * run the process more than once, we will see multiple files.
-	 */
-	private File generateTimestampedFilename(File upgradeDirectory,
-			String prefix) {
-		SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH-mm-sss");
-		String filename = prefix + "." + sdf.format(new Date()) + ".txt";
-		return new File(upgradeDirectory, filename);
-	}
-
-	/**
-	 * Where are we writing the output?
-	 */
-	String getFilename() {
-		return this.logFile.getAbsolutePath();
-	}
-
-	/**
-	 * Write this message.
-	 */
-	void log(String message) {
-		writer.println(timeStamper.format(new Date()) + " INFO  " + message);
-	}
-
-	/**
-	 * Write this message about this resource.
-	 */
-	void log(Resource resource, String message) {
-		log(showResource(resource) + message);
-	}
-
-	/**
-	 * Write this warning message.
-	 */
-	public void warn(String message) {
-		writer.println(timeStamper.format(new Date()) + " WARN  " + message);
-	}
-
-	/**
-	 * Write this warning message about this resource.
-	 */
-	public void warn(Resource resource, String message) {
-		warn(showResource(resource) + message);
-	}
-
-	/**
-	 * Write this error message.
-	 */
-	void error(String message) {
-		writer.println(timeStamper.format(new Date()) + " ERROR " + message);
-	}
-
-	/**
-	 * Write this exception as an error message..
-	 */
-	void error(Exception e) {
-		error(e.toString());
-		e.printStackTrace(writer);
-	}
-
-	/**
-	 * Write an error message with this exception.
-	 */
-	public void error(String message, Exception e) {
-		error(message);
-		e.printStackTrace(writer);
-	}
-
-	/**
-	 * Write an error message about this resource and with this exception.
-	 */
-	public void error(Resource resource, String message) {
-		error(showResource(resource) + message);
-	}
-
-	/**
-	 * Write an error message about this resource and with this exception.
-	 */
-	public void error(Resource resource, String message, Exception e) {
-		error(showResource(resource) + message, e);
-	}
-
-	/**
-	 * Write a section heading.
-	 */
-	public void section(String message) {
-		log(">>>>>>>>>> ");
-		log(">>>>>>>>>> " + message);
-		log(">>>>>>>>>> ");
-	}
-
-	/**
-	 * Close the writer, if not already closed.
-	 */
-	public void close() {
-		if (open) {
-			writer.close();
-			open = false;
-		}
-	}
-
-	/**
-	 * Format the resource label and URI for output in a message.
-	 */
-	private String showResource(Resource resource) {
-		return "On resource '" + getLabel(resource) + "' (" + getUri(resource)
-				+ "), ";
-	}
-
-	/**
-	 * Find the URI for this resource, if there is one.
-	 */
-	private String getUri(Resource resource) {
-		if (resource != null) {
-			String uri = resource.getURI();
-			if (uri != null) {
-				return uri;
-			}
-		}
-		return "no URI";
-	}
-
-	/**
-	 * Find the label for this resource, if there is one.
-	 */
-	private String getLabel(Resource resource) {
-		if (resource != null) {
-			Model model = resource.getModel();
-			if (model != null) {
-				Property prop = model.createProperty(VitroVocabulary.LABEL);
-				Statement stmt = resource.getProperty(prop);
-				if (stmt != null) {
-					RDFNode node = stmt.getObject();
-					if (node.isLiteral()) {
-						return ((Literal) node).getString();
-					}
-				}
-			}
-		}
-		return "no label";
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/FileStorageAliasAdder.java

@@ -1,352 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.query.Query;
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.QuerySolution;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-
-import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
-
-/**
- * Check all of the FileByteStream objects. If there are any that don't have
- * alias URLs, fix them.
- */
-public class FileStorageAliasAdder {
-	private static final Log log = LogFactory
-			.getLog(FileStorageAliasAdder.class);
-
-	private static final String FILE_PATH = "/file/";
-
-	/**
-	 * Query: get all bytestream resources that do not have alias URLs.
-	 */
-	private static final String QUERY_BYTESTREAMS_WITHOUT_ALIASES = ""
-			+ "PREFIX rdf:    <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
-			+ "PREFIX public: <http://vitro.mannlib.cornell.edu/ns/vitro/public#>\n"
-			+ "SELECT ?bs\n" + "WHERE {\n"
-			+ "  ?bs rdf:type public:FileByteStream\n"
-			+ "  OPTIONAL { ?bs public:directDownloadUrl ?alias }\n"
-			+ "  FILTER ( !BOUND(?alias) )\n" + "}\n";
-
-	/**
-	 * Query: get the filenames for all bytestream resources that do not have
-	 * alias URLs.
-	 */
-	private static final String QUERY_FILENAMES_FOR_BYTESTREAMS = ""
-			+ "PREFIX rdf:    <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
-			+ "PREFIX public: <http://vitro.mannlib.cornell.edu/ns/vitro/public#>\n"
-			+ "SELECT ?bs ?fn\n" + "WHERE {\n"
-			+ "  ?bs rdf:type public:FileByteStream . \n"
-			+ "  ?f public:downloadLocation ?bs . \n"
-			+ "  ?f public:filename ?fn . \n"
-			+ "  OPTIONAL { ?bs public:directDownloadUrl ?alias . }\n"
-			+ "  FILTER ( !BOUND(?alias) )\n" + "}\n";
-
-	private final Model model;
-	private final File upgradeDirectory;
-	private final String vivoDefaultNamespace;
-
-	private FSULog updateLog;
-
-	private Set<String> bytestreamUrisWithoutAliases;
-	private Map<String, String> bytestreamUrisAndFilenames;
-
-	public FileStorageAliasAdder(Model model, File uploadDirectory,
-			String vivoDefaultNamespace) {
-		this.model = model;
-		this.upgradeDirectory = new File(uploadDirectory, "upgrade");
-		this.vivoDefaultNamespace = vivoDefaultNamespace;
-	}
-
-	/**
-	 * Go through all of the FileByteStream objects in the model, creating Alias
-	 * URLs for any objects that don't have them.
-	 * 
-	 * If there is nothing to do, don't even create a log file, just exit.
-	 * 
-	 * If there is something to do, go through the whole process.
-	 * 
-	 * At the end, there should be nothing to do.
-	 */
-	public void update() {
-		// If there is nothing to do, we're done: don't even create a log file.
-		if (!isThereAnythingToDo()) {
-			log.debug("Found no FileByteStreams without alias URLs.");
-			return;
-		}
-
-		setup();
-
-		try {
-			findAndAddMissingAliasUrls();
-
-			if (isThereAnythingToDo()) {
-				throw new IllegalStateException("FileStorageAliasAdder "
-						+ "was unsuccessful -- model still contains "
-						+ "FileByteStreams without alias URLs.");
-			}
-
-			updateLog.section("Finished adding alias URLs to FileByteStreams.");
-		} finally {
-			updateLog.close();
-		}
-
-		log.info("Finished adding alias URLs to FileByteStreams.");
-	}
-
-	/**
-	 * Query the model. If there are any FileByteStream objects with no Alias
-	 * URL, we have work to do.
-	 */
-	private boolean isThereAnythingToDo() {
-		String queryString = QUERY_BYTESTREAMS_WITHOUT_ALIASES;
-		log.debug("query: " + queryString);
-
-		QueryExecution qexec = null;
-		try {
-			qexec = createQueryExecutor(queryString);
-			ResultSet results = qexec.execSelect();
-
-			boolean foundSome = results.hasNext();
-			log.debug("any work to do? " + foundSome);
-
-			return foundSome;
-		} catch (Exception e) {
-			log.error(e, e);
-			return false;
-		} finally {
-			if (qexec != null) {
-				qexec.close();
-			}
-		}
-	}
-
-	/**
-	 * Create the upgrade directory. Create the log file. If we fail, drop dead.
-	 */
-	private void setup() {
-		try {
-			this.upgradeDirectory.mkdirs();
-			updateLog = new FSULog(this.upgradeDirectory,
-					"FileStorageAliasAdder-log");
-			log.info("Updating pre-1.1 file references. Log file is "
-					+ updateLog.getFilename());
-		} catch (IOException e) {
-			if (updateLog != null) {
-				updateLog.close();
-			}
-			throw new IllegalStateException("can't create log file: '"
-					+ updateLog.getFilename() + "'", e);
-		}
-	}
-
-	/**
-	 * Add an alias URL to any FileByteStream object that doesn't have one.
-	 */
-	private void findAndAddMissingAliasUrls() {
-		findBytestreamsWithoutAliasUrls();
-		findFilenamesForBytestreams();
-		addAliasUrlsToModel();
-	}
-
-	/**
-	 * Find every bytestream that doesn't have an alias URL.
-	 */
-	private void findBytestreamsWithoutAliasUrls() {
-		BytestreamUriUnpacker unpacker = new BytestreamUriUnpacker();
-
-		runQuery(QUERY_BYTESTREAMS_WITHOUT_ALIASES, unpacker);
-		this.bytestreamUrisWithoutAliases = unpacker.getUris();
-
-		log.debug("Found " + unpacker.getUris().size()
-				+ " bytestreams without alias URLs");
-	}
-
-	/**
-	 * Find the filename for every bytestream that doesn't have an alias URL.
-	 */
-	private void findFilenamesForBytestreams() {
-		FilenameUnpacker unpacker = new FilenameUnpacker();
-
-		runQuery(QUERY_FILENAMES_FOR_BYTESTREAMS, unpacker);
-		this.bytestreamUrisAndFilenames = unpacker.getFilenameMap();
-
-		log.debug("Found " + unpacker.getFilenameMap().size()
-				+ " bytestreams with filenames but no alias URLs");
-	}
-
-	/** Add an alias URL to each resource in the list. */
-	private void addAliasUrlsToModel() {
-		if (this.bytestreamUrisWithoutAliases.isEmpty()) {
-			updateLog.warn("Found no bytestreams without aliases. "
-					+ "Why am I here?");
-			return;
-		}
-
-		Property aliasProperty = model
-				.createProperty(VitroVocabulary.FS_ALIAS_URL);
-
-		for (String bytestreamUri : this.bytestreamUrisWithoutAliases) {
-			String aliasUrl = figureAliasUrl(bytestreamUri);
-			Resource resource = model.getResource(bytestreamUri);
-
-			ModelWrapper.add(model, resource, aliasProperty, aliasUrl);
-			updateLog.log(resource, "added alias URL: '" + aliasUrl + "'");
-		}
-	}
-
-	/**
-	 * Convert the bytestream URI and the filename into an alias URL.
-	 * 
-	 * If they aren't in our default namespace, or they don't have a filename,
-	 * then their URI is the best we can do for an alias URL.
-	 */
-	private String figureAliasUrl(String bytestreamUri) {
-		if (!bytestreamUri.startsWith(vivoDefaultNamespace)) {
-			updateLog.warn("bytestream uri does not start "
-					+ "with the default namespace: '" + bytestreamUri + "'");
-			return bytestreamUri;
-		}
-
-		String filename = this.bytestreamUrisAndFilenames.get(bytestreamUri);
-		if (filename == null) {
-			updateLog.warn("bytestream has no surrogate or no filename: '"
-					+ bytestreamUri + "'");
-			return "filename_not_found";
-		}
-
-		try {
-			String remainder = bytestreamUri.substring(vivoDefaultNamespace
-					.length());
-			String encodedFilename = URLEncoder.encode(filename, "UTF-8");
-			String separator = remainder.endsWith("/") ? "" : "/";
-
-			return FILE_PATH + remainder + separator + encodedFilename;
-		} catch (UnsupportedEncodingException e) {
-			throw new IllegalStateException(e); // No UTF-8? Can't happen.
-		}
-	}
-
-	private void runQuery(String queryString, QueryResultUnpacker unpacker) {
-		log.debug("query: " + queryString);
-
-		QueryExecution qexec = null;
-		try {
-			qexec = createQueryExecutor(queryString);
-
-			Iterator<QuerySolution> results = qexec.execSelect();
-			while (results.hasNext()) {
-				QuerySolution result = results.next();
-				if (log.isDebugEnabled()) {
-					log.debug("Query result variables: "
-							+ listVariables(result));
-				}
-				unpacker.unpack(result);
-			}
-		} catch (Exception e) {
-			log.error(e, e);
-		} finally {
-			if (qexec != null) {
-				qexec.close();
-			}
-		}
-	}
-
-	private QueryExecution createQueryExecutor(String queryString) {
-		Query query = QueryFactory.create(queryString);
-		return QueryExecutionFactory.create(query, model);
-	}
-
-	/** For debug logging. */
-	private List<String> listVariables(QuerySolution result) {
-		List<String> list = new ArrayList<String>();
-		for (Iterator<String> names = result.varNames(); names.hasNext();) {
-			String name = names.next();
-			RDFNode value = result.get(name);
-			list.add(name + "=" + value);
-		}
-		return list;
-	}
-
-	// ----------------------------------------------------------------------
-	// Helper classes
-	// ----------------------------------------------------------------------
-
-	private interface QueryResultUnpacker {
-		public abstract void unpack(QuerySolution result);
-	}
-
-	private class BytestreamUriUnpacker implements QueryResultUnpacker {
-		private final Set<String> uris = new HashSet<String>();
-
-		@Override
-		public void unpack(QuerySolution result) {
-			Resource bytestream = result.getResource("bs");
-			if (bytestream == null) {
-				updateLog.error("Query result contains no "
-						+ "bytestream resource: " + result);
-				return;
-			}
-
-			uris.add(bytestream.getURI());
-		}
-
-		public Set<String> getUris() {
-			return uris;
-		}
-	}
-
-	private class FilenameUnpacker implements QueryResultUnpacker {
-		private final Map<String, String> filenameMap = new HashMap<String, String>();
-
-		@Override
-		public void unpack(QuerySolution result) {
-			Resource bytestream = result.getResource("bs");
-			if (bytestream == null) {
-				updateLog.error("Query result contains no "
-						+ "bytestream resource: " + result);
-				return;
-			}
-			String bytestreamUri = bytestream.getURI();
-
-			Literal filenameLiteral = result.getLiteral("fn");
-			if (filenameLiteral == null) {
-				updateLog.error("Query result for '" + bytestreamUri
-						+ "' contains no filename.");
-				return;
-			}
-			String filename = filenameLiteral.getString();
-
-			filenameMap.put(bytestreamUri, filename);
-		}
-
-		public Map<String, String> getFilenameMap() {
-			return filenameMap;
-		}
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/FileStorageUpdater.java

@@ -1,268 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Collection;
-
-import javax.servlet.ServletContext;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.rdf.model.Model;
-
-import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-import edu.cornell.mannlib.vitro.webapp.filestorage.UploadedFileHelper;
-import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorage;
-
-/**
- * <p>
- * Clean up any files that are stored in the old directory structure and
- * referenced by old-style image properties.
- * </p>
- * <p>
- * Besides converting the files to the new framework, this process will produce
- * these artifacts:
- * <ul>
- * <li>A log file in the uploaded files directory, with a timestamped name, such
- * as <code>upgrade/upgradeLog2010-06-20T14-55-00.txt</code>, for example. If
- * for any reason, the upgrade process must run again, the log will not be
- * overwritten.</li>
- * <li>A directory of "deleted" files - these were extra thumbnail files or
- * extra main image files -- see the details below.</li>
- * <li>A directory of "unreferenced" files - these were in the image directory,
- * but not connected to any entity.</li>
- * </ul>
- * </p>
- * <p>
- * We consider some special cases:
- * <ul>
- * <li>An individual may refer to an image file that does not actually exist. If
- * so, that reference will be deleted.</li>
- * <li>There may be more than one reference to the same image file. If so, all
- * but the first such reference will be deleted.</li>
- * <li>
- * In the old style, it was possible to have a main image without a thumbnail.
- * If we find that, we will generate a scaled down copy of the main image, store
- * that as a thumbnail image file, and then proceed.</li>
- * <li>
- * In the old style, it was possible to have a thumbnail without a main image.
- * If we find that, we will make a copy of the thumbnail image file, declare
- * that copy to be the main image, and then proceed.</li>
- * <li>
- * We may find individuals with more than one main image, or more than one
- * thumbnail. If so, we will discard all but the first one (move them to the
- * "deleted" directory).</li>
- * </ul>
- * </p>
- * <p>
- * Aside from these special cases, we will:
- * <ul>
- * <li>Translate the main image.
- * <ul>
- * <li>Store the image in the new file system.</li>
- * <li>Delete the image from the old images directory.</li>
- * <li>Create a ByteStream individual for the main image.</li>
- * <li>Create a Surrogate individual for the main image.</li>
- * <li>Tie these together and attach to the entity that owns the image.</li>
- * </ul>
- * </li>
- * <li>Translate the thumbnail.
- * <ul>
- * <li>Store the thumbnail in the new file system.</li>
- * <li>Create a ByteStream individual for the thumbnail.</li>
- * <li>Create a Surrogate individual for the thumbnail.</li>
- * <li>Tie these together and attach to the Surrogate for the main image.</li>
- * </ul>
- * </li>
- * </ul>
- * </p>
- * <p>
- * After processing all of these cases, there may be some images remaining in
- * the "images" directory. These will be moved to the "unreferenced" directory,
- * while preserving any internal tree structure.
- * </p>
- */
-public class FileStorageUpdater implements FSUController {
-	private static final Log log = LogFactory.getLog(FileStorageUpdater.class);
-
-	/** How wide should a generated thumbnail image be (in pixels)? */
-	public static final int THUMBNAIL_WIDTH = 200;
-
-	/** How high should a generated thumbnail image be (in pixels)? */
-	public static final int THUMBNAIL_HEIGHT = 200;
-
-	/** How is the main image referenced in the old scheme? */
-	public static final String IMAGEFILE = VitroVocabulary.vitroURI
-			+ "imageFile";
-
-	/** How is the thumbnail referenced in the old scheme? */
-	public static final String IMAGETHUMB = VitroVocabulary.vitroURI
-			+ "imageThumb";
-
-	private final Model model;
-
-	private final FileStorage fileStorage;
-	private final UploadedFileHelper uploadedFileHelper;
-	private final ImageDirectoryWithBackup imageDirectoryWithBackup;
-	private final File upgradeDirectory;
-
-	private FSULog updateLog;
-
-	public FileStorageUpdater(WebappDaoFactory wadf, Model model,
-			FileStorage fileStorage, File uploadDirectory,
-			File webappImageDirectory, ServletContext ctx) {
-		this.model = model;
-		this.fileStorage = fileStorage;
-		this.uploadedFileHelper = new UploadedFileHelper(fileStorage, wadf, ctx);
-		this.upgradeDirectory = new File(uploadDirectory, "upgrade");
-
-		this.imageDirectoryWithBackup = new ImageDirectoryWithBackup(new File(
-				uploadDirectory, "images"), webappImageDirectory);
-	}
-
-	/**
-	 * <p>
-	 * Go through all of the individuals who have image files or thumbnail
-	 * files, adjusting them to the new way.
-	 * </p>
-	 * <p>
-	 * If there is nothing to do, don't even create a log file, just exit.
-	 * </p>
-	 * <p>
-	 * If there is something to do, go through the whole process.
-	 * </p>
-	 * <p>
-	 * At the end, there should be nothing to do. If that's true, clean out the
-	 * old images directory.
-	 * </p>
-	 */
-	public void update() {
-		// If there is nothing to do, we're done: don't even create a log file.
-		if (!isThereAnythingToDo()) {
-			log.debug("Found no pre-1.1 file references.");
-			return;
-		}
-
-		// Create the upgrade directory and the log file.
-		setup();
-
-		try {
-			// Remove any image properties that don't point to literals.
-			new NonLiteralPropertyRemover(this).remove();
-
-			// Remove any image properties that point to files that don't exist.
-			new DeadEndPropertyRemover(this).remove();
-
-			// No resource may have multiple main images or multiple thumbnails.
-			new MultiplePropertyRemover(this).remove();
-
-			// Create a main image for any thumbnail that doesn't have one.
-			new AllThumbsAdjuster(this).adjust();
-
-			// Create a thumbnail for any main image that doesn't have one.
-			new NoThumbsAdjuster(this).adjust();
-
-			// Copy all images into the new file storage system, translating
-			// into the new schema. Get a list of all the images we translated.
-			ImageSchemaTranslater translater = new ImageSchemaTranslater(this);
-			Collection<String> translatedFiles = translater.translate();
-
-			if (isThereAnythingToDo()) {
-				throw new IllegalStateException(
-						"FileStorageUpdate was unsuccessful -- "
-								+ "model still contains pre-1.1 file references.");
-			}
-
-			// Clean out the old image directory, separating into files which
-			// were translated, and files for which we found no reference.
-			new ImageDirectoryCleaner(this).clean(translatedFiles);
-
-			updateLog.section("File Storage update is complete.");
-		} finally {
-			updateLog.close();
-		}
-
-		log.info("Finished updating pre-1.1 file references.");
-	}
-
-	/**
-	 * Query the model. If there are any resources with old-style image
-	 * properties, we have work to do.
-	 */
-	private boolean isThereAnythingToDo() {
-		if (!ModelWrapper.listResourcesWithProperty(model,
-				model.createProperty(IMAGEFILE)).isEmpty()) {
-			return true;
-		}
-
-		if (!ModelWrapper.listResourcesWithProperty(model,
-				model.createProperty(IMAGETHUMB)).isEmpty()) {
-			return true;
-		}
-
-		return false;
-	}
-
-	/**
-	 * Create the upgrade directory. Create the log file. If we fail, drop dead.
-	 */
-	private void setup() {
-		try {
-			this.upgradeDirectory.mkdirs();
-			updateLog = new FSULog(this.upgradeDirectory,
-					"FileStorageUpdater-log");
-			log.info("Updating pre-1.1 file references. Log file is "
-					+ updateLog.getFilename());
-		} catch (IOException e) {
-			if (updateLog != null) {
-				updateLog.close();
-			}
-			throw new IllegalStateException("can't create log file: '"
-					+ updateLog.getFilename() + "'", e);
-		}
-	}
-
-	// ----------------------------------------------------------------------
-	// Methods to set up the individual scanners.
-	// ----------------------------------------------------------------------
-
-	@Override
-	public Model getModel() {
-		return this.model;
-	}
-
-	@Override
-	public FSULog getUpdateLog() {
-		return this.updateLog;
-	}
-
-	@Override
-	public UploadedFileHelper getUploadedFileHelper() {
-		return this.uploadedFileHelper;
-	}
-
-	@Override
-	public FileStorage getFileStorage() {
-		return this.fileStorage;
-	}
-
-	@Override
-	public ImageDirectoryWithBackup getImageDirectoryWithBackup() {
-		return this.imageDirectoryWithBackup;
-	}
-
-	@Override
-	public File getTranslatedDirectory() {
-		return new File(this.upgradeDirectory, "translatedImages");
-	}
-
-	@Override
-	public File getUnreferencedDirectory() {
-		return new File(this.upgradeDirectory, "unreferencedImages");
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/FileUtil.java

@@ -1,107 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-
-/**
- * A collection of static routines for moving, copying and deleting files.
- */
-public class FileUtil {
-	/**
-	 * Copy a file from one location to another, and remove it from the original
-	 * location.
-	 */
-	public static void moveFile(File from, File to) throws IOException {
-		copyFile(from, to);
-		deleteFile(from);
-	}
-
-	/**
-	 * Copy a file from one location to another.
-	 */
-	public static void copyFile(File from, File to) throws IOException {
-		if (!from.exists()) {
-			throw new FileNotFoundException("File '" + from.getAbsolutePath()
-					+ "' does not exist.");
-		}
-
-		InputStream in = null;
-		try {
-			in = new FileInputStream(from);
-			writeFile(in, to);
-		} finally {
-			if (in != null) {
-				try {
-					in.close();
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-		}
-	}
-
-	/**
-	 * Create a file with the contents of this data stream.
-	 * 
-	 * @param stream
-	 *            the data stream. You must close it afterward.
-	 */
-	public static void writeFile(InputStream stream, File to)
-			throws IOException {
-		if (to.exists()) {
-			throw new IOException("File '" + to.getAbsolutePath()
-					+ "' already exists.");
-		}
-
-		File parent = to.getParentFile();
-		if (!parent.exists()) {
-			parent.mkdirs();
-			if (!parent.exists()) {
-				throw new IOException("Can't create parent directory for '"
-						+ to.getAbsolutePath() + "'");
-			}
-		}
-
-		OutputStream out = null;
-		try {
-			out = new FileOutputStream(to);
-			byte[] buffer = new byte[8192];
-			int howMany;
-			while (-1 != (howMany = stream.read(buffer))) {
-				out.write(buffer, 0, howMany);
-			}
-		} finally {
-			if (out != null) {
-				try {
-					out.close();
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-		}
-	}
-
-	/**
-	 * Delete this file, and make sure that it's gone.
-	 */
-	public static void deleteFile(File file) throws IOException {
-		file.delete();
-		if (file.exists()) {
-			throw new IOException("Failed to delete file '"
-					+ file.getAbsolutePath() + "'");
-		}
-	}
-
-	/** No need to instantiate it -- all methods are static. */
-	private FileUtil() {
-		// Nothing to instantiate.
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/FsuScanner.java

@@ -1,126 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.shared.Lock;
-
-/**
- * Base class for the tools that scan the model. Holds some useful fields and
- * some utility methods.
- */
-public abstract class FsuScanner {
-	protected final Model model;
-	protected final FSULog updateLog;
-
-	protected final Property imageProperty;
-	protected final Property thumbProperty;
-
-	public FsuScanner(FSUController controller) {
-		this.model = controller.getModel();
-		this.updateLog = controller.getUpdateLog();
-
-		this.imageProperty = model.createProperty(FileStorageUpdater.IMAGEFILE);
-		this.thumbProperty = model
-				.createProperty(FileStorageUpdater.IMAGETHUMB);
-	}
-
-	/**
-	 * Read all of the specified properties on a resource, and return a
-	 * {@link List} of the {@link String} values.
-	 */
-	protected List<String> getValues(Resource resource, Property property) {
-		List<String> list = new ArrayList<String>();
-		StmtIterator stmts = resource.listProperties(property);
-		try {
-			while (stmts.hasNext()) {
-				Statement stmt = stmts.next();
-				RDFNode object = stmt.getObject();
-				if (object.isLiteral()) {
-					list.add(((Literal) object).getString());
-				} else {
-					updateLog.error(resource,
-							"property value was not a literal: "
-									+ "property is '" + property.getURI()
-									+ "', value is '" + object + "'");
-				}
-			}
-		} finally {
-			stmts.close();
-		}
-		return list;
-	}
-
-	/**
-	 * Read all of the specified properties on a resource, and return a
-	 * {@link List} of the {@link Statement}s.
-	 */
-	protected List<Statement> getStatements(Resource resource, Property property) {
-		List<Statement> list = new ArrayList<Statement>();
-		
-		resource.getModel().enterCriticalSection(Lock.READ);
-		StmtIterator stmts = resource.listProperties(property);
-		try {
-			while (stmts.hasNext()) {
-				list.add(stmts.next());
-			}
-		} finally {
-			stmts.close();
-			resource.getModel().leaveCriticalSection();
-		}
-		return list;
-	}
-
-	/**
-	 * Find the filename within a path so we can add this prefix to it, while
-	 * retaining the path.
-	 */
-	protected String addFilenamePrefix(String prefix, String path) {
-		int slashHere = Math.max(path.lastIndexOf('/'), path.lastIndexOf('\\'));
-		if (slashHere == -1) {
-			return prefix + path;
-		} else {
-			String dirs = path.substring(0, slashHere + 1);
-			String filename = path.substring(slashHere + 1);
-			return dirs + prefix + filename;
-		}
-	}
-
-	/**
-	 * We are about to create a file - if a file of this name already exists,
-	 * increment the name until we have no collision.
-	 * 
-	 * @return the original file, or the file with the incremented name.
-	 */
-	protected File checkNameConflicts(final File file) {
-		if (!file.exists()) {
-			// No conflict.
-			return file;
-		}
-
-		File parent = file.getParentFile();
-		String filename = file.getName();
-		for (int i = 0; i < 100; i++) {
-			File newFile = new File(parent, i + filename);
-			if (!newFile.exists()) {
-				updateLog.log("File '" + file + "' already exists, using '"
-						+ newFile + "' to avoid conflict.");
-				return newFile;
-			}
-		}
-
-		updateLog.error("File '" + file
-				+ "' already exists. Unable to avoid conflict.");
-		return file;
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/ImageDirectoryCleaner.java

@@ -1,134 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Collection;
-
-/**
- * Clean out the old image directory. Copy the files into the upgrade directory,
- * separating into the ones that we translated, and the ones that weren't
- * referenced.
- */
-public class ImageDirectoryCleaner extends FsuScanner {
-	private final ImageDirectoryWithBackup imageDirectoryWithBackup;
-	protected final File translatedDirectory;
-	protected final File unreferencedDirectory;
-
-	public ImageDirectoryCleaner(FSUController controller) {
-		super(controller);
-		this.imageDirectoryWithBackup = controller
-				.getImageDirectoryWithBackup();
-
-		this.translatedDirectory = controller.getTranslatedDirectory();
-		this.unreferencedDirectory = controller.getUnreferencedDirectory();
-	}
-
-	/**
-	 * Remove all of the files from the old image directory.
-	 */
-	public void clean(Collection<String> translatedFiles) {
-		updateLog.section("Cleaning the old image directory of "
-				+ "files that were translated.");
-		removeTranslatedFiles(translatedFiles);
-
-		updateLog.section("Cleaning the old image directory of "
-				+ "files that were not referenced.");
-		removeRemainingFiles(imageDirectoryWithBackup
-				.getPrimaryImageDirectory());
-	}
-
-	/**
-	 * Move all of the files that we translated into the new system.
-	 */
-	private void removeTranslatedFiles(Collection<String> translatedFiles) {
-		for (String path : translatedFiles) {
-			File oldFile = new File(
-					imageDirectoryWithBackup.getPrimaryImageDirectory(), path);
-			if (oldFile.exists()) {
-				updateLog.log("moving image file '" + path
-						+ "' to the 'translated' directory.");
-				File deletedFile = new File(translatedDirectory, path);
-				try {
-					FileUtil.moveFile(oldFile, deletedFile);
-				} catch (IOException e) {
-					updateLog.error("Failed to move translated file '"
-							+ oldFile.getAbsolutePath() + "'");
-				}
-			} else {
-				updateLog.log("Not moving image file '" + path
-						+ "' to the 'translated' directory -- "
-						+ "found it in the backup directory.");
-			}
-		}
-	}
-
-	/**
-	 * Go through the images directory, and discard any that remain. They must
-	 * not have been referenced by any existing individuals.
-	 */
-	private void removeRemainingFiles(File directory) {
-		updateLog.log("Cleaning image directory '" + directory + "'");
-		try {
-			File targetDirectory = makeCorrespondingDirectory(directory);
-			File[] children = directory.listFiles();
-			if (children != null) {
-				for (File child : children) {
-					if (child.isDirectory()) {
-						removeRemainingFiles(child);
-					} else {
-						moveUnreferencedFile(targetDirectory, child);
-					}
-				}
-			}
-		} catch (IOException e) {
-			updateLog.error(
-					"Failed to clean images directory '"
-							+ directory.getAbsolutePath() + "'", e);
-		}
-	}
-
-	/**
-	 * Move this file from its current location to its new home in the
-	 * "unreferenced" directory. Log it.
-	 */
-	private void moveUnreferencedFile(File targetDirectory, File file) {
-		updateLog.log("Moving image file '" + file.getPath()
-				+ "' to the 'unreferenced' directory");
-		try {
-			File newFile = new File(targetDirectory, file.getName());
-			FileUtil.moveFile(file, newFile);
-		} catch (IOException e) {
-			updateLog.error(
-					"Can't move unreferenced file '" + file.getAbsolutePath()
-							+ "'", e);
-		}
-	}
-
-	/**
-	 * Figure out the path from the "images" directory to this one, and create a
-	 * corresponding directory in the "unreferenced" area.
-	 */
-	private File makeCorrespondingDirectory(File directory) throws IOException {
-		String imagesPath = imageDirectoryWithBackup.getPrimaryImageDirectory()
-				.getAbsolutePath();
-		String thisPath = directory.getAbsolutePath();
-
-		if (!thisPath.startsWith(imagesPath)) {
-			throw new IOException("Can't make a corresponding directory for '"
-					+ thisPath + "'");
-		}
-
-		String suffix = thisPath.substring(imagesPath.length());
-
-		File corresponding = new File(unreferencedDirectory, suffix);
-		corresponding.mkdirs();
-		if (!corresponding.exists()) {
-			throw new IOException("Failed to create corresponding directory '"
-					+ corresponding.getAbsolutePath() + "'");
-		}
-
-		return corresponding;
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/ImageDirectoryWithBackup.java

@@ -1,77 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * A way to look for files in TOMCAT_WEBAPP/vivo/images, if they are not found
- * in upload.directory/images.
- */
-public class ImageDirectoryWithBackup {
-	private static final Log log = LogFactory
-			.getLog(ImageDirectoryWithBackup.class);
-
-	/** The primary image directory, where we do most of the manipulation. */
-	private final File uploadImageDirectory;
-
-	/**
-	 * If we are looking for a file and don't find it in the primary directory,
-	 * look for it here.
-	 */
-	private final File webappImageDirectory;
-
-	/**
-	 * Be careful! webappImageDirectory may be null.
-	 */
-	public ImageDirectoryWithBackup(File uploadImageDirectory,
-			File webappImageDirectory) {
-		this.uploadImageDirectory = uploadImageDirectory;
-		this.webappImageDirectory = webappImageDirectory;
-	}
-
-	/**
-	 * When looking to read a file, start by looking in the
-	 * {@link #uploadImageDirectory}.
-	 * 
-	 * If the file isn't found there, look in the {@link #webappImageDirectory}
-	 * as a fallback.
-	 * 
-	 * If not there either, return the pointer to the nonexistent file in the
-	 * {@link #uploadImageDirectory}.
-	 */
-	File getExistingFile(String relativePath) {
-		File file1 = new File(uploadImageDirectory, relativePath);
-		if (file1.exists()) {
-			log.trace("Found file: " + file1.getAbsolutePath());
-			return file1;
-		}
-		if (webappImageDirectory != null) {
-			File file2 = new File(webappImageDirectory, relativePath);
-			if (file2.exists()) {
-				log.trace("Found file: " + file2.getAbsolutePath());
-				return file2;
-			}
-		}
-		log.trace("Didn't find file: " + file1.getAbsolutePath());
-		return file1;
-	}
-
-	/**
-	 * New files will always be created in the primary directory.
-	 */
-	File getNewfile(String relativePath) {
-		return new File(uploadImageDirectory, relativePath);
-	}
-
-	/**
-	 * You can get a direct reference to the primary image directory, but it
-	 * should only be used for directory-base operations, like final cleanup.
-	 */
-	public File getPrimaryImageDirectory() {
-		return uploadImageDirectory;
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/ImageSchemaTranslater.java

@@ -1,170 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Collection;
-import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.apache.commons.io.FilenameUtils;
-
-import com.hp.hpl.jena.rdf.model.ResIterator;
-import com.hp.hpl.jena.rdf.model.Resource;
-
-import edu.cornell.mannlib.vitro.webapp.filestorage.UploadedFileHelper;
-import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorage;
-import edu.cornell.mannlib.vitro.webapp.filestorage.model.FileInfo;
-
-/**
- * Make copies of the main image and thumbnail in the new file storage system,
- * and in the model. Remove the old properties, but don't remove the old files
- * yet, in case someone else is referring to them also.
- */
-public class ImageSchemaTranslater extends FsuScanner {
-	private final ImageDirectoryWithBackup imageDirectoryWithBackup;
-	protected final FileStorage fileStorage;
-	protected final UploadedFileHelper uploadedFileHelper;
-
-	public ImageSchemaTranslater(FSUController controller) {
-		super(controller);
-		this.imageDirectoryWithBackup = controller
-				.getImageDirectoryWithBackup();
-		this.fileStorage = controller.getFileStorage();
-		this.uploadedFileHelper = controller.getUploadedFileHelper();
-	}
-
-	/**
-	 * By the time we get here, any individual with a main image also has a
-	 * thumbnail, and vice versa, and exactly one of each. For each one,
-	 * translate the main image and the thumbnail into the new system.
-	 */
-	public Collection<String> translate() {
-		updateLog.section("Copying images into the new file storage, "
-				+ "and adding them to the new model.");
-
-		SortedSet<String> translated = new TreeSet<String>();
-		ResIterator haveImage = model.listResourcesWithProperty(imageProperty);
-		try {
-			while (haveImage.hasNext()) {
-				Resource resource = haveImage.next();
-				translateImages(resource, translated);
-			}
-		} finally {
-			haveImage.close();
-		}
-		return translated;
-	}
-
-	/**
-	 * This individual should have exactly one main image and exactly one
-	 * thumbnail.
-	 * <ul>
-	 * <li>Translate the first main image into the new system.</li>
-	 * <li>Translate the first thumbnail into the new system.</li>
-	 * <li>Remove all old-style main image properties.</li>
-	 * <li>Remove all old-style thumbnail properties.</li>
-	 * </ul>
-	 */
-	private void translateImages(Resource resource,
-			Collection<String> translated) {
-		List<String> mainImages = getValues(resource, imageProperty);
-		if (mainImages.size() != 1) {
-			updateLog.error(resource, "has " + mainImages.size()
-					+ " main images: " + mainImages);
-			return;
-		}
-
-		List<String> thumbnails = getValues(resource, thumbProperty);
-		if (thumbnails.size() != 1) {
-			updateLog.error(resource, "has " + thumbnails.size()
-					+ " thumbnails: " + thumbnails);
-			return;
-		}
-
-		FileInfo main = translateFile(resource, mainImages.get(0), "main image");
-		FileInfo thumb = translateFile(resource, thumbnails.get(0), "thumbnail");
-		if ((main == null) || (thumb == null)) {
-			return;
-		}
-		uploadedFileHelper.setImagesOnEntity(resource.getURI(), main, thumb);
-
-		translated.add(mainImages.get(0));
-		ResourceWrapper.removeAll(resource, imageProperty);
-
-		translated.add(thumbnails.get(0));
-		ResourceWrapper.removeAll(resource, thumbProperty);
-
-	}
-
-	/**
-	 * Translate an image file into the new system
-	 * <ul>
-	 * <li>Attempt to infer MIME type.</li>
-	 * <li>Copy into the File system.</li>
-	 * <li>Create the File and Bytestream individuals in the model.</li>
-	 * </ul>
-	 */
-	private FileInfo translateFile(Resource resource, String path, String label) {
-		File oldFile = imageDirectoryWithBackup.getExistingFile(path);
-		String filename = getSimpleFilename(path);
-		String mimeType = guessMimeType(resource, filename);
-
-		InputStream inputStream = null;
-		try {
-			inputStream = new FileInputStream(oldFile);
-			// Create the file individuals in the model
-			FileInfo fileInfo = uploadedFileHelper.createFile(filename,
-					mimeType, inputStream);
-			updateLog.log(resource, "translating " + label + " '" + path
-					+ "' into the file storage as '" + fileInfo.getUri() + "'");
-			return fileInfo;
-		} catch (IOException e) {
-			updateLog.error(resource, "Can't create the " + label + " file. ",
-					e);
-			return null;
-		} finally {
-			if (inputStream != null) {
-				try {
-					inputStream.close();
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-		}
-	}
-
-	/**
-	 * Remove any path parts, and just get the filename and extension.
-	 */
-	private String getSimpleFilename(String path) {
-		return FilenameUtils.getName(path);
-	}
-
-	/**
-	 * Guess what the MIME type might be.
-	 */
-	private String guessMimeType(Resource resource, String filename) {
-		if (filename.endsWith(".gif") || filename.endsWith(".GIF")) {
-			return "image/gif";
-		} else if (filename.endsWith(".png") || filename.endsWith(".PNG")) {
-			return "image/png";
-		} else if (filename.endsWith(".jpg") || filename.endsWith(".JPG")) {
-			return "image/jpeg";
-		} else if (filename.endsWith(".jpeg") || filename.endsWith(".JPEG")) {
-			return "image/jpeg";
-		} else if (filename.endsWith(".jpe") || filename.endsWith(".JPE")) {
-			return "image/jpeg";
-		} else {
-			updateLog.warn(resource,
-					"can't recognize the MIME type of this image file: '"
-							+ filename + "'");
-			return "image";
-		}
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/ModelWrapper.java

@@ -1,54 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.ResIterator;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.shared.Lock;
-
-/**
- * Utility methods that operate against the Model with proper locks.
- */
-public class ModelWrapper {
-
-	public static Collection<Resource> listResourcesWithProperty(Model model,
-			Property property) {
-		List<Resource> list = new ArrayList<Resource>();
-		ResIterator iterator = model.listResourcesWithProperty(property);
-		try {
-			while (iterator.hasNext()) {
-				Resource resource = iterator.next();
-				list.add(resource);
-			}
-		} finally {
-			iterator.close();
-		}
-		return list;
-	}
-
-	public static void removeStatement(Model model, Statement stmt) {
-		model.enterCriticalSection(Lock.WRITE);
-		try {
-			model.remove(stmt);
-		} finally {
-			model.leaveCriticalSection();
-		}
-	}
-
-	public static void add(Model model, Resource subject, Property predicate,
-			String value) {
-		model.enterCriticalSection(Lock.WRITE);
-		try {
-			model.add(subject, predicate, value);
-		} finally {
-			model.leaveCriticalSection();
-		}
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/MultiplePropertyRemover.java

@@ -1,65 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.util.List;
-
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-
-/**
- * If a resource has more than one image or more than one thumbnail, this
- * discards the extras.
- */
-public class MultiplePropertyRemover extends FsuScanner {
-
-	public MultiplePropertyRemover(FSUController controller) {
-		super(controller);
-	}
-
-	/**
-	 * By now, we have removed any non-literals or dead ends, so keep the first
-	 * one and discard any extras.
-	 */
-	public void remove() {
-		updateLog.section("Checking for resources with more "
-				+ "than one main image, or more than one thumbnail.");
-
-		removeExtraProperties(imageProperty, "main image");
-		removeExtraProperties(thumbProperty, "thumbnail");
-	}
-
-	/**
-	 * Check each resource that has this property.
-	 */
-	public void removeExtraProperties(Property prop, String label) {
-		for (Resource resource : ModelWrapper.listResourcesWithProperty(model,
-				prop)) {
-			removeExtraProperties(resource, prop, label);
-		}
-	}
-
-	/**
-	 * If this resource has more than one of this property, delete the extras.
-	 */
-	private void removeExtraProperties(Resource resource, Property prop,
-			String label) {
-		List<Statement> stmts = getStatements(resource, prop);
-		for (int i = 1; i < stmts.size(); i++) {
-			Statement stmt = stmts.get(i);
-			RDFNode node = stmt.getObject();
-			if (node.isLiteral()) {
-				String value = ((Literal) node).getString();
-				updateLog.warn(resource, "removing extra " + label
-						+ " property: '" + value + "'");
-			} else {
-				updateLog.warn(resource, "removing extra " + label
-						+ " property: '" + node + "'");
-			}
-			ModelWrapper.removeStatement(model, stmt);
-		}
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/NoThumbsAdjuster.java

@@ -1,173 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import static edu.cornell.mannlib.vitro.webapp.controller.freemarker.ImageUploadController.THUMBNAIL_HEIGHT;
-import static edu.cornell.mannlib.vitro.webapp.controller.freemarker.ImageUploadController.THUMBNAIL_WIDTH;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-
-import javax.media.jai.JAI;
-import javax.media.jai.RenderedOp;
-
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.sun.media.jai.codec.MemoryCacheSeekableStream;
-
-import edu.cornell.mannlib.vitro.webapp.controller.freemarker.ImageUploadController.CropRectangle;
-import edu.cornell.mannlib.vitro.webapp.controller.freemarker.ImageUploadThumbnailer;
-
-/**
- * Adjust any individual that has a main image but no thumbnail.
- */
-public class NoThumbsAdjuster extends FsuScanner {
-	private ImageDirectoryWithBackup imageDirectoryWithBackup;
-
-	public NoThumbsAdjuster(FSUController controller) {
-		super(controller);
-		this.imageDirectoryWithBackup = controller
-				.getImageDirectoryWithBackup();
-	}
-
-	/**
-	 * For every individual with main images but no thumbnails, create a
-	 * thumbnail from the first main image.
-	 */
-	public void adjust() {
-		updateLog.section("Creating thumbnails to match main images.");
-
-		for (Resource resource : ModelWrapper.listResourcesWithProperty(model,
-				imageProperty)) {
-			if (resource.getProperty(thumbProperty) == null) {
-				createThumbnailFromMainImage(resource);
-			}
-		}
-	}
-
-	/**
-	 * This individual has a main image but no thumbnail. Create one.
-	 * <ul>
-	 * <li>Figure a name for the thumbnail image.</li>
-	 * <li>Make a scaled copy of the main image into the thumbnail.</li>
-	 * <li>Set that file as a thumbnail (old-style) on the individual.</li>
-	 * </ul>
-	 */
-	private void createThumbnailFromMainImage(Resource resource) {
-		String mainFilename = getValues(resource, imageProperty).get(0);
-		String thumbFilename = addFilenamePrefix("_thumbnail_", mainFilename);
-		updateLog.log(resource, "creating a thumbnail at '" + thumbFilename
-				+ "' from the main image at '" + mainFilename + "'");
-
-		File mainFile = imageDirectoryWithBackup.getExistingFile(mainFilename);
-		File thumbFile = imageDirectoryWithBackup.getNewfile(thumbFilename);
-		thumbFile = checkNameConflicts(thumbFile);
-
-		try {
-			CropRectangle crop = getImageSize(mainFile);
-			if (imageIsSmallEnoughAlready(crop)) {
-				copyMainImageToThumbnail(mainFile, thumbFile);
-			} else {
-				cropScaleAndStore(crop, mainFile, thumbFile);
-			}
-
-			ResourceWrapper.addProperty(resource, thumbProperty, thumbFilename);
-		} catch (IOException e) {
-			updateLog.error(resource, "failed to create thumbnail file '"
-					+ thumbFilename + "'", e);
-		}
-	}
-
-	private CropRectangle getImageSize(File file) throws IOException {
-		InputStream imageSource = null;
-		try {
-			imageSource = new FileInputStream(file);
-			MemoryCacheSeekableStream stream = new MemoryCacheSeekableStream(
-					imageSource);
-			RenderedOp image = JAI.create("stream", stream);
-			return new CropRectangle(0, 0, image.getHeight(), image.getWidth());
-		} finally {
-			if (imageSource != null) {
-				try {
-					imageSource.close();
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-		}
-	}
-
-	private boolean imageIsSmallEnoughAlready(CropRectangle crop) {
-		return (crop.height <= THUMBNAIL_HEIGHT)
-				&& (crop.width <= THUMBNAIL_WIDTH);
-	}
-
-	private void copyMainImageToThumbnail(File mainFile, File thumbFile)
-			throws IOException {
-		InputStream imageSource = null;
-		try {
-			imageSource = new FileInputStream(mainFile);
-			storeImage(imageSource, thumbFile);
-		} finally {
-			if (imageSource != null) {
-				try {
-					imageSource.close();
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-		}
-	}
-
-	private void cropScaleAndStore(CropRectangle crop, File mainFile,
-			File thumbFile) throws IOException {
-		InputStream mainImageStream = null;
-		InputStream imageSource = null;
-		try {
-			mainImageStream = new FileInputStream(mainFile);
-			ImageUploadThumbnailer iut = new ImageUploadThumbnailer(
-					THUMBNAIL_HEIGHT, THUMBNAIL_WIDTH);
-			imageSource = iut.cropAndScale(mainImageStream, crop);
-			storeImage(imageSource, thumbFile);
-		} finally {
-			if (mainImageStream != null) {
-				try {
-					mainImageStream.close();
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-			if (imageSource != null) {
-				try {
-					imageSource.close();
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-		}
-	}
-
-	private void storeImage(InputStream source, File file) throws IOException {
-		OutputStream sink = null;
-		try {
-			sink = new FileOutputStream(file);
-			
-			byte[] buffer = new byte[8192];
-			int howMany;
-			while (-1 != (howMany = source.read(buffer))) {
-				sink.write(buffer, 0, howMany);
-			}
-		} finally {
-			if (sink != null) {
-				try {
-					sink.close();
-				} catch (IOException e) {
-					e.printStackTrace();
-				}
-			}
-		}
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/NonLiteralPropertyRemover.java

@@ -1,71 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.shared.Lock;
-
-/**
- * All image properties should have literal values. Burn any that don't.
- */
-public class NonLiteralPropertyRemover extends FsuScanner {
-
-	public NonLiteralPropertyRemover(FSUController controller) {
-		super(controller);
-	}
-
-	/**
-	 * Remove any image properties whose objects are not {@link Literal}s.
-	 */
-	public void remove() {
-		updateLog.section("Checking for image properties whose objects "
-				+ "are not literals.");
-
-		removeNonLiterals(imageProperty, "image file");
-		removeNonLiterals(thumbProperty, "thumbnail");
-	}
-
-	/**
-	 * Check all resources for bogus values on this property.
-	 */
-	private void removeNonLiterals(Property prop, String label) {
-		for (Resource resource : ModelWrapper.listResourcesWithProperty(model,
-				prop)) {
-			removeNonLiterals(resource, prop, label);
-		}
-	}
-
-	/**
-	 * Check this resource for bogus values onthis property.
-	 */
-	private void removeNonLiterals(Resource resource, Property prop,
-			String label) {
-		List<RDFNode> bogusValues = new ArrayList<RDFNode>();
-		for (Statement stmt : ResourceWrapper.listProperties(resource, prop)) {
-			RDFNode object = stmt.getObject();
-			if (!object.isLiteral()) {
-				bogusValues.add(object);
-			}
-		}
-
-		for (RDFNode bogusValue : bogusValues) {
-			updateLog.warn(resource, "discarding " + label
-					+ " property with non-literal as object: '" + bogusValue
-					+ "'");
-			model.enterCriticalSection(Lock.WRITE);
-			try {
-				model.createStatement(resource, prop, bogusValue).remove();
-			} finally {
-				model.leaveCriticalSection();
-			}
-		}
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/updater/ResourceWrapper.java

@@ -1,63 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.filestorage.updater;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.shared.Lock;
-
-/**
- * Utility methods that get the appropriate model locks before manipluating
- * resources.
- */
-public class ResourceWrapper {
-
-	public static Statement getProperty(Resource resource, Property property) {
-		resource.getModel().enterCriticalSection(Lock.READ);
-		try {
-			return resource.getProperty(property);
-		} finally {
-			resource.getModel().leaveCriticalSection();
-		}
-	}
-
-	public static void addProperty(Resource resource, Property property,
-			String value) {
-		resource.getModel().enterCriticalSection(Lock.WRITE);
-		try {
-			resource.addProperty(property, value);
-		} finally {
-			resource.getModel().leaveCriticalSection();
-		}
-	}
-
-	public static void removeAll(Resource resource, Property property) {
-		resource.getModel().enterCriticalSection(Lock.WRITE);
-		try {
-			resource.removeAll(property);
-		} finally {
-			resource.getModel().leaveCriticalSection();
-		}
-	}
-
-	public static Collection<Statement> listProperties(Resource resource,
-			Property prop) {
-		List<Statement> list = new ArrayList<Statement>();
-		StmtIterator stmts = resource.listProperties(prop);
-		try {
-			while (stmts.hasNext()) {
-				list.add(stmts.next());
-			}
-			return list;
-		} finally {
-			stmts.close();
-		}
-	}
-
-}

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

@@ -5,6 +5,10 @@ package edu.cornell.mannlib.vitro.webapp.filters;
 import java.io.IOException;
 import java.sql.Connection;
 import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Locale;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -21,18 +25,27 @@ import org.apache.commons.dbcp.BasicDataSource;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.graph.Graph;
+import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.query.DataSource;
 import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.DatasetFactory;
+import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.sdb.SDBFactory;
 import com.hp.hpl.jena.sdb.Store;
 import com.hp.hpl.jena.sdb.StoreDesc;
 import com.hp.hpl.jena.sdb.sql.SDBConnection;
 
+import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryConfig;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.SingleContentOntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraphMultilingual;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
@@ -89,6 +102,15 @@ public class WebappDaoFactorySDBPrep implements Filter {
 		Dataset dataset = null;
 		WebappDaoFactory wadf = null;
 		
+		// temporary scaffolding in the rdfapi dev branch
+        // TODO remove me
+        if (ConfigurationProperties.getBean(request).getProperty(
+                "VitroConnection.DataSource.endpointURI") != null) {
+            filterSparql(request, oms, defaultNamespace);
+            filterChain.doFilter(request, response);
+            return;
+        }
+		
 		try {		
 		    if (bds == null || storeDesc == null || oms == null) {
 		        throw new RuntimeException("SDB store not property set up");
@@ -140,6 +162,56 @@ public class WebappDaoFactorySDBPrep implements Filter {
 		
 	}
 	
+	private void filterSparql(ServletRequest request, OntModelSelector oms, String defaultNamespace) {
+	    log.info("---------");
+	    
+	    VitroRequest vreq = new VitroRequest((HttpServletRequest) request);
+	    
+        Enumeration<String> headStrs = vreq.getHeaderNames();
+        while (headStrs.hasMoreElements()) {
+            String head = headStrs.nextElement(); 
+            log.info(head + " : "  + vreq.getHeader(head));                     
+        }
+        
+        List<String> langs = new ArrayList<String>();
+        
+        log.info("Accept-Language: " + vreq.getHeader("Accept-Language"));
+        Enumeration<Locale> locs = vreq.getLocales();
+        while (locs.hasMoreElements()) {
+            Locale locale = locs.nextElement();
+            langs.add(locale.toString().replace("_", "-"));
+            log.info(locale.toString() + " / " + locale.getLanguage() + " + " + locale.getCountry() + " : " + locale.getDisplayCountry() + " | " + locale.getLanguage() + " : " + locale.getDisplayLanguage());
+        }
+        WebappDaoFactoryConfig config = new WebappDaoFactoryConfig();
+        config.setDefaultNamespace(defaultNamespace);
+        config.setPreferredLanguages(langs);
+        
+        //okay let's make a graph-backed model
+        String endpointURI = ConfigurationProperties.getBean(
+                request).getProperty("VitroConnection.DataSource.endpointURI");
+        
+        Graph g = new SparqlGraphMultilingual(endpointURI, langs);
+        //Graph g = new SparqlGraph(endpointURI);
+        
+        Model m = ModelFactory.createModelForGraph(g);
+        OntModel om = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, m);
+        oms = new SingleContentOntModelSelector(om, oms.getDisplayModel(), oms.getUserAccountsModel());
+                        
+        DataSource dataset = DatasetFactory.create();
+        dataset.addNamedModel("fake:fake", m);           
+        
+        WebappDaoFactory wadf = new WebappDaoFactoryJena(oms, config);
+        //wadf = new WebappDaoFactorySDB(oms, dataset, config);
+        vreq.setWebappDaoFactory(wadf);
+        vreq.setFullWebappDaoFactory(wadf);
+        vreq.setUnfilteredWebappDaoFactory(wadf);
+        vreq.setWebappDaoFactory(wadf);
+        vreq.setAssertionsWebappDaoFactory(wadf);
+        vreq.setDataset(dataset);
+        vreq.setJenaOntModel(om);
+        vreq.setOntModelSelector(oms);
+	}
+
 	@Override
 	public void init(FilterConfig filterConfig) throws ServletException {
 		try {

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java

@@ -43,12 +43,12 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent;
  * Allows for real-time incremental materialization or retraction of RDFS-
  * style class and property subsumption based ABox inferences as statements
  * are added to or removed from the (ABox or TBox) knowledge base. 
+ * @author sjm222
  */
 
 public class SimpleReasoner extends StatementListener {
 
 	private static final Log log = LogFactory.getLog(SimpleReasoner.class);
-	//private static final MyTempLogger log = new MyTempLogger();
 	
 	private OntModel tboxModel;             // asserted and inferred TBox axioms
 	private OntModel aboxModel;             // ABox assertions
@@ -120,9 +120,9 @@ public class SimpleReasoner extends StatementListener {
 	}
 	
 	/*
-	 * Performs selected incremental ABox reasoning based
+	 * Performs incremental ABox reasoning based
-	 * on the addition of a new statement (aka assertion) 
+	 * on the addition of a new statement
-	 * to the ABox.
+	 *  (aka assertion) to the ABox.
 	 */
 	@Override
 	public void addedStatement(Statement stmt) {
@@ -142,7 +142,7 @@ public class SimpleReasoner extends StatementListener {
 	}
 	
 	/*
-	 * Performs selected incremental ABox reasoning based
+	 * Performs incremental ABox reasoning based
 	 * on the retraction of a statement (aka assertion)
 	 * from the ABox. 
 	 */
@@ -160,7 +160,12 @@ public class SimpleReasoner extends StatementListener {
 		}
 	}
 	
-	public synchronized void handleRemovedStatement(Statement stmt) {
+	
+	/*
+	 * Synchronized part of removedStatement. Interacts
+	 * with DeltaComputer.
+	 */
+	protected synchronized void handleRemovedStatement(Statement stmt) {
 		
 		if (batchMode1) {
 			 aBoxDeltaModeler1.removedStatement(stmt);
@@ -176,7 +181,7 @@ public class SimpleReasoner extends StatementListener {
 	}
 	
 	/*
-	 * Performs incremental selected ABox reasoning based
+	 * Performs incremental ABox reasoning based
 	 * on changes to the class hierarchy.
 	 * 
 	 * Handles rdfs:subclassOf, owl:equivalentClass, 
@@ -229,7 +234,7 @@ public class SimpleReasoner extends StatementListener {
 	}
 
 	/*
-	 * Performs incremental selected ABox reasoning based
+	 * Performs incremental ABox reasoning based
 	 * on changes to the class hierarchy.
 	 * 
 	 * Handles rdfs:subclassOf, owl:equivalentClass, 
@@ -281,10 +286,10 @@ public class SimpleReasoner extends StatementListener {
 		}
 	}
 
-	/*
+    /*
-	 * 
+     * This signature used when recomputing the whole ABox
-	 */
+     */
-	public void addedABoxTypeAssertion(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
+	protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
 
 		StmtIterator iter = null;
 		
@@ -302,6 +307,7 @@ public class SimpleReasoner extends StatementListener {
 			aboxModel.leaveCriticalSection();
 		}
 	}
+	
 	/*
 	 * Performs incremental reasoning based on a new type assertion
 	 * added to the ABox (assertion that an individual is of a certain
@@ -309,9 +315,8 @@ public class SimpleReasoner extends StatementListener {
 	 * 
 	 * If it is added that B is of type A, then for each superclass of
 	 * A assert that B is of that type.
-	 * 
 	 */
-	public void addedABoxTypeAssertion(Statement stmt, Model inferenceModel, HashSet<String> unknownTypes) {
+	protected void addedABoxTypeAssertion(Statement stmt, Model inferenceModel, HashSet<String> unknownTypes) {
 		
 		tboxModel.enterCriticalSection(Lock.READ);
 		
@@ -377,13 +382,10 @@ public class SimpleReasoner extends StatementListener {
 	 * that B is of that type.
 	 * 
 	 */
-	public void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
+	protected void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
 				
 		tboxModel.enterCriticalSection(Lock.READ);
 				
-		// convert this method to use generic resources - not get ontclass, not cls.listSuperClasses...
-		// use model contains if want to log warning about type owl class
-		
 		try {
 			
 			OntClass cls = null;
@@ -431,7 +433,6 @@ public class SimpleReasoner extends StatementListener {
 						inferenceModel.enterCriticalSection(Lock.WRITE);
 						try {
 							if (inferenceModel.contains(infStmt)) {
-								//log.debug("Removing this inferred statement:  " + infStmt.toString() + " - " + infStmt.getSubject().toString() + " - " + infStmt.getPredicate().toString() + " - " + infStmt.getObject().toString());
 								inferenceModel.remove(infStmt);
 							}
 						} finally {
@@ -454,7 +455,7 @@ public class SimpleReasoner extends StatementListener {
 	
 	// Returns true if it is entailed by class subsumption that
 	// subject is of type cls; otherwise returns false.
-	public boolean entailedType(Resource subject, OntClass cls) {
+	protected boolean entailedType(Resource subject, OntClass cls) {
 		aboxModel.enterCriticalSection(Lock.READ);
 		tboxModel.enterCriticalSection(Lock.READ);
 		
@@ -485,9 +486,9 @@ public class SimpleReasoner extends StatementListener {
 	/*
 	 * If it is added that B is a subClass of A, then for each
 	 * individual that is typed as B, either in the ABox or in the
-	 * inferred model, assert that it is of type A.
+	 * inferred model, infer that it is of type A.
 	 */
-	public void addedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) {
+	protected void addedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) {
 		log.debug("subClass = " + subClass.getURI() + " superClass = " + superClass.getURI());
 		OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); 
 		unionModel.addSubModel(aboxModel);
@@ -530,7 +531,7 @@ public class SimpleReasoner extends StatementListener {
 	 * UNLESS the individual is of some type C that is a subClass 
 	 * of A (including A itself)
 	 */
-	public void removedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) {
+	protected void removedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) {
 		OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); 
 		unionModel.addSubModel(aboxModel);
 		unionModel.addSubModel(inferenceModel);
@@ -567,10 +568,10 @@ public class SimpleReasoner extends StatementListener {
 
 	/*
      * Find the most specific types (classes) of an individual and
-     * indicate them for the individual with the core:mostSpecificType
+     * indicate them for the individual with the mostSpecificType
      * annotation.
 	 */
-	public void setMostSpecificTypes(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
+	protected void setMostSpecificTypes(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
 			
 		tboxModel.enterCriticalSection(Lock.READ);
 		aboxModel.enterCriticalSection(Lock.READ);
@@ -665,13 +666,13 @@ public class SimpleReasoner extends StatementListener {
 	    return;	
 	}
 	
-	public void setMostSpecificTypes(Resource individual, HashSet<String> typeURIs, Model inferenceModel) {
+	protected void setMostSpecificTypes(Resource individual, HashSet<String> typeURIs, Model inferenceModel) {
 		
 		inferenceModel.enterCriticalSection(Lock.WRITE);
 		
 		try {
 		    Model retractions = ModelFactory.createDefaultModel();
-			// remove obsolete most-specific-type assertions
+			// remove obsolete mostSpecificType assertions
 			StmtIterator iter = inferenceModel.listStatements(individual, mostSpecificType, (RDFNode) null);
 			
 			while (iter.hasNext()) {
@@ -689,7 +690,7 @@ public class SimpleReasoner extends StatementListener {
 			
 			inferenceModel.remove(retractions);
 			
-			// add new most-specific-type assertions 
+			// add new mostSpecificType assertions 
 			Iterator<String> typeIter = typeURIs.iterator();
 			
 			while (typeIter.hasNext()) {
@@ -707,12 +708,12 @@ public class SimpleReasoner extends StatementListener {
 	    return;	
 	}
 		
-	private boolean recomputing = false;
-	
 	/**
 	 * Returns true if the reasoner is in the process of recomputing all
 	 * inferences.
 	 */
+	private boolean recomputing = false;
+	
 	public boolean isRecomputing() {
 	    return recomputing;
 	}
@@ -731,14 +732,14 @@ public class SimpleReasoner extends StatementListener {
 
 	/*
 	 * Recompute the entire ABox inference graph. The new 
-	 * inference graph is built up in a separate model and
+	 * inference graph is built in a separate model and
-	 * then reconciled with the inference graph used by the
+	 * then reconciled with the inference graph in active
-	 * application. The model reconciliation must be done
+	 * use. The model reconciliation must be done
 	 * without reading the whole inference models into 
 	 * memory in order to support very large ABox 
 	 * inference models.	  
 	 */
-	public synchronized void recomputeABox() {
+	protected synchronized void recomputeABox() {
 		
 		HashSet<String> unknownTypes = new HashSet<String>();
 		
@@ -799,8 +800,8 @@ public class SimpleReasoner extends StatementListener {
 		
 		log.info("Finished computing class-based ABox inferences");
 		
-		// reflect the recomputed inferences into the application inference
+		// reflect the recomputed inferences into the application
-		// model.
+		// inference model.
 	    log.info("Updating ABox inference model");
 	    StmtIterator iter = null;
  
@@ -913,23 +914,16 @@ public class SimpleReasoner extends StatementListener {
 		log.info("ABox inference model updated");
 	}
 			
-	public synchronized boolean isABoxReasoningAsynchronous() {
+	/*
-         if (batchMode1 || batchMode2) {
+	 * Get the URIs for all individuals in the system
-        	 return true;
+	 */
-         } else {
+	protected ArrayList<String> getAllIndividualURIs() {
-        	 return false;
-         }
-	}
-		
-
-   
-	public ArrayList<String> getAllIndividualURIs() {
 	    
 		String queryString = "select distinct ?subject where {?subject <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type}";
         return getIndividualURIs(queryString);
 	}
 
-	public ArrayList<String> getIndividualURIs(String queryString) {
+	protected ArrayList<String> getIndividualURIs(String queryString) {
 	    
 		ArrayList<String> individuals = new ArrayList<String>();
 		aboxModel.enterCriticalSection(Lock.READ);	
@@ -960,6 +954,19 @@ public class SimpleReasoner extends StatementListener {
 		return individuals;
 	}
     
+	
+	// system-configured reasoning modules (plugins)
+	public boolean isInterestedInRemovedStatement(Statement stmt) {
+		
+		if (stmt.getPredicate().equals(RDF.type)) return true;
+
+		for (ReasonerPlugin plugin : getPluginList()) {
+			if (plugin.isInterestedInRemovedStatement(stmt)) return true;
+		}
+		
+        return false;
+	}
+	
 	protected void doPlugins(ModelUpdate.Operation op, Statement stmt) {
 		
 		for (ReasonerPlugin plugin : getPluginList()) {
@@ -983,29 +990,16 @@ public class SimpleReasoner extends StatementListener {
 		}
 	}
 		
-	public boolean isInterestedInRemovedStatement(Statement stmt) {
-		
-		if (stmt.getPredicate().equals(RDF.type)) return true;
-
-		for (ReasonerPlugin plugin : getPluginList()) {
-			if (plugin.isInterestedInRemovedStatement(stmt)) return true;
-		}
-		
-        return false;
-	}
-	
-	//TODO remove this for 1.5
-	public synchronized void computeMostSpecificType() {
-
-	}
-	
 	/**
-	 * This is called when the system shuts down.
+	 * This is called when the application shuts down.
 	 */
 	public void setStopRequested() {
 	    this.stopRequested = true;
 	}
 	
+	/*
+	 * Utility method for logging
+	 */
     public static String stmtString(Statement statement) {
     	return  " [subject = " + statement.getSubject().getURI() +
     			"] [property = " + statement.getPredicate().getURI() +
@@ -1013,6 +1007,20 @@ public class SimpleReasoner extends StatementListener {
                 		                                          : ((Resource)statement.getObject()).getURI() + " (Resource)") + "]";	
     }  
 	
+    
+    // DeltaComputer
+    
+	/*
+	 * Asynchronous reasoning mode (DeltaComputer) is used in the case of batch removals. 
+	 */
+	public synchronized boolean isABoxReasoningAsynchronous() {
+         if (batchMode1 || batchMode2) {
+        	 return true;
+         } else {
+        	 return false;
+         }
+	}
+    
 	private volatile boolean deltaComputerProcessing = false;
 	private int eventCount = 0;
     
@@ -1083,7 +1091,7 @@ public class SimpleReasoner extends StatementListener {
     		   }
     	    }
 	   } else { 
-		    log.warn("unexpected condition, invoked when batchMode1 and batchMode2 were both false");
+		    log.warn("unexpected condition, invoked when batchMode1 and batchMode2 are both false");
             deltaComputerProcessing = false;
 	   }
        

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerTBoxListener.java

@@ -13,12 +13,11 @@ import com.hp.hpl.jena.rdf.model.Statement;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
 
-
 /**
  * Route notification of changes to TBox to the incremental ABox reasoner.
- * The incremental ABox reasoner handles only subclass, superclass
+ * The incremental ABox reasoner handles only subClass and
- * and equivalent class axioms.
+ * equivalentClass class axioms. Reasoning dones as a result of TBox
- *  
+ * changes is always done in a separate thread.
  */
 
 public class SimpleReasonerTBoxListener extends StatementListener {

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

@@ -20,7 +20,9 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.ontology.OntDocumentManager;
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.sdb.SDBFactory;
@@ -48,6 +50,8 @@ public class FileGraphSetup implements ServletContextListener {
 		OntModelSelector baseOms = null;
 		
 		try {
+			
+			OntDocumentManager.getInstance().setProcessImports(true);
 			baseOms = ModelContext.getBaseOntModelSelector(sce.getServletContext());
 			Store kbStore = (Store) sce.getServletContext().getAttribute("kbStore");
 						
@@ -78,6 +82,8 @@ public class FileGraphSetup implements ServletContextListener {
 			System.out.println("Throwable in listener " + this.getClass().getName());
 			log.error(t);
 			t.printStackTrace();
+		} finally {
+			OntDocumentManager.getInstance().setProcessImports(false);
 		}
 		
 		if (isUpdateRequired(sce.getServletContext()))  {
@@ -114,7 +120,7 @@ public class FileGraphSetup implements ServletContextListener {
 			try {
 				FileInputStream fis = new FileInputStream( file );
 				try {
-					Model model = ModelFactory.createDefaultModel(); 
+					OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); 
 					if ( p.endsWith(".n3") || p.endsWith(".N3") || p.endsWith(".ttl") || p.endsWith(".TTL") ) {
 						model.read( fis, null, "N3" );
 					} else if ( p.endsWith(".owl") || p.endsWith(".OWL") || p.endsWith(".rdf") || p.endsWith(".RDF") || p.endsWith(".xml") || p.endsWith(".XML") ) {

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

@@ -68,6 +68,14 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase
         ServletContext ctx = sce.getServletContext();
         StartupStatus ss = StartupStatus.getBean(ctx);
         
+        // temporary scaffolding in the rdfapi dev branch
+        // TODO remove me
+        if (ConfigurationProperties.getBean(ctx).getProperty(
+                "VitroConnection.DataSource.endpointURI") != null) {
+            (new JenaDataSourceSetupSparql()).contextInitialized(sce);
+            return;
+        }
+        
         try {
             long startTime = System.currentTimeMillis();
             setUpJenaDataSource(ctx);

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

@@ -2,9 +2,9 @@
 
 package edu.cornell.mannlib.vitro.webapp.servlet.setup;
 
+import java.io.File;
 import java.io.FileInputStream;
 import java.io.InputStream;
-import java.io.File;
 import java.sql.SQLException;
 import java.util.Set;
 

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

@@ -2,10 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.servlet.setup;
 
-import java.util.Collection;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;

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

@@ -16,7 +16,6 @@ import javax.servlet.ServletContextListener;
 import org.apache.commons.dbcp.BasicDataSource;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.mindswap.pellet.PelletOptions;
 
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.vocabulary.OWL;
@@ -45,6 +44,14 @@ public class SimpleReasonerSetup implements ServletContextListener {
 
     @Override
     public void contextInitialized(ServletContextEvent sce) {
+        
+        // temporary scaffolding in the rdfapi dev branch
+        // TODO remove me
+        if (ConfigurationProperties.getBean(sce).getProperty(
+                "VitroConnection.DataSource.endpointURI") != null) {
+            return;
+        }
+        
         try {    
             // set up Pellet reasoning for the TBox    
             
@@ -60,12 +67,12 @@ public class SimpleReasonerSetup implements ServletContextListener {
             }
             
             // Set various Pellet options for incremental consistency checking, etc.
-            PelletOptions.DL_SAFE_RULES = true;
+            //PelletOptions.DL_SAFE_RULES = true;
-            PelletOptions.USE_COMPLETION_QUEUE = true;
+            //PelletOptions.USE_COMPLETION_QUEUE = true;
-            PelletOptions.USE_TRACING = true;
+            //PelletOptions.USE_TRACING = true;
-            PelletOptions.TRACK_BRANCH_EFFECTS = true;
+            //PelletOptions.TRACK_BRANCH_EFFECTS = true;
-            PelletOptions.USE_INCREMENTAL_CONSISTENCY = true;
+            //PelletOptions.USE_INCREMENTAL_CONSISTENCY = true;
-            PelletOptions.USE_INCREMENTAL_DELETION = true;
+            //PelletOptions.USE_INCREMENTAL_DELETION = true;
              
             PelletListener pelletListener = new PelletListener(unionOms.getTBoxModel(),assertionsOms.getTBoxModel(),inferencesOms.getTBoxModel(),ReasonerConfiguration.DEFAULT);
             sce.getServletContext().setAttribute("pelletListener",pelletListener);

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

@@ -20,16 +20,8 @@ import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
-import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Property;
-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.vocabulary.RDF;
 
-import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;

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

@@ -1,144 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.servlet.setup;
-
-import java.io.File;
-
-import javax.servlet.ServletContext;
-import javax.servlet.ServletContextEvent;
-import javax.servlet.ServletContextListener;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.ontology.OntModel;
-
-import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
-import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorage;
-import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorageSetup;
-import edu.cornell.mannlib.vitro.webapp.filestorage.updater.FileStorageAliasAdder;
-import edu.cornell.mannlib.vitro.webapp.filestorage.updater.FileStorageUpdater;
-import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
-
-/**
- * Check that the conditions are met for updating uploaded files. If everything
- * is in place, call the two updaters.
- * 
- * The first updater converts from old-style (pre 1.0) to new-style (post 1.0)
- * file storage.
- * 
- * The second updater insures that all bytestreams store their own alias URLs
- * (post 1.1.1).
- */
-public class UpdateUploadedFiles implements ServletContextListener {
-	private static final Log log = LogFactory.getLog(UpdateUploadedFiles.class);
-
-	/**
-	 * Nothing to do on teardown.
-	 */
-	@Override
-	public void contextDestroyed(ServletContextEvent sce) {
-		return;
-	}
-
-	/**
-	 * Check that the ontology model, the old upload directory, and the file
-	 * storage system are all valid. Then do the update.
-	 */
-	@Override
-	public void contextInitialized(ServletContextEvent sce) {
-		ServletContext ctx = sce.getServletContext();
-		
-		try {
-			WebappDaoFactory wadf = (WebappDaoFactory) ctx
-					.getAttribute("assertionsWebappDaoFactory");
-			if (wadf == null) {
-				throw new IllegalStateException("Webapp DAO Factory is null. "
-						+ "The ServletContext does not contain an attribute "
-						+ "for '" + "assertionsWebappDaoFactory" + "'. "
-						+ "Does the log contain a previous exception from "
-						+ "JenaDataSourceSetup? Is it possible that web.xml "
-						+ "is not set up to run JenaDataSourceSetup before "
-						+ "UpdateUploadedFiles?");
-			}
-
-			OntModel jenaOntModel = (OntModel) ctx
-					.getAttribute(JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME);
-			if (jenaOntModel == null) {
-				throw new IllegalStateException("Ontology model is null. "
-						+ "The ServletContext does not contain an attribute "
-						+ "for '"
-						+ JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME
-						+ "'. "
-						+ "Does the log contain a previous exception from "
-						+ "JenaDataSourceSetup? Is it possible that web.xml "
-						+ "is not set up to run JenaDataSourceSetup before "
-						+ "UpdateUploadedFiles?");
-			}
-
-			FileStorage fileStorage = (FileStorage) ctx
-					.getAttribute(FileStorageSetup.ATTRIBUTE_NAME);
-			if (fileStorage == null) {
-				throw new IllegalStateException("File storage system is null. "
-						+ "The ServletContext does not contain an attribute "
-						+ "for '" + FileStorageSetup.ATTRIBUTE_NAME + "'. "
-						+ "Does the log contain a previous exception from "
-						+ "FileStorageSetup? Is it possible that web.xml is "
-						+ "not set up to run FileStorageSetup before "
-						+ "UpdateUploadedFiles?");
-			}
-
-			String vitroHomeDirectoryName = ConfigurationProperties
-					.getBean(ctx).getProperty(
-							FileStorageSetup.PROPERTY_VITRO_HOME_DIR);
-			if (vitroHomeDirectoryName == null) {
-				throw new IllegalStateException("Upload directory name is null");
-			}
-			File vitroHomeDirectory = new File(vitroHomeDirectoryName);
-			if (!vitroHomeDirectory.exists()) {
-				throw new IllegalStateException("Vitro home directory '"
-						+ vitroHomeDirectory.getAbsolutePath()
-						+ "' does not exist.");
-			}
-			File uploadDirectory = new File(vitroHomeDirectory,
-					FileStorageSetup.FILE_STORAGE_SUBDIRECTORY);
-			if (!uploadDirectory.exists()) {
-				uploadDirectory.mkdir();
-				if (!uploadDirectory.exists()) {
-					throw new IllegalStateException(
-							"Failed to create the file uploads directory: "
-									+ uploadDirectory.getAbsolutePath());
-				}
-			}
-
-			String vivoDefaultNamespace = ConfigurationProperties.getBean(ctx)
-					.getProperty(FileStorageSetup.PROPERTY_DEFAULT_NAMESPACE);
-			if (vivoDefaultNamespace == null) {
-				throw new IllegalStateException("Default namespace is null.");
-			}
-
-			String webappImagePath = ctx.getRealPath("images");
-			File webappImageDirectory = (webappImagePath == null) ? null
-					: new File(webappImagePath);
-
-			/*
-			 * Update from old-style storage to new-style storage.
-			 */
-			FileStorageUpdater fsu = new FileStorageUpdater(wadf, jenaOntModel,
-					fileStorage, uploadDirectory, webappImageDirectory, ctx);
-			fsu.update();
-
-			/*
-			 * Insure that every FileByteStream object has an alias URL.
-			 */
-			FileStorageAliasAdder fsaa = new FileStorageAliasAdder(
-					jenaOntModel, uploadDirectory, vivoDefaultNamespace);
-			fsaa.update();
-		} catch (Exception e) {
-			log.fatal("Unknown problem", e);
-			StartupStatus.getBean(ctx).fatal(this, "Unknown problem", e);
-		}
-	}
-}

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

@@ -1,485 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.servlet.setup;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Date;
-import java.util.List;
-import java.util.Set;
-
-import javax.servlet.ServletContext;
-import javax.servlet.ServletContextEvent;
-import javax.servlet.ServletContextListener;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntResource;
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.util.iterator.ClosableIterator;
-import com.hp.hpl.jena.vocabulary.RDF;
-
-import edu.cornell.mannlib.vitro.webapp.auth.permissions.PermissionSetsLoader;
-import edu.cornell.mannlib.vitro.webapp.beans.UserAccount;
-import edu.cornell.mannlib.vitro.webapp.beans.UserAccount.Status;
-import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
-import edu.cornell.mannlib.vitro.webapp.dao.UserAccountsDao;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
-import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
-
-/**
- * Convert any existing User resources (up to rel 1.2) in the UserAccounts Model
- * to UserAccount resources (rel 1.3 and on).
- */
-public class UpdateUserAccounts implements ServletContextListener {
-	private static final Log log = LogFactory.getLog(UpdateUserAccounts.class);
-
-	public static final String NS = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#";
-	public static final String USER = NS + "User";
-	public static final String USER_USERNAME = NS + "username";
-	public static final String USER_MD5PASSWORD = NS + "md5password";
-	public static final String USER_OLDPASSWORD = NS + "oldpassword";
-	public static final String USER_FIRSTTIME = NS + "firstTime";
-	public static final String USER_LOGINCOUNT = NS + "loginCount";
-	public static final String USER_ROLE = NS + "roleURI";
-	public static final String USER_LASTNAME = NS + "lastName";
-	public static final String USER_FIRSTNAME = NS + "firstName";
-	public static final String MAY_EDIT_AS = NS + "mayEditAs";
-
-	@Override
-	public void contextInitialized(ServletContextEvent sce) {
-		ServletContext ctx = sce.getServletContext();
-		StartupStatus ss = StartupStatus.getBean(ctx);
-		
-		try {
-			Updater updater = new Updater(ctx);
-			if (updater.isThereAnythingToDo()) {
-				updater.update();
-			}
-		} catch (Exception e) {
-			log.fatal("Failed to update user accounts information", e);
-			ss.fatal(this, "Failed to update user accounts information", e);
-		}
-	}
-
-	@Override
-	public void contextDestroyed(ServletContextEvent sce) {
-		// Nothing to destroy.
-	}
-
-	// ----------------------------------------------------------------------
-	// The Updater class
-	// ----------------------------------------------------------------------
-
-	private static class Updater {
-		private final ServletContext ctx;
-		private final MockUserDao userDao;
-		private final UserAccountsDao userAccountsDao;
-
-		public Updater(ServletContext ctx) {
-			this.ctx = ctx;
-
-			WebappDaoFactory wadf = (WebappDaoFactory) ctx
-					.getAttribute("webappDaoFactory");
-			userAccountsDao = wadf.getUserAccountsDao();
-
-			userDao = new MockUserDao(ctx);
-		}
-
-		/**
-		 * If there is nothing to do, we shouldn't even create a Journal.
-		 */
-		public boolean isThereAnythingToDo() {
-			return !userDao.getAllUsers().isEmpty();
-		}
-
-		/**
-		 * We found some old User resources, so convert them.
-		 */
-		public void update() throws IOException {
-			Journal journal = new Journal(ctx);
-			log.info("Updating user accounts info. Journal is in '"
-					+ journal.getPath() + "'");
-
-			try {
-				for (MockUser user : userDao.getAllUsers()) {
-					try {
-						UserAccount ua = getConvertedUser(user);
-						if (ua != null) {
-							journal.noteAlreadyConverted(user, ua);
-						} else {
-							journal.writeUser(user);
-
-							ua = convertToUserAccount(user);
-							userAccountsDao.insertUserAccount(ua);
-							journal.noteUserAccount(ua);
-						}
-
-						userDao.deleteUser(user);
-						journal.noteDeletedUser(user);
-					} catch (Exception e) {
-						log.error(e, e);
-						journal.noteException(e);
-					}
-				}
-			} finally {
-				journal.close();
-			}
-		}
-
-		private UserAccount getConvertedUser(MockUser user) {
-			return userAccountsDao.getUserAccountByEmail(user.getUsername());
-		}
-
-		private UserAccount convertToUserAccount(MockUser u) {
-			UserAccount ua = new UserAccount();
-			ua.setEmailAddress(nonNull(u.getUsername()));
-			ua.setFirstName(nonNull(u.getFirstName()));
-			ua.setLastName(nonNull(u.getLastName()));
-			ua.setMd5Password(nonNull(u.getMd5password()));
-			ua.setLoginCount(nonNegative(u.getLoginCount()));
-			ua.setPasswordChangeRequired(u.getLoginCount() == 0);
-			ua.setPasswordLinkExpires(0L);
-			ua.setStatus(Status.ACTIVE);
-			ua.setExternalAuthId(nonNull(u.getUsername()));
-			ua.setPermissionSetUris(translateFromRoleUri(u.getRoleURI()));
-			return ua;
-		}
-
-		private String nonNull(String value) {
-			return (value == null) ? "" : value;
-		}
-
-		private int nonNegative(int value) {
-			return Math.max(0, value);
-		}
-
-		private Set<String> translateFromRoleUri(String roleUri) {
-			String permissionSetUri = PermissionSetsLoader.URI_SELF_EDITOR;
-			if ("role:/4".equals(roleUri)) {
-				permissionSetUri = PermissionSetsLoader.URI_EDITOR;
-			} else if ("role:/5".equals(roleUri)) {
-				permissionSetUri = PermissionSetsLoader.URI_CURATOR;
-			} else if ("role:/50".equals(roleUri)) {
-				permissionSetUri = PermissionSetsLoader.URI_DBA;
-			}
-			return Collections.singleton(permissionSetUri);
-		}
-	}
-
-	// ----------------------------------------------------------------------
-	// The Journal class
-	// ----------------------------------------------------------------------
-
-	private static class Journal {
-		private final File file;
-		private final PrintWriter w;
-		private int errorCount;
-
-		Journal(ServletContext ctx) throws IOException {
-			String homeDirectoryPath = ConfigurationProperties.getBean(ctx)
-					.getProperty("vitro.home.directory");
-			if (homeDirectoryPath == null) {
-				throw new IllegalStateException(
-						"No value found for vitro.home.directory");
-			}
-			File homeDirectory = new File(homeDirectoryPath);
-			confirmIsDirectory(homeDirectory);
-
-			File upgradeDirectory = createDirectory(homeDirectory, "upgrade");
-			String filename = timestampedFilename("UpgradeUserAccounts", ".txt");
-			this.file = new File(upgradeDirectory, filename);
-
-			this.w = new PrintWriter(this.file);
-
-			w.println("PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>");
-			w.println("PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#>");
-			w.println("PREFIX xsd:   <http://www.w3.org/2001/XMLSchema#>");
-			w.println("PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>");
-			w.println("");
-		}
-
-		public String getPath() {
-			return file.getAbsolutePath();
-		}
-
-		public void note(String... notes) {
-			w.println();
-			for (String note : notes) {
-				w.println("# " + note);
-			}
-		}
-
-		public void noteAlreadyConverted(MockUser user, UserAccount ua) {
-			note("UserAccount '" + ua.getUri() + "' already exists for User '"
-					+ user.getURI() + "', " + user.getFirstName() + " "
-					+ user.getLastName());
-		}
-
-		public void writeUser(MockUser u) {
-			w.println();
-			w.println("# converting User: ");
-			w.println(u.getURI());
-			w.println("    a vitro:User ;");
-			w.println("    vitro:username \"" + u.getUsername() + "\" ;");
-			w.println("    vitro:firstName \"" + u.getFirstName() + "\" ;");
-			w.println("    vitro:lastName \"" + u.getLastName() + "\" ;");
-			w.println("    vitro:md5password \"" + u.getMd5password() + "\" ;");
-			w.println("    vitro:loginCount " + u.getLoginCount() + " ;");
-			w.println("    vitro:roleUri \"" + u.getRoleURI() + "\" ;");
-			w.println("    .");
-		}
-
-		public void noteUserAccount(UserAccount ua) {
-			note("Created UserAccount '" + ua.getUri() + "' for "
-					+ ua.getFirstName() + " " + ua.getLastName());
-		}
-
-		public void noteDeletedUser(MockUser user) {
-			note("Delete User: '" + user.getURI() + "'");
-		}
-
-		public void noteException(Exception e) {
-			errorCount++;
-			note("Exception: " + e, "    (full stack trace in Vitro log file)");
-		}
-
-		public void close() {
-			w.println("upgrade complete with " + errorCount + " errors.");
-			w.close();
-		}
-
-		private void confirmIsDirectory(File home) {
-			if (!home.exists()) {
-				throw new IllegalStateException("Vitro home directory '"
-						+ home.getPath() + "' does not exist.");
-			}
-			if (!home.isDirectory()) {
-				throw new IllegalStateException("Vitro home '" + home.getPath()
-						+ "' is not a directory.");
-			}
-			if (!home.canWrite()) {
-				throw new IllegalStateException(
-						"Can't write to Vitro home directory '"
-								+ home.getPath() + "'.");
-			}
-		}
-
-		private File createDirectory(File home, String name) {
-			File upgradeDirectory = new File(home, name);
-			if (!upgradeDirectory.exists()) {
-				upgradeDirectory.mkdirs();
-				if (!upgradeDirectory.exists()) {
-					throw new IllegalStateException(
-							"Failed to create the upgrade directory '"
-									+ upgradeDirectory.getPath() + "'");
-				}
-			}
-
-			if (!upgradeDirectory.isDirectory()) {
-				throw new IllegalStateException("Upgrade directory '"
-						+ upgradeDirectory.getPath() + "' is not a directory.");
-			}
-			if (!upgradeDirectory.canWrite()) {
-				throw new IllegalStateException(
-						"Can't write to Upgrade directory '"
-								+ upgradeDirectory.getPath() + "'.");
-			}
-
-			return upgradeDirectory;
-		}
-
-		private String timestampedFilename(String prefix, String suffix) {
-			SimpleDateFormat sdf = new SimpleDateFormat(
-					"yyyy-MM-dd'T'HH-mm-sss");
-			return prefix + "." + sdf.format(new Date()) + suffix;
-		}
-	}
-
-	// ----------------------------------------------------------------------
-	// Classes to replace the User and UserDao, just for the upgrade.
-	// ----------------------------------------------------------------------
-
-	private static class MockUser {
-		private String username;
-		private String roleURI;
-		private int loginCount;
-		private String md5password;
-		private String lastName;
-		private String firstName;
-		private String URI;
-
-		public String getUsername() {
-			return username;
-		}
-
-		public void setUsername(String username) {
-			this.username = username;
-		}
-
-		public String getRoleURI() {
-			return roleURI;
-		}
-
-		public void setRoleURI(String roleURI) {
-			this.roleURI = roleURI;
-		}
-
-		public int getLoginCount() {
-			return loginCount;
-		}
-
-		public void setLoginCount(int loginCount) {
-			this.loginCount = loginCount;
-		}
-
-		public String getMd5password() {
-			return md5password;
-		}
-
-		public void setMd5password(String md5password) {
-			this.md5password = md5password;
-		}
-
-		public String getLastName() {
-			return lastName;
-		}
-
-		public void setLastName(String lastName) {
-			this.lastName = lastName;
-		}
-
-		public String getFirstName() {
-			return firstName;
-		}
-
-		public void setFirstName(String firstName) {
-			this.firstName = firstName;
-		}
-
-		public String getURI() {
-			return URI;
-		}
-
-		public void setURI(String uRI) {
-			URI = uRI;
-		}
-
-	}
-
-	private static class MockUserDao {
-		private final OntModel model;
-
-		public MockUserDao(ServletContext ctx) {
-			this.model = ModelContext.getBaseOntModelSelector(ctx)
-					.getUserAccountsModel();
-		}
-
-		public Collection<MockUser> getAllUsers() {
-			List<MockUser> allUsersList = new ArrayList<MockUser>();
-			model.enterCriticalSection(Lock.READ);
-			try {
-				ClosableIterator<Statement> userStmtIt = model.listStatements(
-						null, RDF.type, resource(USER));
-				try {
-					while (userStmtIt.hasNext()) {
-						Statement stmt = userStmtIt.next();
-						OntResource subjRes = stmt.getSubject().as(
-								OntResource.class);
-						allUsersList.add(userFromUserInd(subjRes));
-					}
-				} finally {
-					userStmtIt.close();
-				}
-			} finally {
-				model.leaveCriticalSection();
-			}
-			return allUsersList;
-		}
-
-		private MockUser userFromUserInd(OntResource userInd) {
-			MockUser user = new MockUser();
-			user.setURI(userInd.getURI());
-
-			try {
-				user.setUsername(getStringPropertyValue(userInd, USER_USERNAME));
-			} catch (Exception e) {
-				// ignore it.
-			}
-
-			try {
-				user.setMd5password(getStringPropertyValue(userInd,
-						USER_MD5PASSWORD));
-			} catch (Exception e) {
-				// ignore it.
-			}
-
-			try {
-				user.setLoginCount(getIntegerPropertyValue(userInd,
-						USER_LOGINCOUNT));
-			} catch (Exception e) {
-				user.setLoginCount(0);
-			}
-
-			try {
-				user.setRoleURI(getStringPropertyValue(userInd, USER_ROLE));
-			} catch (Exception e) {
-				log.error("Unable to set user role\n", e);
-				e.printStackTrace();
-				user.setRoleURI("1");
-			}
-			try {
-				user.setLastName(getStringPropertyValue(userInd, USER_LASTNAME));
-			} catch (Exception e) {
-				// ignore it.
-			}
-
-			try {
-				user.setFirstName(getStringPropertyValue(userInd,
-						USER_FIRSTNAME));
-			} catch (Exception e) {
-				// ignore it.
-			}
-
-			return user;
-		}
-
-		private String getStringPropertyValue(OntResource userInd,
-				String propertyUri) {
-			Property property = model.getProperty(propertyUri);
-			Literal object = (Literal) userInd.getProperty(property)
-					.getObject();
-			return object.getString();
-		}
-
-		private int getIntegerPropertyValue(OntResource userInd,
-				String propertyUri) {
-			Property property = model.getProperty(propertyUri);
-			Literal object = (Literal) userInd.getProperty(property)
-					.getObject();
-			return object.getInt();
-		}
-
-		public void deleteUser(MockUser user) {
-			model.removeAll(resource(user.getURI()), null, null);
-		}
-		
-		private Resource resource(String uri) {
-			return model.getResource(uri);
-		}
-
-	}
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/ImageUtil.java

@@ -1,61 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.utils;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
-
-/**
- * Some static methods that help in dealing with image files.
- */
-public class ImageUtil {
-	private static final String DEFAULT_IMAGE_PATH = "/images/placeholders/thumbnail.jpg";
-
-	private static final Map<String, String> DEFAULT_IMAGE_PATHS_BY_TYPE = initImagePaths();
-
-	private static Map<String, String> initImagePaths() {
-		Map<String, String> map = new HashMap<String, String>();
-		// No images other than the default.
-		return Collections.unmodifiableMap(map);
-	}
-
-	/**
-	 * If we have a placeholder image for this exact type, return it. Otherwise,
-	 * return the default.
-	 */
-	public static String getPlaceholderImagePathForType(String typeUri) {
-		for (Entry<String, String> entry : DEFAULT_IMAGE_PATHS_BY_TYPE
-				.entrySet()) {
-			if (typeUri.equals(entry.getKey())) {
-				return entry.getValue();
-			}
-		}
-		return DEFAULT_IMAGE_PATH;
-	}
-
-	/**
-	 * If there is a placeholder image for any type that this Individual
-	 * instantiates, return that image. Otherwise, return the default.
-	 */
-	public static String getPlaceholderImagePathForIndividual(
-			VitroRequest vreq, String individualUri) {
-		IndividualDao indDao = vreq.getWebappDaoFactory().getIndividualDao();
-		for (Entry<String, String> entry : DEFAULT_IMAGE_PATHS_BY_TYPE
-				.entrySet()) {
-			if (indDao.isIndividualOfClass(entry.getKey(), individualUri)) {
-				return entry.getValue();
-			}
-		}
-		return DEFAULT_IMAGE_PATH;
-	}
-
-	/** Never need to instantiate this -- all methods are static. */
-	private ImageUtil() {
-		// Nothing to do
-	}
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/ClassGroupPageData.java

@@ -97,7 +97,7 @@ public class ClassGroupPageData extends DataGetterBase implements DataGetter{
                       setAllClassCountsToZero(group);
                   }
               }else{
-                  log.error("classgroup " + classGroupUri + " does not exist in the system");
+                  throw new RuntimeException("classgroup " + classGroupUri + " does not exist in the system");
               }
               
           }

webapp/src/edu/cornell/mannlib/vitro/webapp/web/images/PlaceholderUtil.java

@@ -0,0 +1,238 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.web.images;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import javax.servlet.ServletContext;
+import javax.servlet.ServletContextEvent;
+import javax.servlet.ServletContextListener;
+
+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.dao.IndividualDao;
+import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
+
+/**
+ * A utility for finding the URL of the correct Placeholder image.
+ * 
+ * The mapping of image URLs to classes is created at startup, and stored in the
+ * ServletContext.
+ */
+public class PlaceholderUtil {
+	private static final Log log = LogFactory.getLog(PlaceholderUtil.class);
+
+	private static final String ATTRIBUTE_NAME = PlaceholderUtil.class
+			.getName();
+	private static final String PROPERTIES_FILE_PATH = "/images/placeholders/placeholders.properties";
+	private static final String DEFAULT_IMAGE_PATH = "/images/placeholders/thumbnail.jpg";
+
+	// ----------------------------------------------------------------------
+	// Static methods
+	// ----------------------------------------------------------------------
+
+	/**
+	 * If we have a placeholder image for this exact type, return it. Otherwise,
+	 * return the default.
+	 */
+	public static String getPlaceholderImagePathForType(VitroRequest vreq,
+			String typeUri) {
+		PlaceholderUtil pu = getPlaceholderUtil(vreq);
+		if (pu == null) {
+			return DEFAULT_IMAGE_PATH;
+		} else {
+			return pu.getPlaceholderImagePathForType(typeUri);
+		}
+	}
+
+	/**
+	 * If there is a placeholder image for any type that this Individual
+	 * instantiates, return that image. Otherwise, return the default.
+	 */
+	public static String getPlaceholderImagePathForIndividual(
+			VitroRequest vreq, String individualUri) {
+		PlaceholderUtil pu = getPlaceholderUtil(vreq);
+		if (pu == null) {
+			return DEFAULT_IMAGE_PATH;
+		} else {
+			IndividualDao iDao = vreq.getWebappDaoFactory().getIndividualDao();
+			return pu.getPlaceholderImagePathForIndividual(iDao, individualUri);
+		}
+	}
+
+	/** Get the PlaceholderUtil instance from the context, or null if none. */
+	private static PlaceholderUtil getPlaceholderUtil(VitroRequest vreq) {
+		if (vreq == null) {
+			return null;
+		}
+		ServletContext ctx = vreq.getSession().getServletContext();
+		Object attrib = ctx.getAttribute(ATTRIBUTE_NAME);
+		if (attrib instanceof PlaceholderUtil) {
+			return (PlaceholderUtil) attrib;
+		} else {
+			log.warn("Looked for a PlaceholerUtil, but found " + attrib);
+			return null;
+		}
+	}
+
+	// ----------------------------------------------------------------------
+	// The object
+	// ----------------------------------------------------------------------
+
+	private final Map<String, String> mapUrlsByClass;
+
+	private PlaceholderUtil(Map<String, String> map) {
+		this.mapUrlsByClass = Collections
+				.unmodifiableMap(new HashMap<String, String>(map));
+	}
+
+	/**
+	 * If we have a placeholder image for this exact type, return it. Otherwise,
+	 * return the default.
+	 */
+	private String getPlaceholderImagePathForType(String typeUri) {
+		if (typeUri == null) {
+			log.debug("getPlaceholderImagePathForType: typeUri is null");
+			return DEFAULT_IMAGE_PATH;
+		}
+		String url = mapUrlsByClass.get(typeUri);
+		if (url == null) {
+			log.debug("getPlaceholderImagePathForType: no value for '"
+					+ typeUri + "'");
+			return DEFAULT_IMAGE_PATH;
+		}
+		log.debug("getPlaceholderImagePathForType: value for '" + typeUri
+				+ "' is '" + url + "'");
+		return url;
+	}
+
+	/**
+	 * If there is a placeholder image for any type that this Individual
+	 * instantiates, return that image. Otherwise, return the default.
+	 */
+	private String getPlaceholderImagePathForIndividual(IndividualDao iDao,
+			String individualUri) {
+		if (individualUri == null) {
+			log.debug("getPlaceholderImagePathForIndividual: "
+					+ "individualUri is null");
+			return DEFAULT_IMAGE_PATH;
+		}
+		for (String classUri : mapUrlsByClass.keySet()) {
+			String imageUrl = mapUrlsByClass.get(classUri);
+			if (iDao.isIndividualOfClass(classUri, individualUri)) {
+				log.debug("getPlaceholderImagePathForIndividual: individual '"
+						+ individualUri + "' is of class '" + classUri
+						+ "', value is '" + imageUrl + "'");
+				return imageUrl;
+			}
+		}
+		log.debug("getPlaceholderImagePathForIndividual: individual '"
+				+ individualUri + "' is not of any recognized class");
+		return DEFAULT_IMAGE_PATH;
+	}
+
+	// ----------------------------------------------------------------------
+	// Classes used for setup
+	// ----------------------------------------------------------------------
+
+	public static class Setup implements ServletContextListener {
+		@Override
+		public void contextInitialized(ServletContextEvent sce) {
+			ServletContext ctx = sce.getServletContext();
+			StartupStatus ss = StartupStatus.getBean(ctx);
+
+			try {
+				File propertiesFile = confirmRealPath(ctx, PROPERTIES_FILE_PATH);
+				Map<String, String> map = loadPropertiesToMap(propertiesFile);
+				confirmImagesArePresent(ctx, map);
+				ctx.setAttribute(ATTRIBUTE_NAME, new PlaceholderUtil(map));
+			} catch (SetupException e) {
+				if (e.getCause() == null) {
+					ss.warning(this, e.getMessage());
+				} else {
+					ss.warning(this, e.getMessage(), e.getCause());
+				}
+			}
+		}
+
+		private Map<String, String> loadPropertiesToMap(File propertiesFile)
+				throws SetupException {
+			Properties props = new Properties();
+			try {
+				props.load(new FileReader(propertiesFile));
+			} catch (IOException e) {
+				throw new SetupException(
+						"Can't load properties from the file at '"
+								+ PROPERTIES_FILE_PATH
+								+ "'. Is it in a valid format?", e);
+			}
+
+			Map<String, String> map = new HashMap<String, String>();
+			for (Enumeration<Object> keys = props.keys(); keys
+					.hasMoreElements();) {
+				String key = (String) keys.nextElement();
+				String value = props.getProperty(key);
+				map.put(key, value);
+			}
+
+			return map;
+		}
+
+		private void confirmImagesArePresent(ServletContext ctx,
+				Map<String, String> map) throws SetupException {
+			Set<String> imageUrls = new HashSet<String>();
+			imageUrls.add(DEFAULT_IMAGE_PATH);
+			imageUrls.addAll(map.values());
+			for (String imageUrl : imageUrls) {
+				confirmRealPath(ctx, imageUrl);
+			}
+
+		}
+
+		private File confirmRealPath(ServletContext ctx, String url)
+				throws SetupException {
+			String path = ctx.getRealPath(url);
+			if (path == null) {
+				throw new SetupException("Can't translate to real path: '"
+						+ url + "'");
+			}
+			File file = new File(path);
+			if (!file.exists()) {
+				throw new SetupException("No file found at '" + url + "'.");
+			}
+			if (!file.canRead()) {
+				throw new SetupException("Can't read the file at '" + url
+						+ "'.");
+			}
+			return file;
+		}
+
+		@Override
+		public void contextDestroyed(ServletContextEvent sce) {
+			sce.getServletContext().removeAttribute(ATTRIBUTE_NAME);
+		}
+
+	}
+
+	private static class SetupException extends Exception {
+		public SetupException(String message) {
+			super(message);
+		}
+
+		public SetupException(String message, Throwable cause) {
+			super(message, cause);
+		}
+	}
+}

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

@@ -0,0 +1,57 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.web.methods;
+
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.servlet.http.HttpServletRequest;
+
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
+import edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil;
+import freemarker.core.Environment;
+import freemarker.template.TemplateModelException;
+
+/**
+ * Get a URL for the placeholder image for this Individual, based on the VClass 
+ * that the Individual belongs to.
+ */
+public class IndividualPlaceholderImageUrlMethod extends BaseTemplateMethodModel {
+
+    @SuppressWarnings("rawtypes")
+    @Override
+    public String exec(List args) throws TemplateModelException {
+        if (args.size() != 1) {
+            throw new TemplateModelException("Wrong number of arguments");
+        }
+
+        String uri = (String) args.get(0);        
+        Environment env = Environment.getCurrentEnvironment();
+        HttpServletRequest request = (HttpServletRequest) env.getCustomAttribute("request");
+        VitroRequest vreq = new VitroRequest(request);
+        String imageUrl = PlaceholderUtil.getPlaceholderImagePathForIndividual(vreq, uri);
+        return UrlBuilder.getUrl(imageUrl);
+    }
+
+    @Override
+    public Map<String, Object> help(String name) {
+        Map<String, Object> map = new LinkedHashMap<String, Object>();
+
+        map.put("return value", "The URL of the placeholder image for this individual, " +
+        		"based on the VClasses that the individual belongs to.");
+
+        List<String>params = new ArrayList<String>();
+        params.add("Uri of individual");
+        map.put("parameters", params);
+        
+        List<String> examples = new ArrayList<String>();
+        examples.add(name + "(individual.uri)");
+        map.put("examples", examples);
+        
+        return map;
+    }
+    
+}

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

@@ -76,15 +76,11 @@ public abstract class BaseIndividualTemplateModel extends BaseTemplateModel {
         return UrlBuilder.getIndividualProfileUrl(individual, vreq);        
     }
 
-    // For image, we use the default list view and Individual methods to reconstruct the image
-    // url from various triples. A custom list view would require that logic to be duplicated here.
     public String getImageUrl() {
         String imageUrl = individual.getImageUrl();
         return imageUrl == null ? null : getUrl(imageUrl);
     }
 
-    // For image, we use the default list view and Individual methods to reconstruct the image
-    // url from various triples. A custom list view would require that logic to be duplicated here.
     public String getThumbUrl() {
         String thumbUrl = individual.getThumbUrl();
         return thumbUrl == null ? null : getUrl(thumbUrl);

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

@@ -207,7 +207,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
         ObjectPropertyDao opDao = wdf.getObjectPropertyDao();
         ObjectProperty op = opDao.getObjectPropertyByURI(propertyUri);
         if (op == null) {
-            log.error("ObjectProperty op returned null from opDao.getObjectPropertyByURI()");
+            log.error("ObjectProperty op returned null from opDao.getObjectPropertyByURI(" + propertyUri + ")");
         } else if (op.getURI() == null) {
             log.error("ObjectProperty op returned with null propertyURI from opDao.getObjectPropertyByURI()");
         } else {

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

@@ -111,7 +111,8 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
     }
     
     public String getAddUrl() {
-        return addUrl;
+        //log.info("addUrl=" + addUrl);
+        return (addUrl != null) ? addUrl : "";
     }
     
     public Map<String, Object> getVerboseDisplay() {

webapp/test/edu/cornell/mannlib/vitro/webapp/dao/filtering/IndividualFilteringByStatementTest.java

@@ -638,18 +638,6 @@ public class IndividualFilteringByStatementTest extends AbstractTestClass {
 		// Un-implemented methods
 		// ----------------------------------------------------------------------
 
-		@Override
-		public boolean isSubjectOriented() {
-			throw new RuntimeException(
-					"ObjectPropertyStatement.isSubjectOriented() not implemented.");
-		}
-
-		@Override
-		public void setSubjectOriented(boolean subjectOriented) {
-			throw new RuntimeException(
-					"ObjectPropertyStatement.setSubjectOriented() not implemented.");
-		}
-
 		@Override
 		public void setSubjectURI(String subjectURI) {
 			throw new RuntimeException(

webapp/test/edu/cornell/mannlib/vitro/webapp/edit/n3editing/VTwo/ProcessRdfFormTest.java

@@ -9,12 +9,16 @@ import java.util.Map;
 import static org.junit.Assert.*;
 import org.junit.Test;
 
+import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfigurationConstants;
 
 public class ProcessRdfFormTest extends AbstractTestClass{
      
@@ -243,6 +247,137 @@ public class ProcessRdfFormTest extends AbstractTestClass{
                 ResourceFactory.createResource("http://test.com/uri3")));
     }
 
+    @Test
+    //Edit existing statement
+    public void forcedNewResourceTest() throws Exception{       
+        /* A very basic new statement edit. */        
+        EditConfigurationVTwo config = new EditConfigurationVTwo();
+        config.setEditKey("mockEditKey");
+        config.setN3Required(Arrays.asList("?newRes ?test2 ?test3 ." ));
+        config.setUrisOnform(Arrays.asList( "newRes", "test2", "test3"));
+        //set uris in scope to include an existing value for new resource
+        config.addUrisInScope("newRes", Arrays.asList("<http://test.com/uri1>"));
+        config.addNewResource("newRes", null);
+        config.setEntityToReturnTo("?newRes");        
+        
+        Map<String,String[]> values = new HashMap<String, String[]>(); 
+        //value from form should indicate that newRes should have new uri created
+        values.put("newRes", (new String[] {EditConfigurationConstants.NEW_URI_SENTINEL}));
+        values.put("test2", (new String[] {"http://test.com/uri2"}));
+        values.put("test3", (new String[] {"http://test.com/uri3"}));
+        values.put("editKey", (new String[] {"mockEditKey"}));
+                
+        MultiValueEditSubmission submission = new MultiValueEditSubmission(values, config);
+        
+        ProcessRdfForm processor = new ProcessRdfForm(config,getMockNewURIMaker());
+        
+        /* test just the N3 substitution part */
+        List<String>req = config.getN3Required();
+        List<String>opt = config.getN3Optional();
+        processor.subInValuesToN3( config , submission, req, opt, null , null);
+        assertNotNull(req);
+        assertTrue( req.size() > 0);
+        assertNotNull(req.get(0));
+        assertEquals("<"+NEWURI_STRING + "0> <http://test.com/uri2> <http://test.com/uri3> .", req.get(0));
+        
+        assertEquals("<" + NEWURI_STRING + "0>", submission.getEntityToReturnTo());
+        
+        /* test the N3 and parse RDF parts */
+        AdditionsAndRetractions changes = processor.process( config, submission );
+        
+        assertNotNull( changes );
+        assertNotNull( changes.getAdditions() );
+        assertNotNull( changes.getRetractions());
+        assertTrue( changes.getAdditions().size() == 1 );
+        //the old uri should be removed
+        assertTrue( changes.getRetractions().size() == 0 );
+        
+        assertTrue( changes.getAdditions().contains(
+                ResourceFactory.createResource(NEWURI_STRING + "0"), 
+                ResourceFactory.createProperty("http://test.com/uri2"),
+                ResourceFactory.createResource("http://test.com/uri3")));
+        
+
+    }
+    
+    /* An edit of an existing statement set where some statements need to be replaced while
+     * others must be retained. */
+    @Test
+    public void basicEditReplaceStatement() throws Exception{
+        String testXURI = "http://test.com/uriX";
+        String testYURI = "http://test.com/uriY";
+        String testZURIOrginal = "http://test.com/uriZ";
+        String testZURIChanged = "http://test.com/uriZChanged";
+        String zType = "http://test.com/TestType";
+        String rdfsLabel = "http://www.w3.org/2000/01/rdf-schema#label";
+        /* set up model */
+        Model model = ModelFactory.createDefaultModel();
+        //?x ?y ?zOriginal.
+        model.add(model.createResource(testXURI), 
+                  model.createProperty(testYURI), 
+                  model.createResource(testZURIOrginal));
+        //?zOriginal a TestType.
+
+        model.add(model.createResource(testZURIOrginal), 
+                RDF.type, 
+                model.createResource(zType));
+        //?zOriginal label "zLabel";
+
+        model.add(model.createResource(testZURIOrginal), 
+                RDFS.label, 
+                model.createLiteral("Z Original Label"));
+        
+        /* set up EditConfiguration */
+        EditConfigurationVTwo config = new EditConfigurationVTwo();
+        config.setEditKey("mockEditKey");        
+        config.setLiteralsOnForm(Arrays.asList("zLabel"));
+        config.setUrisOnform(Arrays.asList("testX", "testY", "testZ"));
+        config.setN3Required( Arrays.asList("?testX ?testY ?testZ ." ));
+        config.setN3Optional( Arrays.asList("?testZ a <" + zType + "> . \n" + 
+        		"?testZ <" + rdfsLabel + "> ?zLabel ." ));
+        //mimicking an existing value for the label
+        config.addLiteralInScope("zLabel", model.createLiteral("Z Original Label"));        
+        
+        config.setVarNameForSubject("testX");
+        config.setSubjectUri(testXURI);
+        
+        config.setPredicateUri(testYURI);
+        config.setVarNameForPredicate("testY");
+        
+        config.setObject(testZURIOrginal);
+        config.setVarNameForObject("testZ");                
+                
+        config.addField(new FieldVTwo().setName("zLabel"));
+        config.prepareForObjPropUpdate(model);    
+        /* set up Submission */        
+        Map<String,String[]> values = new HashMap<String, String[]>();                
+        values.put("testZ", (new String[] {testZURIChanged}));
+        values.put("zLabel", (new String[] {"New Z Label"}));
+        values.put("editKey", (new String[] {"mockEditKey"}));               
+        MultiValueEditSubmission submission = new MultiValueEditSubmission(values, config);
+        
+        ProcessRdfForm processor = new ProcessRdfForm(config,getMockNewURIMaker());        
+        AdditionsAndRetractions changes = processor.process( config, submission );
+             
+        assertNotNull( changes );
+        assertNotNull( changes.getAdditions() );
+        assertNotNull( changes.getRetractions());
+        
+       // assertTrue( changes.getAdditions().size() == 3 );
+        //only one statement should be retracted
+       // assertTrue( changes.getRetractions().size() == 1 );
+        
+        assertTrue( changes.getAdditions().contains(
+                ResourceFactory.createResource(testXURI), 
+                ResourceFactory.createProperty(testYURI),
+                ResourceFactory.createResource(testZURIChanged)));
+        
+        assertTrue( changes.getRetractions().contains(
+                ResourceFactory.createResource(testXURI), 
+                ResourceFactory.createProperty(testYURI),
+                ResourceFactory.createResource(testZURIOrginal)));        
+    }
+    
     
     String NEWURI_STRING= "http://newURI/n";
     

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/dao/ObjectPropertyStatementDaoStub.java

@@ -55,16 +55,6 @@ public class ObjectPropertyStatementDaoStub implements
 					.getObjectURI());
 		}
 
-		@Override
-		public boolean isSubjectOriented() {
-			return false;
-		}
-
-		@Override
-		public void setSubjectOriented(boolean subjectOriented) {
-			throw new UnsupportedOperationException();
-		}
-
 		@Override
 		public String getSubjectURI() {
 			return s;

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactoryStub.java

@@ -7,7 +7,6 @@ import java.util.Map;
 import java.util.Set;
 
 import edu.cornell.mannlib.vitro.webapp.dao.ApplicationDao;
-import edu.cornell.mannlib.vitro.webapp.dao.Classes2ClassesDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
@@ -144,12 +143,6 @@ return this.objectPropertyStatementDao;	}
 	// Un-implemented methods
 	// ----------------------------------------------------------------------
 
-	@Override
-	public Map<String, String> getProperties() {
-		throw new RuntimeException(
-				"WebappDaoFactory.getProperties() not implemented.");
-	}
-
 	@Override
 	public String checkURI(String uriStr) {
 		throw new RuntimeException(
@@ -169,7 +162,7 @@ return this.objectPropertyStatementDao;	}
 	}
 
 	@Override
-	public String[] getPreferredLanguages() {
+	public List<String> getPreferredLanguages() {
 		throw new RuntimeException(
 				"WebappDaoFactory.getPreferredLanguages() not implemented.");
 	}
@@ -192,12 +185,6 @@ return this.objectPropertyStatementDao;	}
 				"WebappDaoFactory.getUserURI() not implemented.");
 	}
 
-	@Override
-	public Classes2ClassesDao getClasses2ClassesDao() {
-		throw new RuntimeException(
-				"WebappDaoFactory.getClasses2ClassesDao() not implemented.");
-	}
-
 	@Override
 	public DatatypeDao getDatatypeDao() {
 		throw new RuntimeException(

webapp/web/WEB-INF/ontologies/app/menu.n3

@@ -32,4 +32,4 @@ display:Home
 ########## Data Getter ############
     
 <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#homeDataGetter>
-      a <java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.BrowseDataGetter> .    
+      a <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter> .    

webapp/web/WEB-INF/resources/permission_config.n3

@@ -22,6 +22,7 @@ auth:ADMIN
     auth:hasPermission simplePermission:SeeStartupStatus ;
     auth:hasPermission simplePermission:UseAdvancedDataToolsPages ;
     auth:hasPermission simplePermission:UseMiscellaneousAdminPages ;
+    auth:hasPermission simplePermission:UseSparqlQueryPage ;
     
     # permissions for CURATOR and above.
     auth:hasPermission simplePermission:EditOntology ;

webapp/web/WEB-INF/resources/startup_listeners.txt

@@ -24,6 +24,8 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase
 
 edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorageSetup
 
+edu.cornell.mannlib.vitro.webapp.web.images.PlaceholderUtil$Setup
+
 # Update the URIs on Permission Sets on UserAccounts from model (1.4) to 1.5.
 edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdatePermissionSetUris
 

webapp/web/admin/sparqlquery/sparqlForm.jsp

@@ -7,7 +7,7 @@
 
 <%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
 <%@page import="edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission" %>
-<% request.setAttribute("requestedActions", SimplePermission.MANAGE_PORTALS.ACTION); %>
+<% request.setAttribute("requestedActions", SimplePermission.USE_SPARQL_QUERY_PAGE.ACTION); %>
 <vitro:confirmAuthorization />
 
 <body>

webapp/web/css/jquery_plugins/jquery.realperson.css

@@ -0,0 +1,38 @@
+/* http://keith-wood.name/realPerson.html
+   Real Person Form Submission for jQuery v1.0.1.
+   Written by Keith Wood (kwood{at}iinet.com.au) June 2009.
+   Dual licensed under the GPL (http://dev.jquery.com/browser/trunk/jquery/GPL-LICENSE.txt) and 
+   MIT (http://dev.jquery.com/browser/trunk/jquery/MIT-LICENSE.txt) licenses. 
+   Please attribute the author if you use it. */
+   
+/* Real Person jQuery plugin styles v1.0.1. */
+.realperson-challenge {
+	display: inline-block;
+	background-color: #ddd;
+	width: 150px;
+	padding-top: 10px;
+	padding-left: 12px;
+}
+.realperson-text {
+	font-family: "Courier New",monospace;
+	font-size: 6px;
+	font-weight: bold;
+	letter-spacing: -1px;
+	line-height: 3px;
+	color: #000;
+}
+.realperson-regen {
+	padding-top: 4px;
+	padding-right: 6px;
+	font-size: 12px;
+	text-align: center;
+	cursor: pointer;
+}
+.realpersonLabel { 
+    display: block; 
+}
+#defaultReal {
+    margin-left: 20px;
+    vertical-align: top;
+    margin-top: 3px;
+}

webapp/web/images/placeholders/placeholders.properties

@@ -0,0 +1,17 @@
+#
+# Assign placeholder images to classes of individuals.
+#
+# If showing an individual that has no image, a placeholder image may be shown.
+# By default, the placeholder is /images/placeholders/thumbnail.jpg. However,
+# this file allows you to associate classes with special placeholder images, and
+# if the individual belongs to such a class, the special placeholder is shown
+# instead of the default.
+#
+# EXAMPLE:
+#   http\://xmlns.com/foaf/0.1/Person = /images/placeholders/person.thumbnail.jpg
+# means that any individual of type foaf:Person will be represented by
+# person.thumbnail.jpg
+#
+# NOTE: a colon is a special character in a properties file, and must be escaped 
+# by a backslash.
+

webapp/web/js/account/accountProxyCommon.js

@@ -44,7 +44,7 @@ function itemElement(template, uri, label, classLabel, imageUrl, removeInfo) {
 	this.uri = uri;
 	this.label = label;
 	this.classLabel = classLabel;
-	this.imageUrl = (imageUrl) ? imageUrl : imageUrl="../images/placeholders/person.thumbnail.jpg";
+	this.imageUrl = imageUrl;
 	this.removeInfo = removeInfo;
 	
 	this.toString = function() {

webapp/web/js/commentForm.js

@@ -6,41 +6,9 @@ function ValidateForm(formName) {
     errors = false;
     var errorList;
 
-    if (document.forms[formName].RequiredFields) {
-        errorList = 'Please fill out the following required fields:\n';
-        // build array of required fields
-        reqStr = document.forms[formName].RequiredFields.value;
-        requiredFields = reqStr.split(',');
-        // build array holding the names of required fields as
-        // displayed in error box
-        if (document.forms[formName].RequiredFieldsNames) {
-            reqNameStr = document.forms[formName].RequiredFieldsNames.value;
-        } else {
-            reqNameStr = document.forms[formName].RequiredFields.value;
-        }
-        requiredNames = reqNameStr.split(',');
-        // Loop through form elements, checking for required fields
-        while ((x < document.forms[formName].elements.length)) {
-            if (document.forms[formName].elements[x].name == requiredFields[y]) {
-                if (document.forms[formName].elements[x].value == '') {
-                    errorList += requiredNames[y] + '\n';
-                    errors = true;
-                }
-                y++;
-            }
-            x++;
-        }
-        if (errors) {
-            alert(errorList);
-            return false;
-        }
-    x = 0;
-    y = 0;
-    }
-
     // Check for Email formatting
     if (document.forms[formName].EmailFields) {
-        errorList = 'Please format your e-mail address as: \"userid@institution.edu\" or enter another complete email address';
+        errorList = '\nPlease format your e-mail address as:\n \"userid@institution.edu\" or enter another complete and valid email address';
         // build array of required fields
         emailStr = document.forms[formName].EmailFields.value;
         emailFields = emailStr.split(',');