committing revision 8270. Merged from trunk.

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

@@ -151,17 +151,12 @@ public class SparqlQueryServlet extends BaseEditController {
 		
 		String queryParam = vreq.getParameter("query");
 		boolean graphPresent = false;
-		StringTokenizer tokenizer = new StringTokenizer(queryParam, " ");
+		String[] tokens = queryParam.split("\\s");
-	    while(tokenizer.hasMoreTokens()){
+	    for(int i = 0; i < tokens.length; i++){
-	    	if("graph".equalsIgnoreCase(tokenizer.nextToken())){
+	    	if("graph".equalsIgnoreCase(tokens[i])){
-	    		graphPresent = true;
+	    		return vreq.getDataset();
-	    		break;
 	    	}
 	    }
-		Dataset dataset = vreq.getDataset();
-		if (dataset != null && graphPresent) {
-			return dataset;
-		}
 		
 		DataSource dataSource = DatasetFactory.create();
 		dataSource.setDefaultModel(vreq.getJenaOntModel());

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

@@ -70,6 +70,10 @@ public class VitroRequest extends HttpServletRequestWrapper {
     	setAttribute("dataset", dataset);
     }
     
+    public void setJenaOntModel(OntModel ontModel) {
+    	setAttribute("jenaOntModel", ontModel);
+    }
+    
     /** gets assertions + inferences WebappDaoFactory with no filtering **/
     public WebappDaoFactory getFullWebappDaoFactory() {
     	Object webappDaoFactoryAttr = _req.getAttribute("fullWebappDaoFactory");
@@ -106,6 +110,10 @@ public class VitroRequest extends HttpServletRequestWrapper {
     }
     
     public OntModel getJenaOntModel() {
+    	Object ontModel = getAttribute("jenaOntModel");
+    	if (ontModel instanceof OntModel) {
+    		return (OntModel) ontModel;
+    	}
     	OntModel jenaOntModel = (OntModel)_req.getSession().getAttribute( JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME );
     	if ( jenaOntModel == null ) {
     		jenaOntModel = (OntModel)_req.getSession().getServletContext().getAttribute( JenaBaseDao.JENA_ONT_MODEL_ATTRIBUTE_NAME );

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

@@ -78,6 +78,7 @@ public class IndividualController extends FreemarkerHttpServlet {
     private static final String INCLUDE_ALL = "all";
     
     private static final Map<String, String> namespaces = new HashMap<String, String>() {{
+        put("display", VitroVocabulary.DISPLAY);
         put("vitro", VitroVocabulary.vitroURI);
         put("vitroPublic", VitroVocabulary.VITRO_PUBLIC);
     }};
@@ -334,13 +335,7 @@ public class IndividualController extends FreemarkerHttpServlet {
 	private ResponseValues doRdf(VitroRequest vreq, Individual individual,
 			ContentType rdfFormat) throws IOException, ServletException {    	
 				
-		OntModel ontModel = null;
+		OntModel ontModel = vreq.getJenaOntModel();		
-		HttpSession session = vreq.getSession(false);
-		if( session != null )
-			ontModel = (OntModel)session.getAttribute("jenaOntModel");		
-		if( ontModel == null)
-			ontModel = (OntModel)getServletContext().getAttribute("jenaOntModel");
-		
                 
         String[] includes = vreq.getParameterValues("include");
 		Model newModel = getRDF(individual,ontModel,ModelFactory.createDefaultModel(),0,includes);		

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

@@ -10,6 +10,7 @@ import java.util.Iterator;
 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 org.joda.time.DateTime;
@@ -26,18 +27,14 @@ import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
 import com.hp.hpl.jena.rdf.model.AnonId;
 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.ResIterator;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
-import com.hp.hpl.jena.vocabulary.OWL;
-import com.hp.hpl.jena.vocabulary.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
@@ -105,11 +102,65 @@ public class IndividualDaoSDB extends IndividualDaoJena {
         		ents.addAll(getIndividualsByVClass(vc));
         	}
         } else {
+        	
+        	List<Individual> individualList;
+        	
+        	// Check if there is a graph filter.
+        	// If so, we will use it in a slightly strange way.  Unfortunately,
+        	// performance is quite bad if we add several graph variables in 
+        	// order to account for the fact that an individual's type 
+        	// declaration may be in a different graph from its label or 
+        	// moniker.  Thus, we will run two queries: one with a single
+        	// graph variable to get the list of URIs, and a second against
+        	// the union graph to get individuals with their labels and 
+        	// monikers.  We will then toss out any individual in the second
+        	// list that is not also in the first list.
+        	// Annoying, yes, but better than the alternative.
+        	// Note that both queries need to sort identically or 
+        	// the results may be very strange.
+        	String[] graphVars = {"?g"};
+        	String filterStr = WebappDaoFactorySDB.getFilterBlock(
+        			graphVars, datasetMode);
+        	if (!StringUtils.isEmpty(filterStr)) {
+        		List<Individual> graphFilteredIndividualList = 
+        			    getGraphFilteredIndividualList(theClass, filterStr);
+        		List<Individual> unfilteredIndividualList = getIndividualList(
+        				theClass);
+        		Iterator<Individual> unfilteredIt  = unfilteredIndividualList
+        													.iterator(); 
+        		for (Individual filt : graphFilteredIndividualList) {
+        			Individual unfilt = unfilteredIt.next();
+        			while (!unfilt.getURI().equals(filt.getURI())) {
+        				unfilt = unfilteredIt.next();
+        			}
+        			ents.add(unfilt);
+        		}	
+        	} else {
+        		ents = getIndividualList(theClass);
+        	}
+        }
+        
+        java.util.Collections.sort(ents);
+        
+        if (quantity > 0 && offset > 0) {
+            List<Individual> sublist = new ArrayList<Individual>();
+            for (int i = offset - 1; i < ((offset - 1) + quantity); i++) {
+                sublist.add(ents.get(i));
+            }
+            return sublist;
+        }
+        
+        return ents;
+
+    }
+        
+    private List<Individual> getIndividualList(Resource theClass) {
+    	List<Individual> ents = new ArrayList<Individual>();
    	    DatasetWrapper w = getDatasetWrapper();
 	    Dataset dataset = w.getDataset();
     	dataset.getLock().enterCriticalSection(Lock.READ);
     	try {
-        	    String[] graphVars = {"?g", "?h", "?i"};
+    	    
     		String query = 
 	    		"SELECT DISTINCT ?ind ?label ?moniker " +
 	    		"WHERE " +
@@ -166,20 +217,40 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     		dataset.getLock().leaveCriticalSection();
     		w.close();
     	} 
-        }
-        
-        java.util.Collections.sort(ents);
-        
-        if (quantity > 0 && offset > 0) {
-            List<Individual> sublist = new ArrayList<Individual>();
-            for (int i = offset - 1; i < ((offset - 1) + quantity); i++) {
-                sublist.add(ents.get(i));
-            }
-            return sublist;
-        }
-        
         return ents;
+    }
     
+    private List<Individual> getGraphFilteredIndividualList(Resource theClass, 
+    		                                                String filterStr) {
+		List<Individual> filteredIndividualList = new ArrayList<Individual>();
+		DatasetWrapper w = getDatasetWrapper();
+   	    Dataset dataset = w.getDataset();
+       	dataset.getLock().enterCriticalSection(Lock.READ);
+       	try {
+    		String query = 
+    			"SELECT DISTINCT ?ind ?label ?moniker " +
+    			"WHERE " +
+    			"{ GRAPH ?g { \n" +
+                	"{   ?ind a <" + theClass.getURI() + "> } \n" +
+                "  } \n" + filterStr +
+                "} ORDER BY ?ind";
+    		ResultSet rs =QueryExecutionFactory.create(
+    		        QueryFactory.create(query), dataset)
+    		        .execSelect();
+    		while (rs.hasNext()) {
+    		    QuerySolution sol = rs.nextSolution();
+    		    Resource currRes = sol.getResource("ind");
+    		    if (currRes.isAnon()) {
+    		        continue;
+    		    }
+    		    filteredIndividualList.add(
+    		    		makeIndividual(currRes.getURI(), null, null));
+    		}
+       	} finally {
+    		dataset.getLock().leaveCriticalSection();
+    		w.close();
+		}
+       	return filteredIndividualList;
     }
     
     private Individual makeIndividual(String uri, String label, String moniker) {

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

@@ -933,21 +933,18 @@ public class IndividualSDB extends IndividualImpl implements Individual {
 		if (ind.getModel().contains((Resource) null, RDF.type, (RDFNode) null)){
 		    tempModel = ind.getModel();
 		} else {
+			String[] graphVars = { "?g" };
     		String getTypes = 
         		"CONSTRUCT{ <" + this.individualURI + "> <" + RDF.type +
         		        "> ?types }\n" +
-        		"WHERE{ GRAPH " + 
+        		"WHERE{ GRAPH ?g"   
-        		((direct) 
+        		+ " { <" + this.individualURI +"> <" +RDF.type+ "> ?types } \n" 
-        		    ? "<http://vitro.mannlib.cornell.edu/default/vitro-kb-2>" 
+   		        + WebappDaoFactorySDB.getFilterBlock(
-        		    : "?g") 
+   		        		graphVars, (direct 
-        		+ " { <" + this.individualURI +"> <" +RDF.type+ "> ?types } \n" ;
+   		        				? WebappDaoFactorySDB.SDBDatasetMode
-    		
+   		        						.ASSERTIONS_ONLY 
-    		    if (!direct) {
+   		        			    : datasetMode)) 
-    		        String[] graphVars = { "?g" };
+        		+ "} \n";        	
-    		        getTypes += WebappDaoFactorySDB.getFilterBlock(graphVars, datasetMode);
-    		    }
-    		
-        		getTypes += "} \n";        	
         	DatasetWrapper w = getDatasetWrapper();
         	Dataset dataset = w.getDataset();
         	dataset.getLock().enterCriticalSection(Lock.READ);

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

@@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 public class WebappDaoFactorySDB extends WebappDaoFactoryJena {
 	
+	public static final String UNION_GRAPH = "urn:x-arq:UnionGraph"; 
     private SDBDatasetMode datasetMode = SDBDatasetMode.ASSERTIONS_AND_INFERENCES;
     
 	/**

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

@@ -21,7 +21,9 @@ import org.apache.commons.dbcp.BasicDataSource;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.sdb.SDBFactory;
 import com.hp.hpl.jena.sdb.Store;
 import com.hp.hpl.jena.sdb.StoreDesc;
@@ -106,6 +108,9 @@ public class WebappDaoFactorySDBPrep implements Filter {
 				vreq.setWebappDaoFactory(wadf);
 				vreq.setFullWebappDaoFactory(wadf);
 				vreq.setDataset(dataset);
+				vreq.setJenaOntModel(ModelFactory.createOntologyModel(
+						OntModelSpec.OWL_MEM, dataset.getNamedModel(
+								WebappDaoFactorySDB.UNION_GRAPH)));
 			}
 		} catch (Throwable t) {
 			log.error("Unable to filter request to set up SDB connection", t);

webapp/web/css/vitro.css

@@ -114,3 +114,92 @@
     display: block;
     padding-left: 15px;
 }
+
+/* ------------------------------------------------->  */
+/* DROP DOWN USER MENU  ---------------------------->  */
+/* ------------------------------------------------->  */
+
+/* LEVEL ONE */
+ul.dropdown { 
+    position: relative; 
+}
+ul.dropdown li {  
+    float: left; 
+    zoom: 1; 
+    padding: 0 !important;
+}
+ul.dropdown li a { 
+    display: block; 
+    font-size: 1.4em;
+}
+ul.dropdown li#user-menu { 
+    background: url(../images/arrowDownOverAccount.gif) right 9px no-repeat;
+    min-width:110px;
+}
+ul.dropdown li#user-menu a { 
+    margin-right: 28px;
+    margin-left:10px;
+}
+ul.dropdown li#user-menu.hover,
+ul.dropdown li#user-menu:hover { 
+    color: #000 !important; 
+    position: relative; 
+    background: #fff url(../images/arrowDownAccount.gif) right 9px no-repeat;
+    border-bottom: 1px solid #cdcfcf;
+}
+ul.dropdown li.hover a,
+ul.dropdown li:hover a { 
+    color: #000 !important; 
+    margin-left:10px;
+}
+/* LEVEL TWO */
+ul.dropdown ul.sub_menu {  
+    background-color: #fff;
+    font-size: 1.4em;
+    visibility: hidden; 
+    position: absolute; 
+    top: 100%; 
+    right: 0; 
+    z-index: 999;
+    color: #000;
+}
+ul.dropdown ul.sub_menu li { 
+    float: none; 
+    clear: both;
+    padding-left: 14px !important;
+    width: 96px;
+    border-right: none !important;
+    border-bottom: 1px solid #cdcfcf;
+    background: #fff url(../images/arrowMenuAccount.gif) 7px 8px no-repeat;
+}
+ul.dropdown ul.sub_menu li:last-child { 
+    width: 96px;
+}
+/* IE 6 & 7 Needs Inline Block */
+/* ADD IN IE6.css and IE7.css*/
+ul.dropdown ul.sub_menu li a { 
+    width: 90%; 
+    display: inline-block; 
+    color: #000 !important;
+    background-color: #fff;
+    padding: 0;
+    padding-left: 0px;
+    height: 24px;
+}
+ul.dropdown ul.sub_menu li.inactive { 
+    color: #aab0ae !important;
+    font-size: 1em !important;
+    padding-left: 22px !important; 
+    width: 88px; 
+}
+ul.dropdown ul.sub_menu li a:hover,
+ul.dropdown ul.sub_menu li a.hover { 
+    color: #999 !important;
+}
+/*  LEVEL THREE */
+ul.dropdown ul ul { 
+    left: 100%; top: 0; 
+}
+ul.dropdown li:hover > ul { 
+    visibility: visible; 
+}

webapp/web/templates/freemarker/body/accounts/userAccounts-edit.ftl

@@ -65,7 +65,7 @@
             <label for="last-name">Last name<span class="requiredHint"> *</span></label> 
             <input type="text" name="lastName" value="${lastName}" id="last-name" role="input" />
 
-            <label for="external-auth-id">External authorization ID (optional)</label> 
+            <label for="external-auth-id">External authorization ID</label> 
             <input type="text" name="externalAuthId" value="${externalAuthId}" id="external-auth-id" role="input "/>
 
             <#if roles?has_content>

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

@@ -1,25 +1,29 @@
 <#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
 
-<#-- Default VIVO individual profile page template (extends individual.ftl in vitro) -->
+<#-- Menu management page (uses individual display mechanism) -->
 
 <#include "individual-setup.ftl">
 
-<#assign individualProductExtension>
-    <#-- Include for any class specific template additions -->
-    ${classSpecificExtension!}
-    
-    <#include "individual-overview.ftl">
-        </section> <!-- #individual-info -->
-    </section> <!-- #individual-intro -->
-</#assign>
-
-<#assign nameForOtherGroup = "other"> <#-- used by both individual-propertyGroupMenu.ftl and individual-properties.ftl -->
-
 <h3>Menu management</h3>
 
-<#-- Menu Ontology properties -->
+<#assign hasElement = propertyGroups.pullProperty("${namespaces.display}hasElement")>
-<#include "individual-menu-properties.ftl">
 
+<#-- List the menu items -->
+<#list hasElement.statements as statement>
+    Position | <#include "${hasElement.template}"> | <@p.editingLinks "hasElement" statement editable /> <br />
+</#list>
+
+<br /> <#-- remove this once styles are applied -->
+
+<#-- Link to add a new menu item -->
+<#if editable>
+    <#assign addUrl = hasElement.addUrl>
+    <#if addUrl?has_content>
+        <a class="add-hasElement green button" href="${addUrl}" title="Add new menu item">Add menu item</a>
+    </#if>
+</#if>
+
+<#-- Remove unneeded scripts and stylesheets -->
 ${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/individual/individual.css" />',
                   '<link rel="stylesheet" href="${urls.base}/css/individual/individual-vivo.css" />')}
 

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

@@ -1,24 +0,0 @@
-<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
-
-<#-- Template for menu management page -->
-
-<#import "lib-properties.ftl" as p>
-
-<#list propertyGroups.all as group>
-    <#assign groupName = group.getName(nameForOtherGroup)>
-    
-        <#-- Display the group heading --> 
-        <#if groupName?has_content>
-            <h2 id="${groupName}">${groupName?capitalize}</h2>
-        </#if>
-        
-        <#-- List the menu items(properties) in the group -->
-        <#list group.properties as property>
-            <#if property.localName == "hasElement">
-                <#-- List menu Items -->
-                <@p.objectProperty property editable property.template />
-                <br /><#--remove break-->
-                <@p.addLink property editable />             
-            </#if>
-        </#list>
-</#list>

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

@@ -75,11 +75,7 @@ Assumes property is non-null. -->
 
 <#macro objectPropertyList property editable statements=property.statements template=property.template>
     <#list statements as statement>
-     <#if property.localName == "hasElement">
-        <@menuItem property statement editable><#include "${template}"></@menuItem>
-     <#else>
         <@propertyListItem property statement editable><#include "${template}"></@propertyListItem>
-     </#if>
     </#list>
 </#macro>
 
@@ -96,16 +92,11 @@ name will be used as the label. -->
 
 <#macro addLink property editable label="${property.name}" extraParams="">
     <#if editable>
-    	<#--@dump var="property"/-->
         <#local url = property.addUrl>
         <#if url?has_content>
-            <#if property.localName == "hasElement">
-                <@showAddMenuItemLink property.localName label addParamsToEditUrl(url, extraParams) />
-            <#else>
             <@showAddLink property.localName label addParamsToEditUrl(url, extraParams) />
         </#if>
     </#if>
-    </#if>
 </#macro>
 
 <#function addParamsToEditUrl url extraParams="">
@@ -249,12 +240,3 @@ name will be used as the label. -->
     <@editingLinks "label" label editable />
 </#macro>
 
-<#-- Add menu item button  -->
-<#macro showAddMenuItemLink propertyLocalName label url>
-    <a class="add-${propertyLocalName} green button" href="${url}" title="Add new ${label?lower_case} entry">Add menu item</a>
-</#macro>
-
-<#-- List menu items -->
-<#macro menuItem property statement editable >
-        Position | <#nested> | <@editingLinks "${property.localName}" statement editable/> <br />
-</#macro>

webapp/web/themes/vitro/css/vitroTheme.css

@@ -422,6 +422,7 @@ ul#header-nav li.last {
     border-right: none;
 }
 ul#header-nav li:last-child {
+    padding-left: 1px;
     padding-right: 0;
     border-right: none;
 }
@@ -437,6 +438,9 @@ ul#header-nav  a:active {
     text-decoration: none;
     color: #999;
 }
+ul#header-nav a.log-out {
+    padding-left: 10px;
+}
 /* SEARCH ------>  */
 #search {
     position: absolute;
@@ -1319,7 +1323,7 @@ p.view-all-coauthors {
 }
 section.property-group h2 {
     font-size: 1.25em;
-    color: #47B6D0;
+    color: #006279;
     font-weight: normal;
 }
 article.property {
@@ -1328,7 +1332,7 @@ article.property {
 article.property h3 {
     background: #fafaf9;
     font-size: 1.063em;
-    color: #8aa149;
+    color: #a8833e;
 }
 article.property ul.property-list li.subclass h3 {
     font-size: 1.063em;

webapp/web/themes/vitro/templates/footer.ftl

@@ -25,6 +25,7 @@
             <#if urls.contact??>
                 <li role="listitem"><a href="${urls.contact}">Contact Us</a></li>
             </#if> 
+            <li role="listitem"><a href="http://www.vivoweb.org/support" target="blank">Support</a></li>
         </ul>
     </nav>
 </footer>

webapp/web/themes/vitro/templates/identity.ftl

@@ -9,23 +9,29 @@
 
     <nav role="navigation">
         <ul id="header-nav" role="list">
+            <li role="listitem"><a href="${urls.index}">Index</a></li>
             <#if user.loggedIn>
-                <li role="listitem"><img class="middle" src="${urls.images}/userIcon.png" alt="user icon" />${user.loginName}</li>
-                <li role="listitem"><a href="${urls.logout}">Log out</a></li>
                 <#if user.hasSiteAdminAccess>
                     <li role="listitem"><a href="${urls.siteAdmin}">Site Admin</a></li>
                 </#if>
-            <#else>
+                    <li>
-                <li role="listitem"><a title="log in to manage this site" href="${urls.login}">Log in</a></li>
+                        <ul class="dropdown">
-            </#if>
+                            <li id="user-menu"><a href="#">${user.loginName}</a>
-            <#-- List of links that appear in submenus, like the header and footer. -->
+                                <ul class="sub_menu">
-                <li role="listitem"><a href="${urls.about}">About</a></li>
+                                     <li role="listitem"><a href="${urls.myAccount}">My account</a></li>
-            <#if urls.contact??>
+                                     <li role="listitem"><a href="${urls.logout}">Log out</a></li>
-                <li role="listitem"><a href="${urls.contact}">Contact Us</a></li>
-            </#if>
-                <li role="listitem"><a href="http://www.vivoweb.org/support" target="blank">Support</a></li>
-                <li role="listitem"><a href="${urls.index}">Index</a></li>
                                 </ul>
+                            </li>
+                         </ul>
+                     </li>
+                
+                ${scripts.add('<script type="text/javascript" src="${urls.base}/js/userMenu/userMenuUtils.js"></script>')}
+                
+            <#else>
+                <li role="listitem"><a class="log-out" title="log in to manage this site" href="${urls.login}">Log in</a></li>
+            </#if>
+        </ul>
+        
     </nav>
     
     <section id="search" role="region">