Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop

webapp/rdf/auth/everytime/permission_config.n3

@@ -25,12 +25,12 @@ auth:ADMIN
     auth:hasPermission simplePermission:UseAdvancedDataToolsPages ;
     auth:hasPermission simplePermission:UseMiscellaneousAdminPages ;
     auth:hasPermission simplePermission:UseSparqlQueryPage ;
-   	auth:hasPermission simplePermission:PageViewableAdmin ;  
+    auth:hasPermission simplePermission:PageViewableAdmin ;  
    	
-		# Uncomment the following permission line to enable the SPARQL update API. 
+    # Uncomment the following permission line to enable the SPARQL update API. 
-		# Before enabling, be sure that the URL api/sparqlUpdate is secured by SSH, 
+    # Before enabling, be sure that the URL api/sparqlUpdate is secured by HTTPS, 
-		# so passwords will not be sent in clear text.   	  
+    # so passwords will not be sent in clear text.   	  
-#  	auth:hasPermission simplePermission:UseSparqlUpdateApi ;    
+    #auth:hasPermission simplePermission:UseSparqlUpdateApi ;    
     
     # permissions for CURATOR and above.
     auth:hasPermission simplePermission:EditOntology ;

webapp/rdf/display/everytime/vitroSearchProhibited.n3

@@ -0,0 +1,25 @@
+# $This file is distributed under the terms of the license in /doc/license.txt$ 
+
+# All instances of a class can be excluded from the search index by adding a 
+# vitroDisplay:excludeClass property between vitroDisplay:SearchIndex and the 
+# URI of the class that you would like to exclude.
+
+# .n3 or .rdf files can be created in this directory to configure the search 
+# exclusions.  Each file must be a valid file in the format specified by its 
+# extension. Each file will be loaded individually and must be a complete 
+# stand alone example of its format.  Each file must contain all the necessary 
+# prefixes, namespaces and preambles required by the format specified by its 
+# extension.  
+
+# If you would like to add classes to the exclusions, add a file to this 
+# directory ending in .n3 with N3 statements similar to this example.
+
+#
+# @prefix owl: <http://www.w3.org/2002/07/owl#> .
+# @prefix vitroDisplay: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> .
+# @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+# @prefix example: <http://example/ns/> .
+#
+# vitroDisplay:SearchIndex 
+#    rdf:type owl:Thing ; 
+#    vitroDisplay:excludeClass example:classToExclude ;

webapp/src/edu/cornell/mannlib/vitro/webapp/migration/Release18Migrator.java

@@ -16,6 +16,7 @@ public class Release18Migrator implements ServletContextListener {
 		ServletContext ctx = sce.getServletContext();
 
 		new FauxPropertiesUpdater(ctx, this).migrate();
+		new RemoveObsoleteMetadataGraphs(ctx, this).migrate();
 	}
 
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/migration/RemoveObsoleteMetadataGraphs.java

@@ -0,0 +1,67 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.migration;
+
+import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService.CONFIGURATION;
+import static edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService.CONTENT;
+
+import javax.servlet.ServletContext;
+import javax.servlet.ServletContextListener;
+
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena;
+import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
+
+/**
+ * The graphs http://vitro.mannlib.cornell.edu/ns/vitro/sdb/metadata were used
+ * in Content models through release 1.7 and in Configuration models in release
+ * 1.7
+ * 
+ * In release 1.8, they area no longer used, and produce annoying warning
+ * messages.
+ */
+public class RemoveObsoleteMetadataGraphs {
+	private static final String OBSOLETE_METADATA_MODEL = "http://vitro.mannlib.cornell.edu/ns/vitro/sdb/metadata";
+
+	private final ServletContext ctx;
+	private final ServletContextListener parent;
+
+	public RemoveObsoleteMetadataGraphs(ServletContext ctx,
+			ServletContextListener parent) {
+		this.ctx = ctx;
+		this.parent = parent;
+	}
+
+	public void migrate() {
+		StartupStatus ss = StartupStatus.getBean(ctx);
+		removeMetadataModel(ctx, ss, CONTENT);
+		removeMetadataModel(ctx, ss, CONFIGURATION);
+	}
+
+	/**
+	 * Ordinarily, RDFServiceJena will issue a warning when a single triple is
+	 * removed from a blank node. In this case, however, that's exactly what we
+	 * want, so stifle those warnings while we remove these models.
+	 */
+	private void removeMetadataModel(ServletContext ctx, StartupStatus ss,
+			WhichService which) {
+		Logger rdfServiceLogger = Logger.getLogger(RDFServiceJena.class);
+		Level rdfServiceLogLevel = rdfServiceLogger.getLevel();
+
+		rdfServiceLogger.setLevel(Level.ERROR);
+		try {
+			ModelAccess.on(ctx).getModelMaker(which)
+					.removeModel(OBSOLETE_METADATA_MODEL);
+		} catch (Exception e) {
+			ss.warning(parent, "Failed to remove '" + OBSOLETE_METADATA_MODEL
+					+ "' from " + which, e);
+		} finally {
+			rdfServiceLogger.setLevel(rdfServiceLogLevel);
+		}
+	}
+
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/searchindex/SearchIndexerImpl.java

@@ -374,7 +374,7 @@ public class SearchIndexerImpl implements SearchIndexer {
 		private final TaskQueue taskQueue;
 		private final List<Task> deferredQueue;
 		private volatile boolean started;
-		private volatile boolean paused = true;
+		private volatile boolean paused;
 
 		public Scheduler(TaskQueue taskQueue) {
 			this.taskQueue = taskQueue;

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

@@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -139,39 +140,31 @@ public class CollatedObjectPropertyTemplateModel extends
 		// others will be removed
 		List<Map<String, String>> filteredList = new ArrayList<Map<String, String>>();
 		Set<String> processedObjects = new HashSet<String>();
-		//Useful to keep track of objects where statement data may not match the most specific type
-		//returne for some reason, in which case useful to keep track
-		Set<String> filteredObjects = new HashSet<String>();
 		for (Map<String, String> outerMap : statementData) {
 
 			String objectUri = outerMap.get(objectVariableName);
+
 			if (processedObjects.contains(objectUri)) {
 				continue;
 			}
 			processedObjects.add(objectUri);
-			//Get most specific type for this particular
+			List<Map<String, String>> dataForThisObject = new ArrayList<Map<String, String>>();
-			List<String> mostSpecificTypes = this.getSortedMostSpecificType(objectUri);
+			//Retrieve the statements that are related to this specific object
-			//If more than one most specific type, will compare against both of them
-			//and if the first one matches, the object will be placed under that
-			//otherwise subclass will be checked against the other
 			for (Map<String, String> innerMap : statementData) {
-				//Check both the object uri and that the subclass returned matches
+				if (innerMap.get(objectVariableName).equals(objectUri)) {
-				//the most specific type
+					// Subclass should at this point contain the most specific
-				if (innerMap.get(objectVariableName) == objectUri) {
+					// type already
-					//At this point, the statement data will already have the most specific type
+					dataForThisObject.add(innerMap);
-					//represented
-					String subclass = innerMap.get(SUBCLASS_VARIABLE_NAME);
-					if(mostSpecificTypes.contains(subclass)) {
-						filteredList.add(innerMap);
-						filteredObjects.add(objectUri);
-					} else {
-						if(log.isDebugEnabled()) {
-							log.debug("Iterating through statement data, Subclass does not match most specific type for Object URI - " + objectUri + " - subclass:" + subclass + " - most specific types=" + mostSpecificTypes.toString());
-						}
-					}
 				}
 			}
-		
+			
+			if(log.isDebugEnabled()) {
+				log.debug("Object URI " + objectUri + " has number of statements = " + dataForThisObject.size());
+			}
+			//Subclass variable should already reflect most specifick types but there may be more than one most specific type
+			Collections.sort(dataForThisObject, new DataComparatorBySubclass());
+			filteredList.add(dataForThisObject.get(0));
+
 		}
 
 		statementData.retainAll(filteredList);
@@ -179,33 +172,25 @@ public class CollatedObjectPropertyTemplateModel extends
 		if (log.isDebugEnabled()) {
 			log.debug("Data after subclass filtering");
 			logData(statementData);
-			//check and see if filteredObjects and processedObjects not the same size
-			if(filteredObjects.size() < processedObjects.size()) {
-				log.debug("Certain objects not included in statements displayed for collated subclasses");
-				processedObjects.removeAll(filteredObjects);
-				log.debug("These object uris not represented" + processedObjects.toString());
-			}
 		}
 	}
-	
+
-	//Get the most specific type
+	//Subclass variable should already contain most specific type
-	//An alternative would be to ensure that the default form, or any form that utilizes collation
+	//If there is more than one most specific type, then order alphabetically
-	//will return most specific type within the listview select/construct queries so the resulting
+	private class DataComparatorBySubclass implements
-	//statement data has that value
+			Comparator<Map<String, String>> {
-	List<String> getMostSpecificTypesForObject(String objectURI) {
+
-		WebappDaoFactory wadf = ModelAccess.on(vreq).getWebappDaoFactory();
+		@Override
-		return wadf.getIndividualDao().getIndividualByURI(objectURI).getMostSpecificTypeURIs();
+		public int compare(Map<String, String> map1, Map<String, String> map2) {
+
+			String subclass1 = map1.get(SUBCLASS_VARIABLE_NAME);
+			String subclass2 = map2.get(SUBCLASS_VARIABLE_NAME);
+
+			return subclass1.compareTo(subclass2);
+
+		}
 	}
 
-	//This will return a single most specific type for an object
-	//If there are multiple most specific types, the list will be sorted alphabetically and
-	//the first one will be returned
-	List<String> getSortedMostSpecificType(String objectURI) {
-		List<String> mostSpecificTypeURIs = this.getMostSpecificTypesForObject(objectURI);
-		Collections.sort(mostSpecificTypeURIs);
-		return mostSpecificTypeURIs;
-	}
-	
 	
 
 	// Collate the statements by subclass.

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

@@ -65,6 +65,7 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
     private String objectKey;   
     private String queryString;
     private Set<String> constructQueries;
+    private int displayLimit;
     
     DataPropertyTemplateModel(DataProperty dp, Individual subject, VitroRequest vreq, 
             boolean editing, List<DataProperty> populatedDataPropertyList) {
@@ -82,7 +83,7 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
         constructQueries = getConstructQueries();
 
         statements = new ArrayList<DataPropertyStatementTemplateModel>();
-        
+		displayLimit = dp.getDisplayLimit();
         // If the property is populated, get the data property statements via a sparql query
         if (populatedDataPropertyList.contains(dp)) {
             log.debug("Getting data for populated data property " + getUri());
@@ -108,14 +109,22 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
             return;
         }
         
-        // If the display limit has already been reached, we can't add a new statement.
+/*       If the display limit has already been reached, we can't add a new statement.
-        // NB This appears to be a misuse of a value called "display limit". Note that it's 
+         NB This appears to be a misuse of a value called "display limit". Note that it's 
-        // not used to limit display, either, so should be renamed.
+         not used to limit display, either, so should be renamed.
         int displayLimit = dp.getDisplayLimit();
-        // Display limit of -1 (default value for new property) means no display limit
+         Display limit of -1 (default value for new property) means no display limit
         if ( displayLimit >= 0 && statements.size() >= displayLimit ) {
             return;
         }
+*/
+		// Rewriting the above per jc55. If the data property is functional, there should only
+		// be 1 statement. The Display Limit is for determining how many statements to display
+		// before a "more..." link is used to hide statements exceeding the display limit. tlw72
+		boolean functional = dp.getFunctional();
+		if ( functional && statements.size() >= 1 ) {
+			return;
+		}
           
         // Determine whether a new statement can be added
 		RequestedAction action = new AddDataPropertyStatement(
@@ -146,6 +155,11 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
     protected Route getPropertyEditRoute() {
         return Route.DATA_PROPERTY_EDIT;
     }
+
+	@Override
+	public int getDisplayLimit() {
+			return displayLimit;
+	}	
     
     public ConfigError checkQuery(String queryString) {
         if (StringUtils.isBlank(queryString)) {
@@ -191,6 +205,7 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
     public String getTemplate() {
         return getTemplateName();
     }
+
     
     /* Template methods */
     

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

@@ -41,6 +41,7 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
     
     private String name;
     private FauxProperty fauxProperty;
+    private int displayLimit;
        
     PropertyTemplateModel(Property property, Individual subject, VitroRequest vreq, String name) {
         this.vreq = vreq;
@@ -49,11 +50,13 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
         propertyUri = property.getURI();
         localName = property.getLocalName();
         this.name = name;
+		this.displayLimit = displayLimit;
         addUrl = "";
         
         fauxProperty = isFauxProperty(property);
         if (fauxProperty != null) {
         	this.name = fauxProperty.getDisplayName();
+			this.displayLimit = fauxProperty.getDisplayLimit();
         } 
 
         setVerboseDisplayValues(property);
@@ -142,6 +145,10 @@ public abstract class PropertyTemplateModel extends BaseTemplateModel {
         return name;
     }
 
+    public int getDisplayLimit() {
+        return displayLimit;
+    }
+
     public String getLocalName() {
         return localName;
     }

webapp/web/WEB-INF/ontologies/search/vitroSearchProhibited.n3

@@ -1,27 +0,0 @@
-# $This file is distributed under the terms of the license in /doc/license.txt$ 
-
-# All instances of a class can be excluded from the search index
-# by adding a vitroDisplay:excludeClass property between 
-# vitroDisplay:SearchIndex and the URI of the class 
-# that you would like to exclude.
-
-# All .n3 or .rdf files in this directory will be used to configure 
-# the search exclusions.  Each file must be a valid file in the format
-# specified by its extension. Each file will be loaded individually and
-# must be a complete stand alone example of its format.  Each file must contain all
-# the necessary prefixes, namespaces and preambles required by the format
-# specified by its extension.  
-
-# If you would like to add classes to the
-# exclusions, add a file to this directory ending in .n3 with
-# N3 statements similar to this example.
-
-#
-# @prefix owl: <http://www.w3.org/2002/07/owl#> .
-# @prefix vitroDisplay: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> .
-# @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-# @prefix example: <http://example/ns/> .
-#
-# vitroDisplay:SearchIndex 
-#    rdf:type owl:Thing ; 
-#    vitroDisplay:excludeClass example:classToExclude ;

webapp/web/css/individual/individual-property-groups.css

@@ -67,4 +67,7 @@ li.selectedGroupTab {
 }
 li.groupTabSpacer {
     float:left;border-bottom: 1px solid #DFE6E5;background-color:#fff;width:3px;height:37px
+}
+div.additionalItems {
+	margin-top: 0 !important;
 }

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

@@ -25,7 +25,7 @@
     <section class="account-feedback">
         <p>
             ${strings.updated_account_1}
-            <a href="${updatedUserAccount.editUrl}" title="${strings.updated_account_title}}">${updatedUserAccount.firstName} ${updatedUserAccount.lastName}</a>
+            <a href="${updatedUserAccount.editUrl}" title="${strings.updated_account_title}">${updatedUserAccount.firstName} ${updatedUserAccount.lastName}</a>
             ${strings.updated_account_2}
             <#if emailWasSent?? >${strings.updated_account_notification(updatedUserAccount.emailAddress)}</#if>
         </p>
@@ -186,4 +186,4 @@
 </script>
 
 ${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/account/account.css" />')}
-${scripts.add('<script type="text/javascript" src="${urls.base}/js/account/accountUtils.js"></script>')}
+${scripts.add('<script type="text/javascript" src="${urls.base}/js/account/accountUtils.js"></script>')}

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

@@ -1,4 +1,6 @@
 <#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+<#import "lib-microformats.ftl" as mf>
+
 <#--Number of labels present-->
 <#if !labelCount??>
     <#assign labelCount = 0 >
@@ -14,7 +16,7 @@
 
 <#-- Default individual profile page template -->
 <#--@dumpAll /-->
-<section id="individual-intro" class="vcard" role="region">
+<section id="individual-intro" class="vcard" role="region" <@mf.sectionSchema individual/>>
     <section id="share-contact" role="region">
         <#-- Image -->
         <#assign individualImage>
@@ -39,7 +41,7 @@
                 <h2>${relatedSubject.relatingPredicateDomainPublic} for ${relatedSubject.name}</h2>
                 <p><a href="${relatedSubject.url}" title="${i18n().return_to(relatedSubject.name)}">&larr; ${i18n().return_to(relatedSubject.name)}</a></p>                
             <#else>                
-                <h1 class="fn">
+                <h1 class="fn" itemprop="name">
                     <#-- Label -->
                     <@p.label individual editable labelCount localesCount languageCount/>
 

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

@@ -42,7 +42,11 @@
                     <h3 id="${property.localName}">${property.name} <@p.addLink property editable /> <@p.verboseDisplay property /> </h3>
                 </#if>
                 <#-- List the statements for each property -->
-                <ul class="property-list" role="list" id="${property.localName}-${rangeClass}-List">
+					<#assign limit = property.getDisplayLimit()!5 />
+					<#if limit == -1 || limit == 0 >
+						<#assign limit = 5 />
+					</#if>
+                <ul class="property-list" role="list" id="${property.localName}-${rangeClass}-List" displayLimit="${limit}">
                     <#-- data property -->
                     <#if property.type == "data">
                         <@p.dataPropertyList property editable />

webapp/web/templates/freemarker/body/partials/shortview/view-browse-default.ftl

@@ -9,11 +9,11 @@
 <#if (individual.thumbUrl)??>
     <img src="${individual.thumbUrl}" width="90" alt="${individual.name}" />
     <h1 class="thumb">
-        <a href="${individual.profileUrl}" title="${i18n().view_profile_page_for} ${individual.name}}">${individual.name}</a>
+        <a href="${individual.profileUrl}" title="${i18n().view_profile_page_for} ${individual.name}">${individual.name}</a>
     </h1>
 <#else>
     <h1>
-        <a href="${individual.profileUrl}" title="${i18n().view_profile_page_for} ${individual.name}}">${individual.name}</a>
+        <a href="${individual.profileUrl}" title="${i18n().view_profile_page_for} ${individual.name}">${individual.name}</a>
     </h1>
 </#if>
 

webapp/web/templates/freemarker/lib/lib-microformats.ftl

@@ -0,0 +1,5 @@
+<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<#macro sectionSchema individual>
+	<#-- Placeholder macro only. Will generate errors if this file is removed from the Vitro source. -->
+</#macro>