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

webapp/rdf/auth/everytime/permission_config.n3

@@ -28,9 +28,9 @@ auth:ADMIN
     auth:hasPermission simplePermission:PageViewableAdmin ;  
    	
     # 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.   	  
-#  	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/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;
@@ -139,38 +140,30 @@ 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());
+				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));
 
 		}
 
@@ -179,31 +172,23 @@ 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();
-		return wadf.getIndividualDao().getIndividualByURI(objectURI).getMostSpecificTypeURIs();
-	}
 
-	//This will return a single most specific type for an object
+		@Override
-	//If there are multiple most specific types, the list will be sorted alphabetically and
+		public int compare(Map<String, String> map1, Map<String, String> map2) {
-	//the first one will be returned
+
-	List<String> getSortedMostSpecificType(String objectURI) {
+			String subclass1 = map1.get(SUBCLASS_VARIABLE_NAME);
-		List<String> mostSpecificTypeURIs = this.getMostSpecificTypesForObject(objectURI);
+			String subclass2 = map2.get(SUBCLASS_VARIABLE_NAME);
-		Collections.sort(mostSpecificTypeURIs);
+
-		return mostSpecificTypeURIs;
+			return subclass1.compareTo(subclass2);
+
+		}
 	}
 
 	

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/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>

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>