From e51da9ac4e4a6c078923eceb3ab2aa0f60f61c51 Mon Sep 17 00:00:00 2001
From: Ted Lawless <lawlesst@gmail.com>
Date: Thu, 8 Jan 2015 08:11:41 -0500
Subject: [PATCH 1/4] SPARQL update API comments in permission_config.n3

Change security update comment from SSH to HTTPs.  Adjust formatting to match rest of file.
---
 webapp/rdf/auth/everytime/permission_config.n3 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/webapp/rdf/auth/everytime/permission_config.n3 b/webapp/rdf/auth/everytime/permission_config.n3
index f4d4b0665..172c55ca8 100644
--- a/webapp/rdf/auth/everytime/permission_config.n3
+++ b/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. 
-		# Before enabling, be sure that the URL api/sparqlUpdate is secured by SSH, 
-		# so passwords will not be sent in clear text.   	  
-#  	auth:hasPermission simplePermission:UseSparqlUpdateApi ;    
+    # Uncomment the following permission line to enable the SPARQL update API. 
+    # 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 ;    
     
     # permissions for CURATOR and above.
     auth:hasPermission simplePermission:EditOntology ;

From 76668990c435da83d2ae92085a362f52c250a06e Mon Sep 17 00:00:00 2001
From: Nate Prewitt <Nate.Prewitt@Colorado.edu>
Date: Tue, 10 Feb 2015 12:10:28 -0700
Subject: [PATCH 2/4] removed extra } from title attributes in vitro templates

---
 .../templates/freemarker/body/accounts/userAccounts-list.ftl  | 4 ++--
 .../body/partials/shortview/view-browse-default.ftl           | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/webapp/web/templates/freemarker/body/accounts/userAccounts-list.ftl b/webapp/web/templates/freemarker/body/accounts/userAccounts-list.ftl
index f76707992..ee9a542c9 100644
--- a/webapp/web/templates/freemarker/body/accounts/userAccounts-list.ftl
+++ b/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>')}
\ No newline at end of file
+${scripts.add('<script type="text/javascript" src="${urls.base}/js/account/accountUtils.js"></script>')}
diff --git a/webapp/web/templates/freemarker/body/partials/shortview/view-browse-default.ftl b/webapp/web/templates/freemarker/body/partials/shortview/view-browse-default.ftl
index bf0e84143..c0fab916b 100644
--- a/webapp/web/templates/freemarker/body/partials/shortview/view-browse-default.ftl
+++ b/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>
 

From f9361f4cd6f0646c194bf58230c77576b9209edd Mon Sep 17 00:00:00 2001
From: hudajkhan <hjk54@cornell.edu>
Date: Tue, 10 Feb 2015 14:23:50 -0500
Subject: [PATCH 3/4] VIVO-957 updating to utilize subclass variable which is
 now most specific type

---
 .../CollatedObjectPropertyTemplateModel.java  | 77 ++++++++-----------
 1 file changed, 31 insertions(+), 46 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/CollatedObjectPropertyTemplateModel.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/CollatedObjectPropertyTemplateModel.java
index e3ba1e473..7a074acb9 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/CollatedObjectPropertyTemplateModel.java
+++ b/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<String> mostSpecificTypes = this.getSortedMostSpecificType(objectUri);
-			//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
+			List<Map<String, String>> dataForThisObject = new ArrayList<Map<String, String>>();
+			//Retrieve the statements that are related to this specific object
 			for (Map<String, String> innerMap : statementData) {
-				//Check both the object uri and that the subclass returned matches
-				//the most specific type
-				if (innerMap.get(objectVariableName) == objectUri) {
-					//At this point, the statement data will already have the most specific type
-					//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 (innerMap.get(objectVariableName).equals(objectUri)) {
+					// Subclass should at this point contain the most specific
+					// type already
+					dataForThisObject.add(innerMap);
 				}
 			}
-		
+			
+			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
-	//An alternative would be to ensure that the default form, or any form that utilizes collation
-	//will return most specific type within the listview select/construct queries so the resulting
-	//statement data has that value
-	List<String> getMostSpecificTypesForObject(String objectURI) {
-		WebappDaoFactory wadf = ModelAccess.on(vreq).getWebappDaoFactory();
-		return wadf.getIndividualDao().getIndividualByURI(objectURI).getMostSpecificTypeURIs();
+
+	//Subclass variable should already contain most specific type
+	//If there is more than one most specific type, then order alphabetically
+	private class DataComparatorBySubclass implements
+			Comparator<Map<String, String>> {
+
+		@Override
+		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.

From 9cf0233d8122c56434aeb4c797b145ca3ab44bc9 Mon Sep 17 00:00:00 2001
From: Jim Blake <jeb228@cornell.edu>
Date: Tue, 10 Feb 2015 15:23:42 -0500
Subject: [PATCH 4/4] VIVO-845 move vitroSearchProhibited.n3 to
 rdf/display/everytime

---
 .../everytime/vitroSearchProhibited.n3        | 25 +++++++++++++++++
 .../search/vitroSearchProhibited.n3           | 27 -------------------
 2 files changed, 25 insertions(+), 27 deletions(-)
 create mode 100644 webapp/rdf/display/everytime/vitroSearchProhibited.n3
 delete mode 100644 webapp/web/WEB-INF/ontologies/search/vitroSearchProhibited.n3

diff --git a/webapp/rdf/display/everytime/vitroSearchProhibited.n3 b/webapp/rdf/display/everytime/vitroSearchProhibited.n3
new file mode 100644
index 000000000..7110c0fbc
--- /dev/null
+++ b/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 ;
\ No newline at end of file
diff --git a/webapp/web/WEB-INF/ontologies/search/vitroSearchProhibited.n3 b/webapp/web/WEB-INF/ontologies/search/vitroSearchProhibited.n3
deleted file mode 100644
index ba3ed6838..000000000
--- a/webapp/web/WEB-INF/ontologies/search/vitroSearchProhibited.n3
+++ /dev/null
@@ -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 ;
\ No newline at end of file