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

.gitignore

@@ -9,4 +9,3 @@
 /ontology/public/catalog-v0001.xml
 
 rdf/auth/firsttime/test-user-model.owl
-utilities/rdbmigration/.work

build.xml

@@ -134,14 +134,4 @@
 		</sync>
 	</target>
 	
-	<!-- ================================= 
-          target: migrateConfigurationModels              
-         ================================= -->
-    <target name="migrateConfigurationModels" description="description">
-    	<dirname property="nihvivobase.dir" file="${ant.file.nihvivo}" />
-    	<property name="rdbmigration.dir" location="${nihvivobase.dir}/utilities/rdbmigration" />
-        <ant dir="${rdbmigration.dir}" target="all"></ant>
-    </target>
-
-
 </project>

doc/README.txt

@@ -8,12 +8,12 @@ find these files in this directory:
               Instructions for installing VIVO on your machine, including 
               a simple installation and several options.
 
-    Upgrade Instructions for VIVO release 1.6.pdf
+    Upgrade Instructions for VIVO release 1.7.pdf
               Instructions for migrating a VIVO installation from release
-              1.5 to release 1.6
+              1.6 to release 1.7
               
 If these files are not present, or to obtain the latest version of the 
 instructions, go to:
     
-    https://wiki.duraspace.org/display/VIVO/VIVO+Documentation
+    https://wiki.duraspace.org/display/VIVO/
               

productMods/config/listViewConfig-informationResourceInAuthorship.xml

@@ -12,7 +12,7 @@
         PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>
         PREFIX vcard:  <http://www.w3.org/2006/vcard/ns#>
                 
-        SELECT DISTINCT <collated> ?subclass </collated>
+        SELECT DISTINCT ?subclass
                         ?authorship
                         ?author ?authorName 
         WHERE {
@@ -21,13 +21,12 @@
                 OPTIONAL { ?authorship core:relates ?author .
                            ?author a foaf:Agent .                      
                            ?author rdfs:label ?authorName 
-                <collated> 
+                
                 OPTIONAL { ?authorship core:relates ?author .
                            ?author a foaf:Agent .  
                            ?author vitro:mostSpecificType ?subclass .
                            ?subclass rdfs:subClassOf foaf:Agent 
                 } 
-                </collated>
                 }
                 OPTIONAL { ?authorship core:relates ?author .
                            ?author a vcard:Kind .                      
@@ -39,13 +38,12 @@
 				           bind ( COALESCE(?middleName, "") As ?middleName1) .
 				           bind ( COALESCE(?lastName, "") As ?lastName1) .
 				           bind (concat(str(?lastName1 + ", "),str(?middleName1 + " "),str(?firstName1)) as ?authorName) .
-                <collated> 
+                 
                 OPTIONAL { ?authorship core:relates ?author .
                            ?author a vcard:Kind .  
                            ?author vitro:mostSpecificType ?subclass .
                            ?subclass rdfs:subClassOf vcard:Kind 
                 } 
-                </collated>
             }
             <critical-data-required>
             FILTER ( bound(?author) )

productMods/config/listViewConfig-scopusId.xml

@@ -14,7 +14,7 @@
                 ?subject ?property ?value
                 FILTER isLiteral(?value) 
             
-        } ORDER BY ?object
+        } ORDER BY ?value
     </query-select>
 
     <query-construct>

productMods/templates/freemarker/body/partials/individual/propStatement-hasRole.ftl

@@ -17,8 +17,8 @@
     <span class="hideThis">&nbsp;</span>
     <script type="text/javascript" >
         $('span.hideThis').parent().parent().addClass("hideThis");
-        if ( $('h3#hasResearcherRole').attr('class').length == 0 ) {
+        if ( $('h3#RO_0000053-ResearcherRole').attr('class').length == 0 ) {
-            $('h3#hasResearcherRole').addClass('hiddenGrants');
+            $('h3#RO_0000053-ResearcherRole').addClass('hiddenGrants');
         }
         $('span.hideThis').parent().remove();
     </script>

productMods/templates/freemarker/body/partials/individual/propStatement-informationResourceInAuthorship.ftl

@@ -13,7 +13,11 @@
      next statement -->
 <#macro showAuthorship statement>
     <#if statement.author??>
-        <a href="${profileUrl(statement.uri("author"))}" title="${i18n().author_name}">${statement.authorName}</a>
+    	<#if statement.subclass?? && statement.subclass?contains("vcard")>
+        	${statement.authorName}
+    	<#else>
+        	<a href="${profileUrl(statement.uri("author"))}" title="${i18n().author_name}">${statement.authorName}</a>
+    	</#if>
     <#else>
         <#-- This shouldn't happen, but we must provide for it -->
         <a href="${profileUrl(statement.uri("authorship"))}" title="${i18n().missing_author}">${i18n().missing_author}</a>

productMods/templates/freemarker/edit/forms/js/addAuthorsToInformationResource.js

@@ -581,6 +581,10 @@ var addAuthorForm = {
             
             this.labelField.val(name);
         }
+		// If user selected org via autocomplete, clear the org name field
+		if ( this.orgUriField.val() != '' ) {
+			this.orgName.val("");
+		}
 
     },    
     
@@ -765,6 +769,7 @@ var addAuthorForm = {
 	    if ( authType == "org" ) {
 	        this.personSection.hide();
 	        this.orgSection.show();
+			this.orgNameWrapper.show();
 	        // person fields
             this.personRadio.attr('checked', false);  // needed for reset when cancel button is clicked
 	        this.acSelector.removeClass("acSelector");

productMods/templates/freemarker/edit/forms/js/manageHideShowStatus.js

@@ -1,6 +1,6 @@
 /* $This file is distributed under the terms of the license in /doc/license.txt$ */
 
-var manageGrants = {
+var manageHideShowStatus = {
 
     /* *** Initial page setup *** */
    
@@ -20,7 +20,7 @@ var manageGrants = {
     // Initial page setup. Called only at page load.
     initPage: function() {
 
-        this.initGrantData();
+        this.initItemData();
        
         this.bindEventListeners();
                        
@@ -29,28 +29,28 @@ var manageGrants = {
     // On page load, associate data with each list item. Then we don't
     // have to keep retrieving data from or modifying the DOM as we manipulate the
     // items.
-    initGrantData: function() {
+    initItemData: function() {
-        $('.grantCheckbox').each(function(index) {
+        $('.itemCheckbox').each(function(index) {
-            $(this).data(grantData[index]);  
+            $(this).data(itemData[index]);  
         });
     },
     
     bindEventListeners: function() {
 
-        $('.grantCheckbox').click(function() {
+        $('.itemCheckbox').click(function() {
-            manageGrants.processGrant(this);
+            manageHideShowStatus.processItem(this);
             //return false;
         });
                
     },
                       
-    processGrant: function(grant) {
+    processItem: function(item) {
         
         var add = "";
         var retract = "";
-        var n3String = "<" + $(grant).data('roleUri') + "> <http://vivoweb.org/ontology/core#hideFromDisplay> \"true\" ." ;
+        var n3String = "<" + $(item).data('relatedUri') + "> <http://vivoweb.org/ontology/core#hideFromDisplay> \"true\" ." ;
 
-        if ( $(grant).is(':checked') ) {
+        if ( $(item).is(':checked') ) {
             add = n3String;
         }
         else {
@@ -58,22 +58,22 @@ var manageGrants = {
         } 
         
         $.ajax({
-            url: manageGrants.processingUrl,
+            url: manageHideShowStatus.processingUrl,
             type: 'POST', 
             data: {
                 additions: add,
                 retractions: retract
             },
             dataType: 'json',
-            context: grant, // context for callback
+            context: item, // context for callback
             complete: function(request, status) {
             
                 if (status === 'success') {
-                    window.status = manageGrants.grantSuccessfullyExcluded; 
+                    window.status = manageHideShowStatus.itemSuccessfullyExcluded; 
 
                 } else {
-                    alert(manageGrants.errorExcludingGrant);
+                    alert(manageHideShowStatus.errorExcludingItem);
-                    $(grant).removeAttr('checked');
+                    $(item).removeAttr('checked');
                 }
             }
         });        
@@ -82,5 +82,5 @@ var manageGrants = {
 };
 
 $(document).ready(function() {   
-    manageGrants.onLoad();
+    manageHideShowStatus.onLoad();
 }); 

productMods/templates/freemarker/edit/forms/js/managePeopleForOrganization.js

@@ -1,86 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-var managePeople = {
-
-    /* *** Initial page setup *** */
-   
-    onLoad: function() {
-    
-            this.mixIn();               
-            this.initPage();       
-        },
-
-    mixIn: function() {
-
-        // Get the custom form data from the page
-        $.extend(this, customFormData);
-        $.extend(this, i18nStrings);
-    },
-
-    // Initial page setup. Called only at page load.
-    initPage: function() {
-
-        this.initPeopleData();
-       
-        this.bindEventListeners();
-                       
-    },
-
-    // On page load, associate data with each list item. Then we don't
-    // have to keep retrieving data from or modifying the DOM as we manipulate the
-    // items.
-    initPeopleData: function() {
-        $('.pubCheckbox').each(function(index) {
-            $(this).data(peopleData[index]);  
-        });
-    },
-    
-    bindEventListeners: function() {
-
-        $('.pubCheckbox').click(function() {
-            managePeople.processPeople(this);
-            //return false;
-        });
-               
-    },
-                      
-    processPeople: function(person) {
-        
-        var add = "";
-        var retract = "";
-        var n3String = "<" + $(person).data('positionUri') + "> <http://vivoweb.org/ontology/core#hideFromDisplay> \"true\" ." ;
-
-        if ( $(person).is(':checked') ) {
-            add = n3String;
-        }
-        else {
-            retract = n3String;
-        } 
-        
-        $.ajax({
-            url: managePeople.processingUrl,
-            type: 'POST', 
-            data: {
-                additions: add,
-                retractions: retract
-            },
-            dataType: 'json',
-            context: person, // context for callback
-            complete: function(request, status) {
-            
-                if (status === 'success') {
-                    window.status = managePeople.personSuccessfullyExcluded; 
-
-                } else {
-                    alert(managePeople.errorExcludingPerson);
-                    $(person).removeAttr('checked');
-                }
-            }
-        });        
-    },
-
-};
-
-$(document).ready(function() {   
-    managePeople.onLoad();
-}); 

productMods/templates/freemarker/edit/forms/js/managePublicationsForIndividual.js

@@ -1,86 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-var managePublications = {
-
-    /* *** Initial page setup *** */
-   
-    onLoad: function() {
-    
-            this.mixIn();               
-            this.initPage();       
-        },
-
-    mixIn: function() {
-
-        // Get the custom form data from the page
-        $.extend(this, customFormData);
-        $.extend(this, i18nStrings);
-    },
-
-    // Initial page setup. Called only at page load.
-    initPage: function() {
-
-        this.initPublicationData();
-       
-        this.bindEventListeners();
-                       
-    },
-
-    // On page load, associate data with each list item. Then we don't
-    // have to keep retrieving data from or modifying the DOM as we manipulate the
-    // items.
-    initPublicationData: function() {
-        $('.pubCheckbox').each(function(index) {
-            $(this).data(publicationData[index]);  
-        });
-    },
-    
-    bindEventListeners: function() {
-
-        $('.pubCheckbox').click(function() {
-            managePublications.processPublication(this);
-            //return false;
-        });
-               
-    },
-                      
-    processPublication: function(publication) {
-        
-        var add = "";
-        var retract = "";
-        var n3String = "<" + $(publication).data('authorshipUri') + "> <http://vivoweb.org/ontology/core#hideFromDisplay> \"true\" ." ;
-
-        if ( $(publication).is(':checked') ) {
-            add = n3String;
-        }
-        else {
-            retract = n3String;
-        } 
-        
-        $.ajax({
-            url: managePublications.processingUrl,
-            type: 'POST', 
-            data: {
-                additions: add,
-                retractions: retract
-            },
-            dataType: 'json',
-            context: publication, // context for callback
-            complete: function(request, status) {
-            
-                if (status === 'success') {
-                    window.status = managePublications.publicationSuccessfullyExcluded; 
-
-                } else {
-                    alert(managePublications.errorExcludingPublication);
-                    $(publication).removeAttr('checked');
-                }
-            }
-        });        
-    },
-
-};
-
-$(document).ready(function() {   
-    managePublications.onLoad();
-}); 

productMods/templates/freemarker/edit/forms/manageGrantsForIndividual.ftl

@@ -13,7 +13,7 @@
 <p style="margin-left:25px;margin-bottom:12px">
 ${i18n().check_grants_to_exclude}
 <script type="text/javascript">
-    var grantData = [];
+    var itemData = [];
 </script>
 </p>
 <@lvf.unsupportedBrowser urls.base /> 
@@ -25,11 +25,11 @@ ${i18n().check_grants_to_exclude}
         <ul >
             <#list grantList as grant>
             <li>
-                <input type="checkbox" class="grantCheckbox" <#if grant.hideThis??>checked</#if> />${grant.label!grant.activity!}
+                <input type="checkbox" class="itemCheckbox" <#if grant.hideThis??>checked</#if> />${grant.label!grant.activity!}
             </li>
             <script type="text/javascript">
-                grantData.push({
+                itemData.push({
-                    "roleUri": "${grant.role!}"              
+                    "relatedUri": "${grant.role!}"              
                 });
             </script>      
             
@@ -48,8 +48,8 @@ var customFormData = {
     processingUrl: '${urls.base}/edit/primitiveRdfEdit'
 };
 var i18nStrings = {
-    grantSuccessfullyExcluded: '${i18n().grant_successfully_excluded}',
+    itemSuccessfullyExcluded: '${i18n().grant_successfully_excluded}',
-    errorExcludingGrant: '${i18n().error_excluding_grant}'
+    errorExcludingItem: '${i18n().error_excluding_grant}'
 };
 </script>
 
@@ -59,5 +59,5 @@ ${stylesheets.add('<link rel="stylesheet" href="${urls.base}/templates/freemarke
 ${scripts.add('<script type="text/javascript" src="${urls.base}/js/utils.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/jquery-ui/js/jquery-ui-1.8.9.custom.min.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/customFormUtils.js"></script>',
-                '<script type="text/javascript" src="${urls.base}/templates/freemarker/edit/forms/js/manageGrantsForIndividual.js"></script>')}
+                '<script type="text/javascript" src="${urls.base}/templates/freemarker/edit/forms/js/manageHideShowStatus.js"></script>')}
               

productMods/templates/freemarker/edit/forms/managePeopleForOrganization.ftl

@@ -7,7 +7,7 @@
 <p style="margin-left:25px;margin-bottom:12px">
 ${i18n().check_people_to_exclude}
 <script type="text/javascript">
-    var peopleData = [];
+    var itemData = [];
 </script>
 </p>
 
@@ -21,11 +21,11 @@ ${i18n().check_people_to_exclude}
         <ul >
             <#list peeps as person>
             <li>
-                <input type="checkbox" class="pubCheckbox" <#if person.hideThis??>checked</#if> />${person.name}
+                <input type="checkbox" class="itemCheckbox" <#if person.hideThis??>checked</#if> />${person.name}
             </li>
             <script type="text/javascript">
-                peopleData.push({
+                itemData.push({
-                    "positionUri": "${person.position}"              
+                    "relatedUri": "${person.position}"              
                 });
             </script>      
             
@@ -44,8 +44,8 @@ var customFormData = {
     processingUrl: '${urls.base}/edit/primitiveRdfEdit'
 };
 var i18nStrings = {
-    personSuccessfullyExcluded: '${i18n().person_successfully_excluded}',
+    itemSuccessfullyExcluded: '${i18n().person_successfully_excluded}',
-    errorExcludingPerson: '${i18n().error_excluding_person}'
+    errorExcludingItem: '${i18n().error_excluding_person}'
 };
 </script>
 
@@ -55,5 +55,5 @@ ${stylesheets.add('<link rel="stylesheet" href="${urls.base}/templates/freemarke
 ${scripts.add('<script type="text/javascript" src="${urls.base}/js/utils.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/jquery-ui/js/jquery-ui-1.8.9.custom.min.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/customFormUtils.js"></script>',
-                '<script type="text/javascript" src="${urls.base}/templates/freemarker/edit/forms/js/managePeopleForOrganization.js"></script>')}
+                '<script type="text/javascript" src="${urls.base}/templates/freemarker/edit/forms/js/manageHideShowStatus.js"></script>')}
               

productMods/templates/freemarker/edit/forms/managePublicationsForIndividual.ftl

@@ -13,7 +13,7 @@
 <p style="margin-left:25px;margin-bottom:12px">
 ${i18n().check_pubs_to_exclude}
 <script type="text/javascript">
-    var publicationData = [];
+    var itemData = [];
 </script>
 </p>
 
@@ -37,12 +37,12 @@ ${i18n().check_pubs_to_exclude}
         <ul >
             <#list pubs as pub>
             <li>
-                <input type="checkbox" class="pubCheckbox" <#if pub.hideThis??>checked</#if> />
+                <input type="checkbox" class="itemCheckbox" <#if pub.hideThis??>checked</#if> />
                 <#if pub.title?has_content>${pub.title!}<#else>${i18n().title_not_found}</#if>
             </li>
             <script type="text/javascript">
-                publicationData.push({
+                itemData.push({
-                    "authorshipUri": "${pub.authorship}"              
+                    "relatedUri": "${pub.authorship}"              
                 });
             </script>      
             
@@ -61,8 +61,8 @@ var customFormData = {
     processingUrl: '${urls.base}/edit/primitiveRdfEdit'
 };
 var i18nStrings = {
-    publicationSuccessfullyExcluded: '${i18n().publication_successfully_excluded}',
+    itemSuccessfullyExcluded: '${i18n().publication_successfully_excluded}',
-    errorExcludingPublication: '${i18n().error_excluding_publication}'
+    errorExcludingItem: '${i18n().error_excluding_publication}'
 };
 </script>
 
@@ -72,5 +72,5 @@ ${stylesheets.add('<link rel="stylesheet" href="${urls.base}/templates/freemarke
 ${scripts.add('<script type="text/javascript" src="${urls.base}/js/utils.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/jquery-ui/js/jquery-ui-1.8.9.custom.min.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/customFormUtils.js"></script>',
-                '<script type="text/javascript" src="${urls.base}/templates/freemarker/edit/forms/js/managePublicationsForIndividual.js"></script>')}
+                '<script type="text/javascript" src="${urls.base}/templates/freemarker/edit/forms/js/manageHideShowStatus.js"></script>')}
               

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonBody.ftl

@@ -53,7 +53,7 @@
                     <div id="error-notification" class="ui-state-error" style="padding:10px; -moz-box-shadow:0 0 6px #980000; -webkit-box-shadow:0 0 6px #980000; box-shadow:0 0 6px #980000;">
                         <a class="ui-notify-close" href="#" title="${i18n().error_notification}"><span class="ui-icon ui-icon-close" style="float:right"></span></a>
                         <span style="float:left; margin:0 5px 0 0;" class="ui-icon ui-icon-alert"></span>
-                        <h1>&#035;{title}</h1>
+                        <h1>&#035;{title!}</h1>
                         <p>&#035;{text}</p>
                         <p style="text-align:center"><a class="ui-notify-close" href="#">${i18n().close_me}</a></p>
                     </div>
@@ -61,7 +61,7 @@
                     <div id="warning-notification" class="ui-state-highlight ui-corner-all" >
                     <a class="ui-notify-close ui-notify-cross" href="#" title="${i18n().error_notification}">x</a>
                     <span style="float: left; margin-right: 0.3em;" class="ui-icon ui-icon-info"></span>
-                        <h1>&#035;{title}</h1>
+                        <h1>&#035;{title!}</h1>
                         <p>&#035;{text}</p>
                     </div>
                 

productMods/templates/freemarker/visualization/mapOfScience/mapOfScienceStandalone.ftl

@@ -27,7 +27,7 @@ corresponding changes in the included Templates. -->
         <div id="error-notification" class="ui-state-error" style="padding:10px; -moz-box-shadow:0 0 6px #980000; -webkit-box-shadow:0 0 6px #980000; box-shadow:0 0 6px #980000;">
             <a class="ui-notify-close" href="#" title="${i18n().error_notification}"><span class="ui-icon ui-icon-close" style="float:right"></span></a>
             <span style="float:left; margin:0 5px 0 0;" class="ui-icon ui-icon-alert"></span>
-            <h1>&#035;{title}</h1>
+            <h1>&#035;{title!}</h1>
             <p>&#035;{text}</p>
             <p style="text-align:center"><a class="ui-notify-close" href="#">${i18n().close_me}</a></p>
         </div>
@@ -35,7 +35,7 @@ corresponding changes in the included Templates. -->
         <div id="warning-notification" class="ui-state-highlight ui-corner-all" >
 	        <a class="ui-notify-close ui-notify-cross" href="#" title="${i18n().error_notification}">x</a>
 	        <span style="float: left; margin-right: 0.3em;" class="ui-icon ui-icon-info"></span>
-	        <h1>&#035;{title}</h1>
+	        <h1>&#035;{title!}</h1>
 	        <p>&#035;{text}</p>
         </div>
     </div>

src/edu/cornell/mannlib/semservices/util/XMLUtils.java

@@ -28,21 +28,16 @@ import javax.xml.xpath.XPathConstants;
 import javax.xml.xpath.XPathExpressionException;
 import javax.xml.xpath.XPathFactory;
 
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.apache.xml.serialize.XMLSerializer;
 import org.w3c.dom.Document;
 import org.w3c.dom.DocumentType;
-import org.w3c.dom.Element;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
-import edu.cornell.mannlib.semservices.util.MetadataNamespaceContext;
-
 /**
  * Convenience Class to parse XML strings to DOM Document for XML contents
  * retrieval.
@@ -117,14 +112,16 @@ public class XMLUtils {
     * @param doc
     * @throws IOException
     */
+    @SuppressWarnings("deprecation")
    public static void serializeDoc(Document doc) throws IOException {
-       XMLSerializer serializer = new XMLSerializer();
+       org.apache.xml.serialize.XMLSerializer serializer = new org.apache.xml.serialize.XMLSerializer();
        serializer.setOutputByteStream(System.out);
        serializer.serialize(doc);
     }
 
+   @SuppressWarnings("deprecation")
    public static String serializeDoctoString(Document doc) throws IOException {
-      XMLSerializer serializer = new XMLSerializer();
+	   org.apache.xml.serialize.XMLSerializer serializer = new org.apache.xml.serialize.XMLSerializer();
       ByteArrayOutputStream bout = new ByteArrayOutputStream();
 
       serializer.setOutputByteStream(bout);

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

@@ -72,8 +72,11 @@ public class ManagePeopleForOrganizationController extends FreemarkerHttpServlet
         + "    OPTIONAL { ?position core:relates  ?person . " 
         + "               ?person a foaf:Person . \n"
         + "               ?person rdfs:label ?label } \n"
-        + "    OPTIONAL { ?position vitro:mostSpecificType ?subclass } \n"
+        + "    OPTIONAL { ?position vitro:mostSpecificType ?subclass . \n"
+        + "               OPTIONAL { ?subclass vitro:displayRankAnnot ?displayRank } \n"
+		+ "    } \n "
         + "    OPTIONAL { ?position core:hideFromDisplay ?hideThis } \n "
+        + "    FILTER ( ?displayRank < 500 )"
         + "} ORDER BY ?subclass ?name";    
        
     HashMap<String, List<Map<String,String>>>  getPeople(String subjectUri, VitroRequest vreq) {

themes/wilma/templates/gadgetDetails.ftl

@@ -2,7 +2,7 @@
 
 <#-- Template for the body of the GadgetDetails page -->
 
-<div class="pageTitle" id="gadgets-title"><h2>${title}</h2></div>
+<div class="pageTitle" id="gadgets-title"><h2>${title!}</h2></div>
 
 <#-- VIVO OpenSocial Extension by UCSF -->
 <#if openSocial??>

themes/wilma/templates/gadgetLogin.ftl

@@ -11,7 +11,7 @@ th {
 }
 </style>	
 
-<div class="pageTitle" id="gadgets-title"><h2>${title}</h2></div>
+<div class="pageTitle" id="gadgets-title"><h2>${title!}</h2></div>
 
 <#-- VIVO OpenSocial Extension by UCSF -->
 <#if openSocial??>

themes/wilma/templates/head.ftl

@@ -4,7 +4,7 @@
 <!-- Google Chrome Frame open source plug-in brings Google Chrome's open web technologies and speedy JavaScript engine to Internet Explorer-->
 <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
 
-<title>${title}</title>
+<title>${siteName!}</title>
 
 <#-- VIVO OpenSocial Extension by UCSF -->
 <#if openSocial??>

utilities/rdbmigration/build.xml

@@ -1,132 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
-
-<!-- ====================================================================== 
-     A tool to migrate RDB data into TDB.
-     ====================================================================== -->
-
-<project name="RDB-migration" default="describe">
-
-	<property name="working.dir" location=".work" />
-	<property name="src.dir" location="src" />
-	<property name="lib.dir" location="lib" />
-
-	<!-- ================================= 
-	      target: describe              
-	     ================================= -->
-	<target name="describe"
-	        description="--> Describe the targets (this is the default).">
-		<echo>
-	all - Compiles and runs the RDB migration tool.
-	    </echo>
-	</target>
-
-	<!-- ================================= 
-	      target: all              
-	     ================================= -->
-	<target name="all"
-	        depends="clean, run"
-	        description="Build from scratch and run the migration.">
-	</target>
-
-	<!-- - - - - - - - - - - - - - - - - - 
-          target: clean                      
-         - - - - - - - - - - - - - - - - - -->
-	<target name="clean">
-		<delete dir="${working.dir}" />
-	</target>
-
-	<!-- - - - - - - - - - - - - - - - - - 
-          target: setup                      
-         - - - - - - - - - - - - - - - - - -->
-	<target name="setup" depends="getBuildProperties, getRuntimeProperties">
-		<mkdir dir="${working.dir}" />
-	</target>
-
-	<!-- - - - - - - - - - - - - - - - - - 
-		  target: getBuildProperties                      
-		 - - - - - - - - - - - - - - - - - -->
-	<target name="getBuildProperties">
-		<property name="vivo.distribution.dir" location="../.." />
-		<property name="build.properties.file"
-		          location="${vivo.distribution.dir}/build.properties" />
-		<fail message="You must create a &quot;${build.properties.file}&quot; file.">
-			<condition>
-				<not>
-					<available file="${build.properties.file}" />
-				</not>
-			</condition>
-		</fail>
-
-		<property file="${build.properties.file}" />
-		<fail unless="vitro.core.dir"
-		      message="${build.properties.file} must contain a value for vitro.core.dir" />
-		<fail unless="vitro.home"
-		      message="${build.properties.file} must contain a value for vitro.home" />
-	</target>
-
-	<!-- - - - - - - - - - - - - - - - - - 
-		  target: getRuntimeProperties                      
-		 - - - - - - - - - - - - - - - - - -->
-	<target name="getRuntimeProperties">
-		<property name="runtime.properties.file"
-		          location="${vitro.home}/runtime.properties" />
-		<fail message="You must create a &quot;${runtime.properties.file}&quot; file.">
-			<condition>
-				<not>
-					<available file="${runtime.properties.file}" />
-				</not>
-			</condition>
-		</fail>
-
-		<property file="${runtime.properties.file}" />
-		<fail unless="VitroConnection.DataSource.url"
-		      message="${runtime.properties.file} must contain a value for VitroConnection.DataSource.url" />
-		<fail unless="VitroConnection.DataSource.username"
-		      message="${runtime.properties.file} must contain a value for VitroConnection.DataSource.username" />
-		<fail unless="VitroConnection.DataSource.password"
-		      message="${runtime.properties.file} must contain a value for VitroConnection.DataSource.password" />
-	</target>
-
-	<!-- - - - - - - - - - - - - - - - - - 
-          target: compile                      
-         - - - - - - - - - - - - - - - - - -->
-	<target name="compile" depends="setup">
-		<path id="main.compile.classpath">
-			<fileset dir="${lib.dir}" includes="*.jar" />
-		</path>
-
-		<javac srcdir="${src.dir}"
-		       destdir="${working.dir}"
-		       debug="true"
-		       deprecation="true"
-		       encoding="UTF8"
-		       includeantruntime="false"
-		       optimize="true"
-		       source="1.7">
-			<classpath refid="main.compile.classpath" />
-		</javac>
-	</target>
-
-	<!-- - - - - - - - - - - - - - - - - - 
-          target: run                      
-         - - - - - - - - - - - - - - - - - -->
-	<target name="run" depends="compile">
-		<path id="migrate.run.classpath">
-			<pathelement location="${working.dir}" />
-			<path refid="main.compile.classpath" />
-		</path>
-
-		<java classname="edu.cornell.mannlib.vivo.utilities.rdbmigration.RdbMigrator"
-		      fork="yes"
-		      failonerror="true">
-			<arg value="${vitro.home}" />
-			<arg value="${VitroConnection.DataSource.url}" />
-			<arg value="${VitroConnection.DataSource.username}" />
-			<arg value="${VitroConnection.DataSource.password}" />
-			<classpath refid="migrate.run.classpath" />
-		</java>
-	</target>
-
-</project>

utilities/rdbmigration/src/edu/cornell/mannlib/vivo/utilities/rdbmigration/RdbMigrator.java

@@ -1,303 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vivo.utilities.rdbmigration;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.sql.Connection;
-import java.sql.DatabaseMetaData;
-import java.sql.Date;
-import java.sql.DriverManager;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.sql.Statement;
-import java.util.Properties;
-
-import com.hp.hpl.jena.db.DBConnection;
-import com.hp.hpl.jena.db.GraphRDB;
-import com.hp.hpl.jena.db.IDBConnection;
-import com.hp.hpl.jena.graph.Graph;
-import com.hp.hpl.jena.graph.Node;
-import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.sparql.core.DatasetGraph;
-import com.hp.hpl.jena.tdb.TDBFactory;
-
-/**
- * TODO
- */
-public class RdbMigrator {
-	private static final String TABLE_RDB = "jena_graph";
-	private static final String TABLE_MIGRATED = "vivo_rdb_migrated";
-	private final String vivoHomeDir;
-	private final String jdbcUrl;
-	private final String username;
-	private final String password;
-
-	private File targetDir;
-	private boolean alreadyMigrated;
-
-	public RdbMigrator(String vivoHomeDir, String jdbcUrl, String username,
-			String password) throws UserDeclinedException, IOException, SQLException {
-		this.vivoHomeDir = vivoHomeDir;
-		this.jdbcUrl = jdbcUrl;
-		this.username = username;
-		this.password = password;
-
-		confirmTargetDirectory();
-
-		if (doesTdbExist()) {
-			askContinueOverTdb();
-		}
-
-		testDbConnection();
-
-		checkThatRdbExists();
-
-		if (isAlreadyMigrated()) {
-			askMigrateAgain();
-		}
-
-		askApprovalForMigrationPlan();
-	}
-
-	private void confirmTargetDirectory() {
-		File vivoHome = new File(vivoHomeDir);
-		if (!vivoHome.isDirectory()) {
-			quit("'" + vivoHome + "' is not a directory.");
-		}
-		if (!vivoHome.canWrite()) {
-			quit("Can't write to '" + vivoHome + "'.");
-		}
-		targetDir = new File(vivoHome, "tdbmodels");
-	}
-
-	private boolean doesTdbExist() {
-		if (!targetDir.exists()) {
-			return false;
-		}
-
-		if (!targetDir.isDirectory()) {
-			quit("'" + targetDir + "' is not a directory.");
-		}
-		if (!targetDir.canWrite()) {
-			quit("Can't write to '" + targetDir + "'.");
-		}
-
-		String[] filenames = targetDir.list();
-		if (filenames == null || filenames.length == 0) {
-			return false;
-		}
-
-		return true;
-	}
-
-	private void askContinueOverTdb() throws UserDeclinedException, IOException {
-		ask("A directory of TDB files exists at '" + targetDir + "'.\n"
-				+ "   Migration will replace the existing triples.\n"
-				+ "Continue? (y/n)");
-	}
-
-	private void testDbConnection() {
-		try (Connection conn = getSqlConnection()) {
-			// Just open and close it.
-		} catch (SQLException e) {
-			quit("Can't log in to database: '" + jdbcUrl + "', '" + username
-					+ "', '" + password + "'\n" + e.getMessage());
-		}
-	}
-
-	private void checkThatRdbExists() throws SQLException {
-		try (Connection conn = getSqlConnection()) {
-			DatabaseMetaData md = conn.getMetaData();
-			try (ResultSet rs = md.getTables(null, null, TABLE_RDB, null);) {
-				if (!rs.next()) {
-					quit("The database at '" + jdbcUrl
-							+ "' contains no RDB tables.");
-				}
-			}
-		}
-	}
-
-	private boolean isAlreadyMigrated() throws SQLException {
-		try (Connection conn = getSqlConnection()) {
-			DatabaseMetaData md = conn.getMetaData();
-			try (ResultSet rs = md.getTables(null, null, TABLE_MIGRATED, null);) {
-				if (rs.next()) {
-					alreadyMigrated = true;
-					announceMigrationDate(conn);
-					return true;
-				} else {
-					return false;
-				}
-			}
-		}
-	}
-
-	private void announceMigrationDate(Connection conn) {
-		String migrationDate = "UNKNOWN DATE";
-		String query = String.format("SELECT date FROM %s LIMIT 1",
-				TABLE_MIGRATED);
-
-		try (Statement stmt = conn.createStatement();
-				java.sql.ResultSet rs = stmt.executeQuery(query)) {
-			if (rs.next()) {
-				migrationDate = rs.getString("DATE");
-			}
-		} catch (SQLException e) {
-			// go with default answer.
-		}
-
-		System.out.println("It looks like this RDB data has already been "
-				+ "migrated to TDB, on " + migrationDate
-				+ "\n   (found a table named '" + TABLE_MIGRATED + "')");
-	}
-
-	private void askMigrateAgain() throws UserDeclinedException, IOException {
-		ask("Migrate again? (y/n)");
-	}
-
-	private void askApprovalForMigrationPlan() throws SQLException,
-			UserDeclinedException, IOException {
-		int modelCount = 0;
-		int tripleCount = 0;
-		try (Connection conn = getSqlConnection()) {
-			IDBConnection rdb = null;
-			try {
-				rdb = getRdbConnection(conn);
-				for (String modelName : rdb.getAllModelNames().toList()) {
-					modelCount++;
-					Graph graph = new GraphRDB(
-							rdb,
-							modelName,
-							null,
-							GraphRDB.OPTIMIZE_ALL_REIFICATIONS_AND_HIDE_NOTHING,
-							false);
-					tripleCount += graph.size();
-					graph.close();
-				}
-			} finally {
-				if (rdb != null) {
-					rdb.close();
-				}
-			}
-		}
-		String warning = alreadyMigrated ? "   Existing triples will be over-written.\n"
-				: "";
-		String question = String.format("Migrating %d triples in %d models "
-				+ "to TDB files in '%s'\n%sContinue? (y/n)", tripleCount,
-				modelCount, targetDir, warning);
-		ask(question);
-	}
-
-	public void migrate() throws SQLException {
-		copyData();
-		writeMigratedRecord();
-	}
-
-	private void copyData() throws SQLException {
-		try (Connection conn = getSqlConnection()) {
-			IDBConnection rdbConnection = null;
-			try {
-				rdbConnection = getRdbConnection(conn);
-				Dataset tdbDataset = TDBFactory.createDataset(targetDir
-						.getAbsolutePath());
-				copyGraphs(rdbConnection, tdbDataset);
-			} finally {
-				if (rdbConnection != null) {
-					rdbConnection.close();
-				}
-			}
-		}
-	}
-
-	@SuppressWarnings("deprecation")
-	private void copyGraphs(IDBConnection rdbConnection, Dataset tdbDataset) {
-		DatasetGraph tdbDsGraph = tdbDataset.asDatasetGraph();
-		for (String modelName : rdbConnection.getAllModelNames().toList()) {
-			Graph graph = null;
-			try {
-				graph = new GraphRDB(rdbConnection, modelName, null,
-						GraphRDB.OPTIMIZE_ALL_REIFICATIONS_AND_HIDE_NOTHING,
-						false);
-				tdbDsGraph.addGraph(Node.createURI(modelName), graph);
-				System.out
-						.println(String.format("  copied %4d triples from %s",
-								graph.size(), modelName));
-			} finally {
-				if (graph != null) {
-					graph.close();
-				}
-			}
-		}
-	}
-
-	private void writeMigratedRecord() throws SQLException {
-		String createTable = String.format("CREATE TABLE %s (date DATE)",
-				TABLE_MIGRATED);
-		String deleteOldDates = String.format("DELETE FROM %s", TABLE_MIGRATED);
-		String insertDate = String.format("INSERT INTO %s (date) VALUES (?)",
-				TABLE_MIGRATED);
-		try (Connection conn = getSqlConnection();
-				Statement stmt = conn.createStatement();
-				PreparedStatement pstmt = conn.prepareStatement(insertDate)) {
-			if (alreadyMigrated) {
-				stmt.executeUpdate(deleteOldDates);
-			} else {
-				stmt.executeUpdate(createTable);
-			}
-			pstmt.setDate(1, new Date(System.currentTimeMillis()));
-			pstmt.executeUpdate();
-		}
-	}
-
-	private void quit(String message) {
-		throw new IllegalArgumentException(message);
-	}
-
-	private void ask(String string) throws UserDeclinedException, IOException {
-		System.out.println(string);
-		BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
-		String s = br.readLine();
-		if ((s == null) || (!s.trim().toLowerCase().equals("y"))) {
-			throw new UserDeclinedException("OK.");
-		}
-	}
-
-	private static class UserDeclinedException extends Exception {
-		public UserDeclinedException(String message) {
-			super(message);
-		}
-	}
-
-	private Connection getSqlConnection() throws SQLException {
-		Properties connectionProps;
-		connectionProps = new Properties();
-		connectionProps.put("user", username);
-		connectionProps.put("password", password);
-		return DriverManager.getConnection(jdbcUrl, connectionProps);
-	}
-
-	private IDBConnection getRdbConnection(Connection sqlConnection) {
-		return new DBConnection(sqlConnection, "MySQL");
-	}
-
-	public static void main(String[] args) throws SQLException {
-		if (args.length != 4) {
-			System.out.println("Usage: RdbMigrator vivoHomeDir, jdbcUrl, "
-					+ "username, password");
-		}
-	
-		try {
-			RdbMigrator rdbm = new RdbMigrator(args[0], args[1], args[2], args[3]);
-			rdbm.migrate();
-		} catch (IllegalArgumentException | UserDeclinedException e) {
-			System.out.println(e.getMessage());
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-	}
-
-}

utilities/releaseScripts/6_insert_documentation.rb

@@ -0,0 +1,15 @@
+=begin
+--------------------------------------------------------------------------------
+
+Create PDF versions of the Installation Instructions and the Upgrade Guide, 
+from the VIVONEXT Wiki space. 
+
+Store them in the docs directory.
+
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+=end
+puts "-------------------------------------------------------------------"
+puts "    Not automated yet. Get Installation and Upgrade PDFs and put   "
+puts "    them into the /doc directory.                                  "
+puts "-------------------------------------------------------------------"