Merge branch 'maint-rel-1.6' of https://github.com/vivo-project/VIVO into maint-rel-1.6

productMods/js/homePageMaps.js

@@ -6,11 +6,12 @@ $(document).ready(function(){
     var countryMapBuilt = false;
     var localMapBuilt = false;
     var researchAreas = { "type": "FeatureCollection", "features": []};
+    var geoResearcherCount = "0";
     
     $.extend(this, urlsBase);
     $.extend(this, i18nStrings);
-    $.extend(this, geoResearcherCount);
     
+    getGeoFocusResearcherCount();
     getGeoJsonForMaps();
     
     $('a#globalLink').click(function() {
@@ -367,9 +368,26 @@ $(document).ready(function(){
        });        
     }
 
+    function getGeoFocusResearcherCount() {
+        $.ajax({
+            url: urlsBase + "/homePageAjax",
+            dataType: "json",
+            data: {
+                action: "getGeoFocusResearcherCount",
+            },
+            complete: function(xhr, status) {
+                
+                var results = $.parseJSON(xhr.responseText);
+                // there will only ever be one key/value pair
+                if ( results != null ) {
+                    geoResearcherCount = results.count;
+                }
+            }
+       });        
+    }
+
     function getResearcherCount(area) {
         
-        var researcherCount = this.geoResearcherCount;
         var areaCount = 0;
         var text = "";
         if ( area == "global" ) {
@@ -391,7 +409,7 @@ $(document).ready(function(){
         if ( areaCount == 1 && text == " states.") {
             text = " " + i18nStrings.stateString;
         }
-        if ( researcherCount == 1 ) {
+        if ( geoResearcherCount == 1 ) {
             researcherText = " " + i18nStrings.researcherString + " " + i18nStrings.inString;
         }
         else {
@@ -399,7 +417,7 @@ $(document).ready(function(){
         }
 
         $('div#researcherTotal').html("<font style='font-size:1.05em;color:#167093'>" 
-                                        + researcherCount 
+                                        + geoResearcherCount 
                                         + "</font> " + researcherText + " <font style='font-size:1.05em;color:#167093'>" 
                                         + areaCount + "</font>" + text);
     }

productMods/templates/freemarker/lib/lib-home-page.ftl

@@ -204,17 +204,3 @@ var urlsBase = "${urls.base}";
        -->
     </section>
 </#macro>
-
-<#-- retrieves a count, the number of researchers with a geographic focus, -->
-<#-- and saves it as a js variable to be used by the homePageMaps.js file  -->
-<#macro getGeoResearcherCount>
-<script>
- 
-<#if researcherCountDG?has_content>
-    <#assign theCount = researcherCountDG[0].count />
-<#else>
-     <#assign theCount = 0 />
-</#if>
-var geoResearcherCount = ${theCount};
-</script>
-</#macro>

rdf/display/everytime/homePageDataGetters.n3

@@ -17,35 +17,14 @@ display:academicDeptsDataGetter
     display:saveToVar "academicDeptDG" ;
     display:query """
     PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-    PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
     PREFIX vivo: <http://vivoweb.org/ontology/core#>
 
     SELECT DISTINCT ?theURI (str(?label) as ?name)
     WHERE
     {
-          ?theURI rdf:type vivo:AcademicDepartment .
+          ?theURI a vivo:AcademicDepartment .
           ?theURI rdfs:label ?label 
     }
     
     """ .
 
-<freemarker:lib-home-page.ftl> display:hasDataGetter display:researcherCountDataGetter .
-
-display:researcherCountDataGetter
-    a <java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter> ;
-    display:saveToVar "researcherCountDG" ;
-    display:query """
-    PREFIX geo: <http://aims.fao.org/aos/geopolitical.owl#>
-    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-    PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-    PREFIX core: <http://vivoweb.org/ontology/core#>
-    PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-    PREFIX vivoc: <http://vivo.library.cornell.edu/ns/0.1#>
-
-    SELECT DISTINCT (COUNT(DISTINCT ?person) AS ?count)  
-    WHERE { 
-        ?person rdf:type foaf:Person .
-        ?person core:geographicFocus ?focus  
-    }
-
-    """ .

rdf/display/everytime/vivoSearchProhibited.n3

@@ -27,7 +27,7 @@
     vitroDisplay:excludeClass core:DateTimeValuePrecision ;
 	vitroDisplay:excludeClass core:DateTimeInterval ;
 	vitroDisplay:excludeClass core:AcademicDegree ;
-	vitroDisplay:excludeClass core:URLLink ;
+	vitroDisplay:excludeClass vcard:URL ;
 	vitroDisplay:excludeClass vcard:Communication ;
 	vitroDisplay:excludeClass vcard:Code ;
 	vitroDisplay:excludeClass vcard:Explanatory ;

src/edu/cornell/mannlib/vitro/webapp/controller/ajax/GeoFocusResearcherCount.java

@@ -0,0 +1,83 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+package edu.cornell.mannlib.vitro.webapp.controller.ajax;
+
+import java.io.IOException;
+import java.lang.Integer;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletResponse;
+import javax.servlet.http.HttpSession;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.json.JSONException;
+
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
+
+public class GeoFocusResearcherCount extends AbstractAjaxResponder {
+
+    private static final Log log = LogFactory.getLog(GeoFocusResearcherCount.class.getName());
+    private List<Map<String,String>>  geoFocusCount;
+    private static String GEO_FOCUS_COUNT_QUERY = ""
+        + "PREFIX core: <http://vivoweb.org/ontology/core#>  \n"
+        + "PREFIX foaf: <http://xmlns.com/foaf/0.1/>  \n"
+        + "SELECT DISTINCT (COUNT(DISTINCT ?person) AS ?count)  \n"
+        + "WHERE {  \n"
+        + "    ?person a foaf:Person .  \n"
+        + "    ?person core:geographicFocus ?focus   \n"
+        + "}" ;
+    
+	public GeoFocusResearcherCount(HttpServlet parent, VitroRequest vreq,
+			HttpServletResponse resp) {
+		super(parent, vreq, resp);
+    }
+
+	@Override
+	public String prepareResponse() throws IOException, JSONException {
+		try {
+            geoFocusCount = getGeoFocusCount(vreq);
+            
+            String response = "{ ";
+            
+            for (Map<String, String> map: geoFocusCount) {
+                String theCount  = map.get("count");
+                response += "\"count\": \"" + theCount + "\"";
+            }
+			response += " }";
+			log.debug(response);
+			return response;
+		} catch (Exception e) {
+			log.error("Failed geographic focus count", e);
+			return EMPTY_RESPONSE;
+		}
+	}
+           
+    private List<Map<String,String>>  getGeoFocusCount(VitroRequest vreq) {
+          
+        String queryStr = GEO_FOCUS_COUNT_QUERY;
+        log.debug("queryStr = " + queryStr);
+        List<Map<String,String>>  count = new ArrayList<Map<String,String>>();
+        try {
+            ResultSet results = QueryUtils.getQueryResults(queryStr, vreq);
+            while (results.hasNext()) {
+                QuerySolution soln = results.nextSolution();
+                count.add(QueryUtils.querySolutionToStringValueMap(soln));
+            }
+        } catch (Exception e) {
+            log.error(e, e);
+        }    
+       
+        return count;
+    }
+}

src/edu/cornell/mannlib/vitro/webapp/controller/ajax/HomePageAjaxController.java

@@ -1,42 +1,46 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.controller.ajax;
-
-import java.io.IOException;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;
-
-/**
- * Handle the AJAX functions that are specific to the "new" home page sections, at
- * this point just the mapping of geographic locations.
- */
-public class HomePageAjaxController extends VitroAjaxController {
-	private static final Log log = LogFactory
-			.getLog(HomePageAjaxController.class);
-
-	private static final String PARAMETER_ACTION = "action";
-
-	@Override
-	protected void doRequest(VitroRequest vreq, HttpServletResponse resp)
-			throws ServletException, IOException {
-		try {
-			String function = vreq.getParameter(PARAMETER_ACTION);
-			if ("getGeoFocusLocations".equals(function)) {
-				new GeoFocusMapLocations(this, vreq, resp).processRequest();
-			} else {
-				resp.getWriter().write("[]");
-			}
-		} catch (Exception e) {
-			log.error(e, e);
-			resp.getWriter().write("[]");
-		}
-	}
-
-}
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.controller.ajax;
+
+import java.io.IOException;
+
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;
+
+/**
+ * Handle the AJAX functions that are specific to the "new" home page sections, at
+ * this point just the mapping of geographic locations.
+ */
+public class HomePageAjaxController extends VitroAjaxController {
+	private static final Log log = LogFactory
+			.getLog(HomePageAjaxController.class);
+
+	private static final String PARAMETER_ACTION = "action";
+
+	@Override
+	protected void doRequest(VitroRequest vreq, HttpServletResponse resp)
+			throws ServletException, IOException {
+		try {
+			String function = vreq.getParameter(PARAMETER_ACTION);
+			if ("getGeoFocusLocations".equals(function)) {
+				new GeoFocusMapLocations(this, vreq, resp).processRequest();
+			}
+			else if ("getGeoFocusResearcherCount".equals(function)) {
+			    new GeoFocusResearcherCount(this, vreq, resp).processRequest();
+			} 
+			else {
+				resp.getWriter().write("[]");
+			}
+		} catch (Exception e) {
+			log.error(e, e);
+			resp.getWriter().write("[]");
+		}
+	}
+
+}

themes/wilma/templates/page-home.ftl

@@ -110,6 +110,5 @@
              $('input.search-homepage').attr("value","${i18n().limit_search} \u2192");
         }  
     </script>
-    <@lh.getGeoResearcherCount/>
     </body>
 </html>

themes/wilma/templates/page.ftl

@@ -10,20 +10,7 @@
     
     <body class="${bodyClasses!}" onload="${bodyOnload!}">
         <#include "identity.ftl">
-        
-        <section id="search" role="region">
-            <fieldset>
-                <legend>${i18n().search_form}</legend>
-
-                <form id="search-form" action="${urls.search}" name="search" role="search" accept-charset="UTF-8" method="POST"> 
-                    <div id="search-field">
-                        <input type="text" name="querytext" class="search-vivo" value="${querytext!}" autocapitalize="off" />
-                        <input type="submit" value="${i18n().search_button}" class="search">
-                    </div>
-                </form>
-            </fieldset>
-        </section>
-        
+        <#include "search.ftl" >
         <#include "menu.ftl">
 
 		<#-- VIVO OpenSocial Extension by UCSF -->

themes/wilma/templates/search.ftl

@@ -0,0 +1,17 @@
+<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<#--Breaking this out so this can be utilized by other pages such as the jsp advanced tools pages-->
+
+<section id="search" role="region">
+    <fieldset>
+        <legend>${i18n().search_form}</legend>
+
+        <form id="search-form" action="${urls.search}" name="search" role="search" accept-charset="UTF-8" method="POST"> 
+            <div id="search-field">
+                <input type="text" name="querytext" class="search-vivo" value="${querytext!}" autocapitalize="off" />
+                <input type="submit" value="${i18n().search_button}" class="search">
+            </div>
+        </form>
+    </fieldset>
+</section>
+        

utilities/ISF-transition/obsoleteUris/directory_walker.rb

@@ -10,6 +10,8 @@ class DirectoryWalker
       if FileTest.directory?(path)
         if File.basename(path).start_with?(".")
           Find.prune       # Don't look any further into this directory.
+        elsif @known_exceptions.skip?(path)
+          Find.prune
         else
           next
         end
@@ -33,13 +35,13 @@ class DirectoryWalker
   
   def scan_line(path, line_number, line)
     @obsolete_uris.uris.each do |uri|
-      next if @known_exceptions.skip?(path, line_number, uri)
+#     next if @known_exceptions.skip?(path, line_number, uri)
       @report.add_event(Event.new(path, line_number, line, uri)) if line =~ Regexp.new("\\b#{Regexp.quote(uri)}\\b") 
     end
     if @complete
       @obsolete_uris.localnames.each do |localname|
         term = ":#{localname}"
-        next if @known_exceptions.skip?(path, line_number, term)
+#       next if @known_exceptions.skip?(path, line_number, term)
         @report.add_event(Event.new(path, line_number, line, term)) if line =~ Regexp.new("#{Regexp.quote(term)}\\b") 
       end
     end

utilities/ISF-transition/obsoleteUris/doit

@@ -1,7 +1,7 @@
 ruby obsoleteUriChecker.rb /Users/jeb228/git/VIVO  \
    ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt \
-   vivo_known_exceptions_2.txt complete > scan_VIVO_maint_branch
+   vivo_known_exceptions.txt complete > scan_VIVO_maint_branch
 ruby obsoleteUriChecker.rb /Users/jeb228/git/Vitro  \
    ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt \
-   vivo_known_exceptions_2.txt complete > scan_Vitro_maint_branch
+   vivo_known_exceptions.txt complete > scan_Vitro_maint_branch
 

utilities/ISF-transition/obsoleteUris/doit_old

@@ -0,0 +1,2 @@
+ruby obsoleteUriChecker.rb /Users/jeb228/Documents/Releases/VIVO\ 1.6/vivo-rel-1.6-rc1  ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt vivo_known_exceptions.txt complete
+

utilities/ISF-transition/obsoleteUris/vivo_known_exceptions.txt

@@ -1,17 +1,23 @@
-.GIF
-.as
-.class
-.fla
-.gif
-.gz
-.ico
-.jar
-.jpg
-.psd
-.png
-.swf
-.war
-.zip
+
+bin
+utilities/ISF-transition/obsoleteUris
+
+*.GIF
+*.as
+*.class
+*.fla
+*.gif
+*.gz
+*.ico
+*.jar
+*.jpg
+*.psd
+*.png
+*.swf
+*.war
+*.zip
+
+**/.*
 
 #
 # first_pass: no excluded files. everything was duplicated in the .bin directory, and
@@ -39,3 +45,25 @@ productMods/WEB-INF/ontologies/update/oldVersion/vivo-bibo-1.5.owl
 productMods/WEB-INF/ontologies/update/oldVersion/scires-1.5.owl 
 productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcterms-1.5.owl
 productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcelements-1.5.owl
+
+#
+# Exclude old performance tests
+#
+utilities/LoadTesting/distros/release1.4/deploy.properties.template
+
+#
+# Exclude the migration code itself
+#
+productMods/WEB-INF/ontologies/update/**/*
+
+#
+# This is commented out.
+#
+src/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java 
+
+#
+# The URI is obsolete, but it has been replaced by another URI with the same localname.
+# http://purl.org/dc/terms/publisher	http://vivoweb.org/ontology/core#publisher
+# How to catch this?
+#
+

utilities/ISF-transition/obsoleteUris/vivo_known_exceptions_old.txt

@@ -1,22 +1,17 @@
-.*
-bin
-
-*.GIF
-*.as
-*.class
-*.fla
-*.gif
-*.gz
-*.ico
-*.jar
-*.jpg
-*.psd
-*.png
-*.swf
-*.war
-*.zip
-
-**/.*
+.GIF
+.as
+.class
+.fla
+.gif
+.gz
+.ico
+.jar
+.jpg
+.psd
+.png
+.swf
+.war
+.zip
 
 #
 # first_pass: no excluded files. everything was duplicated in the .bin directory, and