anchor.diff:              case "custom":
                   enableOncoKBandHotspots = "\"custom\"";
           }
  -        
  -        out.println(String.format("\"%s\" : %s,", "oncoprintOncoKbHotspotsDefault", enableOncoKBandHotspots)); 
  +             
  +        obj.put("oncoprintOncoKbHotspotsDefault",enableOncoKBandHotspots);        
                   
  +        out.println(obj.toJSONString());       
                         
         
        %>
   
  -});
  +);
  +
  
positive.code: <%@ page language="java" contentType="text/javascript; charset=UTF-8"
      pageEncoding="UTF-8"%>
      
  <%@ page import="org.mskcc.cbio.portal.servlet.CheckDarwinAccessServlet" %>
  <%@ page import="org.mskcc.cbio.portal.util.GlobalProperties" %>
  
  <%--
  legacyConfig = 
  {
      enableDarwin : <%=CheckDarwinAccessServlet.CheckDarwinAccess.existsDarwinProperties()%>,
      appVersion : '<%=GlobalProperties.getAppVersion()%>',
      maxTreeDepth : <%=GlobalProperties.getMaxTreeDepth()%>,
      showOncoKB : <%=GlobalProperties.showOncoKB()%>,
      oncoKBApiUrl : '<%=GlobalProperties.getOncoKBPublicApiUrl()%>',
      genomeNexusApiUrl : '<%=GlobalProperties.getGenomeNexusApiUrl()%>',
      showCivic : <%=GlobalProperties.showCivic()%>,
      showHotspot : <%=GlobalProperties.showHotspot()%>,
      showMyCancerGenome : <%=GlobalProperties.showMyCancerGenomeUrl()%>,
      showGenomeNexus : <%=GlobalProperties.showGenomeNexus()%>,
      querySetsOfGenes : JSON.parse('<%=GlobalProperties.getQuerySetsOfGenes()%>'),
      bitlyToken: '<%=GlobalProperties.getBitlyAccessToken()%>',
      skinBlurb : '<%=GlobalProperties.getBlurb()%>',
  
      skinExampleStudyQueries : '<%=GlobalProperties.getExampleStudyQueries().replace("\n","\\n")%>'.split("\n"),
  
      skinDatasetHeader : '<%=GlobalProperties.getDataSetsHeader()%>',
      skinDatasetFooter : '<%=GlobalProperties.getDataSetsFooter()%>',
      skinRightNavShowDatasets : <%=GlobalProperties.showRightNavDataSets()%>,
      skinRightNavShowExamples : <%=GlobalProperties.showRightNavExamples()%>,
      skinRightNavShowTestimonials : <%=GlobalProperties.showRightNavTestimonials()%>,
      skinRightNavExamplesHTML : '<%=GlobalProperties.getExamplesRightColumnHtml()%>',
      skinRightNavExamplesHTML : '<%=GlobalProperties.getExamplesRightColumnHtml()%>',
      skinRightNavWhatsNewBlurb : '<%=GlobalProperties.getRightNavWhatsNewBlurb()%>',
      skinRightLogo : '<%=GlobalProperties.getRightLogo()%>',
      skinTitle : '<%=GlobalProperties.getTitle()%>',
      
      userEmailAddress : '<%=GlobalProperties.getAuthenticatedUserName()%>',
      
      oncoprintCustomDriverAnnotationBinaryMenuLabel: '<%=GlobalProperties.getBinaryCustomDriverAnnotationMenuLabel()%>',
      oncoprintCustomDriverAnnotationTiersMenuLabel: '<%=GlobalProperties.getTiersCustomDriverAnnotationMenuLabel()%>',
      oncoprintCustomDriverAnnotationDefault:'<%=GlobalProperties.enableDriverAnnotations()%>' !== "false", // true unless "false"
      oncoprintCustomDriverTiersAnnotationDefault:'<%=GlobalProperties.enableTiers()%>' !== "false", // true unless "false"
      oncoprintOncoKbHotspotsDefault:{"true":undefined, "false":"disable", "custom":"custom"}['<%=GlobalProperties.enableOncoKBandHotspots()%>'],
      oncoprintHideVUSDefault:'<%=GlobalProperties.hidePassengerMutations()%>' === "true", // false unless "true"
      priorityStudies : <%=studies%>,  //done
      sessionServiceIsEnabled: '<%=GlobalProperties.getSessionServiceUrl()%>' !== "",
      sessionServiceUrl: '<%=GlobalProperties.getSessionServiceUrl()%>',
      baseUrl:"<%=baseURL%>",
      fontendCongfigOveride:JSON.parse('<%=GlobalProperties.getFrontendConfig()%>'),
      skinShowDataTabSets: (<%=GlobalProperties.showDataTab()%> === true),
      skinShowNewsTab: (<%=GlobalProperties.showNewsTab()%> === true),
      skinShowFAQSTab: (<%=GlobalProperties.showFaqsTab()%> === true),
      skinShowToolsTab: (<%=GlobalProperties.showToolsTab()%> === true),
      skinShowAboutTab: (<%=GlobalProperties.showAboutTab()%> === true),
      skinShowWebAPITab: (<%=GlobalProperties.showWebApiTab()%> === true),
      skinShowRmatLABTab : (<%=GlobalProperties.showRMatlabTab()%> === true),
      skinShowTutorialsTab: (<%=GlobalProperties.showTutorialsTab()%> === true),
      emailContactAddress: "<%=GlobalProperties.getContactEmailAddress()%>",
      skinDocumentationBaseUrl: "<%=GlobalProperties.getBaseUrl()%>",
      skinIsMarkdownDocumentation: (<%=GlobalProperties.isMarkdownDocumentation()%> === true),
      skinFaqSourceURL: "<%=GlobalProperties.getFaqHtml()%>",
      skinAboutSourceURL: "<%=GlobalProperties.getAboutHtml()%>",
      skinNewsSourceURL: "<%=GlobalProperties.getNewsHtml()%>",
      skinOQLSourceURL: "<%=GlobalProperties.getOqlHtml()%>",
      googleAnalyticsProfile: "<%=GlobalProperties.getGoogleAnalyticsProfileId()%>",
      
     
  };
  --%>
  
  // an empty string means the property is listed but not assigned to in portal.props 
  // a null value means it was entirely missing 
  
  <%= request.getParameter("callback") %>({
  
      <%
      
          // Set API root variable for cbioportal-frontend repo
          String url = request.getRequestURL().toString();
          String baseURL = url.substring(0, url.length() - request.getRequestURI().length()) + request.getContextPath();
  
negative.code:            
          }; 
      
     
          JSONObject obj = new JSONObject();
             
          // for each above, add json prop and lookup value in portal.properties
          for (int i = 0; i < propNameArray.length; i++){
              
                String value = GlobalProperties.getProperty(propNameArray[i]);
                
                String key = propNameArray[i].replace(".","_");
                              
                // booleans should be non-string in json
                if ("true".equals(value) || "false".equals(value)) {
                   obj.put(key, Boolean.parseBoolean(value));
                } else {
                   obj.put(key, value);
                }
  
          }
          
          // these are some custom props which are not read directly from portal.props
          obj.put("enable_darwin", CheckDarwinAccessServlet.CheckDarwinAccess.existsDarwinProperties());
              
          obj.put("query_sets_of_genes", GlobalProperties.getQuerySetsOfGenes());
          
          obj.put("base_url", baseURL);
            
          obj.put("user_email_address",GlobalProperties.getAuthenticatedUserName());
          
          obj.put("frontendConfigOverride",GlobalProperties.getFrontendConfig());
          
          obj.put("authenticationMethod",GlobalProperties.authenticationMethod());
                    
          String enableOncoKBandHotspots = "";
          switch(GlobalProperties.enableOncoKBandHotspots()){
              case "true":
  