Merge pull request #1389 from angelicaochoa/darwin-fix

Darwin patient view updates
cBioPortal · Jun 24, 2016 · 19c94bc · 19c94bc
2 parents a9d4ef8 + 91ac408
commit 19c94bc
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Showing 4 changed files with 36 additions and 27 deletions.
diff --git a/core/src/main/java/org/mskcc/cbio/portal/util/CheckDarwinAccessMain.java b/core/src/main/java/org/mskcc/cbio/portal/util/CheckDarwinAccessMain.java
@@ -69,10 +69,10 @@
 public class CheckDarwinAccessMain {
 
     public static class CheckDarwinAccess {
-        private static String DARWIN_AUTH_URL = GlobalProperties.getDarwinAuthCheckUrl();
-        private static String DARWIN_RESPONSE_URL = GlobalProperties.getDarwinResponseUrl();
-        private static String DARWIN_AUTHORITY = GlobalProperties.getDarwinAuthority();
-        private static String CIS_USER = GlobalProperties.getCisUser();
+        private static String darwinAuthUrl = GlobalProperties.getDarwinAuthCheckUrl();
+        private static String darwinResponseUrl = GlobalProperties.getDarwinResponseUrl();
+        private static String darwinAuthority = GlobalProperties.getDarwinAuthority();
+        private static String cisUser = GlobalProperties.getCisUser();
 
         public static String checkAccess(HttpServletRequest request) {
             CancerStudy cancerStudy = (CancerStudy)request.getAttribute(PatientView.CANCER_STUDY);
@@ -83,14 +83,14 @@ public static String checkAccess(HttpServletRequest request) {
         }
 
         public static String getResponse(String cancerStudy, String userName, String patientId){   
-            if (!DARWIN_AUTHORITY.equals(cancerStudy) || CIS_USER.equals(userName)) return "";
+            if (!darwinAuthority.equals(cancerStudy) || cisUser.equals(userName)) return "";
 
             RestTemplate restTemplate = new RestTemplate();                 
             HttpEntity<LinkedMultiValueMap<String, Object>> requestEntity = getRequestEntity(userName, patientId);  
-            ResponseEntity<DarwinAccess> responseEntity = restTemplate.exchange(DARWIN_AUTH_URL, HttpMethod.POST, requestEntity, DarwinAccess.class);  
+            ResponseEntity<DarwinAccess> responseEntity = restTemplate.exchange(darwinAuthUrl, HttpMethod.POST, requestEntity, DarwinAccess.class);  
             String darwinResponse = responseEntity.getBody().getDarwinAuthResponse();
 
-            return darwinResponse.equals("valid")?DARWIN_RESPONSE_URL+patientId:"";
+            return darwinResponse.equals("valid")?darwinResponseUrl+patientId:"";
         }
 
         private static HttpEntity<LinkedMultiValueMap<String, Object>> getRequestEntity(String userName, String patientId) {
@@ -100,7 +100,7 @@ private static HttpEntity<LinkedMultiValueMap<String, Object>> getRequestEntity(
             HttpHeaders headers = new HttpHeaders();
             headers.setContentType(MediaType.APPLICATION_FORM_URLENCODED);
             return new HttpEntity<LinkedMultiValueMap<String, Object>>(map, headers);
-        }      
+        }
     }
 
     public static class DarwinAccess {

diff --git a/core/src/main/java/org/mskcc/cbio/portal/util/GlobalProperties.java b/core/src/main/java/org/mskcc/cbio/portal/util/GlobalProperties.java
@@ -32,6 +32,7 @@
 
 package org.mskcc.cbio.portal.util;
 
+import com.mysql.jdbc.StringUtils;
 import org.mskcc.cbio.portal.servlet.QueryBuilder;
 
 import org.apache.commons.logging.Log;
@@ -722,35 +723,43 @@ public static String getDbVersion() {
     }
 
     public static String getDarwinAuthCheckUrl() {
-        String darwinAuthUrl = properties.getProperty(DARWIN_AUTH_URL);
-        if (darwinAuthUrl == null || darwinAuthUrl.isEmpty()) {
-            return "";
+        String darwinAuthUrl = "";
+        try{
+            darwinAuthUrl = properties.getProperty(DARWIN_AUTH_URL).trim();            
         }
-        return darwinAuthUrl.trim();
+        catch (NullPointerException e){}
+
+        return darwinAuthUrl;
     }
 
     public static String getDarwinResponseUrl() {
-        String darwinResponseUrl = properties.getProperty(DARWIN_RESPONSE_URL);
-        if (darwinResponseUrl == null || darwinResponseUrl.isEmpty()) {
-            return "";
+        String darwinResponseUrl = "";
+        try{
+            darwinResponseUrl = properties.getProperty(DARWIN_RESPONSE_URL).trim();
         }
-        return darwinResponseUrl.trim();        
+        catch (NullPointerException e) {}
+
+        return darwinResponseUrl;
     }
 
-    public static String getDarwinAuthority() {
-        String darwinAuthority = properties.getProperty(DARWIN_AUTHORITY);
-        if (darwinAuthority == null || darwinAuthority.isEmpty()) {
-            return "";
+    public static String getDarwinAuthority() { 
+        String darwinAuthority = "";
+        try{
+            darwinAuthority = properties.getProperty(DARWIN_AUTHORITY).trim();
         }
-        return darwinAuthority.trim();
+        catch (NullPointerException e) {}
+
+        return darwinAuthority;
     }
 
     public static String getCisUser() {
-        String cisUser = properties.getProperty(CIS_USER).trim();
-        if (cisUser == null || cisUser.isEmpty()) {
-            return "";
-        }            
-        return cisUser;
+        String cisUser = "";
+        try{
+            cisUser = properties.getProperty(CIS_USER).trim();
+        }
+        catch (NullPointerException e) {}
+
+        return cisUser;         
     }
 
     public static void main(String[] args)

diff --git a/portal/src/main/webapp/WEB-INF/jsp/patient_view/patient_view.jsp b/portal/src/main/webapp/WEB-INF/jsp/patient_view/patient_view.jsp
@@ -962,7 +962,7 @@ function outputClinicalData() {
     row += "</a></span><span id='topbar-cancer-study' style='text-align: right; float: right'>" + formatCancerStudyInfo(55)+ "</span>";
     if (darwinAccessUrl !== null && darwinAccessUrl !== '') {
         //add link to darwin
-        row += "&nbsp;<a target='_blank' href='"+darwinAccessUrl+"'><font color='green'><b>DARWIN</b></font></a>";
+        row += "&nbsp;<a target='_blank' href='"+darwinAccessUrl+"'><img src='images/darwin_logo.png'/></a>";
     }
     row += "<br />";
     $("#clinical_div").append(row);

diff --git a/portal/src/main/webapp/images/darwin_logo.png b/portal/src/main/webapp/images/darwin_logo.png