tidied the exceptions and ws server error behaviour

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 3842e15..232d6d6 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -67,6 +67,7 @@ public class JPredClient extends WSClient
     JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
     try {\r
       this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
+      ((JpredSoapBindingStub) this.server).setTimeout(60000); // one minute stub\r
     }\r
     catch (Exception ex) {\r
       JOptionPane.showMessageDialog(Desktop.desktop, "The Secondary Structure Prediction Service named "\r
@@ -74,6 +75,7 @@ public class JPredClient extends WSClient
                                     "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
       wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"\r
                      +WsURL+"\n"+ex.getMessage());\r
+      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
     }\r
 \r
     JPredThread jthread = new JPredThread(seq);\r
@@ -120,7 +122,8 @@ public class JPredClient extends WSClient
       {\r
         try\r
         {\r
-          result = server.getresult(jobId);\r
+          if ((result = server.getresult(jobId))==null)\r
+            throw(new Exception("Timed out when communicating with server\nTry again later.\n"));\r
 \r
          if( result.isRunning() )\r
            wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
@@ -138,7 +141,13 @@ public class JPredClient extends WSClient
             wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());\r
             if (! (result.isJobFailed() || result.isServerError()))\r
             {\r
-              Thread.sleep(5000);\r
+              try\r
+              {\r
+                Thread.sleep(5000);\r
+              }\r
+              catch (InterruptedException ex1)\r
+              {\r
+              }\r
               //  System.out.println("I'm alive "+seqid+" "+jobid);\r
             } else {\r
               wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
@@ -149,6 +158,14 @@ public class JPredClient extends WSClient
         {\r
           allowedServerExceptions--;\r
           wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());\r
+          try\r
+          {\r
+            if (allowedServerExceptions>0)\r
+              Thread.sleep(5000);\r
+          }\r
+          catch (InterruptedException ex1)\r
+          {\r
+          }\r
         }\r
       }\r
 \r
@@ -167,13 +184,26 @@ public class JPredClient extends WSClient
         } else {\r
           jobId = server.predict(sequence);\r
         }\r
-        System.out.println(WsURL+" Job Id '"+jobId+"'");\r
+        if (jobId!=null) {\r
+          if (jobId.startsWith("Broken")) {\r
+            throw new Exception("Submission " + jobId);\r
+          } else {\r
+            System.out.println(WsURL+" Job Id '"+jobId+"'");\r
+          }\r
+        } else {\r
+          throw new Exception("Server timed out - try again later\n");\r
+\r
+        }\r
       }\r
       catch (Exception e)\r
       {\r
-        System.err.println("JPredWS Client: Failed to submit the prediction\n" +\r
-                           e.toString() + "\n");\r
-        e.printStackTrace();\r
+         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+         allowedServerExceptions=0;\r
+         jobComplete=false;\r
+         wsInfo.appendProgressText("Failed to submit the prediction: "+e.toString()+"\nJust close the window\n");\r
+         System.err.println("JPredWS Client: Failed to submit the prediction\n" +\r
+                            e.toString() + "\n");\r
+         // e.printStackTrace(); TODO: JBPNote DEBUG\r
       }\r
     }\r
 \r

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 9626132..faf2faf 100755 (executable)
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -53,6 +53,7 @@ public class MsaWSClient
     MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
     try {
       this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+      ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout
     }
     catch (Exception ex) {
       wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
@@ -60,7 +61,7 @@ public class MsaWSClient
       wsInfo.setStatus(wsInfo.ERROR);
       ex.printStackTrace();
     }
-
+    loc.getEngine().setOption("axis","1");
     MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
     wsInfo.setthisService(musclethread);
     musclethread.start();
@@ -119,7 +120,7 @@ public class MsaWSClient
     boolean jobComplete = false;
 
     public void cancelJob() {
-      if (!jobComplete) {
+      if (jobId!=null && !jobId.equals("") && !jobComplete) {
         String cancelledMessage="";
         try {
           vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
@@ -147,6 +148,11 @@ public class MsaWSClient
           exc.printStackTrace();
         }
         wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");
+      } else {
+        if (!jobComplete)
+        {
+          wsInfo.setProgressText(OutputHeader + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+        }
       }
     }
 
@@ -159,7 +165,8 @@ public class MsaWSClient
       {
         try
         {
-          result = server.getResult(jobId);
+          if ((result = server.getResult(jobId))==null)
+            throw(new Exception("Timed out when communicating with server\nTry again later.\n"));
 
           if (result.isRunning())
             wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
@@ -192,7 +199,18 @@ public class MsaWSClient
           allowedServerExceptions--;
           wsInfo.appendProgressText("\n" + ServiceName + " Server exception!\n" +
                                     ex.getMessage());
-          ex.printStackTrace();
+          System.err.println(ServiceName + " Server exception: " +
+                                    ex.getMessage());
+          //          ex.printStackTrace(); JBPNote Debug
+          try
+          {
+            if (allowedServerExceptions>0)
+              Thread.sleep(5000);
+          }
+          catch (InterruptedException ex1)
+          {
+          }
+
         }
       }
       if (allowedServerExceptions == 0)
@@ -217,18 +235,26 @@ public class MsaWSClient
       try
       {
         vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
-        if (jobsubmit.getStatus()==1) {
+        if (jobsubmit!=null && jobsubmit.getStatus()==1) {
           jobId=jobsubmit.getJobId();
           System.out.println(WsURL+" Job Id '"+jobId+"'");
         } else {
+          if (jobsubmit == null) {
+            throw new Exception("Server at "+WsURL+" returned null object, it probably cannot be contacted. Try again later ?");
+          }
           throw new Exception(jobsubmit.getJobId());
         }
       }
       catch (Exception e)
       {
-        System.err.println(ServiceName + " Client: Failed to submit the prediction\n" +
+        // TODO: JBPNote catch timeout or other fault types explicitly
+        // For unexpected errors
+        System.err.println(WebServiceName + " Client: Failed to submit the sequences for alignment.\n"+WsURL+" : " +
                            e.toString() + "\n");
-        e.printStackTrace();
+        this.allowedServerExceptions=0;
+        wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+        wsInfo.appendProgressText("Server problems! "+e.toString()+"\nFailed to submit sequences for alignment. Just close the window\n");
+        // e.printStackTrace(); // TODO: JBPNote DEBUG
       }
     }