X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=faf2fafd8dec89f4c6275022ac9d3a2deb65b29a;hb=bd6e2f14dd1a60bb11e1be975574e462a1a6b256;hp=9626132dadd37b9c1abb0a53eeeef825f7aa6d34;hpb=8891eedbf7430d8a98edc1cccb32fceac8e3a9bb;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 9626132..faf2faf 100755
--- 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
       }
     }