JAL-849 try harder and wait for longer for JABAWS to send back job output.

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 86f5fbc..6ef07c6 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -516,7 +516,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
           try
           {
             boolean cancelledJob = server.cancelJob(jobs[job].getJobId());
-            if (cancelledJob || true)
+            if (true) // cancelledJob || true)
             {
               // CANCELLED_JOB
               // if the Jaba server indicates the job can't be cancelled, its
@@ -594,9 +594,12 @@ class MsaWSThread extends AWS2Thread implements WSClientI
               .pullExecStatistics(j.getJobId(), lastchunk);
       if (chunk != null)
       {
-        changed=chunk.getChunk().length()>0;
+        changed|=chunk.getChunk().length()>0;
         response.append(chunk.getChunk());
         lastchunk = chunk.getNextPosition();
+        try {
+          Thread.sleep(50);
+        } catch (InterruptedException x){};
       }
       ;
     } while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
@@ -737,12 +740,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         MsaWSJob msjob = ((MsaWSJob) jobs[j]);
         if (jobs[j].isFinished() && msjob.alignment == null)
         {
+          int nunchanged=3,nexcept=3;
           boolean jpchanged=false,jpex=false;
           do {
             try
             {
               jpchanged = updateJobProgress(msjob);
               jpex=false;
+              if (jpchanged) {
+                nexcept=3;
+              }
             } catch (Exception e)
             {
               
@@ -750,26 +757,24 @@ class MsaWSThread extends AWS2Thread implements WSClientI
                       .warn("Exception when retrieving remaining Job progress data for job "
                               + msjob.getJobId() + " on server " + WsUrl);
               e.printStackTrace();
-              if (jpex) {
-                // give up polling after two consecutive exceptions
-                jpchanged=false;
-              } else {
-                jpchanged=true;
-              }
+              nexcept--;
+              nunchanged=3;
               // set flag remember that we've had an exception.
               jpex=true;
+              jpchanged=false;
             }
-            if (jpchanged)
+            if (!jpchanged)
             {
               try
               {
-                Thread.sleep(jpex ? 400 : 200); // wait a bit longer if we experienced an exception.
+                Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we experienced an exception.
               } catch (Exception ex)
               {
               }
               ;
-            }
-          } while (jpchanged);
+              nunchanged--;
+            } 
+          } while (nunchanged>0 && nexcept>0);
           
           if (Cache.log.isDebugEnabled())
           {
@@ -789,6 +794,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
             Cache.log
                     .debug("Results not available for finished job - marking as broken job.",
                             e);
+            msjob.jobProgress
+                    .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+                            + e.getLocalizedMessage());
             msjob.setjobStatus(JobStatus.FAILED);
           } catch (Exception e)
           {