formatting

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index bd86bf0..9af205f 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -37,26 +37,6 @@ import jalview.ws.JobStateSummary;
 import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.params.WsParamSetI;
 
-/**
- * <p>
- * Title:
- * </p>
- * 
- * <p>
- * Description:
- * </p>
- * 
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- * 
- * <p>
- * Company: Dundee University
- * </p>
- * 
- * @author not attributable
- * @version 1.0
- */
 class MsaWSThread extends AWS2Thread implements WSClientI
 {
   boolean submitGaps = false; // pass sequences including gaps to alignment
@@ -536,7 +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
@@ -596,10 +576,17 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     updateJobProgress(j);
   }
 
-  protected void updateJobProgress(MsaWSJob j) throws Exception
+  /**
+   * 
+   * @param j
+   * @return true if more job progress data was available
+   * @throws Exception
+   */
+  protected boolean updateJobProgress(MsaWSJob j) throws Exception
   {
     StringBuffer response = j.jobProgress;
     long lastchunk = j.getLastChunk();
+    boolean changed = false;
     do
     {
       j.setLastChunk(lastchunk);
@@ -607,11 +594,20 @@ class MsaWSThread extends AWS2Thread implements WSClientI
               .pullExecStatistics(j.getJobId(), lastchunk);
       if (chunk != null)
       {
+        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);
+    return changed;
   }
 
   public void StartJob(AWsJob job)
@@ -651,7 +647,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       }
       else if (j.hasArguments())
       {
-        j.setJobId(server.customAlign(j.seqs,j.getJabaArguments()));
+        j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
       }
       else
       {
@@ -737,6 +733,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
   public void parseResult()
   {
+    long progbar = System.currentTimeMillis();
+    wsInfo.setProgressBar("Collecting job results.", progbar);
     int results = 0; // number of result sets received
     JobStateSummary finalState = new JobStateSummary();
     try
@@ -746,16 +744,45 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         MsaWSJob msjob = ((MsaWSJob) jobs[j]);
         if (jobs[j].isFinished() && msjob.alignment == null)
         {
-          try
+          int nunchanged = 3, nexcept = 3;
+          boolean jpchanged = false, jpex = false;
+          do
           {
-            updateJobProgress(msjob);
-          } catch (Exception e)
-          {
-            Cache.log
-                    .warn("Exception when retrieving remaining Job progress data for job "
-                            + msjob.getJobId() + " on server " + WsUrl);
-            e.printStackTrace();
-          }
+            try
+            {
+              jpchanged = updateJobProgress(msjob);
+              jpex = false;
+              if (jpchanged)
+              {
+                nexcept = 3;
+              }
+            } catch (Exception e)
+            {
+
+              Cache.log
+                      .warn("Exception when retrieving remaining Job progress data for job "
+                              + msjob.getJobId() + " on server " + WsUrl);
+              e.printStackTrace();
+              nexcept--;
+              nunchanged = 3;
+              // set flag remember that we've had an exception.
+              jpex = true;
+              jpchanged = false;
+            }
+            if (!jpchanged)
+            {
+              try
+              {
+                Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we
+                                                  // experienced an exception.
+              } catch (Exception ex)
+              {
+              }
+              ;
+              nunchanged--;
+            }
+          } while (nunchanged > 0 && nexcept > 0);
+
           if (Cache.log.isDebugEnabled())
           {
             System.out.println("Job Execution file for job: "
@@ -774,6 +801,9 @@ 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)
           {
@@ -830,9 +860,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
     else
     {
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
       wsInfo.setFinishedNoResults();
     }
+    updateGlobalStatus(finalState);
+    wsInfo.setProgressBar(null, progbar);
   }
 
   void displayResults(boolean newFrame)