X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=f0602c43812bbb138483609e92c956aeb91ad559;hb=1fe15a0bb2006a51a24f4757c89337d99db4ad26;hp=4c75756cd37a92b3490f1984940dda2c39a6048a;hpb=e3947854073b52cf92a3f924deed0fda77dc88e6;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 4c75756..f0602c4 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,13 +1,13 @@
 /*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -20,8 +20,6 @@ package jalview.ws.jws2;
 import java.util.*;
 
 import compbio.data.msa.MsaWS;
-import compbio.data.sequence.AlignmentMetadata;
-import compbio.data.sequence.Program;
 import compbio.metadata.Argument;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
@@ -37,26 +35,6 @@ 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 +514,7 @@ 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
@@ -606,7 +584,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   {
     StringBuffer response = j.jobProgress;
     long lastchunk = j.getLastChunk();
-    boolean changed=false;
+    boolean changed = false;
     do
     {
       j.setLastChunk(lastchunk);
@@ -614,9 +592,16 @@ 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);
@@ -660,7 +645,7 @@ 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
       {
@@ -746,6 +731,8 @@ 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
@@ -755,40 +742,45 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         MsaWSJob msjob = ((MsaWSJob) jobs[j]);
         if (jobs[j].isFinished() && msjob.alignment == null)
         {
-          boolean jpchanged=false,jpex=false;
-          do {
+          int nunchanged = 3, nexcept = 3;
+          boolean jpchanged = false, jpex = false;
+          do
+          {
             try
             {
               jpchanged = updateJobProgress(msjob);
-              jpex=false;
+              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();
-              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;
+              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)
               {
               }
               ;
+              nunchanged--;
             }
-          } while (jpchanged);
-          
+          } while (nunchanged > 0 && nexcept > 0);
+
           if (Cache.log.isDebugEnabled())
           {
             System.out.println("Job Execution file for job: "
@@ -807,6 +799,9 @@ 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)
           {
@@ -863,9 +858,10 @@ 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)