X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=08accbac5d9e91c50f7756662209b6db8020f431;hb=4272f31e9cc505f9a1496e2cd002dc9250c77928;hp=bd86bf0f39c158d88f888b9f6f9a1504629920cd;hpb=bf16f469383285628cdae9743c008095f9662605;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index bd86bf0..08accba 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,27 +1,26 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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 +36,6 @@ 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 +515,7 @@ 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
@@ -566,6 +545,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI
           }
           wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
                   + cancelledMessage + "\n");
+        } else {
+          // if we hadn't submitted then just mark the job as cancelled.
+          jobs[job].setSubjobComplete(true);
+          wsInfo.setStatus(jobs[job].getJobnum(), WebserviceInfo.STATE_CANCELLED_OK);
+          
         }
       }
       if (cancelled)
@@ -596,10 +580,17 @@ 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 +598,20 @@ 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 +651,7 @@ 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 +737,8 @@ 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 +748,45 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         MsaWSJob msjob = ((MsaWSJob) jobs[j]);
         if (jobs[j].isFinished() && msjob.alignment == null)
         {
-          try
-          {
-            updateJobProgress(msjob);
-          } catch (Exception e)
+          int nunchanged = 3, nexcept = 3;
+          boolean jpchanged = false, jpex = false;
+          do
           {
-            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 +805,9 @@ 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 +864,10 @@ 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)