X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FAWSThread.java;h=36e51c5c5d71fd1da02b2f9c2d13c11ab45d3bd0;hb=b3eead416d4a16141910b7dae1eda4eaf2272b6a;hp=2074f9f54c99870a05f1a61b0803e110bc327906;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 2074f9f..36e51c5 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -31,8 +31,8 @@ import jalview.gui.WebserviceInfo;
 import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
-import java.util.LinkedHashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
 
 public abstract class AWSThread extends Thread
 {
@@ -60,7 +60,7 @@ public abstract class AWSThread extends Thread
   /**
    * dataset sequence relationships to be propagated onto new results
    */
-  protected Set<AlignedCodonFrame> codonframe = null;
+  protected List<AlignedCodonFrame> codonframe = null;
 
   /**
    * are there jobs still running in this thread.
@@ -98,6 +98,7 @@ public abstract class AWSThread extends Thread
   /**
    * generic web service job/subjob poll loop
    */
+  @Override
   public void run()
   {
     JobStateSummary jstate = null;
@@ -115,9 +116,13 @@ public abstract class AWSThread extends Thread
         {
           StartJob(jobs[j]);
         }
-
+        Cache.log.debug("Job " + jobs[j] + " is " + (jobs[j].submitted ? "submitted" : "not submitted"));
         if (jobs[j].submitted && !jobs[j].subjobComplete)
         {
+          jalview.bin.Cache.log.debug(
+              "Polling Job " + j + " Result state was:" + jobs[j].getState() + "(ServerError=" + jobs[j].isServerError()
+                  + ")"
+          );
           try
           {
             pollJob(jobs[j]);
@@ -133,8 +138,8 @@ public abstract class AWSThread extends Thread
           {
             // Deal with Transaction exceptions
             wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
-                    .formatMessage("info.server_exception", new Object[] {
-                        WebServiceName, ex.getMessage() }));
+                    .formatMessage("info.server_exception", new Object[]
+                    { WebServiceName, ex.getMessage() }));
             // always output the exception's stack trace to the log
             Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
                     + ") Server exception.");
@@ -168,8 +173,8 @@ public abstract class AWSThread extends Thread
                     WebserviceInfo.STATE_STOPPED_ERROR);
             Cache.log.error("Out of memory when retrieving Job " + j
                     + " id:" + WsUrl + "/" + jobs[j].jobId, er);
-            new jalview.gui.OOMWarning("retrieving result for "
-                    + WebServiceName, er);
+            new jalview.gui.OOMWarning(
+                    "retrieving result for " + WebServiceName, er);
             System.gc();
           }
         }
@@ -184,10 +189,10 @@ public abstract class AWSThread extends Thread
           Thread.sleep(5000);
         } catch (InterruptedException e)
         {
-          Cache.log
-                  .debug("Interrupted sleep waiting for next job poll.", e);
+          Cache.log.debug("Interrupted sleep waiting for next job poll.",
+                  e);
         }
-        // System.out.println("I'm alive "+alTitle);
+        // System.out.println("I'm alive ?");
       }
     }
     if (jobComplete && jobs != null)
@@ -196,11 +201,11 @@ public abstract class AWSThread extends Thread
     }
     else
     {
-      Cache.log
-              .debug("WebServiceJob poll loop finished with no jobs created.");
+      Cache.log.debug(
+              "WebServiceJob poll loop finished with no jobs created.");
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-      wsInfo.appendProgressText(MessageManager
-              .getString("info.no_jobs_ran"));
+      wsInfo.appendProgressText(
+              MessageManager.getString("info.no_jobs_ran"));
       wsInfo.setFinishedNoResults();
     }
   }
@@ -378,11 +383,11 @@ public abstract class AWSThread extends Thread
     WsUrl = wsurl2;
     if (alframe != null)
     {
-      Set<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
+      List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
               .getCodonFrames();
       if (cf != null)
       {
-        codonframe = new LinkedHashSet<AlignedCodonFrame>();
+        codonframe = new ArrayList<>();
         codonframe.addAll(cf);
       }
     }