X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=4c75756cd37a92b3490f1984940dda2c39a6048a;hb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;hp=0049001ba33774db1a1d8787ca6acca9daa76e67;hpb=478cdf5b2350d055e0da878c5f54ba5a8ae4af4b;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 0049001..4c75756 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -34,6 +34,8 @@ import jalview.gui.*;
 import jalview.ws.AWsJob;
 import jalview.ws.WSClientI;
 import jalview.ws.JobStateSummary;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
 
 /**
  * <p>
@@ -69,7 +71,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   {
     long lastChunk = 0;
 
-    Preset preset = null;
+    WsParamSetI preset = null;
 
     List<Argument> arguments = null;
 
@@ -373,6 +375,67 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       return alignmentProgram;
     }
 
+    public boolean hasArguments()
+    {
+      return (arguments != null && arguments.size() > 0)
+              || (preset != null && preset instanceof JabaWsParamSet);
+    }
+
+    public List<Argument> getJabaArguments()
+    {
+      List<Argument> newargs = new ArrayList<Argument>();
+      if (preset != null && preset instanceof JabaWsParamSet)
+      {
+        newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
+      }
+      if (arguments != null && arguments.size() > 0)
+      {
+        newargs.addAll(arguments);
+      }
+      return newargs;
+    }
+
+    /**
+     * add a progess header to status string containing presets/args used
+     */
+    public void addInitialStatus()
+    {
+      if (preset != null)
+      {
+        jobProgress.append("Using "
+                + (preset instanceof JabaPreset ? "Server" : "User")
+                + "Preset: " + preset.getName());
+        if (preset instanceof JabaWsParamSet)
+        {
+          for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
+          {
+            jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
+                    + "\n");
+          }
+        }
+      }
+      if (arguments != null && arguments.size() > 0)
+      {
+        jobProgress.append("With custom parameters : \n");
+        // merge arguments with preset's own arguments.
+        for (Argument opt : arguments)
+        {
+          jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
+                  + "\n");
+        }
+      }
+      jobProgress.append("\nJob Output:\n");
+    }
+
+    public boolean isPresetJob()
+    {
+      return preset != null && preset instanceof JabaPreset;
+    }
+
+    public Preset getServerPreset()
+    {
+      return (isPresetJob()) ? ((JabaPreset) preset).p : null;
+    }
   }
 
   String alTitle; // name which will be used to form new alignment window.
@@ -416,7 +479,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
    * @param seqset
    *          Alignment
    */
-  MsaWSThread(MsaWS server2, Preset preset, List<Argument> paramset,
+  MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
           String wsUrl, WebserviceInfo wsinfo,
           jalview.gui.AlignFrame alFrame, String wsname, String title,
           AlignmentView _msa, boolean subgaps, boolean presorder,
@@ -533,10 +596,17 @@ 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);
@@ -544,11 +614,13 @@ 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();
       }
       ;
     } while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
+    return changed;
   }
 
   public void StartJob(AWsJob job)
@@ -580,21 +652,15 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
     try
     {
-      // TODO: get the parameters (if any) for this job and submit the job
-      if (j.arguments != null && j.arguments.size() > 0)
+      j.addInitialStatus(); // list the presets/parameters used for the job in
+                            // status
+      if (j.isPresetJob())
       {
-        StringBuffer pset = new StringBuffer();
-        for (Argument arg : j.arguments)
-        {
-          pset.append(arg.getName() + " " + arg.getDefaultValue() + "\n");
-        }
-        j.setStatus("Custom Parameters:\n" + pset.toString()
-                + "\nJob Output:\n");
-        j.setJobId(server.customAlign(j.seqs, j.arguments));
+        j.setJobId(server.presetAlign(j.seqs, j.getServerPreset()));
       }
-      else if (j.preset != null)
+      else if (j.hasArguments())
       {
-        j.setJobId(server.presetAlign(j.seqs, j.preset));
+        j.setJobId(server.customAlign(j.seqs,j.getJabaArguments()));
       }
       else
       {
@@ -689,16 +755,40 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         MsaWSJob msjob = ((MsaWSJob) jobs[j]);
         if (jobs[j].isFinished() && msjob.alignment == null)
         {
-          try
-          {
-            updateJobProgress(msjob);
-          } catch (Exception e)
-          {
-            Cache.log
-                    .warn("Exception when retrieving remaining Job progress data for job "
-                            + msjob.getJobId() + " on server " + WsUrl);
-            e.printStackTrace();
-          }
+          boolean jpchanged=false,jpex=false;
+          do {
+            try
+            {
+              jpchanged = updateJobProgress(msjob);
+              jpex=false;
+            } 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;
+              }
+              // set flag remember that we've had an exception.
+              jpex=true;
+            }
+            if (jpchanged)
+            {
+              try
+              {
+                Thread.sleep(jpex ? 400 : 200); // wait a bit longer if we experienced an exception.
+              } catch (Exception ex)
+              {
+              }
+              ;
+            }
+          } while (jpchanged);
+          
           if (Cache.log.isDebugEnabled())
           {
             System.out.println("Job Execution file for job: "