X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=a54d0b548dffc39c5bbaea61073a23dfbb849319;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;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..a54d0b5 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 2.5)
- * 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;
@@ -34,27 +33,9 @@ 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>
- * 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
@@ -69,7 +50,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   {
     long lastChunk = 0;
 
-    Preset preset = null;
+    WsParamSetI preset = null;
 
     List<Argument> arguments = null;
 
@@ -373,6 +354,67 @@ 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 +458,7 @@ 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,
@@ -473,7 +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
@@ -533,10 +575,17 @@ 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 +593,20 @@ 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)
@@ -580,21 +638,15 @@ 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
       {
@@ -680,6 +732,8 @@ 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
@@ -689,16 +743,45 @@ 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: "
@@ -717,6 +800,9 @@ 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)
           {
@@ -773,9 +859,10 @@ 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)