X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=7d65cebb08cfd5f3b3476a2ea288fb3b0968fc95;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=91f8ebbfd4d751f3055d015fd2d49f9569d8900d;hpb=24ad8bbb87343e317452c0dcb22efd800e7986d6;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 91f8ebb..7d65ceb 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,88 +1,212 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
-import org.apache.axis.client.*;
-import javax.xml.namespace.QName;
-import java.util.*;
+import ext.vamsas.*;
+
+import jalview.analysis.AlignSeq;
+
 import jalview.datamodel.*;
+
 import jalview.gui.*;
-import javax.swing.*;
+
 import java.util.*;
-import java.awt.*;
-import jalview.analysis.AlignSeq;
-import ext.vamsas.*;
-import vamsas.objects.*;
 
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class MsaWSClient
+    extends WSClient
 {
-  int jobsRunning = 0;
+  /**
+   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+   */
   ext.vamsas.MuscleWS server;
-  WebserviceInfo wsInfo;
+  AlignFrame alignFrame;
+
+
   /**
-   * MsaWSClient
+   * Creates a new MsaWSClient object that uses a service
+   * given by an externally retrieved ServiceHandle
    *
-   * @param msa SequenceI[]
+   * @param sh service handle of type AbstractName(MsaWS)
+   * @param altitle DOCUMENT ME!
+   * @param msa DOCUMENT ME!
+   * @param submitGaps DOCUMENT ME!
+   * @param preserveOrder DOCUMENT ME!
    */
-  public MsaWSClient(SequenceI[] msa)
+
+  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+                     SequenceI[] msa,
+                     boolean submitGaps, boolean preserveOrder,
+                     Alignment seqdataset,
+                     AlignFrame _alignFrame)
   {
-    wsInfo = new jalview.gui.WebserviceInfo("Muscle Alignment job",
-                                "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.");
 
+    alignFrame = _alignFrame;
+    if (!sh.getAbstractName().equals("MsaWS"))
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Service called \n" + sh.getName() +
+          "\nis not a \nMultiple Sequence Alignment Service !",
+                                    "Internal Jalview Error",
+                                    JOptionPane.WARNING_MESSAGE);
 
-    wsInfo.setProgressText("Job details\n");
+      return;
+    }
 
+    if ((wsInfo = this.setWebService(sh))==null)
+     {
+       JOptionPane.showMessageDialog(Desktop.desktop,
+                                     "The Multiple Sequence Alignment Service named " +
+                                     sh.getName() +
+                                     " is unknown", "Internal Jalview Error",
+                                     JOptionPane.WARNING_MESSAGE);
 
-    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
-    try {
-      this.server = (MuscleWS) loc.getMuscleWS(); // JBPNote will be set from properties
-    }
-    catch (Exception ex) {
-      wsInfo.setProgressText("Serious! MuscleWS Service location failed\nfor URL :"
-                     +loc.getMuscleWSAddress()+"\n"+ex.getMessage());
-      ex.printStackTrace();
+       return;
+     }
+    startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
+
+  }
+
+
+  private void startMsaWSClient(String altitle, SequenceI[] msa,
+                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+  {
+    if (!locateWebService())
+    {
+      return;
     }
 
-    MsaWSThread musclethread = new MsaWSThread(msa);
+    wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +
+                           " of " + altitle + "\nJob details\n");
+
+    MsaWSThread musclethread = new MsaWSThread(WebServiceName +
+                                               " alignment of " + altitle, msa,
+                                               submitGaps, preserveOrder, seqdataset);
     wsInfo.setthisService(musclethread);
     musclethread.start();
   }
 
-
-  protected class MsaWSThread extends Thread implements WSClientI
+  /**
+   * Initializes the server field with a valid service implementation.
+   *
+   * @return true if service was located.
+   */
+  private boolean locateWebService()
   {
-    String ServiceName = "MuscleWS";
-    public boolean isCancellable()
+    // TODO: MuscleWS transmuted to generic MsaWS client
+    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
+
+    try
     {
-      return true;
+      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+      ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
+    }
+    catch (Exception ex)
+    {
+      wsInfo.setProgressText("Serious! " + WebServiceName +
+                             " Service location failed\nfor URL :" + WsURL +
+                             "\n" +
+                             ex.getMessage());
+      wsInfo.setStatus(WebserviceInfo.ERROR);
+      ex.printStackTrace();
+
+      return false;
     }
 
+    loc.getEngine().setOption("axis", "1");
+
+    return true;
+  }
+
+  protected class MsaWSThread
+      extends Thread implements WSClientI
+  {
+    String ServiceName = WebServiceName;
     String OutputHeader;
     vamsas.objects.simple.MsaResult result = null;
     vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
         SequenceSet();
+    Hashtable SeqNames = null;
+    boolean submitGaps = false; // pass sequences including gaps to alignment service
+    boolean preserveOrder = true; // and always store and recover sequence order
     String jobId;
+    String alTitle; // name which will be used to form new alignment window.
     int allowedServerExceptions = 3; // thread dies if too many exceptions.
-    MsaWSThread(SequenceI[] msa)
+    boolean jobComplete = false;
+
+    Alignment dataset; // dataset to which the new alignment will be associated.
+
+    MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
+                boolean presorder, Alignment seqset)
     {
+      alTitle = title;
+      submitGaps = subgaps;
+      preserveOrder = presorder;
+      dataset = seqset;
       OutputHeader = wsInfo.getProgressText();
+      SeqNames = new Hashtable();
+
       vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
           Sequence[msa.length];
+
       for (int i = 0; i < msa.length; i++)
       {
+        String newname = jalview.analysis.SeqsetUtils.unique_name(i);
+
+        // uniquify as we go
+        // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
+        SeqNames.put(newname,
+                     jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
         seqarray[i] = new vamsas.objects.simple.Sequence();
-        seqarray[i].setId(msa[i].getName());
-        seqarray[i].setSeq(AlignSeq.extractGaps("-. ", msa[i].getSequence()));
+        seqarray[i].setId(newname);
+        seqarray[i].setSeq( (submitGaps) ? msa[i].getSequence()
+                           : AlignSeq.extractGaps(
+                               jalview.util.Comparison.GapChars,
+                               msa[i].getSequence()));
       }
+
       this.seqs = new vamsas.objects.simple.SequenceSet();
       this.seqs.setSeqs(seqarray);
     }
 
-    boolean jobComplete = false;
+    public boolean isCancellable()
+    {
+      return true;
+    }
+
+    public void cancelJob()
+    {
+      if ( (jobId != null) && !jobId.equals("") && !jobComplete)
+      {
+        String cancelledMessage = "";
 
-    public void cancelJob() {
-      if (!jobComplete) {
-        String cancelledMessage="";
-        try {
+        try
+        {
           vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
+
           if (cancelledJob.getStatus() == 2)
           {
             // CANCELLED_JOB
@@ -92,68 +216,158 @@ public class MsaWSClient
             jobsRunning--;
             result = null;
           }
-          else
-          if (cancelledJob.getStatus() == 3)
+          else if (cancelledJob.getStatus() == 3)
           {
             // VALID UNSTOPPABLE JOB
             cancelledMessage +=
                 "Server cannot cancel this job. just close the window.\n";
           }
+
           if (cancelledJob.getJobId() != null)
-            cancelledMessage += "[" + cancelledJob.getJobId() + "]";
-          cancelledMessage +="\n";
-        } catch (Exception exc) {
-          cancelledMessage +="\nProblems cancelling the job : Exception received...\n"+exc+"\n";
+          {
+            cancelledMessage += ("[" + cancelledJob.getJobId() +
+                                 "]");
+          }
+
+          cancelledMessage += "\n";
+        }
+        catch (Exception exc)
+        {
+          cancelledMessage +=
+              ("\nProblems cancelling the job : Exception received...\n" +
+               exc + "\n");
           exc.printStackTrace();
         }
-        wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");
+
+        wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");
+      }
+      else
+      {
+        if (!jobComplete)
+        {
+          wsInfo.setProgressText(OutputHeader +
+                                 "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+        }
       }
     }
 
     public void run()
     {
-
       StartJob();
 
       while (!jobComplete && (allowedServerExceptions > 0))
       {
         try
         {
-          result = server.getResult(jobId);
-
-         if( result.isRunning() )
-           wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-         else if( result.isQueued() )
-           wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+          if ( (result = server.getResult(jobId)) == null)
+          {
+            throw (new Exception(
+                "Timed out when communicating with server\nTry again later.\n"));
+          }
+          jalview.bin.Cache.log.debug("Result state " + result.getState() +
+                                        "(ServerError=" + result.isServerError() +
+                                        ")");
+          if (result.isRunning())
+          {
+            wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+          }
+          else if (result.isQueued())
+          {
+            wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+          }
 
           if (result.isFinished())
           {
+            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
             parseResult();
             jobComplete = true;
             jobsRunning--;
           }
           else
           {
-            wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
-            if (! (result.isJobFailed() || result.isServerError()))
+            if (result.getStatus() != null)
+            {
+              wsInfo.setProgressText(OutputHeader + "\n"+   result.getStatus());
+            }
+            if (result.isServerError())
+            {
+              jobComplete = true;
+              jobsRunning--;
+
+              break;
+            }
+            if (! (result.isJobFailed() || result.isServerError() ||
+                   result.isBroken() || result.isFailed()))
             {
               Thread.sleep(5000);
+
               //  System.out.println("I'm alive "+seqid+" "+jobid);
             }
+            else
+            {
+              jobComplete = true;
+              jobsRunning--;
+              break;
+            }
           }
         }
         catch (Exception ex)
         {
           allowedServerExceptions--;
-          wsInfo.appendProgressText("\n"+ServiceName+" Server exception!\n" + ex.getMessage());
-          ex.printStackTrace();
+          wsInfo.appendProgressText("\n" + ServiceName +
+                                    " Server exception!\n" + ex.getMessage());
+          System.err.println(ServiceName + " Server exception: " +
+                             ex.getMessage());
+
+          //          ex.printStackTrace(); JBPNote Debug
+          try
+          {
+            if (allowedServerExceptions > 0)
+            {
+              Thread.sleep(5000);
+            }
+          }
+          catch (InterruptedException ex1)
+          {
+          }
+        }
+        catch(OutOfMemoryError er)
+        {
+          jobComplete = true;
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "Out of memory handling result!!"
+             +"\nSee help files for increasing Java Virtual Machine memory."
+             ,"Out of memory", JOptionPane.WARNING_MESSAGE );
+          System.out.println("MsaWSClient: "+er);
+          System.gc();
         }
       }
 
-      if (! (result!=null && (result.isJobFailed() || result.isServerError())))
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+      if (allowedServerExceptions == 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      }
       else
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+      {
+        if (result != null)
+        {
+          if ( !(result.isJobFailed() || result.isServerError()))
+          {
+            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+          }
+
+          if (result.isBroken() || result.isFailed())
+          {
+            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+          }
+
+          if (result.isServerError())
+          {
+            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+          }
+        }
+      }
     }
 
     void StartJob()
@@ -161,74 +375,126 @@ public class MsaWSClient
       try
       {
         vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
-        if (jobsubmit.getStatus()==1) {
-          System.out.println(jobId=jobsubmit.getJobId());
-        } else {
+
+        if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
+        {
+          jobId = jobsubmit.getJobId();
+          System.out.println(WsURL + " Job Id '" + jobId + "'");
+        }
+        else
+        {
+          if (jobsubmit == null)
+          {
+            throw new Exception("Server at " + WsURL +
+                                " returned null object, it probably cannot be contacted. Try again later ?");
+          }
+
           throw new Exception(jobsubmit.getJobId());
         }
       }
       catch (Exception e)
       {
-        System.out.println(ServiceName + " Client: Failed to submit the prediction\n" +
-                           e.toString() + "\n");
-        e.printStackTrace();
+        // TODO: JBPNote catch timeout or other fault types explicitly
+        // For unexpected errors
+        System.err.println(WebServiceName +
+                           "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" +
+                           "When contacting Server:" + WsURL + "\n" +
+                           e.toString() +
+                           "\n");
+        this.allowedServerExceptions = 0;
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        wsInfo.appendProgressText(
+            "Failed to submit sequences for alignment.\n" +
+            "It is most likely that there is a problem with the server.\n" +
+            "Just close the window\n");
+
+        // e.printStackTrace(); // TODO: JBPNote DEBUG
       }
     }
 
-    private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) {
+    private jalview.datamodel.Sequence[] getVamsasAlignment(
+        vamsas.objects.simple.Alignment valign)
+    {
+      vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+      jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
+          length];
 
-      Annotation[] annotations = new Annotation[al.getWidth()];
-      for (int j = 0; j < values.size(); j++)
+      for (int i = 0, j = seqs.length; i < j; i++)
       {
-        float value = Float.parseFloat(values.get(j).toString());
-        annotations[gapmap[j]] = new Annotation("", value+"",' ',value);
+        msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
+                                                seqs[i].getSeq());
       }
-      al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength));
-    }
-    private jalview.datamodel.Sequence[] getVamsasAlignment(vamsas.objects.simple.Alignment valign) {
-      vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
-      jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
-      for (int i=0, j=seqs.length; i<j;i++)
-        msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i].getSeq());
+
       return msa;
     }
+
     void parseResult()
     {
-      SequenceI[] seqs=null;
-      try {
+      SequenceI[] seqs = null;
+
+      try
+      {
         // OutputHeader = output.getText();
-        if (result.isFailed()) {
-          OutputHeader +="Job failed.\n";
+        if (result.isFailed())
+        {
+          OutputHeader += "Job failed.\n";
         }
-        if (result.getStatus()!=null) {
-          OutputHeader += "\n"+result.getStatus();
+
+        if (result.getStatus() != null)
+        {
+          OutputHeader += ("\n" + result.getStatus());
         }
-        if (result.getMsa()!=null) {
+
+        if (result.getMsa() != null)
+        {
           OutputHeader += "\nAlignment Object Method Notes\n";
-          String lines[] = result.getMsa().getMethod();
-          for (int line=0;line<lines.length; line++)
-            OutputHeader+=lines[line]+"\n";
+
+          String[] lines = result.getMsa().getMethod();
+
+          for (int line = 0; line < lines.length; line++)
+          {
+            OutputHeader += (lines[line] + "\n");
+          }
 
           // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
           seqs = getVamsasAlignment(result.getMsa());
         }
 
         wsInfo.setProgressText(OutputHeader);
-        if (seqs!=null) {
-          Alignment al;
-          al = new Alignment(seqs);
 
+        if (seqs != null)
+        {
+          AlignmentOrder msaorder = new AlignmentOrder(seqs);
+
+          if (preserveOrder)
+          {
+            jalview.analysis.AlignmentSorter.recoverOrder(seqs);
+          }
+
+          jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
+
+          Alignment al = new Alignment(seqs);
+          if (dataset!=null) {
+            al.setDataset(dataset);
+          }
           // TODO: JBPNote Should also rename the query sequence sometime...
           AlignFrame af = new AlignFrame(al);
-          Desktop.addInternalFrame(af,
-                                   ServiceName + " Alignment",
+
+          //>>>This is a fix for the moment, until a better solution is found!!<<<
+          af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+          af.addSortByOrderMenuItem(ServiceName + " Ordering",
+                                    msaorder);
+
+          Desktop.addInternalFrame(af, alTitle,
                                    AlignFrame.NEW_WINDOW_WIDTH,
                                    AlignFrame.NEW_WINDOW_HEIGHT);
         }
-      }catch(Exception ex){ex.printStackTrace();}
-
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
     }
-
   }
-  }
-
+}