X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=94e19e794c1efd0d1f4a5d2fb29514a5f94d5d05;hb=c954e7c8d0953fee214bf897608410a1bc41ec13;hp=44ffa113e73171c3491e94b263663d64d07a9e36;hpb=895aec0787b4b2104c1a78d98fab530d586693ac;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 44ffa11..94e19e7 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,233 +1,378 @@
+/*
+* 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 org.apache.axis.client.*;
+
 import vamsas.objects.*;
 
-public class MsaWSClient
-{
-  int jobsRunning = 0;
-  ext.vamsas.MuscleWS server;
-  WebserviceInfo wsInfo;
-  /**
-   * MsaWSClient
-   *
-   * @param msa SequenceI[]
-   */
-  public MsaWSClient(SequenceI[] msa)
-  {
-    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.");
+import java.awt.*;
 
+import java.util.*;
 
-    wsInfo.setProgressText("Job details\n");
+import javax.swing.*;
 
+import javax.xml.namespace.QName;
 
-    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();
-    }
 
-    MsaWSThread musclethread = new MsaWSThread(msa);
-    wsInfo.setthisService(musclethread);
-    musclethread.start();
-  }
+public class MsaWSClient extends WSClient {
+    /**
+ * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+ */
+    ext.vamsas.MuscleWS server;
 
+    public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,
+        boolean submitGaps, boolean preserveOrder) {
+        if (setWebService(MsaWSName) == false) {
+            JOptionPane.showMessageDialog(Desktop.desktop,
+                "The Multiple Sequence Alignment Service named " + MsaWSName +
+                " is unknown", "Internal Jalview Error",
+                JOptionPane.WARNING_MESSAGE);
 
-  protected class MsaWSThread extends Thread implements WSClientI
-  {
-    String ServiceName = "MuscleWS";
-    public boolean isCancellable()
-    {
-      return true;
+            return;
+        }
+
+        wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,
+                WebServiceReference);
+
+        if (!locateWebService()) {
+            return;
+        }
+
+        wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") +
+            " of " + altitle + "\nJob details\n");
+
+        MsaWSThread musclethread = new MsaWSThread(WebServiceName +
+                " alignment of " + altitle, msa, submitGaps, preserveOrder);
+        wsInfo.setthisService(musclethread);
+        musclethread.start();
     }
 
-    String OutputHeader;
-    vamsas.objects.simple.MsaResult result = null;
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
-        SequenceSet();
-    String jobId;
-    int allowedServerExceptions = 3; // thread dies if too many exceptions.
-    MsaWSThread(SequenceI[] msa)
-    {
-      OutputHeader = wsInfo.getProgressText();
-      vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
-          Sequence[msa.length];
-      for (int i = 0; i < msa.length; i++)
-      {
-        seqarray[i] = new vamsas.objects.simple.Sequence();
-        seqarray[i].setId(msa[i].getName());
-        seqarray[i].setSeq(AlignSeq.extractGaps("-. ", msa[i].getSequence()));
-      }
-      this.seqs = new vamsas.objects.simple.SequenceSet();
-      this.seqs.setSeqs(seqarray);
+    // JBPNote Nasty object-global state setting methods shouldn't be allowed
+    private boolean setWebService(String MsaWSName) {
+        if (MsaWServices.info.containsKey(MsaWSName)) {
+            WebServiceName = MsaWSName;
+
+            String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
+            WsURL = wsinfo[0];
+            WebServiceJobTitle = wsinfo[1];
+            WebServiceReference = wsinfo[2];
+
+            return true;
+        } else {
+            return false;
+        }
     }
 
-    boolean jobComplete = false;
+    private boolean locateWebService() {
+        // TODO: MuscleWS transmuted to generic MsaWS client
+        MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
 
-    public void cancelJob() {
-      if (!jobComplete) {
-        String cancelledMessage="";
         try {
-          vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
-          if (cancelledJob.getStatus() == 2)
-          {
-            // CANCELLED_JOB
-            cancelledMessage = "Job cancelled.";
-            jobComplete = true;
-            jobsRunning--;
-            result = null;
-          }
-          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";
-          exc.printStackTrace();
+            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(wsInfo.ERROR);
+            ex.printStackTrace();
+
+            return false;
         }
-        wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");
-      }
+
+        loc.getEngine().setOption("axis", "1");
+
+        return true;
     }
 
-    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.isFinished())
-          {
-            parseResult();
-            jobComplete = true;
-            jobsRunning--;
-          }
-          else
-          {
-            wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
-            if (! (result.isJobFailed() || result.isServerError()))
-            {
-              Thread.sleep(5000);
-              //  System.out.println("I'm alive "+seqid+" "+jobid);
+    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; // and always store and recover sequence order
+        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.
+        boolean jobComplete = false;
+
+        MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
+            boolean presorder) {
+            alTitle = title;
+            submitGaps = subgaps;
+            preserveOrder = presorder;
+
+            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(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);
         }
-        catch (Exception ex)
-        {
-          allowedServerExceptions--;
-          wsInfo.appendProgressText("\n"+ServiceName+" Server exception!\n" + ex.getMessage());
-          ex.printStackTrace();
+
+        public boolean isCancellable() {
+            return true;
         }
-      }
 
-      if (! (result!=null && (result.isJobFailed() || result.isServerError())))
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-      else
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-    }
+        public void cancelJob() {
+            if ((jobId != null) && !jobId.equals("") && !jobComplete) {
+                String cancelledMessage = "";
 
-    void StartJob()
-    {
-      try
-      {
-        vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
-        if (jobsubmit.getStatus()==1) {
-          System.out.println(jobId=jobsubmit.getJobId());
-        } else {
-          throw new Exception(jobsubmit.getJobId());
+                try {
+                    vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
+
+                    if (cancelledJob.getStatus() == 2) {
+                        // CANCELLED_JOB
+                        cancelledMessage = "Job cancelled.";
+                        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+                        jobComplete = true;
+                        jobsRunning--;
+                        result = null;
+                    } 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");
+                    exc.printStackTrace();
+                }
+
+                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");
+                }
+            }
         }
-      }
-      catch (Exception e)
-      {
-        System.out.println(ServiceName + " Client: Failed to submit the prediction\n" +
-                           e.toString() + "\n");
-        e.printStackTrace();
-      }
-    }
 
-    private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) {
+        public void run() {
+            StartJob();
 
-      Annotation[] annotations = new Annotation[al.getWidth()];
-      for (int j = 0; j < values.size(); j++)
-      {
-        float value = Float.parseFloat(values.get(j).toString());
-        annotations[gapmap[j]] = new Annotation("", value+"",' ',value);
-      }
-      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 {
-        // OutputHeader = output.getText();
-        if (result.isFailed()) {
-          OutputHeader +="Job failed.\n";
+            while (!jobComplete && (allowedServerExceptions > 0)) {
+                try {
+                    if ((result = server.getResult(jobId)) == null) {
+                        throw (new Exception(
+                            "Timed out when communicating with server\nTry again later.\n"));
+                    }
+
+                    if (result.isRunning()) {
+                        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+                    } else if (result.isQueued()) {
+                        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+                    }
+
+                    if (result.isFinished()) {
+                        parseResult();
+                        jobComplete = true;
+                        jobsRunning--;
+                    } else {
+                        if (result.getStatus() != null) {
+                            wsInfo.setProgressText(OutputHeader + "\n" +
+                                result.getStatus());
+                        }
+
+                        if (!(result.isJobFailed() || result.isServerError())) {
+                            Thread.sleep(5000);
+
+                            //  System.out.println("I'm alive "+seqid+" "+jobid);
+                        } else {
+                            break;
+                        }
+                    }
+                } catch (Exception ex) {
+                    allowedServerExceptions--;
+                    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) {
+                    }
+                }
+            }
+
+            if (allowedServerExceptions == 0) {
+                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+            } else {
+                if (!((result != null) &&
+                        (result.isJobFailed() || result.isServerError()))) {
+                    wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+                } else {
+                    if (result.isFailed()) {
+                        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+                    }
+
+                    if (result.isServerError()) {
+                        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+                    }
+                }
+            }
         }
-        if (result.getStatus()!=null) {
-          OutputHeader += "\n"+result.getStatus();
+
+        void StartJob() {
+            try {
+                vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
+
+                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) {
+                // 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(wsInfo.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
+            }
         }
-        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";
-
-          // 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());
+
+        private void addFloatAnnotations(Alignment al, int[] gapmap,
+            Vector values, String Symname, String Visname, float min,
+            float max, int winLength) {
+            Annotation[] annotations = new Annotation[al.getWidth()];
+
+            for (int j = 0; j < values.size(); j++) {
+                float value = Float.parseFloat(values.get(j).toString());
+                annotations[gapmap[j]] = new Annotation("", value + "", ' ',
+                        value);
+            }
+
+            al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
+                    annotations, min, max, winLength));
         }
 
-        wsInfo.setProgressText(OutputHeader);
-        if (seqs!=null) {
-          Alignment al;
-          al = new Alignment(seqs);
-
-          // TODO: JBPNote Should also rename the query sequence sometime...
-          AlignFrame af = new AlignFrame(al);
-          Desktop.addInternalFrame(af,
-                                   ServiceName + " Alignment",
-                                   AlignFrame.NEW_WINDOW_WIDTH,
-                                   AlignFrame.NEW_WINDOW_HEIGHT);
+        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;
         }
-      }catch(Exception ex){ex.printStackTrace();}
 
-    }
+        void parseResult() {
+            SequenceI[] seqs = null;
+
+            try {
+                // OutputHeader = output.getText();
+                if (result.isFailed()) {
+                    OutputHeader += "Job failed.\n";
+                }
+
+                if (result.getStatus() != null) {
+                    OutputHeader += ("\n" + result.getStatus());
+                }
+
+                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");
 
+                    // 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) {
+                    AlignmentOrder msaorder = new AlignmentOrder(seqs);
+
+                    if (preserveOrder) {
+                        jalview.analysis.AlignmentSorter.recoverOrder(seqs);
+                    }
+
+                    jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
+
+                    Alignment al = new Alignment(seqs);
+
+                    // TODO: JBPNote Should also rename the query sequence sometime...
+                    AlignFrame af = new AlignFrame(al);
+                    af.addSortByOrderMenuItem(ServiceName + " Ordering",
+                        msaorder);
+
+                    Desktop.addInternalFrame(af, alTitle,
+                        AlignFrame.NEW_WINDOW_WIDTH,
+                        AlignFrame.NEW_WINDOW_HEIGHT);
+                }
+            } catch (Exception ex) {
+                ex.printStackTrace();
+            }
+        }
+    }
+}