X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FWSThread.java;h=72d1e4f76c1e3e4ba40d2a584f360f897e65a0a7;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=f3dd9694a78f4388827aadb3471f292872a819e1;hpb=01f128f638fcb801e19fa39041a160f18ae1e4ab;p=jalview.git

diff --git a/src/jalview/ws/WSThread.java b/src/jalview/ws/WSThread.java
index f3dd969..72d1e4f 100644
--- a/src/jalview/ws/WSThread.java
+++ b/src/jalview/ws/WSThread.java
@@ -1,349 +1,480 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 javax.swing.*;
-
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-
-public abstract class WSThread
-    extends Thread
-{
-  /**
-   * Generic properties for Web Service Client threads.
-   */
-  AlignFrame alignFrame = null;
-  WebserviceInfo wsInfo = null;
-  AlignmentView input = null;
-  AlignedCodonFrame[] codonframe = null;
-  boolean jobComplete = false;
-  
-  abstract class WSJob
-  {
-    /**
-     * Generic properties for an individual job within a Web Service Client thread
-     */
-    int jobnum = 0; // WebServiceInfo pane for this job
-    String jobId; // ws job ticket
-    boolean cancelled = false;
-    int allowedServerExceptions = 3; // job dies if too many exceptions.
-    boolean submitted = false;
-    boolean subjobComplete = false;
-    /**
-     *
-     * @return true if job has completed and valid results are available
-     */
-    abstract boolean hasResults();
-
-    /**
-     *
-     * @return boolean true if job can be submitted.
-     */
-    abstract boolean hasValidInput();
-
-    vamsas.objects.simple.Result result;
-  }
-
-  class JobStateSummary
-  {
-    int running = 0;
-    int queuing = 0;
-    int finished = 0;
-    int error = 0;
-    int serror = 0;
-    int cancelled = 0;
-    int results = 0;
-    void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
-                             WSJob j)
-    {
-      if (j.result != null)
-      {
-        String progheader = "";
-        // Parse state of job[j]
-        if (j.result.isRunning())
-        {
-          running++;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
-        }
-        else if (j.result.isQueued())
-        {
-          queuing++;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
-        }
-        else if (j.result.isFinished())
-        {
-          finished++;
-          j.subjobComplete = true;
-          if (j.hasResults())
-          {
-            results++;
-          }
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else if (j.result.isFailed())
-        {
-          progheader += "Job failed.\n";
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-          error++;
-        }
-        else if (j.result.isServerError())
-        {
-          serror++;
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum,
-                           WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        }
-        else if (j.result.isBroken() || j.result.isFailed())
-        {
-          error++;
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-        }
-        // and pass on any sub-job messages to the user
-        wsInfo.setProgressText(j.jobnum, OutputHeader);
-        wsInfo.appendProgressText(j.jobnum, progheader);
-        if (j.result.getStatus() != null)
-        {
-          wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
-        }
-      }
-      else
-      {
-        if (j.submitted && j.subjobComplete)
-        {
-          if (j.allowedServerExceptions == 0)
-          {
-            serror++;
-          }
-          else if (j.result == null)
-          {
-            error++;
-          }
-        }
-      }
-    }
-  }
-
-  WSJob jobs[] = null;
-  String WebServiceName = null;
-  String OutputHeader;
-  String WsUrl = null;
-  abstract void pollJob(WSJob job)
-      throws Exception;
-
-  public void run()
-  {
-    JobStateSummary jstate = null;
-    if (jobs == null)
-    {
-      jobComplete = true;
-    }
-    while (!jobComplete)
-    {
-      jstate = new JobStateSummary();
-      for (int j = 0; j < jobs.length; j++)
-      {
-
-        if (!jobs[j].submitted && jobs[j].hasValidInput())
-        {
-          StartJob(jobs[j]);
-        }
-
-        if (jobs[j].submitted && !jobs[j].subjobComplete)
-        {
-          try
-          {
-            pollJob(jobs[j]);
-            if (jobs[j].result == null)
-            {
-              throw (new Exception(
-                  "Timed out when communicating with server\nTry again later.\n"));
-            }
-            jalview.bin.Cache.log.debug("Job " + j + " Result state " +
-                                        jobs[j].result.getState()
-                                        + "(ServerError=" +
-                                        jobs[j].result.isServerError() + ")");
-          }
-          catch (Exception ex)
-          {
-            // Deal with Transaction exceptions
-            wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
-                                      + " Server exception!\n" + ex.getMessage());
-            Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
-                           + ") Server exception: " + ex.getMessage());
-
-            if (jobs[j].allowedServerExceptions > 0)
-            {
-              jobs[j].allowedServerExceptions--;
-              Cache.log.debug("Sleeping after a server exception.");
-              try
-              {
-                Thread.sleep(5000);
-              }
-              catch (InterruptedException ex1)
-              {
-              }
-            }
-            else
-            {
-              Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
-              jobs[j].subjobComplete = true;
-              wsInfo.setStatus(jobs[j].jobnum,
-                               WebserviceInfo.STATE_STOPPED_SERVERERROR);
-            }
-          }
-          catch (OutOfMemoryError er)
-          {
-            jobComplete = true;
-            jobs[j].subjobComplete = true;
-            jobs[j].result = null; // may contain out of date result object
-            wsInfo.setStatus(jobs[j].jobnum,
-                             WebserviceInfo.STATE_STOPPED_ERROR);
-            JOptionPane
-                .showInternalMessageDialog(
-                    Desktop.desktop,
-                    "Out of memory handling result for job !!"
-                    +
-                    "\nSee help files for increasing Java Virtual Machine memory.",
-                    "Out of memory", JOptionPane.WARNING_MESSAGE);
-            Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
-                            WsUrl + "/" + jobs[j].jobId, er);
-            System.gc();
-          }
-        }
-        jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-      }
-      // Decide on overall state based on collected jobs[] states
-      if (jstate.running > 0)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-      }
-      else if (jstate.queuing > 0)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-      }
-      else
-      {
-        jobComplete = true;
-        if (jstate.finished > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else if (jstate.error > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-        }
-        else if (jstate.serror > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        }
-      }
-      if (!jobComplete)
-      {
-        try
-        {
-          Thread.sleep(5000);
-        }
-        catch (InterruptedException e)
-        {
-          Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
-        }
-        // System.out.println("I'm alive "+alTitle);
-      }
-    }
-    if (jobComplete && jobs != null)
-    {
-      parseResult(); // tidy up and make results available to user
-    }
-    else
-    {
-      Cache.log.debug("WebServiceJob poll loop finished with no jobs created.");
-    }
-  }
-
-  abstract void StartJob(WSJob job);
-
-  abstract void parseResult();
-
-  protected void propagateDatasetMappings(Alignment al)
-  {
-    if (codonframe!=null)
-    {
-      SequenceI[] alignment = al.getSequencesArray();
-      for (int sq = 0; sq<alignment.length; sq++)
-      {
-        for (int i=0; i<codonframe.length; i++)
-        {
-          if (codonframe[i]!=null &&
-                  codonframe[i].involvesSequence(alignment[sq]))
-          {
-            al.addCodonFrame(codonframe[i]);
-            codonframe[i] = null;
-            break;
-          }
-        }
-      }
-    }
-  }
-
-  /**
-   * 
-   * @param alignFrame reference for copying mappings across
-   * @param wsInfo gui attachment point
-   * @param input input data for the calculation
-   * @param webServiceName name of service
-   * @param wsUrl  url of the service being invoked
-   */
-  public WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
-          AlignmentView input, String webServiceName,
-          String wsUrl)
-  {
-    this(alignFrame, wsinfo, input, wsUrl);
-    WebServiceName = webServiceName;
-  }
-
-  /**
-   * 
-   * @param alframe - reference for copying mappings across
-   * @param wsinfo2 - gui attachment point
-   * @param alview - input data for the calculation
-   * @param wsurl2 - url of the service being invoked
-   */
-  public WSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
-          AlignmentView alview, String wsurl2)
-  {
-    super();
-    this.alignFrame = alframe;
-    this.wsInfo = wsinfo2;
-    this.input = alview;
-    WsUrl = wsurl2;
-    if (alignFrame!=null)
-    {
-      AlignedCodonFrame[] cf = alignFrame.getViewport().getAlignment().getCodonFrames();
-      if (cf!=null)
-      {
-        codonframe = new AlignedCodonFrame[cf.length];
-        System.arraycopy(cf, 0, codonframe, 0, cf.length);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 javax.swing.*;
+
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+
+public abstract class WSThread extends Thread
+{
+  /**
+   * Generic properties for Web Service Client threads.
+   */
+  /**
+   * view that this job was associated with
+   */
+  AlignmentI currentView = null;
+
+  /**
+   * feature settings from view that job was associated with
+   */
+  FeatureRendererSettings featureSettings = null;
+
+  /**
+   * metadata about this web service
+   */
+  WebserviceInfo wsInfo = null;
+
+  /**
+   * original input data for this job
+   */
+  AlignmentView input = null;
+
+  /**
+   * dataset sequence relationships to be propagated onto new results
+   */
+  AlignedCodonFrame[] codonframe = null;
+
+  /**
+   * are there jobs still running in this thread.
+   */
+  boolean jobComplete = false;
+
+  abstract class WSJob
+  {
+    /**
+     * Generic properties for an individual job within a Web Service Client
+     * thread
+     */
+    int jobnum = 0; // WebServiceInfo pane for this job
+
+    String jobId; // ws job ticket
+
+    /**
+     * has job been cancelled
+     */
+    boolean cancelled = false;
+
+    /**
+     * number of exceptions left before job dies
+     */
+    int allowedServerExceptions = 3;
+
+    /**
+     * has job been submitted
+     */
+    boolean submitted = false;
+
+    /**
+     * are all sub-jobs complete
+     */
+    boolean subjobComplete = false;
+
+    /**
+     * 
+     * @return true if job has completed and valid results are available
+     */
+    abstract boolean hasResults();
+
+    /**
+     * 
+     * @return boolean true if job can be submitted.
+     */
+    abstract boolean hasValidInput();
+
+    /**
+     * The last result object returned by the service.
+     */
+    vamsas.objects.simple.Result result;
+  }
+
+  class JobStateSummary
+  {
+    /**
+     * number of jobs running
+     */
+    int running = 0;
+
+    /**
+     * number of jobs queued
+     */
+    int queuing = 0;
+
+    /**
+     * number of jobs finished
+     */
+    int finished = 0;
+
+    /**
+     * number of jobs failed
+     */
+    int error = 0;
+
+    /**
+     * number of jobs stopped due to server error
+     */
+    int serror = 0;
+
+    /**
+     * number of jobs cancelled
+     */
+    int cancelled = 0;
+
+    /**
+     * number of jobs finished with results
+     */
+    int results = 0;
+
+    /**
+     * processes WSJob and updates job status counters and WebService status
+     * displays
+     * 
+     * @param wsInfo
+     * @param OutputHeader
+     * @param j
+     */
+    void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
+            WSJob j)
+    {
+      if (j.result != null)
+      {
+        String progheader = "";
+        // Parse state of job[j]
+        if (j.result.isRunning())
+        {
+          running++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
+        }
+        else if (j.result.isQueued())
+        {
+          queuing++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
+        }
+        else if (j.result.isFinished())
+        {
+          finished++;
+          j.subjobComplete = true;
+          if (j.hasResults())
+          {
+            results++;
+          }
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else if (j.result.isFailed())
+        {
+          progheader += "Job failed.\n";
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+          error++;
+        }
+        else if (j.result.isServerError())
+        {
+          serror++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum,
+                  WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        }
+        else if (j.result.isBroken() || j.result.isFailed())
+        {
+          error++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        // and pass on any sub-job messages to the user
+        wsInfo.setProgressText(j.jobnum, OutputHeader);
+        wsInfo.appendProgressText(j.jobnum, progheader);
+        if (j.result.getStatus() != null)
+        {
+          wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
+        }
+      }
+      else
+      {
+        if (j.submitted && j.subjobComplete)
+        {
+          if (j.allowedServerExceptions == 0)
+          {
+            serror++;
+          }
+          else if (j.result == null)
+          {
+            error++;
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * one or more jobs being managed by this thread.
+   */
+  WSJob jobs[] = null;
+
+  /**
+   * full name of service
+   */
+  String WebServiceName = null;
+
+  String OutputHeader;
+
+  String WsUrl = null;
+
+  /**
+   * query web service for status of job. on return, job.result must not be null -
+   * if it is then it will be assumed that the job status query timed out and a
+   * server exception will be logged.
+   * 
+   * @param job
+   * @throws Exception
+   *                 will be logged as a server exception for this job
+   */
+  abstract void pollJob(WSJob job) throws Exception;
+
+  public void run()
+  {
+    JobStateSummary jstate = null;
+    if (jobs == null)
+    {
+      jobComplete = true;
+    }
+    while (!jobComplete)
+    {
+      jstate = new JobStateSummary();
+      for (int j = 0; j < jobs.length; j++)
+      {
+
+        if (!jobs[j].submitted && jobs[j].hasValidInput())
+        {
+          StartJob(jobs[j]);
+        }
+
+        if (jobs[j].submitted && !jobs[j].subjobComplete)
+        {
+          try
+          {
+            pollJob(jobs[j]);
+            if (jobs[j].result == null)
+            {
+              throw (new Exception(
+                      "Timed out when communicating with server\nTry again later.\n"));
+            }
+            jalview.bin.Cache.log.debug("Job " + j + " Result state "
+                    + jobs[j].result.getState() + "(ServerError="
+                    + jobs[j].result.isServerError() + ")");
+          } catch (Exception ex)
+          {
+            // Deal with Transaction exceptions
+            wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
+                    + " Server exception!\n" + ex.getMessage());
+            Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+                    + ") Server exception: " + ex.getMessage());
+
+            if (jobs[j].allowedServerExceptions > 0)
+            {
+              jobs[j].allowedServerExceptions--;
+              Cache.log.debug("Sleeping after a server exception.");
+              try
+              {
+                Thread.sleep(5000);
+              } catch (InterruptedException ex1)
+              {
+              }
+            }
+            else
+            {
+              Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+              jobs[j].subjobComplete = true;
+              wsInfo.setStatus(jobs[j].jobnum,
+                      WebserviceInfo.STATE_STOPPED_SERVERERROR);
+            }
+          } catch (OutOfMemoryError er)
+          {
+            jobComplete = true;
+            jobs[j].subjobComplete = true;
+            jobs[j].result = null; // may contain out of date result object
+            wsInfo.setStatus(jobs[j].jobnum,
+                    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);
+            System.gc();
+          }
+        }
+        jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+      }
+      // Decide on overall state based on collected jobs[] states
+      if (jstate.running > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+      }
+      else if (jstate.queuing > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+      }
+      else
+      {
+        jobComplete = true;
+        if (jstate.finished > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else if (jstate.error > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        else if (jstate.serror > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        }
+      }
+      if (!jobComplete)
+      {
+        try
+        {
+          Thread.sleep(5000);
+        } catch (InterruptedException e)
+        {
+          Cache.log
+                  .debug("Interrupted sleep waiting for next job poll.", e);
+        }
+        // System.out.println("I'm alive "+alTitle);
+      }
+    }
+    if (jobComplete && jobs != null)
+    {
+      parseResult(); // tidy up and make results available to user
+    }
+    else
+    {
+      Cache.log
+              .debug("WebServiceJob poll loop finished with no jobs created.");
+      wsInfo.setFinishedNoResults();
+    }
+  }
+
+  /**
+   * submit job to web service
+   * 
+   * @param job
+   */
+  abstract void StartJob(WSJob job);
+
+  /**
+   * process the set of WSJob objects into a set of results, and tidy up.
+   */
+  abstract void parseResult();
+
+  /**
+   * helper function to conserve dataset references to sequence objects returned
+   * from web services 1. Propagates AlCodonFrame data from
+   * <code>codonframe</code> to <code>al</code>
+   * 
+   * @param al
+   */
+  protected void propagateDatasetMappings(Alignment al)
+  {
+    if (codonframe != null)
+    {
+      SequenceI[] alignment = al.getSequencesArray();
+      for (int sq = 0; sq < alignment.length; sq++)
+      {
+        for (int i = 0; i < codonframe.length; i++)
+        {
+          if (codonframe[i] != null
+                  && codonframe[i].involvesSequence(alignment[sq]))
+          {
+            al.addCodonFrame(codonframe[i]);
+            codonframe[i] = null;
+            break;
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * 
+   * @param alignFrame
+   *                reference for copying mappings across
+   * @param wsInfo
+   *                gui attachment point
+   * @param input
+   *                input data for the calculation
+   * @param webServiceName
+   *                name of service
+   * @param wsUrl
+   *                url of the service being invoked
+   */
+  public WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
+          AlignmentView input, String webServiceName, String wsUrl)
+  {
+    this(alignFrame, wsinfo, input, wsUrl);
+    WebServiceName = webServiceName;
+  }
+
+  char defGapChar = '-';
+
+  /**
+   * 
+   * @return gap character to use for any alignment generation
+   */
+  public char getGapChar()
+  {
+    return defGapChar;
+  }
+
+  /**
+   * 
+   * @param alframe -
+   *                reference for copying mappings and display styles across
+   * @param wsinfo2 -
+   *                gui attachment point
+   * @param alview -
+   *                input data for the calculation
+   * @param wsurl2 -
+   *                url of the service being invoked
+   */
+  public WSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
+          AlignmentView alview, String wsurl2)
+  {
+    super();
+    // this.alignFrame = alframe;
+    currentView = alframe.getCurrentView().getAlignment();
+    featureSettings = alframe.getFeatureRenderer().getSettings();
+    defGapChar = alframe.getViewport().getGapCharacter();
+    this.wsInfo = wsinfo2;
+    this.input = alview;
+    WsUrl = wsurl2;
+    if (alframe != null)
+    {
+      AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+              .getCodonFrames();
+      if (cf != null)
+      {
+        codonframe = new AlignedCodonFrame[cf.length];
+        System.arraycopy(cf, 0, codonframe, 0, cf.length);
+      }
+    }
+  }
+}