JAL-1517 update copyright to version 2.8.2

[jalview.git] / src / jalview / ws / AWSThread.java

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index d49b245..0167690 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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;
 
 import jalview.bin.Cache;
@@ -17,47 +35,57 @@ public abstract class AWSThread extends Thread
    * view that this job was associated with
    */
   protected AlignmentI currentView = null;
+
   /**
    * feature settings from view that job was associated with
    */
   protected FeatureRendererSettings featureSettings = null;
+
   /**
    * metadata about this web service
    */
   protected WebserviceInfo wsInfo = null;
+
   /**
    * original input data for this job
    */
   protected AlignmentView input = null;
+
   /**
    * dataset sequence relationships to be propagated onto new results
    */
   protected AlignedCodonFrame[] codonframe = null;
+
   /**
    * are there jobs still running in this thread.
    */
   protected boolean jobComplete = false;
+
   /**
    * one or more jobs being managed by this thread.
    */
   protected AWsJob jobs[] = null;
+
   /**
    * full name of service
    */
   protected String WebServiceName = null;
+
   protected char defGapChar = '-';
+
   /**
    * header prepended to all output from job
    */
   protected String OutputHeader;
 
   /**
-   * only used when reporting a web service out of memory error - the job ID will be concatenated to the URL
+   * only used when reporting a web service out of memory error - the job ID
+   * will be concatenated to the URL
    */
   protected String WsUrl = null;
 
   /**
-   * generic web service job/subjob poll loop 
+   * generic web service job/subjob poll loop
    */
   public void run()
   {
@@ -97,7 +125,9 @@ public abstract class AWSThread extends Thread
                     + " Server exception!\n" + ex.getMessage());
             // always output the exception's stack trace to the log
             Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
-                    + ") Server exception.",ex);
+                    + ") Server exception.");
+            // todo: could limit trace to cause if this is a SOAPFaultException.
+            ex.printStackTrace();
 
             if (jobs[j].allowedServerExceptions > 0)
             {
@@ -134,30 +164,7 @@ public abstract class AWSThread extends Thread
         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);
-        }
-      }
+      updateGlobalStatus(jstate);
       if (!jobComplete)
       {
         try
@@ -179,10 +186,39 @@ public abstract class AWSThread extends Thread
     {
       Cache.log
               .debug("WebServiceJob poll loop finished with no jobs created.");
+      wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
+      wsInfo.appendProgressText("No jobs ran.");
       wsInfo.setFinishedNoResults();
     }
   }
 
+  protected void updateGlobalStatus(JobStateSummary jstate)
+  {
+    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);
+      }
+    }
+  }
 
   public AWSThread()
   {
@@ -245,8 +281,8 @@ public abstract class AWSThread extends Thread
   /**
    * 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>
-   * TODO: refactor to datamodel
+   * <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
+   * 
    * @param al
    */
   public void propagateDatasetMappings(Alignment al)
@@ -306,11 +342,12 @@ public abstract class AWSThread extends Thread
   }
 
   /**
+   * Extracts additional info from alignment view's context.
    * 
    * @param alframe
    *          - reference for copying mappings and display styles across
    * @param wsinfo2
-   *          - gui attachment point
+   *          - gui attachment point - may be null
    * @param alview
    *          - input data for the calculation
    * @param wsurl2