JAL-974 JAL-975 try to cope with temporary server errors and timeouts

diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index 630faae..1d23ec0 100644 (file)
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -4,8 +4,11 @@ import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.IProgressIndicator;
@@ -14,13 +17,18 @@ import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
+import com.sun.xml.internal.ws.client.ClientTransportException;
+
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.Score;
 import compbio.data.sequence.ScoreManager;
 import compbio.metadata.Argument;
 import compbio.metadata.ChunkHolder;
@@ -117,6 +125,8 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     }
     long progressId = -1;
 
+    int serverErrorsLeft = 3;
+
     String rslt = "JOB NOT DEFINED";
     StringBuffer msg=new StringBuffer();
     try
@@ -189,30 +199,42 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
           return;
         }
         long cpos;
-        ChunkHolder stats;
+        ChunkHolder stats = null;
         do
         {
           cpos = rpos;
-          try
+          boolean retry = false;
+          do
           {
-            stats = aaservice.pullExecStatistics(rslt, rpos);
-          } catch (Exception x)
-          {
-
-            if (x.getMessage().contains(
-                    "Position in a file could not be negative!"))
+            try
             {
-              // squash index out of bounds exception- seems to happen for
-              // disorder predictors which don't (apparently) produce any
-              // progress information and JABA server throws an exception
-              // because progress length is -1.
-              stats = null;
-            }
-            else
+              stats = aaservice.pullExecStatistics(rslt, rpos);
+            }  catch (Exception x)
             {
-              throw x;
+
+              if (x.getMessage().contains(
+                      "Position in a file could not be negative!"))
+              {
+                // squash index out of bounds exception- seems to happen for
+                // disorder predictors which don't (apparently) produce any
+                // progress information and JABA server throws an exception
+                // because progress length is -1.
+                stats = null;
+              }
+              else
+              {
+                if (--serverErrorsLeft > 0)
+                {
+                  retry = true;
+                  try {
+                    Thread.sleep(200);
+                  } catch (InterruptedException q) {};
+                } else {
+                  throw x;
+                }
+              }
             }
-          }
+          } while (retry);
           if (stats != null)
           {
             System.out.print(stats.getChunk());
@@ -232,23 +254,31 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
           ;
         }
       } while (!finished);
-      try
+      if (serverErrorsLeft>0)
       {
-        Thread.sleep(200);
-      } catch (InterruptedException x)
-      {
-      }
-      ;
-      scoremanager = aaservice.getAnnotation(rslt);
-      if (scoremanager != null)
-      {
-        jalview.bin.Cache.log.debug("Updating result annotation from Job "+rslt+" at "+service.getUri());
-        updateResultAnnotation(true);
+        try
+        {
+          Thread.sleep(200);
+        } catch (InterruptedException x)
+        {
+        }
+        ;
+        scoremanager = aaservice.getAnnotation(rslt);
+        if (scoremanager != null)
+        {
+          jalview.bin.Cache.log
+                  .debug("Updating result annotation from Job " + rslt
+                          + " at " + service.getUri());
+          updateResultAnnotation(true);
+        }
       }
-    } catch (JobSubmissionException x)
+    }
+
+    catch (JobSubmissionException x)
     {
 
-      System.err.println("submission error with "+getServiceActionText()+" :");
+      System.err.println("submission error with " + getServiceActionText()
+              + " :");
       x.printStackTrace();
       calcMan.workerCannotRun(this);
     } catch (ResultNotAvailableException x)