Merge branch 'bug/JAL-3810_annotation_ws_stopping_abruptly' into bug/JAL-3809_ws_para...

diff --git a/src/jalview/javascript/log4j/Logger.java b/src/jalview/javascript/log4j/Logger.java
index 183328d..340e1f9 100644 (file)
--- a/src/jalview/javascript/log4j/Logger.java
+++ b/src/jalview/javascript/log4j/Logger.java
@@ -56,7 +56,7 @@ public class Logger
     if (logger == null)
     {
       registry.put(name, logger = new Logger(name));
-      logger.setLevel(Level.INFO);
+      logger.setLevel(Level.DEBUG);
     }
     return logger;
   }
@@ -80,6 +80,21 @@ public class Logger
   {
     return isEnabled;
   }
+  
+  public void trace(Object o)
+  {
+    trace(o, null);
+  }
+  
+  public void trace(Object o, Throwable e)
+  {
+    switch (level.level)
+    {
+    case Level.TRACE_INT:
+      log(o, e);
+      break;
+    }
+  }
 
   public void debug(Object o)
   {
@@ -91,6 +106,7 @@ public class Logger
     switch (level.level)
     {
     case Priority.DEBUG_INT:
+    case Level.TRACE_INT:
       log(o, e);
       break;
     }
@@ -107,6 +123,7 @@ public class Logger
     {
     case Priority.INFO_INT:
     case Priority.DEBUG_INT:
+    case Level.TRACE_INT:
       log(o, e);
       break;
     }
@@ -125,6 +142,7 @@ public class Logger
     case Priority.WARN_INT:
     case Priority.INFO_INT:
     case Priority.DEBUG_INT:
+    case Level.TRACE_INT:
       log(o, e);
       break;
     }
@@ -144,6 +162,7 @@ public class Logger
     case Priority.WARN_INT:
     case Priority.INFO_INT:
     case Priority.DEBUG_INT:
+    case Level.TRACE_INT:
       log(o, e);
       break;
     }
@@ -155,27 +174,15 @@ public class Logger
     switch (level.level)
     {
     case Priority.ERROR_INT:
-      if (appender == null)
-      {
-        System.err.println(s);
-        return;
-      }
-      break;
     case Priority.WARN_INT:
       if (appender == null)
       {
         System.err.println(s);
         return;
       }
-      break;
     case Priority.INFO_INT:
-      if (appender == null)
-      {
-        System.out.println(s);
-        return;
-      }
-      break;
     case Priority.DEBUG_INT:
+    case Level.TRACE_INT:
       if (appender == null)
       {
         System.out.println(s);
@@ -183,7 +190,10 @@ public class Logger
       }
       break;
     }
-    e.printStackTrace();
+    if (e != null)
+    {
+      e.printStackTrace();
+    }
     appender.append(new LoggingEvent(this, s.toString(), level));
   }
 

diff --git a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
index 4c807e1..aafbbab 100644 (file)
--- a/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
+++ b/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java
@@ -274,7 +274,6 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
     // TODO: handle job submission error reporting here.
     Cache.log.debug("Service " + service.getUri() + "\nSubmitted job ID: "
             + rslt);
-    ;
     // ///
     // otherwise, construct WsJob and any UI handlers
     running = new AnnotationWsJob();
@@ -336,7 +335,7 @@ public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
       Cache.log.debug("Ignoring exception during progress update.",
               thr);
     }
-    Cache.log.trace("Result of poll: " + running.getStatus());
+    Cache.log.debug("Result of poll: " + running.getStatus());
     
     
     if (finished)