only indicate that job is broken if it wasn't submitted correctly

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index d2b4ce9..0049001 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -606,6 +606,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         j.setSubmitted(true);
         j.setSubjobComplete(false);
         // System.out.println(WsURL + " Job Id '" + jobId + "'");
+        return;
       }
       else
       {
@@ -630,8 +631,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
               + _lex.getMessage());
       wsInfo.warnUser(_lex.getMessage(), "Input is too big!");
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-      wsInfo.setStatus(j.getJobnum(),
-              WebserviceInfo.STATE_STOPPED_ERROR);
+      wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
     } catch (compbio.metadata.WrongParameterException _lex)
     {
       lex = _lex;
@@ -640,10 +640,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI
               + _lex.getMessage()
               + "\nPlease check to make sure you have used the correct parameter set for this service!\n");
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-      wsInfo.setStatus(j.getJobnum(),
-              WebserviceInfo.STATE_STOPPED_ERROR);
-    }
-    catch (Error e)
+      wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
+    } catch (Error e)
     {
       // For unexpected errors
       System.err
@@ -654,8 +652,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.setStatus(j.getJobnum(),
               WebserviceInfo.STATE_STOPPED_SERVERERROR);
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       // For unexpected errors
       System.err
@@ -668,13 +665,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI
               WebserviceInfo.STATE_STOPPED_SERVERERROR);
     } finally
     {
-      // Boilerplate code here
-      // TODO: JBPNote catch timeout or other fault types explicitly
+      if (!j.isSubmitted())
+      {
+        // Boilerplate code here
+        // TODO: JBPNote catch timeout or other fault types explicitly
 
-      j.setAllowedServerExceptions(0);
-      wsInfo.appendProgressText(j.getJobnum(),
-              "Failed to submit sequences for alignment.\n"
-                      + "Just close the window\n");
+        j.setAllowedServerExceptions(0);
+        wsInfo.appendProgressText(j.getJobnum(),
+                "Failed to submit sequences for alignment.\n"
+                        + "Just close the window\n");
+      }
     }
   }
 
@@ -712,11 +712,13 @@ class MsaWSThread extends AWS2Thread implements WSClientI
             msjob.alignment = server.getResult(msjob.getJobId());
           } catch (compbio.metadata.ResultNotAvailableException e)
           {
-            // job has failed for some reason - probably due to invalid parameters
-            Cache.log.debug("Results not available for finished job - marking as broken job.",e);
+            // job has failed for some reason - probably due to invalid
+            // parameters
+            Cache.log
+                    .debug("Results not available for finished job - marking as broken job.",
+                            e);
             msjob.setjobStatus(JobStatus.FAILED);
-          }
-            catch (Exception e)
+          } catch (Exception e)
           {
             Cache.log.error("Couldn't get Alignment for job.", e);
             // TODO: Increment count and retry ?