From a39e4da5d34f3385ad865ec6d5f7b01e8e5d30a3 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 27 Sep 2011 12:22:33 +0100
Subject: [PATCH] ensure server errors return a URL and response document
 (JAL-715,JAL-724)

---
 src/jalview/ws/rest/RestJobThread.java |  101 +++++++++++++++++++++-----------
 1 file changed, 67 insertions(+), 34 deletions(-)

diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java
index 80e125a..bdd20c9 100644
--- a/src/jalview/ws/rest/RestJobThread.java
+++ b/src/jalview/ws/rest/RestJobThread.java
@@ -255,8 +255,10 @@ public class RestJobThread extends AWSThread
         response = httpclient.execute(request);
       } catch (ClientProtocolException he)
       {
-        rj.statMessage = "Web Protocol Exception when "
-                + getStage(stg) + "Job. <br>Problematic url was <a href=\""+request.getURI()+"\">"+request.getURI()+"</a><br>See Console output for details.";
+        rj.statMessage = "Web Protocol Exception when " + getStage(stg)
+                + "Job. <br>Problematic url was <a href=\""
+                + request.getURI() + "\">" + request.getURI()
+                + "</a><br>See Console output for details.";
         rj.setAllowedServerExceptions(0);// unrecoverable;
         rj.error = true;
         Cache.log.fatal("Unexpected REST Job " + getStage(stg)
@@ -264,8 +266,10 @@ public class RestJobThread extends AWSThread
         throw (he);
       } catch (IOException e)
       {
-        rj.statMessage = "IO Exception when "
-                + getStage(stg) + "Job. <br>Problematic url was <a href=\""+request.getURI()+"\">"+request.getURI()+"</a><br>See Console output for details.";
+        rj.statMessage = "IO Exception when " + getStage(stg)
+                + "Job. <br>Problematic url was <a href=\""
+                + request.getURI() + "\">" + request.getURI()
+                + "</a><br>See Console output for details.";
         Cache.log.warn("IO Exception for REST Job " + getStage(stg)
                 + "exception for URL " + rj.rsd.postUrl);
 
@@ -322,9 +326,22 @@ public class RestJobThread extends AWSThread
         // TODO: deal with all other HTTP response codes from server.
         Cache.log.warn("Unhandled response status when " + getStage(stg)
                 + "for " + postUrl + ": " + response.getStatusLine());
+        rj.error = true;
+        rj.setAllowedServerExceptions(0);
+        rj.setSubjobComplete(true);
+        rj.setSubmitted(true);
         try
         {
-          response.getEntity().consumeContent();
+          completeStatus(
+                  rj,
+                  response,
+                  ""
+                          + getStage(stg)
+                          + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
+                          + request.getURI()
+                          + "\">"
+                          + request.getURI()
+                          + "</a><br/>Filtered response content below:<br/>");
         } catch (IOException e)
         {
           Cache.log.debug("IOException when consuming unhandled response",
@@ -394,7 +411,7 @@ public class RestJobThread extends AWSThread
     int body = f.indexOf("<body");
     if (body > -1)
     {
-      content.delete(0, f.indexOf(">", body));
+      content.delete(0, f.indexOf(">", body) + 1);
     }
     if (body > -1 && sb.length() > 0)
     {
@@ -422,16 +439,15 @@ public class RestJobThread extends AWSThread
     {
       System.err.println("Debug RestJob: Posting Job");
       doPost((RestJob) job);
-    }
-    catch (NoValidInputDataException erex)
+    } catch (NoValidInputDataException erex)
     {
       job.setSubjobComplete(true);
       job.setSubmitted(true);
-      ((RestJob)job).statMessage="<br>It looks like there was a problem with the data sent to the service :<br>"+erex.getMessage()+"\n";
-      ((RestJob)job).error=true;
-      
-    }
-    catch (Exception ex)
+      ((RestJob) job).statMessage = "<br>It looks like there was a problem with the data sent to the service :<br>"
+              + erex.getMessage() + "\n";
+      ((RestJob) job).error = true;
+
+    } catch (Exception ex)
     {
       job.setSubjobComplete(true);
       job.setAllowedServerExceptions(-1);
@@ -471,10 +487,14 @@ public class RestJobThread extends AWSThread
           Cache.log.warn("Failed to finish parsing data for job "
                   + rj.getJobId());
           ex.printStackTrace();
-        }
-        finally {
-          rj.error=true;
-          rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""+rj.resSet.getUrl()+"\">"+rj.resSet.getUrl()+"</a><br>";
+        } finally
+        {
+          rj.error = true;
+          rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""
+                  + rj.resSet.getUrl()
+                  + "\">"
+                  + rj.resSet.getUrl()
+                  + "</a><br>";
         }
       }
     }
@@ -829,7 +849,9 @@ public class RestJobThread extends AWSThread
                   visgrps.add(exsg);
                   exsg.setStartRes(sg.getStartRes() + contigs[ncnt]);
                   exsg.setEndRes(sg.getEndRes() + contigs[ncnt]);
-                } else {
+                }
+                else
+                {
                   recovered = true;
                 }
                 // now replace any references from the result set with
@@ -959,12 +981,14 @@ public class RestJobThread extends AWSThread
                   visan.sequenceRef = sqass;
                   visAlAn.add(visan);
                 }
-                if (contigs[ncnt]+alan[nrj][an].annotations.length>visan.annotations.length)
+                if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length)
                 {
                   // increase width of annotation row
-                  Annotation[] newannv = new Annotation[contigs[ncnt]+alan[nrj][an].annotations.length];
-                  System.arraycopy(visan.annotations, 0, newannv, 0, visan.annotations.length);
-                  visan.annotations=newannv;
+                  Annotation[] newannv = new Annotation[contigs[ncnt]
+                          + alan[nrj][an].annotations.length];
+                  System.arraycopy(visan.annotations, 0, newannv, 0,
+                          visan.annotations.length);
+                  visan.annotations = newannv;
                 }
                 // now copy local annotation data into correct position
                 System.arraycopy(alan[nrj][an].annotations, 0,
@@ -1019,7 +1043,8 @@ public class RestJobThread extends AWSThread
       AlignmentI destal;
       ColumnSelection destcs;
       String alTitle = restClient.service.details.Action + " using "
-              + restClient.service.details.Name + " on "+restClient.viewTitle;
+              + restClient.service.details.Name + " on "
+              + restClient.viewTitle;
       switch (action)
       {
       case newAlignment:
@@ -1027,7 +1052,8 @@ public class RestJobThread extends AWSThread
         destcs = destColsel.get(als);
         destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
-        PaintRefresher.Refresh(destaf, destaf.getViewport().getSequenceSetId());
+        PaintRefresher.Refresh(destaf, destaf.getViewport()
+                .getSequenceSetId());
         // todo transfer any feature settings and colouring
         /*
          * destaf.getFeatureRenderer().transferSettings(this.featureSettings);
@@ -1047,7 +1073,8 @@ public class RestJobThread extends AWSThread
          * i++) { af.addSortByOrderMenuItem( WebServiceName + ((String)
          * names.get(i)) + " Ordering", (AlignmentOrder) alorders.get(i)); } } }
          */
-        // TODO: modify this and previous alignment's title if many alignments have been returned.
+        // TODO: modify this and previous alignment's title if many alignments
+        // have been returned.
         Desktop.addInternalFrame(destaf, alTitle, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
@@ -1227,8 +1254,8 @@ public class RestJobThread extends AWSThread
    */
   public boolean isValid()
   {
-    ArrayList<String> _warnings=new ArrayList<String>();
-    boolean validt=true;
+    ArrayList<String> _warnings = new ArrayList<String>();
+    boolean validt = true;
     if (jobs != null)
     {
       for (RestJob rj : (RestJob[]) jobs)
@@ -1237,42 +1264,48 @@ public class RestJobThread extends AWSThread
         {
           // invalid input for this job
           System.err.println("Job " + rj.getJobnum()
-                  + " has invalid input. ( "+rj.getStatus()+")");
+                  + " has invalid input. ( " + rj.getStatus() + ")");
           if (rj.hasStatus() && !_warnings.contains(rj.getStatus()))
           {
             _warnings.add(rj.getStatus());
           }
-          validt=false;
+          validt = false;
         }
       }
     }
     if (!validt)
     {
       warnings = "";
-      for (String st : _warnings) {
-        if (warnings.length()>0) { warnings+="\n";
+      for (String st : _warnings)
+      {
+        if (warnings.length() > 0)
+        {
+          warnings += "\n";
         }
         warnings += st;
-        
+
       }
     }
     return validt;
   }
 
   protected String warnings;
+
   public boolean hasWarnings()
   {
     // TODO Auto-generated method stub
-    return warnings!=null && warnings.length()>0;
+    return warnings != null && warnings.length() > 0;
   }
 
   /**
    * get any informative messages about why the job thread couldn't start.
+   * 
    * @return
    */
   public String getWarnings()
   {
-    return isValid() ? "Job can be started. No warnings." :  hasWarnings() ? warnings : "";
+    return isValid() ? "Job can be started. No warnings."
+            : hasWarnings() ? warnings : "";
   }
 
 }
-- 
1.7.10.2