X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestJobThread.java;h=5f8eb037fd5f9f5ccae3d1b981bba6e927fe285d;hb=a825b584a274cdabbaf79949a809ecf848f630d5;hp=80e125a4527d59e4927cbcf6438ee4d4ca0c11d0;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java
index 80e125a..5f8eb03 100644
--- a/src/jalview/ws/rest/RestJobThread.java
+++ b/src/jalview/ws/rest/RestJobThread.java
@@ -1,6 +1,6 @@
/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
@@ -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.
Problematic url was "+request.getURI()+"
See Console output for details.";
+ rj.statMessage = "Web Protocol Exception when " + getStage(stg)
+ + "Job.
Problematic url was " + request.getURI()
+ + "
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.
Problematic url was "+request.getURI()+"
See Console output for details.";
+ rj.statMessage = "IO Exception when " + getStage(stg)
+ + "Job.
Problematic url was " + request.getURI()
+ + "
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.
Url concerned was "
+ + request.getURI()
+ + "
Filtered response content below:
");
} catch (IOException e)
{
Cache.log.debug("IOException when consuming unhandled response",
@@ -394,7 +411,7 @@ public class RestJobThread extends AWSThread
int body = f.indexOf("
-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="
It looks like there was a problem with the data sent to the service :
"+erex.getMessage()+"\n";
- ((RestJob)job).error=true;
-
- }
- catch (Exception ex)
+ ((RestJob) job).statMessage = "
It looks like there was a problem with the data sent to the service :
"
+ + 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.
URL for job response is :"+rj.resSet.getUrl()+"
";
+ } finally
+ {
+ rj.error = true;
+ rj.statMessage = "Error whilst parsing data for this job.
URL for job response is :"
+ + rj.resSet.getUrl()
+ + "
";
}
}
}
@@ -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
@@ -838,10 +860,8 @@ public class RestJobThread extends AWSThread
// TODO: cope with recovering hidden sequences from
// resultContext
{
- Vector sqs = sg.getSequences(null);
- for (int sqsi = 0, iSize = sqs.size(); sqsi < iSize; sqsi++)
+ for (SequenceI oseq:sg.getSequences(null))
{
- SequenceI oseq = (SequenceI) sqs.get(sqsi);
SequenceI nseq = getNewSeq(oseq, rseqs[nrj],
ordermap[nrj], destAl);
if (nseq != null)
@@ -959,12 +979,14 @@ 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 +1041,8 @@ 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 +1050,8 @@ 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 +1071,8 @@ 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 +1252,8 @@ public class RestJobThread extends AWSThread
*/
public boolean isValid()
{
- ArrayList _warnings=new ArrayList();
- boolean validt=true;
+ ArrayList _warnings = new ArrayList();
+ boolean validt = true;
if (jobs != null)
{
for (RestJob rj : (RestJob[]) jobs)
@@ -1237,42 +1262,48 @@ 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 : "";
}
}