X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=08accbac5d9e91c50f7756662209b6db8020f431;hb=4272f31e9cc505f9a1496e2cd002dc9250c77928;hp=79ffa906120f445f8af301fde349a7c53c0bf002;hpb=2640ef898b186abf1abffedcb7064103f2c919e4;p=jalview.git
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 79ffa90..08accba 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,27 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import java.util.*;
import compbio.data.msa.MsaWS;
-import compbio.data.sequence.AlignmentMetadata;
-import compbio.data.sequence.Program;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
@@ -34,27 +33,9 @@ import jalview.gui.*;
import jalview.ws.AWsJob;
import jalview.ws.WSClientI;
import jalview.ws.JobStateSummary;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
-/**
- *
- * Title:
- *
- *
- *
- * Description:
- *
- *
- *
- * Copyright: Copyright (c) 2004
- *
- *
- *
- * Company: Dundee University
- *
- *
- * @author not attributable
- * @version 1.0
- */
class MsaWSThread extends AWS2Thread implements WSClientI
{
boolean submitGaps = false; // pass sequences including gaps to alignment
@@ -69,7 +50,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
{
long lastChunk = 0;
- Preset preset = null;
+ WsParamSetI preset = null;
List arguments = null;
@@ -373,6 +354,67 @@ class MsaWSThread extends AWS2Thread implements WSClientI
return alignmentProgram;
}
+ public boolean hasArguments()
+ {
+ return (arguments != null && arguments.size() > 0)
+ || (preset != null && preset instanceof JabaWsParamSet);
+ }
+
+ public List getJabaArguments()
+ {
+ List newargs = new ArrayList();
+ if (preset != null && preset instanceof JabaWsParamSet)
+ {
+ newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
+ }
+ if (arguments != null && arguments.size() > 0)
+ {
+ newargs.addAll(arguments);
+ }
+ return newargs;
+ }
+
+ /**
+ * add a progess header to status string containing presets/args used
+ */
+ public void addInitialStatus()
+ {
+ if (preset != null)
+ {
+ jobProgress.append("Using "
+ + (preset instanceof JabaPreset ? "Server" : "User")
+ + "Preset: " + preset.getName());
+ if (preset instanceof JabaWsParamSet)
+ {
+ for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
+ {
+ jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
+ + "\n");
+ }
+ }
+ }
+ if (arguments != null && arguments.size() > 0)
+ {
+ jobProgress.append("With custom parameters : \n");
+ // merge arguments with preset's own arguments.
+ for (Argument opt : arguments)
+ {
+ jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
+ + "\n");
+ }
+ }
+ jobProgress.append("\nJob Output:\n");
+ }
+
+ public boolean isPresetJob()
+ {
+ return preset != null && preset instanceof JabaPreset;
+ }
+
+ public Preset getServerPreset()
+ {
+ return (isPresetJob()) ? ((JabaPreset) preset).p : null;
+ }
}
String alTitle; // name which will be used to form new alignment window.
@@ -416,7 +458,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
* @param seqset
* Alignment
*/
- MsaWSThread(MsaWS server2, Preset preset, List paramset,
+ MsaWSThread(MsaWS server2, WsParamSetI preset, List paramset,
String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, String wsname, String title,
AlignmentView _msa, boolean subgaps, boolean presorder,
@@ -473,7 +515,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
try
{
boolean cancelledJob = server.cancelJob(jobs[job].getJobId());
- if (cancelledJob || true)
+ if (true) // cancelledJob || true)
{
// CANCELLED_JOB
// if the Jaba server indicates the job can't be cancelled, its
@@ -503,6 +545,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI
}
wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ cancelledMessage + "\n");
+ } else {
+ // if we hadn't submitted then just mark the job as cancelled.
+ jobs[job].setSubjobComplete(true);
+ wsInfo.setStatus(jobs[job].getJobnum(), WebserviceInfo.STATE_CANCELLED_OK);
+
}
}
if (cancelled)
@@ -533,10 +580,17 @@ class MsaWSThread extends AWS2Thread implements WSClientI
updateJobProgress(j);
}
- protected void updateJobProgress(MsaWSJob j) throws Exception
+ /**
+ *
+ * @param j
+ * @return true if more job progress data was available
+ * @throws Exception
+ */
+ protected boolean updateJobProgress(MsaWSJob j) throws Exception
{
StringBuffer response = j.jobProgress;
long lastchunk = j.getLastChunk();
+ boolean changed = false;
do
{
j.setLastChunk(lastchunk);
@@ -544,11 +598,20 @@ class MsaWSThread extends AWS2Thread implements WSClientI
.pullExecStatistics(j.getJobId(), lastchunk);
if (chunk != null)
{
+ changed |= chunk.getChunk().length() > 0;
response.append(chunk.getChunk());
lastchunk = chunk.getNextPosition();
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
}
;
} while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
+ return changed;
}
public void StartJob(AWsJob job)
@@ -580,21 +643,15 @@ class MsaWSThread extends AWS2Thread implements WSClientI
}
try
{
- // TODO: get the parameters (if any) for this job and submit the job
- if (j.arguments != null && j.arguments.size() > 0)
+ j.addInitialStatus(); // list the presets/parameters used for the job in
+ // status
+ if (j.isPresetJob())
{
- StringBuffer pset = new StringBuffer();
- for (Argument arg : j.arguments)
- {
- pset.append(arg.getName() + " " + arg.getDefaultValue() + "\n");
- }
- j.setStatus("Custom Parameters:\n" + pset.toString()
- + "\nJob Output:\n");
- j.setJobId(server.customAlign(j.seqs, j.arguments));
+ j.setJobId(server.presetAlign(j.seqs, j.getServerPreset()));
}
- else if (j.preset != null)
+ else if (j.hasArguments())
{
- j.setJobId(server.presetAlign(j.seqs, j.preset));
+ j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
}
else
{
@@ -606,6 +663,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
j.setSubmitted(true);
j.setSubjobComplete(false);
// System.out.println(WsURL + " Job Id '" + jobId + "'");
+ return;
}
else
{
@@ -630,8 +688,7 @@ 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 +697,8 @@ 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 +709,7 @@ 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
@@ -668,18 +722,23 @@ 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");
+ }
}
}
public void parseResult()
{
+ long progbar = System.currentTimeMillis();
+ wsInfo.setProgressBar("Collecting job results.", progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
@@ -689,16 +748,45 @@ class MsaWSThread extends AWS2Thread implements WSClientI
MsaWSJob msjob = ((MsaWSJob) jobs[j]);
if (jobs[j].isFinished() && msjob.alignment == null)
{
- try
- {
- updateJobProgress(msjob);
- } catch (Exception e)
+ int nunchanged = 3, nexcept = 3;
+ boolean jpchanged = false, jpex = false;
+ do
{
- Cache.log
- .warn("Exception when retrieving remaining Job progress data for job "
- + msjob.getJobId() + " on server " + WsUrl);
- e.printStackTrace();
- }
+ try
+ {
+ jpchanged = updateJobProgress(msjob);
+ jpex = false;
+ if (jpchanged)
+ {
+ nexcept = 3;
+ }
+ } catch (Exception e)
+ {
+
+ Cache.log
+ .warn("Exception when retrieving remaining Job progress data for job "
+ + msjob.getJobId() + " on server " + WsUrl);
+ e.printStackTrace();
+ nexcept--;
+ nunchanged = 3;
+ // set flag remember that we've had an exception.
+ jpex = true;
+ jpchanged = false;
+ }
+ if (!jpchanged)
+ {
+ try
+ {
+ Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we
+ // experienced an exception.
+ } catch (Exception ex)
+ {
+ }
+ ;
+ nunchanged--;
+ }
+ } while (nunchanged > 0 && nexcept > 0);
+
if (Cache.log.isDebugEnabled())
{
System.out.println("Job Execution file for job: "
@@ -710,9 +798,22 @@ class MsaWSThread extends AWS2Thread implements WSClientI
try
{
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);
+ msjob.jobProgress
+ .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ + e.getLocalizedMessage());
+ msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
Cache.log.error("Couldn't get Alignment for job.", e);
+ // TODO: Increment count and retry ?
+ msjob.setjobStatus(JobStatus.UNDEFINED);
}
}
finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
@@ -765,6 +866,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI
{
wsInfo.setFinishedNoResults();
}
+ updateGlobalStatus(finalState);
+ wsInfo.setProgressBar(null, progbar);
}
void displayResults(boolean newFrame)