/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ 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;
import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import java.util.ArrayList;
import java.util.List;
import static java.lang.String.format;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.Timer;
public abstract class AWSThread
{
private javax.swing.Timer timer;
/**
* view that this job was associated with
*/
protected AlignmentI currentView = null;
/**
* feature settings from view that job was associated with
*/
protected FeatureRendererSettings featureSettings = null;
/**
* metadata about this web service
*/
protected WebserviceInfo wsInfo = null;
/**
* original input data for this job
*/
protected AlignmentView input = null;
/**
* dataset sequence relationships to be propagated onto new results
*/
protected List codonframe = null;
/**
* are there jobs still running in this thread.
*
* fixme: initialize with an empty array?
*/
protected boolean jobComplete = false;
/**
* one or more jobs being managed by this thread.
*/
protected AWsJob[] jobs = null;
/**
* full name of service
*/
protected String WebServiceName = null;
protected char defGapChar = '-';
/**
* header prepended to all output from job
*/
protected String OutputHeader;
/**
* only used when reporting a web service out of memory error - the job ID
* will be concatenated to the URL
*/
protected String WsUrl = null;
/*
* The AlignFrame from which the service was requested.
*/
private AlignFrame alignFrame;
public void start()
{
if (jobs == null)
{
jobComplete = true;
Cache.log.debug(
"WebServiceJob poll loop finished with no jobs created.");
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(
MessageManager.getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
return;
}
timer = new Timer(5000, new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
JobStateSummary jstate = new JobStateSummary();
for (final AWsJob job : jobs)
{
if (!job.submitted && job.hasValidInput())
{
StartJob(job);
}
Cache.log.debug(format(
"Job %s is %ssubmitted", job, job.submitted ? "" : "not "));
if (job.submitted && !job.subjobComplete)
{
Cache.log.debug(format(
"Polling Job %s Result state was:%s(ServerError=%b)",
job, job.getState(), job.isServerError()));
try
{
pollJob(job);
if (!job.hasResponse())
throw new Exception("Timed out when communicating with server. Try again later.");
else
Cache.log.debug(format("Job %s Result state:%s(ServerError=%b)",
job, job.getState(), job.isServerError()));
} catch (Exception exc)
{
// Deal with Transaction exceptions
wsInfo.appendProgressText(job.jobnum, MessageManager
.formatMessage("info.server_exception", WebServiceName,
exc.getMessage()));
// always output the exception's stack trace to the log
Cache.log.warn(format("%s job(%s) Server exception.",
WebServiceName, job.jobnum));
exc.printStackTrace();
if (job.allowedServerExceptions > 0)
{
job.allowedServerExceptions--;
}
else
{
Cache.log.warn(format("Dropping job %s %s", job, job.jobId));
job.subjobComplete = true;
wsInfo.setStatus(job.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
} catch (OutOfMemoryError oomerror)
{
jobComplete = true;
job.subjobComplete = true;
job.clearResponse();
wsInfo.setStatus(job.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
Cache.log.error(format("Out of memory when retrieving Job %s id:%s/%s",
job, WsUrl, job.jobId), oomerror);
new jalview.gui.OOMWarning("retrieving result for " + WebServiceName, oomerror);
System.gc();
}
}
jstate.updateJobPanelState(wsInfo, OutputHeader, job);
}
// Decide on overall state based on collected jobs[] states
updateGlobalStatus(jstate);
if (jobComplete)
{
timer.stop();
// jobs should never be null at this point
parseResult(); // tidy up and make results available to user
}
}
});
timer.setInitialDelay(0);
timer.start();
}
protected void updateGlobalStatus(JobStateSummary jstate)
{
if (jstate.running > 0)
{
wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
}
else if (jstate.queuing > 0)
{
wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
}
else
{
jobComplete = true;
if (jstate.finished > 0)
{
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
}
else if (jstate.error > 0)
{
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
}
else if (jstate.serror > 0)
{
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
}
}
public void interrupt()
{
timer.stop();
}
/**
* query web service for status of job. on return, job.result must not be null
* - if it is then it will be assumed that the job status query timed out and
* a server exception will be logged.
*
* @param job
* @throws Exception
* will be logged as a server exception for this job
*/
public abstract void pollJob(AWsJob job) throws Exception;
/**
* submit job to web service
*
* @param job
*/
public abstract void StartJob(AWsJob job);
/**
* process the set of AWsJob objects into a set of results, and tidy up.
*/
public abstract void parseResult();
/**
* helper function to conserve dataset references to sequence objects returned
* from web services 1. Propagates AlCodonFrame data from
* codonframe
to al
TODO: refactor to datamodel
*
* @param al
*/
public void propagateDatasetMappings(Alignment al)
{
if (codonframe != null)
{
SequenceI[] alignment = al.getSequencesArray();
for (int sq = 0; sq < alignment.length; sq++)
{
for (AlignedCodonFrame acf : codonframe)
{
final SequenceI seq = alignment[sq];
if (acf != null && acf.involvesSequence(seq))
{
al.addCodonFrame(acf);
break;
}
}
}
}
}
/**
*
* @return gap character to use for any alignment generation
*/
public char getGapChar()
{
return defGapChar;
}
/**
*
* @param alignFrame
* reference for copying mappings across
* @param wsinfo
* gui attachment point
* @param input
* input data for the calculation
* @param webServiceName
* name of service
* @param wsUrl
* url of the service being invoked
*/
public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
AlignmentView input, String webServiceName, String wsUrl)
{
this(alignFrame, wsinfo, input, wsUrl);
WebServiceName = webServiceName;
}
/**
* Extracts additional info from alignment view's context.
*
* @param alframe
* - reference for copying mappings and display styles across
* @param wsinfo2
* - gui attachment point - may be null
* @param alview
* - input data for the calculation
* @param wsurl2
* - url of the service being invoked
*/
public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
AlignmentView alview, String wsurl2)
{
super();
this.alignFrame = alframe;
currentView = alframe.getCurrentView().getAlignment();
featureSettings = alframe.getFeatureRenderer().getSettings();
defGapChar = alframe.getViewport().getGapCharacter();
this.wsInfo = wsinfo2;
this.input = alview;
WsUrl = wsurl2;
if (alframe != null)
{
List cf = alframe.getViewport().getAlignment()
.getCodonFrames();
if (cf != null)
{
codonframe = new ArrayList<>();
codonframe.addAll(cf);
}
}
}
protected AlignFrame getRequestingAlignFrame()
{
return this.alignFrame;
}
}