From b13d4ee2f7839be680d23ce157aff4e204377a8f Mon Sep 17 00:00:00 2001 From: Mateusz Warowny Date: Wed, 22 Jul 2020 14:13:00 +0100 Subject: [PATCH] JAL-3690 changed AWSThread to use Timer instead --- src/jalview/ws/AWSThread.java | 214 +++++++++++++++-------------------------- 1 file changed, 79 insertions(+), 135 deletions(-) diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java index 36e51c5..096f4ee 100644 --- a/src/jalview/ws/AWSThread.java +++ b/src/jalview/ws/AWSThread.java @@ -33,9 +33,15 @@ import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import java.util.ArrayList; import java.util.List; +import java.util.Timer; +import java.util.TimerTask; -public abstract class AWSThread extends Thread +import static java.lang.String.format; + +public abstract class AWSThread { + + private final Timer timer = new Timer(); /** * view that this job was associated with @@ -64,13 +70,15 @@ public abstract class AWSThread extends Thread /** * 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; + protected AWsJob[] jobs = null; /** * full name of service @@ -95,119 +103,91 @@ public abstract class AWSThread extends Thread */ private AlignFrame alignFrame; - /** - * generic web service job/subjob poll loop - */ - @Override - public void run() + public void start() { - JobStateSummary jstate = null; 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; } - while (!jobComplete) - { - jstate = new JobStateSummary(); - for (int j = 0; j < jobs.length; j++) + TimerTask task = new TimerTask() { + @Override + public void run() { - - if (!jobs[j].submitted && jobs[j].hasValidInput()) - { - StartJob(jobs[j]); - } - Cache.log.debug("Job " + jobs[j] + " is " + (jobs[j].submitted ? "submitted" : "not submitted")); - if (jobs[j].submitted && !jobs[j].subjobComplete) + JobStateSummary jstate = new JobStateSummary(); + for (final AWsJob job : jobs) { - jalview.bin.Cache.log.debug( - "Polling Job " + j + " Result state was:" + jobs[j].getState() + "(ServerError=" + jobs[j].isServerError() - + ")" - ); - try + if (!job.submitted && job.hasValidInput()) { - pollJob(jobs[j]); - if (!jobs[j].hasResponse()) - { - throw (new Exception( - "Timed out when communicating with server\nTry again later.\n")); - } - jalview.bin.Cache.log.debug("Job " + j + " Result state " - + jobs[j].getState() + "(ServerError=" - + jobs[j].isServerError() + ")"); - } catch (Exception ex) + StartJob(job); + } + Cache.log.debug(format( + "Job %s is %ssubmitted", job, job.submitted ? "" : "not ")); + if (job.submitted && !job.subjobComplete) { - // Deal with Transaction exceptions - wsInfo.appendProgressText(jobs[j].jobnum, MessageManager - .formatMessage("info.server_exception", new Object[] - { WebServiceName, ex.getMessage() })); - // always output the exception's stack trace to the log - Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum - + ") Server exception."); - // todo: could limit trace to cause if this is a SOAPFaultException. - ex.printStackTrace(); - - if (jobs[j].allowedServerExceptions > 0) + 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) { - jobs[j].allowedServerExceptions--; - Cache.log.debug("Sleeping after a server exception."); - try + // 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) { - Thread.sleep(5000); - } catch (InterruptedException ex1) + 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); } - } - else + } catch (OutOfMemoryError oomerror) { - Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId); - jobs[j].subjobComplete = true; - wsInfo.setStatus(jobs[j].jobnum, - WebserviceInfo.STATE_STOPPED_SERVERERROR); + 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(); } - } catch (OutOfMemoryError er) - { - jobComplete = true; - jobs[j].subjobComplete = true; - jobs[j].clearResponse(); // may contain out of date result data - wsInfo.setStatus(jobs[j].jobnum, - WebserviceInfo.STATE_STOPPED_ERROR); - Cache.log.error("Out of memory when retrieving Job " + j - + " id:" + WsUrl + "/" + jobs[j].jobId, er); - new jalview.gui.OOMWarning( - "retrieving result for " + WebServiceName, er); - System.gc(); } + jstate.updateJobPanelState(wsInfo, OutputHeader, job); } - jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]); - } - // Decide on overall state based on collected jobs[] states - updateGlobalStatus(jstate); - if (!jobComplete) - { - try + // Decide on overall state based on collected jobs[] states + updateGlobalStatus(jstate); + if (jobComplete) { - Thread.sleep(5000); - } catch (InterruptedException e) - { - Cache.log.debug("Interrupted sleep waiting for next job poll.", - e); + // jobs should never be null at this point + parseResult(); // tidy up and make results available to user + timer.cancel(); } - // System.out.println("I'm alive ?"); } - } - if (jobComplete && jobs != null) - { - parseResult(); // tidy up and make results available to user - } - else - { - 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(); - } + }; + timer.schedule(task, 0, 5000); } protected void updateGlobalStatus(JobStateSummary jstate) @@ -237,40 +217,10 @@ public abstract class AWSThread extends Thread } } } - - public AWSThread() - { - super(); - } - - public AWSThread(Runnable target) + + public void interrupt() { - super(target); - } - - public AWSThread(String name) - { - super(name); - } - - public AWSThread(ThreadGroup group, Runnable target) - { - super(group, target); - } - - public AWSThread(ThreadGroup group, String name) - { - super(group, name); - } - - public AWSThread(Runnable target, String name) - { - super(target, name); - } - - public AWSThread(ThreadGroup group, Runnable target, String name) - { - super(group, target, name); + timer.cancel(); } /** @@ -323,12 +273,6 @@ public abstract class AWSThread extends Thread } } - public AWSThread(ThreadGroup group, Runnable target, String name, - long stackSize) - { - super(group, target, name, stackSize); - } - /** * * @return gap character to use for any alignment generation @@ -342,7 +286,7 @@ public abstract class AWSThread extends Thread * * @param alignFrame * reference for copying mappings across - * @param wsInfo + * @param wsinfo * gui attachment point * @param input * input data for the calculation -- 1.7.10.2