--- /dev/null
+package jalview.ws;
+
+import jalview.gui.AlignFrame;
+import jalview.gui.WebserviceInfo;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.Desktop;
+import javax.swing.JOptionPane;
+import jalview.bin.Cache;
+
+public abstract class WSThread extends Thread
+{
+ /**
+ * Generic properties for Web Service Client threads.
+ */
+ AlignFrame alignFrame;
+ WebserviceInfo wsInfo = null;
+ AlignmentView input;
+ boolean jobComplete = false;
+ abstract class WSJob {
+ /**
+ * Generic properties for an individual job within a Web Service Client thread
+ */
+ int jobnum = 0; // WebServiceInfo pane for this job
+ String jobId; // ws job ticket
+ boolean cancelled = false;
+ int allowedServerExceptions = 3; // job dies if too many exceptions.
+ boolean submitted = false;
+ boolean subjobComplete = false;
+ /**
+ *
+ * @return true if job has completed and valid results are available
+ */
+ abstract boolean hasResults();
+ /**
+ *
+ * @return boolean true if job can be submitted.
+ */
+ abstract boolean hasValidInput();
+ vamsas.objects.simple.Result result;
+ }
+ class JobStateSummary {
+ int running = 0;
+ int queuing = 0;
+ int finished = 0;
+ int error = 0;
+ int serror = 0;
+ int cancelled = 0;
+ int results = 0;
+ void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
+ WSJob j)
+ {
+ if (j.result != null)
+ {
+ String progheader = "";
+ // Parse state of job[j]
+ if (j.result.isRunning())
+ {
+ running++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
+ }
+ else if (j.result.isQueued())
+ {
+ queuing++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
+ }
+ else if (j.result.isFinished())
+ {
+ finished++;
+ j.subjobComplete = true;
+ if (j.hasResults())
+ results++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else if (j.result.isFailed())
+ {
+ progheader += "Job failed.\n";
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ error++;
+ }
+ else if (j.result.isServerError())
+ {
+ serror++;
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum,
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ else if (j.result.isBroken() || j.result.isFailed())
+ {
+ error++;
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ // and pass on any sub-job messages to the user
+ wsInfo.setProgressText(j.jobnum, OutputHeader);
+ wsInfo.appendProgressText(j.jobnum, progheader);
+ if (j.result.getStatus() != null)
+ {
+ wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
+ }
+ }
+ else
+ {
+ if (j.submitted && j.subjobComplete)
+ {
+ if (j.allowedServerExceptions == 0)
+ {
+ serror++;
+ }
+ else if (j.result == null)
+ {
+ error++;
+ }
+ }
+ }
+ }
+ }
+
+ WSJob jobs[] = null;
+ String WebServiceName = null;
+ String OutputHeader;
+ String WsUrl = null;
+ abstract void pollJob(WSJob job) throws Exception;
+ public void run()
+ {
+ JobStateSummary jstate=null;
+ if (jobs==null)
+ jobComplete=true;
+ while (!jobComplete)
+ {
+ jstate = new JobStateSummary();
+ for (int j = 0; j < jobs.length; j++)
+ {
+
+ if (!jobs[j].submitted && jobs[j].hasValidInput())
+ {
+ StartJob(jobs[j]);
+ }
+
+ if (jobs[j].submitted && !jobs[j].subjobComplete)
+ {
+ try
+ {
+ pollJob(jobs[j]);
+ if (jobs[j].result == null)
+ {
+ throw (new Exception(
+ "Timed out when communicating with server\nTry again later.\n"));
+ }
+ jalview.bin.Cache.log.debug("Job " + j + " Result state " +
+ jobs[j].result.getState()
+ + "(ServerError=" +
+ jobs[j].result.isServerError() + ")");
+ }
+ catch (Exception ex)
+ {
+ // Deal with Transaction exceptions
+ wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
+ + " Server exception!\n" + ex.getMessage());
+ Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ + ") Server exception: " + ex.getMessage());
+
+ if (jobs[j].allowedServerExceptions > 0)
+ {
+ jobs[j].allowedServerExceptions--;
+ Cache.log.debug("Sleeping after a server exception.");
+ try
+ {
+ Thread.sleep(5000);
+ }
+ catch (InterruptedException ex1)
+ {
+ }
+ }
+ else
+ {
+ Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+ jobs[j].subjobComplete = true;
+ wsInfo.setStatus(jobs[j].jobnum,
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ }
+ catch (OutOfMemoryError er)
+ {
+ jobComplete = true;
+ jobs[j].subjobComplete = true;
+ jobs[j].result = null; // may contain out of date result object
+ wsInfo.setStatus(jobs[j].jobnum,
+ WebserviceInfo.STATE_STOPPED_ERROR);
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Out of memory handling result for job !!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory.",
+ "Out of memory", JOptionPane.WARNING_MESSAGE);
+ Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
+ WsUrl + "/" + jobs[j].jobId, er);
+ System.gc();
+ }
+ }
+ jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+ }
+ // Decide on overall state based on collected jobs[] states
+ 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);
+ }
+ }
+ if (!jobComplete)
+ {
+ try
+ {
+ Thread.sleep(5000);
+ }
+ catch (InterruptedException e)
+ {
+ Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
+ }
+ // System.out.println("I'm alive "+alTitle);
+ }
+ }
+ if (jobComplete)
+ {
+ parseResult(); // tidy up and make results available to user
+ }
+}
+abstract void StartJob(WSJob job);
+abstract void parseResult();
+}
git://source.jalview.org / jalview.git / blobdiff