/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
- package jalview.ws;
+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;
+import javax.swing.*;
-public abstract class WSThread extends Thread
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+public abstract class WSThread
+ extends Thread
{
- /**
- * Generic properties for Web Service Client threads.
- */
- AlignFrame alignFrame=null;
+ /**
+ * Generic properties for Web Service Client threads.
+ */
+ AlignFrame alignFrame = null;
WebserviceInfo wsInfo = null;
- AlignmentView input=null;
+ AlignmentView input = null;
boolean jobComplete = false;
- abstract class WSJob {
- /**
- * Generic properties for an individual job within a Web Service Client thread
- */
+ 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;
* @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 {
+
+ class JobStateSummary
+ {
int running = 0;
int queuing = 0;
int finished = 0;
finished++;
j.subjobComplete = true;
if (j.hasResults())
+ {
results++;
+ }
wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
}
else if (j.result.isFailed())
String WebServiceName = null;
String OutputHeader;
String WsUrl = null;
- abstract void pollJob(WSJob job) throws Exception;
+ 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++)
+ JobStateSummary jstate = null;
+ if (jobs == null)
{
-
- if (!jobs[j].submitted && jobs[j].hasValidInput())
+ jobComplete = true;
+ }
+ while (!jobComplete)
+ {
+ jstate = new JobStateSummary();
+ for (int j = 0; j < jobs.length; j++)
{
- StartJob(jobs[j]);
- }
- if (jobs[j].submitted && !jobs[j].subjobComplete)
- {
- try
+ if (!jobs[j].submitted && jobs[j].hasValidInput())
{
- 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() + ")");
+ StartJob(jobs[j]);
}
- 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)
+ if (jobs[j].submitted && !jobs[j].subjobComplete)
+ {
+ try
{
- jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
- try
+ pollJob(jobs[j]);
+ if (jobs[j].result == null)
{
- Thread.sleep(5000);
+ throw (new Exception(
+ "Timed out when communicating with server\nTry again later.\n"));
}
- catch (InterruptedException ex1)
+ 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);
}
}
- else
+ catch (OutOfMemoryError er)
{
- Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+ 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_SERVERERROR);
+ 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();
}
}
- 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);
+ jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
}
- else if (jstate.error > 0)
+ // Decide on overall state based on collected jobs[] states
+ if (jstate.running > 0)
{
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
}
- else if (jstate.serror > 0)
+ else if (jstate.queuing > 0)
{
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
}
- }
- if (!jobComplete)
- {
- try
+ else
{
- Thread.sleep(5000);
+ 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);
+ }
}
- catch (InterruptedException e)
+ if (!jobComplete)
{
- Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
+ 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);
}
- // System.out.println("I'm alive "+alTitle);
+ }
+ 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.");
}
}
- 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.");
- }
-}
-abstract void StartJob(WSJob job);
-abstract void parseResult();
+
+ abstract void StartJob(WSJob job);
+
+ abstract void parseResult();
}
git://source.jalview.org / jalview.git / blobdiff