+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
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.*;
+import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+
+public abstract class WSThread
+ extends Thread
{
- /**
- * Generic properties for Web Service Client threads.
- */
- AlignFrame alignFrame=null;
+ /**
+ * Generic properties for Web Service Client threads.
+ */
+ /**
+ * view that this job was associated with
+ */
+ AlignmentI currentView = null;
+ /**
+ * feature settings from view that job was associated with
+ */
+ FeatureRendererSettings featureSettings = null;
+ /**
+ * metadata about this web service
+ */
WebserviceInfo wsInfo = null;
- AlignmentView input=null;
+ /**
+ * original input data for this job
+ */
+ AlignmentView input = null;
+ /**
+ * dataset sequence relationships to be propagated onto new results
+ */
+ AlignedCodonFrame[] codonframe = null;
+ /**
+ * are there jobs still running in this thread.
+ */
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
+ /**
+ * has job been cancelled
+ */
boolean cancelled = false;
- int allowedServerExceptions = 3; // job dies if too many exceptions.
+ /**
+ * number of exceptions left before job dies
+ */
+ int allowedServerExceptions = 3;
+ /**
+ * has job been submitted
+ */
boolean submitted = false;
+ /**
+ * are all sub-jobs complete
+ */
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();
+
+ /**
+ * The last result object returned by the service.
+ */
vamsas.objects.simple.Result result;
}
- class JobStateSummary {
+
+ class JobStateSummary
+ {
+ /**
+ * number of jobs running
+ */
int running = 0;
+ /**
+ * number of jobs queued
+ */
int queuing = 0;
+ /**
+ * number of jobs finished
+ */
int finished = 0;
+ /**
+ * number of jobs failed
+ */
int error = 0;
+ /**
+ * number of jobs stopped due to server error
+ */
int serror = 0;
+ /**
+ * number of jobs cancelled
+ */
int cancelled = 0;
+ /**
+ * number of jobs finished with results
+ */
int results = 0;
+ /**
+ * processes WSJob and updates job status counters and WebService status displays
+ * @param wsInfo
+ * @param OutputHeader
+ * @param j
+ */
void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
WSJob j)
{
finished++;
j.subjobComplete = true;
if (j.hasResults())
+ {
results++;
+ }
wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
}
else if (j.result.isFailed())
}
}
}
-
+ /**
+ * one or more jobs being managed by this thread.
+ */
WSJob jobs[] = null;
+ /**
+ * full name of service
+ */
String WebServiceName = null;
String OutputHeader;
String WsUrl = null;
- abstract void pollJob(WSJob job) throws Exception;
+ /**
+ * 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
+ */
+ 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())
+ {
+ StartJob(jobs[j]);
+ }
+
+ if (jobs[j].submitted && !jobs[j].subjobComplete)
{
- pollJob(jobs[j]);
- if (jobs[j].result == null)
+ try
{
- throw (new Exception(
- "Timed out when communicating with server\nTry again later.\n"));
+ 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() + ")");
}
- 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)
+ catch (Exception ex)
{
- jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
- try
+ // 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)
{
- Thread.sleep(5000);
+ jobs[j].allowedServerExceptions--;
+ Cache.log.debug("Sleeping after a server exception.");
+ try
+ {
+ Thread.sleep(5000);
+ }
+ catch (InterruptedException ex1)
+ {
+ }
}
- 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);
+ }
+ else if (jstate.error > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ else if (jstate.serror > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
}
- jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+ 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);
+ }
}
- // Decide on overall state based on collected jobs[] states
- if (jstate.running > 0)
+ if (jobComplete && jobs != null)
{
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ parseResult(); // tidy up and make results available to user
}
- else if (jstate.queuing > 0)
+ else
{
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ Cache.log.debug("WebServiceJob poll loop finished with no jobs created.");
+ wsInfo.setFinishedNoResults();
}
- else
+ }
+
+ /**
+ * submit job to web service
+ * @param job
+ */
+ abstract void StartJob(WSJob job);
+
+ /**
+ * process the set of WSJob objects into a set of results, and tidy up.
+ */
+ abstract void parseResult();
+
+ /**
+ * helper function to conserve dataset references to sequence objects returned from web services
+ * 1. Propagates AlCodonFrame data from <code>codonframe</code> to <code>al</code>
+ * @param al
+ */
+ protected void propagateDatasetMappings(Alignment al)
+ {
+ if (codonframe!=null)
{
- jobComplete = true;
- if (jstate.finished > 0)
+ SequenceI[] alignment = al.getSequencesArray();
+ for (int sq = 0; sq<alignment.length; sq++)
{
- 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);
+ for (int i=0; i<codonframe.length; i++)
+ {
+ if (codonframe[i]!=null &&
+ codonframe[i].involvesSequence(alignment[sq]))
+ {
+ al.addCodonFrame(codonframe[i]);
+ codonframe[i] = null;
+ break;
+ }
+ }
}
}
- if (!jobComplete)
+ }
+
+ /**
+ *
+ * @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 WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
+ AlignmentView input, String webServiceName,
+ String wsUrl)
+ {
+ this(alignFrame, wsinfo, input, wsUrl);
+ WebServiceName = webServiceName;
+ }
+ char defGapChar = '-';
+ /**
+ *
+ * @return gap character to use for any alignment generation
+ */
+ public char getGapChar()
+ {
+ return defGapChar;
+ }
+
+ /**
+ *
+ * @param alframe - reference for copying mappings and display styles across
+ * @param wsinfo2 - gui attachment point
+ * @param alview - input data for the calculation
+ * @param wsurl2 - url of the service being invoked
+ */
+ public WSThread(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)
{
- try
- {
- Thread.sleep(5000);
- }
- catch (InterruptedException e)
+ AlignedCodonFrame[] cf = alframe.getViewport().getAlignment().getCodonFrames();
+ if (cf!=null)
{
- Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
+ codonframe = new AlignedCodonFrame[cf.length];
+ System.arraycopy(cf, 0, codonframe, 0, cf.length);
}
- // 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.");
- }
-}
-abstract void StartJob(WSJob job);
-abstract void parseResult();
}
git://source.jalview.org / jalview.git / blobdiff