X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2FAWSThread.java;h=5748414ab2e8438a114ba0d9e55dbeede4a56021;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=8d9dce5f38a5d523a10dfe49f1dbb0c3b4c7e325;hpb=9b2272a1679b87760b193ecc87f994d7f5141c75;p=jalview.git
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 8d9dce5..5748414a 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -8,216 +28,205 @@ import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
-import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
-public abstract class AWSThread extends Thread
+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 AlignedCodonFrame[] codonframe = null;
+ 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;
+ 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
+ * only used when reporting a web service out of memory error - the job ID
+ * will be concatenated to the URL
*/
protected String WsUrl = null;
- /**
- * generic web service job/subjob poll loop
+ /*
+ * The AlignFrame from which the service was requested.
*/
- public void run()
+ private AlignFrame alignFrame;
+
+ 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)
+ timer = new Timer(5000, new ActionListener()
{
- jstate = new JobStateSummary();
- for (int j = 0; j < jobs.length; j++)
+
+ @Override
+ public void actionPerformed(ActionEvent e)
{
-
- if (!jobs[j].submitted && jobs[j].hasValidInput())
+ JobStateSummary jstate = new JobStateSummary();
+ for (final AWsJob job : jobs)
{
- StartJob(jobs[j]);
- }
-
- if (jobs[j].submitted && !jobs[j].subjobComplete)
- {
- 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, "\n" + WebServiceName
- + " Server exception!\n" + ex.getMessage());
- // always output the exception's stack trace to the log
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
- + ") Server exception.");
- 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
- 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
+ // 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);
+ timer.stop();
+ // jobs should never be null at this point
+ parseResult(); // tidy up and make results available to user
+
}
- // System.out.println("I'm alive "+alTitle);
}
+ });
+ timer.setInitialDelay(0);
+ timer.start();
+ }
+
+ protected void updateGlobalStatus(JobStateSummary jstate)
+ {
+ if (jstate.running > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
}
- if (jobComplete && jobs != null)
+ else if (jstate.queuing > 0)
{
- parseResult(); // tidy up and make results available to user
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
}
else
{
- Cache.log
- .debug("WebServiceJob poll loop finished with no jobs created.");
- wsInfo.setFinishedNoResults();
+ 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 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.stop();
}
/**
@@ -246,8 +255,8 @@ public abstract class AWSThread extends Thread
/**
* 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
+ * codonframe to al TODO: refactor to datamodel
+ *
* @param al
*/
public void propagateDatasetMappings(Alignment al)
@@ -257,13 +266,12 @@ public abstract class AWSThread extends Thread
SequenceI[] alignment = al.getSequencesArray();
for (int sq = 0; sq < alignment.length; sq++)
{
- for (int i = 0; i < codonframe.length; i++)
+ for (AlignedCodonFrame acf : codonframe)
{
- if (codonframe[i] != null
- && codonframe[i].involvesSequence(alignment[sq]))
+ final SequenceI seq = alignment[sq];
+ if (acf != null && acf.involvesSequence(seq))
{
- al.addCodonFrame(codonframe[i]);
- codonframe[i] = null;
+ al.addCodonFrame(acf);
break;
}
}
@@ -271,12 +279,6 @@ 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
@@ -290,7 +292,7 @@ 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
@@ -307,11 +309,12 @@ public abstract class AWSThread extends Thread
}
/**
+ * Extracts additional info from alignment view's context.
*
* @param alframe
* - reference for copying mappings and display styles across
* @param wsinfo2
- * - gui attachment point
+ * - gui attachment point - may be null
* @param alview
* - input data for the calculation
* @param wsurl2
@@ -321,7 +324,7 @@ public abstract class AWSThread extends Thread
AlignmentView alview, String wsurl2)
{
super();
- // this.alignFrame = alframe;
+ this.alignFrame = alframe;
currentView = alframe.getCurrentView().getAlignment();
featureSettings = alframe.getFeatureRenderer().getSettings();
defGapChar = alframe.getViewport().getGapCharacter();
@@ -330,13 +333,18 @@ public abstract class AWSThread extends Thread
WsUrl = wsurl2;
if (alframe != null)
{
- AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+ List cf = alframe.getViewport().getAlignment()
.getCodonFrames();
if (cf != null)
{
- codonframe = new AlignedCodonFrame[cf.length];
- System.arraycopy(cf, 0, codonframe, 0, cf.length);
+ codonframe = new ArrayList<>();
+ codonframe.addAll(cf);
}
}
}
+
+ protected AlignFrame getRequestingAlignFrame()
+ {
+ return this.alignFrame;
+ }
}