import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
+import jalview.api.PollableAlignCalcWorkerI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import java.util.Map;
public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
- implements WSAnnotationCalcManagerI
+ implements WSAnnotationCalcManagerI, PollableAlignCalcWorkerI
{
protected ServiceWithParameters service;
return gapMap;
}
- public SeqAnnotationServiceCalcWorker(AlignViewportI alignViewport,
- AlignmentViewPanel alignPanel)
- {
- super(alignViewport, alignPanel);
- }
-
public SeqAnnotationServiceCalcWorker(ServiceWithParameters service,
AlignFrame alignFrame,
WsParamSetI preset, List<ArgumentI> paramset)
{
- this(alignFrame.getCurrentView(), alignFrame.alignPanel);
+ super(alignFrame.getCurrentView(), alignFrame.alignPanel);
// TODO: both these fields needed ?
this.alignFrame = alignFrame;
this.guiProgress = alignFrame;
.getEndpoint();
} catch (ClassCastException cce)
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ annotService = null;
+ JvOptionPane.showMessageDialog(Desktop.getInstance(),
MessageManager.formatMessage(
"label.service_called_is_not_an_annotation_service",
new String[]
JvOptionPane.WARNING_MESSAGE);
}
+ cancellable = CancellableI.class.isInstance(annotService);
// configure submission flags
proteinAllowed = service.isProteinService();
nucleotidesAllowed = service.isNucleotideService();
return annotService != null;
}
- protected jalview.ws.api.SequenceAnnotationServiceI annotService = null;
+ protected SequenceAnnotationServiceI annotService;
+ protected final boolean cancellable;
volatile JobId rslt = null;
private int min_valid_seqs;
- @Override
- public void run()
+
+ private long progressId = -1;
+ JobStateSummary job = null;
+ WebserviceInfo info = null;
+ List<SequenceI> seqs = null;
+
+ @Override public void startUp() throws Throwable
{
- if (checkDone())
+ if (alignViewport.isClosed())
{
+ abortAndDestroy();
return;
}
if (!hasService())
{
- calcMan.workerComplete(this);
return;
}
- long progressId = -1;
-
- int serverErrorsLeft = 3;
- final boolean cancellable = CancellableI.class
- .isAssignableFrom(annotService.getClass());
StringBuffer msg = new StringBuffer();
- JobStateSummary job = new JobStateSummary();
- WebserviceInfo info = new WebserviceInfo("foo", "bar", false);
- try
+ job = new JobStateSummary();
+ info = new WebserviceInfo("foo", "bar", false);
+
+ seqs = getInputSequences(
+ alignViewport.getAlignment(),
+ bySequence ? alignViewport.getSelectionGroup() : null);
+
+ if (seqs == null || !checkValidInputSeqs(seqs))
{
- List<SequenceI> seqs = getInputSequences(
- alignViewport.getAlignment(),
- bySequence ? alignViewport.getSelectionGroup() : null);
+ jalview.bin.Console.debug(
+ "Sequences for analysis service were null or not valid");
+ return;
+ }
- if (seqs == null || !checkValidInputSeqs(seqs))
- {
- jalview.bin.Cache.log.debug(
- "Sequences for analysis service were null or not valid");
- calcMan.workerComplete(this);
- return;
- }
+ if (guiProgress != null)
+ {
+ guiProgress.setProgressBar(service.getActionText(),
+ progressId = System.currentTimeMillis());
+ }
+ jalview.bin.Console.debug("submitted " + seqs.size()
+ + " sequences to " + service.getActionText());
- if (guiProgress != null)
- {
- guiProgress.setProgressBar(service.getActionText(),
- progressId = System.currentTimeMillis());
- }
- jalview.bin.Cache.log.debug("submitted " + seqs.size()
- + " sequences to " + service.getActionText());
+ rslt = annotService.submitToService(seqs, getPreset(),
+ getArguments());
+ if (rslt == null)
+ {
+ return;
+ }
+ // TODO: handle job submission error reporting here.
+ Console.debug("Service " + service.getUri() + "\nSubmitted job ID: "
+ + rslt);
+ // ///
+ // otherwise, construct WsJob and any UI handlers
+ running = new AnnotationWsJob();
+ running.setJobHandle(rslt);
+ running.setSeqNames(seqNames);
+ running.setStartPos(start);
+ running.setSeqs(seqs);
+ job.updateJobPanelState(info, "", running);
+ if (guiProgress != null)
+ {
+ guiProgress.registerHandler(progressId,
+ new IProgressIndicatorHandler()
+ {
- rslt = annotService.submitToService(seqs, getPreset(),
- getArguments());
- if (rslt == null)
- {
- return;
- }
- // TODO: handle job submission error reporting here.
- Cache.log.debug("Service " + service.getUri() + "\nSubmitted job ID: "
- + rslt);
- ;
- // ///
- // otherwise, construct WsJob and any UI handlers
- running = new AnnotationWsJob();
- running.setJobHandle(rslt);
- running.setSeqNames(seqNames);
- running.setStartPos(start);
- running.setSeqs(seqs);
- job.updateJobPanelState(info, "", running);
- if (guiProgress != null)
- {
- guiProgress.registerHandler(progressId,
- new IProgressIndicatorHandler()
+ @Override
+ public boolean cancelActivity(long id)
{
+ calcMan.cancelWorker(SeqAnnotationServiceCalcWorker.this);
+ return true;
+ }
- @Override
- public boolean cancelActivity(long id)
- {
- ((CancellableI) annotService).cancel(running);
- return true;
- }
-
- @Override
- public boolean canCancel()
- {
- return cancellable;
- }
- });
- }
-
- // ///
- // and poll for updates until job finishes, fails or becomes stale
-
- boolean finished = false;
- do
- {
- Cache.log.debug("Updating status for annotation service.");
- annotService.updateStatus(running);
- job.updateJobPanelState(info, "", running);
- if (running.isSubjobComplete())
- {
- Cache.log.debug(
- "Finished polling analysis service job: status reported is "
- + running.getState());
- finished = true;
- }
- else
- {
- Cache.log.debug("Status now " + running.getState());
- }
-
- if (calcMan.isPending(this) && isInteractiveUpdate())
- {
- Cache.log.debug("Analysis service job is stale. aborting.");
- // job has become stale.
- if (!finished) {
- finished = true;
- // cancel this job and yield to the new job
- try
- {
- if (cancellable
- && ((CancellableI) annotService).cancel(running))
- {
- System.err.println("Cancelled job: " + rslt);
- }
- else
- {
- System.err.println("FAILED TO CANCEL job: " + rslt);
- }
-
- } catch (Exception x)
- {
+ @Override
+ public boolean canCancel()
+ {
+ return cancellable;
+ }
+ });
+ }
+ }
- }
- }
- rslt = running.getJobHandle();
- return;
- }
-
- // pull any stats - some services need to flush log output before
- // results are available
- Cache.log.debug("Updating progress log for annotation service.");
+ @Override public boolean poll() throws Throwable
+ {
+ boolean finished = false;
+
+ Console.debug("Updating status for annotation service.");
+ annotService.updateStatus(running);
+ job.updateJobPanelState(info, "", running);
+ if (running.isSubjobComplete())
+ {
+ Console.debug(
+ "Finished polling analysis service job: status reported is "
+ + running.getState());
+ finished = true;
+ }
+ else
+ {
+ Console.debug("Status now " + running.getState());
+ }
- try
- {
- annotService.updateJobProgress(running);
- } catch (Throwable thr)
- {
- Cache.log.debug("Ignoring exception during progress update.",
- thr);
- }
- Cache.log.trace("Result of poll: " + running.getStatus());
+ // pull any stats - some services need to flush log output before
+ // results are available
+ Console.debug("Updating progress log for annotation service.");
- if (!finished && !running.isFailed())
- {
- try
- {
- Cache.log.debug("Analysis service job thread sleeping.");
- Thread.sleep(200);
- Cache.log.debug("Analysis service job thread woke.");
- } catch (InterruptedException x)
- {
- }
- ;
- }
- } while (!finished);
-
- Cache.log.debug("Job poll loop exited. Job is " + running.getState());
- // TODO: need to poll/retry
- if (serverErrorsLeft > 0)
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- }
+ try
+ {
+ annotService.updateJobProgress(running);
+ } catch (Throwable thr)
+ {
+ Console.debug("Ignoring exception during progress update.",
+ thr);
+ }
+ Console.debug("Result of poll: " + running.getStatus());
+
+
+ if (finished)
+ {
+ Console.debug("Job poll loop exited. Job is " + running.getState());
if (running.isFinished())
{
// expect there to be results to collect
// features automatically according to user preferences
running.setFeatureRenderer(
((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
- Cache.log.debug("retrieving job results.");
+ Console.debug("retrieving job results.");
final Map<String, FeatureColourI> featureColours = new HashMap<>();
final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
List<AlignmentAnnotation> returnedAnnot = annotService
.getAnnotationResult(running.getJobHandle(), seqs,
featureColours, featureFilters);
- Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
+ Console.debug("Obtained " + (returnedAnnot == null ? "no rows"
: ("" + returnedAnnot.size())));
- Cache.log.debug("There were " + featureColours.size()
+ Console.debug("There were " + featureColours.size()
+ " feature colours and " + featureFilters.size()
+ " filters defined.");
if (running.hasResults())
{
- jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ jalview.bin.Console.debug("Updating result annotation from Job "
+ rslt + " at " + service.getUri());
updateResultAnnotation(true);
if (running.isTransferSequenceFeatures())
// regions
// not annotated due to gapMap/column visibility
- jalview.bin.Cache.log.debug(
+ jalview.bin.Console.debug(
"Updating feature display settings and transferring features from Job "
+ rslt + " at " + service.getUri());
// TODO: consider merge rather than apply here
ap.adjustAnnotationHeight();
}
}
- Cache.log.debug("Annotation Service Worker thread finished.");
- }
-// TODO: use service specitic exception handlers
-// catch (JobSubmissionException x)
-// {
-//
-// System.err.println(
-// "submission error with " + getServiceActionText() + " :");
-// x.printStackTrace();
-// calcMan.disableWorker(this);
-// } catch (ResultNotAvailableException x)
-// {
-// System.err.println("collection error:\nJob ID: " + rslt);
-// x.printStackTrace();
-// calcMan.disableWorker(this);
-//
-// } catch (OutOfMemoryError error)
-// {
-// calcMan.disableWorker(this);
-//
-// ap.raiseOOMWarning(getServiceActionText(), error);
-// }
- catch (Throwable x)
- {
- calcMan.disableWorker(this);
+ Console.debug("Annotation Service Worker thread finished.");
- System.err
- .println("Blacklisting worker due to unexpected exception:");
- x.printStackTrace();
- } finally
+ }
+
+ return finished;
+ }
+
+ @Override public void cancel()
+ {
+ cancelCurrentJob();
+ }
+
+ @Override public void done()
+ {
+ if (ap != null)
{
-
- calcMan.workerComplete(this);
- if (ap != null)
+ if (guiProgress != null && progressId != -1)
{
- if (guiProgress != null && progressId != -1)
- {
- guiProgress.setProgressBar("", progressId);
- }
- // TODO: may not need to paintAlignment again !
- ap.paintAlignment(false, false);
- }
- if (msg.length() > 0)
- {
- // TODO: stash message somewhere in annotation or alignment view.
- // code below shows result in a text box popup
- /*
- * jalview.gui.CutAndPasteTransfer cap = new
- * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
- * jalview.gui.Desktop.addInternalFrame(cap,
- * "Job Status for "+getServiceActionText(), 600, 400);
- */
+ guiProgress.removeProgressBar(progressId);
}
+ // TODO: may not need to paintAlignment again !
+ ap.paintAlignment(false, false);
}
-
}
/**
try
{
String id = running.getJobId();
- if (((CancellableI) annotService).cancel(running))
+ if (cancellable && ((CancellableI) annotService).cancel(running))
{
System.err.println("Cancelled job " + id);
}
{
ala.graphGroup += graphGroup;
}
- SequenceI aseq = null;
-
- /**
+ SequenceI aseq = (ala.sequenceRef == null) ? null
+ : running.getSeqNames().get(ala.sequenceRef.getName());
+ /*
* transfer sequence refs and adjust gapmap
+ * Prepare an array for annotations and copy returned annotations to it
+ * according to gapMap if present.
*/
- if (ala.sequenceRef != null)
- {
- SequenceI seq = running.getSeqNames()
- .get(ala.sequenceRef.getName());
- aseq = seq;
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- }
Annotation[] resAnnot = ala.annotations,
gappedAnnot = new Annotation[Math.max(
alignViewport.getAlignment().getWidth(),
gapMap.length)];
- for (int p = 0, ap = start; ap < gappedAnnot.length; ap++)
+ for (int p = 0, ap = 0; ap < gappedAnnot.length; ap++)
{
if (gapMap != null && gapMap.length > ap && !gapMap[ap])
{
}
}
ala.sequenceRef = aseq;
- ala.annotations = gappedAnnot;
AlignmentAnnotation newAnnot = getAlignViewport().getAlignment()
.updateFromOrCopyAnnotation(ala);
+ newAnnot.annotations = gappedAnnot;
if (aseq != null)
{
-
+ newAnnot.createSequenceMapping(aseq, aseq.findPosition(start), false);
aseq.addAlignmentAnnotation(newAnnot);
newAnnot.adjustForAlignment();
}
}
- /**
- * notify manager that we have started, and wait for a free calculation slot
- *
- * @return true if slot is obtained and work still valid, false if another
- * thread has done our work for us.
- */
- protected boolean checkDone()
- {
- calcMan.notifyStart(this);
- ap.paintAlignment(false, false);
- while (!calcMan.notifyWorking(this))
- {
- if (calcMan.isWorking(this))
- {
- return true;
- }
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false, false);
- }
-
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return true;
- }
- return false;
- }
-
protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
{
List<AlignmentAnnotation> our = ourAnnots;
git://source.jalview.org / jalview.git / blobdiff