X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FWSThread.java;h=121533b0d6b650a33146acda6eacf6b2bc04da5e;hb=93642d621a7f86318a7777b0a70f6113dcd299dc;hp=a9e9b0b4dda801fb9120b451073409db214ff6d8;hpb=08bde8d252a69d4d6a3b2497f759bd5d6f154a3f;p=jalview.git
diff --git a/src/jalview/ws/WSThread.java b/src/jalview/ws/WSThread.java
index a9e9b0b..121533b 100644
--- a/src/jalview/ws/WSThread.java
+++ b/src/jalview/ws/WSThread.java
@@ -1,449 +1,479 @@
-/*
- * 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 javax.swing.*;
-
-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.
- */
- /**
- * 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;
- /**
- * 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
- */
- int jobnum = 0; // WebServiceInfo pane for this job
- String jobId; // ws job ticket
- /**
- * has job been cancelled
- */
- boolean cancelled = false;
- /**
- * 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
- {
- /**
- * 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)
- {
- 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++;
- }
- }
- }
- }
- }
- /**
- * one or more jobs being managed by this thread.
- */
- WSJob jobs[] = null;
- /**
- * full name of service
- */
- String WebServiceName = null;
- String OutputHeader;
- String WsUrl = null;
- /**
- * 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++)
- {
-
- 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 && jobs != null)
- {
- parseResult(); // tidy up and make results available to user
- }
- else
- {
- Cache.log.debug("WebServiceJob poll loop finished with no jobs created.");
- wsInfo.setFinishedNoResults();
- }
- }
-
- /**
- * 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 codonframe to al
- * @param al
- */
- protected void propagateDatasetMappings(Alignment al)
- {
- if (codonframe!=null)
- {
- SequenceI[] alignment = al.getSequencesArray();
- for (int sq = 0; sq.
+ */
+package jalview.ws;
+
+import javax.swing.*;
+
+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.
+ */
+ /**
+ * 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;
+
+ /**
+ * 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
+ */
+ int jobnum = 0; // WebServiceInfo pane for this job
+
+ String jobId; // ws job ticket
+
+ /**
+ * has job been cancelled
+ */
+ boolean cancelled = false;
+
+ /**
+ * 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
+ {
+ /**
+ * 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)
+ {
+ 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++;
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * one or more jobs being managed by this thread.
+ */
+ WSJob jobs[] = null;
+
+ /**
+ * full name of service
+ */
+ String WebServiceName = null;
+
+ String OutputHeader;
+
+ String WsUrl = null;
+
+ /**
+ * 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++)
+ {
+
+ 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);
+ 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, 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 && jobs != null)
+ {
+ parseResult(); // tidy up and make results available to user
+ }
+ else
+ {
+ Cache.log
+ .debug("WebServiceJob poll loop finished with no jobs created.");
+ wsInfo.setFinishedNoResults();
+ }
+ }
+
+ /**
+ * 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
+ * codonframe to al
+ *
+ * @param al
+ */
+ protected void propagateDatasetMappings(Alignment al)
+ {
+ if (codonframe != null)
+ {
+ SequenceI[] alignment = al.getSequencesArray();
+ for (int sq = 0; sq < alignment.length; sq++)
+ {
+ 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;
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ *
+ * @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)
+ {
+ AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+ .getCodonFrames();
+ if (cf != null)
+ {
+ codonframe = new AlignedCodonFrame[cf.length];
+ System.arraycopy(cf, 0, codonframe, 0, cf.length);
+ }
+ }
+ }
+}