2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.bin.Cache;
24 import jalview.datamodel.AlignedCodonFrame;
25 import jalview.datamodel.Alignment;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.AlignmentView;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.AlignFrame;
30 import jalview.gui.WebserviceInfo;
31 import jalview.util.MessageManager;
32 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
34 import java.util.LinkedHashSet;
35 import java.util.List;
38 public abstract class AWSThread extends Thread
42 * view that this job was associated with
44 protected AlignmentI currentView = null;
47 * feature settings from view that job was associated with
49 protected FeatureRendererSettings featureSettings = null;
52 * metadata about this web service
54 protected WebserviceInfo wsInfo = null;
57 * original input data for this job
59 protected AlignmentView input = null;
62 * dataset sequence relationships to be propagated onto new results
64 protected Set<AlignedCodonFrame> codonframe = null;
67 * are there jobs still running in this thread.
69 protected boolean jobComplete = false;
72 * one or more jobs being managed by this thread.
74 protected AWsJob jobs[] = null;
77 * full name of service
79 protected String WebServiceName = null;
81 protected char defGapChar = '-';
84 * header prepended to all output from job
86 protected String OutputHeader;
89 * only used when reporting a web service out of memory error - the job ID
90 * will be concatenated to the URL
92 protected String WsUrl = null;
95 * The AlignFrame from which the service was requested.
97 private AlignFrame alignFrame;
100 * generic web service job/subjob poll loop
105 JobStateSummary jstate = null;
112 jstate = new JobStateSummary();
113 for (int j = 0; j < jobs.length; j++)
116 if (!jobs[j].submitted && jobs[j].hasValidInput())
121 if (jobs[j].submitted && !jobs[j].subjobComplete)
126 if (!jobs[j].hasResponse())
128 throw (new Exception(
129 "Timed out when communicating with server\nTry again later.\n"));
131 jalview.bin.Cache.log.debug("Job " + j + " Result state "
132 + jobs[j].getState() + "(ServerError="
133 + jobs[j].isServerError() + ")");
134 } catch (Exception ex)
136 // Deal with Transaction exceptions
137 wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
138 .formatMessage("info.server_exception", new Object[] {
139 WebServiceName, ex.getMessage() }));
140 // always output the exception's stack trace to the log
141 Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
142 + ") Server exception.");
143 // todo: could limit trace to cause if this is a SOAPFaultException.
144 ex.printStackTrace();
146 if (jobs[j].allowedServerExceptions > 0)
148 jobs[j].allowedServerExceptions--;
149 Cache.log.debug("Sleeping after a server exception.");
153 } catch (InterruptedException ex1)
159 Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
160 jobs[j].subjobComplete = true;
161 wsInfo.setStatus(jobs[j].jobnum,
162 WebserviceInfo.STATE_STOPPED_SERVERERROR);
164 } catch (OutOfMemoryError er)
167 jobs[j].subjobComplete = true;
168 jobs[j].clearResponse(); // may contain out of date result data
169 wsInfo.setStatus(jobs[j].jobnum,
170 WebserviceInfo.STATE_STOPPED_ERROR);
171 Cache.log.error("Out of memory when retrieving Job " + j
172 + " id:" + WsUrl + "/" + jobs[j].jobId, er);
173 new jalview.gui.OOMWarning("retrieving result for "
174 + WebServiceName, er);
178 jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
180 // Decide on overall state based on collected jobs[] states
181 updateGlobalStatus(jstate);
187 } catch (InterruptedException e)
190 .debug("Interrupted sleep waiting for next job poll.", e);
192 // System.out.println("I'm alive "+alTitle);
195 if (jobComplete && jobs != null)
197 parseResult(); // tidy up and make results available to user
202 .debug("WebServiceJob poll loop finished with no jobs created.");
203 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
204 wsInfo.appendProgressText(MessageManager
205 .getString("info.no_jobs_ran"));
206 wsInfo.setFinishedNoResults();
210 protected void updateGlobalStatus(JobStateSummary jstate)
212 if (jstate.running > 0)
214 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
216 else if (jstate.queuing > 0)
218 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
223 if (jstate.finished > 0)
225 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
227 else if (jstate.error > 0)
229 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
231 else if (jstate.serror > 0)
233 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
243 public AWSThread(Runnable target)
248 public AWSThread(String name)
253 public AWSThread(ThreadGroup group, Runnable target)
255 super(group, target);
258 public AWSThread(ThreadGroup group, String name)
263 public AWSThread(Runnable target, String name)
268 public AWSThread(ThreadGroup group, Runnable target, String name)
270 super(group, target, name);
274 * query web service for status of job. on return, job.result must not be null
275 * - if it is then it will be assumed that the job status query timed out and
276 * a server exception will be logged.
280 * will be logged as a server exception for this job
282 public abstract void pollJob(AWsJob job) throws Exception;
285 * submit job to web service
289 public abstract void StartJob(AWsJob job);
292 * process the set of AWsJob objects into a set of results, and tidy up.
294 public abstract void parseResult();
297 * helper function to conserve dataset references to sequence objects returned
298 * from web services 1. Propagates AlCodonFrame data from
299 * <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
303 public void propagateDatasetMappings(Alignment al)
305 if (codonframe != null)
307 SequenceI[] alignment = al.getSequencesArray();
308 for (int sq = 0; sq < alignment.length; sq++)
310 for (AlignedCodonFrame acf : codonframe)
312 final SequenceI seq = alignment[sq];
313 if (acf != null && acf.involvesSequence(seq))
315 al.addCodonFrame(acf);
323 public AWSThread(ThreadGroup group, Runnable target, String name,
326 super(group, target, name, stackSize);
331 * @return gap character to use for any alignment generation
333 public char getGapChar()
341 * reference for copying mappings across
343 * gui attachment point
345 * input data for the calculation
346 * @param webServiceName
349 * url of the service being invoked
351 public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
352 AlignmentView input, String webServiceName, String wsUrl)
354 this(alignFrame, wsinfo, input, wsUrl);
355 WebServiceName = webServiceName;
359 * Extracts additional info from alignment view's context.
362 * - reference for copying mappings and display styles across
364 * - gui attachment point - may be null
366 * - input data for the calculation
368 * - url of the service being invoked
370 public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
371 AlignmentView alview, String wsurl2)
374 this.alignFrame = alframe;
375 currentView = alframe.getCurrentView().getAlignment();
376 featureSettings = alframe.getFeatureRenderer().getSettings();
377 defGapChar = alframe.getViewport().getGapCharacter();
378 this.wsInfo = wsinfo2;
383 List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
387 codonframe = new LinkedHashSet<AlignedCodonFrame>();
388 codonframe.addAll(cf);
393 protected AlignFrame getRequestingAlignFrame()
395 return this.alignFrame;