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.ArrayList;
35 import java.util.List;
37 public abstract class AWSThread extends Thread
41 * view that this job was associated with
43 protected AlignmentI currentView = null;
46 * feature settings from view that job was associated with
48 protected FeatureRendererSettings featureSettings = null;
51 * metadata about this web service
53 protected WebserviceInfo wsInfo = null;
56 * original input data for this job
58 protected AlignmentView input = null;
61 * dataset sequence relationships to be propagated onto new results
63 protected List<AlignedCodonFrame> codonframe = null;
66 * are there jobs still running in this thread.
68 protected boolean jobComplete = false;
71 * one or more jobs being managed by this thread.
73 protected AWsJob jobs[] = null;
76 * full name of service
78 protected String WebServiceName = null;
80 protected char defGapChar = '-';
83 * header prepended to all output from job
85 protected String OutputHeader;
88 * only used when reporting a web service out of memory error - the job ID
89 * will be concatenated to the URL
91 protected String WsUrl = null;
94 * The AlignFrame from which the service was requested.
96 private AlignFrame alignFrame;
99 * generic web service job/subjob poll loop
104 JobStateSummary jstate = null;
111 jstate = new JobStateSummary();
112 for (int j = 0; j < jobs.length; j++)
115 if (!jobs[j].submitted && jobs[j].hasValidInput())
119 Cache.log.debug("Job " + jobs[j] + " is " + (jobs[j].submitted ? "submitted" : "not submitted"));
120 if (jobs[j].submitted && !jobs[j].subjobComplete)
122 jalview.bin.Cache.log.debug(
123 "Polling Job " + j + " Result state was:" + jobs[j].getState() + "(ServerError=" + jobs[j].isServerError()
129 if (!jobs[j].hasResponse())
131 throw (new Exception(
132 "Timed out when communicating with server\nTry again later.\n"));
134 jalview.bin.Cache.log.debug("Job " + j + " Result state "
135 + jobs[j].getState() + "(ServerError="
136 + jobs[j].isServerError() + ")");
137 } catch (Exception ex)
139 // Deal with Transaction exceptions
140 wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
141 .formatMessage("info.server_exception", new Object[]
142 { WebServiceName, ex.getMessage() }));
143 // always output the exception's stack trace to the log
144 Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
145 + ") Server exception.");
146 // todo: could limit trace to cause if this is a SOAPFaultException.
147 ex.printStackTrace();
149 if (jobs[j].allowedServerExceptions > 0)
151 jobs[j].allowedServerExceptions--;
152 Cache.log.debug("Sleeping after a server exception.");
156 } catch (InterruptedException ex1)
162 Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
163 jobs[j].subjobComplete = true;
164 wsInfo.setStatus(jobs[j].jobnum,
165 WebserviceInfo.STATE_STOPPED_SERVERERROR);
167 } catch (OutOfMemoryError er)
170 jobs[j].subjobComplete = true;
171 jobs[j].clearResponse(); // may contain out of date result data
172 wsInfo.setStatus(jobs[j].jobnum,
173 WebserviceInfo.STATE_STOPPED_ERROR);
174 Cache.log.error("Out of memory when retrieving Job " + j
175 + " id:" + WsUrl + "/" + jobs[j].jobId, er);
176 new jalview.gui.OOMWarning(
177 "retrieving result for " + WebServiceName, er);
181 jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
183 // Decide on overall state based on collected jobs[] states
184 updateGlobalStatus(jstate);
190 } catch (InterruptedException e)
192 Cache.log.debug("Interrupted sleep waiting for next job poll.",
195 // System.out.println("I'm alive ?");
198 if (jobComplete && jobs != null)
200 parseResult(); // tidy up and make results available to user
205 "WebServiceJob poll loop finished with no jobs created.");
206 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
207 wsInfo.appendProgressText(
208 MessageManager.getString("info.no_jobs_ran"));
209 wsInfo.setFinishedNoResults();
213 protected void updateGlobalStatus(JobStateSummary jstate)
215 if (jstate.running > 0)
217 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
219 else if (jstate.queuing > 0)
221 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
226 if (jstate.finished > 0)
228 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
230 else if (jstate.error > 0)
232 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
234 else if (jstate.serror > 0)
236 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
246 public AWSThread(Runnable target)
251 public AWSThread(String name)
256 public AWSThread(ThreadGroup group, Runnable target)
258 super(group, target);
261 public AWSThread(ThreadGroup group, String name)
266 public AWSThread(Runnable target, String name)
271 public AWSThread(ThreadGroup group, Runnable target, String name)
273 super(group, target, name);
277 * query web service for status of job. on return, job.result must not be null
278 * - if it is then it will be assumed that the job status query timed out and
279 * a server exception will be logged.
283 * will be logged as a server exception for this job
285 public abstract void pollJob(AWsJob job) throws Exception;
288 * submit job to web service
292 public abstract void StartJob(AWsJob job);
295 * process the set of AWsJob objects into a set of results, and tidy up.
297 public abstract void parseResult();
300 * helper function to conserve dataset references to sequence objects returned
301 * from web services 1. Propagates AlCodonFrame data from
302 * <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
306 public void propagateDatasetMappings(Alignment al)
308 if (codonframe != null)
310 SequenceI[] alignment = al.getSequencesArray();
311 for (int sq = 0; sq < alignment.length; sq++)
313 for (AlignedCodonFrame acf : codonframe)
315 final SequenceI seq = alignment[sq];
316 if (acf != null && acf.involvesSequence(seq))
318 al.addCodonFrame(acf);
326 public AWSThread(ThreadGroup group, Runnable target, String name,
329 super(group, target, name, stackSize);
334 * @return gap character to use for any alignment generation
336 public char getGapChar()
344 * reference for copying mappings across
346 * gui attachment point
348 * input data for the calculation
349 * @param webServiceName
352 * url of the service being invoked
354 public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
355 AlignmentView input, String webServiceName, String wsUrl)
357 this(alignFrame, wsinfo, input, wsUrl);
358 WebServiceName = webServiceName;
362 * Extracts additional info from alignment view's context.
365 * - reference for copying mappings and display styles across
367 * - gui attachment point - may be null
369 * - input data for the calculation
371 * - url of the service being invoked
373 public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
374 AlignmentView alview, String wsurl2)
377 this.alignFrame = alframe;
378 currentView = alframe.getCurrentView().getAlignment();
379 featureSettings = alframe.getFeatureRenderer().getSettings();
380 defGapChar = alframe.getViewport().getGapCharacter();
381 this.wsInfo = wsinfo2;
386 List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
390 codonframe = new ArrayList<>();
391 codonframe.addAll(cf);
396 protected AlignFrame getRequestingAlignFrame()
398 return this.alignFrame;