2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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;
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 Set<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 * generic web service job/subjob poll loop
98 JobStateSummary jstate = null;
105 jstate = new JobStateSummary();
106 for (int j = 0; j < jobs.length; j++)
109 if (!jobs[j].submitted && jobs[j].hasValidInput())
114 if (jobs[j].submitted && !jobs[j].subjobComplete)
119 if (!jobs[j].hasResponse())
121 throw (new Exception(
122 "Timed out when communicating with server\nTry again later.\n"));
124 jalview.bin.Cache.log.debug("Job " + j + " Result state "
125 + jobs[j].getState() + "(ServerError="
126 + jobs[j].isServerError() + ")");
127 } catch (Exception ex)
129 // Deal with Transaction exceptions
130 wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
131 .formatMessage("info.server_exception", new Object[]
132 { WebServiceName, ex.getMessage() }));
133 // always output the exception's stack trace to the log
134 Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
135 + ") Server exception.");
136 // todo: could limit trace to cause if this is a SOAPFaultException.
137 ex.printStackTrace();
139 if (jobs[j].allowedServerExceptions > 0)
141 jobs[j].allowedServerExceptions--;
142 Cache.log.debug("Sleeping after a server exception.");
146 } catch (InterruptedException ex1)
152 Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
153 jobs[j].subjobComplete = true;
154 wsInfo.setStatus(jobs[j].jobnum,
155 WebserviceInfo.STATE_STOPPED_SERVERERROR);
157 } catch (OutOfMemoryError er)
160 jobs[j].subjobComplete = true;
161 jobs[j].clearResponse(); // may contain out of date result data
162 wsInfo.setStatus(jobs[j].jobnum,
163 WebserviceInfo.STATE_STOPPED_ERROR);
164 Cache.log.error("Out of memory when retrieving Job " + j
165 + " id:" + WsUrl + "/" + jobs[j].jobId, er);
166 new jalview.gui.OOMWarning("retrieving result for "
167 + WebServiceName, er);
171 jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
173 // Decide on overall state based on collected jobs[] states
174 updateGlobalStatus(jstate);
180 } catch (InterruptedException e)
183 .debug("Interrupted sleep waiting for next job poll.", e);
185 // System.out.println("I'm alive "+alTitle);
188 if (jobComplete && jobs != null)
190 parseResult(); // tidy up and make results available to user
195 .debug("WebServiceJob poll loop finished with no jobs created.");
196 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
197 wsInfo.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
198 wsInfo.setFinishedNoResults();
202 protected void updateGlobalStatus(JobStateSummary jstate)
204 if (jstate.running > 0)
206 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
208 else if (jstate.queuing > 0)
210 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
215 if (jstate.finished > 0)
217 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
219 else if (jstate.error > 0)
221 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
223 else if (jstate.serror > 0)
225 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
235 public AWSThread(Runnable target)
240 public AWSThread(String name)
245 public AWSThread(ThreadGroup group, Runnable target)
247 super(group, target);
250 public AWSThread(ThreadGroup group, String name)
255 public AWSThread(Runnable target, String name)
260 public AWSThread(ThreadGroup group, Runnable target, String name)
262 super(group, target, name);
266 * query web service for status of job. on return, job.result must not be null
267 * - if it is then it will be assumed that the job status query timed out and
268 * a server exception will be logged.
272 * will be logged as a server exception for this job
274 public abstract void pollJob(AWsJob job) throws Exception;
277 * submit job to web service
281 public abstract void StartJob(AWsJob job);
284 * process the set of AWsJob objects into a set of results, and tidy up.
286 public abstract void parseResult();
289 * helper function to conserve dataset references to sequence objects returned
290 * from web services 1. Propagates AlCodonFrame data from
291 * <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
295 public void propagateDatasetMappings(Alignment al)
297 if (codonframe != null)
299 SequenceI[] alignment = al.getSequencesArray();
300 for (int sq = 0; sq < alignment.length; sq++)
302 for (AlignedCodonFrame acf : codonframe)
304 final SequenceI seq = alignment[sq];
305 if (acf != null && acf.involvesSequence(seq))
307 al.addCodonFrame(acf);
315 public AWSThread(ThreadGroup group, Runnable target, String name,
318 super(group, target, name, stackSize);
323 * @return gap character to use for any alignment generation
325 public char getGapChar()
333 * reference for copying mappings across
335 * gui attachment point
337 * input data for the calculation
338 * @param webServiceName
341 * url of the service being invoked
343 public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
344 AlignmentView input, String webServiceName, String wsUrl)
346 this(alignFrame, wsinfo, input, wsUrl);
347 WebServiceName = webServiceName;
351 * Extracts additional info from alignment view's context.
354 * - reference for copying mappings and display styles across
356 * - gui attachment point - may be null
358 * - input data for the calculation
360 * - url of the service being invoked
362 public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
363 AlignmentView alview, String wsurl2)
366 // this.alignFrame = alframe;
367 currentView = alframe.getCurrentView().getAlignment();
368 featureSettings = alframe.getFeatureRenderer().getSettings();
369 defGapChar = alframe.getViewport().getGapCharacter();
370 this.wsInfo = wsinfo2;
375 Set<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
379 codonframe = new LinkedHashSet<AlignedCodonFrame>();
380 codonframe.addAll(cf);