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;
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 * The AlignFrame from which the service was requested.
96 private AlignFrame alignFrame;
99 * generic web service job/subjob poll loop
103 JobStateSummary jstate = null;
110 jstate = new JobStateSummary();
111 for (int j = 0; j < jobs.length; j++)
114 if (!jobs[j].submitted && jobs[j].hasValidInput())
119 if (jobs[j].submitted && !jobs[j].subjobComplete)
124 if (!jobs[j].hasResponse())
126 throw (new Exception(
127 "Timed out when communicating with server\nTry again later.\n"));
129 jalview.bin.Cache.log.debug("Job " + j + " Result state "
130 + jobs[j].getState() + "(ServerError="
131 + jobs[j].isServerError() + ")");
132 } catch (Exception ex)
134 // Deal with Transaction exceptions
135 wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
136 .formatMessage("info.server_exception", new Object[] {
137 WebServiceName, ex.getMessage() }));
138 // always output the exception's stack trace to the log
139 Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
140 + ") Server exception.");
141 // todo: could limit trace to cause if this is a SOAPFaultException.
142 ex.printStackTrace();
144 if (jobs[j].allowedServerExceptions > 0)
146 jobs[j].allowedServerExceptions--;
147 Cache.log.debug("Sleeping after a server exception.");
151 } catch (InterruptedException ex1)
157 Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
158 jobs[j].subjobComplete = true;
159 wsInfo.setStatus(jobs[j].jobnum,
160 WebserviceInfo.STATE_STOPPED_SERVERERROR);
162 } catch (OutOfMemoryError er)
165 jobs[j].subjobComplete = true;
166 jobs[j].clearResponse(); // may contain out of date result data
167 wsInfo.setStatus(jobs[j].jobnum,
168 WebserviceInfo.STATE_STOPPED_ERROR);
169 Cache.log.error("Out of memory when retrieving Job " + j
170 + " id:" + WsUrl + "/" + jobs[j].jobId, er);
171 new jalview.gui.OOMWarning("retrieving result for "
172 + WebServiceName, er);
176 jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
178 // Decide on overall state based on collected jobs[] states
179 updateGlobalStatus(jstate);
185 } catch (InterruptedException e)
188 .debug("Interrupted sleep waiting for next job poll.", e);
190 // System.out.println("I'm alive "+alTitle);
193 if (jobComplete && jobs != null)
195 parseResult(); // tidy up and make results available to user
200 .debug("WebServiceJob poll loop finished with no jobs created.");
201 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
202 wsInfo.appendProgressText(MessageManager
203 .getString("info.no_jobs_ran"));
204 wsInfo.setFinishedNoResults();
208 protected void updateGlobalStatus(JobStateSummary jstate)
210 if (jstate.running > 0)
212 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
214 else if (jstate.queuing > 0)
216 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
221 if (jstate.finished > 0)
223 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
225 else if (jstate.error > 0)
227 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
229 else if (jstate.serror > 0)
231 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
241 public AWSThread(Runnable target)
246 public AWSThread(String name)
251 public AWSThread(ThreadGroup group, Runnable target)
253 super(group, target);
256 public AWSThread(ThreadGroup group, String name)
261 public AWSThread(Runnable target, String name)
266 public AWSThread(ThreadGroup group, Runnable target, String name)
268 super(group, target, name);
272 * query web service for status of job. on return, job.result must not be null
273 * - if it is then it will be assumed that the job status query timed out and
274 * a server exception will be logged.
278 * will be logged as a server exception for this job
280 public abstract void pollJob(AWsJob job) throws Exception;
283 * submit job to web service
287 public abstract void StartJob(AWsJob job);
290 * process the set of AWsJob objects into a set of results, and tidy up.
292 public abstract void parseResult();
295 * helper function to conserve dataset references to sequence objects returned
296 * from web services 1. Propagates AlCodonFrame data from
297 * <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
301 public void propagateDatasetMappings(Alignment al)
303 if (codonframe != null)
305 SequenceI[] alignment = al.getSequencesArray();
306 for (int sq = 0; sq < alignment.length; sq++)
308 for (AlignedCodonFrame acf : codonframe)
310 final SequenceI seq = alignment[sq];
311 if (acf != null && acf.involvesSequence(seq))
313 al.addCodonFrame(acf);
321 public AWSThread(ThreadGroup group, Runnable target, String name,
324 super(group, target, name, stackSize);
329 * @return gap character to use for any alignment generation
331 public char getGapChar()
339 * reference for copying mappings across
341 * gui attachment point
343 * input data for the calculation
344 * @param webServiceName
347 * url of the service being invoked
349 public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
350 AlignmentView input, String webServiceName, String wsUrl)
352 this(alignFrame, wsinfo, input, wsUrl);
353 WebServiceName = webServiceName;
357 * Extracts additional info from alignment view's context.
360 * - reference for copying mappings and display styles across
362 * - gui attachment point - may be null
364 * - input data for the calculation
366 * - url of the service being invoked
368 public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
369 AlignmentView alview, String wsurl2)
372 this.alignFrame = alframe;
373 currentView = alframe.getCurrentView().getAlignment();
374 featureSettings = alframe.getFeatureRenderer().getSettings();
375 defGapChar = alframe.getViewport().getGapCharacter();
376 this.wsInfo = wsinfo2;
381 Set<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
385 codonframe = new LinkedHashSet<AlignedCodonFrame>();
386 codonframe.addAll(cf);
391 protected AlignFrame getRequestingAlignFrame()
393 return this.alignFrame;