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 import static java.lang.String.format;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import javax.swing.Timer;
43 public abstract class AWSThread
46 private javax.swing.Timer timer;
49 * view that this job was associated with
51 protected AlignmentI currentView = null;
54 * feature settings from view that job was associated with
56 protected FeatureRendererSettings featureSettings = null;
59 * metadata about this web service
61 protected WebserviceInfo wsInfo = null;
64 * original input data for this job
66 protected AlignmentView input = null;
69 * dataset sequence relationships to be propagated onto new results
71 protected List<AlignedCodonFrame> codonframe = null;
74 * are there jobs still running in this thread.
76 * fixme: initialize with an empty array?
78 protected boolean jobComplete = false;
81 * one or more jobs being managed by this thread.
83 protected AWsJob[] jobs = null;
86 * full name of service
88 protected String WebServiceName = null;
90 protected char defGapChar = '-';
93 * header prepended to all output from job
95 protected String OutputHeader;
98 * only used when reporting a web service out of memory error - the job ID
99 * will be concatenated to the URL
101 protected String WsUrl = null;
104 * The AlignFrame from which the service was requested.
106 private AlignFrame alignFrame;
114 "WebServiceJob poll loop finished with no jobs created.");
115 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
116 wsInfo.appendProgressText(
117 MessageManager.getString("info.no_jobs_ran"));
118 wsInfo.setFinishedNoResults();
121 timer = new Timer(5000, new ActionListener()
125 public void actionPerformed(ActionEvent e)
127 JobStateSummary jstate = new JobStateSummary();
128 for (final AWsJob job : jobs)
130 if (!job.submitted && job.hasValidInput())
134 Cache.log.debug(format(
135 "Job %s is %ssubmitted", job, job.submitted ? "" : "not "));
136 if (job.submitted && !job.subjobComplete)
138 Cache.log.debug(format(
139 "Polling Job %s Result state was:%s(ServerError=%b)",
140 job, job.getState(), job.isServerError()));
144 if (!job.hasResponse())
145 throw new Exception("Timed out when communicating with server. Try again later.");
147 Cache.log.debug(format("Job %s Result state:%s(ServerError=%b)",
148 job, job.getState(), job.isServerError()));
149 } catch (Exception exc)
151 // Deal with Transaction exceptions
152 wsInfo.appendProgressText(job.jobnum, MessageManager
153 .formatMessage("info.server_exception", WebServiceName,
155 // always output the exception's stack trace to the log
156 Cache.log.warn(format("%s job(%s) Server exception.",
157 WebServiceName, job.jobnum));
158 exc.printStackTrace();
160 if (job.allowedServerExceptions > 0)
162 job.allowedServerExceptions--;
166 Cache.log.warn(format("Dropping job %s %s", job, job.jobId));
167 job.subjobComplete = true;
168 wsInfo.setStatus(job.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
170 } catch (OutOfMemoryError oomerror)
173 job.subjobComplete = true;
175 wsInfo.setStatus(job.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
176 Cache.log.error(format("Out of memory when retrieving Job %s id:%s/%s",
177 job, WsUrl, job.jobId), oomerror);
178 new jalview.gui.OOMWarning("retrieving result for " + WebServiceName, oomerror);
182 jstate.updateJobPanelState(wsInfo, OutputHeader, job);
184 // Decide on overall state based on collected jobs[] states
185 updateGlobalStatus(jstate);
189 // jobs should never be null at this point
190 parseResult(); // tidy up and make results available to user
195 timer.setInitialDelay(0);
199 protected void updateGlobalStatus(JobStateSummary jstate)
201 if (jstate.running > 0)
203 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
205 else if (jstate.queuing > 0)
207 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
212 if (jstate.finished > 0)
214 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
216 else if (jstate.error > 0)
218 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
220 else if (jstate.serror > 0)
222 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
227 public void interrupt()
233 * query web service for status of job. on return, job.result must not be null
234 * - if it is then it will be assumed that the job status query timed out and
235 * a server exception will be logged.
239 * will be logged as a server exception for this job
241 public abstract void pollJob(AWsJob job) throws Exception;
244 * submit job to web service
248 public abstract void StartJob(AWsJob job);
251 * process the set of AWsJob objects into a set of results, and tidy up.
253 public abstract void parseResult();
256 * helper function to conserve dataset references to sequence objects returned
257 * from web services 1. Propagates AlCodonFrame data from
258 * <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
262 public void propagateDatasetMappings(Alignment al)
264 if (codonframe != null)
266 SequenceI[] alignment = al.getSequencesArray();
267 for (int sq = 0; sq < alignment.length; sq++)
269 for (AlignedCodonFrame acf : codonframe)
271 final SequenceI seq = alignment[sq];
272 if (acf != null && acf.involvesSequence(seq))
274 al.addCodonFrame(acf);
284 * @return gap character to use for any alignment generation
286 public char getGapChar()
294 * reference for copying mappings across
296 * gui attachment point
298 * input data for the calculation
299 * @param webServiceName
302 * url of the service being invoked
304 public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
305 AlignmentView input, String webServiceName, String wsUrl)
307 this(alignFrame, wsinfo, input, wsUrl);
308 WebServiceName = webServiceName;
312 * Extracts additional info from alignment view's context.
315 * - reference for copying mappings and display styles across
317 * - gui attachment point - may be null
319 * - input data for the calculation
321 * - url of the service being invoked
323 public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
324 AlignmentView alview, String wsurl2)
327 this.alignFrame = alframe;
328 currentView = alframe.getCurrentView().getAlignment();
329 featureSettings = alframe.getFeatureRenderer().getSettings();
330 defGapChar = alframe.getViewport().getGapCharacter();
331 this.wsInfo = wsinfo2;
336 List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
340 codonframe = new ArrayList<>();
341 codonframe.addAll(cf);
346 protected AlignFrame getRequestingAlignFrame()
348 return this.alignFrame;