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.Console;
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)
128 JobStateSummary jstate = new JobStateSummary();
129 for (final AWsJob job : jobs)
131 if (!job.submitted && job.hasValidInput())
135 Console.debug(format(
136 "Job %s is %ssubmitted", job, job.submitted ? "" : "not "));
137 if (job.submitted && !job.subjobComplete)
139 Console.debug(format(
140 "Polling Job %s Result state was:%s(ServerError=%b)",
141 job, job.getState(), job.isServerError()));
145 if (!job.hasResponse())
146 throw new Exception("Timed out when communicating with server. Try again later.");
148 Console.debug(format("Job %s Result state:%s(ServerError=%b)",
149 job, job.getState(), job.isServerError()));
150 } catch (Exception exc)
152 // Deal with Transaction exceptions
153 wsInfo.appendProgressText(job.jobnum, MessageManager
154 .formatMessage("info.server_exception", WebServiceName,
156 // always output the exception's stack trace to the log
157 Console.warn(format("%s job(%s) Server exception.",
158 WebServiceName, job.jobnum));
159 exc.printStackTrace();
161 if (job.allowedServerExceptions > 0)
163 job.allowedServerExceptions--;
167 Console.warn(format("Dropping job %s %s", job, job.jobId));
168 job.subjobComplete = true;
169 wsInfo.setStatus(job.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
171 } catch (OutOfMemoryError oomerror)
174 job.subjobComplete = true;
176 wsInfo.setStatus(job.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
177 Console.error(format("Out of memory when retrieving Job %s id:%s/%s",
178 job, WsUrl, job.jobId), oomerror);
179 new jalview.gui.OOMWarning("retrieving result for " + WebServiceName, oomerror);
183 jstate.updateJobPanelState(wsInfo, OutputHeader, job);
185 // Decide on overall state based on collected jobs[] states
186 updateGlobalStatus(jstate);
190 // jobs should never be null at this point
191 parseResult(); // tidy up and make results available to user
196 timer.setInitialDelay(0);
200 protected void updateGlobalStatus(JobStateSummary jstate)
202 if (jstate.running > 0)
204 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
206 else if (jstate.queuing > 0)
208 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
213 if (jstate.finished > 0)
215 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
217 else if (jstate.error > 0)
219 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
221 else if (jstate.serror > 0)
223 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
229 public void interrupt()
235 * query web service for status of job. on return, job.result must not be null
236 * - if it is then it will be assumed that the job status query timed out and
237 * a server exception will be logged.
241 * will be logged as a server exception for this job
243 public abstract void pollJob(AWsJob job) throws Exception;
246 * submit job to web service
250 public abstract void StartJob(AWsJob job);
253 * process the set of AWsJob objects into a set of results, and tidy up.
255 public abstract void parseResult();
258 * helper function to conserve dataset references to sequence objects returned
259 * from web services 1. Propagates AlCodonFrame data from
260 * <code>codonframe</code> to <code>al</code> TODO: refactor to datamodel
264 public void propagateDatasetMappings(Alignment al)
266 if (codonframe != null)
268 SequenceI[] alignment = al.getSequencesArray();
269 for (int sq = 0; sq < alignment.length; sq++)
271 for (AlignedCodonFrame acf : codonframe)
273 final SequenceI seq = alignment[sq];
274 if (acf != null && acf.involvesSequence(seq))
276 al.addCodonFrame(acf);
287 * @return gap character to use for any alignment generation
289 public char getGapChar()
297 * reference for copying mappings across
299 * gui attachment point
301 * input data for the calculation
302 * @param webServiceName
305 * url of the service being invoked
307 public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
308 AlignmentView input, String webServiceName, String wsUrl)
310 this(alignFrame, wsinfo, input, wsUrl);
311 WebServiceName = webServiceName;
315 * Extracts additional info from alignment view's context.
318 * - reference for copying mappings and display styles across
320 * - gui attachment point - may be null
322 * - input data for the calculation
324 * - url of the service being invoked
326 public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
327 AlignmentView alview, String wsurl2)
330 this.alignFrame = alframe;
331 currentView = alframe.getCurrentView().getAlignment();
332 featureSettings = alframe.getFeatureRenderer().getSettings();
333 defGapChar = alframe.getViewport().getGapCharacter();
334 this.wsInfo = wsinfo2;
339 List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
343 codonframe = new ArrayList<>();
344 codonframe.addAll(cf);
349 protected AlignFrame getRequestingAlignFrame()
351 return this.alignFrame;