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Coverage Report

  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.ws2.actions

File BaseTask.java

 

Coverage histogram

../../../img/srcFileCovDistChart6.png
37% of files have more coverage

Code metrics

24
95
18
1
312
243
38
0.4
5.28
18
2.11

Classes

Class Line # Actions
BaseTask 23 95 38
0.583941658.4%
 

Contributing tests

This file is covered by 49 tests. .

Source view

1    package jalview.ws2.actions;
2   
3    import java.io.IOException;
4    import java.util.ArrayList;
5    import java.util.Collections;
6    import java.util.List;
7    import java.util.Objects;
8   
9    import jalview.bin.Console;
10    import jalview.util.ArrayUtils;
11    import jalview.util.MathUtils;
12    import jalview.ws.params.ArgumentI;
13    import jalview.ws2.actions.api.TaskEventListener;
14    import jalview.ws2.actions.api.TaskI;
15    import jalview.ws2.api.Credentials;
16    import jalview.ws2.api.JobStatus;
17    import jalview.ws2.client.api.WebServiceClientI;
18    import jalview.ws2.helpers.DelegateJobEventListener;
19    import jalview.ws2.helpers.TaskEventSupport;
20   
21    import static java.lang.String.format;
22   
 
23    public abstract class BaseTask<T extends BaseJob, R> implements TaskI<R>
24    {
25    protected final long uid = MathUtils.getUID();
26   
27    protected final WebServiceClientI webClient;
28   
29    protected final List<ArgumentI> args;
30   
31    protected final Credentials credentials;
32   
33    private final TaskEventSupport<R> eventHandler;
34   
35    protected JobStatus status = JobStatus.CREATED;
36   
37    protected List<T> jobs = Collections.emptyList();
38   
39    protected R result = null;
40   
41    protected Runnable cancelAction = () -> {
42    };
43   
 
44  48 toggle protected BaseTask(WebServiceClientI webClient, List<ArgumentI> args,
45    Credentials credentials)
46    {
47  48 this.webClient = webClient;
48  48 this.args = args;
49  48 this.credentials = credentials;
50  48 this.eventHandler = new TaskEventSupport<>(this);
51    }
52   
 
53  0 toggle @Override
54    public final long getUid()
55    {
56  0 return uid;
57    }
58   
 
59  32 toggle @Override
60    public final JobStatus getStatus()
61    {
62  32 return status;
63    }
64   
 
65  0 toggle @Override
66    public final List<T> getSubJobs()
67    {
68  0 return jobs;
69    }
70   
 
71  26 toggle @Override
72    public final void addTaskEventListener(TaskEventListener<R> listener)
73    {
74  26 eventHandler.addListener(listener);
75    }
76   
 
77  0 toggle @Override
78    public final void removeTaskEventListener(TaskEventListener<R> listener)
79    {
80  0 eventHandler.addListener(listener);
81    }
82   
 
83  3 toggle @Override
84    public final R getResult()
85    {
86  3 return result;
87    }
88   
 
89  29 toggle @Override
90    public final void init() throws Exception
91    {
92  29 try
93    {
94  29 jobs = prepareJobs();
95    } catch (ServiceInputInvalidException e)
96    {
97  0 setStatus(JobStatus.INVALID);
98  0 eventHandler.fireTaskException(e);
99  0 throw e;
100    }
101  29 setStatus(JobStatus.READY);
102  29 eventHandler.fireTaskStarted(jobs);
103  29 var jobListener = new DelegateJobEventListener<>(eventHandler);
104  29 for (var job : jobs)
105  29 job.addPropertyChangeListener(jobListener);
106  29 submitJobs(jobs);
107    }
108   
109    static final int MAX_SUBMIT_RETRY = 5;
110   
 
111  29 toggle protected final void submitJobs(List<T> jobs) throws IOException
112    {
113  29 var retryCounter = 0;
114  29 while (true)
115    {
116  29 try
117    {
118  29 submitJobs0(jobs);
119  29 setStatus(JobStatus.SUBMITTED);
120  29 break;
121    } catch (IOException e)
122    {
123  0 eventHandler.fireTaskException(e);
124  0 if (++retryCounter > MAX_SUBMIT_RETRY)
125    {
126  0 cancel();
127  0 setStatus(JobStatus.SERVER_ERROR);
128  0 throw e;
129    }
130    }
131    }
132    }
133   
 
134  29 toggle private final void submitJobs0(List<T> jobs) throws IOException
135    {
136  29 IOException exception = null;
137  29 for (BaseJob job : jobs)
138    {
139  29 if (job.getStatus() != JobStatus.READY || !job.isInputValid())
140  0 continue;
141  29 try
142    {
143  29 var jobRef = webClient.submit(job.getInputSequences(), args, credentials);
144  29 job.setServerJob(jobRef);
145  29 job.setStatus(JobStatus.SUBMITTED);
146    } catch (IOException e)
147    {
148  0 exception = e;
149    }
150    }
151  29 if (exception != null)
152  0 throw exception;
153    }
154   
155    /**
156    * Poll all running jobs and update their status and logs. Polling is repeated
157    * periodically until this method return true when all jobs are done.
158    *
159    * @return {@code true] if all jobs are done @throws IOException if server
160    * error occurred
161    */
 
162  35 toggle @Override
163    public final boolean poll() throws IOException
164    {
165  35 boolean allDone = true;
166  35 IOException exception = null;
167  36 for (BaseJob job : jobs)
168    {
169  35 if (job.isInputValid() && !job.getStatus().isDone())
170    {
171  35 var serverJob = job.getServerJob();
172  36 try
173    {
174  36 job.setStatus(webClient.getStatus(serverJob));
175  36 job.setLog(webClient.getLog(serverJob));
176  37 job.setErrorLog(webClient.getErrorLog(serverJob));
177    } catch (IOException e)
178    {
179  0 exception = e;
180    }
181    }
182  37 allDone &= job.isCompleted();
183    }
184  37 updateGlobalStatus();
185  37 if (exception != null)
186  0 throw exception;
187  37 return allDone;
188    }
189   
 
190  29 toggle @Override
191    public final void complete() throws IOException
192    {
193  29 for (var job : jobs)
194    {
195  29 if (!job.isCompleted())
196    {
197    // a fallback in case the executor decides to finish prematurely
198  0 cancelJob(job);
199  0 job.setStatus(JobStatus.SERVER_ERROR);
200    }
201    }
202  29 updateGlobalStatus();
203  29 try {
204  29 result = collectResult(jobs);
205  29 eventHandler.fireTaskCompleted(result);
206    }
207    catch (Exception e)
208    {
209  0 eventHandler.fireTaskException(e);
210  0 setStatus(JobStatus.SERVER_ERROR);
211  0 throw e;
212    }
213    }
214   
215    /**
216    * Cancel all running jobs. Used in case of task failure to cleanup the
217    * resources or when the task has been cancelled.
218    */
 
219  0 toggle @Override
220    public final void cancel()
221    {
222  0 cancelAction.run();
223  0 for (T job : jobs)
224    {
225  0 cancelJob(job);
226    }
227  0 setStatus(JobStatus.CANCELLED);
228    }
229   
 
230  0 toggle private final void cancelJob(T job)
231    {
232  0 if (!job.isCompleted())
233    {
234  0 try
235    {
236  0 if (job.getServerJob() != null)
237  0 webClient.cancel(job.getServerJob());
238  0 job.setStatus(JobStatus.CANCELLED);
239    } catch (IOException e)
240    {
241  0 Console.error(format("failed to cancel job %s", job.getServerJob()), e);
242    }
243    }
244    }
245   
 
246  124 toggle protected final void setStatus(JobStatus status)
247    {
248  124 Objects.requireNonNull(status);
249  124 if (this.status != status)
250    {
251  93 this.status = status;
252  93 eventHandler.fireTaskStatusChanged(status);
253    }
254    }
255   
256    protected abstract List<T> prepareJobs() throws ServiceInputInvalidException;
257   
258    protected abstract R collectResult(List<T> jobs) throws IOException;
259   
260    /**
261    * Update task status according to the overall status of its jobs. The rules
262    * of setting the status are following:
263    * <ul>
264    * <li>task is invalid if all jobs are invalid</li>
265    * <li>task is completed if all but invalid jobs are completed</li>
266    * <li>task is ready, submitted or queued if at least one job is ready,
267    * submitted or queued an none proceeded to the next stage excluding
268    * completed.</li>
269    * <li>task is running if at least one job is running and none are failed or
270    * cancelled</li>
271    * <li>task is cancelled if at least one job is cancelled and none failed</li>
272    * <li>task is failed or server error if at least one job is failed or server
273    * error</li>
274    * </ul>
275    */
 
276  66 toggle protected final void updateGlobalStatus()
277    {
278  66 int precedence = -1;
279  66 for (BaseJob job : jobs)
280    {
281  66 JobStatus status = job.getStatus();
282  66 int jobPrecedence = ArrayUtils.indexOf(JobStatus.statusPrecedence, status);
283  66 if (precedence < jobPrecedence)
284  66 precedence = jobPrecedence;
285    }
286  66 if (precedence >= 0)
287    {
288  66 setStatus(JobStatus.statusPrecedence[precedence]);
289    }
290    }
291   
292    /**
293    * Set the action that will be run when the {@link #cancel()} method is
294    * invoked. The action should typically stop the executor polling the task and
295    * release resources and threads running the task.
296    *
297    * @param action
298    * runnable to be executed when the task is cancelled
299    */
 
300  0 toggle public void setCancelAction(Runnable action)
301    {
302  0 Objects.requireNonNull(action);
303  0 this.cancelAction = action;
304    }
305   
 
306  0 toggle @Override
307    public String toString()
308    {
309  0 var statusName = status != null ? status.name() : "UNSET";
310  0 return String.format("%s(%x, %s)", getClass().getSimpleName(), uid, statusName);
311    }
312    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
  • OpenClover is free and open-source software.