Examples with Task net.sf.mzmine.taskcontrol.Task used on opensource projects

Example 16 with Task

use of net.sf.mzmine.taskcontrol.Task in project mzmine2 by mzmine.

the class HierarAlignerGcModule method runModule.

@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
    Task newTask = new HierarAlignerGCTask(project, parameters);
    tasks.add(newTask);
    return ExitCode.OK;
}

Example 17 with Task

use of net.sf.mzmine.taskcontrol.Task in project mzmine2 by mzmine.

the class SmoothingModule method runModule.

@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
    PeakList[] peakLists = parameters.getParameter(SmoothingParameters.peakLists).getValue().getMatchingPeakLists();
    for (final PeakList peakList : peakLists) {
        Task newTask = new SmoothingTask(project, peakList, parameters);
        tasks.add(newTask);
    }
    return ExitCode.OK;
}

Example 18 with Task

use of net.sf.mzmine.taskcontrol.Task in project mzmine2 by mzmine.

the class DataPointProcessingController method execute.

/**
 * This will execute the modules associated with the plot. It will start with the first one and
 * execute the following ones afterwards automatically. This method is called by the public method
 * execute(). The status listener in this method starts the next task recursively after the
 * previous one has finished.
 *
 * @param dp
 * @param module
 * @param plot
 */
private void execute(DataPoint[] dp, MZmineProcessingStep<DataPointProcessingModule> step, SpectraPlot plot) {
    if (queue == null || queue.isEmpty() || plot == null) {
        logger.warning("execute called, without queue or plot being set.");
        setStatus(ControllerStatus.FINISHED);
        return;
    }
    if (getForcedStatus() == ForcedControllerStatus.CANCEL || getStatus() == ControllerStatus.CANCELED) {
        setResults(ProcessedDataPoint.convert(dp));
        logger.finest("Canceled controller, not starting new tasks. Results are set to latest array.");
        setStatus(ControllerStatus.CANCELED);
        return;
    }
    List<String> err = new ArrayList<>();
    if (!step.getParameterSet().checkParameterValues(err)) {
        setResults(ProcessedDataPoint.convert(dp));
        setStatus(ControllerStatus.CANCELED);
        logger.warning(step.getModule().getName() + " - Not all parameters set." + Arrays.toString(err.toArray(new String[0])));
        return;
    }
    if (step.getModule() instanceof DataPointProcessingModule) {
        DataPointProcessingModule inst = step.getModule();
        ParameterSet parameters = step.getParameterSet();
        Task t = ((DataPointProcessingModule) inst).createTask(dp, parameters, plot, this, new TaskStatusListener() {

            @Override
            public void taskStatusChanged(Task task, TaskStatus newStatus, TaskStatus oldStatus) {
                if (!(task instanceof DataPointProcessingTask)) {
                    // TODO: Throw exception?
                    logger.warning("This should have been a DataPointProcessingTask.");
                    return;
                }
                // logger.finest("Task status changed to " + newStatus.toString());
                switch(newStatus) {
                    case FINISHED:
                        if (queue.hasNextStep(step)) {
                            if (DataPointProcessingManager.getInst().isRunning(((DataPointProcessingTask) task).getController())) {
                                MZmineProcessingStep<DataPointProcessingModule> next = queue.getNextStep(step);
                                // pass results to next task and start recursively
                                ProcessedDataPoint[] result = ((DataPointProcessingTask) task).getResults();
                                ((DataPointProcessingTask) task).displayResults();
                                execute(result, next, plot);
                            } else {
                                logger.warning("This controller was already removed from the running list, although it " + "had not finished processing. Exiting");
                                break;
                            }
                        } else {
                            setResults(((DataPointProcessingTask) task).getResults());
                            ((DataPointProcessingTask) task).displayResults();
                            setStatus(ControllerStatus.FINISHED);
                        }
                        break;
                    case PROCESSING:
                        setStatus(ControllerStatus.PROCESSING);
                        break;
                    case WAITING:
                        // should we even set to WAITING here?
                        break;
                    case ERROR:
                        setStatus(ControllerStatus.ERROR);
                        break;
                    case CANCELED:
                        setStatus(ControllerStatus.CANCELED);
                        break;
                }
            }
        });
        logger.finest("Start processing of " + t.getClass().getName());
        MZmineCore.getTaskController().addTask(t);
        // maybe we need this some time
        setCurrentTask((DataPointProcessingTask) t);
        setCurrentStep(step);
    }
}

Example 19 with Task

use of net.sf.mzmine.taskcontrol.Task in project mzmine2 by mzmine.

the class TaskQueue method getValueAt.

/**
 * @see javax.swing.table.TableModel#getValueAt(int, int)
 */
public synchronized Object getValueAt(int row, int column) {
    if (row < size) {
        WrappedTask wrappedTask = queue[row];
        Task actualTask = wrappedTask.getActualTask();
        switch(column) {
            case 0:
                return actualTask.getTaskDescription();
            case 1:
                return wrappedTask.getPriority();
            case 2:
                return actualTask.getStatus();
            case 3:
                double finishedPercentage = actualTask.getFinishedPercentage();
                LabeledProgressBar progressBar = progressBars.get(row);
                if (progressBar == null) {
                    progressBar = new LabeledProgressBar(finishedPercentage);
                    progressBars.put(row, progressBar);
                } else {
                    progressBar.setValue(finishedPercentage);
                }
                return progressBar;
        }
    }
    return null;
}

Example 20 with Task

use of net.sf.mzmine.taskcontrol.Task in project mzmine2 by mzmine.

the class WorkerThread method run.

/**
 * @see java.lang.Runnable#run()
 */
public void run() {
    Task actualTask = wrappedTask.getActualTask();
    try {
        // Log the start (INFO level events go to the Status bar, too)
        logger.info("Starting processing of task " + actualTask.getTaskDescription());
        // Process the actual task
        actualTask.run();
        // Check if task finished with an error
        if (actualTask.getStatus() == TaskStatus.ERROR) {
            String errorMsg = actualTask.getErrorMessage();
            if (errorMsg == null)
                errorMsg = "Unspecified error";
            // Log the error
            logger.severe("Error of task " + actualTask.getTaskDescription() + ": " + errorMsg);
            MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Error of task " + actualTask.getTaskDescription(), errorMsg);
        } else {
            // Log the finish
            logger.info("Processing of task " + actualTask.getTaskDescription() + " done, status " + actualTask.getStatus());
        }
        /*
       * This is important to allow the garbage collector to remove the task, while keeping the task
       * description in the "Tasks in progress" window
       */
        wrappedTask.removeTaskReference();
    } catch (Throwable e) {
        /*
       * This should never happen, it means the task did not handle its exception properly, or there
       * was some severe error, like OutOfMemoryError
       */
        logger.log(Level.SEVERE, "Unhandled exception " + e + " while processing task " + actualTask.getTaskDescription(), e);
        e.printStackTrace();
        MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "Unhandled exception in task " + actualTask.getTaskDescription() + ": " + ExceptionUtils.exceptionToString(e));
    }
    /*
     * Mark this thread as finished
     */
    finished = true;
}