Examples with MZmineProcessingModule net.sf.mzmine.modules.MZmineProcessingModule used on opensource projects

Example 1 with MZmineProcessingModule

use of net.sf.mzmine.modules.MZmineProcessingModule in project mzmine2 by mzmine.

the class BatchQueue method loadFromXml.

/**
 * De-serialize from XML.
 *
 * @param xmlElement the element that holds the XML.
 * @return the de-serialized value.
 */
public static BatchQueue loadFromXml(final Element xmlElement) {
    // Set the parameter choice for the RowsFilterModule
    String[] choices;
    choices = new String[1];
    choices[0] = "No parameters defined";
    MZmineCore.getConfiguration().getModuleParameters(RowsFilterModule.class).getParameter(RowsFilterParameters.GROUPSPARAMETER).setChoices(choices);
    // Create an empty queue.
    final BatchQueue queue = new BatchQueue();
    // Get the loaded modules.
    final Collection<MZmineModule> allModules = MZmineCore.getAllModules();
    // Process the batch step elements.
    final NodeList nodes = xmlElement.getElementsByTagName(BATCH_STEP_ELEMENT);
    final int nodesLength = nodes.getLength();
    for (int i = 0; i < nodesLength; i++) {
        final Element stepElement = (Element) nodes.item(i);
        final String methodName = stepElement.getAttribute(METHOD_ELEMENT);
        // Find a matching module.
        for (final MZmineModule module : allModules) {
            if (module instanceof MZmineProcessingModule && module.getClass().getName().equals(methodName)) {
                // Get parameters and add step to queue.
                final ParameterSet parameterSet = MZmineCore.getConfiguration().getModuleParameters(module.getClass());
                final ParameterSet methodParams = parameterSet.cloneParameterSet();
                methodParams.loadValuesFromXML(stepElement);
                queue.add(new MZmineProcessingStepImpl<MZmineProcessingModule>((MZmineProcessingModule) module, methodParams));
                break;
            }
        }
    }
    return queue;
}

Example 2 with MZmineProcessingModule

use of net.sf.mzmine.modules.MZmineProcessingModule in project mzmine2 by mzmine.

the class BatchSetupComponent method actionPerformed.

@Override
public void actionPerformed(final ActionEvent e) {
    final Object src = e.getSource();
    if (btnAdd.equals(src)) {
        // Processing module selected?
        final Object selectedItem = methodsCombo.getSelectedItem();
        if (selectedItem instanceof BatchModuleWrapper) {
            // Show method's set-up dialog.
            final BatchModuleWrapper wrappedModule = (BatchModuleWrapper) selectedItem;
            final MZmineProcessingModule selectedMethod = (MZmineProcessingModule) wrappedModule.getModule();
            final ParameterSet methodParams = MZmineCore.getConfiguration().getModuleParameters(selectedMethod.getClass());
            // Clone the parameter set
            final ParameterSet stepParams = methodParams.cloneParameterSet();
            // data file and feature list selection
            if (!batchQueue.isEmpty()) {
                for (Parameter<?> param : stepParams.getParameters()) {
                    if (param instanceof RawDataFilesParameter) {
                        final RawDataFilesParameter rdfp = (RawDataFilesParameter) param;
                        final RawDataFilesSelection selection = new RawDataFilesSelection();
                        selection.setSelectionType(RawDataFilesSelectionType.BATCH_LAST_FILES);
                        rdfp.setValue(selection);
                    }
                    if (param instanceof PeakListsParameter) {
                        final PeakListsParameter plp = (PeakListsParameter) param;
                        final PeakListsSelection selection = new PeakListsSelection();
                        selection.setSelectionType(PeakListsSelectionType.BATCH_LAST_PEAKLISTS);
                        plp.setValue(selection);
                    }
                }
            }
            // Configure parameters
            if (stepParams.getParameters().length > 0) {
                Window parent = (Window) SwingUtilities.getAncestorOfClass(Window.class, this);
                ExitCode exitCode = stepParams.showSetupDialog(parent, false);
                if (exitCode != ExitCode.OK)
                    return;
            }
            // Make a new batch step
            final MZmineProcessingStep<MZmineProcessingModule> step = new MZmineProcessingStepImpl<MZmineProcessingModule>(selectedMethod, stepParams);
            // Add step to queue.
            batchQueue.add(step);
            currentStepsList.setListData(batchQueue);
            currentStepsList.setSelectedIndex(currentStepsList.getModel().getSize() - 1);
        }
    }
    if (btnRemove.equals(src)) {
        // Remove selected step.
        final MZmineProcessingStep<?> selected = (MZmineProcessingStep<?>) currentStepsList.getSelectedValue();
        if (selected != null) {
            final int index = currentStepsList.getSelectedIndex();
            batchQueue.remove(selected);
            currentStepsList.setListData(batchQueue);
            selectStep(index);
        }
    }
    if (btnClear.equals(src)) {
        // Clear the queue.
        batchQueue.clear();
        currentStepsList.setListData(batchQueue);
    }
    if (btnConfig.equals(src)) {
        // Configure the selected item.
        final MZmineProcessingStep<?> selected = (MZmineProcessingStep<?>) currentStepsList.getSelectedValue();
        final ParameterSet parameters = selected == null ? null : selected.getParameterSet();
        if (parameters != null) {
            Window parent = (Window) SwingUtilities.getAncestorOfClass(Window.class, this);
            parameters.showSetupDialog(parent, false);
        }
    }
    if (btnSave.equals(src)) {
        try {
            final File file = chooser.getSaveFile(this, XML_EXTENSION);
            if (file != null) {
                saveBatchSteps(file);
            }
        } catch (Exception ex) {
            JOptionPane.showMessageDialog(this, "A problem occurred saving the file.\n" + ex.getMessage(), "Saving Failed", JOptionPane.ERROR_MESSAGE);
        }
    }
    if (btnLoad.equals(src)) {
        try {
            // Load the steps.
            final File file = chooser.getLoadFile(this);
            if (file != null) {
                // Load the batch steps.
                loadBatchSteps(file);
            }
        } catch (Exception ex) {
            JOptionPane.showMessageDialog(this, "A problem occurred loading the file.\n" + ex.getMessage(), "Loading Failed", JOptionPane.ERROR_MESSAGE);
        }
    }
}

Example 3 with MZmineProcessingModule

use of net.sf.mzmine.modules.MZmineProcessingModule in project mzmine2 by mzmine.

the class BatchQueue method clone.

@Override
public BatchQueue clone() {
    // Clone the parameters.
    final BatchQueue clonedQueue = new BatchQueue();
    for (final MZmineProcessingStep<MZmineProcessingModule> step : this) {
        final ParameterSet parameters = step.getParameterSet();
        final MZmineProcessingStepImpl<MZmineProcessingModule> stepCopy = new MZmineProcessingStepImpl<MZmineProcessingModule>(step.getModule(), parameters.cloneParameterSet());
        clonedQueue.add(stepCopy);
    }
    return clonedQueue;
}

Example 4 with MZmineProcessingModule

use of net.sf.mzmine.modules.MZmineProcessingModule in project mzmine2 by mzmine.

the class BatchTask method processQueueStep.

private void processQueueStep(int stepNumber) {
    logger.info("Starting step # " + (stepNumber + 1));
    // Run next step of the batch
    MZmineProcessingStep<?> currentStep = queue.get(stepNumber);
    MZmineProcessingModule method = (MZmineProcessingModule) currentStep.getModule();
    ParameterSet batchStepParameters = currentStep.getParameterSet();
    // the ones from the previous step
    if (createdDataFiles.isEmpty())
        createdDataFiles.addAll(previousCreatedDataFiles);
    if (createdPeakLists.isEmpty())
        createdPeakLists.addAll(previousCreatedPeakLists);
    // state of the batch
    for (Parameter<?> p : batchStepParameters.getParameters()) {
        if (p instanceof RawDataFilesParameter) {
            RawDataFilesParameter rdp = (RawDataFilesParameter) p;
            RawDataFile[] createdFiles = createdDataFiles.toArray(new RawDataFile[0]);
            final RawDataFilesSelection selectedFiles = rdp.getValue();
            if (selectedFiles == null) {
                setStatus(TaskStatus.ERROR);
                setErrorMessage("Invalid parameter settings for module " + method.getName() + ": " + "Missing parameter value for " + p.getName());
                return;
            }
            selectedFiles.setBatchLastFiles(createdFiles);
        }
    }
    // state of the batch
    for (Parameter<?> p : batchStepParameters.getParameters()) {
        if (p instanceof PeakListsParameter) {
            PeakListsParameter rdp = (PeakListsParameter) p;
            PeakList[] createdPls = createdPeakLists.toArray(new PeakList[0]);
            final PeakListsSelection selectedPeakLists = rdp.getValue();
            if (selectedPeakLists == null) {
                setStatus(TaskStatus.ERROR);
                setErrorMessage("Invalid parameter settings for module " + method.getName() + ": " + "Missing parameter value for " + p.getName());
                return;
            }
            selectedPeakLists.setBatchLastPeakLists(createdPls);
        }
    }
    // Clear the saved data files and feature lists. Save them to the
    // "previous" lists, in case the next step does not produce any new data
    previousCreatedDataFiles.clear();
    previousCreatedDataFiles.addAll(createdDataFiles);
    previousCreatedPeakLists.clear();
    previousCreatedPeakLists.addAll(createdPeakLists);
    createdDataFiles.clear();
    createdPeakLists.clear();
    // Check if the parameter settings are valid
    ArrayList<String> messages = new ArrayList<String>();
    boolean paramsCheck = batchStepParameters.checkParameterValues(messages);
    if (!paramsCheck) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Invalid parameter settings for module " + method.getName() + ": " + Arrays.toString(messages.toArray()));
    }
    ArrayList<Task> currentStepTasks = new ArrayList<Task>();
    ExitCode exitCode = method.runModule(project, batchStepParameters, currentStepTasks);
    if (exitCode != ExitCode.OK) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Could not start batch step " + method.getName());
        return;
    }
    // If current step didn't produce any tasks, continue with next step
    if (currentStepTasks.isEmpty())
        return;
    boolean allTasksFinished = false;
    // Submit the tasks to the task controller for processing
    MZmineCore.getTaskController().addTasks(currentStepTasks.toArray(new Task[0]));
    while (!allTasksFinished) {
        // If we canceled the batch, cancel all running tasks
        if (isCanceled()) {
            for (Task stepTask : currentStepTasks) stepTask.cancel();
            return;
        }
        // First set to true, then check all tasks
        allTasksFinished = true;
        for (Task stepTask : currentStepTasks) {
            TaskStatus stepStatus = stepTask.getStatus();
            // If any of them is not finished, keep checking
            if (stepStatus != TaskStatus.FINISHED)
                allTasksFinished = false;
            // If there was an error, we have to stop the whole batch
            if (stepStatus == TaskStatus.ERROR) {
                setStatus(TaskStatus.ERROR);
                setErrorMessage(stepTask.getTaskDescription() + ": " + stepTask.getErrorMessage());
                return;
            }
            // whole batch
            if (stepStatus == TaskStatus.CANCELED) {
                setStatus(TaskStatus.CANCELED);
                for (Task t : currentStepTasks) t.cancel();
                return;
            }
        }
        // Wait 1s before checking the tasks again
        if (!allTasksFinished) {
            synchronized (this) {
                try {
                    this.wait(1000);
                } catch (InterruptedException e) {
                // ignore
                }
            }
        }
    }
}