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

Example 31 with Task

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

the class GnpsGcExportAndSubmitTask method run.

@Override
public void run() {
    final AbstractTask thistask = this;
    setStatus(TaskStatus.PROCESSING);
    List<AbstractTask> list = new ArrayList<>(3);
    // add mgf export task
    list.add(addAdapMgfTask(parameters));
    // add csv quant table
    list.add(addQuantTableTask(parameters, null));
    // finish listener to submit
    final File fileName = file;
    final File folder = file.getParentFile();
    new AllTasksFinishedListener(list, true, // succeed
    l -> {
        try {
            LOG.info("succeed" + thistask.getStatus().toString());
            if (submit) {
                GnpsGcSubmitParameters param = parameters.getParameter(GnpsGcExportAndSubmitParameters.SUBMIT).getEmbeddedParameters();
                submit(fileName, param);
            }
            // open folder
            try {
                if (openFolder && Desktop.isDesktopSupported()) {
                    Desktop.getDesktop().open(folder);
                }
            } catch (Exception ex) {
            }
        } finally {
            // finish task
            if (thistask.getStatus() == TaskStatus.PROCESSING)
                thistask.setStatus(TaskStatus.FINISHED);
        }
    }, lerror -> {
        setErrorMessage("GNPS-GC submit was not started due too errors while file export");
        thistask.setStatus(TaskStatus.ERROR);
        throw new MSDKRuntimeException("GNPS-GC submit was not started due too errors while file export");
    }, // cancel if one was cancelled
    listCancelled -> cancel()) {

        @Override
        public void taskStatusChanged(Task task, TaskStatus newStatus, TaskStatus oldStatus) {
            super.taskStatusChanged(task, newStatus, oldStatus);
            // show progress
            progress.getAndSet(getProgress());
        }
    };
    MZmineCore.getTaskController().addTasks(list.toArray(new AbstractTask[list.size()]));
    // wait till finish
    while (!(isCanceled() || isFinished())) {
        try {
            Thread.sleep(100);
        } catch (InterruptedException e) {
            LOG.log(Level.SEVERE, "Error in GNPS-GC export/submit task", e);
        }
    }
}

Example 32 with Task

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

the class PathAlignerModule method runModule.

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

Example 33 with Task

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

the class JoinAlignerModule method runModule.

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

Example 34 with Task

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

the class BatchModeModule method runBatch.

public static ExitCode runBatch(@Nonnull MZmineProject project, File batchFile) {
    logger.info("Running batch from file " + batchFile);
    try {
        DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
        Document parsedBatchXML = docBuilder.parse(batchFile);
        BatchQueue newQueue = BatchQueue.loadFromXml(parsedBatchXML.getDocumentElement());
        ParameterSet parameters = new BatchModeParameters();
        parameters.getParameter(BatchModeParameters.batchQueue).setValue(newQueue);
        Task batchTask = new BatchTask(project, parameters);
        batchTask.run();
        if (batchTask.getStatus() == TaskStatus.FINISHED)
            return ExitCode.OK;
        else
            return ExitCode.ERROR;
    } catch (Throwable e) {
        logger.log(Level.SEVERE, "Error while running batch", e);
        e.printStackTrace();
        return ExitCode.ERROR;
    }
}

Example 35 with Task

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

the class ProjectTreeMouseHandler method actionPerformed.

@Override
public void actionPerformed(ActionEvent e) {
    String command = e.getActionCommand();
    if (command.equals("SHOW_TIC")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        TICVisualizerModule.setupNewTICVisualizer(selectedFiles);
    }
    if (command.equals("SHOW_SPECTRUM")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        SpectraVisualizerModule module = MZmineCore.getModuleInstance(SpectraVisualizerModule.class);
        ParameterSet parameters = MZmineCore.getConfiguration().getModuleParameters(SpectraVisualizerModule.class);
        parameters.getParameter(SpectraVisualizerParameters.dataFiles).setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles);
        ExitCode exitCode = parameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(), true);
        MZmineProject project = MZmineCore.getProjectManager().getCurrentProject();
        if (exitCode == ExitCode.OK)
            module.runModule(project, parameters, new ArrayList<Task>());
    }
    if (command.equals("SHOW_IDA")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        MsMsVisualizerModule.showIDAVisualizerSetupDialog(selectedFiles[0]);
    }
    if (command.equals("SHOW_2D")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        TwoDVisualizerModule.show2DVisualizerSetupDialog(selectedFiles[0]);
    }
    if (command.equals("SHOW_3D")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        Fx3DVisualizerModule.setupNew3DVisualizer(selectedFiles[0]);
    }
    if (command.equals("SORT_FILES")) {
        // save current selection
        TreePath[] savedSelection = tree.getSelectionPaths();
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        SortDataFilesModule module = MZmineCore.getModuleInstance(SortDataFilesModule.class);
        ParameterSet params = MZmineCore.getConfiguration().getModuleParameters(SortDataFilesModule.class);
        params.getParameter(SortDataFilesParameters.dataFiles).setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles);
        module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params, new ArrayList<Task>());
        // restore selection
        tree.setSelectionPaths(savedSelection);
    }
    if (command.equals("REMOVE_EXTENSION")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        for (RawDataFile file : selectedFiles) {
            file.setName(FilenameUtils.removeExtension(file.toString()));
        }
        tree.updateUI();
    }
    if (command.equals("EXPORT_FILE")) {
        RawDataExportModule exportModule = MZmineCore.getModuleInstance(RawDataExportModule.class);
        ParameterSet params = MZmineCore.getConfiguration().getModuleParameters(RawDataExportModule.class);
        ExitCode ec = params.showSetupDialog(null, true);
        if (ec == ExitCode.OK) {
            ParameterSet parametersCopy = params.cloneParameterSet();
            ArrayList<Task> tasks = new ArrayList<>();
            MZmineProject project = MZmineCore.getProjectManager().getCurrentProject();
            exportModule.runModule(project, parametersCopy, tasks);
            MZmineCore.getTaskController().addTasks(tasks.toArray(new Task[0]));
        }
    }
    if (command.equals("RENAME_FILE")) {
        TreePath path = tree.getSelectionPath();
        if (path == null)
            return;
        else
            tree.startEditingAtPath(path);
    }
    if (command.equals("REMOVE_FILE")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        PeakList[] allPeakLists = MZmineCore.getProjectManager().getCurrentProject().getPeakLists();
        for (RawDataFile file : selectedFiles) {
            for (PeakList peakList : allPeakLists) {
                if (peakList.hasRawDataFile(file)) {
                    String msg = "Cannot remove file " + file.getName() + ", because it is present in the feature list " + peakList.getName();
                    MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), msg);
                    return;
                }
            }
            MZmineCore.getProjectManager().getCurrentProject().removeFile(file);
        }
    }
    if (command.equals("SHOW_SCAN")) {
        Scan[] selectedScans = tree.getSelectedObjects(Scan.class);
        for (Scan scan : selectedScans) {
            SpectraVisualizerModule.showNewSpectrumWindow(scan.getDataFile(), scan.getScanNumber());
        }
    }
    if (command.equals("EXPORT_SCAN")) {
        Scan[] selectedScans = tree.getSelectedObjects(Scan.class);
        ExportScansModule.showSetupDialog(selectedScans);
    }
    if (command.equals("SHOW_MASSLIST")) {
        MassList[] selectedMassLists = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            Scan scan = massList.getScan();
            SpectraVisualizerWindow window = SpectraVisualizerModule.showNewSpectrumWindow(scan.getDataFile(), scan.getScanNumber());
            MassListDataSet dataset = new MassListDataSet(massList);
            window.addDataSet(dataset, Color.green);
        }
    }
    if (command.equals("REMOVE_MASSLIST")) {
        MassList[] selectedMassLists = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            Scan scan = massList.getScan();
            scan.removeMassList(massList);
        }
    }
    if (command.equals("REMOVE_ALL_MASSLISTS")) {
        MassList[] selectedMassLists = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            String massListName = massList.getName();
            RawDataFile[] dataFiles = MZmineCore.getProjectManager().getCurrentProject().getDataFiles();
            for (RawDataFile dataFile : dataFiles) {
                int[] scanNumbers = dataFile.getScanNumbers();
                for (int scanNum : scanNumbers) {
                    Scan scan = dataFile.getScan(scanNum);
                    MassList ml = scan.getMassList(massListName);
                    if (ml != null)
                        scan.removeMassList(ml);
                }
            }
        }
    }
    if (command.equals("SHOW_PEAKLIST_TABLES")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            PeakListTableModule.showNewPeakListVisualizerWindow(peakList);
        }
    }
    if (command.equals("SHOW_PEAKLIST_INFO")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            InfoVisualizerModule.showNewPeakListInfo(peakList);
        }
    }
    if (command.equals("SHOW_SCATTER_PLOT")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            ScatterPlotVisualizerModule.showNewScatterPlotWindow(peakList);
        }
    }
    if (command.equals("SORT_PEAKLISTS")) {
        // save current selection
        TreePath[] savedSelection = tree.getSelectionPaths();
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        SortPeakListsModule module = MZmineCore.getModuleInstance(SortPeakListsModule.class);
        ParameterSet params = MZmineCore.getConfiguration().getModuleParameters(SortPeakListsModule.class);
        params.getParameter(SortPeakListsParameters.peakLists).setValue(PeakListsSelectionType.SPECIFIC_PEAKLISTS, selectedPeakLists);
        module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params, new ArrayList<Task>());
        // restore selection
        tree.setSelectionPaths(savedSelection);
    }
    if (command.equals("RENAME_FEATURELIST")) {
        TreePath path = tree.getSelectionPath();
        if (path == null)
            return;
        else
            tree.startEditingAtPath(path);
    }
    if (command.equals("REMOVE_PEAKLIST")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) MZmineCore.getProjectManager().getCurrentProject().removePeakList(peakList);
    }
    if (command.equals("SHOW_PEAK_SUMMARY")) {
        PeakListRow[] selectedRows = tree.getSelectedObjects(PeakListRow.class);
        for (PeakListRow row : selectedRows) {
            PeakSummaryVisualizerModule.showNewPeakSummaryWindow(row);
        }
    }
}