Examples with RawDataImportModule net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule used on opensource projects

Example 1 with RawDataImportModule

use of net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule in project mzmine2 by mzmine.

the class MzTabImportTask method importRawDataFiles.

private SortedMap<Integer, RawDataFile> importRawDataFiles(MZTabFile mzTabFile) throws Exception {
    SortedMap<Integer, MsRun> msrun = mzTabFile.getMetadata().getMsRunMap();
    SortedMap<Integer, RawDataFile> rawDataFiles = new TreeMap<>();
    // If we are importing files, let's run RawDataImportModule
    if (importRawFiles) {
        List<File> filesToImport = new ArrayList<>();
        for (Entry<Integer, MsRun> entry : msrun.entrySet()) {
            File fileToImport = new File(entry.getValue().getLocation().getPath());
            if (fileToImport.exists() && fileToImport.canRead())
                filesToImport.add(fileToImport);
            else {
                // Check if the raw file exists in the same folder as the mzTab file
                File checkFile = new File(inputFile.getParentFile(), fileToImport.getName());
                if (checkFile.exists() && checkFile.canRead())
                    filesToImport.add(checkFile);
                else {
                    // Append .gz & check again if file exists as a workaround to .gz not getting preserved
                    // when .mzML.gz importing
                    checkFile = new File(inputFile.getParentFile(), fileToImport.getName() + ".gz");
                    if (checkFile.exists() && checkFile.canRead())
                        filesToImport.add(checkFile);
                    else {
                        // One more level of checking, appending .zip & checking as a workaround
                        checkFile = new File(inputFile.getParentFile(), fileToImport.getName() + ".zip");
                        if (checkFile.exists() && checkFile.canRead())
                            filesToImport.add(checkFile);
                    }
                }
            }
        }
        RawDataImportModule RDI = MZmineCore.getModuleInstance(RawDataImportModule.class);
        ParameterSet rdiParameters = RDI.getParameterSetClass().newInstance();
        rdiParameters.getParameter(RawDataImportParameters.fileNames).setValue(filesToImport.toArray(new File[0]));
        synchronized (underlyingTasks) {
            RDI.runModule(project, rdiParameters, underlyingTasks);
        }
        if (underlyingTasks.size() > 0) {
            MZmineCore.getTaskController().addTasks(underlyingTasks.toArray(new Task[0]));
        }
        // Wait until all raw data file imports have completed
        while (true) {
            if (isCanceled())
                return null;
            boolean tasksFinished = true;
            for (Task task : underlyingTasks) {
                if ((task.getStatus() == TaskStatus.WAITING) || (task.getStatus() == TaskStatus.PROCESSING))
                    tasksFinished = false;
            }
            if (tasksFinished)
                break;
            Thread.sleep(1000);
        }
    /*
       * // Sort raw data files based on order in mzTab file MainWindow mainWindow = (MainWindow)
       * MZmineCore.getDesktop(); ProjectTree rawDataTree = mainWindow.getMainPanel()
       * .getRawDataTree(); final RawDataTreeModel treeModel = ((MZmineProjectImpl)
       * project).getRawDataTreeModel(); final DefaultMutableTreeNode rootNode =
       * treeModel.getRoot(); int[] selectedRows = new int[rootNode.getChildCount()]; for (int i =
       * 1; i < rootNode.getChildCount() + 1; i++) { selectedRows[i - 1] = i; } final
       * ArrayList<DefaultMutableTreeNode> selectedNodes = new ArrayList<DefaultMutableTreeNode>();
       * for (int row : selectedRows) { TreePath path = rawDataTree.getPathForRow(row);
       * DefaultMutableTreeNode selectedNode = (DefaultMutableTreeNode) path
       * .getLastPathComponent(); selectedNodes.add(selectedNode); }
       * 
       * // Reorder the nodes in the tree model based on order in mzTab // file int fileCounter = 0;
       * for (Entry<Integer, MsRun> entry : msrun.entrySet()) { fileCounter++; File f = new
       * File(entry.getValue().getLocation().getPath()); for (DefaultMutableTreeNode node :
       * selectedNodes) { if (node.toString().equals(f.getName())) {
       * treeModel.removeNodeFromParent(node); treeModel.insertNodeInto(node, rootNode, fileCounter
       * - 1); } } }
       */
    } else {
        finishedPercentage = 0.5;
    }
    // Find a matching RawDataFile for each MsRun entry
    for (Entry<Integer, MsRun> entry : msrun.entrySet()) {
        String rawFileName = new File(entry.getValue().getLocation().getPath()).getName();
        RawDataFile rawDataFile = null;
        // Check if we already have a RawDataFile of that name
        for (RawDataFile f : project.getDataFiles()) {
            if (f.getName().equals(rawFileName)) {
                rawDataFile = f;
                break;
            }
        }
        // If no data file of that name exists, create a dummy one
        if (rawDataFile == null) {
            RawDataFileWriter writer = MZmineCore.createNewFile(rawFileName);
            rawDataFile = writer.finishWriting();
            project.addFile(rawDataFile);
        }
        // Save a reference to the new raw data file
        rawDataFiles.put(entry.getKey(), rawDataFile);
    }
    return rawDataFiles;
}