예제 #1
0
  @Override
  protected BufferedDataTable[] execute(
      final BufferedDataTable[] inData, final ExecutionContext exec) throws Exception {
    final BufferedDataContainer con = exec.createDataContainer(m_spec);
    final ImgPlusCellFactory imgCellFactory = new ImgPlusCellFactory(exec);
    int id = 1;
    for (final SerializableSetting<Img<T>[]> conf : m_kernelList.getObjects()) {
      for (final Img<T> img : conf.get()) {
        if (img instanceof ImgPlus<?>) {
          con.addRowToTable(
              new DefaultRow("Kernel " + id, imgCellFactory.createCell((ImgPlus<T>) img)));
        } else {
          con.addRowToTable(
              new DefaultRow("Kernel " + id, imgCellFactory.createCell(new ImgPlus<T>(img))));
        }
        id++;
      }
    }

    con.close();

    // data for the table cell view
    m_data = con.getTable();
    return new BufferedDataTable[] {m_data};
  }
  @Override
  protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec)
      throws Exception {
    BufferedDataContainer cont = exec.createDataContainer(outspec[0]);

    List<DataCell> cells = new ArrayList<DataCell>();
    CloseableRowIterator iter = inData[0].iterator();
    while (iter.hasNext()) {
      cells.add(iter.next().getCell(0));
    }

    ListCell lc = CollectionCellFactory.createListCell(cells);
    DataRow row = new DefaultRow("Row 1", lc);
    cont.addRowToTable(row);
    cont.close();

    return new BufferedDataTable[] {cont.getTable()};
  }
  @Override
  protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec)
      throws Exception {

    List<File> inputFiles =
        FileSelectPanel.getInputFiles(propInputDir.getStringValue(), getAllowedFileExtensions());

    if (inputFiles.isEmpty()) {
      throw new RuntimeException("No files selected");
    }

    // first group files into plate-groups
    Map<String, List<File>> plateFiles = splitFilesIntoPlates(inputFiles);

    if (inputFiles.isEmpty()) {
      throw new RuntimeException("No valid envision-files in selection " + inputFiles);
    }

    // split files
    List<String> allAttributes = mergeAttributes(plateFiles);
    List<Attribute> colAttributes = compileColumnModel(allAttributes);

    DataTableSpec outputSpec = AttributeUtils.compileTableSpecs(colAttributes);
    BufferedDataContainer container = exec.createDataContainer(outputSpec);

    // populate the table
    int fileCounter = 0, rowCounter = 0;
    for (String barcode : plateFiles.keySet()) {

      logger.info("Processing plate " + barcode);

      Plate plate = new Plate();

      // invalidate plate-dims as these become fixed in the loop
      plate.setNumColumns(-1);
      plate.setNumRows(-1);

      for (File file : plateFiles.get(barcode)) {
        String attributeName = getAttributeNameOfEnvisionFile(file);
        parseFile(plate, attributeName, file);

        BufTableUtils.updateProgress(exec, fileCounter++, inputFiles.size());
      }

      // now create the data-rows for this table
      for (Well well : plate.getWells()) {
        if (well.getReadOutNames().isEmpty()) {
          continue;
        }

        DataCell[] knimeRow = new DataCell[colAttributes.size()];

        // first add the barcode-column
        knimeRow[0] = new StringCell(barcode);

        knimeRow[1] = colAttributes.get(1).createCell(well.getPlateRow());
        knimeRow[2] = colAttributes.get(2).createCell(well.getPlateColumn());

        for (String attributeName : allAttributes) {
          int rowIndex = allAttributes.indexOf(attributeName);
          Double value = well.getReadout(attributeName);

          if (value != null) {
            knimeRow[3 + rowIndex] = new DoubleCell(value);
          } else {
            knimeRow[3 + rowIndex] = DataType.getMissingCell();
          }
        }

        DataRow tableRow = new DefaultRow(new RowKey("" + rowCounter++), knimeRow);
        container.addRowToTable(tableRow);
      }
    }

    container.close();

    return new BufferedDataTable[] {container.getTable()};
  }
예제 #4
0
  /** {@inheritDoc} */
  @Override
  protected BufferedDataTable[] execute(
      final BufferedDataTable[] inData, final ExecutionContext exec) throws Exception {
    if (m_email.equals(DEFAULT_EMAIL)) {
      throw new Exception(
          "You must set a valid E-Mail for EBI to contact you in the event of problems with the service!");
    }
    int n_rows = inData[0].getRowCount();
    int seq_idx =
        inData[0].getSpec().findColumnIndex(((SettingsModelString) m_seq_col).getStringValue());
    int accsn_idx =
        inData[0].getSpec().findColumnIndex(((SettingsModelString) m_accsn_col).getStringValue());
    if (seq_idx < 0 || accsn_idx < 0) {
      throw new Exception("Cannot find columns... valid data?");
    }
    int done = 0;

    // create the output columns (raw format for use with R)
    DataTableSpec outputSpec = new DataTableSpec(inData[0].getDataTableSpec(), make_output_spec());
    BufferedDataContainer container = exec.createDataContainer(outputSpec, false, 0);

    // instantiate MUSCLE client
    MuscleClient cli = new MuscleClient();

    // each row is a separate MUSCLE job, the sequences are in one collection cell, the accessions
    // (IDs) in the other
    RowIterator it = inData[0].iterator();
    while (it.hasNext()) {
      DataRow r = it.next();
      ListCell seqs = (ListCell) r.getCell(seq_idx);
      ListCell accsns = (ListCell) r.getCell(accsn_idx);
      if (seqs.size() != accsns.size()) {
        throw new Exception(
            "Every sequence must have a corresponding accession: error at row "
                + r.getKey().getString());
      }
      if (seqs.size() < 1) {
        throw new Exception("Cannot MUSCLE zero sequences: error at row " + r.getKey().getString());
      }
      if (seqs.size() > 1000) {
        throw new Exception("Too many sequences in row " + r.getKey().getString());
      }
      // dummy a fake "FASTA" file (in memory) and then submit that to MUSCLE@EBI along with other
      // necessary parameters
      StringBuffer seq_as_fasta = new StringBuffer();
      for (int i = 0; i < seqs.size(); i++) {
        seq_as_fasta.append(">");
        seq_as_fasta.append(accsns.get(i).toString());
        seq_as_fasta.append("\n");
        seq_as_fasta.append(seqs.get(i).toString());
        seq_as_fasta.append("\n");
      }
      // System.err.println(seq_as_fasta);

      // lodge the muscle job and store the results in the output table
      InputParameters ip = new InputParameters();
      ip.setSequence(seq_as_fasta.toString());

      // start the job
      String jobId = cli.runApp(m_email.getStringValue(), r.getKey().getString(), ip);

      exec.checkCanceled();
      exec.setProgress(((double) done) / n_rows, "Executing " + jobId);
      Thread.sleep(20 * 1000); // 20 seconds
      waitForCompletion(cli, exec, jobId);
      done++;

      // process results and add them into the table...
      // 1. fasta alignment data
      byte[] bytes = cli.getSrvProxy().getResult(jobId, "aln-fasta", null);

      DataCell[] cells = new DataCell[3];
      cells[0] = new StringCell(jobId);

      // compute the base64 encoded phylip aligned sequences suitable for use by R's phangorn
      // package
      String fasta = new String(bytes);
      String ret = fasta2phylip(fasta);

      // it must be encoded (I chose base64) as it is common to both Java and R and it must be
      // encoded due to containing multiple lines, which confuses the CSV passed between KNIME and R
      String rk = r.getKey().getString();
      DataCell mac = AlignmentCellFactory.createCell(fasta, AlignmentType.AL_AA);
      if (mac instanceof MultiAlignmentCell) m_muscle_map.put(rk, (MultiAlignmentCell) mac);
      cells[1] = mac;

      bytes = cli.getSrvProxy().getResult(jobId, "out", null);
      cells[2] = new StringCell("<html><pre>" + new String(bytes));

      container.addRowToTable(new JoinedRow(r, new DefaultRow(r.getKey(), cells)));
    }
    container.close();
    BufferedDataTable out = container.getTable();
    return new BufferedDataTable[] {out};
  }
  @Override
  protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec)
      throws Exception {

    BufferedDataTable input = inData[0];

    // Get the condition attribute
    Attribute treatmentAttribute =
        new InputTableAttribute(this.treatmentAttribute.getStringValue(), input);

    // Get the library and reference condition names
    String libraryName = AbstractScreenTrafoModel.getAndValidateTreatment(reference);
    String referenceName = AbstractScreenTrafoModel.getAndValidateTreatment(library);

    // Get the parameter and make sure there all double value columns
    List<Attribute> parameters = getParameterList(input);

    // Split the columns according to groups contained in the condition column
    Map<String, List<DataRow>> groupedRows = AttributeUtils.splitRows(input, treatmentAttribute);
    List<DataRow> libraryRows = groupedRows.get(libraryName);
    List<DataRow> referenceRows = groupedRows.get(referenceName);

    int progress = parameters.size();
    BufTableUtils.updateProgress(exec, progress / 2, progress);

    // Initialize
    BufferedDataContainer container = exec.createDataContainer(new DataTableSpec(getListSpec()));
    MutualInformation mutualinfo = new MutualInformation();
    mutualinfo.set_base(logbase.getDoubleValue());
    mutualinfo.set_method(method.getStringValue());
    mutualinfo.set_axeslinking(linkaxes.getBooleanValue());

    DataCell[] cells = new DataCell[container.getTableSpec().getNumColumns()];
    int p = 0;

    // Calculate mutual information
    for (Attribute parameter : parameters) {

      Double[] x = getDataVec(libraryRows, parameter);
      Double[] y = getDataVec(referenceRows, parameter);
      mutualinfo.set_vectors(x, y);

      if (binning.getIntValue() == 0) {
        mutualinfo.set_binning();
      } else {
        mutualinfo.set_binning(binning.getIntValue());
      }
      int[] bins = mutualinfo.get_binning();

      Double[] res = mutualinfo.calculate();

      cells[0] = new StringCell(parameter.getName());
      cells[1] = new DoubleCell(res[0]);
      cells[2] = new DoubleCell(res[1]);
      cells[3] = new DoubleCell(res[2]);
      cells[4] = new IntCell(bins[0]);
      cells[5] = new IntCell(bins[1]);
      cells[6] = new DoubleCell(mutualinfo.get_logbase());
      cells[7] = new StringCell(mutualinfo.get_method());

      container.addRowToTable(new DefaultRow("row" + p, cells));

      BufTableUtils.updateProgress(exec, (progress + p++) / 2, progress);
      exec.checkCanceled();
    }

    container.close();
    return new BufferedDataTable[] {container.getTable()};
  }