@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()}; }
/** {@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()}; }