@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()};
}
