/** {@inheritDoc} */
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings)
throws InvalidSettingsException {
foodFile.loadSettingsFrom(settings);
outPath.loadSettingsFrom(settings);
method.loadSettingsFrom(settings);
}
/** {@inheritDoc} */
@Override
protected BufferedDataTable[] execute(
final BufferedDataTable[] inData, final ExecutionContext exec) throws Exception {
GenerateFoodSensitivitySpecificity.exec(
foodFile.getStringValue(),
outPath.getStringValue(),
method.getStringValue().equals(SPEARMAN_METHOD),
exec);
return new BufferedDataTable[] {};
}
protected XMLWriterNodeDialog() {
super();
addDialogComponent(
new DialogComponentColumnNameSelection(
new SettingsModelString(XMLWriterNodeModel.CFGKEY_XML_COL, "XML Data"),
"XML Column",
0,
true,
false,
new ColumnFilter() {
@Override
public boolean includeColumn(DataColumnSpec colSpec) {
if (colSpec != null && colSpec.getType().equals(XMLCell.TYPE)) {
return true;
}
return false;
}
@Override
public String allFilteredMsg() {
return "No XML columns available for selection!";
}
}));
createNewGroup("Filename conventions");
final SettingsModelBoolean sb_use_rowid =
new SettingsModelBoolean(XMLWriterNodeModel.CFGKEY_USE_ROWID, true);
final SettingsModelString sb_basename =
new SettingsModelString(XMLWriterNodeModel.CFGKEY_BASENAME, "document");
sb_basename.setEnabled(!sb_use_rowid.getBooleanValue());
addDialogComponent(
new DialogComponentString(
new SettingsModelString(XMLWriterNodeModel.CFGKEY_EXTN, ".xml"), "Filename extension"));
addDialogComponent(new DialogComponentBoolean(sb_use_rowid, "Use Row ID?"));
addDialogComponent(new DialogComponentString(sb_basename, "Basename"));
sb_use_rowid.addChangeListener(
new ChangeListener() {
@Override
public void stateChanged(ChangeEvent arg0) {
sb_basename.setEnabled(!sb_use_rowid.getBooleanValue());
}
});
createNewGroup("Save XML files to folder...");
addDialogComponent(
new DialogComponentString(
new SettingsModelString(XMLWriterNodeModel.CFGKEY_FOLDER, "c:/temp"),
"Folder to save to..."));
}
private UnaryOutputOperation<ImgPlus<T>, ImgPlus<V>> getSlidingOperation(
final ImgPlus<T> img, final V type) {
final Shape neighborhood =
NeighborhoodType.getNeighborhood(
NeighborhoodType.valueOf(m_neighborhoodType.getStringValue()),
m_intervalExtend.getIntValue());
final OutOfBoundsFactory<T, ImgPlus<T>> outStrat =
OutOfBoundsStrategyFactory.<T, ImgPlus<T>>getStrategy(
m_outOfBoundsStrategy.getStringValue(), img.firstElement());
return getSlidingOperation(img, type, neighborhood, outStrat);
}
private DataColumnSpec[] getListSpec() {
DataColumnSpec[] listSpecs = new DataColumnSpec[8];
String columnName =
"mutual info. " + reference.getStringValue() + " - " + library.getStringValue();
listSpecs[0] = new DataColumnSpecCreator("Parameter name", StringCell.TYPE).createSpec();
listSpecs[1] = new DataColumnSpecCreator(columnName, DoubleCell.TYPE).createSpec();
listSpecs[2] = new DataColumnSpecCreator("sigma", DoubleCell.TYPE).createSpec();
listSpecs[3] = new DataColumnSpecCreator("bias", DoubleCell.TYPE).createSpec();
listSpecs[4] = new DataColumnSpecCreator("N bins x", DoubleCell.TYPE).createSpec();
listSpecs[5] = new DataColumnSpecCreator("N bins y", DoubleCell.TYPE).createSpec();
listSpecs[6] = new DataColumnSpecCreator("log-base", DoubleCell.TYPE).createSpec();
listSpecs[7] = new DataColumnSpecCreator("method", StringCell.TYPE).createSpec();
return listSpecs;
}
private void addLabelingOptions() {
setHorizontalPlacement(true);
m_useCustomTrackPrefixModel.addChangeListener(
e -> m_customTrackPrefixModel.setEnabled(m_useCustomTrackPrefixModel.getBooleanValue()));
addDialogComponent(
new DialogComponentBoolean(
m_useCustomTrackPrefixModel, "Tracks are labeled with a custom prefix"));
m_customTrackPrefixModel.setEnabled(false);
addDialogComponent(new DialogComponentString(m_customTrackPrefixModel, "Prefix:"));
setHorizontalPlacement(false);
}
/** {@inheritDoc} */
@Override
protected void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
m_email.validateSettings(settings);
m_seq_col.validateSettings(settings);
m_accsn_col.validateSettings(settings);
m_alignment_type.validateSettings(settings);
}
/** {@inheritDoc} */
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
m_email.saveSettingsTo(settings);
m_seq_col.saveSettingsTo(settings);
m_accsn_col.saveSettingsTo(settings);
m_alignment_type.saveSettingsTo(settings);
}
/** {@inheritDoc} */
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings)
throws InvalidSettingsException {
m_email.loadSettingsFrom(settings);
m_seq_col.loadSettingsFrom(settings);
m_accsn_col.loadSettingsFrom(settings);
m_alignment_type.loadSettingsFrom(settings);
}
@Override
protected DataTableSpec[] configure(DataTableSpec[] inSpecs) throws InvalidSettingsException {
List<File> inputFiles =
FileSelectPanel.getInputFiles(propInputDir.getStringValue(), getAllowedFileExtensions());
if (inputFiles.isEmpty()) {
return new DataTableSpec[] {new DataTableSpec()};
}
// 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);
}
// compile the column-model
List<Attribute> colAttributes = compileColumnModel(mergeAttributes(plateFiles));
return new DataTableSpec[] {AttributeUtils.compileTableSpecs(colAttributes)};
}
@Override
protected void updateComponent() {
if (beforeLoad) { // This is immediately *after* load!
newColumns.clear();
newColumns.addAll(
Arrays.asList(((SettingsModelStringArray) getModel()).getStringArrayValue()));
beforeLoad = false; // Never again
}
final PortObjectSpec lastTableSpec = getLastTableSpec(portIndex);
final List<DataRow> dataRows = new ArrayList<DataRow>();
final List<DataColumnSpec> colSpecs = new ArrayList<DataColumnSpec>();
if (lastTableSpec instanceof DataTableSpec) {
final DataTableSpec spec = (DataTableSpec) lastTableSpec;
try {
final Map<List<String>, Map<String, Integer>> parts =
UnpivotNodeModel.createParts(pattern.getStringValue(), spec);
final Set<Integer> participating = new HashSet<Integer>();
for (final Map<String, Integer> map : parts.values()) {
for (final Integer i : map.values()) {
participating.add(i);
}
}
for (int i = 0; i < spec.getNumColumns(); ++i) {
if (!participating.contains(Integer.valueOf(i))) {
colSpecs.add(spec.getColumnSpec(i));
}
}
singleCount = colSpecs.size();
int rowCount = 0;
if (parts.isEmpty() || newColumns.size() != parts.keySet().iterator().next().size()) {
newColumns.clear();
if (!parts.isEmpty()) { // Fill with defaults
for (int i = parts.keySet().iterator().next().size(); i-- > 0; ) {
final String colName = "Col_" + i;
newColumns.add(colName);
colSpecs.add(new DataColumnSpecCreator(colName, StringCell.TYPE).createSpec());
}
}
} else {
for (final String colName : newColumns) {
colSpecs.add(new DataColumnSpecCreator(colName, StringCell.TYPE).createSpec());
}
}
final Map<String, DataType> types = new LinkedHashMap<String, DataType>();
for (final Entry<List<String>, Map<String, Integer>> outer : parts.entrySet()) {
final Map<String, Integer> map = outer.getValue();
for (final Entry<String, Integer> entry : map.entrySet()) {
final String colName = entry.getKey();
final DataType origType = types.get(colName);
if (origType == null) {
types.put(colName, spec.getColumnSpec(entry.getValue().intValue()).getType());
} else {
types.put(
colName,
DataType.getCommonSuperType(
origType, spec.getColumnSpec(entry.getValue().intValue()).getType()));
}
}
}
for (final Entry<String, DataType> entry : types.entrySet()) {
colSpecs.add(new DataColumnSpecCreator(entry.getKey(), entry.getValue()).createSpec());
}
for (final Entry<List<String>, Map<String, Integer>> entry : parts.entrySet()) {
final List<DataCell> cells = new ArrayList<DataCell>(colSpecs.size());
for (int i = singleCount; i-- > 0; ) {
cells.add(DataType.getMissingCell());
}
for (final String val : entry.getKey()) {
cells.add(new StringCell(val));
}
for (final Entry<String, Integer> inner : entry.getValue().entrySet()) {
final DataColumnDomain domain =
spec.getColumnSpec(inner.getValue().intValue()).getDomain();
cells.add(
domain.getLowerBound() == null
? domain.getValues() == null || domain.getValues().isEmpty()
? DataType.getMissingCell()
: domain.getValues().iterator().next()
: domain.getLowerBound());
}
dataRows.add(new DefaultRow("Row" + rowCount, cells));
++rowCount;
}
} catch (final PatternSyntaxException e) {
for (final DataColumnSpec dataColumnSpec : spec) {
colSpecs.add(dataColumnSpec);
}
}
}
@SuppressWarnings("deprecation")
final DataTable data =
new org.knime.core.data.def.DefaultTable(
dataRows.toArray(new DataRow[dataRows.size()]),
new DataTableSpec(colSpecs.toArray(new DataColumnSpec[colSpecs.size()])));
table.setDataTable(data);
table.repaint();
}
@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 void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
foodFile.validateSettings(settings);
outPath.validateSettings(settings);
method.validateSettings(settings);
}
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
fileName.saveSettingsTo(settings);
packageName.saveSettingsTo(settings);
}
/** {@inheritDoc} */
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
foodFile.saveSettingsTo(settings);
outPath.saveSettingsTo(settings);
method.saveSettingsTo(settings);
}
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings)
throws InvalidSettingsException {
fileName.loadSettingsFrom(settings);
packageName.loadSettingsFrom(settings);
}
/** {@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 void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
fileName.validateSettings(settings);
packageName.validateSettings(settings);
}