de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/runner/FsxkRunnerNodeModel.java
package de.bund.bfr.knime.pmm.fskx.runner;
import java.awt.Image;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.stream.Collectors;
import org.apache.commons.io.FilenameUtils;
import org.eclipse.core.runtime.Platform;
import org.knime.base.node.util.exttool.ExtToolOutputNodeModel;
import org.knime.core.data.DataRow;
import org.knime.core.data.container.CloseableRowIterator;
import org.knime.core.data.def.StringCell;
import org.knime.core.data.image.png.PNGImageContent;
import org.knime.core.node.BufferedDataTable;
import org.knime.core.node.CanceledExecutionException;
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.ExecutionMonitor;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;
import org.knime.core.node.port.PortObject;
import org.knime.core.node.port.PortObjectSpec;
import org.knime.core.node.port.PortType;
import org.knime.core.node.port.image.ImagePortObject;
import org.knime.core.node.port.image.ImagePortObjectSpec;
import org.knime.core.util.FileUtil;
import org.knime.ext.r.node.local.port.RPortObject;
import org.knime.ext.r.node.local.port.RPortObjectSpec;
import org.rosuda.REngine.REXPMismatchException;
import de.bund.bfr.knime.fsklab.nodes.common.RunnerNodeInternalSettings;
import de.bund.bfr.knime.fsklab.nodes.port.FskPortObject;
import de.bund.bfr.knime.fsklab.nodes.port.FskPortObjectSpec;
import de.bund.bfr.knime.fsklab.r.client.IRController.RException;
import de.bund.bfr.knime.fsklab.r.client.LibRegistry;
import de.bund.bfr.knime.fsklab.r.client.RController;
import de.bund.bfr.knime.fsklab.r.client.ScriptExecutor;
import de.bund.bfr.knime.pmm.fskx.FskMetaDataTuple;
public class FsxkRunnerNodeModel extends ExtToolOutputNodeModel {
private static final NodeLogger LOGGER = NodeLogger.getLogger("Fskx Runner Node Model");
/** Output spec for an FSK object. */
private static final FskPortObjectSpec FSK_SPEC = FskPortObjectSpec.INSTANCE;
/** Output spec for an R object. */
private static final RPortObjectSpec R_SPEC = RPortObjectSpec.INSTANCE;
/** Output spec for a PNG image. */
private static final ImagePortObjectSpec PNG_SPEC = new ImagePortObjectSpec(PNGImageContent.TYPE);
private static final PortType[] inPortTypes = new PortType[] { FskPortObject.TYPE,
BufferedDataTable.TYPE_OPTIONAL };
private static final PortType[] outPortTypes = new PortType[] { FskPortObject.TYPE, RPortObject.TYPE,
ImagePortObject.TYPE_OPTIONAL };
private final RunnerNodeInternalSettings internalSettings = new RunnerNodeInternalSettings();
public FsxkRunnerNodeModel() {
super(inPortTypes, outPortTypes);
}
// --- internal settings methods ---
@Override
protected void loadInternals(File nodeInternDir, ExecutionMonitor exec)
throws IOException, CanceledExecutionException {
internalSettings.loadInternals(nodeInternDir);
}
@Override
protected void saveInternals(File nodeInternDir, ExecutionMonitor exec)
throws IOException, CanceledExecutionException {
internalSettings.saveInternals(nodeInternDir);
}
@Override
protected void reset() {
internalSettings.reset();
}
// --- node settings methods ---
@Override
protected void saveSettingsTo(NodeSettingsWO settings) {
// no settings
}
@Override
protected void validateSettings(NodeSettingsRO settings) throws InvalidSettingsException {
// no settings
}
@Override
protected void loadValidatedSettingsFrom(NodeSettingsRO settings) throws InvalidSettingsException {
// no settings
}
@Override
protected PortObjectSpec[] configure(PortObjectSpec[] inSpecs) throws InvalidSettingsException {
return new PortObjectSpec[] { FSK_SPEC, R_SPEC, PNG_SPEC };
}
@Override
protected PortObject[] execute(PortObject[] inObjects, ExecutionContext exec) throws Exception {
exec.checkCanceled();
FskPortObject fskObj = (FskPortObject) inObjects[0];
if (!fskObj.template.independentVariables.isEmpty()) {
fskObj.param = fskObj.template.independentVariables.stream().map(v -> v.name + " <- " + v.value)
.collect(Collectors.joining("\n"));
}
// If a metadata table is connected then update the model metadata
else if (inObjects.length == 2 && inObjects[1] != null) {
BufferedDataTable metadataTable = (BufferedDataTable) inObjects[1];
if (metadataTable.size() == 1) {
try (CloseableRowIterator iterator = metadataTable.iterator()) {
DataRow dataRow = iterator.next();
iterator.close();
// Gets independent variables and their values
StringCell varCell = (StringCell) dataRow.getCell(FskMetaDataTuple.Key.indepvars.ordinal());
String[] vars = varCell.getStringValue().split("\\|\\|");
StringCell valuesCell = (StringCell) dataRow
.getCell(FskMetaDataTuple.Key.indepvars_values.ordinal());
String[] values = valuesCell.getStringValue().split("\\|\\|");
if (vars != null && values != null && vars.length == values.length) {
StringBuilder sb = new StringBuilder();
for (int i = 0; i < vars.length; i++) {
sb.append(vars[i] + " <- " + values[i] + "\n");
}
fskObj.param = sb.toString();
}
}
}
}
try (RController controller = new RController()) {
fskObj = runSnippet(controller, fskObj, exec, internalSettings.imageFile);
}
RPortObject rObj = new RPortObject(fskObj.workspace);
try (FileInputStream fis = new FileInputStream(internalSettings.imageFile)) {
final PNGImageContent content = new PNGImageContent(fis);
internalSettings.plot = content.getImage();
ImagePortObject imgObj = new ImagePortObject(content, PNG_SPEC);
return new PortObject[] { fskObj, rObj, imgObj };
} catch (IOException e) {
LOGGER.warn("There is no image created");
return new PortObject[] { fskObj, rObj };
}
}
private FskPortObject runSnippet(final RController controller, final FskPortObject fskObj,
final ExecutionMonitor monitor, final File imageFile)
throws RException, CanceledExecutionException, InterruptedException, IOException, REXPMismatchException {
ScriptExecutor executor = new ScriptExecutor(controller);
monitor.setMessage("Setting up output capturing");
executor.setupOutputCapturing(monitor);
monitor.setMessage("Add paths to libraries");
controller.addPackagePath(LibRegistry.instance().getInstallationPath());
monitor.setMessage("Run parameters script");
executor.executeIgnoreResult(fskObj.param, monitor);
monitor.setMessage("Run model script");
executor.executeIgnoreResult(fskObj.model, monitor);
monitor.setMessage("Run visualization script");
try {
plot(imageFile, fskObj.viz, 640, 640, 12, "NA", executor, monitor);
} catch (final RException exception) {
LOGGER.warn("Visualization script failed", exception);
}
monitor.setMessage("Restore library paths");
controller.restorePackagePath();
monitor.setMessage("Collecting captured output");
executor.finishOutputCapturing(monitor);
// Save workspace
if (fskObj.workspace == null) {
fskObj.workspace = FileUtil.createTempFile("workspace", ".R");
}
controller.saveWorkspace(fskObj.workspace.toPath(), monitor);
// process the return value of error capturing and update error
// and output views accordingly
if (!executor.getStdErr().isEmpty()) {
setExternalOutput(getLinkedListFromOutput(executor.getStdErr()));
}
if (!executor.getStdErr().isEmpty()) {
final LinkedList<String> output = getLinkedListFromOutput(executor.getStdErr());
setExternalErrorOutput(output);
for (final String line : output) {
if (line.startsWith(ScriptExecutor.ERROR_PREFIX)) {
throw new RException("Error in R code: \"" + line + "\"", null);
}
}
}
// cleanup temporary variables of output capturing and consoleLikeCommand stuff
monitor.setMessage("Cleaning up");
executor.cleanup(monitor);
return fskObj;
}
private static final LinkedList<String> getLinkedListFromOutput(final String output) {
return Arrays.stream(output.split("\\r?\\n")).collect(Collectors.toCollection(LinkedList::new));
}
Image getResultImage() {
return internalSettings.plot;
}
/**
* Plots model results and generates a chart using a visualization script.
*
* @param imgFile
* Chart file
* @param vizScript
* Visualization script
* @param executor
* R executor
* @param monitor
* KNIME {@link ExecutionMonitor}
* @throws InterruptedException
* @throws CanceledExecutionException
* @throws RException
*
*/
private static void plot(final File imageFile, final String vizScript, final int width, final int height,
final int pointSize, final String res, final ScriptExecutor executor, final ExecutionMonitor monitor)
throws RException, CanceledExecutionException, InterruptedException {
// Initialize necessary R stuff to plot
if (Platform.getOS().equals(Platform.OS_MACOSX)) {
executor.executeIgnoreResult("library('Cairo')", monitor);
executor.executeIgnoreResult("options(device='png', bitmapType='cairo')", monitor);
} else {
executor.executeIgnoreResult("options(device='png')", monitor);
}
// Get image path (with proper slashes)
final String path = FilenameUtils.separatorsToUnix(imageFile.getAbsolutePath());
// Gets values
String pngCommand = "png('" + path + "', width=" + width + ", height=" + height + ", pointsize=" + pointSize
+ ", res='" + res + "')";
executor.executeIgnoreResult(pngCommand, monitor);
executor.executeIgnoreResult(vizScript, monitor);
executor.executeIgnoreResult("dev.off()", monitor);
}
}