Examples with PortObject org.knime.core.node.port.PortObject used on opensource projects

Example 91 with PortObject

use of org.knime.core.node.port.PortObject in project knime-core by knime.

the class VirtualSubNodeInputNodeModel method createStreamableOperator.

@Override
public StreamableOperator createStreamableOperator(final PartitionInfo partitionInfo, final PortObjectSpec[] inSpecs) throws InvalidSettingsException {
    return new StreamableOperator() {

        @Override
        public void runFinal(final PortInput[] inputs, final PortOutput[] outputs, final ExecutionContext exec) throws Exception {
            assert inputs.length == 0;
            PortObject[] dataFromParent = ArrayUtils.remove(m_subNodeContainer.fetchInputDataFromParent(), 0);
            for (int i = 0; i < outputs.length; i++) {
                if (BufferedDataTable.TYPE.equals(getOutPortType(i))) {
                    // stream port content if it's data
                    BufferedDataTable bdt = (BufferedDataTable) (dataFromParent[i]);
                    RowOutput rowOutput = (RowOutput) outputs[i];
                    for (DataRow dr : bdt) {
                        rowOutput.push(dr);
                    }
                    rowOutput.close();
                } else {
                    ((PortObjectOutput) outputs[i]).setPortObject(dataFromParent[i]);
                }
            }
        }
    };
}

Example 92 with PortObject

use of org.knime.core.node.port.PortObject in project knime-core by knime.

the class DecisionTreeLearnerNodeModel method execute.

/**
 * Start of decision tree induction.
 *
 * @param exec the execution context for this run
 * @param data the input data to build the decision tree from
 * @return an empty data table array, as just a model is provided
 * @throws Exception any type of exception, e.g. for cancellation,
 *         invalid input,...
 * @see NodeModel#execute(BufferedDataTable[],ExecutionContext)
 */
@Override
protected PortObject[] execute(final PortObject[] data, final ExecutionContext exec) throws Exception {
    // holds the warning message displayed after execution
    StringBuilder warningMessageSb = new StringBuilder();
    ParallelProcessing parallelProcessing = new ParallelProcessing(m_parallelProcessing.getIntValue());
    if (LOGGER.isDebugEnabled()) {
        LOGGER.debug("Number available threads: " + parallelProcessing.getMaxNumberThreads() + " used threads: " + parallelProcessing.getCurrentThreadsInUse());
    }
    exec.setProgress("Preparing...");
    // check input data
    assert (data != null && data[DATA_INPORT] != null);
    BufferedDataTable inData = (BufferedDataTable) data[DATA_INPORT];
    // get column with color information
    String colorColumn = null;
    for (DataColumnSpec s : inData.getDataTableSpec()) {
        if (s.getColorHandler() != null) {
            colorColumn = s.getName();
            break;
        }
    }
    // the data table must have more than 2 records
    if (inData.getRowCount() <= 1) {
        throw new IllegalArgumentException("Input data table must have at least 2 records!");
    }
    // get class column index
    int classColumnIndex = inData.getDataTableSpec().findColumnIndex(m_classifyColumn.getStringValue());
    assert classColumnIndex > -1;
    // create initial In-Memory table
    exec.setProgress("Create initial In-Memory table...");
    InMemoryTableCreator tableCreator = new InMemoryTableCreator(inData, classColumnIndex, m_minNumberRecordsPerNode.getIntValue(), m_skipColumns.getBooleanValue());
    InMemoryTable initialTable = tableCreator.createInMemoryTable(exec.createSubExecutionContext(0.05));
    int removedRows = tableCreator.getRemovedRowsDueToMissingClassValue();
    if (removedRows == inData.getRowCount()) {
        throw new IllegalArgumentException("Class column contains only " + "missing values");
    }
    if (removedRows > 0) {
        warningMessageSb.append(removedRows);
        warningMessageSb.append(" rows removed due to missing class value;");
    }
    // the all over row count is used to report progress
    m_alloverRowCount = initialTable.getSumOfWeights();
    // set the finishing counter
    // this counter will always be incremented when a leaf node is
    // created, as this determines the recursion end and can thus
    // be used for progress indication
    m_finishedCounter = new AtomicDouble(0);
    // get the number of attributes
    m_numberAttributes = initialTable.getNumAttributes();
    // create the quality measure
    final SplitQualityMeasure splitQualityMeasure;
    if (m_splitQualityMeasureType.getStringValue().equals(SPLIT_QUALITY_GINI)) {
        splitQualityMeasure = new SplitQualityGini();
    } else {
        splitQualityMeasure = new SplitQualityGainRatio();
    }
    // build the tree
    // before this set the node counter to 0
    m_counter.set(0);
    exec.setMessage("Building tree...");
    DecisionTreeNode root = null;
    root = buildTree(initialTable, exec, 0, splitQualityMeasure, parallelProcessing);
    boolean isBinaryNominal = m_binaryNominalSplitMode.getBooleanValue();
    boolean isFilterInvalidAttributeValues = m_filterNominalValuesFromParent.getBooleanValue();
    if (isBinaryNominal && isFilterInvalidAttributeValues) {
        // traverse tree nodes and remove from the children the attribute
        // values that were filtered out further up in the tree. "Bug" 3124
        root.filterIllegalAttributes(Collections.EMPTY_MAP);
    }
    // the decision tree model saved as PMML at the second out-port
    DecisionTree decisionTree = new DecisionTree(root, m_classifyColumn.getStringValue(), /* strategy has to be set explicitly as the default in PMML is
                    none, which means rows with missing values are not
                    classified. */
    PMMLMissingValueStrategy.LAST_PREDICTION);
    decisionTree.setColorColumn(colorColumn);
    // prune the tree
    exec.setMessage("Prune tree with " + m_pruningMethod.getStringValue() + "...");
    pruneTree(decisionTree);
    // add highlight patterns and color information
    exec.setMessage("Adding hilite and color info to tree...");
    addHiliteAndColorInfo(inData, decisionTree);
    LOGGER.info("Decision tree consisting of " + decisionTree.getNumberNodes() + " nodes created with pruning method " + m_pruningMethod.getStringValue());
    // set the warning message if available
    if (warningMessageSb.length() > 0) {
        setWarningMessage(warningMessageSb.toString());
    }
    // reset the number available threads
    parallelProcessing.reset();
    parallelProcessing = null;
    // no data out table is created -> return an empty table array
    exec.setMessage("Creating PMML decision tree model...");
    // handle the optional PMML input
    PMMLPortObject inPMMLPort = (PMMLPortObject) data[1];
    DataTableSpec inSpec = inData.getSpec();
    PMMLPortObjectSpec outPortSpec = createPMMLPortObjectSpec(inPMMLPort == null ? null : inPMMLPort.getSpec(), inSpec);
    PMMLPortObject outPMMLPort = new PMMLPortObject(outPortSpec, inPMMLPort, inData.getSpec());
    outPMMLPort.addModelTranslater(new PMMLDecisionTreeTranslator(decisionTree));
    m_decisionTree = decisionTree;
    return new PortObject[] { outPMMLPort };
}

Example 93 with PortObject

use of org.knime.core.node.port.PortObject in project knime-core by knime.

the class SubNodeContainer method performLoadContent.

/**
 * {@inheritDoc}
 */
@Override
WorkflowCopyContent performLoadContent(final SingleNodeContainerPersistor nodePersistor, final Map<Integer, BufferedDataTable> tblRep, final FlowObjectStack inStack, final ExecutionMonitor exec, final LoadResult loadResult, final boolean preserveNodeMessage) throws CanceledExecutionException {
    SubNodeContainerPersistor subNodePersistor = (SubNodeContainerPersistor) nodePersistor;
    WorkflowPersistor workflowPersistor = subNodePersistor.getWorkflowPersistor();
    // TODO pass in a filter input stack
    m_wfm.loadContent(workflowPersistor, tblRep, inStack, exec, loadResult, preserveNodeMessage);
    if (workflowPersistor.isDirtyAfterLoad() || m_wfm.isDirty()) {
        setDirty();
    }
    InternalNodeContainerState loadState = nodePersistor.getMetaPersistor().getState();
    if (!m_wfm.getInternalState().equals(loadState)) {
        // can happen for workflows that were exported without data;
        // the same check is done by the caller (WorkflowManager#postLoad) and handled appropriately
        setInternalState(m_wfm.getInternalState(), false);
    }
    NodeSettingsRO modelSettings = subNodePersistor.getSNCSettings().getModelSettings();
    if (modelSettings != null) {
        try {
            loadModelSettingsIntoDialogNodes(modelSettings, false);
        } catch (InvalidSettingsException e) {
            final String msg = "Could not load Wrapped Metanode configuration into dialog-nodes: " + e.getMessage();
            LOGGER.error(msg, e);
            loadResult.addError(msg);
            setDirty();
        }
    }
    checkInOutNodesAfterLoad(subNodePersistor, loadResult);
    // put data input output node if it was executed;
    final NativeNodeContainer virtualOutNode = getVirtualOutNode();
    LoadVersion l = nodePersistor instanceof FileSingleNodeContainerPersistor ? ((FileSingleNodeContainerPersistor) nodePersistor).getLoadVersion() : LoadVersion.V3010;
    if (l.isOlderThan(LoadVersion.V3010) && virtualOutNode.getInternalState().isExecuted()) {
        VirtualSubNodeOutputNodeModel outNodeModel = getVirtualOutNodeModel();
        PortObject[] outputData = new PortObject[virtualOutNode.getNrInPorts()];
        m_wfm.assembleInputData(getVirtualOutNodeID(), outputData);
        outNodeModel.postLoadExecute(ArrayUtils.removeAll(outputData, 0));
        // allow node to receive the internal held objects so that the next save operation also persists the
        // array of internal held objects - otherwise we get strange errors with nodes saved in 2.x, then loaded
        // and saved in 3.1+ (and converted ... although unmodified)
        getVirtualOutNode().getNode().assignInternalHeldObjects(outputData, null, getVirtualOutNode().createExecutionContext(), new PortObject[0]);
    }
    setVirtualOutputIntoOutport(m_wfm.getInternalState());
    m_wfmStateChangeListener = createAndAddStateListener();
    getInPort(0).setPortName("Variable Inport");
    getOutPort(0).setPortName("Variable Outport");
    getVirtualInNode().addNodeStateChangeListener(new RefreshPortNamesListener());
    getVirtualOutNode().addNodeStateChangeListener(new RefreshPortNamesListener());
    refreshPortNames();
    return null;
}

Example 94 with PortObject

use of org.knime.core.node.port.PortObject in project knime-core by knime.

the class SubNodeContainer method setVirtualOutputIntoOutport.

/**
 * Copies data from virtual output node into m_outputs, notifies state listeners if not
 * processing call from parent.
 * @param newState State of the internal WFM to decide whether to publish ports and/or specs.
 */
@SuppressWarnings("null")
private boolean setVirtualOutputIntoOutport(final InternalNodeContainerState newState) {
    // retrieve results and copy to outports
    final VirtualSubNodeOutputNodeModel virtualOutNodeModel = getVirtualOutNodeModel();
    final boolean isInactive = getVirtualOutNode().isInactive();
    final VirtualSubNodeExchange outputExchange = virtualOutNodeModel.getOutputExchange();
    // put objects into output if state of WFM is executed
    boolean publishObjects = newState.isExecuted();
    // publishObjects implies that output node has data or is inactive
    assert !publishObjects || (isInactive || (outputExchange != null && outputExchange.getPortObjects() != null)) : String.format("output node must have data or be inactive, status: %s, inactive: %b, exhange is null: %b, " + "exchange content is null: %s", newState, isInactive, outputExchange == null, outputExchange == null ? "<invalid>" : String.valueOf(outputExchange.getPortObjects() == null));
    boolean publishSpecs = (isInactive || outputExchange != null) && (newState.isConfigured() || newState.isExecuted() || newState.isExecutionInProgress());
    boolean changed = false;
    for (int i = 1; i < m_outputs.length; i++) {
        // not publish spec:     null output
        // inactive output node: inactive branch port object
        // otherwise:            use data from output node
        final PortObjectSpec spec = publishSpecs ? (isInactive ? InactiveBranchPortObjectSpec.INSTANCE : outputExchange.getPortSpecs()[i - 1]) : null;
        changed = m_outputs[i].setSpec(spec) || changed;
        final PortObject object = publishObjects ? (isInactive ? InactiveBranchPortObject.INSTANCE : outputExchange.getPortObjects()[i - 1]) : null;
        changed = m_outputs[i].setObject(object) || changed;
    }
    final PortObjectSpec spec = publishSpecs ? (isInactive ? InactiveBranchPortObjectSpec.INSTANCE : FlowVariablePortObjectSpec.INSTANCE) : null;
    changed = m_outputs[0].setSpec(spec) || changed;
    final PortObject object = publishObjects ? (isInactive ? InactiveBranchPortObject.INSTANCE : FlowVariablePortObject.INSTANCE) : null;
    changed = m_outputs[0].setObject(object) || changed;
    final FlowObjectStack outgoingFlowObjectStack = getOutgoingFlowObjectStack();
    // TODO API to remove variables from stack, then remove variables no longer in output node and update "changed"
    if (publishObjects && !isInactive) {
        for (FlowVariable f : outputExchange.getFlowVariables()) {
            outgoingFlowObjectStack.push(f.cloneAndUnsetOwner());
        }
    } else {
        // outgoing stack may be null if reset is called twice in a row (or once but no configure was called)
        if (outgoingFlowObjectStack != null) {
            while (!outgoingFlowObjectStack.isEmpty()) {
                outgoingFlowObjectStack.pop(FlowObject.class);
            }
        }
    }
    if (changed && !m_isPerformingActionCalledFromParent) {
        // updates port views
        notifyStateChangeListeners(new NodeStateEvent(this));
    }
    return changed;
}

Example 95 with PortObject

use of org.knime.core.node.port.PortObject in project knime-core by knime.

the class SubNodeContainer method fetchInputDataFromParent.

/* -------------------- Virtual node callbacks -------------- */
/**
 * Called from virtual input node when executed - in possibly executes nodes in the parent wfm and then
 * fetches the data from it.
 * @return the subnode data input (incl. mandatory flow var port object).
 * @throws ExecutionException any exception thrown while waiting for upstream nodes to finish execution.
 */
public PortObject[] fetchInputDataFromParent() throws ExecutionException {
    Callable<PortObject[]> c = new Callable<PortObject[]>() {

        @Override
        public PortObject[] call() throws Exception {
            final WorkflowManager parent = getParent();
            // might be not yet or no longer in workflow (e.g. part of construction)
            if (parent.containsNodeContainer(getID())) {
                PortObject[] results = new PortObject[getNrInPorts()];
                parent.executePredecessorsAndWait(getID());
                if (parent.assembleInputData(getID(), results)) {
                    return results;
                }
            }
            return null;
        }
    };
    ThreadPool currentPool = ThreadPool.currentPool();
    if (currentPool != null) {
        return currentPool.runInvisible(c);
    } else {
        try {
            return c.call();
        } catch (Exception e) {
            throw new ExecutionException(e);
        }
    }
}