Examples with BufferedDataContainer org.knime.core.node.BufferedDataContainer used on opensource projects

Example 36 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class PortObjectRepository method copy.

/**
 * Copies the argument object by means of the associated serializer.
 * @param object The port object to be copied.
 * @param exec Host for BDTs being created
 * @param progress For progress/cancelation
 * @return The deep copy.
 * @throws IOException In case of exceptions while accessing the streams
 * @throws CanceledExecutionException If canceled.
 */
public static final PortObject copy(final PortObject object, final ExecutionContext exec, final ExecutionMonitor progress) throws IOException, CanceledExecutionException {
    if (object instanceof BufferedDataTable) {
        // need to copy the table cell by cell
        // this is to workaround the standard knime philosophy according
        // to which tables are referenced. A row-based copy will not work
        // as it still will reference blobs
        BufferedDataTable in = (BufferedDataTable) object;
        BufferedDataContainer con = exec.createDataContainer(in.getSpec(), true, 0);
        final long rowCount = in.size();
        long row = 0;
        boolean hasLoggedCloneProblem = false;
        for (DataRow r : in) {
            DataCell[] cells = new DataCell[r.getNumCells()];
            for (int i = 0; i < cells.length; i++) {
                // deserialize blob
                DataCell c = r.getCell(i);
                if (c instanceof BlobDataCell) {
                    try {
                        c = cloneBlobCell(c);
                    } catch (Exception e) {
                        if (!hasLoggedCloneProblem) {
                            LOGGER.warn("Can't clone blob object: " + e.getMessage(), e);
                            hasLoggedCloneProblem = true;
                            LOGGER.debug("Suppressing futher warnings.");
                        }
                    }
                }
                cells[i] = c;
            }
            con.addRowToTable(new DefaultRow(r.getKey(), cells));
            progress.setProgress(row / (double) rowCount, "Copied row " + row + "/" + rowCount);
            progress.checkCanceled();
            row++;
        }
        con.close();
        return con.getTable();
    }
    return Node.copyPortObject(object, exec);
}

Example 37 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class BlobsInSetCellWorkflowTest method createBDT.

/**
 * {@inheritDoc}
 */
@Override
protected BufferedDataTable createBDT(final ExecutionContext exec) {
    DataType t = ListCell.getCollectionType(DataType.getType(DataCell.class));
    BufferedDataContainer c = exec.createDataContainer(new DataTableSpec(new DataColumnSpecCreator("Sequence", t).createSpec()));
    for (int i = 0; i < ROW_COUNT; i++) {
        String s = "someName_" + i;
        // every other a ordinary string cell
        Collection<DataCell> cells = new ArrayList<DataCell>();
        for (int j = 0; j < LIST_SIZE * 2; j++) {
            String val = "Row_" + i + "; Cell index " + j;
            if (j % 2 == 0) {
                cells.add(new LargeBlobCell(val, LargeBlobCell.SIZE_OF_CELL));
            } else {
                cells.add(new StringCell(val));
            }
        }
        ListCell cell = CollectionCellFactory.createListCell(cells);
        c.addRowToTable(new DefaultRow(s, cell));
    }
    c.close();
    return c.getTable();
}

Example 38 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class TreeEnsembleModelExtractorNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] inObjects, final ExecutionContext exec) throws Exception {
    TreeEnsembleModelPortObject treeEnsembleModel = (TreeEnsembleModelPortObject) inObjects[0];
    DataTableSpec outSpec = createOutSpec();
    BufferedDataContainer container = exec.createDataContainer(outSpec, false, 0);
    int nrModels = treeEnsembleModel.getEnsembleModel().getNrModels();
    for (int i = 0; i < nrModels; i++) {
        PMMLPortObject pmmlObject = treeEnsembleModel.createDecisionTreePMMLPortObject(i);
        DataCell cell = PMMLCellFactory.create(pmmlObject.getPMMLValue().toString());
        RowKey key = RowKey.createRowKey(i);
        container.addRowToTable(new DefaultRow(key, cell));
        exec.checkCanceled();
        exec.setProgress(i / (double) nrModels, "Exported model " + (i + 1) + "/" + nrModels);
    }
    container.close();
    return new BufferedDataTable[] { container.getTable() };
}

Example 39 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class MedianTableTest method setUp.

/**
 * @throws java.lang.Exception
 */
@Before
public void setUp() throws Exception {
    Random random = new Random(37);
    DataColumnSpec[] colSpecs = new DataColumnSpec[] { new DataColumnSpecCreator("AscendingDouble", DoubleCell.TYPE).createSpec(), new DataColumnSpecCreator("DescendingDouble", DoubleCell.TYPE).createSpec(), new DataColumnSpecCreator("ThreeValuesSingleMedian", DoubleCell.TYPE).createSpec(), new DataColumnSpecCreator("ThreeValuesDifferentMedian", DoubleCell.TYPE).createSpec() // new DataColumnSpecCreator("FourValuesSingleMedian", DoubleCell.TYPE).createSpec(),
    // new DataColumnSpecCreator("FourValuesDifferentMedian", DoubleCell.TYPE).createSpec()
    };
    DataTableSpec spec = new DataTableSpec(colSpecs);
    final BufferedDataContainer container = EXEC_CONTEXT.createDataContainer(spec);
    try {
        int count = 100;
        for (int i = 0; i < count; ++i) {
            int col = 0;
            DataCell[] rowVals = new DataCell[colSpecs.length];
            rowVals[col++] = new DoubleCell(i);
            rowVals[col++] = new DoubleCell(count - i - 1);
            rowVals[col++] = i == 4 ? DataType.getMissingCell() : new DoubleCell(i < count / 2 ? 0 : i * 2 >= count + 2 ? 4 : 1);
            rowVals[col++] = new DoubleCell(i < count / 2 ? 0 : i * 2 >= count + 2 ? 4 : 1);
            container.addRowToTable(new DefaultRow(Integer.toString(i), rowVals));
        }
    } finally {
        container.close();
    }
    smallTable = container.getTable();
    NodeLogger.getLogger(getClass()).debug("Contents of test table:");
    for (DataRow row : smallTable) {
        StringBuilder buf = new StringBuilder();
        for (DataCell dataCell : row) {
            buf.append(dataCell + "\t");
        }
        NodeLogger.getLogger(getClass()).debug(buf.toString());
    }
}

Example 40 with BufferedDataContainer

use of org.knime.core.node.BufferedDataContainer in project knime-core by knime.

the class CovarianceMatrixCalculatorTest method generateData.

/**
 * @param random
 * @param size
 * @param data
 */
private BufferedDataContainer generateData(final Random random, final double[][] data, final DataTableSpec spec) {
    BufferedDataContainer createDataContainer = m_exec.createDataContainer(spec);
    for (int j = 0; j < data.length; j++) {
        double[] row = new double[spec.getNumColumns()];
        for (int i = 0; i < spec.getNumColumns(); i++) {
            {
                row[i] = random.nextDouble();
            }
        }
        data[j] = row;
        createDataContainer.addRowToTable(new DefaultRow(RowKey.createRowKey(j), row));
    }
    return createDataContainer;
}