Examples with DataContainer org.knime.core.data.container.DataContainer used on opensource projects

Example 26 with DataContainer

use of org.knime.core.data.container.DataContainer in project knime-core by knime.

the class HierarchicalClusterNodeModel method createResultTable.

/**
 * Creates a standard table as the result table. The result table is
 * constructed for the desired number of clusters.
 *
 * @param inputData
 *            the input data table which has the meta information like
 *            column names classes, and so on
 *
 * @param clusters
 *            the vector with the clusters
 * @param exec
 *            to check for user cancelations
 * @return the result data table which contains the data rows with the class
 *         information
 * @throws CanceledExecutionException
 *             if user canceled
 */
private DataTable createResultTable(final DataTable inputData, final List<ClusterNode> clusters, final ExecutionContext exec) throws CanceledExecutionException {
    DataTableSpec inputSpec = inputData.getDataTableSpec();
    DataTableSpec outputSpec = generateOutSpec(inputSpec);
    DataContainer resultTable = exec.createDataContainer(outputSpec);
    for (int i = 0; i < clusters.size(); i++) {
        DataRow[] memberRows = clusters.get(i).getAllDataRows();
        for (DataRow dataRow : memberRows) {
            DataCell[] cells = new DataCell[dataRow.getNumCells() + 1];
            for (int j = 0; j < dataRow.getNumCells(); j++) {
                cells[j] = dataRow.getCell(j);
            }
            // append the cluster id the row belongs to
            cells[cells.length - 1] = new StringCell("cluster_" + i);
            resultTable.addRowToTable(new DefaultRow(dataRow.getKey(), cells));
            exec.checkCanceled();
        }
    }
    resultTable.close();
    return resultTable.getTable();
}

Example 27 with DataContainer

use of org.knime.core.data.container.DataContainer in project knime-core by knime.

the class DBReaderImpl method createTable.

/**
 * Called from the database port to read the first n-number of rows.
 *
 * @param useDbRowId <code>true</code> if the KNIME row id should based on the db row id
 * @param cachedNoRows number of rows cached for data preview
 * @param cp {@link CredentialsProvider} providing user/password
 * @return buffered data table read from database
 * @throws SQLException if the connection could not be opened
 */
DataTable createTable(final boolean useDbRowId, final int cachedNoRows, final CredentialsProvider cp) throws SQLException {
    if (m_blobFactory == null) {
        m_blobFactory = new BinaryObjectCellFactory();
    }
    // retrieve connection
    // final Connection conn = initConnection(cp);
    final DatabaseQueryConnectionSettings dbConn = getQueryConnection();
    // synchronized (dbConn.syncConnection(conn)) {
    return dbConn.execute(cp, conn -> {
        // remember auto-commit flag
        final boolean autoCommit = conn.getAutoCommit();
        final Statement stmt = initStatement(cp, conn);
        try {
            final String[] oQueries = dbConn.getQuery().split(SQL_QUERY_SEPARATOR);
            if (cachedNoRows < 0) {
                int fetchsize = (DatabaseConnectionSettings.FETCH_SIZE != null) ? DatabaseConnectionSettings.FETCH_SIZE : -1;
                dbConn.getUtility().getStatementManipulator().setFetchSize(stmt, fetchsize);
            } else {
                final int hashAlias = System.identityHashCode(this);
                final int selectIdx = oQueries.length - 1;
                // replace last element in statement(s) with wrapped SQL
                oQueries[selectIdx] = "SELECT * FROM (" + oQueries[selectIdx] + ") table_" + hashAlias;
                try {
                    // bugfix 2925: may fail, e.g. on sqlite
                    stmt.setMaxRows(cachedNoRows);
                } catch (SQLException ex) {
                    Throwable cause = ExceptionUtils.getRootCause(ex);
                    if (cause == null) {
                        cause = ex;
                    }
                    LOGGER.warn("Can't set max rows on statement, reason: " + cause.getMessage(), ex);
                }
            }
            // execute all except the last query
            for (int i = 0; i < oQueries.length - 1; i++) {
                LOGGER.debug("Executing SQL statement as execute: " + oQueries[i]);
                stmt.execute(oQueries[i]);
            }
            final String lastQuery = oQueries[oQueries.length - 1];
            LOGGER.debug("Executing SQL statement as executeQuery: " + lastQuery);
            final ResultSet result = stmt.executeQuery(lastQuery);
            LOGGER.debug("Reading meta data from database ResultSet...");
            m_spec = createTableSpec(result.getMetaData());
            LOGGER.debug("Parsing database ResultSet...");
            // final DBRowIterator dbIt = createRowIterator(useDbRowId, result);
            final RowIterator it = createDBRowIterator(m_spec, dbConn, m_blobFactory, useDbRowId, result);
            DataContainer buf = new DataContainer(m_spec);
            while (it.hasNext()) {
                buf.addRowToTable(it.next());
            }
            buf.close();
            return buf.getTable();
        } finally {
            if (stmt != null) {
                if (!conn.getAutoCommit()) {
                    conn.commit();
                }
                DatabaseConnectionSettings.setAutoCommit(conn, autoCommit);
                stmt.close();
            }
        }
    });
}

Example 28 with DataContainer

use of org.knime.core.data.container.DataContainer in project knime-core by knime.

the class MissingValueApplyNodeModel method execute.

/**
 * {@inheritDoc}
 */
@Override
protected PortObject[] execute(final PortObject[] inData, final ExecutionContext exec) throws Exception {
    BufferedDataTable inTable = (BufferedDataTable) inData[DATA_PORT_IDX];
    DataTableSpec inSpec = inTable.getDataTableSpec();
    PMMLPortObject pmmlIn = (PMMLPortObject) inData[PMML_PORT_IDX];
    MissingCellReplacingDataTable mvTable;
    try (LockedSupplier<Document> supplier = pmmlIn.getPMMLValue().getDocumentSupplier()) {
        mvTable = new MissingCellReplacingDataTable(inSpec, PMMLDocument.Factory.parse(supplier.get()));
    }
    // Calculate the statistics
    mvTable.init(inTable, exec.createSubExecutionContext(0.5));
    long rowCounter = 0;
    final long numOfRows = inTable.size();
    DataContainer container = exec.createDataContainer(mvTable.getDataTableSpec());
    for (DataRow row : mvTable) {
        exec.checkCanceled();
        if (row != null) {
            exec.setProgress(++rowCounter / (double) numOfRows, "Processed row " + rowCounter + "/" + numOfRows + " (\"" + row.getKey() + "\")");
            container.addRowToTable(row);
        } else {
            exec.setProgress(++rowCounter / (double) numOfRows, "Processed row " + rowCounter + "/" + numOfRows);
        }
    }
    container.close();
    // Collect warning messages
    String warnings = mvTable.finish();
    // Handle the warnings
    if (warnings.length() > 0) {
        setWarningMessage(warnings);
    }
    return new PortObject[] { (BufferedDataTable) container.getTable() };
}

Example 29 with DataContainer

use of org.knime.core.data.container.DataContainer in project knime-core by knime.

the class InteractiveHiLiteCollectorNodeModel method getHiLiteAnnotationsTable.

/**
 * @return table with hilit rows first and then all rows with annotations
 */
DataTable getHiLiteAnnotationsTable() {
    // return null if not executed
    if (m_data == null) {
        return null;
    }
    DataContainer buf;
    if (m_annotationMap.isEmpty()) {
        buf = new DataContainer(new DataTableSpec());
    } else {
        buf = new DataContainer(new DataTableSpec(createSpecs(null)));
    }
    HiLiteHandler hdl = getInHiLiteHandler(0);
    if (hdl != null) {
        for (RowKey key : hdl.getHiLitKeys()) {
            DataCell[] cells = new DataCell[buf.getTableSpec().getNumColumns()];
            for (int i = 0; i < cells.length; i++) {
                Map<Integer, String> map = m_annotationMap.get(key);
                if (map == null) {
                    cells[i] = DataType.getMissingCell();
                } else {
                    String str = m_annotationMap.get(key).get(i);
                    if (str == null) {
                        cells[i] = DataType.getMissingCell();
                    } else {
                        cells[i] = new StringCell(str);
                    }
                }
            }
            buf.addRowToTable(new DefaultRow(key, cells));
        }
        for (RowKey key : m_annotationMap.keySet()) {
            if (!hdl.isHiLit(key)) {
                DataCell[] cells = new DataCell[buf.getTableSpec().getNumColumns()];
                for (int i = 0; i < cells.length; i++) {
                    String str = m_annotationMap.get(key).get(i);
                    if (str == null) {
                        cells[i] = DataType.getMissingCell();
                    } else {
                        cells[i] = new StringCell(str);
                    }
                }
                buf.addRowToTable(new DefaultRow(key, cells));
            }
        }
    }
    buf.close();
    return buf.getTable();
}

Example 30 with DataContainer

use of org.knime.core.data.container.DataContainer in project knime-core by knime.

the class NominalValueRowFilterNodeModel method execute.

/**
 * {@inheritDoc}
 */
@SuppressWarnings("null")
@Override
protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec) throws Exception {
    // include data container
    DataContainer positive = exec.createDataContainer(inData[0].getDataTableSpec());
    DataContainer negative = m_splitter ? exec.createDataContainer(inData[0].getDataTableSpec()) : null;
    long currentRow = 0;
    for (DataRow row : inData[0]) {
        // if row matches to included...
        if (matches(row)) {
            positive.addRowToTable(row);
        } else if (m_splitter) {
            negative.addRowToTable(row);
        }
        exec.setProgress(currentRow / (double) inData[0].size(), "filtering row # " + currentRow);
        currentRow++;
        exec.checkCanceled();
    }
    positive.close();
    BufferedDataTable positiveTable = exec.createBufferedDataTable(positive.getTable(), exec);
    if (positiveTable.size() <= 0) {
        String warning = "No rows matched!";
        if (m_splitter) {
            warning = warning + " Input mirrored at out-port 1 (excluded)";
        }
        setWarningMessage(warning);
    }
    if (m_splitter) {
        negative.close();
        BufferedDataTable negativeTable = exec.createBufferedDataTable(negative.getTable(), exec);
        if (negativeTable.size() <= 0) {
            setWarningMessage("All rows matched! Input mirrored at out-port 0 (included)");
        }
        return new BufferedDataTable[] { positiveTable, negativeTable };
    }
    return new BufferedDataTable[] { positiveTable };
}