de.bund.bfr.knime.pmm.xml2table.XML2TableNodeModel.java Source code

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Here is the source code for de.bund.bfr.knime.pmm.xml2table.XML2TableNodeModel.java

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/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Department Biological Safety - BfR
 *******************************************************************************/
package de.bund.bfr.knime.pmm.xml2table;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.knime.core.data.DataCell;
import org.knime.core.data.DataColumnSpec;
import org.knime.core.data.DataColumnSpecCreator;
import org.knime.core.data.DataRow;
import org.knime.core.data.DataTableSpec;
import org.knime.core.data.DataType;
import org.knime.core.data.StringValue;
import org.knime.core.data.def.DefaultRow;
import org.knime.core.data.def.StringCell;
import org.knime.core.node.BufferedDataContainer;
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.NodeModel;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;

import de.bund.bfr.knime.pmm.common.PmmXmlDoc;

/**
 * This is the model implementation of XML2Table.
 * 
 * 
 * @author BfR
 */
public class XML2TableNodeModel extends NodeModel {

    private SettingsHelper set;

    /**
     * Constructor for the node model.
     */
    protected XML2TableNodeModel() {
        super(1, 1);
        set = new SettingsHelper();
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec)
            throws Exception {
        BufferedDataTable table = inData[0];
        DataTableSpec inSpec = table.getSpec();
        int columnIndex = inSpec.findColumnIndex(set.getColumn());

        int n = 0;

        for (DataRow row : table) {
            PmmXmlDoc xml = createXml(row.getCell(columnIndex));

            if (xml != null) {
                n = Math.max(n, xml.size());
            }
        }

        DataTableSpec outSpec = createSpec(inSpec, n, Arrays.asList(set.getXmlElements()));
        BufferedDataContainer container = exec.createDataContainer(outSpec);
        int index = 0;

        for (DataRow row : table) {
            DataCell[] cells = new DataCell[outSpec.getNumColumns()];

            for (String column : inSpec.getColumnNames()) {
                cells[outSpec.findColumnIndex(column)] = row.getCell(inSpec.findColumnIndex(column));
            }

            PmmXmlDoc xml = createXml(row.getCell(columnIndex));

            for (int i = 0; i < n; i++) {
                Element e = null;

                if (xml != null && i < xml.size()) {
                    e = xml.getElementSet().get(i).toXmlElement();
                }

                for (String element : set.getXmlElements()) {
                    String column = createColumnName(element, i, n);

                    if (e != null) {
                        cells[outSpec.findColumnIndex(column)] = new StringCell(e.getAttributeValue(element));
                    } else {
                        cells[outSpec.findColumnIndex(column)] = DataType.getMissingCell();
                    }
                }
            }

            exec.checkCanceled();
            exec.setProgress((double) index / (double) table.size());
            container.addRowToTable(new DefaultRow(row.getKey(), cells));
        }

        container.close();

        return new BufferedDataTable[] { container.getTable() };
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected void reset() {
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected DataTableSpec[] configure(final DataTableSpec[] inSpecs) throws InvalidSettingsException {
        // Spec at output is not known in advance. It depends on the XML.
        return null;
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected void saveSettingsTo(final NodeSettingsWO settings) {
        set.saveSettings(settings);
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected void loadValidatedSettingsFrom(final NodeSettingsRO settings) throws InvalidSettingsException {
        set.loadSettings(settings);
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected void loadInternals(final File internDir, final ExecutionMonitor exec)
            throws IOException, CanceledExecutionException {
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected void saveInternals(final File internDir, final ExecutionMonitor exec)
            throws IOException, CanceledExecutionException {
    }

    protected static PmmXmlDoc createXml(DataCell cell) {
        if (cell instanceof StringValue) {
            try {
                return new PmmXmlDoc(((StringValue) cell).getStringValue());
            } catch (IOException e) {
            } catch (JDOMException e) {
            }
        }

        return null;
    }

    private DataTableSpec createSpec(DataTableSpec spec, int n, List<String> elements) {
        List<DataColumnSpec> columns = new ArrayList<>();

        for (DataColumnSpec column : spec) {
            columns.add(column);
        }

        for (int i = 0; i < n; i++) {
            for (String element : elements) {
                columns.add(
                        new DataColumnSpecCreator(createColumnName(element, i, n), StringCell.TYPE).createSpec());
            }
        }

        return new DataTableSpec(columns.toArray(new DataColumnSpec[0]));
    }

    private String createColumnName(String element, int i, int n) {
        String column = set.getColumn() + "_" + element;

        if (n > 1) {
            column += "_" + (i + 1);
        }

        return column;
    }

}