SiLeBAT/FSK-Lab

/*******************************************************************************
 * 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.xlstimeseriesreader;

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

import org.knime.core.data.DataTableSpec;
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.AgentXml;
import de.bund.bfr.knime.pmm.common.KnimeUtils;
import de.bund.bfr.knime.pmm.common.LiteratureItem;
import de.bund.bfr.knime.pmm.common.MatrixXml;
import de.bund.bfr.knime.pmm.common.PmmXmlDoc;
import de.bund.bfr.knime.pmm.common.XLSReader;
import de.bund.bfr.knime.pmm.common.generictablemodel.KnimeTuple;
import de.bund.bfr.knime.pmm.common.pmmtablemodel.SchemaFactory;
import de.bund.bfr.knime.pmm.common.pmmtablemodel.TimeSeriesSchema;

/**
 * This is the model implementation of XLSTimeSeriesReader.
 * 
 * 
 * @author Christian Thoens
 */
public class XLSTimeSeriesReaderNodeModel extends NodeModel {

    private SettingsHelper set;

    /**
     * Constructor for the node model.
     */
    protected XLSTimeSeriesReaderNodeModel() {
        super(0, 1);
        set = new SettingsHelper();
    }

    /**
     * {@inheritDoc}
     */
    @Override
    protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec)
            throws Exception {
        XLSReader xlsReader = new XLSReader();
        List<KnimeTuple> tuples = new ArrayList<>(xlsReader
                .getTimeSeriesTuples(KnimeUtils.getFile(set.getFileName()), set.getSheetName(), set.getColumnMappings(),
                        set.getTimeUnit(), set.getConcentrationUnit(), set.getAgentColumn(), set.getAgentMappings(),
                        set.getMatrixColumn(), set.getMatrixMappings(), set.isPreserveIds(), set.getUsedIds())
                .values());

        for (String warning : xlsReader.getWarnings()) {
            setWarningMessage(warning);
        }

        if (set.getAgentColumn() == null && set.getAgent() != null) {
            for (KnimeTuple tuple : tuples) {
                PmmXmlDoc agentXml = tuple.getPmmXml(TimeSeriesSchema.ATT_AGENT);

                ((AgentXml) agentXml.get(0)).id = set.getAgent().id;
                ((AgentXml) agentXml.get(0)).name = set.getAgent().name;
                ((AgentXml) agentXml.get(0)).dbuuid = set.getAgent().dbuuid;
                tuple.setValue(TimeSeriesSchema.ATT_AGENT, agentXml);
            }
        }

        if (set.getMatrixColumn() == null && set.getMatrix() != null) {
            for (KnimeTuple tuple : tuples) {
                PmmXmlDoc matrixXml = tuple.getPmmXml(TimeSeriesSchema.ATT_MATRIX);

                ((MatrixXml) matrixXml.get(0)).id = set.getMatrix().id;
                ((MatrixXml) matrixXml.get(0)).name = set.getMatrix().name;
                ((MatrixXml) matrixXml.get(0)).dbuuid = set.getMatrix().dbuuid;
                tuple.setValue(TimeSeriesSchema.ATT_MATRIX, matrixXml);
            }
        }

        PmmXmlDoc literatureXML = new PmmXmlDoc();

        for (LiteratureItem item : set.getLiterature()) {
            literatureXML.add(item);
        }

        for (KnimeTuple tuple : tuples) {
            tuple.setValue(TimeSeriesSchema.ATT_LITMD, literatureXML);
        }

        BufferedDataContainer container = exec.createDataContainer(SchemaFactory.createDataSchema().createSpec());

        for (KnimeTuple tuple : tuples) {
            container.addRowToTable(tuple);
        }

        container.close();

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

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

    /**
     * {@inheritDoc}
     */
    @Override
    protected DataTableSpec[] configure(final DataTableSpec[] inSpecs) throws InvalidSettingsException {
        if (set.getFileName() == null) {
            throw new InvalidSettingsException("");
        }

        return new DataTableSpec[] { SchemaFactory.createDataSchema().createSpec() };
    }

    /**
     * {@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 {
    }

}