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.pmfreader;

import java.io.File;
import java.io.IOException;

import org.jdom2.Element;
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 org.knime.core.node.defaultnodesettings.SettingsModelString;

import de.bund.bfr.knime.pmm.common.KnimeUtils;
import de.bund.bfr.knime.pmm.common.reader.ReaderUtils;
import de.bund.bfr.pmfml.file.PMFMetadataNode;
import de.unirostock.sems.cbarchive.CombineArchive;
import de.unirostock.sems.cbarchive.meta.MetaDataObject;

public class PMFReaderNodeModel extends NodeModel {

  // configuration keys
  public static final String CFGKEY_FILE = "filename";
  // defaults for persistent state
  private static final String DEFAULT_FILE = "c:/temp/foo.xml";

  // persistent state
  private SettingsModelString filename = new SettingsModelString(CFGKEY_FILE, DEFAULT_FILE);

  private final boolean isPmfx;
  
  /**
   * Constructor for the node model.
   */
  public PMFReaderNodeModel(final boolean isPmfx) {
    // 0 input ports and 2 input ports
    super(0, 2);
    this.isPmfx = isPmfx;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  protected BufferedDataTable[] execute(final BufferedDataTable[] inData,
      final ExecutionContext exec) throws Exception {
    BufferedDataTable[] tables = null;
    tables = loadPMF(exec);
    return tables;
  }

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

  /**
   * {@inheritDoc}
   */
  @Override
  protected DataTableSpec[] configure(final DataTableSpec[] inSpecs)
      throws InvalidSettingsException {
    return new DataTableSpec[] {null, null};
  }

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

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

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

    // TODO check if the settings could be applied to our model
    // e.g. if the count is in a certain range (which is ensured by the
    // SettingsModel).
    // Do not actually set any values of any member variables.
    filename.validateSettings(settings);
  }

  /**
   * {@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 {}

  // Load PMF file
  private BufferedDataTable[] loadPMF(final ExecutionContext exec) throws Exception {
    // Get model type from annotation in the metadata file

    // a) Open archive
    File file = KnimeUtils.getFile(filename.getStringValue());
    CombineArchive ca = new CombineArchive(file, true);

    // b) Get annotation
    MetaDataObject mdo = ca.getDescriptions().get(0);
    Element metaParent = mdo.getXmlDescription();
    PMFMetadataNode pmfMetadataNode = new PMFMetadataNode(metaParent);

    // c) Close archive
    ca.close();

    BufferedDataContainer[] containers =
        ReaderUtils.readPMF(file, isPmfx, exec, pmfMetadataNode.getModelType());
    BufferedDataTable[] tables = {containers[0].getTable(), containers[1].getTable()};
    return tables;
  }
}