mnb.io.tabular.xls.HSSFPreparsedSheet.java Source code

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Here is the source code for mnb.io.tabular.xls.HSSFPreparsedSheet.java

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/*
 * Copyright (c) 2013. EMBL, European Bioinformatics Institute
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser 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 Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package mnb.io.tabular.xls;

import java.lang.reflect.InvocationTargetException;
import java.util.List;
import mnb.io.tabular.type.EntityColumn;
import mnb.io.tabular.ExcelEntityResolver;
import mnb.io.tabular.ExcelModelProperties;
import mnb.io.tabular.preparse.PreparsedMetabolite;
import mnb.io.tabular.type.TableDescription;
import mnb.io.tabular.preparse.PreparsedSheet;
import mnb.io.tabular.preparse.PreparsedEntry;
import mnb.io.tabular.preparse.PreparsedReaction;
import mnb.io.tabular.type.ReactionColumn;
import org.apache.log4j.Logger;
import org.apache.poi.hssf.usermodel.HSSFCell;
import org.apache.poi.hssf.usermodel.HSSFRow;
import org.apache.poi.hssf.usermodel.HSSFSheet;
import org.apache.poi.hssf.util.HSSFCellUtil;
import org.apache.poi.ss.format.CellFormatType;

/**
 *          HSSFPreparsedSheet  2011.08.30 <br>
 *          Class description
 * @version $Rev$ : Last Changed $Date$
 * @author  johnmay
 * @author  $Author$ (this version)
 */
public class HSSFPreparsedSheet extends PreparsedSheet {

    private static final Logger LOGGER = Logger.getLogger(HSSFPreparsedSheet.class);
    private final HSSFSheet worksheet;
    private Class dataType;

    /**
     *
     *
     * @param worksheet
     * @param properties An instance of ExcelModelProperties describing the location of the data in
     *                   the excel workbook
     * @param header     Whether the bounding box includes a single header row. This will
     *                   be used as the column names in the PreparsedReaction. If the header
     *                   is false columns without names will not be loaded into the
     *                   PreparsedEntry
     *
     */
    public HSSFPreparsedSheet(HSSFSheet worksheet, ExcelModelProperties properties, TableDescription bounds) {
        super(worksheet, properties, bounds);
        dataType = bounds.getClass();
        this.worksheet = worksheet;
    }

    @Override
    public PreparsedEntry getEntry(int i, List<TableDescription> cols) {

        PreparsedEntry entry = null;

        // otherwise we can't cast
        if (dataType == ReactionColumn.class) {
            entry = new PreparsedReaction();
        } else if (dataType == EntityColumn.class) {
            entry = new PreparsedMetabolite();
        }

        // add others

        HSSFRow row = worksheet.getRow(i);
        ExcelModelProperties properties = super.getProperties();

        // for the described columns add them to the preparsed entry
        for (TableDescription col : cols) {
            int index = properties.getColumnIndex(col);
            HSSFCell cell = row.getCell(index);
            if (cell != null) {
                int type = cell.getCellType();
                if (type == HSSFCell.CELL_TYPE_NUMERIC) {
                    entry.addValue(col, Double.toString(cell.getNumericCellValue()));
                } else if (type != HSSFCell.CELL_TYPE_BLANK) {
                    cell.setCellType(HSSFCell.CELL_TYPE_STRING);
                    entry.addValue(col, cell.getStringCellValue());
                }
            }
        }

        return entry;
    }

}