org.cytoscape.tableimport.internal.reader.ExcelNetworkSheetReader.java Source code

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Here is the source code for org.cytoscape.tableimport.internal.reader.ExcelNetworkSheetReader.java

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package org.cytoscape.tableimport.internal.reader;

/*
 * #%L
 * Cytoscape Table Import Impl (table-import-impl)
 * $Id:$
 * $HeadURL:$
 * %%
 * Copyright (C) 2006 - 2013 The Cytoscape Consortium
 * %%
 * 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 2.1 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 Lesser Public License for more details.
 * 
 * You should have received a copy of the GNU General Lesser Public 
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/lgpl-2.1.html>.
 * #L%
 */

import java.io.IOException;
import java.util.Map;

import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.DataFormatter;
import org.apache.poi.ss.usermodel.FormulaEvaluator;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.service.util.CyServiceRegistrar;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Reader for Network file in Excel (.xls) format.<br>
 *
 * <p>
 * Currently supports only one sheet.
 * </p>
 *
 * @since Cytoscape 2.4
 * @version 0.6
 * @author Keiichiro Ono
 */
public class ExcelNetworkSheetReader extends NetworkTableReader {

    private final Sheet sheet;
    private final DataFormatter formatter;
    private final FormulaEvaluator evaluator;
    private static final Logger logger = LoggerFactory.getLogger(ExcelNetworkSheetReader.class);

    /*
     * Reader will read entries from this line.
     */
    /**
     * Creates a new ExcelNetworkSheetReader object.
     */
    public ExcelNetworkSheetReader(final String networkName, final Sheet sheet,
            final NetworkTableMappingParameters nmp, final Map<Object, CyNode> nMap,
            final CyRootNetwork rootNetwork, final CyServiceRegistrar serviceRegistrar) {
        super(networkName, null, nmp, nMap, rootNetwork, serviceRegistrar);
        this.sheet = sheet;
        this.evaluator = sheet.getWorkbook().getCreationHelper().createFormulaEvaluator();
        this.formatter = new DataFormatter();
    }

    @Override
    public void readTable(CyTable table) throws IOException {
        network.getRow(network).set("name", this.getNetworkName());
        parser.setNetwork(network);

        Row row;
        int rowCount = startLineNumber;
        String[] cellsInOneRow;

        while ((row = sheet.getRow(rowCount)) != null) {
            cellsInOneRow = createElementStringArray(row);
            try {
                parser.parseEntry(cellsInOneRow);
            } catch (Exception e) {
                logger.warn("Couldn't parse row: " + rowCount, e);
            }
            rowCount++;
        }
    }

    /**
     * For a given Excel row, convert the cells into String.
     *
     * @param row
     * @return
     */
    private String[] createElementStringArray(final Row row) {
        if (mapping.getColumnCount() == -1)
            return null;
        String[] cells = new String[mapping.getColumnCount()];
        Cell cell;

        for (short i = 0; i < mapping.getColumnCount(); i++) {
            cell = row.getCell(i);

            if (cell == null || cell.getCellType() == Cell.CELL_TYPE_ERROR
                    || (cell.getCellType() == Cell.CELL_TYPE_FORMULA
                            && cell.getCachedFormulaResultType() == Cell.CELL_TYPE_ERROR)) {
                cells[i] = null;
            } else {
                cells[i] = formatter.formatCellValue(cell, evaluator);
            }
        }

        return cells;
    }
}