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

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Here is the source code for org.cytoscape.tableimport.internal.reader.ExcelAttributeSheetReader.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.Arrays;
import java.util.List;
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.CyTable;
import org.cytoscape.service.util.CyServiceRegistrar;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Reader for Excel attribute workbook.<br>
 * This class creates string array and pass it to the AttributeLineParser.<br>
 *
 * <p>
 * This reader takes one sheet at a time.
 * </p>
 */
public class ExcelAttributeSheetReader implements TextTableReader {

    private final Sheet sheet;
    private final AttributeMappingParameters mapping;
    private final AttributeLineParser parser;
    private final DataFormatter formatter;
    private final FormulaEvaluator evaluator;
    private final int startLineNumber;
    private int globalCounter = 0;

    private static final Logger logger = LoggerFactory.getLogger(ExcelAttributeSheetReader.class);

    public ExcelAttributeSheetReader(final Sheet sheet, final AttributeMappingParameters mapping,
            final CyServiceRegistrar serviceRegistrar) {
        this.sheet = sheet;
        this.mapping = mapping;
        this.startLineNumber = mapping.getStartLineNumber();
        this.parser = new AttributeLineParser(mapping, serviceRegistrar);
        this.evaluator = sheet.getWorkbook().getCreationHelper().createFormulaEvaluator();
        this.formatter = new DataFormatter();
    }

    @Override
    public List<String> getColumnNames() {
        return Arrays.asList(mapping.getAttributeNames());
    }

    @Override
    public void readTable(CyTable table) throws IOException {
        Row row;
        int rowCount = startLineNumber;
        String[] cellsInOneRow;

        while ((row = sheet.getRow(rowCount)) != null) {
            cellsInOneRow = createElementStringArray(row);
            try {
                //if(importAll)
                parser.parseAll(table, cellsInOneRow);
                //else 
                //   parser.parseEntry(table, cellsInOneRow);
            } catch (Exception ex) {
                logger.warn("Couldn't parse row: " + rowCount, ex);
            }

            rowCount++;
            globalCounter++;
        }
    }

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

        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;
    }

    @Override
    public String getReport() {
        final StringBuilder sb = new StringBuilder();
        final Map<String, Object> invalid = parser.getInvalidMap();
        sb.append(globalCounter + " entries are loaded and mapped into table.");

        int limit = 10;
        if (invalid.size() > 0) {
            sb.append("\n\nThe following enties are invalid and were not imported:\n");

            for (String key : invalid.keySet()) {
                sb.append(key + " = " + invalid.get(key) + "\n");
                if (limit-- <= 0) {
                    sb.append(
                            "Approximately " + (invalid.size() - 10) + " additional entries were not imported...");
                    break;
                }

            }
        }

        return sb.toString();
    }

    @Override
    public MappingParameter getMappingParameter() {
        return mapping;
    }
}