Java tutorial
/* Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org) The Cytoscape Consortium is: - Institute for Systems Biology - University of California San Diego - Memorial Sloan-Kettering Cancer Center - Institut Pasteur - Agilent Technologies This library 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 any later version. This library 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. The software and documentation provided hereunder is on an "as is" basis, and the Institute for Systems Biology and the Whitehead Institute have no obligations to provide maintenance, support, updates, enhancements or modifications. In no event shall the Institute for Systems Biology and the Whitehead Institute be liable to any party for direct, indirect, special, incidental or consequential damages, including lost profits, arising out of the use of this software and its documentation, even if the Institute for Systems Biology and the Whitehead Institute have been advised of the possibility of such damage. 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 library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. */ package edu.ucsd.bioeng.coreplugin.tableImport.reader; 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.Row; import org.apache.poi.ss.usermodel.Sheet; import cytoscape.data.CyAttributes; import cytoscape.logger.CyLogger; /** * 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> * * @version 0.7 * @since Cytoscape 2.4 * @author kono * */ public class ExcelAttributeSheetReader implements TextTableReader { private final Sheet sheet; private final AttributeMappingParameters mapping; private final AttributeLineParser parser; private final int startLineNumber; private int globalCounter = 0; private boolean importAll = false; private CyLogger logger = CyLogger.getLogger(ExcelAttributeSheetReader.class); /** * Constructor.<br> * * Takes one Excel sheet as parameter. * * @param sheet * @param mapping */ public ExcelAttributeSheetReader(final Sheet sheet, final AttributeMappingParameters mapping, final int startLineNumber) { this(sheet, mapping, startLineNumber, false); } /** * Creates a new ExcelAttributeSheetReader object. * * @param sheet DOCUMENT ME! * @param mapping DOCUMENT ME! * @param startLineNumber DOCUMENT ME! * @param importAll DOCUMENT ME! */ public ExcelAttributeSheetReader(final Sheet sheet, final AttributeMappingParameters mapping, final int startLineNumber, boolean importAll) { this.sheet = sheet; this.mapping = mapping; this.startLineNumber = startLineNumber; this.parser = new AttributeLineParser(mapping); this.importAll = importAll; } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public List<String> getColumnNames() { return Arrays.asList(mapping.getAttributeNames()); } /** * DOCUMENT ME! * * @throws IOException DOCUMENT ME! */ public void readTable() throws IOException { Row row; int rowCount = startLineNumber; String[] cellsInOneRow; while ((row = sheet.getRow(rowCount)) != null) { cellsInOneRow = createElementStringArray(row); try { if (importAll) parser.parseAll(cellsInOneRow); else parser.parseEntry(cellsInOneRow); } catch (Exception ex) { logger.warn("Couldn't parse row: " + rowCount, ex); } rowCount++; globalCounter++; } } /** * For a given Excell row, convert the cells into String. * * @param row * @return */ 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) { cells[i] = null; } else if (cell.getCellType() == Cell.CELL_TYPE_STRING) { cells[i] = cell.getRichStringCellValue().getString(); } else if (cell.getCellType() == Cell.CELL_TYPE_NUMERIC) { if (mapping.getAttributeTypes()[i] == CyAttributes.TYPE_INTEGER) { Double dblValue = cell.getNumericCellValue(); Integer intValue = dblValue.intValue(); cells[i] = intValue.toString(); } else { cells[i] = Double.toString(cell.getNumericCellValue()); } } else if (cell.getCellType() == Cell.CELL_TYPE_BOOLEAN) { cells[i] = Boolean.toString(cell.getBooleanCellValue()); } else if (cell.getCellType() == Cell.CELL_TYPE_BLANK) { cells[i] = null; } else if (cell.getCellType() == Cell.CELL_TYPE_ERROR) { cells[i] = null; logger.warn("Error found when reading a cell!"); } } return cells; } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public String getReport() { final StringBuilder sb = new StringBuilder(); final Map<String, Object> invalid = parser.getInvalidMap(); sb.append(globalCounter + " entries are loaded and mapped onto\n"); sb.append(mapping.getObjectType().toString() + " attributes."); 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(); } }