Java tutorial
package org.cytoscape.tableimport.internal.task; /* * #%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.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; import org.apache.poi.openxml4j.exceptions.InvalidFormatException; import org.apache.poi.ss.usermodel.Sheet; import org.apache.poi.ss.usermodel.Workbook; import org.apache.poi.ss.usermodel.WorkbookFactory; import org.cytoscape.io.read.CyTableReader; import org.cytoscape.model.CyTable; import org.cytoscape.model.CyTableFactory; import org.cytoscape.service.util.CyServiceRegistrar; import org.cytoscape.tableimport.internal.reader.AttributeMappingParameters; import org.cytoscape.tableimport.internal.reader.DefaultAttributeTableReader; import org.cytoscape.tableimport.internal.reader.ExcelAttributeSheetReader; import org.cytoscape.tableimport.internal.reader.SupportedFileType; import org.cytoscape.tableimport.internal.reader.TextTableReader; import org.cytoscape.tableimport.internal.util.AttributeDataType; import org.cytoscape.tableimport.internal.util.SourceColumnSemantic; import org.cytoscape.tableimport.internal.util.TypeUtil; import org.cytoscape.view.model.CyNetworkView; import org.cytoscape.view.vizmap.VisualStyle; import org.cytoscape.work.AbstractTask; import org.cytoscape.work.TaskMonitor; import org.cytoscape.work.Tunable; import org.cytoscape.work.TunableValidator; public class ImportAttributeTableReaderTask extends AbstractTask implements CyTableReader, TunableValidator { private InputStream is; private final String fileType; protected CyNetworkView[] cyNetworkViews; protected VisualStyle[] visualstyles; private final String inputName; private CyTable[] cyTables; private static int numImports; @Tunable(description = "Attribute Mapping Parameters:") public AttributeMappingParameters amp; TextTableReader reader; private final CyServiceRegistrar serviceRegistrar; public ImportAttributeTableReaderTask(final InputStream is, final String fileType, final String inputName, final CyServiceRegistrar serviceRegistrar) { this.fileType = fileType; this.inputName = inputName; this.is = is; this.serviceRegistrar = serviceRegistrar; try { File tempFile = File.createTempFile("temp", this.fileType); tempFile.deleteOnExit(); FileOutputStream os = new FileOutputStream(tempFile); int read = 0; byte[] bytes = new byte[1024]; while ((read = is.read(bytes)) != -1) { os.write(bytes, 0, read); } os.flush(); os.close(); amp = new AttributeMappingParameters(new FileInputStream(tempFile), fileType); this.is = new FileInputStream(tempFile); } catch (IOException e) { try { is.close(); } catch (IOException e1) { } this.is = null; throw new IllegalStateException("Could not initialize object", e); } } @Override public void run(TaskMonitor tm) throws Exception { tm.setTitle("Loading table data"); tm.setProgress(0.0); tm.setStatusMessage("Loading table..."); Workbook workbook = null; // Load Spreadsheet data for preview. if (fileType != null && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) && workbook == null) { try { workbook = WorkbookFactory.create(is); } catch (InvalidFormatException e) { e.printStackTrace(); throw new IllegalArgumentException("Could not read Excel file. Maybe the file is broken?"); } finally { if (is != null) is.close(); } } if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension()) || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) { // Fixed bug# 1668, Only load data from the first sheet, ignore the rest sheets // UPDATE: From the user perspective it makes more sense to get the selected tab/sheet instead. String networkName = amp.getName(); if (networkName == null) networkName = workbook.getSheetName(0); final Sheet sheet = workbook.getSheet(networkName); if (sheet != null) { reader = new ExcelAttributeSheetReader(sheet, amp, serviceRegistrar); loadAnnotation(tm); } } else { try { reader = new DefaultAttributeTableReader(null, amp, this.is, serviceRegistrar); loadAnnotation(tm); } catch (Exception ioe) { tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage()); } } } @Override public CyTable[] getTables() { return cyTables; } private void loadAnnotation(TaskMonitor tm) { tm.setProgress(0.0); final TextTableReader reader = this.reader; final AttributeMappingParameters readerAMP = (AttributeMappingParameters) reader.getMappingParameter(); final String primaryKey = readerAMP.getAttributeNames()[readerAMP.getKeyIndex()]; final AttributeDataType dataType = readerAMP.getDataTypes()[readerAMP.getKeyIndex()]; final Class<?> keyType; switch (dataType) { case TYPE_INTEGER: keyType = Integer.class; break; case TYPE_LONG: keyType = Long.class; break; default: keyType = String.class; } tm.setProgress(0.1); final CyTable table = serviceRegistrar.getService(CyTableFactory.class).createTable("AttrTable " + inputName.substring(inputName.lastIndexOf('/') + 1) + " " + Integer.toString(numImports++), primaryKey, keyType, true, true); cyTables = new CyTable[] { table }; tm.setProgress(0.3); try { this.reader.readTable(table); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } tm.setProgress(1.0); } @Override public ValidationState getValidationState(Appendable errMsg) { if (amp.getKeyIndex() == -1) { try { errMsg.append("The primary key column needs to be selected."); } catch (IOException e) { e.printStackTrace(); return ValidationState.INVALID; } return ValidationState.INVALID; } final AttributeDataType keyDataType = amp.getDataTypes()[amp.getKeyIndex()]; if (!TypeUtil.isValid(SourceColumnSemantic.KEY, keyDataType)) { try { errMsg.append("The primary key column must be an Integer, Long or String."); } catch (IOException e) { e.printStackTrace(); return ValidationState.INVALID; } return ValidationState.INVALID; } if (amp.getSelectedColumnCount() < 2) { try { errMsg.append( "Table should have more than one column. Please check the selected delimeters and columns."); } catch (IOException e) { e.printStackTrace(); return ValidationState.INVALID; } return ValidationState.INVALID; } return ValidationState.OK; } }