/**
ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
License:
ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
EXHIBIT A. CPAL version 1.0
The contents of this file are subject to the CPAL version 1.0 (the License);
you may not use this file except in compliance with the License. You may obtain a
copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html.
The License is based on the Mozilla Public License version 1.1 but Sections
14 and 15 have been added to cover use of software over a computer network and
provide for limited attribution for the Original Developer. In addition, Exhibit
A has been modified to be consistent with Exhibit B.
Software distributed under the License is distributed on an AS IS basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
the specific language governing rights and limitations under the License.
The Original Code is ISAcreator.
The Original Developer is the Initial Developer. The Initial Developer of the
Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com;
Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com;
http://www.isa-tools.org). All portions of the code written by the ISA Team are
Copyright (c) 2007-2011 ISA Team. All Rights Reserved.
EXHIBIT B. Attribution Information
Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team
Attribution Phrase: Developed by the ISA Team
Attribution URL: http://www.isa-tools.org
Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png
Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL.
Sponsors:
The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone).
*/
package org.isatools.isacreator.gui.menu;
import org.apache.log4j.Logger;
import org.isatools.errorreporter.model.ErrorMessage;
import org.isatools.errorreporter.model.FileType;
import org.isatools.errorreporter.model.ISAFileErrorReport;
import org.isatools.isacreator.api.ImportConfiguration;
import org.isatools.isacreator.gs.GSLocalFilesManager;
import org.isatools.isacreator.gui.ISAcreator;
import org.isatools.isacreator.gui.modeselection.Mode;
import org.isatools.isacreator.launch.ISAcreatorCLArgs;
import org.isatools.isacreator.utils.GeneralUtils;
import org.isatools.isacreator.utils.PropertyFileIO;
import org.jdesktop.fuse.InjectedResource;
import uk.ac.ebi.utils.io.DownloadUtils;
import javax.swing.*;
import java.awt.*;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* ImportFilesMenu provides the interface to allow users to import previously saved ISATAB
* submissions into the software for editing/viewing.
* <p/>
* Date: Mar 3, 2010
*
* @author eamonnmaguire
* @author <a href="mailto:alejandra.gonzalez.beltran@gmail.com">Alejandra Gonzalez-Beltran</a>
*/
public class ImportConfigurationMenu extends AbstractImportFilesMenu {
private static Logger log = Logger.getLogger(ImportConfigurationMenu.class);
@InjectedResource
private ImageIcon panelHeader, listImage, filterLeft, filterRight;
//private boolean initialLoadingPassed = true;
public ImportConfigurationMenu(ISAcreatorMenu menu) {
super(menu);
setPreferredSize(new Dimension(400, 400));
previousNonLocalFiles = new ArrayList<File>();
}
public JPanel createAlternativeExitDisplay() {
return new JPanel();
}
public void getSelectedFileAndLoad() {
if (previousFilesExtendedJList.getSelectedIndex() != -1) {
// select file from list
for (File candidate : previousFiles) {
if (candidate.getName()
.equals(previousFilesExtendedJList.getSelectedValue()
.toString())) {
menu.showProgressPanel("attempting to load configuration in " +
candidate.getName() + "...");
//loadFile(ISAcreator.DEFAULT_CONFIGURATIONS_DIRECTORY + File.separator +
// candidate.getName() + File.separator);
loadFile(candidate.getAbsolutePath());
}
}
}
}
public void loadFile(final String dir) {
// show infinite panel. if successful, hide glass panel and show either the errors, or the data entry panel containing the submission
Thread performer = new Thread(new Runnable() {
public void run() {
// success, so load
SwingUtilities.invokeLater(new Runnable() {
public void run() {
ImportConfiguration importConfiguration = new ImportConfiguration(dir);
boolean successful = importConfiguration.loadConfiguration();
menu.stopProgressIndicator();
if (!successful) {
menu.resetViewAfterProgress();
System.out.println("Problem encountered");
problemReport.setText(importConfiguration.getProblemLog());
problemScroll.setVisible(true);
revalidate();
repaint();
} else {
System.out.println("Loaded configuration");
try {
if (!dir.contains(ISAcreator.DEFAULT_CONFIGURATIONS_DIRECTORY)) {
//check it doesn't exit already
boolean exists = false;
for (File file : previousNonLocalFiles) {
if (dir.equals(file.getCanonicalPath())) {
exists = true;
break;
}
}
if (!exists)
previousNonLocalFiles.add(new File(dir));
}
}catch(IOException ioex){
ioex.printStackTrace();
}
menu.resetViewAfterProgress();
menu.hideGlassPane();
if (ISAcreatorCLArgs.mode() == Mode.GS) {
if (ISAcreatorCLArgs.isatabDir() != null || ISAcreatorCLArgs.isatabFiles() != null) {
List<ErrorMessage> errors = GSLocalFilesManager.downloadFiles(menu.getAuthentication());
if (!errors.isEmpty()) {
ISAFileErrorReport error = new ISAFileErrorReport("", FileType.INVESTIGATION, errors);
java.util.List<ISAFileErrorReport> list = new ArrayList<ISAFileErrorReport>();
list.add(error);
ErrorMenu errorMenu = new ErrorMenu(menu, list, false, menu.getMainMenuGUI());
errorMenu.createGUI();
} else {
menu.loadFiles(ISAcreatorCLArgs.isatabDir(), true);
}
} else {
//the ISAtab files were not given as parameter, show main menu
menu.changeView(menu.getMainMenuGUI());
}
} else {
//mode is not GS
if (ISAcreatorCLArgs.isatabDir() != null) {
menu.loadFiles(ISAcreatorCLArgs.isatabDir(), true);
} else {
menu.changeView(menu.getMainMenuGUI());
}
}
}
problemScroll.setVisible(false);
}
}
);
}
}
);
performer.start();
}
public java.util.List<File> getPreviousFiles() {
previousFilesExtendedJList.clearItems();
File f = new File(ISAcreator.DEFAULT_CONFIGURATIONS_DIRECTORY);
if (!f.exists() || !f.isDirectory()) {
f.mkdir();
}
previousFiles = new ArrayList<File>(Arrays.asList(f.listFiles()));
if (previousFiles.size() == 0) {
String configurationFilesLocation = PropertyFileIO.retrieveDefaultSettings().getProperty("configurationFilesLocation");
String tmpDirectory = GeneralUtils.createTmpDirectory("Configurations");
String downloadedFile = tmpDirectory + "config.zip";
boolean downloaded = DownloadUtils.downloadFile(configurationFilesLocation, downloadedFile);
System.out.println("downloadedFile=" + downloadedFile);
ISAcreator.DEFAULT_CONFIGURATIONS_DIRECTORY = tmpDirectory;
try {
String unzipped = GeneralUtils.unzip(downloadedFile);
System.out.println("Configurations downloaded and unzipped =" + unzipped);
f = new File(ISAcreator.DEFAULT_CONFIGURATIONS_DIRECTORY);
previousFiles = new ArrayList<File>(Arrays.asList(f.listFiles()));
} catch (IOException ex) {
ex.printStackTrace();
}
}
for (File prevSubmission : previousFiles) {
if (prevSubmission.isDirectory()) {
previousFilesExtendedJList.addItem(prevSubmission.getName());
}
}
for (File prevSubmission : previousNonLocalFiles) {
if (prevSubmission.isDirectory()) {
previousFilesExtendedJList.addItem(prevSubmission.getName());
previousFiles.add(prevSubmission);
}
}
return previousFiles;
}
public String getBorderTitle() {
return "selected configuration to load";
}
public ImageIcon getPanelHeaderImage() {
return panelHeader;
}
public void setListRenderer() {
previousFilesExtendedJList.setCellRenderer(new ImportFilesListCellRenderer(listImage));
}
@Override
public ImageIcon getLeftFilterImage() {
return filterLeft;
}
@Override
public ImageIcon getRightFilterImage() {
return filterRight;
}
}