/**
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.ErrorLevel;
import org.isatools.errorreporter.model.ErrorMessage;
import org.isatools.errorreporter.model.FileType;
import org.isatools.errorreporter.model.ISAFileErrorReport;
import org.isatools.isacreator.common.UIHelper;
import org.isatools.isacreator.common.button.ButtonType;
import org.isatools.isacreator.common.button.FlatButton;
import org.isatools.isacreator.gui.ISAcreator;
import org.isatools.isacreator.gui.io.importisa.ISAtabFilesImporterFromGUI;
import org.isatools.isacreator.io.importisa.ISAtabImporter;
import org.isatools.isacreator.managers.ApplicationManager;
import org.isatools.isacreator.settings.ISAcreatorProperties;
import org.jdesktop.fuse.InjectedResource;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.File;
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.
*
* @author Eamonn Maguire
* @date Mar 3, 2010
*/
public class ImportFilesMenu extends AbstractImportFilesMenu {
private static Logger log = Logger.getLogger(ImportFilesMenu.class);
@InjectedResource
private ImageIcon panelHeader, listImage, backButton, backButtonOver, filterLeft, filterRight;
private JButton back;
private JPanel loadingImagePanel;
public ImportFilesMenu(ISAcreatorMenu menu) {
super(menu, false);
previousNonLocalFiles = new ArrayList<File>();
}
public JPanel createAlternativeExitDisplay() {
JPanel previousButtonPanel = new JPanel(new GridLayout(1, 1));
previousButtonPanel.setOpaque(false);
back = new FlatButton(ButtonType.GREY, "Back", UIHelper.DARK_GREEN_COLOR);
back.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
if (problemScroll != null)
problemScroll.setVisible(false);
ApplicationManager.getCurrentApplicationInstance().setGlassPanelContents(menu.getMainMenuGUI());
}
});
previousButtonPanel.add(back);
return previousButtonPanel;
}
public void getSelectedFileAndLoad() {
if (previousFilesExtendedJList.getSelectedIndex() != -1) {
// select file from list
for (File candidate : previousFiles) {
if (candidate.getName()
.equals(previousFilesExtendedJList.getSelectedValue()
.toString())) {
getSelectedFileAndLoad(candidate, true);
}
}
}
}
public void getSelectedFileAndLoad(File candidate, boolean loadingImagePane) {
if (loadingImagePane) {
showLoadingImagePane();
}
ApplicationManager.setCurrentLocalISATABFolder(candidate.getAbsolutePath());
loadFile(candidate.getAbsolutePath());
}
public void showLoadingImagePane() {
// capture the current glass pane. This is required when an error occurs on loading and we need to show the error screen etc..
menu.captureCurrentGlassPaneContents();
// we hide the glass pane which is currently holding the menu items, loading interface etc.
menu.hideGlassPane();
// add the loading image panel to the view. No need to use the glass pane here.
menu.add(createLoadingImagePanel(), BorderLayout.CENTER);
}
private JPanel createLoadingImagePanel() {
if (loadingImagePanel == null) {
loadingImagePanel = new JPanel();
loadingImagePanel.setLayout(new BoxLayout(loadingImagePanel, BoxLayout.PAGE_AXIS));
loadingImagePanel.setPreferredSize(new Dimension(400, 400));
loadingImagePanel.setOpaque(false);
JPanel loadingImageContainer = UIHelper.wrapComponentInPanel(new JLabel(loadISAanimation));
loadingImageContainer.setSize(new Dimension(125, 256));
loadingImagePanel.add(loadingImageContainer);
JPanel infoContainer = UIHelper.wrapComponentInPanel(
UIHelper.createLabel("<html><p>In this version of the tool, we automatically upgrade elements annotated with ontology terms from using ontology accessions to using URIs. " +
"This is an artifact of the upgrades to BioPortal's new REST web services (version 4).</p> <p>Loading might take a little bit longer than normal during this upgrade for some ISA-TAB datasets.</p> </html>", UIHelper.VER_12_BOLD, UIHelper.ASPHALT));
infoContainer.setBorder(new EmptyBorder(0, 50, 50, 0));
loadingImagePanel.add(infoContainer);
}
return loadingImagePanel;
}
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() {
try {
final ISAtabImporter iISA = new ISAtabFilesImporterFromGUI(ApplicationManager.getCurrentApplicationInstance());
boolean successfulImport = iISA.importFile(dir);
if (successfulImport && iISA.getMessages().size() == 0) {
System.out.println("ISA-TAB dataset loaded");
// success, so load
ApplicationManager.getCurrentApplicationInstance().setCurrentPage(ApplicationManager.getCurrentApplicationInstance().getDataEntryEnvironment());
menu.resetViewAfterProgress();
ApplicationManager.setModified(false);
ISAcreatorProperties.setProperty(ISAcreatorProperties.CURRENT_ISATAB, new File(dir).getAbsolutePath());
if (!dir.contains(ISAcreator.DEFAULT_ISATAB_SAVE_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));
}
} else if (successfulImport) {
log.error("The following problems were encountered when importing the ISAtab files in " + dir);
for (ISAFileErrorReport report : iISA.getMessages()) {
if (report.getMessages().size() > 0) {
log.info("For " + report.getFileName());
for (ErrorMessage message : report.getMessages()) {
log.error("\t" + message.getMessage());
}
}
}
ISAcreatorProperties.setProperty(ISAcreatorProperties.CURRENT_ISATAB, new File(dir).getAbsolutePath());
SwingUtilities.invokeLater(new Runnable() {
public void run() {
createErrorView(iISA.getMessages(), true);
}
});
} else {
log.error("The following problems were encountered when importing the ISAtab files in " + dir);
for (ISAFileErrorReport report : iISA.getMessages()) {
if (report.getMessages().size() > 0) {
log.info("For " + report.getFileName());
for (ErrorMessage message : report.getMessages()) {
log.error("\t" + message.getMessage());
}
}
}
SwingUtilities.invokeLater(new Runnable() {
public void run() {
createErrorView(iISA.getMessages(), false);
}
});
}
} catch (OutOfMemoryError outOfMemory) {
System.gc();
menu.resetViewAfterProgress();
List<ErrorMessage> messages = new ArrayList<ErrorMessage>();
messages.add(new ErrorMessage(ErrorLevel.ERROR, "ISAcreator ran out of memory whilst loading. We have attempted to clear the memory now and you can try again." +
"Alternatively, if this fails you may want to increase the memory available to ISAcreator..."));
ISAFileErrorReport report = new ISAFileErrorReport("memory issue", FileType.INVESTIGATION, messages);
List<ISAFileErrorReport> reports = new ArrayList<ISAFileErrorReport>();
reports.add(report);
createErrorView(reports, false);
} catch (Exception e) {
menu.resetViewAfterProgress();
e.printStackTrace();
log.error(e.toString());
List<ErrorMessage> messages = new ArrayList<ErrorMessage>();
messages.add(new ErrorMessage(ErrorLevel.ERROR, "Unexpected problem occurred." + e.getMessage()));
ISAFileErrorReport report = new ISAFileErrorReport("Unexpected Problem", FileType.INVESTIGATION, messages);
List<ISAFileErrorReport> reports = new ArrayList<ISAFileErrorReport>();
reports.add(report);
createErrorView(reports, false);
} finally {
if (loadingImagePanel != null) {
menu.remove(loadingImagePanel);
}
menu.hideGlassPane();
}
}
});
performer.start();
}
public List<File> getPreviousFiles() {
previousFilesExtendedJList.clearItems();
File f = new File(ISAcreator.DEFAULT_ISATAB_SAVE_DIRECTORY);
if (!f.exists() || !f.isDirectory()) {
f.mkdir();
}
previousFiles = new ArrayList<File>(Arrays.asList(f.listFiles()));
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;
}
private void createErrorView(List<ISAFileErrorReport> errors, boolean showContinue) {
ErrorMenu errorMenu = new ErrorMenu(menu, errors, showContinue, this);
errorMenu.createGUI();
}
public String getBorderTitle() {
return "select ISA-TAB 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;
}
}