/*
* #%L
* gitools-ui-app
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 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 Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.ui.app.actions.file;
import org.apache.commons.io.FilenameUtils;
import org.gitools.api.ApplicationContext;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.modulemap.IModuleMap;
import org.gitools.api.resource.IResourceFormat;
import org.gitools.api.resource.IResourceLocator;
import org.gitools.datasources.kegg.modules.EnsemblKeggModulesImporter;
import org.gitools.matrix.MatrixUtils;
import org.gitools.matrix.modulemap.format.GmtModuleMapFormat;
import org.gitools.matrix.modulemap.format.GmxModuleMapFormat;
import org.gitools.persistence.locators.UrlResourceLocator;
import org.gitools.ui.app.wizard.ModulesImportWizard;
import org.gitools.ui.core.Application;
import org.gitools.ui.core.actions.AbstractAction;
import org.gitools.ui.platform.progress.JobRunnable;
import org.gitools.ui.platform.progress.JobThread;
import org.gitools.ui.platform.wizard.WizardDialog;
import javax.swing.*;
import java.awt.event.ActionEvent;
import java.io.File;
import java.io.PrintWriter;
import java.util.HashMap;
import java.util.Map;
public abstract class AbstractImportModulesAction extends AbstractAction {
public AbstractImportModulesAction(String name) {
super(name);
setDefaultEnabled(true);
}
protected abstract EnsemblKeggModulesImporter getImporter();
protected abstract ModulesImportWizard getWizard(EnsemblKeggModulesImporter importer);
@Override
public void actionPerformed(ActionEvent e) {
final EnsemblKeggModulesImporter importer = getImporter();
final ModulesImportWizard wz = getWizard(importer);
WizardDialog dlg = new WizardDialog(Application.get(), wz);
dlg.open();
if (dlg.isCancelled()) {
return;
}
JobThread.execute(Application.get(), new JobRunnable() {
@Override
public void run(IProgressMonitor monitor) {
try {
Map<String, String> descriptions = new HashMap<>();
IModuleMap mmap = importer.importMap(monitor, descriptions);
if (!monitor.isCancelled()) {
String extension = wz.getSaveFilePage().getFormat().getExtension();
File file = wz.getSaveFilePage().getPathAsFile();
IResourceLocator resourceLocator = new UrlResourceLocator(file);
if (GmxModuleMapFormat.EXTENSION.equals(extension) || GmtModuleMapFormat.EXTENSION.equals(extension)) {
IMatrix mat = MatrixUtils.moduleMapToMatrix(mmap);
IResourceFormat format = ApplicationContext.getPersistenceManager().getFormat(extension, mat.getClass());
ApplicationContext.getPersistenceManager().store(resourceLocator, mat, format, monitor);
} else {
IResourceFormat format = ApplicationContext.getPersistenceManager().getFormat(extension, mmap.getClass());
ApplicationContext.getPersistenceManager().store(resourceLocator, mmap, format, monitor);
}
//TODO Use PersistenceManager
String prefix = FilenameUtils.getName(file.getName());
file = new File(file.getParentFile(), prefix + "_annotations.tsv");
monitor.begin("Saving module annotations ...", mmap.getModules().size());
PrintWriter pw = new PrintWriter(file);
pw.println("id\tname");
for (String module : mmap.getModules()) {
pw.print(module);
pw.print('\t');
pw.println(descriptions.get(module));
monitor.worked(1);
}
pw.close();
} else {
setStatus("Operation cancelled");
}
} catch (Throwable ex) {
monitor.exception(ex);
}
}
});
}
private void setStatus(final String msg) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
Application.get().showNotification(msg);
}
});
}
}