/*
* #%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.gitools.api.analysis.IProgressMonitor;
import org.gitools.datasources.biomart.BiomartService;
import org.gitools.datasources.biomart.restful.model.Query;
import org.gitools.ui.app.datasources.biomart.wizard.BiomartModulesWizard;
import org.gitools.ui.app.datasources.biomart.wizard.BiomartTableWizard;
import org.gitools.ui.core.Application;
import org.gitools.ui.core.actions.AbstractAction;
import org.gitools.ui.platform.icons.IconNames;
import org.gitools.ui.platform.progress.JobRunnable;
import org.gitools.ui.platform.progress.JobThread;
import org.gitools.ui.platform.wizard.WizardDialog;
import java.awt.event.ActionEvent;
import java.io.File;
public class ImportBiomartTableAction extends AbstractAction {
private static final long serialVersionUID = 4381993756203388654L;
public ImportBiomartTableAction() {
super("Biomart table...");
setLargeIconFromResource(IconNames.biomart24);
setSmallIconFromResource(IconNames.biomart16);
setDefaultEnabled(true);
}
@Override
public void actionPerformed(ActionEvent e) {
final BiomartTableWizard wizard = new BiomartTableWizard();
WizardDialog wdlg = new WizardDialog(Application.get(), wizard);
wdlg.open();
if (wdlg.isCancelled()) {
return;
}
final File file = wizard.getSelectedFile();
JobThread.execute(Application.get(), new JobRunnable() {
@Override
public void run(IProgressMonitor monitor) {
monitor.begin("Downloading data...", 1);
Query query = wizard.getQuery();
String format = wizard.getFormat().getExtension();
format = (format.endsWith("gz") ? BiomartModulesWizard.FORMAT_COMPRESSED_GZ : BiomartModulesWizard.FORMAT_PLAIN);
BiomartService service = wizard.getService();
try {
service.queryTable(query, file, format, wizard.isSkipRowsWithEmptyValuesEnabled(), wizard.emptyValuesReplacement(), monitor);
} catch (Exception ex) {
monitor.exception(ex);
}
}
});
}
}