/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.ui.action;
//~--- non-JDK imports --------------------------------------------------------
import org.apache.log4j.Logger;
import org.broad.igv.PreferenceManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.ResourceLocator;
import javax.swing.*;
import java.awt.event.ActionEvent;
import java.util.Arrays;
/**
* @author jrobinso
*/
public class LoadFromDatabaseAction extends MenuAction {
static Logger log = Logger.getLogger(LoadFromDatabaseAction.class);
IGV mainFrame;
public LoadFromDatabaseAction(String label, int mnemonic, IGV mainFrame) {
super(label, null, mnemonic);
this.mainFrame = mainFrame;
setToolTipText(UIConstants.LOAD_SERVER_DATA_TOOLTIP);
}
@Override
public void actionPerformed(ActionEvent evt) {
SwingWorker worker = new SwingWorker() {
@Override
protected Object doInBackground() throws Exception {
String host = PreferenceManager.getInstance().get(PreferenceManager.DB_HOST);
if (host == null || host.trim().length() == 0) {
MessageUtils.showMessage("Please set database configuration in user preferences (View > Preferences)");
return null;
}
final PreferenceManager preferenceManager = PreferenceManager.getInstance();
String db = preferenceManager.get(PreferenceManager.DB_NAME);
String port = preferenceManager.get(PreferenceManager.DB_PORT);
String url = "jdbc:mysql://" + host;
if (!port.equals("-1")) {
url += ":" + port;
}
url += "/" + db;
String table2 = "SAMPLE_INFO";
ResourceLocator loc2 = new ResourceLocator(url, table2);
loc2.setDescription("SELECT * FROM " + table2);
//
String table1 = "CNV";
ResourceLocator loc1 = new ResourceLocator(url, table1);
// TODO -- get these mappings from a config table
String query = "SELECT Sample Sample, `Probe Median` Value, " +
"Chromosome chr, Start start, Stop end, " +
"CONCAT('<br>Event: ', Event,'<br>% CNV Overlap = ', `% of CNV Overlap`) description " +
" FROM CNV " +
" WHERE Event = 'CN Gain' OR Event = 'CN Loss' OR Event = 'High Copy Gain'";
// + "INNER JOIN SAMPLE_INFO ON SAMPLE_INFO.SAMPLE = CNV.SAMPLE " +
// "WHERE SAMPLE_INFO.SUBTYPE like 'Classical'";
// String query = "select * from cnv";
loc1.setDescription(query);
loc1.setType(".seg");
mainFrame.loadTracks(Arrays.asList(loc1, loc2));
return null;
}
@Override
protected void done() {
mainFrame.showLoadedTrackCount();
}
};
worker.execute();
}
}