/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.dev.db;
import org.apache.log4j.Logger;
import org.broad.igv.track.AttributeManager;
import org.broad.igv.util.ResourceLocator;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
/**
* @author Jim Robinson
* @date 10/15/11
*/
public class SampleInfoSQLReader extends WholeTableDBReader<Void> {
private static Logger log = Logger.getLogger(SampleInfoSQLReader.class);
String sampleColumn; // = "SAMPLE_ID_ARRAY";
public SampleInfoSQLReader(DBProfile.DBTable table, String sampleColumn) {
super(table);
this.sampleColumn = sampleColumn;
}
public SampleInfoSQLReader(ResourceLocator locator, String tableName, String sampleColumn) {
super(locator, tableName, null);
this.sampleColumn = sampleColumn;
}
@Override
protected Void processResultSet(ResultSet rs) throws SQLException {
ResultSetMetaData metaData = rs.getMetaData();
int nCol = metaData.getColumnCount();
String[] columnNames = new String[nCol];
for (int i = 0; i < nCol; i++) {
columnNames[i] = metaData.getColumnName(i + 1);
}
while (rs.next()) {
String sample = rs.getString(sampleColumn);
for (String col : columnNames) {
if (col.equals(sampleColumn)) {
continue;
}
String value = rs.getString(col);
AttributeManager.getInstance().addAttribute(sample, col, value);
}
}
return null;
}
}