/* * 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; } }