/*
* 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.util.ResourceLocator;
import org.broad.igv.util.StringUtils;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.Map;
/**
* General class for reading from a SQL Database.
* Each instance is attached to a specific database, table, and
* configuration of columns.
*
* @author Jacob Silterra
* @date 2012/05/30
*/
public class DBReader {
private static Logger log = Logger.getLogger(DBReader.class);
protected ResourceLocator locator;
protected String baseQueryString;
private String tableName;
public static String buildBaseQueryString(String tableName, Map<Integer, String> columnLabelMap) {
String colListing = "*";
if (columnLabelMap != null) {
String[] colNames = new String[columnLabelMap.size()];
for (Map.Entry<Integer, String> entry : columnLabelMap.entrySet()) {
colNames[entry.getKey()] = entry.getValue();
}
colListing = StringUtils.join(colNames, ",");
}
return String.format("SELECT %s FROM %s", colListing, tableName);
}
public DBReader(DBProfile.DBTable table) {
this(table.getDbLocator(), table.getName(), table.getBaseQuery());
}
/**
* @param locator
* @param tableName
* @param baseQueryString Can be null, in which case all columns from {@code tableName} are selected
*/
public DBReader(ResourceLocator locator, String tableName, String baseQueryString) {
this.locator = locator;
assert tableName != null;
this.tableName = tableName;
this.baseQueryString = baseQueryString;
if (baseQueryString == null) {
this.baseQueryString = buildBaseQueryString(this.tableName, null);
}
}
protected ResultSet executeQuery(String queryString) {
try {
Connection conn = DBManager.getConnection(locator);
Statement st = conn.createStatement();
return st.executeQuery(queryString);
} catch (SQLException e) {
log.error("Database error", e);
throw new RuntimeException("Database error", e);
}
}
public String getTableName() {
return tableName;
}
}