/*
 * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * Copyright [2016-2017] EMBL-European Bioinformatics Institute
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *      http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.ensembl.healthcheck.testcase.eg_core;

import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.Statement;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.util.DBUtils;

/**
 * @author mnuhn
 * 
 * <p>
 * 	Checks that the length given in seq_region is the length of the sequence
 * in the dna table.
 * </p>
 *
 */
public class SeqRegionLength extends AbstractEgCoreTestCase {
	
	private final String sql_find_wrong_lengths 
	
		= "select seq_region_id, name, length(sequence) as len, length "
		+ "from dna join seq_region using (seq_region_id) "
		+ "where length(sequence) != length"
	;

	private final String error_msg 
	
		= "Some seq region lengths do not match the actual length of the "
		+ "sequence stored in the dna table. The ones found by this test can "
		+ "be corrected like this:"
	;
	
	@Override
	protected boolean runTest(DatabaseRegistryEntry dbre) {

		Connection con = dbre.getConnection();
		
		int numRows = DBUtils.getRowCount(con, sql_find_wrong_lengths);
		
		boolean passed = numRows==0; 
		
		if (!passed) {

			ReportManager.problem(this, con, error_msg + "\n");
			
			try {
				Statement stmt = con.createStatement();
				ResultSet rs = stmt.executeQuery(sql_find_wrong_lengths);
				if (rs != null) {
					
					while (rs.next()) {
						
						ReportManager.problem(
							this, 
							con, 
							"update seq_region set length=" 
							+ rs.getInt("len") 
							+ " where seq_region_id=" 
							+ rs.getInt("seq_region_id")
							+ ";"
						);
					}
				}
				rs.close();
				stmt.close();
			} catch (Exception e) {
				e.printStackTrace();
			}
		}
		return passed;
	}

	/* (non-Javadoc)
	 * @see org.ensembl.healthcheck.testcase.eg_core.AbstractEgCoreTestCase#getEgDescription()
	 */
	@Override
	protected String getEgDescription() {
		return "Checks that the length given in seq_region is the length of the sequence in the dna table.";
	}
}