/*
 * 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.compara;

import java.sql.Connection;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;

/**
 * An EnsEMBL Healthcheck test case that looks for broken foreign-key
 * relationships.
 */

public class CheckHomology extends SingleDatabaseTestCase {

	/**
	 * Create an CheckHomology that applies to a specific set of databases.
	 */
	public CheckHomology() {
		setDescription("Check for broken foreign-key relationships in ensembl_compara databases.");
		setTeamResponsible(Team.COMPARA);
	}

	/**
	 * Run the test.
	 * 
	 * @param dbre
	 *          The database to use.
	 * @return true if the test passed.
	 *  
	 */
	public boolean run(DatabaseRegistryEntry dbre) {

		boolean result = true;

		Connection con = dbre.getConnection();

		result &= checkForSingles(con, "homology_member", "homology_id");

		String sql_main = "SELECT hm1.gene_member_id gene_member_id1, hm2.gene_member_id gene_member_id2, COUNT(*) num, GROUP_CONCAT(h1.description order by h1.description) descs" +
			" FROM homology h1 CROSS JOIN homology_member hm1 USING (homology_id)" +
			" CROSS JOIN homology_member hm2 USING (homology_id)" +
			" WHERE hm1.gene_member_id < hm2.gene_member_id" +
			" GROUP BY hm1.gene_member_id, hm2.gene_member_id HAVING COUNT(*) > 1";
		String sql_count = sql_main;
		String sql_summary = "SELECT descs, num, count(*) FROM (" + sql_main + ") tt1 GROUP BY descs, num";
		int numRows = DBUtils.getRowCount(con, sql_count);
		if (numRows > 0) {
			ReportManager.problem(this, con, "FAILED homology contains redundant entries");
			ReportManager.problem(this, con, "FAILURE DETAILS: There are " + numRows + " redundant homology relationships in the DB");
			ReportManager.problem(this, con, "USEFUL SQL: " + sql_summary);
			result = false;
		}

		return result;

	}

} // CheckHomology