/*
* 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 CheckSynteny extends SingleDatabaseTestCase {
/**
* Create an CheckSynteny that applies to a specific set of databases.
*/
public CheckSynteny() {
setDescription("Check for missing syntenies in the compara database.");
setTeamResponsible(Team.COMPARA);
}
/**
* Run the test.
*
* @param dbre
* The database to use.
* @return true if the test passed.
*
*/
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
if (!tableHasRows(con, "synteny_region")) {
ReportManager.problem(this, con, "NO ENTRIES in the synteny_region table");
return false;
} else if (!tableHasRows(con, "dnafrag_region")) {
ReportManager.problem(this, con, "NO ENTRIES in the dnafrag_region table");
return false;
} else if (!tableHasRows(con, "dnafrag")) {
ReportManager.problem(this, con, "NO ENTRIES in the dnafrag table");
return false;
} else {
boolean result = true;
result &= checkForSingles(con, "dnafrag_region", "synteny_region_id");
return result;
}
}
} // CheckHomology