/*
* 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.generic;
import java.sql.Connection;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
/**
* Healthcheck for the dna table. Should be empty in an est database
*/
public class DNAEmpty extends SingleDatabaseTestCase {
/**
* Check the assembly_exception table.
*/
public DNAEmpty() {
setDescription("Check that dna table is empty");
setTeamResponsible(Team.GENEBUILD);
}
/**
* This applies to all core schema databases apart from 'core', 'presite' and 'sangervega'
*/
public void types() {
removeAppliesToType(DatabaseType.CORE);
removeAppliesToType(DatabaseType.PRE_SITE);
removeAppliesToType(DatabaseType.SANGER_VEGA);
}
/**
* Run the test.
*
* @param dbre
* The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
int rows = DBUtils.getRowCount(con, "SELECT COUNT(*) FROM dna");
if (rows > 0) {
result = false;
ReportManager.problem(this, con, "dna table contains " + rows + " rows - it should be empty unless it's a core database ");
} else {
ReportManager.correct(this, con, "dna table is empty");
}
return result;
}
} // DNAEmpty