/*
* 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;
/**
* Check for any coord_system.versions that are blank ('') - they should be NULL for various other things to work.
*/
public class BlankCoordSystemVersions extends SingleDatabaseTestCase {
/**
* Create a new BlankCoordSystem testcase.
*/
public BlankCoordSystemVersions() {
setDescription("Check for any coord_system.version that are blank ('') - they should be NULL.");
setTeamResponsible(Team.GENEBUILD);// this is now inaccurate for funcgen usecase
}
/**
* Data is only tested in core database, as the tables are in sync
*/
public void types() {
removeAppliesToType(DatabaseType.OTHERFEATURES);
removeAppliesToType(DatabaseType.ESTGENE);
removeAppliesToType(DatabaseType.RNASEQ);
removeAppliesToType(DatabaseType.CDNA);
}
/**
* 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();
int rows = DBUtils.getRowCount(con, "SELECT COUNT(*) FROM coord_system WHERE version = ''");
if (rows > 0) {
ReportManager.problem(this, con, rows + " rows in coord_system have a blank versions - should be set to null");
result = false;
} else {
ReportManager.correct(this, con, "No blank versions in coord_system");
}
return result;
} // run
} // BlankCoordSystemVersions