/*
* 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_compara;
import java.util.List;
import org.apache.commons.lang.StringUtils;
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.AbstractTemplatedTestCase;
public class EGCheckEmptyLocators extends AbstractTemplatedTestCase {
public EGCheckEmptyLocators() {
setTeamResponsible(Team.ENSEMBL_GENOMES);
appliesToType(DatabaseType.COMPARA);
setDescription("Checks the consistency of GenomeDB locators");
}
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean pass = true;
String sql = "select name from genome_db where locator IS NOT NULL";
List<String> names = getTemplate(dbre).queryForDefaultObjectList(sql, String.class);
if(! names.isEmpty()) {
String joinedNames = StringUtils.join(names, ',');
int count = names.size();
String message = String.format("%d GenomeDB(s) [%s] did not have empty locators", count, joinedNames);
ReportManager.problem(this, dbre.getConnection(), message);
pass = false;
}
return pass;
}
}