/*
* 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.variation;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
/**
* An EnsEMBL Healthcheck test case that looks for variation feature entries
* with no alleles
*/
public class VariationFeatureAlleles extends SingleDatabaseTestCase {
/**
* Create an OrphanTestCase that applies to a specific set of databases.
*/
public VariationFeatureAlleles() {
addToGroup("variation-release");
setDescription("Check for variation features with no alleles.");
setTeamResponsible(Team.VARIATION);
}
/**
* Look for variation feature entries with no alleles
*
* @param dbre
* The database to use.
* @return true Ff all foreign key relationships are valid.
*/
public boolean run(DatabaseRegistryEntry dbre) {
return checkForOrphans(dbre.getConnection(), "variation_feature", "variation_id", "allele", "variation_id",
true);
}
}