/*
* 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;
/**
* An EnsEMBL Healthcheck test case that checks that
* method_link_species_set_id is the same across joinable genomic_align
* entries
*/
public class CheckMLSSIDConsistencyInGenomicAlign extends SingleDatabaseTestCase {
public CheckMLSSIDConsistencyInGenomicAlign() {
setDescription("Check the consistency of the genomic-alignment tables.");
setTeamResponsible(Team.COMPARA);
}
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
boolean result = true;
result &= checkCountIsZero(con, "genomic_align ga LEFT JOIN genomic_align_block gab USING (genomic_align_block_id)", "ga.method_link_species_set_id != gab.method_link_species_set_id");
return result;
}
} // CheckMLSSIDConsistencyInGenomicAlign