/*
* 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
* wga_coverage and goc_score thresholds are defined for all the mlss_ids
* that need them
*/
public class CheckOrthologQCThresholds extends SingleDatabaseTestCase {
public CheckOrthologQCThresholds() {
setDescription("Check that the wga_coverage and goc_score thresholds are defined where needed");
setTeamResponsible(Team.COMPARA);
}
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
boolean result = true;
result &= checkCountIsZero(con, "homology JOIN method_link_species_set_attr USING (method_link_species_set_id)", "goc_score IS NOT NULL AND goc_quality_threshold IS NULL");
result &= checkCountIsZero(con, "homology JOIN method_link_species_set_attr USING (method_link_species_set_id)", "wga_coverage IS NOT NULL AND wga_quality_threshold IS NULL");
return result;
}
} // CheckOrthologQCThresholds