/*
* 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 to check for "threshold_on_ds" in the
* method_link_species_set_attr table
*/
public class MLSSTagThresholdDs extends SingleDatabaseTestCase {
public MLSSTagThresholdDs() {
setDescription("Tests that proper 'threshold_on_ds' entries are in method_link_species_set_attr.");
setTeamResponsible(Team.COMPARA);
}
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
if (!tableHasRows(con, "homology")) {
ReportManager.problem(this, con, "NO ENTRIES in homology or homology_member tables");
return false;
}
boolean result = true;
result &= checkCountIsNonZero(con, "method_link_species_set_attr", "threshold_on_ds IS NOT NULL");
result &= checkCountIsZero(con, "method_link_species_set_attr", "(threshold_on_ds IS NOT NULL) AND (threshold_on_ds NOT IN (1,2))");
return result;
}
}