CheckOrthologQCThresholds.java

/*
 * 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