/*
* 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 java.sql.Connection;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Species;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
/**
* Check for duplicate synonym names which may have different import sources despite having the same original source
*/
public class VariationSynonym extends SingleDatabaseTestCase {
/**
* Creates a new instance of Check Variation Synonym
*/
public VariationSynonym() {
addToGroup("variation-release");
setDescription("Check for duplicate variation synonyms");
setTeamResponsible(Team.VARIATION);
}
/**
* Run the test
*
* @param dbre
* The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
if (dbre.getSpecies() != Species.HOMO_SAPIENS) {
ReportManager.info(this, con, "This test is only for human at moment");
return true;
}
boolean result = true;
try {
int rows = DBUtils.getRowCount(con, "select vs1.variation_synonym_id, vs1.variation_id, vs1.name from variation_synonym vs1, variation_synonym vs2 where vs2.variation_id = vs1.variation_id and vs2.name = vs1.name and vs2.variation_synonym_id > vs1.variation_synonym_id and vs1.source_id = vs2.source_id");
if (rows > 0) {
result = false;
ReportManager.problem(this, con, rows + " duplicate variation_synonyms detected");
} else {
ReportManager.correct(this, con, "No duplicate variation_synonyms detected");
}
} catch (Exception e) {
ReportManager.problem(this, con, "HealthCheck generated an error: " + e.getMessage());
result = false;
}
return result;
} // run
} // VariationSynonym