/*
* 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.generic;
import java.sql.Connection;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.Priority;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
/**
* Check for newlines & tabs in gene descriptions - causes problems for TSV dumping.
*/
public class DescriptionNewlines extends SingleDatabaseTestCase {
/**
* Creates a new instance of DescriptionNewlines.
*/
public DescriptionNewlines() {
setDescription("Check for newlines and tabs in gene descriptions.");
setPriority(Priority.AMBER);
setEffect("Will cause problems for TSV file dumping and importing");
setFix("Remove newlines and tabs; useful SQL for identifying affected genes:\nSELECT gene_id, stable_id, description FROM gene WHERE (LOCATE('\\n', description) > 0 or LOCATE('\\t', description) > 0);");
setTeamResponsible(Team.CORE);
}
/**
* Run the test.
*
* @param dbre
* The database to use.
* @return true if the test passed.
*
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
int rows = DBUtils.getRowCount(con, "SELECT COUNT(*) FROM gene WHERE (LOCATE('\n', description) > 0 OR LOCATE('\t', description) > 0)");
if (rows > 0) {
result = false;
ReportManager.problem(this, con, rows + " genes have newlines and/or tabs in their descriptions");
} else {
ReportManager.correct(this, con, "No genes have newlines or tabs in their descriptions");
}
return result;
} // run
// -------------------------------------------------------------------------
} // DescriptionNewlines