/*
* 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 java.util.Iterator;
import java.util.List;
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 columns of type ENUM that have blank values - probably means there was a problem importing them.
*/
public class BlankEnums extends SingleDatabaseTestCase {
/**
* Create a new BlankEnums testcase.
*/
public BlankEnums() {
setDescription("Check for columns of type ENUM that have blank values - probably means there was a problem importing them.");
setPriority(Priority.AMBER);
setEffect("Will have blank values where NULL or one of the enum values is expected.");
setFix("Re-import after identifying source of problem - possibly the word NULL in import files instead of \\N");
setTeamResponsible(Team.GENEBUILD);
}
/**
* 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();
String[] tables = DBUtils.getTableNames(con);
for (int i = 0; i < tables.length; i++) {
String table = tables[i];
List columnsAndTypes = DBUtils.getTableInfo(con, table, "enum");
Iterator it = columnsAndTypes.iterator();
while (it.hasNext()) {
String[] columnAndType = (String[]) it.next();
String column = columnAndType[0];
int rows = DBUtils.getRowCount(con, "SELECT COUNT(*) FROM " + table + " WHERE " + column + "=''");
if (rows > 0) {
ReportManager.problem(this, con, rows + " rows in " + table + "." + column + " are blank, should be NULL or one of the ENUM values");
result = false;
}
}
}
return result;
} // run
} // BlankEnums