/*
* 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.
*/
/**
* File: EgMetaTest.java
* Created by: dstaines
* Created on: May 26, 2009
* CVS: $$
*/
package org.ensembl.healthcheck.testcase.eg_core;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Map;
import java.util.Map.Entry;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.util.CollectionUtils;
import org.ensembl.healthcheck.util.MapRowMapper;
import org.ensembl.healthcheck.util.SqlTemplate;
/**
* Test to find duplicate taxids entries
*
* @author dstaines
*
*/
public class DuplicateTaxonomyIds extends AbstractEgCoreTestCase {
private final static String META_QUERY = "select meta_value,count(*) from meta where meta_key='species.taxonomy_id' group by meta_value having count(*)>1";
private final MapRowMapper<String, Integer> mapper = new MapRowMapper<String, Integer>() {
public void existingObject(Integer currentValue, ResultSet resultSet,
int position) throws SQLException {
throw new SQLException(
"Duplicate key found - aggregate expression not working");
}
public String getKey(ResultSet resultSet) throws SQLException {
return resultSet.getString(1);
}
public Map<String, Integer> getMap() {
return CollectionUtils.createHashMap();
}
public Integer mapRow(ResultSet resultSet, int position)
throws SQLException {
return resultSet.getInt(2);
}
};
public DuplicateTaxonomyIds() {
}
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
SqlTemplate template = getTemplate(dbre);
Map<String, Integer> map = template.queryForMap(META_QUERY, mapper);
for (Entry<String, Integer> e : map.entrySet()) {
if (e.getValue() > 1) {
ReportManager.problem(this, dbre.getConnection(),
"Duplicate taxonomy ID " + e.getKey() + " found for "
+ e.getValue() + " species");
passes = false;
}
}
return passes;
}
/* (non-Javadoc)
* @see org.ensembl.healthcheck.testcase.AbstractTemplatedTestCase#getEgDescription()
*/
@Override
protected String getEgDescription() {
return "Test to find duplicate taxids entries";
}
}