/*
* 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.funcgen;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.Team;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashMap;
/**
* Check that every result_set has an associated BAM file entry stored in
* dbfile_registry table. Check that the file actually exists on the disk.
*
* @author ilavidas
*/
public class ResultSetHasBamFile extends DBFileRegistryHasFile {
public ResultSetHasBamFile() {
setTeamResponsible(Team.FUNCGEN);
setDescription("Check that every result_set has an associated BAM " +
"file entry stored in dbfile_registry table. Check that the " +
"file actually exists on the disk.");
}
@Override
protected FileType getFileType() {
return FileType.BAM;
}
@Override
protected TableName getTableName() {
return TableName.result_set;
}
@Override
HashMap<Integer, String> getTableIDs(DatabaseRegistryEntry dbre) {
HashMap<Integer, String> tableIDs = new HashMap<Integer, String>();
Connection con = dbre.getConnection();
try {
Statement stmt = con.createStatement();
ResultSet rs = stmt.executeQuery("SELECT result_set_id, name " +
"FROM" + " result_set");
while(rs!=null && rs.next()){
tableIDs.put(rs.getInt(1),rs.getString(2));
}
} catch (SQLException e) {
e.printStackTrace();
}
return tableIDs;
}
}