/*
* Copyright (C) 2013 SeqWare
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sourceforge.seqware.pipeline.plugins.checkdb.plugins;
import java.sql.SQLException;
import java.util.List;
import java.util.Set;
import java.util.SortedMap;
import net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB;
import net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface;
import net.sourceforge.seqware.pipeline.plugins.checkdb.SelectQueryRunner;
import org.apache.commons.dbutils.handlers.ColumnListHandler;
import org.openide.util.lookup.ServiceProvider;
/**
* Checks the metadb for issues specifically with the sample hierarchy.
*
* @author dyuen
*/
@ServiceProvider(service = CheckDBPluginInterface.class)
public class SampleHierarchyPlugin implements CheckDBPluginInterface {
@Override
public void check(SelectQueryRunner qRunner, SortedMap<Level, Set<String>> result) throws SQLException {
String query = "WITH sample_parent_count AS (\n"
+ " select sample_id, count(parent_id) AS parent_count from sample_hierarchy GROUP BY sample_id\n" + ")\n"
+ "SELECT * from sample s \n" + "JOIN sample_parent_count spc ON s.sample_id=spc.sample_id \n" + "WHERE parent_count > 1;";
List<Integer> executeQuery = qRunner.executeQuery(query, new ColumnListHandler<Integer>());
CheckDB.processOutput(result, Level.SEVERE, "Samples with more than one parent: ", executeQuery);
}
}