/*
* 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.io.IOException;
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.apache.commons.io.IOUtils;
import org.openide.util.lookup.ServiceProvider;
/**
* Checks the metadb for issues with attributes.
*
* This plugin also acts as a demo for reading external sql files
*
* @author dyuen
*/
@ServiceProvider(service = CheckDBPluginInterface.class)
public class AttributePlugin implements CheckDBPluginInterface {
@Override
public void check(SelectQueryRunner qRunner, SortedMap<Level, Set<String>> result) throws SQLException {
try {
String query = IOUtils.toString(AttributePlugin.class.getResourceAsStream("duplicate_attribute_keys.sql"));
List<Integer> executeQuery = qRunner.executeQuery(query, new ColumnListHandler<Integer>());
CheckDB.processOutput(result, Level.SEVERE, "Entities with duplicate attribute keys in non-sample tables: ", executeQuery);
query = IOUtils.toString(AttributePlugin.class.getResourceAsStream("duplicate_sample_attribute_keys.sql"));
executeQuery = qRunner.executeQuery(query, new ColumnListHandler<Integer>());
CheckDB.processOutput(result, Level.SEVERE, "Samples with duplicate attribute keys: ", executeQuery);
} catch (IOException ex) {
throw new RuntimeException(ex);
}
}
}