HadoopDefaultVariantStatisticsManager.java

package org.opencb.opencga.storage.hadoop.variant.stats;

import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.opencga.storage.core.metadata.StudyConfiguration;
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
import org.opencb.opencga.storage.core.variant.io.db.VariantStatsDBWriter;
import org.opencb.opencga.storage.core.variant.stats.DefaultVariantStatisticsManager;
import org.opencb.opencga.storage.hadoop.variant.adaptors.VariantHadoopDBAdaptor;

import java.sql.SQLException;

/**
 * Created on 07/12/16.
 *
 * @author Jacobo Coll <jacobo167@gmail.com>
 */
public class HadoopDefaultVariantStatisticsManager extends DefaultVariantStatisticsManager {
    public HadoopDefaultVariantStatisticsManager(VariantDBAdaptor dbAdaptor) {
        super(dbAdaptor);
    }

    @Override
    protected VariantStatsDBWriter newVariantStatisticsDBWriter(VariantDBAdaptor dbAdaptor, StudyConfiguration studyConfiguration,
                                                                QueryOptions options) {
        if (!(dbAdaptor instanceof VariantHadoopDBAdaptor)) {
            throw new IllegalStateException("Expected " + VariantHadoopDBAdaptor.class + " dbAdaptor");
        }
        return new VariantStatsDBWriter(dbAdaptor, studyConfiguration, options) {
            @Override
            public boolean pre() {
                super.pre();
                try {
                    ((VariantHadoopDBAdaptor) dbAdaptor).updateStatsColumns(studyConfiguration);
                } catch (SQLException e) {
                    throw new RuntimeException(e);
                }
                return true;
            }

        };
    }


}