edu.harvard.i2b2.crc.dao.setfinder.PatientSetCollectionSpringDao.java Source code

Introduction

Here is the source code for edu.harvard.i2b2.crc.dao.setfinder.PatientSetCollectionSpringDao.java

Source

/*
 * Copyright (c) 2006-2007 Massachusetts General Hospital 
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the i2b2 Software License v1.0 
 * which accompanies this distribution. 
 * 
 * Contributors: 
 *     Rajesh Kuttan
 */
package edu.harvard.i2b2.crc.dao.setfinder;

import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.util.Arrays;

import javax.sql.DataSource;

import org.springframework.jdbc.core.BatchPreparedStatementSetter;
import org.springframework.jdbc.core.JdbcTemplate;

import edu.harvard.i2b2.common.exception.I2B2DAOException;
import edu.harvard.i2b2.crc.dao.CRCDAO;
import edu.harvard.i2b2.crc.dao.DAOFactoryHelper;
import edu.harvard.i2b2.crc.datavo.db.DataSourceLookup;
import edu.harvard.i2b2.crc.datavo.db.QtPatientSetCollection;
import edu.harvard.i2b2.crc.datavo.db.QtQueryResultInstance;

/**
 * Class to support batch inserts of patients to PatientSetCollection This class
 * uses single Session to persist all the patients to collection. To have
 * limited memory usage, it will flush and clear the session manually for every
 * 1000 inserts. $Id: PatientSetCollectionDao.java,v 1.4 2007/08/31 14:44:26
 * rk903 Exp $
 * 
 * @author rkuttan
 * @see QtPatientSetCollection
 */
public class PatientSetCollectionSpringDao extends CRCDAO implements IPatientSetCollectionDao {
    /** patient set collection index * */
    private int setIndex = 0, batchDataIndex = 0;
    private JdbcTemplate jdbcTemplate = null;
    private String insert_sql = "";

    QtPatientSetCollection[] patientSetColl = null;
    /** master table for patient set collection * */
    QtQueryResultInstance resultInstance = null;
    String resultInstanceId = null;
    private static final int INITIAL_ARRAY_SIZE = 1100;
    private DataSourceLookup dataSourceLookup = null;

    private SQLServerSequenceDAO sqlServerSequenceDao = null;

    /**
     * Construc with patientset id Initialize hibernate session and creates
     * Query reuslt instance class
     * 
     * @param patientSetId
     */
    public PatientSetCollectionSpringDao(DataSource dataSource, DataSourceLookup dataSourceLookup) {
        setDataSource(dataSource);
        setDbSchemaName(dataSourceLookup.getFullSchema());
        jdbcTemplate = new JdbcTemplate(dataSource);
        this.dataSourceLookup = dataSourceLookup;
        if (dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.ORACLE)) {
            insert_sql = "insert into " + getDbSchemaName()
                    + "qt_patient_set_collection(patient_set_coll_id,result_instance_id,set_index,patient_num) values ("
                    + getDbSchemaName() + "QT_SQ_QPR_PCID.nextval,?,?,?)";
        } else if (dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.SQLSERVER)
                || dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.POSTGRESQL)) {
            insert_sql = "insert into " + getDbSchemaName()
                    + "qt_patient_set_collection(result_instance_id,set_index,patient_num) values (?,?,?)";
        }
        sqlServerSequenceDao = new SQLServerSequenceDAO(dataSource, dataSourceLookup);
        resultInstance = new QtQueryResultInstance();
        patientSetColl = new QtPatientSetCollection[INITIAL_ARRAY_SIZE];

    }

    public void createPatientSetCollection(String resultInstanceId) {
        resultInstance = new QtQueryResultInstance();
        resultInstance.setResultInstanceId(resultInstanceId);

    }

    public String getResultInstanceId() {
        return resultInstance.getResultInstanceId();
    }

    /**
     * function to add patient to patient set without out creating new db
     * session
     * 
     * @param patientId
     */
    public void addPatient(long patientId) {
        setIndex++;

        QtPatientSetCollection collElement = new QtPatientSetCollection();
        int patientSetCollId = 0;
        collElement.setPatientId(patientId);
        collElement.setQtQueryResultInstance(resultInstance);
        collElement.setSetIndex(setIndex);
        patientSetColl[batchDataIndex++] = collElement;

        if ((setIndex % 1000) == 0) {
            InsertStatementSetter batchSetter = new InsertStatementSetter(patientSetColl, batchDataIndex);
            jdbcTemplate.batchUpdate(insert_sql, batchSetter);

            Arrays.fill(patientSetColl, null);
            batchDataIndex = 0;
        }
    }

    /**
     * Call this function at the end. i.e. after loading all patient with
     * addPatient function, finally call this function to clear session
     */
    public void flush() {
        InsertStatementSetter batchSetter = new InsertStatementSetter(patientSetColl, batchDataIndex);
        jdbcTemplate.batchUpdate(insert_sql, batchSetter);
        Arrays.fill(patientSetColl, null);
        batchDataIndex = 0;
        setIndex = 0;
    }

    class InsertStatementSetter implements BatchPreparedStatementSetter {

        private QtPatientSetCollection[] data;
        private int batchSize = 0;

        public InsertStatementSetter(QtPatientSetCollection[] data, int batchSize) {
            this.data = data;
            this.batchSize = batchSize;
        }

        public int getBatchSize() {
            return batchSize;
        }

        // this is called for each row
        public void setValues(PreparedStatement ps, int i) throws SQLException {

            //ps.setLong(1, data[i].getPatientSetCollId()); // set first value
            ps.setInt(1, Integer.parseInt(data[i].getQtQueryResultInstance().getResultInstanceId()));
            ps.setInt(2, data[i].getSetIndex());
            ps.setLong(3, data[i].getPatientId());

        }

    }

}