edu.harvard.i2b2.ontology.dao.SchemesDao.java Source code

Introduction

Here is the source code for edu.harvard.i2b2.ontology.dao.SchemesDao.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:
 *       Lori Phillips
 */
package edu.harvard.i2b2.ontology.dao;

import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.List;

import javax.sql.DataSource;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.dao.DataAccessException;
import org.springframework.jdbc.core.simple.ParameterizedRowMapper;
import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
import org.springframework.jdbc.core.support.JdbcDaoSupport;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.ontology.datavo.vdo.ConceptType;
import edu.harvard.i2b2.ontology.datavo.vdo.GetReturnType;
import edu.harvard.i2b2.ontology.util.OntologyUtil;
import edu.harvard.i2b2.ontology.ejb.DBInfoType;

public class SchemesDao extends JdbcDaoSupport {

    private static Log log = LogFactory.getLog(SchemesDao.class);
    final static String DEFAULT = " c_key, c_name ";

    private SimpleJdbcTemplate jt;

    private void setDataSource(String dataSource) {
        DataSource ds = null;
        try {
            ds = OntologyUtil.getInstance().getDataSource(dataSource);
        } catch (I2B2Exception e2) {
            log.error(e2.getMessage());
            ;
        }
        this.jt = new SimpleJdbcTemplate(ds);
    }

    private String getMetadataSchema() throws I2B2Exception {

        return OntologyUtil.getInstance().getMetaDataSchemaName();
    }

    public List findSchemes(final GetReturnType returnType, final DBInfoType dbInfo) throws DataAccessException {

        // find return parameters
        String parameters = DEFAULT;

        String metadataSchema = dbInfo.getDb_fullSchema();
        setDataSource(dbInfo.getDb_dataSource());

        String schemesSql = "select distinct " + parameters + " from " + metadataSchema + "schemes order by c_name";

        ParameterizedRowMapper<ConceptType> mapper = new ParameterizedRowMapper<ConceptType>() {
            public ConceptType mapRow(ResultSet rs, int rowNum) throws SQLException {
                ConceptType scheme = new ConceptType();

                //assume key is "" unless we explicitly determine otherwise
                // "" is valid
                scheme.setKey("");
                String c_key = rs.getString("c_key");
                if ((c_key != null) && (c_key.trim().length() > 0) && (!c_key.equals("(null)")))
                    scheme.setKey(c_key);
                scheme.setName(rs.getString("c_name"));
                return scheme;
            }
        };

        List queryResult = null;
        try {
            queryResult = jt.query(schemesSql, mapper);
        } catch (DataAccessException e) {
            log.error(e.getMessage());
            throw e;
        }
        log.debug("result size = " + queryResult.size());

        return queryResult;

    }

}