/*
* 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.pdo;
import java.io.IOException;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.List;
import javax.sql.DataSource;
import oracle.sql.ArrayDescriptor;
//import org.jboss.resource.adapter.jdbc.WrappedConnection;
import edu.harvard.i2b2.common.exception.I2B2DAOException;
import edu.harvard.i2b2.common.util.db.JDBCUtil;
import edu.harvard.i2b2.crc.dao.CRCDAO;
import edu.harvard.i2b2.crc.dao.DAOFactoryHelper;
import edu.harvard.i2b2.crc.dao.pdo.input.FactRelatedQueryHandler;
import edu.harvard.i2b2.crc.dao.pdo.input.IInputOptionListHandler;
import edu.harvard.i2b2.crc.dao.pdo.input.SQLServerFactRelatedQueryHandler;
import edu.harvard.i2b2.crc.dao.pdo.output.ConceptFactRelated;
import edu.harvard.i2b2.crc.dao.pdo.output.ModifierFactRelated;
import edu.harvard.i2b2.crc.datavo.db.DataSourceLookup;
import edu.harvard.i2b2.crc.datavo.pdo.ConceptSet;
import edu.harvard.i2b2.crc.datavo.pdo.ConceptType;
import edu.harvard.i2b2.crc.datavo.pdo.ModifierSet;
import edu.harvard.i2b2.crc.datavo.pdo.ModifierType;
/**
* Class to support concept section of table pdo query $Id:
* TablePdoQueryConceptDao.java,v 1.13 2008/07/21 19:53:40 rk903 Exp $
*
* @author rkuttan
*/
public class TablePdoQueryModifierDao extends CRCDAO implements
ITablePdoQueryModifierDao {
private DataSourceLookup dataSourceLookup = null;
private String schemaName = null;
public TablePdoQueryModifierDao(DataSourceLookup dataSourceLookup,
DataSource dataSource) {
this.dataSourceLookup = dataSourceLookup;
this.setDbSchemaName(dataSourceLookup.getFullSchema());
setDataSource(dataSource);
}
public ModifierSet getModifierByFact(List<String> panelSqlList,
List<Integer> sqlParamCountList,
IInputOptionListHandler inputOptionListHandler, boolean detailFlag,
boolean blobFlag, boolean statusFlag) throws I2B2DAOException {
ModifierSet modifierSet = new ModifierSet();
RPDRPdoFactory.ModifierBuilder modifierBuilder = new RPDRPdoFactory.ModifierBuilder(
detailFlag, blobFlag, statusFlag);
ModifierFactRelated modifierFactRelated = new ModifierFactRelated(
buildOutputOptionType(detailFlag, blobFlag, statusFlag));
String selectClause = modifierFactRelated.getSelectClause();
String serverType = dataSourceLookup.getServerType();
String factTempTable = "";
Connection conn = null;
PreparedStatement query = null;
try {
conn = dataSource.getConnection();
if (serverType.equalsIgnoreCase(DAOFactoryHelper.ORACLE)) {
factTempTable = this.getDbSchemaName()
+ FactRelatedQueryHandler.TEMP_FACT_PARAM_TABLE;
} else if (serverType.equalsIgnoreCase(DAOFactoryHelper.SQLSERVER) ||
serverType.equalsIgnoreCase(DAOFactoryHelper.POSTGRESQL)) {
log.debug("creating temp table");
java.sql.Statement tempStmt = conn.createStatement();
factTempTable = this.getDbSchemaName()
+ SQLServerFactRelatedQueryHandler.TEMP_FACT_PARAM_TABLE;
try {
tempStmt.executeUpdate("drop table " + factTempTable);
} catch (SQLException sqlex) {
;
}
String createTempInputListTable = "create table "
+ factTempTable
+ " ( set_index int, char_param1 varchar(500) )";
tempStmt.executeUpdate(createTempInputListTable);
log.debug("created temp table" + factTempTable);
}
// if the inputlist is enumeration, then upload the enumerated input
// to temp table.
// the uploaded enumerated input will be used in the fact join.
if (inputOptionListHandler.isEnumerationSet()) {
inputOptionListHandler.uploadEnumerationValueToTempTable(conn);
}
String insertSql = "";
int i = 0;
int sqlParamCount = 0;
ResultSet resultSet = null;
for (String panelSql : panelSqlList) {
insertSql = " insert into "
+ factTempTable
+ "(char_param1) select distinct obs_modifier_cd from ( "
+ panelSql + ") b";
log.debug("Executing SQL [ " + insertSql + "]");
sqlParamCount = sqlParamCountList.get(i++);
// conn.createStatement().executeUpdate(insertSql);
executeTotalSql(insertSql, conn, sqlParamCount,
inputOptionListHandler);
}
String finalSql = "SELECT "
+ selectClause
+ " FROM "
+ getDbSchemaName()
+ "modifier_dimension modifier where modifier_cd in (select distinct char_param1 from "
+ factTempTable + ") order by modifier_path";
log.debug("Executing SQL [" + finalSql + "]");
query = conn.prepareStatement(finalSql);
resultSet = query.executeQuery();
while (resultSet.next()) {
ModifierType modifier = modifierBuilder.buildModifierSet(resultSet);
modifierSet.getModifier().add(modifier);
}
} catch (SQLException sqlEx) {
log.error("", sqlEx);
throw new I2B2DAOException("sql exception", sqlEx);
} catch (IOException ioEx) {
log.error("", ioEx);
throw new I2B2DAOException("IO exception", ioEx);
} finally {
PdoTempTableUtil tempTableUtil = new PdoTempTableUtil();
tempTableUtil.clearTempTable(serverType, conn, factTempTable);
if (inputOptionListHandler != null
&& inputOptionListHandler.isEnumerationSet()) {
try {
inputOptionListHandler.deleteTempTable(conn);
} catch (SQLException e) {
e.printStackTrace();
}
}
try {
JDBCUtil.closeJdbcResource(null, query, conn);
} catch (SQLException sqlEx) {
sqlEx.printStackTrace();
}
}
return modifierSet;
}
private void executeTotalSql(String totalSql, Connection conn,
int sqlParamCount, IInputOptionListHandler inputOptionListHandler)
throws SQLException {
PreparedStatement stmt = conn.prepareStatement(totalSql);
log.debug(totalSql + " [ " + sqlParamCount + " ]");
if (inputOptionListHandler.isCollectionId()) {
for (int i = 1; i <= sqlParamCount; i++) {
stmt.setInt(i, Integer.parseInt(inputOptionListHandler
.getCollectionId()));
}
}
stmt.executeUpdate();
}
/**
* Function returns concepts based on list of concept codes
*
* @param conceptCdList
* @param detailFlag
* @param blobFlag
* @param statusFlag
* @return ConceptSet
* @throws I2B2DAOException
*/
public ModifierSet getModifierByModifierCd(List<String> modifierCdList,
boolean detailFlag, boolean blobFlag, boolean statusFlag)
throws I2B2DAOException {
ModifierSet modifierSet = new ModifierSet();
RPDRPdoFactory.ModifierBuilder modifierBuilder = new RPDRPdoFactory.ModifierBuilder(
detailFlag, blobFlag, statusFlag);
log.debug("input concept cd list size " + modifierCdList.size());
Connection conn = null;
PreparedStatement query = null;
String tempTableName = "";
try {
conn = getDataSource().getConnection();
ModifierFactRelated modifierFactRelated = new ModifierFactRelated(
buildOutputOptionType(detailFlag, blobFlag, statusFlag));
String selectClause = modifierFactRelated.getSelectClause();
String serverType = dataSourceLookup.getServerType();
if (serverType.equalsIgnoreCase(DAOFactoryHelper.ORACLE)) {
oracle.jdbc.driver.OracleConnection conn1 = null;// (oracle.jdbc.driver.OracleConnection) ((WrappedConnection) conn)
// .getUnderlyingConnection();
String finalSql = "SELECT "
+ selectClause
+ " FROM "
+ getDbSchemaName()
+ "modifier_dimension modifier WHERE modifier.modifier_cd IN (SELECT * FROM TABLE (?))";
log.debug("Executing sql[" + finalSql + "]");
query = conn1.prepareStatement(finalSql);
ArrayDescriptor desc = ArrayDescriptor.createDescriptor(
"QT_PDO_QRY_STRING_ARRAY", conn1);
oracle.sql.ARRAY paramArray = new oracle.sql.ARRAY(desc, conn1,
modifierCdList.toArray(new String[] {}));
query.setArray(1, paramArray);
} else if (serverType.equalsIgnoreCase(DAOFactoryHelper.SQLSERVER) ||
serverType.equalsIgnoreCase(DAOFactoryHelper.POSTGRESQL)) {
log.debug("creating temp table");
java.sql.Statement tempStmt = conn.createStatement();
tempTableName = this.getDbSchemaName()
+ SQLServerFactRelatedQueryHandler.TEMP_PDO_INPUTLIST_TABLE;
try {
tempStmt.executeUpdate("drop table " + tempTableName);
} catch (SQLException sqlex) {
;
}
uploadTempTable(tempStmt, tempTableName, modifierCdList);
String finalSql = "SELECT "
+ selectClause
+ " FROM "
+ getDbSchemaName()
+ "modifier_dimension modifier WHERE modifier.modifier_cd IN (select distinct char_param1 FROM "
+ tempTableName + ") order by modifier_path";
log.debug("Executing [" + finalSql + "]");
query = conn.prepareStatement(finalSql);
}
ResultSet resultSet = query.executeQuery();
while (resultSet.next()) {
ModifierType modifier = modifierBuilder.buildModifierSet(resultSet);
modifierSet.getModifier().add(modifier);
}
} catch (SQLException sqlEx) {
log.error("", sqlEx);
throw new I2B2DAOException("sql exception", sqlEx);
} catch (IOException ioEx) {
log.error("", ioEx);
throw new I2B2DAOException("IO exception", ioEx);
} finally {
PdoTempTableUtil tempTableUtil = new PdoTempTableUtil();
tempTableUtil.deleteTempTableSqlServer(conn, tempTableName);
try {
JDBCUtil.closeJdbcResource(null, query, conn);
} catch (SQLException sqlEx) {
sqlEx.printStackTrace();
}
}
return modifierSet;
}
private void uploadTempTable(Statement tempStmt, String tempTableName,
List<String> patientNumList) throws SQLException {
String createTempInputListTable = "create table " + tempTableName
+ " ( char_param1 varchar(100) )";
tempStmt.executeUpdate(createTempInputListTable);
log.debug("created temp table" + tempTableName);
// load to temp table
// TempInputListInsert inputListInserter = new
// TempInputListInsert(dataSource,TEMP_PDO_INPUTLIST_TABLE);
// inputListInserter.setBatchSize(100);
int i = 0;
for (String singleValue : patientNumList) {
tempStmt.addBatch("insert into " + tempTableName + " values ('"
+ singleValue + "' )");
log.debug("adding batch" + singleValue);
i++;
if (i % 100 == 0) {
log.debug("batch insert");
tempStmt.executeBatch();
}
}
log.debug("batch insert1");
tempStmt.executeBatch();
}
}