/*
* 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.Iterator;
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.PatientListTypeHandler;
import edu.harvard.i2b2.crc.dao.pdo.input.SQLServerFactRelatedQueryHandler;
import edu.harvard.i2b2.crc.dao.pdo.input.VisitListTypeHandler;
import edu.harvard.i2b2.crc.dao.pdo.output.VisitFactRelated;
import edu.harvard.i2b2.crc.datavo.db.DataSourceLookup;
import edu.harvard.i2b2.crc.datavo.pdo.EventSet;
import edu.harvard.i2b2.crc.datavo.pdo.EventType;
import edu.harvard.i2b2.crc.datavo.pdo.ParamType;
import edu.harvard.i2b2.crc.datavo.pdo.query.EventListType;
import edu.harvard.i2b2.crc.datavo.pdo.query.PatientListType;
/**
* Class to support event section of table pdo query $Id:
* TablePdoQueryVisitDao.java,v 1.11 2008/03/19 22:42:08 rk903 Exp $
*
* @author rkuttan
*/
public class TablePdoQueryVisitDao extends CRCDAO implements
ITablePdoQueryVisitDao {
private DataSourceLookup dataSourceLookup = null;
private String schemaName = null;
private List<ParamType> metaDataParamList = null;
public TablePdoQueryVisitDao(DataSourceLookup dataSourceLookup,
DataSource dataSource) {
this.dataSourceLookup = dataSourceLookup;
setDataSource(dataSource);
this.setDbSchemaName(dataSourceLookup.getFullSchema());
}
public void setMetaDataParamList(List<ParamType> metaDataParamList) {
this.metaDataParamList = metaDataParamList;
}
/**
* Function to return EventSet from visit information
*
* @param encounterNumList
* @param detailFlag
* @param blobFlag
* @param statusFlag
* @return EventSet
* @throws I2B2DAOException
*/
public EventSet getVisitsByEncounterNum(List<String> encounterNumList,
boolean detailFlag, boolean blobFlag, boolean statusFlag)
throws I2B2DAOException {
EventSet eventSet = new EventSet();
RPDRPdoFactory.EventBuilder eventBuilder = new RPDRPdoFactory.EventBuilder(
detailFlag, blobFlag, statusFlag);
System.out.println("input encounter list size "
+ encounterNumList.size());
Connection conn = null;
PreparedStatement query = null;
String tempTableName = "";
try {
conn = getDataSource().getConnection();
// create type StudentIdArrayType as varray(1000) of integer;
String selectClause = getSelectClause(detailFlag, blobFlag,
statusFlag);
String joinClause = getLookupJoinClause(detailFlag, blobFlag,
statusFlag);
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()
+ "visit_dimension visit \n"
+ joinClause
+ " WHERE visit.encounter_num IN (SELECT * FROM TABLE (cast (? as QT_PDO_QRY_STRING_ARRAY)))";
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,
encounterNumList.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 = getDbSchemaName()
+ SQLServerFactRelatedQueryHandler.TEMP_PDO_INPUTLIST_TABLE;
try {
tempStmt.executeUpdate("drop table " + tempTableName);
} catch (SQLException sqlex) {
;
}
uploadTempTable(tempStmt, tempTableName, encounterNumList);
String finalSql = "SELECT "
+ selectClause
+ " FROM "
+ getDbSchemaName()
+ "visit_dimension visit \n"
+ joinClause
+ " WHERE visit.encounter_num IN (select distinct CAST(coalesce(char_param1, '0') as integer) FROM "
+ tempTableName + " ) order by encounter_num,patient_num ";
log.debug("Executing [" + finalSql + "]");
query = conn.prepareStatement(finalSql);
}
long startTimeSql = System.currentTimeMillis();
ResultSet resultSet = query.executeQuery();
long endTimeSql = System.currentTimeMillis();
long totalTimeSql = endTimeSql - startTimeSql;
log.debug("********* Total time for visit sql ****"
+ totalTimeSql);
long startTime = System.currentTimeMillis();
while (resultSet.next()) {
EventType event = eventBuilder.buildEventSet(resultSet, "i2b2",this.metaDataParamList);
eventSet.getEvent().add(event);
}
long endTime = System.currentTimeMillis();
long totalTime = endTimeSql - startTimeSql;
log.debug("********* Total time for visit objects ****"
+ totalTime);
} 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 {
if (dataSourceLookup.getServerType().equalsIgnoreCase(
DAOFactoryHelper.SQLSERVER)) {
PdoTempTableUtil tempUtil = new PdoTempTableUtil();
tempUtil.deleteTempTableSqlServer(conn, tempTableName);
}
try {
JDBCUtil.closeJdbcResource(null, query, conn);
} catch (SQLException sqlEx) {
sqlEx.printStackTrace();
}
}
return eventSet;
}
/**
* Function to return EventSet from visit information
*
* @param visitListType
* @param detailFlag
* @param blobFlag
* @param statusFlag
* @return EventSet
* @throws I2B2DAOException
*/
public EventSet getVisitDimensionSetFromVisitList(
EventListType visitListType, boolean detailFlag, boolean blobFlag,
boolean statusFlag) throws I2B2DAOException {
VisitListTypeHandler visitListTypeHandler = new VisitListTypeHandler(
dataSourceLookup, visitListType);
String inSqlClause = visitListTypeHandler.generateWhereClauseSql();
String selectClause = getSelectClause(detailFlag, blobFlag, statusFlag);
String joinClause = getLookupJoinClause(detailFlag, blobFlag,
statusFlag);
String mainSqlString = " SELECT " + selectClause + " FROM "
+ getDbSchemaName() + "visit_dimension visit " + joinClause
+ " WHERE visit.encounter_num IN ( ";
mainSqlString += inSqlClause;
mainSqlString += " ) order by visit.encounter_num,visit.patient_num \n";
EventSet eventSet = new EventSet();
RPDRPdoFactory.EventBuilder eventBuilder = new RPDRPdoFactory.EventBuilder(
detailFlag, blobFlag, statusFlag);
Connection conn = null;
PreparedStatement preparedStmt = null;
try {
// execute fullsql
conn = getDataSource().getConnection();
log.debug("Executing sql[" + mainSqlString + "]");
if (visitListTypeHandler.isCollectionId()) {
String patientEncCollectionId = visitListTypeHandler
.getCollectionId();
preparedStmt = conn.prepareStatement(mainSqlString);
preparedStmt
.setInt(1, Integer.parseInt(patientEncCollectionId));
} else if (visitListTypeHandler.isEnumerationSet()) {
String serverType = dataSourceLookup.getServerType();
visitListTypeHandler.uploadEnumerationValueToTempTable(conn);
preparedStmt = conn.prepareStatement(mainSqlString);
} else {
preparedStmt = conn.prepareStatement(mainSqlString);
}
ResultSet resultSet = preparedStmt.executeQuery();
while (resultSet.next()) {
// VisitDimensionType visitDimensionType =
// getVisitDimensionType(resultSet);
EventType event = eventBuilder.buildEventSet(resultSet, "i2b2",this.metaDataParamList);
eventSet.getEvent().add(event);
}
} 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 {
if (dataSourceLookup.getServerType().equalsIgnoreCase(
DAOFactoryHelper.SQLSERVER)) {
try {
visitListTypeHandler.deleteTempTable(conn);
} catch (SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
try {
JDBCUtil.closeJdbcResource(null, preparedStmt, conn);
} catch (SQLException sqlEx) {
sqlEx.printStackTrace();
}
}
return eventSet;
}
/**
* Function to return EventSet for given patient set
*
* @param patientListType
* @param detailFlag
* @param blobFlag
* @param statusFlag
* @return
* @throws I2B2DAOException
*/
public EventSet getVisitDimensionSetFromPatientList(
PatientListType patientListType, boolean detailFlag,
boolean blobFlag, boolean statusFlag) throws I2B2DAOException {
String selectClause = getSelectClause(detailFlag, blobFlag, statusFlag);
String joinClause = getLookupJoinClause(detailFlag, blobFlag,
statusFlag);
String mainSqlString = " SELECT " + selectClause + " FROM "
+ getDbSchemaName() + "visit_dimension visit " + joinClause
+ " WHERE visit.patient_num IN ( ";
PatientListTypeHandler patientListTypeHandler = new PatientListTypeHandler(
dataSourceLookup, patientListType);
String inSqlClause = patientListTypeHandler.generateWhereClauseSql();
mainSqlString += inSqlClause;
mainSqlString += " ) order by visit.encounter_num,visit.patient_num \n";
log.debug("Visit dimension sql " + mainSqlString);
EventSet eventSet = new EventSet();
RPDRPdoFactory.EventBuilder eventBuilder = new RPDRPdoFactory.EventBuilder(
detailFlag, blobFlag, statusFlag);
Connection conn = null;
PreparedStatement preparedStmt = null;
try {
// execute fullsql
conn = getDataSource().getConnection();
log.debug("Executing sql[" + mainSqlString + "]");
if (patientListTypeHandler.isCollectionId()) {
preparedStmt = conn.prepareStatement(mainSqlString);
preparedStmt.setInt(1, Integer.parseInt(patientListTypeHandler
.getCollectionId()));
} else if (patientListTypeHandler.isEnumerationSet()) {
String serverType = dataSourceLookup.getServerType();
patientListTypeHandler.uploadEnumerationValueToTempTable(conn);
preparedStmt = conn.prepareStatement(mainSqlString);
} else if (patientListTypeHandler.isEntireSet()) {
// log.debug("No need to pass parameter to sql");
preparedStmt = conn.prepareStatement(mainSqlString);
}
ResultSet resultSet = preparedStmt.executeQuery();
while (resultSet.next()) {
EventType event = eventBuilder.buildEventSet(resultSet, "i2b2",this.metaDataParamList);
eventSet.getEvent().add(event);
}
} 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 {
if (patientListTypeHandler.isEnumerationSet()) {
try {
patientListTypeHandler.deleteTempTable(conn);
} catch (SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
try {
JDBCUtil.closeJdbcResource(null, preparedStmt, conn);
} catch (SQLException sqlEx) {
sqlEx.printStackTrace();
}
}
return eventSet;
}
private String buildCustomSelectClause(String prefix) {
String detailSelectClause = " ";
for (Iterator<ParamType> iterator = this.metaDataParamList.iterator();iterator.hasNext();) {
ParamType paramType = iterator.next();
detailSelectClause += prefix + "." + paramType.getColumn() + " " + prefix + "_" + paramType.getColumn();
if (iterator.hasNext()) {
detailSelectClause += " , ";
}
}
return detailSelectClause;
}
private String buildCustomLookupSelectClause() {
String detailSelectClause = " ";
for (Iterator<ParamType> iterator = this.metaDataParamList.iterator();iterator.hasNext();) {
ParamType paramType = iterator.next();
if (paramType.getType().equalsIgnoreCase("string")) {
detailSelectClause += " , " + paramType.getColumn() + "_lookup" + ".name_char" + " " + paramType.getColumn() + "_name";
}
}
return detailSelectClause;
}
private String getSelectClause(boolean detailFlag, boolean blobFlag,
boolean statusFlag) {
String selectClause = "";
selectClause = " visit.encounter_num visit_encounter_num, visit.patient_num visit_patient_num ";
if (detailFlag) {
selectClause += " ," + buildCustomSelectClause("visit");
selectClause += buildCustomLookupSelectClause() ;
selectClause += ", visit.start_date visit_start_date,visit.end_date visit_end_date ";
//selectClause += ", inout_lookup.name_char inout_name,location_lookup.name_char location_name, active_status_lookup.name_char active_status_name";
}
if (blobFlag) {
selectClause += ", visit.visit_blob visit_visit_blob ";
}
if (statusFlag) {
selectClause += " , visit.update_date visit_update_date, visit.download_date visit_download_date, visit.import_date visit_import_date, visit.sourcesystem_cd visit_sourcesystem_cd, visit.upload_id visit_upload_id ";
}
return selectClause;
}
private String getLookupJoinClause(boolean detailFlag, boolean blobFlag,
boolean statusFlag) {
String joinClause = " ";
if (detailFlag) {
for (Iterator<ParamType> iterator = this.metaDataParamList.iterator();iterator.hasNext();) {
ParamType paramType = iterator.next();
if (paramType.getType().equalsIgnoreCase("string")) {
String columnName = paramType.getColumn();
joinClause += " left JOIN "
+ this.getDbSchemaName()
+ "code_lookup " + columnName + "_lookup \n"
+ " ON (visit." + columnName + " = " + columnName + "_lookup.code_Cd AND upper(" + columnName +"_lookup.column_cd) = '" + columnName.toUpperCase() + "') \n";
}
}
}
return joinClause;
}
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();
}
public EventSet getVisitByFact(List<String> panelSqlList,
List<Integer> sqlParamCountList,
IInputOptionListHandler inputOptionListHandler, boolean detailFlag,
boolean blobFlag, boolean statusFlag) throws I2B2DAOException {
EventSet eventSet = new EventSet();
RPDRPdoFactory.EventBuilder eventBuilder = new RPDRPdoFactory.EventBuilder(
detailFlag, blobFlag, statusFlag);
VisitFactRelated eventFactRelated = new VisitFactRelated(
buildOutputOptionType(detailFlag, blobFlag, statusFlag));
String selectClause = getSelectClause(detailFlag, blobFlag, statusFlag);
String joinClause = getLookupJoinClause(detailFlag, blobFlag,
statusFlag);
String serverType = dataSourceLookup.getServerType();
String factTempTable = "";
Connection conn = null;
PreparedStatement query = null;
try {
conn = dataSource.getConnection();
if (serverType.equalsIgnoreCase(DAOFactoryHelper.ORACLE)) {
factTempTable = 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 = 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_encounter_num from ( "
+ panelSql + ") b";
log.debug("Executing SQL [ " + insertSql + "]");
sqlParamCount = sqlParamCountList.get(i++);
// conn.createStatement().executeUpdate(insertSql);
executeUpdateSql(insertSql, conn, sqlParamCount,
inputOptionListHandler);
}
String finalSql = "SELECT "
+ selectClause
+ " FROM "
+ getDbSchemaName()
+ "visit_dimension visit "
+ joinClause
+ " where encounter_num in (select distinct CAST(coalesce(char_param1, '0') as integer) from "
+ factTempTable + ") order by encounter_num";
log.debug("Executing SQL [" + finalSql + "]");
query = conn.prepareStatement(finalSql);
resultSet = query.executeQuery();
while (resultSet.next()) {
EventType event = eventBuilder.buildEventSet(resultSet, "i2b2",this.metaDataParamList);
eventSet.getEvent().add(event);
}
} 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 tempUtil = new PdoTempTableUtil();
tempUtil.clearTempTable(dataSourceLookup.getServerType(), 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 eventSet;
}
private void executeUpdateSql(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();
}
}