Java tutorial
/* * 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.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; //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; import edu.harvard.i2b2.crc.datavo.pdo.PatientDataType; /** * This class handles Concept dimension query's related to PDO request $Id: * PdoQueryConceptDao.java,v 1.11 2008/03/19 22:42:08 rk903 Exp $ * * @author rkuttan */ public class PdoQueryModifierDao extends CRCDAO implements IPdoQueryModifierDao { private DataSourceLookup dataSourceLookup = null; public PdoQueryModifierDao(DataSourceLookup dataSourceLookup, DataSource dataSource) { this.dataSourceLookup = dataSourceLookup; setDataSource(dataSource); setDbSchemaName(dataSourceLookup.getFullSchema()); } /** log * */ protected final Log log = LogFactory.getLog(getClass()); /** * Get concepts detail from concept code list * * @param conceptCdList * @param detailFlag * @param blobFlag * @param statusFlag * @return {@link PatientDataType.ConceptDimensionSet} * @throws I2B2DAOException */ public ModifierSet getModifierByModifierCd(List<String> modifierCdList, boolean detailFlag, boolean blobFlag, boolean statusFlag) throws I2B2DAOException { ModifierSet modifierDimensionSet = new ModifierSet(); log.debug("Size of input modifier cd list " + 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)) { // get oracle connection from jboss wrapped connection // Otherwise Jboss wrapped connection fails when using oracle // Arrays 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("Pdo modifier 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 = 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(); I2B2PdoFactory.ModifierBuilder modifierBuilder = new I2B2PdoFactory().new ModifierBuilder(detailFlag, blobFlag, statusFlag, dataSourceLookup.getServerType()); while (resultSet.next()) { ModifierType modifierDimensionType = modifierBuilder.buildModifierSet(resultSet); modifierDimensionSet.getModifier().add(modifierDimensionType); } } catch (SQLException sqlEx) { log.error("", sqlEx); throw new I2B2DAOException("", sqlEx); } catch (IOException ioEx) { log.error("", ioEx); throw new I2B2DAOException("", 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 modifierDimensionSet; } private void uploadTempTable(Statement tempStmt, String tempTable, List<String> patientNumList) throws SQLException { String createTempInputListTable = "create table " + tempTable + " ( char_param1 varchar(100) )"; tempStmt.executeUpdate(createTempInputListTable); log.debug("created temp table" + tempTable); PreparedStatement preparedStmt = tempStmt.getConnection() .prepareStatement("insert into " + tempTable + " values (?)"); // load to temp table // TempInputListInsert inputListInserter = new // TempInputListInsert(dataSource,TEMP_PDO_INPUTLIST_TABLE); // inputListInserter.setBatchSize(100); int i = 0; for (String singleValue : patientNumList) { preparedStmt.setString(1, singleValue); preparedStmt.addBatch(); log.debug("adding batch [" + i + "] " + singleValue); i++; if (i % 100 == 0) { log.debug("batch insert [" + i + "]"); preparedStmt.executeBatch(); } } log.debug("batch insert [" + i + "]"); preparedStmt.executeBatch(); } public ModifierSet getModifierByFact(List<String> panelSqlList, List<Integer> sqlParamCountList, IInputOptionListHandler inputOptionListHandler, boolean detailFlag, boolean blobFlag, boolean statusFlag) throws I2B2DAOException { ModifierSet modifierSet = new ModifierSet(); I2B2PdoFactory.ModifierBuilder modifierBuilder = new I2B2PdoFactory().new ModifierBuilder(detailFlag, blobFlag, statusFlag, dataSourceLookup.getServerType()); ModifierFactRelated modifierFactRelated = new ModifierFactRelated( buildOutputOptionType(detailFlag, blobFlag, statusFlag)); String selectClause = modifierFactRelated.getSelectClause(); String serverType = dataSourceLookup.getServerType(); String tempTable = ""; Connection conn = null; PreparedStatement query = null; try { conn = dataSource.getConnection(); if (serverType.equalsIgnoreCase(DAOFactoryHelper.ORACLE)) { tempTable = 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(); tempTable = SQLServerFactRelatedQueryHandler.TEMP_FACT_PARAM_TABLE; try { tempStmt.executeUpdate("drop table " + tempTable); } catch (SQLException sqlex) { ; } String createTempInputListTable = "create table " + tempTable + " ( set_index int, char_param1 varchar(500) )"; tempStmt.executeUpdate(createTempInputListTable); log.debug("created temp table" + tempTable); } // 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 " + tempTable + "(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 " + tempTable + ") order by modifier_path"; log.debug("Executing SQL [" + finalSql + "]"); System.out.println("Final 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 tempUtil = new PdoTempTableUtil(); tempUtil.clearTempTable(dataSourceLookup.getServerType(), conn, tempTable); 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); System.out.println(totalSql + " [ " + sqlParamCount + " ]"); if (inputOptionListHandler.isCollectionId()) { for (int i = 1; i <= sqlParamCount; i++) { stmt.setInt(i, Integer.parseInt(inputOptionListHandler.getCollectionId())); } } stmt.executeUpdate(); } }