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.util; import java.io.IOException; import java.sql.Connection; import java.sql.DriverManager; import java.sql.SQLException; import java.util.Properties; import javax.naming.InitialContext; import javax.naming.NamingException; import javax.sql.DataSource; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.quartz.Scheduler; import org.quartz.impl.SchedulerRepository; import org.springframework.beans.factory.BeanFactory; import org.springframework.beans.factory.config.PropertiesFactoryBean; import org.springframework.context.support.FileSystemXmlApplicationContext; import org.springframework.core.io.FileSystemResource; import edu.harvard.i2b2.common.exception.I2B2Exception; import edu.harvard.i2b2.common.util.ServiceLocator; import edu.harvard.i2b2.common.util.ServiceLocatorException; import edu.harvard.i2b2.crc.ejb.ProcessQueue; import edu.harvard.i2b2.crc.ejb.QueryManagerBeanUtil; import edu.harvard.i2b2.crc.ejb.analysis.AnalysisPluginInfoLocal; import edu.harvard.i2b2.crc.ejb.analysis.CronEjbLocal; import edu.harvard.i2b2.crc.ejb.analysis.StartAnalysisLocal; import edu.harvard.i2b2.crc.ejb.role.PriviledgeBean; import edu.harvard.i2b2.crc.ejb.role.PriviledgeLocal; import edu.harvard.i2b2.crc.quartz.QuartzFactory; /** * This is the CRC application's main utility class This utility class provides * support for fetching resources like datasouce, to read application * properties, to get ejb home,etc. $Id: QueryProcessorUtil.java,v 1.7 * 2007/04/25 15:05:11 rk903 Exp $ * * @author rkuttan */ public class QueryProcessorUtil { /** log **/ protected final static Log log = LogFactory.getLog(QueryProcessorUtil.class); /** property file name which holds application directory name **/ public static final String APPLICATION_DIRECTORY_PROPERTIES_FILENAME = "crc_application_directory.properties"; /** application directory property name **/ public static final String APPLICATIONDIR_PROPERTIES = "edu.harvard.i2b2.crc.applicationdir"; /** application property filename* */ public static final String APPLICATION_PROPERTIES_FILENAME = "crc.properties"; /** property name for query manager ejb present in app property file* */ private static final String EJB_LOCAL_JNDI_QUERYMANAGER_PROPERTIES = "queryprocessor.jndi.querymanagerlocal"; /** property name for query info ejb present in app property file* */ private static final String EJB_LOCAL_JNDI_QUERYINFO_PROPERTIES = "queryprocessor.jndi.queryinfolocal"; /** property name for query run ejb present in app property file* */ private static final String EJB_LOCAL_JNDI_QUERYRUN_PROPERTIES = "queryprocessor.jndi.queryrunlocal"; /** property name for query result ejb present in app property file* */ private static final String EJB_LOCAL_JNDI_QUERYRESULT_PROPERTIES = "queryprocessor.jndi.queryresultlocal"; /** property name for pdo query ejb present in app property file* */ private static final String EJB_LOCAL_JNDI_PDOQUERY_PROPERTIES = "queryprocessor.jndi.pdoquerylocal"; /** property name for datasource present in app property file* */ private static final String DATASOURCE_JNDI_PROPERTIES = "queryprocessor.jndi.datasource_name"; /** property name for database connection string in app property file* */ private static final String DATABASE_CONNECTION_STRING_PROPERTIES = "queryprocessor.database.connection_string"; /** property name for database user in app property file* */ private static final String DATABASE_CONNECTION_USER_PROPERTIES = "queryprocessor.database.user"; /** property name for database password in app property file* */ private static final String DATABASE_CONNECTION_PASSWORD_PROPERTIES = "queryprocessor.database.password"; /** property name for metadata schema name* */ private static final String METADATA_SCHEMA_NAME_PROPERTIES = "queryprocessor.db.metadataschema"; /** property name for metadata schema name* */ private static final String PMCELL_WS_URL_PROPERTIES = "queryprocessor.ws.pm.url"; /** property name for PM bypass flag **/ private static final String PMCELL_BYPASS_FLAG_PROPERTIES = "queryprocessor.ws.pm.bypass"; /** property name for PM bypass project role name* */ private static final String PMCELL_BYPASS_ROLE_PROPERTIES = "queryprocessor.ws.pm.bypass.role"; /** property name for pm bypass project name **/ private static final String PMCELL_BYPASS_PROJECT_PROPERTIES = "queryprocessor.ws.pm.bypass.project"; /** property name for metadata schema name* */ private static final String DS_LOOKUP_DATASOURCE_PROPERTIES = "queryprocessor.ds.lookup.datasource"; /** property name for metadata schema name* */ private static final String DS_LOOKUP_SCHEMANAME_PROPERTIES = "queryprocessor.ds.lookup.schemaname"; /** property name for metadata schema name* */ private static final String DS_LOOKUP_SERVERTYPE_PROPERTIES = "queryprocessor.ds.lookup.servertype"; /** property name for ontology url schema name **/ private static final String ONTOLOGYCELL_WS_URL_PROPERTIES = "queryprocessor.ws.ontology.url"; public static final String ONTOLOGYCELL_ROOT_WS_URL_PROPERTIES = "edu.harvard.i2b2.crc.delegate.ontology.url"; public static final String ONTOLOGYCELL_GETTERMINFO_URL_PROPERTIES = "edu.harvard.i2b2.crc.delegate.ontology.operation.getterminfo"; public static final String ONTOLOGYCELL_GETCHILDREN_URL_PROPERTIES = "edu.harvard.i2b2.crc.delegate.ontology.operation.getchildren"; public static final String ONTOLOGYCELL_GETMODIFIERINFO_URL_PROPERTIES = "edu.harvard.i2b2.crc.delegate.ontology.operation.getmodifierinfo"; public static final String SINGLEPANEL_SKIPTEMPTABLE_PROPERTIES = "edu.harvard.i2b2.crc.setfinderquery.singlepanel.skiptemptable"; public static final String SINGLEPANEL_SKIPTEMPTABLE_MAXCONCEPT_PROPERTIES = "edu.harvard.i2b2.crc.setfinderquery.skiptemptable.maxconcept"; /** spring bean name for datasource **/ private static final String DATASOURCE_BEAN_NAME = "dataSource"; public static final String DEFAULT_SETFINDER_RESULT_BEANNAME = "defaultSetfinderResultType"; public static final String PAGING_OBSERVATION_SIZE = "edu.harvard.i2b2.crc.pdo.paging.observation.size"; public static final String PAGING_MINPERCENT = "edu.harvard.i2b2.crc.pdo.paging.inputlist.minpercent"; public static final String PAGING_MINSIZE = "edu.harvard.i2b2.crc.pdo.paging.inputlist.minsize"; public static final String PAGING_METHOD = "edu.harvard.i2b2.crc.pdo.paging.method"; public static final String PAGING_ITERATION = "edu.harvard.i2b2.crc.pdo.paging.iteration"; /** class instance field* */ private static QueryProcessorUtil thisInstance = null; /** service locator field* */ private static ServiceLocator serviceLocator = null; /** field to store application properties * */ private static Properties appProperties = null; private static Properties loadProperties = null; /** field to store app datasource* */ private DataSource dataSource = null; /** single instance of spring bean factory* */ private BeanFactory beanFactory = null; private ProcessQueue pqMedium = new ProcessQueue(QueryManagerBeanUtil.MEDIUM_QUEUE); private ProcessQueue pqLarge = new ProcessQueue(QueryManagerBeanUtil.LARGE_QUEUE); /** * Private constructor to make the class singleton */ private QueryProcessorUtil() { log.debug("Starting queue"); //Start queues //TURN OFF QUEUE pqMedium.start(); pqLarge.start(); } static { try { Class.forName("oracle.jdbc.OracleDriver"); } catch (ClassNotFoundException e) { log.error(e); } } /** * Return this class instance * * @return QueryProcessorUtil */ public static QueryProcessorUtil getInstance() { if (thisInstance == null) { thisInstance = new QueryProcessorUtil(); serviceLocator = ServiceLocator.getInstance(); } // start cron job // startCronJob(); return thisInstance; } private static void startCronJob() { CronEjbLocal cronLocal; try { cronLocal = thisInstance.getCronLocal(); cronLocal.start(); } catch (I2B2Exception e) { e.printStackTrace(); } } public StartAnalysisLocal getStartAnalysisLocal() throws I2B2Exception { InitialContext ctx; try { ctx = new InitialContext(); return (StartAnalysisLocal) ctx.lookup("QP1/StartAnalysis/local"); } catch (NamingException e) { throw new I2B2Exception("Bean lookup error Analysis ", e); } } public AnalysisPluginInfoLocal getAnalysisPluginInfoLocal() throws I2B2Exception { InitialContext ctx; try { ctx = new InitialContext(); return (AnalysisPluginInfoLocal) ctx.lookup("QP1/AnalysisPluginInfo/local"); } catch (NamingException e) { throw new I2B2Exception("Bean lookup error Anaylysis Plugin", e); } } public CronEjbLocal getCronLocal() throws I2B2Exception { InitialContext ctx; try { ctx = new InitialContext(); return (CronEjbLocal) ctx.lookup("QP1/CronEjb/local"); } catch (NamingException e) { throw new I2B2Exception("Bean lookup error Cron ", e); } } public PriviledgeLocal getPriviledgeLocal() throws I2B2Exception { return new PriviledgeBean(); /* removed ejb InitialContext ctx; try { ctx = new InitialContext(); return (PriviledgeLocal) ctx.lookup("QP1/PriviledgeBean/local"); } catch (NamingException e) { throw new I2B2Exception("Bean lookup error Priviledge", e); } */ } public Scheduler getQuartzScheduler() throws I2B2Exception { return QuartzFactory.getInstance().getScheduler(); } /** * Function to create spring bean factory * * @return BeanFactory */ public BeanFactory getSpringBeanFactory() { if (beanFactory == null) { String appDir = null; try { // read application directory property file via classpath loadProperties = ServiceLocator.getProperties(APPLICATION_DIRECTORY_PROPERTIES_FILENAME); // read directory property appDir = loadProperties.getProperty(APPLICATIONDIR_PROPERTIES); } catch (I2B2Exception e) { log.error(APPLICATION_DIRECTORY_PROPERTIES_FILENAME + "could not be located from classpath "); } if (appDir != null) { FileSystemXmlApplicationContext ctx = new FileSystemXmlApplicationContext( "file:" + appDir + "/" + "CRCApplicationContext.xml"); beanFactory = ctx.getBeanFactory(); } else { FileSystemXmlApplicationContext ctx = new FileSystemXmlApplicationContext( "classpath:" + "CRCApplicationContext.xml"); beanFactory = ctx.getBeanFactory(); } } return beanFactory; } /** * Function returns database connection from app server * * @return * @throws I2B2Exception * @throws SQLException */ public Connection getConnection() throws I2B2Exception, SQLException { String dataSourceName = getPropertyValue(DATASOURCE_JNDI_PROPERTIES); dataSource = (DataSource) serviceLocator.getAppServerDataSource(dataSourceName); Connection conn = dataSource.getConnection(); return conn; } /** * Function returns database connection from app server * * @return * @throws I2B2Exception * @throws SQLException */ public Connection getManualConnection() throws I2B2Exception, SQLException { String dbConnectionString = getPropertyValue(DATABASE_CONNECTION_STRING_PROPERTIES); String dbUser = getPropertyValue(DATABASE_CONNECTION_USER_PROPERTIES); String dbPassword = getPropertyValue(DATABASE_CONNECTION_PASSWORD_PROPERTIES); return DriverManager.getConnection(dbConnectionString, dbUser, dbPassword); } /** * Function to return metadata schema name, which is specified in property * file * * @return String * @throws I2B2Exception */ public String getMetaDataSchemaName() throws I2B2Exception { return getPropertyValue(METADATA_SCHEMA_NAME_PROPERTIES); } /** * Get Project managment cell's service url * * @return * @throws I2B2Exception */ public String getProjectManagementCellUrl() throws I2B2Exception { return getPropertyValue(PMCELL_WS_URL_PROPERTIES); } /** * Get Project management bypass flag * * @return * @throws I2B2Exception */ public boolean getProjectManagementByPassFlag() throws I2B2Exception { String pmByPassFlag = getPropertyValue(PMCELL_BYPASS_FLAG_PROPERTIES); if (pmByPassFlag == null) { return false; } else if (pmByPassFlag.trim().equalsIgnoreCase("true")) { return true; } else { return false; } } public long getPagingObservationSize() throws I2B2Exception { String obsPageSizeStr = getPropertyValue(PAGING_OBSERVATION_SIZE); return Long.parseLong(obsPageSizeStr); } public int getPagingInputListMinPercent() throws I2B2Exception { String pagingMinPercent = getPropertyValue(PAGING_MINPERCENT); return Integer.parseInt(pagingMinPercent); } public int getPagingInputListMinSize() throws I2B2Exception { String pagingMinSize = getPropertyValue(PAGING_MINSIZE); return Integer.parseInt(pagingMinSize); } public String getPagingMethod() throws I2B2Exception { String pagingMethod = getPropertyValue(PAGING_METHOD); return pagingMethod; } public int getPagingIterationCount() throws I2B2Exception { String pagingIteration = getPropertyValue(PAGING_ITERATION); return Integer.parseInt(pagingIteration); } /** * Get Project management bypass project role * * @return * @throws I2B2Exception */ public String getProjectManagementByPassRole() throws I2B2Exception { return getPropertyValue(PMCELL_BYPASS_ROLE_PROPERTIES); } /** * Get Project management bypass project * * @return * @throws I2B2Exception */ public String getProjectManagementByPassProject() throws I2B2Exception { return getPropertyValue(PMCELL_BYPASS_PROJECT_PROPERTIES); } public String getCRCDBLookupDataSource() throws I2B2Exception { return getPropertyValue(DS_LOOKUP_DATASOURCE_PROPERTIES); } public String getCRCDBLookupServerType() throws I2B2Exception { return getPropertyValue(DS_LOOKUP_SERVERTYPE_PROPERTIES); } public String getCRCDBLookupSchemaName() throws I2B2Exception { return getPropertyValue(DS_LOOKUP_SCHEMANAME_PROPERTIES); } public String getOntologyUrl() throws I2B2Exception { return getPropertyValue(ONTOLOGYCELL_WS_URL_PROPERTIES); } /** * Return app server datasource * * @return datasource * @throws I2B2Exception * @throws SQLException */ public DataSource getDataSource(String dataSourceName) throws I2B2Exception { dataSource = (DataSource) serviceLocator.getAppServerDataSource(dataSourceName); // DataSource dataSource = (DataSource) getSpringBeanFactory().getBean( // dataSourceName); return dataSource; } public DataSource getSpringDataSource(String dataSourceName) throws I2B2Exception { return getDataSource(dataSourceName); } public String getCRCPropertyValue(String propertyName) throws I2B2Exception { return getPropertyValue(propertyName); } // --------------------- // private methods here // --------------------- /** * Load application property file into memory */ private String getPropertyValue(String propertyName) throws I2B2Exception { if (appProperties == null) { // read application directory property file loadProperties = ServiceLocator.getProperties(APPLICATION_DIRECTORY_PROPERTIES_FILENAME); // read application directory property String appDir = loadProperties.getProperty(APPLICATIONDIR_PROPERTIES); if (appDir == null) { throw new I2B2Exception("Could not find " + APPLICATIONDIR_PROPERTIES + "from " + APPLICATION_DIRECTORY_PROPERTIES_FILENAME); } String appPropertyFile = appDir + "/" + APPLICATION_PROPERTIES_FILENAME; try { FileSystemResource fileSystemResource = new FileSystemResource(appPropertyFile); PropertiesFactoryBean pfb = new PropertiesFactoryBean(); pfb.setLocation(fileSystemResource); pfb.afterPropertiesSet(); appProperties = (Properties) pfb.getObject(); } catch (IOException e) { throw new I2B2Exception("Application property file(" + appPropertyFile + ") missing entries or not loaded properly"); } if (appProperties == null) { throw new I2B2Exception("Application property file(" + appPropertyFile + ") missing entries or not loaded properly"); } } String propertyValue = appProperties.getProperty(propertyName); if ((propertyValue != null) && (propertyValue.trim().length() > 0)) { ; } else { throw new I2B2Exception("Application property file(" + APPLICATION_PROPERTIES_FILENAME + ") missing " + propertyName + " entry"); } return propertyValue; } }