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MedCoUtil.java
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Wed, Sep 18, 00:18

MedCoUtil.java
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/*
* 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:
* Raj Kuttan
* Lori Phillips
*/
package ch.epfl.lca1.medco.util;
import java.io.IOException;
import java.io.StringWriter;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.List;
import java.util.ListIterator;
import java.util.Properties;
import javax.sql.DataSource;
import ch.epfl.lca1.medco.i2b2.MessagesUtil;
import org.springframework.beans.factory.config.PropertiesFactoryBean;
import org.springframework.core.io.FileSystemResource;
import ch.epfl.lca1.medco.util.exceptions.MedCoError;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.common.util.ServiceLocator;
import org.springframework.util.StopWatch;
// TODO: reorganize this file, split in 2 (have a config file)
/**
* This is the PM service's main utility class
* This utility class provides support for
* fetching resources like datasouce, to read application
* properties, to get ejb home,etc.
* $Id: PMUtil.java,v 1.3 2009/07/10 18:40:07 mem61 Exp $
* @author rkuttan
*/
//TODO: add exception config not valid TODO TODO
// TODO: reorganize!!!
//TODO: get rid of the application dir and use that:
/*
String fileName = System.getProperty("jboss.server.config.dir") + "/my.properties";
try(FileInputStream fis = new FileInputStream(fileName)) {
properties.load(fis);
}
*/
/**
* todo:
* required = true -> no default value
* required = false -> default value provided (have default vals as constant)
*/
//todo: split config / util, ocnfig used only at high level
public class MedCoUtil {
/**
* Names of general MedCo properties.
*/
public static final String MEDCO_APP_NAME_PROPERTIES = "medco.app.name",
MEDCO_APP_VERSION_PROPERTIES = "medco.app.version";
/**
* Names of properties related to the I2B2 communications.
*/
public static final String PMCELL_WS_URL_PROPERTIES = "medco.i2b2.pm.url",
ONTCELL_WS_URL_PROPERTIES = "medco.i2b2.ont.url",
CRCCELL_WS_URL_PROPERTIES = "medco.i2b2.crc.url",
FRCELL_WS_URL_PROPERTIES = "medco.i2b2.fr.url",
MEDCOCELL_WS_URL_PROPERTIES = "medco.i2b2.medco.url",
I2B2CELLS_WS_WAITTIME_PROPERTIES = "medco.i2b2.waittimems";
/**
* Names of properties related to the Unlynx communications.
*/
public static final String UNLYNX_BINARY_PATH_PROPERTIES = "medco.unlynx.binarypath",
UNLYNX_DEBUG_LEVEL_PROPERTIES = "medco.unlynx.debuglevel",
UNLYNX_GROUP_FILE_PATH_PROPERTIES = "medco.unlynx.groupfilepath",
UNLYNX_ENTRY_POINT_IDX_PROPERTIES = "medco.unlynx.entrypointidx",
UNLYNX_PROOFS_PROPERTIES = "medco.unlynx.proofs";
public static final String JBOSS_CONFIG_DIR_PROPERTIES = "jboss.server.config.dir";
/** application property filename**/
public static final String APPLICATION_PROPERTIES_FILENAME = "medco.properties";
/** todo:property name for datasource present in app property file**/
private static final String DATASOURCE_JNDI_PROPERTIES = "medco.jndi.datasource_name";
/** property name for metadata schema name**/
private static final String METADATA_SCHEMA_NAME_PROPERTIES = "medco.bootstrapdb.metadataschema";
/** class instance field**/
private static MedCoUtil thisInstance = null;
/** service locator field**/
private static ServiceLocator serviceLocator = null;
/** field to store application properties **/
private static Properties appProperties = null;
/** field to store app datasource**/
private DataSource dataSource = null;
/**
* Names of JAXB packages that will be loaded.
*/
private static final String[] JAXB_PACKAGES = new String[]{
"edu.harvard.i2b2.crc.datavo.i2b2message",
"edu.harvard.i2b2.crc.datavo.pdo",
"edu.harvard.i2b2.crc.datavo.pdo.query",
"edu.harvard.i2b2.crc.datavo.setfinder.query",
"edu.harvard.i2b2.crc.datavo.pm",
"edu.harvard.i2b2.crc.datavo.ontology",
"edu.harvard.i2b2.crc.datavo.i2b2result",
"edu.harvard.i2b2.crc.loader.datavo.fr",
"edu.harvard.i2b2.crc.loader.datavo.loader.query"
};
/**
* Private constructor to make the class singleton.
* @param requireSuccess if method should throw exception when configuration fails to be loaded (set false for testing environment)
*/
private MedCoUtil(boolean requireSuccess) {
this.initAppProperties(requireSuccess);
}
private static MessagesUtil jaxbUtil;
public static MessagesUtil getMsgUtil() {
if (jaxbUtil == null) {
jaxbUtil = new MessagesUtil(JAXB_PACKAGES);
}
return jaxbUtil;
}
/**
* Return this class instance
* @return OntologyUtil
*/
public static MedCoUtil getInstance() {
if (thisInstance == null) {
thisInstance = new MedCoUtil(true);
}
serviceLocator = ServiceLocator.getInstance();
return thisInstance;
}
public static MedCoUtil getTestInstance() {
if (thisInstance == null) {
thisInstance = new MedCoUtil(false);
}
serviceLocator = ServiceLocator.getInstance();
return thisInstance;
}
/**
* Return metadata schema name
* @return
* @throws I2B2Exception
*/
public String getMetaDataSchemaName() throws I2B2Exception {
return getPropertyValue(METADATA_SCHEMA_NAME_PROPERTIES, true).trim()+ ".";
}
/**
* Get Project managment cell's service url
*
* @return
* @throws I2B2Exception
*/
public String getProjectManagementCellUrl() {
return getPropertyValue(PMCELL_WS_URL_PROPERTIES, false);
}
public int getI2b2Waittimems() {
String timems = getPropertyValue(I2B2CELLS_WS_WAITTIME_PROPERTIES, true);
try {
int timemsLong = Integer.parseInt(timems);
if (timemsLong < 0) {
Logger.warn("Invalid wait time value, returning default");
return 180000;
} else {
return timemsLong;
}
} catch (NumberFormatException e) {
Logger.warn("Cannot parse int", e);
return 180000;
}
}
public String getOntologyCellUrl() {
return getPropertyValue(ONTCELL_WS_URL_PROPERTIES, true);
}
public String getMedCoCellUrl() {
return getPropertyValue(MEDCOCELL_WS_URL_PROPERTIES, true);
}
public String getDataRepositoryCellUrl() {
return getPropertyValue(CRCCELL_WS_URL_PROPERTIES, true);
}
public String getFileRepositoryCellUrl() {
return getPropertyValue(FRCELL_WS_URL_PROPERTIES, true);
}
public String getApplicationName() {
String prop = getPropertyValue(MEDCO_APP_NAME_PROPERTIES, false);
return prop == null ? "MedCo I2B2 cell" : prop;
}
public String getApplicationVersion() {
String prop = getPropertyValue(MEDCO_APP_VERSION_PROPERTIES, false);
return prop == null ? "0.01" : prop;
}
/**
* Get Project managment cell's service url
*
* @return
* @throws I2B2Exception
*/
public String getUnlynxBinPath() {
return getPropertyValue(UNLYNX_BINARY_PATH_PROPERTIES, true);
}
/**
* Ensures 0 <= debug level <= 5.
*
* @return the unlynx debug level
*/
public int getUnlynxDebugLevel() {
String lvl = getPropertyValue(UNLYNX_DEBUG_LEVEL_PROPERTIES, false);
try {
int lvlInt = Integer.parseInt(lvl);
if (lvlInt >= 0 && lvlInt <= 5) {
return lvlInt;
} else {
return 0;
}
} catch (NumberFormatException e) {
Logger.warn("Cannot parse int", e);
return 0;
}
}
public String getUnlynxGroupFilePath() {
return getPropertyValue(UNLYNX_GROUP_FILE_PATH_PROPERTIES, true);
}
public int getUnlynxEntryPointIdx() {
String idx = getPropertyValue(UNLYNX_ENTRY_POINT_IDX_PROPERTIES, true);
try {
int idxInt = Integer.parseInt(idx);
if (idxInt >= 0) {
return idxInt;
} else {
throw Logger.error(new MedCoError("Invalid entry point index in configuration"));
}
} catch (NumberFormatException e) {
throw Logger.error(new MedCoError("Invalid entry point index in configuration"));
}
}
/**
*
* @return true if proofs should be computed
*/
public int getUnlynxProofsFlag() {
String proofs = getPropertyValue(UNLYNX_PROOFS_PROPERTIES, false);
try {
int proofsBool = Integer.parseInt(proofs);
if (proofsBool >= 0 && proofsBool <= 1) {
return proofsBool;
} else {
return 0;
}
} catch (NumberFormatException e) {
Logger.warn("Cannot parse int: " + e.getMessage());
return 0;
}
}
/**
* Return app server datasource
* @return datasource
* @throws I2B2Exception
*/
public DataSource getDataSource(String dataSourceName) throws I2B2Exception {
if (dataSource == null) {
dataSource = serviceLocator.getAppServerDataSource(dataSourceName);
}
return dataSource;
}
/**
* Set the datasource, for tests purposes.
*/
public void setDataSource(DataSource ds) {
dataSource = ds;
}
//---------------------
// private methods here
//---------------------
/**
* Initialize the application properties.
*
* @throws MedCoError if they cannot be loaded (unrecoverable)
*/
private void initAppProperties(boolean requireSuccess) {
try {
// read application directory property
String appDir = System.getProperty(JBOSS_CONFIG_DIR_PROPERTIES) == null ?
"./etc/spring/medcoapp" :
System.getProperty(JBOSS_CONFIG_DIR_PROPERTIES) + "/medcoapp";
// prepare to read the properties
String appPropertyFile = appDir + "/" + APPLICATION_PROPERTIES_FILENAME;
FileSystemResource fileSystemResource = new FileSystemResource(appPropertyFile);
PropertiesFactoryBean pfb = new PropertiesFactoryBean();
pfb.setLocation(fileSystemResource);
// read and parse the properties
pfb.afterPropertiesSet();
appProperties = (Properties) pfb.getObject();
if (appProperties == null) {
throw new I2B2Exception("appProperties null at end of initialization");
}
} catch (I2B2Exception | IOException | NullPointerException e) {
if (requireSuccess) {
throw new MedCoError("Could not load application properties " + JBOSS_CONFIG_DIR_PROPERTIES +
" - " + APPLICATION_PROPERTIES_FILENAME, e);
} else {
Logger.warn(e);
appProperties = new Properties();
}
}
}
/**
* Returns a property from the properties file.
* If the property is required and is not found, throws error.
*
* @param propertyName the property name
* @param required flag to indicate if the property is required
* @return the value of the property or null if not found and not required
*
* @throws MedCoError if a required property if not found
*
*/
private String getPropertyValue(String propertyName, boolean required) {
String propertyValue = appProperties.getProperty(propertyName);
if (required && (propertyValue == null || propertyValue.trim().length() <= 0)) {
throw new MedCoError("Application property file (" + APPLICATION_PROPERTIES_FILENAME + ") missing " + propertyName + " required entry");
}
return propertyValue;
}
/**
* Sets via a method a property. Mainly used for testing purposes.
*
* @param propertyName name of the property (use the static fields name in this class)
* @param propertyValue value of the property
*/
public void setProperty(String propertyName, String propertyValue) {
appProperties.setProperty(propertyName, propertyValue);
}
}

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