diff --git a/build.gradle b/build.gradle
index 63ac93f199ff13d7dc16e4fc00fa1279e9cf75b0..0d0a783917c38a4eed3eb0921b2142de2f4fd8ac 100644
--- a/build.gradle
+++ b/build.gradle
@@ -105,6 +105,8 @@ configurations {
all*.exclude group: 'avalon-logkit'
all*.exclude group: 'com.metaparadigm'
all*.exclude group: 'com.sun.mail'
+ all*.exclude group: 'commons-dbcp'
+ all*.exclude group: 'commons-pool'
all*.exclude group: 'excalibur-component'
all*.exclude group: 'excalibur-instrument'
all*.exclude group: 'excalibur-logger'
@@ -221,6 +223,7 @@ dependencies {
compile "org.json:json:20151123"
compile "xerces:xercesImpl:2.11.0"
+ compile "commons-beanutils:commons-beanutils:1.9.2"
compile "commons-codec:commons-codec:1.10"
compile "commons-collections:commons-collections:3.2.2"
compile "commons-configuration:commons-configuration:1.10"
@@ -228,7 +231,6 @@ dependencies {
compile "commons-discovery:commons-discovery:0.5"
compile "commons-fileupload:commons-fileupload:1.3.1"
compile "commons-net:commons-net:3.4"
- compile "commons-pool:commons-pool:1.6"
compile "org.apache.commons:commons-email:1.4"
compile "org.apache.commons:commons-math:2.2"
diff --git a/src/main/java/org/nrg/xnat/configuration/DatabaseConfig.java b/src/main/java/org/nrg/xnat/configuration/DatabaseConfig.java
index 6fe2217cba7ecb1777d277aadc1cc97c5a252d05..8fb7d5a1b0c11ff86d4be07dd694abba036c544b 100644
--- a/src/main/java/org/nrg/xnat/configuration/DatabaseConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/DatabaseConfig.java
@@ -1,40 +1,99 @@
package org.nrg.xnat.configuration;
-import org.apache.commons.dbcp.BasicDataSource;
-import org.springframework.beans.factory.annotation.Value;
+import org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory;
+import org.hibernate.cache.spi.RegionFactory;
+import org.hibernate.cfg.ImprovedNamingStrategy;
+import org.nrg.framework.exceptions.NrgServiceError;
+import org.nrg.framework.exceptions.NrgServiceException;
+import org.nrg.framework.orm.hibernate.AggregatedAnnotationSessionFactoryBean;
+import org.nrg.framework.orm.hibernate.PrefixedTableNamingStrategy;
+import org.nrg.framework.utilities.Beans;
+import org.springframework.beans.factory.config.PropertiesFactoryBean;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
+import org.springframework.core.env.Environment;
import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.datasource.SimpleDriverDataSource;
+import org.springframework.orm.hibernate4.HibernateTransactionManager;
+import org.springframework.orm.hibernate4.LocalSessionFactoryBean;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
+import javax.inject.Inject;
import javax.sql.DataSource;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+import java.util.Properties;
/**
* Sets up the database configuration for XNAT.
*/
@Configuration
+@EnableTransactionManagement(proxyTargetClass = true)
public class DatabaseConfig {
-
@Bean
- public DataSource dataSource() {
- final BasicDataSource dataSource = new BasicDataSource();
- dataSource.setDriverClassName(_driver);
- dataSource.setUrl(_url);
- dataSource.setUsername(_username);
- dataSource.setPassword(_password);
- return dataSource;
+ public DataSource dataSource() throws NrgServiceException {
+ final Properties properties = Beans.getNamespacedProperties(_environment, "datasource", true);
+ final String dataSourceClassName = properties.getProperty("class", SimpleDriverDataSource.class.getName());
+ try {
+ final Class<? extends DataSource> clazz = Class.forName(dataSourceClassName).asSubclass(DataSource.class);
+ if (properties.containsKey("driver")) {
+ final String driver = (String) properties.get("driver");
+ properties.put("driver", Class.forName(driver).newInstance());
+ }
+ return Beans.getInitializedBean(properties, clazz);
+ } catch (ClassNotFoundException e) {
+ throw new NrgServiceException(NrgServiceError.ConfigurationError, "Couldn't find the specified data-source class name: " + dataSourceClassName);
+ } catch (IllegalAccessException | InstantiationException | InvocationTargetException e) {
+ throw new NrgServiceException(NrgServiceError.ConfigurationError, "An error occurred trying to access a property in the specified data-source class: " + dataSourceClassName, e);
+ }
}
@Bean
- public JdbcTemplate jdbcTemplate() {
+ public JdbcTemplate jdbcTemplate() throws NrgServiceException {
return new JdbcTemplate(dataSource());
}
- @Value("${datasource.driver}")
- private String _driver;
- @Value("${datasource.url}")
- private String _url;
- @Value("${datasource.username}")
- private String _username;
- @Value("${datasource.password}")
- private String _password;
+ @Bean
+ public ImprovedNamingStrategy namingStrategy() {
+ return new PrefixedTableNamingStrategy("xhbm");
+ }
+
+ @Bean
+ public PropertiesFactoryBean hibernateProperties() {
+ final PropertiesFactoryBean bean = new PropertiesFactoryBean();
+ bean.setProperties(Beans.getNamespacedProperties(_environment, "hibernate", false));
+ return bean;
+ }
+
+ @Bean
+ public RegionFactory regionFactory() throws NrgServiceException {
+ try {
+ return new SingletonEhCacheRegionFactory(hibernateProperties().getObject());
+ } catch (IOException e) {
+ throw new NrgServiceException(NrgServiceError.Unknown, "An error occurred trying to retrieve the Hibernate properties", e);
+ }
+ }
+
+ @Bean
+ public LocalSessionFactoryBean sessionFactory() throws NrgServiceException {
+ try {
+ final AggregatedAnnotationSessionFactoryBean bean = new AggregatedAnnotationSessionFactoryBean();
+ bean.setDataSource(dataSource());
+ bean.setCacheRegionFactory(regionFactory());
+ bean.setHibernateProperties(hibernateProperties().getObject());
+ bean.setNamingStrategy(namingStrategy());
+ return bean;
+ } catch (IOException e) {
+ throw new NrgServiceException(NrgServiceError.Unknown, "An error occurred trying to retrieve the Hibernate properties", e);
+ }
+ }
+
+ @Bean
+ public PlatformTransactionManager transactionManager() throws NrgServiceException {
+ return new HibernateTransactionManager(sessionFactory().getObject());
+ }
+
+ @Inject
+ private Environment _environment;
}
diff --git a/src/main/java/org/nrg/xnat/configuration/PropertiesConfig.java b/src/main/java/org/nrg/xnat/configuration/PropertiesConfig.java
index 4e54061a2e675b1d62ac93541484d8a70b486c45..b2e133d440606f1ab92e082f5ad726d9841a9f9d 100644
--- a/src/main/java/org/nrg/xnat/configuration/PropertiesConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/PropertiesConfig.java
@@ -25,9 +25,6 @@ import java.util.List;
*/
@Configuration
@PropertySources({
- @PropertySource(value = "file:${HOME}/config/services.properties", ignoreResourceNotFound = true),
- @PropertySource(value = "file:${HOME}/xnat/config/services.properties", ignoreResourceNotFound = true),
- @PropertySource(value = "file:${XNAT_HOME}/config/services.properties", ignoreResourceNotFound = true),
@PropertySource(value = "file:${xnat.home}/config/services.properties", ignoreResourceNotFound = true),
@PropertySource(value = "file:${xnat.config.home}/services.properties", ignoreResourceNotFound = true),
@PropertySource(value = "file:${xnat.config}", ignoreResourceNotFound = true)})
diff --git a/src/main/java/org/nrg/xnat/initialization/RootConfig.java b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
index e00af60cadb2d0b2c1a06a006ed0eeae76ede0ec..6ae818e422bad777c60226fdf8bef428a53179b9 100644
--- a/src/main/java/org/nrg/xnat/initialization/RootConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
@@ -36,11 +36,11 @@ import java.util.List;
"org.nrg.prefs.repositories",
"org.nrg.prefs.services.impl.hibernate",
"org.nrg.dicomtools.filters"})
-@ImportResource({"WEB-INF/conf/xnat-security.xml", "WEB-INF/conf/orm-config.xml", "WEB-INF/conf/mq-context.xml"})
+@ImportResource({"WEB-INF/conf/xnat-security.xml", "WEB-INF/conf/mq-context.xml"})
public class RootConfig {
- public static final List<String> DEFAULT_ENTITY_PACKAGES = Arrays.asList("org.nrg.framework.datacache", "org.nrg.xft.entities", "org.nrg.xdat.entities",
- "org.nrg.xnat.entities", "org.nrg.prefs.entities", "org.nrg.config.entities");
+ private static final List<String> DEFAULT_ENTITY_PACKAGES = Arrays.asList("org.nrg.framework.datacache", "org.nrg.xft.entities", "org.nrg.xdat.entities",
+ "org.nrg.xnat.entities", "org.nrg.prefs.entities", "org.nrg.config.entities");
@Bean
public String siteId() {
diff --git a/src/main/webapp/WEB-INF/conf/orm-config.xml b/src/main/webapp/WEB-INF/conf/orm-config.xml
deleted file mode 100644
index 4bea2ff4e64029bfaef813aca208f481a8ff63af..0000000000000000000000000000000000000000
--- a/src/main/webapp/WEB-INF/conf/orm-config.xml
+++ /dev/null
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
- ~ D:/Development/XNAT/1.6/xnat_builder_1_6dev/plugin-resources/conf/orm-config.xml
- ~ XNAT http://www.xnat.org
- ~ Copyright (c) 2014, Washington University School of Medicine
- ~ All Rights Reserved
- ~
- ~ Released under the Simplified BSD.
- ~
- ~ Last modified 2/7/14 12:19 PM
- -->
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:p="http://www.springframework.org/schema/p"
- xmlns:tx="http://www.springframework.org/schema/tx"
- xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx.xsd">
-
- <!-- Used the prefixed table naming strategy, class FooBar gives you prefix_foo_bar instead of FooBar. -->
- <bean id="namingStrategy" class="org.nrg.framework.orm.hibernate.PrefixedTableNamingStrategy" p:prefix="xhbm" />
-
- <!-- Set up default hibernate properties. -->
- <bean id="hibernateProperties" class="org.springframework.beans.factory.config.PropertiesFactoryBean">
- <property name="properties">
- <props>
- <prop key="hibernate.dialect">org.hibernate.dialect.PostgreSQL9Dialect</prop>
- <prop key="hibernate.hbm2ddl.auto">update</prop>
- <prop key="hibernate.show_sql">false</prop>
- <prop key="hibernate.cache.use_second_level_cache">true</prop>
- <prop key="hibernate.cache.use_query_cache">true</prop>
- </props>
- </property>
- </bean>
-
- <bean id="regionFactory" class="org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory">
- <constructor-arg index="0" ref="hibernateProperties" />
- </bean>
-
- <bean id="sessionFactory" class="org.nrg.framework.orm.hibernate.AggregatedAnnotationSessionFactoryBean"
- p:cacheRegionFactory-ref="regionFactory" p:dataSource-ref="dataSource"
- p:hibernateProperties-ref="hibernateProperties" p:namingStrategy-ref="namingStrategy" />
-
- <bean id="transactionManager" class="org.springframework.orm.hibernate4.HibernateTransactionManager" p:sessionFactory-ref="sessionFactory" />
-
- <tx:annotation-driven proxy-target-class="true" transaction-manager="transactionManager"/>
-
-</beans>
diff --git a/src/main/webapp/WEB-INF/conf/services.properties b/src/main/webapp/WEB-INF/conf/services.properties
index 17081f1e259c05cd75b9755771a3583cc46d0e9d..de1d5c7fac4e77dbee428cf9994d40c80eea32e3 100644
--- a/src/main/webapp/WEB-INF/conf/services.properties
+++ b/src/main/webapp/WEB-INF/conf/services.properties
@@ -16,6 +16,12 @@ datasource.url=jdbc:postgresql://localhost/xnat
datasource.username=xnat
datasource.password=xnat
+hibernate.dialect=org.hibernate.dialect.PostgreSQL9Dialect
+hibernate.hbm2ddl.auto=update
+hibernate.show_sql=false
+hibernate.cache.use_second_level_cache=true
+hibernate.cache.use_query_cache=true
+
mailserver.host=mail.server
mailserver.port=25
mailserver.username=