Made data source and Hibernate configurations populate from...

Made data source and Hibernate configurations populate from services.properties. Moved ORM configuration into DatabaseConfig and removed XML configuration file.

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"

src/main/java/org/nrg/xnat/configuration/DatabaseConfig.java

 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;
 }

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)})

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() {

src/main/webapp/WEB-INF/conf/orm-config.xml

-<?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>

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=