Move to Spring 4 [WIP]

Include depreacted SimpleFormController from Spring 3.2.18 by extracting specific files with Maven depdendency plugin. Update xsi:schemaLocations mentions to 4.3. Update Hibernate to 4.3.11. Update DWR to 3.0.2.
PavlidisLab · Dec 4, 2022 · ac20945 · ac20945
1 parent 2bce979
commit ac20945
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Showing 26 changed files with 188 additions and 173 deletions.
diff --git a/gemma-cli/src/main/resources/ubic/gemma/cliContext-component-scan.xml b/gemma-cli/src/main/resources/ubic/gemma/cliContext-component-scan.xml
@@ -2,8 +2,8 @@
 <beans xmlns="http://www.springframework.org/schema/beans"
 	xmlns:context="http://www.springframework.org/schema/context"
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
-   http://www.springframework.org/schema/context  http://www.springframework.org/schema/context/spring-context-3.2.xsd">
+	xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.3.xsd
+   http://www.springframework.org/schema/context  http://www.springframework.org/schema/context/spring-context-4.3.xsd">
 
 	<!-- Standard CLI tools -->
 	<context:component-scan base-package="ubic.gemma.core.apps"

diff --git a/gemma-core/src/main/java/ubic/gemma/core/security/audit/AuditAdvice.java b/gemma-core/src/main/java/ubic/gemma/core/security/audit/AuditAdvice.java
@@ -25,7 +25,9 @@
 import org.aspectj.lang.annotation.Before;
 import org.hibernate.*;
 import org.hibernate.engine.spi.CascadeStyle;
+import org.hibernate.engine.spi.CascadeStyles;
 import org.hibernate.engine.spi.CascadingAction;
+import org.hibernate.engine.spi.CascadingActions;
 import org.hibernate.persister.entity.EntityPersister;
 import org.hibernate.type.Type;
 import org.slf4j.Logger;
@@ -75,7 +77,7 @@ private enum OperationType {
     /**
      * Perform the audit advice on when entities are created.
      * <p>
-     * This audit will cascade on {@link CascadeStyle#PERSIST}.
+     * This audit will cascade on {@link CascadeStyles#PERSIST}.
      *
      * @see Pointcuts#creator()
      * @see ubic.gemma.persistence.service.BaseDao#create(Object)
@@ -89,7 +91,7 @@ public void doCreateAdvice( JoinPoint pjp ) {
     /**
      * Perform auditing when entities are updated.
      * <p>
-     * This audit will cascade on {@link CascadeStyle#UPDATE}.
+     * This audit will cascade on {@link CascadeStyles#UPDATE}.
      *
      * @see Pointcuts#updater()
      * @see ubic.gemma.persistence.service.BaseDao#update(Object)
@@ -103,8 +105,8 @@ public void doUpdateAdvice( JoinPoint pjp ) {
     /**
      * Perform auditing when entities are saved.
      * <p>
-     * This audit will cascade on {@link CascadeStyle#PERSIST} if the audited entity is transient else
-     * {@link CascadeStyle#MERGE}.
+     * This audit will cascade on {@link CascadeStyles#PERSIST} if the audited entity is transient else
+     * {@link CascadeStyles#MERGE}.
      *
      * @see Pointcuts#saver()
      * @see ubic.gemma.persistence.service.BaseDao#save(Object)
@@ -118,7 +120,7 @@ public void doSaveAdvice( JoinPoint pjp ) {
     /**
      * Perform auditing when entities are deleted.
      * <p>
-     * This audit will cascade on {@link CascadeStyle#DELETE}.
+     * This audit will cascade on {@link CascadeStyles#DELETE}.
      *
      * @see Pointcuts#deleter()
      * @see ubic.gemma.persistence.service.BaseDao#remove(Object)
@@ -180,18 +182,18 @@ private void processAuditable( Signature method, OperationType operationType, Au
      */
     private void addCreateAuditEvent( Signature method, Auditable auditable, User user, Date date ) {
         addAuditEvent( method, auditable, AuditAction.CREATE, "", user, date );
-        cascadeAuditEvent( method, AuditAction.CREATE, auditable, user, date, CascadingAction.PERSIST );
+        cascadeAuditEvent( method, AuditAction.CREATE, auditable, user, date, CascadingActions.PERSIST );
     }
 
     private void addSaveAuditEvent( Signature method, Auditable auditable, User user, Date date ) {
         AuditAction auditAction;
         CascadingAction cascadingAction;
         if ( auditable.getId() != null ) {
             auditAction = AuditAction.UPDATE;
-            cascadingAction = CascadingAction.MERGE;
+            cascadingAction = CascadingActions.MERGE;
         } else {
             auditAction = AuditAction.CREATE;
-            cascadingAction = CascadingAction.PERSIST;
+            cascadingAction = CascadingActions.PERSIST;
         }
         addAuditEvent( method, auditable, auditAction, "", user, date );
         // we only propagate a CREATE event through cascade for entities that were created in the save
@@ -214,15 +216,15 @@ private void addUpdateAuditEvent( Signature method, Auditable auditable, User us
         addAuditEvent( method, auditable, AuditAction.UPDATE, "", user, date );
         // we only propagate a CREATE event through cascade for entities that were created in the update
         // Note: CREATE events are skipped if the audit trail already contains one
-        cascadeAuditEvent( method, AuditAction.CREATE, auditable, user, date, CascadingAction.SAVE_UPDATE );
+        cascadeAuditEvent( method, AuditAction.CREATE, auditable, user, date, CascadingActions.SAVE_UPDATE );
     }
 
     private void addDeleteAuditEvent( Signature method, Auditable auditable, User user, Date date ) {
         if ( auditable.getId() == null ) {
             throw new IllegalArgumentException( String.format( "Transient instance passed to delete auditing [%s on %s by %s]", method, auditable, user.getUserName() ) );
         }
         addAuditEvent( method, auditable, AuditAction.DELETE, "", user, date );
-        cascadeAuditEvent( method, AuditAction.DELETE, auditable, user, date, CascadingAction.DELETE );
+        cascadeAuditEvent( method, AuditAction.DELETE, auditable, user, date, CascadingActions.DELETE );
     }
 
     /**

diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/util/ObjectFilter.java b/gemma-core/src/main/java/ubic/gemma/persistence/util/ObjectFilter.java
@@ -62,7 +62,7 @@ public class ObjectFilter {
      */
     private static final ConfigurableConversionService conversionService = new GenericConversionService();
 
-    private static <T> void addConverter( Class<?> targetClass, Converter<String, T> converter ) {
+    private static <T> void addConverter( Class<T> targetClass, Converter<? super String, ? extends T> converter ) {
         conversionService.addConverter( String.class, targetClass, converter );
     }
 

diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-component-scan.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-component-scan.xml
@@ -2,8 +2,8 @@
 <beans xmlns="http://www.springframework.org/schema/beans"
        xmlns:context="http://www.springframework.org/schema/context"
        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
-   http://www.springframework.org/schema/context  http://www.springframework.org/schema/context/spring-context-3.2.xsd">
+       xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.3.xsd
+   http://www.springframework.org/schema/context  http://www.springframework.org/schema/context/spring-context-4.3.xsd">
 
     <!-- This defines which classes are picked up by annotation-scanning for beans (e.g. @Component or @Service or @Repository
         or @Controller). We exclude ubic.gemma.web here, it is brought in by gemma-servlet.xml. -->

diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-hibernate.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-hibernate.xml
@@ -3,9 +3,9 @@
 <beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
 	   xmlns:tx="http://www.springframework.org/schema/tx" xmlns:p="http://www.springframework.org/schema/p"
 	   xmlns="http://www.springframework.org/schema/beans"
-	   xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-3.2.xsd
-   http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-3.2.xsd
-   http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-3.2.xsd">
+	   xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.3.xsd
+   http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-4.3.xsd
+   http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-4.3.xsd">
 
 	<!-- Enable AspectJ autoproxy -->
 	<aop:aspectj-autoproxy/>

diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-search.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-search.xml
@@ -1,7 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.springframework.org/schema/beans"
-       xsi:schemaLocation="http://www.springframework.org/schema/beans
-   http://www.springframework.org/schema/beans/spring-beans-3.2.xsd">
+       xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.3.xsd">
     <!-- author: keshav -->
 
     <!-- See LuceneEnvironment for documentation of these parameters -->
@@ -31,7 +30,7 @@
         <property name="compass" ref="compassExpression"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -40,7 +39,7 @@
         <property name="compass" ref="compassGene"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -49,7 +48,7 @@
         <property name="compass" ref="compassArray"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -58,7 +57,7 @@
         <property name="compass" ref="compassBibliographic"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -67,7 +66,7 @@
         <property name="compass" ref="compassProbe"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -76,7 +75,7 @@
         <property name="compass" ref="compassBiosequence"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -85,7 +84,7 @@
         <property name="compass" ref="compassGeneSet"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -94,7 +93,7 @@
         <property name="compass" ref="compassExperimentSet"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>

diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-security.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-security.xml
@@ -7,13 +7,13 @@
        xmlns="http://www.springframework.org/schema/beans"
        xsi:schemaLocation="
             http://www.springframework.org/schema/beans
-            http://www.springframework.org/schema/beans/spring-beans-3.2.xsd
+            http://www.springframework.org/schema/beans/spring-beans-4.3.xsd
             http://www.springframework.org/schema/security
             http://www.springframework.org/schema/security/spring-security-3.2.xsd
             http://www.springframework.org/schema/util
-            http://www.springframework.org/schema/util/spring-util-3.2.xsd
+            http://www.springframework.org/schema/util/spring-util-4.3.xsd
             http://www.springframework.org/schema/aop
-            http://www.springframework.org/schema/aop/spring-aop-3.2.xsd">
+            http://www.springframework.org/schema/aop/spring-aop-4.3.xsd">
 
     <bean id="authenticationLoggerListener" class="org.springframework.security.authentication.event.LoggerListener"/>
 

diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml
@@ -3,7 +3,7 @@
 <beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xmlns="http://www.springframework.org/schema/beans"
        xsi:schemaLocation="http://www.springframework.org/schema/beans
-            http://www.springframework.org/schema/beans/spring-beans-3.2.xsd">
+            http://www.springframework.org/schema/beans/spring-beans-4.3.xsd">
 
     <!-- Local tasks executor -->
     <bean id="taskExecutor" class="org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor">
@@ -20,9 +20,7 @@
         are listed in a resource. If the resource is in your classpath, list in in 'locations'. Other config files can be added by
         defining PropertiesConfiguration instances -->
     <bean id="userPropertiesFileHandler" class="org.apache.commons.configuration2.io.FileHandler" init-method="load">
-        <constructor-arg index="0">
-            <ref local="userProperties"/>
-        </constructor-arg>
+        <constructor-arg index="0" ref="userProperties"/>
         <property name="fileName" value="Gemma.properties"/>
     </bean>
 
@@ -31,9 +29,7 @@
     <bean id="configurationPropertyConfigurer"
           class="ubic.gemma.persistence.util.CommonsConfigurationPropertyPlaceholderConfigurer"
           depends-on="userPropertiesFileHandler">
-        <property name="configuration">
-            <ref local="userProperties"/>
-        </property>
+        <property name="configuration" ref="userProperties"/>
         <property name="locations">
             <list>
                 <value>classpath:default.properties</value>

diff --git a/gemma-core/src/main/resources/ubic/gemma/dataSource.xml b/gemma-core/src/main/resources/ubic/gemma/dataSource.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.springframework.org/schema/beans"
        xsi:schemaLocation="http://www.springframework.org/schema/beans
-   http://www.springframework.org/schema/beans/spring-beans-3.2.xsd">
+   http://www.springframework.org/schema/beans/spring-beans-4.3.xsd">
 
     <!-- Database connection information -->
     <bean id="dataSource" class="org.apache.commons.dbcp2.BasicDataSource" destroy-method="close">

diff --git a/gemma-core/src/main/resources/ubic/gemma/testDataSource.xml b/gemma-core/src/main/resources/ubic/gemma/testDataSource.xml
@@ -4,7 +4,7 @@
 <beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xmlns="http://www.springframework.org/schema/beans"
        xsi:schemaLocation="http://www.springframework.org/schema/beans
-   http://www.springframework.org/schema/beans/spring-beans-3.2.xsd">
+   http://www.springframework.org/schema/beans/spring-beans-4.3.xsd">
 
     <bean id="dataSource" class="org.apache.commons.dbcp2.BasicDataSource" destroy-method="close">
         <property name="driverClassName" value="${gemma.testdb.driver}"/>

diff --git a/gemma-web/pom.xml b/gemma-web/pom.xml
@@ -102,6 +102,30 @@
 				<artifactId>maven-war-plugin</artifactId>
 				<version>3.3.2</version>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-dependency-plugin</artifactId>
+				<version>3.3.0</version>
+				<executions>
+					<execution>
+						<phase>generate-sources</phase>
+						<goals>
+							<goal>unpack</goal>
+						</goals>
+						<configuration>
+							<artifactItems>
+								<artifactItem>
+									<groupId>org.springframework</groupId>
+									<artifactId>spring-webmvc</artifactId>
+									<version>3.2.18.RELEASE</version>
+								</artifactItem>
+							</artifactItems>
+							<includes>org/springframework/web/servlet/mvc/AbstractFormController.class,org/springframework/web/servlet/mvc/BaseCommandController.class,org/springframework/web/servlet/mvc/SimpleFormController.class</includes>
+							<outputDirectory>${project.build.directory}/classes</outputDirectory>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 		</plugins>
 		<pluginManagement>
 			<plugins>
@@ -198,7 +222,7 @@
 		<dependency>
 			<groupId>org.springframework.ws</groupId>
 			<artifactId>spring-ws-core</artifactId>
-			<version>2.1.4.RELEASE</version>
+			<version>2.4.7.RELEASE</version>
 		</dependency>
 
 		<!-- Apache Commons -->
@@ -224,19 +248,19 @@
 		<dependency>
 			<groupId>org.quartz-scheduler</groupId>
 			<artifactId>quartz</artifactId>
-			<version>1.8.6</version>
+			<version>2.3.2</version>
 		</dependency>
 
 		<!-- RSS feeds (depends on spring-web version) -->
 		<dependency>
-			<groupId>rome</groupId>
+			<groupId>com.rometools</groupId>
 			<artifactId>rome</artifactId>
-			<version>1.0</version>
+			<version>1.18.0</version>
 		</dependency>
 		<dependency>
-			<groupId>rome</groupId>
+			<groupId>com.rometools</groupId>
 			<artifactId>rome-fetcher</artifactId>
-			<version>1.0</version>
+			<version>1.18.0</version>
 		</dependency>
 
 		<!-- JSON -->
@@ -250,7 +274,7 @@
 		<dependency>
 			<groupId>org.directwebremoting</groupId>
 			<artifactId>dwr</artifactId>
-			<version>2.0.11-RELEASE</version>
+			<version>3.0.2-RELEASE</version>
 		</dependency>
 
 		<!-- Templating -->

diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/common/rss/CustomRssViewer.java b/gemma-web/src/main/java/ubic/gemma/web/controller/common/rss/CustomRssViewer.java
@@ -18,9 +18,9 @@
  */
 package ubic.gemma.web.controller.common.rss;
 
-import com.sun.syndication.feed.rss.Channel;
-import com.sun.syndication.feed.rss.Content;
-import com.sun.syndication.feed.rss.Item;
+import com.rometools.rome.feed.rss.Channel;
+import com.rometools.rome.feed.rss.Content;
+import com.rometools.rome.feed.rss.Item;
 import org.apache.commons.lang3.time.DateUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;

diff --git a/gemma-web/src/main/java/ubic/gemma/web/feed/FeedReader.java b/gemma-web/src/main/java/ubic/gemma/web/feed/FeedReader.java
@@ -18,12 +18,12 @@
  */
 package ubic.gemma.web.feed;
 
-import com.sun.syndication.feed.synd.SyndEntry;
-import com.sun.syndication.feed.synd.SyndFeed;
-import com.sun.syndication.fetcher.FeedFetcher;
-import com.sun.syndication.fetcher.impl.FeedFetcherCache;
-import com.sun.syndication.fetcher.impl.HashMapFeedInfoCache;
-import com.sun.syndication.fetcher.impl.HttpURLFeedFetcher;
+import com.rometools.fetcher.FeedFetcher;
+import com.rometools.fetcher.impl.FeedFetcherCache;
+import com.rometools.fetcher.impl.HashMapFeedInfoCache;
+import com.rometools.fetcher.impl.HttpURLFeedFetcher;
+import com.rometools.rome.feed.synd.SyndEntry;
+import com.rometools.rome.feed.synd.SyndFeed;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.stereotype.Controller;