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 DWR to 3.0.2. Update Jersey to 2.27.
PavlidisLab · Dec 26, 2022 · 0a59b75 · 0a59b75
1 parent 7011459
commit 0a59b75
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Showing 20 changed files with 132 additions and 128 deletions.
diff --git a/gemma-core/pom.xml b/gemma-core/pom.xml
@@ -112,8 +112,8 @@
                 <version>1.5</version>
                 <dependencies><!-- yes, this needs to be here. -->
                     <dependency>
-                        <groupId>mysql</groupId>
-                        <artifactId>mysql-connector-java</artifactId>
+                        <groupId>com.mysql</groupId>
+                        <artifactId>mysql-connector-j</artifactId>
                         <version>${mysql.version}</version>
                         <scope>runtime</scope>
                     </dependency>

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
@@ -26,6 +26,7 @@
 import org.hibernate.*;
 import org.hibernate.engine.spi.CascadeStyle;
 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;
@@ -180,18 +181,18 @@ 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 +215,15 @@ 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/Filter.java b/gemma-core/src/main/java/ubic/gemma/persistence/util/Filter.java
@@ -59,7 +59,7 @@ public class Filter {
      */
     private static final ConfigurableConversionService conversionService = new GenericConversionService();
 
-    private static <T> void addConverter( Class<?> targetClass, Converter<String, T> converter, Converter<T, String> reverseConverter ) {
+    private static <T> void addConverter( Class<T> targetClass, Converter<String, T> converter, Converter<T, String> reverseConverter ) {
         conversionService.addConverter( String.class, targetClass, converter );
         conversionService.addConverter( targetClass, String.class, reverseConverter );
     }

diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-search.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-search.xml
@@ -31,7 +31,7 @@
         <property name="compass" ref="compassExpression"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -40,7 +40,7 @@
         <property name="compass" ref="compassGene"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -49,7 +49,7 @@
         <property name="compass" ref="compassArray"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -58,7 +58,7 @@
         <property name="compass" ref="compassBibliographic"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -67,7 +67,7 @@
         <property name="compass" ref="compassProbe"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -76,7 +76,7 @@
         <property name="compass" ref="compassBiosequence"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -85,7 +85,7 @@
         <property name="compass" ref="compassGeneSet"/>
         <property name="gpsDevices">
             <list>
-                <ref local="hibernateGpsDevice"/>
+                <ref bean="hibernateGpsDevice"/>
             </list>
         </property>
     </bean>
@@ -94,7 +94,7 @@
         <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-serviceBeans.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml
@@ -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/test/resources/test.spring.config.xml b/gemma-core/src/test/resources/test.spring.config.xml
@@ -5,9 +5,7 @@
 
     <bean id="configurationPropertyConfigurer"
           class="ubic.gemma.persistence.util.CommonsConfigurationPropertyPlaceholderConfigurer">
-        <property name="configuration">
-            <ref local="buildProperties"/>
-        </property>
+        <property name="configuration" ref="buildProperties"/>
         <property name="locations">
             <list>
                 <value>classpath:default.properties</value>
@@ -18,9 +16,7 @@
     </bean>
 
     <bean id="buildPropertiesFileHandler" class="org.apache.commons.configuration2.io.FileHandler" init-method="load">
-        <constructor-arg index="0">
-            <ref local="buildProperties"/>
-        </constructor-arg>
+        <constructor-arg index="0" ref="buildProperties"/>
         <property name="fileName" value="default.properties"/>
     </bean>
 

diff --git a/gemma-web/.gitignore b/gemma-web/.gitignore
@@ -1 +1,2 @@
 /bin
+/src/main/java/org
diff --git a/gemma-web/pom.xml b/gemma-web/pom.xml
@@ -102,6 +102,31 @@
 				<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>
+									<classifier>sources</classifier>
+								</artifactItem>
+							</artifactItems>
+							<includes>org/springframework/web/servlet/mvc/AbstractFormController.java,org/springframework/web/servlet/mvc/BaseCommandController.java,org/springframework/web/servlet/mvc/SimpleFormController.java</includes>
+							<outputDirectory>${project.build.sourceDirectory}</outputDirectory>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 		</plugins>
 		<pluginManagement>
 			<plugins>
@@ -187,18 +212,18 @@
 		</dependency>
 
 		<!-- Spring extra modules -->
-		<!-- latest for Spring 3 -->
+		<!-- latest for Spring 4 -->
 		<dependency>
 			<groupId>org.springframework.social</groupId>
 			<artifactId>spring-social-core</artifactId>
-			<version>1.0.3.RELEASE</version>
+			<version>1.1.6.RELEASE</version>
 			<scope>runtime</scope>
 		</dependency>
-		<!-- latest for Spring 3 -->
+		<!-- latest for Spring 4 -->
 		<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 +249,19 @@
 		<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 +275,7 @@
 		<dependency>
 			<groupId>org.directwebremoting</groupId>
 			<artifactId>dwr</artifactId>
-			<version>2.0.11-RELEASE</version>
+			<version>3.0.2-RELEASE</version>
 		</dependency>
 
 		<!-- Templating -->
@@ -274,7 +299,7 @@
 			<scope>runtime</scope>
 		</dependency>
 
-		<!-- Jersey (latest for Spring 3) -->
+		<!-- Jersey (latest for Spring 4 and javax.servlet namespace) -->
 		<dependency>
 			<groupId>org.glassfish.jersey.core</groupId>
 			<artifactId>jersey-server</artifactId>
@@ -288,7 +313,7 @@
 		</dependency>
 		<dependency>
 			<groupId>org.glassfish.jersey.ext</groupId>
-			<artifactId>jersey-spring3</artifactId>
+			<artifactId>jersey-spring4</artifactId>
 			<version>${jersey.version}</version>
 		</dependency>
 		<dependency>
@@ -312,7 +337,7 @@
 		<dependency>
 			<groupId>javax.ws.rs</groupId>
 			<artifactId>javax.ws.rs-api</artifactId>
-			<version>2.0.1</version>
+			<version>2.1.1</version>
 		</dependency>
 
 		<!-- Tomcat (defined by production deployment constraints) -->

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;