Move to Spring 4

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>

gemma-core/src/main/java/ubic/gemma/core/association/phenotype/PhenotypeAssoManagerServiceHelperImpl.java

@@ -18,7 +18,7 @@
  */
 package ubic.gemma.core.association.phenotype;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import ubic.gemma.core.annotation.reference.BibliographicReferenceService;

gemma-core/src/main/java/ubic/gemma/core/metrics/MeterRegistryEhcacheConfigurer.java

@@ -1,15 +1,15 @@
 package ubic.gemma.core.metrics;
 
 import io.micrometer.core.instrument.MeterRegistry;
+import io.micrometer.core.instrument.binder.cache.EhCache2Metrics;
 import net.sf.ehcache.Ehcache;
 import org.springframework.cache.Cache;
 import org.springframework.cache.CacheManager;
-import ubic.gemma.core.metrics.binder.cache.EhCache24Metrics;
 
 /**
  * Add metrics from each available {@link Ehcache} in the given {@link CacheManager} to the supplied meter registry.
  * @author poirigui
- * @see EhCache24Metrics
+ * @see EhCache2Metrics
  */
 public class MeterRegistryEhcacheConfigurer extends AbstractMeterRegistryConfigurer {
 
@@ -25,7 +25,7 @@ public void configure( MeterRegistry registry ) {
         for ( String cacheName : cacheManager.getCacheNames() ) {
             Cache cache = cacheManager.getCache( cacheName );
             if ( cache.getNativeCache() instanceof Ehcache ) {
-                EhCache24Metrics.monitor( registry, ( Ehcache ) cache.getNativeCache() );
+                EhCache2Metrics.monitor( registry, ( Ehcache ) cache.getNativeCache() );
             }
         }
     }

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 );
     }
 
     /**

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 );
     }

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>

gemma-core/src/main/resources/ubic/gemma/applicationContext-serviceBeans.xml

@@ -22,9 +22,7 @@
         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>
 
@@ -33,9 +31,7 @@
     <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>

gemma-core/src/test/java/ubic/gemma/persistence/service/common/description/CharacteristicDaoImplTest.java

@@ -1,6 +1,6 @@
 package ubic.gemma.persistence.service.common.description;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;

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>
 

gemma-web/.gitignore

@@ -1 +1,2 @@
 /bin
+/src/main/java/org