Update Jersey to 2.25.1

PavlidisLab · Jun 9, 2021 · 1cf1565 · 1cf1565
1 parent 80bf648
commit 1cf1565
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Showing 13 changed files with 28 additions and 71 deletions.
diff --git a/gemma-web/pom.xml b/gemma-web/pom.xml
@@ -409,60 +409,24 @@
 		</dependency>
 		<!-- Jersey -->
 		<dependency>
-			<groupId>com.sun.jersey</groupId>
+			<groupId>org.glassfish.jersey.core</groupId>
 			<artifactId>jersey-server</artifactId>
-			<version>1.8</version>
+			<version>${jersey.version}</version>
 		</dependency>
 		<dependency>
-			<groupId>com.sun.jersey</groupId>
-			<artifactId>jersey-json</artifactId>
-			<version>1.8</version>
-			<exclusions>
-				<exclusion>
-					<groupId>javax.xml.stream</groupId>
-					<artifactId>stax-api</artifactId>
-				</exclusion>
-				<exclusion>
-					<artifactId>stax-api</artifactId>
-					<groupId>stax</groupId>
-				</exclusion>
-				<exclusion>
-					<groupId>javax.activation</groupId>
-					<artifactId>activation</artifactId>
-				</exclusion>
-			</exclusions>
+			<groupId>org.glassfish.jersey.containers</groupId>
+			<artifactId>jersey-container-servlet</artifactId>
+			<version>${jersey.version}</version>
 		</dependency>
-		<!-- Jersey + Spring -->
 		<dependency>
-			<groupId>com.sun.jersey.contribs</groupId>
-			<artifactId>jersey-spring</artifactId>
-			<version>1.8</version>
-			<exclusions>
-				<exclusion>
-					<groupId>org.springframework</groupId>
-					<artifactId>spring</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.springframework</groupId>
-					<artifactId>spring-core</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.springframework</groupId>
-					<artifactId>spring-web</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.springframework</groupId>
-					<artifactId>spring-beans</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.springframework</groupId>
-					<artifactId>spring-context</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.springframework</groupId>
-					<artifactId>spring-aop</artifactId>
-				</exclusion>
-			</exclusions>
+			<groupId>org.glassfish.jersey.ext</groupId>
+			<artifactId>jersey-spring3</artifactId>
+			<version>${jersey.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.glassfish.jersey.media</groupId>
+			<artifactId>jersey-media-json-jackson</artifactId>
+			<version>${jersey.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>pavlab</groupId>

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/ExceptionHandlerFilter.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/ExceptionHandlerFilter.java
@@ -1,6 +1,6 @@
 package ubic.gemma.web.services.rest.util;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.springframework.web.filter.OncePerRequestFilter;
 
 import javax.servlet.FilterChain;

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/JsonMappingExceptionMapper.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/JsonMappingExceptionMapper.java
@@ -1,7 +1,7 @@
 package ubic.gemma.web.services.rest.util;
 
+import com.fasterxml.jackson.databind.JsonMappingException;
 import org.apache.commons.logging.LogFactory;
-import org.codehaus.jackson.map.JsonMappingException;
 
 import javax.ws.rs.core.Response;
 import javax.ws.rs.ext.ExceptionMapper;

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/RestAuthEntryPoint.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/RestAuthEntryPoint.java
@@ -1,6 +1,6 @@
 package ubic.gemma.web.services.rest.util;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.springframework.security.core.AuthenticationException;
 import org.springframework.security.web.authentication.www.BasicAuthenticationEntryPoint;
 

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/WellComposedErrorBody.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/WellComposedErrorBody.java
@@ -1,7 +1,7 @@
 package ubic.gemma.web.services.rest.util;
 
-import org.codehaus.jackson.annotate.JsonIgnore;
-import org.codehaus.jackson.annotate.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.ws.rs.core.Response;
 import java.util.HashMap;

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/CompositeSequenceArg.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/CompositeSequenceArg.java
@@ -22,8 +22,7 @@ public abstract class CompositeSequenceArg<T>
      * @return instance of CompositeSequenceArg.
      */
     @SuppressWarnings("unused")
-    public static MutableArg<?, CompositeSequence, CompositeSequenceValueObject, CompositeSequenceService> valueOf(
-            final String s ) {
+    public static CompositeSequenceArg<?> valueOf( final String s ) {
         try {
             return new CompositeSequenceIdArg( Long.parseLong( s.trim() ) );
         } catch ( NumberFormatException e ) {

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/DatabaseEntryArg.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/DatabaseEntryArg.java
@@ -19,7 +19,7 @@ public abstract class DatabaseEntryArg<T>
      * @return instance of appropriate implementation of DatabaseEntryArg based on the actual Type the argument represents.
      */
     @SuppressWarnings("unused")
-    public static DatabaseEntryArg valueOf( final String s ) {
+    public static DatabaseEntryArg<?> valueOf( final String s ) {
         try {
             return new DatabaseEntryIdArg( Long.parseLong( s.trim() ) );
         } catch ( NumberFormatException e ) {

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/DatasetArg.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/DatasetArg.java
@@ -26,8 +26,7 @@ public abstract class DatasetArg<T>
      * @return instance of appropriate implementation of DatasetArg based on the actual Type the argument represents.
      */
     @SuppressWarnings("unused")
-    public static MutableArg<?, ExpressionExperiment, ExpressionExperimentValueObject, ExpressionExperimentService> valueOf(
-            final String s ) {
+    public static DatasetArg<?> valueOf( final String s ) {
         try {
             return new DatasetIdArg( Long.parseLong( s.trim() ) );
         } catch ( NumberFormatException e ) {

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/GeneArg.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/GeneArg.java
@@ -38,7 +38,7 @@ public abstract class GeneArg<T> extends MutableArg<T, Gene, GeneValueObject, Ge
      * @return instance of appropriate implementation of GeneArg based on the actual property the argument represents.
      */
     @SuppressWarnings("unused")
-    public static MutableArg<?, Gene, GeneValueObject, GeneService> valueOf( final String s ) {
+    public static GeneArg<?> valueOf( final String s ) {
         try {
             return new GeneNcbiIdArg( Integer.parseInt( s.trim() ) );
         } catch ( NumberFormatException e ) {

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/PlatformArg.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/PlatformArg.java
@@ -27,7 +27,7 @@ public abstract class PlatformArg<T> extends MutableArg<T, ArrayDesign, ArrayDes
      * @return   instance of appropriate implementation of DatasetArg based on the actual Type the argument represents.
      */
     @SuppressWarnings("unused")
-    public static MutableArg<?, ArrayDesign, ArrayDesignValueObject, ArrayDesignService> valueOf( final String s ) {
+    public static PlatformArg<?> valueOf( final String s ) {
         try {
             return new PlatformIdArg( Long.parseLong( s.trim() ) );
         } catch ( NumberFormatException e ) {

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/TaxonArg.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/util/args/TaxonArg.java
@@ -35,10 +35,10 @@ public abstract class TaxonArg<T> extends MutableArg<T, Taxon, TaxonValueObject,
      * Used by RS to parse value of request parameters.
      *
      * @param  s the request taxon argument
-     * @return   instance of appropriate implementation of TaxonArg based on the actual Type the argument represents.
+     * @return instance of appropriate implementation of TaxonArg based on the actual Type the argument represents.
      */
     @SuppressWarnings("unused")
-    public static MutableArg<?, Taxon, TaxonValueObject, TaxonService> valueOf( final String s ) {
+    public static TaxonArg<?> valueOf( final String s ) {
         try {
             Long id = Long.parseLong( s.trim() );
             return id < TaxonArg.MIN_NCBI_ID ? new TaxonIdArg( id ) : new TaxonNcbiIdArg( id );

diff --git a/gemma-web/src/main/webapp/WEB-INF/web.xml b/gemma-web/src/main/webapp/WEB-INF/web.xml
@@ -193,17 +193,11 @@
     <!-- REST web service -->
     <servlet>
         <servlet-name>rest-ws-servlet</servlet-name>
-        <servlet-class>
-            com.sun.jersey.spi.spring.container.servlet.SpringServlet
-        </servlet-class>
+        <servlet-class>org.glassfish.jersey.servlet.ServletContainer</servlet-class>
         <init-param>
-            <param-name>com.sun.jersey.config.property.packages</param-name>
+            <param-name>jersey.config.server.provider.packages</param-name>
             <param-value>ubic.gemma.web.services.rest</param-value>
         </init-param>
-        <init-param>
-            <param-name>com.sun.jersey.api.json.POJOMappingFeature</param-name>
-            <param-value>true</param-value>
-        </init-param>
         <load-on-startup>1</load-on-startup>
     </servlet>
 

diff --git a/pom.xml b/pom.xml
@@ -534,6 +534,7 @@
 		<spring.security.version>3.1.4.RELEASE</spring.security.version>
 		<hibernate.version>3.6.7.Final</hibernate.version>
 		<ehcache.version>2.6.6</ehcache.version>
+		<jersey.version>2.25.1</jersey.version>
 		<tomcat.version>8.5.60</tomcat.version>
 	</properties>
 </project>