PD 5312 jdk 17 , spring 6, jakarta migration

orcid-activemq/pom.xml

@@ -24,35 +24,35 @@
 	  <dependency>
 	      <groupId>org.apache.activemq</groupId>
 	      <artifactId>activemq-broker</artifactId>
-	      <version>5.13.3</version>
+          <version>${activemq.version}</version>
 	  </dependency>
   	  <dependency>
 	      <groupId>org.apache.activemq</groupId>
 	      <artifactId>activemq-spring</artifactId>
-	  	  <version>5.13.3</version>
+      	  <version>${activemq.version}</version>
 	  </dependency>
 	  <!-- https://mvnrepository.com/artifact/org.apache.activemq/activemq-kahadb-store -->
  	<dependency>
  	    <groupId>org.apache.activemq</groupId>
 	    <artifactId>activemq-kahadb-store</artifactId>
-	    <version>5.13.3</version>
+        <version>${activemq.version}</version>
 	</dependency>
 
 	<!-- javax.xml -->
     <dependency>
     <groupId>jakarta.xml.bind</groupId>
     <artifactId>jakarta.xml.bind-api</artifactId>
-    <version>2.3.3</version>
+    <version>3.0.1</version>
 </dependency>
 <dependency>
 <groupId>com.sun.xml.bind</groupId>
 <artifactId>jaxb-impl</artifactId>
-<version>2.3.3</version>
+<version>3.0.2</version>
 </dependency>
 	<dependency>
-         <groupId>javax.annotation</groupId>
-         <artifactId>javax.annotation-api</artifactId>
-         <version>1.3.2</version>
+         <groupId>jakarta.annotation</groupId>
+     <artifactId>jakarta.annotation-api</artifactId>
+     <version>2.1.1</version>
     </dependency>
 
      <!-- Test dependencies -->

orcid-activemq/src/main/resources/activemq.xml

@@ -5,7 +5,7 @@
 	xmlns:context="http://www.springframework.org/schema/context"
 	xsi:schemaLocation="
        http://activemq.apache.org/schema/core http://activemq.apache.org/schema/core/activemq-core.xsd
-       http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-4.3.xsd
+       http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context.xsd
        http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd">
 
 	<context:property-placeholder

orcid-activemq/src/main/resources/orcid-activemq-web-context.xml

@@ -4,11 +4,11 @@
 	xmlns:cache="http://www.springframework.org/schema/cache" xmlns:aop="http://www.springframework.org/schema/aop"
 	xmlns:jms="http://www.springframework.org/schema/jms"
 	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
+        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.xsd
         http://www.springframework.org/schema/cache http://www.springframework.org/schema/cache/spring-cache.xsd
-        http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-4.3.xsd 
-        http://www.springframework.org/schema/jms http://www.springframework.org/schema/jms/spring-jms-4.3.xsd" >
+        http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop.xsd 
+        http://www.springframework.org/schema/jms http://www.springframework.org/schema/jms/spring-jms.xsd" >
 
 	<bean id="broker" class="org.apache.activemq.xbean.BrokerFactoryBean">
 	  <property name="config" value="classpath:activemq.xml" />

orcid-activemq/src/test/java/org/orcid/activemq/AppContextActiveMQTest.java

@@ -2,7 +2,7 @@
 
 import static org.junit.Assert.*;
 
-import javax.annotation.Resource;
+import jakarta.annotation.Resource;
 
 import org.apache.activemq.xbean.BrokerFactoryBean;
 import org.junit.Test;

orcid-activemq/src/test/resources/test-orcid-activemq-web-context.xml

@@ -4,11 +4,11 @@
 	xmlns:cache="http://www.springframework.org/schema/cache" xmlns:aop="http://www.springframework.org/schema/aop"
 	xmlns:jms="http://www.springframework.org/schema/jms"
 	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
+        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.xsd
         http://www.springframework.org/schema/cache http://www.springframework.org/schema/cache/spring-cache.xsd
-        http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-4.3.xsd 
-        http://www.springframework.org/schema/jms http://www.springframework.org/schema/jms/spring-jms-4.3.xsd" >
+        http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop.xsd 
+        http://www.springframework.org/schema/jms http://www.springframework.org/schema/jms/spring-jms.xsd" >
 
 	<bean id="broker" class="org.apache.activemq.xbean.BrokerFactoryBean">
 	  <property name="config" value="classpath:test-activemq.xml" />

orcid-activities-indexer/pom.xml

@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
 
   <artifactId>orcid-activities-indexer</artifactId>
-  <version>0.0.1-SNAPSHOT</version>
+    <version>release-2.0.0</version>
   <packaging>war</packaging>
 
   <name>ORCID - Activities Indexer</name>
@@ -22,7 +22,6 @@
          <dependency>
             <groupId>org.orcid</groupId>
             <artifactId>orcid-model</artifactId>
-            <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.orcid</groupId>
@@ -50,18 +49,34 @@
         <dependency>
             <groupId>org.apache.activemq</groupId>
             <artifactId>activemq-broker</artifactId>
-            <version>5.13.3</version>
+            <version>${activemq.version}</version>
         </dependency>
   	  <dependency>
 	      <groupId>org.apache.activemq</groupId>
 	      <artifactId>activemq-spring</artifactId>
-	  	  <version>5.13.3</version>
+	  	  <version>${activemq.version}</version>
 	  </dependency>
 
 	    <dependency>
-            <groupId>com.sun.jersey</groupId>              
+            <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-client</artifactId>
-        </dependency> 
+            <version>${jersey.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.inject</groupId>
+            <artifactId>jersey-hk2</artifactId>
+            <version>${jersey.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.media</groupId>
+            <artifactId>jersey-media-jaxb</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>org.liquibase</groupId>
@@ -85,28 +100,27 @@
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-c3p0</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-entitymanager</artifactId>
-            <scope>compile</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-core</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.hibernate.javax.persistence</groupId>
-            <artifactId>hibernate-jpa-2.1-api</artifactId>
-        </dependency>
+            <dependency>
+                <groupId>org.hibernate.orm</groupId>
+                <artifactId>hibernate-core</artifactId>
+            </dependency>
+            <dependency>
+                <groupId>org.hibernate.orm</groupId>
+                <artifactId>hibernate-agroal</artifactId>
+            </dependency>
+            <dependency>
+                <groupId>org.hibernate.orm</groupId>
+                <artifactId>hibernate-c3p0</artifactId>
+            </dependency>
+            <dependency>
+                <groupId>org.hibernate.validator</groupId>
+                <artifactId>hibernate-validator</artifactId>
+            </dependency>
   </dependencies>
   <parent>
   	<groupId>org.orcid</groupId>
   	<artifactId>orcid-parent</artifactId>
-        <version>${project.version}</version>
+      <version>release-2.0.0</version>
   	<relativePath>../pom.xml</relativePath>
   </parent>
 

orcid-activities-indexer/src/main/java/org/orcid/activitiesindexer/cron/RetryFailedRecords.java

@@ -6,7 +6,12 @@
 import java.util.List;
 import java.util.Map;
 
-import javax.annotation.Resource;
+import jakarta.annotation.Resource;
+import jakarta.ws.rs.client.Client;
+import jakarta.ws.rs.client.ClientBuilder;
+import jakarta.ws.rs.client.Entity;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
 
 import org.apache.commons.lang3.StringUtils;
 import org.orcid.activitiesindexer.persistence.entities.ActivitiesStatusEntity;
@@ -22,9 +27,6 @@
 import org.springframework.scheduling.annotation.Scheduled;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.sun.jersey.api.client.Client;
-import com.sun.jersey.api.client.ClientResponse;
-import com.sun.jersey.api.client.WebResource;
 
 @Configuration
 @EnableScheduling
@@ -50,7 +52,7 @@ public class RetryFailedRecords {
     private S3MessageProcessor s3Processor;
 
     public RetryFailedRecords() {
-        client = Client.create();
+        client = ClientBuilder.newClient();
         mapper = new ObjectMapper();
     }
 
@@ -156,11 +158,13 @@ private void sendSystemAlert(String message) {
                 throw new RuntimeException(e);
             }
 
-            WebResource resource = client.resource(webhookUrl);
-            ClientResponse response = resource.entity(bodyJson).post(ClientResponse.class);
-            int status = response.getStatus();
-            if (status != 200) {
-                LOGGER.warn("Unable to send message to Slack, status={}, error={}, message={}", new Object[] { status, response.getEntity(String.class), message });
+            try (Response response = client.target(webhookUrl)
+                    .request()
+                    .post(Entity.entity(bodyJson, MediaType.APPLICATION_JSON_TYPE))) {
+                int status = response.getStatus();
+                if (status != 200) {
+                    LOGGER.warn("Unable to send message to Slack, status={}, error={}, message={}", new Object[] { status, response.readEntity(String.class), message });
+                }
             }
         }
     }

orcid-activities-indexer/src/main/java/org/orcid/activitiesindexer/jersey/OrcidJerseyClientHandler.java

@@ -16,37 +16,39 @@
  */
 package org.orcid.activitiesindexer.jersey;
 
+import java.util.HashMap;
 import java.util.Map;
 import java.util.Set;
 
 import org.orcid.activitiesindexer.util.DevJerseyClientConfig;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.jaxrs.json.JacksonJaxbJsonProvider;
-import com.sun.jersey.api.client.Client;
-import com.sun.jersey.api.client.config.ClientConfig;
-import com.sun.jersey.api.client.config.DefaultClientConfig;
+import org.glassfish.jersey.jackson.JacksonFeature;
+
+import jakarta.ws.rs.client.Client;
+import jakarta.ws.rs.client.ClientBuilder;
 
 public class OrcidJerseyClientHandler {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(OrcidJerseyClientHandler.class);
 
     public static Client create(boolean isDevelopmentMode, Map<String, Object> properties) {
-        ClientConfig config = null;
+        ClientBuilder builder = ClientBuilder.newBuilder();
         if (isDevelopmentMode) {
             // DANGER!!! Trust all certs
             LOGGER.info("TRUSTING ALL SSL CERTS IN DEV MODE!!!");
-            config = new DevJerseyClientConfig();
-        } else {
-            config = new DefaultClientConfig();
+            DevJerseyClientConfig.apply(builder);
         }
-        Set<String> keyset = properties.keySet();
+
+        Client client = builder.register(JacksonFeature.class).build();
+
+        Set<String> keyset = new HashMap<>(properties).keySet();
         for (String key : keyset) {
-            config.getProperties().put(key, properties.get(key));
+            client.property(key, properties.get(key));
         }
-        config.getClasses().add(JacksonJaxbJsonProvider.class);
-        return Client.create(config);
+
+        return client;
     }
 
 }

orcid-activities-indexer/src/main/java/org/orcid/activitiesindexer/listener/BaseListener.java

@@ -19,8 +19,8 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import javax.jms.JMSException;
-import javax.jms.Message;
+import jakarta.jms.JMSException;
+import jakarta.jms.Message;
 
 import org.apache.activemq.command.ActiveMQMapMessage;
 import org.fusesource.hawtbuf.UTF8Buffer;

orcid-activities-indexer/src/main/java/org/orcid/activitiesindexer/listener/ReIndexListener.java

@@ -20,10 +20,10 @@
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 
-import javax.annotation.Resource;
-import javax.jms.Message;
-import javax.jms.MessageListener;
-import javax.xml.bind.JAXBException;
+import jakarta.annotation.Resource;
+import jakarta.jms.Message;
+import jakarta.jms.MessageListener;
+import jakarta.xml.bind.JAXBException;
 
 import org.orcid.activitiesindexer.s3.S3MessageProcessor;
 import org.orcid.utils.listener.LastModifiedMessage;

orcid-activities-indexer/src/main/java/org/orcid/activitiesindexer/listener/UpdatedOrcidListener.java

@@ -18,9 +18,9 @@
 
 import java.util.Map;
 
-import javax.annotation.Resource;
-import javax.jms.Message;
-import javax.jms.MessageListener;
+import jakarta.annotation.Resource;
+import jakarta.jms.Message;
+import jakarta.jms.MessageListener;
 
 import org.orcid.utils.listener.LastModifiedMessage;
 import org.slf4j.Logger;

orcid-activities-indexer/src/main/java/org/orcid/activitiesindexer/listener/UpdatedOrcidWorker.java

@@ -16,7 +16,7 @@
  */
 package org.orcid.activitiesindexer.listener;
 
-import javax.annotation.Resource;
+import jakarta.annotation.Resource;
 
 import org.orcid.activitiesindexer.s3.S3MessageProcessor;
 import org.orcid.utils.listener.LastModifiedMessage;

orcid-activities-indexer/src/main/java/org/orcid/activitiesindexer/listener/persistence/dao/ActivitiesStatusDao.java

@@ -20,10 +20,10 @@
 import java.util.Date;
 import java.util.List;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
 
 import org.orcid.activitiesindexer.persistence.entities.ActivitiesStatusEntity;
 import org.orcid.activitiesindexer.persistence.util.ActivityType;