switching to opensource jakarta from proprietary javax for reading xml

Author: adamjohnwright

pom.xml

@@ -21,8 +21,7 @@
         <maven.compiler.source>11</maven.compiler.source>
         <maven.compiler.target>11</maven.compiler.target>
 
-        <jaxb.version>2.3.1</jaxb.version>
-        <jaxb-core.version>3.0.1</jaxb-core.version>
+        <jaxb.version>4.0.0</jaxb.version>
         <commons-csv.version>1.8</commons-csv.version>
         <commons-collections4.version>4.4</commons-collections4.version>
     </properties>
@@ -45,22 +44,17 @@
             <artifactId>jsap</artifactId>
             <version>${jsap.version}</version>
         </dependency>
-        <!--JAXB-->
+        <!--JAXB (Jakarta)-->
         <dependency>
-            <groupId>javax.xml.bind</groupId>
-            <artifactId>jaxb-api</artifactId>
+            <groupId>jakarta.xml.bind</groupId>
+            <artifactId>jakarta.xml.bind-api</artifactId>
             <version>${jaxb.version}</version>
         </dependency>
         <dependency>
-            <groupId>com.sun.xml.bind</groupId>
-            <artifactId>jaxb-impl</artifactId>
+            <groupId>org.glassfish.jaxb</groupId>
+            <artifactId>jaxb-runtime</artifactId>
             <version>${jaxb.version}</version>
         </dependency>
-        <dependency>
-            <groupId>com.sun.xml.bind</groupId>
-            <artifactId>jaxb-core</artifactId>
-            <version>${jaxb-core.version}</version>
-        </dependency>
 
         <dependency>
             <groupId>org.apache.commons</groupId>

src/main/java/org/reactome/server/tools/DuplicateChecker.java

@@ -8,9 +8,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Unmarshaller;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.IOException;

src/main/java/org/reactome/server/tools/IconValidator.java

@@ -11,9 +11,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Unmarshaller;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;

src/main/java/org/reactome/server/tools/model/Icon.java

@@ -3,7 +3,7 @@
 import lombok.Data;
 import lombok.NoArgsConstructor;
 
-import javax.xml.bind.annotation.*;
+import jakarta.xml.bind.annotation.*;
 import java.util.List;
 
 /**

src/main/java/org/reactome/server/tools/model/Person.java

@@ -1,6 +1,6 @@
 package org.reactome.server.tools.model;
 
-import javax.xml.bind.annotation.*;
+import jakarta.xml.bind.annotation.*;
 
 /**
  * Created by Chuqiao on 2019/11/12.

src/main/java/org/reactome/server/tools/model/Reference.java

@@ -4,10 +4,10 @@
 import lombok.Data;
 import lombok.NoArgsConstructor;
 
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlRootElement;
 
 /**
  * Created by Chuqiao on 2019/11/12.