[WIP] Try with jaxb 3.0 and xjc

build.gradle

@@ -173,9 +173,9 @@ dependencies {
 
     implementation 'de.undercouch:citeproc-java:2.1.0-SNAPSHOT'
 
-    implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
-    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
-    implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.2'
+    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '3.0.0'
+    implementation group: 'com.sun.xml.bind', name: 'jaxb-core', version: '3.0.0'
+    implementation group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '3.0.0'
 
     implementation ('com.github.tomtung:latex2unicode_2.12:0.2.6') {
         exclude module: 'fastparse_2.12'
@@ -208,7 +208,8 @@ dependencies {
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:8.38'
-    xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
+    xjc group: 'com.sun.xml.bind', name: 'jaxb-xjc', version: '3.0.0'
+    xjc group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '3.0.0'
 }
 
 dependencyUpdates {
@@ -561,7 +562,6 @@ jlink {
     // Execute ./gradlew suggestMergedModuleInfo and include the suggested directives here.
     mergedModule {
         requires 'java.xml'
-        requires 'com.sun.xml.txw2'
         requires 'java.desktop'
         requires 'org.objectweb.asm'
         requires 'jdk.jfr'
@@ -590,6 +590,8 @@ jlink {
         requires 'java.transaction.xa'
         requires 'org.graalvm.sdk'
         requires 'org.slf4j'
+        requires 'jakarta.xml.bind';
+        requires 'jakarta.activation';
         uses 'org.apache.logging.log4j.util.PropertySource'
         uses 'org.apache.logging.log4j.core.util.WatchEventService'
         uses 'org.apache.logging.log4j.plugins.processor.PluginService'
@@ -603,7 +605,7 @@ jlink {
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
         uses 'org.mariadb.jdbc.LocalInfileInterceptor'
-        uses 'javax.xml.bind.JAXBContextFactory'
+        uses 'jakarta.xml.bind.JAXBContextFactory'
         provides 'javax.annotation.processing.Processor' with 'org.apache.logging.log4j.plugins.processor.PluginProcessor'
         provides 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
         provides 'org.apache.logging.log4j.message.ThreadDumpMessage.ThreadInfoFactory' with 'org.apache.logging.log4j.core.message.ExtendedThreadInfoFactory'

src/main/java/module-info.java

@@ -37,7 +37,7 @@
 
     // Preferences and XML
     requires java.prefs;
-    requires java.xml.bind;
+    requires jakarta.xml.bind;
     requires jdk.xml.dom;
 
     // Annotations (@PostConstruct)

src/main/java/org/jabref/logic/exporter/BibTeXMLExporter.java

@@ -13,10 +13,6 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
 import javax.xml.datatype.DatatypeConfigurationException;
 import javax.xml.datatype.DatatypeFactory;
 import javax.xml.datatype.XMLGregorianCalendar;
@@ -47,6 +43,10 @@
 import org.jabref.model.entry.types.EntryType;
 import org.jabref.model.entry.types.StandardEntryType;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/logic/exporter/ModsExporter.java

@@ -9,10 +9,6 @@
 import java.util.Objects;
 import java.util.TreeMap;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
 import javax.xml.namespace.QName;
 
 import org.jabref.logic.importer.fileformat.mods.AbstractDefinition;
@@ -52,6 +48,11 @@
 import org.jabref.model.entry.field.UnknownField;
 import org.jabref.model.entry.types.EntryType;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+
 /**
  * TemplateExporter for exporting in MODS XML format.
  */

src/main/java/org/jabref/logic/importer/fileformat/BibTeXMLImporter.java

@@ -14,10 +14,6 @@
 import java.util.Optional;
 import java.util.regex.Pattern;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Unmarshaller;
 import javax.xml.datatype.XMLGregorianCalendar;
 
 import org.jabref.logic.importer.Importer;
@@ -34,6 +30,10 @@
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.types.StandardEntryType;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/logic/importer/fileformat/EndnoteXmlImporter.java

@@ -14,9 +14,6 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Unmarshaller;
 import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
@@ -58,6 +55,9 @@
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.OptionalUtil;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java

@@ -15,10 +15,6 @@
 import java.util.Objects;
 import java.util.Optional;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Unmarshaller;
 import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
@@ -84,6 +80,10 @@
 import org.jabref.model.strings.StringUtil;
 
 import com.google.common.base.Joiner;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/logic/importer/fileformat/ModsImporter.java

@@ -15,11 +15,6 @@
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Unmarshaller;
-
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.Importer;
 import org.jabref.logic.importer.ParseException;
@@ -63,6 +58,10 @@
 import org.jabref.model.entry.types.EntryTypeFactory;
 
 import com.google.common.base.Joiner;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/logic/importer/fileformat/mods/package-info.java

@@ -7,8 +7,8 @@
 
 // This needs to be in the src/main/java to ensure that the Namespace is mapped to the prefix "mods"
 // this cannot be done by a gradle task at the moment
-@javax.xml.bind.annotation.XmlSchema(namespace = "http://www.loc.gov/mods/v3", xmlns = {
-        @XmlNs(prefix = "mods", namespaceURI = "http://www.loc.gov/mods/v3")}, elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@jakarta.xml.bind.annotation.XmlSchema(namespace = "http://www.loc.gov/mods/v3", xmlns = {
+        @XmlNs(prefix = "mods", namespaceURI = "http://www.loc.gov/mods/v3")}, elementFormDefault = jakarta.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package org.jabref.logic.importer.fileformat.mods;
 
-import javax.xml.bind.annotation.XmlNs;
+import jakarta.xml.bind.annotation.XmlNs;

src/main/resources/xjc/mods/mods-binding.xjb

@@ -1,4 +1,4 @@
-<jxb:bindings version="2.0" xmlns:jxb="http://java.sun.com/xml/ns/jaxb" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
+<jxb:bindings version="3.0" xmlns:jxb="https://jakarta.ee/xml/ns/jaxb" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
 
     <jxb:bindings schemaLocation="mods-3-7.xsd" node="/xsd:schema">