Jaxb context 9539

build.gradle

@@ -189,7 +189,10 @@ dependencies {
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.10.0.202406032230-r'
 
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.17.2'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-xml', version: '2.17.2'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.17.2'
+    implementation group: 'com.fasterxml.jackson.module', name: 'jackson-module-jaxb-annotations', version: '2.17.2'
+
 
     implementation 'com.fasterxml:aalto-xml:1.3.3'
 

src/main/java/module-info.java

@@ -79,7 +79,9 @@
     requires com.google.gson;
     requires com.fasterxml.jackson.databind;
     requires com.fasterxml.jackson.dataformat.yaml;
+    requires com.fasterxml.jackson.dataformat.xml;
     requires com.fasterxml.jackson.datatype.jsr310;
+    requires com.fasterxml.jackson.module.jaxb;
     // needs to be loaded here as it's otherwise not found at runtime
     requires org.glassfish.jaxb.runtime;
     // endregion

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

@@ -1,9 +1,12 @@
 package org.jabref.logic.importer.fileformat;
 
+import java.io.BufferedInputStream;
 import java.io.BufferedReader;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.PushbackInputStream;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -49,9 +52,8 @@
 import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.model.strings.StringUtil;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBException;
-import jakarta.xml.bind.Unmarshaller;
+import com.fasterxml.jackson.dataformat.xml.XmlMapper;
+import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
 import org.apache.commons.io.ByteOrderMark;
 import org.apache.commons.io.input.BOMInputStream;
 import org.slf4j.Logger;
@@ -85,7 +87,7 @@ public class CitaviXmlImporter extends Importer implements Parser {
     private CitaviExchangeData.ReferenceKeywords refKeywords;
     private CitaviExchangeData.ReferencePublishers refPublishers;
 
-    private Unmarshaller unmarshaller;
+    private XmlMapper mapper;
 
     public CitaviXmlImporter() {
         xmlInputFactory = XMLInputFactory.newFactory();
@@ -135,16 +137,13 @@ public boolean isRecognizedFormat(Path filePath) throws IOException {
     @Override
     public ParserResult importDatabase(Path filePath) throws IOException {
         try (BufferedReader reader = getReaderFromZip(filePath)) {
-            Object unmarshalledObject = unmarshallRoot(reader);
-
-            if (unmarshalledObject instanceof CitaviExchangeData data) {
+            if (mapperRoot(reader) instanceof CitaviExchangeData data) {
                 List<BibEntry> bibEntries = parseDataList(data);
-
                 return new ParserResult(bibEntries);
             } else {
                 return ParserResult.fromErrorMessage("File does not start with xml tag.");
             }
-        } catch (JAXBException | XMLStreamException e) {
+        } catch (XMLStreamException e) {
             LOGGER.debug("could not parse document", e);
             return ParserResult.fromError(e);
         }
@@ -406,25 +405,31 @@ private String removeSpacesBeforeLineBreak(String string) {
               .replaceAll(" +\n", "\n");
     }
 
-    private void initUnmarshaller() throws JAXBException {
-        if (unmarshaller == null) {
-            // Lazy init because this is expensive
-            JAXBContext context = JAXBContext.newInstance("org.jabref.logic.importer.fileformat.citavi");
-            unmarshaller = context.createUnmarshaller();
+    private void initMapper() throws Exception {
+        // Lazy init because this is expensive
+        if (mapper == null) {
+            mapper = XmlMapper.xmlBuilder().addModule(new JaxbAnnotationModule()).build();
         }
     }
 
-    private Object unmarshallRoot(BufferedReader reader) throws XMLStreamException, JAXBException {
-        initUnmarshaller();
+    private Object mapperRoot(BufferedReader reader) throws XMLStreamException {
+        Objects.requireNonNull(reader);
 
-        XMLStreamReader xmlStreamReader = xmlInputFactory.createXMLStreamReader(reader);
+        try {
+            initMapper();
 
-        // Go to the root element
-        while (!xmlStreamReader.isStartElement()) {
-            xmlStreamReader.next();
-        }
+            XMLStreamReader xmlStreamReader = xmlInputFactory.createXMLStreamReader(reader);
 
-        return unmarshaller.unmarshal(xmlStreamReader);
+            // Go to the root element
+            while (!xmlStreamReader.isStartElement()) {
+                xmlStreamReader.next();
+            }
+
+            return mapper.readValue(xmlStreamReader, Object.class);
+        } catch (Exception e) {
+            LOGGER.debug("could not read document", e);
+            return ParserResult.fromError(e);
+        }
     }
 
     @Override