WIP convert to jackson 3

.github/workflows/tests-code.yml

@@ -576,6 +576,7 @@ jobs:
               echo "//SOURCES ../../$f" >> "${{ matrix.script }}"
             fi
           done
+      - run: cat ${{ matrix.script }}
       - run: jbang build "${{ matrix.script }}"
         shell: bash
       - run: jbang "${{ matrix.script }}" --help

.jbang/JabKitLauncher.java

@@ -30,6 +30,10 @@
 //DEPS io.github.darvil82:terminal-text-formatter:2.3.0c
 //DEPS info.picocli:picocli:4.7.7
 //DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
+//DEPS com.fasterxml.jackson.core:jackson-annotations:2.20
+//DEPS tools.jackson.core:jackson-core:3.0.2
+//DEPS tools.jackson.core:jackson-databind:3.0.2
+//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
 
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabKitLauncher {

.jbang/JabLsLauncher.java

@@ -36,7 +36,10 @@
 //DEPS org.jspecify:jspecify:1.0.0
 
 // from jabls
-//DEPS com.fasterxml.jackson.core:jackson-databind:2.20.1
+//DEPS com.fasterxml.jackson.core:jackson-annotations:2.20
+//DEPS tools.jackson.core:jackson-core:3.0.2
+//DEPS tools.jackson.core:jackson-databind:3.0.2
+//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
 //DEPS info.picocli:picocli:4.7.7
 //DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.2
 //DEPS org.eclipse.lsp4j:org.eclipse.lsp4j:0.24.0

.jbang/JabSrvLauncher.java

@@ -80,6 +80,9 @@
 //DEPS net.harawata:appdirs:1.5.0
 //DEPS de.undercouch:citeproc-java:3.4.0
 //DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
+//DEPS tools.jackson.core:jackson-core:3.0.2
+//DEPS tools.jackson.core:jackson-databind:3.0.2
+//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
 //DEPS org.apache.commons:commons-lang3:3.19.0
 
 /// This class is required for [jbang](https://www.jbang.dev/)

jablib-examples/jbang/ieee_pdf_references_to_bibtex.java

@@ -18,6 +18,10 @@
 //DEPS org.jabref:jablib:6.0-SNAPSHOT
 // JabRef relies on PR https://github.com/unicode-org/icu/pull/2127; for experiments the release version is OK.
 //DEPS com.ibm.icu:icu4j:78.1
+//DEPS com.fasterxml.jackson.core:jackson-annotations:2.20
+//DEPS tools.jackson.core:jackson-core:3.0.2
+//DEPS tools.jackson.core:jackson-databind:3.0.2
+//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
 
 void main() throws Exception {
     var preferences = JabRefCliPreferences.getInstance();

jablib/build.gradle.kts

@@ -103,8 +103,8 @@ dependencies {
 
     implementation("org.eclipse.jgit:org.eclipse.jgit")
 
-    implementation("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml")
-    implementation("com.fasterxml.jackson.datatype:jackson-datatype-jsr310")
+    implementation("tools.jackson.dataformat:jackson-dataformat-yaml")
+    implementation("tools.jackson.core:jackson-databind")
     // TODO: Somwewhere we get a warning: unknown enum constant Id.CLASS reason: class file for com.fasterxml.jackson.annotation.JsonTypeInfo$Id not found
     // implementation("com.fasterxml.jackson.core:jackson-annotations:2.19.1")
 

jablib/src/main/java/module-info.java

@@ -155,9 +155,9 @@
     // region: data mapping
     requires jdk.xml.dom;
     requires com.google.gson;
-    requires com.fasterxml.jackson.databind;
-    requires com.fasterxml.jackson.dataformat.yaml;
-    requires com.fasterxml.jackson.datatype.jsr310;
+    requires tools.jackson.databind;
+    requires tools.jackson.dataformat.yaml;
+    requires tools.jackson.core;
     // endregion
 
     // region HTTP clients

jablib/src/main/java/org/jabref/logic/citationstyle/CSLStyleLoader.java

@@ -9,12 +9,12 @@
 
 import org.jabref.logic.openoffice.OpenOfficePreferences;
 
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import org.jspecify.annotations.NonNull;
 import org.jspecify.annotations.Nullable;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import tools.jackson.core.type.TypeReference;
+import tools.jackson.databind.ObjectMapper;
 
 /**
  * Manages the loading of CitationStyles from both internal resources and external files.

jablib/src/main/java/org/jabref/logic/crawler/StudyYamlParser.java

@@ -7,9 +7,10 @@
 
 import org.jabref.model.study.Study;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
-import com.fasterxml.jackson.dataformat.yaml.YAMLGenerator;
+import tools.jackson.databind.ObjectMapper;
+import tools.jackson.dataformat.yaml.YAMLFactory;
+import tools.jackson.dataformat.yaml.YAMLMapper;
+import tools.jackson.dataformat.yaml.YAMLWriteFeature;
 
 /**
  * Example use: <code>new StudyYamlParser().parseStudyYamlFile(studyDefinitionFile);</code>
@@ -30,8 +31,10 @@ public Study parseStudyYamlFile(Path studyYamlFile) throws IOException {
      * Writes the given study instance into a yaml file to the given path
      */
     public void writeStudyYamlFile(Study study, Path studyYamlFile) throws IOException {
-        ObjectMapper yamlMapper = new ObjectMapper(new YAMLFactory().disable(YAMLGenerator.Feature.WRITE_DOC_START_MARKER)
-                                                                    .enable(YAMLGenerator.Feature.MINIMIZE_QUOTES));
+
+        ObjectMapper yamlMapper = new YAMLMapper(YAMLFactory.builder()
+                                                            .disable(YAMLWriteFeature.WRITE_DOC_START_MARKER)
+                                                            .enable(YAMLWriteFeature.MINIMIZE_QUOTES).build());
         yamlMapper.writeValue(studyYamlFile.toFile(), study);
     }
 }

jablib/src/main/java/org/jabref/logic/importer/fileformat/CffImporter.java

@@ -26,10 +26,12 @@
 
 import com.fasterxml.jackson.annotation.JsonAnySetter;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 import com.google.common.collect.HashBiMap;
 import org.jspecify.annotations.NonNull;
+import tools.jackson.core.JacksonException;
+import tools.jackson.databind.ObjectMapper;
+import tools.jackson.dataformat.yaml.YAMLFactory;
+import tools.jackson.dataformat.yaml.YAMLMapper;
 
 public class CffImporter extends Importer {
 
@@ -171,7 +173,7 @@ private void setValues(String key, String value) {
 
     @Override
     public ParserResult importDatabase(@NonNull BufferedReader reader) throws IOException {
-        ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
+        ObjectMapper mapper = new YAMLMapper(new YAMLFactory());
         CffFormat citation = mapper.readValue(reader, CffFormat.class);
         List<BibEntry> entriesList = new ArrayList<>();
 
@@ -263,14 +265,13 @@ public ParserResult importDatabase(@NonNull BufferedReader reader) throws IOExce
 
     @Override
     public boolean isRecognizedFormat(@NonNull BufferedReader reader) throws IOException {
-
-        ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
+        ObjectMapper mapper = new YAMLMapper(new YAMLFactory());
         CffFormat citation;
 
         try {
             citation = mapper.readValue(reader, CffFormat.class);
             return (citation != null) && (citation.values.get("title") != null);
-        } catch (IOException e) {
+        } catch (JacksonException e) {
             return false;
         }
     }

jablib/src/main/java/org/jabref/logic/util/MscCodeUtils.java

@@ -7,14 +7,15 @@
 
 import org.jabref.logic.shared.exception.MscCodeLoadingException;
 
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.JsonMappingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.HashBiMap;
 import org.jspecify.annotations.NonNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import tools.jackson.core.exc.StreamReadException;
+import tools.jackson.core.type.TypeReference;
+import tools.jackson.databind.DatabindException;
+import tools.jackson.databind.ObjectMapper;
+import tools.jackson.databind.json.JsonMapper;
 
 public class MscCodeUtils {
     private static final Logger LOGGER = LoggerFactory.getLogger(MscCodeUtils.class);
@@ -29,10 +30,10 @@ public class MscCodeUtils {
     @NonNull
     public static Optional<HashBiMap<String, String>> loadMscCodesFromJson(URL resourceUrl) throws MscCodeLoadingException {
 
-        ObjectMapper mapper = new ObjectMapper();
+        ObjectMapper mapper = new JsonMapper();
         try {
             Map<String, String> mapping =
-                    mapper.readValue(resourceUrl, new TypeReference<>() {
+                    mapper.readValue(resourceUrl.openStream(), new TypeReference<>() {
                     });
             HashBiMap<String, String> result = HashBiMap.create(mapping);
 
@@ -41,7 +42,7 @@ public static Optional<HashBiMap<String, String>> loadMscCodesFromJson(URL resou
             }
 
             return Optional.of(result);
-        } catch (JsonParseException | JsonMappingException e) {
+        } catch (StreamReadException | DatabindException e) {
             LOGGER.error("Error parsing MSC codes from JSON", e);
             throw new MscCodeLoadingException("Failed to parse MSC codes from JSON", e);
         } catch (IOException e) {

jabls/src/main/java/module-info.java

@@ -6,7 +6,7 @@
 
     requires org.jabref.jablib;
 
-    requires com.fasterxml.jackson.databind;
+    requires tools.jackson.databind;
 
     requires com.google.common;
     requires com.google.gson;

jabls/src/main/java/org/jabref/languageserver/ExtensionSettings.java

@@ -1,10 +1,11 @@
 package org.jabref.languageserver;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.gson.JsonObject;
 import org.slf4j.Logger;
+import tools.jackson.core.JacksonException;
+import tools.jackson.databind.JsonNode;
+import tools.jackson.databind.ObjectMapper;
+import tools.jackson.databind.json.JsonMapper;
 
 public class ExtensionSettings {
 
@@ -29,15 +30,15 @@ public static ExtensionSettings getDefaultSettings() {
     }
 
     public void copyFromJsonObject(JsonObject object) {
-        ObjectMapper mapper = new ObjectMapper();
+        ObjectMapper mapper = new JsonMapper();
         try {
             JsonNode node = mapper.readTree(object.toString());
             this.consistencyCheck = node.at("/jabref/consistencyCheck/enabled").asBoolean(this.consistencyCheck);
             this.consistencyCheckRequired = node.at("/jabref/consistencyCheck/required").asBoolean(this.consistencyCheckRequired);
             this.consistencyCheckOptional = node.at("/jabref/consistencyCheck/optional").asBoolean(this.consistencyCheckOptional);
             this.consistencyCheckUnknown = node.at("/jabref/consistencyCheck/unknown").asBoolean(this.consistencyCheckUnknown);
             this.integrityCheck = node.at("/jabref/integrityCheck/enabled").asBoolean(this.integrityCheck);
-        } catch (JsonProcessingException processingException) {
+        } catch (JacksonException processingException) {
             LOGGER.error("Error parsing settings from JSON", processingException);
         }
     }

jabsrv/src/main/java/module-info.java

@@ -10,7 +10,7 @@
     exports org.jabref.http.server.command to jersey.server;
     opens org.jabref.http.server.cayw to com.google.gson, org.glassfish.hk2.locator, org.glassfish.hk2.utilities;
     opens org.jabref.http.dto to com.google.gson;
-    opens org.jabref.http.server.command to com.google.gson, org.glassfish.hk2.locator, org.glassfish.hk2.utilities, com.fasterxml.jackson.databind;
+    opens org.jabref.http.server.command to com.google.gson, org.glassfish.hk2.locator, org.glassfish.hk2.utilities, tools.jackson.databind;
     exports org.jabref.http.server.services;
     exports org.jabref.http;
     opens org.jabref.http.server.resources to org.glassfish.hk2.locator, org.glassfish.hk2.utilities;
@@ -58,6 +58,5 @@
     requires java.logging;
     requires jersey.container.grizzly2.http;
     requires jersey.server;
-    requires com.fasterxml.jackson.annotation;
-    requires com.fasterxml.jackson.databind;
+    requires tools.jackson.databind;
 }

jabsrv/src/main/java/org/jabref/http/server/command/CommandResource.java

@@ -1,7 +1,5 @@
 package org.jabref.http.server.command;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import jakarta.inject.Inject;
 import jakarta.ws.rs.Consumes;
 import jakarta.ws.rs.POST;
@@ -10,6 +8,9 @@
 import jakarta.ws.rs.core.MediaType;
 import jakarta.ws.rs.core.Response;
 import org.glassfish.hk2.api.ServiceLocator;
+import tools.jackson.core.JacksonException;
+import tools.jackson.databind.ObjectMapper;
+import tools.jackson.databind.json.JsonMapper;
 
 @Path("commands")
 public class CommandResource {
@@ -21,13 +22,13 @@ public class CommandResource {
     @Consumes({MediaType.APPLICATION_JSON})
     @Produces({MediaType.APPLICATION_JSON})
     public Response dispatchCommand(String jsonCommand) {
-        ObjectMapper objectMapper = new ObjectMapper();
+        ObjectMapper objectMapper = new JsonMapper();
         try {
             Command command = objectMapper.readValue(jsonCommand, Command.class);
             command.setServiceLocator(serviceLocator);
 
             return command.execute();
-        } catch (JsonProcessingException e) {
+        } catch (JacksonException e) {
             return Response.serverError().entity(e.getMessage()).build();
         }
     }

versions/build.gradle.kts

@@ -32,6 +32,10 @@ dependencies {
     api("org.junit.jupiter:junit-jupiter")
     api("org.junit.platform:junit-platform-launcher")
 
+    api(platform("tools.jackson:jackson-bom:3.0.2"))
+    api("tools.jackson.core:jackson-core")
+    api("tools.jackson.core:jackson-databind")
+    api("tools.jackson.dataformat:jackson-dataformat-yaml")
 }
 
 dependencies.constraints {
@@ -47,8 +51,6 @@ dependencies.constraints {
     api("com.dlsc.gemsfx:gemsfx:3.6.2")
     api("com.dlsc.pdfviewfx:pdfviewfx:3.3.2")
     api("com.ibm.icu:icu4j:72.0.1!!")
-    api("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.20.1")
-    api("com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.20.1")
     api("com.fasterxml:aalto-xml:1.3.4")
     api("org.eclipse.lsp4j:org.eclipse.lsp4j:0.24.0")
     api("org.eclipse.lsp4j:org.eclipse.lsp4j.websocket:0.24.0")