Switch to Jakarta libraries (#5247)

* Move to jakarta

https://wiki.eclipse.org/New_Maven_Coordinates

* Revert "Switch from tika-parsers to tika-core (#5217)"

This reverts commit 29cf4f2

* Revert "Revert "Switch from tika-parsers to tika-core (#5217)""

This reverts commit be558fe

* Fix build

* Fix build

Author: tobiasdiez

build.gradle

@@ -102,9 +102,10 @@ configurations {
     errorprone
     libreoffice
 
-    // TODO: Workaround for "ResolutionException: Modules java.annotation and jsr305 export package javax.annotation to module httpcore.nio"
+    // TODO: Remove the following workaround for split error messages such as
+    // error: module java.xml.bind reads package javax.annotation from both jsr305 and java.annotation
     compile {
-        exclude group: 'com.google.code.findbugs', module: 'jsr305'
+        exclude group: "javax.activation"
     }
 }
 
@@ -149,9 +150,12 @@ dependencies {
 
     compile 'org.postgresql:postgresql:42.2.6'
 
-    compile 'com.google.guava:guava:28.0-jre'
+    compile ('com.google.guava:guava:28.0-jre') {
+        // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
+        exclude module: "jsr305"
+    }
 
-    compile group: 'javax.annotation', name: 'javax.annotation-api', version: '1.3.2'
+    compile group: 'jakarta.annotation', name: 'jakarta.annotation-api', version: '1.3.4'
 
     // JavaFX stuff
     compile 'de.jensd:fontawesomefx-commons:11.0'
@@ -161,7 +165,7 @@ dependencies {
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
     compile 'org.fxmisc.richtext:richtextfx:0.10.1'
-    compile 'javax.inject:javax.inject:1'
+    compile group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     compile 'com.jfoenix:jfoenix:9.0.9'
     compile 'org.controlsfx:controlsfx:11.0.0'
 
@@ -177,9 +181,9 @@ dependencies {
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 
-    compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.1'
-    compile group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.1'
-    compile 'com.sun.activation:javax.activation:1.2.0'
+    compile group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
+    compile group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
+    compile group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.2'
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.6'
 
@@ -198,7 +202,9 @@ dependencies {
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.12.1'
     testCompile 'org.mockito:mockito-core:3.0.0'
     //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
-    testCompile 'org.reflections:reflections:0.9.11'
+    testCompile ('org.reflections:reflections:0.9.11') {
+        exclude module: "jsr305"
+    }
     testCompile 'org.xmlunit:xmlunit-core:2.6.3'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
     testCompile 'com.tngtech.archunit:archunit-junit5-api:0.11.0'
@@ -604,7 +610,7 @@ jlink {
     // The pom.xml associated with such a non-modular artifact does not mention that the artifact depends on the removed code
     // (because the artifact was published when this code was still available in the JDK).
     forceMerge "javafx"
-    forceMerge "controlsfx", "bcprov", "jaxb", "javax", "istack", "stax", "log4j"
+    forceMerge "controlsfx", "bcprov", "jaxb", "istack", "stax", "log4j"
 
     // TODO: Remove the following correction to the merged module
     // The module descriptor automatically generated by the plugin for the merged module contained some invalid entries.
@@ -637,7 +643,6 @@ jlink {
         provides 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
         provides 'org.apache.commons.logging.LogFactory' with 'org.apache.logging.log4j.jcl.LogFactoryImpl'
         provides 'org.slf4j.spi.SLF4JServiceProvider' with 'org.apache.logging.slf4j.SLF4JServiceProvider'
-        provides 'javax.annotation.processing.Processor' with 'org.apache.logging.log4j.core.config.plugins.processor.PluginProcessor'
         provides 'com.microsoft.applicationinsights.core.dependencies.io.grpc.ServerProvider' with 'com.microsoft.applicationinsights.core.dependencies.io.grpc.netty.shaded.io.grpc.netty.NettyServerProvider'
         provides 'com.microsoft.applicationinsights.core.dependencies.io.grpc.NameResolverProvider' with 'com.microsoft.applicationinsights.core.dependencies.io.grpc.internal.DnsNameResolverProvider'
         provides 'java.security.Provider' with 'org.bouncycastle.jce.provider.BouncyCastleProvider', 'org.bouncycastle.pqc.jcajce.provider.BouncyCastlePQCProvider'

src/main/java/module-info.java

@@ -1,74 +1,75 @@
 open module org.jabref {
-  exports org.jabref;
+    exports org.jabref;
 
-  exports org.jabref.gui;
-  exports org.jabref.gui.logging;
-  exports org.jabref.gui.maintable;
-  exports org.jabref.gui.specialfields;
+    exports org.jabref.gui;
+    exports org.jabref.gui.logging;
+    exports org.jabref.gui.maintable;
+    exports org.jabref.gui.specialfields;
 
-  exports org.jabref.model.database;
+    exports org.jabref.model.database;
 
-  exports org.jabref.logic;
-  exports org.jabref.logic.citationstyle;
-  exports org.jabref.logic.search;
+    exports org.jabref.logic;
+    exports org.jabref.logic.citationstyle;
+    exports org.jabref.logic.search;
 
-  // Swing
-  requires java.desktop;
+    // Swing
+    requires java.desktop;
 
-  // SQL
-  requires java.sql;
+    // SQL
+    requires java.sql;
 
-  // JavaFX
-  requires javafx.graphics;
-  requires javafx.swing;
-  requires javafx.controls;
-  requires javafx.web;
-  requires javafx.fxml;
-  requires afterburner.fx;
-  requires com.jfoenix;
-  requires de.saxsys.mvvmfx;
-  requires de.jensd.fx.fontawesomefx.commons;
-  requires de.jensd.fx.fontawesomefx.materialdesignicons;
-  requires org.controlsfx.controls;
+    // JavaFX
+    requires javafx.graphics;
+    requires javafx.swing;
+    requires javafx.controls;
+    requires javafx.web;
+    requires javafx.fxml;
+    requires afterburner.fx;
+    requires com.jfoenix;
+    requires de.saxsys.mvvmfx;
+    requires de.jensd.fx.fontawesomefx.commons;
+    requires de.jensd.fx.fontawesomefx.materialdesignicons;
+    requires org.controlsfx.controls;
 
-  provides com.airhacks.afterburner.views.ResourceLocator
-      with org.jabref.gui.util.JabRefResourceLocator;
+    provides com.airhacks.afterburner.views.ResourceLocator
+            with org.jabref.gui.util.JabRefResourceLocator;
 
-  provides com.airhacks.afterburner.injection.PresenterFactory
-      with org.jabref.gui.DefaultInjector;
+    provides com.airhacks.afterburner.injection.PresenterFactory
+            with org.jabref.gui.DefaultInjector;
 
-  // Logging
-  requires org.slf4j;
-  requires org.apache.logging.log4j;
-  requires org.apache.logging.log4j.core;
-  requires applicationinsights.logging.log4j2;
+    // Logging
+    requires org.slf4j;
+    requires org.apache.logging.log4j;
+    requires org.apache.logging.log4j.core;
+    requires applicationinsights.logging.log4j2;
 
-  // Preferences and XML
-  requires java.prefs;
-  requires java.xml.bind;
-  requires jdk.xml.dom;
+    // Preferences and XML
+    requires java.prefs;
+    requires java.xml.bind;
+    requires jdk.xml.dom;
 
-  // Annotations (@PostConstruct)
-  requires java.annotation;
+    // Annotations (@PostConstruct)
+    requires java.annotation;
 
-  // Microsoft application insights
-  requires applicationinsights.core;
+    // Microsoft application insights
+    requires applicationinsights.core;
 
-  // Libre Office
-  requires org.jabref.thirdparty.libreoffice;
+    // Libre Office
+    requires org.jabref.thirdparty.libreoffice;
 
-  // Other modules
-  requires commons.logging;
-  requires com.google.common;
-  requires easybind;
-  requires javax.inject;
-  requires pdfbox;
-  requires reactfx;
-  requires commons.cli;
-  requires httpclient;
-  requires com.github.tomtung.latex2unicode;
-  requires jbibtex;
-  requires citeproc.java;
-  requires antlr.runtime;
-  requires commons.lang3;
+    // Other modules
+    requires commons.logging;
+    requires com.google.common;
+    requires easybind;
+    requires jakarta.inject;
+    requires pdfbox;
+    requires reactfx;
+    requires commons.cli;
+    requires httpclient;
+    requires com.github.tomtung.latex2unicode;
+    requires jbibtex;
+    requires citeproc.java;
+    requires antlr.runtime;
+    requires commons.lang3;
+    requires xmpbox;
 }

src/main/java/org/jabref/logic/l10n/Localization.java

@@ -66,7 +66,7 @@ public static String lang(String key, String... params) {
     public static void setLanguage(Language language) {
         Optional<Locale> knownLanguage = Language.convertToSupportedLocale(language);
         final Locale defaultLocale = Locale.getDefault();
-        if (!knownLanguage.isPresent()) {
+        if (knownLanguage.isEmpty()) {
             LOGGER.warn("Language " + language + " is not supported by JabRef (Default:" + defaultLocale + ")");
             setLanguage(Language.ENGLISH);
             return;