Upgrade citeproc to 3.x snapshot without graal (#7370)

Author: Siedlerchr

build.gradle

@@ -171,7 +171,7 @@ dependencies {
     implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
 
-    implementation 'de.undercouch:citeproc-java:2.1.0-SNAPSHOT'
+    implementation 'de.undercouch:citeproc-java:3.0.0-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'
@@ -390,7 +390,6 @@ run {
                 'org.controlsfx.controls/impl.org.controlsfx.skin' : 'org.jabref',
 
                 'javafx.controls/com.sun.javafx.scene.control.behavior' : 'com.jfoenix',
-                'com.oracle.truffle.regex/com.oracle.truffle.regex' : 'org.graalvm.truffle',
 
                 // Not sure why we need to restate the controlfx exports
                 // Taken from here: https://github.com/controlsfx/controlsfx/blob/9.0.0/build.gradle#L1
@@ -567,56 +566,51 @@ jlink {
     // The module descriptor automatically generated by the plugin for the merged module contained some invalid entries.
     // 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'
-        requires 'jdk.unsupported'
-        requires 'com.google.gson'
-        requires 'java.management'
-        requires 'java.naming'
-        requires 'java.security.sasl'
-        requires 'jdk.security.jgss'
-        requires 'java.logging'
-        requires 'jdk.xml.dom'
-        requires 'java.sql'
-        requires 'java.rmi'
-        requires 'java.security.jgss'
-        requires 'com.oracle.truffle.regex'
-        requires 'jdk.jsobject'
-        requires 'jdk.management'
-        requires 'jdk.unsupported.desktop'
-        requires 'org.objectweb.asm.util'
-        requires 'java.scripting'
-        requires 'org.objectweb.asm.commons'
-        requires 'org.graalvm.truffle'
-        requires 'java.datatransfer'
-        requires 'java.compiler'
-        requires 'java.sql.rowset'
-        requires 'java.transaction.xa'
-        requires 'org.graalvm.sdk'
+        requires 'java.compiler';
+        requires 'java.datatransfer';
+        requires 'java.desktop';
+        requires 'java.logging';
+        requires 'java.management';
+        requires 'java.naming';
+        requires 'java.net.http';
+        requires 'java.scripting';
+        requires 'java.security.jgss';
+        requires 'java.security.sasl';
+        requires 'java.sql';
+        requires 'java.sql.rowset';
+        requires 'java.transaction.xa';
+        requires 'java.rmi';
+        requires 'java.xml';
+        requires 'jdk.jfr';
+        requires 'jdk.jsobject';
+        requires 'jdk.unsupported';
+        requires 'jdk.unsupported.desktop';
+        requires 'jdk.security.jgss';
+        requires 'jdk.xml.dom';
+        requires 'com.google.gson';
+        requires 'com.sun.xml.fastinfoset';
+        requires 'com.sun.xml.txw2';
         requires 'org.slf4j'
         uses 'org.apache.logging.log4j.util.PropertySource'
         uses 'org.apache.logging.log4j.core.util.WatchEventService'
         uses 'org.apache.logging.log4j.plugins.processor.PluginService'
         uses 'org.controlsfx.glyphfont.GlyphFont'
         uses 'com.airhacks.afterburner.views.ResourceLocator'
-        uses 'com.oracle.truffle.js.runtime.Evaluator'
         uses 'org.apache.logging.log4j.message.ThreadDumpMessage.ThreadInfoFactory'
         uses 'com.airhacks.afterburner.injection.PresenterFactory'
-        uses 'com.oracle.truffle.js.runtime.builtins.JSFunctionLookup'
         uses 'org.apache.logging.log4j.spi.Provider'
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
         uses 'org.mariadb.jdbc.LocalInfileInterceptor'
+        uses 'org.eclipse.jgit.transport.SshSessionFactory';
+        uses 'org.eclipse.jgit.lib.GpgSigner';
         uses 'javax.xml.bind.JAXBContextFactory'
+        provides 'org.apache.lucene.codecs.DocValuesFormat' with 'org.apache.lucene.codecs.lucene80.Lucene80DocValuesFormat';
         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'
         provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'
         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.oracle.truffle.js.runtime.Evaluator' with 'com.oracle.truffle.js.parser.GraalJSEvaluator'
         provides 'com.microsoft.applicationinsights.core.dependencies.io.grpc.NameResolverProvider' with 'com.microsoft.applicationinsights.core.dependencies.io.grpc.internal.DnsNameResolverProvider'
         provides 'org.apache.logging.log4j.util.PropertySource' with 'org.apache.logging.log4j.util.EnvironmentPropertySource',
                 'org.apache.logging.log4j.util.SystemPropertiesPropertySource'
@@ -639,7 +633,6 @@ jlink {
         provides 'java.security.Provider' with 'org.bouncycastle.jce.provider.BouncyCastleProvider',
                 'org.bouncycastle.pqc.jcajce.provider.BouncyCastlePQCProvider'
         provides 'com.microsoft.applicationinsights.core.dependencies.io.grpc.ManagedChannelProvider' with 'com.microsoft.applicationinsights.core.dependencies.io.grpc.netty.shaded.io.grpc.netty.NettyChannelProvider'
-        provides 'com.oracle.truffle.js.runtime.builtins.JSFunctionLookup' with 'com.oracle.truffle.js.builtins.JSDefaultBuiltinLookup'
     }
 
     jpackage {

eclipse.gradle

@@ -34,9 +34,6 @@ eclipse {
                 def javafxfxml = entries.find { isJavafxFXML(it) };
                 javafxfxml.entryAttributes['add-opens'] = 'javafx.fxml/javafx.fxml=org.jabref';
 
-                def graaltruffle = entries.find{ isTruffleGraal(it) } ;
-                graaltruffle.entryAttributes['add-exports'] = 'com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle';
-
                 entries.findAll { isLibrary(it) && isTestScope(it) }.each { //mark test source files
                     it.entryAttributes['test'] = 'true'
                 }
@@ -66,8 +63,6 @@ boolean isJavafxGraphics(entry) { return entry.properties.path.contains('javafx-
 
 boolean isJavafxFXML(entry) { return entry.properties.path.contains('javafx-fxml'); }
 
-boolean isTruffleGraal(entry)  {return entry.properties.path.contains('org.graalvm.regex'); }
-
 // add formatter and cleanup settings to Eclipse settings
 // see http://stackoverflow.com/a/27461890/873282
 

src/main/java/module-info.java

@@ -61,11 +61,6 @@
     requires jbibtex;
     requires citeproc.java;
     requires antlr.runtime;
-    requires org.graalvm.truffle;
-    requires org.graalvm.sdk;
-    requires transitive org.graalvm.js;
-    requires java.scripting;
-    requires jdk.internal.vm.compiler;
     requires org.apache.xmpbox;
     requires de.saxsys.mvvmfx.validation;
     requires com.google.gson;

src/main/java/org/jabref/gui/maintable/MainTableDataModel.java

@@ -54,6 +54,7 @@ public MainTableDataModel(BibDatabaseContext context, PreferencesService prefere
         // We need to wrap the list since otherwise sorting in the table does not work
         entriesSorted = new SortedList<>(entriesFiltered);
         groupViewMode = preferencesService.getGroupViewMode();
+
     }
 
     private boolean isMatched(ObservableList<GroupTreeNode> groups, Optional<SearchQuery> query, BibEntryTableViewModel entry) {

src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java

@@ -68,7 +68,7 @@ private void initialize(String newStyle, CitationStyleOutputFormat newFormat) th
         if ((cslInstance == null) || !Objects.equals(newStyle, style)) {
             // lang and forceLang are set to the default values of other CSL constructors
             cslInstance = new CSL(dataProvider, new JabRefLocaleProvider(),
-                    new DefaultAbbreviationProvider(), null, newStyle, "en-US", false, true);
+                    new DefaultAbbreviationProvider(), null, newStyle, "en-US");
             style = newStyle;
         }