Upgrade lucence to 9.x with proper JPMS

CHANGELOG.md

@@ -19,6 +19,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Changed
 
+- We upgraded to Lucene 9.1 for the fulltext search. Thus, the now created search index cannot be read from older versions of JabRef anylonger and would need to be recreated if you switch back to an older version [#8362](https://github.com/JabRef/jabref/pull/8362)
 - We changed the list of CSL styles to those that support formatting bibliographies [#8421](https://github.com/JabRef/jabref/issues/8421) [citeproc-java#116](https://github.com/michel-kraemer/citeproc-java/issues/116)
 - The CSL preview styles now also support displaying data from cross references entries that are linked via the `crossref` field [#7378](https://github.com/JabRef/jabref/issues/7378)
 - We made the Search button in Web Search wider. We also skewed the panel titles to the left [#8397](https://github.com/JabRef/jabref/issues/8397)

build.gradle

@@ -114,6 +114,12 @@ dependencies {
     implementation 'org.apache.pdfbox:fontbox:3.0.0-RC1'
     implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1'
 
+    implementation 'org.apache.lucene:lucene-core:9.1.0'
+    implementation 'org.apache.lucene:lucene-queryparser:9.1.0'
+    implementation 'org.apache.lucene:lucene-queries:9.1.0'
+    implementation 'org.apache.lucene:lucene-analysis-common:9.1.0'
+    implementation 'org.apache.lucene:lucene-highlighter:9.1.0'
+
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
     implementation 'com.h2database:h2-mvstore:2.1.210'
@@ -557,7 +563,6 @@ jlink {
         requires 'com.google.gson'
         requires 'org.slf4j'
         requires 'jakarta.xml.bind'
-        uses 'org.controlsfx.glyphfont.GlyphFont'
         uses 'com.airhacks.afterburner.views.ResourceLocator'
         uses 'com.airhacks.afterburner.injection.PresenterFactory'
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
@@ -566,11 +571,7 @@ jlink {
         uses 'org.mariadb.jdbc.LocalInfileInterceptor'
         uses 'org.eclipse.jgit.transport.SshSessionFactory'
         uses 'org.eclipse.jgit.lib.GpgSigner'
-        provides 'org.apache.lucene.codecs.DocValuesFormat' with 'org.apache.lucene.codecs.lucene80.Lucene80DocValuesFormat'
-        provides 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
         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.microsoft.applicationinsights.core.dependencies.io.grpc.NameResolverProvider' with 'com.microsoft.applicationinsights.core.dependencies.io.grpc.internal.DnsNameResolverProvider'
         provides 'java.sql.Driver' with 'org.postgresql.Driver'
         provides 'org.mariadb.jdbc.authentication.AuthenticationPlugin' with 'org.mariadb.jdbc.internal.com.send.authentication.CachingSha2PasswordPlugin',
                 'org.mariadb.jdbc.internal.com.send.authentication.ClearPasswordPlugin',
@@ -584,9 +585,7 @@ jlink {
                 'org.mariadb.jdbc.credential.env.EnvCredentialPlugin',
                 'org.mariadb.jdbc.credential.system.PropertiesCredentialPlugin'
         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'
-    }
+                'org.bouncycastle.pqc.jcajce.provider.BouncyCastlePQCProvider'    }
 
     jpackage {
         outputDir = "distribution"

src/main/java/module-info.java

@@ -46,8 +46,6 @@
     with org.jabref.gui.logging.GuiWriter,
          org.jabref.gui.logging.ApplicationInsightsWriter;
 
-    requires applicationinsights.logging.log4j2;
-
     // Preferences and XML
     requires java.prefs;
     requires jakarta.xml.bind;
@@ -65,7 +63,6 @@
     requires org.libreoffice.uno;
 
     // Other modules
-    requires commons.logging;
     requires com.google.common;
     requires jakarta.inject;
     requires reactfx;
@@ -101,10 +98,20 @@
     requires flexmark.util.ast;
     requires flexmark.util.data;
     requires com.h2database.mvstore;
-    requires lucene;
-    requires org.eclipse.jgit;
+
+    // fulltext search
+    requires org.apache.lucene.core;
+    uses org.apache.lucene.codecs.lucene91.Lucene91Codec;
+
+    requires org.apache.lucene.queryparser;
+    uses org.apache.lucene.queryparser.classic.MultiFieldQueryParser;
+    requires org.apache.lucene.analysis.common;
+    requires org.apache.lucene.highlighter;
+
+
     requires com.fasterxml.jackson.databind;
     requires com.fasterxml.jackson.dataformat.yaml;
     requires com.fasterxml.jackson.datatype.jsr310;
     requires net.harawata.appdirs;
+
 }

src/main/java/org/jabref/gui/documentviewer/DocumentViewerViewModel.java

@@ -19,6 +19,7 @@
 
 import org.jabref.gui.AbstractViewModel;
 import org.jabref.gui.StateManager;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.preferences.PreferencesService;
@@ -105,10 +106,13 @@ private void setCurrentEntry(BibEntry entry) {
     }
 
     private void setCurrentDocument(Path path) {
-        try (PDDocument document = Loader.loadPDF(path.toFile())) {
-            currentDocument.set(new PdfDocumentViewModel(document));
+        try {
+            if (FileUtil.isPDFFile(path)) {
+                PDDocument document = Loader.loadPDF(path.toFile());
+                currentDocument.set(new PdfDocumentViewModel(document));
+            }
         } catch (IOException e) {
-            LOGGER.error("Could not set Document Viewer", e);
+            LOGGER.error("Could not set Document Viewer for path {}", path, e);
         }
     }
 

src/main/java/org/jabref/logic/pdf/search/retrieval/PdfSearcher.java

@@ -12,6 +12,7 @@
 import org.jabref.model.pdf.search.SearchResult;
 import org.jabref.model.strings.StringUtil;
 
+import org.apache.lucene.codecs.Codec;
 import org.apache.lucene.index.DirectoryReader;
 import org.apache.lucene.index.IndexReader;
 import org.apache.lucene.queryparser.classic.MultiFieldQueryParser;
@@ -35,6 +36,8 @@ public final class PdfSearcher {
 
     private PdfSearcher(Directory indexDirectory) {
         this.indexDirectory = indexDirectory;
+        Codec.forName("Lucene91");
+
     }
 
     public static PdfSearcher of(BibDatabaseContext databaseContext) throws IOException {
@@ -72,6 +75,7 @@ public PdfSearchResults search(final String searchString, final int maxHits)
                 resultDocs.add(new SearchResult(searcher, query, scoreDoc));
             }
             return new PdfSearchResults(resultDocs);
+
         } catch (ParseException e) {
             LOGGER.warn("Could not parse query: '{}'!\n{}", searchString, e.getMessage());
             return new PdfSearchResults();