Add encoding detection (and pin export to UTF-8)

CHANGELOG.md

@@ -18,16 +18,21 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
 - We introduced a preference to disable fulltext indexing [#8468](https://github.com/JabRef/jabref/issues/8468)
+- When exporting entries, the encoding is always UTF-8
+- When embedding BibTeX data into a PDF, the encoding is always UTF-8
 
 ### Fixed
 
 - We fixed an issue where an exception could occur when saving the preferences [#7614](https://github.com/JabRef/jabref/issues/7614)
 - We fixed an issue where "Copy DOI url" in the right-click menu of the Entry List would just copy the DOI and not the DOI url. [#8389](https://github.com/JabRef/jabref/issues/8389)
 - We fixed an issue where opening the console from the drop-down menu would cause an exception. [#8466](https://github.com/JabRef/jabref/issues/8466)
+- We fixed an issue when reading non-UTF-8 encoded. When no encoding header is present, the encoding is now detected from the file content (and the preference option is disregarded) [#8417](https://github.com/JabRef/jabref/issues/8417)
+- We fixed an issue where modifying a library would trigger reindexing of all PDFs [#8420](https://github.com/JabRef/jabref/issues/8420)
 
 ### Removed
 
 - We removed the option to copy CSL Citation styles data as `XSL_FO`, `ASCIIDOC`, and `RTF` as these have not been working since a long time and are no longer supported in the external library used for processing the styles [#7378](https://github.com/JabRef/jabref/issues/7378)
+- We removed the option to configure the default encoding. The default encoding is now hard-coded to the modern UTF-8 encoding.
 
 
 

build.gradle

@@ -1,12 +1,8 @@
-import groovy.json.JsonSlurper
 import org.gradle.internal.os.OperatingSystem
 import org.jabref.build.JournalAbbreviationConverter
 import org.jabref.build.xjc.XjcPlugin
 import org.jabref.build.xjc.XjcTask
 
-// to update the gradle wrapper, execute
-// ./gradlew wrapper --gradle-version=6.0 --distribution-type=bin
-
 plugins {
     id 'application'
 
@@ -122,6 +118,7 @@ dependencies {
     implementation 'com.h2database:h2-mvstore:2.1.210'
 
     implementation group: 'org.apache.tika', name: 'tika-core', version: '2.3.0'
+    implementation 'com.ibm.icu:icu4j-charset:70.1'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk15on:1.70'

src/main/java/module-info.java

@@ -91,6 +91,7 @@
     requires org.antlr.antlr4.runtime;
     requires org.fxmisc.flowless;
     requires org.apache.tika.core;
+    requires com.ibm.icu;
 
     requires flexmark;
     requires flexmark.ext.gfm.strikethrough;

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -1,7 +1,7 @@
 package org.jabref.cli;
 
 import java.io.IOException;
-import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
@@ -236,7 +236,6 @@ private List<ParserResult> processArguments() {
             if (!loaded.isEmpty()) {
                 writeMetadatatoPdf(loaded,
                         cli.getWriteMetadatatoPdf(),
-                        preferencesService.getGeneralPreferences().getDefaultEncoding(),
                         preferencesService.getXmpPreferences(),
                         preferencesService.getFilePreferences(),
                         preferencesService.getGeneralPreferences().getDefaultBibDatabaseMode(),
@@ -271,7 +270,7 @@ private List<ParserResult> processArguments() {
         return loaded;
     }
 
-    private void writeMetadatatoPdf(List<ParserResult> loaded, String filesAndCitekeys, Charset encoding, XmpPreferences xmpPreferences, FilePreferences filePreferences, BibDatabaseMode databaseMode, BibEntryTypesManager entryTypesManager, FieldWriterPreferences fieldWriterPreferences, boolean writeXMP, boolean embeddBibfile) {
+    private void writeMetadatatoPdf(List<ParserResult> loaded, String filesAndCitekeys, XmpPreferences xmpPreferences, FilePreferences filePreferences, BibDatabaseMode databaseMode, BibEntryTypesManager entryTypesManager, FieldWriterPreferences fieldWriterPreferences, boolean writeXMP, boolean embeddBibfile) {
         if (loaded.isEmpty()) {
             LOGGER.error("The write xmp option depends on a valid import option.");
             return;
@@ -285,7 +284,7 @@ private void writeMetadatatoPdf(List<ParserResult> loaded, String filesAndCiteke
 
         if ("all".equals(filesAndCitekeys)) {
             for (BibEntry entry : dataBase.getEntries()) {
-                writeMetadatatoPDFsOfEntry(databaseContext, entry.getCitationKey().orElse("<no cite key defined>"), entry, encoding, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
+                writeMetadatatoPDFsOfEntry(databaseContext, entry.getCitationKey().orElse("<no cite key defined>"), entry, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
             }
             return;
         }
@@ -300,22 +299,22 @@ private void writeMetadatatoPdf(List<ParserResult> loaded, String filesAndCiteke
             }
         }
 
-        writeMetadatatoPdfByCitekey(databaseContext, dataBase, citeKeys, encoding, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
-        writeMetadatatoPdfByFileNames(databaseContext, dataBase, pdfs, encoding, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
+        writeMetadatatoPdfByCitekey(databaseContext, dataBase, citeKeys, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
+        writeMetadatatoPdfByFileNames(databaseContext, dataBase, pdfs, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
 
     }
 
-    private void writeMetadatatoPDFsOfEntry(BibDatabaseContext databaseContext, String citeKey, BibEntry entry, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
+    private void writeMetadatatoPDFsOfEntry(BibDatabaseContext databaseContext, String citeKey, BibEntry entry, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
         try {
             if (writeXMP) {
-                if (xmpPdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, List.of(entry))) {
+                if (xmpPdfExporter.exportToAllFilesOfEntry(databaseContext, filePreferences, entry, List.of(entry))) {
                     System.out.printf("Successfully written XMP metadata on at least one linked file of %s%n", citeKey);
                 } else {
                     System.err.printf("Cannot write XMP metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.%n", citeKey);
                 }
             }
             if (embeddBibfile) {
-                if (embeddedBibFilePdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, List.of(entry))) {
+                if (embeddedBibFilePdfExporter.exportToAllFilesOfEntry(databaseContext, filePreferences, entry, List.of(entry))) {
                     System.out.printf("Successfully embedded metadata on at least one linked file of %s%n", citeKey);
                 } else {
                     System.out.printf("Cannot embedd metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.%n", citeKey);
@@ -326,20 +325,20 @@ private void writeMetadatatoPDFsOfEntry(BibDatabaseContext databaseContext, Stri
         }
     }
 
-    private void writeMetadatatoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> citeKeys, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
+    private void writeMetadatatoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> citeKeys, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
         for (String citeKey : citeKeys) {
             List<BibEntry> bibEntryList = dataBase.getEntriesByCitationKey(citeKey);
             if (bibEntryList.isEmpty()) {
                 System.err.printf("Skipped - Cannot find %s in library.%n", citeKey);
                 continue;
             }
             for (BibEntry entry : bibEntryList) {
-                writeMetadatatoPDFsOfEntry(databaseContext, citeKey, entry, encoding, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
+                writeMetadatatoPDFsOfEntry(databaseContext, citeKey, entry, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
             }
         }
     }
 
-    private void writeMetadatatoPdfByFileNames(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> fileNames, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
+    private void writeMetadatatoPdfByFileNames(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> fileNames, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
         for (String fileName : fileNames) {
             Path filePath = Path.of(fileName);
             if (!filePath.isAbsolute()) {
@@ -348,14 +347,14 @@ private void writeMetadatatoPdfByFileNames(BibDatabaseContext databaseContext, B
             if (Files.exists(filePath)) {
                 try {
                     if (writeXMP) {
-                        if (xmpPdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
+                        if (xmpPdfExporter.exportToFileByPath(databaseContext, dataBase, filePreferences, filePath)) {
                             System.out.printf("Successfully written XMP metadata of at least one entry to %s%n", fileName);
                         } else {
                             System.out.printf("File %s is not linked to any entry in database.%n", fileName);
                         }
                     }
                     if (embeddBibfile) {
-                        if (embeddedBibFilePdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
+                        if (embeddedBibFilePdfExporter.exportToFileByPath(databaseContext, dataBase, filePreferences, filePath)) {
                             System.out.printf("Successfully embedded XMP metadata of at least one entry to %s%n", fileName);
                         } else {
                             System.out.printf("File %s is not linked to any entry in database.%n", fileName);
@@ -410,9 +409,7 @@ private boolean exportMatches(List<ParserResult> loaded) {
                 // We have an TemplateExporter instance:
                 try {
                     System.out.println(Localization.lang("Exporting") + ": " + data[1]);
-                    exporter.get().export(databaseContext, Path.of(data[1]),
-                            databaseContext.getMetaData().getEncoding().orElse(preferencesService.getGeneralPreferences().getDefaultEncoding()),
-                            matches);
+                    exporter.get().export(databaseContext, Path.of(data[1]), matches);
                 } catch (Exception ex) {
                     System.err.println(Localization.lang("Could not export file") + " '" + data[1] + "': "
                             + Throwables.getStackTraceAsString(ex));
@@ -455,7 +452,6 @@ private List<ParserResult> importAndOpenFiles() {
                     try {
                         pr = OpenDatabase.loadDatabase(
                                 Path.of(aLeftOver),
-                                preferencesService.getGeneralPreferences(),
                                 preferencesService.getImportFormatPreferences(),
                                 Globals.getFileUpdateMonitor());
                     } catch (IOException ex) {
@@ -530,7 +526,7 @@ private void saveDatabase(BibDatabase newBase, String subName) {
             System.out.println(Localization.lang("Saving") + ": " + subName);
             GeneralPreferences generalPreferences = preferencesService.getGeneralPreferences();
             SavePreferences savePreferences = preferencesService.getSavePreferences();
-            AtomicFileWriter fileWriter = new AtomicFileWriter(Path.of(subName), generalPreferences.getDefaultEncoding());
+            AtomicFileWriter fileWriter = new AtomicFileWriter(Path.of(subName), StandardCharsets.UTF_8);
             BibWriter bibWriter = new BibWriter(fileWriter, OS.NEWLINE);
             BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(bibWriter, generalPreferences, savePreferences, Globals.entryTypesManager);
             databaseWriter.saveDatabase(new BibDatabaseContext(newBase));
@@ -539,9 +535,8 @@ private void saveDatabase(BibDatabase newBase, String subName) {
             if (fileWriter.hasEncodingProblems()) {
                 System.err.println(Localization.lang("Warning") + ": "
                         + Localization.lang(
-                        "The chosen encoding '%0' could not encode the following characters:",
-                        generalPreferences.getDefaultEncoding().displayName())
-                        + " " + fileWriter.getEncodingProblems());
+                        "UTF-8 could not be used to encode the following characters:"
+                        + " " + fileWriter.getEncodingProblems()));
             }
         } catch (IOException ex) {
             System.err.println(Localization.lang("Could not save file.") + "\n" + ex.getLocalizedMessage());
@@ -581,8 +576,6 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
                 // We have an exporter:
                 try {
                     exporter.get().export(pr.getDatabaseContext(), Path.of(data[0]),
-                            pr.getDatabaseContext().getMetaData().getEncoding()
-                              .orElse(preferencesService.getGeneralPreferences().getDefaultEncoding()),
                             pr.getDatabaseContext().getDatabase().getEntries());
                 } catch (Exception ex) {
                     System.err.println(Localization.lang("Could not export file") + " '" + data[0] + "': "

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -826,7 +826,7 @@ private MenuBar createMenu() {
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.WRITE_METADATA_TO_PDF, new WriteMetadataToPdfAction(stateManager, prefs.getGeneralPreferences().getDefaultBibDatabaseMode(), Globals.entryTypesManager, prefs.getFieldWriterPreferences(), dialogService, taskExecutor, prefs.getFilePreferences(), prefs.getXmpPreferences(), prefs.getGeneralPreferences().getDefaultEncoding())),
+                factory.createMenuItem(StandardActions.WRITE_METADATA_TO_PDF, new WriteMetadataToPdfAction(stateManager, prefs.getGeneralPreferences().getDefaultBibDatabaseMode(), Globals.entryTypesManager, prefs.getFieldWriterPreferences(), dialogService, taskExecutor, prefs.getFilePreferences(), prefs.getXmpPreferences())),
                 factory.createMenuItem(StandardActions.COPY_LINKED_FILES, new CopyFilesAction(dialogService, prefs, stateManager)),
 
                 new SeparatorMenuItem(),

src/main/java/org/jabref/gui/JabRefGUI.java

@@ -279,7 +279,6 @@ private void openLastEditedDatabases() {
             try {
                 parsedDatabase = OpenDatabase.loadDatabase(
                         dbFile,
-                        preferencesService.getGeneralPreferences(),
                         preferencesService.getImportFormatPreferences(),
                         Globals.getFileUpdateMonitor());
             } catch (IOException ex) {

src/main/java/org/jabref/gui/collab/ChangeScanner.java

@@ -55,7 +55,7 @@ public List<DatabaseChangeViewModel> scanForChanges() {
             // Important: apply all post-load actions
             ImportFormatPreferences importFormatPreferences = preferencesService.getImportFormatPreferences();
             GeneralPreferences generalPreferences = preferencesService.getGeneralPreferences();
-            ParserResult result = OpenDatabase.loadDatabase(database.getDatabasePath().get(), generalPreferences, importFormatPreferences, new DummyFileUpdateMonitor());
+            ParserResult result = OpenDatabase.loadDatabase(database.getDatabasePath().get(), importFormatPreferences, new DummyFileUpdateMonitor());
             BibDatabaseContext databaseOnDisk = result.getDatabaseContext();
 
             // Start looking at changes.

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -370,8 +370,7 @@ private void setupToolBar() {
                 preferencesService.getImporterPreferences(),
                 preferencesService.getImportFormatPreferences(),
                 preferencesService.getFilePreferences(),
-                databaseContext,
-                preferencesService.getGeneralPreferences().getDefaultEncoding());
+                databaseContext);
         for (EntryBasedFetcher fetcher : entryBasedFetchers) {
             MenuItem fetcherMenuItem = new MenuItem(fetcher.getName());
             if (fetcher instanceof PdfMergeMetadataImporter.EntryBasedFetcherWrapper) {
@@ -383,8 +382,7 @@ private void setupToolBar() {
                                     preferencesService.getImporterPreferences(),
                                     preferencesService.getImportFormatPreferences(),
                                     preferencesService.getFilePreferences(),
-                                    databaseContext,
-                                    preferencesService.getGeneralPreferences().getDefaultEncoding());
+                                    databaseContext);
                     fetchAndMerge(pdfMergeMetadataImporter);
                 });
             } else {

src/main/java/org/jabref/gui/exporter/ExportCommand.java

@@ -118,10 +118,6 @@ private void export(Path file, FileChooser.ExtensionFilter selectedExtensionFilt
                 .wrap(() -> {
                     format.export(stateManager.getActiveDatabase().get(),
                             file,
-                            stateManager.getActiveDatabase().get()
-                                 .getMetaData()
-                                 .getEncoding()
-                                 .orElse(preferences.getGeneralPreferences().getDefaultEncoding()),
                             finEntries);
                     return null; // can not use BackgroundTask.wrap(Runnable) because Runnable.run() can't throw Exceptions
                 })