Merge remote-tracking branch 'upstream/main' into adddeletemultiplefi…

…les#

* upstream/main:
  Add lucence backwards codec (#8667)
  Fix XMP write (#8658)

build.gradle

@@ -119,10 +119,11 @@ dependencies {
     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 'org.apache.lucene:lucene-backward-codecs: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:2.1.212'
+    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'
@@ -187,7 +188,7 @@ dependencies {
 
     implementation 'de.undercouch:citeproc-java:3.0.0-alpha.6'
 
-    // jakarta.activation is already depdency of glassfish
+    // jakarta.activation is already dependency of glassfish
     implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '3.0.1'
     implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 

src/main/java/module-info.java

@@ -102,6 +102,8 @@
     // fulltext search
     requires org.apache.lucene.core;
     uses org.apache.lucene.codecs.lucene91.Lucene91Codec;
+    requires org.apache.lucene.backward_codecs;
+    uses org.apache.lucene.backward_codecs.lucene87.Lucene87Codec;
 
     requires org.apache.lucene.queryparser;
     uses org.apache.lucene.queryparser.classic.MultiFieldQueryParser;

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())),
+                factory.createMenuItem(StandardActions.WRITE_METADATA_TO_PDF, new WriteMetadataToPdfAction(stateManager, 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/exporter/WriteMetadataToPdfAction.java

@@ -34,7 +34,6 @@
 import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.preferences.FilePreferences;
@@ -44,11 +43,12 @@
 public class WriteMetadataToPdfAction extends SimpleCommand {
 
     private final StateManager stateManager;
+    private final BibEntryTypesManager entryTypesManager;
+    private final FieldWriterPreferences fieldWriterPreferences;
     private final DialogService dialogService;
     private final TaskExecutor taskExecutor;
     private final FilePreferences filePreferences;
     private final XmpPreferences xmpPreferences;
-    private final EmbeddedBibFilePdfExporter embeddedBibExporter;
 
     private OptionsDialog optionsDialog;
 
@@ -60,13 +60,14 @@ public class WriteMetadataToPdfAction extends SimpleCommand {
     private int entriesChanged;
     private int errors;
 
-    public WriteMetadataToPdfAction(StateManager stateManager, BibDatabaseMode databaseMode, BibEntryTypesManager entryTypesManager, FieldWriterPreferences fieldWriterPreferences, DialogService dialogService, TaskExecutor taskExecutor, FilePreferences filePreferences, XmpPreferences xmpPreferences) {
+    public WriteMetadataToPdfAction(StateManager stateManager, BibEntryTypesManager entryTypesManager, FieldWriterPreferences fieldWriterPreferences, DialogService dialogService, TaskExecutor taskExecutor, FilePreferences filePreferences, XmpPreferences xmpPreferences) {
         this.stateManager = stateManager;
+        this.entryTypesManager = entryTypesManager;
+        this.fieldWriterPreferences = fieldWriterPreferences;
         this.dialogService = dialogService;
         this.taskExecutor = taskExecutor;
         this.filePreferences = filePreferences;
         this.xmpPreferences = xmpPreferences;
-        this.embeddedBibExporter = new EmbeddedBibFilePdfExporter(databaseMode, entryTypesManager, fieldWriterPreferences);
 
         this.executable.bind(needsDatabase(stateManager));
     }
@@ -189,10 +190,12 @@ private void writeMetadata() {
     }
 
     /**
-     * This writes both XMP data and embeddeds the .bib file
+     * This writes both XMP data and embeds a corresponding .bib file
      */
-    private void writeMetadataToFile(Path file, BibEntry entry, BibDatabaseContext databaseContext, BibDatabase database) throws Exception {
+    synchronized private void writeMetadataToFile(Path file, BibEntry entry, BibDatabaseContext databaseContext, BibDatabase database) throws Exception {
         XmpUtilWriter.writeXmp(file, entry, database, xmpPreferences);
+
+        EmbeddedBibFilePdfExporter embeddedBibExporter = new EmbeddedBibFilePdfExporter(databaseContext.getMode(), entryTypesManager, fieldWriterPreferences);
         embeddedBibExporter.exportToFileByPath(databaseContext, database, filePreferences, file);
     }
 

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -423,16 +423,19 @@ public void writeMetadataToPdf() {
             if (file.isEmpty()) {
                 dialogService.notify(Localization.lang("Failed to write metadata, file %1 not found.", file.map(Path::toString).orElse("")));
             } else {
-                try {
-                    XmpUtilWriter.writeXmp(file.get(), entry, databaseContext.getDatabase(), preferences.getXmpPreferences());
-
-                    EmbeddedBibFilePdfExporter embeddedBibExporter = new EmbeddedBibFilePdfExporter(preferences.getGeneralPreferences().getDefaultBibDatabaseMode(), Globals.entryTypesManager, preferences.getFieldWriterPreferences());
-                    embeddedBibExporter.exportToFileByPath(databaseContext, databaseContext.getDatabase(), preferences.getFilePreferences(), file.get());
-
-                    dialogService.notify(Localization.lang("Success! Finished writing metadata."));
-                } catch (IOException | TransformerException ex) {
-                    dialogService.notify(Localization.lang("Error while writing metadata. See the error log for details."));
-                    LOGGER.error("Error while writing metadata to {}", file.map(Path::toString).orElse(""), ex);
+                synchronized (linkedFile) {
+                    try {
+                        // Similar code can be found at {@link org.jabref.gui.exporter.WriteMetadataToPdfAction.writeMetadataToFile}
+                        XmpUtilWriter.writeXmp(file.get(), entry, databaseContext.getDatabase(), preferences.getXmpPreferences());
+
+                        EmbeddedBibFilePdfExporter embeddedBibExporter = new EmbeddedBibFilePdfExporter(databaseContext.getMode(), Globals.entryTypesManager, preferences.getFieldWriterPreferences());
+                        embeddedBibExporter.exportToFileByPath(databaseContext, databaseContext.getDatabase(), preferences.getFilePreferences(), file.get());
+
+                        dialogService.notify(Localization.lang("Success! Finished writing metadata."));
+                    } catch (IOException | TransformerException ex) {
+                        dialogService.notify(Localization.lang("Error while writing metadata. See the error log for details."));
+                        LOGGER.error("Error while writing metadata to {}", file.map(Path::toString).orElse(""), ex);
+                    }
                 }
             }
             return null;

src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java

@@ -26,7 +26,7 @@
  * This class monitors a set of files for changes. Upon detecting a change it notifies the registered {@link
  * FileUpdateListener}s.
  * <p>
- * Implementation based on https://stackoverflow.com/questions/16251273/can-i-watch-for-single-file-change-with-watchservice-not-the-whole-directory
+ * Implementation based on <a href="https://stackoverflow.com/questions/16251273/can-i-watch-for-single-file-change-with-watchservice-not-the-whole-directory">https://stackoverflow.com/questions/16251273/can-i-watch-for-single-file-change-with-watchservice-not-the-whole-directory</a>.
  */
 public class DefaultFileUpdateMonitor implements Runnable, FileUpdateMonitor {
 

src/main/java/org/jabref/logic/exporter/EmbeddedBibFilePdfExporter.java

@@ -19,6 +19,7 @@
 import org.jabref.logic.util.OS;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.logic.util.io.FileUtil;
+import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
@@ -64,12 +65,19 @@ public void export(BibDatabaseContext databaseContext, Path file, List<BibEntry>
         embedBibTex(bibString, file);
     }
 
-    private void embedBibTex(String bibTeX, Path file) throws IOException {
-        if (!Files.exists(file) || !FileUtil.isPDFFile(file)) {
+    /**
+     * Similar method: {@link XmpUtilWriter#writeXmp(java.nio.file.Path, java.util.List, org.jabref.model.database.BibDatabase, org.jabref.logic.xmp.XmpPreferences)}
+     */
+    private void embedBibTex(String bibTeX, Path path) throws IOException {
+        if (!Files.exists(path) || !FileUtil.isPDFFile(path)) {
             return;
         }
 
-        try (PDDocument document = Loader.loadPDF(file.toFile())) {
+        // Read from another file
+        // Reason: Apache PDFBox does not support writing while the file is opened
+        // See https://issues.apache.org/jira/browse/PDFBOX-4028
+        Path newFile = Files.createTempFile("JabRef", "pdf");
+        try (PDDocument document = Loader.loadPDF(path.toFile())) {
             PDDocumentNameDictionary nameDictionary = document.getDocumentCatalog().getNames();
             PDEmbeddedFilesNameTreeNode efTree;
             Map<String, PDComplexFileSpecification> names;
@@ -111,19 +119,19 @@ private void embedBibTex(String bibTeX, Path file) throws IOException {
                     try {
                         names.put(EMBEDDED_FILE_NAME, fileSpecification);
                     } catch (UnsupportedOperationException e) {
-                        throw new IOException(Localization.lang("File '%0' is write protected.", file.toString()));
+                        throw new IOException(Localization.lang("File '%0' is write protected.", path.toString()));
                     }
                 }
 
                 efTree.setNames(names);
                 nameDictionary.setEmbeddedFiles(efTree);
                 document.getDocumentCatalog().setNames(nameDictionary);
             }
-            Path newFile = Files.createTempFile("JabRef", "pdf");
             document.save(newFile.toFile());
-            FileUtil.copyFile(newFile, file, true);
-            Files.delete(newFile);
+            FileUtil.copyFile(newFile, path, true);
+
         }
+        Files.delete(newFile);
     }
 
     private String getBibString(List<BibEntry> entries) throws IOException {

src/main/java/org/jabref/logic/xmp/DublinCoreExtractor.java

@@ -98,7 +98,7 @@ private void extractAbstract() {
         try {
             description = dcSchema.getDescription();
         } catch (BadFieldValueException e) {
-            LOGGER.warn("Could not get abstract, e");
+            LOGGER.warn("Could not get abstract", e);
         }
         if (!StringUtil.isNullOrEmpty(description)) {
             bibEntry.setField(StandardField.ABSTRACT, description);

src/main/java/org/jabref/logic/xmp/XmpUtilWriter.java

@@ -16,6 +16,7 @@
 
 import javax.xml.transform.TransformerException;
 
+import org.jabref.logic.exporter.EmbeddedBibFilePdfExporter;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
@@ -60,7 +61,8 @@ public class XmpUtilWriter {
      * @throws IOException          If the file could not be written to or could not be found.
      */
     public static void writeXmp(String fileName, BibEntry entry,
-                                BibDatabase database, XmpPreferences xmpPreferences) throws IOException, TransformerException {
+                                BibDatabase database, XmpPreferences xmpPreferences)
+        throws IOException, TransformerException {
         XmpUtilWriter.writeXmp(Path.of(fileName), entry, database, xmpPreferences);
     }
 
@@ -84,7 +86,8 @@ public static void writeXmp(String fileName, BibEntry entry,
      * @throws IOException          If the file could not be written to or could not be found.
      */
     public static void writeXmp(Path file, BibEntry entry,
-                                BibDatabase database, XmpPreferences xmpPreferences) throws IOException, TransformerException {
+                                BibDatabase database, XmpPreferences xmpPreferences)
+        throws IOException, TransformerException {
         List<BibEntry> bibEntryList = new ArrayList<>();
         bibEntryList.add(entry);
         XmpUtilWriter.writeXmp(file, bibEntryList, database, xmpPreferences);
@@ -132,8 +135,8 @@ private static void writeToDCSchema(DublinCoreSchema dcSchema, BibEntry entry, X
      *                 resolve strings. If the database is null the strings will not be resolved.
      */
     private static void writeDublinCore(PDDocument document,
-            List<BibEntry> entries, BibDatabase database, XmpPreferences xmpPreferences)
-            throws IOException, TransformerException {
+                                        List<BibEntry> entries, BibDatabase database, XmpPreferences xmpPreferences)
+        throws IOException, TransformerException {
 
         List<BibEntry> resolvedEntries;
         if (database == null) {
@@ -297,6 +300,8 @@ private static void writeDocumentInformation(PDDocument document,
      * The method will overwrite existing BibTeX-XMP-data, but keep other
      * existing metadata.
      *
+     * The code for using PDFBox is also used at {@link EmbeddedBibFilePdfExporter#embedBibTex(java.lang.String, java.nio.file.Path)}.
+     *
      * @param path          The file to write the entries to.
      * @param bibtexEntries The entries to write to the file. *
      * @param database      maybenull An optional database which the given bibtex entries belong to, which will be used
@@ -307,17 +312,20 @@ private static void writeDocumentInformation(PDDocument document,
      */
     public static void writeXmp(Path path,
                                 List<BibEntry> bibtexEntries, BibDatabase database,
-                                XmpPreferences xmpPreferences) throws IOException, TransformerException {
-
+                                XmpPreferences xmpPreferences)
+        throws IOException, TransformerException {
         List<BibEntry> resolvedEntries;
         if (database == null) {
             resolvedEntries = bibtexEntries;
         } else {
             resolvedEntries = database.resolveForStrings(bibtexEntries, false);
         }
 
+        // Read from another file
+        // Reason: Apache PDFBox does not support writing while the file is opened
+        // See https://issues.apache.org/jira/browse/PDFBOX-4028
+        Path newFile = Files.createTempFile("JabRef", "pdf");
         try (PDDocument document = Loader.loadPDF(path.toFile())) {
-
             if (document.isEncrypted()) {
                 throw new EncryptedPdfsNotSupportedException();
             }
@@ -328,17 +336,16 @@ public static void writeXmp(Path path,
                 XmpUtilWriter.writeDublinCore(document, resolvedEntries, null, xmpPreferences);
             }
 
-            // Save
+            // Save updates to original file
             try {
-                Path newFile = Files.createTempFile("JabRef", "pdf");
                 document.save(newFile.toFile());
                 FileUtil.copyFile(newFile, path, true);
-                Files.delete(newFile);
             } catch (IOException e) {
                 LOGGER.debug("Could not write XMP metadata", e);
                 throw new TransformerException("Could not write XMP metadata: " + e.getLocalizedMessage(), e);
             }
         }
+        Files.delete(newFile);
     }
 
     private static BibEntry getDefaultOrDatabaseEntry(BibEntry defaultEntry, BibDatabase database) {

src/main/java/org/jabref/model/util/FileUpdateMonitor.java

@@ -20,7 +20,7 @@ public interface FileUpdateMonitor {
     void removeListener(Path path, FileUpdateListener listener);
 
     /**
-     * Indicates whether or not the native system's file monitor has successfully started.
+     * Indicates whether the native system's file monitor has successfully started.
      * @return true is process is running; false otherwise.
      */
     boolean isActive();