Git Integration and UI Improvements

build.gradle

@@ -156,7 +156,7 @@ jacoco {
 dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
-
+    implementation 'org.eclipse.jgit:org.eclipse.jgit:6.7.0.202309050840-r'
     def pdfbox = "3.0.3"
     implementation ("org.apache.pdfbox:pdfbox:$pdfbox") {
         exclude group: 'commons-logging'

src/jmh/java/module-info.java

@@ -0,0 +1,8 @@
+/**
+ * 
+ */
+/**
+ * 
+ */
+module JabRef {
+}

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

@@ -42,7 +42,7 @@
 import org.jabref.gui.autocompleter.SuggestionProvider;
 import org.jabref.gui.autocompleter.SuggestionProviders;
 import org.jabref.gui.autosaveandbackup.AutosaveManager;
-import org.jabref.gui.autosaveandbackup.BackupManager;
+import org.jabref.gui.autosaveandbackup.BackupManagerGit;
 import org.jabref.gui.collab.DatabaseChangeMonitor;
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.entryeditor.EntryEditor;
@@ -105,6 +105,7 @@
 import com.tobiasdiez.easybind.Subscription;
 import org.controlsfx.control.NotificationPane;
 import org.controlsfx.control.action.Action;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -308,7 +309,7 @@ private void onDatabaseLoadingStarted() {
         getMainTable().placeholderProperty().setValue(loadingLayout);
     }
 
-    private void onDatabaseLoadingSucceed(ParserResult result) {
+    private void onDatabaseLoadingSucceed(ParserResult result) throws GitAPIException, IOException {
         OpenDatabaseAction.performPostOpenActions(result, dialogService, preferences);
         if (result.getChangedOnMigration()) {
             this.markBaseChanged();
@@ -343,7 +344,7 @@ private void onDatabaseLoadingFailed(Exception ex) {
         dialogService.showErrorDialogAndWait(title, content, ex);
     }
 
-    private void setDatabaseContext(BibDatabaseContext bibDatabaseContext) {
+    private void setDatabaseContext(BibDatabaseContext bibDatabaseContext) throws GitAPIException, IOException {
         TabPane tabPane = this.getTabPane();
         if (tabPane == null) {
             LOGGER.debug("User interrupted loading. Not showing any library.");
@@ -367,13 +368,13 @@ private void setDatabaseContext(BibDatabaseContext bibDatabaseContext) {
         installAutosaveManagerAndBackupManager();
     }
 
-    public void installAutosaveManagerAndBackupManager() {
+    public void installAutosaveManagerAndBackupManager() throws GitAPIException, IOException {
         if (isDatabaseReadyForAutoSave(bibDatabaseContext)) {
             AutosaveManager autosaveManager = AutosaveManager.start(bibDatabaseContext);
             autosaveManager.registerListener(new AutosaveUiManager(this, dialogService, preferences, entryTypesManager));
         }
         if (isDatabaseReadyForBackup(bibDatabaseContext) && preferences.getFilePreferences().shouldCreateBackup()) {
-            BackupManager.start(this, bibDatabaseContext, Injector.instantiateModelOrService(BibEntryTypesManager.class), preferences);
+            BackupManagerGit.start(this, bibDatabaseContext, Injector.instantiateModelOrService(BibEntryTypesManager.class), preferences);
         }
     }
 
@@ -753,7 +754,7 @@ private boolean confirmClose() {
         }
 
         if (buttonType.equals(discardChanges)) {
-            BackupManager.discardBackup(bibDatabaseContext, preferences.getFilePreferences().getBackupDirectory());
+            LOGGER.debug("Discarding changes");
             return true;
         }
 
@@ -801,9 +802,9 @@ private void onClosed(Event event) {
             LOGGER.error("Problem when shutting down autosave manager", e);
         }
         try {
-            BackupManager.shutdown(bibDatabaseContext,
-                    preferences.getFilePreferences().getBackupDirectory(),
-                    preferences.getFilePreferences().shouldCreateBackup());
+            BackupManagerGit.shutdown(bibDatabaseContext,
+                    preferences.getFilePreferences().shouldCreateBackup(),
+                    preferences.getFilePreferences().getBackupDirectory());
         } catch (RuntimeException e) {
             LOGGER.error("Problem when shutting down backup manager", e);
         }
@@ -1082,7 +1083,15 @@ public static LibraryTab createLibraryTab(BackgroundTask<ParserResult> dataLoadi
 
         newTab.setDataLoadingTask(dataLoadingTask);
         dataLoadingTask.onRunning(newTab::onDatabaseLoadingStarted)
-                       .onSuccess(newTab::onDatabaseLoadingSucceed)
+                       .onSuccess(result -> {
+                           try {
+                               newTab.onDatabaseLoadingSucceed(result);
+                           } catch (Exception e) {
+                               // We need to handle the exception.
+                               // Handle the exception, e.g., log it or show an error dialog
+                               LOGGER.error("An error occurred while loading the database", e);
+                           }
+                       })
                        .onFailure(newTab::onDatabaseLoadingFailed)
                        .executeWith(taskExecutor);
 

src/main/java/org/jabref/gui/autosaveandbackup/BackupManager.java

@@ -41,7 +41,6 @@
 import org.jabref.model.metadata.SaveOrder;
 import org.jabref.model.metadata.SelfContainedSaveOrder;
 
-import com.google.common.eventbus.Subscribe;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -51,6 +50,7 @@
  * rejects all redundant backup tasks. This class does not manage the .bak file which is created when opening a
  * database.
  */
+
 public class BackupManager {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(BackupManager.class);
@@ -107,10 +107,10 @@ static Optional<Path> getLatestBackupPath(Path originalPath, Path backupDir) {
      * @param bibDatabaseContext Associated {@link BibDatabaseContext}
      */
     public static BackupManager start(LibraryTab libraryTab, BibDatabaseContext bibDatabaseContext, BibEntryTypesManager entryTypesManager, CliPreferences preferences) {
-        BackupManager backupManager = new BackupManager(libraryTab, bibDatabaseContext, entryTypesManager, preferences);
-        backupManager.startBackupTask(preferences.getFilePreferences().getBackupDirectory());
-        runningInstances.add(backupManager);
-        return backupManager;
+        BackupManager BackupManager = new BackupManager(libraryTab, bibDatabaseContext, entryTypesManager, preferences);
+        BackupManager.startBackupTask(preferences.getFilePreferences().getBackupDirectory());
+        runningInstances.add(BackupManager);
+        return BackupManager;
     }
 
     /**
@@ -119,7 +119,7 @@ public static BackupManager start(LibraryTab libraryTab, BibDatabaseContext bibD
      * @param bibDatabaseContext Associated {@link BibDatabaseContext}
      */
     public static void discardBackup(BibDatabaseContext bibDatabaseContext, Path backupDir) {
-        runningInstances.stream().filter(instance -> instance.bibDatabaseContext == bibDatabaseContext).forEach(backupManager -> backupManager.discardBackup(backupDir));
+        runningInstances.stream().filter(instance -> instance.bibDatabaseContext == bibDatabaseContext).forEach(BackupManager -> BackupManager.discardBackup(backupDir));
     }
 
     /**
@@ -130,7 +130,7 @@ public static void discardBackup(BibDatabaseContext bibDatabaseContext, Path bac
      * @param backupDir The path to the backup directory
      */
     public static void shutdown(BibDatabaseContext bibDatabaseContext, Path backupDir, boolean createBackup) {
-        runningInstances.stream().filter(instance -> instance.bibDatabaseContext == bibDatabaseContext).forEach(backupManager -> backupManager.shutdown(backupDir, createBackup));
+        runningInstances.stream().filter(instance -> instance.bibDatabaseContext == bibDatabaseContext).forEach(BackupManager -> BackupManager.shutdown(backupDir, createBackup));
         runningInstances.removeIf(instance -> instance.bibDatabaseContext == bibDatabaseContext);
     }
 
@@ -237,6 +237,9 @@ void performBackup(Path backupPath) {
             }
         }
 
+        // l'ordre dans lequel les entrées BibTeX doivent être écrites dans le fichier de sauvegarde.
+        // Si l'utilisateur a trié la table d'affichage des entrées dans JabRef, cet ordre est récupéré.
+        // Sinon, un ordre par défaut est utilisé.
         // code similar to org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase
         SelfContainedSaveOrder saveOrder = bibDatabaseContext
                 .getMetaData().getSaveOrder()
@@ -256,20 +259,26 @@ void performBackup(Path backupPath) {
                     }
                 })
                 .orElse(SaveOrder.getDefaultSaveOrder());
+
+        // Elle configure la sauvegarde, en indiquant qu'aucune sauvegarde supplémentaire (backup) ne doit être créée,
+        // que l'ordre de sauvegarde doit être celui défini, et que les entrées doivent être formatées selon les préférences
+        // utilisateur.
         SelfContainedSaveConfiguration saveConfiguration = (SelfContainedSaveConfiguration) new SelfContainedSaveConfiguration()
                 .withMakeBackup(false)
                 .withSaveOrder(saveOrder)
                 .withReformatOnSave(preferences.getLibraryPreferences().shouldAlwaysReformatOnSave());
 
         // "Clone" the database context
         // We "know" that "only" the BibEntries might be changed during writing (see [org.jabref.logic.exporter.BibDatabaseWriter.savePartOfDatabase])
+        // Chaque entrée BibTeX (comme un article, livre, etc.) est clonée en utilisant la méthode clone().
+        // Cela garantit que les modifications faites pendant la sauvegarde n'affecteront pas l'entrée originale.
         List<BibEntry> list = bibDatabaseContext.getDatabase().getEntries().stream()
                                                 .map(BibEntry::clone)
                                                 .map(BibEntry.class::cast)
                                                 .toList();
         BibDatabase bibDatabaseClone = new BibDatabase(list);
         BibDatabaseContext bibDatabaseContextClone = new BibDatabaseContext(bibDatabaseClone, bibDatabaseContext.getMetaData());
-
+        // Elle définit l'encodage à utiliser pour écrire le fichier. Cela garantit que les caractères spéciaux sont bien sauvegardés.
         Charset encoding = bibDatabaseContext.getMetaData().getEncoding().orElse(StandardCharsets.UTF_8);
         // We want to have successful backups only
         // Thus, we do not use a plain "FileWriter", but the "AtomicFileWriter"
@@ -327,23 +336,25 @@ private void logIfCritical(Path backupPath, IOException e) {
         }
     }
 
-    @Subscribe
-    public synchronized void listen(@SuppressWarnings("unused") BibDatabaseContextChangedEvent event) {
+    public synchronized void listen(BibDatabaseContextChangedEvent event) {
         if (!event.isFilteredOut()) {
             this.needsBackup = true;
         }
     }
 
     private void startBackupTask(Path backupDir) {
         fillQueue(backupDir);
+        // remplie backupFilesQueue les files .sav de le meme bibl
 
         executor.scheduleAtFixedRate(
-                                     // We need to determine the backup path on each action, because we use the timestamp in the filename
-                                     () -> determineBackupPathForNewBackup(backupDir).ifPresent(path -> this.performBackup(path)),
-                                     DELAY_BETWEEN_BACKUP_ATTEMPTS_IN_SECONDS,
-                                     DELAY_BETWEEN_BACKUP_ATTEMPTS_IN_SECONDS,
-                                     TimeUnit.SECONDS);
+                // We need to determine the backup path on each action, because we use the timestamp in the filename
+                () -> determineBackupPathForNewBackup(backupDir).ifPresent(path -> this.performBackup(path)),
+                DELAY_BETWEEN_BACKUP_ATTEMPTS_IN_SECONDS,
+                DELAY_BETWEEN_BACKUP_ATTEMPTS_IN_SECONDS,
+                TimeUnit.SECONDS);
     }
+    // La méthode fillQueue(backupDir) est définie dans le code et son rôle est de lister et d'ajouter
+    // les fichiers de sauvegarde existants dans une file d'attente,
 
     private void fillQueue(Path backupDir) {
         if (!Files.exists(backupDir)) {
@@ -356,6 +367,7 @@ private void fillQueue(Path backupDir) {
                 List<Path> allSavFiles = Files.list(backupDir)
                                               // just list the .sav belonging to the given targetFile
                                               .filter(p -> p.getFileName().toString().startsWith(prefix))
+                                              // tous les files .sav commencerait par ce prefix
                                               .sorted().toList();
                 backupFilesQueue.addAll(allSavFiles);
             } catch (IOException e) {