Merge branch 'main' into build-journal-lists-on-deployment

koppor · Sep 2, 2023 · c80630e · c80630e
2 parents d78ce5a + 57f97f2
commit c80630e
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -12,8 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.9 (latest release)"
-        - "3.8.2"
+        - "5.10 (latest release)"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.
@@ -42,7 +41,7 @@ body:
 
   - type: checkboxes
     attributes:
-      label: Checked with the latest development build
+      label: Checked with the latest development build (copy version output from About dialog)
       description: |
         Please always test if the bug is still reproducible in the latest development version. We are constantly improving JabRef and some bugs may already be fixed. If you already use a development version, ensure that you use the latest one.
         You can download the latest development build at: https://builds.jabref.org/main/ . **Please make a backup of your library before you try out this version.**

diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -163,7 +163,7 @@ jobs:
           xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.pkg --keychain-profile "notarytool-profile" --keychain ${{runner.temp}}/keychain/notarization.keychain --wait
           xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.pkg
       - name: Upload with rsync
-        if: ! startsWith(github.ref, 'refs/heads/gh-readonly-queue')
+        if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
         shell: bash
         run: |
           mkdir ${{runner.temp}}/sshkey
@@ -173,7 +173,7 @@ jobs:
           fi
           rsync -Pavz --itemize-changes --stats --partial-dir=/tmp/partial --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i ~/.ssh/id_rsa' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
       - name: Upload to GitHub workflow artifacts store
-        if: ! startsWith(github.ref, 'refs/heads/gh-readonly-queue')
+        if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-${{ matrix.displayName }}

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -229,7 +229,7 @@ jobs:
           rm debian-binary control.tar.* data.tar.*
           mv -f jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64_repackaged.deb  jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64.deb
       - name: Upload to builds.jabref.org (ubuntu)
-        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (! startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
+        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
         uses: Pendect/[email protected]
         env:
           DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -240,13 +240,13 @@ jobs:
           src: 'build/distribution/'
           dest: [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
       - name: Upload to GitHub workflow artifacts store (windows)
-        if: (matrix.os == 'windows-latest') && (! startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
+        if: (matrix.os == 'windows-latest') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-${{ matrix.displayName }}
           path: build/distribution
       - name: Upload to GitHub workflow artifacts store (macos)
-        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (! startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
         uses: actions/upload-artifact@v3
         with:
           # tbn = to-be-notarized
@@ -307,7 +307,7 @@ jobs:
         shell: bash
         run: ${{ matrix.archivePortable }}
       - name: Upload to GitHub workflow artifacts store
-        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (! startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
+        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-macOS
@@ -318,7 +318,7 @@ jobs:
     name: Upload binaries on builds.jabref.org
     runs-on: ubuntu-latest
     needs: [build, notarize]
-    if: ! startsWith(github.ref, 'refs/heads/gh-readonly-queue')
+    if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
     steps:
       - name: Check secrets presence
         id: checksecrets
@@ -353,7 +353,7 @@ jobs:
           name: JabRef-windows
           path: build/distribution
       - name: Get macOS binaries unsigned
-        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (inputs.notarization == false && ! startsWith(github.ref, 'refs/tags/'))
+        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (inputs.notarization == false && !startsWith(github.ref, 'refs/tags/'))
         uses: actions/download-artifact@master
         with:
           name: JabRef-macOS-tbn

diff --git a/.gitignore b/.gitignore
@@ -478,5 +478,7 @@ lib/ojdbc.jar
 # do not ignore JabRef icons (they are ignored by the macos setting above)
 !src/main/java/org/jabref/gui/icon
 
+!**/autosaveandbackup/*.bak
+
 # generated during release process
 CHANGELOG.html
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- It is possible again to use "current table sort order" for the order of entries when saving. [#9869](https://github.com/JabRef/jabref/issues/9869)
+
 ### Removed
 
 ## [5.10] - 2023-09-02

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -54,6 +54,8 @@
 import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.actions.StandardActions;
+import org.jabref.gui.autosaveandbackup.AutosaveManager;
+import org.jabref.gui.autosaveandbackup.BackupManager;
 import org.jabref.gui.auximport.NewSubLibraryAction;
 import org.jabref.gui.bibtexextractor.ExtractBibtexAction;
 import org.jabref.gui.citationkeypattern.GenerateCitationKeyAction;
@@ -118,8 +120,6 @@
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.TaskExecutor;
-import org.jabref.logic.autosaveandbackup.AutosaveManager;
-import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.citationstyle.CitationStyleOutputFormat;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.IdFetcher;

diff --git a/src/main/java/org/jabref/gui/LibraryTab.java b/src/main/java/org/jabref/gui/LibraryTab.java
@@ -26,6 +26,8 @@
 import org.jabref.gui.autocompleter.AutoCompletePreferences;
 import org.jabref.gui.autocompleter.PersonNameSuggestionProvider;
 import org.jabref.gui.autocompleter.SuggestionProviders;
+import org.jabref.gui.autosaveandbackup.AutosaveManager;
+import org.jabref.gui.autosaveandbackup.BackupManager;
 import org.jabref.gui.collab.DatabaseChangeMonitor;
 import org.jabref.gui.dialogs.AutosaveUiManager;
 import org.jabref.gui.entryeditor.EntryEditor;
@@ -39,8 +41,6 @@
 import org.jabref.gui.undo.UndoableRemoveEntries;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.logic.autosaveandbackup.AutosaveManager;
-import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.citationstyle.CitationStyleCache;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.util.FileFieldParser;
@@ -294,7 +294,7 @@ public void installAutosaveManagerAndBackupManager() {
             autosaveManager.registerListener(new AutosaveUiManager(this, preferencesService, entryTypesManager));
         }
         if (isDatabaseReadyForBackup(bibDatabaseContext) && preferencesService.getFilePreferences().shouldCreateBackup()) {
-            BackupManager.start(bibDatabaseContext, Globals.entryTypesManager, preferencesService);
+            BackupManager.start(this, bibDatabaseContext, Globals.entryTypesManager, preferencesService);
         }
     }
 

diff --git a/...ic/autosaveandbackup/AutosaveManager.java → ...ui/autosaveandbackup/AutosaveManager.java b/...ic/autosaveandbackup/AutosaveManager.java → ...ui/autosaveandbackup/AutosaveManager.java
@@ -1,4 +1,4 @@
-package org.jabref.logic.autosaveandbackup;
+package org.jabref.gui.autosaveandbackup;
 
 import java.util.HashSet;
 import java.util.Set;

diff --git a/...ogic/autosaveandbackup/BackupManager.java → .../gui/autosaveandbackup/BackupManager.java b/...ogic/autosaveandbackup/BackupManager.java → .../gui/autosaveandbackup/BackupManager.java
@@ -1,4 +1,4 @@
-package org.jabref.logic.autosaveandbackup;
+package org.jabref.gui.autosaveandbackup;
 
 import java.io.IOException;
 import java.io.Writer;
@@ -19,6 +19,11 @@
 import java.util.concurrent.ScheduledThreadPoolExecutor;
 import java.util.concurrent.TimeUnit;
 
+import javafx.scene.control.TableColumn;
+
+import org.jabref.gui.LibraryTab;
+import org.jabref.gui.maintable.BibEntryTableViewModel;
+import org.jabref.gui.maintable.columns.MainTableColumn;
 import org.jabref.logic.bibtex.InvalidFieldValueException;
 import org.jabref.logic.exporter.AtomicFileWriter;
 import org.jabref.logic.exporter.BibWriter;
@@ -31,6 +36,7 @@
 import org.jabref.model.database.event.BibDatabaseContextChangedEvent;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.metadata.SaveOrder;
+import org.jabref.model.metadata.SelfContainedSaveOrder;
 import org.jabref.preferences.PreferencesService;
 
 import com.google.common.eventbus.Subscribe;
@@ -58,17 +64,19 @@ public class BackupManager {
     private final ScheduledThreadPoolExecutor executor;
     private final CoarseChangeFilter changeFilter;
     private final BibEntryTypesManager entryTypesManager;
+    private final LibraryTab libraryTab;
 
     // Contains a list of all backup paths
     // During a write, the less recent backup file is deleted
     private final Queue<Path> backupFilesQueue = new LinkedBlockingQueue<>();
     private boolean needsBackup = false;
 
-    BackupManager(BibDatabaseContext bibDatabaseContext, BibEntryTypesManager entryTypesManager, PreferencesService preferences) {
+    BackupManager(LibraryTab libraryTab, BibDatabaseContext bibDatabaseContext, BibEntryTypesManager entryTypesManager, PreferencesService preferences) {
         this.bibDatabaseContext = bibDatabaseContext;
         this.entryTypesManager = entryTypesManager;
         this.preferences = preferences;
         this.executor = new ScheduledThreadPoolExecutor(2);
+        this.libraryTab = libraryTab;
 
         changeFilter = new CoarseChangeFilter(bibDatabaseContext);
         changeFilter.registerListener(this);
@@ -96,8 +104,8 @@ static Optional<Path> getLatestBackupPath(Path originalPath, Path backupDir) {
      *
      * @param bibDatabaseContext Associated {@link BibDatabaseContext}
      */
-    public static BackupManager start(BibDatabaseContext bibDatabaseContext, BibEntryTypesManager entryTypesManager, PreferencesService preferences) {
-        BackupManager backupManager = new BackupManager(bibDatabaseContext, entryTypesManager, preferences);
+    public static BackupManager start(LibraryTab libraryTab, BibDatabaseContext bibDatabaseContext, BibEntryTypesManager entryTypesManager, PreferencesService preferences) {
+        BackupManager backupManager = new BackupManager(libraryTab, bibDatabaseContext, entryTypesManager, preferences);
         backupManager.startBackupTask(preferences.getFilePreferences().getBackupDirectory());
         runningInstances.add(backupManager);
         return backupManager;
@@ -215,18 +223,36 @@ void performBackup(Path backupPath) {
 
         // We opted for "while" to delete backups in case there are more than 10
         while (backupFilesQueue.size() >= MAXIMUM_BACKUP_FILE_COUNT) {
-            Path lessRecentBackupFile = backupFilesQueue.poll();
+            Path oldestBackupFile = backupFilesQueue.poll();
             try {
-                Files.delete(lessRecentBackupFile);
+                Files.delete(oldestBackupFile);
             } catch (IOException e) {
-                LOGGER.error("Could not delete backup file {}", lessRecentBackupFile, e);
+                LOGGER.error("Could not delete backup file {}", oldestBackupFile, e);
             }
         }
 
         // code similar to org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase
+        SelfContainedSaveOrder saveOrder = bibDatabaseContext
+                .getMetaData().getSaveOrder()
+                .map(so -> {
+                    if (so.getOrderType() == SaveOrder.OrderType.TABLE) {
+                        // We need to "flatten out" SaveOrder.OrderType.TABLE as BibWriter does not have access to preferences
+                        List<TableColumn<BibEntryTableViewModel, ?>> sortOrder = libraryTab.getMainTable().getSortOrder();
+                        return new SelfContainedSaveOrder(
+                                SaveOrder.OrderType.SPECIFIED,
+                                sortOrder.stream()
+                                         .filter(col -> col instanceof MainTableColumn<?>)
+                                         .map(column -> ((MainTableColumn<?>) column).getModel())
+                                         .flatMap(model -> model.getSortCriteria().stream())
+                                         .toList());
+                    } else {
+                        return SelfContainedSaveOrder.of(so);
+                    }
+                })
+                .orElse(SaveOrder.getDefaultSaveOrder());
         SaveConfiguration saveConfiguration = new SaveConfiguration()
                 .withMakeBackup(false)
-                .withSaveOrder(bibDatabaseContext.getMetaData().getSaveOrder().orElse(SaveOrder.getDefaultSaveOrder()))
+                .withSaveOrder(saveOrder)
                 .withReformatOnSave(preferences.getLibraryPreferences().shouldAlwaysReformatOnSave());
 
         Charset encoding = bibDatabaseContext.getMetaData().getEncoding().orElse(StandardCharsets.UTF_8);

diff --git a/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java b/src/main/java/org/jabref/gui/collab/metedatachange/MetadataChangeDetailsView.java
@@ -1,6 +1,7 @@
 package org.jabref.gui.collab.metedatachange;
 
 import javafx.scene.control.Label;
+import javafx.scene.control.ScrollPane;
 import javafx.scene.layout.VBox;
 
 import org.jabref.gui.collab.DatabaseChangeDetailsView;
@@ -17,20 +18,24 @@ public MetadataChangeDetailsView(MetadataChange metadataChange, PreferencesServi
         header.getStyleClass().add("sectionHeader");
         container.getChildren().add(header);
 
-        for (MetaDataDiff.Difference change : metadataChange.getMetaDataDiff().getDifferences(preferencesService)) {
-            container.getChildren().add(new Label(getDifferenceString(change)));
+        for (MetaDataDiff.Difference diff : metadataChange.getMetaDataDiff().getDifferences(preferencesService)) {
+            container.getChildren().add(new Label(getDifferenceString(diff.differenceType())));
+            container.getChildren().add(new Label(diff.originalObject().toString()));
+            container.getChildren().add(new Label(diff.newObject().toString()));
         }
 
-        setLeftAnchor(container, 8d);
-        setTopAnchor(container, 8d);
-        setRightAnchor(container, 8d);
-        setBottomAnchor(container, 8d);
+        ScrollPane scrollPane = new ScrollPane(container);
+        scrollPane.setFitToWidth(true);
+        getChildren().setAll(scrollPane);
 
-        getChildren().setAll(container);
+        setLeftAnchor(scrollPane, 8d);
+        setTopAnchor(scrollPane, 8d);
+        setRightAnchor(scrollPane, 8d);
+        setBottomAnchor(scrollPane, 8d);
     }
 
-    private String getDifferenceString(MetaDataDiff.Difference change) {
-        return switch (change) {
+    private String getDifferenceString(MetaDataDiff.DifferenceType changeType) {
+        return switch (changeType) {
             case PROTECTED ->
                     Localization.lang("Library protection");
             case GROUPS_ALTERED ->

diff --git a/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java b/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java
@@ -8,13 +8,13 @@
 import javafx.scene.control.ButtonType;
 
 import org.jabref.gui.DialogService;
+import org.jabref.gui.autosaveandbackup.BackupManager;
 import org.jabref.gui.backup.BackupResolverDialog;
 import org.jabref.gui.collab.DatabaseChange;
 import org.jabref.gui.collab.DatabaseChangeList;
 import org.jabref.gui.collab.DatabaseChangeResolverFactory;
 import org.jabref.gui.collab.DatabaseChangesResolverDialog;
 import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.ParserResult;

diff --git a/src/main/java/org/jabref/gui/entryeditor/RequiredFieldsTab.java b/src/main/java/org/jabref/gui/entryeditor/RequiredFieldsTab.java
@@ -56,7 +56,7 @@ protected Set<Field> determineFieldsToShow(BibEntry entry) {
         Set<Field> fields = new LinkedHashSet<>();
         if (entryType.isPresent()) {
             for (OrFields orFields : entryType.get().getRequiredFields()) {
-                fields.addAll(orFields);
+                fields.addAll(orFields.getFields());
             }
             // Add the edit field for Bibtex-key.
             fields.add(InternalField.KEY_FIELD);