Merge branch 'main' into fix-issue-11189-part-00-refactor-citation-re…

…lation-tab-logic

CHANGELOG.md

@@ -11,10 +11,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a feature for copying entries to libraries, available via the context menu, with an option to include cross-references. [#12374](https://github.com/JabRef/jabref/pull/12374)
 - We introduced a settings parameters to manage citations' relations local storage time-to-live with a default value set to 30 days. [#11189](https://github.com/JabRef/jabref/issues/11189)
 
 ### Changed
 
+- We moved the "Generate a new key for imported entries" option from the "Web search" tab to the "Citation key generator" tab in preferences. [#12436](https://github.com/JabRef/jabref/pull/12436)
 - We improved the offline parsing of BibTeX data from PDF-documents. [#12278](https://github.com/JabRef/jabref/issues/12278)
 - The tab bar is now hidden when only one library is open. [#9971](https://github.com/JabRef/jabref/issues/9971)
 - We improved the citations relations caching by implementing a two levels cache aside strategy including offline storage. [#11189](https://github.com/JabRef/jabref/issues/11189)
@@ -28,6 +30,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where removing the sort from the table did not restore the original order. [#12371](https://github.com/JabRef/jabref/pull/12371)
 - We fixed an issue where JabRef icon merges with dark background [#7771](https://github.com/JabRef/jabref/issues/7771)
 - We fixed an issue where an entry's group was no longer highlighted on selection [#12413](https://github.com/JabRef/jabref/issues/12413)
+- We fixed an issue where BibTeX Strings were not included in the backup file [#12462](https://github.com/JabRef/jabref/issues/12462)
 
 ### Removed
 

build.gradle

@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '7.0.0'
+    id 'org.openrewrite.rewrite' version '7.0.5'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }

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

@@ -38,6 +38,7 @@
 import org.jabref.model.database.event.BibDatabaseContextChangedEvent;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.BibtexString;
 import org.jabref.model.metadata.SaveOrder;
 import org.jabref.model.metadata.SelfContainedSaveOrder;
 
@@ -59,7 +60,7 @@ public class BackupManager {
 
     private static final int DELAY_BETWEEN_BACKUP_ATTEMPTS_IN_SECONDS = 19;
 
-    private static Set<BackupManager> runningInstances = new HashSet<>();
+    private static final Set<BackupManager> RUNNING_INSTANCES = new HashSet<>();
 
     private final BibDatabaseContext bibDatabaseContext;
     private final CliPreferences preferences;
@@ -109,7 +110,7 @@ static Optional<Path> getLatestBackupPath(Path originalPath, Path backupDir) {
     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);
+        RUNNING_INSTANCES.add(backupManager);
         return backupManager;
     }
 
@@ -119,7 +120,7 @@ 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));
+        RUNNING_INSTANCES.stream().filter(instance -> instance.bibDatabaseContext == bibDatabaseContext).forEach(backupManager -> backupManager.discardBackup(backupDir));
     }
 
     /**
@@ -130,8 +131,8 @@ 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.removeIf(instance -> instance.bibDatabaseContext == bibDatabaseContext);
+        RUNNING_INSTANCES.stream().filter(instance -> instance.bibDatabaseContext == bibDatabaseContext).forEach(backupManager -> backupManager.shutdown(backupDir, createBackup));
+        RUNNING_INSTANCES.removeIf(instance -> instance.bibDatabaseContext == bibDatabaseContext);
     }
 
     /**
@@ -268,6 +269,9 @@ void performBackup(Path backupPath) {
                                                 .map(BibEntry.class::cast)
                                                 .toList();
         BibDatabase bibDatabaseClone = new BibDatabase(list);
+        bibDatabaseContext.getDatabase().getStringValues().stream().map(BibtexString::clone)
+                          .map(BibtexString.class::cast)
+                          .forEach(bibDatabaseClone::addString);
         BibDatabaseContext bibDatabaseContextClone = new BibDatabaseContext(bibDatabaseClone, bibDatabaseContext.getMetaData());
 
         Charset encoding = bibDatabaseContext.getMetaData().getEncoding().orElse(StandardCharsets.UTF_8);

src/main/java/org/jabref/gui/externalfiles/ImportHandler.java

@@ -351,7 +351,7 @@ private void addToGroups(List<BibEntry> entries, Collection<GroupTreeNode> group
      * @param entries entries to generate keys for
      */
     private void generateKeys(List<BibEntry> entries) {
-        if (!preferences.getImporterPreferences().isGenerateNewKeyOnImport()) {
+        if (!preferences.getImporterPreferences().shouldGenerateNewKeyOnImport()) {
             return;
         }
         CitationKeyGenerator keyGenerator = new CitationKeyGenerator(

src/main/java/org/jabref/gui/preferences/citationkeypattern/CitationKeyPatternTab.fxml

@@ -27,6 +27,7 @@
         </padding>
     </CheckBox>
     <CheckBox fx:id="generateOnSave" text="%Generate keys before saving (for entries without a key)"/>
+    <CheckBox fx:id="generateNewKeyOnImport" text="%Generate a new key for imported entries (overwriting their default)"/>
 
     <Label text="%Letters after duplicate generated keys"/>
     <VBox spacing="10.0">

src/main/java/org/jabref/gui/preferences/citationkeypattern/CitationKeyPatternTab.java

@@ -24,6 +24,7 @@ public class CitationKeyPatternTab extends AbstractPreferenceTabView<CitationKey
     @FXML private CheckBox overwriteAllow;
     @FXML private CheckBox overwriteWarning;
     @FXML private CheckBox generateOnSave;
+    @FXML private CheckBox generateNewKeyOnImport;
     @FXML private RadioButton letterStartA;
     @FXML private RadioButton letterStartB;
     @FXML private RadioButton letterAlwaysAdd;
@@ -45,11 +46,12 @@ public String getTabName() {
     }
 
     public void initialize() {
-        this.viewModel = new CitationKeyPatternTabViewModel(preferences.getCitationKeyPatternPreferences());
+        this.viewModel = new CitationKeyPatternTabViewModel(preferences.getCitationKeyPatternPreferences(), preferences.getImporterPreferences());
 
         overwriteAllow.selectedProperty().bindBidirectional(viewModel.overwriteAllowProperty());
         overwriteWarning.selectedProperty().bindBidirectional(viewModel.overwriteWarningProperty());
         generateOnSave.selectedProperty().bindBidirectional(viewModel.generateOnSaveProperty());
+        generateNewKeyOnImport.selectedProperty().bindBidirectional(viewModel.generateKeyOnImportProperty());
         letterStartA.selectedProperty().bindBidirectional(viewModel.letterStartAProperty());
         letterStartB.selectedProperty().bindBidirectional(viewModel.letterStartBProperty());
         letterAlwaysAdd.selectedProperty().bindBidirectional(viewModel.letterAlwaysAddProperty());

src/main/java/org/jabref/gui/preferences/citationkeypattern/CitationKeyPatternTabViewModel.java

@@ -15,12 +15,14 @@
 import org.jabref.gui.preferences.PreferenceTabViewModel;
 import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
 import org.jabref.logic.citationkeypattern.GlobalCitationKeyPatterns;
+import org.jabref.logic.importer.ImporterPreferences;
 
 public class CitationKeyPatternTabViewModel implements PreferenceTabViewModel {
 
     private final BooleanProperty overwriteAllowProperty = new SimpleBooleanProperty();
     private final BooleanProperty overwriteWarningProperty = new SimpleBooleanProperty();
     private final BooleanProperty generateOnSaveProperty = new SimpleBooleanProperty();
+    private final BooleanProperty generateKeyOnImportProperty = new SimpleBooleanProperty();
     private final BooleanProperty letterStartAProperty = new SimpleBooleanProperty();
     private final BooleanProperty letterStartBProperty = new SimpleBooleanProperty();
     private final BooleanProperty letterAlwaysAddProperty = new SimpleBooleanProperty();
@@ -36,15 +38,25 @@ public class CitationKeyPatternTabViewModel implements PreferenceTabViewModel {
 
     private final CitationKeyPatternPreferences keyPatternPreferences;
 
-    public CitationKeyPatternTabViewModel(CitationKeyPatternPreferences keyPatternPreferences) {
+    /**
+     * The preference for whether to use the key generator on import is different from how it is configured.
+     * In the UI, there is no better place to put the option than the Citation Key Generator tab.
+     * However, shifting the preference to {@link CitationKeyPatternPreferences} would break the abstraction or hierarchy.
+     * Hence, we keep the preference in {@link ImporterPreferences}, but for the UI, we initialize it here.
+     */
+    private final ImporterPreferences importerPreferences;
+
+    public CitationKeyPatternTabViewModel(CitationKeyPatternPreferences keyPatternPreferences, ImporterPreferences importerPreferences) {
         this.keyPatternPreferences = keyPatternPreferences;
+        this.importerPreferences = importerPreferences;
     }
 
     @Override
     public void setValues() {
         overwriteAllowProperty.setValue(!keyPatternPreferences.shouldAvoidOverwriteCiteKey());
         overwriteWarningProperty.setValue(keyPatternPreferences.shouldWarnBeforeOverwriteCiteKey());
         generateOnSaveProperty.setValue(keyPatternPreferences.shouldGenerateCiteKeysBeforeSaving());
+        generateKeyOnImportProperty.setValue(importerPreferences.shouldGenerateNewKeyOnImport());
 
         if (keyPatternPreferences.getKeySuffix()
                 == CitationKeyPatternPreferences.KeySuffix.ALWAYS) {
@@ -97,6 +109,7 @@ public void storeSettings() {
         keyPatternPreferences.setAvoidOverwriteCiteKey(!overwriteAllowProperty.getValue());
         keyPatternPreferences.setWarnBeforeOverwriteCiteKey(overwriteWarningProperty.getValue());
         keyPatternPreferences.setGenerateCiteKeysBeforeSaving(generateOnSaveProperty.getValue());
+        importerPreferences.setGenerateNewKeyOnImport(generateKeyOnImportProperty.getValue());
         keyPatternPreferences.setKeySuffix(keySuffix);
         keyPatternPreferences.setKeyPatternRegex(keyPatternRegexProperty.getValue());
         keyPatternPreferences.setKeyPatternReplacement(keyPatternReplacementProperty.getValue());
@@ -116,6 +129,10 @@ public BooleanProperty generateOnSaveProperty() {
         return generateOnSaveProperty;
     }
 
+    public BooleanProperty generateKeyOnImportProperty() {
+        return generateKeyOnImportProperty;
+    }
+
     public BooleanProperty letterStartAProperty() {
         return letterStartAProperty;
     }

src/main/java/org/jabref/gui/preferences/websearch/WebSearchTab.fxml

@@ -18,7 +18,6 @@
 
     <Label styleClass="sectionHeader" text="%General"/>
     <CheckBox fx:id="enableWebSearch" text="%Enable web search"/>
-    <CheckBox fx:id="generateNewKeyOnImport" text="%Generate a new key for imported entries (overwriting their default)"/>
     <CheckBox fx:id="warnAboutDuplicatesOnImport" text="%Warn about duplicates on import"/>
     <CheckBox fx:id="downloadLinkedOnlineFiles" text="%Download linked online files"/>
     <CheckBox fx:id="keepDownloadUrl" text="%Store url for downloaded file" />

src/main/java/org/jabref/gui/preferences/websearch/WebSearchTab.java

@@ -31,7 +31,6 @@
 public class WebSearchTab extends AbstractPreferenceTabView<WebSearchTabViewModel> implements PreferencesTab {
 
     @FXML private CheckBox enableWebSearch;
-    @FXML private CheckBox generateNewKeyOnImport;
     @FXML private CheckBox warnAboutDuplicatesOnImport;
     @FXML private CheckBox downloadLinkedOnlineFiles;
     @FXML private CheckBox keepDownloadUrl;
@@ -75,7 +74,6 @@ public void initialize() {
         this.viewModel = new WebSearchTabViewModel(preferences, dialogService, refAiEnabled);
 
         enableWebSearch.selectedProperty().bindBidirectional(viewModel.enableWebSearchProperty());
-        generateNewKeyOnImport.selectedProperty().bindBidirectional(viewModel.generateKeyOnImportProperty());
         warnAboutDuplicatesOnImport.selectedProperty().bindBidirectional(viewModel.warnAboutDuplicatesOnImportProperty());
         downloadLinkedOnlineFiles.selectedProperty().bindBidirectional(viewModel.shouldDownloadLinkedOnlineFiles());
         keepDownloadUrl.selectedProperty().bindBidirectional(viewModel.shouldKeepDownloadUrl());

src/main/java/org/jabref/gui/preferences/websearch/WebSearchTabViewModel.java

@@ -42,7 +42,6 @@
 
 public class WebSearchTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty enableWebSearchProperty = new SimpleBooleanProperty();
-    private final BooleanProperty generateKeyOnImportProperty = new SimpleBooleanProperty();
     private final BooleanProperty warnAboutDuplicatesOnImportProperty = new SimpleBooleanProperty();
     private final BooleanProperty shouldDownloadLinkedOnlineFiles = new SimpleBooleanProperty();
     private final BooleanProperty shouldkeepDownloadUrl = new SimpleBooleanProperty();
@@ -130,7 +129,6 @@ private void setupPlainCitationParsers(CliPreferences preferences) {
     @Override
     public void setValues() {
         enableWebSearchProperty.setValue(importerPreferences.areImporterEnabled());
-        generateKeyOnImportProperty.setValue(importerPreferences.isGenerateNewKeyOnImport());
         warnAboutDuplicatesOnImportProperty.setValue(importerPreferences.shouldWarnAboutDuplicatesOnImport());
         shouldDownloadLinkedOnlineFiles.setValue(filePreferences.shouldDownloadLinkedFiles());
         shouldkeepDownloadUrl.setValue(filePreferences.shouldKeepDownloadUrl());
@@ -163,7 +161,6 @@ public void setValues() {
     @Override
     public void storeSettings() {
         importerPreferences.setImporterEnabled(enableWebSearchProperty.getValue());
-        importerPreferences.setGenerateNewKeyOnImport(generateKeyOnImportProperty.getValue());
         importerPreferences.setWarnAboutDuplicatesOnImport(warnAboutDuplicatesOnImportProperty.getValue());
         filePreferences.setDownloadLinkedFiles(shouldDownloadLinkedOnlineFiles.getValue());
         filePreferences.setKeepDownloadUrl(shouldkeepDownloadUrl.getValue());
@@ -190,10 +187,6 @@ public BooleanProperty enableWebSearchProperty() {
         return enableWebSearchProperty;
     }
 
-    public BooleanProperty generateKeyOnImportProperty() {
-        return generateKeyOnImportProperty;
-    }
-
     public ListProperty<PlainCitationParserChoice> plainCitationParsers() {
         return plainCitationParsers;
     }

src/main/java/org/jabref/logic/ai/chatting/model/Gpt4AllModel.java

@@ -65,7 +65,7 @@ public Response<AiMessage> generate(List<ChatMessage> list) {
                     .uri(URLUtil.createUri(fullUrl))
                     .header("Content-Type", "application/json")
                     .POST(HttpRequest.BodyPublishers.ofString(requestBody))
-                    .timeout(Duration.ofSeconds(60))
+                    .timeout(Duration.ofMinutes(1))
                     .build();
 
             HttpResponse<String> response = httpClient.send(httpRequest, HttpResponse.BodyHandlers.ofString());

src/main/java/org/jabref/logic/importer/ImporterPreferences.java

@@ -70,7 +70,7 @@ public void setImporterEnabled(boolean importerEnabled) {
         this.importerEnabled.set(importerEnabled);
     }
 
-    public boolean isGenerateNewKeyOnImport() {
+    public boolean shouldGenerateNewKeyOnImport() {
         return generateNewKeyOnImport.get();
     }
 

src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

@@ -354,21 +354,18 @@ private void parseJabRefComment(Map<String, String> meta) {
         // We remove all line breaks in the metadata
         // These have been inserted to prevent too long lines when the file was saved, and are not part of the data.
         String comment = buffer.toString().replaceAll("[\\x0d\\x0a]", "");
-        if (MetaData.META_FLAG.equals(comment.substring(0, Math.min(comment.length(), MetaData.META_FLAG.length())))) {
-            if (comment.startsWith(MetaData.META_FLAG)) {
-                String rest = comment.substring(MetaData.META_FLAG.length());
+        if (comment.startsWith(MetaData.META_FLAG)) {
+            String rest = comment.substring(MetaData.META_FLAG.length());
 
-                int pos = rest.indexOf(':');
+            int pos = rest.indexOf(':');
 
-                if (pos > 0) {
-                    meta.put(rest.substring(0, pos), rest.substring(pos + 1));
+            if (pos > 0) {
+                meta.put(rest.substring(0, pos), rest.substring(pos + 1));
 
-                    // meta comments are always re-written by JabRef and not stored in the file
-                    dumpTextReadSoFarToString();
-                }
+                // meta comments are always re-written by JabRef and not stored in the file
+                dumpTextReadSoFarToString();
             }
-        } else if (MetaData.ENTRYTYPE_FLAG
-                          .equals(comment.substring(0, Math.min(comment.length(), MetaData.ENTRYTYPE_FLAG.length())))) {
+        } else if (comment.startsWith(MetaData.ENTRYTYPE_FLAG)) {
             // A custom entry type can also be stored in a
             // "@comment"
             Optional<BibEntryType> typ = MetaDataParser.parseCustomEntryType(comment);

src/test/java/org/jabref/gui/entryeditor/citationrelationtab/CitationsRelationsTabViewModelTest.java

@@ -60,7 +60,7 @@ void setUp() {
         when(preferences.getImportFormatPreferences()).thenReturn(importFormatPreferences);
 
         ImporterPreferences importerPreferences = mock(ImporterPreferences.class, Answers.RETURNS_DEEP_STUBS);
-        when(importerPreferences.isGenerateNewKeyOnImport()).thenReturn(false);
+        when(importerPreferences.shouldGenerateNewKeyOnImport()).thenReturn(false);
         when(preferences.getImporterPreferences()).thenReturn(importerPreferences);
 
         FieldPreferences fieldPreferences = mock(FieldPreferences.class);