Add pref switch to not store url

CHANGELOG.md

@@ -26,6 +26,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We enabled creating a new file link manually. [#11017](https://github.com/JabRef/jabref/issues/11017)
 - We added a toggle button to invert the selected groups. [#9073](https://github.com/JabRef/jabref/issues/9073)
 - We reintroduced the floating search in the main table. [#4237](https://github.com/JabRef/jabref/issues/4237)
+- We added a switch not to store the linked file URL, because it caused troubles at other apps. [#11735](https://github.com/JabRef/jabref/pull/11735)
 - When starting a new SLR, the selected catalogs now persist within and across JabRef sessions. [koppor#614](https://github.com/koppor/jabref/issues/614)
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
 

src/main/java/org/jabref/gui/linkedfile/DownloadLinkedFileAction.java

@@ -169,9 +169,9 @@ private void onSuccess(Path targetDirectory, Path downloadedFile) {
         if (newLinkedFile.getDescription().isEmpty() && !linkedFile.getDescription().isEmpty()) {
             newLinkedFile.setDescription((linkedFile.getDescription()));
         }
-        if (linkedFile.getSourceUrl().isEmpty() && LinkedFile.isOnlineLink(linkedFile.getLink())) {
+        if (linkedFile.getSourceUrl().isEmpty() && LinkedFile.isOnlineLink(linkedFile.getLink()) && filePreferences.shouldKeepDownloadUrl()) {
             newLinkedFile.setSourceURL(linkedFile.getLink());
-        } else {
+        } else if (filePreferences.shouldKeepDownloadUrl()) {
             newLinkedFile.setSourceURL(linkedFile.getSourceUrl());
         }
 

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

@@ -20,6 +20,7 @@
     <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" />
 
     <Label styleClass="sectionHeader" text="%Custom DOI URI"/>
     <HBox alignment="CENTER_LEFT" spacing="10.0">

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

@@ -29,6 +29,7 @@ public class WebSearchTab extends AbstractPreferenceTabView<WebSearchTabViewMode
     @FXML private CheckBox generateNewKeyOnImport;
     @FXML private CheckBox warnAboutDuplicatesOnImport;
     @FXML private CheckBox downloadLinkedOnlineFiles;
+    @FXML private CheckBox keepDownloadUrl;
 
     @FXML private CheckBox useCustomDOI;
     @FXML private TextField useCustomDOIName;
@@ -66,6 +67,7 @@ public void initialize() {
         generateNewKeyOnImport.selectedProperty().bindBidirectional(viewModel.generateKeyOnImportProperty());
         warnAboutDuplicatesOnImport.selectedProperty().bindBidirectional(viewModel.warnAboutDuplicatesOnImportProperty());
         downloadLinkedOnlineFiles.selectedProperty().bindBidirectional(viewModel.shouldDownloadLinkedOnlineFiles());
+        keepDownloadUrl.selectedProperty().bindBidirectional(viewModel.shouldKeepDownloadUrl());
 
         grobidEnabled.selectedProperty().bindBidirectional(viewModel.grobidEnabledProperty());
         grobidURL.textProperty().bindBidirectional(viewModel.grobidURLProperty());

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

@@ -46,6 +46,7 @@ public class WebSearchTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty generateKeyOnImportProperty = new SimpleBooleanProperty();
     private final BooleanProperty warnAboutDuplicatesOnImportProperty = new SimpleBooleanProperty();
     private final BooleanProperty shouldDownloadLinkedOnlineFiles = new SimpleBooleanProperty();
+    private final BooleanProperty shouldkeepDownloadUrl = new SimpleBooleanProperty();
 
     private final BooleanProperty useCustomDOIProperty = new SimpleBooleanProperty();
     private final StringProperty useCustomDOINameProperty = new SimpleStringProperty("");
@@ -83,7 +84,7 @@ public void setValues() {
         generateKeyOnImportProperty.setValue(importerPreferences.isGenerateNewKeyOnImport());
         warnAboutDuplicatesOnImportProperty.setValue(importerPreferences.shouldWarnAboutDuplicatesOnImport());
         shouldDownloadLinkedOnlineFiles.setValue(filePreferences.shouldDownloadLinkedFiles());
-
+        shouldkeepDownloadUrl.setValue(filePreferences.shouldKeepDownloadUrl());
         useCustomDOIProperty.setValue(doiPreferences.isUseCustom());
         useCustomDOINameProperty.setValue(doiPreferences.getDefaultBaseURI());
 
@@ -110,7 +111,7 @@ public void storeSettings() {
         importerPreferences.setGenerateNewKeyOnImport(generateKeyOnImportProperty.getValue());
         importerPreferences.setWarnAboutDuplicatesOnImport(warnAboutDuplicatesOnImportProperty.getValue());
         filePreferences.setDownloadLinkedFiles(shouldDownloadLinkedOnlineFiles.getValue());
-
+        filePreferences.setKeepDownloadUrl(shouldkeepDownloadUrl.getValue());
         grobidPreferences.setGrobidEnabled(grobidEnabledProperty.getValue());
         grobidPreferences.setGrobidOptOut(grobidPreferences.isGrobidOptOut());
         grobidPreferences.setGrobidURL(grobidURLProperty.getValue());
@@ -172,6 +173,10 @@ public BooleanProperty shouldDownloadLinkedOnlineFiles() {
         return shouldDownloadLinkedOnlineFiles;
     }
 
+    public BooleanProperty shouldKeepDownloadUrl() {
+        return shouldkeepDownloadUrl;
+    }
+
     public ReadOnlyBooleanProperty apiKeyPersistAvailable() {
         return apikeyPersistAvailableProperty;
     }

src/main/java/org/jabref/preferences/FilePreferences.java

@@ -38,6 +38,7 @@ public class FilePreferences {
     private final ObjectProperty<Path> backupDirectory = new SimpleObjectProperty<>();
     private final BooleanProperty confirmDeleteLinkedFile = new SimpleBooleanProperty();
     private final BooleanProperty moveToTrash = new SimpleBooleanProperty();
+    private final BooleanProperty shouldKeepDownloadUrl = new SimpleBooleanProperty();
 
     public FilePreferences(String userAndHost,
                            String mainFileDirectory,
@@ -51,7 +52,8 @@ public FilePreferences(String userAndHost,
                            boolean createBackup,
                            Path backupDirectory,
                            boolean confirmDeleteLinkedFile,
-                           boolean moveToTrash) {
+                           boolean moveToTrash,
+                           boolean shouldKeepDownloadUrl) {
         this.userAndHost.setValue(userAndHost);
         this.mainFileDirectory.setValue(mainFileDirectory);
         this.storeFilesRelativeToBibFile.setValue(storeFilesRelativeToBibFile);
@@ -65,6 +67,7 @@ public FilePreferences(String userAndHost,
         this.backupDirectory.setValue(backupDirectory);
         this.confirmDeleteLinkedFile.setValue(confirmDeleteLinkedFile);
         this.moveToTrash.setValue(moveToTrash);
+        this.shouldKeepDownloadUrl.setValue(shouldKeepDownloadUrl);
     }
 
     public String getUserAndHost() {
@@ -214,4 +217,16 @@ public BooleanProperty moveToTrashProperty() {
     public void moveToTrash(boolean moveToTrash) {
         this.moveToTrash.set(moveToTrash);
     }
+
+    public boolean shouldKeepDownloadUrl() {
+        return shouldKeepDownloadUrl.get();
+    }
+
+    public BooleanProperty shouldKeepDownloadUrlProperty() {
+        return shouldKeepDownloadUrl;
+    }
+
+    public void setKeepDownloadUrl(boolean shouldKeepDownloadUrl) {
+        this.shouldKeepDownloadUrl.set(shouldKeepDownloadUrl);
+    }
 }

src/main/java/org/jabref/preferences/JabRefPreferences.java

@@ -453,6 +453,7 @@ public class JabRefPreferences implements PreferencesService {
     private static final String PREFS_EXPORT_PATH = "prefsExportPath";
     private static final String DOWNLOAD_LINKED_FILES = "downloadLinkedFiles";
     private static final String FULLTEXT_INDEX_LINKED_FILES = "fulltextIndexLinkedFiles";
+    private static final String KEEP_DOWNLOAD_URL = "keepDownloadUrl";
 
     // Helper string
     private static final String USER_HOME = System.getProperty("user.home");
@@ -774,6 +775,7 @@ private JabRefPreferences() {
         defaults.put(WARN_BEFORE_OVERWRITING_KEY, Boolean.TRUE);
         defaults.put(CONFIRM_DELETE, Boolean.TRUE);
         defaults.put(CONFIRM_LINKED_FILE_DELETE, Boolean.TRUE);
+        defaults.put(KEEP_DOWNLOAD_URL, Boolean.TRUE);
         defaults.put(DEFAULT_CITATION_KEY_PATTERN, "[auth][year]");
         defaults.put(UNWANTED_CITATION_KEY_CHARACTERS, "-`ʹ:!;?^");
         defaults.put(RESOLVE_STRINGS_FOR_FIELDS, "author;booktitle;editor;editora;editorb;editorc;institution;issuetitle;journal;journalsubtitle;journaltitle;mainsubtitle;month;publisher;shortauthor;shorteditor;subtitle;titleaddon");
@@ -2257,7 +2259,8 @@ public FilePreferences getFilePreferences() {
                 getPath(BACKUP_DIRECTORY, OS.getNativeDesktop().getBackupDirectory()),
                 getBoolean(CONFIRM_LINKED_FILE_DELETE),
                 // We make use of the fallback, because we need AWT being initialized, which is not the case at the constructor JabRefPreferences()
-                getBoolean(TRASH_INSTEAD_OF_DELETE, OS.getNativeDesktop().moveToTrashSupported()));
+                getBoolean(TRASH_INSTEAD_OF_DELETE, OS.getNativeDesktop().moveToTrashSupported()),
+                getBoolean(KEEP_DOWNLOAD_URL));
 
         EasyBind.listen(getInternalPreferences().getUserAndHostProperty(), (obs, oldValue, newValue) -> filePreferences.getUserAndHostProperty().setValue(newValue));
         EasyBind.listen(filePreferences.mainFileDirectoryProperty(), (obs, oldValue, newValue) -> put(MAIN_FILE_DIRECTORY, newValue));
@@ -2273,6 +2276,7 @@ public FilePreferences getFilePreferences() {
         EasyBind.listen(filePreferences.backupDirectoryProperty(), (obs, oldValue, newValue) -> put(BACKUP_DIRECTORY, newValue.toString()));
         EasyBind.listen(filePreferences.confirmDeleteLinkedFileProperty(), (obs, oldValue, newValue) -> putBoolean(CONFIRM_LINKED_FILE_DELETE, newValue));
         EasyBind.listen(filePreferences.moveToTrashProperty(), (obs, oldValue, newValue) -> putBoolean(TRASH_INSTEAD_OF_DELETE, newValue));
+        EasyBind.listen(filePreferences.shouldKeepDownloadUrlProperty(), (obs, oldValue, newValue) -> putBoolean(KEEP_DOWNLOAD_URL, newValue));
 
         return filePreferences;
     }

src/main/resources/l10n/JabRef_en.properties

@@ -2780,3 +2780,4 @@ Warning\:\ The\ selected\ directory\ is\ not\ a\ valid\ directory.=Warning: The
 
 Currently\ selected\ JStyle\:\ '%0' = Currently selected JStyle: '%0'
 Currently\ selected\ CSL\ Style\:\ '%0' = Currently selected CSL Style: '%0'
+Store\ url\ for\ downloaded\ file=Store url for downloaded file

src/test/java/org/jabref/gui/linkedfile/DownloadLinkedFileActionTest.java

@@ -77,6 +77,7 @@ void replacesLinkedFiles(@TempDir Path tempFolder) throws Exception {
         when(databaseContext.getFirstExistingFileDir(any())).thenReturn(Optional.of(tempFolder));
         when(filePreferences.getFileNamePattern()).thenReturn("[citationkey]");
         when(filePreferences.getFileDirectoryPattern()).thenReturn("");
+        when(filePreferences.shouldKeepDownloadUrl()).thenReturn(true);
 
         DownloadLinkedFileAction downloadLinkedFileAction = new DownloadLinkedFileAction(
                 databaseContext,
@@ -100,6 +101,7 @@ void doesntReplaceSourceURL(boolean keepHtml) throws Exception {
         when(databaseContext.getFirstExistingFileDir(any())).thenReturn(Optional.of(tempFolder));
         when(filePreferences.getFileNamePattern()).thenReturn("[citationkey]");
         when(filePreferences.getFileDirectoryPattern()).thenReturn("");
+        when(filePreferences.shouldKeepDownloadUrl()).thenReturn(true);
 
         DownloadLinkedFileAction downloadLinkedFileAction = new DownloadLinkedFileAction(
                 databaseContext,