Changed default value of "search and store files relative to bibtex f…

…ile" to true (#6928) * Fixes #6863 * CHANGELOG.md * Reworded bibLocationAsPrimary to reflect real meaning of the preference setting, changed default val to true * Cleanup of deprecated methods LinkedFiles(String, String, String) and List<String> getFileDirectories(...) * Reworded package filelist to linkedfile * Fixed SpringerFetcher
JabRef · Sep 25, 2020 · 3123090 · 3123090
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We completed the rebranding of `bibtexkey` as `citationkey` which was started in JabRef 5.1.
 - JabRef no longer opens the entry editor with the first entry on startup [#6855](https://github.com/JabRef/jabref/issues/6855)
 - Fetch by ID: (long) "SAO/NASA Astrophysics Data System" replaced by (short) "SAO/NASA ADS" [#6876](https://github.com/JabRef/jabref/pull/6876)
+- We changed the default preference option "Search and store files relative to library file location" to on, as this seems to be a more intuitive behaviour. [#6863](https://github.com/JabRef/jabref/issues/6863)
 - We changed the title of the window  "Manage field names and content":  to have the same title as the corresponding menu item  [#6895](https://github.com/JabRef/jabref/pull/6895)
 - Improved detection of "short" DOIs [6880](https://github.com/JabRef/jabref/issues/6880)
 

diff --git a/src/main/java/org/jabref/gui/JabRefGUI.java b/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -145,7 +145,7 @@ private void openDatabases() {
                     new SharedDatabaseUIManager(mainFrame).openSharedDatabaseFromParserResult(pr);
                 } catch (SQLException | DatabaseNotSupportedException | InvalidDBMSConnectionPropertiesException |
                         NotASharedDatabaseException e) {
-                    pr.getDatabaseContext().clearDatabaseFile(); // do not open the original file
+                    pr.getDatabaseContext().clearDatabasePath(); // do not open the original file
                     pr.getDatabase().clearSharedDatabaseID();
 
                     LOGGER.error("Connection error", e);

diff --git a/src/main/java/org/jabref/gui/SendAsEMailAction.java b/src/main/java/org/jabref/gui/SendAsEMailAction.java
@@ -90,7 +90,7 @@ private String sendEmail() throws Exception {
         //   the unofficial "mailto:attachment" property
         boolean openFolders = JabRefPreferences.getInstance().getBoolean(JabRefPreferences.OPEN_FOLDERS_OF_ATTACHED_FILES);
 
-        List<Path> fileList = FileUtil.getListOfLinkedFiles(entries, databaseContext.getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()));
+        List<Path> fileList = FileUtil.getListOfLinkedFiles(entries, databaseContext.getFileDirectories(Globals.prefs.getFilePreferences()));
         for (Path path : fileList) {
             attachments.add(path.toAbsolutePath().toString());
             if (openFolders) {

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -55,7 +55,7 @@ public static void openExternalViewer(BibDatabaseContext databaseContext, String
         Field field = initialField;
         if (StandardField.PS.equals(field) || StandardField.PDF.equals(field)) {
             // Find the default directory for this field type:
-            List<Path> directories = databaseContext.getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences());
+            List<Path> directories = databaseContext.getFileDirectories(Globals.prefs.getFilePreferences());
 
             Optional<Path> file = FileHelper.find(link, directories);
 

diff --git a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
@@ -103,7 +103,8 @@ private ExportResult exportToClipboard(Exporter exporter) throws Exception {
         // Set the global variable for this database's file directory before exporting,
         // so formatters can resolve linked files correctly.
         // (This is an ugly hack!)
-        Globals.prefs.fileDirForDatabase = panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()).stream().map(Path::toString).collect(Collectors.toList());
+        Globals.prefs.fileDirForDatabase = panel.getBibDatabaseContext()
+                                                .getFileDirectories(Globals.prefs.getFilePreferences());
 
         // Add chosen export type to last used pref, to become default
         Globals.prefs.put(JabRefPreferences.LAST_USED_EXPORT, exporter.getName());

diff --git a/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java b/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
@@ -37,7 +37,7 @@ public class AutoSetFileLinksUtil {
     private ExternalFileTypes externalFileTypes;
 
     public AutoSetFileLinksUtil(BibDatabaseContext databaseContext, FilePreferences filePreferences, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {
-        this(databaseContext.getFileDirectoriesAsPaths(filePreferences), autoLinkPreferences, externalFileTypes);
+        this(databaseContext.getFileDirectories(filePreferences), autoLinkPreferences, externalFileTypes);
     }
 
     private AutoSetFileLinksUtil(List<Path> directories, AutoLinkPreferences autoLinkPreferences, ExternalFileTypes externalFileTypes) {

diff --git a/src/main/java/org/jabref/gui/externalfiles/DownloadFullTextAction.java b/src/main/java/org/jabref/gui/externalfiles/DownloadFullTextAction.java
@@ -160,7 +160,7 @@ private void addLinkedFileFromURL(BibDatabaseContext databaseContext, URL url, B
                 downloadTask.onSuccess(destination -> {
                     LinkedFile downloadedFile = LinkedFilesEditorViewModel.fromFile(
                             destination,
-                            databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences()),
+                            databaseContext.getFileDirectories(preferences.getFilePreferences()),
                             ExternalFileTypes.getInstance());
                     entry.addFile(downloadedFile);
                     dialogService.notify(Localization.lang("Finished downloading full text document for entry %0.",

diff --git a/src/main/java/org/jabref/gui/externalfiles/ExternalFilesEntryLinker.java b/src/main/java/org/jabref/gui/externalfiles/ExternalFilesEntryLinker.java
@@ -56,8 +56,8 @@ public void addFilesToEntry(BibEntry entry, List<Path> files) {
             FileUtil.getFileExtension(file).ifPresent(ext -> {
                 ExternalFileType type = externalFileTypes.getExternalFileTypeByExt(ext)
                                                          .orElse(new UnknownExternalFileType(ext));
-                Path relativePath = FileUtil.relativize(file, bibDatabaseContext.getFileDirectoriesAsPaths(filePreferences));
-                LinkedFile linkedfile = new LinkedFile("", relativePath.toString(), type.getName());
+                Path relativePath = FileUtil.relativize(file, bibDatabaseContext.getFileDirectories(filePreferences));
+                LinkedFile linkedfile = new LinkedFile("", relativePath, type.getName());
                 entry.addFile(linkedfile);
             });
         }

diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
@@ -29,9 +29,9 @@
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.externalfiletype.StandardExternalFileType;
-import org.jabref.gui.filelist.LinkedFileEditDialogView;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.icon.JabRefIcon;
+import org.jabref.gui.linkedfile.LinkedFileEditDialogView;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.ControlHelper;
 import org.jabref.gui.util.TaskExecutor;
@@ -187,7 +187,7 @@ public Observable[] getObservables() {
         observables.add(downloadOngoing);
         observables.add(downloadProgress);
         observables.add(isAutomaticallyFound);
-        return observables.toArray(new Observable[observables.size()]);
+        return observables.toArray(new Observable[0]);
     }
 
     public void open() {
@@ -426,7 +426,7 @@ public void download() {
             URLDownload urlDownload = new URLDownload(linkedFile.getLink());
             BackgroundTask<Path> downloadTask = prepareDownloadTask(targetDirectory.get(), urlDownload);
             downloadTask.onSuccess(destination -> {
-                LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectoriesAsPaths(filePreferences), externalFileTypes);
+                LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectories(filePreferences), externalFileTypes);
 
                 List<LinkedFile> linkedFiles = entry.getFiles();
                 int oldFileIndex = -1;

diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java
@@ -54,7 +54,11 @@ public class LinkedFilesEditor extends HBox implements FieldEditorFX {
     private final BibDatabaseContext databaseContext;
     private final UiThreadObservableList<LinkedFileViewModel> decoratedModelList;
 
-    public LinkedFilesEditor(Field field, DialogService dialogService, BibDatabaseContext databaseContext, TaskExecutor taskExecutor, SuggestionProvider<?> suggestionProvider,
+    public LinkedFilesEditor(Field field,
+                             DialogService dialogService,
+                             BibDatabaseContext databaseContext,
+                             TaskExecutor taskExecutor,
+                             SuggestionProvider<?> suggestionProvider,
                              FieldCheckers fieldCheckers,
                              JabRefPreferences preferences) {
         this.viewModel = new LinkedFilesEditorViewModel(field, suggestionProvider, dialogService, databaseContext, taskExecutor, fieldCheckers, preferences);

diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java
@@ -94,11 +94,11 @@ public static LinkedFile fromFile(Path file, List<Path> fileDirectories, Externa
                 .getExternalFileTypeByExt(fileExtension)
                 .orElse(new UnknownExternalFileType(fileExtension));
         Path relativePath = FileUtil.relativize(file, fileDirectories);
-        return new LinkedFile("", relativePath.toString(), suggestedFileType.getName());
+        return new LinkedFile("", relativePath, suggestedFileType.getName());
     }
 
     public LinkedFileViewModel fromFile(Path file) {
-        List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences());
+        List<Path> fileDirectories = databaseContext.getFileDirectories(preferences.getFilePreferences());
 
         LinkedFile linkedFile = fromFile(file, fileDirectories, externalFileTypes);
         return new LinkedFileViewModel(
@@ -150,7 +150,7 @@ public void addNewFile() {
                 .withInitialDirectory(workingDirectory)
                 .build();
 
-        List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences());
+        List<Path> fileDirectories = databaseContext.getFileDirectories(preferences.getFilePreferences());
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(newFile -> {
             LinkedFile newLinkedFile = fromFile(newFile, fileDirectories, externalFileTypes);
             files.add(new LinkedFileViewModel(

diff --git a/src/main/java/org/jabref/gui/filelist/FileListEntry.java b/src/main/java/org/jabref/gui/filelist/FileListEntry.java
diff --git a/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java b/src/main/java/org/jabref/gui/importer/actions/OpenDatabaseAction.java
@@ -192,7 +192,7 @@ private ParserResult loadDatabase(Path file) throws Exception {
                 new SharedDatabaseUIManager(frame).openSharedDatabaseFromParserResult(result);
             } catch (SQLException | DatabaseNotSupportedException | InvalidDBMSConnectionPropertiesException |
                     NotASharedDatabaseException e) {
-                result.getDatabaseContext().clearDatabaseFile(); // do not open the original file
+                result.getDatabaseContext().clearDatabasePath(); // do not open the original file
                 result.getDatabase().clearSharedDatabaseID();
                 LOGGER.error("Connection error", e);
 

diff --git a/...jabref/gui/filelist/AttachFileAction.java → ...bref/gui/linkedfile/AttachFileAction.java b/...jabref/gui/filelist/AttachFileAction.java → ...bref/gui/linkedfile/AttachFileAction.java
@@ -1,4 +1,4 @@
-package org.jabref.gui.filelist;
+package org.jabref.gui.linkedfile;
 
 import java.nio.file.Path;
 import java.util.Optional;
@@ -60,7 +60,7 @@ public void execute() {
 
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(newFile -> {
             LinkedFile linkedFile = LinkedFilesEditorViewModel.fromFile(newFile,
-                    databaseContext.getFileDirectoriesAsPaths(preferencesService.getFilePreferences()),
+                    databaseContext.getFileDirectories(preferencesService.getFilePreferences()),
                     ExternalFileTypes.getInstance());
 
             LinkedFileEditDialogView dialog = new LinkedFileEditDialogView(linkedFile);

diff --git a/...ef/gui/filelist/LinkedFileEditDialog.fxml → .../gui/linkedfile/LinkedFileEditDialog.fxml b/...ef/gui/filelist/LinkedFileEditDialog.fxml → .../gui/linkedfile/LinkedFileEditDialog.fxml
@@ -9,7 +9,7 @@
 <?import javafx.scene.layout.ColumnConstraints?>
 <?import javafx.scene.layout.GridPane?>
 <?import javafx.scene.layout.RowConstraints?>
-<DialogPane minHeight="-Infinity" prefHeight="150.0" prefWidth="536.0" xmlns="http://javafx.com/javafx/8.0.141" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.filelist.LinkedFileEditDialogView">
+<DialogPane minHeight="-Infinity" prefHeight="150.0" prefWidth="536.0" xmlns="http://javafx.com/javafx/8.0.141" xmlns:fx="http://javafx.com/fxml/1" fx:controller="org.jabref.gui.linkedfile.LinkedFileEditDialogView">
     <content>
         <GridPane>
             <columnConstraints>
@@ -22,19 +22,21 @@
                 <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
                 <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES"/>
             </rowConstraints>
-            <children>
-                <Label minWidth="95.0" text="%Link"/>
-                <TextField fx:id="link" minHeight="-Infinity" minWidth="-Infinity" prefHeight="25.0" prefWidth="150.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS"/>
-                <Label text="Description" GridPane.rowIndex="1"/>
-                <TextField fx:id="description" minHeight="-Infinity" minWidth="-Infinity" prefHeight="25.0" prefWidth="150.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" GridPane.rowIndex="1"/>
-                <ComboBox fx:id="fileType" minHeight="-Infinity" prefWidth="150.0" GridPane.columnIndex="1" GridPane.columnSpan="2" GridPane.hgrow="ALWAYS" GridPane.rowIndex="2"/>
-                <Button id="browse" mnemonicParsing="false" onAction="#openBrowseDialog" text="%Browse" GridPane.columnIndex="2">
-                    <GridPane.margin>
-                        <Insets left="10.0"/>
-                    </GridPane.margin>
-                </Button>
-                <Label text="Filetype" GridPane.rowIndex="2"/>
-            </children>
+            <Label minWidth="95.0" text="%Link"/>
+            <TextField fx:id="link" minHeight="-Infinity" minWidth="-Infinity" prefHeight="25.0" prefWidth="150.0"
+                       GridPane.columnIndex="1" GridPane.hgrow="ALWAYS"/>
+            <Label text="Description" GridPane.rowIndex="1"/>
+            <TextField fx:id="description" minHeight="-Infinity" minWidth="-Infinity" prefHeight="25.0"
+                       prefWidth="150.0" GridPane.columnIndex="1" GridPane.hgrow="ALWAYS" GridPane.rowIndex="1"/>
+            <ComboBox fx:id="fileType" minHeight="-Infinity" prefWidth="150.0" GridPane.columnIndex="1"
+                      GridPane.columnSpan="2" GridPane.hgrow="ALWAYS" GridPane.rowIndex="2"/>
+            <Button id="browse" mnemonicParsing="false" onAction="#openBrowseDialog" text="%Browse"
+                    GridPane.columnIndex="2">
+                <GridPane.margin>
+                    <Insets left="10.0"/>
+                </GridPane.margin>
+            </Button>
+            <Label text="Filetype" GridPane.rowIndex="2"/>
         </GridPane>
     </content>
 </DialogPane>
diff --git a/...ui/filelist/LinkedFileEditDialogView.java → .../linkedfile/LinkedFileEditDialogView.java b/...ui/filelist/LinkedFileEditDialogView.java → .../linkedfile/LinkedFileEditDialogView.java
@@ -1,4 +1,4 @@
-package org.jabref.gui.filelist;
+package org.jabref.gui.linkedfile;
 
 import javax.inject.Inject;
 

diff --git a/...elist/LinkedFilesEditDialogViewModel.java → ...dfile/LinkedFilesEditDialogViewModel.java b/...elist/LinkedFilesEditDialogViewModel.java → ...dfile/LinkedFilesEditDialogViewModel.java
@@ -1,4 +1,4 @@
-package org.jabref.gui.filelist;
+package org.jabref.gui.linkedfile;
 
 import java.nio.file.Path;
 import java.util.List;
@@ -125,11 +125,11 @@ public ObjectProperty<ExternalFileType> selectedExternalFileTypeProperty() {
     }
 
     public LinkedFile getNewLinkedFile() {
-        return new LinkedFile(description.getValue(), link.getValue(), monadicSelectedExternalFileType.getValue().map(ExternalFileType::toString).orElse(""));
+        return new LinkedFile(description.getValue(), Path.of(link.getValue()), monadicSelectedExternalFileType.getValue().map(ExternalFileType::toString).orElse(""));
     }
 
     private String relativize(Path filePath) {
-        List<Path> fileDirectories = database.getFileDirectoriesAsPaths(preferences.getFilePreferences());
+        List<Path> fileDirectories = database.getFileDirectories(preferences.getFilePreferences());
         return FileUtil.relativize(filePath, fileDirectories).toString();
     }
 }
diff --git a/src/main/java/org/jabref/gui/maintable/RightClickMenu.java b/src/main/java/org/jabref/gui/maintable/RightClickMenu.java
@@ -15,8 +15,8 @@
 import org.jabref.gui.edit.CopyMoreAction;
 import org.jabref.gui.edit.EditAction;
 import org.jabref.gui.exporter.ExportToClipboardAction;
-import org.jabref.gui.filelist.AttachFileAction;
 import org.jabref.gui.keyboard.KeyBindingRepository;
+import org.jabref.gui.linkedfile.AttachFileAction;
 import org.jabref.gui.menus.ChangeEntryTypeMenu;
 import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.mergeentries.MergeWithFetchedEntryAction;

diff --git a/src/main/java/org/jabref/gui/preferences/LinkedFilesTabViewModel.java b/src/main/java/org/jabref/gui/preferences/LinkedFilesTabViewModel.java
@@ -73,7 +73,7 @@ public LinkedFilesTabViewModel(DialogService dialogService, PreferencesService p
     public void setValues() {
         // External files preferences / Attached files preferences / File preferences
         mainFileDirectoryProperty.setValue(initialFilePreferences.getFileDirectory().orElse(Path.of("")).toString());
-        useBibLocationAsPrimaryProperty.setValue(initialFilePreferences.isBibLocationAsPrimary());
+        useBibLocationAsPrimaryProperty.setValue(initialFilePreferences.shouldStoreFilesRelativeToBib());
         searchFilesOnOpenProperty.setValue(initialFilePreferences.shouldSearchFilesOnOpen());
         openBrowseOnCreateProperty.setValue(initialFilePreferences.shouldOpenBrowseOnCreate());
         fileNamePatternProperty.setValue(initialFilePreferences.getFileNamePattern());

diff --git a/src/main/java/org/jabref/logic/cleanup/RelativePathsCleanup.java b/src/main/java/org/jabref/logic/cleanup/RelativePathsCleanup.java
@@ -39,12 +39,12 @@ public List<FieldChange> cleanup(BibEntry entry) {
             } else {
                 // only try to transform local file path to relative one
                 newFileName = FileUtil
-                        .relativize(Path.of(oldFileName), databaseContext.getFileDirectoriesAsPaths(filePreferences))
+                        .relativize(Path.of(oldFileName), databaseContext.getFileDirectories(filePreferences))
                         .toString();
             }
             LinkedFile newFileEntry = fileEntry;
             if (!oldFileName.equals(newFileName)) {
-                newFileEntry = new LinkedFile(fileEntry.getDescription(), newFileName, fileEntry.getFileType());
+                newFileEntry = new LinkedFile(fileEntry.getDescription(), Path.of(newFileName), fileEntry.getFileType());
                 changed = true;
             }
             newFileList.add(newFileEntry);