Changed default value of "search and store files relative to bibtex file" to true

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)
 
 ### Fixed

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);

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) {

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);
 

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());

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) {

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.",

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);
             });
         }

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -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;

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);

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(

src/main/java/org/jabref/gui/filelist/AttachFileAction.java

@@ -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);

src/main/java/org/jabref/gui/filelist/FileListEntry.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.filelist;
 
+import java.nio.file.Path;
 import java.util.Objects;
 import java.util.Optional;
 
@@ -48,7 +49,7 @@ public String toString() {
     }
 
     public LinkedFile toParsedFileField() {
-        return new LinkedFile(getDescription(), getLink(), getType().isPresent() ? getType().get().getName() : "");
+        return new LinkedFile(getDescription(), Path.of(getLink()), getType().isPresent() ? getType().get().getName() : "");
     }
 
     public String getDescription() {

src/main/java/org/jabref/gui/filelist/LinkedFilesEditDialogViewModel.java

@@ -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();
     }
 }

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);
 

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());

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);

src/main/java/org/jabref/logic/cleanup/UpgradePdfPsToFileCleanup.java

@@ -1,6 +1,6 @@
 package org.jabref.logic.cleanup;
 
-import java.io.File;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -36,16 +36,16 @@ public List<FieldChange> cleanup(BibEntry entry) {
         List<LinkedFile> fileList = new ArrayList<>(entry.getFiles());
         int oldItemCount = fileList.size();
         for (Map.Entry<Field, String> field : fields.entrySet()) {
-            entry.getField(field.getKey()).ifPresent(o -> {
-                if (o.trim().isEmpty()) {
+            entry.getField(field.getKey()).ifPresent(fieldContent -> {
+                if (fieldContent.trim().isEmpty()) {
                     return;
                 }
-                File f = new File(o);
-                LinkedFile flEntry = new LinkedFile(f.getName(), o, field.getValue());
+                Path path = Path.of(fieldContent);
+                LinkedFile flEntry = new LinkedFile(path.getFileName().toString(), path, field.getValue());
                 fileList.add(flEntry);
 
                 entry.clearField(field.getKey());
-                changes.add(new FieldChange(entry, field.getKey(), o, null));
+                changes.add(new FieldChange(entry, field.getKey(), fieldContent, null));
             });
         }
 

src/main/java/org/jabref/logic/externalfiles/LinkedFileHandler.java

@@ -117,7 +117,7 @@ public boolean renameToName(String targetFileName, boolean overwriteExistingFile
     }
 
     private String relativize(Path path) {
-        List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(filePreferences);
+        List<Path> fileDirectories = databaseContext.getFileDirectories(filePreferences);
         return FileUtil.relativize(path, fileDirectories).toString();
     }
 

src/main/java/org/jabref/logic/importer/fetcher/SpringerFetcher.java

@@ -5,6 +5,7 @@
 import java.net.MalformedURLException;
 import java.net.URISyntaxException;
 import java.net.URL;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
@@ -118,7 +119,7 @@ public static BibEntry parseSpringerJSONtoBibtex(JSONObject springerJsonEntry) {
                 urls.forEach(data -> {
                     JSONObject url = (JSONObject) data;
                     if (url.optString("format").equalsIgnoreCase("pdf")) {
-                        entry.addFile(new LinkedFile("online", url.optString("value"), "PDF"));
+                        entry.addFile(new LinkedFile("online", Path.of(url.optString("value")), "PDF"));
                     }
                 });
             }

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

@@ -4,6 +4,8 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.util.Collections;
 import java.util.List;
@@ -21,7 +23,6 @@
 
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.Importer;
-import org.jabref.logic.importer.ParseException;
 import org.jabref.logic.importer.Parser;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fileformat.endnote.Abstract;
@@ -158,23 +159,14 @@ private void initUnmarshaller() throws JAXBException {
     }
 
     private static EntryType convertRefNameToType(String refName) {
-        switch (refName.toLowerCase().trim()) {
-            case "artwork":
-                return StandardEntryType.Misc;
-            case "generic":
-                return StandardEntryType.Misc;
-            case "electronic article":
-                return IEEETranEntryType.Electronic;
-            case "book section":
-                return StandardEntryType.InBook;
-            case "book":
-                return StandardEntryType.Book;
-            case "journal article":
-                return StandardEntryType.Article;
-
-            default:
-                return StandardEntryType.Article;
-        }
+        return switch (refName.toLowerCase().trim()) {
+            case "artwork", "generic" -> StandardEntryType.Misc;
+            case "electronic article" -> IEEETranEntryType.Electronic;
+            case "book section" -> StandardEntryType.InBook;
+            case "book" -> StandardEntryType.Book;
+            // case "journal article" -> StandardEntryType.Article;
+            default -> StandardEntryType.Article;
+        };
     }
 
     private BibEntry parseRecord(Record record) {
@@ -247,7 +239,14 @@ private List<LinkedFile> getLinkedFiles(Record record) {
         return OptionalUtil.toStream(urls)
                            .flatMap(pdfUrls -> pdfUrls.getUrl().stream())
                            .flatMap(url -> OptionalUtil.toStream(getUrlValue(url)))
-                           .map(url -> new LinkedFile("", url, "PDF"))
+                           .map(url -> {
+                               try {
+                                   return new LinkedFile(new URL(url), "PDF");
+                               } catch (MalformedURLException e) {
+                                   LOGGER.info("Unable to parse {}", url);
+                                   return null;
+                               }
+                           })
                            .collect(Collectors.toList());
     }
 
@@ -295,7 +294,7 @@ private String clean(String input) {
     }
 
     @Override
-    public List<BibEntry> parseEntries(InputStream inputStream) throws ParseException {
+    public List<BibEntry> parseEntries(InputStream inputStream) {
         try {
             return importDatabase(
                     new BufferedReader(new InputStreamReader(inputStream, StandardCharsets.UTF_8))).getDatabase().getEntries();

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

@@ -212,7 +212,7 @@ public ParserResult importDatabase(Path filePath, Charset defaultEncoding) {
                 ParserResult parserResult = new ParserResult(result);
                 Optional<BibEntry> entry = new DoiFetcher(importFormatPreferences).performSearchById(doi.get().getDOI());
                 entry.ifPresent(parserResult.getDatabase()::insertEntry);
-                entry.ifPresent(bibEntry -> bibEntry.addFile(new LinkedFile("", filePath.toAbsolutePath().toString(), "PDF")));
+                entry.ifPresent(bibEntry -> bibEntry.addFile(new LinkedFile("", filePath.toAbsolutePath(), "PDF")));
                 return parserResult;
             }
 
@@ -226,7 +226,7 @@ public ParserResult importDatabase(Path filePath, Charset defaultEncoding) {
             return ParserResult.fromErrorMessage(e.getMessage());
         }
 
-        result.forEach(entry -> entry.addFile(new LinkedFile("", filePath.toAbsolutePath().toString(), "PDF")));
+        result.forEach(entry -> entry.addFile(new LinkedFile("", filePath.toAbsolutePath(), "PDF")));
         return new ParserResult(result);
     }