Implement journal abbreviation storage in separate directory (Closes #10557)

CHANGELOG.md

@@ -64,41 +64,76 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We changed instances of 'Search Selected' to 'Search Pre-configured' in Web Search Preferences UI. [#11871](https://github.com/JabRef/jabref/pull/11871)
 - We added a new CSS style class `main-table` for the main table. [#11881](https://github.com/JabRef/jabref/pull/11881)
 - When renaming a file, the old extension is now used if there is none provided in the new name. [#11903](https://github.com/JabRef/jabref/issues/11903)
+- We added the ability for users to change the journal abbreviation directory via the preferences dialog. The chosen directory is stored as a preference. [#10557](https://github.com/JabRef/jabref/issues/10557)
 
 ### Fixed
 
 - We fixed an issue where certain actions were not disabled when no libraries were open. [#11923](https://github.com/JabRef/jabref/issues/11923)
+
 - We fixed an issue where the "Check for updates" preference was not saved. [#11485](https://github.com/JabRef/jabref/pull/11485)
+
 - We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11515](https://github.com/JabRef/jabref/pull/11515)
+
 - We fixed an issue where JabRef put file paths as absolute path when an entry was created using drag and drop of a PDF file. [#11173](https://github.com/JabRef/jabref/issues/11173)
+
 - We fixed an issue that online and offline mode for new library creation were handled incorrectly. [#11565](https://github.com/JabRef/jabref/pull/11565)
+
 - We fixed an issue with colors in the search bar when dark theme is enabled. [#11569](https://github.com/JabRef/jabref/issues/11569)
+
 - We fixed an issue with query transformers (JStor and others). [#11643](https://github.com/JabRef/jabref/pull/11643)
+
 - We fixed an issue where a new unsaved library was not marked with an asterisk. [#11519](https://github.com/JabRef/jabref/pull/11519)
+
 - We fixed an issue where JabRef starts without window decorations. [#11440](https://github.com/JabRef/jabref/pull/11440)
+
 - We fixed an issue where the entry preview highlight was not working when searching before opening the entry editor. [#11659](https://github.com/JabRef/jabref/pull/11659)
+
 - We fixed an issue where text in Dark mode inside "Citation information" was not readable. [#11512](https://github.com/JabRef/jabref/issues/11512)
+
 - We fixed an issue where the selection of an entry in the table lost after searching for a group. [#3176](https://github.com/JabRef/jabref/issues/3176)
+
 - We fixed the non-functionality of the option "Automatically sync bibliography when inserting citations" in the OpenOffice panel, when enabled in case of JStyles. [#11684](https://github.com/JabRef/jabref/issues/11684)
+
 - We fixed an issue where the library was not marked changed after a migration. [#11542](https://github.com/JabRef/jabref/pull/11542)
+
 - We fixed an issue where rebuilding the full-text search index was not working. [#11374](https://github.com/JabRef/jabref/issues/11374)
+
 - We fixed an issue where the progress of indexing linked files showed an incorrect number of files. [#11378](https://github.com/JabRef/jabref/issues/11378)
+
 - We fixed an issue where the full-text search results were incomplete. [#8626](https://github.com/JabRef/jabref/issues/8626)
+
 - We fixed an issue where search result highlighting was incorrectly highlighting the boolean operators. [#11595](https://github.com/JabRef/jabref/issues/11595)
+
 - We fixed an issue where search result highlighting was broken at complex searches. [#8067](https://github.com/JabRef/jabref/issues/8067)
+
 - We fixed an exception when searching for unlinked files. [#11731](https://github.com/JabRef/jabref/issues/11731)
+
 - We fixed an issue with the link to the full text at the BVB fetcher. [#11852](https://github.com/JabRef/jabref/pull/11852)
+
 - We fixed an issue where two contradicting notifications were shown when cutting an entry in the main table. [#11724](https://github.com/JabRef/jabref/pull/11724)
+
 - We fixed an issue where unescaped braces in the arXiv fetcher were not treated. [#11704](https://github.com/JabRef/jabref/issues/11704)
+
 - We fixed an issue where HTML instead of the fulltext pdf was downloaded when importing arXiv entries. [#4913](https://github.com/JabRef/jabref/issues/4913)
+
 - We fixed an issue where the keywords and crossref fields were not properly focused. [#11177](https://github.com/JabRef/jabref/issues/11177)
+
 - We fixed handling of `\"` in [bracketed patterns](https://docs.jabref.org/setup/citationkeypatterns) containing a RegEx. [#11967](https://github.com/JabRef/jabref/pull/11967)
+
 - We fixed an issue where the Undo/Redo buttons were active even when all libraries are closed. [#11837](https://github.com/JabRef/jabref/issues/11837)
+
 - We fixed an issue where recently opened files were not displayed in the main menu properly. [#9042](https://github.com/JabRef/jabref/issues/9042)
+
 - We fixed an issue where the DOI lookup would show an error when a DOI was found for an entry. [#11850](https://github.com/JabRef/jabref/issues/11850)
+
 - We fixed an issue where <kbd>Tab</kbd> cannot be used to jump to next field in some single-line fields. [#11785](https://github.com/JabRef/jabref/issues/11785)
+
 - We fixed an issue where web search preferences "Custom API key" table modifications not discarded. [#11925](https://github.com/JabRef/jabref/issues/11925)
 
+- We fixed an issue where JabRef did not automatically create and add a `custom.csv` file to the Journal lists when it was missing from the specified directory. [#10557](https://github.com/JabRef/jabref/issues/10557)
+
+
+
 ### Removed
 
 - We removed support for case-sensitive and exact search. [#11542](https://github.com/JabRef/jabref/pull/11542)

src/main/java/org/jabref/gui/preferences/journals/JournalAbbreviationsTab.fxml

@@ -49,6 +49,11 @@
         </Button>
     </HBox>
 
+    <HBox spacing="10.0" alignment="CENTER_LEFT">
+        <Button fx:id="changeDirectoryButton" onAction="#handleChangeDirectory" text="Change Directory"/>
+        <CustomTextField fx:id="directoryPathField" editable="false" minWidth="200"/>
+    </HBox>
+
     <VBox spacing="10.0" HBox.hgrow="ALWAYS">
         <CustomTextField fx:id="searchBox" promptText="%Filter" VBox.vgrow="NEVER">
             <VBox.margin>

src/main/java/org/jabref/gui/preferences/journals/JournalAbbreviationsTab.java

@@ -57,6 +57,9 @@ public class JournalAbbreviationsTab extends AbstractPreferenceTabView<JournalAb
     @FXML private Button addAbbreviationButton;
     @FXML private Button removeAbbreviationListButton;
 
+    @FXML private Button changeDirectoryButton;
+    @FXML private CustomTextField directoryPathField;
+
     @FXML private CustomTextField searchBox;
     @FXML private CheckBox useFJournal;
 
@@ -87,6 +90,8 @@ private void initialize() {
 
         searchBox.setPromptText(Localization.lang("Search..."));
         searchBox.setLeft(IconTheme.JabRefIcons.SEARCH.getGraphicNode());
+
+        directoryPathField.textProperty().bind(viewModel.directoryPathProperty());
     }
 
     private void setUpTable() {
@@ -168,6 +173,11 @@ private void removeList() {
         viewModel.removeCurrentFile();
     }
 
+    @FXML
+    private void handleChangeDirectory() {
+        viewModel.handleChangeDirectory();
+    }
+
     @FXML
     private void addAbbreviation() {
         if (!searchBox.getText().isEmpty()) {

src/main/java/org/jabref/gui/preferences/journals/JournalAbbreviationsTabViewModel.java

@@ -4,17 +4,21 @@
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Objects;
+import java.util.Optional;
 import java.util.stream.Collectors;
 
 import javafx.beans.property.SimpleBooleanProperty;
 import javafx.beans.property.SimpleIntegerProperty;
 import javafx.beans.property.SimpleListProperty;
 import javafx.beans.property.SimpleObjectProperty;
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
 import javafx.collections.FXCollections;
 import javafx.collections.ListChangeListener;
 
 import org.jabref.gui.DialogService;
 import org.jabref.gui.preferences.PreferenceTabViewModel;
+import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.journals.Abbreviation;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
@@ -50,6 +54,8 @@ public class JournalAbbreviationsTabViewModel implements PreferenceTabViewModel
     private final SimpleBooleanProperty isAbbreviationEditableAndRemovable = new SimpleBooleanProperty(false);
     private final SimpleBooleanProperty useFJournal = new SimpleBooleanProperty(true);
 
+    private final StringProperty directoryPath = new SimpleStringProperty();
+
     private final DialogService dialogService;
     private final TaskExecutor taskExecutor;
 
@@ -103,6 +109,7 @@ public JournalAbbreviationsTabViewModel(JournalAbbreviationPreferences abbreviat
                 }
             }
         });
+        directoryPath.set(abbreviationsPreferences.getJournalAbbreviationDir().toString());
     }
 
     @Override
@@ -211,6 +218,39 @@ public void removeCurrentFile() {
         }
     }
 
+    public void handleChangeDirectory() {
+        DirectoryDialogConfiguration config = new DirectoryDialogConfiguration.Builder()
+                .withInitialDirectory(Path.of(directoryPath.get()))
+                .build();
+
+        Optional<Path> newDirectory = dialogService.showDirectorySelectionDialog(config);
+        newDirectory.ifPresent(path -> {
+            directoryPath.set(path.toString());
+            abbreviationsPreferences.setJournalAbbreviationDir(path);
+            updateJournalFiles();
+            storeSettings();
+            // Optionally trigger any updates needed due to directory change
+        });
+    }
+
+    private void updateJournalFiles() {
+        List<String> externalLists = abbreviationsPreferences.getExternalJournalLists();
+
+        // Remove files that are no longer in the external lists
+        journalFiles.removeIf(file -> !externalLists.contains(file.getAbsolutePath().map(Path::toString).orElse("")));
+
+        // Add new files
+        for (String filePath : externalLists) {
+            if (journalFiles.stream().noneMatch(file -> file.getAbsolutePath().map(Path::toString).orElse("").equals(filePath))) {
+                openFile(Path.of(filePath));
+            }
+        }
+    }
+
+    public StringProperty directoryPathProperty() {
+        return directoryPath;
+    }
+
     /**
      * Method to add a new abbreviation to the abbreviations list property. It also sets the currentAbbreviation
      * property to the new abbreviation.
@@ -334,6 +374,7 @@ public void storeSettings() {
                                                                  .collect(Collectors.toList());
 
                     abbreviationsPreferences.setExternalJournalLists(journalStringList);
+                    abbreviationsPreferences.setJournalAbbreviationDir(Path.of(directoryPath.get()));
                     abbreviationsPreferences.setUseFJournalField(useFJournal.get());
 
                     if (shouldWriteLists) {

src/main/java/org/jabref/logic/journals/JournalAbbreviationLoader.java

@@ -24,6 +24,24 @@ public class JournalAbbreviationLoader {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(JournalAbbreviationLoader.class);
 
+    public static Path ensureJournalAbbreviationFileExists(Path baseDirectory) {
+        try {
+            // Ensure the subdirectory 'journal-abbreviations' exists
+            Path directory = baseDirectory.resolve("journal-abbreviations");
+            Files.createDirectories(directory);
+
+            Path customCsvPath = directory.resolve("custom.csv");
+            if (!Files.exists(customCsvPath)) {
+                Files.createFile(customCsvPath);
+                LOGGER.info("Created custom.csv at {}", customCsvPath);
+            }
+            return customCsvPath;
+        } catch (IOException e) {
+            LOGGER.error("Could not initialize journal abbreviation directory or file", e);
+            return null;
+        }
+    }
+
     public static Collection<Abbreviation> readAbbreviationsFromCsvFile(Path file) throws IOException {
         LOGGER.debug("Reading journal list from file {}", file);
         AbbreviationParser parser = new AbbreviationParser();

src/main/java/org/jabref/logic/journals/JournalAbbreviationPreferences.java

@@ -1,21 +1,75 @@
 package org.jabref.logic.journals;
 
+import java.nio.file.Path;
 import java.util.List;
 
 import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.ObjectProperty;
 import javafx.beans.property.SimpleBooleanProperty;
+import javafx.beans.property.SimpleObjectProperty;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 
 public class JournalAbbreviationPreferences {
 
     private final ObservableList<String> externalJournalLists;
     private final BooleanProperty useFJournalField;
+    private final ObjectProperty<Path> journalAbbreviationDir;
+
+    public JournalAbbreviationPreferences(List<String> externalJournalLists, boolean useFJournalField) {
+        this(externalJournalLists, useFJournalField, getDefaultAbbreviationDir().toString());
+    }
 
     public JournalAbbreviationPreferences(List<String> externalJournalLists,
-                                          boolean useFJournalField) {
+                                          boolean useFJournalField, String directory) {
         this.externalJournalLists = FXCollections.observableArrayList(externalJournalLists);
         this.useFJournalField = new SimpleBooleanProperty(useFJournalField);
+        this.journalAbbreviationDir = new SimpleObjectProperty<>(
+                directory != null ? Path.of(directory) : getDefaultAbbreviationDir()
+        );
+
+        updateCustomCsvFile(this.journalAbbreviationDir.get());
+
+        this.journalAbbreviationDir.addListener((observable, oldValue, newValue) -> {
+            updateCustomCsvFile(newValue);
+        });
+    }
+
+    private void updateCustomCsvFile(Path directory) {
+        if (directory == null) {
+            return;
+        }
+        Path newFilePath = JournalAbbreviationLoader.ensureJournalAbbreviationFileExists(directory);
+        if (newFilePath != null) {
+            String newFilePathString = newFilePath.toString();
+            // Remove old custom.csv path if it exists
+            externalJournalLists.removeIf(path -> path.endsWith("custom.csv"));
+            // Add new custom.csv path
+            if (!externalJournalLists.contains(newFilePathString)) {
+                externalJournalLists.add(newFilePathString);
+            }
+        }
+    }
+
+    public Path getJournalAbbreviationDir() {
+        Path dir = journalAbbreviationDir.get();
+        return dir != null ? dir : getDefaultAbbreviationDir();
+    }
+
+    public static Path getDefaultAbbreviationDir() {
+        String appData = System.getenv("APPDATA");
+        if (appData == null) {
+            appData = System.getProperty("user.home");
+        }
+        return Path.of(appData, ".jabref", "journals");
+    }
+
+    public void setJournalAbbreviationDir(Path journalAbbreviationDir) {
+        this.journalAbbreviationDir.set(journalAbbreviationDir);
+    }
+
+    public ObjectProperty<Path> journalAbbreviationDirProperty() {
+        return journalAbbreviationDir;
     }
 
     public ObservableList<String> getExternalJournalLists() {