Removed Globals from BibDatabaseContext (JabRef#1856)

* Removed Globals from BibDatabaseContext

* Removed the temporarily introduced Globals dependency in logic

CHANGELOG.md

@@ -17,7 +17,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Fixed NullPointerException when opening search result window for an untitled database 
 
 ### Removed
-
+- The non-supported feature of being able to define file directories for any extension is removed. Still, it should work for older databases using the legacy `ps` and `pdf` fields, although we strongly encourage using the `file` field. 
 
 
 

src/main/java/net/sf/jabref/BibDatabaseContext.java

@@ -6,13 +6,11 @@
 import java.util.Objects;
 import java.util.Optional;
 
-import net.sf.jabref.logic.layout.format.FileLinkPreferences;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.model.database.BibDatabaseMode;
 import net.sf.jabref.model.database.BibDatabaseModeDetection;
 import net.sf.jabref.model.database.DatabaseLocation;
 import net.sf.jabref.model.entry.FieldName;
-import net.sf.jabref.preferences.JabRefPreferences;
 import net.sf.jabref.shared.DBMSSynchronizer;
 
 /**
@@ -120,27 +118,32 @@ public boolean isBiblatexMode() {
         return getMode() == BibDatabaseMode.BIBLATEX;
     }
 
+    public List<String> getFileDirectory(FileDirectoryPreferences preferences) {
+        return getFileDirectory(FieldName.FILE, preferences);
+    }
+
     /**
-     * Look up the directory set up for the given field type for this database.
-     * If no directory is set up, return that defined in global preferences.
-     * There can be up to three directory definitions for these files:
-     * the database's metadata can specify a general directory and/or a user-specific directory
-     * or the preferences can specify one.
-     * <p>
-     * The settings are prioritized in the following order and the first defined setting is used:
-     * 1. metadata user-specific directory
-     * 2. metadata general directory
-     * 3. preferences directory
-     * 4. BIB file directory
-     *
-     * @param fieldName The field type
-     * @return The default directory for this field type.
-     */
-    public List<String> getFileDirectory(String fieldName) {
+    * Look up the directory set up for the given field type for this database.
+    * If no directory is set up, return that defined in global preferences.
+    * There can be up to three directory definitions for these files:
+    * the database's metadata can specify a general directory and/or a user-specific directory
+    * or the preferences can specify one.
+    * <p>
+    * The settings are prioritized in the following order and the first defined setting is used:
+    * 1. metadata user-specific directory
+    * 2. metadata general directory
+    * 3. preferences directory
+    * 4. BIB file directory
+    *
+    * @param
+    * @param fieldName The field type
+    * @return The default directory for this field type.
+    */
+    public List<String> getFileDirectory(String fieldName, FileDirectoryPreferences preferences) {
         List<String> fileDirs = new ArrayList<>();
 
         // 1. metadata user-specific directory
-        Optional<String> userFileDirectory = metaData.getUserFileDirectory(Globals.prefs.getUser());
+        Optional<String> userFileDirectory = metaData.getUserFileDirectory(preferences.getUser());
         if(userFileDirectory.isPresent()) {
             fileDirs.add(getFileDirectoryPath(userFileDirectory.get()));
         }
@@ -152,16 +155,13 @@ public List<String> getFileDirectory(String fieldName) {
         }
 
         // 3. preferences directory
-        String dir = Globals.prefs.get(fieldName + FileLinkPreferences.DIR_SUFFIX); // FILE_DIR
-        if (dir != null) {
-            fileDirs.add(dir);
-        }
+        preferences.getFileDirectory(fieldName).ifPresent(fileDirs::add);
 
         // 4. BIB file directory
         getDatabaseFile().ifPresent(databaseFile -> {
             String parentDir = databaseFile.getParent();
             // Check if we should add it as primary file dir (first in the list) or not:
-            if (Globals.prefs.getBoolean(JabRefPreferences.BIB_LOC_AS_PRIMARY_DIR)) {
+            if (preferences.isBibLocationAsPrimary()) {
                 fileDirs.add(0, parentDir);
             } else {
                 fileDirs.add(parentDir);
@@ -193,10 +193,6 @@ private String getFileDirectoryPath(String directoryName) {
         return dir;
     }
 
-    public List<String> getFileDirectory() {
-        return getFileDirectory(FieldName.FILE);
-    }
-
     public DBMSSynchronizer getDBSynchronizer() {
         return this.dbmsSynchronizer;
     }

src/main/java/net/sf/jabref/FileDirectoryPreferences.java

@@ -0,0 +1,36 @@
+package net.sf.jabref;
+
+import java.util.Map;
+import java.util.Optional;
+
+import net.sf.jabref.model.entry.FieldName;
+
+public class FileDirectoryPreferences {
+    private final String user;
+    private final Map<String, String> fieldFileDirectories;
+    private final boolean bibLocationAsPrimary;
+
+
+    public FileDirectoryPreferences(String user, Map<String, String> fieldFileDirectories,
+            boolean bibLocationAsPrimary) {
+        this.user = user;
+        this.fieldFileDirectories = fieldFileDirectories;
+        this.bibLocationAsPrimary = bibLocationAsPrimary;
+    }
+
+    public String getUser() {
+        return user;
+    }
+
+    public Optional<String> getFileDirectory(String field) {
+        return Optional.ofNullable(fieldFileDirectories.get(field));
+    }
+
+    public Optional<String> getFileDirectory() {
+        return getFileDirectory(FieldName.FILE);
+    }
+
+    public boolean isBibLocationAsPrimary() {
+        return bibLocationAsPrimary;
+    }
+}

src/main/java/net/sf/jabref/cli/ArgumentProcessor.java

@@ -372,7 +372,8 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
             }
             BibDatabaseContext databaseContext = pr.getDatabaseContext();
             databaseContext.setDatabaseFile(theFile);
-            Globals.prefs.fileDirForDatabase = databaseContext.getFileDirectory();
+            Globals.prefs.fileDirForDatabase = databaseContext
+                    .getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
             System.out.println(Localization.lang("Exporting") + ": " + data[0]);
             IExportFormat format = ExportFormats.getExportFormat(data[1]);
             if (format == null) {

src/main/java/net/sf/jabref/external/AutoSetLinks.java

@@ -92,7 +92,7 @@ public static Runnable autoSetLinks(final List<BibEntry> entries, final NamedCom
             public void run() {
                 // determine directories to search in
                 List<File> dirs = new ArrayList<>();
-                List<String> dirsS = databaseContext.getFileDirectory();
+                List<String> dirsS = databaseContext.getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
                 dirs.addAll(dirsS.stream().map(File::new).collect(Collectors.toList()));
 
                 // determine extensions

src/main/java/net/sf/jabref/external/DownloadExternalFile.java

@@ -147,7 +147,7 @@ public void download(URL url, final DownloadCallback callback) throws IOExceptio
         }
 
         String suggestedName = getSuggestedFileName(suffix);
-        List<String> fDirectory = databaseContext.getFileDirectory();
+        List<String> fDirectory = databaseContext.getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
         String directory;
         if (fDirectory.isEmpty()) {
             directory = null;

src/main/java/net/sf/jabref/external/DroppedFileHandler.java

@@ -140,7 +140,10 @@ public void handleDroppedfile(String fileName, ExternalFileType fileType, BibEnt
         String destFilename;
 
         if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.shortenFileName(new File(fileName), panel.getBibDatabaseContext().getFileDirectory()).toString();
+            destFilename = FileUtil
+                    .shortenFileName(new File(fileName),
+                            panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences()))
+                    .toString();
         } else {
             destFilename = renameCheckBox.isSelected() ? renameToTextBox.getText() : new File(fileName).getName();
             if (copyRadioButton.isSelected()) {
@@ -190,7 +193,10 @@ public void linkPdfToEntry(String fileName, BibEntry entry) {
         NamedCompound edits = new NamedCompound(Localization.lang("Drop %0", fileType.getExtension()));
 
         if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.shortenFileName(new File(fileName), panel.getBibDatabaseContext().getFileDirectory()).toString();
+            destFilename = FileUtil
+                    .shortenFileName(new File(fileName),
+                            panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences()))
+                    .toString();
         } else {
             destFilename = renameCheckBox.isSelected() ? renameToTextBox.getText() : new File(fileName).getName();
             if (copyRadioButton.isSelected()) {
@@ -264,7 +270,10 @@ private boolean tryXmpImport(String fileName, ExternalFileType fileType, NamedCo
         String destFilename;
 
         if (linkInPlace.isSelected()) {
-            destFilename = FileUtil.shortenFileName(new File(fileName), panel.getBibDatabaseContext().getFileDirectory()).toString();
+            destFilename = FileUtil
+                    .shortenFileName(new File(fileName),
+                            panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences()))
+                    .toString();
         } else {
             if (renameCheckBox.isSelected()) {
                 destFilename = fileName;
@@ -301,7 +310,7 @@ private boolean showLinkMoveCopyRenameDialog(String linkFileName, ExternalFileTy
             BibDatabase database) {
 
         String dialogTitle = Localization.lang("Link to file %0", linkFileName);
-        List<String> dirs = panel.getBibDatabaseContext().getFileDirectory();
+        List<String> dirs = panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
         int found = -1;
         for (int i = 0; i < dirs.size(); i++) {
             if (new File(dirs.get(i)).exists()) {
@@ -388,7 +397,8 @@ private void doLink(BibEntry entry, ExternalFileType fileType, String filename,
         // If avoidDuplicate==true, we should check if this file is already linked:
         if (avoidDuplicate) {
             // For comparison, find the absolute filename:
-            List<String> dirs = panel.getBibDatabaseContext().getFileDirectory();
+            List<String> dirs = panel.getBibDatabaseContext()
+                    .getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
             String absFilename;
             if (new File(filename).isAbsolute() || dirs.isEmpty()) {
                 absFilename = filename;
@@ -448,7 +458,7 @@ private void doLink(BibEntry entry, ExternalFileType fileType, String filename,
      */
     private boolean doMove(String fileName, String destFilename,
                            NamedCompound edits) {
-        List<String> dirs = panel.getBibDatabaseContext().getFileDirectory();
+        List<String> dirs = panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
         int found = -1;
         for (int i = 0; i < dirs.size(); i++) {
             if (new File(dirs.get(i)).exists()) {
@@ -498,7 +508,7 @@ private boolean doMove(String fileName, String destFilename,
      */
     private boolean doCopy(String fileName, String toFile, NamedCompound edits) {
 
-        List<String> dirs = panel.getBibDatabaseContext().getFileDirectory();
+        List<String> dirs = panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
         int found = -1;
         for (int i = 0; i < dirs.size(); i++) {
             if (new File(dirs.get(i)).exists()) {

src/main/java/net/sf/jabref/external/FindFullTextAction.java

@@ -7,6 +7,7 @@
 
 import javax.swing.JOptionPane;
 
+import net.sf.jabref.Globals;
 import net.sf.jabref.gui.BasePanel;
 import net.sf.jabref.gui.FileListTableModel;
 import net.sf.jabref.gui.undo.UndoableFieldChange;
@@ -53,7 +54,8 @@ public void run() {
     @Override
     public void update() {
         if (result.isPresent()) {
-            List<String> dirs = basePanel.getBibDatabaseContext().getFileDirectory();
+            List<String> dirs = basePanel.getBibDatabaseContext()
+                    .getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
             if (dirs.isEmpty()) {
                 JOptionPane.showMessageDialog(basePanel.frame(),
                         Localization.lang("Main file directory not set!") + " " + Localization.lang("Preferences")

src/main/java/net/sf/jabref/external/MoveFileAction.java

@@ -69,7 +69,8 @@ public void actionPerformed(ActionEvent event) {
         }
 
         // Get an absolute path representation:
-        List<String> dirs = frame.getCurrentBasePanel().getBibDatabaseContext().getFileDirectory();
+        List<String> dirs = frame.getCurrentBasePanel().getBibDatabaseContext()
+                .getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
         int found = -1;
         for (int i = 0; i < dirs.size(); i++) {
             if (new File(dirs.get(i)).exists()) {

src/main/java/net/sf/jabref/external/SynchronizeFileField.java

@@ -137,7 +137,8 @@ public void run() {
                     tableModel.setContentDontGuessTypes(old.get());
 
                     // We need to specify which directories to search in for Util.expandFilename:
-                    List<String> dirsS = panel.getBibDatabaseContext().getFileDirectory();
+                    List<String> dirsS = panel.getBibDatabaseContext()
+                            .getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
                     List<File> dirs = new ArrayList<>();
                     for (String dirs1 : dirsS) {
                         dirs.add(new File(dirs1));
@@ -365,7 +366,7 @@ public void setVisible(boolean visible) {
                 canceled = true;
             }
 
-            List<String> dirs = databaseContext.getFileDirectory();
+            List<String> dirs = databaseContext.getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
             if (dirs.isEmpty()) {
                 autoSetNone.setSelected(true);
                 autoSetNone.setEnabled(false);

src/main/java/net/sf/jabref/external/TransferableFileLinkSelection.java

@@ -8,6 +8,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import net.sf.jabref.Globals;
 import net.sf.jabref.gui.BasePanel;
 import net.sf.jabref.gui.FileListTableModel;
 import net.sf.jabref.logic.util.io.FileUtil;
@@ -32,7 +33,8 @@ public TransferableFileLinkSelection(BasePanel panel, List<BibEntry> selection)
         selection.get(0).getFieldOptional(FieldName.FILE).ifPresent(tm::setContent);
         if (tm.getRowCount() > 0) {
             // Find the default directory for this field type, if any:
-            List<String> dirs = panel.getBibDatabaseContext().getFileDirectory();
+            List<String> dirs = panel.getBibDatabaseContext()
+                    .getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
             FileUtil.expandFilename(tm.getEntry(0).link, dirs).ifPresent(fileList::add);
         }
 

src/main/java/net/sf/jabref/external/WriteXMPAction.java

@@ -121,11 +121,16 @@ public void run() {
             List<File> files = new ArrayList<>();
 
             // First check the (legacy) "pdf" field:
-            entry.getFieldOptional(FieldName.PDF).ifPresent(pdf ->
-                FileUtil.expandFilename(pdf, panel.getBibDatabaseContext().getFileDirectory("pdf"))
-                    .ifPresent(files::add));
+            entry.getFieldOptional(FieldName.PDF)
+                    .ifPresent(
+                            pdf -> FileUtil
+                                    .expandFilename(pdf,
+                                            panel.getBibDatabaseContext().getFileDirectory(FieldName.PDF,
+                                                    Globals.prefs.getFileDirectoryPreferences()))
+                            .ifPresent(files::add));
             // Then check the "file" field:
-            List<String> dirs = panel.getBibDatabaseContext().getFileDirectory();
+            List<String> dirs = panel.getBibDatabaseContext()
+                    .getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
             if (entry.hasField(FieldName.FILE)) {
                 FileListTableModel tm = new FileListTableModel();
                 entry.getFieldOptional(FieldName.FILE).ifPresent(tm::setContent);

src/main/java/net/sf/jabref/external/WriteXMPEntryEditorAction.java

@@ -55,11 +55,13 @@ public void actionPerformed(ActionEvent actionEvent) {
         List<File> files = new ArrayList<>();
 
         // First check the (legacy) "pdf" field:
-        entry.getFieldOptional(FieldName.PDF).ifPresent(pdf -> FileUtil
-                .expandFilename(pdf, panel.getBibDatabaseContext().getFileDirectory("pdf")).ifPresent(files::add));
+        entry.getFieldOptional(FieldName.PDF)
+                .ifPresent(pdf -> FileUtil.expandFilename(pdf, panel.getBibDatabaseContext()
+                        .getFileDirectory(FieldName.PDF, Globals.prefs.getFileDirectoryPreferences()))
+                .ifPresent(files::add));
 
         // Then check the "file" field:
-        List<String> dirs = panel.getBibDatabaseContext().getFileDirectory();
+        List<String> dirs = panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
         if (entry.hasField(FieldName.FILE)) {
             FileListTableModel tm = new FileListTableModel();
             entry.getFieldOptional(FieldName.FILE).ifPresent(tm::setContent);

src/main/java/net/sf/jabref/gui/BasePanel.java

@@ -538,7 +538,7 @@ public void update() {
 
         actions.put(Actions.OPEN_FOLDER, (BaseAction) () -> JabRefExecutorService.INSTANCE.execute(() -> {
             final List<File> files = FileUtil.getListOfLinkedFiles(mainTable.getSelectedEntries(),
-                    bibDatabaseContext.getFileDirectory());
+                    bibDatabaseContext.getFileDirectory(Globals.prefs.getFileDirectoryPreferences()));
             for (final File f : files) {
                 try {
                     JabRefDesktop.openFolderAndSelectFile(f.getAbsolutePath());
@@ -2359,12 +2359,10 @@ public Optional<String> searchAndOpen() {
 
             final Set<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
             final List<File> dirs = new ArrayList<>();
-            if (!basePanel.getBibDatabaseContext().getFileDirectory().isEmpty()) {
-                final List<String> mdDirs = basePanel.getBibDatabaseContext().getFileDirectory();
-                for (final String mdDir : mdDirs) {
-                    dirs.add(new File(mdDir));
-
-                }
+            final List<String> mdDirs = basePanel.getBibDatabaseContext()
+                    .getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
+            for (final String mdDir : mdDirs) {
+                dirs.add(new File(mdDir));
             }
             final List<String> extensions = new ArrayList<>();
             for (final ExternalFileType type : types) {

src/main/java/net/sf/jabref/gui/FileListEntryEditor.java

@@ -295,7 +295,7 @@ private void storeSettings(FileListEntry entry) {
         String link = "";
         // See if we should trim the file link to be relative to the file directory:
         try {
-            List<String> dirs = databaseContext.getFileDirectory();
+            List<String> dirs = databaseContext.getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
             if (dirs.isEmpty()) {
                 link = this.link.getText().trim();
             } else {
@@ -335,7 +335,8 @@ public boolean okPressed() {
 
     private final ActionListener browsePressed = e -> {
         String filePath = link.getText().trim();
-        Optional<File> file = FileUtil.expandFilename(this.databaseContext, filePath);
+        Optional<File> file = FileUtil.expandFilename(this.databaseContext, filePath,
+                Globals.prefs.getFileDirectoryPreferences());
         String workingDir;
         // no file set yet or found
         if (file.isPresent()) {
@@ -352,7 +353,7 @@ public boolean okPressed() {
             Globals.prefs.put(JabRefPreferences.FILE_WORKING_DIRECTORY, newFile.getPath());
 
             // If the file is below the file directory, make the path relative:
-            List<String> fileDirs = this.databaseContext.getFileDirectory();
+            List<String> fileDirs = this.databaseContext.getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
             newFile = FileUtil.shortenFileName(newFile, fileDirs);
 
             link.setText(newFile.getPath());