Removed JabRefPreferences dependency in FileUtil and removed TimeStam…

…p class (#1791)

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

@@ -18,9 +18,11 @@
 import net.sf.jabref.gui.JabRefFrame;
 import net.sf.jabref.gui.net.MonitoredURLDownload;
 import net.sf.jabref.logic.l10n.Localization;
+import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.logic.net.URLDownload;
 import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.logic.util.io.FileUtil;
+import net.sf.jabref.preferences.JabRefPreferences;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -255,8 +257,9 @@ private void downloadFinished() {
     // FIXME: will break download if no bibtexkey is present!
     private String getSuggestedFileName(String suffix) {
         String plannedName = FileUtil.createFileNameFromPattern(databaseContext.getDatabase(),
-                frame.getCurrentBasePanel().getSelectedEntries().get(0), Globals.journalAbbreviationLoader,
-                Globals.prefs);
+                frame.getCurrentBasePanel().getSelectedEntries().get(0),
+                Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN),
+                LayoutFormatterPreferences.fromPreferences(Globals.prefs, Globals.journalAbbreviationLoader));
 
         if (!suffix.isEmpty()) {
             plannedName += "." + suffix;

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

@@ -25,6 +25,7 @@
 import net.sf.jabref.gui.undo.UndoableFieldChange;
 import net.sf.jabref.gui.undo.UndoableInsertEntry;
 import net.sf.jabref.logic.l10n.Localization;
+import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.logic.util.io.FileUtil;
 import net.sf.jabref.logic.xmp.XMPPreferences;
@@ -334,8 +335,9 @@ private boolean showLinkMoveCopyRenameDialog(String linkFileName, ExternalFileTy
         renameCheckBox.setText(Localization.lang("Rename file to").concat(": "));
 
         // Determine which name to suggest:
-        String targetName = FileUtil.createFileNameFromPattern(database, entry, Globals.journalAbbreviationLoader,
-                Globals.prefs);
+        String targetName = FileUtil.createFileNameFromPattern(database, entry,
+                Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN),
+                LayoutFormatterPreferences.fromPreferences(Globals.prefs, Globals.journalAbbreviationLoader));
 
         renameToTextBox.setText(targetName.concat(".").concat(fileType.getExtension()));
 

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

@@ -20,6 +20,7 @@
 import net.sf.jabref.gui.fieldeditors.FileListEditor;
 import net.sf.jabref.gui.util.component.CheckBoxMessage;
 import net.sf.jabref.logic.l10n.Localization;
+import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.logic.util.io.FileUtil;
 import net.sf.jabref.preferences.JabRefPreferences;
 
@@ -97,7 +98,9 @@ public void actionPerformed(ActionEvent event) {
                     // Determine which name to suggest:
                     String suggName = FileUtil
                             .createFileNameFromPattern(eEditor.getDatabase(), eEditor.getEntry(),
-                                    Globals.journalAbbreviationLoader, Globals.prefs)
+                                    Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN),
+                                    LayoutFormatterPreferences.fromPreferences(Globals.prefs,
+                                            Globals.journalAbbreviationLoader))
                             .concat(entry.type.isPresent() ? "." + entry.type.get().getExtension() : "");
                     CheckBoxMessage cbm = new CheckBoxMessage(Localization.lang("Move file to file directory?"),
                             Localization.lang("Rename to '%0'", suggName),

src/main/java/net/sf/jabref/gui/actions/CleanupAction.java

@@ -17,6 +17,7 @@
 import net.sf.jabref.logic.cleanup.CleanupPreset;
 import net.sf.jabref.logic.cleanup.CleanupWorker;
 import net.sf.jabref.logic.l10n.Localization;
+import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.model.FieldChange;
 import net.sf.jabref.model.entry.BibEntry;
 import net.sf.jabref.preferences.JabRefPreferences;
@@ -146,7 +147,9 @@ private int showDialog(CleanupPresetPanel presetPanel) {
     private void doCleanup(CleanupPreset preset, BibEntry entry, NamedCompound ce) {
         // Create and run cleaner
         BibDatabaseContext bibDatabaseContext = panel.getBibDatabaseContext();
-        CleanupWorker cleaner = new CleanupWorker(bibDatabaseContext, Globals.journalAbbreviationLoader, Globals.prefs);
+        CleanupWorker cleaner = new CleanupWorker(bibDatabaseContext,
+                Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN),
+                LayoutFormatterPreferences.fromPreferences(Globals.prefs, Globals.journalAbbreviationLoader));
         List<FieldChange> changes = cleaner.cleanup(preset, entry);
 
         unsuccessfulRenames = cleaner.getUnsuccessfulRenames();

src/main/java/net/sf/jabref/gui/date/DatePickerButton.java

@@ -12,6 +12,7 @@
 import net.sf.jabref.gui.fieldeditors.FieldEditor;
 import net.sf.jabref.gui.util.FocusRequester;
 import net.sf.jabref.logic.util.date.EasyDateFormat;
+import net.sf.jabref.preferences.JabRefPreferences;
 
 import com.michaelbaranov.microba.calendar.DatePicker;
 
@@ -43,7 +44,9 @@ public void actionPerformed(ActionEvent e) {
             if (isoFormat) {
                 editor.setText(EasyDateFormat.isoDateFormat().getDateAt(date));
             } else {
-                editor.setText(EasyDateFormat.fromPreferences(Globals.prefs).getDateAt(date));
+                editor.setText(EasyDateFormat
+                        .fromTimeStampFormat(Globals.prefs.get(JabRefPreferences.TIME_STAMP_FORMAT))
+                        .getDateAt(date));
             }
             // Set focus to editor component after changing its text:
             new FocusRequester(editor.getTextComponent());

src/main/java/net/sf/jabref/gui/entryeditor/EntryEditor.java

@@ -88,8 +88,10 @@
 import net.sf.jabref.logic.importer.fileformat.BibtexParser;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.search.SearchQueryHighlightListener;
-import net.sf.jabref.logic.util.date.TimeStamp;
+import net.sf.jabref.logic.util.UpdateField;
+import net.sf.jabref.logic.util.date.EasyDateFormat;
 import net.sf.jabref.model.EntryTypes;
+import net.sf.jabref.model.FieldChange;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.model.database.BibDatabaseMode;
 import net.sf.jabref.model.entry.BibEntry;
@@ -1129,11 +1131,10 @@ public void actionPerformed(ActionEvent event) {
 
                 // Add an UndoableKeyChange to the baseframe's undoManager.
                 UndoableKeyChange undoableKeyChange = new UndoableKeyChange(panel.getDatabase(), entry, oldValue, newValue);
-                if (TimeStamp.updateTimeStampIsSet(Globals.prefs)) {
+                if (updateTimeStampIsSet()) {
                     NamedCompound ce = new NamedCompound(undoableKeyChange.getPresentationName());
                     ce.addEdit(undoableKeyChange);
-                    TimeStamp.doUpdateTimeStamp(entry, Globals.prefs)
-                            .ifPresent(fieldChange -> ce.addEdit(new UndoableFieldChange(fieldChange)));
+                    doUpdateTimeStamp().ifPresent(fieldChange -> ce.addEdit(new UndoableFieldChange(fieldChange)));
                     ce.end();
                     panel.getUndoManager().addEdit(ce);
                 } else {
@@ -1196,11 +1197,11 @@ public void actionPerformed(ActionEvent event) {
 
                         // Add an UndoableFieldChange to the baseframe's undoManager.
                         UndoableFieldChange undoableFieldChange = new UndoableFieldChange(entry, fieldEditor.getFieldName(), oldValue, toSet);
-                        if (TimeStamp.updateTimeStampIsSet(Globals.prefs)) {
+                        if (updateTimeStampIsSet()) {
                             NamedCompound ce = new NamedCompound(undoableFieldChange.getPresentationName());
                             ce.addEdit(undoableFieldChange);
 
-                            TimeStamp.doUpdateTimeStamp(entry, Globals.prefs)
+                            doUpdateTimeStamp()
                                     .ifPresent(fieldChange -> ce.addEdit(new UndoableFieldChange(fieldChange)));
                             ce.end();
 
@@ -1503,4 +1504,20 @@ public void actionPerformed(ActionEvent event) {
         }
     }
 
+
+    private boolean updateTimeStampIsSet() {
+        return Globals.prefs.getBoolean(JabRefPreferences.USE_TIME_STAMP)
+                && Globals.prefs.getBoolean(JabRefPreferences.UPDATE_TIMESTAMP);
+    }
+
+    /**
+     * Updates the timestamp of the given entry and returns the FieldChange
+     */
+    private Optional<FieldChange> doUpdateTimeStamp() {
+        String timeStampField = Globals.prefs.get(JabRefPreferences.TIME_STAMP_FIELD);
+        String timeStampFormat = Globals.prefs.get(JabRefPreferences.TIME_STAMP_FORMAT);
+        String timestamp = EasyDateFormat.fromTimeStampFormat(timeStampFormat).getCurrentDate();
+        return UpdateField.updateField(entry, timeStampField, timestamp);
+    }
+
 }

src/main/java/net/sf/jabref/logic/cleanup/CleanupWorker.java

@@ -6,24 +6,23 @@
 import java.util.Objects;
 
 import net.sf.jabref.BibDatabaseContext;
-import net.sf.jabref.logic.journals.JournalAbbreviationLoader;
+import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.model.FieldChange;
 import net.sf.jabref.model.entry.BibEntry;
 import net.sf.jabref.model.entry.FieldName;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 public class CleanupWorker {
 
     private final BibDatabaseContext databaseContext;
-    private final JournalAbbreviationLoader repositoryLoader;
-    private final JabRefPreferences prefs;
+    private final String fileNamePattern;
+    private final LayoutFormatterPreferences prefs;
     private int unsuccessfulRenames;
 
 
-    public CleanupWorker(BibDatabaseContext databaseContext, JournalAbbreviationLoader repositoryLoader,
-            JabRefPreferences prefs) {
+    public CleanupWorker(BibDatabaseContext databaseContext, String fileNamePattern,
+            LayoutFormatterPreferences prefs) {
         this.databaseContext = databaseContext;
-        this.repositoryLoader = repositoryLoader;
+        this.fileNamePattern = fileNamePattern;
         this.prefs = prefs;
     }
 
@@ -68,7 +67,7 @@ private List<CleanupJob> determineCleanupActions(CleanupPreset preset) {
         }
         if (preset.isRenamePDF()) {
             RenamePdfCleanup cleaner = new RenamePdfCleanup(preset.isRenamePdfOnlyRelativePaths(), databaseContext,
-                    repositoryLoader, prefs);
+                    fileNamePattern, prefs);
             jobs.add(cleaner);
             unsuccessfulRenames += cleaner.getUnsuccessfulRenames();
         }

src/main/java/net/sf/jabref/logic/cleanup/RenamePdfCleanup.java

@@ -9,29 +9,28 @@
 
 import net.sf.jabref.BibDatabaseContext;
 import net.sf.jabref.logic.TypedBibEntry;
-import net.sf.jabref.logic.journals.JournalAbbreviationLoader;
+import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.logic.util.io.FileUtil;
 import net.sf.jabref.model.FieldChange;
 import net.sf.jabref.model.entry.BibEntry;
 import net.sf.jabref.model.entry.ParsedFileField;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 public class RenamePdfCleanup implements CleanupJob {
 
     private final BibDatabaseContext databaseContext;
     private final boolean onlyRelativePaths;
-    private final JournalAbbreviationLoader repositoryLoader;
-    private final JabRefPreferences prefs;
+    private final String fileNamePattern;
+    private final LayoutFormatterPreferences prefs;
 
     private int unsuccessfulRenames;
 
 
     public RenamePdfCleanup(boolean onlyRelativePaths, BibDatabaseContext databaseContext,
-            JournalAbbreviationLoader repositoryLoader, JabRefPreferences prefs) {
+            String fileNamePattern, LayoutFormatterPreferences prefs) {
         this.databaseContext = Objects.requireNonNull(databaseContext);
         this.onlyRelativePaths = onlyRelativePaths;
-        this.repositoryLoader = Objects.requireNonNull(repositoryLoader);
+        this.fileNamePattern = Objects.requireNonNull(fileNamePattern);
         this.prefs = Objects.requireNonNull(prefs);
     }
 
@@ -50,9 +49,8 @@ public List<FieldChange> cleanup(BibEntry entry) {
                 continue;
             }
 
-            StringBuilder newFilename = new StringBuilder(
-                    FileUtil.createFileNameFromPattern(databaseContext.getDatabase(), entry, repositoryLoader, prefs)
-                            .trim());
+            StringBuilder newFilename = new StringBuilder(FileUtil
+                    .createFileNameFromPattern(databaseContext.getDatabase(), entry, fileNamePattern, prefs).trim());
 
             //Add extension to newFilename
             newFilename.append('.').append(FileUtil.getFileExtension(realOldFilename).orElse("pdf"));

src/main/java/net/sf/jabref/logic/util/date/EasyDateFormat.java

@@ -5,8 +5,6 @@
 import java.time.format.DateTimeFormatter;
 import java.util.Date;
 
-import net.sf.jabref.preferences.JabRefPreferences;
-
 public class EasyDateFormat {
 
     /**
@@ -59,10 +57,6 @@ public static EasyDateFormat fromTimeStampFormat(String timeStampFormat) {
         return new EasyDateFormat(timeStampFormat);
     }
 
-    public static EasyDateFormat fromPreferences(JabRefPreferences preferences) {
-     return new EasyDateFormat(preferences.get(JabRefPreferences.TIME_STAMP_FORMAT));
-    }
-
     public static EasyDateFormat isoDateFormat() {
         return new EasyDateFormat(DateTimeFormatter.ISO_LOCAL_DATE);
     }

src/main/java/net/sf/jabref/logic/util/io/FileUtil.java

@@ -21,7 +21,6 @@
 import java.util.regex.Pattern;
 
 import net.sf.jabref.BibDatabaseContext;
-import net.sf.jabref.logic.journals.JournalAbbreviationLoader;
 import net.sf.jabref.logic.layout.Layout;
 import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.logic.layout.LayoutHelper;
@@ -31,7 +30,6 @@
 import net.sf.jabref.model.entry.FieldName;
 import net.sf.jabref.model.entry.FileField;
 import net.sf.jabref.model.entry.ParsedFileField;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -371,19 +369,19 @@ public static List<File> getListOfLinkedFiles(List<BibEntry> bes, List<String> f
     /**
      * Determines filename provided by an entry in a database
      *
-     * @param database the database, where the entry is located
-     * @param entry    the entry to which the file should be linked to
-     * @param repositoryLoader
+     * @param database        the database, where the entry is located
+     * @param entry           the entry to which the file should be linked to
+     * @param fileNamePattern the filename pattern
+     * @param prefs           the layout preferences
      * @return a suggested fileName
      */
     public static String createFileNameFromPattern(BibDatabase database, BibEntry entry,
-            JournalAbbreviationLoader repositoryLoader, JabRefPreferences prefs) {
+            String fileNamePattern, LayoutFormatterPreferences prefs) {
         String targetName = entry.getCiteKeyOptional().orElse("default");
-        StringReader sr = new StringReader(prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN));
+        StringReader sr = new StringReader(fileNamePattern);
         Layout layout = null;
         try {
-            layout = new LayoutHelper(sr, LayoutFormatterPreferences.fromPreferences(prefs, repositoryLoader))
-                    .getLayoutFromText();
+            layout = new LayoutHelper(sr, prefs).getLayoutFromText();
         } catch (IOException e) {
             LOGGER.info("Wrong format " + e.getMessage(), e);
         }

src/test/java/net/sf/jabref/logic/cleanup/CleanupWorkerTest.java

@@ -19,7 +19,7 @@
 import net.sf.jabref.logic.formatter.bibtexfields.NormalizePagesFormatter;
 import net.sf.jabref.logic.formatter.bibtexfields.UnitsToLatexFormatter;
 import net.sf.jabref.logic.formatter.casechanger.ProtectTermsFormatter;
-import net.sf.jabref.logic.journals.JournalAbbreviationLoader;
+import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.logic.protectedterms.ProtectedTermsLoader;
 import net.sf.jabref.logic.protectedterms.ProtectedTermsPreferences;
 import net.sf.jabref.model.FieldChange;
@@ -52,16 +52,14 @@ public void setUp() throws IOException {
         if (Globals.prefs == null) {
             Globals.prefs = JabRefPreferences.getInstance();
         }
-        if (Globals.journalAbbreviationLoader == null) {
-            Globals.journalAbbreviationLoader = mock(JournalAbbreviationLoader.class);
-        }
 
         pdfFolder = bibFolder.newFolder();
 
         MetaData metaData = new MetaData();
         metaData.setDefaultFileDirectory(pdfFolder.getAbsolutePath());
         BibDatabaseContext context = new BibDatabaseContext(new BibDatabase(), metaData, bibFolder.newFile("test.bib"));
-        worker = new CleanupWorker(context, mock(JournalAbbreviationLoader.class), Globals.prefs);
+        worker = new CleanupWorker(context, Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN),
+                mock(LayoutFormatterPreferences.class));
     }
 
     @Test(expected = NullPointerException.class)

src/test/java/net/sf/jabref/logic/cleanup/ISSNCleanupTest.java

@@ -3,9 +3,8 @@
 import java.util.Optional;
 
 import net.sf.jabref.BibDatabaseContext;
-import net.sf.jabref.logic.journals.JournalAbbreviationLoader;
+import net.sf.jabref.logic.layout.LayoutFormatterPreferences;
 import net.sf.jabref.model.entry.BibEntry;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 import org.junit.Assert;
 import org.junit.Before;
@@ -20,8 +19,7 @@ public class ISSNCleanupTest {
 
     @Before
     public void setUp() {
-        worker = new CleanupWorker(mock(BibDatabaseContext.class), mock(JournalAbbreviationLoader.class),
-                JabRefPreferences.getInstance());
+        worker = new CleanupWorker(mock(BibDatabaseContext.class), "", mock(LayoutFormatterPreferences.class));
     }
 
     @Test