Finalize code, fix Localization, do some renames

Add changelog enty and missing dots in previous entries

CHANGELOG.md

@@ -34,6 +34,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We integrated support for the [paper recommender system Mr.DLib](http://help.jabref.org/en/EntryEditor#related-articles-tab) in a new tab in the entry editor.
 - We renamed "database" to "library" to have a real distinction to SQL and NoSQL databases. [#2095](https://github.com/JabRef/jabref/issues/2095)
 - Removed the apache.commons.collections library
+- The `Move linked files to default file directory`-Cleanup operation respects the `File directory pattern` setting 
+- We separated the `Move file` and `Rename Pdfs` logic and context menu entries in the `General`-Tab for the Field `file` to improve the semantics
 
 ### Fixed
  - We fixed an issue where authors with multiple surnames were not presented correctly in the main table. [#2534](https://github.com/JabRef/jabref/issues/2534)
@@ -43,11 +45,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - The field `issue` is now always exported to the corresponding `issue` field in MS-Office XML.
  - We fixed an issue with repeated escaping of the %-sign when running the LaTeXCleanup more than once. [#2451](https://github.com/JabRef/jabref/issues/2451)
  - We fixed the import of MS-Office XML files, when the `month` field contained an invalid value.
- - ArXiV fetcher now checks similarity of entry when using DOI retrieval to avoid false positives [#2575](https://github.com/JabRef/jabref/issues/2575)
- - Sciencedirect/Elsevier fetcher is now able to scrape new HTML structure [#2576](https://github.com/JabRef/jabref/issues/2576)
- - Fixed the synchronization logic of keywords and special fields and vice versa [#2580](https://github.com/JabRef/jabref/issues/2580)
-
-
+ - ArXiV fetcher now checks similarity of entry when using DOI retrieval to avoid false positives. [#2575](https://github.com/JabRef/jabref/issues/2575)
+ - Sciencedirect/Elsevier fetcher is now able to scrape new HTML structure. [#2576](https://github.com/JabRef/jabref/issues/2576)
+ - Fixed the synchronization logic of keywords and special fields and vice versa. [#2580](https://github.com/JabRef/jabref/issues/2580)
+ - We fixed an issue introduced with Version 3.8.2 where executing the `Rename PDFs`-Cleanup operation moved the files to the file directory. [#2526](https://github.com/JabRef/jabref/issues/2526)
+ - We fixed an issue where the `Move linked files to default file directory`-Cleanup operation did not move the files to the location of the bib-file. [#2454](https://github.com/JabRef/jabref/issues/2454)
+ - We fixed an issue where executeing `Move file` on a selected file in the `General`-Tab could overwrite an existing file. [#2385](https://github.com/JabRef/jabref/issues/2358)
 ### Removed
 
 

src/main/java/org/jabref/gui/externalfiles/MoveFileAction.java

@@ -22,19 +22,13 @@
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.FieldChange;
 import org.jabref.model.entry.ParsedFileField;
 
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
 /**
  * Action for moving a file that is linked  from an entry in JabRef.
  */
 public class MoveFileAction extends AbstractAction {
 
-    private static final Log LOGGER = LogFactory.getLog(MoveFileAction.class);
-
     private final JabRefFrame frame;
     private final EntryEditor eEditor;
     private final FileListEditor editor;
@@ -56,7 +50,6 @@ public void actionPerformed(ActionEvent event) {
         }
 
         FileListEntry entry = editor.getTableModel().getEntry(selected);
-
         // Check if the current file exists:
         String ln = entry.link;
         ParsedFileField field = entry.toParsedFileField();
@@ -66,14 +59,13 @@ public void actionPerformed(ActionEvent event) {
             // TODO: notify that this operation cannot be done on remote links
             return;
         }
-        System.out.println("Parsed file Field " + field);
         // Get an absolute path representation:
         List<String> dirs = frame.getCurrentBasePanel().getBibDatabaseContext()
                 .getFileDirectories(prefs.getFileDirectoryPreferences());
         Optional<Path> fileDir = frame.getCurrentBasePanel().getBibDatabaseContext()
                 .getFirstExistingFileDir(prefs.getFileDirectoryPreferences());
         if (!fileDir.isPresent()) {
-            JOptionPane.showMessageDialog(frame, Localization.lang("File_directory_is_not_set_or_does_not_exist!"),
+            JOptionPane.showMessageDialog(frame, Localization.lang("File directory is not set or does not exist!"),
                     Localization.lang("Move file"), JOptionPane.ERROR_MESSAGE);
             return;
         }
@@ -83,122 +75,22 @@ public void actionPerformed(ActionEvent event) {
         }
 
         if ((file != null) && Files.exists(file)) {
-            // Ok, we found the file. Now get a new name:
-            System.out.println("Cleanup of file " + file);
 
-            //Problem: All listed files are cleaned up
             MoveFilesCleanup moveFiles = new MoveFilesCleanup(frame.getCurrentBasePanel().getBibDatabaseContext(),
                     prefs.getFileDirPattern(), prefs.getFileDirectoryPreferences(),
                     prefs.getLayoutFormatterPreferences(), field);
 
             String[] options = {Localization.lang("Move file"), Localization.lang("Cancel")};
 
-            int dialogResult = JOptionPane.showOptionDialog(frame, "Move file to file directory" + fileDir.get(),
-                    "Move",
+            int dialogResult = JOptionPane.showOptionDialog(frame,
+                    Localization.lang("Move file to file directory?") + " " + fileDir.get(),
+                    Localization.lang("Move file"),
                     JOptionPane.INFORMATION_MESSAGE, JOptionPane.YES_NO_CANCEL_OPTION, null, options, options[0]);
 
             if (dialogResult == JOptionPane.YES_OPTION) {
-                List<FieldChange> fieldChanges = moveFiles.cleanup((eEditor.getEntry()));
-                fieldChanges.stream().findFirst().ifPresent(x -> System.out.println(x.getNewValue()));
-            }
-
-            //myCleanUp.cleanup();
-            /*  File newFile = null;
-            boolean repeat = true;
-            while (repeat) {
-                repeat = false;
-                String chosenFile;
-                if (toFileDir) {
-                    // Determine which name to suggest:
-                    String suggName = FileUtil
-                            .createFileNameFromPattern(eEditor.getDatabase(), eEditor.getEntry(),
-                                    Globals.prefs.get(JabRefPreferences.IMPORT_FILENAMEPATTERN),
-                                    Globals.prefs.getLayoutFormatterPreferences(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),
-                            Globals.prefs.getBoolean(JabRefPreferences.RENAME_ON_MOVE_FILE_TO_FILE_DIR));
-                    int answer;
-                    // Only ask about renaming file if the file doesn't have the proper name already:
-                    if (suggName.equals(file.getName())) {
-                        answer = JOptionPane.showConfirmDialog(frame, Localization.lang("Move file to file directory?"),
-                                MOVE_RENAME, JOptionPane.YES_NO_OPTION);
-                    } else {
-                        answer = JOptionPane.showConfirmDialog(frame, cbm, MOVE_RENAME, JOptionPane.YES_NO_OPTION);
-                    }
-                    if (answer != JOptionPane.YES_OPTION) {
-                        return;
-                    }
-                    Globals.prefs.putBoolean(JabRefPreferences.RENAME_ON_MOVE_FILE_TO_FILE_DIR, cbm.isSelected());
-                    StringBuilder sb = new StringBuilder(dirs.get(found));
-                    if (!dirs.get(found).endsWith(File.separator)) {
-                        sb.append(File.separator);
-                    }
-                    if (cbm.isSelected()) {
-                        // Rename:
-                        sb.append(suggName);
-                    } else {
-                        // Do not rename:
-                        sb.append(file.getName());
-                    }
-                    chosenFile = sb.toString();
-                } else {
-                    Optional<Path> path = new FileDialog(frame, file.getPath()).saveNewFile();
-                    if (path.isPresent()) {
-                        chosenFile = path.get().toString();
-                    } else {
-                        return;
-                    }
-                }
-                newFile = new File(chosenFile);
-
+                moveFiles.cleanup((eEditor.getEntry()));
             }
 
-            if ((newFile != null) && !newFile.equals(file)) {
-                try {
-                    boolean success = file.renameTo(newFile);
-                    if (!success) {
-                        success = FileUtil.copyFile(file.toPath(), newFile.toPath(), true);
-                    }
-                    if (success) {
-                        // Remove the original file:
-                        Files.deleteIfExists(file.toPath());
-
-                        // Relativise path, if possible.
-                        String canPath = new File(dirs.get(found)).getCanonicalPath();
-                        if (newFile.getCanonicalPath().startsWith(canPath)) {
-                            if ((newFile.getCanonicalPath().length() > canPath.length())
-                                    && (newFile.getCanonicalPath().charAt(canPath.length()) == File.separatorChar)) {
-
-                                String newLink = newFile.getCanonicalPath().substring(1 + canPath.length());
-                                editor.getTableModel().setEntry(selected,
-                                        new FileListEntry(entry.description, newLink, entry.type));
-                            } else {
-                                String newLink = newFile.getCanonicalPath().substring(canPath.length());
-                                editor.getTableModel().setEntry(selected,
-                                        new FileListEntry(entry.description, newLink, entry.type));
-                            }
-
-                        } else {
-                            String newLink = newFile.getCanonicalPath();
-                            editor.getTableModel().setEntry(selected,
-                                    new FileListEntry(entry.description, newLink, entry.type));
-                        }
-                        eEditor.updateField(editor);
-                        frame.output(Localization.lang("File moved"));
-                    } else {
-                        JOptionPane.showMessageDialog(frame, Localization.lang("Move file failed"), MOVE_RENAME,
-                                JOptionPane.ERROR_MESSAGE);
-                    }
-
-                } catch (SecurityException | IOException ex) {
-                    LOGGER.warn("Could not move file", ex);
-                    JOptionPane.showMessageDialog(frame,
-                            Localization.lang("Could not move file '%0'.", file.getAbsolutePath()) + ex.getMessage(),
-                            MOVE_RENAME, JOptionPane.ERROR_MESSAGE);
-                }
-
-            }*/
         } else {
             // File doesn't exist, so we can't move it.
             JOptionPane.showMessageDialog(frame, Localization.lang("Could not find file '%0'.", entry.link),

src/main/java/org/jabref/gui/externalfiles/RenameFileAction.java

@@ -22,7 +22,6 @@
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.FieldChange;
 import org.jabref.model.entry.ParsedFileField;
 
 public class RenameFileAction extends AbstractAction {
@@ -48,9 +47,7 @@ public void actionPerformed(ActionEvent e) {
         }
 
         FileListEntry entry = editor.getTableModel().getEntry(selected);
-
         ParsedFileField field = entry.toParsedFileField();
-        System.out.println("Parsed file Field " + field);
         // Check if the current file exists:
         String ln = entry.link;
         boolean httpLink = ln.toLowerCase(Locale.ENGLISH).startsWith("http");
@@ -63,7 +60,7 @@ public void actionPerformed(ActionEvent e) {
         Optional<Path> fileDir = frame.getCurrentBasePanel().getBibDatabaseContext()
                 .getFirstExistingFileDir(prefs.getFileDirectoryPreferences());
         if (!fileDir.isPresent()) {
-            JOptionPane.showMessageDialog(frame, Localization.lang("File_directory_is_not_set_or_does_not_exist!"),
+            JOptionPane.showMessageDialog(frame, Localization.lang("File directory is not set or does not exist!"),
                     Localization.lang("Rename file"), JOptionPane.ERROR_MESSAGE);
             return;
         }
@@ -73,25 +70,23 @@ public void actionPerformed(ActionEvent e) {
         }
 
         if ((file != null) && Files.exists(file)) {
-            System.out.println("Cleanup Rename of file " + file);
 
             RenamePdfCleanup pdfCleanup = new RenamePdfCleanup(false,
                     frame.getCurrentBasePanel().getBibDatabaseContext(), prefs.getFileNamePattern(),
                     prefs.getLayoutFormatterPreferences(),
                     prefs.getFileDirectoryPreferences(), field);
 
             String targetFileName = pdfCleanup.getTargetFileName(field, eEditor.getEntry());
-            System.out.println("TargetFileName " + targetFileName);
 
             String[] options = {Localization.lang("Rename file"), Localization.lang("Cancel")};
-
-            int dialogResult = JOptionPane.showOptionDialog(frame, "Rename file to " + targetFileName, "Rename",
+            int dialogResult = JOptionPane.showOptionDialog(frame,
+                    Localization.lang("Rename file to") + " " + targetFileName,
+                    Localization.lang("Rename file"),
                     JOptionPane.INFORMATION_MESSAGE, JOptionPane.YES_NO_CANCEL_OPTION, null, options, options[0]);
 
             //indicates Rename pressed
             if (dialogResult == JOptionPane.YES_OPTION) {
-                List<FieldChange> fieldChanges = pdfCleanup.cleanup(eEditor.getEntry());
-                fieldChanges.stream().findFirst().ifPresent(System.out::println);
+                pdfCleanup.cleanup(eEditor.getEntry());
             }
 
         }

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

@@ -35,7 +35,7 @@ public class MoveFilesCleanup implements CleanupJob {
     private final String fileDirPattern;
     private static final Log LOGGER = LogFactory.getLog(MoveFilesCleanup.class);
 
-    private ParsedFileField singleFieldCleanup;
+    private ParsedFileField singleFileFieldCleanup;
 
     public MoveFilesCleanup(BibDatabaseContext databaseContext, String fileDirPattern,
             FileDirectoryPreferences fileDirectoryPreferences, LayoutFormatterPreferences layoutPrefs) {
@@ -50,7 +50,7 @@ public MoveFilesCleanup(BibDatabaseContext databaseContext, String fileDirPatter
             ParsedFileField field) {
 
         this(databaseContext, fileDirPattern, fileDirectoryPreferences, prefs);
-        this.singleFieldCleanup = field;
+        this.singleFileFieldCleanup = field;
     }
 
     @Override
@@ -73,10 +73,10 @@ public List<FieldChange> cleanup(BibEntry entry) {
         List<ParsedFileField> fileList;
         List<ParsedFileField> newFileList;
 
-        if (singleFieldCleanup != null) {
-            fileList = Arrays.asList(singleFieldCleanup);
-
-            newFileList = typedEntry.getFiles().stream().filter(x -> !x.equals(singleFieldCleanup))
+        if (singleFileFieldCleanup != null) {
+            fileList = Arrays.asList(singleFileFieldCleanup);
+            //Add all other except the current selected file
+            newFileList = typedEntry.getFiles().stream().filter(name -> !name.equals(singleFileFieldCleanup))
                     .collect(Collectors.toList());
         } else {
             newFileList = new ArrayList<>();

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

@@ -163,12 +163,9 @@ public String getTargetFileName(ParsedFileField flEntry, BibEntry entry) {
         StringBuilder targetFileName = new StringBuilder(FileUtil
                 .createFileNameFromPattern(databaseContext.getDatabase(), entry, fileNamePattern, layoutPrefs)
                 .trim());
-
         //Add extension to newFilename
         targetFileName.append('.').append(FileUtil.getFileExtension(realOldFilename).orElse("pdf"));
-
         return targetFileName.toString();
-
     }
 
     public int getUnsuccessfulRenames() {

src/main/resources/l10n/JabRef_da.properties

@@ -1386,7 +1386,6 @@ Query_'%0'_with_fetcher_'%1'_did_not_return_any_results.=Forespørgsel_'%0'_med_
 Move_file=Flyt_fil
 Rename_file=omdøb_fil
 
-File_moved=Fil_flyttet
 Move_file_failed=Flytning_af_fil_mislykkedes
 Could_not_move_file_'%0'.=Kunne_ikke_flytte_fil_'%0'.
 Could_not_find_file_'%0'.=Kunne_ikke_finde_filen_'%0'.
@@ -1400,7 +1399,6 @@ Show_search_results_in_a_window=Vis_søgeresultater_i_et_vindue
 Show_global_search_results_in_a_window=
 Search_in_all_open_libraries=
 Move_file_to_file_directory?=Flyt_fil_til_filbibliotek?
-Rename_to_'%0'=Omdøb_til_'%0'
 You_have_changed_the_menu_and_label_font_size.=Du_har_ændret_menu-_og_tekst-skriftstørrelsen.
 
 Library_is_protected._Cannot_save_until_external_changes_have_been_reviewed.=Libraryn_er_beskyttet._Kan_ikke_gemme_før_eksterne_ændringer_er_gennemset.

src/main/resources/l10n/JabRef_de.properties

@@ -1386,7 +1386,6 @@ Query_'%0'_with_fetcher_'%1'_did_not_return_any_results.=Die_Abfrage_'%0'_mit_de
 Move_file=Datei_verschoben
 Rename_file=Datei_umbenennen
 
-File_moved=Datei_verschoben
 Move_file_failed=Fehler_beim_Verschieben_der_Datei
 Could_not_move_file_'%0'.=Datei_'%0'_konnte_nicht_verschoben_werden.
 Could_not_find_file_'%0'.=Datei_'%0'_nicht_gefunden.
@@ -1400,7 +1399,6 @@ Show_search_results_in_a_window=Suchergebnisse_in_einem_Fenster_anzeigen
 Show_global_search_results_in_a_window=Globale_Suchergebnisse_in_einem_Fenster_anzeigen
 Search_in_all_open_libraries=Suche_in_allen_offenen_Datenbanken
 Move_file_to_file_directory?=Datei_in_Dateiverzeichnis_verschieben?
-Rename_to_'%0'=Umbenennen_in_'%0'
 You_have_changed_the_menu_and_label_font_size.=Sie_haben_die_Schriftgröße_für_Menüs_und_Label_geändert.
 
 Library_is_protected._Cannot_save_until_external_changes_have_been_reviewed.=Die_Datenbank_ist_geschützt._Speichern_nicht_möglich,_bis_externe_Änderungen_geprüft_wurden.

src/main/resources/l10n/JabRef_en.properties

@@ -1386,7 +1386,6 @@ Query_'%0'_with_fetcher_'%1'_did_not_return_any_results.=Query_'%0'_with_fetcher
 Move_file=Move_file
 Rename_file=Rename_file
 
-File_moved=File_moved
 Move_file_failed=Move_file_failed
 Could_not_move_file_'%0'.=Could_not_move_file_'%0'.
 Could_not_find_file_'%0'.=Could_not_find_file_'%0'.
@@ -1400,7 +1399,6 @@ Show_search_results_in_a_window=Show_search_results_in_a_window
 Show_global_search_results_in_a_window=Show_global_search_results_in_a_window
 Search_in_all_open_libraries=Search_in_all_open_libraries
 Move_file_to_file_directory?=Move_file_to_file_directory?
-Rename_to_'%0'=Rename_to_'%0'
 You_have_changed_the_menu_and_label_font_size.=You_have_changed_the_menu_and_label_font_size.
 
 Library_is_protected._Cannot_save_until_external_changes_have_been_reviewed.=Library_is_protected._Cannot_save_until_external_changes_have_been_reviewed.