Refactor cleanup code

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

@@ -36,12 +36,12 @@
 import javax.swing.*;
 
 import net.sf.jabref.gui.*;
-import net.sf.jabref.gui.actions.CleanUpAction;
 import net.sf.jabref.gui.entryeditor.EntryEditorTabList;
 import net.sf.jabref.gui.maintable.PersistenceTableColumnListener;
 import net.sf.jabref.gui.preftabs.ImportSettingsTab;
 import net.sf.jabref.importer.fileformat.ImportFormat;
 import net.sf.jabref.logic.autocompleter.AutoCompletePreferences;
+import net.sf.jabref.logic.cleanup.CleanupPreset;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.labelPattern.GlobalLabelPattern;
 import net.sf.jabref.logic.util.OS;
@@ -310,6 +310,33 @@ public final class JabRefPreferences {
     public static final String USE_CONVERT_TO_EQUATION = "useConvertToEquation";
     public static final String USE_IEEE_ABRV = "useIEEEAbrv";
 
+    public static final String AKS_AUTO_NAMING_PDFS_AGAIN = "AskAutoNamingPDFsAgain";
+    public static final String CLEANUP_DOI = "CleanUpDOI";
+    public static final String CLEANUP_MONTH = "CleanUpMonth";
+    public static final String CLEANUP_PAGE_NUMBERS = "CleanUpPageNumbers";
+    public static final String CLEANUP_DATE = "CleanUpDate";
+    public static final String CLEANUP_MAKE_PATHS_RELATIVE = "CleanUpMakePathsRelative";
+    public static final String CLEANUP_RENAME_PDF = "CleanUpRenamePDF";
+    public static final String CLEANUP_RENAME_PDF_ONLY_RELATIVE_PATHS = "CleanUpRenamePDFonlyRelativePaths";
+    public static final String CLEANUP_UPGRADE_EXTERNAL_LINKS = "CleanUpUpgradeExternalLinks";
+    public static final String CLEANUP_SUPERSCRIPTS = "CleanUpSuperscripts";
+    public static final String CLEANUP_HTML = "CleanUpHTML";
+    public static final String CLEANUP_CASE = "CleanUpCase";
+    public static final String CLEANUP_LATEX = "CleanUpLaTeX";
+    public static final String CLEANUP_UNITS = "CleanUpUnits";
+    public static final String CLEANUP_UNICODE = "CleanUpUnicode";
+    public static final String CLEANUP_CONVERT_TO_BIBLATEX = "CleanUpConvertToBiblatex";
+    public static final String CLEANUP_FIX_FILE_LINKS = "CleanUpFixFileLinks";
+    public static final CleanupPreset CLEANUP_DEFAULT_PRESET;
+    static {
+        EnumSet<CleanupPreset.CleanupStep> deactivedJobs = EnumSet.of(
+                CleanupPreset.CleanupStep.CLEAN_UP_UPGRADE_EXTERNAL_LINKS,
+                CleanupPreset.CleanupStep.RENAME_PDF_ONLY_RELATIVE_PATHS,
+                CleanupPreset.CleanupStep.CONVERT_TO_BIBLATEX);
+        CLEANUP_DEFAULT_PRESET = new CleanupPreset(EnumSet.complementOf(deactivedJobs));
+    }
+
+
     public static final String PUSH_TO_APPLICATION = "pushToApplication";
 
     // OpenOffice/LibreOffice preferences
@@ -336,6 +363,7 @@ public final class JabRefPreferences {
 
     private static final char[][] VALUE_DELIMITERS = new char[][] { {'"', '"'}, {'{', '}'}};
 
+
     public String WRAPPED_USERNAME;
     public final String MARKING_WITH_NUMBER_PATTERN;
 
@@ -729,7 +757,9 @@ private JabRefPreferences() {
         defaults.put(DB_CONNECT_HOSTNAME, "localhost");
         defaults.put(DB_CONNECT_DATABASE, "jabref");
         defaults.put(DB_CONNECT_USERNAME, "root");
-        CleanUpAction.putDefaults(defaults);
+
+        defaults.put(AKS_AUTO_NAMING_PDFS_AGAIN, Boolean.TRUE);
+        insertCleanupPreset(defaults, CLEANUP_DEFAULT_PRESET);
 
         // defaults for DroppedFileHandler UI
         defaults.put(DroppedFileHandler.DFH_LEAVE, Boolean.FALSE);
@@ -1279,4 +1309,24 @@ public Charset getDefaultEncoding() {
     public void setDefaultEncoding(Charset encoding) {
         put(JabRefPreferences.DEFAULT_ENCODING, encoding.name());
     }
+
+    private static void insertCleanupPreset(Map<String, Object> storage, CleanupPreset preset) {
+
+        storage.put(CLEANUP_SUPERSCRIPTS, preset.isCleanUpSuperscripts());
+        storage.put(CLEANUP_DOI, preset.isCleanUpDOI());
+        storage.put(CLEANUP_MONTH, preset.isCleanUpMonth());
+        storage.put(CLEANUP_PAGE_NUMBERS, preset.isCleanUpPageNumbers());
+        storage.put(CLEANUP_DATE, preset.isCleanUpDate());
+        storage.put(CLEANUP_MAKE_PATHS_RELATIVE, preset.isMakePathsRelative());
+        storage.put(CLEANUP_RENAME_PDF, preset.isRenamePDF());
+        storage.put(CLEANUP_RENAME_PDF_ONLY_RELATIVE_PATHS, preset.isRenamePdfOnlyRelativePaths());
+        storage.put(CLEANUP_UPGRADE_EXTERNAL_LINKS, preset.isCleanUpUpgradeExternalLinks());
+        storage.put(CLEANUP_HTML, preset.isConvertHTMLToLatex());
+        storage.put(CLEANUP_CASE, preset.isConvertCase());
+        storage.put(CLEANUP_LATEX, preset.isConvertLaTeX());
+        storage.put(CLEANUP_UNITS, preset.isConvertUnits());
+        storage.put(CLEANUP_UNICODE, preset.isConvertUnicodeToLatex());
+        storage.put(CLEANUP_CONVERT_TO_BIBLATEX, preset.isConvertToBiblatex());
+        storage.put(CLEANUP_FIX_FILE_LINKS, preset.isFixFileLinks());
+    }
 }

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

@@ -38,7 +38,7 @@
 import net.sf.jabref.groups.GroupTreeNode;
 import net.sf.jabref.gui.actions.Actions;
 import net.sf.jabref.gui.actions.BaseAction;
-import net.sf.jabref.gui.actions.CleanUpAction;
+import net.sf.jabref.gui.actions.CleanupAction;
 import net.sf.jabref.gui.desktop.JabRefDesktop;
 import net.sf.jabref.gui.entryeditor.EntryEditor;
 import net.sf.jabref.gui.fieldeditors.FieldEditor;
@@ -294,7 +294,7 @@ public void output(String s) {
 
     private void setupActions() {
         SaveDatabaseAction saveAction = new SaveDatabaseAction(this);
-        CleanUpAction cleanUpAction = new CleanUpAction(this);
+        CleanupAction cleanUpAction = new CleanupAction(this, Globals.prefs);
 
         actions.put(Actions.UNDO, undoAction);
         actions.put(Actions.REDO, redoAction);

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

@@ -0,0 +1,175 @@
+package net.sf.jabref.gui;
+
+import java.util.EnumSet;
+import java.util.Objects;
+
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import com.jgoodies.forms.builder.FormBuilder;
+import com.jgoodies.forms.layout.FormLayout;
+
+import net.sf.jabref.Globals;
+import net.sf.jabref.gui.preftabs.ImportSettingsTab;
+import net.sf.jabref.logic.cleanup.CleanupPreset;
+import net.sf.jabref.logic.l10n.Localization;
+
+public class CleanupPresetPanel {
+
+    private JCheckBox cleanUpSuperscripts;
+    private JCheckBox cleanUpDOI;
+    private JCheckBox cleanUpMonth;
+    private JCheckBox cleanUpPageNumbers;
+    private JCheckBox cleanUpDate;
+    private JCheckBox cleanUpMakePathsRelative;
+    private JCheckBox cleanUpRenamePDF;
+    private JCheckBox cleanUpRenamePDFonlyRelativePaths;
+    private JCheckBox cleanUpUpgradeExternalLinks;
+    private JCheckBox cleanUpHTML;
+    private JCheckBox cleanUpCase;
+    private JCheckBox cleanUpLaTeX;
+    private JCheckBox cleanUpUnits;
+    private JCheckBox cleanUpUnicode;
+    private JCheckBox cleanUpBibLatex;
+
+    private JPanel panel;
+    private CleanupPreset cleanupPreset;
+
+    public CleanupPresetPanel(CleanupPreset cleanupPreset) {
+        this.cleanupPreset = Objects.requireNonNull(cleanupPreset);
+
+        init();
+    }
+
+    private void init() {
+        cleanUpSuperscripts = new JCheckBox(Localization.lang("Convert 1st, 2nd, ... to real superscripts"));
+        cleanUpDOI = new JCheckBox(
+                Localization.lang("Move DOIs from note and URL field to DOI field and remove http prefix"));
+        cleanUpMonth = new JCheckBox(Localization.lang("Format content of month field to #mon#"));
+        cleanUpPageNumbers = new JCheckBox(Localization.lang("Ensure that page ranges are of the form num1--num2"));
+        cleanUpDate = new JCheckBox(Localization.lang("Format date field in the form yyyy-mm or yyyy-mm-dd"));
+        cleanUpMakePathsRelative = new JCheckBox(
+                Localization.lang("Make paths of linked files relative (if possible)"));
+        cleanUpRenamePDF = new JCheckBox(Localization.lang("Rename PDFs to given filename format pattern"));
+        cleanUpRenamePDF.addChangeListener(
+                event -> cleanUpRenamePDFonlyRelativePaths.setEnabled(cleanUpRenamePDF.isSelected()));
+        cleanUpRenamePDFonlyRelativePaths = new JCheckBox(Localization.lang("Rename only PDFs having a relative path"));
+        cleanUpUpgradeExternalLinks = new JCheckBox(
+                Localization.lang("Upgrade external PDF/PS links to use the '%0' field.", Globals.FILE_FIELD));
+        cleanUpHTML = new JCheckBox(Localization.lang("Run HTML converter on title"));
+        cleanUpCase = new JCheckBox(Localization.lang("Run filter on title keeping the case of selected words"));
+        cleanUpLaTeX = new JCheckBox(
+                Localization.lang("Remove unneccessary $, {, and } and move adjacent numbers into equations"));
+        cleanUpUnits = new JCheckBox(
+                Localization.lang("Add brackets and replace separators with their non-breaking version for units"));
+        cleanUpUnicode = new JCheckBox(Localization.lang("Run Unicode converter on title, author(s), and abstract"));
+        cleanUpBibLatex = new JCheckBox(Localization
+                .lang("Convert to BibLatex format (for example, move the value of the 'journal' field to 'journaltitle')"));
+        updateDisplay(cleanupPreset);
+
+        FormLayout layout = new FormLayout("left:15dlu,pref:grow",
+                "pref, pref, pref, pref, pref, pref, pref, pref, pref, pref, pref, pref, pref, pref, pref, pref");
+        FormBuilder builder = FormBuilder.create().layout(layout);
+        builder.add(cleanUpHTML).xyw(1, 1, 2);
+        builder.add(cleanUpUnicode).xyw(1, 2, 2);
+        builder.add(cleanUpCase).xyw(1, 3, 2);
+        builder.add(cleanUpLaTeX).xyw(1, 4, 2);
+        builder.add(cleanUpUnits).xyw(1, 5, 2);
+        builder.add(cleanUpSuperscripts).xyw(1, 6, 2);
+        builder.add(cleanUpDOI).xyw(1, 7, 2);
+        builder.add(cleanUpMonth).xyw(1, 8, 2);
+        builder.add(cleanUpPageNumbers).xyw(1, 9, 2);
+        builder.add(cleanUpDate).xyw(1, 10, 2);
+        builder.add(cleanUpUpgradeExternalLinks).xyw(1, 11, 2);
+        builder.add(cleanUpMakePathsRelative).xyw(1, 12, 2);
+        builder.add(cleanUpRenamePDF).xyw(1, 13, 2);
+        String currentPattern = Localization.lang("Filename format pattern").concat(": ").concat(
+                Globals.prefs.get(ImportSettingsTab.PREF_IMPORT_FILENAMEPATTERN));
+        builder.add(new JLabel(currentPattern)).xy(2, 14);
+        builder.add(cleanUpRenamePDFonlyRelativePaths).xy(2, 15);
+        builder.add(cleanUpBibLatex).xyw(1, 16, 2);
+        panel = builder.build();
+    }
+
+    private void updateDisplay(CleanupPreset preset) {
+        cleanUpSuperscripts.setSelected(preset.isCleanUpSuperscripts());
+        cleanUpDOI.setSelected(preset.isCleanUpDOI());
+        cleanUpMonth.setSelected(preset.isCleanUpMonth());
+        cleanUpPageNumbers.setSelected(preset.isCleanUpPageNumbers());
+        cleanUpDate.setSelected(preset.isCleanUpDate());
+        cleanUpMakePathsRelative.setSelected(preset.isMakePathsRelative());
+        cleanUpRenamePDF.setSelected(preset.isRenamePDF());
+        cleanUpRenamePDFonlyRelativePaths.setSelected(preset.isRenamePdfOnlyRelativePaths());
+        cleanUpRenamePDFonlyRelativePaths.setEnabled(cleanUpRenamePDF.isSelected());
+        cleanUpUpgradeExternalLinks.setSelected(preset.isCleanUpUpgradeExternalLinks());
+        cleanUpHTML.setSelected(preset.isConvertHTMLToLatex());
+        cleanUpCase.setSelected(preset.isConvertCase());
+        cleanUpLaTeX.setSelected(preset.isConvertLaTeX());
+        cleanUpUnits.setSelected(preset.isConvertUnits());
+        cleanUpUnicode.setSelected(preset.isConvertUnicodeToLatex());
+        cleanUpBibLatex.setSelected(preset.isConvertToBiblatex());
+    }
+
+    public JPanel getPanel() {
+        return panel;
+    }
+
+    public CleanupPreset getCleanupPreset() {
+
+        EnumSet<CleanupPreset.CleanupStep> activeJobs = EnumSet.noneOf(CleanupPreset.CleanupStep.class);
+
+        if (cleanUpSuperscripts.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CLEAN_UP_SUPERSCRIPTS);
+        }
+        if (cleanUpDOI.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CLEAN_UP_DOI);
+        }
+        if (cleanUpMonth.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CLEAN_UP_MONTH);
+        }
+        if (cleanUpPageNumbers.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CLEAN_UP_PAGE_NUMBERS);
+        }
+        if (cleanUpDate.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CLEAN_UP_DATE);
+        }
+        if (cleanUpMakePathsRelative.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.MAKE_PATHS_RELATIVE);
+        }
+        if (cleanUpRenamePDF.isSelected()) {
+            if (cleanUpRenamePDFonlyRelativePaths.isSelected()) {
+                activeJobs.add(CleanupPreset.CleanupStep.RENAME_PDF_ONLY_RELATIVE_PATHS);
+            } else {
+                activeJobs.add(CleanupPreset.CleanupStep.RENAME_PDF);
+            }
+        }
+
+        if (cleanUpUpgradeExternalLinks.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CLEAN_UP_UPGRADE_EXTERNAL_LINKS);
+        }
+        if (cleanUpHTML.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CONVERT_HTML_TO_LATEX);
+        }
+        if (cleanUpCase.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CONVERT_CASE);
+        }
+        if (cleanUpLaTeX.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CONVERT_LATEX);
+        }
+        if (cleanUpUnits.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CONVERT_UNITS);
+        }
+        if (cleanUpUnicode.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CONVERT_UNICODE_TO_LATEX);
+        }
+        if (cleanUpBibLatex.isSelected()) {
+            activeJobs.add(CleanupPreset.CleanupStep.CONVERT_TO_BIBLATEX);
+        }
+
+        activeJobs.add(CleanupPreset.CleanupStep.FIX_FILE_LINKS);
+
+        cleanupPreset = new CleanupPreset(activeJobs);
+        return cleanupPreset;
+    }
+}

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

@@ -50,8 +50,4 @@ private String getTypeName() {
     public String toString() {
         return description + " : " + link + " : " + type;
     }
-
-    public FileListEntry switchLinkAndDescription() {
-        return new FileListEntry(link, description, type);
-    }
 }