/**
* This method performs the actual changes.
*
* @param panel
* @param pr
* @param fileDir The path to the file directory to set, or null if it should not be set.
*/
private void makeChanges(
BasePanel panel,
ParserResult pr,
boolean upgradePrefs,
boolean upgradeDatabase,
String fileDir) {
if (upgradeDatabase) {
// Update file links links in the database:
NamedCompound ce =
Util.upgradePdfPsToFile(pr.getDatabase(), FileLinksUpgradeWarning.FIELDS_TO_LOOK_FOR);
panel.undoManager.addEdit(ce);
panel.markBaseChanged();
}
if (fileDir != null) {
Globals.prefs.put(GUIGlobals.FILE_FIELD + "Directory", fileDir);
}
if (upgradePrefs) {
// Exchange table columns:
Globals.prefs.putBoolean(JabRefPreferences.PDF_COLUMN, Boolean.FALSE);
Globals.prefs.putBoolean(JabRefPreferences.FILE_COLUMN, Boolean.TRUE);
// Modify General fields if necessary:
// If we don't find the file field, insert it at the bottom of the first tab:
if (!showsFileInGenFields()) {
String gfs = Globals.prefs.get(JabRefPreferences.CUSTOM_TAB_FIELDS + "0");
// System.out.println(gfs);
StringBuilder sb = new StringBuilder(gfs);
if (gfs.length() > 0) {
sb.append(";");
}
sb.append(GUIGlobals.FILE_FIELD);
Globals.prefs.put(JabRefPreferences.CUSTOM_TAB_FIELDS + "0", sb.toString());
Globals.prefs.updateEntryEditorTabList();
panel.frame().removeCachedEntryEditors();
}
panel.frame().setupAllTables();
}
}
@Override
public void run() {
if (cancelled) {
return;
}
int choice = showCleanUpDialog();
if (choice != JOptionPane.OK_OPTION) {
cancelled = true;
return;
}
storeSettings();
boolean choiceCleanUpSuperscripts = cleanUpSuperscripts.isSelected();
boolean choiceCleanUpDOI = cleanUpDOI.isSelected();
boolean choiceCleanUpMonth = cleanUpMonth.isSelected();
boolean choiceCleanUpPageNumbers = cleanUpPageNumbers.isSelected();
boolean choiceCleanUpDate = cleanUpDate.isSelected();
boolean choiceCleanUpUpgradeExternalLinks = cleanUpUpgradeExternalLinks.isSelected();
boolean choiceMakePathsRelative = cleanUpMakePathsRelative.isSelected();
boolean choiceRenamePDF = cleanUpRenamePDF.isSelected();
boolean choiceConvertHTML = cleanUpHTML.isSelected();
boolean choiceConvertCase = cleanUpCase.isSelected();
boolean choiceConvertLaTeX = cleanUpLaTeX.isSelected();
boolean choiceConvertUnits = cleanUpUnits.isSelected();
boolean choiceConvertUnicode = cleanUpUnicode.isSelected();
boolean choiceConvertToBiblatex = cleanUpBibLatex.isSelected();
if (choiceRenamePDF && Globals.prefs.getBoolean(CleanUpAction.AKS_AUTO_NAMING_PDFS_AGAIN)) {
CheckBoxMessage cbm =
new CheckBoxMessage(
Localization.lang("Auto-generating PDF-Names does not support undo. Continue?"),
Localization.lang("Disable this confirmation dialog"),
false);
int answer =
JOptionPane.showConfirmDialog(
frame, cbm, Localization.lang("Autogenerate PDF Names"), JOptionPane.YES_NO_OPTION);
if (cbm.isSelected()) {
Globals.prefs.putBoolean(CleanUpAction.AKS_AUTO_NAMING_PDFS_AGAIN, false);
}
if (answer == JOptionPane.NO_OPTION) {
cancelled = true;
return;
}
}
// first upgrade the external links
// we have to use it separately as the Utils function generates a separate Named Compound
if (choiceCleanUpUpgradeExternalLinks) {
NamedCompound ce =
Util.upgradePdfPsToFile(
Arrays.asList(panel.getSelectedEntries()), new String[] {"pdf", "ps"});
if (ce.hasEdits()) {
panel.undoManager.addEdit(ce);
panel.markBaseChanged();
panel.updateEntryEditorIfShowing();
panel.output(Localization.lang("Upgraded links."));
}
}
for (BibtexEntry entry : panel.getSelectedEntries()) {
// undo granularity is on entry level
NamedCompound ce = new NamedCompound(Localization.lang("Cleanup entry"));
if (choiceCleanUpSuperscripts) {
doCleanUpSuperscripts(entry, ce);
}
if (choiceCleanUpDOI) {
doCleanUpDOI(entry, ce);
}
if (choiceCleanUpMonth) {
doCleanUpMonth(entry, ce);
}
if (choiceCleanUpPageNumbers) {
doCleanUpPageNumbers(entry, ce);
}
if (choiceCleanUpDate) {
doCleanUpDate(entry, ce);
}
fixWrongFileEntries(entry, ce);
if (choiceMakePathsRelative) {
doMakePathsRelative(entry, ce);
}
if (choiceRenamePDF) {
doRenamePDFs(entry, ce);
}
if (choiceConvertHTML) {
doConvertHTML(entry, ce);
}
if (choiceConvertUnits) {
doConvertUnits(entry, ce);
}
if (choiceConvertCase) {
doConvertCase(entry, ce);
}
if (choiceConvertLaTeX) {
doConvertLaTeX(entry, ce);
}
if (choiceConvertUnicode) {
doConvertUnicode(entry, ce);
}
if (choiceConvertToBiblatex) {
convertToBiblatex(entry, ce);
}
ce.end();
if (ce.hasEdits()) {
modifiedEntriesCount++;
panel.undoManager.addEdit(ce);
}
}
}