@Override
public void update() {
if (cancelled) {
frame.unblock();
return;
}
if (unsuccessfulRenames > 0) { // Rename failed for at least one entry
JOptionPane.showMessageDialog(
frame,
Localization.lang(
"File rename failed for %0 entries.", Integer.toString(unsuccessfulRenames)),
Localization.lang("Autogenerate PDF Names"),
JOptionPane.INFORMATION_MESSAGE);
}
if (modifiedEntriesCount > 0) {
panel.updateEntryEditorIfShowing();
panel.markBaseChanged();
}
String message;
switch (modifiedEntriesCount) {
case 0:
message = Localization.lang("No entry needed a clean up");
break;
case 1:
message = Localization.lang("One entry needed a clean up");
break;
default:
message =
Localization.lang(
"%0 entries needed a clean up", Integer.toString(modifiedEntriesCount));
break;
}
panel.output(message);
frame.unblock();
}
private Optional<BibEntry> createNewEntry() {
// Find out what type is desired
EntryTypeDialog etd = new EntryTypeDialog(frame);
// We want to center the dialog, to make it look nicer.
etd.setLocationRelativeTo(frame);
etd.setVisible(true);
EntryType type = etd.getChoice();
if (type != null) { // Only if the dialog was not canceled.
String id = IdGenerator.next();
final BibEntry bibEntry = new BibEntry(id, type.getName());
try {
panel.getDatabase().insertEntry(bibEntry);
// Set owner/timestamp if options are enabled:
List<BibEntry> list = new ArrayList<>();
list.add(bibEntry);
UpdateField.setAutomaticFields(list, true, true, Globals.prefs.getUpdateFieldPreferences());
// Create an UndoableInsertEntry object.
panel
.getUndoManager()
.addEdit(new UndoableInsertEntry(panel.getDatabase(), bibEntry, panel));
panel.output(
Localization.lang("Added new")
+ " '"
+ type.getName().toLowerCase()
+ "' "
+ Localization.lang("entry")
+ ".");
// We are going to select the new entry. Before that, make sure that we are in
// show-entry mode. If we aren't already in that mode, enter the WILL_SHOW_EDITOR
// mode which makes sure the selection will trigger display of the entry editor
// and adjustment of the splitter.
if (panel.getMode() != BasePanelMode.SHOWING_EDITOR) {
panel.setMode(BasePanelMode.WILL_SHOW_EDITOR);
}
SwingUtilities.invokeLater(() -> panel.showEntry(bibEntry));
// The database just changed.
panel.markBaseChanged();
return Optional.of(bibEntry);
} catch (KeyCollisionException ex) {
LOGGER.info("Key collision occurred", ex);
}
}
return Optional.empty();
}
@Override
public void update() {
if (!goOn) {
return;
}
panel.output(
Localization.lang(
"Finished synchronizing file links. Entries changed: %0.",
String.valueOf(entriesChangedCount)));
panel.frame().setProgressBarVisible(false);
if (entriesChangedCount > 0) {
panel.markBaseChanged();
}
}
@Override
public void update() {
if (databases == null) {
return;
}
for (DBImporterResult res : databases) {
databaseContext = res.getDatabaseContext();
if (databaseContext != null) {
BasePanel pan = frame.addTab(databaseContext, true);
pan.getBibDatabaseContext().getMetaData().setDBStrings(dbs);
frame.setTabTitle(pan, res.getName() + "(Imported)", "Imported DB");
pan.markBaseChanged();
}
}
frame.output(
Localization.lang(
"Imported %0 databases successfully", Integer.toString(databases.size())));
}
private void doContentImport(String fileName, List<BibEntry> res) {
PdfContentImporter contentImporter =
new PdfContentImporter(Globals.prefs.getImportFormatPreferences());
Path filePath = Paths.get(fileName);
ParserResult result =
contentImporter.importDatabase(filePath, Globals.prefs.getDefaultEncoding());
if (result.hasWarnings()) {
frame.showMessage(result.getErrorMessage());
}
if (!result.getDatabase().hasEntries()) {
// import failed -> generate default entry
createNewBlankEntry(fileName).ifPresent(res::add);
return;
}
// only one entry is imported
BibEntry entry = result.getDatabase().getEntries().get(0);
// insert entry to database and link file
panel.getDatabase().insertEntry(entry);
panel.markBaseChanged();
BibtexKeyPatternUtil.makeLabel(
panel
.getBibDatabaseContext()
.getMetaData()
.getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
panel.getDatabase(),
entry,
Globals.prefs.getBibtexKeyPatternPreferences());
DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
dfh.linkPdfToEntry(fileName, entry);
panel.highlightEntry(entry);
if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_OPEN_FORM)) {
EntryEditor editor = panel.getEntryEditor(entry);
panel.showEntryEditor(editor);
}
res.add(entry);
}
/**
* 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(Globals.FILE_FIELD + Globals.DIR_SUFFIX, fileDir);
}
if (upgradePrefs) {
// Exchange table columns:
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");
StringBuilder sb = new StringBuilder(gfs);
if (!gfs.isEmpty()) {
sb.append(";");
}
sb.append(Globals.FILE_FIELD);
Globals.prefs.put(JabRefPreferences.CUSTOM_TAB_FIELDS + "0", sb.toString());
Globals.prefs.updateEntryEditorTabList();
panel.frame().removeCachedEntryEditors();
}
panel.frame().setupAllTables();
}
}
private void doXMPImport(String fileName, List<BibEntry> res) {
List<BibEntry> localRes = new ArrayList<>();
PdfXmpImporter importer = new PdfXmpImporter(Globals.prefs.getXMPPreferences());
Path filePath = Paths.get(fileName);
ParserResult result = importer.importDatabase(filePath, Globals.prefs.getDefaultEncoding());
if (result.hasWarnings()) {
frame.showMessage(result.getErrorMessage());
}
localRes.addAll(result.getDatabase().getEntries());
BibEntry entry;
if (localRes.isEmpty()) {
// import failed -> generate default entry
LOGGER.info("Import failed");
createNewBlankEntry(fileName).ifPresent(res::add);
return;
}
// only one entry is imported
entry = localRes.get(0);
// insert entry to database and link file
panel.getDatabase().insertEntry(entry);
panel.markBaseChanged();
FileListTableModel tm = new FileListTableModel();
File toLink = new File(fileName);
// Get a list of file directories:
List<String> dirsS =
panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
tm.addEntry(
0,
new FileListEntry(
toLink.getName(),
FileUtil.shortenFileName(toLink, dirsS).getPath(),
ExternalFileTypes.getInstance().getExternalFileTypeByName("PDF")));
entry.setField(FieldName.FILE, tm.getStringRepresentation());
res.add(entry);
}
@Override
public void actionPerformed(ActionEvent evt) {
final List<BibEntry> entries = panel.getSelectedEntries();
// if an editor is showing, its fields must be updated after the assignment,
// and before that, the current edit has to be stored:
panel.storeCurrentEdit();
NamedCompound undoAll = new NamedCompound(Localization.lang("change assignment of entries"));
if (move) {
moveToGroup(entries, undoAll);
} else {
addToGroup(entries, undoAll);
}
undoAll.end();
panel.getUndoManager().addEdit(undoAll);
panel.markBaseChanged();
panel.updateEntryEditorIfShowing();
panel.getGroupSelector().valueChanged(null);
}
@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);
}
}
}
@Override
public void run() {
if (!goOn) {
panel.output(
Localization.lang("This operation requires one or more entries to be selected."));
return;
}
entriesChangedCount = 0;
panel.frame().setProgressBarValue(0);
panel.frame().setProgressBarVisible(true);
int weightAutoSet = 10; // autoSet takes 10 (?) times longer than checkExisting
int progressBarMax =
(autoSet ? weightAutoSet * sel.size() : 0) + (checkExisting ? sel.size() : 0);
panel.frame().setProgressBarMaximum(progressBarMax);
int progress = 0;
final NamedCompound ce = new NamedCompound(Localization.lang("Automatically set file links"));
Set<BibEntry> changedEntries = new HashSet<>();
// First we try to autoset fields
if (autoSet) {
Collection<BibEntry> entries = new ArrayList<>(sel);
// Start the automatically setting process:
Runnable r =
AutoSetLinks.autoSetLinks(
entries, ce, changedEntries, null, panel.getBibDatabaseContext(), null, null);
JabRefExecutorService.INSTANCE.executeAndWait(r);
}
progress += sel.size() * weightAutoSet;
panel.frame().setProgressBarValue(progress);
// The following loop checks all external links that are already set.
if (checkExisting) {
boolean removeAllBroken = false;
mainLoop:
for (BibEntry aSel : sel) {
panel.frame().setProgressBarValue(progress++);
final String old = aSel.getField(Globals.FILE_FIELD);
// Check if a extension is set:
if ((old != null) && !(old.isEmpty())) {
FileListTableModel tableModel = new FileListTableModel();
tableModel.setContentDontGuessTypes(old);
// We need to specify which directories to search in for Util.expandFilename:
List<String> dirsS = panel.getBibDatabaseContext().getFileDirectory();
List<File> dirs = new ArrayList<>();
for (String dirs1 : dirsS) {
dirs.add(new File(dirs1));
}
for (int j = 0; j < tableModel.getRowCount(); j++) {
FileListEntry flEntry = tableModel.getEntry(j);
// See if the link looks like an URL:
boolean httpLink = flEntry.link.toLowerCase(Locale.ENGLISH).startsWith("http");
if (httpLink) {
continue; // Don't check the remote file.
// TODO: should there be an option to check remote links?
}
// A variable to keep track of whether this link gets deleted:
boolean deleted = false;
// Get an absolute path representation:
Optional<File> file = FileUtil.expandFilename(flEntry.link, dirsS);
if ((!file.isPresent()) || !file.get().exists()) {
int answer;
if (removeAllBroken) {
answer = 2; // We should delete this link.
} else {
answer =
JOptionPane.showOptionDialog(
panel.frame(),
Localization.lang(
"<HTML>Could not find file '%0'<BR>linked from entry '%1'</HTML>",
flEntry.link, aSel.getCiteKey()),
Localization.lang("Broken link"),
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE,
null,
brokenLinkOptions,
brokenLinkOptions[0]);
}
switch (answer) {
case 1:
// Assign new file.
FileListEntryEditor flEditor =
new FileListEntryEditor(
panel.frame(), flEntry, false, true, panel.getBibDatabaseContext());
flEditor.setVisible(true, true);
break;
case 2:
// Clear field:
tableModel.removeEntry(j);
deleted = true; // Make sure we don't investigate this link further.
j--; // Step back in the iteration, because we removed an entry.
break;
case 3:
// Clear field:
tableModel.removeEntry(j);
deleted = true; // Make sure we don't investigate this link further.
j--; // Step back in the iteration, because we removed an entry.
removeAllBroken = true; // Notify for further cases.
break;
default:
// Cancel
break mainLoop;
}
}
// Unless we deleted this link, see if its file type is recognized:
if (!deleted
&& flEntry.type.isPresent()
&& (flEntry.type.get() instanceof UnknownExternalFileType)) {
String[] options =
new String[] {
Localization.lang("Define '%0'", flEntry.type.get().getName()),
Localization.lang("Change file type"),
Localization.lang("Cancel")
};
String defOption = options[0];
int answer =
JOptionPane.showOptionDialog(
panel.frame(),
Localization.lang(
"One or more file links are of the type '%0', which is undefined. What do you want to do?",
flEntry.type.get().getName()),
Localization.lang("Undefined file type"),
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE,
null,
options,
defOption);
if (answer == JOptionPane.CANCEL_OPTION) {
// User doesn't want to handle this unknown link type.
} else if (answer == JOptionPane.YES_OPTION) {
// User wants to define the new file type. Show the dialog:
ExternalFileType newType =
new ExternalFileType(
flEntry.type.get().getName(),
"",
"",
"",
"new",
IconTheme.JabRefIcon.FILE.getSmallIcon());
ExternalFileTypeEntryEditor editor =
new ExternalFileTypeEntryEditor(panel.frame(), newType);
editor.setVisible(true);
if (editor.okPressed()) {
// Get the old list of types, add this one, and update the list in prefs:
List<ExternalFileType> fileTypes =
new ArrayList<>(
ExternalFileTypes.getInstance().getExternalFileTypeSelection());
fileTypes.add(newType);
Collections.sort(fileTypes);
ExternalFileTypes.getInstance().setExternalFileTypes(fileTypes);
panel.getMainTable().repaint();
}
} else {
// User wants to change the type of this link.
// First get a model of all file links for this entry:
FileListEntryEditor editor =
new FileListEntryEditor(
panel.frame(), flEntry, false, true, panel.getBibDatabaseContext());
editor.setVisible(true, false);
}
}
}
if (!tableModel.getStringRepresentation().equals(old)) {
// The table has been modified. Store the change:
String toSet = tableModel.getStringRepresentation();
if (toSet.isEmpty()) {
ce.addEdit(new UndoableFieldChange(aSel, Globals.FILE_FIELD, old, null));
aSel.clearField(Globals.FILE_FIELD);
} else {
ce.addEdit(new UndoableFieldChange(aSel, Globals.FILE_FIELD, old, toSet));
aSel.setField(Globals.FILE_FIELD, toSet);
}
changedEntries.add(aSel);
}
}
}
}
if (!changedEntries.isEmpty()) {
// Add the undo edit:
ce.end();
panel.getUndoManager().addEdit(ce);
panel.markBaseChanged();
entriesChangedCount = changedEntries.size();
}
}