@Override
public void operationCompleted(BasePanel panel) {
if (couldNotConnect) {
JOptionPane.showMessageDialog(
panel.frame(),
"<HTML>"
+ Localization.lang(
"Could not connect to a running gnuserv process. Make sure that "
+ "Emacs or XEmacs is running,<BR>and that the server has been started "
+ "(by running the command 'server-start'/'gnuserv-start').")
+ "</HTML>",
Localization.lang("Error"),
JOptionPane.ERROR_MESSAGE);
} else if (couldNotCall) {
JOptionPane.showMessageDialog(
panel.frame(),
Localization.lang(
"Could not run the gnuclient/emacsclient program. Make sure you have "
+ "the emacsclient/gnuclient program installed and available in the PATH."),
Localization.lang("Error"),
JOptionPane.ERROR_MESSAGE);
} else {
super.operationCompleted(panel);
}
}
@Override
public void actionPerformed(ActionEvent actionEvent) {
setEnabled(false);
panel.output(Localization.lang("Writing XMP-metadata..."));
panel.frame().setProgressBarIndeterminate(true);
panel.frame().setProgressBarVisible(true);
BibEntry entry = editor.getEntry();
// Make a list of all PDFs linked from this entry:
List<File> files = new ArrayList<>();
// First check the (legacy) "pdf" field:
entry
.getField(FieldName.PDF)
.ifPresent(
pdf ->
FileUtil.expandFilename(
pdf,
panel
.getBibDatabaseContext()
.getFileDirectory(
FieldName.PDF, Globals.prefs.getFileDirectoryPreferences()))
.ifPresent(files::add));
// Then check the "file" field:
List<String> dirs =
panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
if (entry.hasField(FieldName.FILE)) {
FileListTableModel tm = new FileListTableModel();
entry.getField(FieldName.FILE).ifPresent(tm::setContent);
for (int j = 0; j < tm.getRowCount(); j++) {
FileListEntry flEntry = tm.getEntry(j);
if ((flEntry.type.isPresent()) && "pdf".equalsIgnoreCase(flEntry.type.get().getName())) {
FileUtil.expandFilename(flEntry.link, dirs).ifPresent(files::add);
}
}
}
// We want to offload the actual work to a background thread, so we have a worker
// thread:
AbstractWorker worker = new WriteXMPWorker(files, entry);
// Using Spin, we get a thread that gets synchronously offloaded to a new thread,
// blocking the execution of this method:
worker.getWorker().run();
// After the worker thread finishes, we are unblocked and ready to print the
// status message:
panel.output(message);
panel.frame().setProgressBarVisible(false);
setEnabled(true);
}
public void moveToGroup(List<BibEntry> entries, NamedCompound undoAll) {
List<GroupTreeNode> groupsContainingEntries =
node.getNode()
.getRoot()
.getContainingGroups(entries, false)
.stream()
.filter(node -> node.getGroup().supportsRemove())
.collect(Collectors.toList());
List<AbstractGroup> affectedGroups =
groupsContainingEntries.stream().map(GroupTreeNode::getGroup).collect(Collectors.toList());
affectedGroups.add(node.getNode().getGroup());
if (!WarnAssignmentSideEffects.warnAssignmentSideEffects(affectedGroups, panel.frame())) {
return; // user aborted operation
}
// first remove
for (GroupTreeNode group : groupsContainingEntries) {
Optional<EntriesGroupChange> undoRemove = group.getGroup().remove(entries);
if (undoRemove.isPresent()) {
undoAll.addEdit(UndoableChangeEntriesOfGroup.getUndoableEdit(node, undoRemove.get()));
}
}
// then add
Optional<EntriesGroupChange> undoAdd = node.addEntriesToGroup(entries);
if (undoAdd.isPresent()) {
undoAll.addEdit(UndoableChangeEntriesOfGroup.getUndoableEdit(node, undoAdd.get()));
}
}
public void addToGroup(List<BibEntry> entries, NamedCompound undo) {
if (!WarnAssignmentSideEffects.warnAssignmentSideEffects(
node.getNode().getGroup(), panel.frame())) {
return; // user aborted operation
}
Optional<EntriesGroupChange> undoAdd = node.addEntriesToGroup(entries);
if (undoAdd.isPresent()) {
undo.addEdit(UndoableChangeEntriesOfGroup.getUndoableEdit(node, undoAdd.get()));
}
}
/**
* 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();
}
}
@Override
public void init() {
Collection<BibEntry> col = panel.getDatabase().getEntries();
goOn = true;
sel = new ArrayList<>(col);
// Ask about rules for the operation:
if (optDiag == null) {
optDiag =
new SynchronizeFileField.OptionsDialog(panel.frame(), panel.getBibDatabaseContext());
}
optDiag.setLocationRelativeTo(panel.frame());
optDiag.setVisible(true);
if (optDiag.canceled()) {
goOn = false;
return;
}
autoSet = !optDiag.isAutoSetNone();
checkExisting = optDiag.isCheckLinks();
panel.output(Localization.lang("Synchronizing file links..."));
}
@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();
}
}
/**
* Set up a mouse listener for opening an external viewer and fetching by DOI
*
* @param fieldEditor
* @param panel
* @return
*/
public static Optional<JComponent> getDoiExtraComponent(
BasePanel panel, EntryEditor entryEditor, FieldEditor fieldEditor) {
JPanel controls = new JPanel();
controls.setLayout(new BorderLayout());
// open doi link
JButton button = new JButton(Localization.lang("Open"));
button.setEnabled(false);
button.addActionListener(
actionEvent -> {
try {
JabRefDesktop.openExternalViewer(
panel.getBibDatabaseContext(), fieldEditor.getText(), fieldEditor.getFieldName());
} catch (IOException ex) {
panel.output(Localization.lang("Unable to open link."));
}
});
// lookup doi
JButton doiButton = new JButton(Localization.lang("Lookup DOI"));
doiButton.addActionListener(
actionEvent -> {
Optional<DOI> doi = DOI.fromBibEntry(entryEditor.getEntry());
if (doi.isPresent()) {
entryEditor.getEntry().setField(FieldName.DOI, doi.get().getDOI());
} else {
panel
.frame()
.setStatus(
Localization.lang("No %0 found", FieldName.getDisplayName(FieldName.DOI)));
}
});
// fetch bibtex data
JButton fetchButton =
new JButton(
Localization.lang("Get BibTeX data from %0", FieldName.getDisplayName(FieldName.DOI)));
fetchButton.setEnabled(false);
fetchButton.addActionListener(
actionEvent -> {
BibEntry entry = entryEditor.getEntry();
new FetchAndMergeEntry(entry, panel, FieldName.DOI);
});
controls.add(button, BorderLayout.NORTH);
controls.add(doiButton, BorderLayout.CENTER);
controls.add(fetchButton, BorderLayout.SOUTH);
// enable/disable button
JTextComponent doi = (JTextComponent) fieldEditor;
doi.getDocument()
.addDocumentListener(
new DocumentListener() {
@Override
public void changedUpdate(DocumentEvent documentEvent) {
checkDoi();
}
@Override
public void insertUpdate(DocumentEvent documentEvent) {
checkDoi();
}
@Override
public void removeUpdate(DocumentEvent documentEvent) {
checkDoi();
}
private void checkDoi() {
Optional<DOI> doiUrl = DOI.build(doi.getText());
if (doiUrl.isPresent()) {
button.setEnabled(true);
fetchButton.setEnabled(true);
} else {
button.setEnabled(false);
fetchButton.setEnabled(false);
}
}
});
return Optional.of(controls);
}
/**
* This method presents a dialog box explaining and offering to make the changes. If the user
* confirms, the changes are performed.
*
* @param panel
* @param parserResult
*/
@Override
public void performAction(BasePanel panel, ParserResult parserResult) {
if (!isThereSomethingToBeDone()) {
return; // Nothing to do, just return.
}
JCheckBox changeSettings =
new JCheckBox(
Localization.lang(
"Change table column and General fields settings to use the new feature"),
offerChangeSettings);
JCheckBox changeDatabase =
new JCheckBox(
Localization.lang("Upgrade old external file links to use the new feature"),
offerChangeDatabase);
JCheckBox setFileDir =
new JCheckBox(Localization.lang("Set main external file directory") + ":", offerSetFileDir);
JTextField fileDir = new JTextField(30);
JCheckBox doNotShowDialog =
new JCheckBox(Localization.lang("Do not show these options in the future"), false);
JPanel message = new JPanel();
FormBuilder formBuilder = FormBuilder.create().layout(new FormLayout("left:pref", "p"));
// Keep the formatting of these lines. Otherwise, strings have to be translated again.
// See updated JabRef_en.properties modifications by python syncLang.py -s -u
int row = 1;
formBuilder
.add(
new JLabel(
"<html>"
+ Localization.lang("This database uses outdated file links.")
+ "<br><br>"
+ Localization.lang(
"JabRef no longer supports 'ps' or 'pdf' fields.<br>File links are now stored in the 'file' field and files are stored in an external file directory.<br>To make use of this feature, JabRef needs to upgrade file links.<br><br>")
+ "<p>"
+ Localization.lang("Do you want JabRef to do the following operations?")
+ "</html>"))
.xy(1, row);
if (offerChangeSettings) {
formBuilder.appendRows("2dlu, p");
row += 2;
formBuilder.add(changeSettings).xy(1, row);
}
if (offerChangeDatabase) {
formBuilder.appendRows("2dlu, p");
row += 2;
formBuilder.add(changeDatabase).xy(1, row);
}
if (offerSetFileDir) {
if (Globals.prefs.hasKey("pdfDirectory")) {
fileDir.setText(Globals.prefs.get("pdfDirectory"));
} else {
fileDir.setText(Globals.prefs.get("psDirectory"));
}
JPanel builderPanel = new JPanel();
builderPanel.add(setFileDir);
builderPanel.add(fileDir);
JButton browse = new JButton(Localization.lang("Browse"));
browse.addActionListener(BrowseAction.buildForDir(fileDir));
builderPanel.add(browse);
formBuilder.appendRows("2dlu, p");
row += 2;
formBuilder.add(builderPanel).xy(1, row);
}
formBuilder.appendRows("6dlu, p");
formBuilder.add(doNotShowDialog).xy(1, row + 2);
message.add(formBuilder.build());
int answer =
JOptionPane.showConfirmDialog(
panel.frame(), message, Localization.lang("Upgrade file"), JOptionPane.YES_NO_OPTION);
if (doNotShowDialog.isSelected()) {
Globals.prefs.putBoolean(JabRefPreferences.SHOW_FILE_LINKS_UPGRADE_WARNING, false);
}
if (answer == JOptionPane.YES_OPTION) {
makeChanges(
panel,
parserResult,
changeSettings.isSelected(),
changeDatabase.isSelected(),
setFileDir.isSelected() ? fileDir.getText() : null);
}
}
public CleanupAction(BasePanel panel, JabRefPreferences preferences) {
this.panel = panel;
this.frame = panel.frame();
this.preferences = Objects.requireNonNull(preferences);
this.presetPanel = new CleanupPresetPanel(CleanupPreset.loadFromPreferences(preferences));
}
public CleanUpAction(BasePanel panel) {
this.panel = panel;
this.frame = panel.frame();
initOptionsPanel();
}
@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();
}
}