@Override
public String format(String field) {
FileListTableModel tableModel = new FileListTableModel();
if (field == null) {
return "";
}
tableModel.setContent(field);
String link = null;
if (fileType == null) {
// No file type specified. Simply take the first link.
if (tableModel.getRowCount() > 0) {
link = tableModel.getEntry(0).getLink();
}
} else {
// A file type is specified:
for (int i = 0; i < tableModel.getRowCount(); i++) {
FileListEntry flEntry = tableModel.getEntry(i);
if (flEntry.getType().getName().toLowerCase().equals(fileType)) {
link = flEntry.getLink();
break;
}
}
}
if (link == null) {
return "";
}
String[] dirs;
// We need to resolve the file directory from the database's metadata,
// but that is not available from a formatter. Therefore, as an
// ugly hack, the export routine has set a global variable before
// starting the export, which contains the database's file directory:
if (Globals.prefs.fileDirForDatabase != null) {
dirs = Globals.prefs.fileDirForDatabase;
} else {
dirs = new String[] {Globals.prefs.get(Globals.FILE_FIELD + "Directory")};
}
File f = FileUtil.expandFilename(link, dirs);
/*
* Stumbled over this while investigating
*
* https://sourceforge.net/tracker/index.php?func=detail&aid=1469903&group_id=92314&atid=600306
*/
if (f != null) {
try {
return f.getCanonicalPath(); // f.toURI().toString();
} catch (IOException e) {
e.printStackTrace();
return f.getPath();
}
} else {
return link;
}
}
private void doMakePathsRelative(BibtexEntry entry, NamedCompound ce) {
String oldValue = entry.getField(Globals.FILE_FIELD);
if (oldValue == null) {
return;
}
FileListTableModel flModel = new FileListTableModel();
flModel.setContent(oldValue);
if (flModel.getRowCount() == 0) {
return;
}
boolean changed = false;
for (int i = 0; i < flModel.getRowCount(); i++) {
FileListEntry flEntry = flModel.getEntry(i);
String oldFileName = flEntry.getLink();
String newFileName =
FileUtil.shortenFileName(
new File(oldFileName), panel.metaData().getFileDirectory(Globals.FILE_FIELD))
.toString();
if (!oldFileName.equals(newFileName)) {
flEntry.setLink(newFileName);
changed = true;
}
}
if (changed) {
String newValue = flModel.getStringRepresentation();
assert (!oldValue.equals(newValue));
entry.setField(Globals.FILE_FIELD, newValue);
ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
}
}
private static void fixWrongFileEntries(BibtexEntry entry, NamedCompound ce) {
String oldValue = entry.getField(Globals.FILE_FIELD);
if (oldValue == null) {
return;
}
FileListTableModel flModel = new FileListTableModel();
flModel.setContent(oldValue);
if (flModel.getRowCount() == 0) {
return;
}
boolean changed = false;
for (int i = 0; i < flModel.getRowCount(); i++) {
FileListEntry flEntry = flModel.getEntry(i);
String link = flEntry.getLink();
String description = flEntry.getDescription();
if ("".equals(link) && (!"".equals(description))) {
// link and description seem to be switched, quickly fix that
flEntry.setLink(flEntry.getDescription());
flEntry.setDescription("");
changed = true;
}
}
if (changed) {
String newValue = flModel.getStringRepresentation();
assert (!oldValue.equals(newValue));
entry.setField(Globals.FILE_FIELD, newValue);
ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
}
}
public Object getColumnValue(BibtexEntry entry, int column) {
if (column < PAD) {
Object o;
switch (column) {
case FILE_COL:
o = entry.getField(GUIGlobals.FILE_FIELD);
if (o != null) {
FileListTableModel model = new FileListTableModel();
model.setContent((String) o);
fileLabel.setToolTipText(model.getToolTipHTMLRepresentation());
if (model.getRowCount() > 0) fileLabel.setIcon(model.getEntry(0).getType().getIcon());
return fileLabel;
} else return null;
case URL_COL:
o = entry.getField("url");
if (o != null) {
urlLabel.setToolTipText((String) o);
return urlLabel;
} else return null;
default:
return null;
}
} else {
String field = fields[column - PAD];
if (field.equals("author") || field.equals("editor")) {
// For name fields, tap into a MainTableFormat instance and use
// the same name formatting as is used in the entry table:
if (frame.basePanel() != null)
return frame.basePanel().tableFormat.formatName(entry.getField(field));
}
return entry.getField(field);
}
}
/**
* If the user has signalled the opening of a context menu, the event gets redirected to this
* method. Here we open a file link menu if the user is pointing at a file link icon. Otherwise
* a general context menu should be shown.
*
* @param e The triggering mouse event.
*/
public void processPopupTrigger(MouseEvent e) {
BibtexEntry entry = sortedEntries.get(entryTable.rowAtPoint(e.getPoint()));
BasePanel p = entryHome.get(entry);
int col = entryTable.columnAtPoint(e.getPoint());
JPopupMenu menu = new JPopupMenu();
int count = 0;
if (col == FILE_COL) {
// We use a FileListTableModel to parse the field content:
Object o = entry.getField(GUIGlobals.FILE_FIELD);
FileListTableModel fileList = new FileListTableModel();
fileList.setContent((String) o);
// If there are one or more links, open the first one:
for (int i = 0; i < fileList.getRowCount(); i++) {
FileListEntry flEntry = fileList.getEntry(i);
String description = flEntry.getDescription();
if ((description == null) || (description.trim().length() == 0))
description = flEntry.getLink();
menu.add(
new ExternalFileMenuItem(
p.frame(),
entry,
description,
flEntry.getLink(),
flEntry.getType().getIcon(),
p.metaData(),
flEntry.getType()));
count++;
}
}
if (count > 0) menu.show(entryTable, e.getX(), e.getY());
}
public void mouseClicked(MouseEvent e) {
if (e.isPopupTrigger()) {
processPopupTrigger(e);
return;
}
// if (e.)
final int col = entryTable.columnAtPoint(e.getPoint()),
row = entryTable.rowAtPoint(e.getPoint());
if (col < PAD) {
BibtexEntry entry = sortedEntries.get(row);
BasePanel p = entryHome.get(entry);
switch (col) {
case FILE_COL:
Object o = entry.getField(GUIGlobals.FILE_FIELD);
if (o != null) {
FileListTableModel tableModel = new FileListTableModel();
tableModel.setContent((String) o);
if (tableModel.getRowCount() == 0) return;
FileListEntry fl = tableModel.getEntry(0);
(new ExternalFileMenuItem(
frame, entry, "", fl.getLink(), null, p.metaData(), fl.getType()))
.actionPerformed(null);
}
break;
case URL_COL:
Object link = entry.getField("url");
try {
if (link != null) Util.openExternalViewer(p.metaData(), (String) link, "url");
} catch (IOException ex) {
ex.printStackTrace();
}
break;
}
}
}
@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 String format(String field) {
StringBuilder sb = new StringBuilder();
// Build the table model containing the links:
FileListTableModel tableModel = new FileListTableModel();
if (field == null) return "";
tableModel.setContent(field);
int piv = 1; // counter for relevant iterations
for (int i = 0; i < tableModel.getRowCount(); i++) {
FileListEntry flEntry = tableModel.getEntry(i);
// Use this entry if we don't discriminate on types, or if the type fits:
if ((fileType == null) || flEntry.getType().getName().toLowerCase().equals(fileType)) {
for (FormatEntry entry : format) {
switch (entry.getType()) {
case STRING:
sb.append(entry.getString());
break;
case ITERATION_COUNT:
sb.append(String.valueOf(piv));
break;
case FILE_PATH:
if (flEntry.getLink() == null) break;
String dir;
// We need to resolve the file directory from the database's metadata,
// but that is not available from a formatter. Therefore, as an
// ugly hack, the export routine has set a global variable before
// starting the export, which contains the database's file directory:
if (Globals.prefs.fileDirForDatabase != null) dir = Globals.prefs.fileDirForDatabase;
else dir = Globals.prefs.get(GUIGlobals.FILE_FIELD + "Directory");
File f = Util.expandFilename(flEntry.getLink(), new String[] {dir});
/*
* Stumbled over this while investigating
*
* https://sourceforge.net/tracker/index.php?func=detail&aid=1469903&group_id=92314&atid=600306
*/
if (f != null) {
try {
sb.append(replaceStrings(f.getCanonicalPath())); // f.toURI().toString();
} catch (IOException ex) {
ex.printStackTrace();
sb.append(replaceStrings(f.getPath()));
}
} else {
sb.append(replaceStrings(flEntry.getLink()));
}
break;
case RELATIVE_FILE_PATH:
if (flEntry.getLink() == null) break;
/*
* Stumbled over this while investigating
*
* https://sourceforge.net/tracker/index.php?func=detail&aid=1469903&group_id=92314&atid=600306
*/
sb.append(replaceStrings(flEntry.getLink())); // f.toURI().toString();
break;
case FILE_EXTENSION:
if (flEntry.getLink() == null) break;
int index = flEntry.getLink().lastIndexOf('.');
if ((index >= 0) && (index < flEntry.getLink().length() - 1))
sb.append(replaceStrings(flEntry.getLink().substring(index + 1)));
break;
case FILE_TYPE:
sb.append(replaceStrings(flEntry.getType().getName()));
break;
case FILE_DESCRIPTION:
sb.append(replaceStrings(flEntry.getDescription()));
break;
}
}
piv++; // update counter
}
}
return sb.toString();
}
private void doRenamePDFs(BibtexEntry entry, NamedCompound ce) {
// Extract the path
String oldValue = entry.getField(Globals.FILE_FIELD);
if (oldValue == null) {
return;
}
FileListTableModel flModel = new FileListTableModel();
flModel.setContent(oldValue);
if (flModel.getRowCount() == 0) {
return;
}
boolean changed = false;
for (int i = 0; i < flModel.getRowCount(); i++) {
String realOldFilename = flModel.getEntry(i).getLink();
if (cleanUpRenamePDFonlyRelativePaths.isSelected()
&& (new File(realOldFilename).isAbsolute())) {
continue;
}
String newFilename = Util.getLinkedFileName(panel.database(), entry);
// String oldFilename = bes.getField(GUIGlobals.FILE_FIELD); // would have to be stored for
// undoing purposes
// Add extension to newFilename
newFilename = newFilename + "." + flModel.getEntry(i).getType().getExtension();
// get new Filename with path
// Create new Path based on old Path and new filename
File expandedOldFile =
FileUtil.expandFilename(
realOldFilename, panel.metaData().getFileDirectory(Globals.FILE_FIELD));
if (expandedOldFile.getParent() == null) {
// something went wrong. Just skip this entry
continue;
}
String newPath =
expandedOldFile
.getParent()
.concat(System.getProperty("file.separator"))
.concat(newFilename);
if (new File(newPath).exists()) {
// we do not overwrite files
// TODO: we could check here if the newPath file is linked with the current entry. And if
// not, we could add a link
continue;
}
// do rename
boolean renameSuccessful = FileUtil.renameFile(expandedOldFile.toString(), newPath);
if (renameSuccessful) {
changed = true;
// Change the path for this entry
String description = flModel.getEntry(i).getDescription();
ExternalFileType type = flModel.getEntry(i).getType();
flModel.removeEntry(i);
// we cannot use "newPath" to generate a FileListEntry as newPath is absolute, but we want
// to keep relative paths whenever possible
File parent = (new File(realOldFilename)).getParentFile();
String newFileEntryFileName;
if (parent == null) {
newFileEntryFileName = newFilename;
} else {
newFileEntryFileName =
parent.toString().concat(System.getProperty("file.separator")).concat(newFilename);
}
flModel.addEntry(i, new FileListEntry(description, newFileEntryFileName, type));
} else {
unsuccessfulRenames++;
}
}
if (changed) {
String newValue = flModel.getStringRepresentation();
assert (!oldValue.equals(newValue));
entry.setField(Globals.FILE_FIELD, newValue);
// we put an undo of the field content here
// the file is not being renamed back, which leads to inconsistencies
// if we put a null undo object here, the change by "doMakePathsRelative" would overwrite the
// field value nevertheless.
ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
}
}
public void run() {
if (!goOn) return;
for (int i = 0; i < entries.length; i++) {
BibtexEntry entry = entries[i];
// Make a list of all PDFs linked from this entry:
List<File> files = new ArrayList<File>();
// First check the (legacy) "pdf" field:
String pdf = entry.getField("pdf");
String dir = panel.metaData().getFileDirectory("pdf");
File f = Util.expandFilename(pdf, new String[] {dir, "."});
if (f != null) files.add(f);
// Then check the "file" field:
dir = panel.metaData().getFileDirectory(GUIGlobals.FILE_FIELD);
String field = entry.getField(GUIGlobals.FILE_FIELD);
if (field != null) {
FileListTableModel tm = new FileListTableModel();
tm.setContent(field);
for (int j = 0; j < tm.getRowCount(); j++) {
FileListEntry flEntry = tm.getEntry(j);
if ((flEntry.getType() != null)
&& (flEntry.getType().getName().toLowerCase().equals("pdf"))) {
f = Util.expandFilename(flEntry.getLink(), new String[] {dir, "."});
if (f != null) files.add(f);
}
}
}
optDiag.progressArea.append(entry.getCiteKey() + "\n");
if (files.size() == 0) {
skipped++;
optDiag.progressArea.append(" " + Globals.lang("Skipped - No PDF linked") + ".\n");
} else
for (File file : files) {
if (!file.exists()) {
skipped++;
optDiag.progressArea.append(
" " + Globals.lang("Skipped - PDF does not exist") + ":\n");
optDiag.progressArea.append(" " + file.getPath() + "\n");
} else {
try {
XMPUtil.writeXMP(file, entry, database);
optDiag.progressArea.append(" " + Globals.lang("Ok") + ".\n");
entriesChanged++;
} catch (Exception e) {
optDiag.progressArea.append(
" " + Globals.lang("Error while writing") + " '" + file.getPath() + "':\n");
optDiag.progressArea.append(" " + e.getLocalizedMessage() + "\n");
errors++;
}
}
}
if (optDiag.canceled) {
optDiag.progressArea.append("\n" + Globals.lang("Operation canceled.\n"));
break;
}
}
optDiag.progressArea.append(
"\n"
+ Globals.lang(
"Finished writing XMP for %0 file (%1 skipped, %2 errors).",
String.valueOf(entriesChanged), String.valueOf(skipped), String.valueOf(errors)));
optDiag.done();
}
@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();
}
}