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));
}
}
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));
}
}
@Test
@Ignore
public void testInsertTestData() throws Exception {
entry1 = new BibtexEntry();
JabRefPreferences jabRefPreferences = JabRefPreferences.getInstance();
ExternalFileType fileType = jabRefPreferences.getExternalFileTypeByExt("PDF");
FileListEntry fileListEntry =
new FileListEntry("", ImportDataTest.FILE_IN_DATABASE.getAbsolutePath(), fileType);
FileListTableModel model = new FileListTableModel();
model.addEntry(0, fileListEntry);
entry1.setField("file", model.getStringRepresentation());
database.insertEntry(entry1);
// #################### SETUP END ##################### //
UnlinkedFilesCrawler crawler = new UnlinkedFilesCrawler(database);
CheckableTreeNode treeNode =
crawler.searchDirectory(ImportDataTest.EXISTING_FOLDER, new EntryFromPDFCreator());
Assert.assertNotNull(treeNode);
/** Select all nodes manually. */
@SuppressWarnings("unchecked")
Enumeration<CheckableTreeNode> enumeration = treeNode.breadthFirstEnumeration();
while (enumeration.hasMoreElements()) {
CheckableTreeNode nextElement = enumeration.nextElement();
nextElement.setSelected(true);
}
List<File> resultList = getFileListFromNode(treeNode);
Assert.assertFalse(resultList.isEmpty());
Assert.assertTrue(resultList.contains(ImportDataTest.FILE_NOT_IN_DATABASE));
Assert.assertFalse(resultList.contains(ImportDataTest.FILE_IN_DATABASE));
}
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));
}
}
@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();
}
}