private static String getKeyString(BibEntry[] bibentries) {
StringBuilder result = new StringBuilder();
String citeKey;
boolean first = true;
for (BibEntry bes : bibentries) {
citeKey = bes.getCiteKey();
// if the key is empty we give a warning and ignore this entry
if ((citeKey == null) || citeKey.isEmpty()) {
continue;
}
if (first) {
result.append(citeKey);
first = false;
} else {
result.append(',').append(citeKey);
}
}
return result.toString();
}
/**
* 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();
}
}
private BibtexDatabase parseBibtexDatabase(List<String> id, boolean abs) throws IOException {
if (id.isEmpty()) {
return null;
}
URLConnection conn;
try {
conn = new URL(IEEEXploreFetcher.IMPORT_URL).openConnection();
} catch (MalformedURLException e) {
e.printStackTrace();
return null;
}
conn.setDoInput(true);
conn.setDoOutput(true);
conn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");
conn.setRequestProperty("Referer", searchUrl);
PrintWriter out = new PrintWriter(conn.getOutputStream());
String recordIds = "";
for (String anId : id) {
recordIds += anId + " ";
}
recordIds = recordIds.trim();
String citation = abs ? "citation-abstract" : "citation-only";
String content =
"recordIds="
+ recordIds.replaceAll(" ", "%20")
+ "&fromPageName=&citations-format="
+ citation
+ "&download-format=download-bibtex";
System.out.println(content);
out.write(content);
out.flush();
out.close();
BufferedReader bufr = new BufferedReader(new InputStreamReader(conn.getInputStream()));
StringBuilder sb = new StringBuilder();
char[] buffer = new char[256];
while (true) {
int bytesRead = bufr.read(buffer);
if (bytesRead == -1) {
break;
}
for (int i = 0; i < bytesRead; i++) {
sb.append(buffer[i]);
}
}
System.out.println(sb);
ParserResult results = new BibtexParser(bufr).parse();
bufr.close();
return results.getDatabase();
}
/**
* Read results from a file instead of an URL. Just for faster debugging.
*
* @param f
* @return
* @throws IOException
*/
public String getResultsFromFile(File f) throws IOException {
InputStream in = new BufferedInputStream(new FileInputStream(f));
StringBuilder sb = new StringBuilder();
byte[] buffer = new byte[256];
while (true) {
int bytesRead = in.read(buffer);
if (bytesRead == -1) {
break;
}
for (int i = 0; i < bytesRead; i++) {
sb.append((char) buffer[i]);
}
}
return sb.toString();
}
/**
* Download the URL and return contents as a String.
*
* @param source
* @return
* @throws IOException
*/
private String getResults(URL source) throws IOException {
InputStream in = source.openStream();
StringBuilder sb = new StringBuilder();
byte[] buffer = new byte[256];
while (true) {
int bytesRead = in.read(buffer);
if (bytesRead == -1) {
break;
}
for (int i = 0; i < bytesRead; i++) {
sb.append((char) buffer[i]);
}
}
return sb.toString();
}
public void actionPerformed(ActionEvent event) {
int selected = editor.getSelectedRow();
if (selected == -1) return;
FileListEntry flEntry = editor.getTableModel().getEntry(selected);
// Check if the current file exists:
String ln = flEntry.getLink();
boolean httpLink = ln.toLowerCase().startsWith("http");
if (httpLink) {
// TODO: notify that this operation cannot be done on remote links
}
// Get an absolute path representation:
String dir = frame.basePanel().metaData().getFileDirectory(GUIGlobals.FILE_FIELD);
if ((dir == null) || (dir.trim().length() == 0) || !(new File(dir)).exists()) {
JOptionPane.showMessageDialog(
frame,
Globals.lang("File_directory_is_not_set_or_does_not_exist!"),
Globals.lang("Move/Rename file"),
JOptionPane.ERROR_MESSAGE);
return;
}
File file = new File(ln);
if (!file.isAbsolute()) {
file = Util.expandFilename(ln, new String[] {dir});
}
if ((file != null) && file.exists()) {
// Ok, we found the file. Now get a new name:
String extension = null;
if (flEntry.getType() != null) extension = "." + flEntry.getType().getExtension();
File newFile = null;
boolean repeat = true;
while (repeat) {
repeat = false;
String chosenFile;
if (toFileDir) {
String suggName = eEditor.getEntry().getCiteKey() + extension;
CheckBoxMessage cbm =
new CheckBoxMessage(
Globals.lang("Move file to file directory?"),
Globals.lang("Rename to '%0'", suggName),
Globals.prefs.getBoolean("renameOnMoveFileToFileDir"));
int answer;
// Only ask about renaming file if the file doesn't have the proper name already:
if (!suggName.equals(file.getName()))
answer =
JOptionPane.showConfirmDialog(
frame, cbm, Globals.lang("Move/Rename file"), JOptionPane.YES_NO_OPTION);
else
answer =
JOptionPane.showConfirmDialog(
frame,
Globals.lang("Move file to file directory?"),
Globals.lang("Move/Rename file"),
JOptionPane.YES_NO_OPTION);
if (answer != JOptionPane.YES_OPTION) return;
Globals.prefs.putBoolean("renameOnMoveFileToFileDir", cbm.isSelected());
StringBuilder sb = new StringBuilder(dir);
if (!dir.endsWith(File.separator)) sb.append(File.separator);
if (cbm.isSelected()) {
// Rename:
sb.append(suggName);
} else {
// Do not rename:
sb.append(file.getName());
}
chosenFile = sb.toString();
} else {
chosenFile =
FileDialogs.getNewFile(frame, file, extension, JFileChooser.SAVE_DIALOG, false);
}
if (chosenFile == null) {
return; // cancelled
}
newFile = new File(chosenFile);
// Check if the file already exists:
if (newFile.exists()
&& (JOptionPane.showConfirmDialog(
frame,
"'" + newFile.getName() + "' " + Globals.lang("exists. Overwrite file?"),
Globals.lang("Move/Rename file"),
JOptionPane.OK_CANCEL_OPTION)
!= JOptionPane.OK_OPTION)) {
if (!toFileDir) repeat = true;
else return;
}
}
if (!newFile.equals(file)) {
try {
boolean success = file.renameTo(newFile);
if (!success) {
success = Util.copyFile(file, newFile, true);
}
if (success) {
// Remove the original file:
file.delete();
// Relativise path, if possible.
String canPath = (new File(dir)).getCanonicalPath();
if (newFile.getCanonicalPath().startsWith(canPath)) {
if ((newFile.getCanonicalPath().length() > canPath.length())
&& (newFile.getCanonicalPath().charAt(canPath.length()) == File.separatorChar))
flEntry.setLink(newFile.getCanonicalPath().substring(1 + canPath.length()));
else flEntry.setLink(newFile.getCanonicalPath().substring(canPath.length()));
} else flEntry.setLink(newFile.getCanonicalPath());
eEditor.updateField(editor);
JOptionPane.showMessageDialog(
frame,
Globals.lang("File moved"),
Globals.lang("Move/Rename file"),
JOptionPane.INFORMATION_MESSAGE);
} else {
JOptionPane.showMessageDialog(
frame,
Globals.lang("Move file failed"),
Globals.lang("Move/Rename file"),
JOptionPane.ERROR_MESSAGE);
}
} catch (SecurityException ex) {
ex.printStackTrace();
JOptionPane.showMessageDialog(
frame,
Globals.lang("Could not move file") + ": " + ex.getMessage(),
Globals.lang("Move/Rename file"),
JOptionPane.ERROR_MESSAGE);
} catch (IOException ex) {
ex.printStackTrace();
JOptionPane.showMessageDialog(
frame,
Globals.lang("Could not move file") + ": " + ex.getMessage(),
Globals.lang("Move/Rename file"),
JOptionPane.ERROR_MESSAGE);
}
}
} else {
// File doesn't exist, so we can't move it.
JOptionPane.showMessageDialog(
frame,
Globals.lang("Could not find file '%0'.", flEntry.getLink()),
Globals.lang("File not found"),
JOptionPane.ERROR_MESSAGE);
}
}
@Override
public String getShortDescription() {
StringBuilder sb = new StringBuilder();
sb.append("<b>");
if (Globals.prefs.getBoolean(JabRefPreferences.GROUP_SHOW_DYNAMIC)) {
sb.append("<i>").append(StringUtil.quoteForHTML(getName())).append("</i>");
} else {
sb.append(StringUtil.quoteForHTML(getName()));
}
sb.append("</b> - ");
sb.append(Globals.lang("dynamic group"));
sb.append("<b>");
sb.append(searchField);
sb.append("</b>");
sb.append(Globals.lang("contains"));
sb.append(" <b>");
sb.append(StringUtil.quoteForHTML(searchExpression));
sb.append("</b>)");
switch (getHierarchicalContext()) {
case INCLUDING:
sb.append(", ").append(Globals.lang("includes subgroups"));
break;
case REFINING:
sb.append(", ").append(Globals.lang("refines supergroup"));
break;
default:
break;
}
return sb.toString();
}
private BibtexEntry parseNextEntry(String allText, int startIndex) {
BibtexEntry entry = null;
int index = allText.indexOf("<div class=\"detail", piv);
int endIndex = allText.indexOf("</div>", index);
if (index >= 0 && endIndex > 0) {
endIndex += 6;
piv = endIndex;
String text = allText.substring(index, endIndex);
BibtexEntryType type = null;
String sourceField = null;
String typeName = "";
Matcher typeMatcher = typePattern.matcher(text);
if (typeMatcher.find()) {
typeName = typeMatcher.group(1);
if (typeName.equalsIgnoreCase("IEEE Journals & Magazines")
|| typeName.equalsIgnoreCase("IEEE Early Access Articles")
|| typeName.equalsIgnoreCase("IET Journals & Magazines")
|| typeName.equalsIgnoreCase("AIP Journals & Magazines")
|| typeName.equalsIgnoreCase("AVS Journals & Magazines")
|| typeName.equalsIgnoreCase("IBM Journals & Magazines")
|| typeName.equalsIgnoreCase("TUP Journals & Magazines")
|| typeName.equalsIgnoreCase("BIAI Journals & Magazines")) {
type = BibtexEntryType.getType("article");
sourceField = "journal";
} else if (typeName.equalsIgnoreCase("IEEE Conference Publications")
|| typeName.equalsIgnoreCase("IET Conference Publications")
|| typeName.equalsIgnoreCase("VDE Conference Publications")) {
type = BibtexEntryType.getType("inproceedings");
sourceField = "booktitle";
} else if (typeName.equalsIgnoreCase("IEEE Standards")
|| typeName.equalsIgnoreCase("Standards")) {
type = BibtexEntryType.getType("standard");
sourceField = "number";
} else if (typeName.equalsIgnoreCase("IEEE eLearning Library Courses")) {
type = BibtexEntryType.getType("Electronic");
sourceField = "note";
} else if (typeName.equalsIgnoreCase("Wiley-IEEE Press eBook Chapters")
|| typeName.equalsIgnoreCase("MIT Press eBook Chapters")
|| typeName.equalsIgnoreCase("IEEE USA Books & eBooks")) {
type = BibtexEntryType.getType("inCollection");
sourceField = "booktitle";
}
}
if (type == null) {
type = BibtexEntryType.getType("misc");
sourceField = "note";
System.err.println("Type detection failed. Use MISC instead.");
unparseable++;
System.err.println(text);
}
entry = new BibtexEntry(IdGenerator.next(), type);
if (typeName.equalsIgnoreCase("IEEE Standards")) {
entry.setField("organization", "IEEE");
}
if (typeName.equalsIgnoreCase("Wiley-IEEE Press eBook Chapters")) {
entry.setField("publisher", "Wiley-IEEE Press");
} else if (typeName.equalsIgnoreCase("MIT Press eBook Chapters")) {
entry.setField("publisher", "MIT Press");
} else if (typeName.equalsIgnoreCase("IEEE USA Books & eBooks")) {
entry.setField("publisher", "IEEE USA");
}
if (typeName.equalsIgnoreCase("IEEE Early Access Articles")) {
entry.setField("note", "Early Access");
}
Set<String> fields = fieldPatterns.keySet();
for (String field : fields) {
Matcher fieldMatcher = Pattern.compile(fieldPatterns.get(field)).matcher(text);
if (fieldMatcher.find()) {
entry.setField(field, htmlConverter.format(fieldMatcher.group(1)));
if (field.equals("title") && fieldMatcher.find()) {
String sec_title = htmlConverter.format(fieldMatcher.group(1));
if (entry.getType() == BibtexEntryType.getStandardType("standard")) {
sec_title = sec_title.replaceAll("IEEE Std ", "");
}
entry.setField(sourceField, sec_title);
}
if (field.equals("pages") && fieldMatcher.groupCount() == 2) {
entry.setField(field, fieldMatcher.group(1) + "-" + fieldMatcher.group(2));
}
}
}
Matcher authorMatcher = authorPattern.matcher(text);
// System.out.println(text);
StringBuilder authorNames = new StringBuilder("");
int authorCount = 0;
while (authorMatcher.find()) {
if (authorCount >= 1) {
authorNames.append(" and ");
}
authorNames.append(htmlConverter.format(authorMatcher.group(1)));
// System.out.println(authorCount + ": " + authorMatcher.group(1));
authorCount++;
}
entry.setField("author", authorNames.toString());
if (entry.getField("author") == null
|| entry.getField("author").startsWith("a href")
|| entry
.getField("author")
.startsWith("Topic(s)")) { // Fix for some documents without authors
entry.setField("author", "");
}
if (entry.getType() == BibtexEntryType.getStandardType("inproceedings")
&& entry.getField("author").equals("")) {
entry.setType(BibtexEntryType.getStandardType("proceedings"));
}
if (includeAbstract) {
index = text.indexOf("id=\"abstract");
if (index >= 0) {
endIndex = text.indexOf("</div>", index) + 6;
text = text.substring(index, endIndex);
Matcher absMatcher = absPattern.matcher(text);
if (absMatcher.find()) {
// Clean-up abstract
String abstr = absMatcher.group(1);
abstr = abstr.replaceAll("<span class='snippet'>([\\w]+)</span>", "$1");
entry.setField("abstract", htmlConverter.format(abstr));
}
}
}
}
if (entry == null) {
return null;
} else {
return cleanup(entry);
}
}
/**
* Formats the content of a field.
*
* @param s the content of the field
* @param fieldName the name of the field - used to trigger different serializations, e.g.,
* turning off resolution for some strings
* @return a formatted string suitable for output
* @throws IllegalArgumentException if s is not a correct bibtex string, e.g., because of
* improperly balanced braces or using # not paired
*/
public String format(String text, String fieldName) throws IllegalArgumentException {
if (text == null) {
return valueDelimiterStartOfValue + "" + valueDelimiterEndOfValue;
}
if (Globals.prefs.putBracesAroundCapitals(fieldName) && !BIBTEX_STRING.equals(fieldName)) {
text = StringUtil.putBracesAroundCapitals(text);
}
// normalize newlines
if (!text.contains(Globals.NEWLINE) && text.contains("\n")) {
// if we don't have real new lines, but pseudo newlines, we replace them
// On Win 8.1, this is always true for multiline fields
text = text.replaceAll("\n", Globals.NEWLINE);
}
// If the field is non-standard, we will just append braces,
// wrap and write.
boolean resolveStrings = true;
if (resolveStringsAllFields) {
// Resolve strings for all fields except some:
String[] exceptions = doNotResolveStringsFors;
for (String exception : exceptions) {
if (exception.equals(fieldName)) {
resolveStrings = false;
break;
}
}
} else {
// Default operation - we only resolve strings for standard fields:
resolveStrings = BibtexFields.isStandardField(fieldName) || BIBTEX_STRING.equals(fieldName);
}
if (!resolveStrings) {
int numberOfBrackets = 0;
boolean ok = true;
for (int i = 0; i < text.length(); i++) {
char c = text.charAt(i);
// Util.pr(""+c);
if (c == '{') {
numberOfBrackets++;
}
if (c == '}') {
numberOfBrackets--;
}
if (numberOfBrackets < 0) {
ok = false;
break;
}
}
if (numberOfBrackets > 0) {
ok = false;
}
if (!ok) {
throw new IllegalArgumentException("Curly braces { and } must be balanced.");
}
stringBuilder = new StringBuilder(valueDelimiterStartOfValue + "");
// No formatting at all for these fields, to allow custom formatting?
// if (Globals.prefs.getBoolean("preserveFieldFormatting"))
// sb.append(text);
// else
// currently, we do not do any more wrapping
// these two are also hard coded in
// net.sf.jabref.importer.fileformat.FieldContentParser.multiLineFields
// there, JabRefPreferences.NON_WRAPPABLE_FIELDS are also included
boolean isAbstract = "abstract".equals(fieldName);
boolean isReview = "review".equals(fieldName);
boolean doWrap = !isAbstract || !isReview;
boolean strangePrefSettings =
writefieldWrapfield && !Globals.prefs.isNonWrappableField(fieldName);
if (strangePrefSettings && doWrap) {
stringBuilder.append(
parser.format(StringUtil.wrap(text, GUIGlobals.LINE_LENGTH), fieldName));
} else {
stringBuilder.append(parser.format(text, fieldName));
}
stringBuilder.append(valueDelimiterEndOfValue);
return stringBuilder.toString();
}
stringBuilder = new StringBuilder();
int pivot = 0;
int pos1;
int pos2;
// Here we assume that the user encloses any bibtex strings in #, e.g.:
// #jan# - #feb#
// ...which will be written to the file like this:
// jan # { - } # feb
checkBraces(text);
while (pivot < text.length()) {
int goFrom = pivot;
pos1 = pivot;
while (goFrom == pos1) {
pos1 = text.indexOf('#', goFrom);
if (pos1 > 0 && text.charAt(pos1 - 1) == '\\') {
goFrom = pos1 + 1;
pos1++;
} else {
goFrom = pos1 - 1; // Ends the loop.
}
}
if (pos1 == -1) {
pos1 = text.length(); // No more occurrences found.
pos2 = -1;
} else {
pos2 = text.indexOf('#', pos1 + 1);
if (pos2 == -1) {
if (!neverFailOnHashes) {
throw new IllegalArgumentException(
Localization.lang(
"The # character is not allowed in BibTeX strings unless escaped as in '\\#'.")
+ '\n'
+ Localization.lang(
"In JabRef, use pairs of # characters to indicate a string.")
+ '\n'
+ Localization.lang(
"Note that the entry causing the problem has been selected."));
} else {
pos1 = text.length(); // just write out the rest of the text, and throw no exception
}
}
}
if (pos1 > pivot) {
writeText(text, pivot, pos1);
}
if (pos1 < text.length() && pos2 - 1 > pos1) {
// We check that the string label is not empty. That means
// an occurrence of ## will simply be ignored. Should it instead
// cause an error message?
writeStringLabel(text, pos1 + 1, pos2, pos1 == pivot, pos2 + 1 == text.length());
}
if (pos2 > -1) {
pivot = pos2 + 1;
} else {
pivot = pos1 + 1;
// if (tell++ > 10) System.exit(0);
}
}
// currently, we do not add newlines and new formatting
if (writefieldWrapfield && !Globals.prefs.isNonWrappableField(fieldName)) {
// introduce a line break to be read at the parser
return parser.format(
StringUtil.wrap(stringBuilder.toString(), GUIGlobals.LINE_LENGTH),
fieldName); // , but that lead to ugly .tex
} else {
return parser.format(stringBuilder.toString(), fieldName);
}
}
private void putIn(String s) {
stringBuilder.append(StringUtil.wrap(s, GUIGlobals.LINE_LENGTH));
}
private void writeText(String text, int start_pos, int end_pos) {
/*sb.append("{");
sb.append(text.substring(start_pos, end_pos));
sb.append("}");*/
stringBuilder.append(valueDelimiterStartOfValue);
boolean escape = false;
boolean inCommandName = false;
boolean inCommand = false;
boolean inCommandOption = false;
int nestedEnvironments = 0;
StringBuilder commandName = new StringBuilder();
char c;
for (int i = start_pos; i < end_pos; i++) {
c = text.charAt(i);
// Track whether we are in a LaTeX command of some sort.
if (Character.isLetter(c) && (escape || inCommandName)) {
inCommandName = true;
if (!inCommandOption) {
commandName.append(c);
}
} else if (Character.isWhitespace(c) && (inCommand || inCommandOption)) {
// System.out.println("whitespace here");
} else if (inCommandName) {
// This means the command name is ended.
// Perhaps the beginning of an argument:
if (c == '[') {
inCommandOption = true;
}
// Or the end of an argument:
else if (inCommandOption && c == ']') {
inCommandOption = false;
} else if (!inCommandOption && c == '{') {
// System.out.println("Read command: '"+commandName.toString()+"'");
inCommandName = false;
inCommand = true;
}
// Or simply the end of this command altogether:
else {
// System.out.println("I think I read command: '"+commandName.toString()+"'");
commandName.delete(0, commandName.length());
inCommandName = false;
}
}
// If we are in a command body, see if it has ended:
if (inCommand && c == '}') {
// System.out.println("nestedEnvironments = " + nestedEnvironments);
// System.out.println("Done with command: '"+commandName.toString()+"'");
if (commandName.toString().equals("begin")) {
nestedEnvironments++;
}
if (nestedEnvironments > 0 && commandName.toString().equals("end")) {
nestedEnvironments--;
}
// System.out.println("nestedEnvironments = " + nestedEnvironments);
commandName.delete(0, commandName.length());
inCommand = false;
}
// We add a backslash before any ampersand characters, with one exception: if
// we are inside an \\url{...} command, we should write it as it is. Maybe.
if (c == '&'
&& !escape
&& !(inCommand && commandName.toString().equals("url"))
&& nestedEnvironments == 0) {
stringBuilder.append("\\&");
} else {
stringBuilder.append(c);
}
escape = c == '\\';
}
stringBuilder.append(valueDelimiterEndOfValue);
}