/**
* Will parse the BibTex-Data found when reading from reader.
*
* <p>The reader will be consumed.
*
* <p>Multiple calls to parse() return the same results
*
* @return ParserResult
* @throws IOException
*/
public ParserResult parse() throws IOException {
// If we already parsed this, just return it.
if (_pr != null) return _pr;
_db = new BibtexDatabase(); // Bibtex related contents.
_meta = new HashMap<String, String>(); // Metadata in comments for Bibkeeper.
entryTypes = new HashMap<String, BibtexEntryType>(); // To store custem entry types parsed.
_pr = new ParserResult(_db, _meta, entryTypes);
// First see if we can find the version number of the JabRef version that
// wrote the file:
String versionNum = readJabRefVersionNumber();
if (versionNum != null) {
_pr.setJabrefVersion(versionNum);
setMajorMinorVersions();
} else {
// No version number found. However, we have only
}
skipWhitespace();
try {
while (!_eof) {
boolean found = consumeUncritically('@');
if (!found) break;
skipWhitespace();
String entryType = parseTextToken();
BibtexEntryType tp = BibtexEntryType.getType(entryType);
boolean isEntry = (tp != null);
// Util.pr(tp.getName());
if (!isEntry) {
// The entry type name was not recognized. This can mean
// that it is a string, preamble, or comment. If so,
// parse and set accordingly. If not, assume it is an entry
// with an unknown type.
if (entryType.toLowerCase().equals("preamble")) {
_db.setPreamble(parsePreamble());
} else if (entryType.toLowerCase().equals("string")) {
BibtexString bs = parseString();
try {
_db.addString(bs);
} catch (KeyCollisionException ex) {
_pr.addWarning(Globals.lang("Duplicate string name") + ": " + bs.getName());
// ex.printStackTrace();
}
} else if (entryType.toLowerCase().equals("comment")) {
StringBuffer commentBuf = parseBracketedTextExactly();
/**
* Metadata are used to store Bibkeeper-specific information in .bib files.
*
* <p>Metadata are stored in bibtex files in the format
*
* @comment{jabref-meta: type:data0;data1;data2;...}
* <p>Each comment that starts with the META_FLAG is stored in the meta HashMap,
* with type as key. Unluckily, the old META_FLAG bibkeeper-meta: was used in JabRef
* 1.0 and 1.1, so we need to support it as well. At least for a while. We'll always
* save with the new one.
*/
String comment = commentBuf.toString().replaceAll("[\\x0d\\x0a]", "");
if (comment
.substring(0, Math.min(comment.length(), GUIGlobals.META_FLAG.length()))
.equals(GUIGlobals.META_FLAG)
|| comment
.substring(0, Math.min(comment.length(), GUIGlobals.META_FLAG_OLD.length()))
.equals(GUIGlobals.META_FLAG_OLD)) {
String rest;
if (comment.substring(0, GUIGlobals.META_FLAG.length()).equals(GUIGlobals.META_FLAG))
rest = comment.substring(GUIGlobals.META_FLAG.length());
else rest = comment.substring(GUIGlobals.META_FLAG_OLD.length());
int pos = rest.indexOf(':');
if (pos > 0) _meta.put(rest.substring(0, pos), rest.substring(pos + 1));
// We remove all line breaks in the metadata - these
// will have been inserted
// to prevent too long lines when the file was
// saved, and are not part of the data.
}
/**
* A custom entry type can also be stored in a
*
* @comment:
*/
if (comment
.substring(0, Math.min(comment.length(), GUIGlobals.ENTRYTYPE_FLAG.length()))
.equals(GUIGlobals.ENTRYTYPE_FLAG)) {
CustomEntryType typ = CustomEntryType.parseEntryType(comment);
entryTypes.put(typ.getName().toLowerCase(), typ);
}
} else {
// The entry type was not recognized. This may mean that
// it is a custom entry type whose definition will
// appear
// at the bottom of the file. So we use an
// UnknownEntryType
// to remember the type name by.
tp = new UnknownEntryType(entryType.toLowerCase());
// System.out.println("unknown type: "+entryType);
isEntry = true;
}
}
if (isEntry) // True if not comment, preamble or string.
{
/**
* Morten Alver 13 Aug 2006: Trying to make the parser more robust. If an exception is
* thrown when parsing an entry, drop the entry and try to resume parsing. Add a warning
* for the user.
*
* <p>An alternative solution is to try rescuing the entry for which parsing failed, by
* returning the entry with the exception and adding it before parsing is continued.
*/
try {
BibtexEntry be = parseEntry(tp);
boolean duplicateKey = _db.insertEntry(be);
if (duplicateKey) // JZTODO lyrics
_pr.addWarning(
Globals.lang("duplicate BibTeX key")
+ ": "
+ be.getCiteKey()
+ " ("
+ Globals.lang("grouping may not work for this entry")
+ ")");
else if (be.getCiteKey() == null || be.getCiteKey().equals("")) {
_pr.addWarning(
Globals.lang("empty BibTeX key")
+ ": "
+ be.getAuthorTitleYear(40)
+ " ("
+ Globals.lang("grouping may not work for this entry")
+ ")");
}
} catch (IOException ex) {
ex.printStackTrace();
_pr.addWarning(
Globals.lang("Error occured when parsing entry")
+ ": '"
+ ex.getMessage()
+ "'. "
+ Globals.lang("Skipped entry."));
}
}
skipWhitespace();
}
// Before returning the database, update entries with unknown type
// based on parsed type definitions, if possible.
checkEntryTypes(_pr);
return _pr;
} catch (KeyCollisionException kce) {
// kce.printStackTrace();
throw new IOException("Duplicate ID in bibtex file: " + kce.toString());
}
}
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();
}
public void update() {
// pdfURL = new URL("http://geog-www.sbs.ohio-state.edu/faculty/bmark/abbott_etal_ppp03.pdf");
if (result.url != null) {
// System.out.println("PDF URL: "+result.url);
String bibtexKey = entry.getCiteKey();
String fileDir = basePanel.metaData().getFileDirectory(GUIGlobals.FILE_FIELD);
if (fileDir == null) {
// TODO: error message if file dir not defined
// JOptionPane.showMessageDialog(frame, Globals.lang);
return;
}
DownloadExternalFile def =
new DownloadExternalFile(basePanel.frame(), basePanel.metaData(), bibtexKey);
try {
def.download(
result.url,
new DownloadExternalFile.DownloadCallback() {
public void downloadComplete(FileListEntry file) {
System.out.println("finished");
FileListTableModel tm = new FileListTableModel();
String oldValue = entry.getField(GUIGlobals.FILE_FIELD);
tm.setContent(oldValue);
tm.addEntry(tm.getRowCount(), file);
String newValue = tm.getStringRepresentation();
UndoableFieldChange edit =
new UndoableFieldChange(entry, GUIGlobals.FILE_FIELD, oldValue, newValue);
entry.setField(GUIGlobals.FILE_FIELD, newValue);
basePanel.undoManager.addEdit(edit);
basePanel.markBaseChanged();
}
});
} catch (IOException e) {
e.printStackTrace();
}
basePanel.output(Globals.lang("Finished downloading full text document"));
} else {
String message = null;
switch (result.status) {
case FindFullText.UNKNOWN_DOMAIN:
message =
Globals.lang(
"Unable to find full text article. No search algorithm "
+ "defined for the '%0' web site.",
result.host);
break;
case FindFullText.WRONG_MIME_TYPE:
message =
Globals.lang(
"Found pdf link, but received the wrong MIME type. "
+ "This could indicate that you don't have access to the fulltext article.");
break;
case FindFullText.LINK_NOT_FOUND:
message = Globals.lang("Unable to find full text document in the linked web page.");
break;
case FindFullText.IO_EXCEPTION:
message = Globals.lang("Connection error when trying to find full text document.");
break;
case FindFullText.NO_URLS_DEFINED:
message = Globals.lang("This entry provides no URL or DOI links.");
break;
}
basePanel.output(Globals.lang("Full text article download failed"));
JOptionPane.showMessageDialog(
basePanel.frame(),
message,
Globals.lang("Full text article download failed"),
JOptionPane.ERROR_MESSAGE);
}
}
