@Test
public void roundtripWithContentSelectorsAndUmlauts() throws IOException, SaveException {
String fileContent =
"% Encoding: UTF-8"
+ OS.NEWLINE
+ OS.NEWLINE
+ "@Comment{jabref-meta: selector_journal:Test {\\\\\"U}mlaut;}"
+ OS.NEWLINE;
Charset encoding = StandardCharsets.UTF_8;
ParserResult firstParse =
new BibtexParser(importFormatPreferences).parse(new StringReader(fileContent));
SavePreferences preferences =
new SavePreferences().withEncoding(encoding).withSaveInOriginalOrder(true);
BibDatabaseContext context =
new BibDatabaseContext(
firstParse.getDatabase(),
firstParse.getMetaData(),
new Defaults(BibDatabaseMode.BIBTEX));
StringSaveSession session =
databaseWriter.savePartOfDatabase(
context, firstParse.getDatabase().getEntries(), preferences);
assertEquals(fileContent, session.getStringValue());
}
@Test
public void roundtripWithUserCommentBeforeStringAndChange() throws Exception {
Path testBibtexFile = Paths.get("src/test/resources/testbib/complex.bib");
Charset encoding = StandardCharsets.UTF_8;
ParserResult result =
new BibtexParser(importFormatPreferences)
.parse(Importer.getReader(testBibtexFile, encoding));
for (BibtexString string : result.getDatabase().getStringValues()) {
// Mark them as changed
string.setContent(string.getContent());
}
SavePreferences preferences =
new SavePreferences().withEncoding(encoding).withSaveInOriginalOrder(true);
BibDatabaseContext context =
new BibDatabaseContext(
result.getDatabase(), result.getMetaData(), new Defaults(BibDatabaseMode.BIBTEX));
StringSaveSession session =
databaseWriter.savePartOfDatabase(context, result.getDatabase().getEntries(), preferences);
try (Scanner scanner = new Scanner(testBibtexFile, encoding.name())) {
assertEquals(scanner.useDelimiter("\\A").next(), session.getStringValue());
}
}
@Test
public void roundtripWithUserCommentAndEntryChange() throws Exception {
Path testBibtexFile = Paths.get("src/test/resources/testbib/bibWithUserComments.bib");
Charset encoding = StandardCharsets.UTF_8;
ParserResult result =
new BibtexParser(importFormatPreferences)
.parse(Importer.getReader(testBibtexFile, encoding));
BibEntry entry = result.getDatabase().getEntryByKey("1137631").get();
entry.setField("author", "Mr. Author");
SavePreferences preferences =
new SavePreferences().withEncoding(encoding).withSaveInOriginalOrder(true);
BibDatabaseContext context =
new BibDatabaseContext(
result.getDatabase(), result.getMetaData(), new Defaults(BibDatabaseMode.BIBTEX));
StringSaveSession session =
databaseWriter.savePartOfDatabase(context, result.getDatabase().getEntries(), preferences);
try (Scanner scanner =
new Scanner(
Paths.get("src/test/resources/testbib/bibWithUserCommentAndEntryChange.bib"),
encoding.name())) {
assertEquals(scanner.useDelimiter("\\A").next(), session.getStringValue());
}
}
@Test
public void duplicateBibDatabaseConfiguration() throws URISyntaxException, IOException {
InputStream originalStream = AuxParserTest.class.getResourceAsStream("config.bib");
File auxFile = Paths.get(AuxParserTest.class.getResource("paper.aux").toURI()).toFile();
try (InputStreamReader originalReader =
new InputStreamReader(originalStream, StandardCharsets.UTF_8)) {
ParserResult result = new BibtexParser(importFormatPreferences).parse(originalReader);
AuxParser auxParser = new AuxParser(auxFile.getAbsolutePath(), result.getDatabase());
AuxParserResult auxResult = auxParser.parse();
BibDatabase db = auxResult.getGeneratedBibDatabase();
assertEquals(Optional.of("\"Maintained by \" # maintainer"), db.getPreamble());
assertEquals(1, db.getStringCount());
}
}
private void doContentImport(String fileName, List<BibEntry> res) {
PdfContentImporter contentImporter =
new PdfContentImporter(Globals.prefs.getImportFormatPreferences());
Path filePath = Paths.get(fileName);
ParserResult result =
contentImporter.importDatabase(filePath, Globals.prefs.getDefaultEncoding());
if (result.hasWarnings()) {
frame.showMessage(result.getErrorMessage());
}
if (!result.getDatabase().hasEntries()) {
// import failed -> generate default entry
createNewBlankEntry(fileName).ifPresent(res::add);
return;
}
// only one entry is imported
BibEntry entry = result.getDatabase().getEntries().get(0);
// insert entry to database and link file
panel.getDatabase().insertEntry(entry);
panel.markBaseChanged();
BibtexKeyPatternUtil.makeLabel(
panel
.getBibDatabaseContext()
.getMetaData()
.getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
panel.getDatabase(),
entry,
Globals.prefs.getBibtexKeyPatternPreferences());
DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
dfh.linkPdfToEntry(fileName, entry);
panel.highlightEntry(entry);
if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_OPEN_FORM)) {
EntryEditor editor = panel.getEntryEditor(entry);
panel.showEntryEditor(editor);
}
res.add(entry);
}
private void doXMPImport(String fileName, List<BibEntry> res) {
List<BibEntry> localRes = new ArrayList<>();
PdfXmpImporter importer = new PdfXmpImporter(Globals.prefs.getXMPPreferences());
Path filePath = Paths.get(fileName);
ParserResult result = importer.importDatabase(filePath, Globals.prefs.getDefaultEncoding());
if (result.hasWarnings()) {
frame.showMessage(result.getErrorMessage());
}
localRes.addAll(result.getDatabase().getEntries());
BibEntry entry;
if (localRes.isEmpty()) {
// import failed -> generate default entry
LOGGER.info("Import failed");
createNewBlankEntry(fileName).ifPresent(res::add);
return;
}
// only one entry is imported
entry = localRes.get(0);
// insert entry to database and link file
panel.getDatabase().insertEntry(entry);
panel.markBaseChanged();
FileListTableModel tm = new FileListTableModel();
File toLink = new File(fileName);
// Get a list of file directories:
List<String> dirsS =
panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
tm.addEntry(
0,
new FileListEntry(
toLink.getName(),
FileUtil.shortenFileName(toLink, dirsS).getPath(),
ExternalFileTypes.getInstance().getExternalFileTypeByName("PDF")));
entry.setField(FieldName.FILE, tm.getStringRepresentation());
res.add(entry);
}
@Override
public ParserResult importDatabase(BufferedReader reader) throws IOException {
Objects.requireNonNull(reader);
List<BibEntry> bibItems = new ArrayList<>();
try {
JAXBContext context =
JAXBContext.newInstance("net.sf.jabref.logic.importer.fileformat.medline");
XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory();
XMLStreamReader xmlStreamReader = xmlInputFactory.createXMLStreamReader(reader);
// go to the root element
while (!xmlStreamReader.isStartElement()) {
xmlStreamReader.next();
}
Unmarshaller unmarshaller = context.createUnmarshaller();
Object unmarshalledObject = unmarshaller.unmarshal(xmlStreamReader);
// check whether we have an article set, an article, a book article or a book article set
if (unmarshalledObject instanceof PubmedArticleSet) {
PubmedArticleSet articleSet = (PubmedArticleSet) unmarshalledObject;
for (Object article : articleSet.getPubmedArticleOrPubmedBookArticle()) {
if (article instanceof PubmedArticle) {
PubmedArticle currentArticle = (PubmedArticle) article;
parseArticle(currentArticle, bibItems);
}
if (article instanceof PubmedBookArticle) {
PubmedBookArticle currentArticle = (PubmedBookArticle) article;
parseBookArticle(currentArticle, bibItems);
}
}
} else if (unmarshalledObject instanceof PubmedArticle) {
PubmedArticle article = (PubmedArticle) unmarshalledObject;
parseArticle(article, bibItems);
} else if (unmarshalledObject instanceof PubmedBookArticle) {
PubmedBookArticle currentArticle = (PubmedBookArticle) unmarshalledObject;
parseBookArticle(currentArticle, bibItems);
} else {
PubmedBookArticleSet bookArticleSet = (PubmedBookArticleSet) unmarshalledObject;
for (PubmedBookArticle bookArticle : bookArticleSet.getPubmedBookArticle()) {
parseBookArticle(bookArticle, bibItems);
}
}
} catch (JAXBException | XMLStreamException e) {
LOGGER.debug("could not parse document", e);
return ParserResult.fromErrorMessage(e.getLocalizedMessage());
}
return new ParserResult(bibItems);
}
@Test
public void testNormal() throws URISyntaxException, IOException {
InputStream originalStream = AuxParserTest.class.getResourceAsStream("origin.bib");
File auxFile = Paths.get(AuxParserTest.class.getResource("paper.aux").toURI()).toFile();
try (InputStreamReader originalReader =
new InputStreamReader(originalStream, StandardCharsets.UTF_8)) {
ParserResult result = new BibtexParser(importFormatPreferences).parse(originalReader);
AuxParser auxParser = new AuxParser(auxFile.getAbsolutePath(), result.getDatabase());
AuxParserResult auxResult = auxParser.parse();
assertTrue(auxResult.getGeneratedBibDatabase().hasEntries());
assertEquals(0, auxResult.getUnresolvedKeysCount());
BibDatabase newDB = auxResult.getGeneratedBibDatabase();
assertEquals(2, newDB.getEntries().size());
assertEquals(2, auxResult.getResolvedKeysCount());
assertEquals(2, auxResult.getFoundKeysInAux());
assertEquals(
auxResult.getFoundKeysInAux() + auxResult.getCrossRefEntriesCount(),
auxResult.getResolvedKeysCount() + auxResult.getUnresolvedKeysCount());
assertEquals(0, auxResult.getCrossRefEntriesCount());
}
}