Examples with BibtexParser org.jabref.logic.importer.fileformat.BibtexParser used on opensource projects

Example 31 with BibtexParser

use of org.jabref.logic.importer.fileformat.BibtexParser in project jabref by JabRef.

the class CrossrefFetcherEvaluator method main.

public static void main(String[] args) throws IOException, InterruptedException {
    Globals.prefs = JabRefPreferences.getInstance();
    try (FileReader reader = new FileReader(args[0])) {
        BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences());
        ParserResult result = parser.parse(reader);
        BibDatabase db = result.getDatabase();
        List<BibEntry> entries = db.getEntries();
        AtomicInteger dois = new AtomicInteger();
        AtomicInteger doiFound = new AtomicInteger();
        AtomicInteger doiNew = new AtomicInteger();
        AtomicInteger doiIdentical = new AtomicInteger();
        int total = entries.size();
        CountDownLatch countDownLatch = new CountDownLatch(total);
        ExecutorService executorService = Executors.newFixedThreadPool(5);
        for (BibEntry entry : entries) {
            executorService.execute(new Runnable() {

                @Override
                public void run() {
                    Optional<DOI> origDOI = entry.getField(FieldName.DOI).flatMap(DOI::parse);
                    if (origDOI.isPresent()) {
                        dois.incrementAndGet();
                        try {
                            Optional<DOI> crossrefDOI = new CrossRef().findIdentifier(entry);
                            if (crossrefDOI.isPresent()) {
                                doiFound.incrementAndGet();
                                if (origDOI.get().getDOI().equalsIgnoreCase(crossrefDOI.get().getDOI())) {
                                    doiIdentical.incrementAndGet();
                                } else {
                                    System.out.println("DOI not identical for : " + entry);
                                }
                            } else {
                                System.out.println("DOI not found for: " + entry);
                            }
                        } catch (FetcherException e) {
                            e.printStackTrace();
                        }
                    } else {
                        try {
                            Optional<DOI> crossrefDOI = new CrossRef().findIdentifier(entry);
                            if (crossrefDOI.isPresent()) {
                                System.out.println("New DOI found for: " + entry);
                                doiNew.incrementAndGet();
                            }
                        } catch (FetcherException e) {
                            e.printStackTrace();
                        }
                    }
                    countDownLatch.countDown();
                }
            });
        }
        countDownLatch.await();
        System.out.println("---------------------------------");
        System.out.println("Total DB size: " + total);
        System.out.println("Total DOIs: " + dois);
        System.out.println("DOIs found: " + doiFound);
        System.out.println("DOIs identical: " + doiIdentical);
        System.out.println("New DOIs found: " + doiNew);
        executorService.shutdown();
    }
}

Example 32 with BibtexParser

use of org.jabref.logic.importer.fileformat.BibtexParser in project jabref by JabRef.

the class EntryEditor method storeSource.

private boolean storeSource() {
    BibtexParser bibtexParser = new BibtexParser(Globals.prefs.getImportFormatPreferences());
    try {
        ParserResult parserResult = bibtexParser.parse(new StringReader(source.getText()));
        BibDatabase database = parserResult.getDatabase();
        if (database.getEntryCount() > 1) {
            throw new IllegalStateException("More than one entry found.");
        }
        if (!database.hasEntries()) {
            if (parserResult.hasWarnings()) {
                // put the warning into as exception text -> it will be displayed to the user
                throw new IllegalStateException(parserResult.warnings().get(0));
            } else {
                throw new IllegalStateException("No entries found.");
            }
        }
        NamedCompound compound = new NamedCompound(Localization.lang("source edit"));
        BibEntry newEntry = database.getEntries().get(0);
        String newKey = newEntry.getCiteKeyOptional().orElse(null);
        boolean entryChanged = false;
        boolean emptyWarning = (newKey == null) || newKey.isEmpty();
        if (newKey != null) {
            entry.setCiteKey(newKey);
        } else {
            entry.clearCiteKey();
        }
        // First, remove fields that the user has removed.
        for (Entry<String, String> field : entry.getFieldMap().entrySet()) {
            String fieldName = field.getKey();
            String fieldValue = field.getValue();
            if (InternalBibtexFields.isDisplayableField(fieldName) && !newEntry.hasField(fieldName)) {
                compound.addEdit(new UndoableFieldChange(entry, fieldName, fieldValue, null));
                entry.clearField(fieldName);
                entryChanged = true;
            }
        }
        // Then set all fields that have been set by the user.
        for (Entry<String, String> field : newEntry.getFieldMap().entrySet()) {
            String fieldName = field.getKey();
            String oldValue = entry.getField(fieldName).orElse(null);
            String newValue = field.getValue();
            if (!Objects.equals(oldValue, newValue)) {
                // Test if the field is legally set.
                new LatexFieldFormatter(Globals.prefs.getLatexFieldFormatterPreferences()).format(newValue, fieldName);
                compound.addEdit(new UndoableFieldChange(entry, fieldName, oldValue, newValue));
                entry.setField(fieldName, newValue);
                entryChanged = true;
            }
        }
        // See if the user has changed the entry type:
        if (!Objects.equals(newEntry.getType(), entry.getType())) {
            compound.addEdit(new UndoableChangeType(entry, entry.getType(), newEntry.getType()));
            entry.setType(newEntry.getType());
            entryChanged = true;
        }
        compound.end();
        if (!entryChanged) {
            return true;
        }
        panel.getUndoManager().addEdit(compound);
        if (panel.getDatabase().getDuplicationChecker().isDuplicateCiteKeyExisting(entry)) {
            warnDuplicateBibtexkey();
        } else if (emptyWarning) {
            warnEmptyBibtexkey();
        } else {
            panel.output(Localization.lang("Stored entry") + '.');
        }
        lastSourceStringAccepted = source.getText();
        // Update UI
        // TODO: we need to repaint the entryeditor if fields that are not displayed have been added
        panel.updateEntryEditorIfShowing();
        lastSourceAccepted = true;
        updateSource = true;
        // TODO: does updating work properly after source stored?
        panel.markBaseChanged();
        panel.highlightEntry(entry);
        return true;
    } catch (InvalidFieldValueException | IOException ex) {
        // The source couldn't be parsed, so the user is given an
        // error message, and the choice to keep or revert the contents
        // of the source text field.
        updateSource = false;
        lastSourceAccepted = false;
        tabbed.setSelectedComponent(srcPanel);
        Object[] options = { Localization.lang("Edit"), Localization.lang("Revert to original source") };
        if (!SwingUtilities.isEventDispatchThread()) {
            int answer = JOptionPane.showOptionDialog(frame, Localization.lang("Error") + ": " + ex.getMessage(), Localization.lang("Problem with parsing entry"), JOptionPane.YES_NO_OPTION, JOptionPane.ERROR_MESSAGE, null, options, options[0]);
            if (answer != 0) {
                updateSource = true;
                lastSourceAccepted = true;
                updateSource();
            }
        }
        LOGGER.debug("Incorrect source", ex);
        return false;
    }
}

Example 33 with BibtexParser

use of org.jabref.logic.importer.fileformat.BibtexParser in project jabref by JabRef.

the class INSPIREFetcher method importInspireEntries.

/**
     * Constructs a INSPIRE query url from slaccitation field
     *
     * @param slaccitation
     * @return query string
     *
     *         public static String constructUrlFromSlaccitation(String slaccitation) { String cmd = "j"; String key =
     *         slaccitation.replaceAll("^%%CITATION = ", "").replaceAll( ";%%$", ""); if (key.matches("^\\w*-\\w*[ /].*"
     *         )) cmd = "eprint"; try { key = URLEncoder.encode(key, "UTF-8"); } catch (UnsupportedEncodingException e)
     *         { } StringBuffer sb = new StringBuffer("http://").append(INSPIRE_HOST) .append("/");
     *         sb.append("spires/find/hep/www").append("?"); sb.append("rawcmd=find+").append(cmd).append("+");
     *         sb.append(key); return sb.toString(); }
     *
     *         /** Construct an INSPIRE query url from eprint field
     *
     * @param eprint
     * @return query string
     *
     *         public static String constructUrlFromEprint(String eprint) { String key = eprint.replaceAll(" [.*]$",
     *         ""); try { key = URLEncoder.encode(key, "UTF-8"); } catch (UnsupportedEncodingException e) { return ""; }
     *         StringBuffer sb = new StringBuffer("http://").append(INSPIRE_HOST) .append("/");
     *         sb.append("spires/find/hep/www").append("?"); sb.append("rawcmd=find+eprint+"); sb.append(key); return
     *         sb.toString(); }
     */
/**
     * Import an entry from an OAI2 archive. The BibEntry provided has to have the field OAI2_IDENTIFIER_FIELD set to
     * the search string.
     *
     * @param key The OAI2 key to fetch from ArXiv.
     * @return The imported BibEntry or null if none.
     */
private BibDatabase importInspireEntries(String key) throws IOException {
    String url = constructUrl(key);
    HttpURLConnection conn = (HttpURLConnection) new URL(url).openConnection();
    conn.setRequestProperty("User-Agent", "JabRef");
    InputStream inputStream = conn.getInputStream();
    try (INSPIREBibtexFilterReader reader = new INSPIREBibtexFilterReader(new InputStreamReader(inputStream, StandardCharsets.UTF_8))) {
        ParserResult pr = new BibtexParser(Globals.prefs.getImportFormatPreferences()).parse(reader);
        return pr.getDatabase();
    }
}

Example 34 with BibtexParser

use of org.jabref.logic.importer.fileformat.BibtexParser in project jabref by JabRef.

the class IEEEXploreFetcher method processQuery.

@Override
public boolean processQuery(String query, ImportInspector dialog, OutputPrinter status) {
    //IEEE API seems to use .QT. as a marker for the quotes for exact phrase searching
    String terms = query.replaceAll("\"", "\\.QT\\.");
    shouldContinue = true;
    int parsed = 0;
    int pageNumber = 1;
    String postData = makeSearchPostRequestPayload(pageNumber, terms);
    try {
        //open the search URL
        URLDownload dl = new URLDownload(IEEEXploreFetcher.URL_SEARCH);
        //add request header
        dl.addHeader("Accept", "application/json");
        dl.addHeader("Content-Type", "application/json");
        dl.addHeader("Referer", "http://ieeexplore.ieee.org/search/searchresult.jsp");
        // set post data
        dl.setPostData(postData);
        //retrieve the search results
        String page = dl.asString();
        //the page can be blank if the search did not work (not sure the exact conditions that lead to this, but declaring it an invalid search for now)
        if (page.isEmpty()) {
            status.showMessage(Localization.lang("You have entered an invalid search '%0'.", query), DIALOG_TITLE, JOptionPane.INFORMATION_MESSAGE);
            return false;
        }
        //parses the JSON data returned by the query
        //TODO: a faster way would be to parse the JSON tokens one at a time just to extract the article number, but this seems to be fast enough...
        JSONObject searchResultsJson = new JSONObject(page);
        int hits = searchResultsJson.getInt("totalRecords");
        //if no search results were found
        if (hits == 0) {
            status.showMessage(Localization.lang("No entries found for the search string '%0'", query), DIALOG_TITLE, JOptionPane.INFORMATION_MESSAGE);
            return false;
        }
        //if max hits were exceeded, display the warning
        if (hits > IEEEXploreFetcher.MAX_FETCH) {
            status.showMessage(Localization.lang("%0 entries found. To reduce server load, only %1 will be downloaded.", String.valueOf(hits), String.valueOf(IEEEXploreFetcher.MAX_FETCH)), DIALOG_TITLE, JOptionPane.INFORMATION_MESSAGE);
        }
        //fetch the raw Bibtex results from IEEEXplore
        String bibtexPage = new URLDownload(createBibtexQueryURL(searchResultsJson)).asString(Globals.prefs.getDefaultEncoding());
        //preprocess the result (eg. convert HTML escaped characters to latex and do other formatting not performed by BibtexParser)
        bibtexPage = preprocessBibtexResultsPage(bibtexPage);
        //parse the page into Bibtex entries
        Collection<BibEntry> parsedBibtexCollection = new BibtexParser(Globals.prefs.getImportFormatPreferences()).parseEntries(bibtexPage);
        int nEntries = parsedBibtexCollection.size();
        Iterator<BibEntry> parsedBibtexCollectionIterator = parsedBibtexCollection.iterator();
        while (parsedBibtexCollectionIterator.hasNext() && shouldContinue) {
            dialog.addEntry(cleanup(parsedBibtexCollectionIterator.next()));
            dialog.setProgress(parsed, nEntries);
            parsed++;
        }
        return true;
    } catch (ParseException | IOException | JSONException e) {
        LOGGER.error("Error while fetching from " + getTitle(), e);
        ((ImportInspectionDialog) dialog).showErrorMessage(this.getTitle(), e.getLocalizedMessage());
    }
    return false;
}

Example 35 with BibtexParser

use of org.jabref.logic.importer.fileformat.BibtexParser in project jabref by JabRef.

the class AuxParserTest method testNotAllFound.

@Test
public void testNotAllFound() throws URISyntaxException, IOException {
    InputStream originalStream = AuxParserTest.class.getResourceAsStream("origin.bib");
    File auxFile = Paths.get(AuxParserTest.class.getResource("badpaper.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(1, auxResult.getUnresolvedKeysCount());
        BibDatabase newDB = auxResult.getGeneratedBibDatabase();
        assertEquals(2, newDB.getEntries().size());
        assertEquals(2, auxResult.getResolvedKeysCount());
        assertEquals(3, auxResult.getFoundKeysInAux());
        assertEquals(auxResult.getFoundKeysInAux() + auxResult.getCrossRefEntriesCount(), auxResult.getResolvedKeysCount() + auxResult.getUnresolvedKeysCount());
        assertEquals(0, auxResult.getCrossRefEntriesCount());
    }
}