Examples with FetcherException org.jabref.logic.importer.FetcherException used on opensource projects

Example 1 with FetcherException

use of org.jabref.logic.importer.FetcherException in project jabref by JabRef.

the class ClipBoardManager method extractBibEntriesFromClipboard.

public List<BibEntry> extractBibEntriesFromClipboard() {
    // Get clipboard contents, and see if TransferableBibtexEntry is among the content flavors offered
    Transferable content = CLIPBOARD.getContents(null);
    List<BibEntry> result = new ArrayList<>();
    if (content.isDataFlavorSupported(TransferableBibtexEntry.entryFlavor)) {
        // We have determined that the clipboard data is a set of entries.
        try {
            @SuppressWarnings("unchecked") List<BibEntry> contents = (List<BibEntry>) content.getTransferData(TransferableBibtexEntry.entryFlavor);
            result = contents;
        } catch (UnsupportedFlavorException | ClassCastException ex) {
            LOGGER.warn("Could not paste this type", ex);
        } catch (IOException ex) {
            LOGGER.warn("Could not paste", ex);
        }
    } else if (content.isDataFlavorSupported(DataFlavor.stringFlavor)) {
        try {
            String data = (String) content.getTransferData(DataFlavor.stringFlavor);
            // fetch from doi
            if (DOI.parse(data).isPresent()) {
                LOGGER.info("Found DOI in clipboard");
                Optional<BibEntry> entry = new DoiFetcher(Globals.prefs.getImportFormatPreferences()).performSearchById(new DOI(data).getDOI());
                entry.ifPresent(result::add);
            } else {
                // parse bibtex string
                BibtexParser bp = new BibtexParser(Globals.prefs.getImportFormatPreferences());
                BibDatabase db = bp.parse(new StringReader(data)).getDatabase();
                LOGGER.info("Parsed " + db.getEntryCount() + " entries from clipboard text");
                if (db.hasEntries()) {
                    result = db.getEntries();
                }
            }
        } catch (UnsupportedFlavorException ex) {
            LOGGER.warn("Could not parse this type", ex);
        } catch (IOException ex) {
            LOGGER.warn("Data is no longer available in the requested flavor", ex);
        } catch (FetcherException ex) {
            LOGGER.error("Error while fetching", ex);
        }
    }
    return result;
}

Example 2 with FetcherException

use of org.jabref.logic.importer.FetcherException in project jabref by JabRef.

the class LookupIdentifiersWorker method run.

@Override
public void run() {
    BasePanel basePanel = Objects.requireNonNull(frame.getCurrentBasePanel());
    List<BibEntry> bibEntries = basePanel.getSelectedEntries();
    if (!bibEntries.isEmpty()) {
        String totalCount = Integer.toString(bibEntries.size());
        NamedCompound namedCompound = new NamedCompound(Localization.lang("Look up %0", fetcher.getIdentifierName()));
        int count = 0;
        int foundCount = 0;
        for (BibEntry bibEntry : bibEntries) {
            count++;
            frame.output(Localization.lang("Looking up %0... - entry %1 out of %2 - found %3", fetcher.getIdentifierName(), Integer.toString(count), totalCount, Integer.toString(foundCount)));
            Optional<T> identifier = Optional.empty();
            try {
                identifier = fetcher.findIdentifier(bibEntry);
            } catch (FetcherException e) {
                LOGGER.error("Could not fetch " + fetcher.getIdentifierName(), e);
            }
            if (identifier.isPresent() && !bibEntry.hasField(identifier.get().getDefaultField())) {
                Optional<FieldChange> fieldChange = bibEntry.setField(identifier.get().getDefaultField(), identifier.get().getNormalized());
                if (fieldChange.isPresent()) {
                    namedCompound.addEdit(new UndoableFieldChange(fieldChange.get()));
                    foundCount++;
                    frame.output(Localization.lang("Looking up %0... - entry %1 out of %2 - found %3", Integer.toString(count), totalCount, Integer.toString(foundCount)));
                }
            }
        }
        namedCompound.end();
        if (foundCount > 0) {
            basePanel.getUndoManager().addEdit(namedCompound);
            basePanel.markBaseChanged();
        }
        message = Localization.lang("Determined %0 for %1 entries", fetcher.getIdentifierName(), Integer.toString(foundCount));
    }
}

Example 3 with FetcherException

use of org.jabref.logic.importer.FetcherException in project jabref by JabRef.

the class IsbnViaChimboriFetcher method performSearchById.

@Override
public Optional<BibEntry> performSearchById(String identifier) throws FetcherException {
    if (StringUtil.isBlank(identifier)) {
        return Optional.empty();
    }
    this.ensureThatIsbnIsValid(identifier);
    HttpResponse<String> postResponse;
    try {
        postResponse = Unirest.post("https://bibtex.chimbori.com/isbn-bibtex").field("isbn", identifier).asString();
    } catch (UnirestException e) {
        throw new FetcherException("Could not retrieve data from chimbori.com", e);
    }
    if (postResponse.getStatus() != 200) {
        throw new FetcherException("Error while retrieving data from chimbori.com: " + postResponse.getBody());
    }
    List<BibEntry> fetchedEntries;
    try {
        fetchedEntries = getParser().parseEntries(postResponse.getRawBody());
    } catch (ParseException e) {
        throw new FetcherException("An internal parser error occurred", e);
    }
    if (fetchedEntries.isEmpty()) {
        return Optional.empty();
    } else if (fetchedEntries.size() > 1) {
        LOGGER.info("Fetcher " + getName() + "found more than one result for identifier " + identifier + ". We will use the first entry.");
    }
    BibEntry entry = fetchedEntries.get(0);
    // chimbori does not return an ISBN. Thus, we add the one searched for
    entry.setField("isbn", identifier);
    doPostCleanup(entry);
    return Optional.of(entry);
}

Example 4 with FetcherException

use of org.jabref.logic.importer.FetcherException in project jabref by JabRef.

the class ArXiv method searchForEntries.

private List<ArXivEntry> searchForEntries(BibEntry entry) throws FetcherException {
    // 1. Eprint
    Optional<String> identifier = entry.getField(FieldName.EPRINT);
    if (StringUtil.isNotBlank(identifier)) {
        try {
            // Get pdf of entry with the specified id
            return OptionalUtil.toList(searchForEntryById(identifier.get()));
        } catch (FetcherException e) {
            LOGGER.warn("arXiv eprint API request failed", e);
        }
    }
    // 2. DOI and other fields
    String query;
    Optional<String> doi = entry.getField(FieldName.DOI).flatMap(DOI::parse).map(DOI::getNormalized);
    if (doi.isPresent()) {
        // Search for an entry in the ArXiv which is linked to the doi
        query = "doi:" + doi.get();
    } else {
        Optional<String> authorQuery = entry.getField(FieldName.AUTHOR).map(author -> "au:" + author);
        Optional<String> titleQuery = entry.getField(FieldName.TITLE).map(title -> "ti:" + title);
        query = OptionalUtil.toList(authorQuery, titleQuery).stream().collect(Collectors.joining("+AND+"));
    }
    Optional<ArXivEntry> arxivEntry = searchForEntry(query);
    if (arxivEntry.isPresent()) {
        // Check if entry is a match
        StringSimilarity match = new StringSimilarity();
        String arxivTitle = arxivEntry.get().title.orElse("");
        String entryTitle = entry.getField(FieldName.TITLE).orElse("");
        if (match.isSimilar(arxivTitle, entryTitle)) {
            return OptionalUtil.toList(arxivEntry);
        }
    }
    return Collections.emptyList();
}

Example 5 with FetcherException

use of org.jabref.logic.importer.FetcherException in project jabref by JabRef.

the class GoogleScholar method downloadEntry.

private BibEntry downloadEntry(String link) throws IOException, FetcherException {
    String downloadedContent = new URLDownload(link).asString();
    BibtexParser parser = new BibtexParser(importFormatPreferences);
    ParserResult result = parser.parse(new StringReader(downloadedContent));
    if ((result == null) || (result.getDatabase() == null)) {
        throw new FetcherException("Parsing entries from Google Scholar bib file failed.");
    } else {
        Collection<BibEntry> entries = result.getDatabase().getEntries();
        if (entries.size() != 1) {
            LOGGER.debug(entries.size() + " entries found! (" + link + ")");
            throw new FetcherException("Parsing entries from Google Scholar bib file failed.");
        } else {
            BibEntry entry = entries.iterator().next();
            return entry;
        }
    }
}