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

Example 1 with PubmedArticle

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

the class MedlineImporter method importDatabase.

@Override
public ParserResult importDatabase(BufferedReader reader) throws IOException {
    Objects.requireNonNull(reader);
    List<BibEntry> bibItems = new ArrayList<>();
    try {
        JAXBContext context = JAXBContext.newInstance("org.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.fromError(e);
    }
    return new ParserResult(bibItems);
}