Examples with Reference org.ambraproject.wombat.model.Reference used on opensource projects

Example 1 with Reference

use of org.ambraproject.wombat.model.Reference in project wombat by PLOS.

the class ArticleController method getXmlContent.

/**
 * Gets article xml from cache if it exists; otherwise, gets it from rhino and caches it. Then it parses the
 * references and does html transform
 *
 * @param articlePointer
 * @param request
 * @return an XmlContent containing the list of references and article html
 * @throws IOException
 */
private XmlContent getXmlContent(Site site, ArticlePointer articlePointer, HttpServletRequest request) throws IOException {
    return corpusContentApi.readManuscript(articlePointer, site, "html", (InputStream stream) -> {
        byte[] xml = ByteStreams.toByteArray(stream);
        final Document document = parseXmlService.getDocument(new ByteArrayInputStream(xml));
        List<Reference> references = parseXmlService.parseArticleReferences(document, doi -> getLinkText(site, request, doi));
        StringWriter articleHtml = new StringWriter(XFORM_BUFFER_SIZE);
        try (OutputStream outputStream = new WriterOutputStream(articleHtml, charset)) {
            articleTransformService.transformArticle(site, articlePointer, references, new ByteArrayInputStream(xml), outputStream);
        }
        return new XmlContent(articleHtml.toString(), references);
    });
}

Example 2 with Reference

use of org.ambraproject.wombat.model.Reference in project wombat by PLOS.

the class ParseReferenceService method buildReferences.

/**
 * Builds a list of Reference objects for each <ref></ref> element
 *
 * @param refElement a <ref></ref> node which can contain (label?, (element-citation | mixed-citation | nlm-citation)+)
 * @return list of Reference objects
 */
public List<Reference> buildReferences(Element refElement, DoiToJournalLinkService linkService) throws XMLParseException, IOException {
    List<Node> citationElements = null;
    for (CitationElement elementType : CitationElement.values()) {
        NodeList nodes = refElement.getElementsByTagName(elementType.getValue());
        if (!ParseXmlUtil.isNullOrEmpty(nodes)) {
            citationElements = NodeListAdapter.wrap(nodes);
            break;
        }
    }
    List<Reference> references = new ArrayList<>();
    // a <ref></ref> element can have one or more of citation elements
    for (Node citationNode : citationElements) {
        if (citationNode.getNodeType() != Node.ELEMENT_NODE) {
            throw new XMLParseException("<element-citation>, <mixed-citation>, <nlm-citation> is not an element.");
        }
        Element element = (Element) citationNode;
        String unstructuredReference = null;
        String uri = null;
        String doi = null;
        String year = ParseXmlUtil.getElementSingleValue(element, "year");
        String volume = ParseXmlUtil.getElementSingleValue(element, "volume");
        String title = buildTitle(element);
        if (Strings.isNullOrEmpty(title)) {
            unstructuredReference = getUnstructuredCitation(element);
        }
        NodeList extLinkList = element.getElementsByTagName("ext-link");
        if (!ParseXmlUtil.isNullOrEmpty(extLinkList)) {
            Element extLink = (Element) extLinkList.item(0);
            // use the ext-link as doi, only if ext-link previous text is "doi:" or "doi"
            boolean useDoi = false;
            Node previousNode = extLink.getPreviousSibling();
            if (previousNode != null) {
                String previousText = previousNode.getTextContent();
                if (!Strings.isNullOrEmpty(previousText)) {
                    previousText = previousText.trim();
                    useDoi = previousText.equalsIgnoreCase("doi:") || previousText.equalsIgnoreCase("doi");
                }
            }
            String linkType = ParseXmlUtil.getElementAttributeValue(extLink, "ext-link-type");
            if (linkType.equals("uri")) {
                uri = ParseXmlUtil.getElementAttributeValue(extLink, "xlink:href");
                // TODO: add a validation check for the doi and add it to the meta-tags
                if (useDoi) {
                    doi = extLink.getFirstChild() == null ? null : extLink.getFirstChild().getNodeValue();
                }
            }
        }
        PageRange pages = buildPages(element);
        String fullArticleLink = null;
        if (doi != null) {
            fullArticleLink = linkService.getLink(doi);
        }
        Reference reference = Reference.build().setJournal(parseJournal(element)).setFullArticleLink(fullArticleLink).setTitle(title).setChapterTitle(buildChapterTitle(element)).setUnStructuredReference(unstructuredReference).setAuthors(parseAuthors(element)).setCollabAuthors(parseCollabAuthors(element)).setYear(parseYear(year)).setVolume(volume).setVolumeNumber(parseVolumeNumber(volume)).setIssue(ParseXmlUtil.getElementSingleValue(element, "issue")).setPublisherName(ParseXmlUtil.getElementSingleValue(element, "publisher-name")).setIsbn(ParseXmlUtil.getElementSingleValue(element, "isbn")).setUri(uri).setDoi(doi).setfPage(pages.firstPage).setlPage(pages.lastPage).build();
        references.add(reference);
    }
    return references;
}

Example 3 with Reference

use of org.ambraproject.wombat.model.Reference in project wombat by PLOS.

the class ParseXmlServiceImpl method parseArticleReferences.

/**
 * {@inheritDoc}
 */
@Override
public List<Reference> parseArticleReferences(Document doc, ParseReferenceService.DoiToJournalLinkService linkService) throws IOException {
    List<Reference> references = new ArrayList<>();
    List<Node> refListNodes = NodeListAdapter.wrap(doc.getElementsByTagName("ref-list"));
    if (ParseXmlUtil.isNullOrEmpty(refListNodes)) {
        log.info("No <ref-list> element was found in the xml.");
        return references;
    }
    for (Node refListNode : refListNodes) {
        if (refListNode.getNodeType() != Node.ELEMENT_NODE) {
            throw new XmlContentException("<ref-list> is not an element.");
        }
        Element refListElement = (Element) refListNode;
        List<Node> refNodes = NodeListAdapter.wrap(refListElement.getElementsByTagName("ref"));
        references.addAll(refNodes.stream().map(ref -> {
            try {
                return parseReferenceService.buildReferences((Element) ref, linkService);
            } catch (XMLParseException | IOException e) {
                throw new RuntimeException(e);
            }
        }).flatMap(Collection::stream).collect(Collectors.toList()));
    }
    return references;
}