Examples with ArticleIngestion org.ambraproject.rhino.model.ArticleIngestion used on opensource projects

Example 11 with ArticleIngestion

use of org.ambraproject.rhino.model.ArticleIngestion in project rhino by PLOS.

the class ArticleCrudServiceImpl method buildOverview.

@Override
public ArticleOverview buildOverview(Article article) {
    return hibernateTemplate.execute(session -> {
        Query ingestionQuery = session.createQuery("FROM ArticleIngestion WHERE article = :article");
        ingestionQuery.setParameter("article", article);
        List<ArticleIngestion> ingestions = ingestionQuery.list();
        Query revisionQuery = session.createQuery("" + "FROM ArticleRevision WHERE ingestion IN " + "  (FROM ArticleIngestion WHERE article = :article)");
        revisionQuery.setParameter("article", article);
        List<ArticleRevision> revisions = revisionQuery.list();
        ArticleIdentifier id = ArticleIdentifier.create(article.getDoi());
        return ArticleOverview.build(id, ingestions, revisions);
    });
}

Example 12 with ArticleIngestion

use of org.ambraproject.rhino.model.ArticleIngestion in project rhino by PLOS.

the class IngestionServiceTest method createStubArticleItem.

private static ArticleItem createStubArticleItem() {
    ArticleItem articleItem = new ArticleItem();
    ArticleIngestion articleIngestion = new ArticleIngestion();
    Article article = new Article();
    article.setDoi("test");
    articleItem.setIngestion(articleIngestion);
    articleIngestion.setArticle(article);
    return articleItem;
}

Example 13 with ArticleIngestion

use of org.ambraproject.rhino.model.ArticleIngestion in project rhino by PLOS.

the class TaxonomyClassificationServiceImpl method getRawTerms.

/**
   * @inheritDoc
   */
@Override
public List<String> getRawTerms(Document articleXml, Article article, boolean isTextRequired) {
    RuntimeConfiguration.TaxonomyConfiguration configuration = getTaxonomyConfiguration();
    String toCategorize = getCategorizationContent(articleXml);
    ArticleIngestion latest = articleCrudService.readLatestRevision(article).getIngestion();
    String header = String.format(MESSAGE_HEADER, new SimpleDateFormat("yyyy-MM-dd").format(latest.getPublicationDate()), latest.getJournal().getTitle(), latest.getArticleType(), article.getDoi());
    String aiMessage = String.format(MESSAGE_BEGIN, configuration.getThesaurus()) + StringEscapeUtils.escapeXml10(String.format(MESSAGE_DOC_ELEMENT, header, toCategorize)) + MESSAGE_END;
    HttpPost post = new HttpPost(configuration.getServer().toString());
    post.setEntity(new StringEntity(aiMessage, APPLICATION_XML_UTF_8));
    DocumentBuilder documentBuilder = newDocumentBuilder();
    Document response;
    try (CloseableHttpResponse httpResponse = httpClient.execute(post);
        InputStream stream = httpResponse.getEntity().getContent()) {
        response = documentBuilder.parse(stream);
    } catch (IOException e) {
        throw new TaxonomyRemoteServiceNotAvailableException(e);
    } catch (SAXException e) {
        throw new TaxonomyRemoteServiceInvalidBehaviorException("Invalid XML returned from " + configuration.getServer(), e);
    }
    //parse result
    NodeList vectorElements = response.getElementsByTagName("VectorElement");
    List<String> results = new ArrayList<>(vectorElements.getLength());
    // Add the text that is sent to taxonomy server if isTextRequired is true
    if (isTextRequired) {
        toCategorize = StringEscapeUtils.unescapeXml(toCategorize);
        results.add(toCategorize);
    }
    //The first and last elements of the vector response are just MAITERMS
    for (int i = 1; i < vectorElements.getLength() - 1; i++) {
        results.add(vectorElements.item(i).getTextContent());
    }
    if ((isTextRequired && results.size() == 1) || results.isEmpty()) {
        log.error("Taxonomy server returned 0 terms. " + article.getDoi());
    }
    return results;
}

Example 14 with ArticleIngestion

use of org.ambraproject.rhino.model.ArticleIngestion in project rhino by PLOS.

the class IssueOutputView method getIssueImageFigureDoi.

private static String getIssueImageFigureDoi(ArticleCrudService articleCrudService, Article imageArticle) {
    ArticleRevision latestArticleRevision = articleCrudService.getLatestRevision(imageArticle).orElseThrow(() -> new RuntimeException("Image article has no published revisions. " + imageArticle.getDoi()));
    ArticleIngestion ingestion = latestArticleRevision.getIngestion();
    Collection<ArticleItem> allArticleItems = articleCrudService.getAllArticleItems(ingestion);
    List<ArticleItem> figureImageItems = allArticleItems.stream().filter(item -> FIGURE_IMAGE_TYPES.contains(item.getItemType())).collect(Collectors.toList());
    if (figureImageItems.size() != 1) {
        throw new RuntimeException("Image article does not contain exactly one image file. " + imageArticle.getDoi());
    }
    return figureImageItems.get(0).getDoi();
}

Example 15 with ArticleIngestion

use of org.ambraproject.rhino.model.ArticleIngestion in project rhino by PLOS.

the class TaxonomyClassificationServiceImpl method populateCategories.

/**
   * {@inheritDoc}
   */
@Override
public void populateCategories(ArticleRevision revision) {
    ArticleIngestion ingestion = revision.getIngestion();
    Article article = ingestion.getArticle();
    Document xml = articleCrudService.getManuscriptXml(ingestion);
    List<WeightedTerm> terms;
    String doi = article.getDoi();
    //todo: fix or remove this when we find a home for article types
    boolean isAmendment = false;
    if (!isAmendment) {
        terms = classifyArticle(article, xml);
        if (terms != null && terms.size() > 0) {
            List<WeightedTerm> leafNodes = getDistinctLeafNodes(CATEGORY_COUNT, terms);
            persistCategories(leafNodes, article);
        } else {
            log.error("Taxonomy server returned 0 terms. Cannot populate Categories. " + doi);
        }
    }
}