Examples with Doi org.ambraproject.rhino.identity.Doi used on opensource projects

Example 6 with Doi

use of org.ambraproject.rhino.identity.Doi in project rhino by PLOS.

the class CommentCrudServiceImpl method createComment.

@Override
public ServiceResponse<CommentOutputView> createComment(Optional<ArticleIdentifier> articleId, CommentInputView input) {
    final Optional<String> parentCommentUri = Optional.ofNullable(input.getParentCommentId());
    final Article article;
    final Comment parentComment;
    if (parentCommentUri.isPresent()) {
        parentComment = readComment(CommentIdentifier.create(parentCommentUri.get()));
        if (parentComment == null) {
            throw new RestClientException("Parent comment not found: " + parentCommentUri, HttpStatus.BAD_REQUEST);
        }
        article = parentComment.getArticle();
        ArticleIdentifier articleDoiFromDb = ArticleIdentifier.create(parentComment.getArticle().getDoi());
        if (!articleId.isPresent()) {
            articleId = Optional.of(articleDoiFromDb);
        } else if (!articleId.get().equals(articleDoiFromDb)) {
            String message = String.format("Parent comment (%s) not from declared article (%s).", parentCommentUri.get(), articleId.get());
            throw new RestClientException(message, HttpStatus.BAD_REQUEST);
        }
    } else {
        // The comment is a root-level reply to an article (no parent comment).
        if (!articleId.isPresent()) {
            throw new RestClientException("Must provide articleId or parentCommentUri", HttpStatus.BAD_REQUEST);
        }
        article = articleCrudService.readArticle(articleId.get());
        parentComment = null;
    }
    // comment receives same DOI prefix as article
    String doiPrefix = extractDoiPrefix(articleId.get());
    // generate a new DOI out of a random UUID
    UUID uuid = UUID.randomUUID();
    Doi createdCommentUri = Doi.create(doiPrefix + "annotation/" + uuid);
    Comment created = new Comment();
    created.setArticle(article);
    created.setParent(parentComment);
    created.setCommentUri(createdCommentUri.getName());
    created.setUserProfileID(Long.valueOf(Strings.nullToEmpty(input.getCreatorUserId())));
    created.setTitle(Strings.nullToEmpty(input.getTitle()));
    created.setBody(Strings.nullToEmpty(input.getBody()));
    created.setHighlightedText(Strings.nullToEmpty(input.getHighlightedText()));
    created.setCompetingInterestBody(Strings.nullToEmpty(input.getCompetingInterestStatement()));
    created.setIsRemoved(Boolean.valueOf(Strings.nullToEmpty(input.getIsRemoved())));
    hibernateTemplate.save(created);
    // the new comment can't have any children yet
    List<Comment> childComments = ImmutableList.of();
    CompetingInterestPolicy competingInterestPolicy = new CompetingInterestPolicy(runtimeConfiguration);
    CommentOutputView.Factory viewFactory = new CommentOutputView.Factory(competingInterestPolicy, childComments, article);
    CommentOutputView view = viewFactory.buildView(created);
    return ServiceResponse.reportCreated(view);
}

Example 7 with Doi

use of org.ambraproject.rhino.identity.Doi in project rhino by PLOS.

the class ArticleCrudServiceImpl method getLatestRevision.

@Override
public Optional<ArticleRevision> getLatestRevision(Article article) {
    Integer maxRevisionNumber = hibernateTemplate.execute(session -> {
        Query query = session.createQuery("" + "SELECT MAX(rev.revisionNumber) " + "FROM ArticleRevision rev, ArticleItem item " + "WHERE item.doi = :doi " + "  AND rev.ingestion = item.ingestion");
        query.setParameter("doi", Doi.create(article.getDoi()).getName());
        return (Integer) query.uniqueResult();
    });
    if (maxRevisionNumber == null)
        return Optional.empty();
    return Optional.ofNullable(hibernateTemplate.execute(session -> {
        Query query = session.createQuery("" + "FROM ArticleRevision as av " + "WHERE av.ingestion.article = :article " + "AND av.revisionNumber = :latestRevision");
        query.setParameter("article", article);
        query.setParameter("latestRevision", maxRevisionNumber);
        return (ArticleRevision) query.uniqueResult();
    }));
}

Example 8 with Doi

use of org.ambraproject.rhino.identity.Doi in project rhino by PLOS.

the class ArticleXml method disambiguateAssetNodes.

/**
   * @param assetNodesMetadata metadata for at least two asset nodes with the same DOI and unequal content
   * @return the metadata with the most non-empty fields
   * @throws XmlContentException if two or more asset nodes have non-empty, inconsistent title or description
   */
@VisibleForTesting
static AssetMetadata disambiguateAssetNodes(Collection<AssetMetadata> assetNodesMetadata) {
    // Find the node with the most substantial content
    AssetMetadata bestNode = assetNodesMetadata.stream().min(ASSET_NODE_PREFERENCE).orElseThrow(() -> new IllegalArgumentException("Argument list must not be empty"));
    // If any other nodes have non-empty fields that are inconsistent with bestNode, complain about ambiguity
    Collection<AssetMetadata> ambiguous = assetNodesMetadata.stream().filter(node -> {
        String title = node.getTitle();
        boolean ambiguousTitle = !title.isEmpty() && !title.equals(bestNode.getTitle());
        String description = node.getDescription();
        boolean ambiguousDescription = !description.isEmpty() && !description.equals(bestNode.getDescription());
        return ambiguousTitle || ambiguousDescription;
    }).collect(Collectors.toList());
    if (!ambiguous.isEmpty()) {
        throw new XmlContentException(String.format("Ambiguous asset nodes: %s, %s", bestNode, ambiguous));
    }
    return bestNode;
}

Example 9 with Doi

use of org.ambraproject.rhino.identity.Doi in project rhino by PLOS.

the class ArticlePackageBuilder method findAssetType.

private static AssetType findAssetType(AssetNodesByDoi assetNodeMap, ManifestXml.Asset asset) {
    if (asset.getAssetTagName().equals(ManifestXml.AssetTagName.ARTICLE)) {
        return AssetType.ARTICLE;
    }
    Doi assetIdentity = Doi.create(asset.getUri());
    if (!assetNodeMap.getDois().contains(assetIdentity)) {
        if (asset.isStrikingImage()) {
            return AssetType.STANDALONE_STRIKING_IMAGE;
        } else {
            throw new RestClientException("Asset not mentioned in manuscript: " + asset.getUri(), HttpStatus.BAD_REQUEST);
        }
    }
    List<Node> nodes = assetNodeMap.getNodes(assetIdentity);
    AssetType identifiedType = null;
    for (Node node : nodes) {
        String nodeName = node.getNodeName();
        AssetType assetType = getByXmlNodeName(nodeName);
        if (assetType != null) {
            if (identifiedType == null) {
                identifiedType = assetType;
            } else if (!identifiedType.equals(assetType)) {
                String message = String.format("Ambiguous nodes: %s, %s", identifiedType, assetType);
                throw new RestClientException(message, HttpStatus.BAD_REQUEST);
            }
        }
    }
    if (identifiedType == null) {
        throw new RestClientException("Type not recognized", HttpStatus.BAD_REQUEST);
    }
    return identifiedType;
}

Example 10 with Doi

use of org.ambraproject.rhino.identity.Doi in project rhino by PLOS.

the class ArticleXml method findAllAssetNodes.

/**
   * Find each node within this object's XML whose name is expected to be associated with an asset entity.
   *
   * @return the list of asset nodes
   */
public AssetNodesByDoi findAllAssetNodes() {
    // Find all nodes of an asset type and map them by DOI
    List<Node> rawNodes = readNodeList(ASSET_EXPRESSION);
    ListMultimap<Doi, Node> nodeMap = LinkedListMultimap.create(rawNodes.size());
    for (Node node : rawNodes) {
        Doi assetDoi = getAssetDoi(node);
        if (assetDoi != null) {
            nodeMap.put(assetDoi, node);
        } else {
            findNestedDoi(node, nodeMap);
        }
    }
    // Replace <graphic> nodes without changing keys or iteration order
    for (Map.Entry<Doi, Node> entry : nodeMap.entries()) {
        Node node = entry.getValue();
        if (node.getNodeName().equals(GRAPHIC)) {
            entry.setValue(replaceGraphicNode(node));
        }
    }
    return new AssetNodesByDoi(nodeMap);
}