jats-xml/dist/utils.js

Types and utilities for working with JATS in Typescript

import { toText } from 'myst-common';
import { doi } from 'doi-utils';
import { select, selectAll } from 'unist-util-select';
import { Tags } from 'jats-tags';
import { remove } from 'unist-util-remove';
export function findArticleId(node, pubIdType = 'doi') {
    if (!node)
        return undefined;
    const id = select(`[pub-id-type=${pubIdType}]`, node);
    if (id && toText(id))
        return toText(id);
    const doiTag = selectAll(`${Tags.articleId},${Tags.pubId}`, node).find((t) => doi.validate(toText(t)));
    return toText(doiTag) || undefined;
}
export function processContributor(contrib) {
    const author = {
        name: `${toText(select(Tags.givenNames, contrib))} ${toText(select(Tags.surname, contrib))}`,
    };
    const orcid = select('[contrib-id-type=orcid]', contrib);
    if (orcid) {
        author.orcid = toText(orcid).replace(/(https?:\/\/)?orcid\.org\//, '');
    }
    const affiliationRefs = selectAll('xref[ref-type=aff]', contrib);
    const affiliationIds = affiliationRefs.map((xref) => xref.rid);
    if (affiliationIds.length > 0) {
        author.affiliations = affiliationIds;
    }
    const uri = select('uri', contrib);
    if (uri === null || uri === void 0 ? void 0 : uri['xlink:href']) {
        author.url = uri['xlink:href'];
    }
    // If there are no aff xrefs AND contrib is in a contrib group with affs AND those affs do not have IDs, add them as affiliations...
    return author;
}
/**
 * Perform standard toText, trim, remove trailing comma and semicolon
 *
 * Additionally, this returns undefined instead of empty string if node is undefined
 */
function toTextAndTrim(content) {
    const text = toText(content);
    if (!text)
        return undefined;
    return text.replace(/^[\s;,]+/, '').replace(/[\s;,]+$/, '');
}
function markForDeletion(nodes) {
    nodes.forEach((node) => {
        if (node)
            node.type = '__delete__';
    });
}
export function processAffiliation(aff) {
    var _a, _b;
    const id = aff.id;
    let ror;
    let isni;
    const rorNode = select(`institution-id[institution-id-type=ror]`, aff);
    if (rorNode) {
        ror = toTextAndTrim(rorNode);
    }
    const isniNode = select(`institution-id[institution-id-type=ISNI]`, aff);
    if (isniNode) {
        isni = toTextAndTrim(isniNode);
    }
    markForDeletion(selectAll('institution-id', aff));
    remove(aff, '__delete__');
    const institutions = selectAll('institution', aff);
    const textAddress = selectAll('addr-line > text', aff);
    const namedContent = selectAll('named-content', aff);
    const departmentNode = (_a = institutions.find((inst) => inst['content-type'] === 'dept')) !== null && _a !== void 0 ? _a : namedContent.find((content) => content['content-type'] === 'organisation-division');
    const addressNode = namedContent.find((content) => content['content-type'] === 'street');
    const cityNode = namedContent.find((content) => content['content-type'] === 'city');
    const stateNode = namedContent.find((content) => content['content-type'] === 'country-part');
    const postalCodeNode = namedContent.find((content) => content['content-type'] === 'post-code');
    const countryNode = (_b = select('country', aff)) !== null && _b !== void 0 ? _b : namedContent.find((content) => content['content-type'] === 'country');
    markForDeletion([
        ...textAddress,
        ...namedContent,
        departmentNode,
        addressNode,
        cityNode,
        stateNode,
        postalCodeNode,
        countryNode,
    ]);
    remove(aff, '__delete__');
    const affChildren = aff.children.filter((child) => child.type !== 'label');
    let institution;
    if (affChildren.filter((child) => ['text', 'institution-wrap', 'institution'].includes(child.type))
        .length === affChildren.length) {
        institution = toTextAndTrim(affChildren);
    }
    else {
        institution = toTextAndTrim(institutions.find((inst) => inst['content-type'] !== 'dept'));
    }
    const addressLines = textAddress
        .map((line) => toTextAndTrim(line))
        .filter((line) => !!line);
    let department = departmentNode
        ? toTextAndTrim(departmentNode)
        : addressLines.find((line) => line.toLowerCase().includes('department'));
    let address = addressNode
        ? toTextAndTrim(addressNode)
        : addressLines.find((line) => !line.toLowerCase().includes('department'));
    if (address && !institution) {
        institution = address;
        address = undefined;
    }
    if (department && !institution) {
        institution = department;
        department = undefined;
    }
    const city = toTextAndTrim(cityNode);
    const state = toTextAndTrim(stateNode);
    const postal_code = toTextAndTrim(postalCodeNode);
    const country = toTextAndTrim(countryNode);
    return { id, ror, isni, department, institution, address, city, state, postal_code, country };
}