myst-cli/dist/build/jats/single.js

Command line tools for MyST

import path from 'node:path';
import { tic, writeFileToFolder } from 'myst-cli-utils';
import { FRONTMATTER_ALIASES, PAGE_FRONTMATTER_KEYS } from 'myst-frontmatter';
import { writeJats } from 'myst-to-jats';
import { filterKeys } from 'simple-validators';
import { VFile } from 'vfile';
import { combineCitationRenderers } from '../../process/citations.js';
import { finalizeMdast } from '../../process/mdast.js';
import { castSession } from '../../session/cache.js';
import { logMessagesFromVFile } from '../../utils/logging.js';
import { KNOWN_IMAGE_EXTENSIONS } from '../../utils/resolveExtension.js';
import { resolveFrontmatterParts } from '../../utils/resolveFrontmatterParts.js';
import { cleanOutput } from '../utils/cleanOutput.js';
import { getFileContent } from '../utils/getFileContent.js';
/**
 * Build a MyST project as JATS XML
 *
 * @param session session with logging
 * @param opts configuration options
 */
export async function runJatsExport(session, sourceFile, exportOptions, opts) {
    const toc = tic();
    const { output, articles, sub_articles } = exportOptions;
    const { clean, projectPath, extraLinkTransformers, execute } = opts !== null && opts !== void 0 ? opts : {};
    // At this point, export options are resolved to contain one-and-only-one article
    const article = articles[0];
    if (!(article === null || article === void 0 ? void 0 : article.file))
        return { tempFolders: [] };
    if (clean)
        cleanOutput(session, output);
    const processedContents = (await getFileContent(session, [article.file, ...(sub_articles !== null && sub_articles !== void 0 ? sub_articles : [])], {
        projectPath,
        imageExtensions: KNOWN_IMAGE_EXTENSIONS,
        extraLinkTransformers,
        preFrontmatters: [
            filterKeys(article, [...PAGE_FRONTMATTER_KEYS, ...Object.keys(FRONTMATTER_ALIASES)]),
        ], // only apply to article, not sub_articles
        execute,
    })).map((content) => {
        const { kind, file, mdast, frontmatter, slug } = content;
        const rendererFiles = projectPath ? [projectPath, file] : [file];
        const citations = combineCitationRenderers(castSession(session), ...rendererFiles);
        return { mdast, kind, frontmatter, citations, slug, file };
    });
    await Promise.all(processedContents.map(({ mdast, frontmatter, file }) => {
        return finalizeMdast(session, mdast, frontmatter, file, {
            imageWriteFolder: path.join(path.dirname(output), 'files'),
            imageAltOutputFolder: 'files/',
            imageExtensions: KNOWN_IMAGE_EXTENSIONS,
            simplifyFigures: false,
        });
    }));
    const [processedArticle, ...processedSubArticles] = processedContents.map(({ frontmatter, ...contents }) => {
        const parts = resolveFrontmatterParts(session, frontmatter);
        return { frontmatter: { ...frontmatter, parts }, ...contents };
    });
    const vfile = new VFile();
    vfile.path = output;
    const jats = writeJats(vfile, processedArticle, {
        subArticles: processedSubArticles,
        writeFullArticle: true,
        format: 'pretty',
        abstractParts: [
            { part: 'abstract' },
            {
                part: [
                    'plain-language-summary',
                    'plain-language-abstract',
                    'summary',
                    'plain language summary',
                ],
                type: 'plain-language-summary',
                title: 'Plain Language Summary',
            },
            { part: 'keypoints', type: 'key-points', title: 'Key Points' },
        ],
        backSections: [
            {
                part: ['data-availability', 'data_availability', 'availability', 'data availability'],
                type: 'data-availability',
                title: 'Data Availability',
            },
        ],
        // if we want to add templating here, we have access to { ...processedArticle.frontmatter.options, ...exportOptions }
    });
    logMessagesFromVFile(session, jats);
    session.log.info(toc(`📑 Exported JATS in %s, copying to ${output}`));
    writeFileToFolder(output, jats.result);
    return { tempFolders: [] };
}