jackwener/OpenCLI · error · EmptyResultError

pubmed article

Error message

pubmed article

What it means

EmptyResultError('pubmed article') thrown at clis/pubmed/article.js:28 when eutilsFetch('efetch') succeeded but parseArticleXml returned null/undefined for the requested PMID. The CLI treats this as 'no data' rather than a crash: the XML came back but contained no parseable article matching the PMID.

Source

Thrown at clis/pubmed/article.js:28

    description: 'Get detailed information for a PubMed article by PMID',
    domain: 'pubmed.ncbi.nlm.nih.gov',
    strategy: Strategy.PUBLIC,
    browser: false,
    defaultFormat: 'plain',
    args: [
        { name: 'pmid', positional: true, required: true, help: 'PubMed ID, e.g. 37780221' },
        { name: 'full-abstract', type: 'boolean', default: false, help: 'Do not truncate the abstract in table output' },
    ],
    columns: ['pmid', 'title', 'authors', 'journal', 'year', 'date', 'article_type', 'language', 'doi', 'pmc', 'affiliations', 'grants', 'mesh_terms', 'keywords', 'abstract', 'url'],
    func: async (args) => {
        const pmid = requirePmid(args.pmid);
        const xml = await eutilsFetch('efetch', {
            id: pmid,
            rettype: 'abstract',
        }, { retmode: 'xml', label: 'pubmed article' });
        const article = parseArticleXml(xml, pmid);
        if (!article) {
            throw new EmptyResultError('pubmed article', `No article found for PMID ${pmid}.`);
        }
        if (!article.title) {
            throw new CommandExecutionError(`pubmed article ${pmid} did not include a title`, 'PubMed EFetch response shape may have changed.');
        }
        const abstract = args['full-abstract'] ? article.abstract : truncateText(article.abstract, 500);
        return [
            {
                pmid: article.pmid,
                title: article.title,
                authors: article.authors.join(', '),
                journal: article.journal,
                year: article.year,
                date: article.date || null,
                article_type: article.article_type,
                language: article.language || null,
                doi: article.doi || null,
                pmc: article.pmc || null,
                affiliations: article.affiliations || null,

View on GitHub (pinned to 49907e53dc)

Solutions

1. Verify the PMID exists by opening https://pubmed.ncbi.nlm.nih.gov/<pmid>/ in a browser
2. Check the raw EFetch response (add debug logging on xml) to see if NCBI returned an error or empty document
3. If you have a DOI or other id, resolve it to a PMID first via esearch before calling efetch
4. Validate the PMID input (digits only) before calling the command
5. Retry later if NCBI is having a transient issue; confirm status at the NCBI status page

Example fix

// before
const article = parseArticleXml(xml, pmid);
if (!article) {
    throw new EmptyResultError('pubmed article', `No article found for PMID ${pmid}.`);
}
// after
if (!/^\d+$/.test(pmid)) {
    throw new ArgumentError(`"${pmid}" is not a valid PMID (expected numeric id)`);
}
const article = parseArticleXml(xml, pmid);
if (!article) {
    throw new EmptyResultError('pubmed article', `No article found for PMID ${pmid}.`);
}

// validate the PMID before calling the command
if (!/^\d{1,9}$/.test(pmid)) {
  throw new Error(`"${pmid}" is not a numeric PMID`);
}

try {
  const article = await runCli('pubmed article', { pmid });
} catch (e) {
  if (e instanceof EmptyResultError || /No article found/.test(e.message)) {
    console.warn(`PMID ${pmid} not found in PubMed — verify the id.`);
    return null;
  }
  throw e;
}

When it happens

Trigger: parseArticleXml(xml, pmid) returns falsy because: (a) the PMID does not exist or was withdrawn/removed from PubMed, (b) EFetch returned an error XML (e.g. <eFetchResult> with no <PubmedArticle>) for an invalid id, (c) the rettype 'abstract' XML has a shape parseArticleXml does not recognize.

Common situations: Passing a DOI instead of a PMID; a typo'd or stale PMID from an old reference list; querying a book/in-process record whose XML differs; NCBI returns an error document for an id that was suppressed.

Related errors

• pubmed author
• pubmed citations
• pubmed clinical-trial
• No cruise departure port matching "${port}" (try a listed se
• devto/${id}

AI-assisted analysis of jackwener/OpenCLI@49907e53dc (2026-08-29). Data as JSON: /api/errors/ee7e0546e73f7f2d. Report an issue: GitHub.