jackwener/OpenCLI · error · CommandExecutionError

pubmed article response did not include a PMID

Error message

pubmed article response did not include a PMID

What it means

parseArticleXml extracts the PMID from the EFetch XML response and throws 'pubmed article response did not include a PMID' when no <PMID> element can be found, even though the body looked like a PubmedArticle. The library throws this because without the returned PMID it cannot verify the response corresponds to the requested article.

Source

Thrown at clis/pubmed/utils.js:275

        }
        terms.push(`${from}:${to}[PDAT]`);
    }
    if (filters.articleType) terms.push(`${requireText(filters.articleType, 'article-type')}[PT]`);
    if (filters.hasAbstract) terms.push('hasabstract[text]');
    if (filters.hasFullText) terms.push('free full text[sb]');
    if (filters.humanOnly) terms.push('humans[mesh]');
    if (filters.englishOnly) terms.push('english[lang]');
    return terms.join(' AND ');
}

export function parseArticleXml(xml, pmid) {
    const text = String(xml ?? '');
    if (!text || /<ERROR\b/i.test(text) || !/<PubmedArticle\b/i.test(text)) {
        return null;
    }
    const returnedPmid = extractFirst(text, 'PMID');
    if (!returnedPmid) {
        throw new CommandExecutionError('pubmed article response did not include a PMID', 'PubMed EFetch response shape may have changed.');
    }
    if (returnedPmid !== pmid) {
        throw new CommandExecutionError(`pubmed article response PMID ${returnedPmid} did not match requested PMID ${pmid}`, 'Refusing to return metadata for a different article.');
    }
    const articleBlock = text.match(/<Article\b[^>]*>([\s\S]*?)<\/Article>/i)?.[1] || text;
    const journalBlock = articleBlock.match(/<Journal\b[^>]*>([\s\S]*?)<\/Journal>/i)?.[1] || '';
    const journalIssue = journalBlock.match(/<JournalIssue\b[^>]*>([\s\S]*?)<\/JournalIssue>/i)?.[1] || '';
    const pubDate = journalIssue.match(/<PubDate\b[^>]*>([\s\S]*?)<\/PubDate>/i)?.[1] || '';
    const authorBlocks = [...text.matchAll(/<Author\b[^>]*>([\s\S]*?)<\/Author>/gi)].map(match => match[1]);
    const authors = authorBlocks.map(block => {
        const name = extractFirst(block, 'CollectiveName') || [extractFirst(block, 'LastName'), extractFirst(block, 'ForeName') || extractFirst(block, 'Initials')].filter(Boolean).join(' ');
        return name;
    }).filter(Boolean);
    const abstract = extractAll(articleBlock, 'AbstractText').join(' ');
    const pubTypes = extractAll(articleBlock, 'PublicationType');
    const meshTerms = extractAll(text, 'DescriptorName');
    const keywords = extractAll(text, 'Keyword');
    const affiliations = extractAll(text, 'Affiliation');

View on GitHub (pinned to 49907e53dc)

Solutions

1. Retry the request — a transient truncation can drop elements
2. Inspect the raw XML to confirm whether <PMID> is genuinely absent
3. Check for NCBI DTD/schema updates and update the parser if tags changed
4. Fall back to fetching metadata from the PubMed web page instead of EFetch

// Pre-flight: confirm the article exists before parsing
const res = await fetch(`https://pubmed.ncbi.nlm.nih.gov/${pmid}/`);
if (!res.ok) throw new Error(`PMID ${pmid} not found on PubMed`);

function hasPmidElement(xmlText) {
  return /<PMID\b[^>]*>[^<]+<\/PMID>/i.test(String(xmlText));
}

try {
  const meta = await article(pmid);
} catch (e) {
  if (/did not include a PMID/.test(e.message)) {
    console.error('EFetch XML had no <PMID>; inspect raw response:', e.detail);
  }
  throw e;
}

When it happens

Trigger: Calling the article command when NCBI's EFetch returns a PubmedArticle-shaped document with no <PMID> tag inside — typically due to an NCBI response format change, a heavily truncated/garbled XML body, or XML where the PMID tag is namespaced/renamed.

Common situations: NCBI schema updates altering tag placement; proxies mangling XML; NCBI returning an unusual article encoding (e.g. PMC-sourced records without PMID).

Related errors

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AI-assisted analysis of jackwener/OpenCLI@49907e53dc (2026-08-29). Data as JSON: /api/errors/bfbef0889b9e01dc. Report an issue: GitHub.