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  "Slug": "pubmed-mcp-server",
  "Name": "pubmed-mcp-server",
  "CanonicalUrl": "https://askpod.ai/mcp/pubmed-mcp-server/issues",
  "ServerUrl": "https://askpod.ai/mcp/pubmed-mcp-server",
  "IssueTotal": 16,
  "Held": 16,
  "Issues": [
    {
      "Title": "bug(fetch_fulltext): mixed-citation glues italic journal title to bold volume number",
      "Excerpt": "### Server version\n\n2.10.7\n\n### mcp-ts-core version\n\n0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nIn `pubmed_fetch_fulltext` with `includeReferences: true`, a JATS `mixed-citation` whose italic journal title is immediately followed by a bold volume number (no text node between them) renders the two glued together on both output surfaces, e.g. `Nat. Methods16, 603–606 (2019)`.\n\nRelated: #115 (same zero-separator flattening, but for…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/123",
      "PublishedAt": "2026-09-09T10:54:31.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(fetch_fulltext): unavailable reason skips over an unconfigured tier, hiding an incomplete search",
      "Excerpt": "### Server version\n\n2.10.5\n\n### mcp-ts-core version\n\n0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.x\n\n### Transport\n\nstdio\n\n### Description\n\n`pubmed_fetch_fulltext`'s `reasonFromChain` (`src/mcp-server/tools/definitions/fetch-fulltext.tool.ts`) derives an unavailable entry's top-level `reason` from the last chain entry whose `outcome` isn't `not-attempted`, skipping over any tiers the deployment never tried:\n\n```ts\nfunction reasonFromChain(chain) {\n  let lastSignal;\n  for (const t of…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/110",
      "PublishedAt": "2026-09-09T06:10:40.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(format_citations): invalid format value collapses to a generic union error, hiding accepted values",
      "Excerpt": "### Server version\n\n2.10.5\n\n### mcp-ts-core version\n\n0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.x\n\n### Transport\n\nstdio\n\n### Description\n\n`pubmed_format_citations` accepts `format` as a Zod union — a bare `CitationStyleEnum` or an array of it (`src/mcp-server/tools/definitions/format-citations.tool.ts`):\n\n```ts\nformat: z\n  .union([\n    CitationStyleEnum.describe('Single citation style. One of: apa, mla, bibtex, ris, vancouver.'),\n    z.array(CitationStyleEnum).min(1).describe(…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/109",
      "PublishedAt": "2026-09-09T06:10:20.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(spell_check): all-numeric query is coerced to a number by the XML parser and fails output validation",
      "Excerpt": "### Server version\n\n2.10.4\n\n### mcp-ts-core version\n\n^0.12.3\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.x\n\n### Transport\n\nhttp\n\n### Description\n\n`NcbiService.eSpell` (`src/services/ncbi/ncbi-service.ts`) reads `Query` / `CorrectedQuery` from `NcbiResponseHandler`'s default `xmlParser`, which is configured with `parseTagValue: true`. For an all-numeric term — a PMID pasted into the spell checker is the common case — `<Query>33306283</Query>` parses to the number `33306283` before any…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/108",
      "PublishedAt": "2026-08-22T20:48:44.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(fetch_fulltext): HTML served at Unpaywall's url_for_pdf is parsed as a PDF, so the landing-page fallback never runs",
      "Excerpt": "### Server version\n\n2.10.5 (also present at 2.10.2, when this was filed)\n\n### mcp-ts-core version\n\n0.12.7 (also present at 0.12.3, when this was filed)\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0\n\n### Transport\n\nHTTP (Streamable)\n\n### Description\n\nWhen [Unpaywall](https://unpaywall.org/) reports a `url_for_pdf` that the publisher answers with an HTML paywall or interstitial page — `200 OK`, `content-type: text/html` — `pubmed_fetch_fulltext` hands those HTML bytes to the PDF parser. The…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/104",
      "PublishedAt": "2026-08-21T22:40:54.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(find_related): all-provider failure returns an empty success",
      "Excerpt": "### Server version\n\n2.10.5\n\n### mcp-ts-core version\n\n^0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.x\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### OS\n\nmacOS 26.x\n\n### Description\n\n`pubmed_find_related` converts a complete provider outage into a successful empty result. When NCBI fails and every other eligible fallback also fails, the handler's `providerResult === null` branch returns `articles: []` with an invented `source: \"ncbi\"` and `totalCount: 0` — callers cannot distinguish…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/103",
      "PublishedAt": "2026-08-11T14:37:54.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(europepmc): title markup leaks into both output surfaces",
      "Excerpt": "### Server version\n\n2.10.2\n\n### mcp-ts-core version\n\n^0.11.0\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.14\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### OS\n\nmacOS 26.1\n\n### Description\n\nEurope PMC's `title`, `authors` (`authorString`), and `journal` (`journalTitle`) fields are passed straight through from the upstream JSON to both `structuredContent` and the Markdown `content[]` render, in `pubmed_europepmc_fetch` and `pubmed_europepmc_search` alike. `abstractText` goes through…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/102",
      "PublishedAt": "2026-08-11T14:37:49.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(find_related): Europe PMC fallback can return false-empty pages",
      "Excerpt": "### Server version\n\n2.10.5\n\n### mcp-ts-core version\n\n^0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.3.x\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### OS\n\nmacOS 26.x\n\n### Description\n\n`pubmed_find_related`'s Europe PMC fallback (`epmcProvider()` in `src/mcp-server/tools/definitions/find-related.tool.ts`) reports Europe PMC's raw `hitCount` as the tool's `totalFound`, but `EuropePmcService.citations()`/`references()` (`src/services/europe-pmc/europe-pmc-service.ts`) silently drop link…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/101",
      "PublishedAt": "2026-08-11T14:37:44.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "enhancement(lookup_citation): duplicate keys render identical headings in content[]",
      "Excerpt": "### Server version\n\n2.10.7\n\n### mcp-ts-core version\n\n0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nWhen two `pubmed_lookup_citation` inputs share a `key`, the results are correct and distinct in `structuredContent`, but the `content[]` markdown renders each under an identical `### <key>` heading, so a reader of the text surface cannot tell which result belongs to which submitted citation.\n\n### Steps to reproduce\n\n1. Call…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/128",
      "PublishedAt": "2026-09-09T12:03:59.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(fetch_fulltext): Europe PMC XML parser coerces numeric text, unlike the PMC path",
      "Excerpt": "### Server version\n\n2.10.7\n\n### mcp-ts-core version\n\n0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nThe Europe PMC full-text parser is built with `parseTagValue: true`, under a comment saying its config \"mirrors `NcbiResponseHandler.orderedXmlParser`\". The NCBI parser sets `parseTagValue: false` specifically so bibliographic tokens stay verbatim (page ranges like `4002.e26`, zero-padded pages). On the Europe PMC path,…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/127",
      "PublishedAt": "2026-09-09T12:03:57.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(fetch_fulltext): sections filter matches top-level titles only and does not say so",
      "Excerpt": "### Server version\n\n2.10.7\n\n### mcp-ts-core version\n\n0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`pubmed_fetch_fulltext`'s `sections` filter matches top-level section titles only. Its description says \"Filter to specific sections by title\" with no scope qualifier, while the sibling `maxSections` says \"Maximum top-level body sections\". A caller who names a subsection title gets zero sections and the filter-miss notice, with…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/126",
      "PublishedAt": "2026-09-09T12:03:55.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(lookup_citation): a key containing \"|\" turns a matched citation into not_found",
      "Excerpt": "### Server version\n\n2.10.7\n\n### mcp-ts-core version\n\n0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`pubmed_lookup_citation` accepts any string as a citation `key`, but the key is embedded verbatim into the pipe-delimited `bdata` line sent to NCBI ECitMatch. A key containing `|` shifts the field layout of that line, so NCBI's echoed response no longer reconciles to the submitted citation and a citation NCBI matched comes back as…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/125",
      "PublishedAt": "2026-09-09T12:03:52.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(fetch_fulltext): mixed-citation glues surname to given names inside <name>",
      "Excerpt": "### Server version\n\n2.10.7\n\n### mcp-ts-core version\n\n0.12.8\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nIn `pubmed_fetch_fulltext` with `includeReferences: true`, a JATS `mixed-citation` author written as `<name><surname>…</surname><given-names>…</given-names></name>` with no text between the two parts renders the surname glued to the initials, e.g. `NybakkenJW Marine Biology: An Ecological Approach, 4th ed.; …`.\n\nRelated: #115, #123…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/124",
      "PublishedAt": "2026-09-09T11:43:18.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(search_articles): blank queries retry as an NCBI outage",
      "Excerpt": "### Server version\n\n2.10.7\n\n### mcp-ts-core version\n\n0.12.7\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nA whitespace-only PubMed query passes validation, becomes an empty upstream term, and is retried as a service outage. The resulting recovery hint asks the caller to retry instead of correcting the query.\n\n### Steps to reproduce\n\nCall `pubmed_search_articles` with `{\"query\":\"   \",\"maxResults\":2}`.\n\n### Actual behavior\n\nWith the default…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/122",
      "PublishedAt": "2026-09-09T09:25:44.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(fetch_fulltext): add a true response-wide budget",
      "Excerpt": "Related: #81\n\n## Use case\n\nThe character controls added in #81 bound body text only, not the complete `pubmed_fetch_fulltext` response. Callers can set a small `maxCharacters` and still receive a much larger payload from the abstract, references, metadata, and additional articles.\n\nField-tested on v2.10.6 over the same DOI the original report used:\n\n```json\n{\n  \"dois\": [\"10.1093/nar/gks1195\"],\n  \"maxCharacters\": 1000,\n  \"includeReferences\": true\n}\n```\n\nThe body was correctly capped to 1,000 of…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/100",
      "PublishedAt": "2026-08-11T14:37:38.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(fetch_articles): bound large batch responses",
      "Excerpt": "## Use case\n\n`pubmed_fetch_articles` accepts up to 200 PMIDs and returns complete metadata for every resolved article, but it has no response budget or continuation signal. A normal batch can exceed an MCP client's context window before the caller has a chance to split it.\n\nConfirmed on 2.10.6 (HEAD) by reading `src/mcp-server/tools/definitions/fetch-articles.tool.ts` in full: the handler has no `maxCharacters`/budget input, no `truncated`/`nextOffset`/`remainingPmids` output, and no size…",
      "SourceUrl": "https://github.com/cyanheads/pubmed-mcp-server/issues/99",
      "PublishedAt": "2026-08-11T14:37:34.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    }
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      "16 reported issues below",
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