Changelog

All notable changes to this project. Each entry links to its full per-version file in changelog/.

2.11.1 — 2026-10-25

Framework update from mcp-ts-core 0.13.16 to 0.13.18: the HTTP transport no longer retains memory per request, enrichment trailer values render as code spans, the .mcpb drops repo-local and framework build-only files, and root Agent Plugins plugin.json and mcp.json ship.

2.11.0 — 2026-10-25

New pubmed_fetch_citation_metrics tool for NIH iCite metrics, sectionCap disclosure for maxSections, license metadata on PMC and Europe PMC results, Europe PMC full text gated on open access, and fixes to query encoding, Markdown escaping, and entity decoding.

2.10.23 — 2026-10-23

Markdown-safe content[] across the tools, dataBanks on pubmed_fetch_articles, fairer full-text outline budgets, and citation, spell-check, consortium-author, and Europe PMC fixes.

2.10.22 — 2026-10-12

Author name suffixes carry through records, citations, and full text; citation formatting, full-text cleanup, in-place spell-check corrections, and Europe PMC sort errors are fixed.

2.10.21 — 2026-10-09 · 🛡️ Security

pubmed_fetch_fulltext returns PMC back matter and keeps MathML structure, takes singular id keys, and fetches the first 10 of up to 50 identifiers; pubmed_format_citations notes retractions and errata; upstream fetch errors and logs name only the host.

2.10.20 — 2026-10-04

Text-fidelity fixes across full-text JATS, PubMed record, and Europe PMC parsing, with Bookshelf chapters dated by their own dates and pubmed_fetch_fulltext taking pmcids, pmids, and dois in one call.

2.10.19 — 2026-09-27

pubmed_fetch_articles returns the retraction, erratum, and comment notices NCBI links to a record, and the search tools reject blank queries, filters, and cursors and impossible or reversed date ranges instead of returning unfiltered or falsely empty results.

2.10.18 — 2026-09-22

Moves Europe PMC's request queue onto the framework pacer with retries outside it, so a backoff no longer holds a concurrency slot and an upstream Retry-After is honored; also widens the unkeyed NCBI request delay to 400ms and limits openalex_unreachable to exhausted ServiceUnavailable errors.

2.10.17 — 2026-09-22

Fixes pubmed_fetch_fulltext body parsing (alternatives figures, titled body-level blocks), word-boundary truncation with per-subsection accounting, Unpaywall title/journal/year, and case-insensitive DOI and zero-padded PMC ID matching.

2.10.16 — 2026-09-22

Normalizes a zero-padded PMID to the PMID it spells across every ID-diffing tool, and adds snake_case/synonym parameter aliases (ids, limit, max_results, citation) across the tool surface.

2.10.15 — 2026-09-22

Retries NCBI's proxy_stream() backend relays and Europe PMC's empty-envelope and outage responses instead of surfacing them as caller errors, and closes the NCBI request queue on a 429 for every caller at once.

2.10.14 — 2026-09-18 · 🛡️ Security

Adopts mcp-ts-core 0.13.4: argument rejections carry a Recovery hint, a mistyped key or JSON-stringified array is repaired before validation, and tool-argument copying is hardened against proto injection.

2.10.13 — 2026-09-13

NCBI EFetch backend-timeout envelopes now retry instead of failing as invalid input. Adopts mcp-ts-core 0.13.0: the skill tree moves to framework-skills/, and blank/placeholder env values read as unset without a per-field guard.

2.10.12 — 2026-09-11

pubmed_fetch_fulltext no longer emits LaTeX preambles or duplicate renderings for -wrapped formulas, APA citations for authorless records open on the title instead of the year, and internal NCBI response-parsing helpers are hardened against defects that were silently inert until now.

2.10.11 — 2026-09-10

pubmed_fetch_articles and pubmed_format_citations return NCBI Bookshelf chapters and books instead of reporting them unavailable, journal article locators are preserved through metadata and every citation style, and pubmed_convert_ids and pubmed_lookup_citation reject inputs that could shift NCBI's own field parsing.

2.10.10 — 2026-09-10

pubmed_fetch_fulltext renders JATS block content at its own position and returns figures and supplementary material as a structured assets[] field, pubmed_find_related's OpenAlex fallback pages to the full requested window, and the query tools reject a blank query instead of forwarding it to NCBI.

2.10.9 — 2026-09-10

pubmed_fetch_fulltext now extracts JATS tables as structured cells, finds Europe PMC references nested under at any depth, and matches a sections filter against subsection titles too; mixed-citation author names and Europe PMC's numeric-text coercion are also fixed.

2.10.8 — 2026-09-09

ECitMatch reconciliation now keys on per-request wire tokens so duplicate caller keys no longer misassign results; pubmed_fetch_fulltext folds JATS sections nested three or more levels deep into the deepest surviving subsection's text; mixed-citation references separate zero-gap adjacent pub-ids and title/volume pairs.

2.10.7 — 2026-09-09

pubmed_fetch_articles and pubmed_fetch_fulltext gain an opt-in maxResponseCharacters whole-response budget with deferred-article continuation; fetch_fulltext reports unqueriedTiers when a search skipped an unconfigured tier; format_citations names accepted format values on an invalid input.

2.10.6 — 2026-09-08

Five bug fixes: pubmed_find_related no longer returns false-empty Europe PMC pages or a fake empty success when every provider fails, Europe PMC title/author/journal markup is stripped and Markdown-escaped, an all-numeric spell_check query round-trips as text, and Unpaywall HTML is no longer parsed as a PDF. Adopts mcp-ts-core 0.12.7.

2.10.5 — 2026-09-02 · 🛡️ Security

Adopts mcp-ts-core 0.12.5: no HTTP status classifies as InternalError anymore (500/501 join the rest of 5xx as ServiceUnavailable), and an SSRF DNS-guard bypass on Bun 1.4 Linux is closed. The NCBI, OpenAlex, and Europe PMC retry loops now honor the framework's retryable:false opt-out so a 501 fails on the first attempt instead of retrying.

2.10.4 — 2026-08-21

Pins the Docker build stage to $BUILDPLATFORM so the multi-arch image publishes again — the emulated linux/amd64 leg aborted tsc.

2.10.3 — 2026-08-21

Adopts mcp-ts-core 0.12.3 and the v2 MCP SDK packages; pubmed_fetch_fulltext gains a truncated enrichment flag.

2.10.2 — 2026-07-26

Markup strip no longer eats statistical notation like P<0.001 in Europe PMC abstracts; pubmed_europepmc_fetch now resolves source: "PMC" refs for articles also indexed in PubMed; doi fields across the tool catalog disclose that casing differs by upstream.

2.10.1 — 2026-07-26

eSearch upstream failures now throw instead of masking as zero-hit searches; pubmed_search_articles surfaces ignored field tags, unmatched phrases, and dropped partial dateRange filters via notice; the summaryCount cap message points at pubmed_fetch_articles when maxed; research_plan's includeAgentPrompts is now correctly advertised as optional.

2.10.0 — 2026-07-26

New pubmed_europepmc_fetch tool (11th tool) resolves full Europe PMC records by source + epmcId; pubmed_fetch_fulltext gains maxCharacters/maxCharactersPerSection/overflowMode budget controls; a shared surrogate-pair-safe slice helper backs both.

2.9.10 — 2026-07-26

pubmed_fetch_fulltext: EPMC/PMCID query builders fixed, front-matter-only records fall through the retrieval chain instead of being dropped, pmcids input reaches Unpaywall via a resolved DOI, and Unpaywall articles carry a pmcId backlink. Dead 404-handling branches removed from the Europe PMC and OpenAlex clients.

2.9.9 — 2026-07-26

pubmed_lookup_mesh gets true upstream totalCount plus offset/nextOffset pagination; pubmed_lookup_citation stops false-flagging authors ranked 4th or later; pubmed_spell_check threads ctx.signal into ESpell. Adopts mcp-ts-core 0.11.0.

2.9.8 — 2026-06-30

pubmed_fetch_fulltext surfaces a recovery notice when a sections filter removes every body section from an article that had one — naming the requested terms and affected article ids, still returning the article; detected on both the PMC and Europe PMC paths. Adopts mcp-ts-core 0.10.10.

2.9.7 — 2026-06-20

Adopt mcp-ts-core 0.10.9: devcheck gains a Dependency Specifiers guard (floating latest/*/dist-tags) and plugin-manifest checks in lint:packaging; fresh-scaffold git guards; 14 skills re-synced; dependency refresh

2.9.6 — 2026-06-18

Output cleanups: convert_ids accepts mixed PMC/bare-digit batches; europepmc_search and fetch_articles strip leaked markup and decode entities; europepmc_search splits its silent-rejection diagnosis from its recovery hint; lookup_mesh drops non-navigable SCR tree pointers

2.9.5 — 2026-06-13

Fixes: transient NCBI eutils 500s now reclassify to ServiceUnavailable and retry; pubmed_lookup_mesh returns the canonical MeSH DescriptorUI with a new entrezUid field

2.9.4 — 2026-06-11

mcp-ts-core ^0.10.6: post-pack bundle cleaner, packaging identity checks; lint-packaging checks 8–9 synced; orchestrations skill v1.3

2.9.3 — 2026-06-11

serverInfo title corrected to machine name pubmed-mcp-server

2.9.2 — 2026-06-11

mcp-ts-core ^0.10.5: ctx.enrich.total(), z.stringbool(), server identity fields; totalCount enrichment rename; .mcpbignore anchored

2.9.1 — 2026-06-09

fix(fetch_fulltext): element-citation references now delimited; PMC page/bibliographic tokens preserved verbatim

2.9.0 — 2026-06-09

find_related: offset pagination, multi-source provider fallback (NCBI → EuropePMC → OpenAlex); europepmc_search: date-sort advisory for PPR-only results

2.8.0 — 2026-06-08

Vancouver citation style, full-text reference extraction fix, BibTeX MeSH keyword fix, empty-result notices

2.7.11 — 2026-06-04

fetch_fulltext: DOI→PMCID resolution via PMC ID Converter (#64), config-aware tool description (#65)

2.7.10 — 2026-06-04

Three ECitMatch fixes: HTTP 500 reclassified as retryable, dropped citations synthesized as not_found, citation validation requires journal or year

2.7.9 — 2026-06-02

mcp-ts-core ^0.9.16 → ^0.9.21: per-request log context fix, fetchWithTimeout secret-scrubbing, withRetry fail-fast on non-retryable errors; new scripts/release-github.ts, skill sync

2.7.8 — 2026-05-29

mcp-ts-core ^0.9.13 → ^0.9.16: result-set context (effective query, totals, applied filters, empty-result notices) moved to ctx.enrich and mirrored to structuredContent and content[] via enrichmentTrailer render/label

2.7.7 — 2026-05-28

mcp-ts-core ^0.9.10 → ^0.9.13: 413 request-body cap, auth-gated landing page default, GET /mcp keywords; landing.requireAuth: false explicit opt-out for hosted instance

2.7.6 — 2026-05-27

MCPB install fix — handle unsubstituted ${user_config.X} env values when optional fields are left blank.

2.7.5 — 2026-05-27

Framework ^0.9.6 → ^0.9.10. Plugin metadata scaffolds. Field-test fixes: tool description ↔ enum alignment, PMC ID schema validation, EuropePMC cursor round-trip.

2.7.4 — 2026-05-23

Framework ^0.9.4 → ^0.9.6. .mcpbignore recursive-match fix. Skills synced.

2.7.3 — 2026-05-22

Framework ^0.9.3 → ^0.9.4. Documents opt-in MCP_GC_PRESSURE_INTERVAL_MS for HTTP heap-growth mitigation.

2.7.2 — 2026-05-22

Framework ^0.9.1 → ^0.9.3 (zod peer-dep migration). MCPB bundle scaffolding (manifest.json + install badges). fast-xml-parser unpinned to ^5.8.0 (closes #55).

2.7.1 — 2026-05-19

pubmed_europepmc_search now surfaces silent EPMC rejections (invalid sort field, empty query) as ValidationError instead of falling through to a fake 0-hit response.

2.7.0 — 2026-05-18 · ⚠️ Breaking

New pubmed_europepmc_search tool surfaces preprints, patents, Agricola, and EPMC-only OA records. pubmed_fetch_fulltext chain expands to NCBI PMC → Europe PMC fullTextXML → Unpaywall with a dois input branch (#52).

2.6.12 — 2026-05-16

NCBI queue wait now counts toward totalDeadlineMs, so a slow upstream can't backlog tools into 10+ min latencies (#50). pubmed_find_related similar switches to cmd=neighbor to dodge NCBI's unstable scoring backend (#53).

2.6.11 — 2026-05-13

Adopts @cyanheads/mcp-ts-core 0.9.0 (Workers under nodejs_compat, instructions field, portability lint family). Pins fast-xml-parser to ~5.7.3 to avoid the 5.8.0 XMLValidator deprecation in favor of an unproven sibling package. Server now ships an instructions string.

2.6.10 — 2026-05-10

Reclassify NCBI prolog-only XML responses as transient ServiceUnavailable so the retry chain recovers, fixing intermittent pubmed_find_related (and any eLink) failures caused by upstream TXCLIENT EOFs.

2.6.9 — 2026-05-10

Service-layer error-contracts module with recoveryFor() helper; pubmed_convert_ids 400-leak rewrite; pubmed_find_related ELink <ERROR> folded into ESummary disambiguation. Adopts @cyanheads/mcp-ts-core 0.8.20.

2.6.8 — 2026-05-09

Fix server.json top-level version field missed in v2.6.7 — kept the registry stuck at 2.6.6 even though the two packages[*].version entries advanced. No code changes.

2.6.7 — 2026-05-09

Adopts @cyanheads/mcp-ts-core 0.8.6 → 0.8.19 — HTTP SSE per-request leak fix, OTel double-write fix, ctx.sessionId / ctx.auth.token. Node engine ≥24.0.0; Dockerfile pinned to oven/bun:1.3.

2.6.6 — 2026-04-29 · ⚠️ Breaking

Recovery hints on every error contract; pubmed_convert_ids input renamed idtype → idType for camelCase parity; adopts @cyanheads/mcp-ts-core v0.8.6.

2.6.5 — 2026-04-28 · ⚠️ Breaking

Typed error contracts on NCBI tools, service-layer logger metadata typed end-to-end, fuzz coverage for all 9 tools, plus DX renames on pubmed_format_citations (styles → format) and pubmed_lookup_mesh (term → query).

2.6.4 — 2026-04-26

Description audit follow-up to v2.6.3 — cross-field constraints surface in tool descriptions, and pubmed_format_citations no longer throws on zero matches.

2.6.3 — 2026-04-26

Cross-field input violations on pubmed_fetch_fulltext and pubmed_lookup_citation now classify as -32602 instead of -32603 (closes #46).

2.6.2 — 2026-04-26

Maintenance — @cyanheads/mcp-ts-core 0.7.0 → 0.7.5, fast-xml-parser 5.7.1 → 5.7.2. No runtime API changes for this server.

2.6.1 — 2026-04-24

Field-test correctness + DX pass.

2.6.0 — 2026-04-24

Closes #34 — non-PMC full-text fallback via Unpaywall.

2.5.6 — 2026-04-24

Correctness + ergonomics pass on pubmed_lookup_citation.

2.5.5 — 2026-04-24

Framework minor bump (@cyanheads/mcp-ts-core 0.6.17 → 0.7.0).

2.5.3 — 2026-04-23

Framework patch bump (@cyanheads/mcp-ts-core 0.6.8 → 0.6.10) and agent-protocol polish.

2.5.2 — 2026-04-22

Framework patch series bump (@cyanheads/mcp-ts-core 0.6.5 → 0.6.8) and documentation refresh.

2.5.1 — 2026-04-22

End-to-end cancellation.

2.5.0 — 2026-04-21

Three feature tracks land together: MCPmed-aligned semantic concept tags on every tool, an HTTP landing page with per-tool view-source links, and a framework bump to @cyanheads/mcp-ts-core 0.6.3 that exposes sourceUrl? on definitions so the…

2.4.1 — 2026-04-20

Adopts @cyanheads/mcp-ts-core 0.5.3, whose new format-parity lint rule flagged 20 tool fields that were declared in output but never rendered by format().

2.4.0 — 2026-04-20

Extends the content[]-completeness work from #26 across the rest of the tool surface.

2.3.11 — 2026-04-20

pubmed_fetch_articles format() renders all schema fields in content[] (closes #26); actionable PMID validation errors (#27); parser omits empty arrays for absent fields (#28).

2.3.10 — 2026-04-20

PMC full-text parser preserves document order via preserveOrder: true (closes #19); all-invalid-ID fetches now surface failures (closes #20).

2.3.9 — 2026-04-20

pubmed_search_articles — restores DOI/PMC IDs in brief summaries (closes #17); adds date validation, filter docs, empty-result guidance (closes #18).

2.3.8 — 2026-04-20

pubmed_fetch_fulltext PMID→PMCID resolution switched from eLink to PMC ID Converter (closes #16); @cyanheads/mcp-ts-core 0.3.7 → 0.4.1.

2.3.7 — 2026-04-20

Citation formatter fixes — APA collective-author period, RIS page expansion, BibTeX double-period; adds pub-type mapping, ISSN, PMC URL, MeSH keywords (closes #15).

2.3.6 — 2026-04-19

Maintenance — five deps updated, overrides block removed (all nine pinned transitives patched upstream), tool description strings collapsed to single-paragraph convention.

2.3.5 — 2026-04-13

XML handling — raised entity expansion ceiling, preserved diacritics, wrapped parser failures as SerializationError. Retry tightened: only transient McpError retries. fast-xml-parser ^5.5.12.

2.3.4 — 2026-04-12

HTTP 429 now classified as RateLimited and retried; default maxRetries raised 3 → 6 with 30s backoff cap and ±25% jitter.

2.3.3 — 2026-04-09

Output enrichments — pubmed_search_articles adds effectiveQuery and appliedFilters, pubmed_lookup_citation adds per-citation status, pubmed_format_citations adds partial-result counters.

2.3.2 — 2026-04-04

ESummary date parsing fix (parseNcbiDate), pubmed_fetch_fulltext now propagates eFetch errors, pubmed_search_articles uses effectiveQuery for PubMed link, pubmed_format_citations adds POST mode for large batches.

2.3.1 — 2026-04-01

Fix pubmed_search_articles ignoring empty dateRange strings — skips date clause instead of producing a malformed NCBI query (closes #14).

2.3.0 — 2026-03-31

Adds pubmed_lookup_citation (ECitMatch, batch 25) and pubmed_convert_ids (DOI/PMID/PMCID via PMC ID Converter, batch 50). Refactored retry logic and HTTP error classification in NcbiApiClient.

2.2.6 — 2026-03-30

Skill updates — add-tool v1.1 expands format() template and adds Tool Response Design section; add-resource and design-mcp-server gain coverage guidance and tools-first patterns. Bumps mcp-ts-core ^0.2.10, biome ^2.4.10.

2.2.5 — 2026-03-28

Maintenance — @cyanheads/mcp-ts-core bumped to ^0.2.8. No runtime API changes.

2.2.4 — 2026-03-28

Format output enriched — pubmed_fetch_articles gains affiliations, MeSH/grants; pubmed_fetch_fulltext gains authors, journal, references. Deps: mcp-ts-core →0.2.3, biome →2.4.9.

2.2.3 — 2026-03-24

Retry logic moved to NcbiService.performRequest to cover XML-level NCBI errors; backoff changed to 1s base; HTML rate-limit responses now throw ServiceUnavailable. 8 new retry integration tests.

2.2.2 — 2026-03-24

Format improvements for fetch-articles, fetch-fulltext, and find-related; NCBI raw exception traces replaced with user-friendly messages; @cyanheads/mcp-ts-core 0.1.29.

2.2.1 — 2026-03-23

Fix: adds missing mcpName field to package.json required by the MCP registry for publishing.

2.2.0 — 2026-03-23

The server was migrated to use the @cyanheads/mcp-ts-core framework for MCP plumbing.

2.1.6 — 2026-03-09

Fix: structuredContent removed from error responses (valid for success only); fast-check → 4.6.0, jose → 6.2.1.

2.1.5 — 2026-03-06

NCBI config now logged at startup (API key status, delay, retries, timeout). Dep bumps: @biomejs/biome 2.4.6, jose 6.2.0, @types/node 25.3.5.

2.1.4 — 2026-03-04

pubmed_fetch gains affiliations and articleDates fields; public hosted endpoint added to README; new output-schema coverage tests prevent strict-client rejections.

2.1.3 — 2026-03-04

Fix: OpenTelemetry NodeSDK now initializes on Bun — isBun guard removed, manual spans, custom metrics, and OTLP export all work correctly.

2.1.2 — 2026-03-04

pmc_fetch renamed to pubmed_pmc_fetch; log directory path resolution switched to node:path for cross-platform correctness (#9).

2.1.1 — 2026-03-04

Bug fixes across response handler, PMC/article parsers, and citation formatter — plus comprehensive test coverage for NCBI service and parser edge cases.

2.1.0 — 2026-03-04

Adds pubmed_pmc_fetch tool — fetch full-text articles from PubMed Central via NCBI EFetch, with a JATS XML parser returning structured body sections, metadata, and references.

2.0.1 — 2026-03-04

pubmed_search gains field filters, offset pagination, and PMC URLs; pubmed_mesh_lookup exact-heading sort; pubmed_trending removed; six tool and config defaults revised.

2.0.0 — 2026-03-04

Initial release — 7 PubMed tools, NCBI E-utilities service layer (eSearch/eSummary/eFetch/eLink/eSpell/eInfo with rate-limit + retry), research_plan prompt, and pubmed://database/info resource.