npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.7.9 → 2.7.11 - Mend

@cyanheads/pubmed-mcp-server 2.7.9 → 2.7.11

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (17) hide show

package/AGENTS.md +1 -1
package/CLAUDE.md +1 -1
package/README.md +2 -2
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +14 -3
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +107 -24
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +4 -4
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
package/dist/services/ncbi/api-client.d.ts.map +1 -1
package/dist/services/ncbi/api-client.js +6 -1
package/dist/services/ncbi/api-client.js.map +1 -1
package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
package/dist/services/ncbi/ncbi-service.js +11 -1
package/dist/services/ncbi/ncbi-service.js.map +1 -1
package/package.json +1 -1
package/server.json +3 -3

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.7.9
+**Version:** 2.7.11
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.7.9
+**Version:** 2.7.11
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0

package/README.md CHANGED Viewed

@@ -9,7 +9,7 @@
-[![Version](https://img.shields.io/badge/Version-2.7.9-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-2.7.11-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -78,7 +78,7 @@ Fetch full article metadata by PubMed IDs.
 Fetch full-text articles via a three-stage chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall.
-- Accepts exactly one of `pmcids` (direct PMC IDs), `pmids` (PubMed IDs, auto-resolved), or `dois` (covers preprints and EPMC-only OA records that lack PMID/PMCID)
+- Accepts exactly one of `pmcids` (direct PMC IDs), `pmids` (PubMed IDs, auto-resolved), or `dois` (auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to Europe PMC / Unpaywall)
 - NCBI PMC and Europe PMC both return structured JATS; output records origin via `viaSource: "pmc" | "europepmc" | "unpaywall"`
 - Europe PMC layer (enabled by default; disable with `EUROPEPMC_ENABLED=false`) recovers PMC-counterpart records that NCBI PMC EFetch missed, and resolves DOI input to PMC counterparts when one exists. EPMC's `fullTextXML` is PMC-keyed, so preprints (PPR), patents (PAT), and Agricola (AGR) are reachable via `pubmed_europepmc_search` for metadata but have no full text via this chain.
 - Unpaywall layer (enabled by setting `UNPAYWALL_EMAIL`) resolves DOIs to legal OA copies; extracts HTML landing pages to Markdown via Defuddle or PDFs to text via unpdf

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts CHANGED Viewed

@@ -6,9 +6,9 @@
  *   - `pmcids` — fetch directly by PMC ID. Articles not in PMC fall through to
  *     EPMC by PMC ID, then to Unpaywall when the DOI is available.
  *   - `pmids` — resolve PMID → PMCID via PMC ID Converter, then run the chain.
- *   - `dois` — skip PMC EFetch (no PMCID); resolve via EPMC search-by-DOI →
- *     fullTextXML, then Unpaywall. Covers EPMC-only OA and preprints with no
- *     PubMed presence.
+ *   - `dois` — resolve DOI → PMCID via the PMC ID Converter (mirroring `pmids`),
+ *     then run the chain. DOIs with no PMC counterpart fall through to EPMC
+ *     search-by-DOI → fullTextXML, then Unpaywall (EPMC-only OA, preprints).
  *
  * Output uses a discriminated union on `source` (`pmc` | `unpaywall`) with an
  * extra `viaSource` discriminator that records which layer produced the
@@ -18,6 +18,17 @@
  * @module src/mcp-server/tools/definitions/fetch-fulltext.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
+/**
+ * Compose the tool description for the fallback tiers enabled in this
+ * deployment. PMC EFetch is always present; Europe PMC (`EUROPEPMC_ENABLED`)
+ * and Unpaywall (`UNPAYWALL_EMAIL`) are optional, so the advertised chain must
+ * match what the server can actually deliver — otherwise the model requests
+ * recoveries that silently can't happen.
+ */
+export declare function buildFulltextDescription(tiers: {
+    europePmc: boolean;
+    unpaywall: boolean;
+}): string;
 export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     pmcids: z.ZodOptional<z.ZodArray<z.ZodString>>;
     pmids: z.ZodOptional<z.ZodArray<z.ZodString>>;

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAoR~~/D,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~cAgd5B~~,CAAC"}
1	+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqR/D;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE;IAC9C,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACpB,GAAG,MAAM,CA+BT;AAID,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA4f5B,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED Viewed

@@ -6,9 +6,9 @@
  *   - `pmcids` — fetch directly by PMC ID. Articles not in PMC fall through to
  *     EPMC by PMC ID, then to Unpaywall when the DOI is available.
  *   - `pmids` — resolve PMID → PMCID via PMC ID Converter, then run the chain.
- *   - `dois` — skip PMC EFetch (no PMCID); resolve via EPMC search-by-DOI →
- *     fullTextXML, then Unpaywall. Covers EPMC-only OA and preprints with no
- *     PubMed presence.
+ *   - `dois` — resolve DOI → PMCID via the PMC ID Converter (mirroring `pmids`),
+ *     then run the chain. DOIs with no PMC counterpart fall through to EPMC
+ *     search-by-DOI → fullTextXML, then Unpaywall (EPMC-only OA, preprints).
  *
  * Output uses a discriminated union on `source` (`pmc` | `unpaywall`) with an
  * extra `viaSource` discriminator that records which layer produced the
@@ -19,6 +19,7 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { htmlExtractor, pdfParser } from '@cyanheads/mcp-ts-core/utils';
+import { getServerConfig } from '../../../config/server-config.js';
 import { EUROPEPMC_SERVICE_ERRORS, NCBI_SERVICE_ERRORS, UNPAYWALL_SERVICE_ERRORS, } from '../../../services/error-contracts.js';
 import { getEuropePmcService, } from '../../../services/europe-pmc/europe-pmc-service.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
@@ -221,8 +222,47 @@ const UnavailableSchema = z
 })
     .describe('One identifier that could not be returned, with the full chain it traversed');
 // ─── Tool Definition ─────────────────────────────────────────────────────────
+/**
+ * Compose the tool description for the fallback tiers enabled in this
+ * deployment. PMC EFetch is always present; Europe PMC (`EUROPEPMC_ENABLED`)
+ * and Unpaywall (`UNPAYWALL_EMAIL`) are optional, so the advertised chain must
+ * match what the server can actually deliver — otherwise the model requests
+ * recoveries that silently can't happen.
+ */
+export function buildFulltextDescription(tiers) {
+    const base = 'Fetch full-text articles from PubMed Central with structured sections and references.';
+    const epmcClause = 'Europe PMC `fullTextXML` (structured JATS for records with a PMC counterpart)';
+    const unpaywallClause = 'Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text';
+    let fallback;
+    if (tiers.europePmc && tiers.unpaywall) {
+        fallback = `When PMC misses, transparently falls back to ${epmcClause}, then to ${unpaywallClause}.`;
+    }
+    else if (tiers.europePmc) {
+        fallback = `When PMC misses, transparently falls back to ${epmcClause}.`;
+    }
+    else if (tiers.unpaywall) {
+        fallback = `When PMC misses, falls back to ${unpaywallClause}.`;
+    }
+    else {
+        fallback =
+            'Full text is sourced from PubMed Central only; articles not in PMC return no full text in this configuration.';
+    }
+    const doiTail = tiers.europePmc && tiers.unpaywall
+        ? '; preprints and EPMC-only OA fall through to the Europe PMC and Unpaywall layers'
+        : tiers.europePmc
+            ? '; preprints with a PMC counterpart recover via Europe PMC'
+            : tiers.unpaywall
+                ? '; DOIs with no PMC copy recover via Unpaywall open access'
+                : '';
+    const input = `Provide exactly one of \`pmcids\` (PMC IDs directly), \`pmids\` (PubMed IDs, auto-resolved), or \`dois\` (DOIs, auto-resolved to PMC via the ID Converter${doiTail}).`;
+    return `${base} ${fallback} ${input}`;
+}
+const serverConfig = getServerConfig();
 export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
-    description: 'Fetch full-text articles from PubMed Central with structured sections and references. When PMC misses, transparently falls back to Europe PMC `fullTextXML` (structured JATS for records with a PMC counterpart), then to Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Provide exactly one of `pmcids` (PMC IDs directly), `pmids` (PubMed IDs, auto-resolved), or `dois` (preprints and EPMC-only OA records that lack PMID/PMCID).',
+    description: buildFulltextDescription({
+        europePmc: serverConfig.europepmcEnabled,
+        unpaywall: Boolean(serverConfig.unpaywallEmail),
+    }),
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-fulltext.tool.ts',
@@ -252,7 +292,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             .min(1)
             .max(10)
             .optional()
-            .describe('DOIs to resolve (e.g. ["10.21203/rs.3.rs-9010375/v1"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. Covers preprints and EPMC-only OA records that lack PMID/PMCID. Chain: Europe PMC search-by-DOI → fullTextXML → Unpaywall.'),
+            .describe('DOIs to resolve (e.g. ["10.21203/rs.3.rs-9010375/v1"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled.'),
         includeReferences: z
             .boolean()
             .default(false)
@@ -294,9 +334,10 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         // for, so we can skip them when building `unavailable[]`.
         const chainByInput = new Map();
         const recoveredIds = new Set();
-        // PMCIDs the converter resolved from a pmid → PMID, for back-mapping after
-        // the PMC and EPMC stages.
-        const pmcidToPmid = new Map();
+        // Back-map from a converter-resolved prefixed PMCID to the input id that
+        // seeded it — a PMID for `pmids` input, a DOI for `dois` input — so the PMC
+        // and EPMC stages attribute recoveries and misses to the original input id.
+        const pmcidToInputId = new Map();
         // DOI hints captured during pmids→pmcid routing so PMC-misses on the pmids
         // branch can still reach Unpaywall without re-fetching from PubMed metadata.
         const pmidContext = new Map();
@@ -319,7 +360,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 if (r.pmcid) {
                     const normalized = normalizePmcId(String(r.pmcid));
                     pmcIds.push(normalized);
-                    pmcidToPmid.set(withPmcPrefix(normalized), pmid);
+                    pmcidToInputId.set(withPmcPrefix(normalized), pmid);
                     pmidContext.set(pmid, { pmid, ...(r.doi && { doi: r.doi }) });
                 }
                 else {
@@ -348,17 +389,52 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             pmcIds = input.pmcids.map(normalizePmcId);
         }
         else if (input.dois) {
-            for (const doi of input.dois) {
-                chainByInput.set(doi, [
-                    { tier: 'pmc', outcome: 'not-attempted', detail: 'DOI input bypasses PMC EFetch' },
-                ]);
+            // Mirror the `pmids` branch: resolve DOI → PMCID via the PMC ID Converter
+            // so PMC-indexed DOIs reach PMC EFetch instead of going straight to the
+            // EPMC/Unpaywall fallback (which misses articles whose only OA copy is the
+            // PMC JATS). DOIs the converter can't place in PMC seed `doiCandidates`.
+            const requestedDois = new Set(input.dois);
+            for (const doi of input.dois)
+                chainByInput.set(doi, []);
+            const records = await getNcbiService().idConvert(input.dois, 'doi', ctx.signal ? { signal: ctx.signal } : undefined);
+            const seen = new Set();
+            for (const r of records) {
+                // The converter echoes the submitted id verbatim in `requested-id`;
+                // match on it, not `r.doi` (DOIs aren't case-stable across the API).
+                const doi = String(r['requested-id']);
+                if (!requestedDois.has(doi))
+                    continue;
+                seen.add(doi);
+                if (r.pmcid) {
+                    const normalized = normalizePmcId(String(r.pmcid));
+                    pmcIds.push(normalized);
+                    pmcidToInputId.set(withPmcPrefix(normalized), doi);
+                }
+                else {
+                    chainByInput.get(doi)?.push({
+                        tier: 'pmc',
+                        outcome: 'not-attempted',
+                        detail: 'DOI has no PMC counterpart',
+                    });
+                    doiCandidates.push({ doi });
+                }
+            }
+            for (const requested of input.dois) {
+                if (!seen.has(requested)) {
+                    chainByInput.get(requested)?.push({
+                        tier: 'pmc',
+                        outcome: 'not-attempted',
+                        detail: 'ID Converter returned no record for this DOI',
+                    });
+                    doiCandidates.push({ doi: requested });
+                }
             }
-            doiCandidates = input.dois.map((doi) => ({ doi }));
         }
         // Route PMC-missed prefixed PMCIDs into the fallback buckets so EPMC and
-        // (for pmids) Unpaywall still get a chance. For pmids input we look up the
-        // captured DOI hint via `pmidContext` to avoid an extra PubMed eFetch when
-        // available; the converter often returns the DOI alongside a PMCID match.
+        // (for pmids/dois) Unpaywall still get a chance. For pmids input we look up
+        // the captured DOI hint via `pmidContext` to avoid an extra PubMed eFetch
+        // when available; the converter often returns the DOI alongside a PMCID
+        // match. For dois input the original DOI is the fallback key directly.
         const routePmcMissesToFallback = (missingPrefixed) => {
             if (missingPrefixed.length === 0)
                 return;
@@ -367,11 +443,18 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             }
             else if (input.pmids) {
                 for (const prefixed of missingPrefixed) {
-                    const pmid = pmcidToPmid.get(prefixed);
+                    const pmid = pmcidToInputId.get(prefixed);
                     if (pmid)
                         pmidFallbackCandidates.push(pmidContext.get(pmid) ?? { pmid });
                 }
             }
+            else if (input.dois) {
+                for (const prefixed of missingPrefixed) {
+                    const doi = pmcidToInputId.get(prefixed);
+                    if (doi)
+                        doiCandidates.push({ doi });
+                }
+            }
         };
         // ── Stage 1: PMC EFetch ─────────────────────────────────────────────────
         // Wrapped so transient NCBI failures fall through to EPMC/Unpaywall rather
@@ -399,13 +482,13 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 }));
                 const returnedPmcIds = new Set(pmcArticles.map((a) => a.pmcId).filter((id) => !!id));
                 for (const prefixed of returnedPmcIds) {
-                    recoveredIds.add(pmcidToPmid.get(prefixed) ?? prefixed);
+                    recoveredIds.add(pmcidToInputId.get(prefixed) ?? prefixed);
                 }
                 const missing = pmcIds
                     .map((id) => withPmcPrefix(id))
                     .filter((id) => !returnedPmcIds.has(id));
                 for (const prefixed of missing) {
-                    const inputId = pmcidToPmid.get(prefixed) ?? prefixed;
+                    const inputId = pmcidToInputId.get(prefixed) ?? prefixed;
                     chainByInput.get(inputId)?.push({ tier: 'pmc', outcome: 'miss' });
                 }
                 routePmcMissesToFallback(missing);
@@ -418,7 +501,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 });
                 const allPrefixed = pmcIds.map(withPmcPrefix);
                 for (const prefixed of allPrefixed) {
-                    const inputId = pmcidToPmid.get(prefixed) ?? prefixed;
+                    const inputId = pmcidToInputId.get(prefixed) ?? prefixed;
                     chainByInput.get(inputId)?.push({ tier: 'pmc', outcome: 'service-error', detail });
                 }
                 routePmcMissesToFallback(allPrefixed);
@@ -456,7 +539,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 chainByInput.get(c.pmid)?.push(epmcDisabledEntry);
             for (const c of pmcidFallbackCandidates) {
                 const prefixed = withPmcPrefix(c.pmcid);
-                chainByInput.get(pmcidToPmid.get(prefixed) ?? prefixed)?.push(epmcDisabledEntry);
+                chainByInput.get(pmcidToInputId.get(prefixed) ?? prefixed)?.push(epmcDisabledEntry);
             }
             for (const c of doiCandidates)
                 chainByInput.get(c.doi)?.push(epmcDisabledEntry);
@@ -470,7 +553,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
                 chainByInput.get(pmid)?.push(epmcTierFromOutcome(outcome));
             }
             for (const [prefixed, outcome] of epmcOutcomes.pmcidOutcomes) {
-                const inputId = pmcidToPmid.get(prefixed) ?? prefixed;
+                const inputId = pmcidToInputId.get(prefixed) ?? prefixed;
                 if (outcome.kind === 'hit') {
                     recoveredIds.add(inputId);
                     continue;
@@ -495,7 +578,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         // implementation doesn't resolve PMCID → DOI for that branch.
         for (const c of pmcidFallbackCandidates) {
             const prefixed = withPmcPrefix(c.pmcid);
-            chainByInput.get(pmcidToPmid.get(prefixed) ?? prefixed)?.push({
+            chainByInput.get(pmcidToInputId.get(prefixed) ?? prefixed)?.push({
                 tier: 'unpaywall',
                 outcome: 'not-attempted',
                 detail: 'pmcids input does not resolve a DOI for Unpaywall',

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED Viewed

@@ -22,7 +22,7 @@ function authorSurnames(authors) {
         .filter((s) => s.length > 0 && s !== 'et');
 }
 export const lookupCitationTool = tool('pubmed_lookup_citation', {
-    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName); more fields = better match accuracy.`,
+    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
@@ -47,9 +47,9 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
                 .optional()
                 .describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
         })
-            .describe('Citation to match against PubMed. Must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).')
-            .refine((c) => !!(c.journal || c.year || c.volume || c.firstPage || c.authorName), {
-            message: 'Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).',
+            .describe('Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.')
+            .refine((c) => !!(c.journal || c.year), {
+            message: 'Each citation must include at least a journal or year field — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.',
         }))
             .min(1)
             .max(25)

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/ncbi/api-client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;~~IAoClB~~;;;;;OAKG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC;IA8ClB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAWlB,OAAO,CAAC,WAAW;CAcpB"}
1	+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;IAyClB;;;;;OAKG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC;IA8ClB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAWlB,OAAO,CAAC,WAAW;CAcpB"}

package/dist/services/ncbi/api-client.js CHANGED Viewed

@@ -4,7 +4,7 @@
  * retry logic lives in NcbiService.performRequest to cover both HTTP and XML-level errors.
  * @module src/services/ncbi/api-client
  */
-import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
 import { recoveryFor } from '../../services/error-contracts.js';
 import { NCBI_EUTILS_BASE_URL } from './types.js';
@@ -33,6 +33,11 @@ export class NcbiApiClient {
             if (!response.ok) {
                 throw await httpErrorFromResponse(response, {
                     service: 'NCBI',
+                    // NCBI's eutils proxy returns HTTP 500 for transient mesh-layer failures
+                    // that are safe to retry. Reclassify as ServiceUnavailable so the retry
+                    // loop in NcbiService.withRetry picks it up — 501 (Not Implemented) is
+                    // left as InternalError since those are not transient.
+                    codeOverride: (s) => (s === 500 ? JsonRpcErrorCode.ServiceUnavailable : undefined),
                     data: { endpoint },
                 });
             }

package/dist/services/ncbi/api-client.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/ncbi-service.js CHANGED Viewed

@@ -139,7 +139,7 @@ export class NcbiService {
             .map((c) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${c.key}|`)
             .join('\r');
         const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text', ...(options?.signal && { signal: options.signal }) });
-        return text
+        const parsed = text
             .split(/[\r\n]+/)
             .filter((line) => line.trim().length > 0)
             .map((line) => {
@@ -174,6 +174,16 @@ export class NcbiService {
                 ...(rawOutcome && { detail: rawOutcome }),
             };
         });
+        // ECitMatch omits lines for citations it cannot classify. Reconcile against
+        // the submitted citations so every input gets a result row — callers can rely
+        // on results.length === citations.length and correlate by key.
+        const parsedByKey = new Map(parsed.map((r) => [r.key, r]));
+        return citations.map((c) => parsedByKey.get(c.key) ?? {
+            key: c.key,
+            matched: false,
+            pmid: null,
+            status: 'not_found',
+        });
     }
     /**
      * Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.

package/dist/services/ncbi/ncbi-service.js.map CHANGED Viewed

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.7.9",
+  "version": "2.7.11",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.7.9",
+  "version": "2.7.11",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.7.9",
+      "version": "2.7.11",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.7.9",
+      "version": "2.7.11",
       "packageArguments": [
         {
           "type": "positional",