@cyanheads/pubmed-mcp-server 2.6.12 → 2.7.0

package/dist/services/europe-pmc/types.d.ts

@@ -0,0 +1,123 @@
+/**
+ * @fileoverview Types for the Europe PMC REST API. Covers the search response
+ * shape and the fullTextXML endpoint contract.
+ *
+ * See https://europepmc.org/RestfulWebService for the full API. We use only
+ * the search endpoint (`/webservices/rest/search`) and the fullText endpoint
+ * (`/webservices/rest/{id}/fullTextXML`).
+ *
+ * @module src/services/europe-pmc/types
+ */
+/** Base URL for Europe PMC's RESTful web service. */
+export declare const EUROPEPMC_API_BASE = "https://www.ebi.ac.uk/europepmc/webservices/rest";
+/**
+ * Europe PMC source taxonomy. Determines which corpus a record belongs to and
+ * what identifier scheme applies. PubMed-derived records carry a `pmid`; PMC
+ * preprints carry an EPMC id (`source: PPR`) but no PMID; patents and Agricola
+ * records may carry neither.
+ */
+export type EuropePmcSource = 'MED' | 'PMC' | 'PPR' | 'PAT' | 'AGR' | 'CTX' | 'CBA' | 'ETH' | 'HIR';
+/** Allowed sources for `pubmed_europepmc_search` input. */
+export declare const EUROPEPMC_DEFAULT_SOURCES: readonly ["MED", "PMC", "PPR"];
+export declare const EUROPEPMC_ALL_SOURCES: readonly ["MED", "PMC", "PPR", "PAT", "AGR"];
+/**
+ * Single record from a Europe PMC search response. Only fields the server
+ * actually consumes are typed; the upstream payload carries many more under
+ * `resultType=core`. Field optionality reflects EPMC's real-world sparsity —
+ * preprints often lack `journalTitle`; patents lack `authorString`.
+ */
+export interface EuropePmcSearchHit {
+    abstractText?: string;
+    authorString?: string;
+    bookOrReportDetails?: unknown;
+    citedByCount?: number;
+    doi?: string;
+    /** ISO date (YYYY-MM-DD) of first index in EPMC. */
+    firstIndexDate?: string;
+    /** ISO date (YYYY-MM-DD) of publication where known. */
+    firstPublicationDate?: string;
+    hasBook?: 'Y' | 'N';
+    hasPDF?: 'Y' | 'N';
+    /** "Y"/"N" — whether EPMC believes a full-text XML is available for this record. */
+    hasTextMinedTerms?: 'Y' | 'N';
+    /** EPMC's own record identifier — unique within `source`. Always present. */
+    id: string;
+    inEPMC?: 'Y' | 'N';
+    inPMC?: 'Y' | 'N';
+    isOpenAccess?: 'Y' | 'N';
+    issue?: string;
+    journalTitle?: string;
+    journalVolume?: string;
+    /** Some hits carry their own license. Free-form per EPMC. */
+    license?: string;
+    pageInfo?: string;
+    pmcid?: string;
+    pmid?: string;
+    pubYear?: string;
+    source: EuropePmcSource;
+    title?: string;
+    [extra: string]: unknown;
+}
+/** Wrapper for the `resultList` block in a search response. */
+export interface EuropePmcResultList {
+    result?: EuropePmcSearchHit[] | EuropePmcSearchHit;
+}
+/**
+ * Top-level shape of a Europe PMC JSON search response. EPMC returns scalar
+ * `result` when there's exactly one hit; `request.queryString` echoes the
+ * effective query so callers can preview what EPMC actually searched.
+ */
+export interface EuropePmcSearchResponse {
+    /** Total matching records across all pages. */
+    hitCount?: number;
+    /** Cursor token for the next page; absent on the final page. */
+    nextCursorMark?: string;
+    /** Cursor used for this response, echoed back from the request. */
+    request?: {
+        queryString?: string;
+        resultType?: string;
+        cursorMark?: string;
+        pageSize?: number;
+        sort?: string;
+        [extra: string]: unknown;
+    };
+    resultList?: EuropePmcResultList;
+    version?: string;
+    [extra: string]: unknown;
+}
+/** Normalized search result returned by the service layer. */
+export interface EuropePmcSearchResult {
+    /** Cursor used for this response. Returned as-is so callers can echo it. */
+    cursorMark?: string;
+    hitCount: number;
+    hits: EuropePmcSearchHit[];
+    /** Cursor for the next page. `undefined` when no more pages remain. */
+    nextCursorMark?: string;
+    query: string;
+}
+/** Parameters accepted by the EPMC search endpoint. */
+export interface EuropePmcSearchParams {
+    /** EPMC's cursor pagination token; start with `*` for the first page. */
+    cursorMark?: string;
+    /** Max 100 (per EPMC docs). */
+    pageSize?: number;
+    query: string;
+    /** Default `core` — richest payload with abstract, IDs, dates, license. */
+    resultType?: 'core' | 'lite' | 'idlist';
+    signal?: AbortSignal;
+    /** Optional sort spec, e.g. `FIRST_PIDATE desc`. */
+    sort?: string;
+    /** Allowed sources, comma-joined into the query as `(SRC:"MED" OR ...)`. */
+    sources?: readonly EuropePmcSource[];
+}
+/** Outcome of a fullTextXML lookup. */
+export type EuropePmcFullTextResult = {
+    kind: 'found';
+    xml: string;
+    epmcId: string;
+    source: EuropePmcSource;
+} | {
+    kind: 'not-available';
+    reason: string;
+};
+//# sourceMappingURL=types.d.ts.map

package/dist/services/europe-pmc/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/europe-pmc/types.js

@@ -0,0 +1,16 @@
+/**
+ * @fileoverview Types for the Europe PMC REST API. Covers the search response
+ * shape and the fullTextXML endpoint contract.
+ *
+ * See https://europepmc.org/RestfulWebService for the full API. We use only
+ * the search endpoint (`/webservices/rest/search`) and the fullText endpoint
+ * (`/webservices/rest/{id}/fullTextXML`).
+ *
+ * @module src/services/europe-pmc/types
+ */
+/** Base URL for Europe PMC's RESTful web service. */
+export const EUROPEPMC_API_BASE = 'https://www.ebi.ac.uk/europepmc/webservices/rest';
+/** Allowed sources for `pubmed_europepmc_search` input. */
+export const EUROPEPMC_DEFAULT_SOURCES = ['MED', 'PMC', 'PPR'];
+export const EUROPEPMC_ALL_SOURCES = ['MED', 'PMC', 'PPR', 'PAT', 'AGR'];
+//# sourceMappingURL=types.js.map

package/dist/services/europe-pmc/types.js.map

@@ -0,0 +1 @@
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package/dist/services/ncbi/response-handler.js

@@ -133,7 +133,7 @@ function sanitizeNcbiError(message) {
  * E-utilities use `<ERROR>` for response-level failures, while PMC EFetch
  * uses lowercase `<error id="…">` to flag a single unavailable PMCID. The
  * latter is data (a missing ID), not a transport error, so it falls through
- * to the caller which reports it via `unavailablePmcIds`.
+ * to the caller which reports it via the unified `unavailable[]` list.
  */
 const ERROR_TAG_REGEX = /<ERROR(?:\s[^>]*)?>/;
 /**

package/dist/services/unpaywall/unpaywall-service.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAYH,OAAO,EAEL,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EAEzB,MAAM,YAAY,CAAC;AAIpB;;;GAGG;AACH,qBAAa,gBAAgB;IAEzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS;gBADT,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM;IAGpC;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC;IA2D9E;;;;;OAKG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC;YAsBlF,OAAO;CAkDtB;AAiBD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAc3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

package/dist/services/unpaywall/unpaywall-service.js

@@ -7,7 +7,7 @@
  * resolution; only genuine service failures (5xx, network, timeout) throw.
  * @module src/services/unpaywall/unpaywall-service
  */
-import { 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 { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../../services/error-contracts.js';
@@ -35,6 +35,11 @@ export class UnpaywallService {
             return { kind: 'no-oa', reason: 'Invalid DOI' };
         const url = `${UNPAYWALL_API_BASE}/${encodeURIComponent(normalized)}?email=${encodeURIComponent(this.email)}`;
         const ctx = requestContextService.createRequestContext({ operation: 'UnpaywallResolve', doi });
+        // `fetchWithTimeout` throws on any non-2xx response, so the explicit
+        // `response.status === 404` / `=== 422` checks the API actually returns
+        // arrive as `McpError(NotFound)` / `McpError(ValidationError)` here, not as
+        // a response object. Translate those into the documented `no-oa` outcomes
+        // before falling back to the service-unavailable wrap.
         let response;
         try {
             response = await fetchWithTimeout(url, this.timeoutMs, ctx, {
@@ -43,6 +48,14 @@ export class UnpaywallService {
             });
         }
         catch (error) {
+            if (error instanceof McpError) {
+                if (error.code === JsonRpcErrorCode.NotFound) {
+                    return { kind: 'no-oa', reason: 'DOI unknown to Unpaywall' };
+                }
+                if (error.code === JsonRpcErrorCode.ValidationError) {
+                    return { kind: 'no-oa', reason: 'Invalid DOI format' };
+                }
+            }
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Unpaywall request failed: ${msg}`, {
                 reason: 'unpaywall_unreachable',
@@ -50,18 +63,6 @@ export class UnpaywallService {
                 ...recoveryFor('unpaywall_unreachable'),
             }, { cause: error });
         }
-        if (response.status === 404)
-            return { kind: 'no-oa', reason: 'DOI unknown to Unpaywall' };
-        if (response.status === 422)
-            return { kind: 'no-oa', reason: 'Invalid DOI format' };
-        if (!response.ok) {
-            const body = await response.text().catch(() => '');
-            throw await httpErrorFromResponse(response, {
-                service: 'Unpaywall',
-                captureBody: false,
-                data: { doi: normalized, body: body.substring(0, 300) },
-            });
-        }
         const data = (await response.json());
         if (!data.is_oa)
             return { kind: 'no-oa', reason: 'No open-access copy indexed' };

package/dist/services/unpaywall/unpaywall-service.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.6.12",
+  "version": "2.7.0",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
-  "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.",
+  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -40,7 +40,8 @@
     "e-utilities",
     "open-access",
     "full-text",
-    "unpaywall"
+    "unpaywall",
+    "europe-pmc"
   ],
   "repository": {
     "type": "git",
@@ -81,7 +82,7 @@
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.15",
-    "@types/node": "^25.8.0",
+    "@types/node": "^25.9.0",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^4.1.6",
     "depcheck": "^1.4.7",

package/server.json

@@ -1,12 +1,12 @@
 {
   "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
   "name": "io.github.cyanheads/pubmed-mcp-server",
-  "description": "Search PubMed, fetch articles and full text, generate citations, and explore MeSH terms via NCBI.",
+  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.",
   "repository": {
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.6.12",
+  "version": "2.7.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.12",
+      "version": "2.7.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.12",
+      "version": "2.7.0",
       "packageArguments": [
         {
           "type": "positional",