@cyanheads/pubmed-mcp-server 2.5.6 → 2.6.0

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

@@ -1 +1 @@
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package/dist/services/unpaywall/types.d.ts

@@ -0,0 +1,55 @@
+/**
+ * @fileoverview Types for the Unpaywall API and the content extracted from
+ * open-access copies it indexes.
+ * @module src/services/unpaywall/types
+ */
+export declare const UNPAYWALL_API_BASE = "https://api.unpaywall.org/v2";
+/**
+ * Shape of a single OA location record returned by Unpaywall. Fields mirror
+ * the public API — see https://unpaywall.org/data-format for the full contract.
+ * All fields beyond `url` are best-effort.
+ */
+export interface UnpaywallLocation {
+    /** `open`, `closed`, `embargoed`, `gold`, `hybrid`, `bronze`, `green`, etc. */
+    host_type?: 'publisher' | 'repository' | string | null;
+    /** SPDX-ish license identifier (`cc-by`, `cc0`, `public-domain`, …). */
+    license?: string | null;
+    /** Direct link to the OA copy (HTML landing page or PDF). */
+    url: string;
+    /** Direct link to a PDF when one is known; separate from `url`. */
+    url_for_pdf?: string | null;
+    /** `submittedVersion`, `acceptedVersion`, `publishedVersion`. */
+    version?: 'submittedVersion' | 'acceptedVersion' | 'publishedVersion' | string | null;
+}
+/**
+ * Subset of the Unpaywall `/v2/{doi}` response this server consumes.
+ * Upstream response has many more fields — we narrow to what's actually used.
+ */
+export interface UnpaywallResponse {
+    best_oa_location?: UnpaywallLocation | null;
+    doi?: string;
+    is_oa?: boolean;
+    oa_locations?: UnpaywallLocation[];
+    oa_status?: 'gold' | 'green' | 'hybrid' | 'bronze' | 'closed' | string;
+}
+/** Outcome of resolving a DOI to an OA copy. */
+export type UnpaywallResolution = {
+    kind: 'found';
+    location: UnpaywallLocation;
+} | {
+    kind: 'no-oa';
+    reason: string;
+};
+/** Raw content + type tag, pre-extraction. Discriminated on `kind` so the body type narrows. */
+export type UnpaywallContent = {
+    kind: 'html';
+    fetchedUrl: string;
+    body: string;
+} | {
+    kind: 'pdf';
+    fetchedUrl: string;
+    body: Uint8Array;
+};
+/** Kind of content body returned by a successful Unpaywall fetch. */
+export type UnpaywallContentKind = UnpaywallContent['kind'];
+//# sourceMappingURL=types.d.ts.map

package/dist/services/unpaywall/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/types.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,eAAO,MAAM,kBAAkB,iCAAiC,CAAC;AAEjE;;;;GAIG;AACH,MAAM,WAAW,iBAAiB;IAChC,+EAA+E;IAC/E,SAAS,CAAC,EAAE,WAAW,GAAG,YAAY,GAAG,MAAM,GAAG,IAAI,CAAC;IACvD,wEAAwE;IACxE,OAAO,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,6DAA6D;IAC7D,GAAG,EAAE,MAAM,CAAC;IACZ,mEAAmE;IACnE,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,iEAAiE;IACjE,OAAO,CAAC,EAAE,kBAAkB,GAAG,iBAAiB,GAAG,kBAAkB,GAAG,MAAM,GAAG,IAAI,CAAC;CACvF;AAED;;;GAGG;AACH,MAAM,WAAW,iBAAiB;IAChC,gBAAgB,CAAC,EAAE,iBAAiB,GAAG,IAAI,CAAC;IAC5C,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,YAAY,CAAC,EAAE,iBAAiB,EAAE,CAAC;IACnC,SAAS,CAAC,EAAE,MAAM,GAAG,OAAO,GAAG,QAAQ,GAAG,QAAQ,GAAG,QAAQ,GAAG,MAAM,CAAC;CACxE;AAED,gDAAgD;AAChD,MAAM,MAAM,mBAAmB,GAC3B;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,QAAQ,EAAE,iBAAiB,CAAA;CAAE,GAC9C;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC;AAEtC,gGAAgG;AAChG,MAAM,MAAM,gBAAgB,GACxB;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAClD;IAAE,IAAI,EAAE,KAAK,CAAC;IAAC,UAAU,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,UAAU,CAAA;CAAE,CAAC;AAE1D,qEAAqE;AACrE,MAAM,MAAM,oBAAoB,GAAG,gBAAgB,CAAC,MAAM,CAAC,CAAC"}

package/dist/services/unpaywall/types.js

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Types for the Unpaywall API and the content extracted from
+ * open-access copies it indexes.
+ * @module src/services/unpaywall/types
+ */
+export const UNPAYWALL_API_BASE = 'https://api.unpaywall.org/v2';
+//# sourceMappingURL=types.js.map

package/dist/services/unpaywall/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/unpaywall/types.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,8BAA8B,CAAC"}

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

@@ -0,0 +1,42 @@
+/**
+ * @fileoverview Unpaywall service. Resolves a DOI to an open-access location
+ * and fetches the raw content (HTML or PDF) for downstream extraction. Enabled
+ * only when `UNPAYWALL_EMAIL` is set — absence leaves the fallback disabled.
+ *
+ * Philosophy: best-effort. Upstream 404s and non-OA DOIs return a `no-oa`
+ * resolution; only genuine service failures (5xx, network, timeout) throw.
+ * @module src/services/unpaywall/unpaywall-service
+ */
+import { type UnpaywallContent, type UnpaywallLocation, type UnpaywallResolution } from './types.js';
+/**
+ * Resolves a DOI to an open-access copy via Unpaywall and fetches its bytes.
+ * Constructed only when `UNPAYWALL_EMAIL` is present; absent config → no service.
+ */
+export declare class UnpaywallService {
+    private readonly email;
+    private readonly timeoutMs;
+    constructor(email: string, timeoutMs: number);
+    /**
+     * Look up a DOI in Unpaywall. Returns a structured outcome — never throws
+     * for a DOI that simply has no OA copy or that Unpaywall doesn't know.
+     * Throws `McpError(ServiceUnavailable)` only for network/server failures.
+     */
+    resolve(doi: string, signal?: AbortSignal): Promise<UnpaywallResolution>;
+    /**
+     * Fetch the content at an Unpaywall location. Prefers `url_for_pdf` when
+     * present (direct PDF bytes) and falls back to `url` (HTML landing page).
+     * Throws `McpError(ServiceUnavailable)` on network/server failures or
+     * unreadable responses — caller handles partial failures.
+     */
+    fetchContent(location: UnpaywallLocation, signal?: AbortSignal): Promise<UnpaywallContent>;
+    private fetchAs;
+}
+/**
+ * Initialize the Unpaywall service if `UNPAYWALL_EMAIL` is configured.
+ * Safe to call regardless — absence of the env var leaves the service unset,
+ * and `getUnpaywallService()` returns `undefined`.
+ */
+export declare function initUnpaywallService(): void;
+/** Returns the initialized service, or `undefined` when the fallback is disabled. */
+export declare function getUnpaywallService(): UnpaywallService | undefined;
+//# sourceMappingURL=unpaywall-service.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/services/unpaywall/unpaywall-service.js

@@ -0,0 +1,165 @@
+/**
+ * @fileoverview Unpaywall service. Resolves a DOI to an open-access location
+ * and fetches the raw content (HTML or PDF) for downstream extraction. Enabled
+ * only when `UNPAYWALL_EMAIL` is set — absence leaves the fallback disabled.
+ *
+ * Philosophy: best-effort. Upstream 404s and non-OA DOIs return a `no-oa`
+ * resolution; only genuine service failures (5xx, network, timeout) throw.
+ * @module src/services/unpaywall/unpaywall-service
+ */
+import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
+import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { getServerConfig } from '../../config/server-config.js';
+import { UNPAYWALL_API_BASE, } from './types.js';
+const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
+/**
+ * Resolves a DOI to an open-access copy via Unpaywall and fetches its bytes.
+ * Constructed only when `UNPAYWALL_EMAIL` is present; absent config → no service.
+ */
+export class UnpaywallService {
+    email;
+    timeoutMs;
+    constructor(email, timeoutMs) {
+        this.email = email;
+        this.timeoutMs = timeoutMs;
+    }
+    /**
+     * Look up a DOI in Unpaywall. Returns a structured outcome — never throws
+     * for a DOI that simply has no OA copy or that Unpaywall doesn't know.
+     * Throws `McpError(ServiceUnavailable)` only for network/server failures.
+     */
+    async resolve(doi, signal) {
+        const normalized = normalizeDoi(doi);
+        if (!normalized)
+            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 });
+        let response;
+        try {
+            response = await fetchWithTimeout(url, this.timeoutMs, ctx, {
+                headers: { Accept: 'application/json', 'User-Agent': USER_AGENT },
+                ...(signal && { signal }),
+            });
+        }
+        catch (error) {
+            const msg = error instanceof Error ? error.message : String(error);
+            throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `Unpaywall request failed: ${msg}`, {
+                doi: normalized,
+            });
+        }
+        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 new McpError(response.status >= 500
+                ? JsonRpcErrorCode.ServiceUnavailable
+                : JsonRpcErrorCode.InvalidRequest, `Unpaywall returned HTTP ${response.status}.`, { doi: normalized, status: response.status, body: body.substring(0, 300) });
+        }
+        const data = (await response.json());
+        if (!data.is_oa)
+            return { kind: 'no-oa', reason: 'No open-access copy indexed' };
+        const location = data.best_oa_location ?? data.oa_locations?.[0];
+        if (!location?.url)
+            return { kind: 'no-oa', reason: 'OA flagged but no usable location URL' };
+        logger.debug('Unpaywall resolved DOI', {
+            doi: normalized,
+            hostType: location.host_type ?? null,
+            license: location.license ?? null,
+            version: location.version ?? null,
+        });
+        return { kind: 'found', location };
+    }
+    /**
+     * Fetch the content at an Unpaywall location. Prefers `url_for_pdf` when
+     * present (direct PDF bytes) and falls back to `url` (HTML landing page).
+     * Throws `McpError(ServiceUnavailable)` on network/server failures or
+     * unreadable responses — caller handles partial failures.
+     */
+    async fetchContent(location, signal) {
+        const pdfUrl = location.url_for_pdf ?? undefined;
+        const htmlUrl = location.url;
+        if (pdfUrl) {
+            try {
+                return await this.fetchAs(pdfUrl, 'pdf', signal);
+            }
+            catch (pdfErr) {
+                logger.debug('Unpaywall PDF fetch failed; falling back to HTML URL', {
+                    url: pdfUrl,
+                    error: pdfErr instanceof Error ? pdfErr.message : String(pdfErr),
+                });
+            }
+        }
+        return this.fetchAs(htmlUrl, 'auto', signal);
+    }
+    async fetchAs(url, expected, signal) {
+        const ctx = requestContextService.createRequestContext({
+            operation: 'UnpaywallFetch',
+            url,
+            expected,
+        });
+        const accept = expected === 'pdf'
+            ? 'application/pdf,*/*;q=0.5'
+            : 'text/html,application/pdf;q=0.9,*/*;q=0.5';
+        let response;
+        try {
+            response = await fetchWithTimeout(url, this.timeoutMs, ctx, {
+                headers: { Accept: accept, 'User-Agent': USER_AGENT },
+                redirect: 'follow',
+                ...(signal && { signal }),
+            });
+        }
+        catch (error) {
+            const msg = error instanceof Error ? error.message : String(error);
+            throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `Unpaywall content fetch failed: ${msg}`, { url });
+        }
+        if (!response.ok) {
+            throw new McpError(response.status >= 500
+                ? JsonRpcErrorCode.ServiceUnavailable
+                : JsonRpcErrorCode.InvalidRequest, `Unpaywall content fetch returned HTTP ${response.status}.`, { url, status: response.status });
+        }
+        const contentType = response.headers.get('content-type')?.toLowerCase() ?? '';
+        const fetchedUrl = response.url || url;
+        if (contentType.includes('pdf') || expected === 'pdf') {
+            const bytes = new Uint8Array(await response.arrayBuffer());
+            return { kind: 'pdf', fetchedUrl, body: bytes };
+        }
+        const text = await response.text();
+        return { kind: 'html', fetchedUrl, body: text };
+    }
+}
+/**
+ * Strip a leading `doi:` prefix or URL wrapping and return a clean DOI, or
+ * undefined when the input can't be coerced into one.
+ */
+function normalizeDoi(input) {
+    const trimmed = input.trim();
+    if (!trimmed)
+        return;
+    const withoutScheme = trimmed.replace(/^doi:/i, '').replace(/^https?:\/\/(dx\.)?doi\.org\//i, '');
+    return withoutScheme.startsWith('10.') ? withoutScheme : undefined;
+}
+// ─── Init / Accessor ────────────────────────────────────────────────────────
+let _service;
+/**
+ * Initialize the Unpaywall service if `UNPAYWALL_EMAIL` is configured.
+ * Safe to call regardless — absence of the env var leaves the service unset,
+ * and `getUnpaywallService()` returns `undefined`.
+ */
+export function initUnpaywallService() {
+    const config = getServerConfig();
+    if (!config.unpaywallEmail) {
+        logger.info('Unpaywall fallback disabled (UNPAYWALL_EMAIL not set).');
+        return;
+    }
+    _service = new UnpaywallService(config.unpaywallEmail, config.unpaywallTimeoutMs);
+    logger.info('Unpaywall service initialized.', {
+        timeoutMs: config.unpaywallTimeoutMs,
+    });
+}
+/** Returns the initialized service, or `undefined` when the fallback is disabled. */
+export function getUnpaywallService() {
+    return _service;
+}
+//# sourceMappingURL=unpaywall-service.js.map

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

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.5.6",
+  "version": "2.6.0",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
   "type": "module",
@@ -69,9 +69,12 @@
   },
   "dependencies": {
     "@cyanheads/mcp-ts-core": "^0.7.0",
+    "defuddle": "^0.18.1",
     "fast-xml-parser": "^5.7.1",
+    "linkedom": "^0.18.12",
     "pino-pretty": "^13.1.3",
-    "sanitize-html": "^2.17.3"
+    "sanitize-html": "^2.17.3",
+    "unpdf": "^1.6.0"
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.13",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.5.6",
+  "version": "2.6.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.5.6",
+      "version": "2.6.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -49,6 +49,12 @@
           "description": "Contact email sent with NCBI requests (recommended by NCBI).",
           "format": "string",
           "isRequired": false
+        },
+        {
+          "name": "UNPAYWALL_EMAIL",
+          "description": "Contact email for Unpaywall. When set, pubmed_fetch_fulltext falls back to Unpaywall open-access copies for DOIs not in PMC.",
+          "format": "string",
+          "isRequired": false
         }
       ],
       "transport": {
@@ -60,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.5.6",
+      "version": "2.6.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -124,6 +130,12 @@
           "description": "Contact email sent with NCBI requests (recommended by NCBI).",
           "format": "string",
           "isRequired": false
+        },
+        {
+          "name": "UNPAYWALL_EMAIL",
+          "description": "Contact email for Unpaywall. When set, pubmed_fetch_fulltext falls back to Unpaywall open-access copies for DOIs not in PMC.",
+          "format": "string",
+          "isRequired": false
         }
       ],
       "transport": {