@cyanheads/pubmed-mcp-server 2.5.5 → 2.6.0

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 @@
+{"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAMH,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;IAkD9E;;;;;OAKG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC;YAkBlF,OAAO;CAqDtB;AAiBD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAU3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

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

@@ -0,0 +1 @@
+{"version":3,"file":"unpaywall-service.js","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EACL,kBAAkB,GAKnB,MAAM,YAAY,CAAC;AAEpB,MAAM,UAAU,GAAG,qEAAqE,CAAC;AAEzF;;;GAGG;AACH,MAAM,OAAO,gBAAgB;IAER;IACA;IAFnB,YACmB,KAAa,EACb,SAAiB;QADjB,UAAK,GAAL,KAAK,CAAQ;QACb,cAAS,GAAT,SAAS,CAAQ;IACjC,CAAC;IAEJ;;;;OAIG;IACH,KAAK,CAAC,OAAO,CAAC,GAAW,EAAE,MAAoB;QAC7C,MAAM,UAAU,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC;QACrC,IAAI,CAAC,UAAU;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,CAAC;QAEjE,MAAM,GAAG,GAAG,GAAG,kBAAkB,IAAI,kBAAkB,CAAC,UAAU,CAAC,UAAU,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QAC9G,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,EAAE,CAAC,CAAC;QAE/F,IAAI,QAAkB,CAAC;QACvB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;gBAC1D,OAAO,EAAE,EAAE,MAAM,EAAE,kBAAkB,EAAE,YAAY,EAAE,UAAU,EAAE;gBACjE,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,kBAAkB,EAAE,6BAA6B,GAAG,EAAE,EAAE;gBAC1F,GAAG,EAAE,UAAU;aAChB,CAAC,CAAC;QACL,CAAC;QAED,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,0BAA0B,EAAE,CAAC;QAC1F,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,oBAAoB,EAAE,CAAC;QAEpF,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;YACjB,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC;YACnD,MAAM,IAAI,QAAQ,CAChB,QAAQ,CAAC,MAAM,IAAI,GAAG;gBACpB,CAAC,CAAC,gBAAgB,CAAC,kBAAkB;gBACrC,CAAC,CAAC,gBAAgB,CAAC,cAAc,EACnC,2BAA2B,QAAQ,CAAC,MAAM,GAAG,EAC7C,EAAE,GAAG,EAAE,UAAU,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAC3E,CAAC;QACJ,CAAC;QAED,MAAM,IAAI,GAAG,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAsB,CAAC;QAC1D,IAAI,CAAC,IAAI,CAAC,KAAK;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,6BAA6B,EAAE,CAAC;QAEjF,MAAM,QAAQ,GAAG,IAAI,CAAC,gBAAgB,IAAI,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,CAAC;QACjE,IAAI,CAAC,QAAQ,EAAE,GAAG;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,uCAAuC,EAAE,CAAC;QAE9F,MAAM,CAAC,KAAK,CAAC,wBAAwB,EAAE;YACrC,GAAG,EAAE,UAAU;YACf,QAAQ,EAAE,QAAQ,CAAC,SAAS,IAAI,IAAI;YACpC,OAAO,EAAE,QAAQ,CAAC,OAAO,IAAI,IAAI;YACjC,OAAO,EAAE,QAAQ,CAAC,OAAO,IAAI,IAAI;SACzB,CAAC,CAAC;QAEZ,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAC;IACrC,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,YAAY,CAAC,QAA2B,EAAE,MAAoB;QAClE,MAAM,MAAM,GAAG,QAAQ,CAAC,WAAW,IAAI,SAAS,CAAC;QACjD,MAAM,OAAO,GAAG,QAAQ,CAAC,GAAG,CAAC;QAE7B,IAAI,MAAM,EAAE,CAAC;YACX,IAAI,CAAC;gBACH,OAAO,MAAM,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;YACnD,CAAC;YAAC,OAAO,MAAe,EAAE,CAAC;gBACzB,MAAM,CAAC,KAAK,CAAC,sDAAsD,EAAE;oBACnE,GAAG,EAAE,MAAM;oBACX,KAAK,EAAE,MAAM,YAAY,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC;iBACxD,CAAC,CAAC;YACd,CAAC;QACH,CAAC;QAED,OAAO,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC;IAC/C,CAAC;IAEO,KAAK,CAAC,OAAO,CACnB,GAAW,EACX,QAAwB,EACxB,MAAoB;QAEpB,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC;YACrD,SAAS,EAAE,gBAAgB;YAC3B,GAAG;YACH,QAAQ;SACT,CAAC,CAAC;QAEH,MAAM,MAAM,GACV,QAAQ,KAAK,KAAK;YAChB,CAAC,CAAC,2BAA2B;YAC7B,CAAC,CAAC,2CAA2C,CAAC;QAElD,IAAI,QAAkB,CAAC;QACvB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;gBAC1D,OAAO,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,UAAU,EAAE;gBACrD,QAAQ,EAAE,QAAQ;gBAClB,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAChB,gBAAgB,CAAC,kBAAkB,EACnC,mCAAmC,GAAG,EAAE,EACxC,EAAE,GAAG,EAAE,CACR,CAAC;QACJ,CAAC;QAED,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;YACjB,MAAM,IAAI,QAAQ,CAChB,QAAQ,CAAC,MAAM,IAAI,GAAG;gBACpB,CAAC,CAAC,gBAAgB,CAAC,kBAAkB;gBACrC,CAAC,CAAC,gBAAgB,CAAC,cAAc,EACnC,yCAAyC,QAAQ,CAAC,MAAM,GAAG,EAC3D,EAAE,GAAG,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,CACjC,CAAC;QACJ,CAAC;QAED,MAAM,WAAW,GAAG,QAAQ,CAAC,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;QAC9E,MAAM,UAAU,GAAG,QAAQ,CAAC,GAAG,IAAI,GAAG,CAAC;QAEvC,IAAI,WAAW,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,QAAQ,KAAK,KAAK,EAAE,CAAC;YACtD,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,MAAM,QAAQ,CAAC,WAAW,EAAE,CAAC,CAAC;YAC3D,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC;QAClD,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QACnC,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC;IAClD,CAAC;CACF;AAED;;;GAGG;AACH,SAAS,YAAY,CAAC,KAAa;IACjC,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC;IAC7B,IAAI,CAAC,OAAO;QAAE,OAAO;IACrB,MAAM,aAAa,GAAG,OAAO,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,gCAAgC,EAAE,EAAE,CAAC,CAAC;IAClG,OAAO,aAAa,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC;AACrE,CAAC;AAED,+EAA+E;AAE/E,IAAI,QAAsC,CAAC;AAE3C;;;;GAIG;AACH,MAAM,UAAU,oBAAoB;IAClC,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;IACjC,IAAI,CAAC,MAAM,CAAC,cAAc,EAAE,CAAC;QAC3B,MAAM,CAAC,IAAI,CAAC,wDAAwD,CAAC,CAAC;QACtE,OAAO;IACT,CAAC;IACD,QAAQ,GAAG,IAAI,gBAAgB,CAAC,MAAM,CAAC,cAAc,EAAE,MAAM,CAAC,kBAAkB,CAAC,CAAC;IAClF,MAAM,CAAC,IAAI,CAAC,gCAAgC,EAAE;QAC5C,SAAS,EAAE,MAAM,CAAC,kBAAkB;KAC5B,CAAC,CAAC;AACd,CAAC;AAED,qFAAqF;AACrF,MAAM,UAAU,mBAAmB;IACjC,OAAO,QAAQ,CAAC;AAClB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.5.5",
+  "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": "2.5.5",
+  "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": "2.5.5",
+      "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": "2.5.5",
+      "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": {