@cyanheads/pubmed-mcp-server 2.6.11 → 2.7.0

package/CLAUDE.md

@@ -1,8 +1,8 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.6.11
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.0`
+**Version:** 2.6.12
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.1`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0
 
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.

package/README.md

@@ -1,13 +1,13 @@
 <div align="center">
   <h1>@cyanheads/pubmed-mcp-server</h1>
-  <p><b>MCP server for the NCBI E-utilities API. Search PubMed, fetch article metadata and full text, generate citations, explore MeSH terms, and discover related research. STDIO or Streamable HTTP.</b>
-  <div>9 Tools • 1 Resource • 1 Prompt</div>
+  <p><b>Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.</b>
+  <div>10 Tools • 1 Resource • 1 Prompt</div>
   </p>
 </div>
 
 <div align="center">
 
-[![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) [![Version](https://img.shields.io/badge/Version-2.6.11-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![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) [![Version](https://img.shields.io/badge/Version-2.7.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) 
 
 [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![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/)
 
@@ -23,13 +23,14 @@
 
 ## Tools
 
-Nine tools for working with PubMed and NCBI data:
+10 tools for working with PubMed, PubMed Central, and Europe PMC data:
 
 | Tool | Description |
 |:---|:---|
 | `pubmed_search_articles` | Search PubMed with full query syntax, field-specific filters, date ranges, pagination, and optional brief summaries |
+| `pubmed_europepmc_search` | Search Europe PMC for preprints, patents, Agricola, and EPMC-only OA records that don't surface in PubMed. Cursor-based pagination. |
 | `pubmed_fetch_articles` | Fetch full article metadata by PMIDs — abstract, authors, journal, MeSH terms, grants |
-| `pubmed_fetch_fulltext` | Fetch full-text articles from PubMed Central, with optional Unpaywall fallback for non-PMC DOIs (HTML → Markdown or PDF → text) |
+| `pubmed_fetch_fulltext` | Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs. |
 | `pubmed_format_citations` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, or RIS |
 | `pubmed_find_related` | Find similar articles, citing articles, or references for a given PMID |
 | `pubmed_spell_check` | Spell-check biomedical queries using NCBI's ESpell service |
@@ -67,18 +68,32 @@ Fetch full article metadata by PubMed IDs.
 
 ### `pubmed_fetch_fulltext`
 
-Fetch full-text articles from PubMed Central (PMC), with an optional Unpaywall fallback for articles not in PMC.
+Fetch full-text articles via a three-stage chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall.
 
-- Accepts PMC IDs directly or PubMed IDs (auto-resolved to PMCIDs via ELink)
-- PMC path returns complete article body organized by sections and subsections, plus optional references from back matter
-- Unpaywall fallback (enabled by setting `UNPAYWALL_EMAIL`) resolves DOIs to legal open-access copies hosted by publishers or institutional repositories; extracts HTML landing pages to Markdown via Defuddle or PDFs to text via unpdf
-- Discriminated output contract — `source: "pmc"` (structured sections) or `source: "unpaywall"` (single body + `contentFormat` metadata: `html-markdown` or `pdf-text`)
-- Structured unavailable reasons (`no-pmc-fallback-disabled`, `no-doi`, `no-oa`, `fetch-failed`, `parse-failed`, `service-error`) so callers can retry or explain to users without parsing text
+- 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)
+- 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
+- Discriminated output contract — `source: "pmc"` (structured sections, regardless of whether it came from PMC or EPMC) or `source: "unpaywall"` (best-effort body + `contentFormat`: `html-markdown` or `pdf-text`)
+- Structured unavailable reasons (`not-found`, `no-pmc-fallback-disabled`, `no-epmc-fulltext`, `no-doi`, `no-oa`, `fetch-failed`, `parse-failed`, `service-error`) so callers can retry or explain to users without parsing text
+- Each `unavailable` entry carries `idType` (`pmid` / `pmcid` / `doi`) and `triedTiers` — per-tier outcomes (`not-attempted`, `miss`, `no-fulltext`, `service-error`, …) in execution order, so callers can see which stage failed and why
 - Section filtering by title (case-insensitive match, e.g. `["methods", "results"]`) and configurable max sections apply to PMC output
 - Up to 10 articles per request
 
 ---
 
+### `pubmed_europepmc_search`
+
+Search Europe PMC (EBI/EMBL-EBI), a broader open-access biomedical corpus than PubMed alone.
+
+- Surfaces records PubMed search can't reach: preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC (`PMC`)
+- Default sources `["MED", "PMC", "PPR"]`; pass `sources` to include `PAT` / `AGR`
+- Cursor-based pagination via `cursorMark` (unlike `pubmed_search_articles`, which uses offset) — `*` for the first page, return `nextCursorMark` for the next
+- Output discriminator on `source` plus optional `pmid` / `pmcId` / `doi` cross-walking
+- Disabled when `EUROPEPMC_ENABLED=false`; tool is not registered in that case
+
+---
+
 ### `pubmed_format_citations`
 
 Generate formatted citations for articles.
@@ -97,7 +112,7 @@ Find articles related to a source article via ELink.
 
 - Three relationship types: `similar` (content similarity), `cited_by`, `references`
 - Results enriched with title, authors, publication date, and source via ESummary
-- Similarity scores included for `similar` relationship type
+- Results returned in NCBI's relevance order
 
 ---
 
@@ -285,12 +300,18 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
 | `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |
 | `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
 | `NCBI_ADMIN_EMAIL` | Contact email sent with NCBI requests (recommended by NCBI) | none |
-| `NCBI_REQUEST_DELAY_MS` | Delay between NCBI requests in ms | 334 (100 with key) |
+| `NCBI_REQUEST_DELAY_MS` | Minimum gap between NCBI request starts in ms | 334 (100 with key) |
+| `NCBI_MAX_CONCURRENT` | Max concurrent in-flight NCBI requests | `8` |
 | `NCBI_MAX_RETRIES` | Retry attempts for failed NCBI requests | 6 |
 | `NCBI_TIMEOUT_MS` | Per-request HTTP timeout in ms | `30000` |
 | `NCBI_TOTAL_DEADLINE_MS` | Total deadline across all retry attempts for one NCBI call, in ms | `60000` |
 | `UNPAYWALL_EMAIL` | Contact email for Unpaywall. When set, `pubmed_fetch_fulltext` falls back to Unpaywall open-access copies for non-PMC DOIs | none |
 | `UNPAYWALL_TIMEOUT_MS` | Per-request HTTP timeout for Unpaywall lookups and content fetches, in ms | `20000` |
+| `EUROPEPMC_ENABLED` | Enable Europe PMC search tool and the `pubmed_fetch_fulltext` JATS fallback chain. Set `false` to disable all EPMC calls and skip tool registration. | `true` |
+| `EUROPEPMC_EMAIL` | Optional contact email sent with Europe PMC requests (EBI courtesy). | none |
+| `EUROPEPMC_REQUEST_DELAY_MS` | Minimum gap between Europe PMC request starts in ms | `200` |
+| `EUROPEPMC_MAX_RETRIES` | Retry attempts for failed Europe PMC requests | `3` |
+| `EUROPEPMC_TIMEOUT_MS` | Per-request HTTP timeout for Europe PMC calls, in ms | `20000` |
 | `OTEL_ENABLED` | Enable OpenTelemetry | `false` |
 
 ## Running the server
@@ -319,10 +340,11 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
 
 | Directory | Purpose |
 |:---|:---|
-| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Nine PubMed tools. |
+| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Ten tools across PubMed, PMC, and Europe PMC. |
 | `src/mcp-server/resources` | Resource definitions. Database info resource. |
 | `src/mcp-server/prompts` | Prompt definitions. Research plan prompt. |
 | `src/services/ncbi` | NCBI E-utilities service layer — API client, queue, parser, formatter. |
+| `src/services/europe-pmc` | Europe PMC service — search + `fullTextXML` JATS retrieval. Reuses the NCBI JATS parser. |
 | `src/services/unpaywall` | Unpaywall service — DOI → OA location resolution and content fetch (HTML/PDF). |
 | `src/config` | Server-specific environment variable parsing and validation with Zod. |
 | `tests/` | Unit and integration tests, mirroring the `src/` structure. |

package/dist/config/server-config.d.ts

@@ -10,11 +10,17 @@ declare const ServerConfigSchema: z.ZodObject<{
     toolIdentifier: z.ZodDefault<z.ZodString>;
     adminEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
     requestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    maxConcurrent: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     maxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     timeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     totalDeadlineMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     unpaywallEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
     unpaywallTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    europepmcEnabled: z.ZodDefault<z.ZodPreprocess<z.ZodBoolean>>;
+    europepmcEmail: z.ZodPreprocess<z.ZodOptional<z.ZodEmail>>;
+    europepmcRequestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    europepmcMaxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    europepmcTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
 }, z.core.$strip>;
 export type ServerConfig = z.infer<typeof ServerConfigSchema>;
 export declare function getServerConfig(): ServerConfig;

package/dist/config/server-config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAyB3C,QAAA,MAAM,kBAAkB;;;;;;;;;;;;;;;;iBA2DtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA8B9C"}

package/dist/config/server-config.js

@@ -12,11 +12,33 @@ import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
  * validation instead of being interpreted as "no admin email configured".
  */
 const emptyAsUndefined = (v) => (v === '' ? undefined : v);
+/**
+ * Parse a string env var as a boolean. `z.coerce.boolean()` is unusable for
+ * env vars because it applies JavaScript truthy semantics — `"false"` coerces
+ * to `true`. This mirrors the framework's `envBoolean` so `EUROPEPMC_ENABLED=false`
+ * actually disables the service.
+ */
+const envBoolean = z.preprocess((v) => {
+    if (typeof v === 'string') {
+        const s = v.trim().toLowerCase();
+        if (s === 'true' || s === '1')
+            return true;
+        if (s === 'false' || s === '0' || s === '')
+            return false;
+    }
+    return v;
+}, z.boolean());
 const ServerConfigSchema = z.object({
     apiKey: z.preprocess(emptyAsUndefined, z.string().optional()).describe('NCBI API key'),
     toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
     adminEmail: z.preprocess(emptyAsUndefined, z.email().optional()).describe('Admin contact email'),
     requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
+    maxConcurrent: z.coerce
+        .number()
+        .min(1)
+        .max(16)
+        .default(8)
+        .describe('Max concurrent in-flight NCBI requests'),
     maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
     timeoutMs: z.coerce
         .number()
@@ -39,6 +61,30 @@ const ServerConfigSchema = z.object({
         .max(120000)
         .default(20000)
         .describe('Per-request HTTP timeout for Unpaywall lookups and content fetches, in ms'),
+    europepmcEnabled: envBoolean
+        .default(true)
+        .describe('Enable Europe PMC search tool and `pubmed_fetch_fulltext` JATS fallback chain. Set false to fully disable EPMC calls.'),
+    europepmcEmail: z
+        .preprocess(emptyAsUndefined, z.email().optional())
+        .describe('Optional contact email sent with Europe PMC requests'),
+    europepmcRequestDelayMs: z.coerce
+        .number()
+        .min(50)
+        .max(5000)
+        .default(200)
+        .describe('Minimum gap between Europe PMC request starts in ms'),
+    europepmcMaxRetries: z.coerce
+        .number()
+        .min(0)
+        .max(10)
+        .default(3)
+        .describe('Max retry attempts for failed Europe PMC requests'),
+    europepmcTimeoutMs: z.coerce
+        .number()
+        .min(1000)
+        .max(120000)
+        .default(20000)
+        .describe('Per-request HTTP timeout for Europe PMC calls, in ms'),
 });
 let _config;
 export function getServerConfig() {
@@ -48,11 +94,17 @@ export function getServerConfig() {
             toolIdentifier: 'NCBI_TOOL_IDENTIFIER',
             adminEmail: 'NCBI_ADMIN_EMAIL',
             requestDelayMs: 'NCBI_REQUEST_DELAY_MS',
+            maxConcurrent: 'NCBI_MAX_CONCURRENT',
             maxRetries: 'NCBI_MAX_RETRIES',
             timeoutMs: 'NCBI_TIMEOUT_MS',
             totalDeadlineMs: 'NCBI_TOTAL_DEADLINE_MS',
             unpaywallEmail: 'UNPAYWALL_EMAIL',
             unpaywallTimeoutMs: 'UNPAYWALL_TIMEOUT_MS',
+            europepmcEnabled: 'EUROPEPMC_ENABLED',
+            europepmcEmail: 'EUROPEPMC_EMAIL',
+            europepmcRequestDelayMs: 'EUROPEPMC_REQUEST_DELAY_MS',
+            europepmcMaxRetries: 'EUROPEPMC_MAX_RETRIES',
+            europepmcTimeoutMs: 'EUROPEPMC_TIMEOUT_MS',
         });
         /**
          * An API key raises NCBI's rate ceiling from ~3 req/s to ~10 req/s. If the

package/dist/config/server-config.js.map

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package/dist/index.js

@@ -4,6 +4,7 @@
  * @module index
  */
 import { createApp } from '@cyanheads/mcp-ts-core';
+import { getServerConfig } from './config/server-config.js';
 import { researchPlanPrompt } from './mcp-server/prompts/definitions/research-plan.prompt.js';
 import { databaseInfoResource } from './mcp-server/resources/definitions/database-info.resource.js';
 import { convertIdsTool } from './mcp-server/tools/definitions/convert-ids.tool.js';
@@ -13,25 +14,30 @@ import { findRelatedTool } from './mcp-server/tools/definitions/find-related.too
 import { formatCitationsTool } from './mcp-server/tools/definitions/format-citations.tool.js';
 import { lookupCitationTool } from './mcp-server/tools/definitions/lookup-citation.tool.js';
 import { lookupMeshTool } from './mcp-server/tools/definitions/lookup-mesh.tool.js';
+import { pubmedEuropepmcSearchTool } from './mcp-server/tools/definitions/pubmed-europepmc-search.tool.js';
 import { searchArticlesTool } from './mcp-server/tools/definitions/search-articles.tool.js';
 import { spellCheckTool } from './mcp-server/tools/definitions/spell-check.tool.js';
+import { initEuropePmcService } from './services/europe-pmc/europe-pmc-service.js';
 import { initNcbiService } from './services/ncbi/ncbi-service.js';
 import { initUnpaywallService } from './services/unpaywall/unpaywall-service.js';
+const config = getServerConfig();
+const tools = [
+    searchArticlesTool,
+    fetchArticlesTool,
+    fetchFulltextTool,
+    formatCitationsTool,
+    findRelatedTool,
+    spellCheckTool,
+    lookupMeshTool,
+    lookupCitationTool,
+    convertIdsTool,
+    ...(config.europepmcEnabled ? [pubmedEuropepmcSearchTool] : []),
+];
 await createApp({
-    tools: [
-        searchArticlesTool,
-        fetchArticlesTool,
-        fetchFulltextTool,
-        formatCitationsTool,
-        findRelatedTool,
-        spellCheckTool,
-        lookupMeshTool,
-        lookupCitationTool,
-        convertIdsTool,
-    ],
+    tools,
     resources: [databaseInfoResource],
     prompts: [researchPlanPrompt],
-    instructions: "PubMed/NCBI E-utilities wrapper. Typical research flow: `pubmed_search_articles` → `pubmed_fetch_articles` (metadata) → `pubmed_fetch_fulltext`. Prefer `pubmed_lookup_citation` over free-text search when you have a partial known reference — it's deterministic. Use `pubmed_lookup_mesh` and `pubmed_spell_check` to refine queries before searching, when needed.",
+    instructions: "Use the pubmed_* tools to search PubMed and PubMed Central, fetch article metadata and full text, format citations, and find related articles via NCBI's E-utilities. Articles are keyed by PMID (integer); PMC full text by PMCID (`PMC` prefix); most also carry a DOI. Typical flow: `pubmed_search_articles` → `pubmed_fetch_articles` → `pubmed_fetch_fulltext`. When PubMed itself comes up empty (preprints, EPMC-only OA), broaden via `pubmed_europepmc_search`. Prefer deterministic resolvers when inputs are structured: `pubmed_lookup_citation` for partial references, `pubmed_convert_ids` to crosswalk IDs. Refine queries with `pubmed_lookup_mesh` and `pubmed_spell_check`.",
     landing: {
         tagline: 'Search PubMed, fetch articles, generate citations, explore MeSH terms, and discover related research.',
         repoRoot: 'https://github.com/cyanheads/pubmed-mcp-server',
@@ -58,6 +64,7 @@ await createApp({
     setup() {
         initNcbiService();
         initUnpaywallService();
+        initEuropePmcService();
     },
 });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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

@@ -1,24 +1,39 @@
 /**
- * @fileoverview Full-text fetch tool. Primary source is PubMed Central (NCBI
- * EFetch, `db=pmc`). When a PMID has no PMC copy but does have a DOI,
- * transparently falls back to Unpaywall to retrieve a legally-deposited
- * open-access copy (HTML or PDF). Output uses a discriminated union on
- * `source` so callers can reason about structural reliability per article.
+ * @fileoverview Full-text fetch tool. Resolves full-text articles through a
+ * three-stage chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall.
+ * Accepts three mutually-exclusive input shapes:
+ *
+ *   - `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.
+ *
+ * Output uses a discriminated union on `source` (`pmc` | `unpaywall`) with an
+ * extra `viaSource` discriminator that records which layer produced the
+ * content. EPMC's JATS reuses the `pmc` schema shape because it's the same
+ * DTD; `viaSource: 'europepmc'` distinguishes it from PMC EFetch output.
+ *
  * @module src/mcp-server/tools/definitions/fetch-fulltext.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
-import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 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>>;
+    dois: z.ZodOptional<z.ZodArray<z.ZodString>>;
     includeReferences: z.ZodDefault<z.ZodBoolean>;
     maxSections: z.ZodOptional<z.ZodNumber>;
     sections: z.ZodOptional<z.ZodArray<z.ZodString>>;
 }, z.core.$strip>, z.ZodObject<{
     articles: z.ZodArray<z.ZodDiscriminatedUnion<[z.ZodObject<{
         source: z.ZodLiteral<"pmc">;
-        pmcId: z.ZodString;
-        pmcUrl: z.ZodString;
+        viaSource: z.ZodEnum<{
+            pmc: "pmc";
+            europepmc: "europepmc";
+        }>;
+        pmcId: z.ZodOptional<z.ZodString>;
+        pmcUrl: z.ZodOptional<z.ZodString>;
         pmid: z.ZodOptional<z.ZodString>;
         pubmedUrl: z.ZodOptional<z.ZodString>;
         doi: z.ZodOptional<z.ZodString>;
@@ -59,14 +74,17 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
             id: z.ZodOptional<z.ZodString>;
             label: z.ZodOptional<z.ZodString>;
         }, z.core.$strip>>>;
+        epmcId: z.ZodOptional<z.ZodString>;
+        epmcSource: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>, z.ZodObject<{
         source: z.ZodLiteral<"unpaywall">;
+        viaSource: z.ZodLiteral<"unpaywall">;
         contentFormat: z.ZodEnum<{
             "html-markdown": "html-markdown";
             "pdf-text": "pdf-text";
         }>;
-        pmid: z.ZodString;
-        pubmedUrl: z.ZodString;
+        pmid: z.ZodOptional<z.ZodString>;
+        pubmedUrl: z.ZodOptional<z.ZodString>;
         doi: z.ZodString;
         sourceUrl: z.ZodString;
         title: z.ZodOptional<z.ZodString>;
@@ -79,58 +97,88 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
     }, z.core.$strip>], "source">>;
     totalReturned: z.ZodNumber;
     unavailable: z.ZodOptional<z.ZodArray<z.ZodObject<{
-        pmid: z.ZodString;
+        id: z.ZodString;
+        idType: z.ZodEnum<{
+            pmid: "pmid";
+            pmcid: "pmcid";
+            doi: "doi";
+        }>;
         reason: z.ZodEnum<{
             "no-oa": "no-oa";
+            "not-found": "not-found";
             "no-pmc-fallback-disabled": "no-pmc-fallback-disabled";
+            "no-epmc-fulltext": "no-epmc-fulltext";
             "no-doi": "no-doi";
             "fetch-failed": "fetch-failed";
             "parse-failed": "parse-failed";
             "service-error": "service-error";
         }>;
-        detail: z.ZodOptional<z.ZodString>;
+        triedTiers: z.ZodArray<z.ZodObject<{
+            tier: z.ZodEnum<{
+                pmc: "pmc";
+                europepmc: "europepmc";
+                unpaywall: "unpaywall";
+            }>;
+            outcome: z.ZodEnum<{
+                "no-oa": "no-oa";
+                "no-doi": "no-doi";
+                "fetch-failed": "fetch-failed";
+                "parse-failed": "parse-failed";
+                "service-error": "service-error";
+                "not-attempted": "not-attempted";
+                miss: "miss";
+                "no-fulltext": "no-fulltext";
+            }>;
+            detail: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>;
     }, z.core.$strip>>>;
-    unavailablePmcIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
 }, z.core.$strip>, readonly [{
     readonly reason: "queue_full";
-    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
     readonly when: "Local NCBI request queue is at capacity.";
     readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_unreachable";
-    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
     readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_deadline_exceeded";
-    readonly code: JsonRpcErrorCode.Timeout;
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
     readonly when: "Total request deadline expired before NCBI returned a response.";
     readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_invalid_response";
-    readonly code: JsonRpcErrorCode.SerializationError;
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
     readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
     readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
     readonly retryable: true;
 }, {
     readonly reason: "ncbi_resource_not_found";
-    readonly code: JsonRpcErrorCode.NotFound;
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
     readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
 }, {
     readonly reason: "unpaywall_unreachable";
-    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "Unpaywall was unreachable when resolving a DOI or fetching content.";
     readonly recovery: "Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.";
     readonly retryable: true;
 }, {
-    readonly reason: "invalid_pmc_efetch_response";
-    readonly code: JsonRpcErrorCode.SerializationError;
-    readonly when: "PMC EFetch returned a payload missing the pmc-articleset wrapper.";
-    readonly recovery: "Retry once; if it persists, NCBI returned malformed data — try fewer PMC IDs at once.";
+    readonly reason: "europepmc_unreachable";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Europe PMC was unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.";
+    readonly retryable: true;
+}, {
+    readonly reason: "europepmc_invalid_response";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
+    readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
+    readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
+    readonly retryable: true;
 }]>;
 //# sourceMappingURL=fetch-fulltext.tool.d.ts.map

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

@@ -1 +1 @@
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+{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsc5B,CAAC"}