@cyanheads/pubmed-mcp-server 2.10.13 → 2.10.15

package/dist/services/ncbi/response-handler.d.ts

@@ -2,16 +2,29 @@
  * @fileoverview Handles parsing of NCBI E-utility responses and NCBI-specific error extraction.
  * Creates an NCBI-specific XMLParser instance with `isArray` callback support for handling
  * NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
+ * Also reads the `<ERROR>` envelope of a failed eutils response: a backend failure is
+ * reclassified as transient, and EFetch's all-invalid-ID rejection becomes the empty set
+ * NCBI returns for an unknown ID.
  * @module src/services/ncbi/response-handler
  */
 import type { NcbiRequestOptions } from './types.js';
+/**
+ * The response NCBI would have sent had it answered an all-invalid EFetch ID list the
+ * way it answers an unknown well-formed one. EFetch rejects a list in which no ID is a
+ * real UID (`id=00000000`) with an HTTP 400 `ID list is empty!` envelope, but answers an
+ * unassigned UID (`id=99999999`) with HTTP 200 and an empty set, so the same question —
+ * "which of these exist?" — would otherwise split into an error and an answer depending
+ * on the ID's spelling. Returns the empty-set document to parse in place of the error,
+ * or `undefined` when the error is anything else. (#155)
+ */
+export declare function emptyEFetchResultFor(error: unknown, endpoint: string, db: unknown): string | undefined;
 /**
  * Reclassifies an HTTP error from a eutils request whose captured body is an NCBI
  * `<ERROR>` envelope reporting a backend failure. The status-derived code reads such a
  * response as caller error (400 → InvalidParams), which the retry gate never retries.
  * Any other error — including a genuine invalid-parameter 400 — is returned unchanged.
  * Matches the body text rather than parsing it, since the framework captures only a
- * bounded prefix. (#153)
+ * bounded prefix. (#153, #155)
  */
 export declare function reclassifyNcbiHttpError(error: unknown, endpoint: string): unknown;
 /**

package/dist/services/ncbi/response-handler.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AA2BH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AA4IrD;;;;;;;;GAQG;AACH,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,MAAM,EAChB,EAAE,EAAE,OAAO,GACV,MAAM,GAAG,SAAS,CAKpB;AAED;;;;;;;GAOG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAoBjF;AAsJD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAeD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAkBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}

package/dist/services/ncbi/response-handler.js

@@ -2,6 +2,9 @@
  * @fileoverview Handles parsing of NCBI E-utility responses and NCBI-specific error extraction.
  * Creates an NCBI-specific XMLParser instance with `isArray` callback support for handling
  * NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
+ * Also reads the `<ERROR>` envelope of a failed eutils response: a backend failure is
+ * reclassified as transient, and EFetch's all-invalid-ID rejection becomes the empty set
+ * NCBI returns for an unknown ID.
  * @module src/services/ncbi/response-handler
  */
 import { McpError, notFound, serializationError, serviceUnavailable, } from '@cyanheads/mcp-ts-core/errors';
@@ -107,29 +110,82 @@ const ERROR_PATHS = [
  * NCBI `<ERROR>` messages describing a backend failure rather than the request.
  * EFetch sends the viewer-timeout envelope under HTTP 200 and HTTP 400 alike, so
  * the status cannot tell it from a malformed request; the message can. (#153)
+ *
+ * `proxy_stream()` is the EFetch front end's own backend-proxy method: it prefixes
+ * every failure relayed from the service behind it (a 502 page, "Failed to connect
+ * to PubOne service"), so a client-side 400 cannot carry it. (#155)
+ */
+const NCBI_TRANSIENT_ERROR_PATTERNS = [
+    /External viewer error/i,
+    /Status:\s*Timeout/i,
+    /proxy_stream\(\)/,
+];
+/**
+ * Captures the text of each uppercase `<ERROR>` element in a raw response body. The
+ * framework keeps only the first 500 bytes of an error body, so an envelope relaying a
+ * backend page is cut before its `</ERROR>`: an unterminated element runs to the end of
+ * the capture. Content may hold markup, raw or entity-escaped.
+ */
+const ERROR_TEXT_REGEX = /<ERROR(?:\s[^>]*)?>([\s\S]*?)(?:<\/ERROR>|$)/g;
+/** NCBI's whole-list rejection when not one supplied ID is a real UID. (#155) */
+const EMPTY_ID_LIST_PATTERN = /^ID list is empty\b/i;
+/**
+ * What EFetch answers, HTTP 200, when every requested ID is well-formed but unknown —
+ * an empty set in the database's own wrapper. Keyed by `db`; a database missing here
+ * keeps the rejection as an error.
+ */
+const EMPTY_EFETCH_RESULTS = {
+    pubmed: '<?xml version="1.0" ?>\n<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd">\n<PubmedArticleSet></PubmedArticleSet>\n',
+    pmc: '<?xml version="1.0" ?>\n<!DOCTYPE pmc-articleset PUBLIC "-//NLM//DTD ARTICLE SET 2.0//EN" "https://dtd.nlm.nih.gov/ncbi/pmc/articleset/nlm-articleset-2.0.dtd">\n<pmc-articleset></pmc-articleset>\n',
+};
+/**
+ * The `<ERROR>` messages in the captured body of a non-2xx eutils response, as plain
+ * text: entities decoded, markup dropped (including a tag the capture cut in half),
+ * whitespace collapsed. `undefined` when the error carries no captured body.
+ */
+function ncbiErrorTexts(error) {
+    if (!(error instanceof McpError) || typeof error.data?.body !== 'string')
+        return;
+    return [...error.data.body.matchAll(ERROR_TEXT_REGEX)].map((match) => decodeHtmlEntities(match[1] ?? '')
+        .replace(/<\/?[a-z!][^>]*(?:>|$)/gi, ' ')
+        .replace(/\s+/g, ' ')
+        .trim());
+}
+/**
+ * The response NCBI would have sent had it answered an all-invalid EFetch ID list the
+ * way it answers an unknown well-formed one. EFetch rejects a list in which no ID is a
+ * real UID (`id=00000000`) with an HTTP 400 `ID list is empty!` envelope, but answers an
+ * unassigned UID (`id=99999999`) with HTTP 200 and an empty set, so the same question —
+ * "which of these exist?" — would otherwise split into an error and an answer depending
+ * on the ID's spelling. Returns the empty-set document to parse in place of the error,
+ * or `undefined` when the error is anything else. (#155)
  */
-const NCBI_TRANSIENT_ERROR_PATTERNS = [/External viewer error/i, /Status:\s*Timeout/i];
-/** Captures the text of each uppercase `<ERROR>` element in a raw response body. */
-const ERROR_TEXT_REGEX = /<ERROR(?:\s[^>]*)?>([^<]*)<\/ERROR>/g;
+export function emptyEFetchResultFor(error, endpoint, db) {
+    if (endpoint !== 'efetch' || typeof db !== 'string')
+        return;
+    const empty = EMPTY_EFETCH_RESULTS[db];
+    if (empty === undefined)
+        return;
+    return ncbiErrorTexts(error)?.some((msg) => EMPTY_ID_LIST_PATTERN.test(msg)) ? empty : undefined;
+}
 /**
  * Reclassifies an HTTP error from a eutils request whose captured body is an NCBI
  * `<ERROR>` envelope reporting a backend failure. The status-derived code reads such a
  * response as caller error (400 → InvalidParams), which the retry gate never retries.
  * Any other error — including a genuine invalid-parameter 400 — is returned unchanged.
  * Matches the body text rather than parsing it, since the framework captures only a
- * bounded prefix. (#153)
+ * bounded prefix. (#153, #155)
  */
 export function reclassifyNcbiHttpError(error, endpoint) {
-    if (!(error instanceof McpError) || typeof error.data?.body !== 'string')
-        return error;
-    const ncbiErrors = [...error.data.body.matchAll(ERROR_TEXT_REGEX)].map((match) => decodeHtmlEntities(match[1] ?? '').trim());
-    if (!ncbiErrors.some((msg) => NCBI_TRANSIENT_ERROR_PATTERNS.some((p) => p.test(msg)))) {
+    const ncbiErrors = ncbiErrorTexts(error);
+    if (!(error instanceof McpError) ||
+        !ncbiErrors?.some((msg) => NCBI_TRANSIENT_ERROR_PATTERNS.some((p) => p.test(msg)))) {
         return error;
     }
     return serviceUnavailable(`NCBI API Error: ${ncbiErrors.join('; ')}`, {
         reason: 'ncbi_unreachable',
         endpoint,
-        status: error.data.status,
+        status: error.data?.status,
         ncbiErrors,
         ...recoveryFor('ncbi_unreachable'),
     }, { cause: error });

package/dist/services/ncbi/response-handler.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAQH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AAmFpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd,8EAA8E;YAChE,SAAS;CAmDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}
+{"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAOH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd,8EAA8E;YAChE,SAAS;CAmDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}

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

@@ -17,19 +17,12 @@
  *
  * @module src/services/openalex/openalex-service
  */
-import { internalError, JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
-import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { internalError, McpError } from '@cyanheads/mcp-ts-core/errors';
+import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
-import { isTransient } from '../retry-policy.js';
 import { OpenAlexApiClient } from './api-client.js';
 import { OPENALEX_MAX_FILTER_VALUES, OPENALEX_MAX_PAGE_SIZE, OPENALEX_MAX_UPSTREAM_REQUESTS, } from './types.js';
-/** Transient codes eligible for retry. */
-const RETRYABLE_CODES = new Set([
-    JsonRpcErrorCode.ServiceUnavailable,
-    JsonRpcErrorCode.Timeout,
-    JsonRpcErrorCode.RateLimited,
-]);
 const MAX_BACKOFF_MS = 30_000;
 /** Strip the `https://openalex.org/` prefix an OA ID may carry. */
 function bareOaId(id) {
@@ -218,7 +211,7 @@ export class OpenAlexService {
                     throw signal.reason;
                 if (!(error instanceof McpError))
                     throw error;
-                if (!isTransient(error, RETRYABLE_CODES))
+                if (!defaultIsTransient(error))
                     throw error;
                 if (attempt < this.maxRetries) {
                     const baseDelay = Math.min(1000 * 2 ** attempt, MAX_BACKOFF_MS);

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

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.13",
+  "version": "2.10.15",
   "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",
@@ -9,7 +9,16 @@
   "bin": {
     "pubmed-mcp-server": "dist/index.js"
   },
-  "files": ["dist/", "README.md", "LICENSE", "CLAUDE.md", "AGENTS.md", "Dockerfile", "server.json"],
+  "files": [
+    "changelog/",
+    "dist/",
+    "README.md",
+    "LICENSE",
+    "CLAUDE.md",
+    "AGENTS.md",
+    "Dockerfile",
+    "server.json"
+  ],
   "scripts": {
     "build": "bun run scripts/build.ts",
     "rebuild": "bun run scripts/clean.ts && bun run build",
@@ -83,27 +92,27 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.13.0",
-    "defuddle": "^0.19.3",
+    "@cyanheads/mcp-ts-core": "^0.13.6",
+    "defuddle": "^0.19.4",
     "fast-xml-parser": "^5.11.1",
     "linkedom": "^0.18.13",
     "pino-pretty": "^13.1.3",
     "sanitize-html": "^2.17.7",
     "unpdf": "^1.8.1",
-    "zod": "^4.6.1"
+    "zod": "^4.6.5"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.13",
+    "@biomejs/biome": "^2.5.14",
     "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "^26.5.1",
+    "@types/node": "^26.6.2",
     "@types/sanitize-html": "^2.16.1",
-    "@vitest/coverage-istanbul": "^5.0.0",
+    "@vitest/coverage-istanbul": "^5.0.1",
     "depcheck": "^1.4.7",
-    "fast-check": "^4.9.0",
+    "fast-check": "^4.10.2",
     "ignore": "^7.0.9",
-    "tsc-alias": "^1.9.4",
+    "tsc-alias": "^1.9.5",
     "typescript": "^7.0.2",
-    "vitest": "^5.0.0"
+    "vitest": "^5.0.1"
   },
   "overrides": {
     "@hono/node-server": "^2.0.11",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.13",
+  "version": "2.10.15",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.13",
+      "version": "2.10.15",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.13",
+      "version": "2.10.15",
       "packageArguments": [
         {
           "type": "positional",

package/dist/services/retry-policy.d.ts

@@ -1,18 +0,0 @@
-/**
- * @fileoverview Shared transience check for the hand-rolled retry loops in the NCBI,
- * OpenAlex, and Europe PMC services. Mirrors the framework's `defaultIsTransient`
- * (`withRetry`, `@cyanheads/mcp-ts-core/utils`) so the three gates classify identically
- * to the framework path they don't use.
- * @module src/services/retry-policy
- */
-import type { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
-/**
- * Whether a thrown `McpError` should be retried. An explicit `data.retryable === false`
- * opt-out wins over code-based classification; absent (or `true`) the code decides.
- *
- * The HTTP helpers stamp the opt-out on an upstream 501, which classifies as
- * `ServiceUnavailable` — a transient code — but re-asks for a method the upstream has
- * declared absent, so it must fail on the first attempt.
- */
-export declare function isTransient(error: McpError, transientCodes: ReadonlySet<JsonRpcErrorCode>): boolean;
-//# sourceMappingURL=retry-policy.d.ts.map

package/dist/services/retry-policy.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"retry-policy.d.ts","sourceRoot":"","sources":["../../src/services/retry-policy.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAEhF;;;;;;;GAOG;AACH,wBAAgB,WAAW,CACzB,KAAK,EAAE,QAAQ,EACf,cAAc,EAAE,WAAW,CAAC,gBAAgB,CAAC,GAC5C,OAAO,CAGT"}

package/dist/services/retry-policy.js

@@ -1,21 +0,0 @@
-/**
- * @fileoverview Shared transience check for the hand-rolled retry loops in the NCBI,
- * OpenAlex, and Europe PMC services. Mirrors the framework's `defaultIsTransient`
- * (`withRetry`, `@cyanheads/mcp-ts-core/utils`) so the three gates classify identically
- * to the framework path they don't use.
- * @module src/services/retry-policy
- */
-/**
- * Whether a thrown `McpError` should be retried. An explicit `data.retryable === false`
- * opt-out wins over code-based classification; absent (or `true`) the code decides.
- *
- * The HTTP helpers stamp the opt-out on an upstream 501, which classifies as
- * `ServiceUnavailable` — a transient code — but re-asks for a method the upstream has
- * declared absent, so it must fail on the first attempt.
- */
-export function isTransient(error, transientCodes) {
-    if (error.data?.retryable === false)
-        return false;
-    return transientCodes.has(error.code);
-}
-//# sourceMappingURL=retry-policy.js.map

package/dist/services/retry-policy.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"retry-policy.js","sourceRoot":"","sources":["../../src/services/retry-policy.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAIH;;;;;;;GAOG;AACH,MAAM,UAAU,WAAW,CACzB,KAAe,EACf,cAA6C;IAE7C,IAAI,KAAK,CAAC,IAAI,EAAE,SAAS,KAAK,KAAK;QAAE,OAAO,KAAK,CAAC;IAClD,OAAO,cAAc,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;AACxC,CAAC"}