@cyanheads/pubmed-mcp-server 2.10.20 → 2.10.22

package/dist/services/europe-pmc/europe-pmc-service.js

@@ -14,10 +14,13 @@
  * A search's retry boundary covers fetch and response classification, so
  * Europe PMC's intermittent empty `{ version }` envelope is retried like an
  * HTTP outage; only a sort or cursor that explains it is reported as bad input.
- * Europe PMC answers an unreadable cursor with the HTTP 503 it uses for an
- * outage, so a 503 on a caller-supplied cursor is checked against the first
- * page of the same query, and the cursor is blamed only when a retry draws
- * the 503 again while that first page was served.
+ * A `relevance` sort is sent as none, and a sort whose keys are not each one
+ * field plus `asc`/`desc` fails before the request. Europe PMC answers an
+ * unreadable cursor, and a sort it cannot use, with the HTTP 503 it uses for an
+ * outage, so a 503 on a caller-supplied cursor or a sort is checked against the
+ * first page of the same query — with the sort for the cursor, without it for
+ * the sort — and the input is blamed only when a retry draws the 503 again
+ * while that first page was served.
  * A search reports the effective query Europe PMC echoes back, or — with no
  * echo — the source-filtered query it sent.
  *
@@ -33,6 +36,7 @@ import { defaultIsTransient, logger, requestContextService, withRetry, } from '@
 import { XMLParser, XMLValidator } from 'fast-xml-parser';
 import { getServerConfig } from '../../config/server-config.js';
 import { ORDERED_XML_PARSER_OPTIONS } from '../ncbi/parsing/ordered-xml-parser-options.js';
+import { stripInvisibleFormatChars } from '../ncbi/parsing/text-helpers.js';
 import { ensureArray } from '../ncbi/parsing/xml-helpers.js';
 import { buildSearchQuery, EuropePmcApiClient } from './api-client.js';
 import { createEuropePmcRequestQueue } from './request-queue.js';
@@ -99,27 +103,60 @@ function callerCursor({ cursorMark }) {
 /** Next step for a cursor Europe PMC cannot read, whichever way it signals that. */
 const CURSOR_RECOVERY_HINT = "Pass the previous response's `nextCursorMark` verbatim as `cursorMark`, or `*` to restart from the first page.";
 /** The sort fields Europe PMC documents. */
-const DOCUMENTED_SORT_FIELDS = new Set(['P_PDATE_D', 'CITED', 'AUTH_FIRST', 'PUB_YEAR']);
+const DOCUMENTED_SORT_FIELDS = new Set([
+    'P_PDATE_D',
+    'CITED',
+    'AUTH_FIRST',
+    'PUB_YEAR',
+    'FIRST_IDATE_D',
+]);
+/** Next step for a sort Europe PMC cannot use, whichever way it signals that. */
+const SORT_RECOVERY_HINT = 'Use a documented sort (`P_PDATE_D desc`, `CITED desc`, `AUTH_FIRST asc`, `PUB_YEAR desc`, or `FIRST_IDATE_D desc`), or omit `sort` for relevance ranking.';
+/** `relevance`, alone or with `desc`: Europe PMC's default order, which it refuses as a sort. */
+const RELEVANCE_SORT_RE = /^\s*relevance(?:\s+desc)?\s*$/i;
+/** One sort key: a single field token and an `asc`/`desc` direction, any case and spacing. */
+const SORT_KEY_RE = /^\s*\S+\s+(?:asc|desc)\s*$/i;
 /**
- * Whether a sort is the likely cause of an empty `{ version }` envelope: one of
- * its comma-separated keys has a field outside the documented set, or lacks an
- * `asc`/`desc` direction. Europe PMC answers those shapes with the envelope on
- * every request, and orders by every key of a valid list (`PUB_YEAR desc, CITED
- * desc`). Field and direction compare case-insensitively and tolerate extra
- * whitespace, matching Europe PMC's own parsing.
+ * The sort a search sends. `relevance` and `relevance desc` read as no sort,
+ * since relevance is Europe PMC's default order and it refuses the word as a
+ * sort. Any other sort must be a comma-separated list of keys, each one field
+ * token plus `asc` or `desc`, or it fails here with no request: Europe PMC
+ * refuses every other shape (a key with no direction, an empty key, an extra
+ * token) on every request, with the HTTP 503 it also uses for an outage.
  *
- * Classification only, never a local allowlist: the request always goes out.
- * Europe PMC honors some undocumented fields (`ID asc` reorders results) and
- * silently ignores others (`SCORE desc`), so only the envelope itself decides.
+ * The field itself is never checked locally: Europe PMC honors some
+ * undocumented fields (`ID asc` reorders results), silently ignores others
+ * (`SCORE desc`), and refuses the rest with a 503 the search diagnoses by
+ * probing the same query unsorted. An empty or whitespace-only sort is no sort,
+ * as Europe PMC serves it. (#159, #239)
  */
-function sortExplainsEnvelope(sort) {
-    return sort.split(',').some((key) => {
-        const [field = '', direction = '', ...rest] = key.trim().split(/\s+/);
-        return (rest.length > 0 ||
-            !DOCUMENTED_SORT_FIELDS.has(field.toUpperCase()) ||
-            !/^(asc|desc)$/i.test(direction));
+function effectiveSort(sort) {
+    if (!sort?.trim() || RELEVANCE_SORT_RE.test(sort))
+        return;
+    if (sort.split(',').every((key) => SORT_KEY_RE.test(key)))
+        return sort;
+    throw validationError(`Europe PMC cannot use the sort "${sort}" — each comma-separated key needs one field and an \`asc\` or \`desc\` direction.`, {
+        reason: 'europepmc_invalid_input',
+        retryable: false,
+        sort,
+        recovery: { hint: SORT_RECOVERY_HINT },
     });
 }
+/**
+ * Whether a well-shaped sort is the likely cause of an empty `{ version }`
+ * envelope: one of its keys names a field outside the documented set. Europe
+ * PMC orders by every key of a valid list (`PUB_YEAR desc, CITED desc`); fields
+ * compare case-insensitively, matching its own parsing.
+ *
+ * Classification only, never a local allowlist: the request has already gone
+ * out, and only the envelope decides. Malformed keys never get this far —
+ * {@link effectiveSort} rejects them before the request. (#159)
+ */
+function sortExplainsEnvelope(sort) {
+    return sort
+        .split(',')
+        .some((key) => !DOCUMENTED_SORT_FIELDS.has(key.trim().split(/\s+/)[0]?.toUpperCase() ?? ''));
+}
 /**
  * Facade over the Europe PMC REST API:
  *   - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
@@ -155,38 +192,76 @@ export class EuropePmcService {
      * together, so an empty envelope retries like any other transient failure
      * rather than surfacing after the loop has already returned. (#159)
      *
-     * The first HTTP 503 on a caller-supplied cursor draws one probe of the same
-     * query's first page, and the cursor is retried either way: one 503 is not
-     * enough to tell a bad cursor from a transient outage. A later 503 fails the
-     * search at once as non-retryable input only when that probe was served;
-     * otherwise it goes on through the ordinary retry path. A 503 with no retry
-     * left is never probed, since nothing could use the answer. (#180)
+     * The sort is resolved before any request (see {@link effectiveSort}): a
+     * `relevance` sort is dropped, and a malformed one fails with no request.
+     *
+     * Europe PMC answers both an unreadable cursor and a sort it cannot use with
+     * the HTTP 503 it uses for an outage. The first 503 on a search carrying a
+     * caller-supplied cursor or a sort draws probes of the same query's first
+     * page, and the search is retried either way: one 503 is not enough to tell
+     * bad input from a transient outage. With a cursor, the first page with the
+     * sort is probed first (#180); when it is served, the cursor is the suspect.
+     * Otherwise, with a sort, the first page without the sort is probed — never
+     * with the caller's cursor, which Europe PMC binds to the sort that issued
+     * it — and when that is served, the sort is the suspect (#239). A later 503
+     * fails the search at once as non-retryable input naming the suspect; with
+     * no suspect it goes on through the ordinary retry path. A 503 with no retry
+     * left is never probed, since nothing could use the answer.
      */
-    search(params) {
-        const cursorMark = callerCursor(params);
-        let firstPage = 'unknown';
-        return this.runPaced('search', params.signal, (attempt) => this.searchOnce(params, attempt === this.maxRetries + 1), cursorMark === undefined
+    async search(params) {
+        const { sort: requestedSort, ...rest } = params;
+        const sort = effectiveSort(requestedSort);
+        const request = { ...rest, ...(sort && { sort }) };
+        const cursorMark = callerCursor(request);
+        let suspect;
+        return await this.runPaced('search', request.signal, (attempt) => this.searchOnce(request, attempt === this.maxRetries + 1), cursorMark === undefined && sort === undefined
             ? undefined
             : async (error, signal, attempt) => {
                 if (!(error instanceof McpError) || error.data?.status !== 503)
                     return error;
-                if (firstPage === 'unknown') {
+                if (suspect === undefined) {
                     if (attempt <= this.maxRetries) {
-                        firstPage = (await this.firstPageServed(params, signal)) ? 'served' : 'failed';
+                        suspect = await this.diagnose503(request, signal);
                     }
                     return error;
                 }
-                if (firstPage === 'failed')
-                    return error;
-                return validationError(`Europe PMC answered cursorMark "${cursorMark}" with HTTP 503 twice but served the first page of the same query — the cursor is most likely invalid or expired.`, {
-                    reason: 'europepmc_invalid_input',
-                    cursorMark,
-                    status: 503,
-                    retryable: false,
-                    recovery: { hint: CURSOR_RECOVERY_HINT },
-                }, { cause: error });
+                if (suspect === 'cursor') {
+                    return validationError(`Europe PMC answered cursorMark "${cursorMark}" with HTTP 503 twice but served the first page of the same query — the cursor is most likely invalid or expired.`, {
+                        reason: 'europepmc_invalid_input',
+                        cursorMark,
+                        status: 503,
+                        retryable: false,
+                        recovery: { hint: CURSOR_RECOVERY_HINT },
+                    }, { cause: error });
+                }
+                if (suspect === 'sort') {
+                    return validationError(`Europe PMC answered sort "${sort}" with HTTP 503 twice but served the same query without it — Europe PMC most likely cannot sort by it.`, {
+                        reason: 'europepmc_invalid_input',
+                        sort,
+                        status: 503,
+                        retryable: false,
+                        recovery: { hint: SORT_RECOVERY_HINT },
+                    }, { cause: error });
+                }
+                return error;
             });
     }
+    /**
+     * Which input, if any, explains a 503 on `request`: the caller's cursor when
+     * the first page with the same sort is served, the sort when the first page
+     * without it is served, otherwise neither.
+     */
+    async diagnose503(request, signal) {
+        if (callerCursor(request) !== undefined && (await this.firstPageServed(request, signal))) {
+            return 'cursor';
+        }
+        if (request.sort !== undefined) {
+            const { sort: _sort, ...unsorted } = request;
+            if (await this.firstPageServed(unsorted, signal))
+                return 'sort';
+        }
+        return 'none';
+    }
     /**
      * Whether Europe PMC serves the first page of the search in `params`: one
      * request (`cursorMark: '*'`, `pageSize: 1`), paced like any other, with no
@@ -263,15 +338,13 @@ export class EuropePmcService {
             parsed.resultList === undefined) {
             const cursorMark = callerCursor(params);
             if (params.sort && sortExplainsEnvelope(params.sort)) {
-                throw validationError(`Europe PMC silently rejected the request — most likely the sort "${params.sort}", which needs a documented field and an asc/desc direction.`, {
+                throw validationError(`Europe PMC silently rejected the request — most likely the sort "${params.sort}", which uses a field outside the documented set.`, {
                     reason: 'europepmc_invalid_input',
                     retryable: false,
                     sort: params.sort,
                     ...(cursorMark && { cursorMark }),
                     responseSnippet: text.substring(0, 200),
-                    recovery: {
-                        hint: 'Use a documented sort (`P_PDATE_D desc`, `CITED desc`, `AUTH_FIRST asc`, or `PUB_YEAR desc`), or omit `sort` for relevance ranking.',
-                    },
+                    recovery: { hint: SORT_RECOVERY_HINT },
                 });
             }
             if (cursorMark && isLastAttempt) {
@@ -433,7 +506,9 @@ export class EuropePmcService {
      *
      * Throws `SerializationError` only for fundamentally invalid XML; an
      * article-free but well-formed body returns `undefined` so callers can
-     * surface a `no-epmc-fulltext` outcome without a hard failure.
+     * surface a `no-epmc-fulltext` outcome without a hard failure. Invisible
+     * characters a deposit carries inside words are dropped before parsing, as
+     * on the PMC EFetch tier. (#224)
      */
     parseFullTextXml(xml) {
         const validationResult = XMLValidator.validate(xml.replace(/<!DOCTYPE[^>]*>/gi, ''));
@@ -445,7 +520,7 @@ export class EuropePmcService {
         }
         let parsed;
         try {
-            parsed = this.orderedXmlParser.parse(xml);
+            parsed = this.orderedXmlParser.parse(stripInvisibleFormatChars(xml));
         }
         catch (error) {
             const parserError = error instanceof Error ? error.message : String(error);

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

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

@@ -109,7 +109,11 @@ export interface EuropePmcSearchParams {
     /** Default `core` — richest payload with abstract, IDs, dates, license. */
     resultType?: 'core' | 'lite' | 'idlist';
     signal?: AbortSignal;
-    /** Optional sort spec, e.g. `FIRST_PIDATE desc`. */
+    /**
+     * Optional sort spec: comma-separated `<field> asc|desc` keys, e.g.
+     * `CITED desc` or `PUB_YEAR desc, CITED desc`. `relevance` (Europe PMC's
+     * default order) is sent as no sort.
+     */
     sort?: string;
     /**
      * Allowed sources, OR-joined into a `(SRC:"MED" OR ...)` clause ANDed with the

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

@@ -1 +1 @@
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package/dist/services/fetch-redaction.d.ts

@@ -0,0 +1,23 @@
+/**
+ * @fileoverview Keeps request URLs out of the text of fetch rejections. Runtimes can
+ * quote the whole request URL in a rejection message (Bun 1.4 does, for some malformed
+ * responses, in both the header and the body phase), and these services' query strings
+ * carry an API key, the operator's contact email, and the caller's query. The message
+ * becomes caller-facing error text, and the rejection rides `cause` into the log
+ * record's cause chain, so every URL in it is cut to its origin first.
+ * @module src/services/fetch-redaction
+ */
+/**
+ * A fetch rejection with every URL its text quotes reduced to the URL's origin. An
+ * `Error` is rewritten in place, keeping its identity and transport `code`; one whose
+ * `message` refuses the write is replaced by a stand-in carrying its `name` and `code`.
+ * A non-`Error` rejection comes back as its redacted text.
+ */
+export declare function redactRejection(error: unknown): unknown;
+/**
+ * Awaits a response-body read (`response.text()`, `.json()`, `.arrayBuffer()`),
+ * rethrowing its rejection with {@link redactRejection} applied. A failure while the
+ * body streams is otherwise unchanged: same error, same classification.
+ */
+export declare function readBody<T>(read: Promise<T>): Promise<T>;
+//# sourceMappingURL=fetch-redaction.d.ts.map

package/dist/services/fetch-redaction.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"fetch-redaction.d.ts","sourceRoot":"","sources":["../../src/services/fetch-redaction.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAiBH;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,OAAO,GAAG,OAAO,CAcvD;AAED;;;;GAIG;AACH,wBAAsB,QAAQ,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAM9D"}

package/dist/services/fetch-redaction.js

@@ -0,0 +1,62 @@
+/**
+ * @fileoverview Keeps request URLs out of the text of fetch rejections. Runtimes can
+ * quote the whole request URL in a rejection message (Bun 1.4 does, for some malformed
+ * responses, in both the header and the body phase), and these services' query strings
+ * carry an API key, the operator's contact email, and the caller's query. The message
+ * becomes caller-facing error text, and the rejection rides `cause` into the log
+ * record's cause chain, so every URL in it is cut to its origin first.
+ * @module src/services/fetch-redaction
+ */
+/** An absolute `http:`/`https:` URL inside free text, up to the first quote, bracket, or space. */
+const EMBEDDED_URL = /https?:\/\/[^\s"'`<>]+/gi;
+/**
+ * Names a URL by its origin, path and query elided behind markers
+ * (`https://host/…?…`); an unparseable one becomes a fixed placeholder.
+ */
+function redactUrl(url) {
+    const parsed = URL.parse(url);
+    if (!parsed)
+        return '[unparseable URL]';
+    const path = parsed.pathname === '/' ? '' : '/…';
+    const query = parsed.search ? '?…' : '';
+    return `${parsed.origin}${path}${query}`;
+}
+/**
+ * A fetch rejection with every URL its text quotes reduced to the URL's origin. An
+ * `Error` is rewritten in place, keeping its identity and transport `code`; one whose
+ * `message` refuses the write is replaced by a stand-in carrying its `name` and `code`.
+ * A non-`Error` rejection comes back as its redacted text.
+ */
+export function redactRejection(error) {
+    if (!(error instanceof Error))
+        return String(error).replace(EMBEDDED_URL, redactUrl);
+    const message = error.message.replace(EMBEDDED_URL, redactUrl);
+    if (message === error.message)
+        return error;
+    try {
+        error.message = message;
+    }
+    catch {
+        // A frozen or read-only `message`; the stand-in below takes over.
+    }
+    if (error.message === message)
+        return error;
+    const standIn = new Error(message);
+    standIn.name = error.name;
+    const { code } = error;
+    return typeof code === 'string' ? Object.assign(standIn, { code }) : standIn;
+}
+/**
+ * Awaits a response-body read (`response.text()`, `.json()`, `.arrayBuffer()`),
+ * rethrowing its rejection with {@link redactRejection} applied. A failure while the
+ * body streams is otherwise unchanged: same error, same classification.
+ */
+export async function readBody(read) {
+    try {
+        return await read;
+    }
+    catch (error) {
+        throw redactRejection(error);
+    }
+}
+//# sourceMappingURL=fetch-redaction.js.map

package/dist/services/fetch-redaction.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fetch-redaction.js","sourceRoot":"","sources":["../../src/services/fetch-redaction.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,mGAAmG;AACnG,MAAM,YAAY,GAAG,0BAA0B,CAAC;AAEhD;;;GAGG;AACH,SAAS,SAAS,CAAC,GAAW;IAC5B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;IAC9B,IAAI,CAAC,MAAM;QAAE,OAAO,mBAAmB,CAAC;IACxC,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;IACjD,MAAM,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;IACxC,OAAO,GAAG,MAAM,CAAC,MAAM,GAAG,IAAI,GAAG,KAAK,EAAE,CAAC;AAC3C,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,eAAe,CAAC,KAAc;IAC5C,IAAI,CAAC,CAAC,KAAK,YAAY,KAAK,CAAC;QAAE,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;IACrF,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;IAC/D,IAAI,OAAO,KAAK,KAAK,CAAC,OAAO;QAAE,OAAO,KAAK,CAAC;IAC5C,IAAI,CAAC;QACH,KAAK,CAAC,OAAO,GAAG,OAAO,CAAC;IAC1B,CAAC;IAAC,MAAM,CAAC;QACP,kEAAkE;IACpE,CAAC;IACD,IAAI,KAAK,CAAC,OAAO,KAAK,OAAO;QAAE,OAAO,KAAK,CAAC;IAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC;IACnC,OAAO,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC;IAC1B,MAAM,EAAE,IAAI,EAAE,GAAG,KAA2B,CAAC;IAC7C,OAAO,OAAO,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;AAC/E,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAI,IAAgB;IAChD,IAAI,CAAC;QACH,OAAO,MAAM,IAAI,CAAC;IACpB,CAAC;IAAC,OAAO,KAAc,EAAE,CAAC;QACxB,MAAM,eAAe,CAAC,KAAK,CAAC,CAAC;IAC/B,CAAC;AACH,CAAC"}

package/dist/services/ncbi/api-client.d.ts

@@ -25,6 +25,9 @@ export declare class NcbiApiClient {
      * Uses plain fetch (not fetchWithTimeout) so we can capture response bodies on
      * error status codes — fetchWithTimeout throws before the body can be read.
      * Injects tool and email params but not api_key (eutils-specific).
+     *
+     * Records and error data name the URL's host and the caller's own params,
+     * never the request URL, whose query carries the operator's email.
      */
     makeExternalRequest(url: string, params: NcbiRequestParams, externalSignal?: AbortSignal): Promise<string>;
     private buildParams;

package/dist/services/ncbi/api-client.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAOH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAoBnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,mBAAmB,EAAI;IAEtD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC,CAqCjB;IAED;;;;;;;;OAQG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC,CAwCjB;IAED,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB;;;;OAIG;IACH,OAAO,CAAC,UAAU;IAUlB,sFAAsF;IACtF,OAAO,CAAC,WAAW;IAcnB;;;OAGG;IACH,OAAO,CAAC,kBAAkB;CAI3B"}

package/dist/services/ncbi/api-client.js

@@ -6,9 +6,20 @@
  */
 import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { httpErrorFromResponse, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { redactRejection } from '../fetch-redaction.js';
 import { NCBI_EUTILS_BASE_URL } from './types.js';
 /** Maximum encoded query-string length before automatically switching to POST. */
 const POST_THRESHOLD = 2000;
+/**
+ * Wraps a non-`McpError` fetch rejection — header or body phase — as `ncbi_unreachable`.
+ * The request URL carries `api_key` and the operator's `email`, and a runtime can quote
+ * it in the rejection text, so that text is redacted before it becomes the message.
+ */
+function unreachable(error, data) {
+    const cause = redactRejection(error);
+    const msg = cause instanceof Error ? cause.message : String(cause);
+    return serviceUnavailable(`NCBI request failed: ${msg}`, { reason: 'ncbi_unreachable', ...data }, { cause });
+}
 /**
  * Low-level HTTP client for NCBI E-utilities. Constructs URLs, injects credentials,
  * and chooses GET/POST based on payload size. Single-attempt — retry logic lives
@@ -25,7 +36,7 @@ export class NcbiApiClient {
         const suffix = endpoint.includes('.') ? '' : '.fcgi';
         const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}${suffix}`;
         try {
-            logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, requestContextService.createRequestContext({
+            logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${endpoint}`, requestContextService.createRequestContext({
                 operation: 'NcbiHttpRequest',
                 additionalContext: { endpoint },
             }));
@@ -49,8 +60,7 @@ export class NcbiApiClient {
         catch (error) {
             if (error instanceof McpError)
                 throw error;
-            const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`NCBI request failed: ${msg}`, { reason: 'ncbi_unreachable', endpoint }, { cause: error });
+            throw unreachable(error, { endpoint });
         }
     }
     /**
@@ -58,6 +68,9 @@ export class NcbiApiClient {
      * Uses plain fetch (not fetchWithTimeout) so we can capture response bodies on
      * error status codes — fetchWithTimeout throws before the body can be read.
      * Injects tool and email params but not api_key (eutils-specific).
+     *
+     * Records and error data name the URL's host and the caller's own params,
+     * never the request URL, whose query carries the operator's email.
      */
     async makeExternalRequest(url, params, externalSignal) {
         const finalParams = {
@@ -70,11 +83,12 @@ export class NcbiApiClient {
         }
         const qs = new URLSearchParams(finalParams).toString();
         const fullUrl = qs ? `${url}?${qs}` : url;
+        const host = URL.parse(url)?.host;
         const signal = this.buildTimeoutSignal(externalSignal);
         try {
-            logger.debug(`NCBI external request: GET ${fullUrl}`, requestContextService.createRequestContext({
+            logger.debug('NCBI external request: GET', requestContextService.createRequestContext({
                 operation: 'NcbiExternalRequest',
-                additionalContext: { url },
+                additionalContext: { host, params },
             }));
             const response = await fetch(fullUrl, { signal });
             const body = await response.text();
@@ -82,7 +96,7 @@ export class NcbiApiClient {
                 throw await httpErrorFromResponse(response, {
                     service: 'NCBI',
                     captureBody: false,
-                    data: { url, body: body.substring(0, 500) },
+                    data: { host, body: body.substring(0, 500) },
                 });
             }
             return body;
@@ -90,8 +104,7 @@ export class NcbiApiClient {
         catch (error) {
             if (error instanceof McpError)
                 throw error;
-            const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`NCBI request failed: ${msg}`, { reason: 'ncbi_unreachable', url }, { cause: error });
+            throw unreachable(error, { host });
         }
     }
     buildParams(params) {

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package/dist/services/ncbi/formatting/citation-formatter.d.ts

@@ -4,9 +4,23 @@
  * Pure TypeScript, zero dependencies, Workers-compatible.
  * @module src/services/ncbi/formatting/citation-formatter
  */
-import type { ParsedArticle } from '../types.js';
+import type { ParsedArticle, ParsedCommentsCorrection } from '../types.js';
 /** Supported citation output formats. */
 export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
+/**
+ * NCBI `RefType`s that qualify the cited article itself — it was retracted,
+ * corrected, or questioned. A link from a record that is itself a notice
+ * (`RetractionOf`, `ErratumFor`) and comment or update links are not among them:
+ * citing a retraction notice is not citing a retracted work. (#215)
+ */
+export declare const CITATION_NOTICE_TYPES: readonly ['RetractionIn', 'RetractedandRepublishedIn', 'ExpressionOfConcernIn', 'ErratumIn', 'CorrectedandRepublishedIn'];
+export type CitationNoticeType = (typeof CITATION_NOTICE_TYPES)[number];
+/** A linked notice that qualifies the cited article. */
+export type CitationNotice = ParsedCommentsCorrection & {
+    refType: CitationNoticeType;
+};
+/** The record's linked notices that qualify the cited article, in NCBI's order. */
+export declare function citationNotices(article: ParsedArticle): CitationNotice[];
 /**
  * Format a PubMed article as an APA 7th edition citation.
  *
@@ -18,7 +32,8 @@ export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
  * ```
  * Title. (Year). *Journal*, *Volume*(Issue), Pages. https://doi.org/DOI
  * ```
- * A Bookshelf record routes to {@link formatApaBook}.
+ * A retracted article ends on `(Retraction published <RefSource>)`. A Bookshelf
+ * record routes to {@link formatApaBook}.
  */
 export declare function formatApa(article: ParsedArticle): string;
 /**
@@ -63,8 +78,9 @@ export declare function formatRis(article: ParsedArticle): string;
  * ```
  * Journal name uses the NLM/ISO abbreviation when available; pages are used as
  * PubMed supplies them (often elided, e.g. "583-9"); the DOI carries no trailing
- * period so it stays copy-pasteable. An article number replaces nothing — with
+ * period so it stays copy-pasteable, unless a note follows it. An article number replaces nothing — with
  * no pagination it trails the source as an NLM note (`. pii: 2400512.`). A
+ * retraction or erratum follows as a note (`Retraction in: <RefSource>`). A
  * Bookshelf record routes to {@link formatVancouverBook}.
  */
 export declare function formatVancouver(article: ParsedArticle): string;

package/dist/services/ncbi/formatting/citation-formatter.d.ts.map

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