npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.18 → 2.10.20 - Mend

@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.20

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (121) hide show

package/dist/services/europe-pmc/api-client.js CHANGED Viewed

@@ -10,7 +10,6 @@
  */
 import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
-import { recoveryFor } from '../error-contracts.js';
 import { EUROPEPMC_API_BASE } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**
@@ -36,8 +35,8 @@ export class EuropePmcApiClient {
      * query is HTTP 200 with `hitCount: 0`. A 404 is reclassified from its
      * status-mapped `NotFound` to `ServiceUnavailable` so the service retries it.
      * A retryable 5xx keeps its code, so a 504 stays `Timeout`. Only a failure
-     * that ends up `ServiceUnavailable` carries `europepmc_unreachable` and its
-     * recovery hint, the one code that reason is declared for. An upstream
+     * that ends up `ServiceUnavailable` carries `europepmc_unreachable`, the one
+     * code that reason is declared for. An upstream
      * `retryAfter` is kept. A 429 and every other 4xx pass through unchanged, as
      * does a 501, whose `data.retryable: false` keeps it out of the retry loop.
      * (#152)
@@ -66,14 +65,13 @@ export class EuropePmcApiClient {
                 throw new McpError(code, `Europe PMC search request failed: ${error.message}`, {
                     ...(code === JsonRpcErrorCode.ServiceUnavailable && {
                         reason: 'europepmc_unreachable',
-                        ...recoveryFor('europepmc_unreachable'),
                     }),
                     status,
                     ...(error.data?.retryAfter !== undefined && { retryAfter: error.data.retryAfter }),
                 }, { cause: error });
             }
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`Europe PMC search request failed: ${msg}`, { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') }, { cause: error });
+            throw serviceUnavailable(`Europe PMC search request failed: ${msg}`, { reason: 'europepmc_unreachable' }, { cause: error });
         }
         return response.text();
     }
@@ -112,7 +110,7 @@ export class EuropePmcApiClient {
                 throw error;
             }
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`Europe PMC fullTextXML request failed: ${msg}`, { reason: 'europepmc_unreachable', epmcId, ...recoveryFor('europepmc_unreachable') }, { cause: error });
+            throw serviceUnavailable(`Europe PMC fullTextXML request failed: ${msg}`, { reason: 'europepmc_unreachable', epmcId }, { cause: error });
         }
         const xml = await response.text();
         if (!xml.trim()) {
@@ -159,7 +157,7 @@ export class EuropePmcApiClient {
             if (error instanceof McpError)
                 throw error;
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`Europe PMC links request failed: ${msg}`, { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') }, { cause: error });
+            throw serviceUnavailable(`Europe PMC links request failed: ${msg}`, { reason: 'europepmc_unreachable' }, { cause: error });
         }
         return response.text();
     }
@@ -183,12 +181,19 @@ export class EuropePmcApiClient {
  * optional source filter. EPMC's query syntax supports `SRC:"X"` field tokens —
  * the requested sources are OR-joined into a parenthesized clause and ANDed
  * with the caller's query.
+ *
+ * A single source is repeated (`SRC:"MED" OR SRC:"MED"`). Europe PMC matches
+ * nothing when a query is exactly one `EXT_ID` clause ANDed with one `SRC`
+ * clause and either value is quoted; the repeated clause matches quoted and
+ * unquoted `EXT_ID` alike and returns the same total as a lone clause for any
+ * other query. Multi-source clauses are sent as they are. (#175)
  */
 export function buildSearchQuery(params) {
     const base = params.query.trim();
     if (!params.sources || params.sources.length === 0)
         return base;
-    const sourceClause = params.sources.map((s) => `SRC:"${s}"`).join(' OR ');
+    const sources = params.sources.length === 1 ? [...params.sources, ...params.sources] : params.sources;
+    const sourceClause = sources.map((s) => `SRC:"${s}"`).join(' OR ');
     return `(${base}) AND (${sourceClause})`;
 }
 //# sourceMappingURL=api-client.js.map

package/dist/services/europe-pmc/api-client.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/services/europe-pmc/europe-pmc-service.d.ts CHANGED Viewed

@@ -14,6 +14,10 @@
  * 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 search reports the effective query Europe PMC echoes back, or — with no
  * echo — the source-filtered query it sent.
  *
@@ -51,12 +55,26 @@ export declare class EuropePmcService {
      * The retry boundary covers the fetch and the response classification
      * 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)
      */
     search(params: EuropePmcSearchParams): Promise<EuropePmcSearchResult>;
+    /**
+     * Whether Europe PMC serves the first page of the search in `params`: one
+     * request (`cursorMark: '*'`, `pageSize: 1`), paced like any other, with no
+     * retries of its own. Any failure reads as not served — except the caller's
+     * cancellation, which propagates.
+     */
+    private firstPageServed;
     /**
      * One search attempt: fetch, parse, and classify the body. `isLastAttempt`
-     * lets an empty envelope that has persisted through the whole retry budget
-     * be attributed to a caller-supplied cursor.
+     * lets an empty envelope on the last attempt the retry budget allows be
+     * attributed to a caller-supplied cursor.
      */
     private searchOnce;
     /**
@@ -129,6 +147,11 @@ export declare class EuropePmcService {
      * signal reaches the queue wait and the backoff sleep. `execute` receives the
      * one-based attempt number.
      *
+     * `reclassify`, when given, sees each failed attempt after its queue slot is
+     * released and before the retry decision, with the attempt's signal and its
+     * one-based number. The error it returns is the one the loop judges, so it
+     * can end the retries by returning a non-transient error.
+     *
      * A caller abort rethrows the caller's own reason; an exhausted failure is
      * reshaped by {@link toServiceError}, after the loop.
      */

package/dist/services/europe-pmc/europe-pmc-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AASH,OAAO,EAGL,KAAK,KAAK,EAGX,MAAM,8BAA8B,CAAC;AAMtC,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAoB,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AAEvE,OAAO,KAAK,EACV,uBAAuB,EAEvB,kBAAkB,EAElB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AAsGpB;;;;;;;;;;GAUG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;IAE7C,YACmB,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,MAAM,EAQpC;IAED;;;;;;;;;;;;;;OAcG;IACH,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA+BpE;IAED;;;;;OAKG;YACW,eAAe;IAgB7B;;;;OAIG;YACW,UAAU;IAyHxB;;;;;;;;;;OAUG;IACG,YAAY,CAChB,IAAI,EAAE,SAAS,kBAAkB,EAAE,EACnC,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAQ/B;IAED;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC,CASlC;IAED;;;;;;;;;;OAUG;IACH,SAAS,CACP,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;;;;;;OAUG;IACH,UAAU,CACR,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;OAKG;YACW,iBAAiB;IAkE/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS,CA4BlD;IAED;;;;;;;;;;;;;;;OAeG;YACW,QAAQ;CA8CvB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAyB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

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

@@ -14,6 +14,10 @@
  * 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 search reports the effective query Europe PMC echoes back, or — with no
  * echo — the source-filtered query it sent.
  *
@@ -28,7 +32,6 @@ import { defaultIsTransient, logger, requestContextService, withRetry, } from '@
 // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see ncbi/response-handler.ts
 import { XMLParser, XMLValidator } from 'fast-xml-parser';
 import { getServerConfig } from '../../config/server-config.js';
-import { recoveryFor } from '../error-contracts.js';
 import { ORDERED_XML_PARSER_OPTIONS } from '../ncbi/parsing/ordered-xml-parser-options.js';
 import { ensureArray } from '../ncbi/parsing/xml-helpers.js';
 import { buildSearchQuery, EuropePmcApiClient } from './api-client.js';
@@ -45,8 +48,8 @@ const isTransient = (error) => error instanceof McpError && defaultIsTransient(e
  * Reshapes an error whose retries ran out: the last attempt's code and message with
  * the attempt count appended, `label`, `attempts`, and the upstream `retryAfter`, so a
  * 429 still tells the caller how long to wait. Only a `ServiceUnavailable` gains
- * `europepmc_unreachable` and its hint; a `Timeout` or `RateLimited` keeps its code
- * with no reason, as the NCBI service reports them. Anything never retried — a
+ * `europepmc_unreachable`; a `Timeout` or `RateLimited` keeps its code with no
+ * reason, as the OpenAlex service reports them. Anything never retried — a
  * non-transient failure, or a `Retry-After` longer than the backoff cap — passes
  * through unchanged.
  */
@@ -55,10 +58,9 @@ function toServiceError(error, label) {
         return error;
     const last = error.cause instanceof McpError ? error.cause : error;
     const attempts = error.data.retryAttempts;
-    return new McpError(error.code, `${last.message} (failed after ${attempts} attempts)`, {
+    return new McpError(error.code, `${last.message} (failed after ${attempts} attempt${attempts === 1 ? '' : 's'})`, {
         ...(error.code === JsonRpcErrorCode.ServiceUnavailable && {
             reason: 'europepmc_unreachable',
-            ...recoveryFor('europepmc_unreachable'),
         }),
         label,
         attempts,
@@ -87,6 +89,15 @@ function recordLookupQuery({ epmcId, source }) {
     const extIdClause = `(EXT_ID:${epmcId} AND SRC:${source})`;
     return source === 'PMC' ? `${extIdClause} OR (PMCID:${epmcId})` : extIdClause;
 }
+/**
+ * The caller's cursor when it asks for a page past the first. `*` and an
+ * exactly-empty cursor both read as the first page upstream.
+ */
+function callerCursor({ cursorMark }) {
+    return cursorMark && cursorMark !== '*' ? cursorMark : undefined;
+}
+/** 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']);
 /**
@@ -143,14 +154,60 @@ export class EuropePmcService {
      * The retry boundary covers the fetch and the response classification
      * 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)
      */
     search(params) {
-        return this.runPaced('search', params.signal, (attempt) => this.searchOnce(params, attempt === this.maxRetries + 1));
+        const cursorMark = callerCursor(params);
+        let firstPage = 'unknown';
+        return this.runPaced('search', params.signal, (attempt) => this.searchOnce(params, attempt === this.maxRetries + 1), cursorMark === undefined
+            ? undefined
+            : async (error, signal, attempt) => {
+                if (!(error instanceof McpError) || error.data?.status !== 503)
+                    return error;
+                if (firstPage === 'unknown') {
+                    if (attempt <= this.maxRetries) {
+                        firstPage = (await this.firstPageServed(params, signal)) ? 'served' : 'failed';
+                    }
+                    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 });
+            });
+    }
+    /**
+     * Whether Europe PMC serves the first page of the search in `params`: one
+     * request (`cursorMark: '*'`, `pageSize: 1`), paced like any other, with no
+     * retries of its own. Any failure reads as not served — except the caller's
+     * cancellation, which propagates.
+     */
+    async firstPageServed(params, signal) {
+        try {
+            await this.queue.run(() => this.searchOnce({ ...params, cursorMark: '*', pageSize: 1, signal }, false), { signal });
+            return true;
+        }
+        catch (error) {
+            if (signal.aborted)
+                throw error;
+            return false;
+        }
     }
     /**
      * One search attempt: fetch, parse, and classify the body. `isLastAttempt`
-     * lets an empty envelope that has persisted through the whole retry budget
-     * be attributed to a caller-supplied cursor.
+     * lets an empty envelope on the last attempt the retry budget allows be
+     * attributed to a caller-supplied cursor.
      */
     async searchOnce(params, isLastAttempt) {
         const text = await this.client.search(params);
@@ -162,7 +219,6 @@ export class EuropePmcService {
             throw serializationError('Failed to parse Europe PMC search JSON response.', {
                 reason: 'europepmc_invalid_response',
                 responseSnippet: text.substring(0, 200),
-                ...recoveryFor('europepmc_invalid_response'),
             }, { cause: error });
         }
         /**
@@ -174,6 +230,7 @@ export class EuropePmcService {
         if (errMsg) {
             throw validationError(`Europe PMC rejected the request: ${errMsg}`, {
                 reason: 'europepmc_invalid_input',
+                retryable: false,
                 epmcErrCode: parsed.errCode,
                 epmcErrMsg: errMsg,
                 recovery: { hint: `Europe PMC reported: "${errMsg}". Fix the input and retry.` },
@@ -187,25 +244,28 @@ export class EuropePmcService {
          *
          * - A sort that EPMC rejects every time (see `sortExplainsEnvelope`) fails
          *   fast as non-retryable input — retrying only adds backoff.
-         * - A non-default cursor that draws it on every attempt is most likely
-         *   invalid or expired; EPMC rejects a malformed cursor every time.
+         * - A non-default cursor that draws it on the last attempt the retry budget
+         *   allows is most likely invalid or expired; EPMC rejects a malformed
+         *   cursor every time. Earlier attempts may have failed another way.
          * - Otherwise it is intermittent upstream noise — valid requests, with or
          *   without a documented sort, draw it on a fraction of calls and succeed
          *   when repeated — so it is thrown as a transient `europepmc_unreachable`
          *   for the retry loop, and never names the caller's input. (#159)
          *
          * Each throw keeps the diagnosis (message) apart from the next step
-         * (recovery hint): the framework mirrors `data.recovery.hint` into
-         * `content[]`, and one string passed as both renders byte-identical
-         * Error:/Recovery: blocks. (#75)
+         * (recovery hint): the framework renders `data.recovery.hint` in
+         * `content[]` as a `Recovery:` line only when the message does not already
+         * contain it, so one string passed as both would leave the caller the
+         * diagnosis and no separate next step. (#75)
          */
         if (parsed.hitCount === undefined &&
             parsed.request === undefined &&
             parsed.resultList === undefined) {
-            const cursorMark = params.cursorMark && params.cursorMark !== '*' ? params.cursorMark : undefined;
+            const cursorMark = callerCursor(params);
             if (params.sort && sortExplainsEnvelope(params.sort)) {
                 throw validationError(`Europe PMC silently rejected the request — most likely the sort "${params.sort}", which needs a documented field and an asc/desc direction.`, {
                     reason: 'europepmc_invalid_input',
+                    retryable: false,
                     sort: params.sort,
                     ...(cursorMark && { cursorMark }),
                     responseSnippet: text.substring(0, 200),
@@ -215,16 +275,15 @@ export class EuropePmcService {
                 });
             }
             if (cursorMark && isLastAttempt) {
-                throw validationError(`Europe PMC answered every attempt for cursorMark "${cursorMark}" with an empty response — the cursor is most likely invalid or expired.`, {
+                throw validationError(`Europe PMC answered the last attempt for cursorMark "${cursorMark}" with an empty response — the cursor is most likely invalid or expired.`, {
                     reason: 'europepmc_invalid_input',
+                    retryable: false,
                     cursorMark,
                     responseSnippet: text.substring(0, 200),
-                    recovery: {
-                        hint: 'Restart from the first page with `cursorMark: "*"`, or pass the exact `nextCursorMark` from the previous response.',
-                    },
+                    recovery: { hint: CURSOR_RECOVERY_HINT },
                 });
             }
-            throw serviceUnavailable('Europe PMC returned an empty response with no hit count or result list.', { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') });
+            throw serviceUnavailable('Europe PMC returned an empty response with no hit count or result list.', { reason: 'europepmc_unreachable' });
         }
         const hits = ensureArray(parsed.resultList?.result);
         // Without an echo, report the query actually sent — source filter included —
@@ -325,7 +384,6 @@ export class EuropePmcService {
             throw serializationError(`Failed to parse Europe PMC ${kind} JSON response.`, {
                 reason: 'europepmc_invalid_response',
                 responseSnippet: text.substring(0, 200),
-                ...recoveryFor('europepmc_invalid_response'),
             }, { cause: error });
         }
         /**
@@ -338,6 +396,7 @@ export class EuropePmcService {
         if (errMsg) {
             throw validationError(`Europe PMC rejected the ${kind} request: ${errMsg}`, {
                 reason: 'europepmc_invalid_input',
+                retryable: false,
                 epmcErrCode: parsed.errCode,
                 epmcErrMsg: errMsg,
                 recovery: { hint: `Europe PMC reported: "${errMsg}". Fix the input and retry.` },
@@ -382,7 +441,6 @@ export class EuropePmcService {
             throw serializationError('Received invalid XML from Europe PMC.', {
                 reason: 'europepmc_invalid_response',
                 responseSnippet: xml.substring(0, 200),
-                ...recoveryFor('europepmc_invalid_response'),
             });
         }
         let parsed;
@@ -395,7 +453,6 @@ export class EuropePmcService {
                 reason: 'europepmc_invalid_response',
                 parserError,
                 responseSnippet: xml.substring(0, 200),
-                ...recoveryFor('europepmc_invalid_response'),
             }, { cause: error });
         }
         if (!Array.isArray(parsed))
@@ -411,17 +468,25 @@ export class EuropePmcService {
      * signal reaches the queue wait and the backoff sleep. `execute` receives the
      * one-based attempt number.
      *
+     * `reclassify`, when given, sees each failed attempt after its queue slot is
+     * released and before the retry decision, with the attempt's signal and its
+     * one-based number. The error it returns is the one the loop judges, so it
+     * can end the retries by returning a non-transient error.
+     *
      * A caller abort rethrows the caller's own reason; an exhausted failure is
      * reshaped by {@link toServiceError}, after the loop.
      */
-    async runPaced(label, signal, execute) {
+    async runPaced(label, signal, execute, reclassify) {
         let attempt = 0;
         try {
             return await withRetry(({ signal: attemptSignal }) => {
                 const current = ++attempt;
                 return this.queue
                     .run(() => execute(current), { signal: attemptSignal })
-                    .catch((error) => {
+                    .catch(async (failure) => {
+                    const error = reclassify
+                        ? await reclassify(failure, attemptSignal, current)
+                        : failure;
                     if (current <= this.maxRetries && isTransient(error)) {
                         logger.warning(`Europe PMC ${label} failed on attempt ${current} of ${this.maxRetries + 1}.`, requestContextService.createRequestContext({
                             operation: 'EuropePmcRetry',

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

	@@ -1 +1 @@
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package/dist/services/europe-pmc/types.d.ts CHANGED Viewed

@@ -111,7 +111,12 @@ export interface EuropePmcSearchParams {
     signal?: AbortSignal;
     /** Optional sort spec, e.g. `FIRST_PIDATE desc`. */
     sort?: string;
-    /** Allowed sources, comma-joined into the query as `(SRC:"MED" OR ...)`. */
+    /**
+     * Allowed sources, OR-joined into a `(SRC:"MED" OR ...)` clause ANDed with the
+     * query. A single source is repeated (`SRC:"MED" OR SRC:"MED"`), since Europe
+     * PMC matches nothing for a lone quoted `EXT_ID` clause ANDed with a lone `SRC`
+     * clause. (#175)
+     */
     sources?: readonly EuropePmcSource[];
 }
 /**

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

	@@ -1 +1 @@
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package/dist/services/ncbi/api-client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/api-client.js CHANGED Viewed

@@ -6,7 +6,6 @@
  */
 import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { httpErrorFromResponse, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
-import { recoveryFor } from '../error-contracts.js';
 import { NCBI_EUTILS_BASE_URL } from './types.js';
 /** Maximum encoded query-string length before automatically switching to POST. */
 const POST_THRESHOLD = 2000;
@@ -51,7 +50,7 @@ export class NcbiApiClient {
             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, ...recoveryFor('ncbi_unreachable') }, { cause: error });
+            throw serviceUnavailable(`NCBI request failed: ${msg}`, { reason: 'ncbi_unreachable', endpoint }, { cause: error });
         }
     }
     /**
@@ -92,7 +91,7 @@ export class NcbiApiClient {
             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, ...recoveryFor('ncbi_unreachable') }, { cause: error });
+            throw serviceUnavailable(`NCBI request failed: ${msg}`, { reason: 'ncbi_unreachable', url }, { cause: error });
         }
     }
     buildParams(params) {

package/dist/services/ncbi/api-client.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/formatting/citation-formatter.d.ts CHANGED Viewed

@@ -21,6 +21,15 @@ export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
  * A Bookshelf record routes to {@link formatApaBook}.
  */
 export declare function formatApa(article: ParsedArticle): string;
+/**
+ * Format a PubMed article as an MLA 9th edition citation.
+ *
+ * Pattern:
+ * ```
+ * Last, First, et al. "Title." *Journal*, vol. 12, no. 3, 2024, pp. 45-67. DOI.
+ * ```
+ * A Bookshelf record routes to {@link formatMlaBook}.
+ */
 export declare function formatMla(article: ParsedArticle): string;
 /**
  * Format a PubMed article as a BibTeX entry.
@@ -43,6 +52,21 @@ export declare function formatBibtex(article: ParsedArticle): string;
  * Record ends with `ER  - ` (trailing spaces per spec).
  */
 export declare function formatRis(article: ParsedArticle): string;
+/**
+ * Format a PubMed article as a Vancouver (ICMJE/NLM) reference — the numbered
+ * style used by NEJM, Lancet, JAMA, BMJ, and most biomedical journals.
+ *
+ * Pattern (the leading list number is the consumer's responsibility — entries
+ * are formatted independently, so this returns the unnumbered reference body):
+ * ```
+ * Surname AB, Surname CD, et al. Article title. Abbrev J Name. Year;Vol(Issue):Pages. doi: 10.x/y
+ * ```
+ * 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
+ * no pagination it trails the source as an NLM note (`. pii: 2400512.`). A
+ * Bookshelf record routes to {@link formatVancouverBook}.
+ */
 export declare function formatVancouver(article: ParsedArticle): string;
 /**
  * Format a single article in the requested citation style.

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

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