npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.1 → 2.10.3 - Mend

@cyanheads/pubmed-mcp-server 2.10.1 → 2.10.3

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 (63) hide show

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

@@ -32,7 +32,7 @@ export class EuropePmcApiClient {
         const url = this.buildSearchUrl(params);
         const ctx = requestContextService.createRequestContext({
             operation: 'EuropePmcSearch',
-            query: params.query,
+            additionalContext: { query: params.query },
         });
         let response;
         try {
@@ -63,7 +63,7 @@ export class EuropePmcApiClient {
         const url = `${EUROPEPMC_API_BASE}/${encodeURIComponent(epmcId)}/fullTextXML`;
         const ctx = requestContextService.createRequestContext({
             operation: 'EuropePmcFullTextXml',
-            epmcId,
+            additionalContext: { epmcId },
         });
         let response;
         try {
@@ -90,7 +90,7 @@ export class EuropePmcApiClient {
         if (!xml.trim()) {
             logger.debug('Europe PMC returned an empty fullTextXML body.', requestContextService.createRequestContext({
                 operation: 'EuropePmcFullTextXmlEmpty',
-                epmcId,
+                additionalContext: { epmcId },
             }));
             return { kind: 'not-available', reason: 'EPMC returned an empty fullTextXML body' };
         }
@@ -116,7 +116,10 @@ export class EuropePmcApiClient {
     }
     /** Helper: fetch a links (citations/references) JSON URL and return the body. */
     async fetchLinksJson(url, operation, pmid, signal) {
-        const ctx = requestContextService.createRequestContext({ operation, pmid });
+        const ctx = requestContextService.createRequestContext({
+            operation,
+            additionalContext: { pmid },
+        });
         let response;
         try {
             response = await fetchWithTimeout(url, this.config.timeoutMs, ctx, {

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

@@ -40,12 +40,14 @@ export declare class EuropePmcService {
     search(params: EuropePmcSearchParams): Promise<EuropePmcSearchResult>;
     /**
      * Look up specific records by `source` + EPMC id. One search request covers
-     * the whole batch: each ref becomes an `(EXT_ID:<id> AND SRC:<source>)`
-     * clause, OR-joined into a single query.
+     * the whole batch: each ref becomes a `recordLookupQuery` clause, OR-joined
+     * into a single query.
      *
      * Returns the hits Europe PMC resolved, in the order it returned them.
      * Unmatched refs are simply absent — callers diff against their own request
-     * to report misses rather than getting a padded array back.
+     * to report misses rather than getting a padded array back. A `PMC` ref can
+     * resolve to a `MED`-source hit that reports the requested PMCID in `pmcid`
+     * rather than as its `id`, so that diff matches on the PMCID too.
      */
     fetchRecords(refs: readonly EuropePmcRecordRef[], signal?: AbortSignal): Promise<EuropePmcSearchHit[]>;
     /**

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

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

@@ -53,9 +53,20 @@ function abortableSleep(ms, signal) {
  * `EXT_ID:"<id>" AND SRC:<source>` — quotes survive on an identifier token only
  * while no `AND SRC:` clause follows it. Callers pass ids through a schema that
  * restricts them to identifier characters, so no escaping is applied here.
+ *
+ * `SRC:PMC` alone under-resolves: the PMC corpus holds only articles Europe PMC
+ * has no PubMed record for. Once an article is indexed in PubMed its canonical
+ * record moves to `MED` and carries the PMCID as a field, so `EXT_ID:PMC8371605
+ * AND SRC:PMC` matches nothing while `PMCID:PMC8371605` resolves it. OR the two
+ * together for `PMC` so both corpus placements resolve from one request. The
+ * same asymmetry drove the PMCID branch of `pubmed_fetch_fulltext` (#85); that
+ * path can drop the `SRC:PMC` clause outright because it never takes a
+ * caller-supplied source, whereas this one must still serve genuine PMC-only
+ * records. (#94)
  */
 function recordLookupQuery({ epmcId, source }) {
-    return `(EXT_ID:${epmcId} AND SRC:${source})`;
+    const extIdClause = `(EXT_ID:${epmcId} AND SRC:${source})`;
+    return source === 'PMC' ? `${extIdClause} OR (PMCID:${epmcId})` : extIdClause;
 }
 /**
  * Facade over the Europe PMC REST API:
@@ -176,12 +187,14 @@ export class EuropePmcService {
     }
     /**
      * Look up specific records by `source` + EPMC id. One search request covers
-     * the whole batch: each ref becomes an `(EXT_ID:<id> AND SRC:<source>)`
-     * clause, OR-joined into a single query.
+     * the whole batch: each ref becomes a `recordLookupQuery` clause, OR-joined
+     * into a single query.
      *
      * Returns the hits Europe PMC resolved, in the order it returned them.
      * Unmatched refs are simply absent — callers diff against their own request
-     * to report misses rather than getting a padded array back.
+     * to report misses rather than getting a padded array back. A `PMC` ref can
+     * resolve to a `MED`-source hit that reports the requested PMCID in `pmcid`
+     * rather than as its `id`, so that diff matches on the PMCID too.
      */
     async fetchRecords(refs, signal) {
         const result = await this.search({
@@ -327,9 +340,7 @@ export class EuropePmcService {
                     const retryDelay = Math.round(jitter);
                     logger.warning(`Europe PMC ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, requestContextService.createRequestContext({
                         operation: 'EuropePmcRetry',
-                        label,
-                        attempt: attempt + 1,
-                        retryDelay,
+                        additionalContext: { label, attempt: attempt + 1, retryDelay },
                     }));
                     await abortableSleep(retryDelay, signal);
                     continue;
@@ -372,10 +383,12 @@ export function initEuropePmcService() {
     _service = new EuropePmcService(client, queue, config.europepmcMaxRetries);
     logger.info('Europe PMC service initialized.', requestContextService.createRequestContext({
         operation: 'EuropePmcInit',
-        requestDelayMs: config.europepmcRequestDelayMs,
-        maxRetries: config.europepmcMaxRetries,
-        timeoutMs: config.europepmcTimeoutMs,
-        hasEmail: !!config.europepmcEmail,
+        additionalContext: {
+            requestDelayMs: config.europepmcRequestDelayMs,
+            maxRetries: config.europepmcMaxRetries,
+            timeoutMs: config.europepmcTimeoutMs,
+            hasEmail: !!config.europepmcEmail,
+        },
     }));
 }
 /** Returns the initialized service, or `undefined` when EPMC is disabled. */

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

	@@ -1 +1 @@
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	@@ -1 +1 @@
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1	+ {"version":3,"file":"request-queue.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAeH;;;;;;;;;;;;GAYG;AACH,qBAAa,qBAAqB;IAChC,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAgB;IACxC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAK;IACrB,OAAO,CAAC,aAAa,CAAK;IAC1B,OAAO,CAAC,iBAAiB,CAA4C;IAErE,YAAY,aAAa,EAAE,MAAM,EAAE,aAAa,GAAE,MAA+B,EAGhF;IAED,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,OAAO,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,CA6BlF;IAED,OAAO,CAAC,WAAW;CAwDpB"}

package/dist/services/europe-pmc/request-queue.js CHANGED Viewed

@@ -83,17 +83,21 @@ export class EuropePmcRequestQueue {
             this.inFlight += 1;
             logger.debug(`Executing Europe PMC request via queue: ${waiter.label}`, requestContextService.createRequestContext({
                 operation: 'EuropePmcQueueDispatch',
-                label: waiter.label,
-                inFlight: this.inFlight,
-                queueDepth: this.waiters.length,
+                additionalContext: {
+                    label: waiter.label,
+                    inFlight: this.inFlight,
+                    queueDepth: this.waiters.length,
+                },
             }));
             Promise.resolve()
                 .then(() => waiter.task())
                 .then(waiter.resolve, (err) => {
                 logger.error('Error processing Europe PMC request from queue.', requestContextService.createRequestContext({
                     operation: 'EuropePmcQueueProcess',
-                    label: waiter.label,
-                    errorMessage: err instanceof Error ? err.message : String(err),
+                    additionalContext: {
+                        label: waiter.label,
+                        errorMessage: err instanceof Error ? err.message : String(err),
+                    },
                 }));
                 waiter.reject(err);
             })

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

	@@ -1 +1 @@
1	- {"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE7E,MAAM,sBAAsB,GAAG,CAAC,CAAC;AAWjC;;;;;;;;;;;;GAYG;AACH,MAAM,OAAO,qBAAqB;IACf,OAAO,GAAa,EAAE,CAAC;IACvB,aAAa,CAAS;IACtB,aAAa,CAAS;IAC/B,QAAQ,GAAG,CAAC,CAAC;IACb,aAAa,GAAG,CAAC,CAAC;IAClB,iBAAiB,CAA4C;IAErE,YAAY,aAAqB,EAAE,aAAa,GAAW,sBAAsB;QAC/E,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;QACnC,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;IACrC,CAAC;IAED,OAAO,CAAI,IAAsB,EAAE,KAAa,EAAE,MAAoB;QACpE,OAAO,IAAI,OAAO,CAAI,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;YACxC,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;gBACpB,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACtB,OAAO;YACT,CAAC;YAED,MAAM,MAAM,GAAc;gBACxB,OAAO;gBACP,MAAM;gBACN,IAAI;gBACJ,KAAK;gBACL,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC;YAEF,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,OAAO,GAAG,GAAG,EAAE;oBACnB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,MAAgB,CAAC,CAAC;oBACnD,IAAI,GAAG,KAAK,CAAC,CAAC;wBAAE,OAAO;oBACvB,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC;oBAC5B,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,CAAC,CAAC;gBACF,MAAM,CAAC,OAAO,GAAG,OAAO,CAAC;gBACzB,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;YAC5D,CAAC;YAED,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,MAAgB,CAAC,CAAC;YACpC,IAAI,CAAC,WAAW,EAAE,CAAC;QACrB,CAAC,CAAC,CAAC;IACL,CAAC;IAEO,WAAW;QACjB,IAAI,IAAI,CAAC,iBAAiB,KAAK,SAAS;YAAE,OAAO;QAEjD,OAAO,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACrE,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YACvB,MAAM,GAAG,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC;YAC5D,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,IAAI,CAAC,iBAAiB,GAAG,UAAU,CAAC,GAAG,EAAE;oBACvC,IAAI,CAAC,iBAAiB,GAAG,SAAS,CAAC;oBACnC,IAAI,CAAC,WAAW,EAAE,CAAC;gBACrB,CAAC,EAAE,GAAG,CAAC,CAAC;gBACR,OAAO;YACT,CAAC;YAED,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;YACpC,IAAI,CAAC,MAAM;gBAAE,OAAO;YAEpB,IAAI,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBACpC,MAAM,CAAC,MAAM,CAAC,mBAAmB,CAAC,OAAO,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;YAC7D,CAAC;YAED,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAChC,IAAI,CAAC,QAAQ,IAAI,CAAC,CAAC;YACnB,MAAM,CAAC,KAAK,CACV,2CAA2C,MAAM,CAAC,KAAK,EAAE,EACzD,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,SAAS,EAAE,wBAAwB;gBACnC,KAAK,EAAE,MAAM,CAAC,KAAK;~~gBACnB~~,QAAQ,EAAE,IAAI,CAAC,QAAQ;~~gBACvB~~,UAAU,EAAE,IAAI,CAAC,OAAO,CAAC,MAAM;~~aAChC~~,CAAC,CACH,CAAC;YAEF,OAAO,CAAC,OAAO,EAAE;iBACd,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC;iBACzB,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,GAAG,EAAE,EAAE;gBAC5B,MAAM,CAAC,KAAK,CACV,iDAAiD,EACjD,qBAAqB,CAAC,oBAAoB,CAAC;oBACzC,SAAS,EAAE,uBAAuB;oBAClC,KAAK,EAAE,MAAM,CAAC,KAAK;~~oBACnB~~,YAAY,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;~~iBAC~~/D,CAAC,CACH,CAAC;gBACF,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YACrB,CAAC,CAAC;iBACD,OAAO,CAAC,GAAG,EAAE;gBACZ,IAAI,CAAC,QAAQ,IAAI,CAAC,CAAC;gBACnB,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,CAAC,CAAC,CAAC;QACP,CAAC;IACH,CAAC;CACF"}
1	+ {"version":3,"file":"request-queue.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/request-queue.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE7E,MAAM,sBAAsB,GAAG,CAAC,CAAC;AAWjC;;;;;;;;;;;;GAYG;AACH,MAAM,OAAO,qBAAqB;IACf,OAAO,GAAa,EAAE,CAAC;IACvB,aAAa,CAAS;IACtB,aAAa,CAAS;IAC/B,QAAQ,GAAG,CAAC,CAAC;IACb,aAAa,GAAG,CAAC,CAAC;IAClB,iBAAiB,CAA4C;IAErE,YAAY,aAAqB,EAAE,aAAa,GAAW,sBAAsB;QAC/E,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;QACnC,IAAI,CAAC,aAAa,GAAG,aAAa,CAAC;IACrC,CAAC;IAED,OAAO,CAAI,IAAsB,EAAE,KAAa,EAAE,MAAoB;QACpE,OAAO,IAAI,OAAO,CAAI,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;YACxC,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;gBACpB,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACtB,OAAO;YACT,CAAC;YAED,MAAM,MAAM,GAAc;gBACxB,OAAO;gBACP,MAAM;gBACN,IAAI;gBACJ,KAAK;gBACL,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;aAC1B,CAAC;YAEF,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,OAAO,GAAG,GAAG,EAAE;oBACnB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,MAAgB,CAAC,CAAC;oBACnD,IAAI,GAAG,KAAK,CAAC,CAAC;wBAAE,OAAO;oBACvB,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC;oBAC5B,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,CAAC,CAAC;gBACF,MAAM,CAAC,OAAO,GAAG,OAAO,CAAC;gBACzB,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;YAC5D,CAAC;YAED,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,MAAgB,CAAC,CAAC;YACpC,IAAI,CAAC,WAAW,EAAE,CAAC;QACrB,CAAC,CAAC,CAAC;IACL,CAAC;IAEO,WAAW;QACjB,IAAI,IAAI,CAAC,iBAAiB,KAAK,SAAS;YAAE,OAAO;QAEjD,OAAO,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACrE,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YACvB,MAAM,GAAG,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC;YAC5D,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,IAAI,CAAC,iBAAiB,GAAG,UAAU,CAAC,GAAG,EAAE;oBACvC,IAAI,CAAC,iBAAiB,GAAG,SAAS,CAAC;oBACnC,IAAI,CAAC,WAAW,EAAE,CAAC;gBACrB,CAAC,EAAE,GAAG,CAAC,CAAC;gBACR,OAAO;YACT,CAAC;YAED,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;YACpC,IAAI,CAAC,MAAM;gBAAE,OAAO;YAEpB,IAAI,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBACpC,MAAM,CAAC,MAAM,CAAC,mBAAmB,CAAC,OAAO,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;YAC7D,CAAC;YAED,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAChC,IAAI,CAAC,QAAQ,IAAI,CAAC,CAAC;YACnB,MAAM,CAAC,KAAK,CACV,2CAA2C,MAAM,CAAC,KAAK,EAAE,EACzD,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,SAAS,EAAE,wBAAwB;gBACnC,iBAAiB,EAAE;oBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;oBACnB,QAAQ,EAAE,IAAI,CAAC,QAAQ;oBACvB,UAAU,EAAE,IAAI,CAAC,OAAO,CAAC,MAAM;iBAChC;aACF,CAAC,CACH,CAAC;YAEF,OAAO,CAAC,OAAO,EAAE;iBACd,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC;iBACzB,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,GAAG,EAAE,EAAE;gBAC5B,MAAM,CAAC,KAAK,CACV,iDAAiD,EACjD,qBAAqB,CAAC,oBAAoB,CAAC;oBACzC,SAAS,EAAE,uBAAuB;oBAClC,iBAAiB,EAAE;wBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;wBACnB,YAAY,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;qBAC/D;iBACF,CAAC,CACH,CAAC;gBACF,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YACrB,CAAC,CAAC;iBACD,OAAO,CAAC,GAAG,EAAE;gBACZ,IAAI,CAAC,QAAQ,IAAI,CAAC,CAAC;gBACnB,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,CAAC,CAAC,CAAC;QACP,CAAC;IACH,CAAC;CACF"}

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

	@@ -1 +1 @@
1	- {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,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,~~CAuCjB~~;IAED;;;;;OAKG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC,~~CAyCjB~~;IAED,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB;;;;;OAKG;IACH,OAAO,CAAC,UAAU;IAUlB,sFAAsF;IACtF,OAAO,CAAC,WAAW;IAcnB;;;OAGG;IACH,OAAO,CAAC,kBAAkB;CAI3B"}
1	+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,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,CA0CjB;IAED;;;;;OAKG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC,CA4CjB;IAED,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB;;;;;OAKG;IACH,OAAO,CAAC,UAAU;IAUlB,sFAAsF;IACtF,OAAO,CAAC,WAAW;IAcnB;;;OAGG;IACH,OAAO,CAAC,kBAAkB;CAI3B"}

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

@@ -26,7 +26,10 @@ 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({ operation: 'NcbiHttpRequest', endpoint }));
+            logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, requestContextService.createRequestContext({
+                operation: 'NcbiHttpRequest',
+                additionalContext: { endpoint },
+            }));
             const response = usePost
                 ? await this.postRequest(url, finalParams, options?.signal)
                 : await this.getRequest(url, finalParams, options?.signal);
@@ -69,7 +72,10 @@ export class NcbiApiClient {
         const fullUrl = qs ? `${url}?${qs}` : url;
         const signal = this.buildTimeoutSignal(externalSignal);
         try {
-            logger.debug(`NCBI external request: GET ${fullUrl}`, requestContextService.createRequestContext({ operation: 'NcbiExternalRequest', url }));
+            logger.debug(`NCBI external request: GET ${fullUrl}`, requestContextService.createRequestContext({
+                operation: 'NcbiExternalRequest',
+                additionalContext: { url },
+            }));
             const response = await fetch(fullUrl, { signal });
             const body = await response.text();
             if (!response.ok) {

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

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

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

@@ -131,9 +131,11 @@ export class NcbiService {
         const corrected = spellResult.CorrectedQuery ?? '';
         logger.debug('ESpell result parsed.', requestContextService.createRequestContext({
             operation: 'NcbiESpell',
-            original,
-            corrected,
-            hasSuggestion: corrected.length > 0 && corrected !== original,
+            additionalContext: {
+                original,
+                corrected,
+                hasSuggestion: corrected.length > 0 && corrected !== original,
+            },
         }));
         return {
             original,
@@ -317,9 +319,7 @@ export class NcbiService {
                     const retryDelay = Math.round(jitter);
                     logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, requestContextService.createRequestContext({
                         operation: 'NcbiRetry',
-                        endpoint: label,
-                        attempt: attempt + 1,
-                        retryDelay,
+                        additionalContext: { endpoint: label, attempt: attempt + 1, retryDelay },
                     }));
                     await abortableSleep(retryDelay, signal);
                     continue;
@@ -379,11 +379,13 @@ export function initNcbiService() {
     _service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries, config.totalDeadlineMs);
     logger.info('NCBI service initialized.', requestContextService.createRequestContext({
         operation: 'NcbiInit',
-        toolIdentifier: config.toolIdentifier,
-        hasApiKey: !!config.apiKey,
-        requestDelayMs: config.requestDelayMs,
-        maxConcurrent: config.maxConcurrent,
-        totalDeadlineMs: config.totalDeadlineMs,
+        additionalContext: {
+            toolIdentifier: config.toolIdentifier,
+            hasApiKey: !!config.apiKey,
+            requestDelayMs: config.requestDelayMs,
+            maxConcurrent: config.maxConcurrent,
+            totalDeadlineMs: config.totalDeadlineMs,
+        },
     }));
 }
 /** Get the initialized NCBI service. Throws if not initialized. */

package/dist/services/ncbi/ncbi-service.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/esummary-parser.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,~~CAkC7B~~;~~AAoQD~~;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAkD/B"}
1	+ {"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CA+B7B;AAsQD;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAkD/B"}

package/dist/services/ncbi/parsing/esummary-parser.js CHANGED Viewed

@@ -4,7 +4,7 @@
  * consistent ParsedBriefSummary objects.
  * @module src/services/ncbi/parsing/esummary-parser
  */
-import { dateParser, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { dateParser, logger, requestContextService, withExtra } from '@cyanheads/mcp-ts-core/utils';
 import { ensureArray, getAttribute, getText } from './xml-helpers.js';
 /**
  * Formats an array of ESummary authors into a string.
@@ -85,7 +85,7 @@ export async function standardizeESummaryDate(dateStr, parentContext) {
     const currentContext = parentContext ||
         requestContextService.createRequestContext({
             operation: 'standardizeESummaryDateInternal',
-            inputDate: dateInputString,
+            additionalContext: { inputDate: dateInputString },
         });
     try {
         const parsedDate = await dateParser.parseDate(dateInputString, currentContext);
@@ -95,10 +95,7 @@ export async function standardizeESummaryDate(dateStr, parentContext) {
         logger.debug(`standardizeESummaryDate: could not parse "${dateInputString}", returning undefined.`, currentContext);
     }
     catch (e) {
-        logger.warning(`standardizeESummaryDate: dateParser.parseDate error for "${dateInputString}", returning undefined.`, {
-            ...currentContext,
-            error: e instanceof Error ? e.message : String(e),
-        });
+        logger.warning(`standardizeESummaryDate: dateParser.parseDate error for "${dateInputString}", returning undefined.`, withExtra(currentContext, { error: e instanceof Error ? e.message : String(e) }));
     }
     return;
 }
@@ -141,7 +138,7 @@ function parseESummaryAuthorsFromDocumentSummary(docSummary) {
                 const authInputString = JSON.stringify(authorObj);
                 logger.warning(`Unhandled author structure in parseESummaryAuthorsFromDocumentSummary. authInput: ${authInputString.substring(0, 100)}`, requestContextService.createRequestContext({
                     operation: 'parseESummaryAuthorsFromDocumentSummary',
-                    detail: 'Unhandled author structure',
+                    additionalContext: { detail: 'Unhandled author structure' },
                 }));
                 const keys = Object.keys(authorObj);
                 if (keys.length === 1 &&
@@ -196,8 +193,10 @@ function parseESummaryAuthorsFromDocumentSummary(docSummary) {
         catch (e) {
             logger.debug(`Failed to parse Authors string as JSON: ${authorsProp.substring(0, 100)}`, requestContextService.createRequestContext({
                 operation: 'parseESummaryAuthorsFromString',
-                input: authorsProp.substring(0, 100),
-                error: e instanceof Error ? e.message : String(e),
+                additionalContext: {
+                    input: authorsProp.substring(0, 100),
+                    error: e instanceof Error ? e.message : String(e),
+                },
             }));
         }
         for (const namePart of authorsProp.split(/[,;]/)) {
@@ -312,10 +311,7 @@ export async function extractBriefSummaries(eSummaryResult, context) {
             operation: 'extractBriefSummariesInternal',
         });
     if (eSummaryResult.ERROR) {
-        logger.warning('ESummary result contains an error', {
-            ...opContext,
-            errorDetails: eSummaryResult.ERROR,
-        });
+        logger.warning('ESummary result contains an error', withExtra(opContext, { errorDetails: eSummaryResult.ERROR }));
         return [];
     }
     let rawSummaries = [];

package/dist/services/ncbi/parsing/esummary-parser.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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