npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.9 → 2.10.10 - Mend

@cyanheads/pubmed-mcp-server 2.10.9 → 2.10.10

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 (47) hide show

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

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package/dist/services/ncbi/types.d.ts CHANGED Viewed

@@ -481,6 +481,8 @@ export interface ParsedPmcArticle {
     abstract?: string;
     affiliations?: string[];
     articleType?: string;
+    /** Figures and supplementary material, in document order. Absent when the article carries none. */
+    assets?: ParsedPmcAsset[];
     authors?: ParsedPmcAuthor[];
     doi?: string;
     journal?: ParsedPmcJournal;
@@ -499,6 +501,47 @@ export interface ParsedPmcArticle {
     tables?: ParsedPmcTable[];
     title?: string;
 }
+/** Which captioned element an asset came from. */
+export type ParsedPmcAssetType = 'figure' | 'supplementary-material';
+/**
+ * A captioned asset lifted out of a PMC full-text article — a `<fig>` or a
+ * `<supplementary-material>`. Both are a caption plus a pointer that prose
+ * refers to by label, and a sixth of them sit outside `<body>` with no section
+ * to hang from, so they are reported at article level the way `tables[]` is,
+ * leaving a positional marker in the section text they were lifted from.
+ *
+ * Scalar leaves only: the tool-layer schema that renders these sits under the
+ * framework's `format-parity` walker depth cap.
+ *
+ * There is no per-asset unextractable reason, and deliberately so. A table
+ * promises cells, so a graphic-only deposit has to disclose that it has none; an
+ * asset promises a caption, and an uncaptioned supplement is still fully
+ * represented by its `id` and `href`, with no re-call that would produce more.
+ * There is no media-type field either — `mimetype`/`mime-subtype` are in the
+ * JATS model but appear zero times across a 68-record draw. (#130)
+ */
+export interface ParsedPmcAsset {
+    /** Which element this came from. */
+    assetType: ParsedPmcAssetType;
+    /** Caption text, without the label. */
+    caption?: string;
+    /**
+     * The `<graphic>`/`<media>` `@xlink:href`, verbatim. A deposit-relative
+     * filename (`MOL2-20-1253-g001.jpg`), not a fetchable URL — no absolute form
+     * of it resolves. Use `pmcUrl` for the rendered article.
+     */
+    href?: string;
+    /** The `id` attribute, when the deposit carries one. */
+    id?: string;
+    /** Display label, e.g. `Fig. 1`. */
+    label?: string;
+    /**
+     * Title of the innermost enclosing `<sec>` wherever it sits — body, back
+     * matter, or appendix. Absent for a `<floats-group>` deposit, which sits in no
+     * section at all.
+     */
+    sectionTitle?: string;
+}
 /** Parsed PMC author. */
 export interface ParsedPmcAuthor {
     collectiveName?: string;

package/dist/services/ncbi/types.d.ts.map CHANGED Viewed

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

@@ -36,14 +36,23 @@ export declare class OpenAlexApiClient {
     /**
      * Batch-resolve a list of OpenAlex work IDs to their PMIDs.
      * Uses the filter=openalex:W1|W2|... endpoint with select=id,ids.
-     * Returns only records that carry a `pmid` field.
+     *
+     * One call resolves one batch: the OR-filter accepts at most
+     * `OPENALEX_MAX_FILTER_VALUES` values and the endpoint serves at most
+     * `OPENALEX_MAX_PAGE_SIZE` rows, so splitting a longer list is the caller's
+     * job (`OpenAlexService`). Results arrive in OpenAlex's order, not the
+     * requested one.
      */
     resolveOaIdsToPmids(oaIds: string[], signal?: AbortSignal): Promise<OpenAlexWork[]>;
     /**
-     * Fetch works that cite a given OpenAlex work ID (the cited_by relationship).
-     * Returns up to `perPage` records with PMIDs.
+     * Fetch one page of works that cite a given OpenAlex work ID (the cited_by
+     * relationship). Returns up to `perPage` records plus OpenAlex's own total.
+     *
+     * `page` is 1-based. Basic paging is bounded by `page × per_page ≤ 10,000`;
+     * past that OpenAlex rejects the request and requires cursor paging, so the
+     * caller's page cap must keep the walk inside that ceiling.
      */
-    getCitedBy(oaId: string, perPage: number, signal?: AbortSignal): Promise<{
+    getCitedBy(oaId: string, perPage: number, page: number, signal?: AbortSignal): Promise<{
         works: OpenAlexWork[];
         totalCount: number;
     }>;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAGL,KAAK,YAAY,EAElB,MAAM,YAAY,CAAC;AAIpB,MAAM,WAAW,uBAAuB;IACtC,sEAAsE;IACtE,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;;;;;GAQG;AACH,qBAAa,iBAAiB;IAChB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,uBAAuB,EAAI;IAEhE;;;;;;;;;OASG;IACG,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,GAAG,IAAI,CAAC,CA0CpF;IAED;;;;;;;;;OASG;IACH,mBAAmB,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAiBlF;IAED;;;;;;;OAOG;IACG,UAAU,CACd,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC;QAAE,KAAK,EAAE,YAAY,EAAE,CAAC;QAAC,UAAU,EAAE,MAAM,CAAA;KAAE,CAAC,CAiExD;IAED,gEAAgE;YAClD,cAAc;CAqC7B"}

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

@@ -7,7 +7,7 @@
 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 { OPENALEX_API_BASE } from './types.js';
+import { OPENALEX_API_BASE, OPENALEX_MAX_PAGE_SIZE, } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**
  * Low-level HTTP client for OpenAlex. Single-attempt — retries upstream.
@@ -72,7 +72,12 @@ export class OpenAlexApiClient {
     /**
      * Batch-resolve a list of OpenAlex work IDs to their PMIDs.
      * Uses the filter=openalex:W1|W2|... endpoint with select=id,ids.
-     * Returns only records that carry a `pmid` field.
+     *
+     * One call resolves one batch: the OR-filter accepts at most
+     * `OPENALEX_MAX_FILTER_VALUES` values and the endpoint serves at most
+     * `OPENALEX_MAX_PAGE_SIZE` rows, so splitting a longer list is the caller's
+     * job (`OpenAlexService`). Results arrive in OpenAlex's order, not the
+     * requested one.
      */
     resolveOaIdsToPmids(oaIds, signal) {
         if (oaIds.length === 0)
@@ -82,7 +87,7 @@ export class OpenAlexApiClient {
         const params = new URLSearchParams({
             filter: `openalex:${bareIds.join('|')}`,
             select: 'id,ids',
-            per_page: String(Math.min(oaIds.length, 200)),
+            per_page: String(Math.min(oaIds.length, OPENALEX_MAX_PAGE_SIZE)),
         });
         if (this.config.email)
             params.set('mailto', this.config.email);
@@ -90,10 +95,14 @@ export class OpenAlexApiClient {
         return this.fetchWorksList(url, 'OpenAlexResolveOaIds', signal);
     }
     /**
-     * Fetch works that cite a given OpenAlex work ID (the cited_by relationship).
-     * Returns up to `perPage` records with PMIDs.
+     * Fetch one page of works that cite a given OpenAlex work ID (the cited_by
+     * relationship). Returns up to `perPage` records plus OpenAlex's own total.
+     *
+     * `page` is 1-based. Basic paging is bounded by `page × per_page ≤ 10,000`;
+     * past that OpenAlex rejects the request and requires cursor paging, so the
+     * caller's page cap must keep the walk inside that ceiling.
      */
-    async getCitedBy(oaId, perPage, signal) {
+    async getCitedBy(oaId, perPage, page, signal) {
         // Strip full URL prefix if needed
         const bareId = oaId.startsWith('https://openalex.org/')
             ? oaId.slice('https://openalex.org/'.length)
@@ -101,14 +110,15 @@ export class OpenAlexApiClient {
         const params = new URLSearchParams({
             filter: `cites:${bareId}`,
             select: 'id,ids',
-            per_page: String(Math.min(perPage, 200)),
+            per_page: String(Math.min(perPage, OPENALEX_MAX_PAGE_SIZE)),
+            page: String(page),
         });
         if (this.config.email)
             params.set('mailto', this.config.email);
         const url = `${OPENALEX_API_BASE}/works?${params.toString()}`;
         const ctx = requestContextService.createRequestContext({
             operation: 'OpenAlexGetCitedBy',
-            additionalContext: { oaId: bareId },
+            additionalContext: { oaId: bareId, page },
         });
         let response;
         try {
@@ -135,6 +145,7 @@ export class OpenAlexApiClient {
             operation: 'OpenAlexGetCitedByDone',
             additionalContext: {
                 oaId: bareId,
+                page,
                 totalCount: parsed.meta?.count,
                 resultCount: parsed.results?.length,
             },

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

@@ -5,13 +5,20 @@
  *   - `citedBy(pmid, n)`: cites:W<id> filter → PMIDs (mirrors pubmed_pubmed_citedin)
  *   - `references(pmid, n)`: referenced_works → PMIDs (mirrors pubmed_pubmed_refs)
  *
- * All three methods drop records with no PMID — never mints fake IDs.
+ * Each method returns at least `n` PubMed-addressable rows when OpenAlex has
+ * them: `citedBy` walks pages of the `cites:` filter, and the other two resolve
+ * the work's ID list in batches, both stopping once the window is covered,
+ * upstream runs out, or a cap is reached. Records with no PMID are dropped —
+ * never minted — and counted, so callers can disclose the shortfall instead of
+ * serving an unexplained empty window.
+ *
  * Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
  * `mailto=` parameter when set; omits it when unset.
  *
  * @module src/services/openalex/openalex-service
  */
 import { OpenAlexApiClient } from './api-client.js';
+import { type OpenAlexRelatedResult } from './types.js';
 /** Service facade over the OpenAlex API for the find-related provider chain. */
 export declare class OpenAlexService {
     private readonly client;
@@ -20,33 +27,43 @@ export declare class OpenAlexService {
     /**
      * Find works with similar content to the given PMID via OpenAlex `related_works`.
      * Returns PMIDs only; drops any record with no PMID.
-     * `n` is the number of PMIDs to return (OpenAlex caps related_works at ~10).
+     * `n` is the size of the window the caller needs covered.
      */
-    similar(pmid: string, n: number, signal?: AbortSignal): Promise<{
-        pmids: string[];
-        totalCount: number;
-    }>;
+    similar(pmid: string, n: number, signal?: AbortSignal): Promise<OpenAlexRelatedResult>;
     /**
      * Find works that cite the given PMID via OpenAlex `cites:W<id>` filter.
      * Returns PMIDs only; drops any record with no PMID.
+     *
+     * Pages are all one size and are pulled until the filtered array covers `n`,
+     * upstream runs out, or `OPENALEX_MAX_UPSTREAM_REQUESTS` is hit — the rows OpenAlex
+     * serves count every citing work, but only those with a PubMed PMID are
+     * addressable, so a single page sized on the raw window can under-fill it.
      */
-    citedBy(pmid: string, n: number, signal?: AbortSignal): Promise<{
-        pmids: string[];
-        totalCount: number;
-    }>;
+    citedBy(pmid: string, n: number, signal?: AbortSignal): Promise<OpenAlexRelatedResult>;
     /**
      * Find works referenced by the given PMID via OpenAlex `referenced_works`.
      * Returns PMIDs only; drops any record with no PMID.
      */
-    references(pmid: string, n: number, signal?: AbortSignal): Promise<{
-        pmids: string[];
-        totalCount: number;
-    }>;
+    references(pmid: string, n: number, signal?: AbortSignal): Promise<OpenAlexRelatedResult>;
+    /** Look up the source work by PMID; `null` when OpenAlex doesn't index it. */
+    private fetchWork;
+    /**
+     * Resolve an OpenAlex ID list (a work's references or related works) to PMIDs,
+     * in batches, until the window is covered, the list is exhausted, or the
+     * request cap is reached. The work record carries the whole list, so this
+     * paginates resolution rather than an upstream query.
+     *
+     * Each batch's rows are re-ordered to the requested IDs, so the result follows
+     * the source list — a window at any offset stays stable across calls, whatever
+     * order OpenAlex answers a batch in.
+     */
+    private resolveIdsToPmids;
     /**
-     * Extract unique numeric PMIDs from a list of works, excluding the source PMID.
-     * Any work with no PMID is silently dropped (never minted).
+     * Shape a walk's outcome. Exhausting the fetchable set makes the addressable
+     * count exact; short of that only OpenAlex's own total is known, and a window
+     * the walk never reached is flagged rather than served as a silent empty.
      */
-    private extractPmids;
+    private finish;
     /** Retry wrapper for transient errors, mirroring the EPMC service pattern. */
     private withRetry;
 }

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

	@@ -1 +1 @@
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