@cyanheads/pubmed-mcp-server 2.8.0 → 2.9.1

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

@@ -207,9 +207,68 @@ function extractSection(sec) {
 }
 // ─── References ─────────────────────────────────────────────────────────────
 /**
- * Extract references from a `<back>` node. Prefers mixed-citation over
- * element-citation, descending into `<citation-alternatives>` when a ref carries
- * both forms there rather than as direct children of `<ref>`.
+ * `pub-id-type` → human label, so the trailing identifiers in a rendered
+ * `<element-citation>` read as `PMID 37657419` rather than a bare number run.
+ */
+const PUB_ID_LABELS = {
+    pmid: 'PMID',
+    doi: 'DOI',
+    pmcid: 'PMCID',
+};
+/** Render one `<person-group>` child — a `<name>`, `<collab>`, or `<etal>`. */
+function renderCitationName(node) {
+    const tag = tagNameOf(node);
+    if (tag === 'name' || tag === 'string-name') {
+        const surname = textContent(findOne(node, 'surname'));
+        const given = textContent(findOne(node, 'given-names'));
+        return [surname, given].filter(Boolean).join(' ') || textContent(node);
+    }
+    if (tag === 'collab')
+        return textContent(node);
+    if (tag === 'etal')
+        return 'et al.';
+    return '';
+}
+/**
+ * Render a structured `<element-citation>` as a readable, delimited string.
+ * Its child elements carry no punctuation between them, so a flat
+ * `textContent()` runs every field together (`DomanJ.L.…Cell18618…`). Walk the
+ * direct children in document order, joining author names with `, ` and
+ * labeling typed `<pub-id>`s, so the output reads as a citation rather than a
+ * token run. (#69)
+ */
+function renderElementCitation(node) {
+    const parts = [];
+    for (const child of childrenOf(node)) {
+        const tag = tagNameOf(child);
+        if (tag === 'person-group') {
+            const names = childrenOf(child).map(renderCitationName).filter(Boolean);
+            if (names.length > 0)
+                parts.push(names.join(', '));
+        }
+        else if (tag === 'pub-id') {
+            const value = textContent(child);
+            if (value) {
+                const label = PUB_ID_LABELS[attrOf(child, 'pub-id-type') ?? ''];
+                parts.push(label ? `${label} ${value}` : value);
+            }
+        }
+        else {
+            // Element field (source, volume, year, fpage, …) or a bare text node;
+            // textContent renders both, and empty results drop out of the join.
+            const text = textContent(child);
+            if (text)
+                parts.push(text);
+        }
+    }
+    return parts.join(' ');
+}
+/**
+ * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
+ * `<element-citation>`, descending into `<citation-alternatives>` when a ref
+ * carries both forms there rather than as direct children of `<ref>`. Mixed
+ * citations are read verbatim; structured element citations are rendered
+ * field-by-field with separators (see `renderElementCitation`).
  */
 export function extractReferences(back) {
     if (!back)
@@ -224,10 +283,18 @@ export function extractReferences(back) {
         // <mixed-citation>). findOne matches direct children only, so resolve that
         // container first; refs with a direct citation node fall through to `ref`.
         const container = findOne(ref, 'citation-alternatives') ?? ref;
-        const citationNode = findOne(container, 'mixed-citation') ?? findOne(container, 'element-citation');
-        if (!citationNode)
-            continue;
-        const citation = textContent(citationNode);
+        const mixedCitation = findOne(container, 'mixed-citation');
+        const elementCitation = findOne(container, 'element-citation');
+        // <mixed-citation> carries punctuation in the text nodes between its
+        // elements, so textContent() reads correctly. <element-citation> children
+        // have no separators — render the structured fields explicitly. (#69)
+        let citation = '';
+        if (mixedCitation) {
+            citation = textContent(mixedCitation);
+        }
+        else if (elementCitation) {
+            citation = renderElementCitation(elementCitation);
+        }
         if (!citation)
             continue;
         const id = attrOf(ref, 'id');

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

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

@@ -33,7 +33,12 @@ export declare class NcbiResponseHandler {
      * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
      * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
      * doesn't collapse into reordered text. `trimValues: false` retains spacing
-     * between text nodes and adjacent inline children.
+     * between text nodes and adjacent inline children. `parseTagValue: false`
+     * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
+     * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
+     * every value on this path is `String()`-ed downstream, so coercion is pure
+     * downside. Entity decoding is unaffected (it's governed by `processEntities`/
+     * `htmlEntities`), so page-range en-dashes still resolve. (#69)
      */
     private readonly orderedXmlParser;
     constructor();

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

@@ -1 +1 @@
-{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}
+{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;;;;;;OAUG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}

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

@@ -230,7 +230,12 @@ export class NcbiResponseHandler {
      * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
      * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
      * doesn't collapse into reordered text. `trimValues: false` retains spacing
-     * between text nodes and adjacent inline children.
+     * between text nodes and adjacent inline children. `parseTagValue: false`
+     * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
+     * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
+     * every value on this path is `String()`-ed downstream, so coercion is pure
+     * downside. Entity decoding is unaffected (it's governed by `processEntities`/
+     * `htmlEntities`), so page-range en-dashes still resolve. (#69)
      */
     orderedXmlParser;
     constructor() {
@@ -246,7 +251,7 @@ export class NcbiResponseHandler {
             preserveOrder: true,
             ignoreAttributes: false,
             attributeNamePrefix: '@_',
-            parseTagValue: true,
+            parseTagValue: false,
             trimValues: false,
             processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
             htmlEntities: true,

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

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

@@ -0,0 +1,39 @@
+/**
+ * @fileoverview Low-level HTTP client for the OpenAlex API. Builds URLs,
+ * injects the optional polite-pool email, and exposes single-attempt fetch
+ * calls. Retry logic lives in `OpenAlexService`.
+ * @module src/services/openalex/api-client
+ */
+import { type OpenAlexWork } from './types.js';
+export interface OpenAlexApiClientConfig {
+    /** Admin email for OpenAlex polite pool (mailto= param). Optional. */
+    email?: string;
+    timeoutMs: number;
+}
+/** Low-level HTTP client for OpenAlex. Single-attempt — retries upstream. */
+export declare class OpenAlexApiClient {
+    private readonly config;
+    constructor(config: OpenAlexApiClientConfig);
+    /**
+     * Fetch a single work by PMID. Returns the work record (with related_works
+     * and referenced_works populated) or null when the PMID is unknown.
+     */
+    getWorkByPmid(pmid: string, signal?: AbortSignal): Promise<OpenAlexWork | null>;
+    /**
+     * 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.
+     */
+    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.
+     */
+    getCitedBy(oaId: string, perPage: number, signal?: AbortSignal): Promise<{
+        works: OpenAlexWork[];
+        totalCount: number;
+    }>;
+    /** Helper: fetch a /works?... URL and return parsed results. */
+    private fetchWorksList;
+}
+//# sourceMappingURL=api-client.d.ts.map

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

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

@@ -0,0 +1,174 @@
+/**
+ * @fileoverview Low-level HTTP client for the OpenAlex API. Builds URLs,
+ * injects the optional polite-pool email, and exposes single-attempt fetch
+ * calls. Retry logic lives in `OpenAlexService`.
+ * @module src/services/openalex/api-client
+ */
+import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
+import { recoveryFor } from '../../services/error-contracts.js';
+import { OPENALEX_API_BASE } 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. */
+export class OpenAlexApiClient {
+    config;
+    constructor(config) {
+        this.config = config;
+    }
+    /**
+     * Fetch a single work by PMID. Returns the work record (with related_works
+     * and referenced_works populated) or null when the PMID is unknown.
+     */
+    async getWorkByPmid(pmid, signal) {
+        const params = new URLSearchParams({
+            select: 'id,related_works,referenced_works',
+        });
+        if (this.config.email)
+            params.set('mailto', this.config.email);
+        const url = `${OPENALEX_API_BASE}/works/pmid:${encodeURIComponent(pmid)}?${params.toString()}`;
+        const ctx = requestContextService.createRequestContext({
+            operation: 'OpenAlexGetWorkByPmid',
+            pmid,
+        });
+        let response;
+        try {
+            response = await fetchWithTimeout(url, this.config.timeoutMs, ctx, {
+                headers: { Accept: 'application/json', 'User-Agent': USER_AGENT },
+                ...(signal && { signal }),
+            });
+        }
+        catch (error) {
+            if (error instanceof McpError)
+                throw error;
+            const msg = error instanceof Error ? error.message : String(error);
+            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') }, { cause: error });
+        }
+        if (response.status === 404)
+            return null;
+        if (!response.ok) {
+            throw await httpErrorFromResponse(response, {
+                service: 'OpenAlex',
+                data: { url, reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') },
+            });
+        }
+        const text = await response.text();
+        try {
+            return JSON.parse(text);
+        }
+        catch (error) {
+            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response', ...recoveryFor('openalex_invalid_response') }, { cause: error });
+        }
+    }
+    /**
+     * Batch-resolve a list of OpenAlex work IDs to their PMIDs.
+     * Uses the filter=openalex:W1|W2|... endpoint with select=id,ids.
+     * Returns only records that carry a `pmid` field.
+     */
+    resolveOaIdsToPmids(oaIds, signal) {
+        if (oaIds.length === 0)
+            return Promise.resolve([]);
+        // Strip https://openalex.org/ prefix if present — filter expects bare IDs
+        const bareIds = oaIds.map((id) => id.startsWith('https://openalex.org/') ? id.slice('https://openalex.org/'.length) : id);
+        const params = new URLSearchParams({
+            filter: `openalex:${bareIds.join('|')}`,
+            select: 'id,ids',
+            per_page: String(Math.min(oaIds.length, 200)),
+        });
+        if (this.config.email)
+            params.set('mailto', this.config.email);
+        const url = `${OPENALEX_API_BASE}/works?${params.toString()}`;
+        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.
+     */
+    async getCitedBy(oaId, perPage, signal) {
+        // Strip full URL prefix if needed
+        const bareId = oaId.startsWith('https://openalex.org/')
+            ? oaId.slice('https://openalex.org/'.length)
+            : oaId;
+        const params = new URLSearchParams({
+            filter: `cites:${bareId}`,
+            select: 'id,ids',
+            per_page: String(Math.min(perPage, 200)),
+        });
+        if (this.config.email)
+            params.set('mailto', this.config.email);
+        const url = `${OPENALEX_API_BASE}/works?${params.toString()}`;
+        const ctx = requestContextService.createRequestContext({
+            operation: 'OpenAlexGetCitedBy',
+            oaId: bareId,
+        });
+        let response;
+        try {
+            response = await fetchWithTimeout(url, this.config.timeoutMs, ctx, {
+                headers: { Accept: 'application/json', 'User-Agent': USER_AGENT },
+                ...(signal && { signal }),
+            });
+        }
+        catch (error) {
+            if (error instanceof McpError)
+                throw error;
+            const msg = error instanceof Error ? error.message : String(error);
+            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') }, { cause: error });
+        }
+        if (!response.ok) {
+            throw await httpErrorFromResponse(response, {
+                service: 'OpenAlex',
+                data: { url, reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') },
+            });
+        }
+        const text = await response.text();
+        let parsed;
+        try {
+            parsed = JSON.parse(text);
+        }
+        catch (error) {
+            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response', ...recoveryFor('openalex_invalid_response') }, { cause: error });
+        }
+        logger.debug('OpenAlex cited_by response', requestContextService.createRequestContext({
+            operation: 'OpenAlexGetCitedByDone',
+            oaId: bareId,
+            totalCount: parsed.meta?.count,
+            resultCount: parsed.results?.length,
+        }));
+        return {
+            works: parsed.results ?? [],
+            totalCount: parsed.meta?.count ?? 0,
+        };
+    }
+    /** Helper: fetch a /works?... URL and return parsed results. */
+    async fetchWorksList(url, operation, signal) {
+        const ctx = requestContextService.createRequestContext({ operation });
+        let response;
+        try {
+            response = await fetchWithTimeout(url, this.config.timeoutMs, ctx, {
+                headers: { Accept: 'application/json', 'User-Agent': USER_AGENT },
+                ...(signal && { signal }),
+            });
+        }
+        catch (error) {
+            if (error instanceof McpError)
+                throw error;
+            const msg = error instanceof Error ? error.message : String(error);
+            throw serviceUnavailable(`OpenAlex request failed: ${msg}`, { reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') }, { cause: error });
+        }
+        if (!response.ok) {
+            throw await httpErrorFromResponse(response, {
+                service: 'OpenAlex',
+                data: { url, reason: 'openalex_unreachable', ...recoveryFor('openalex_unreachable') },
+            });
+        }
+        const text = await response.text();
+        let parsed;
+        try {
+            parsed = JSON.parse(text);
+        }
+        catch (error) {
+            throw serviceUnavailable('OpenAlex returned a non-JSON body.', { reason: 'openalex_invalid_response', ...recoveryFor('openalex_invalid_response') }, { cause: error });
+        }
+        return parsed.results ?? [];
+    }
+}
+//# sourceMappingURL=api-client.js.map

package/dist/services/openalex/api-client.js.map

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

@@ -0,0 +1,59 @@
+/**
+ * @fileoverview OpenAlex service for related-article fallback in `pubmed_find_related`.
+ * Provides three capabilities that mirror the NCBI eLink relationships:
+ *   - `similar(pmid, n)`: related_works → PMIDs (mirrors pubmed_pubmed)
+ *   - `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.
+ * 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';
+/** Service facade over the OpenAlex API for the find-related provider chain. */
+export declare class OpenAlexService {
+    private readonly client;
+    private readonly maxRetries;
+    constructor(client: OpenAlexApiClient, maxRetries: number);
+    /**
+     * 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).
+     */
+    similar(pmid: string, n: number, signal?: AbortSignal): Promise<{
+        pmids: string[];
+        totalCount: number;
+    }>;
+    /**
+     * Find works that cite the given PMID via OpenAlex `cites:W<id>` filter.
+     * Returns PMIDs only; drops any record with no PMID.
+     */
+    citedBy(pmid: string, n: number, signal?: AbortSignal): Promise<{
+        pmids: string[];
+        totalCount: number;
+    }>;
+    /**
+     * 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;
+    }>;
+    /**
+     * Extract unique numeric PMIDs from a list of works, excluding the source PMID.
+     * Any work with no PMID is silently dropped (never minted).
+     */
+    private extractPmids;
+    /** Retry wrapper for transient errors, mirroring the EPMC service pattern. */
+    private withRetry;
+}
+/** Initialize the OpenAlex service. Call from `setup()` in createApp. */
+export declare function initOpenAlexService(): void;
+/** Get the initialized OpenAlex service. Throws if not initialized. */
+export declare function getOpenAlexService(): OpenAlexService;
+/** Returns the service if initialized, undefined otherwise (for optional use). */
+export declare function getOpenAlexServiceOptional(): OpenAlexService | undefined;
+//# sourceMappingURL=openalex-service.d.ts.map

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

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