npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.7.11 → 2.9.0 - Mend

@cyanheads/pubmed-mcp-server 2.7.11 → 2.9.0

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 (56) hide show

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

@@ -1,12 +1,12 @@
 /**
  * @fileoverview Hand-rolled citation formatters for PubMed articles.
- * Supports APA 7th, MLA 9th, BibTeX, and RIS formats.
+ * Supports APA 7th, MLA 9th, BibTeX, RIS, and Vancouver (ICMJE/NLM) formats.
  * Pure TypeScript, zero dependencies, Workers-compatible.
  * @module src/services/ncbi/formatting/citation-formatter
  */
 import type { ParsedArticle } from '../types.js';
 /** Supported citation output formats. */
-export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris';
+export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
 /**
  * Format a PubMed article as an APA 7th edition citation.
  *
@@ -46,6 +46,20 @@ 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.
+ */
+export declare function formatVancouver(article: ParsedArticle): string;
 /**
  * Format a single article in the requested citation style.
  * Throws on unsupported style.

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AAEtE,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,GAAG,WAAW,CAAC;AAgM3E;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA6CxD;AAMD;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkF3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA4FxD;AA4CD;;;;;;;;;;;;GAYG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAuC9D;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAanF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}

package/dist/services/ncbi/formatting/citation-formatter.js CHANGED Viewed

@@ -1,6 +1,6 @@
 /**
  * @fileoverview Hand-rolled citation formatters for PubMed articles.
- * Supports APA 7th, MLA 9th, BibTeX, and RIS formats.
+ * Supports APA 7th, MLA 9th, BibTeX, RIS, and Vancouver (ICMJE/NLM) formats.
  * Pure TypeScript, zero dependencies, Workers-compatible.
  * @module src/services/ncbi/formatting/citation-formatter
  */
@@ -370,8 +370,12 @@ export function formatBibtex(article) {
         if (m.descriptorName)
             keywordSet.add(m.descriptorName);
     }
+    // Brace-wrap each term so MeSH descriptors that carry internal commas in
+    // their inverted form (e.g. "Databases, Protein") stay a single keyword —
+    // biblatex's comma-separated list parser reads a braced item as one element.
     if (keywordSet.size > 0) {
-        fields.push(['keywords', escapeBibtex([...keywordSet].join(', '))]);
+        const keywords = [...keywordSet].map((k) => `{${escapeBibtex(k)}}`).join(', ');
+        fields.push(['keywords', keywords]);
     }
     // Build entry
     const maxKeyLen = Math.max(...fields.map(([k]) => k.length));
@@ -468,6 +472,100 @@ export function formatRis(article) {
     return lines.join('\n');
 }
 // ---------------------------------------------------------------------------
+// Vancouver (ICMJE / NLM)
+// ---------------------------------------------------------------------------
+/**
+ * Format a single author in Vancouver style: `Surname AB` — surname, a space,
+ * then initials with no periods or internal spaces. Collective/group authors
+ * return their name directly.
+ */
+function formatAuthorVancouver(author) {
+    if (author.collectiveName)
+        return author.collectiveName;
+    const last = author.lastName ?? '';
+    const initialsSource = author.initials ??
+        author.firstName
+            ?.split(/[\s-]+/)
+            .filter(Boolean)
+            .map((part) => part[0])
+            .join('');
+    // Letters only (Unicode-aware), uppercased, no separators: "AB", not "A. B."
+    const initials = initialsSource
+        ? Array.from(initialsSource)
+            .filter((c) => /\p{L}/u.test(c))
+            .join('')
+            .toUpperCase()
+        : '';
+    if (!last)
+        return initials;
+    if (!initials)
+        return last;
+    return `${last} ${initials}`;
+}
+/**
+ * Format the full author list for Vancouver: list every author for six or
+ * fewer; for seven or more, list the first six followed by `et al.` (ICMJE).
+ */
+function formatAuthorsVancouver(authors) {
+    const names = authors.map(formatAuthorVancouver).filter(Boolean);
+    if (names.length === 0)
+        return '';
+    if (names.length <= 6)
+        return names.join(', ');
+    return `${names.slice(0, 6).join(', ')}, et al.`;
+}
+/**
+ * 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.
+ */
+export function formatVancouver(article) {
+    const segments = [];
+    // Authors — terminate with a period unless the list already ends in "et al."
+    const authorStr = article.authors?.length ? formatAuthorsVancouver(article.authors) : '';
+    if (authorStr) {
+        segments.push(authorStr.endsWith('.') ? authorStr : `${authorStr}.`);
+    }
+    // Title — sentence case as supplied, single terminating period
+    if (article.title) {
+        segments.push(`${article.title.replace(/\.\s*$/, '')}.`);
+    }
+    // Journal — NLM/ISO abbreviation preferred, full title as fallback
+    const journal = article.journalInfo;
+    const journalName = journal?.isoAbbreviation ?? journal?.title;
+    if (journalName) {
+        segments.push(`${journalName.replace(/\.\s*$/, '')}.`);
+    }
+    // Source — "Year;Volume(Issue):Pages."
+    const year = getYear(article);
+    let source = year !== 'n.d.' ? year : '';
+    if (journal?.volume) {
+        source += source ? `;${journal.volume}` : journal.volume;
+        if (journal.issue)
+            source += `(${journal.issue})`;
+        if (journal.pages)
+            source += `:${journal.pages}`;
+    }
+    else if (journal?.pages) {
+        source += source ? `:${journal.pages}` : journal.pages;
+    }
+    if (source)
+        segments.push(`${source}.`);
+    // DOI — NLM "doi: <doi>" form; no trailing period (would corrupt the DOI)
+    if (article.doi) {
+        segments.push(`doi: ${article.doi}`);
+    }
+    return segments.join(' ');
+}
+// ---------------------------------------------------------------------------
 // Dispatchers
 // ---------------------------------------------------------------------------
 /**
@@ -484,6 +582,8 @@ export function formatCitation(article, style) {
             return formatBibtex(article);
         case 'ris':
             return formatRis(article);
+        case 'vancouver':
+            return formatVancouver(article);
     }
 }
 /**

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

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

@@ -18,7 +18,11 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
  * in manuscript-submitted PMC deposits) preserve their main text.
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
-/** Extract references from a `<back>` node. Prefers mixed-citation over element-citation. */
+/**
+ * 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>`.
+ */
 export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
 /**
  * Parse a single JATS `<article>` node (from PMC EFetch via the ordered parser)

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

	@@ -1 +1 @@
1	- {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAKL,KAAK,QAAQ,EAGd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AA0BD~~,6FAA6F~~;~~AAC7F~~,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,~~CAsBlF~~;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}
1	+ {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAKL,KAAK,QAAQ,EAGd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AA0BD;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CA4BlF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}

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

@@ -206,7 +206,11 @@ function extractSection(sec) {
     };
 }
 // ─── References ─────────────────────────────────────────────────────────────
-/** Extract references from a `<back>` node. Prefers mixed-citation over element-citation. */
+/**
+ * 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>`.
+ */
 export function extractReferences(back) {
     if (!back)
         return [];
@@ -215,7 +219,12 @@ export function extractReferences(back) {
         return [];
     const results = [];
     for (const ref of findAll(refList, 'ref')) {
-        const citationNode = findOne(ref, 'mixed-citation') ?? findOne(ref, 'element-citation');
+        // JATS wraps the two citation forms in <citation-alternatives> (the NLM
+        // construct carrying both a structured <element-citation> and a readable
+        // <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);

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

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

@@ -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 ADDED Viewed

@@ -0,0 +1 @@

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

@@ -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

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

@@ -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