@cyanheads/pubmed-mcp-server 2.9.10 → 2.10.0
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.
- package/AGENTS.md +2 -2
- package/CLAUDE.md +2 -2
- package/README.md +19 -4
- package/dist/index.js +3 -2
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/tools/definitions/_text.d.ts +22 -0
- package/dist/mcp-server/tools/definitions/_text.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/_text.js +32 -0
- package/dist/mcp-server/tools/definitions/_text.js.map +1 -0
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +32 -0
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +440 -79
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts +87 -0
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +195 -0
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +28 -7
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts +21 -7
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js +39 -6
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/dist/services/europe-pmc/types.d.ts +9 -0
- package/dist/services/europe-pmc/types.d.ts.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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@@ -18,10 +18,19 @@ import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-ser
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import { EUROPEPMC_ALL_SOURCES, EUROPEPMC_DEFAULT_SOURCES, } from '../../../services/europe-pmc/types.js';
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import { toDisplayText } from '../../../services/ncbi/parsing/text-helpers.js';
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import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
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import { sliceCodeUnits } from './_text.js';
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const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
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/**
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* Character budget for `abstractSnippet`. Keeps a search page bounded no matter
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* how many hits carry long abstracts; `pubmed_europepmc_fetch` serves the
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* complete text for the records a caller actually wants. A cut that would split
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* a surrogate pair backs off a code unit, so a snippet can come back one
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* character under the budget. (#93)
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*/
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const ABSTRACT_SNIPPET_LIMIT = 400;
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// ─── Tool Definition ─────────────────────────────────────────────────────────
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export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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description: 'Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`.',
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description: 'Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit’s `source` and `epmcId` to `pubmed_europepmc_fetch` for the complete abstract.',
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annotations: { readOnlyHint: true, openWorldHint: true },
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_meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
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sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts',
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@@ -71,7 +80,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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source: SourceEnum.describe('Europe PMC source — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola)'),
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epmcId: z
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.string()
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.describe("Europe PMC's internal record id
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.describe("Europe PMC's internal record id. Pass it with this hit's `source` to `pubmed_europepmc_fetch` for the complete record. Europe PMC's `fullTextXML` is keyed on `pmcId`, not on this id, so records without a PMC counterpart have no full text to fetch."),
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title: z.string().optional().describe('Article title'),
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authors: z.string().optional().describe('Formatted author string'),
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journal: z.string().optional().describe('Journal title'),
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@@ -94,7 +103,11 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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abstractSnippet: z
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.string()
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.optional()
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.describe(
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.describe(`First ${ABSTRACT_SNIPPET_LIMIT} characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when \`resultType: "core"\` is requested, with a trailing … appended when the abstract was cut. Check \`abstractTruncated\` before treating it as the whole abstract.`),
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abstractTruncated: z
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.boolean()
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.optional()
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.describe('Whether `abstractSnippet` was cut short of the full abstract. Retrieve the complete text with `pubmed_europepmc_fetch` using this record’s `source` and `epmcId`. Present whenever `abstractSnippet` is; omitted when Europe PMC carries no abstract.'),
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citedByCount: z.number().optional().describe('Citation count reported by Europe PMC'),
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epmcUrl: z.string().describe('Europe PMC article URL'),
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})
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@@ -151,7 +164,8 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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// un-decoded entities, and soft hyphens (no XML parser runs on it). Clean it
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// to display-ready plain text before truncating, so the snippet budget is
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// spent on text and soft hyphens don't corrupt downstream token matching. (#74)
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const
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const abstract = h.abstractText ? toDisplayText(h.abstractText) : '';
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const truncated = abstract.length > ABSTRACT_SNIPPET_LIMIT;
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return {
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source: h.source,
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epmcId: h.id,
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@@ -165,8 +179,11 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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...(h.doi && { doi: h.doi }),
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...(h.isOpenAccess !== undefined && { isOpenAccess: h.isOpenAccess === 'Y' }),
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...(h.inPMC !== undefined && { hasFullTextXml: h.inPMC === 'Y' }),
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...(
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abstractSnippet:
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...(abstract && {
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abstractSnippet: truncated
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? `${sliceCodeUnits(abstract, ABSTRACT_SNIPPET_LIMIT)}…`
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: abstract,
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abstractTruncated: truncated,
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}),
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...(typeof h.citedByCount === 'number' && { citedByCount: h.citedByCount }),
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epmcUrl: `https://europepmc.org/article/${h.source}/${h.id}`,
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@@ -241,8 +258,12 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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if (typeof h.citedByCount === 'number')
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lines.push(`**Cited by:** ${h.citedByCount}`);
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lines.push(`**URL:** ${h.epmcUrl}`);
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if (h.abstractSnippet)
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if (h.abstractSnippet) {
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lines.push(`\n${h.abstractSnippet}`);
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if (h.abstractTruncated) {
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lines.push(`_Abstract truncated at ${ABSTRACT_SNIPPET_LIMIT} characters — call \`pubmed_europepmc_fetch\` with this record's \`source\` and \`epmcId\` for the complete text._`);
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}
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}
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}
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}
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return [{ type: 'text', text: lines.join('\n') }];
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@@ -1 +1 @@
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1
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+
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@@ -1,9 +1,11 @@
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1
1
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/**
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* @fileoverview Europe PMC service. Wraps the EPMC REST API with rate-limiting,
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3
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-
* retries, and JATS XML parsing.
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*
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-
*
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* `
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3
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+
* retries, and JATS XML parsing. `search()` covers keyword discovery across the
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4
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* EPMC corpus (MED/PMC/PPR/PAT/AGR), `fetchRecords()` resolves specific records
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5
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* by `source` + EPMC id, `fullTextXml()` fetches a record's full-text JATS, and
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6
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* `citations()` / `references()` walk EPMC's link graph. The XML parser matches
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7
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* NCBI's ordered config so `parsePmcArticle` consumes the result without
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8
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* modification.
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7
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*
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* Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
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* default). `getEuropePmcService()` returns `undefined` when disabled so
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@@ -14,13 +16,15 @@
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16
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import type { JatsNode } from '../../services/ncbi/parsing/pmc-xml-helpers.js';
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import { EuropePmcApiClient } from './api-client.js';
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import { EuropePmcRequestQueue } from './request-queue.js';
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17
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-
import type { EuropePmcFullTextResult, EuropePmcRelatedResult, EuropePmcSearchParams, EuropePmcSearchResult, EuropePmcSource } from './types.js';
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19
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+
import type { EuropePmcFullTextResult, EuropePmcRecordRef, EuropePmcRelatedResult, EuropePmcSearchHit, EuropePmcSearchParams, EuropePmcSearchResult, EuropePmcSource } from './types.js';
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20
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/**
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19
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-
* Facade over the Europe PMC REST API
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21
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+
* Facade over the Europe PMC REST API:
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20
22
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* - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
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23
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+
* - `fetchRecords()` — batch lookup of specific records by source + EPMC id.
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21
24
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* - `fullTextXml()` — JATS full text for an EPMC record.
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25
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+
* - `citations()` / `references()` — EPMC's link graph for a PubMed article.
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22
26
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*
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23
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-
*
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27
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+
* All honor `ctx.signal` for cancellation and retry transient failures with
|
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24
28
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* capped exponential backoff plus jitter.
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25
29
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*/
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export declare class EuropePmcService {
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@@ -34,6 +38,16 @@ export declare class EuropePmcService {
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* omit) for the first page; pass the returned `nextCursorMark` for the next.
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35
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*/
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36
40
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search(params: EuropePmcSearchParams): Promise<EuropePmcSearchResult>;
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41
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+
/**
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42
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+
* Look up specific records by `source` + EPMC id. One search request covers
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43
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+
* the whole batch: each ref becomes an `(EXT_ID:<id> AND SRC:<source>)`
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44
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+
* clause, OR-joined into a single query.
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+
*
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46
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+
* Returns the hits Europe PMC resolved, in the order it returned them.
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47
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+
* Unmatched refs are simply absent — callers diff against their own request
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48
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+
* to report misses rather than getting a padded array back.
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*/
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fetchRecords(refs: readonly EuropePmcRecordRef[], signal?: AbortSignal): Promise<EuropePmcSearchHit[]>;
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/**
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* Fetch the JATS full text for an EPMC record. Returns:
|
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* - `{ kind: 'found', xml, epmcId, source }` — JATS XML string usable
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA
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1
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+
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAeH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAEvB,kBAAkB,EAElB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AAuCpB;;;;;;;;;GASG;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,qBAAqB,EAC5B,UAAU,EAAE,MAAM,EAiBpC;IAED;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA6F1E;IAED;;;;;;;;OAQG;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,CAgBlC;IAED;;;;;;;;;OASG;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;;;;;;;;;OASG;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;;;OAGG;YACW,iBAAiB;IA6C/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS,CA8BlD;IAED;;;;OAIG;YACW,SAAS;CAsDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAuB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
|
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@@ -1,9 +1,11 @@
|
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1
1
|
/**
|
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2
2
|
* @fileoverview Europe PMC service. Wraps the EPMC REST API with rate-limiting,
|
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3
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-
* retries, and JATS XML parsing.
|
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4
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-
*
|
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5
|
-
*
|
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6
|
-
* `
|
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3
|
+
* retries, and JATS XML parsing. `search()` covers keyword discovery across the
|
|
4
|
+
* EPMC corpus (MED/PMC/PPR/PAT/AGR), `fetchRecords()` resolves specific records
|
|
5
|
+
* by `source` + EPMC id, `fullTextXml()` fetches a record's full-text JATS, and
|
|
6
|
+
* `citations()` / `references()` walk EPMC's link graph. The XML parser matches
|
|
7
|
+
* NCBI's ordered config so `parsePmcArticle` consumes the result without
|
|
8
|
+
* modification.
|
|
7
9
|
*
|
|
8
10
|
* Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
|
|
9
11
|
* default). `getEuropePmcService()` returns `undefined` when disabled so
|
|
@@ -45,11 +47,24 @@ function abortableSleep(ms, signal) {
|
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|
45
47
|
});
|
|
46
48
|
}
|
|
47
49
|
/**
|
|
48
|
-
*
|
|
50
|
+
* Europe PMC lookup clause for one record addressed by `source` + EPMC id.
|
|
51
|
+
*
|
|
52
|
+
* The unquoted form is load-bearing: Europe PMC matches zero records for
|
|
53
|
+
* `EXT_ID:"<id>" AND SRC:<source>` — quotes survive on an identifier token only
|
|
54
|
+
* while no `AND SRC:` clause follows it. Callers pass ids through a schema that
|
|
55
|
+
* restricts them to identifier characters, so no escaping is applied here.
|
|
56
|
+
*/
|
|
57
|
+
function recordLookupQuery({ epmcId, source }) {
|
|
58
|
+
return `(EXT_ID:${epmcId} AND SRC:${source})`;
|
|
59
|
+
}
|
|
60
|
+
/**
|
|
61
|
+
* Facade over the Europe PMC REST API:
|
|
49
62
|
* - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
|
|
63
|
+
* - `fetchRecords()` — batch lookup of specific records by source + EPMC id.
|
|
50
64
|
* - `fullTextXml()` — JATS full text for an EPMC record.
|
|
65
|
+
* - `citations()` / `references()` — EPMC's link graph for a PubMed article.
|
|
51
66
|
*
|
|
52
|
-
*
|
|
67
|
+
* All honor `ctx.signal` for cancellation and retry transient failures with
|
|
53
68
|
* capped exponential backoff plus jitter.
|
|
54
69
|
*/
|
|
55
70
|
export class EuropePmcService {
|
|
@@ -159,6 +174,24 @@ export class EuropePmcService {
|
|
|
159
174
|
query: echoed,
|
|
160
175
|
};
|
|
161
176
|
}
|
|
177
|
+
/**
|
|
178
|
+
* Look up specific records by `source` + EPMC id. One search request covers
|
|
179
|
+
* the whole batch: each ref becomes an `(EXT_ID:<id> AND SRC:<source>)`
|
|
180
|
+
* clause, OR-joined into a single query.
|
|
181
|
+
*
|
|
182
|
+
* Returns the hits Europe PMC resolved, in the order it returned them.
|
|
183
|
+
* Unmatched refs are simply absent — callers diff against their own request
|
|
184
|
+
* to report misses rather than getting a padded array back.
|
|
185
|
+
*/
|
|
186
|
+
async fetchRecords(refs, signal) {
|
|
187
|
+
const result = await this.search({
|
|
188
|
+
query: refs.map(recordLookupQuery).join(' OR '),
|
|
189
|
+
resultType: 'core',
|
|
190
|
+
pageSize: refs.length,
|
|
191
|
+
...(signal && { signal }),
|
|
192
|
+
});
|
|
193
|
+
return result.hits;
|
|
194
|
+
}
|
|
162
195
|
/**
|
|
163
196
|
* Fetch the JATS full text for an EPMC record. Returns:
|
|
164
197
|
* - `{ kind: 'found', xml, epmcId, source }` — JATS XML string usable
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
{"version":3,"file":"europe-pmc-service.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,QAAQ,EACR,kBAAkB,EAClB,eAAe,GAChB,MAAM,+BAA+B,CAAC;AACvC,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAC7E,mHAAmH;AACnH,OAAO,EAAE,SAAS,EAAE,YAAY,EAAE,MAAM,iBAAiB,CAAC;AAE1D,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,WAAW,EAAE,MAAM,+BAA+B,CAAC;AAE5D,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AACrE,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAc3D,sDAAsD;AACtD,MAAM,eAAe,GAAG,IAAI,GAAG,CAAmB;IAChD,gBAAgB,CAAC,kBAAkB;IACnC,gBAAgB,CAAC,OAAO;IACxB,gBAAgB,CAAC,WAAW;CAC7B,CAAC,CAAC;AAEH,MAAM,cAAc,GAAG,MAAM,CAAC;AAE9B,SAAS,cAAc,CAAC,EAAU,EAAE,MAAoB;IACtD,IAAI,CAAC,MAAM;QAAE,OAAO,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;IAC1D,IAAI,MAAM,CAAC,OAAO;QAAE,OAAO,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IACzD,OAAO,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;QAC3C,MAAM,OAAO,GAAG,GAAG,EAAE;YACnB,YAAY,CAAC,KAAK,CAAC,CAAC;YACpB,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QACxB,CAAC,CAAC;QACF,MAAM,KAAK,GAAG,UAAU,CAAC,GAAG,EAAE;YAC5B,MAAM,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;YAC7C,OAAO,EAAE,CAAC;QACZ,CAAC,EAAE,EAAE,CAAC,CAAC;QACP,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;IAC5D,CAAC,CAAC,CAAC;AACL,CAAC;AAED;;;;;;;GAOG;AACH,SAAS,iBAAiB,CAAC,EAAE,MAAM,EAAE,MAAM,EAAsB;IAC/D,OAAO,WAAW,MAAM,YAAY,MAAM,GAAG,CAAC;AAChD,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,OAAO,gBAAgB;IAIR,MAAM;IACN,KAAK;IACL,UAAU;IALZ,gBAAgB,CAAY;IAE7C,YACmB,MAA0B,EAC1B,KAA4B,EAC5B,UAAkB;sBAFlB,MAAM;qBACN,KAAK;0BACL,UAAU;QAE3B;;;;;WAKG;QACH,IAAI,CAAC,gBAAgB,GAAG,IAAI,SAAS,CAAC;YACpC,aAAa,EAAE,IAAI;YACnB,gBAAgB,EAAE,KAAK;YACvB,mBAAmB,EAAE,IAAI;YACzB,aAAa,EAAE,IAAI;YACnB,UAAU,EAAE,KAAK;YACjB,eAAe,EAAE,IAAI;YACrB,YAAY,EAAE,IAAI;SACnB,CAAC,CAAC;IACL,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,MAAM,CAAC,MAA6B;QACxC,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CACnC,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,MAAM,CAAC,EAC/E,QAAQ,EACR,MAAM,CAAC,MAAM,CACd,CAAC;QAEF,IAAI,MAA+B,CAAC;QACpC,IAAI,CAAC;YACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAA4B,CAAC;QACvD,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,kBAAkB,CACtB,kDAAkD,EAClD;gBACE,MAAM,EAAE,4BAA4B;gBACpC,eAAe,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC;gBACvC,GAAG,WAAW,CAAC,4BAA4B,CAAC;aAC7C,EACD,EAAE,KAAK,EAAE,KAAK,EAAE,CACjB,CAAC;QACJ,CAAC;QAED;;;;WAIG;QACH,MAAM,MAAM,GAAG,OAAO,MAAM,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC;QAC7E,IAAI,MAAM,EAAE,CAAC;YACX,MAAM,eAAe,CAAC,oCAAoC,MAAM,EAAE,EAAE;gBAClE,MAAM,EAAE,yBAAyB;gBACjC,WAAW,EAAE,MAAM,CAAC,OAAO;gBAC3B,UAAU,EAAE,MAAM;gBAClB,QAAQ,EAAE,EAAE,IAAI,EAAE,yBAAyB,MAAM,6BAA6B,EAAE;aACjF,CAAC,CAAC;QACL,CAAC;QAED;;;;;;;WAOG;QACH,IACE,MAAM,CAAC,QAAQ,KAAK,SAAS;YAC7B,MAAM,CAAC,OAAO,KAAK,SAAS;YAC5B,MAAM,CAAC,UAAU,KAAK,SAAS,EAC/B,CAAC;YACD,wEAAwE;YACxE,qEAAqE;YACrE,qEAAqE;YACrE,uEAAuE;YACvE,sBAAsB;YACtB,MAAM,EAAE,OAAO,EAAE,IAAI,EAAE,GAAG,MAAM,CAAC,IAAI;gBACnC,CAAC,CAAC;oBACE,OAAO,EAAE,kFAAkF,MAAM,CAAC,IAAI,IAAI;oBAC1G,IAAI,EAAE,qIAAqI;iBAC5I;gBACH,CAAC,CAAC;oBACE,OAAO,EAAE,6EAA6E;oBACtF,IAAI,EAAE,kEAAkE;iBACzE,CAAC;YACN,MAAM,eAAe,CAAC,OAAO,EAAE;gBAC7B,MAAM,EAAE,yBAAyB;gBACjC,GAAG,CAAC,MAAM,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,EAAE,CAAC;gBACzC,GAAG,CAAC,MAAM,CAAC,UAAU,IAAI,MAAM,CAAC,UAAU,KAAK,GAAG,IAAI,EAAE,UAAU,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC;gBACxF,eAAe,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC;gBACvC,QAAQ,EAAE,EAAE,IAAI,EAAE;aACnB,CAAC,CAAC;QACL,CAAC;QAED,MAAM,IAAI,GAAG,WAAW,CAAqB,MAAM,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC;QACxE,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,EAAE,WAAW,IAAI,MAAM,CAAC,KAAK,CAAC;QAE3D,yEAAyE;QACzE,0EAA0E;QAC1E,wEAAwE;QACxE,2DAA2D;QAC3D,MAAM,UAAU,GAAG,MAAM,CAAC,UAAU,IAAI,GAAG,CAAC;QAC5C,MAAM,UAAU,GACd,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,KAAK,UAAU;YAC3D,CAAC,CAAC,MAAM,CAAC,cAAc;YACvB,CAAC,CAAC,SAAS,CAAC;QAEhB,OAAO;YACL,IAAI;YACJ,QAAQ,EAAE,MAAM,CAAC,QAAQ,IAAI,IAAI,CAAC,MAAM;YACxC,GAAG,CAAC,UAAU,IAAI,EAAE,cAAc,EAAE,UAAU,EAAE,CAAC;YACjD,UAAU;YACV,KAAK,EAAE,MAAM;SACd,CAAC;IACJ,CAAC;IAED;;;;;;;;OAQG;IACH,KAAK,CAAC,YAAY,CAChB,IAAmC,EACnC,MAAoB;QAEpB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC;YAC/B,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,iBAAiB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC;YAC/C,UAAU,EAAE,MAAM;YAClB,QAAQ,EAAE,IAAI,CAAC,MAAM;YACrB,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;SAC1B,CAAC,CAAC;QACH,OAAO,MAAM,CAAC,IAAI,CAAC;IACrB,CAAC;IAED;;;;;;;OAOG;IACH,KAAK,CAAC,WAAW,CACf,MAAc,EACd,MAAuB,EACvB,MAAoB;QAEpB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CACtC,GAAG,EAAE,CACH,IAAI,CAAC,SAAS,CACZ,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,EAC7C,eAAe,MAAM,GAAG,EACxB,MAAM,CACP,EACH,eAAe,MAAM,GAAG,EACxB,MAAM,CACP,CAAC;QAEF,IAAI,OAAO,CAAC,IAAI,KAAK,eAAe,EAAE,CAAC;YACrC,OAAO,EAAE,IAAI,EAAE,eAAe,EAAE,MAAM,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC;QAC3D,CAAC;QACD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,E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@@ -114,6 +114,15 @@ export interface EuropePmcSearchParams {
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114
114
|
/** Allowed sources, comma-joined into the query as `(SRC:"MED" OR ...)`. */
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|
115
115
|
sources?: readonly EuropePmcSource[];
|
|
116
116
|
}
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|
117
|
+
/**
|
|
118
|
+
* Address of one Europe PMC record: the corpus it lives in plus EPMC's own
|
|
119
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+
* identifier within that corpus. The pair is the only identifier many PPR,
|
|
120
|
+
* PAT, and AGR records carry — they frequently have no PMID and no DOI.
|
|
121
|
+
*/
|
|
122
|
+
export interface EuropePmcRecordRef {
|
|
123
|
+
epmcId: string;
|
|
124
|
+
source: EuropePmcSource;
|
|
125
|
+
}
|
|
117
126
|
/** Outcome of a fullTextXML lookup. */
|
|
118
127
|
export type EuropePmcFullTextResult = {
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|
119
128
|
kind: 'found';
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@@ -1 +1 @@
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|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.10.0",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/pubmed-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "2.
|
|
9
|
+
"version": "2.10.0",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
21
21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "2.
|
|
22
|
+
"version": "2.10.0",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -66,7 +66,7 @@
|
|
|
66
66
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
67
67
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
68
68
|
"runtimeHint": "bun",
|
|
69
|
-
"version": "2.
|
|
69
|
+
"version": "2.10.0",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|