npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.1 → 2.10.2 - Mend

@cyanheads/pubmed-mcp-server 2.10.1 → 2.10.2

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 (30) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.1
+**Version:** 2.10.2
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.0`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.10.1
+**Version:** 2.10.2
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.0`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0

package/README.md CHANGED Viewed

@@ -9,7 +9,7 @@
-[![Version](https://img.shields.io/badge/Version-2.10.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-2.10.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>

package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAcjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~cA2GzB~~,CAAC"}
1	+ {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAcjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA6GzB,CAAC"}

package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED Viewed

@@ -43,7 +43,7 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
             doi: z
                 .string()
                 .optional()
-                .describe('Digital Object Identifier; absent if no DOI is on record'),
+                .describe('Digital Object Identifier, cased as the PMC ID Converter reports it; absent if no DOI is on record. DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ from a Europe PMC-sourced `doi` — compare the two case-insensitively.'),
             errmsg: z
                 .string()
                 .optional()

package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"convert-ids.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAC;AAE9E;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,gCAAgC,CAAC;AAC1D,MAAM,qBAAqB,GACzB,gIAAgI,CAAC;AAEnI,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EAAE,4NAA4N;IACzO,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,eAAe,EAAE,cAAc,CAAC,CAAC;IACrD,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;aACxB,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,oNAAoN,CACrN;QACH,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,CAAC;aAC9B,QAAQ,CACP,sFAAsF,CACvF;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YAC7D,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;YACjF,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,0DAA0D,CAAC;YACvE,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,6QAA6Q,CAC9Q;YACH,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yHAAyH,CAC1H;SACJ,CAAC;aACD,QAAQ,CAAC,0BAA0B,CAAC,CACxC;aACA,QAAQ,CAAC,sCAAsC,CAAC;QACnD,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KAC/D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;YACvB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QAEH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAE9F,0EAA0E;QAC1E,MAAM,OAAO,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC5B,MAAM,WAAW,GAAG,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;YAC9C,IAAI,MAA0B,CAAC;YAC/B,IAAI,CAAC,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;gBAC3B,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;gBAClC,IAAI,gBAAgB,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;oBACpC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,gCAAgC,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAC,CAAC;oBAC3E,MAAM,GAAG,qBAAqB,CAAC;gBACjC,CAAC;qBAAM,CAAC;oBACN,MAAM,GAAG,QAAQ,CAAC;gBACpB,CAAC;YACH,CAAC;YACD,OAAO;gBACL,WAAW;gBACX,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrD,GAAG,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;gBACxD,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAClD,GAAG,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,CAAC;aACxC,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,cAAc,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC;QAC/D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,cAAc;YACd,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;IACvE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,0BAA0B;YAC1B,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;YAClE,EAAE;YACF,+CAA+C;YAC/C,4BAA4B;SAC7B,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,WAAW,MAAM,CAAC,CAAC,IAAI,IAAI,GAAG,MAAM,CAAC,CAAC,KAAK,IAAI,GAAG,MAAM,CAAC,CAAC,GAAG,IAAI,GAAG,MAAM,CAAC,CAAC,MAAM,IAAI,GAAG,IAAI,CACrG,CAAC;QACJ,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAyGjE~~,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWhB,yBAAyB;;mBAE3B,sEAAsE;uBAE1E,qFAAqF;;;EAsK3F,CAAC"}
1	+ {"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWhB,yBAAyB;;mBAE3B,sEAAsE;uBAE1E,qFAAqF;;;EAsK3F,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED Viewed

@@ -83,7 +83,10 @@ const FetchedArticleSchema = z
     affiliations: z.array(z.string()).optional().describe('Deduplicated author affiliations'),
     authors: z.array(AuthorSchema).optional().describe('Author list'),
     journalInfo: JournalInfoSchema.optional(),
-    doi: z.string().optional().describe('DOI'),
+    doi: z
+        .string()
+        .optional()
+        .describe("DOI, cased as NCBI reports it (usually the publisher's mixed case). DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_europepmc_search` and `pubmed_europepmc_fetch` (NCBI `10.1056/NEJMoa2212948`, Europe PMC `10.1056/nejmoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch."),
     pmcId: z.string().optional().describe('PMC ID'),
     pubmedUrl: z.string().optional().describe('PubMed article URL'),
     pmcUrl: z.string().optional().describe('PMC full text URL'),

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAmoB~~/D;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE;IAC9C,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACpB,GAAG,MAAM,CA+BT;AAID,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2rB5B,CAAC"}
1	+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwoB/D;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE;IAC9C,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACpB,GAAG,MAAM,CA+BT;AAID,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2rB5B,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED Viewed

@@ -169,7 +169,10 @@ const PmcArticleSchema = z
     pmcUrl: z.string().optional().describe('PMC URL — derived from `pmcId` when present'),
     pmid: z.string().optional().describe('PubMed ID'),
     pubmedUrl: z.string().optional().describe('PubMed URL'),
-    doi: z.string().optional().describe('DOI'),
+    doi: z
+        .string()
+        .optional()
+        .describe('DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.'),
     title: z.string().optional().describe('Article title'),
     abstract: z.string().optional().describe('Abstract'),
     authors: z.array(AuthorSchema).optional().describe('Authors'),

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"pubmed-europepmc-fetch.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AA0EjE~~,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWvB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;~~EAyIjG~~,CAAC"}
1	+ {"version":3,"file":"pubmed-europepmc-fetch.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkFjE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWvB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;EAsJjG,CAAC"}

package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js CHANGED Viewed

@@ -29,9 +29,11 @@ const epmcIdSchema = z
     .string()
     .regex(/^[A-Za-z0-9][A-Za-z0-9._-]*$/, 'epmcId must be a Europe PMC record identifier — letters, digits, dots, hyphens, or underscores only (e.g. "PPR1283828", "KR20120031038", "IND609436151"). Copy it verbatim from a pubmed_europepmc_search hit\'s `epmcId`.')
     .max(64);
+/** An `epmcId` in PMCID shape — `pubmed_fetch_fulltext` addresses these directly. */
+const PMCID_SHAPED_RE = /^PMC\d+$/i;
 const RecordRefSchema = z
     .object({
-    source: SourceEnum.describe("Europe PMC source corpus — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola). Copy it from the search hit's `source`."),
+    source: SourceEnum.describe("Europe PMC source corpus — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola). Copy it from the search hit's `source`. `PMC` paired with a PMCID resolves whether or not the article is also indexed in PubMed, and a PubMed-indexed one comes back as its canonical `MED` record carrying that PMCID in `pmcId`."),
     epmcId: epmcIdSchema.describe("Europe PMC's own record id within that source. Copy it from the search hit's `epmcId` — for `MED` records this is the PMID; for the other sources it is an EPMC-native accession."),
 })
     .describe('One record address: the Europe PMC source corpus plus its id within that corpus');
@@ -46,7 +48,10 @@ const FetchedRecordSchema = z
     firstPublicationDate: z.string().optional().describe('First publication date (ISO YYYY-MM-DD)'),
     pmid: z.string().optional().describe('PMID when present in PubMed'),
     pmcId: z.string().optional().describe('PMC ID when present in PMC'),
-    doi: z.string().optional().describe('DOI when present'),
+    doi: z
+        .string()
+        .optional()
+        .describe('DOI when present, cased as Europe PMC reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_fetch_articles` (Europe PMC `10.1056/nejmoa2212948`, NCBI `10.1056/NEJMoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch.'),
     isOpenAccess: z
         .boolean()
         .optional()
@@ -135,20 +140,34 @@ export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
         // Europe PMC treats identifiers case-insensitively, so match the request
         // against the response on an upper-cased key rather than reporting a hit as
         // missing over a casing difference.
-        const refKey = (ref) => `${ref.source}:${ref.epmcId.toUpperCase()}`;
-        const resolved = new Set(records.map(refKey));
-        const notFound = input.records.filter((ref) => !resolved.has(refKey(ref)));
+        const refKey = (source, id) => `${source}:${id.toUpperCase()}`;
+        const resolved = new Set();
+        for (const r of records) {
+            resolved.add(refKey(r.source, r.epmcId));
+            // A `PMC` request for a PubMed-indexed article resolves to that article's
+            // canonical `MED` record, which reports the requested PMCID in `pmcId`
+            // instead of as its own id. Without this alias the record comes back in
+            // `records` and is reported missing in the same response.
+            if (r.pmcId)
+                resolved.add(refKey('PMC', r.pmcId));
+        }
+        const notFound = input.records.filter((ref) => !resolved.has(refKey(ref.source, ref.epmcId)));
         ctx.log.info('pubmed_europepmc_fetch completed', {
             requested: input.records.length,
             returned: records.length,
         });
+        // An unresolved id shaped like a PMCID is reachable by another route:
+        // pubmed_fetch_fulltext addresses PMCIDs directly, with no `source` pair.
+        const pmcidHint = notFound.some((r) => PMCID_SHAPED_RE.test(r.epmcId))
+            ? ' An id shaped like a PMCID also resolves through pubmed_fetch_fulltext, whose `pmcids` input takes it on its own.'
+            : '';
         if (records.length === 0) {
-            ctx.enrich.notice('Europe PMC returned no record for any requested pair. Both fields must be copied verbatim from a pubmed_europepmc_search hit — `epmcId` is Europe PMC\'s own id (the PMID only for `source: "MED"`), and it must be paired with the same hit\'s `source`.');
+            ctx.enrich.notice(`Europe PMC returned no record for any requested pair. Both fields must be copied verbatim from a pubmed_europepmc_search hit — \`epmcId\` is Europe PMC's own id (the PMID only for \`source: "MED"\`), and it must be paired with the same hit's \`source\`.${pmcidHint}`);
         }
         else if (notFound.length > 0) {
             ctx.enrich.notice(`Europe PMC returned no record for ${notFound.length} of ${input.records.length} requested pairs: ${notFound
                 .map((r) => `${r.source}/${r.epmcId}`)
-                .join(', ')}. Verify each against its pubmed_europepmc_search hit — a mismatched \`source\` is the usual cause.`);
+                .join(', ')}. Verify each against its pubmed_europepmc_search hit — a mismatched \`source\` is the usual cause.${pmcidHint}`);
         }
         return {
             records,

package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	- {"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;;~~EAoQjG~~,CAAC"}
1	+ {"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;;EAyQjG,CAAC"}

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js CHANGED Viewed

@@ -91,7 +91,10 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
                 .describe('First publication date (ISO YYYY-MM-DD)'),
             pmid: z.string().optional().describe('PMID when present in PubMed'),
             pmcId: z.string().optional().describe('PMC ID when present in PMC'),
-            doi: z.string().optional().describe('DOI when present'),
+            doi: z
+                .string()
+                .optional()
+                .describe('DOI when present, cased as Europe PMC reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_fetch_articles` (Europe PMC `10.1056/nejmoa2212948`, NCBI `10.1056/NEJMoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch.'),
             isOpenAccess: z
                 .boolean()
                 .optional()

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA+IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EA2V7B~~,CAAC"}
1	+ {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA+IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgW7B,CAAC"}

package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED Viewed

@@ -181,7 +181,10 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             authors: z.string().optional().describe('Formatted author string'),
             source: z.string().optional().describe('Journal source'),
             pubDate: z.string().optional().describe('Publication date'),
-            doi: z.string().optional().describe('DOI'),
+            doi: z
+                .string()
+                .optional()
+                .describe('DOI, cased as NCBI reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ from a Europe PMC-sourced `doi` — compare the two case-insensitively.'),
             pmcId: z.string().optional().describe('PMC ID'),
             pmcUrl: z.string().optional().describe('PMC URL'),
             pubmedUrl: z.string().optional().describe('PubMed URL'),

package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED Viewed

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

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

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

	@@ -1 +1 @@
1	- {"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"}
1	+ {"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;AAkDpB;;;;;;;;;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;;;;;;;;;;OAUG;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"}

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

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

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

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

	@@ -1 +1 @@
1	- {"version":3,"file":"text-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/text-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;~~AAmBH~~;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAcvD;AAED;;;;;;;;GAQG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAKlD"}
1	+ {"version":3,"file":"text-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/text-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAiCH;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAcvD;AAED;;;;;;;;GAQG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAKlD"}

package/dist/services/ncbi/parsing/text-helpers.js CHANGED Viewed

@@ -19,7 +19,21 @@ const NAMED_ENTITIES = {
 };
 /** A well-formed numeric (`&#173;`, `&#xAD;`) or named (`&amp;`) character reference. */
 const ENTITY_RE = /&(#x[0-9a-f]+|#\d+|[a-z][a-z0-9]*);/gi;
-const MARKUP_TAG_RE = /<[^>]+>/g;
+/**
+ * A structural tag: `<` immediately followed by an optional `/` and a tag-name
+ * letter, then a tag body carrying no further angle bracket.
+ *
+ * Both restrictions exist to keep statistical notation intact. Requiring a
+ * leading letter leaves `P<0.001` alone; forbidding `<` inside the body stops a
+ * match that opened on a stray `<` from spanning across the next real tag and
+ * swallowing the prose between them (`n<N ... <bold>` keeps its text). The
+ * remaining gap is a stray `<` and `>` pair with a letter after the `<` and no
+ * tag between them — `a<b and c>d` still strips to `a d`. Closing it would take
+ * a tag-name allowlist, which would silently drop unknown JATS elements, so the
+ * looser pattern is deliberate: it errs toward leaving markup visible rather
+ * than deleting text. (#94)
+ */
+const MARKUP_TAG_RE = /<\/?[A-Za-z][^<>]*>/g;
 const SOFT_HYPHEN_RE = //g;
 const WHITESPACE_RE = /\s+/g;
 /**

package/dist/services/ncbi/parsing/text-helpers.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.1",
+  "version": "2.10.2",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.1",
+  "version": "2.10.2",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.1",
+      "version": "2.10.2",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.1",
+      "version": "2.10.2",
       "packageArguments": [
         {
           "type": "positional",