@cyanheads/pubmed-mcp-server 2.10.21 → 2.10.22

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js

@@ -8,88 +8,62 @@
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { NCBI_SERVICE_ERRORS, QUERY_INPUT_ERRORS } from '../../../services/error-contracts.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
-import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { ensureArray, getOptionalText, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_ONTOLOGY_TERMINOLOGY, SCHEMA_DEFINED_TERM, SCHEMA_DEFINED_TERM_SET, } from './_concepts.js';
 import { hasVisibleText } from './_visible-text.js';
 /**
- * NCBI Entrez mesh UIDs encode the canonical MeSH DescriptorUI as the ASCII code of the
- * UI's letter prefix followed by its 6-digit number: D=68, C=67 (supplementary concept),
- * Q=81 (qualifier). So `68003924` → `D003924`. Modern supplementary-concept records receive
- * plain sequential UIDs that don't encode a UI (e.g. `2025952`); those aren't decodable, so
- * the raw Entrez UID is returned unchanged.
+ * Records the exact-heading (`[MH]`) search reads to choose its pin. A heading
+ * matches one record, or two for a drug class (its pharmacological-action record
+ * and its descriptor); the rest is headroom.
  */
-const ENTREZ_UID_PREFIX = { '67': 'C', '68': 'D', '81': 'Q' };
-function decodeMeshDescriptorUi(entrezUid) {
-    if (/^\d{8}$/.test(entrezUid)) {
-        const letter = ENTREZ_UID_PREFIX[entrezUid.slice(0, 2)];
-        if (letter)
-            return `${letter}${entrezUid.slice(2)}`;
-    }
-    return entrezUid;
-}
-function findItem(items, name) {
-    return items.find((it) => getText(it['@_Name']) === name);
-}
-function getItemText(item) {
-    if (!item)
-        return '';
-    const direct = getText(item, '');
-    if (direct)
-        return direct;
-    const subItems = ensureArray(item.Item);
-    return subItems.length > 0 ? getText(subItems[0]) : '';
-}
-function getItemTexts(item) {
-    if (!item)
-        return [];
-    const subItems = ensureArray(item.Item);
-    return subItems.map((si) => getText(si)).filter((s) => s.length > 0);
-}
-function extractTreeNumbers(items) {
-    const idxLinks = findItem(items, 'DS_IdxLinks');
-    if (!idxLinks)
-        return [];
-    const linkStructures = ensureArray(idxLinks.Item);
-    const treeNums = [];
-    for (const struct of linkStructures) {
-        const structItems = ensureArray(struct.Item);
-        const treeItem = findItem(structItems, 'TreeNum');
-        const val = treeItem ? getText(treeItem) : '';
-        // Supplementary Concept Records (SCRs) surface a non-navigable mapped-heading
-        // pointer (e.g. "@218176") in the same TreeNum field. Drop it so treeNumbers
-        // holds only real, navigable MeSH tree numbers. (#76)
-        if (val && !val.startsWith('@'))
-            treeNums.push(val);
-    }
-    return treeNums;
+const EXACT_MATCH_CANDIDATES = 5;
+/**
+ * The record's tree numbers. Two `TreeNum` values are not tree positions: a
+ * supplementary concept record's mapped-heading pointer (`@218176`, #76), and the
+ * record's own UI, which is the only `TreeNum` a pharmacological-action record
+ * carries (#247).
+ */
+function extractTreeNumbers(doc, meshId) {
+    const idxLinks = doc.DS_IdxLinks;
+    return ensureArray(idxLinks?.LinksType)
+        .map((link) => getText(link.TreeNum))
+        .filter((treeNum) => treeNum && !treeNum.startsWith('@') && treeNum !== meshId);
 }
-function parseSummaryRecords(data, ids, includeDetails) {
-    if (!data || typeof data !== 'object')
-        return ids.map((id) => ({ entrezUid: id, meshId: decodeMeshDescriptorUi(id), name: id }));
-    const root = data;
-    const summaryResult = root.eSummaryResult;
-    const docSums = ensureArray((summaryResult ?? root).DocSum);
-    if (docSums.length === 0)
-        return ids.map((id) => ({ entrezUid: id, meshId: decodeMeshDescriptorUi(id), name: id }));
-    return docSums.map((doc) => {
-        const entrezUid = getText(doc.Id);
-        const meshId = decodeMeshDescriptorUi(entrezUid);
-        const items = ensureArray(doc.Item);
-        const name = getItemText(findItem(items, 'DS_MeshTerms')) || meshId;
-        const record = { entrezUid, meshId, name };
+/**
+ * Index a `version=2.0` MeSH eSummary by Entrez UID. The canonical UI is read from
+ * `DS_MeSHUI`, which every record type carries; the Entrez UID encodes no UI for
+ * records added in recent MeSH years or for pharmacological-action records. A
+ * `<DocumentSummary>` holding only an `<error>` (a UID with no record) yields no
+ * `meshId`. (#238)
+ */
+function parseSummaryRecords(data, includeDetails) {
+    const docs = ensureArray(data?.DocumentSummarySet?.DocumentSummary);
+    const summaries = new Map();
+    for (const doc of docs) {
+        const entrezUid = getText(doc['@_uid']);
+        const meshId = getOptionalText(doc.DS_MeSHUI);
+        const terms = doc.DS_MeshTerms;
+        const entryTerms = ensureArray(terms?.string)
+            .map((term) => getText(term))
+            .filter(Boolean);
+        const record = {
+            entrezUid,
+            ...(meshId !== undefined && { meshId }),
+            name: entryTerms[0] ?? entrezUid,
+        };
         if (includeDetails) {
-            const scopeNote = getItemText(findItem(items, 'DS_ScopeNote'));
+            const scopeNote = getOptionalText(doc.DS_ScopeNote);
             if (scopeNote)
                 record.scopeNote = scopeNote;
-            const entryTerms = getItemTexts(findItem(items, 'DS_MeshTerms'));
             if (entryTerms.length > 0)
                 record.entryTerms = entryTerms;
-            const treeNumbers = extractTreeNumbers(items);
+            const treeNumbers = extractTreeNumbers(doc, meshId);
             if (treeNumbers.length > 0)
                 record.treeNumbers = treeNumbers;
         }
-        return record;
-    });
+        summaries.set(entrezUid, { record, recordType: getOptionalText(doc.DS_RecordType) });
+    }
+    return summaries;
 }
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const lookupMeshTool = tool('pubmed_lookup_mesh', {
@@ -141,7 +115,8 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
             .object({
             meshId: z
                 .string()
-                .describe('Canonical MeSH DescriptorUI (e.g. "D003924") — resolves at the MeSH Browser and NLM linked data. Falls back to the raw Entrez UID when a record is not decodable.'),
+                .optional()
+                .describe('Canonical MeSH unique identifier (e.g. "D003924", "C000626284", "Q000009") — resolves at the MeSH Browser and NLM linked data. A pharmacological-action record carries its descriptor\'s UI. Omitted only when eSummary returned no record for this UID.'),
             entrezUid: z
                 .string()
                 .describe('NCBI Entrez UID for this record — the join key for E-utilities (eSummary/eFetch db=mesh).'),
@@ -149,7 +124,7 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
             treeNumbers: z
                 .array(z.string())
                 .optional()
-                .describe('Navigable MeSH tree numbers (e.g. "D02.078.370.141.450"). Omitted for supplementary concept records (SCRs), which map to a heading rather than occupying a tree position.'),
+                .describe('Navigable MeSH tree numbers (e.g. "D02.078.370.141.450"). Omitted for supplementary concept records (SCRs), which map to a heading rather than occupying a tree position, and for pharmacological-action records, whose descriptor carries the tree positions.'),
             scopeNote: z.string().optional().describe('Scope note'),
             entryTerms: z.array(z.string()).optional().describe('Synonyms / entry terms'),
         })
@@ -187,10 +162,24 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
         // hold back. The first page leads with it; later pages skip it where it ranks.
         const exactSearch = hasFieldTag
             ? undefined
-            : ncbi.eSearch({ db: 'mesh', term: `${query}[MH]`, retmax: 1 }, callOpts);
+            : ncbi.eSearch({ db: 'mesh', term: `${query}[MH]`, retmax: EXACT_MATCH_CANDIDATES }, callOpts);
         const [broadResult, exactResult] = await Promise.all([broadSearch, exactSearch]);
         const totalCount = broadResult.count;
-        const pinnedUid = exactResult?.idList[0];
+        const exactIds = exactResult?.idList ?? [];
+        const fetchSummaries = (uids) => ncbi
+            .eSummary({ db: 'mesh', id: uids.join(','), version: '2.0' }, callOpts)
+            .then((data) => parseSummaryRecords(data, includeDetails));
+        // A drug-class heading matches its pharmacological-action record ahead of its
+        // descriptor. When the heading matches more than one record and this page
+        // leads with the pin or holds a candidate at its rank, read the record types
+        // first — the page's own summaries ride the same request — and pin the first
+        // that is not a pharmacological-action record. (#247)
+        const pinShapesPage = offset === 0 || exactIds.some((id) => broadResult.idList.includes(id));
+        const prefetched = exactIds.length > 1 && pinShapesPage
+            ? await fetchSummaries([...new Set([...exactIds, ...broadResult.idList])])
+            : undefined;
+        const pinnedUid = exactIds.find((id) => prefetched?.get(id)?.recordType !== 'pharmacological-action') ??
+            exactIds[0];
         const ids = [];
         if (pinnedUid !== undefined && offset === 0)
             ids.push(pinnedUid);
@@ -228,8 +217,8 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
             ctx.enrich.notice(notice);
             return { query, offset, ...(hasMore && { nextOffset }), results: [] };
         }
-        const summaryData = await ncbi.eSummary({ db: 'mesh', id: ids.join(',') }, callOpts);
-        const results = parseSummaryRecords(summaryData, ids, includeDetails);
+        const summaries = prefetched ?? (await fetchSummaries(ids));
+        const results = ids.map((id) => summaries.get(id)?.record ?? { entrezUid: id, name: id });
         const queryLower = query.toLowerCase();
         results.sort((a, b) => {
             const aExact = a.name.toLowerCase() === queryLower ? 0 : 1;
@@ -255,7 +244,8 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
         }
         for (const r of result.results) {
             lines.push(`\n## ${r.name}`);
-            lines.push(`- **MeSH ID:** ${r.meshId}`);
+            if (r.meshId)
+                lines.push(`- **MeSH ID:** ${r.meshId}`);
             lines.push(`- **Entrez UID:** ${r.entrezUid}`);
             if (r.treeNumbers?.length)
                 lines.push(`- **Tree Numbers:** ${r.treeNumbers.join(', ')}`);

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map

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package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts

@@ -4,6 +4,7 @@
  * and returns each one's complete, untruncated abstract. That pair is the only
  * identifier many PPR, PAT, and AGR records carry, so `pubmed_fetch_articles`
  * (PMIDs) and `pubmed_fetch_fulltext` (PMCIDs / PMIDs / DOIs) cannot reach them.
+ * A lower-case `source` is read as its upper-case code.
  *
  * Only registered when `EUROPEPMC_ENABLED=true` (the default). The handler
  * fails fast with a configuration error if the service is unset, since the
@@ -15,13 +16,13 @@ import { z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const pubmedEuropepmcFetchTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     records: z.ZodArray<z.ZodObject<{
-        source: z.ZodEnum<{
+        source: z.ZodPreprocess<z.ZodEnum<{
             AGR: "AGR";
             MED: "MED";
             PAT: "PAT";
             PMC: "PMC";
             PPR: "PPR";
-        }>;
+        }>, unknown>;
         epmcId: z.ZodString;
     }, z.core.$strip>>;
     maxResponseCharacters: z.ZodOptional<z.ZodNumber>;
@@ -50,13 +51,13 @@ export declare const pubmedEuropepmcFetchTool: import("@cyanheads/mcp-ts-core").
         epmcUrl: z.ZodString;
     }, z.core.$strip>>;
     notFound: z.ZodOptional<z.ZodArray<z.ZodObject<{
-        source: z.ZodEnum<{
+        source: z.ZodPreprocess<z.ZodEnum<{
             AGR: "AGR";
             MED: "MED";
             PAT: "PAT";
             PMC: "PMC";
             PPR: "PPR";
-        }>;
+        }>, unknown>;
         epmcId: z.ZodString;
     }, z.core.$strip>>>;
     deferred: z.ZodOptional<z.ZodObject<{
@@ -92,7 +93,7 @@ export declare const pubmedEuropepmcFetchTool: import("@cyanheads/mcp-ts-core").
 }, {
     readonly reason: 'europepmc_invalid_input';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: 'Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).';
+    readonly when: 'Europe PMC rejected the request input — an error message in place of results; a sort it cannot use (one whose keys are not each a field plus asc/desc, rejected before any request; an empty response to a sort with an undocumented field; or a second HTTP 503 to a sorted search when the same query without the sort is served); or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).';
     readonly recovery: "Fix the rejected input before retrying — the query, the sort, or the cursorMark (pass the previous response's `nextCursorMark` verbatim, or `*` to restart); the same input will most likely be rejected again.";
     readonly retryable: false;
     readonly thrownBy: 'service';

package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map

@@ -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;AAiIjE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWvB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;EAwNjG,CAAC"}
+{"version":3,"file":"pubmed-europepmc-fetch.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkIjE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWvB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;EA8NjG,CAAC"}

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

@@ -4,6 +4,7 @@
  * and returns each one's complete, untruncated abstract. That pair is the only
  * identifier many PPR, PAT, and AGR records carry, so `pubmed_fetch_articles`
  * (PMIDs) and `pubmed_fetch_fulltext` (PMCIDs / PMIDs / DOIs) cannot reach them.
+ * A lower-case `source` is read as its upper-case code.
  *
  * Only registered when `EUROPEPMC_ENABLED=true` (the default). The handler
  * fails fast with a configuration error if the service is unset, since the
@@ -17,8 +18,9 @@ import { EUROPEPMC_SERVICE_ERRORS } from '../../../services/error-contracts.js';
 import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-service.js';
 import { EUROPEPMC_ALL_SOURCES } from '../../../services/europe-pmc/types.js';
 import { toDisplayText } from '../../../services/ncbi/parsing/text-helpers.js';
-import { fitWholeItems } from './_budget.js';
+import { buildDeferralNotice, fitWholeItems } from './_budget.js';
 import { conceptMeta, EDAM_ACCESSION, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
+import { europePmcSourceInputSchema } from './_schemas.js';
 import { escapeMarkdownInline } from './_text.js';
 const SourceEnum = z.enum(EUROPEPMC_ALL_SOURCES);
 /**
@@ -35,7 +37,7 @@ const epmcIdSchema = z
 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`. `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`."),
+    source: europePmcSourceInputSchema.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');
@@ -95,12 +97,12 @@ const DeferredSchema = z
         .describe("The deferred records, in response order, each as the resolved record's own `source` + `epmcId` — a `PMC` request answered by its `MED` record is listed as that `MED` pair. Pass them back as `records` to retrieve them. Never contains a pair from `notFound`."),
     nextDeferredCharacters: z
         .number()
-        .describe('Serialized size of the next deferred record — the first entry in `records`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller record further down `records` cannot be reached until this one fits.'),
+        .describe('Serialized size of the next deferred record — the first entry in `records`, where the response stopped — and the continuation ceiling: re-calling with the deferred pairs needs `maxResponseCharacters` ≥ this to return anything, and a smaller record further down `records` cannot be reached until this one fits. Repeating this same call needs `maxResponseCharacters` ≥ `returnedCharacters` + this to return this record as well.'),
 })
     .describe('Continuation state for records the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one record.');
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
-    description: "Fetch complete Europe PMC records — including the full, untruncated abstract — for records addressed by `source` plus `epmcId`. Pairs with `pubmed_europepmc_search`, which returns bounded `abstractSnippet` values and flags cut ones with `abstractTruncated: true`; pass those hits' `source` and `epmcId` here to read the whole abstract. This is the retrieval path for preprint (`PPR`), patent (`PAT`), and Agricola (`AGR`) records, which frequently carry no PMID and no DOI, so `pubmed_fetch_articles` and `pubmed_fetch_fulltext` cannot address them. Up to 25 records per call. Set `maxResponseCharacters` to bound the whole response: records past the ceiling are deferred whole and listed in `deferred.records` for a follow-up call.",
+    description: "Fetch complete Europe PMC records — including the full, untruncated abstract — addressed as `records: [{ source, epmcId }]`, an array even for one record. Pairs with `pubmed_europepmc_search`, which returns bounded `abstractSnippet` values and flags cut ones with `abstractTruncated: true`; copy each hit's `source` and `epmcId` into `records` here to read the whole abstract. This is the retrieval path for preprint (`PPR`), patent (`PAT`), and Agricola (`AGR`) records, which frequently carry no PMID and no DOI, so `pubmed_fetch_articles` and `pubmed_fetch_fulltext` cannot address them. Up to 25 records per call. Set `maxResponseCharacters` to bound the whole response: records past the ceiling are deferred whole and listed in `deferred.records` for a follow-up call.",
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_ACCESSION]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.ts',
@@ -244,7 +246,11 @@ export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
         }
         if (deferred) {
             ctx.enrich({ truncated: true });
-            notices.push(buildDeferralNotice(deferred));
+            notices.push(buildDeferralNotice(deferred, {
+                noun: 'record',
+                ids: deferred.records.map(formatPair).join(', '),
+                recall: 'pubmed_europepmc_fetch with those pairs as `records: [{ source, epmcId }]`',
+            }));
         }
         if (notices.length > 0)
             ctx.enrich.notice(notices.join(' '));
@@ -301,16 +307,4 @@ export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
 function formatPair(pair) {
     return `${pair.source}/${pair.epmcId}`;
 }
-/**
- * Compose the recovery notice for a response the whole-response budget bounded.
- * Names what was spent, which pairs are still retrievable, and the ceiling the
- * next call has to clear — so a caller reading only `content[]` can resume
- * without inspecting `deferred`. (#188)
- */
-function buildDeferralNotice(deferred) {
-    const spent = deferred.returnedCharacters === 0
-        ? `The first record alone exceeds the requested maxResponseCharacters of ${deferred.maxResponseCharacters}, so none were returned.`
-        : `Response character budget reached: ${deferred.returnedCharacters} of ${deferred.maxResponseCharacters} characters returned.`;
-    return `${spent} ${deferred.deferredCount} resolved record(s) were deferred whole: ${deferred.records.map(formatPair).join(', ')}. Re-call pubmed_europepmc_fetch with those pairs as \`records\` to retrieve them, or raise maxResponseCharacters to at least ${deferred.nextDeferredCharacters} — the size of the next deferred record.`;
-}
 //# sourceMappingURL=pubmed-europepmc-fetch.tool.js.map

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

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package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts

@@ -6,7 +6,7 @@
  * because EPMC's search API doesn't support offset. `max_results`, `limit`, and
  * `maxResults` are accepted as aliases for `pageSize`. A `query` with no search
  * term (`()`, `<b></b>`) or a blank `cursorMark` is rejected before Europe PMC
- * is called.
+ * is called. A lower-case `sources` code is read as its upper-case form.
  * The total hit count rides in `output` so `format()` can state it in the
  * header, and `searchUrl` opens the source-filtered query Europe PMC actually
  * ran.
@@ -23,13 +23,13 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
     query: z.ZodString;
     pageSize: z.ZodDefault<z.ZodNumber>;
     cursorMark: z.ZodDefault<z.ZodString>;
-    sources: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+    sources: z.ZodOptional<z.ZodArray<z.ZodPreprocess<z.ZodEnum<{
         AGR: "AGR";
         MED: "MED";
         PAT: "PAT";
         PMC: "PMC";
         PPR: "PPR";
-    }>>>;
+    }>, unknown>>>;
     resultType: z.ZodDefault<z.ZodEnum<{
         core: "core";
         lite: "lite";
@@ -81,7 +81,7 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
 }, {
     readonly reason: 'europepmc_invalid_input';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: 'Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).';
+    readonly when: 'Europe PMC rejected the request input — an error message in place of results; a sort it cannot use (one whose keys are not each a field plus asc/desc, rejected before any request; an empty response to a sort with an undocumented field; or a second HTTP 503 to a sorted search when the same query without the sort is served); or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served).';
     readonly recovery: "Fix the rejected input before retrying — the query, the sort, or the cursorMark (pass the previous response's `nextCursorMark` verbatim, or `*` to restart); the same input will most likely be rejected again.";
     readonly retryable: false;
     readonly thrownBy: 'service';

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map

@@ -1 +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;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgCjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAYxB,cAAc;;mBAEhB,gLAAgL;uBAEpL,gIAAgI;;;qBAI1H,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;EAgUjG,CAAC"}
+{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiCjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAYxB,cAAc;;mBAEhB,gLAAgL;uBAEpL,gIAAgI;;;qBAI1H,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;EAgUjG,CAAC"}

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

@@ -6,7 +6,7 @@
  * because EPMC's search API doesn't support offset. `max_results`, `limit`, and
  * `maxResults` are accepted as aliases for `pageSize`. A `query` with no search
  * term (`()`, `<b></b>`) or a blank `cursorMark` is rejected before Europe PMC
- * is called.
+ * is called. A lower-case `sources` code is read as its upper-case form.
  * The total hit count rides in `output` so `format()` can state it in the
  * header, and `searchUrl` opens the source-filtered query Europe PMC actually
  * ran.
@@ -25,6 +25,7 @@ import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-ser
 import { EUROPEPMC_ALL_SOURCES, EUROPEPMC_DEFAULT_SOURCES, } from '../../../services/europe-pmc/types.js';
 import { toDisplayText } from '../../../services/ncbi/parsing/text-helpers.js';
 import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
+import { europePmcSourceInputSchema } from './_schemas.js';
 import { escapeMarkdownInline, sliceCodeUnits } from './_text.js';
 import { hasVisibleText } from './_visible-text.js';
 const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
@@ -38,7 +39,7 @@ const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
 const ABSTRACT_SNIPPET_LIMIT = 400;
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
-    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.',
+    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 to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]` for the complete abstract.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts',
@@ -80,7 +81,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             .default('*')
             .describe("Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` verbatim for subsequent pages. A whitespace-only cursor, invisible characters included, is rejected before the request, and a cursor Europe PMC cannot read fails with `europepmc_invalid_input` once a retry of it fails again while the first page of the same query is served."),
         sources: z
-            .array(SourceEnum)
+            .array(europePmcSourceInputSchema)
             .min(1)
             .optional()
             .describe(`Filter to specific EPMC sources. Defaults to ${EUROPEPMC_DEFAULT_SOURCES.join(', ')} when omitted. Pass an explicit array including PAT or AGR to broaden coverage. Allowed values: ${EUROPEPMC_ALL_SOURCES.join(', ')}.`),
@@ -91,7 +92,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         sort: z
             .string()
             .optional()
-            .describe('Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Field and direction match case-insensitively. A field outside the documented set may be honored, silently ignored, or rejected, and a sort using one — or a key without `asc`/`desc` — can fail with `europepmc_invalid_input` naming it, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: ["PPR"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date.'),
+            .describe('Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year), `FIRST_IDATE_D` (date first indexed in Europe PMC). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking; `relevance` or `relevance desc` is sent as no sort. Field and direction match case-insensitively. Each key must be one field plus `asc` or `desc`: a key without a direction, an empty key, or an extra word fails with `europepmc_invalid_input` before the request. A field outside the documented set may be honored, silently ignored, or refused — a sort Europe PMC refuses fails with `europepmc_invalid_input` naming it, and an empty Europe PMC response to a sort with an undocumented field fails the same way, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: ["PPR"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR desc` to order preprints by date.'),
     }),
     output: z.object({
         hits: z
@@ -100,7 +101,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             source: SourceEnum.describe('Europe PMC source — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola)'),
             epmcId: z
                 .string()
-                .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."),
+                .describe("Europe PMC's internal record id. Pass it with this hit's `source` to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]` 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."),
             title: z
                 .string()
                 .optional()
@@ -139,7 +140,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             abstractTruncated: z
                 .boolean()
                 .optional()
-                .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.'),
+                .describe('Whether `abstractSnippet` was cut short of the full abstract. Retrieve the complete text by passing this record to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]`. Present whenever `abstractSnippet` is; omitted when Europe PMC carries no abstract.'),
             citedByCount: z.number().optional().describe('Citation count reported by Europe PMC'),
             epmcUrl: z.string().describe('Europe PMC article URL'),
         })
@@ -261,7 +262,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         }
         else if (sortField === 'P_PDATE_D' && isPprOnly) {
             notice =
-                'Europe PMC ignores `P_PDATE_D` sort for preprint-only (PPR) results — preprints have no populated publication date, so records are returned in relevance order, not by date. To order preprints by date, sort by `PUB_YEAR`, or re-rank the returned page by each record’s `firstPublicationDate`.';
+                'Europe PMC ignores `P_PDATE_D` sort for preprint-only (PPR) results — preprints have no populated publication date, so records are returned in relevance order, not by date. To order preprints by date, sort by `PUB_YEAR desc`, or re-rank the returned page by each record’s `firstPublicationDate`.';
         }
         ctx.log.info('pubmed_europepmc_search completed', {
             hitCount: result.hitCount,
@@ -323,7 +324,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
                 if (h.abstractSnippet) {
                     lines.push(`\n${h.abstractSnippet}`);
                     if (h.abstractTruncated) {
-                        lines.push(`_Abstract truncated at ${ABSTRACT_SNIPPET_LIMIT} characters — call \`pubmed_europepmc_fetch\` with this record's \`source\` and \`epmcId\` for the complete text._`);
+                        lines.push(`_Abstract truncated at ${ABSTRACT_SNIPPET_LIMIT} characters — pass this hit to \`pubmed_europepmc_fetch\` as \`records: [{ source, epmcId }]\` for the complete text._`);
                     }
                 }
             }