npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.20 → 2.10.22 - Mend

@cyanheads/pubmed-mcp-server 2.10.20 → 2.10.22

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 (110) hide show

package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AA2IjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAwS7B,CAAC"}
1	+ {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAwS7B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED Viewed

@@ -48,12 +48,14 @@ const VISIBLE_TEXT_ERROR = 'Must contain a visible character. Omit the field rat
 const YEAR_RE = /^[ \t]*\d{4}[ \t]*$/;
 /**
  * A safe integer sent for a string field, read as its decimal string — the
- * framework's own repair rule (a safe integer other than `-0`), applied here
- * because that repair cannot reach a lone citation object: it re-reads the
- * failing path `citations.0.year` against the raw arguments, where `citations`
- * is still the object this schema wraps. Converting before validation gives the
- * object and array forms the same citation. Anything else passes through to be
- * rejected as before. (#198)
+ * framework's own repair rule (a safe integer other than `-0`). That repair
+ * reaches a lone citation object and this schema's preprocess output alike, and
+ * hands the handler the same value. What it cannot do is hold a repaired value
+ * to the field's own check: when the digits then fail it, the call is rejected
+ * with the original `expected string, received number`, so an integer year
+ * that is not four digits would be told to resend it as a string. Converting
+ * before validation reports the four-digit rule instead. Anything else passes
+ * through to be rejected as before. (#187, #198)
  */
 const integerAsString = (value) => typeof value === 'number' && Number.isSafeInteger(value) && !Object.is(value, -0)
     ? String(value)

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts CHANGED Viewed

@@ -16,7 +16,7 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
     offset: z.ZodNumber;
     nextOffset: z.ZodOptional<z.ZodNumber>;
     results: z.ZodArray<z.ZodObject<{
-        meshId: z.ZodString;
+        meshId: z.ZodOptional<z.ZodString>;
         entrezUid: z.ZodString;
         name: z.ZodString;
         treeNumbers: z.ZodOptional<z.ZodArray<z.ZodString>>;

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js CHANGED Viewed

@@ -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(', ')}`);

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

@@ -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 CHANGED Viewed

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

@@ -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',
@@ -123,7 +125,6 @@ export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
             .number()
             .int()
             .min(1)
-            .max(1_000_000)
             .optional()
             .describe('Opt-in ceiling for the whole response, in characters. Each record is measured as the JSON record it is returned as — title, authors, journal, abstract, identifiers, every field it carries. Records are kept in the order Europe PMC returned them until the next one would cross the ceiling; that record and the rest are deferred whole (never partially populated) and listed in `deferred.records`. Response envelope fields — `notFound`, `deferred` itself — are not counted. Omit to return every resolved record.'),
     }),
@@ -245,7 +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(' '));
@@ -302,16 +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

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

@@ -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 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;;;;;;;;;;;;;;;;;;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"}