@cyanheads/pubmed-mcp-server 2.10.19 → 2.10.20

package/dist/mcp-server/tools/definitions/find-related.tool.js.map

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

@@ -5,18 +5,22 @@
  * returns a PMID whose author roster doesn't contain the queried author.
  * `citations` is advertised as an array of 1–25 citations. A lone citation
  * object is wrapped into a one-element array before validation, and `citation`
- * is accepted as an alias for `citations`.
+ * is accepted as an alias for `citations`. Every citation-shape rule lives in
+ * the schema, so a citation that cannot match is rejected under its
+ * `citations.N.<field>` path before ECitMatch is called: `year` is four digits,
+ * the other bibliographic fields hold a visible character, and each citation
+ * carries a journal or a year.
  * @module src/mcp-server/tools/definitions/lookup-citation.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
 export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     citations: z.ZodPreprocess<z.ZodArray<z.ZodObject<{
-        journal: z.ZodOptional<z.ZodString>;
-        year: z.ZodOptional<z.ZodString>;
-        volume: z.ZodOptional<z.ZodString>;
-        firstPage: z.ZodOptional<z.ZodString>;
-        authorName: z.ZodOptional<z.ZodString>;
-        key: z.ZodOptional<z.ZodString>;
+        journal: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        year: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        volume: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        firstPage: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        authorName: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+        key: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
     }, z.core.$strip>>, unknown>;
 }, z.core.$strip>, z.ZodObject<{
     results: z.ZodArray<z.ZodObject<{

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

@@ -1 +1 @@
-{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6FjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAoS7B,CAAC"}
+{"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"}

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

@@ -5,7 +5,11 @@
  * returns a PMID whose author roster doesn't contain the queried author.
  * `citations` is advertised as an array of 1–25 citations. A lone citation
  * object is wrapped into a one-element array before validation, and `citation`
- * is accepted as an alias for `citations`.
+ * is accepted as an alias for `citations`. Every citation-shape rule lives in
+ * the schema, so a citation that cannot match is rejected under its
+ * `citations.N.<field>` path before ECitMatch is called: `year` is four digits,
+ * the other bibliographic fields hold a visible character, and each citation
+ * carries a journal or a year.
  * @module src/mcp-server/tools/definitions/lookup-citation.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -13,6 +17,7 @@ import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
+import { hasVisibleText } from './_visible-text.js';
 /** Extract the surname token (first whitespace-separated part) from an author string. */
 function surname(name) {
     return name.trim().split(/\s+/)[0]?.toLowerCase() ?? '';
@@ -30,42 +35,69 @@ function surname(name) {
  * wire (the service submits positional tokens instead), so it stays free-form.
  */
 const BDATA_FIELD_RE = /^[^|\r\n]*$/;
-const BDATA_FIELD_HINT = 'Cannot contain a pipe ("|") or a line break.';
-const BDATA_FIELD_ERROR = `${BDATA_FIELD_HINT} Those characters shift ECitMatch's field layout — remove them or replace them with a space.`;
+const BDATA_FIELD_ERROR = 'Cannot contain a pipe ("|") or a line break. Those characters shift ECitMatch\'s field layout — remove them or replace them with a space.';
+const TEXT_FIELD_HINT = 'Must contain a visible character, and cannot contain a pipe ("|") or a line break.';
+const VISIBLE_TEXT_ERROR = 'Must contain a visible character. Omit the field rather than sending only spaces or invisible characters.';
+/**
+ * The only year ECitMatch matches on: four ASCII digits, padding with spaces or
+ * tabs tolerated. Every other form — `1991a`, `91`, `1991-1992`, `1991 May` —
+ * misses, and a journal-less citation carrying one makes ECitMatch drop that
+ * line and every line after it. No CR or LF, so the bdata layout rule above
+ * holds for this field too. (#187)
+ */
+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)
+ */
+const integerAsString = (value) => typeof value === 'number' && Number.isSafeInteger(value) && !Object.is(value, -0)
+    ? String(value)
+    : value;
+/**
+ * An exactly-empty string from a form client means "unset", never a value to
+ * validate: it parses to `undefined` before the field's checks run, so the
+ * advertised schema keeps its plain `pattern`. Whitespace and invisible-only
+ * values still reach the checks and are rejected. An integer is read as its
+ * decimal string first. (#187, #198)
+ */
+const blankAsUnset = (schema) => z.preprocess((value) => {
+    const read = integerAsString(value);
+    return read === '' ? undefined : read;
+}, schema);
+/**
+ * A bibliographic text field: rejected when it would shift the bdata layout or
+ * holds no visible character — whitespace or a zero-width space sent as a
+ * journal reads as present here but constrains nothing upstream. (#125, #187)
+ */
+const textField = () => blankAsUnset(z
+    .string()
+    .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
+    .refine(hasVisibleText, VISIBLE_TEXT_ERROR)
+    .optional());
 const CitationSchema = z
     .object({
-    journal: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a"). ${BDATA_FIELD_HINT}`),
-    year: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`Publication year (e.g., "1991"). ${BDATA_FIELD_HINT}`),
-    volume: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`Volume number. ${BDATA_FIELD_HINT}`),
-    firstPage: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`First page number. ${BDATA_FIELD_HINT}`),
-    authorName: z
-        .string()
-        .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
-        .optional()
-        .describe(`Author name, typically "lastname initials" (e.g., "mann bj"). ${BDATA_FIELD_HINT}`),
+    journal: textField().describe(`Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a"). ${TEXT_FIELD_HINT}`),
+    year: blankAsUnset(z.string().regex(YEAR_RE, 'Must be a four-digit year, e.g. "1991".').optional()).describe('Publication year as four digits (e.g., "1991").'),
+    volume: textField().describe(`Volume number. ${TEXT_FIELD_HINT}`),
+    firstPage: textField().describe(`First page number. ${TEXT_FIELD_HINT}`),
+    authorName: textField().describe(`Author name, typically "lastname initials" (e.g., "mann bj"). ${TEXT_FIELD_HINT}`),
     key: z
-        .string()
-        .optional()
+        .preprocess(integerAsString, z.string().optional())
         .describe('Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.'),
 })
-    .describe('Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.')
-    .refine((c) => !!(c.journal || c.year), {
+    .describe('Citation to match against PubMed. Must include at least journal or a four-digit year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.')
+    /**
+     * Zod still runs this beside a field that failed its own check, handing it the
+     * raw value, so the rule tests the journal and year itself: a whitespace
+     * journal or a malformed year never satisfies it. (#187)
+     */
+    .refine((c) => (c.journal !== undefined && hasVisibleText(c.journal)) ||
+    (c.year !== undefined && YEAR_RE.test(c.year)), {
     message: 'Each citation must include at least a journal or year field — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.',
 });
 /**
@@ -79,7 +111,7 @@ const CITATIONS_SHAPE_ERROR = 'Invalid input: expected a citation object or an a
 /** A citation sent on its own rather than in an array. JSON input has no other object kind. */
 const isCitationObject = (value) => typeof value === 'object' && value !== null && !Array.isArray(value);
 export const lookupCitationTool = tool('pubmed_lookup_citation', {
-    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
+    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or a four-digit year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
@@ -177,7 +209,11 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
         const matchedPmids = Array.from(new Set(results.filter((r) => r.matched && r.pmid).map((r) => r.pmid)));
         const summaryByPmid = new Map();
         if (matchedPmids.length > 0) {
-            const summaryResult = await ncbi.eSummary({ db: 'pubmed', id: matchedPmids.join(',') }, { signal: ctx.signal });
+            // Version 2.0, because the version 1 DocSum drops what verification
+            // needs: it lists a consortium as a `CollectiveName` item the roster
+            // never reads, and it has no `DocDate`, so a Bookshelf chapter would be
+            // dated by its book's start year. (#199, #201)
+            const summaryResult = await ncbi.eSummary({ db: 'pubmed', version: '2.0', retmode: 'xml', id: matchedPmids.join(',') }, { signal: ctx.signal });
             const summaries = await extractBriefSummaries(summaryResult);
             for (const s of summaries) {
                 summaryByPmid.set(s.pmid, {

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

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

@@ -1,7 +1,8 @@
 /**
  * @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
  * Searches the NCBI MeSH database with offset pagination and optionally
- * retrieves detailed records. `limit` is accepted as an alias for `maxResults`.
+ * retrieves detailed records. `limit`, `retmax`, and `pageSize` are accepted as
+ * aliases for `maxResults`, `retstart` for `offset`, and `term` for `query`.
  * @module src/mcp-server/tools/definitions/lookup-mesh.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';

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

@@ -1 +1 @@
-{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8GjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwMzB,CAAC"}
+{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8GjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+MzB,CAAC"}

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

@@ -1,7 +1,8 @@
 /**
  * @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
  * Searches the NCBI MeSH database with offset pagination and optionally
- * retrieves detailed records. `limit` is accepted as an alias for `maxResults`.
+ * retrieves detailed records. `limit`, `retmax`, and `pageSize` are accepted as
+ * aliases for `maxResults`, `retstart` for `offset`, and `term` for `query`.
  * @module src/mcp-server/tools/definitions/lookup-mesh.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -102,8 +103,15 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
     ]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
     errors: [...NCBI_SERVICE_ERRORS, ...QUERY_INPUT_ERRORS],
-    // Never advertised; rewritten to the canonical key before the schema parses. (#156)
-    inputAliases: { limit: 'maxResults' },
+    // Never advertised; rewritten to the canonical key before the schema parses.
+    // ESearch's own names (`retmax`, `retstart`, `term`) and sibling tools' names. (#156, #190)
+    inputAliases: {
+        limit: 'maxResults',
+        retmax: 'maxResults',
+        pageSize: 'maxResults',
+        retstart: 'offset',
+        term: 'query',
+    },
     input: z.object({
         query: z
             .string()

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

@@ -24,6 +24,7 @@ export declare const pubmedEuropepmcFetchTool: import("@cyanheads/mcp-ts-core").
         }>;
         epmcId: z.ZodString;
     }, z.core.$strip>>;
+    maxResponseCharacters: z.ZodOptional<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     records: z.ZodArray<z.ZodObject<{
         source: z.ZodEnum<{
@@ -58,6 +59,22 @@ export declare const pubmedEuropepmcFetchTool: import("@cyanheads/mcp-ts-core").
         }>;
         epmcId: z.ZodString;
     }, z.core.$strip>>>;
+    deferred: z.ZodOptional<z.ZodObject<{
+        maxResponseCharacters: z.ZodNumber;
+        returnedCharacters: z.ZodNumber;
+        deferredCount: z.ZodNumber;
+        records: z.ZodArray<z.ZodObject<{
+            source: z.ZodEnum<{
+                AGR: "AGR";
+                MED: "MED";
+                PAT: "PAT";
+                PMC: "PMC";
+                PPR: "PPR";
+            }>;
+            epmcId: z.ZodString;
+        }, z.core.$strip>>;
+        nextDeferredCharacters: z.ZodNumber;
+    }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
     readonly reason: 'europepmc_unreachable';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
@@ -86,5 +103,6 @@ export declare const pubmedEuropepmcFetchTool: import("@cyanheads/mcp-ts-core").
     readonly recovery: 'Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.';
 }], {
     readonly notice: z.ZodOptional<z.ZodString>;
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
 }>;
 //# sourceMappingURL=pubmed-europepmc-fetch.tool.d.ts.map

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

@@ -1 +1 @@
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+{"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;;;;EAyNjG,CAAC"}