@cyanheads/pubmed-mcp-server 2.10.0 → 2.10.1

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 (18) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +1 -1
  4. package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts +1 -1
  5. package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts.map +1 -1
  6. package/dist/mcp-server/prompts/definitions/research-plan.prompt.js +9 -2
  7. package/dist/mcp-server/prompts/definitions/research-plan.prompt.js.map +1 -1
  8. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  9. package/dist/mcp-server/tools/definitions/search-articles.tool.js +88 -19
  10. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  11. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  12. package/dist/services/ncbi/ncbi-service.js +19 -2
  13. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  14. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  15. package/dist/services/ncbi/response-handler.js +1 -0
  16. package/dist/services/ncbi/response-handler.js.map +1 -1
  17. package/package.json +1 -1
  18. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.10.0
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+ **Version:** 2.10.1
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.0`
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  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.10.0
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+ **Version:** 2.10.1
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.0`
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  **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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package/README.md CHANGED
@@ -9,7 +9,7 @@
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- [![Version](https://img.shields.io/badge/Version-2.10.0-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/)
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+ [![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/)
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  </div>
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package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts CHANGED
@@ -10,7 +10,7 @@ export declare const researchPlanPrompt: import("@cyanheads/mcp-ts-core").Prompt
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  goal: z.ZodString;
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  keywords: z.ZodString;
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  organism: z.ZodOptional<z.ZodString>;
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- includeAgentPrompts: z.ZodDefault<z.ZodEnum<{
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+ includeAgentPrompts: z.ZodOptional<z.ZodEnum<{
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  false: "false";
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  true: "true";
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  }>>;
package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"research-plan.prompt.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/prompts/definitions/research-plan.prompt.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAU,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgJnD,eAAO,MAAM,kBAAkB;;;;;;;;;kBA6B7B,CAAC"}
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+ {"version":3,"file":"research-plan.prompt.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/prompts/definitions/research-plan.prompt.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAU,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAuJnD,eAAO,MAAM,kBAAkB;;;;;;;;;kBA6B7B,CAAC"}
package/dist/mcp-server/prompts/definitions/research-plan.prompt.js CHANGED
@@ -10,10 +10,17 @@ const ArgsSchema = z.object({
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  goal: z.string().describe('Primary research goal'),
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  keywords: z.string().describe('Research keywords (comma-separated)'),
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  organism: z.string().optional().describe('Target organism'),
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+ /**
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+ * `.optional()` rather than `.default('false')`: the SDK derives each prompt
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+ * argument's `required` flag from whether the field is optional, and a
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+ * `ZodDefault` does not read as optional — a defaulted field is advertised as
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+ * required in `prompts/list`. `buildPlan` compares against `'true'`, so an
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+ * omitted value behaves exactly as `'false'` did.
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+ */
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  includeAgentPrompts: z
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  .enum(['true', 'false'])
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- .default('false')
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- .describe('Include inline guidance blocks under each phase with execution-time hints ("true" or "false")'),
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+ .optional()
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+ .describe('Include inline guidance blocks under each phase with execution-time hints ("true" or "false"; omitted = "false")'),
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  });
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  function agentBlock(text, include) {
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  return include ? `\n> **Agent guidance:** ${text}\n` : '';
package/dist/mcp-server/prompts/definitions/research-plan.prompt.js.map CHANGED
@@ -1 +1 @@
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1
+ 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package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8T7B,CAAC"}
1
+ {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA+IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2V7B,CAAC"}
package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED
@@ -16,23 +16,67 @@ import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION
16
16
  */
17
17
  const DATE_RE = /^$|^\d{4}([/\-.]\d{1,2}([/\-.]\d{1,2})?)?$/;
18
18
  /**
19
- * Produces an optional human- and agent-readable hint for edge cases where
20
- * bare empty arrays leave the caller without enough signal to recover:
19
+ * NCBI's eSearch serves `retstart` up to 9998 for PubMed and fails the whole
20
+ * request above it, so the ceiling is enforced at the edge where the caller can
21
+ * still act on it. The limit is db-specific — it does not apply to db=mesh.
22
+ */
23
+ const OFFSET_MAX = 9998;
24
+ /** Upper bound on brief summaries fetched per call; shared by the schema and the format() cap message. */
25
+ const SUMMARY_COUNT_MAX = 50;
26
+ /** Renders a diagnostic list as a comma-separated set of backticked clauses. */
27
+ function quoteClauses(clauses) {
28
+ return clauses.map((clause) => `\`${clause}\``).join(', ');
29
+ }
30
+ /**
31
+ * Produces an optional human- and agent-readable hint for the cases where the
32
+ * returned PMIDs alone leave the caller without enough signal to recover.
33
+ *
34
+ * The signals are independent and can co-occur, so every applicable one is
35
+ * collected and joined rather than the first match being returned:
36
+ * - A `dateRange` with one bound filled, which drops the date filter entirely
37
+ * - Field tags PubMed did not recognize (results silently unrestricted)
38
+ * - Phrases PubMed matched nothing for
21
39
  * - No matches at all (suggest spell-check / removing filters)
22
- * - Filters applied but nothing matched (suggest relaxing filters)
23
40
  * - Pagination overshoot (offset ≥ totalCount)
41
+ *
42
+ * The one precedence rule: an unmatched phrase names the exact clause that
43
+ * returned nothing, so it replaces the generic empty-result guidance, which
44
+ * would only guess across every filter the request might have set.
24
45
  */
25
46
  function buildNotice(args) {
26
- const { totalCount, pmidCount, offset, hasFilters } = args;
47
+ const { totalCount, pmidCount, offset, hasFilters, partialDateBound, errorList, warningList } = args;
48
+ const notices = [];
49
+ if (partialDateBound) {
50
+ const missing = partialDateBound.name === 'minDate' ? 'maxDate' : 'minDate';
51
+ const sentinel = missing === 'maxDate' ? '3000' : '1800';
52
+ notices.push(`No date filter was applied: dateRange needs both bounds and only \`${partialDateBound.name}\` ("${partialDateBound.value}") was supplied. Set \`${missing}\` as well — for an open-ended range pass a wide sentinel (e.g. \`${missing}: "${sentinel}"\`).`);
53
+ }
54
+ const ignoredFields = [
55
+ ...(errorList?.FieldNotFound ?? []),
56
+ ...(warningList?.FieldNotFound ?? []),
57
+ ];
58
+ if (ignoredFields.length > 0) {
59
+ notices.push(`PubMed did not recognize the field tag(s) ${quoteClauses(ignoredFields)} and searched those terms as free text, so these results are not restricted by that field. Correct the tag or drop it.`);
60
+ }
61
+ const unmatchedPhrases = [
62
+ ...(errorList?.PhraseNotFound ?? []),
63
+ ...(warningList?.PhraseNotFound ?? []),
64
+ ...(warningList?.QuotedPhraseNotFound ?? []),
65
+ ];
66
+ if (unmatchedPhrases.length > 0) {
67
+ notices.push(`PubMed matched nothing for ${quoteClauses(unmatchedPhrases)}, so that clause contributed no results. Check the spelling, or resolve the term with pubmed_lookup_mesh before filtering on it.`);
68
+ }
27
69
  if (totalCount === 0) {
28
- return hasFilters
29
- ? 'No results matched your query with the applied filters. Try removing filters (e.g. dateRange, publicationTypes, meshTerms), broadening dates, or verifying author/journal spelling.'
30
- : 'No results matched your query. Try running pubmed_spell_check for a suggested correction or broaden the query.';
70
+ if (unmatchedPhrases.length === 0) {
71
+ notices.push(hasFilters
72
+ ? 'No results matched your query with the applied filters. Try removing filters (e.g. dateRange, publicationTypes, meshTerms), broadening dates, or verifying author/journal spelling.'
73
+ : 'No results matched your query. Try running pubmed_spell_check for a suggested correction or broaden the query.');
74
+ }
31
75
  }
32
- if (pmidCount === 0 && offset > 0 && offset >= totalCount) {
33
- return `Offset ${offset} exceeds totalCount (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`;
76
+ else if (pmidCount === 0 && offset > 0 && offset >= totalCount) {
77
+ notices.push(`Offset ${offset} exceeds totalCount (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`);
34
78
  }
35
- return;
79
+ return notices.length > 0 ? notices.join(' ') : undefined;
36
80
  }
37
81
  const AppliedFiltersSchema = z.object({
38
82
  dateRange: z
@@ -75,7 +119,13 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
75
119
  input: z.object({
76
120
  query: z.string().min(1).describe('PubMed search query (supports full NCBI syntax)'),
77
121
  maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
78
- offset: z.number().int().min(0).default(0).describe('Result offset for pagination (0-based)'),
122
+ offset: z
123
+ .number()
124
+ .int()
125
+ .min(0)
126
+ .max(OFFSET_MAX)
127
+ .default(0)
128
+ .describe(`Result offset for pagination (0-based). PubMed serves at most the first ${OFFSET_MAX + 1} records of a result set, so this caps at ${OFFSET_MAX}; narrow the query or add filters to reach anything beyond it.`),
79
129
  sort: z
80
130
  .enum(['relevance', 'pub_date', 'author', 'journal'])
81
131
  .default('relevance')
@@ -115,9 +165,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
115
165
  .number()
116
166
  .int()
117
167
  .min(0)
118
- .max(50)
168
+ .max(SUMMARY_COUNT_MAX)
119
169
  .default(0)
120
- .describe('Fetch brief summaries for top N results (0 = PMIDs only)'),
170
+ .describe(`Fetch brief summaries for top N results (0 = PMIDs only). Above the ${SUMMARY_COUNT_MAX} cap, pass the remaining PMIDs to pubmed_fetch_articles.`),
121
171
  }),
122
172
  output: z.object({
123
173
  query: z.string().describe('Original query'),
@@ -153,7 +203,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
153
203
  notice: z
154
204
  .string()
155
205
  .optional()
156
- .describe('Optional guidance when results are empty or paging overshot — e.g. how to broaden filters or reset offset. Absent on successful result pages.'),
206
+ .describe('Optional guidance when the result set does not reflect what was asked for — a field tag PubMed ignored, a phrase it matched nothing for, a dateRange dropped for having one bound, no matches at all, or paging past the end. Absent when nothing applies.'),
157
207
  },
158
208
  // content[] trailer presentation for the enrichment block. structuredContent always
159
209
  // carries the full structured value; this only shapes the human-facing trailer line.
@@ -196,14 +246,24 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
196
246
  let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
197
247
  // Build filters — capture normalized values for both query construction and appliedFilters
198
248
  let normalizedDateRange;
199
- if (input.dateRange?.minDate && input.dateRange?.maxDate) {
249
+ const { dateRange } = input;
250
+ const minDate = dateRange?.minDate.trim() ?? '';
251
+ const maxDate = dateRange?.maxDate.trim() ?? '';
252
+ if (dateRange && minDate && maxDate) {
200
253
  normalizedDateRange = {
201
- minDate: input.dateRange.minDate.trim().replace(/[-.]/g, '/'),
202
- maxDate: input.dateRange.maxDate.trim().replace(/[-.]/g, '/'),
203
- dateType: input.dateRange.dateType,
254
+ minDate: minDate.replace(/[-.]/g, '/'),
255
+ maxDate: maxDate.replace(/[-.]/g, '/'),
256
+ dateType: dateRange.dateType,
204
257
  };
205
258
  effectiveQuery += ` AND (${normalizedDateRange.minDate}[${normalizedDateRange.dateType}] : ${normalizedDateRange.maxDate}[${normalizedDateRange.dateType}])`;
206
259
  }
260
+ // Both bounds are required for the filter to apply, so one filled bound is a
261
+ // dropped date range the caller gets no other signal about.
262
+ const partialDateBound = minDate && !maxDate
263
+ ? { name: 'minDate', value: minDate }
264
+ : maxDate && !minDate
265
+ ? { name: 'maxDate', value: maxDate }
266
+ : undefined;
207
267
  let sanitizedPubTypes;
208
268
  if (input.publicationTypes?.length) {
209
269
  sanitizedPubTypes = await Promise.all(input.publicationTypes.map((pt) => sanitization.sanitizeString(pt, { context: 'text' })));
@@ -297,6 +357,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
297
357
  pmidCount: pmids.length,
298
358
  offset: input.offset,
299
359
  hasFilters: Object.keys(appliedFilters).length > 0,
360
+ ...(partialDateBound && { partialDateBound }),
361
+ ...(esResult.errorList && { errorList: esResult.errorList }),
362
+ ...(esResult.warningList && { warningList: esResult.warningList }),
300
363
  });
301
364
  ctx.enrich({ effectiveQuery, appliedFilters });
302
365
  ctx.enrich.total(esResult.count);
@@ -321,7 +384,13 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
321
384
  lines.push(`\n**PMIDs:** ${result.pmids.join(', ')}`);
322
385
  if (result.summaries?.length) {
323
386
  if (result.summaries.length < result.pmids.length) {
324
- lines.push(`\n> Summaries shown for top ${result.summaries.length} of ${result.pmids.length} PMIDs. Increase \`summaryCount\` (max 50) to fetch more.`);
387
+ const shown = `Summaries shown for top ${result.summaries.length} of ${result.pmids.length} PMIDs`;
388
+ lines.push(
389
+ // At the cap there is no knob left to raise, so point at the tool that
390
+ // can read the rest instead of at `summaryCount`.
391
+ result.summaries.length >= SUMMARY_COUNT_MAX
392
+ ? `\n> ${shown} — \`summaryCount\` is at its maximum (${SUMMARY_COUNT_MAX}). Fetch the remaining ${result.pmids.length - result.summaries.length} with \`pubmed_fetch_articles\` using the PMIDs above.`
393
+ : `\n> ${shown}. Increase \`summaryCount\` (max ${SUMMARY_COUNT_MAX}) to fetch more.`);
325
394
  }
326
395
  lines.push('\n### Summaries');
327
396
  for (const s of result.summaries) {
package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/ncbi/ncbi-service.d.ts.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAgEpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;IALlC,YACmB,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,EACtC;IAEE,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC,CAoB1F;IAEK,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC,CAO5F;IAED,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC,CAIZ;IAED,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC,CAKZ;IAEK,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC,CAyBxF;IAED,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC,CAK5E;IAED;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAkE5B;IAED;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAiE5B;IAED,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA4BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
package/dist/services/ncbi/ncbi-service.js CHANGED
@@ -23,6 +23,21 @@ const ID_CONVERT_FORMAT_HINTS = {
23
23
  pmcid: '"PMC" + digits or bare digits, e.g. "PMC3531190" or "3531190"',
24
24
  doi: 'starts with "10.", e.g. "10.1093/nar/gks1195"',
25
25
  };
26
+ /**
27
+ * NCBI collapses a single-entry `ErrorList`/`WarningList` member to a scalar and
28
+ * leaves multi-entry members as arrays, and `parseTagValue` coerces a numeric-looking
29
+ * phrase to a number. Normalize every member to `string[]` so `ESearchErrorList` /
30
+ * `ESearchWarningList` describe what callers actually receive.
31
+ */
32
+ function normalizeDiagnosticList(list) {
33
+ if (!list)
34
+ return;
35
+ const normalized = {};
36
+ for (const [key, value] of Object.entries(list)) {
37
+ normalized[key] = (Array.isArray(value) ? value : [value]).map(String);
38
+ }
39
+ return normalized;
40
+ }
26
41
  /** Sentinel reason used when the service-level deadline expires. */
27
42
  class NcbiDeadlineExceeded extends Error {
28
43
  constructor(deadlineMs) {
@@ -74,6 +89,8 @@ export class NcbiService {
74
89
  ...(options?.signal && { signal: options.signal }),
75
90
  });
76
91
  const esResult = response.eSearchResult;
92
+ const errorList = normalizeDiagnosticList(esResult.ErrorList);
93
+ const warningList = normalizeDiagnosticList(esResult.WarningList);
77
94
  return {
78
95
  count: parseInt(esResult.Count, 10) || 0,
79
96
  retmax: parseInt(esResult.RetMax, 10) || 0,
@@ -82,8 +99,8 @@ export class NcbiService {
82
99
  ...(esResult.WebEnv !== undefined && { webEnv: esResult.WebEnv }),
83
100
  idList: (esResult.IdList?.Id ?? []).map(String),
84
101
  queryTranslation: esResult.QueryTranslation,
85
- ...(esResult.ErrorList !== undefined && { errorList: esResult.ErrorList }),
86
- ...(esResult.WarningList !== undefined && { warningList: esResult.WarningList }),
102
+ ...(errorList !== undefined && { errorList }),
103
+ ...(warningList !== undefined && { warningList }),
87
104
  };
88
105
  }
89
106
  async eSummary(params, options) {
package/dist/services/ncbi/ncbi-service.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;;;;;;OAUG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IAEjD,cAkBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAyNH;CACF"}
1
+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAkMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;;;;;;OAUG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IAEjD,cAkBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAyNH;CACF"}
package/dist/services/ncbi/response-handler.js CHANGED
@@ -61,6 +61,7 @@ const NCBI_ARRAY_JPATHS = new Set([
61
61
  */
62
62
  const ERROR_PATHS = [
63
63
  'eLinkResult.ERROR',
64
+ 'eSearchResult.ERROR',
64
65
  'eSummaryResult.ERROR',
65
66
  'PubmedArticleSet.ErrorList.CannotRetrievePMID',
66
67
  'ERROR',
package/dist/services/ncbi/response-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.10.0",
3
+ "version": "2.10.1",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
6
6
  "type": "module",
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.10.0",
9
+ "version": "2.10.1",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubmed-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "2.10.0",
22
+ "version": "2.10.1",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -66,7 +66,7 @@
66
66
  "registryBaseUrl": "https://registry.npmjs.org",
67
67
  "identifier": "@cyanheads/pubmed-mcp-server",
68
68
  "runtimeHint": "bun",
69
- "version": "2.10.0",
69
+ "version": "2.10.1",
70
70
  "packageArguments": [
71
71
  {
72
72
  "type": "positional",