@cyanheads/pubmed-mcp-server 2.10.15 → 2.10.17

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 (77) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +26 -15
  4. package/changelog/2.10.x/2.10.16.md +26 -0
  5. package/changelog/2.10.x/2.10.17.md +19 -0
  6. package/dist/mcp-server/tools/definitions/_schemas.d.ts +11 -1
  7. package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/_schemas.js +13 -1
  9. package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
  10. package/dist/mcp-server/tools/definitions/_text.d.ts +20 -3
  11. package/dist/mcp-server/tools/definitions/_text.d.ts.map +1 -1
  12. package/dist/mcp-server/tools/definitions/_text.js +35 -3
  13. package/dist/mcp-server/tools/definitions/_text.js.map +1 -1
  14. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +3 -0
  15. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/convert-ids.tool.js +41 -9
  17. package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
  18. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +3 -1
  19. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  20. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +12 -4
  21. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  22. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +25 -31
  23. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  24. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +373 -131
  25. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  26. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +7 -3
  27. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
  28. package/dist/mcp-server/tools/definitions/find-related.tool.js +38 -21
  29. package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
  30. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +3 -1
  31. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  32. package/dist/mcp-server/tools/definitions/format-citations.tool.js +12 -4
  33. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  34. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +11 -2
  35. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  36. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +62 -41
  37. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  38. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +3 -3
  39. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  40. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +3 -1
  41. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  42. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +5 -2
  43. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
  44. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +19 -10
  45. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
  46. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +9 -3
  47. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  48. package/dist/mcp-server/tools/definitions/search-articles.tool.js +71 -11
  49. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  50. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +5 -4
  51. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  52. package/dist/mcp-server/tools/definitions/spell-check.tool.js +4 -3
  53. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  54. package/dist/services/error-contracts.d.ts +7 -5
  55. package/dist/services/error-contracts.d.ts.map +1 -1
  56. package/dist/services/error-contracts.js +7 -5
  57. package/dist/services/error-contracts.js.map +1 -1
  58. package/dist/services/europe-pmc/api-client.d.ts +14 -11
  59. package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
  60. package/dist/services/europe-pmc/api-client.js +21 -18
  61. package/dist/services/europe-pmc/api-client.js.map +1 -1
  62. package/dist/services/europe-pmc/europe-pmc-service.d.ts +2 -0
  63. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  64. package/dist/services/europe-pmc/europe-pmc-service.js +6 -2
  65. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  66. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +8 -0
  67. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  68. package/dist/services/ncbi/parsing/pmc-article-parser.js +159 -16
  69. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  70. package/dist/services/unpaywall/types.d.ts +16 -2
  71. package/dist/services/unpaywall/types.d.ts.map +1 -1
  72. package/dist/services/unpaywall/unpaywall-service.d.ts +4 -3
  73. package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
  74. package/dist/services/unpaywall/unpaywall-service.js +15 -4
  75. package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
  76. package/package.json +1 -1
  77. package/server.json +3 -3
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED
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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts CHANGED
@@ -3,17 +3,29 @@
3
3
  * three-stage chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall.
4
4
  * Accepts three mutually-exclusive input shapes:
5
5
  *
6
- * - `pmcids` — fetch directly by PMC ID. Articles not in PMC fall through to
7
- * EPMC by PMC ID, then to Unpaywall when the DOI is available.
6
+ * - `pmcids` — fetch directly by PMC ID, once per record however it is
7
+ * spelled (`PMC123`, `pmc123`, `123`, zero-padded `PMC0123`), and reported
8
+ * in `PMC<digits>` form. Articles not in PMC fall through to EPMC by PMC ID,
9
+ * then to Unpaywall when the DOI is available.
8
10
  * - `pmids` — resolve PMID → PMCID via PMC ID Converter, then run the chain.
11
+ * A zero-padded PMID runs as the PMID it spells; `unavailable[]` and
12
+ * `deferred.ids` report it as the caller wrote it.
9
13
  * - `dois` — resolve DOI → PMCID via the PMC ID Converter (mirroring `pmids`),
10
14
  * then run the chain. DOIs with no PMC counterpart fall through to EPMC
11
15
  * search-by-DOI → fullTextXML, then Unpaywall (EPMC-only OA, preprints).
16
+ * DOIs are case-insensitive: every casing of one DOI runs the chain once,
17
+ * and `unavailable[]` reports each casing as the caller wrote it.
12
18
  *
13
19
  * Output uses a discriminated union on `source` (`pmc` | `unpaywall`) with an
14
20
  * extra `viaSource` discriminator that records which layer produced the
15
21
  * content. EPMC's JATS reuses the `pmc` schema shape because it's the same
16
- * DTD; `viaSource: 'europepmc'` distinguishes it from PMC EFetch output.
22
+ * DTD; `viaSource: 'europepmc'` distinguishes it from PMC EFetch output. An
23
+ * Unpaywall article takes its title from Unpaywall's record, else the Europe
24
+ * PMC record the chain searched, else (HTML only) the page itself.
25
+ *
26
+ * Europe PMC and Unpaywall failures are folded into each id's `triedTiers`
27
+ * rather than thrown, so the declared `errors[]` covers the NCBI ID routing
28
+ * alone.
17
29
  *
18
30
  * @module src/mcp-server/tools/definitions/fetch-fulltext.tool
19
31
  */
@@ -135,6 +147,8 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
135
147
  doi: z.ZodString;
136
148
  sourceUrl: z.ZodString;
137
149
  title: z.ZodOptional<z.ZodString>;
150
+ journalName: z.ZodOptional<z.ZodString>;
151
+ year: z.ZodOptional<z.ZodNumber>;
138
152
  content: z.ZodString;
139
153
  wordCount: z.ZodOptional<z.ZodNumber>;
140
154
  totalPages: z.ZodOptional<z.ZodNumber>;
@@ -209,9 +223,17 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
209
223
  returnedCharacters: z.ZodNumber;
210
224
  sections: z.ZodOptional<z.ZodArray<z.ZodObject<{
211
225
  title: z.ZodOptional<z.ZodString>;
226
+ label: z.ZodOptional<z.ZodString>;
212
227
  originalCharacters: z.ZodNumber;
213
228
  returnedCharacters: z.ZodNumber;
214
229
  truncated: z.ZodBoolean;
230
+ subsections: z.ZodOptional<z.ZodArray<z.ZodObject<{
231
+ title: z.ZodOptional<z.ZodString>;
232
+ label: z.ZodOptional<z.ZodString>;
233
+ originalCharacters: z.ZodNumber;
234
+ returnedCharacters: z.ZodNumber;
235
+ truncated: z.ZodBoolean;
236
+ }, z.core.$strip>>>;
215
237
  }, z.core.$strip>>>;
216
238
  omittedTables: z.ZodOptional<z.ZodNumber>;
217
239
  omittedTableNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -266,34 +288,6 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
266
288
  readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
267
289
  readonly retryable: false;
268
290
  readonly thrownBy: 'service';
269
- }, {
270
- readonly reason: 'unpaywall_unreachable';
271
- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
272
- readonly when: 'Unpaywall was unreachable when resolving a DOI or fetching content.';
273
- readonly recovery: 'Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.';
274
- readonly retryable: true;
275
- readonly thrownBy: 'service';
276
- }, {
277
- readonly reason: 'europepmc_unreachable';
278
- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
279
- readonly when: 'Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results.';
280
- readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
281
- readonly retryable: true;
282
- readonly thrownBy: 'service';
283
- }, {
284
- readonly reason: 'europepmc_invalid_response';
285
- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
286
- readonly when: 'Europe PMC returned a body that could not be parsed (invalid JSON or XML).';
287
- readonly recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.';
288
- readonly retryable: true;
289
- readonly thrownBy: 'service';
290
- }, {
291
- readonly reason: 'europepmc_invalid_input';
292
- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
293
- readonly when: 'Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt.';
294
- readonly recovery: 'Adjust the input — the query, the sort, or the cursorMark — before retrying; the same input will be rejected again.';
295
- readonly retryable: false;
296
- readonly thrownBy: 'service';
297
291
  }], {
298
292
  readonly notice: z.ZodOptional<z.ZodString>;
299
293
  readonly truncated: z.ZodOptional<z.ZodBoolean>;
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8BG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAi7C/D;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CAAC,KAAK,EAAE;IAC9C,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACpB,GAAG,MAAM,CAiCT;AAID,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA66B5B,CAAC"}