@cyanheads/pubmed-mcp-server 2.10.17 → 2.10.19

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 (105) hide show
  1. package/AGENTS.md +12 -14
  2. package/CLAUDE.md +12 -14
  3. package/Dockerfile +77 -36
  4. package/README.md +86 -109
  5. package/changelog/2.10.x/2.10.17.md +1 -1
  6. package/changelog/2.10.x/2.10.18.md +14 -0
  7. package/changelog/2.10.x/2.10.19.md +42 -0
  8. package/dist/config/server-config.d.ts.map +1 -1
  9. package/dist/config/server-config.js +7 -3
  10. package/dist/config/server-config.js.map +1 -1
  11. package/dist/mcp-server/resources/definitions/database-info.resource.d.ts +43 -1
  12. package/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map +1 -1
  13. package/dist/mcp-server/resources/definitions/database-info.resource.js +2 -0
  14. package/dist/mcp-server/resources/definitions/database-info.resource.js.map +1 -1
  15. package/dist/mcp-server/tools/definitions/_visible-text.d.ts +19 -0
  16. package/dist/mcp-server/tools/definitions/_visible-text.d.ts.map +1 -0
  17. package/dist/mcp-server/tools/definitions/_visible-text.js +22 -0
  18. package/dist/mcp-server/tools/definitions/_visible-text.js.map +1 -0
  19. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +11 -4
  20. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
  21. package/dist/mcp-server/tools/definitions/convert-ids.tool.js +1 -1
  22. package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
  23. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +20 -7
  24. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  25. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +40 -5
  26. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  27. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +11 -4
  28. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  29. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +18 -1
  30. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  31. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
  32. package/dist/mcp-server/tools/definitions/find-related.tool.js +39 -10
  33. package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
  34. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +11 -4
  35. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  36. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +16 -15
  37. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  38. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +40 -22
  39. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  40. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +13 -6
  41. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  42. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +8 -8
  43. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  44. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts +2 -2
  45. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -1
  46. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +1 -1
  47. package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
  48. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +19 -5
  49. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
  50. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +37 -7
  51. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
  52. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +40 -18
  53. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  54. package/dist/mcp-server/tools/definitions/search-articles.tool.js +193 -43
  55. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  56. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +13 -6
  57. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  58. package/dist/mcp-server/tools/definitions/spell-check.tool.js +8 -8
  59. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  60. package/dist/services/error-contracts.d.ts +42 -71
  61. package/dist/services/error-contracts.d.ts.map +1 -1
  62. package/dist/services/error-contracts.js +43 -75
  63. package/dist/services/error-contracts.js.map +1 -1
  64. package/dist/services/europe-pmc/api-client.d.ts +8 -2
  65. package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
  66. package/dist/services/europe-pmc/api-client.js +13 -8
  67. package/dist/services/europe-pmc/api-client.js.map +1 -1
  68. package/dist/services/europe-pmc/europe-pmc-service.d.ts +43 -14
  69. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  70. package/dist/services/europe-pmc/europe-pmc-service.js +165 -85
  71. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  72. package/dist/services/europe-pmc/request-queue.d.ts +11 -27
  73. package/dist/services/europe-pmc/request-queue.d.ts.map +1 -1
  74. package/dist/services/europe-pmc/request-queue.js +17 -104
  75. package/dist/services/europe-pmc/request-queue.js.map +1 -1
  76. package/dist/services/europe-pmc/types.d.ts +6 -1
  77. package/dist/services/europe-pmc/types.d.ts.map +1 -1
  78. package/dist/services/ncbi/api-client.d.ts.map +1 -1
  79. package/dist/services/ncbi/api-client.js +2 -3
  80. package/dist/services/ncbi/api-client.js.map +1 -1
  81. package/dist/services/ncbi/ncbi-service.d.ts +2 -1
  82. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  83. package/dist/services/ncbi/ncbi-service.js +67 -20
  84. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  85. package/dist/services/ncbi/parsing/article-parser.d.ts +15 -1
  86. package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
  87. package/dist/services/ncbi/parsing/article-parser.js +29 -0
  88. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  89. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  90. package/dist/services/ncbi/response-handler.js +22 -19
  91. package/dist/services/ncbi/response-handler.js.map +1 -1
  92. package/dist/services/ncbi/types.d.ts +33 -0
  93. package/dist/services/ncbi/types.d.ts.map +1 -1
  94. package/dist/services/openalex/api-client.d.ts.map +1 -1
  95. package/dist/services/openalex/api-client.js +6 -7
  96. package/dist/services/openalex/api-client.js.map +1 -1
  97. package/dist/services/openalex/openalex-service.d.ts +11 -1
  98. package/dist/services/openalex/openalex-service.d.ts.map +1 -1
  99. package/dist/services/openalex/openalex-service.js +18 -11
  100. package/dist/services/openalex/openalex-service.js.map +1 -1
  101. package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
  102. package/dist/services/unpaywall/unpaywall-service.js +1 -3
  103. package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
  104. package/package.json +6 -5
  105. package/server.json +3 -3
package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED
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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts CHANGED
@@ -40,15 +40,22 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
40
40
  }, {
41
41
  readonly reason: 'ncbi_unreachable';
42
42
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
43
- readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
44
- readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
43
+ readonly when: 'NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline.';
44
+ readonly recovery: 'Retry after a brief delay; NCBI failed on every attempt this call made.';
45
+ readonly retryable: true;
46
+ readonly thrownBy: 'service';
47
+ }, {
48
+ readonly reason: 'ncbi_rate_limited';
49
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
50
+ readonly when: 'NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap.';
51
+ readonly recovery: "Wait as long as `retryAfter` says when present (a number of seconds or an HTTP date), otherwise a few seconds, then retry; NCBI is throttling this server's requests. If the server runs without NCBI_API_KEY, setting it raises the E-utilities ceiling from about 3 to about 10 requests per second and shortens the default gap between requests — an operator setting in the server's environment, not a tool input.";
45
52
  readonly retryable: true;
46
53
  readonly thrownBy: 'service';
47
54
  }, {
48
55
  readonly reason: 'ncbi_deadline_exceeded';
49
56
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
50
- readonly when: 'Total request deadline expired before NCBI returned a response.';
51
- readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
57
+ readonly when: 'The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff.';
58
+ readonly recovery: 'Retry after a brief delay; NCBI may be under temporary load. For a large batch, split it into smaller calls.';
52
59
  readonly retryable: true;
53
60
  readonly thrownBy: 'service';
54
61
  }, {
package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkI9B,CAAC"}
1
+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkI9B,CAAC"}
package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts CHANGED
@@ -3,27 +3,21 @@
3
3
  * to PubMed IDs using NCBI's ECitMatch service, then verifies author agreement
4
4
  * against ESummary to catch cases where ECitMatch's journal+volume+page weighting
5
5
  * returns a PMID whose author roster doesn't contain the queried author.
6
- * `citations` takes an array or a single citation object, and `citation` is
7
- * accepted as an alias for it.
6
+ * `citations` is advertised as an array of 1–25 citations. A lone citation
7
+ * object is wrapped into a one-element array before validation, and `citation`
8
+ * is accepted as an alias for `citations`.
8
9
  * @module src/mcp-server/tools/definitions/lookup-citation.tool
9
10
  */
10
11
  import { z } from '@cyanheads/mcp-ts-core';
11
12
  export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
12
- citations: z.ZodUnion<readonly [z.ZodArray<z.ZodObject<{
13
+ citations: z.ZodPreprocess<z.ZodArray<z.ZodObject<{
13
14
  journal: z.ZodOptional<z.ZodString>;
14
15
  year: z.ZodOptional<z.ZodString>;
15
16
  volume: z.ZodOptional<z.ZodString>;
16
17
  firstPage: z.ZodOptional<z.ZodString>;
17
18
  authorName: z.ZodOptional<z.ZodString>;
18
19
  key: z.ZodOptional<z.ZodString>;
19
- }, z.core.$strip>>, z.ZodObject<{
20
- journal: z.ZodOptional<z.ZodString>;
21
- year: z.ZodOptional<z.ZodString>;
22
- volume: z.ZodOptional<z.ZodString>;
23
- firstPage: z.ZodOptional<z.ZodString>;
24
- authorName: z.ZodOptional<z.ZodString>;
25
- key: z.ZodOptional<z.ZodString>;
26
- }, z.core.$strip>]>;
20
+ }, z.core.$strip>>, unknown>;
27
21
  }, z.core.$strip>, z.ZodObject<{
28
22
  results: z.ZodArray<z.ZodObject<{
29
23
  key: z.ZodString;
@@ -58,15 +52,22 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
58
52
  }, {
59
53
  readonly reason: 'ncbi_unreachable';
60
54
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
61
- readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
62
- readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
55
+ readonly when: 'NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline.';
56
+ readonly recovery: 'Retry after a brief delay; NCBI failed on every attempt this call made.';
57
+ readonly retryable: true;
58
+ readonly thrownBy: 'service';
59
+ }, {
60
+ readonly reason: 'ncbi_rate_limited';
61
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
62
+ readonly when: 'NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap.';
63
+ readonly recovery: "Wait as long as `retryAfter` says when present (a number of seconds or an HTTP date), otherwise a few seconds, then retry; NCBI is throttling this server's requests. If the server runs without NCBI_API_KEY, setting it raises the E-utilities ceiling from about 3 to about 10 requests per second and shortens the default gap between requests — an operator setting in the server's environment, not a tool input.";
63
64
  readonly retryable: true;
64
65
  readonly thrownBy: 'service';
65
66
  }, {
66
67
  readonly reason: 'ncbi_deadline_exceeded';
67
68
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
68
- readonly when: 'Total request deadline expired before NCBI returned a response.';
69
- readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
69
+ readonly when: 'The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff.';
70
+ readonly recovery: 'Retry after a brief delay; NCBI may be under temporary load. For a large batch, split it into smaller calls.';
70
71
  readonly retryable: true;
71
72
  readonly thrownBy: 'service';
72
73
  }, {
package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map CHANGED
@@ -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;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAyFjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAqR7B,CAAC"}
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"}
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED
@@ -3,8 +3,9 @@
3
3
  * to PubMed IDs using NCBI's ECitMatch service, then verifies author agreement
4
4
  * against ESummary to catch cases where ECitMatch's journal+volume+page weighting
5
5
  * returns a PMID whose author roster doesn't contain the queried author.
6
- * `citations` takes an array or a single citation object, and `citation` is
7
- * accepted as an alias for it.
6
+ * `citations` is advertised as an array of 1–25 citations. A lone citation
7
+ * object is wrapped into a one-element array before validation, and `citation`
8
+ * is accepted as an alias for `citations`.
8
9
  * @module src/mcp-server/tools/definitions/lookup-citation.tool
9
10
  */
10
11
  import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -68,34 +69,52 @@ const CitationSchema = z
68
69
  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.',
69
70
  });
70
71
  /**
71
- * The union issue's own message, in place of Zod's bare `Invalid input`. A value
72
- * that fails only a check inside one branch — a pipe in a field, a missing
73
- * journal and year — keeps that branch's issue and path. A value that fails both
74
- * branches outright (a string, or an array element of the wrong type) is one
75
- * union issue carrying this message, with each branch's issues nested under it.
72
+ * Message for a `citations` value the array check refuses (a string, a number, a
73
+ * missing field, or an array outside 1–25) in place of Zod's bare `expected
74
+ * array`, so the caller learns both shapes that parse. A lone object never
75
+ * reaches this check: it is wrapped first, and its own field issues report under
76
+ * `citations.0`.
76
77
  */
77
78
  const CITATIONS_SHAPE_ERROR = 'Invalid input: expected a citation object or an array of 1–25 citation objects';
79
+ /** A citation sent on its own rather than in an array. JSON input has no other object kind. */
80
+ const isCitationObject = (value) => typeof value === 'object' && value !== null && !Array.isArray(value);
78
81
  export const lookupCitationTool = tool('pubmed_lookup_citation', {
79
82
  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.`,
80
83
  annotations: { readOnlyHint: true, openWorldHint: true },
81
84
  _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
82
85
  sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
83
86
  errors: [...NCBI_SERVICE_ERRORS],
84
- // Never advertised; rewritten to the canonical key before the schema parses.
85
- // A single object usually arrives under this name, which the union below
86
- // accepts. (#156)
87
+ /**
88
+ * Never advertised; rewritten to the canonical key before the schema parses.
89
+ * A single object usually arrives under this name, and `citations` wraps it
90
+ * into a one-element array. (#156)
91
+ */
87
92
  inputAliases: { citation: 'citations' },
88
93
  input: z.object({
94
+ /**
95
+ * The wrap runs before validation and stays off the advertised schema, which
96
+ * remains a plain `type: "array"`. A top-level union would advertise
97
+ * `citations` with no `type` for a client to build the parameter from. (#173)
98
+ *
99
+ * A string is refused here, as one `invalid_type` issue: left to the array,
100
+ * its `length` runs the size checks after the type check fails and the shape
101
+ * message reports twice. The pipe stops on this issue, and its code keeps
102
+ * the framework's "Send citations as an array, not a string." recovery.
103
+ */
89
104
  citations: z
90
- .union([
91
- z
92
- .array(CitationSchema)
93
- .min(1)
94
- .max(25)
95
- .describe('Up to 25 citations, each matched independently.'),
96
- CitationSchema,
97
- ], { error: CITATIONS_SHAPE_ERROR })
98
- .describe('Citations to look up — an array of up to 25, or a single citation object. More fields = better match accuracy.'),
105
+ .preprocess((value, ctx) => {
106
+ if (typeof value === 'string') {
107
+ ctx.issues.push({
108
+ code: 'invalid_type',
109
+ expected: 'array',
110
+ input: value,
111
+ message: CITATIONS_SHAPE_ERROR,
112
+ });
113
+ return value;
114
+ }
115
+ return isCitationObject(value) ? [value] : value;
116
+ }, z.array(CitationSchema, { error: CITATIONS_SHAPE_ERROR }).min(1).max(25))
117
+ .describe('Citations to look up, 1–25, each matched independently. More fields = better match accuracy.'),
99
118
  }),
100
119
  output: z.object({
101
120
  results: z
@@ -140,9 +159,8 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
140
159
  .describe('Number of matched citations that carry at least one warning'),
141
160
  }),
142
161
  async handler(input, ctx) {
143
- const submitted = Array.isArray(input.citations) ? input.citations : [input.citations];
144
- ctx.log.info('Executing pubmed_lookup_citation', { count: submitted.length });
145
- const citations = submitted.map((c, i) => ({
162
+ ctx.log.info('Executing pubmed_lookup_citation', { count: input.citations.length });
163
+ const citations = input.citations.map((c, i) => ({
146
164
  journal: c.journal,
147
165
  year: c.year,
148
166
  volume: c.volume,
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1
+ 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package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts CHANGED
@@ -32,15 +32,22 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
32
32
  }, {
33
33
  readonly reason: 'ncbi_unreachable';
34
34
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
35
- readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
36
- readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
35
+ readonly when: 'NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline.';
36
+ readonly recovery: 'Retry after a brief delay; NCBI failed on every attempt this call made.';
37
+ readonly retryable: true;
38
+ readonly thrownBy: 'service';
39
+ }, {
40
+ readonly reason: 'ncbi_rate_limited';
41
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
42
+ readonly when: 'NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap.';
43
+ readonly recovery: "Wait as long as `retryAfter` says when present (a number of seconds or an HTTP date), otherwise a few seconds, then retry; NCBI is throttling this server's requests. If the server runs without NCBI_API_KEY, setting it raises the E-utilities ceiling from about 3 to about 10 requests per second and shortens the default gap between requests — an operator setting in the server's environment, not a tool input.";
37
44
  readonly retryable: true;
38
45
  readonly thrownBy: 'service';
39
46
  }, {
40
47
  readonly reason: 'ncbi_deadline_exceeded';
41
48
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
42
- readonly when: 'Total request deadline expired before NCBI returned a response.';
43
- readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
49
+ readonly when: 'The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff.';
50
+ readonly recovery: 'Retry after a brief delay; NCBI may be under temporary load. For a large batch, split it into smaller calls.';
44
51
  readonly retryable: true;
45
52
  readonly thrownBy: 'service';
46
53
  }, {
@@ -60,8 +67,8 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
60
67
  }, {
61
68
  readonly reason: 'blank_query';
62
69
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
63
- readonly when: 'The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there.';
64
- readonly recovery: 'Supply a nonblank search term — a bare field tag or empty parentheses carry none; NCBI cannot search a blank term and retrying the same input will not help.';
70
+ readonly when: 'The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and `&nbsp;` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`.';
71
+ readonly recovery: 'Supply a nonblank search term; retrying the same blank input will not help.';
65
72
  readonly retryable: false;
66
73
  }], {
67
74
  readonly totalCount: z.ZodNumber;
package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
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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"}
package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js CHANGED
@@ -5,10 +5,11 @@
5
5
  * @module src/mcp-server/tools/definitions/lookup-mesh.tool
6
6
  */
7
7
  import { tool, z } from '@cyanheads/mcp-ts-core';
8
- import { NCBI_QUERY_INPUT_ERRORS, NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
8
+ import { NCBI_SERVICE_ERRORS, QUERY_INPUT_ERRORS } from '../../../services/error-contracts.js';
9
9
  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
10
10
  import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
11
11
  import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_ONTOLOGY_TERMINOLOGY, SCHEMA_DEFINED_TERM, SCHEMA_DEFINED_TERM_SET, } from './_concepts.js';
12
+ import { hasVisibleText } from './_visible-text.js';
12
13
  /**
13
14
  * NCBI Entrez mesh UIDs encode the canonical MeSH DescriptorUI as the ASCII code of the
14
15
  * UI's letter prefix followed by its 6-digit number: D=68, C=67 (supplementary concept),
@@ -100,14 +101,14 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
100
101
  EDAM_DATA_RETRIEVAL,
101
102
  ]),
102
103
  sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
103
- errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
104
+ errors: [...NCBI_SERVICE_ERRORS, ...QUERY_INPUT_ERRORS],
104
105
  // Never advertised; rewritten to the canonical key before the schema parses. (#156)
105
106
  inputAliases: { limit: 'maxResults' },
106
107
  input: z.object({
107
108
  query: z
108
109
  .string()
109
110
  .min(1)
110
- .describe('MeSH descriptor name or free-text term to look up. Must carry a term: a blank or whitespace-only value is rejected rather than searched.'),
111
+ .describe('MeSH descriptor name or free-text term to look up. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than searched.'),
111
112
  maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),
112
113
  offset: z
113
114
  .number()
@@ -165,11 +166,10 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
165
166
  ctx.log.debug('MeSH lookup started', { query, maxResults, offset, includeDetails });
166
167
  // ESearch on db=mesh answers a blank term with Count=0 and a WarningList
167
168
  // rather than an error, so the empty-result branch would report "no MeSH
168
- // descriptors matched" for a term that was never really searched. (#133)
169
- if (query.trim().length === 0) {
170
- throw ctx.fail('blank_query', 'The `query` is blank — there is no term to look up.', {
171
- ...ctx.recoveryFor('blank_query'),
172
- });
169
+ // descriptors matched" for a term that was never really searched. Invisible
170
+ // characters such as a zero-width space count as blank. (#133, #176)
171
+ if (!hasVisibleText(query)) {
172
+ throw ctx.fail('blank_query', 'The `query` is blank — there is no term to look up.');
173
173
  }
174
174
  const hasFieldTag = /\[.+\]/.test(query);
175
175
  const callOpts = { signal: ctx.signal };
package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts CHANGED
@@ -75,8 +75,8 @@ export declare const pubmedEuropepmcFetchTool: import("@cyanheads/mcp-ts-core").
75
75
  }, {
76
76
  readonly reason: 'europepmc_invalid_input';
77
77
  readonly code: JsonRpcErrorCode.ValidationError;
78
- 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.';
79
- readonly recovery: 'Adjust the input — the query, the sort, or the cursorMark — before retrying; the same input will be rejected again.';
78
+ 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).';
79
+ 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.";
80
80
  readonly retryable: false;
81
81
  readonly thrownBy: 'service';
82
82
  }, {
package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map CHANGED
@@ -1 +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;AAkGjE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWvB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;EA+JjG,CAAC"}
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;AAkGjE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWvB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;EA8JjG,CAAC"}
package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js CHANGED
@@ -121,7 +121,7 @@ export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
121
121
  ctx.log.info('Executing pubmed_europepmc_fetch', { recordCount: input.records.length });
122
122
  const epmc = getEuropePmcService();
123
123
  if (!epmc) {
124
- throw ctx.fail('europepmc_disabled', 'Europe PMC service is not available. Set EUROPEPMC_ENABLED=true to use this tool.', { ...ctx.recoveryFor('europepmc_disabled') });
124
+ throw ctx.fail('europepmc_disabled', 'Europe PMC service is not available. Set EUROPEPMC_ENABLED=true to use this tool.');
125
125
  }
126
126
  const hits = await epmc.fetchRecords(input.records, ctx.signal);
127
127
  const records = hits.map((h) => {
package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map CHANGED
@@ -1 +1 @@
1
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