@cyanheads/pubmed-mcp-server 2.10.9 → 2.10.11

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 (83) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +13 -5
  4. package/dist/mcp-server/tools/definitions/_schemas.d.ts +16 -0
  5. package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
  6. package/dist/mcp-server/tools/definitions/_schemas.js +20 -0
  7. package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
  8. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +6 -0
  9. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/convert-ids.tool.js +28 -3
  11. package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +27 -0
  13. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  14. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +166 -24
  15. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  16. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +18 -0
  17. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +307 -68
  19. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +12 -0
  21. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/find-related.tool.js +171 -27
  23. package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  25. package/dist/mcp-server/tools/definitions/format-citations.tool.js +11 -13
  26. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  27. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  28. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +42 -8
  29. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  30. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +6 -0
  31. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  32. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +14 -3
  33. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  34. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +10 -0
  35. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  36. package/dist/mcp-server/tools/definitions/search-articles.tool.js +52 -5
  37. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  38. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +6 -0
  39. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  40. package/dist/mcp-server/tools/definitions/spell-check.tool.js +15 -3
  41. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  42. package/dist/services/error-contracts.d.ts +39 -2
  43. package/dist/services/error-contracts.d.ts.map +1 -1
  44. package/dist/services/error-contracts.js +43 -2
  45. package/dist/services/error-contracts.js.map +1 -1
  46. package/dist/services/ncbi/formatting/citation-formatter.d.ts +0 -29
  47. package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
  48. package/dist/services/ncbi/formatting/citation-formatter.js +381 -30
  49. package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
  50. package/dist/services/ncbi/ncbi-service.d.ts +3 -2
  51. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  52. package/dist/services/ncbi/ncbi-service.js +22 -10
  53. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  54. package/dist/services/ncbi/parsing/article-parser.d.ts +45 -2
  55. package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
  56. package/dist/services/ncbi/parsing/article-parser.js +208 -1
  57. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  58. package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
  59. package/dist/services/ncbi/parsing/esummary-parser.js +32 -1
  60. package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
  61. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +24 -4
  62. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  63. package/dist/services/ncbi/parsing/pmc-article-parser.js +505 -57
  64. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  65. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  66. package/dist/services/ncbi/response-handler.js +42 -1
  67. package/dist/services/ncbi/response-handler.js.map +1 -1
  68. package/dist/services/ncbi/types.d.ts +215 -2
  69. package/dist/services/ncbi/types.d.ts.map +1 -1
  70. package/dist/services/openalex/api-client.d.ts +13 -4
  71. package/dist/services/openalex/api-client.d.ts.map +1 -1
  72. package/dist/services/openalex/api-client.js +19 -8
  73. package/dist/services/openalex/api-client.js.map +1 -1
  74. package/dist/services/openalex/openalex-service.d.ts +34 -17
  75. package/dist/services/openalex/openalex-service.d.ts.map +1 -1
  76. package/dist/services/openalex/openalex-service.js +119 -35
  77. package/dist/services/openalex/openalex-service.js.map +1 -1
  78. package/dist/services/openalex/types.d.ts +34 -1
  79. package/dist/services/openalex/types.d.ts.map +1 -1
  80. package/dist/services/openalex/types.js +20 -0
  81. package/dist/services/openalex/types.js.map +1 -1
  82. package/package.json +1 -1
  83. 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
@@ -35,6 +35,7 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
35
35
  dois: z.ZodOptional<z.ZodArray<z.ZodString>>;
36
36
  includeReferences: z.ZodDefault<z.ZodBoolean>;
37
37
  includeTables: z.ZodDefault<z.ZodBoolean>;
38
+ includeAssets: z.ZodDefault<z.ZodBoolean>;
38
39
  maxSections: z.ZodOptional<z.ZodNumber>;
39
40
  sections: z.ZodOptional<z.ZodArray<z.ZodString>>;
40
41
  maxCharacters: z.ZodOptional<z.ZodNumber>;
@@ -70,6 +71,7 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
70
71
  volume: z.ZodOptional<z.ZodString>;
71
72
  issue: z.ZodOptional<z.ZodString>;
72
73
  pages: z.ZodOptional<z.ZodString>;
74
+ elocationId: z.ZodOptional<z.ZodString>;
73
75
  }, z.core.$strip>>;
74
76
  keywords: z.ZodOptional<z.ZodArray<z.ZodString>>;
75
77
  articleType: z.ZodOptional<z.ZodString>;
@@ -102,6 +104,17 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
102
104
  "no-rows": "no-rows";
103
105
  }>>;
104
106
  }, z.core.$strip>>>;
107
+ assets: z.ZodOptional<z.ZodArray<z.ZodObject<{
108
+ assetType: z.ZodEnum<{
109
+ figure: "figure";
110
+ "supplementary-material": "supplementary-material";
111
+ }>;
112
+ label: z.ZodOptional<z.ZodString>;
113
+ caption: z.ZodOptional<z.ZodString>;
114
+ id: z.ZodOptional<z.ZodString>;
115
+ sectionTitle: z.ZodOptional<z.ZodString>;
116
+ href: z.ZodOptional<z.ZodString>;
117
+ }, z.core.$strip>>>;
105
118
  references: z.ZodOptional<z.ZodArray<z.ZodObject<{
106
119
  citation: z.ZodString;
107
120
  id: z.ZodOptional<z.ZodString>;
@@ -138,6 +151,7 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
138
151
  pmid: "pmid";
139
152
  }>;
140
153
  reason: z.ZodEnum<{
154
+ "doi-lookup-failed": "doi-lookup-failed";
141
155
  "fetch-failed": "fetch-failed";
142
156
  "no-body": "no-body";
143
157
  "no-doi": "no-doi";
@@ -155,6 +169,7 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
155
169
  unpaywall: "unpaywall";
156
170
  }>;
157
171
  outcome: z.ZodEnum<{
172
+ "doi-lookup-failed": "doi-lookup-failed";
158
173
  "fetch-failed": "fetch-failed";
159
174
  miss: "miss";
160
175
  "no-body": "no-body";
@@ -183,6 +198,7 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
183
198
  returnedCharacters: z.ZodNumber;
184
199
  omittedSections: z.ZodNumber;
185
200
  omittedTables: z.ZodOptional<z.ZodNumber>;
201
+ omittedAssets: z.ZodOptional<z.ZodNumber>;
186
202
  articles: z.ZodArray<z.ZodObject<{
187
203
  id: z.ZodString;
188
204
  source: z.ZodEnum<{
@@ -199,6 +215,8 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
199
215
  }, z.core.$strip>>>;
200
216
  omittedTables: z.ZodOptional<z.ZodNumber>;
201
217
  omittedTableNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
218
+ omittedAssets: z.ZodOptional<z.ZodNumber>;
219
+ omittedAssetNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
202
220
  }, z.core.$strip>>;
203
221
  }, z.core.$strip>>;
204
222
  deferred: z.ZodOptional<z.ZodObject<{
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAomC/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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA01B5B,CAAC"}
1
+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAu0C/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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+2B5B,CAAC"}