@cyanheads/pubmed-mcp-server 2.9.8 → 2.9.10

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 (70) hide show
  1. package/AGENTS.md +30 -8
  2. package/CLAUDE.md +30 -8
  3. package/Dockerfile +13 -7
  4. package/README.md +1 -1
  5. package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts +1 -1
  6. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +17 -17
  7. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +18 -18
  8. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  9. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +43 -40
  10. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +206 -56
  12. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  13. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +33 -33
  14. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +17 -17
  15. package/dist/mcp-server/tools/definitions/format-citations.tool.js +1 -1
  16. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  17. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +16 -16
  18. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  19. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +9 -12
  20. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +20 -16
  22. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  23. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +73 -22
  24. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  25. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +18 -18
  26. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
  27. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +1 -1
  28. package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
  29. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +22 -22
  30. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +15 -15
  31. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  32. package/dist/mcp-server/tools/definitions/spell-check.tool.js +2 -2
  33. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  34. package/dist/services/error-contracts.d.ts +33 -33
  35. package/dist/services/error-contracts.d.ts.map +1 -1
  36. package/dist/services/europe-pmc/api-client.d.ts +14 -1
  37. package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
  38. package/dist/services/europe-pmc/api-client.js +22 -25
  39. package/dist/services/europe-pmc/api-client.js.map +1 -1
  40. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  41. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  42. package/dist/services/europe-pmc/request-queue.d.ts.map +1 -1
  43. package/dist/services/europe-pmc/request-queue.js.map +1 -1
  44. package/dist/services/europe-pmc/types.d.ts +2 -2
  45. package/dist/services/europe-pmc/types.d.ts.map +1 -1
  46. package/dist/services/ncbi/api-client.d.ts.map +1 -1
  47. package/dist/services/ncbi/api-client.js.map +1 -1
  48. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  49. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  50. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  51. package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
  52. package/dist/services/ncbi/parsing/esummary-parser.js +3 -0
  53. package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
  54. package/dist/services/ncbi/parsing/xml-helpers.js.map +1 -1
  55. package/dist/services/ncbi/request-queue.d.ts.map +1 -1
  56. package/dist/services/ncbi/request-queue.js.map +1 -1
  57. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  58. package/dist/services/ncbi/types.d.ts +6 -0
  59. package/dist/services/ncbi/types.d.ts.map +1 -1
  60. package/dist/services/openalex/api-client.d.ts +15 -1
  61. package/dist/services/openalex/api-client.d.ts.map +1 -1
  62. package/dist/services/openalex/api-client.js +22 -24
  63. package/dist/services/openalex/api-client.js.map +1 -1
  64. package/dist/services/openalex/openalex-service.d.ts.map +1 -1
  65. package/dist/services/openalex/openalex-service.js.map +1 -1
  66. package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
  67. package/dist/services/unpaywall/unpaywall-service.js +1 -0
  68. package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
  69. package/package.json +24 -17
  70. package/server.json +3 -3
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@cyanheads/pubmed-mcp-server",
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- "version": "2.9.8",
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+ "version": "2.9.10",
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  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
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  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
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  "type": "module",
@@ -60,7 +60,7 @@
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  "url": "https://github.com/cyanheads/pubmed-mcp-server/issues"
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  },
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  "homepage": "https://github.com/cyanheads/pubmed-mcp-server#readme",
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- "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/pubmed-mcp-server#readme)",
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+ "author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
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  "funding": [
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  {
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  "type": "github",
@@ -72,34 +72,41 @@
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  }
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  ],
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  "license": "Apache-2.0",
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- "packageManager": "bun@1.3.2",
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+ "packageManager": "bun@1.3.14",
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  "engines": {
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- "bun": ">=1.3.2",
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+ "bun": ">=1.3.0",
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  "node": ">=24.0.0"
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  },
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  "publishConfig": {
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  "access": "public"
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  },
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  "dependencies": {
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- "@cyanheads/mcp-ts-core": "^0.10.10",
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- "defuddle": "^0.19.0",
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- "fast-xml-parser": "^5.9.3",
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- "linkedom": "^0.18.12",
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+ "@cyanheads/mcp-ts-core": "^0.11.0",
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+ "defuddle": "^0.19.2",
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+ "fast-xml-parser": "^5.10.1",
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+ "linkedom": "^0.18.13",
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  "pino-pretty": "^13.1.3",
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- "sanitize-html": "^2.17.5",
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+ "sanitize-html": "^2.17.6",
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  "unpdf": "^1.6.2",
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  "zod": "^4.4.3"
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  },
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  "devDependencies": {
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- "@biomejs/biome": "^2.5.0",
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- "@types/node": "^26.0.0",
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+ "@biomejs/biome": "^2.5.5",
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+ "@socketsecurity/bun-security-scanner": "^1.1.2",
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+ "@types/node": "^26.1.1",
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  "@types/sanitize-html": "^2.16.1",
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- "@vitest/coverage-istanbul": "^4.1.9",
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+ "@vitest/coverage-istanbul": "^4.1.10",
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  "depcheck": "^1.4.7",
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- "fast-check": "^4.8.0",
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- "ignore": "^7.0.5",
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- "tsc-alias": "^1.8.17",
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- "typescript": "^6.0.3",
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- "vitest": "^4.1.9"
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+ "fast-check": "^4.9.0",
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+ "ignore": "^7.0.6",
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+ "tsc-alias": "^1.9.1",
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+ "typescript": "^7.0.2",
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+ "vitest": "^4.1.10"
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+ },
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+ "overrides": {
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+ "@hono/node-server": "^2.0.11",
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+ "brace-expansion": "^2.1.2",
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+ "fast-uri": "^3.1.4",
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+ "postcss": "^8.5.22"
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  }
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  }
package/server.json CHANGED
@@ -6,7 +6,7 @@
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  "url": "https://github.com/cyanheads/pubmed-mcp-server",
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  "source": "github"
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  },
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- "version": "2.9.8",
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+ "version": "2.9.10",
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  "remotes": [
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  {
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  "type": "streamable-http",
@@ -19,7 +19,7 @@
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/pubmed-mcp-server",
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  "runtimeHint": "bun",
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- "version": "2.9.8",
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+ "version": "2.9.10",
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  "packageArguments": [
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  {
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  "type": "positional",
@@ -66,7 +66,7 @@
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/pubmed-mcp-server",
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  "runtimeHint": "bun",
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- "version": "2.9.8",
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+ "version": "2.9.10",
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  "packageArguments": [
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  {
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  "type": "positional",