@cyanheads/ensembl-mcp-server 0.4.2 → 0.4.4

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 (22) hide show
  1. package/AGENTS.md +83 -49
  2. package/CLAUDE.md +83 -49
  3. package/Dockerfile +6 -5
  4. package/README.md +92 -67
  5. package/changelog/0.4.x/0.4.3.md +29 -0
  6. package/changelog/0.4.x/0.4.4.md +27 -0
  7. package/changelog/template.md +62 -40
  8. package/dist/config/server-config.d.ts.map +1 -1
  9. package/dist/config/server-config.js +1 -2
  10. package/dist/config/server-config.js.map +1 -1
  11. package/dist/index.js +15 -0
  12. package/dist/index.js.map +1 -1
  13. package/dist/mcp-server/resources/definitions/species.resource.d.ts +2 -2
  14. package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts +1 -1
  15. package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts +1 -1
  16. package/dist/mcp-server/tools/definitions/list-species.tool.d.ts +2 -2
  17. package/dist/mcp-server/tools/definitions/query-region.tool.d.ts +1 -1
  18. package/dist/services/ensembl/ensembl-service.d.ts.map +1 -1
  19. package/dist/services/ensembl/ensembl-service.js +1 -1
  20. package/dist/services/ensembl/ensembl-service.js.map +1 -1
  21. package/package.json +13 -12
  22. package/server.json +4 -4
package/dist/services/ensembl/ensembl-service.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"ensembl-service.d.ts","sourceRoot":"","sources":["../../../src/services/ensembl/ensembl-service.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AAGrE,OAAO,KAAK,EAEV,UAAU,EAEV,cAAc,EACd,cAAc,EASd,cAAc,EACd,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,SAAS,EACV,MAAM,YAAY,CAAC;AAqKpB,qBAAa,cAAc;IACzB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IAEjC,YAAY,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc,EAEvD;YAIa,SAAS;IAmFvB,OAAO,CAAC,cAAc;IAuBhB,UAAU,CACd,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,UAAU,CAAC,CAKrB;IAEK,cAAc,CAAC,EAAE,EAAE,MAAM,EAAE,iBAAiB,EAAE,OAAO,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,UAAU,CAAC,CAK9F;IAEK,gBAAgB,CACpB,GAAG,EAAE,MAAM,EAAE,EACb,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,CAYlC;IAEK,kBAAkB,CACtB,OAAO,EAAE,MAAM,EAAE,EACjB,OAAO,EAAE,MAAM,EACf,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,CAalC;IAIK,gBAAgB,CAAC,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,gBAAgB,CAAC,CAI1E;IAIK,eAAe,CACnB,EAAE,EAAE,MAAM,EACV,IAAI,EAAE,MAAM,EACZ,YAAY,EAAE,MAAM,EACpB,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC,CAWzB;IAEK,mBAAmB,CACvB,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC,CAQzB;IAIK,WAAW,CACf,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,EAAE,EAClB,OAAO,EAAE,MAAM,GAAG,SAAS,EAC3B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,EAAE,CAAC,CAO3B;IAIK,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC,CAK9F;IAEK,oBAAoB,CACxB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,EACb,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,SAAS,EAAE,CAAC,CAMtB;IAEK,gBAAgB,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC,CAKtF;IAIK,mBAAmB,CACvB,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,aAAa,EAAE,MAAM,GAAG,SAAS,EACjC,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC,CAKzB;IAEK,eAAe,CACnB,EAAE,EAAE,MAAM,EACV,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,aAAa,EAAE,MAAM,GAAG,SAAS,EACjC,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC,CAKzB;IAIK,YAAY,CAAC,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,SAAS,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC,CAM7F;IAIK,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC,CAKpF;CACF;AAMD,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,cAAc,GAAG,IAAI,CAEnF;AAED,wBAAgB,iBAAiB,IAAI,cAAc,CAKlD"}
package/dist/services/ensembl/ensembl-service.js CHANGED
@@ -227,7 +227,7 @@ export class EnsemblService {
227
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  const operation = `EnsemblService.fetch:${path.split('?')[0]}`;
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  const reqCtx = requestContextService.createRequestContext({
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  operation,
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- parentContext: { requestId: ctx.requestId },
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+ parentContext: ctx,
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  });
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  return withRetry(() => this.fetchJson(path, ctx, options), {
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  operation,
package/dist/services/ensembl/ensembl-service.js.map CHANGED
@@ -1 +1 @@
1
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package/package.json CHANGED
@@ -1,8 +1,8 @@
1
1
  {
2
2
  "name": "@cyanheads/ensembl-mcp-server",
3
- "version": "0.4.2",
3
+ "version": "0.4.4",
4
4
  "mcpName": "io.github.cyanheads/ensembl-mcp-server",
5
- "description": "Look up genes, fetch sequences, predict variant consequences, find orthologs and cross-database xrefs via Ensembl REST via MCP. STDIO or Streamable HTTP.",
5
+ "description": "Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP.",
6
6
  "type": "module",
7
7
  "main": "dist/index.js",
8
8
  "types": "dist/index.d.ts",
@@ -24,6 +24,7 @@
24
24
  "rebuild": "bun run scripts/clean.ts && bun run scripts/build.ts",
25
25
  "clean": "bun run scripts/clean.ts",
26
26
  "devcheck": "bun run scripts/devcheck.ts",
27
+ "audit:fix": "bun audit fix",
27
28
  "audit:refresh": "rm -f bun.lock && bun install && bun audit",
28
29
  "tree": "bun run scripts/tree.ts",
29
30
  "list-skills": "bun run scripts/list-skills.ts",
@@ -81,28 +82,28 @@
81
82
  }
82
83
  ],
83
84
  "license": "Apache-2.0",
84
- "packageManager": "bun@1.3.14",
85
+ "packageManager": "bun@1.4.0",
85
86
  "engines": {
86
- "bun": ">=1.3.0",
87
+ "bun": ">=1.4.0",
87
88
  "node": ">=24.0.0"
88
89
  },
89
90
  "publishConfig": {
90
91
  "access": "public"
91
92
  },
92
93
  "dependencies": {
93
- "@cyanheads/mcp-ts-core": "^0.10.14",
94
+ "@cyanheads/mcp-ts-core": "^0.13.6",
94
95
  "pino-pretty": "^13.1.3",
95
- "zod": "^4.4.3"
96
+ "zod": "^4.6.5"
96
97
  },
97
98
  "devDependencies": {
98
- "@biomejs/biome": "^2.5.0",
99
+ "@biomejs/biome": "^2.5.14",
99
100
  "@socketsecurity/bun-security-scanner": "^1.1.2",
100
- "@types/node": "^26.0.0",
101
+ "@types/node": "^26.6.1",
101
102
  "depcheck": "^1.4.7",
102
- "ignore": "^7.0.5",
103
- "tsc-alias": "^1.9.0",
104
- "typescript": "^6.0.3",
105
- "vitest": "^4.1.10"
103
+ "ignore": "^7.0.9",
104
+ "tsc-alias": "^1.9.5",
105
+ "typescript": "^7.0.2",
106
+ "vitest": "^5.0.1"
106
107
  },
107
108
  "trustedDependencies": ["@socketsecurity/bun-security-scanner"]
108
109
  }
package/server.json CHANGED
@@ -1,12 +1,12 @@
1
1
  {
2
2
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
3
3
  "name": "io.github.cyanheads/ensembl-mcp-server",
4
- "description": "Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.",
4
+ "description": "Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.",
5
5
  "repository": {
6
6
  "url": "https://github.com/cyanheads/ensembl-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.4.2",
9
+ "version": "0.4.4",
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/ensembl-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "0.4.2",
22
+ "version": "0.4.4",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -55,7 +55,7 @@
55
55
  "registryBaseUrl": "https://registry.npmjs.org",
56
56
  "identifier": "@cyanheads/ensembl-mcp-server",
57
57
  "runtimeHint": "bun",
58
- "version": "0.4.2",
58
+ "version": "0.4.4",
59
59
  "packageArguments": [
60
60
  {
61
61
  "type": "positional",