@cyanheads/pubchem-mcp-server 0.1.20 → 0.1.22

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 (29) hide show
  1. package/README.md +2 -2
  2. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts +1 -1
  3. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts +1 -1
  5. package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map +1 -1
  6. package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts +1 -1
  7. package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts +1 -1
  9. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts +1 -1
  11. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map +1 -1
  12. package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts +1 -1
  13. package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map +1 -1
  14. package/dist/mcp-server/tools/definitions/index.d.ts +17 -13
  15. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts +6 -4
  17. package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/search-assays.tool.js +19 -21
  19. package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +5 -3
  21. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/search-compounds.tool.js +18 -9
  23. package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
  24. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  25. package/dist/services/pubchem/pubchem-client.js +13 -7
  26. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  27. package/manifest.json +13 -3
  28. package/package.json +9 -4
  29. package/server.json +3 -3
package/README.md CHANGED
@@ -7,13 +7,13 @@
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.1.20-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-0.1.22-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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  </div>
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  <div align="center">
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- [![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/pubchem-mcp-server/releases/latest/download/pubchem-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=pubchem-mcp-server&config=eyJ0eXBlIjoic3RkaW8iLCJjb21tYW5kIjoiYnVueCIsImFyZ3MiOlsiQGN5YW5oZWFkcy9wdWJjaGVtLW1jcC1zZXJ2ZXJAbGF0ZXN0Il0sImVudiI6eyJNQ1BfVFJBTlNQT1JUX1RZUEUiOiJzdGRpbyIsIk1DUF9MT0dfTEVWRUwiOiJpbmZvIn19) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22pubchem-mcp-server%22%2C%22config%22%3A%7B%22type%22%3A%22stdio%22%2C%22command%22%3A%22bunx%22%2C%22args%22%3A%5B%22%40cyanheads%2Fpubchem-mcp-server%40latest%22%5D%2C%22env%22%3A%7B%22MCP_TRANSPORT_TYPE%22%3A%22stdio%22%2C%22MCP_LOG_LEVEL%22%3A%22info%22%7D%7D%7D)
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+ [![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/pubchem-mcp-server/releases/latest/download/pubchem-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=pubchem-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcHViY2hlbS1tY3Atc2VydmVyIl19) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22pubchem-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads/pubchem-mcp-server%22%5D%7D)
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  [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts CHANGED
@@ -29,5 +29,5 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
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  unit: z.ZodOptional<z.ZodString>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>>;
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- }, z.core.$strip>, undefined>;
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+ }, z.core.$strip>, undefined, undefined>;
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  //# sourceMappingURL=get-bioactivity.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;6BAuIzB,CAAC"}
1
+ {"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;wCAuIzB,CAAC"}
package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts CHANGED
@@ -74,5 +74,5 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
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  meshClasses: z.ZodArray<z.ZodString>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>>;
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- }, z.core.$strip>, undefined>;
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+ }, z.core.$strip>, undefined, undefined>;
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  //# sourceMappingURL=get-compound-details.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAgX7B,CAAC"}
1
+ {"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCAgX7B,CAAC"}
package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts CHANGED
@@ -15,5 +15,5 @@ export declare const getCompoundImage: import("@cyanheads/mcp-ts-core").ToolDefi
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  mimeType: z.ZodString;
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  width: z.ZodNumber;
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  height: z.ZodNumber;
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- }, z.core.$strip>, undefined>;
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+ }, z.core.$strip>, undefined, undefined>;
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  //# sourceMappingURL=get-compound-image.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;6BAoD3B,CAAC"}
1
+ {"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;wCAoD3B,CAAC"}
package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts CHANGED
@@ -21,5 +21,5 @@ export declare const getCompoundSafety: import("@cyanheads/mcp-ts-core").ToolDef
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  }, z.core.$strip>>;
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  }, z.core.$strip>>;
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  source: z.ZodOptional<z.ZodString>;
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- }, z.core.$strip>, undefined>;
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+ }, z.core.$strip>, undefined, undefined>;
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  //# sourceMappingURL=get-compound-safety.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;6BAyG5B,CAAC"}
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+ {"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;wCAyG5B,CAAC"}
package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts CHANGED
@@ -17,5 +17,5 @@ export declare const getCompoundXrefs: import("@cyanheads/mcp-ts-core").ToolDefi
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  totalAvailable: z.ZodNumber;
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  truncated: z.ZodBoolean;
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  }, z.core.$strip>>;
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- }, z.core.$strip>, undefined>;
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+ }, z.core.$strip>, undefined, undefined>;
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  //# sourceMappingURL=get-compound-xrefs.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;6BAmH3B,CAAC"}
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+ {"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;wCAmH3B,CAAC"}
package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts CHANGED
@@ -35,5 +35,5 @@ export declare const getSummary: import("@cyanheads/mcp-ts-core").ToolDefinition
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  lineage: z.ZodOptional<z.ZodArray<z.ZodString>>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>>;
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- }, z.core.$strip>, undefined>;
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+ }, z.core.$strip>, undefined, undefined>;
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  //# sourceMappingURL=get-summary.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsGrB,CAAC"}
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+ {"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCAsGrB,CAAC"}
package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -27,7 +27,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  unit: import("zod").ZodOptional<import("zod").ZodString>;
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  }, import("zod/v4/core").$strip>>;
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  }, import("zod/v4/core").$strip>>;
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- }, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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+ }, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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  cids: import("zod").ZodArray<import("zod").ZodNumber>;
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  properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
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  [x: string]: string;
@@ -97,7 +97,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  meshClasses: import("zod").ZodArray<import("zod").ZodString>;
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  }, import("zod/v4/core").$strip>>;
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  }, import("zod/v4/core").$strip>>;
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- }, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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+ }, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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  cid: import("zod").ZodNumber;
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  size: import("zod").ZodDefault<import("zod").ZodEnum<{
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  small: "small";
@@ -109,7 +109,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  mimeType: import("zod").ZodString;
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  width: import("zod").ZodNumber;
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  height: import("zod").ZodNumber;
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- }, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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+ }, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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  cid: import("zod").ZodNumber;
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  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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  cid: import("zod").ZodNumber;
@@ -127,7 +127,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  }, import("zod/v4/core").$strip>>;
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  }, import("zod/v4/core").$strip>>;
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  source: import("zod").ZodOptional<import("zod").ZodString>;
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- }, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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+ }, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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  cid: import("zod").ZodNumber;
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  xrefTypes: import("zod").ZodArray<import("zod").ZodEnum<{
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  [x: string]: string;
@@ -141,7 +141,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  totalAvailable: import("zod").ZodNumber;
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  truncated: import("zod").ZodBoolean;
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  }, import("zod/v4/core").$strip>>;
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- }, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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+ }, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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  entityType: import("zod").ZodEnum<{
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  assay: "assay";
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  gene: "gene";
@@ -173,7 +173,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  lineage: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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  }, import("zod/v4/core").$strip>>;
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  }, import("zod/v4/core").$strip>>;
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- }, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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+ }, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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  targetType: import("zod").ZodEnum<{
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  proteinaccession: "proteinaccession";
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  genesymbol: "genesymbol";
@@ -183,11 +183,13 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  targetQuery: import("zod").ZodString;
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  maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
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  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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- targetType: import("zod").ZodString;
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- targetQuery: import("zod").ZodString;
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- totalFound: import("zod").ZodNumber;
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  aids: import("zod").ZodArray<import("zod").ZodNumber>;
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- }, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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+ }, import("zod/v4/core").$strip>, undefined, {
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+ readonly targetType: import("zod").ZodString;
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+ readonly targetQuery: import("zod").ZodString;
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+ readonly totalFound: import("zod").ZodNumber;
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+ readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
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+ }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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  searchType: import("zod").ZodEnum<{
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  substructure: "substructure";
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  superstructure: "superstructure";
@@ -214,8 +216,6 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  [x: string]: string;
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  }>>>;
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  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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- searchType: import("zod").ZodString;
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- totalFound: import("zod").ZodNumber;
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  results: import("zod").ZodArray<import("zod").ZodObject<{
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  cid: import("zod").ZodNumber;
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  identifier: import("zod").ZodOptional<import("zod").ZodString>;
@@ -236,5 +236,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
237
237
  readonly when: "substructure/superstructure/similarity search missing query or queryType";
238
238
  readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
239
- }]>)[];
239
+ }], {
240
+ readonly searchType: import("zod").ZodString;
241
+ readonly totalFound: import("zod").ZodNumber;
242
+ readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
243
+ }>)[];
240
244
  //# sourceMappingURL=index.d.ts.map
package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;MAS9B,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAS9B,CAAC"}
package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts CHANGED
@@ -14,9 +14,11 @@ export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefiniti
14
14
  targetQuery: z.ZodString;
15
15
  maxResults: z.ZodDefault<z.ZodNumber>;
16
16
  }, z.core.$strip>, z.ZodObject<{
17
- targetType: z.ZodString;
18
- targetQuery: z.ZodString;
19
- totalFound: z.ZodNumber;
20
17
  aids: z.ZodArray<z.ZodNumber>;
21
- }, z.core.$strip>, undefined>;
18
+ }, z.core.$strip>, undefined, {
19
+ readonly targetType: z.ZodString;
20
+ readonly targetQuery: z.ZodString;
21
+ readonly totalFound: z.ZodNumber;
22
+ readonly notice: z.ZodOptional<z.ZodString>;
23
+ }>;
22
24
  //# sourceMappingURL=search-assays.tool.d.ts.map
package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-assays.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,YAAY;;;;;;;;;;;;;;6BAiFvB,CAAC"}
1
+ {"version":3,"file":"search-assays.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;EAiFvB,CAAC"}
package/dist/mcp-server/tools/definitions/search-assays.tool.js CHANGED
@@ -28,13 +28,21 @@ export const searchAssays = tool('pubchem_search_assays', {
28
28
  .describe('Max AIDs to return (1-200). Popular targets may have thousands of assays. Default: 50.'),
29
29
  }),
30
30
  output: z.object({
31
+ aids: z.array(z.number()).describe('PubChem Assay IDs.'),
32
+ }),
33
+ // Agent-facing context — target echo, total before cap, and an empty-result notice.
34
+ // Reaches structuredContent and content[] automatically; not in the domain return.
35
+ enrichment: {
31
36
  targetType: z
32
37
  .string()
33
38
  .describe('Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession.'),
34
39
  targetQuery: z.string().describe('Target identifier searched.'),
35
- totalFound: z.number().describe('Total AIDs found.'),
36
- aids: z.array(z.number()).describe('PubChem Assay IDs.'),
37
- }),
40
+ totalFound: z.number().describe('Total AIDs found before the maxResults cap.'),
41
+ notice: z
42
+ .string()
43
+ .optional()
44
+ .describe('Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.'),
45
+ },
38
46
  async handler(input, ctx) {
39
47
  const client = getPubChemClient();
40
48
  const allAids = await client.searchAssaysByTarget(input.targetType, input.targetQuery);
@@ -46,28 +54,18 @@ export const searchAssays = tool('pubchem_search_assays', {
46
54
  totalFound,
47
55
  returned: aids.length,
48
56
  });
49
- return {
50
- targetType: input.targetType,
51
- targetQuery: input.targetQuery,
52
- totalFound,
53
- aids,
54
- };
57
+ // Agent-facing context: target echo, total, and empty-result notice.
58
+ ctx.enrich({ targetType: input.targetType, targetQuery: input.targetQuery, totalFound });
59
+ if (aids.length === 0) {
60
+ ctx.enrich.notice(`No assays found for "${input.targetQuery}" (${input.targetType}). Try a different targetType (e.g. switch from proteinname to genesymbol), verify the identifier spelling, or use pubchem_get_summary for gene/protein entity lookups.`);
61
+ }
62
+ return { aids };
55
63
  },
56
64
  format(result) {
57
- const truncated = result.totalFound > result.aids.length
58
- ? ` (showing ${result.aids.length} of ${result.totalFound})`
59
- : '';
60
- const lines = [
61
- `Found ${result.totalFound} assay${result.totalFound !== 1 ? 's' : ''} for "${result.targetQuery}" (${result.targetType})${truncated}`,
62
- '',
63
- ];
64
65
  if (result.aids.length > 0) {
65
- lines.push(`AIDs: ${result.aids.join(', ')}`);
66
- }
67
- else {
68
- lines.push('No assays found.');
66
+ return [{ type: 'text', text: `AIDs: ${result.aids.join(', ')}` }];
69
67
  }
70
- return [{ type: 'text', text: lines.join('\n') }];
68
+ return [{ type: 'text', text: 'No assays found.' }];
71
69
  },
72
70
  });
73
71
  //# sourceMappingURL=search-assays.tool.js.map
package/dist/mcp-server/tools/definitions/search-assays.tool.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-assays.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,CAAC,uBAAuB,EAAE;IACxD,KAAK,EAAE,eAAe;IACtB,WAAW,EACT,qOAAqO;IACvO,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,YAAY,EAAE,aAAa,EAAE,QAAQ,EAAE,kBAAkB,CAAC,CAAC;aACjE,QAAQ,CACP,0JAA0J,CAC3J;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,CACP,mJAAmJ,CACpJ;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,wFAAwF,CACzF;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,oFAAoF,CACrF;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QAC/D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QACpD,IAAI,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;KACzD,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,KAAK,CAAC,UAAU,EAAE,KAAK,CAAC,WAAW,CAAC,CAAC;QAEvF,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC;QAClC,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;QAEhD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,wBAAwB,EAAE;YACrC,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,UAAU;YACV,QAAQ,EAAE,IAAI,CAAC,MAAM;SACtB,CAAC,CAAC;QAEH,OAAO;YACL,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,UAAU;YACV,IAAI;SACL,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,SAAS,GACb,MAAM,CAAC,UAAU,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM;YACpC,CAAC,CAAC,aAAa,MAAM,CAAC,IAAI,CAAC,MAAM,OAAO,MAAM,CAAC,UAAU,GAAG;YAC5D,CAAC,CAAC,EAAE,CAAC;QAET,MAAM,KAAK,GAAG;YACZ,SAAS,MAAM,CAAC,UAAU,SAAS,MAAM,CAAC,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,MAAM,CAAC,WAAW,MAAM,MAAM,CAAC,UAAU,IAAI,SAAS,EAAE;YACtI,EAAE;SACH,CAAC;QAEF,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,KAAK,CAAC,IAAI,CAAC,SAAS,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChD,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC;QACjC,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
1
+ {"version":3,"file":"search-assays.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,CAAC,uBAAuB,EAAE;IACxD,KAAK,EAAE,eAAe;IACtB,WAAW,EACT,qOAAqO;IACvO,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,YAAY,EAAE,aAAa,EAAE,QAAQ,EAAE,kBAAkB,CAAC,CAAC;aACjE,QAAQ,CACP,0JAA0J,CAC3J;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,CACP,mJAAmJ,CACpJ;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,wFAAwF,CACzF;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;KACzD,CAAC;IACF,oFAAoF;IACpF,mFAAmF;IACnF,UAAU,EAAE;QACV,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,oFAAoF,CACrF;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QAC/D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uIAAuI,CACxI;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,KAAK,CAAC,UAAU,EAAE,KAAK,CAAC,WAAW,CAAC,CAAC;QAEvF,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC;QAClC,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;QAEhD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,wBAAwB,EAAE;YACrC,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,UAAU;YACV,QAAQ,EAAE,IAAI,CAAC,MAAM;SACtB,CAAC,CAAC;QAEH,qEAAqE;QACrE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,WAAW,EAAE,KAAK,CAAC,WAAW,EAAE,UAAU,EAAE,CAAC,CAAC;QACzF,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACtB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,KAAK,CAAC,WAAW,MAAM,KAAK,CAAC,UAAU,yKAAyK,CACzO,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,IAAI,EAAE,CAAC;IAClB,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,SAAS,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;QACrE,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,EAAE,CAAC,CAAC;IACtD,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts CHANGED
@@ -32,8 +32,6 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
32
32
  [x: string]: string;
33
33
  }>>>;
34
34
  }, z.core.$strip>, z.ZodObject<{
35
- searchType: z.ZodString;
36
- totalFound: z.ZodNumber;
37
35
  results: z.ZodArray<z.ZodObject<{
38
36
  cid: z.ZodNumber;
39
37
  identifier: z.ZodOptional<z.ZodString>;
@@ -54,5 +52,9 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
54
52
  readonly code: JsonRpcErrorCode.ValidationError;
55
53
  readonly when: "substructure/superstructure/similarity search missing query or queryType";
56
54
  readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
57
- }]>;
55
+ }], {
56
+ readonly searchType: z.ZodString;
57
+ readonly totalFound: z.ZodNumber;
58
+ readonly notice: z.ZodOptional<z.ZodString>;
59
+ }>;
58
60
  //# sourceMappingURL=search-compounds.tool.d.ts.map
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkQ1B,CAAC"}
1
+ {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6Q1B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED
@@ -72,10 +72,6 @@ export const searchCompounds = tool('pubchem_search_compounds', {
72
72
  .describe('Optional: fetch these properties for each result, avoiding a follow-up details call. E.g. ["MolecularFormula", "MolecularWeight", "CanonicalSMILES"].'),
73
73
  }),
74
74
  output: z.object({
75
- searchType: z
76
- .string()
77
- .describe('Search strategy used: identifier, formula, substructure, superstructure, or similarity.'),
78
- totalFound: z.number().describe('Total CIDs found (before maxResults cap).'),
79
75
  results: z
80
76
  .array(z
81
77
  .object({
@@ -92,6 +88,18 @@ export const searchCompounds = tool('pubchem_search_compounds', {
92
88
  .describe('Matching compound entry.'))
93
89
  .describe('Matching compounds.'),
94
90
  }),
91
+ // Agent-facing context — search strategy echo, total before cap, and an empty-result
92
+ // notice. Reaches structuredContent and content[] automatically; not in the domain return.
93
+ enrichment: {
94
+ searchType: z
95
+ .string()
96
+ .describe('Search strategy used: identifier, formula, substructure, superstructure, or similarity.'),
97
+ totalFound: z.number().describe('Total CIDs found before the maxResults cap.'),
98
+ notice: z
99
+ .string()
100
+ .optional()
101
+ .describe('Recovery guidance when no compounds matched — echoes search strategy and suggests how to broaden. Absent when results were returned.'),
102
+ },
95
103
  errors: [
96
104
  {
97
105
  reason: 'missing_identifier_args',
@@ -175,6 +183,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
175
183
  totalFound,
176
184
  returned: cappedCids.length,
177
185
  });
186
+ // Agent-facing context: search strategy echo, total, and empty-result notice.
187
+ ctx.enrich({ searchType: input.searchType, totalFound });
188
+ if (cappedCids.length === 0) {
189
+ ctx.enrich.notice(`No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
190
+ }
178
191
  // Optionally hydrate with properties
179
192
  let propsMap;
180
193
  if (input.properties && input.properties.length > 0 && cappedCids.length > 0) {
@@ -193,14 +206,10 @@ export const searchCompounds = tool('pubchem_search_compounds', {
193
206
  }
194
207
  return result;
195
208
  });
196
- return { searchType: input.searchType, totalFound, results };
209
+ return { results };
197
210
  },
198
211
  format(result) {
199
212
  const lines = [];
200
- const count = result.results.length;
201
- const truncated = result.totalFound > count ? ` (showing ${count} of ${result.totalFound})` : '';
202
- lines.push(`Found ${result.totalFound} compound${result.totalFound !== 1 ? 's' : ''}${truncated} — ${result.searchType} search`);
203
- lines.push('');
204
213
  if (result.results.length === 0) {
205
214
  lines.push('No results.');
206
215
  return [{ type: 'text', text: lines.join('\n') }];
package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/pubchem/pubchem-client.js CHANGED
@@ -4,7 +4,7 @@
4
4
  * @module services/pubchem/pubchem-client
5
5
  */
6
6
  import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
7
- import { httpStatusToErrorCode } from '@cyanheads/mcp-ts-core/utils';
7
+ import { httpErrorFromResponse } from '@cyanheads/mcp-ts-core/utils';
8
8
  const isNotFound = (error) => error instanceof McpError && error.code === JsonRpcErrorCode.NotFound;
9
9
  // ── Rate Limiter ─────────────────────────────────────────────────────
10
10
  /** Sliding-window rate limiter. Queues requests exceeding maxPerSecond. */
@@ -207,14 +207,17 @@ export class PubChemClient {
207
207
  return (await response.json());
208
208
  }
209
209
  const text = await response.text();
210
- const message = parseFaultMessage(text) ?? text.slice(0, 300);
210
+ const fault = parseFaultMessage(text) ?? text.slice(0, 300);
211
211
  // Retry once on 5xx
212
212
  if (response.status >= 500 && attempt < 1) {
213
213
  await sleep(1000 * 2 ** attempt);
214
214
  continue;
215
215
  }
216
- const code = httpStatusToErrorCode(response.status) ?? JsonRpcErrorCode.InternalError;
217
- throw new McpError(code, message, { url, status: response.status });
216
+ throw await httpErrorFromResponse(response, {
217
+ captureBody: false,
218
+ service: 'PubChem',
219
+ data: { fault, url },
220
+ });
218
221
  }
219
222
  catch (error) {
220
223
  // HTTP errors are already classified — surface them, don't retry.
@@ -243,9 +246,12 @@ export class PubChemClient {
243
246
  const response = await fetch(url, { signal: controller.signal });
244
247
  if (!response.ok) {
245
248
  const text = await response.text();
246
- const message = parseFaultMessage(text) ?? text.slice(0, 300);
247
- const code = httpStatusToErrorCode(response.status) ?? JsonRpcErrorCode.InternalError;
248
- throw new McpError(code, message, { url, status: response.status });
249
+ const fault = parseFaultMessage(text) ?? text.slice(0, 300);
250
+ throw await httpErrorFromResponse(response, {
251
+ captureBody: false,
252
+ service: 'PubChem',
253
+ data: { fault, url },
254
+ });
249
255
  }
250
256
  return await response.arrayBuffer();
251
257
  }
package/dist/services/pubchem/pubchem-client.js.map CHANGED
@@ -1 +1 @@
1
- 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package/manifest.json CHANGED
@@ -1,9 +1,17 @@
1
1
  {
2
2
  "manifest_version": "0.3",
3
3
  "name": "pubchem-mcp-server",
4
- "version": "0.1.20",
4
+ "version": "0.1.22",
5
5
  "description": "Search PubChem compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP.",
6
- "author": { "name": "cyanheads" },
6
+ "author": {
7
+ "name": "cyanheads"
8
+ },
9
+ "repository": {
10
+ "type": "git",
11
+ "url": "https://github.com/cyanheads/pubchem-mcp-server"
12
+ },
13
+ "homepage": "https://github.com/cyanheads/pubchem-mcp-server#readme",
14
+ "license": "Apache-2.0",
7
15
  "server": {
8
16
  "type": "node",
9
17
  "entry_point": "dist/index.js",
@@ -18,7 +26,9 @@
18
26
  }
19
27
  },
20
28
  "compatibility": {
21
- "runtimes": { "node": ">=24.0.0" }
29
+ "runtimes": {
30
+ "node": ">=24.0.0"
31
+ }
22
32
  },
23
33
  "tools_generated": true,
24
34
  "prompts_generated": true,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubchem-mcp-server",
3
- "version": "0.1.20",
3
+ "version": "0.1.22",
4
4
  "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.",
5
5
  "mcpName": "io.github.cyanheads/pubchem-mcp-server",
6
6
  "type": "module",
@@ -18,7 +18,8 @@
18
18
  "audit:refresh": "rm -f bun.lock && bun install && bun audit",
19
19
  "tree": "bun scripts/tree.ts",
20
20
  "list-skills": "bun scripts/list-skills.ts",
21
- "format": "biome check --write --unsafe .",
21
+ "format": "biome check --write .",
22
+ "format:unsafe": "biome check --write --unsafe .",
22
23
  "lint:mcp": "bun scripts/lint-mcp.ts",
23
24
  "lint:packaging": "bun scripts/lint-packaging.ts",
24
25
  "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubchem-mcp-server.mcpb",
@@ -42,6 +43,10 @@
42
43
  "mcp",
43
44
  "mcp-server",
44
45
  "model-context-protocol",
46
+ "typescript",
47
+ "bun",
48
+ "stdio",
49
+ "streamable-http",
45
50
  "pubchem",
46
51
  "chemistry",
47
52
  "compounds",
@@ -67,12 +72,12 @@
67
72
  "access": "public"
68
73
  },
69
74
  "dependencies": {
70
- "@cyanheads/mcp-ts-core": "^0.9.6",
75
+ "@cyanheads/mcp-ts-core": "^0.9.16",
71
76
  "pino-pretty": "^13.1.3",
72
77
  "zod": "^4.4.3"
73
78
  },
74
79
  "devDependencies": {
75
- "@biomejs/biome": "^2.4.15",
80
+ "@biomejs/biome": "^2.4.16",
76
81
  "@types/node": "^25.9.1",
77
82
  "depcheck": "^1.4.7",
78
83
  "ignore": "^7.0.5",
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubchem-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.1.20",
9
+ "version": "0.1.22",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
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20
  "identifier": "@cyanheads/pubchem-mcp-server",
21
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  "runtimeHint": "bun",
22
- "version": "0.1.20",
22
+ "version": "0.1.22",
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  "packageArguments": [
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  { "type": "positional", "value": "run" },
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  { "type": "positional", "value": "start:stdio" }
@@ -42,7 +42,7 @@
42
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  "registryBaseUrl": "https://registry.npmjs.org",
43
43
  "identifier": "@cyanheads/pubchem-mcp-server",
44
44
  "runtimeHint": "bun",
45
- "version": "0.1.20",
45
+ "version": "0.1.22",
46
46
  "packageArguments": [
47
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  { "type": "positional", "value": "run" },
48
48
  { "type": "positional", "value": "start:http" }