@cyanheads/pubchem-mcp-server 0.6.3 → 0.6.4

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Files changed (41) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +3 -2
  4. package/changelog/0.6.x/0.6.4.md +23 -0
  5. package/dist/mcp-server/resources/definitions/assay.resource.js +1 -1
  6. package/dist/mcp-server/resources/definitions/assay.resource.js.map +1 -1
  7. package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js +1 -1
  8. package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map +1 -1
  9. package/dist/mcp-server/resources/definitions/compound-image.resource.js +1 -1
  10. package/dist/mcp-server/resources/definitions/compound-image.resource.js.map +1 -1
  11. package/dist/mcp-server/resources/definitions/compound-safety.resource.js +1 -1
  12. package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map +1 -1
  13. package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js +1 -1
  14. package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js.map +1 -1
  15. package/dist/mcp-server/resources/definitions/compound.resource.js +1 -1
  16. package/dist/mcp-server/resources/definitions/compound.resource.js.map +1 -1
  17. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +2 -2
  18. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
  19. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js +3 -3
  20. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/get-compound-details.tool.js +1 -1
  22. package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map +1 -1
  23. package/dist/mcp-server/tools/definitions/get-compound-image.tool.js +1 -1
  24. package/dist/mcp-server/tools/definitions/get-compound-image.tool.js.map +1 -1
  25. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +1 -1
  26. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -1
  27. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js +1 -1
  28. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map +1 -1
  29. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js +1 -1
  30. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map +1 -1
  31. package/dist/mcp-server/tools/definitions/index.d.ts +2 -2
  32. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +2 -2
  33. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
  34. package/dist/mcp-server/tools/definitions/search-compounds.tool.js +8 -5
  35. package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
  36. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  37. package/dist/services/pubchem/pubchem-client.js +37 -8
  38. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  39. package/manifest.json +1 -1
  40. package/package.json +3 -3
  41. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,7 +1,7 @@
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  # Developer Protocol
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  **Server:** pubchem-mcp-server
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- **Version:** 0.6.3
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+ **Version:** 0.6.4
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
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  **Engines:** Bun ≥1.4.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Developer Protocol
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  **Server:** pubchem-mcp-server
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- **Version:** 0.6.3
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+ **Version:** 0.6.4
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
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  **Engines:** Bun ≥1.4.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
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-0.6.3-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-^2.0.0-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-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.4.0-f472b6.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-0.6.4-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-^2.0.0-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-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.4.0-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=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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+ [![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%2Fpubchem-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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@@ -64,6 +64,7 @@ Compound and assay records are also exposed as URI-templated resources, backed b
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  ### `pubchem_search_compounds` <sub>tool</sub>
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  - Five search strategies: identifier (name/SMILES/InChIKey, batched 1-25), formula (Hill notation, optional `allowOtherElements`), substructure/superstructure containment, or 2D Tanimoto similarity (threshold 70-100, default 90)
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+ - Each strategy needs its own fields — identifier: `identifierType` + `identifiers`; formula: `formula`; substructure/superstructure/similarity: `query` + `queryType` — and a missing or blank one is rejected before the upstream call
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  - Caps at 200 CIDs per page (default 20); `offset` pages to a ceiling of 10,000 — identifier lookups resolve every match up front so paging is free, while formula/structure/similarity searches cost more upstream per deep page
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  - Optional `properties` hydration avoids a follow-up `pubchem_get_compound_details` call
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  - Identifier mode reports `unresolvedIdentifiers` for inputs that resolved to no CID, plus notices when multiple inputs collide on one CID
package/changelog/0.6.x/0.6.4.md ADDED
@@ -0,0 +1,23 @@
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+ ---
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+ summary: "pubchem_search_compounds names each mode's required fields and rejects a blank formula or query before calling PubChem, failed PubChem requests log their URL server-side, and integer inputs advertise minimum: 1 instead of exclusiveMinimum."
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+ breaking: false
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+ security: false
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+ ---
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+
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+ # 0.6.4 — 2026-09-24
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+
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+ ## Added
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+
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+ - **Failed PubChem requests log the request URL server-side** ([#50](https://github.com/cyanheads/pubchem-mcp-server/issues/50)) — one module `logger` line per failure after any retry, carrying `url`, `method`, and the HTTP `status` and `fault` or the error message: `debug` for a 404, `warning` for any other non-2xx, a network error, a 30 s timeout, or an SDQ rejection inside a 2xx. The client-facing `error.data` still carries no URL.
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+
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+ ## Fixed
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+
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+ - **`pubchem_search_compounds` `searchType` names each mode's required fields** ([#45](https://github.com/cyanheads/pubchem-mcp-server/issues/45)) — identifier needs `identifierType` + `identifiers`, formula needs `formula`, substructure/superstructure/similarity need `query` + `queryType`. The input root stays a flat object.
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+ - **A whitespace-only `formula` or `query` fails as `missing_formula` / `missing_structure_args`** before any PubChem request, instead of returning unrelated compounds or an upstream HTTP 500. A padded formula such as `" C9H8O4 "` still resolves.
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+ - **Integer inputs use `.min(1)` instead of `.positive()`** ([#51](https://github.com/cyanheads/pubchem-mcp-server/issues/51)) — ten inputs across seven tools now advertise `minimum: 1` rather than a numeric `exclusiveMinimum`, which Microsoft Copilot Studio fails to parse; accepted values are unchanged. The six resource templates' `cid`/`aid` params match.
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+ - **README VS Code install badge** URL-encodes the `/` in `@cyanheads/pubchem-mcp-server`.
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+
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+ ## Dependencies
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+
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+ - `@socketsecurity/bun-security-scanner` ^1.1.2 → ^1.1.3
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+ - `@types/node` 26.6.1 → 26.6.2
package/dist/mcp-server/resources/definitions/assay.resource.js CHANGED
@@ -10,7 +10,7 @@ export const assayResource = resource('pubchem://assay/{aid}', {
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  description: 'Summary for a PubChem BioAssay by AID — name, description, source, protocol, and substance counts.',
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  mimeType: 'application/json',
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  params: z.object({
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- aid: z.coerce.number().int().positive().describe('PubChem Assay ID.'),
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+ aid: z.coerce.number().int().min(1).describe('PubChem Assay ID.'),
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  }),
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  async handler(params) {
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  const client = getPubChemClient();
package/dist/mcp-server/resources/definitions/assay.resource.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js CHANGED
@@ -11,7 +11,7 @@ export const compoundBioactivityResource = resource('pubchem://compound/{cid}/bi
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  description: 'Bioassay activity profile for a PubChem compound by CID. Returns up to 25 assays; use pubchem_get_bioactivity to filter by outcome or molecular target, raise the cap, and page through the rest with offset.',
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  mimeType: 'application/json',
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  params: z.object({
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- cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
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+ cid: z.coerce.number().int().min(1).describe('PubChem Compound ID.'),
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  }),
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  async handler(params) {
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  const client = getPubChemClient();
package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"compound-bioactivity.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-bioactivity.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,gGAAgG;AAChG,MAAM,WAAW,GAAG,EAAE,CAAC;AAEvB,MAAM,CAAC,MAAM,2BAA2B,GAAG,QAAQ,CAAC,sCAAsC,EAAE;IAC1F,IAAI,EAAE,8BAA8B;IACpC,WAAW,EACT,+MAA+M;IACjN,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACtD,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QACtE,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,WAAW,EAAE,IAAI,CAAC,MAAM;YACxB,WAAW;YACX,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,WAAW,CAAC;SACpC,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
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+ {"version":3,"file":"compound-bioactivity.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-bioactivity.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,gGAAgG;AAChG,MAAM,WAAW,GAAG,EAAE,CAAC;AAEvB,MAAM,CAAC,MAAM,2BAA2B,GAAG,QAAQ,CAAC,sCAAsC,EAAE;IAC1F,IAAI,EAAE,8BAA8B;IACpC,WAAW,EACT,+MAA+M;IACjN,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACtD,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QACtE,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,WAAW,EAAE,IAAI,CAAC,MAAM;YACxB,WAAW;YACX,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,WAAW,CAAC;SACpC,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/resources/definitions/compound-image.resource.js CHANGED
@@ -9,7 +9,7 @@ export const compoundImageResource = resource('pubchem://compound/{cid}/image',
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  description: 'A 2D structure diagram (PNG, 300x300) for a PubChem compound by CID. Use pubchem_get_compound_image to choose the image size.',
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  mimeType: 'image/png',
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  params: z.object({
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- cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
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+ cid: z.coerce.number().int().min(1).describe('PubChem Compound ID.'),
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  }),
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  output: z.object({
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  base64: z.string().describe('Base64-encoded PNG image data.'),
package/dist/mcp-server/resources/definitions/compound-image.resource.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"compound-image.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-image.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,gCAAgC,EAAE;IAC9E,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EACT,+HAA+H;IACjI,QAAQ,EAAE,WAAW;IACrB,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;KAC9D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;QAC1D,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE,CAAC;IAC5D,CAAC;IAED,mFAAmF;IACnF,MAAM,CAAC,MAAM,EAAE,IAAI;QACjB,MAAM,EAAE,MAAM,EAAE,GAAG,MAA4B,CAAC;QAChD,OAAO,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;IACzE,CAAC;CACF,CAAC,CAAC"}
1
+ {"version":3,"file":"compound-image.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-image.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,gCAAgC,EAAE;IAC9E,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EACT,+HAA+H;IACjI,QAAQ,EAAE,WAAW;IACrB,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrE,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;KAC9D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;QAC1D,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE,CAAC;IAC5D,CAAC;IAED,mFAAmF;IACnF,MAAM,CAAC,MAAM,EAAE,IAAI;QACjB,MAAM,EAAE,MAAM,EAAE,GAAG,MAA4B,CAAC;QAChD,OAAO,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;IACzE,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/resources/definitions/compound-safety.resource.js CHANGED
@@ -9,7 +9,7 @@ export const compoundSafetyResource = resource('pubchem://compound/{cid}/safety'
9
9
  description: 'GHS hazard classification for a PubChem compound by CID — signal word, pictograms, hazard (H) and precautionary (P) statements. Not every compound carries a deposited classification.',
10
10
  mimeType: 'application/json',
11
11
  params: z.object({
12
- cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
12
+ cid: z.coerce.number().int().min(1).describe('PubChem Compound ID.'),
13
13
  }),
14
14
  async handler(params) {
15
15
  const client = getPubChemClient();
package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"compound-safety.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-safety.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,iCAAiC,EAAE;IAChF,IAAI,EAAE,yBAAyB;IAC/B,WAAW,EACT,wLAAwL;IAC1L,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACtD,2FAA2F;QAC3F,wFAAwF;QACxF,IAAI,MAAM,CAAC,MAAM,KAAK,IAAI,EAAE,CAAC;YAC3B,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;QACpE,CAAC;QACD,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,OAAO,EAAE,IAAI;YACb,MAAM,EAAE,MAAM,CAAC,MAAM;YACrB,GAAG,EAAE;gBACH,UAAU,EAAE,MAAM,CAAC,GAAG,CAAC,UAAU;gBACjC,UAAU,EAAE,MAAM,CAAC,GAAG,CAAC,UAAU;gBACjC,gBAAgB,EAAE,MAAM,CAAC,GAAG,CAAC,gBAAgB;gBAC7C,uBAAuB,EAAE,MAAM,CAAC,GAAG,CAAC,uBAAuB;aAC5D;YACD,MAAM,EAAE,MAAM,CAAC,GAAG,CAAC,MAAM;SAC1B,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
1
+ {"version":3,"file":"compound-safety.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-safety.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,iCAAiC,EAAE;IAChF,IAAI,EAAE,yBAAyB;IAC/B,WAAW,EACT,wLAAwL;IAC1L,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACtD,2FAA2F;QAC3F,wFAAwF;QACxF,IAAI,MAAM,CAAC,MAAM,KAAK,IAAI,EAAE,CAAC;YAC3B,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;QACpE,CAAC;QACD,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,OAAO,EAAE,IAAI;YACb,MAAM,EAAE,MAAM,CAAC,MAAM;YACrB,GAAG,EAAE;gBACH,UAAU,EAAE,MAAM,CAAC,GAAG,CAAC,UAAU;gBACjC,UAAU,EAAE,MAAM,CAAC,GAAG,CAAC,UAAU;gBACjC,gBAAgB,EAAE,MAAM,CAAC,GAAG,CAAC,gBAAgB;gBAC7C,uBAAuB,EAAE,MAAM,CAAC,GAAG,CAAC,uBAAuB;aAC5D;YACD,MAAM,EAAE,MAAM,CAAC,GAAG,CAAC,MAAM;SAC1B,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js CHANGED
@@ -12,7 +12,7 @@ export const compoundXrefsResource = resource('pubchem://compound/{cid}/xrefs',
12
12
  description: 'External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID, up to 25 per type. Use pubchem_get_compound_xrefs for the full set of xref types, a higher per-type cap, and to page through the rest with offset.',
13
13
  mimeType: 'application/json',
14
14
  params: z.object({
15
- cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
15
+ cid: z.coerce.number().int().min(1).describe('PubChem Compound ID.'),
16
16
  }),
17
17
  async handler(params) {
18
18
  const client = getPubChemClient();
package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"compound-xrefs.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-xrefs.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,0FAA0F;AAC1F,MAAM,mBAAmB,GAAG,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,CAAU,CAAC;AACtE,MAAM,YAAY,GAAG,EAAE,CAAC;AAExB,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,gCAAgC,EAAE;IAC9E,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EACT,4OAA4O;IAC9O,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,KAAK,GAA8E,EAAE,CAAC;QAC5F,KAAK,MAAM,IAAI,IAAI,mBAAmB,EAAE,CAAC;YACvC,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;YACpD,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,YAAY,CAAC,EAAE,cAAc,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YACpF,CAAC;QACH,CAAC;QACD,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACpC,CAAC;CACF,CAAC,CAAC"}
1
+ {"version":3,"file":"compound-xrefs.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-xrefs.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,0FAA0F;AAC1F,MAAM,mBAAmB,GAAG,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,CAAU,CAAC;AACtE,MAAM,YAAY,GAAG,EAAE,CAAC;AAExB,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,gCAAgC,EAAE;IAC9E,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EACT,4OAA4O;IAC9O,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,KAAK,GAA8E,EAAE,CAAC;QAC5F,KAAK,MAAM,IAAI,IAAI,mBAAmB,EAAE,CAAC;YACvC,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;YACpD,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,YAAY,CAAC,EAAE,cAAc,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YACpF,CAAC;QACH,CAAC;QACD,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACpC,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/resources/definitions/compound.resource.js CHANGED
@@ -11,7 +11,7 @@ export const compoundResource = resource('pubchem://compound/{cid}', {
11
11
  description: 'Core physicochemical properties for a PubChem compound by CID. Use pubchem_get_compound_details to select properties or add descriptions, synonyms, drug-likeness, and classification.',
12
12
  mimeType: 'application/json',
13
13
  params: z.object({
14
- cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
14
+ cid: z.coerce.number().int().min(1).describe('PubChem Compound ID.'),
15
15
  }),
16
16
  async handler(params) {
17
17
  const client = getPubChemClient();
package/dist/mcp-server/resources/definitions/compound.resource.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"compound.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAC;AAEjE,MAAM,CAAC,MAAM,gBAAgB,GAAG,QAAQ,CAAC,0BAA0B,EAAE;IACnE,IAAI,EAAE,kBAAkB;IACxB,WAAW,EACT,wLAAwL;IAC1L,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,kBAAkB,CAAC,CAAC,CAAC;QAC/E,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACpB,6FAA6F;QAC7F,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,KAAK,CAAC,EAAE,CAAC;YACvD,MAAM,QAAQ,CAAC,qCAAqC,MAAM,CAAC,GAAG,GAAG,EAAE,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC;QAC1F,CAAC;QACD,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,UAAU,EAAE,GAAG,GAAG,CAAC;QACzC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,UAAU,EAAE,CAAC;IACzC,CAAC;CACF,CAAC,CAAC"}
1
+ {"version":3,"file":"compound.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAC;AAEjE,MAAM,CAAC,MAAM,gBAAgB,GAAG,QAAQ,CAAC,0BAA0B,EAAE;IACnE,IAAI,EAAE,kBAAkB;IACxB,WAAW,EACT,wLAAwL;IAC1L,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,kBAAkB,CAAC,CAAC,CAAC;QAC/E,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACpB,6FAA6F;QAC7F,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,KAAK,CAAC,EAAE,CAAC;YACvD,MAAM,QAAQ,CAAC,qCAAqC,MAAM,CAAC,GAAG,GAAG,EAAE,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC;QAC1F,CAAC;QACD,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,UAAU,EAAE,GAAG,GAAG,CAAC;QACzC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,UAAU,EAAE,CAAC;IACzC,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js CHANGED
@@ -18,7 +18,7 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
18
18
  cid: z
19
19
  .number()
20
20
  .int()
21
- .positive()
21
+ .min(1)
22
22
  .describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
23
23
  outcomeFilter: z
24
24
  .enum(['active', 'inactive', 'all'])
@@ -27,7 +27,7 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
27
27
  targetGeneId: z
28
28
  .number()
29
29
  .int()
30
- .positive()
30
+ .min(1)
31
31
  .optional()
32
32
  .describe('Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter="active" to answer "is this compound active against target T?".'),
33
33
  targetAccession: z
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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{"version":3,"file":"get-bioactivity.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,yBAAyB,EAAE;IAC5D,KAAK,EAAE,iBAAiB;IACxB,WAAW,EACT,kYAAkY;IACpY,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,aAAa,EAAE,CAAC;aACb,IAAI,CAAC,CAAC,QAAQ,EAAE,UAAU,EAAE,KAAK,CAAC,CAAC;aACnC,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,+JAA+J,CAChK;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,2OAA2O,CAC5O;QACH,eAAe,EAAE,CAAC;aACf,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,kMAAkM,CACnM;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,+KAA+K,CAChL;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,2JAA2J,CAC5J;KACJ,CAAC;IACF,mFAAmF;IACnF,qFAAqF;IACrF,2DAA2D;IAC3D,YAAY,EAAE,EAAE,MAAM,EAAE,cAAc,EAAE,SAAS,EAAE,iBAAiB,EAAE;IACtE,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC1E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACjE,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QACrE,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC7C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACnD,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,CAAC,gEAAgE,CAAC;YAC7E,eAAe,EAAE,CAAC;iBACf,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,6CAA6C,CAAC;YAC1D,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;YACpE,cAAc,EAAE,CAAC;iBACd,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CACP,oEAAoE,CACrE;gBACH,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;gBAC7C,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CAAC,+DAA+D,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,0CAA0C,CAAC,CACxD;iBACA,QAAQ,CAAC,qCAAqC,CAAC;SACnD,CAAC;aACD,QAAQ,CAAC,qBAAqB,CAAC,CACnC;aACA,QAAQ,CAAC,oCAAoC,CAAC;KAClD,CAAC;IACF,qFAAqF;IACrF,wFAAwF;IACxF,0DAA0D;IAC1D,EAAE;IACF,kFAAkF;IAClF,oFAAoF;IACpF,oFAAoF;IACpF,8EAA8E;IAC9E,UAAU,EAAE;QACV,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACvF,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,qEAAqE,CAAC;QAClF,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,CACP,mFAAmF,CACpF;QACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACnE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QAC5E,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;QAC9F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACtE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8FAA8F,CAC/F;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAExD,MAAM,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QACzE,MAAM,aAAa,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC,MAAM,CAAC;QAE7E,2EAA2E;QAC3E,yFAAyF;QACzF,IAAI,QAAQ,GAAG,OAAO,CAAC;QACvB,IAAI,KAAK,CAAC,aAAa,KAAK,QAAQ,EAAE,CAAC;YACrC,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC;QAC5D,CAAC;aAAM,IAAI,KAAK,CAAC,aAAa,KAAK,UAAU,EAAE,CAAC;YAC9C,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC;QAC9D,CAAC;QAED,MAAM,WAAW,GAAG;YAClB,KAAK,CAAC,YAAY,IAAI,IAAI,CAAC,CAAC,CAAC,UAAU,KAAK,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,SAAS;YACvE,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,aAAa,KAAK,CAAC,eAAe,EAAE,CAAC,CAAC,CAAC,SAAS;SACzE;aACE,MAAM,CAAC,OAAO,CAAC;aACf,IAAI,CAAC,GAAG,CAAC,CAAC;QACb,IAAI,KAAK,CAAC,YAAY,IAAI,IAAI,EAAE,CAAC;YAC/B,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,KAAK,KAAK,CAAC,YAAY,CAAC,CAAC;QAC3E,CAAC;QACD,IAAI,KAAK,CAAC,eAAe,EAAE,CAAC;YAC1B,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,eAAe,KAAK,KAAK,CAAC,eAAe,CAAC,CAAC;QACjF,CAAC;QAED,6EAA6E;QAC7E,iFAAiF;QACjF,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;QAC9E,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;QACjD,MAAM,OAAO,GAAG,UAAU,GAAG,QAAQ,CAAC,MAAM,CAAC;QAE7C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,qBAAqB,EAAE;YAClC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,OAAO,CAAC,MAAM;YACrB,MAAM,EAAE,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package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js CHANGED
@@ -27,7 +27,7 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
27
27
  cid: z
28
28
  .number()
29
29
  .int()
30
- .positive()
30
+ .min(1)
31
31
  .describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
32
32
  format: z
33
33
  .enum(['sdf', 'json'])
@@ -40,13 +40,13 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
40
40
  maxAtoms: z
41
41
  .number()
42
42
  .int()
43
- .positive()
43
+ .min(1)
44
44
  .optional()
45
45
  .describe('Cap the atoms returned in the format="json" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms.'),
46
46
  maxBonds: z
47
47
  .number()
48
48
  .int()
49
- .positive()
49
+ .min(1)
50
50
  .optional()
51
51
  .describe('Cap the bonds returned in the format="json" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds.'),
52
52
  includeRawSdf: z
package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/get-compound-details.tool.js CHANGED
@@ -110,7 +110,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
110
110
  },
111
111
  input: z.object({
112
112
  cids: z
113
- .array(z.number().int().positive())
113
+ .array(z.number().int().min(1))
114
114
  .min(1)
115
115
  .max(100)
116
116
  .describe('PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds.'),
package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/get-compound-image.tool.js CHANGED
@@ -17,7 +17,7 @@ export const getCompoundImage = tool('pubchem_get_compound_image', {
17
17
  cid: z
18
18
  .number()
19
19
  .int()
20
- .positive()
20
+ .min(1)
21
21
  .describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
22
22
  size: z
23
23
  .enum(['small', 'large'])
package/dist/mcp-server/tools/definitions/get-compound-image.tool.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"get-compound-image.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EAAE,iEAAiE;IAC9E,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;aACxB,OAAO,CAAC,OAAO,CAAC;aAChB,QAAQ,CAAC,uEAAuE,CAAC;KACrF,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAClE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAChE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACpD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KACvD,CAAC;IACF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,iFAAiF;YACjF,mFAAmF;YACnF,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,4CAA4C;YAClD,QAAQ,EAAE,+DAA+D;SAC1E;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5D,MAAM,GAAG,GAAG,KAAK,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;QAE/C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC;QAE9F,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,WAAW,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC;YACnD,QAAQ,EAAE,WAAW;YACrB,KAAK,EAAE,GAAG;YACV,MAAM,EAAE,GAAG;SACZ,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,OAAO;YACL,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE;YACtE;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,wBAAwB,MAAM,CAAC,GAAG,KAAK,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,MAAM,GAAG;aAC9E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
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package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js CHANGED
@@ -17,7 +17,7 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
17
17
  cid: z
18
18
  .number()
19
19
  .int()
20
- .positive()
20
+ .min(1)
21
21
  .describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
22
22
  kinds: z
23
23
  .array(z.enum(['drug-drug', 'drug-food', 'target']))
package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js CHANGED
@@ -44,7 +44,7 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
44
44
  },
45
45
  input: z.object({
46
46
  cids: z
47
- .array(z.number().int().positive())
47
+ .array(z.number().int().min(1))
48
48
  .min(1)
49
49
  .max(25)
50
50
  .describe('PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds.'),
package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js CHANGED
@@ -18,7 +18,7 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
18
18
  cid: z
19
19
  .number()
20
20
  .int()
21
- .positive()
21
+ .min(1)
22
22
  .describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
23
23
  xrefTypes: z
24
24
  .array(xrefTypeEnum)
package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -147,12 +147,12 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
147
147
  }, {
148
148
  readonly reason: "missing_formula";
149
149
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
150
- readonly when: "searchType is \"formula\" but the formula field was omitted";
150
+ readonly when: "searchType is \"formula\" but the formula field was omitted or blank";
151
151
  readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
152
152
  }, {
153
153
  readonly reason: "missing_structure_args";
154
154
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
155
- readonly when: "substructure/superstructure/similarity search missing query or queryType";
155
+ readonly when: "substructure/superstructure/similarity search with query or queryType omitted, or a blank query";
156
156
  readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
157
157
  }, {
158
158
  readonly reason: "invalid_cid_query";
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts CHANGED
@@ -47,12 +47,12 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
47
47
  }, {
48
48
  readonly reason: "missing_formula";
49
49
  readonly code: JsonRpcErrorCode.ValidationError;
50
- readonly when: "searchType is \"formula\" but the formula field was omitted";
50
+ readonly when: "searchType is \"formula\" but the formula field was omitted or blank";
51
51
  readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
52
52
  }, {
53
53
  readonly reason: "missing_structure_args";
54
54
  readonly code: JsonRpcErrorCode.ValidationError;
55
- readonly when: "substructure/superstructure/similarity search missing query or queryType";
55
+ readonly when: "substructure/superstructure/similarity search with query or queryType omitted, or a blank query";
56
56
  readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
57
57
  }, {
58
58
  readonly reason: "invalid_cid_query";
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
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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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwb1B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED
@@ -26,7 +26,7 @@ export const searchCompounds = tool('pubchem_search_compounds', {
26
26
  openWorldHint: true,
27
27
  },
28
28
  input: z.object({
29
- searchType: searchTypeEnum.describe('Search strategy. "identifier": name/SMILES/InChIKey lookup. "formula": molecular formula. "substructure": find compounds containing the query as a substructure. "superstructure": find compounds that are themselves substructures of the query. "similarity": 2D Tanimoto similarity to the query.'),
29
+ searchType: searchTypeEnum.describe('Search strategy; each mode needs its own fields. "identifier": name/SMILES/InChIKey lookup — requires identifierType and identifiers. "formula": molecular formula — requires formula. "substructure": find compounds containing the query as a substructure. "superstructure": find compounds that are themselves substructures of the query. "similarity": 2D Tanimoto similarity to the query. substructure, superstructure, and similarity require query and queryType.'),
30
30
  identifierType: identifierTypeEnum
31
31
  .optional()
32
32
  .describe('Required for identifier search. Type of chemical identifier: "name", "smiles", or "inchikey".'),
@@ -145,13 +145,13 @@ export const searchCompounds = tool('pubchem_search_compounds', {
145
145
  {
146
146
  reason: 'missing_formula',
147
147
  code: JsonRpcErrorCode.ValidationError,
148
- when: 'searchType is "formula" but the formula field was omitted',
148
+ when: 'searchType is "formula" but the formula field was omitted or blank',
149
149
  recovery: 'Pass formula in Hill notation, for example "C6H12O6" or "CaH2O2".',
150
150
  },
151
151
  {
152
152
  reason: 'missing_structure_args',
153
153
  code: JsonRpcErrorCode.ValidationError,
154
- when: 'substructure/superstructure/similarity search missing query or queryType',
154
+ when: 'substructure/superstructure/similarity search with query or queryType omitted, or a blank query',
155
155
  recovery: 'Provide both query (SMILES string or CID as string) and queryType ("smiles" or "cid").',
156
156
  },
157
157
  {
@@ -229,7 +229,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
229
229
  break;
230
230
  }
231
231
  case 'formula': {
232
- if (!input.formula) {
232
+ // Blank means missing: PubChem answers a whitespace-only formula with unrelated
233
+ // compounds. A padded formula passes through — PubChem trims it.
234
+ if (!input.formula?.trim()) {
233
235
  throw ctx.fail('missing_formula', undefined, {
234
236
  ...ctx.recoveryFor('missing_formula'),
235
237
  });
@@ -241,7 +243,8 @@ export const searchCompounds = tool('pubchem_search_compounds', {
241
243
  case 'substructure':
242
244
  case 'superstructure':
243
245
  case 'similarity': {
244
- if (!input.query || !input.queryType) {
246
+ // A whitespace-only SMILES query otherwise surfaces as an upstream HTTP 500.
247
+ if (!input.query?.trim() || !input.queryType) {
245
248
  throw ctx.fail('missing_structure_args', undefined, {
246
249
  ...ctx.recoveryFor('missing_structure_args'),
247
250
  });
package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map CHANGED
@@ -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, notFound, serviceUnavailable, } from '@cyanheads/mcp-ts-core/errors';
7
- import { httpErrorFromResponse } from '@cyanheads/mcp-ts-core/utils';
7
+ import { httpErrorFromResponse, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
8
8
  const isNotFound = (error) => error instanceof McpError && error.code === JsonRpcErrorCode.NotFound;
9
9
  /** Distinguishes the two outcomes PUG View hides behind a single HTTP 404.
10
10
  *
@@ -63,6 +63,17 @@ class RateLimiter {
63
63
  }
64
64
  // ── Helpers ──────────────────────────────────────────────────────────
65
65
  const sleep = (ms) => new Promise((r) => setTimeout(r, ms));
66
+ /** Records a failed PubChem request, with its URL, in the server's own log. The error the
67
+ * caller receives deliberately omits the URL, so this line is the only place an operator can
68
+ * see which route failed. The module `logger` writes server-side only — `ctx.log` would also
69
+ * forward the line to the client as `notifications/message`. */
70
+ function logFailedRequest(level, url, method, detail) {
71
+ const summary = 'status' in detail ? `HTTP ${detail.status}` : detail.error;
72
+ logger[level](`PubChem request failed: ${summary}`, requestContextService.createRequestContext({
73
+ operation: 'PubChemClient.fetch',
74
+ additionalContext: { url, method, ...detail },
75
+ }));
76
+ }
66
77
  /** PubChem returns different field names than the request parameter names for some properties.
67
78
  * Request IsomericSMILES → response key "SMILES" (includes stereochemistry).
68
79
  * Request CanonicalSMILES → response key "ConnectivitySMILES" (connectivity only). */
@@ -407,6 +418,7 @@ export class PubChemClient {
407
418
  * one resilience contract — the divergence that left fetchBinary without retry or a clean
408
419
  * timeout message (#16) cannot recur. */
409
420
  async fetchResponse(url, init) {
421
+ const method = init?.method ?? 'GET';
410
422
  for (let attempt = 0;; attempt++) {
411
423
  await this.rateLimiter.acquire();
412
424
  const controller = new AbortController();
@@ -432,10 +444,15 @@ export class PubChemClient {
432
444
  await sleep(1000 * 2 ** attempt);
433
445
  continue;
434
446
  }
447
+ // A 404 is routine — most callers read it as "no data" — so it logs below warning.
448
+ logFailedRequest(response.status === 404 ? 'debug' : 'warning', url, method, {
449
+ status: response.status,
450
+ fault,
451
+ });
435
452
  throw error;
436
453
  }
437
454
  catch (error) {
438
- // HTTP errors are already classified — surface them, don't retry.
455
+ // HTTP errors are already classified and logged — surface them, don't retry.
439
456
  if (error instanceof McpError)
440
457
  throw error;
441
458
  // Retry once on network errors
@@ -443,10 +460,13 @@ export class PubChemClient {
443
460
  await sleep(1000 * 2 ** attempt);
444
461
  continue;
445
462
  }
446
- if (error instanceof Error && error.name === 'AbortError') {
447
- throw new Error('PubChem request timed out (30s)');
448
- }
449
- throw error;
463
+ const failure = error instanceof Error && error.name === 'AbortError'
464
+ ? new Error('PubChem request timed out (30s)')
465
+ : error;
466
+ logFailedRequest('warning', url, method, {
467
+ error: failure instanceof Error ? failure.message : String(failure),
468
+ });
469
+ throw failure;
450
470
  }
451
471
  finally {
452
472
  clearTimeout(timeoutId);
@@ -1098,18 +1118,27 @@ export class PubChemClient {
1098
1118
  return empty;
1099
1119
  throw error;
1100
1120
  }
1121
+ // Both rejections below arrive inside a 2xx, past fetchResponse's failure logging.
1122
+ const reject = (message, data) => {
1123
+ logFailedRequest('warning', url, 'GET', { error: message });
1124
+ throw serviceUnavailable(message, data);
1125
+ };
1101
1126
  let parsed;
1102
1127
  try {
1103
1128
  parsed = JSON.parse(body);
1104
1129
  }
1105
1130
  catch {
1106
- throw serviceUnavailable(`PubChem SDQ returned unparseable JSON for collection "${collection}"`, { collection, cid, snippet: body.slice(0, 200) });
1131
+ return reject(`PubChem SDQ returned unparseable JSON for collection "${collection}"`, {
1132
+ collection,
1133
+ cid,
1134
+ snippet: body.slice(0, 200),
1135
+ });
1107
1136
  }
1108
1137
  const set = parsed.SDQOutputSet?.[0];
1109
1138
  if (!set)
1110
1139
  return empty;
1111
1140
  if (set.status?.error) {
1112
- throw serviceUnavailable(`PubChem SDQ rejected the query for collection "${collection}": ${set.status.error}`, { collection, cid, sdqError: set.status.error });
1141
+ return reject(`PubChem SDQ rejected the query for collection "${collection}": ${set.status.error}`, { collection, cid, sdqError: set.status.error });
1113
1142
  }
1114
1143
  return { rows: set.rows ?? [], totalCount: set.totalCount ?? 0 };
1115
1144
  }
package/dist/services/pubchem/pubchem-client.js.map CHANGED
@@ -1 +1 @@
1
- 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package/manifest.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "manifest_version": "0.3",
3
3
  "name": "pubchem-mcp-server",
4
- "version": "0.6.3",
4
+ "version": "0.6.4",
5
5
  "description": "Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.",
6
6
  "author": {
7
7
  "name": "cyanheads"
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubchem-mcp-server",
3
- "version": "0.6.3",
3
+ "version": "0.6.4",
4
4
  "description": "Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.",
5
5
  "mcpName": "io.github.cyanheads/pubchem-mcp-server",
6
6
  "type": "module",
@@ -90,8 +90,8 @@
90
90
  },
91
91
  "devDependencies": {
92
92
  "@biomejs/biome": "2.5.14",
93
- "@socketsecurity/bun-security-scanner": "^1.1.2",
94
- "@types/node": "26.6.1",
93
+ "@socketsecurity/bun-security-scanner": "^1.1.3",
94
+ "@types/node": "26.6.2",
95
95
  "depcheck": "^1.4.7",
96
96
  "ignore": "^7.0.9",
97
97
  "tsc-alias": "^1.9.5",
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": "0.6.3",
9
+ "version": "0.6.4",
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/pubchem-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "0.6.3",
22
+ "version": "0.6.4",
23
23
  "packageArguments": [
24
24
  { "type": "positional", "value": "run" },
25
25
  { "type": "positional", "value": "start:stdio" }
@@ -42,7 +42,7 @@
42
42
  "registryBaseUrl": "https://registry.npmjs.org",
43
43
  "identifier": "@cyanheads/pubchem-mcp-server",
44
44
  "runtimeHint": "bun",
45
- "version": "0.6.3",
45
+ "version": "0.6.4",
46
46
  "packageArguments": [
47
47
  { "type": "positional", "value": "run" },
48
48
  { "type": "positional", "value": "start:http" }