@cyanheads/pubchem-mcp-server 0.2.0 → 0.2.2

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Files changed (17) hide show
  1. package/README.md +2 -2
  2. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts +1 -0
  3. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +21 -3
  5. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -1
  6. package/dist/mcp-server/tools/definitions/index.d.ts +1 -0
  7. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  8. package/dist/services/pubchem/pubchem-client.d.ts +19 -3
  9. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  10. package/dist/services/pubchem/pubchem-client.js +78 -68
  11. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  12. package/dist/services/pubchem/types.d.ts +11 -0
  13. package/dist/services/pubchem/types.d.ts.map +1 -1
  14. package/dist/services/pubchem/types.js.map +1 -1
  15. package/manifest.json +2 -2
  16. package/package.json +4 -3
  17. package/server.json +4 -4
package/README.md CHANGED
@@ -1,13 +1,13 @@
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  <div align="center">
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  <h1>@cyanheads/pubchem-mcp-server</h1>
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- <p><b>MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.</b>
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+ <p><b>Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.</b>
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  <div>10 Tools • 6 Resources</div>
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  </p>
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  </div>
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.2.0-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-0.2.2-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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package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts CHANGED
@@ -27,6 +27,7 @@ export declare const getCompoundInteractions: import("@cyanheads/mcp-ts-core").T
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  }, z.core.$strip>, undefined, {
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  readonly requestedKinds: z.ZodString;
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  readonly returnedCount: z.ZodNumber;
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+ readonly failedKinds: z.ZodOptional<z.ZodString>;
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  readonly notice: z.ZodOptional<z.ZodString>;
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  }>;
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  //# sourceMappingURL=get-compound-interactions.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;EAmIlC,CAAC"}
package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js CHANGED
@@ -51,11 +51,15 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
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  .describe('A single interaction entry.'))
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  .describe('Interaction entries across the requested kinds.'),
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  }),
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- // Agent-facing context — kind echo, total returned, and an empty-result notice.
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+ // Agent-facing context — kind echo, total returned, failed kinds, and an empty-result notice.
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  // Reaches structuredContent and content[]; keys disjoint from output (cid/entries).
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  enrichment: {
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  requestedKinds: z.string().describe('Interaction kinds requested (comma-separated).'),
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  returnedCount: z.number().describe('Total interaction entries returned across all kinds.'),
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+ failedKinds: z
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+ .string()
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+ .optional()
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+ .describe('Interaction kinds that could not be retrieved (comma-separated). The returned entries cover the kinds that succeeded; retry to re-attempt the failed ones.'),
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  notice: z
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  .string()
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  .optional()
@@ -63,14 +67,28 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
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  },
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  async handler(input, ctx) {
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  const client = getPubChemClient();
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- const entries = await client.getInteractions(input.cid, input.kinds, input.maxEntries);
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+ const { entries, failedKinds } = await client.getInteractions(input.cid, input.kinds, input.maxEntries);
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+ for (const f of failedKinds) {
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+ ctx.log.warning('Interaction kind failed', {
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+ cid: input.cid,
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+ kind: f.kind,
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+ error: f.message,
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+ });
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+ }
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  ctx.log.info('Interactions fetched', {
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  cid: input.cid,
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  kinds: input.kinds,
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  returned: entries.length,
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+ failed: failedKinds.length,
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  });
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  ctx.enrich({ requestedKinds: input.kinds.join(', '), returnedCount: entries.length });
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- if (entries.length === 0) {
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+ if (failedKinds.length > 0) {
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+ const names = failedKinds.map((f) => f.kind).join(', ');
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+ const plural = failedKinds.length > 1;
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+ ctx.enrich({ failedKinds: names });
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+ ctx.enrich.notice(`Could not retrieve ${names} interaction${plural ? 's' : ''} for CID ${input.cid}.${entries.length > 0 ? ' Returned the kinds that succeeded.' : ''} Retry to re-attempt ${plural ? 'them' : 'it'}.`);
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+ }
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+ else if (entries.length === 0) {
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  ctx.enrich.notice(`No ${input.kinds.join('/')} interaction data found for CID ${input.cid}. PubChem has no deposited interaction records for this compound — coverage is richest for approved drugs.`);
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  }
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  return { cid: input.cid, entries };
package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map CHANGED
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1
+ {"version":3,"file":"get-compound-interactions.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,uBAAuB,GAAG,IAAI,CAAC,mCAAmC,EAAE;IAC/E,KAAK,EAAE,2BAA2B;IAClC,WAAW,EACT,oTAAoT;IACtT,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,KAAK,EAAE,CAAC;aACL,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC;aACnD,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,WAAW,CAAC,CAAC;aACtB,QAAQ,CACP,6LAA6L,CAC9L;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,gGAAgG,CACjG;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACpF,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oDAAoD,CAAC;YACjF,QAAQ,EAAE,CAAC;iBACR,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,kJAAkJ,CACnJ;YACH,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;SACxD,CAAC;aACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;aACA,QAAQ,CAAC,iDAAiD,CAAC;KAC/D,CAAC;IACF,8FAA8F;IAC9F,oFAAoF;IACpF,UAAU,EAAE;QACV,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;QAC1F,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,4JAA4J,CAC7J;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,sEAAsE,CAAC;KACpF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAC3D,KAAK,CAAC,GAAG,EACT,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,UAAU,CACjB,CAAC;QAEF,KAAK,MAAM,CAAC,IAAI,WAAW,EAAE,CAAC;YAC5B,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,yBAAyB,EAAE;gBACzC,GAAG,EAAE,KAAK,CAAC,GAAG;gBACd,IAAI,EAAE,CAAC,CAAC,IAAI;gBACZ,KAAK,EAAE,CAAC,CAAC,OAAO;aACjB,CAAC,CAAC;QACL,CAAC;QACD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,sBAAsB,EAAE;YACnC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,QAAQ,EAAE,OAAO,CAAC,MAAM;YACxB,MAAM,EAAE,WAAW,CAAC,MAAM;SAC3B,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,aAAa,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;QAEtF,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACxD,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACtC,GAAG,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,KAAK,EAAE,CAAC,CAAC;YACnC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,sBAAsB,KAAK,eAAe,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,YAAY,KAAK,CAAC,GAAG,IAC9E,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,qCAAqC,CAAC,CAAC,CAAC,EAC/D,wBAAwB,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,GAAG,CAClD,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,MAAM,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,mCAAmC,KAAK,CAAC,GAAG,4GAA4G,CACpL,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,CAAC;IACrC,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,CAAC,yBAAyB,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QAEpE,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,4BAA4B,CAAC,CAAC;YACzC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,MAAM,OAAO,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;YACrD,MAAM,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAChE,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,IAAI,OAAO,GAAG,QAAQ,IAAI,CAAC,CAAC,IAAI,cAAc,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC;QACrF,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"}
package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -176,6 +176,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
176
176
  }, import("zod/v4/core").$strip>, undefined, {
177
177
  readonly requestedKinds: import("zod").ZodString;
178
178
  readonly returnedCount: import("zod").ZodNumber;
179
+ readonly failedKinds: import("zod").ZodOptional<import("zod").ZodString>;
179
180
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
180
181
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
181
182
  cids: import("zod").ZodArray<import("zod").ZodNumber>;
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;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
package/dist/services/pubchem/pubchem-client.d.ts CHANGED
@@ -3,12 +3,18 @@
3
3
  * Wraps both PUG REST and PUG View APIs behind a shared rate limiter.
4
4
  * @module services/pubchem/pubchem-client
5
5
  */
6
- import type { BioactivityRow, CompoundClassification, GHSClassification, InteractionEntry } from './types.js';
6
+ import type { BioactivityRow, CompoundClassification, GHSClassification, InteractionsResult } from './types.js';
7
7
  export declare class PubChemClient {
8
8
  private readonly pugBase;
9
9
  private readonly viewBase;
10
10
  private readonly sdqBase;
11
11
  private readonly rateLimiter;
12
+ /** Shared HTTP core: rate-limit, 30s timeout, retry once on 5xx and once on a transient
13
+ * network error, and surface a clean timeout message. Returns the ok Response; callers
14
+ * extract the body (JSON, bytes, or text). Centralizing this keeps every fetch variant on
15
+ * one resilience contract — the divergence that left fetchBinary without retry or a clean
16
+ * timeout message (#16) cannot recur. */
17
+ private fetchResponse;
12
18
  private fetchJson;
13
19
  private fetchBinary;
14
20
  /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
@@ -42,12 +48,22 @@ export declare class PubChemClient {
42
48
  * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi,
43
49
  * consolidatedcompoundtarget); drug-food is inline PUG View text. Each kind is capped
44
50
  * at maxEntries; absent data for a kind contributes nothing rather than erroring. */
45
- getInteractions(cid: number, kinds: Array<'drug-drug' | 'drug-food' | 'target'>, maxEntries: number): Promise<InteractionEntry[]>;
51
+ getInteractions(cid: number, kinds: Array<'drug-drug' | 'drug-food' | 'target'>, maxEntries: number): Promise<InteractionsResult>;
46
52
  private getInteractionsForKind;
47
53
  private getDrugDrugInteractions;
54
+ /** Chemical-target binding/activity from PubChem's `bioactivity` SDQ collection (BindingDB,
55
+ * ChEMBL, and others). That collection is cid-keyed and scopes correctly to the requested
56
+ * compound; the `consolidatedcompoundtarget` collection used previously is gene-indexed, so
57
+ * its `cid` filter was silently ignored — every CID returned the same default compound (#20).
58
+ * Only rows naming a molecular target are returned; untargeted assay outcomes are the domain
59
+ * of pubchem_get_bioactivity. */
48
60
  private getTargetInteractions;
49
61
  private getDrugFoodInteractions;
50
- /** Query a PubChem SDQ external table for a single CID. Returns [] on not-found. */
62
+ /** Query a PubChem SDQ external table for a single CID, projecting only the columns the
63
+ * caller maps. Projection keeps payloads small and excludes the free-text `citations` column
64
+ * whose unescaped quotes make PubChem emit invalid JSON (#20). Returns [] on not-found; on an
65
+ * unparseable body throws a contextful error rather than the bare `Failed to parse JSON`, so
66
+ * the caller and per-kind isolation can report it cleanly. */
51
67
  private fetchSdq;
52
68
  /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when
53
69
  * PubChem has no computed 3D coordinates (large molecules, mixtures, undefined salts). */
package/dist/services/pubchem/pubchem-client.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/services/pubchem/pubchem-client.js CHANGED
@@ -197,16 +197,20 @@ export class PubChemClient {
197
197
  sdqBase = 'https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi';
198
198
  rateLimiter = new RateLimiter(5);
199
199
  // ── Core HTTP ────────────────────────────────────────────────────
200
- async fetchJson(url, init) {
200
+ /** Shared HTTP core: rate-limit, 30s timeout, retry once on 5xx and once on a transient
201
+ * network error, and surface a clean timeout message. Returns the ok Response; callers
202
+ * extract the body (JSON, bytes, or text). Centralizing this keeps every fetch variant on
203
+ * one resilience contract — the divergence that left fetchBinary without retry or a clean
204
+ * timeout message (#16) cannot recur. */
205
+ async fetchResponse(url, init) {
201
206
  for (let attempt = 0;; attempt++) {
202
207
  await this.rateLimiter.acquire();
203
208
  const controller = new AbortController();
204
209
  const timeoutId = setTimeout(() => controller.abort(), 30_000);
205
210
  try {
206
211
  const response = await fetch(url, { ...init, signal: controller.signal });
207
- if (response.ok) {
208
- return (await response.json());
209
- }
212
+ if (response.ok)
213
+ return response;
210
214
  const text = await response.text();
211
215
  const fault = parseFaultMessage(text) ?? text.slice(0, 300);
212
216
  // Retry once on 5xx
@@ -239,48 +243,18 @@ export class PubChemClient {
239
243
  }
240
244
  }
241
245
  }
246
+ async fetchJson(url, init) {
247
+ const response = await this.fetchResponse(url, init);
248
+ return (await response.json());
249
+ }
242
250
  async fetchBinary(url) {
243
- await this.rateLimiter.acquire();
244
- const controller = new AbortController();
245
- const timeoutId = setTimeout(() => controller.abort(), 30_000);
246
- try {
247
- const response = await fetch(url, { signal: controller.signal });
248
- if (!response.ok) {
249
- const text = await response.text();
250
- const fault = parseFaultMessage(text) ?? text.slice(0, 300);
251
- throw await httpErrorFromResponse(response, {
252
- captureBody: false,
253
- service: 'PubChem',
254
- data: { fault, url },
255
- });
256
- }
257
- return await response.arrayBuffer();
258
- }
259
- finally {
260
- clearTimeout(timeoutId);
261
- }
251
+ const response = await this.fetchResponse(url);
252
+ return response.arrayBuffer();
262
253
  }
263
254
  /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
264
255
  async fetchText(url) {
265
- await this.rateLimiter.acquire();
266
- const controller = new AbortController();
267
- const timeoutId = setTimeout(() => controller.abort(), 30_000);
268
- try {
269
- const response = await fetch(url, { signal: controller.signal });
270
- if (!response.ok) {
271
- const text = await response.text();
272
- const fault = parseFaultMessage(text) ?? text.slice(0, 300);
273
- throw await httpErrorFromResponse(response, {
274
- captureBody: false,
275
- service: 'PubChem',
276
- data: { fault, url },
277
- });
278
- }
279
- return await response.text();
280
- }
281
- finally {
282
- clearTimeout(timeoutId);
283
- }
256
+ const response = await this.fetchResponse(url);
257
+ return response.text();
284
258
  }
285
259
  // ── CID Resolution ──────────────────────────────────────────────
286
260
  /** Fetch CID list, with automatic ListKey polling for async searches */
@@ -701,8 +675,25 @@ export class PubChemClient {
701
675
  * consolidatedcompoundtarget); drug-food is inline PUG View text. Each kind is capped
702
676
  * at maxEntries; absent data for a kind contributes nothing rather than erroring. */
703
677
  async getInteractions(cid, kinds, maxEntries) {
704
- const batches = await Promise.all(kinds.map((kind) => this.getInteractionsForKind(cid, kind, maxEntries)));
705
- return batches.flat();
678
+ // Per-kind isolation: a failure in one source (upstream parse error, timeout, network)
679
+ // must not discard the kinds that succeeded. Failures are reported, not thrown (#21).
680
+ const settled = await Promise.allSettled(kinds.map((kind) => this.getInteractionsForKind(cid, kind, maxEntries)));
681
+ const entries = [];
682
+ const failedKinds = [];
683
+ kinds.forEach((kind, i) => {
684
+ const result = settled[i];
685
+ if (result?.status === 'fulfilled') {
686
+ entries.push(...result.value);
687
+ }
688
+ else if (result?.status === 'rejected') {
689
+ const reason = result.reason;
690
+ failedKinds.push({
691
+ kind,
692
+ message: reason instanceof Error ? reason.message : String(reason),
693
+ });
694
+ }
695
+ });
696
+ return { entries, failedKinds };
706
697
  }
707
698
  getInteractionsForKind(cid, kind, maxEntries) {
708
699
  switch (kind) {
@@ -715,7 +706,7 @@ export class PubChemClient {
715
706
  }
716
707
  }
717
708
  async getDrugDrugInteractions(cid, maxEntries) {
718
- const rows = await this.fetchSdq('drugbankddi', cid, maxEntries);
709
+ const rows = await this.fetchSdq('drugbankddi', cid, ['cid', 'name2', 'descr'], maxEntries);
719
710
  const entries = [];
720
711
  for (const row of rows) {
721
712
  const text = typeof row.descr === 'string' ? row.descr : '';
@@ -728,30 +719,37 @@ export class PubChemClient {
728
719
  }
729
720
  return entries;
730
721
  }
722
+ /** Chemical-target binding/activity from PubChem's `bioactivity` SDQ collection (BindingDB,
723
+ * ChEMBL, and others). That collection is cid-keyed and scopes correctly to the requested
724
+ * compound; the `consolidatedcompoundtarget` collection used previously is gene-indexed, so
725
+ * its `cid` filter was silently ignored — every CID returned the same default compound (#20).
726
+ * Only rows naming a molecular target are returned; untargeted assay outcomes are the domain
727
+ * of pubchem_get_bioactivity. */
731
728
  async getTargetInteractions(cid, maxEntries) {
732
- const rows = await this.fetchSdq('consolidatedcompoundtarget', cid, maxEntries);
729
+ // `targetname` is sparse (most rows are untargeted assay outcomes), so oversample and keep
730
+ // the target-bearing rows, most-potent-first.
731
+ const window = Math.min(Math.max(maxEntries * 4, 20), 100);
732
+ const rows = await this.fetchSdq('bioactivity', cid, ['cid', 'targetname', 'acname', 'acqualifier', 'acvalue', 'aidsrcname'], window, ['acvalue,asc']);
733
733
  const entries = [];
734
734
  for (const row of rows) {
735
- const target = (typeof row.protname === 'string' && row.protname) ||
736
- (typeof row.srctargetname === 'string' && row.srctargetname) ||
737
- (typeof row.genename === 'string' && row.genename) ||
738
- '';
739
- const activity = [row.actname, row.actvalue]
740
- .filter((v) => typeof v === 'string' && v.length > 0)
741
- .join(': ');
742
- const text = [target, activity].filter(Boolean).join(' — ');
743
- if (!text)
735
+ const target = typeof row.targetname === 'string' ? row.targetname.trim() : '';
736
+ if (!target)
744
737
  continue;
745
- const entry = {
738
+ const acname = typeof row.acname === 'string' ? row.acname : '';
739
+ const qualifier = typeof row.acqualifier === 'string' ? row.acqualifier : '';
740
+ const acvalue = row.acvalue == null ? '' : String(row.acvalue).trim();
741
+ // Faithful to the source: the bioactivity collection carries no unit column, so the raw
742
+ // activity value is surfaced without an asserted unit.
743
+ const activity = acname && acvalue ? `${acname} ${qualifier} ${acvalue}`.replace(/\s+/g, ' ').trim() : '';
744
+ entries.push({
746
745
  kind: 'target',
747
- source: typeof row.dsn === 'string' && row.dsn ? row.dsn : 'PubChem',
748
- text,
749
- };
750
- if (target)
751
- entry.partner = target;
752
- entries.push(entry);
746
+ source: typeof row.aidsrcname === 'string' && row.aidsrcname ? row.aidsrcname : 'PubChem',
747
+ partner: target,
748
+ text: activity || 'Activity reported',
749
+ });
753
750
  }
754
- return entries;
751
+ // Collapse duplicate measurements of the same target/value reported across assays.
752
+ return dedupByKey(entries, (e) => `${e.partner ?? ''}|${e.text}`).slice(0, maxEntries);
755
753
  }
756
754
  async getDrugFoodInteractions(cid, maxEntries) {
757
755
  try {
@@ -778,25 +776,37 @@ export class PubChemClient {
778
776
  throw error;
779
777
  }
780
778
  }
781
- /** Query a PubChem SDQ external table for a single CID. Returns [] on not-found. */
782
- async fetchSdq(collection, cid, limit) {
779
+ /** Query a PubChem SDQ external table for a single CID, projecting only the columns the
780
+ * caller maps. Projection keeps payloads small and excludes the free-text `citations` column
781
+ * whose unescaped quotes make PubChem emit invalid JSON (#20). Returns [] on not-found; on an
782
+ * unparseable body throws a contextful error rather than the bare `Failed to parse JSON`, so
783
+ * the caller and per-kind isolation can report it cleanly. */
784
+ async fetchSdq(collection, cid, columns, limit, order) {
783
785
  const query = JSON.stringify({
784
- download: '*',
786
+ download: columns,
785
787
  collection,
786
788
  where: { ands: [{ cid: String(cid) }] },
789
+ ...(order ? { order } : {}),
787
790
  start: 1,
788
791
  limit,
789
792
  });
790
793
  const url = `${this.sdqBase}?infmt=json&outfmt=json&query=${encodeURIComponent(query)}`;
794
+ let body;
791
795
  try {
792
- const data = await this.fetchJson(url);
793
- return Array.isArray(data) ? data : [];
796
+ body = await this.fetchText(url);
794
797
  }
795
798
  catch (error) {
796
799
  if (isNotFound(error))
797
800
  return [];
798
801
  throw error;
799
802
  }
803
+ try {
804
+ const data = JSON.parse(body);
805
+ return Array.isArray(data) ? data : [];
806
+ }
807
+ catch {
808
+ throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `PubChem SDQ returned unparseable JSON for collection "${collection}"`, { collection, cid, snippet: body.slice(0, 200) });
809
+ }
800
810
  }
801
811
  // ── 3D Structure ────────────────────────────────────────────────
802
812
  /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when
package/dist/services/pubchem/pubchem-client.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/pubchem/types.d.ts CHANGED
@@ -144,6 +144,17 @@ export interface InteractionEntry {
144
144
  /** The interaction statement. */
145
145
  text: string;
146
146
  }
147
+ /** Result of a multi-kind interaction fetch. Kinds are fetched independently so a failure in
148
+ * one (upstream parse error, timeout, network) never discards the kinds that succeeded. */
149
+ export interface InteractionsResult {
150
+ /** Interaction entries across the kinds that resolved successfully. */
151
+ entries: InteractionEntry[];
152
+ /** Kinds whose fetch failed, with the failure message. Empty when every kind resolved. */
153
+ failedKinds: Array<{
154
+ kind: string;
155
+ message: string;
156
+ }>;
157
+ }
147
158
  /** A single atom in a 3D conformer (Cartesian coordinates, Angstroms). */
148
159
  export interface Sdf3DAtom {
149
160
  element: string;
package/dist/services/pubchem/types.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/pubchem/types.js.map CHANGED
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package/manifest.json CHANGED
@@ -1,8 +1,8 @@
1
1
  {
2
2
  "manifest_version": "0.3",
3
3
  "name": "pubchem-mcp-server",
4
- "version": "0.2.0",
5
- "description": "Search PubChem compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP.",
4
+ "version": "0.2.2",
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"
8
8
  },
package/package.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "name": "@cyanheads/pubchem-mcp-server",
3
- "version": "0.2.0",
4
- "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.",
3
+ "version": "0.2.2",
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",
7
7
  "main": "dist/index.js",
@@ -26,6 +26,7 @@
26
26
  "changelog:build": "bun scripts/build-changelog.ts",
27
27
  "changelog:check": "bun scripts/build-changelog.ts --check",
28
28
  "publish-mcp": "mcp-publisher publish",
29
+ "release:github": "bun scripts/release-github.ts",
29
30
  "test": "vitest run",
30
31
  "start:stdio": "node dist/index.js",
31
32
  "start:http": "MCP_TRANSPORT_TYPE=http node dist/index.js"
@@ -72,7 +73,7 @@
72
73
  "access": "public"
73
74
  },
74
75
  "dependencies": {
75
- "@cyanheads/mcp-ts-core": "^0.9.16",
76
+ "@cyanheads/mcp-ts-core": "^0.9.21",
76
77
  "pino-pretty": "^13.1.3",
77
78
  "zod": "^4.4.3"
78
79
  },
package/server.json CHANGED
@@ -1,12 +1,12 @@
1
1
  {
2
2
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
3
3
  "name": "io.github.cyanheads/pubchem-mcp-server",
4
- "description": "MCP server for PubChem. Search compounds, properties, safety, bioactivity, xrefs, and summaries.",
4
+ "description": "Search PubChem compounds, properties, safety data, bioactivity, and cross-references.",
5
5
  "repository": {
6
6
  "url": "https://github.com/cyanheads/pubchem-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.2.0",
9
+ "version": "0.2.2",
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": "0.2.0",
22
+ "version": "0.2.2",
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": "0.2.0",
45
+ "version": "0.2.2",
46
46
  "packageArguments": [
47
47
  { "type": "positional", "value": "run" },
48
48
  { "type": "positional", "value": "start:http" }