@cyanheads/pubchem-mcp-server 0.3.0 → 0.3.1

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 (18) hide show
  1. package/README.md +1 -1
  2. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts +3 -1
  3. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js +14 -0
  5. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map +1 -1
  6. package/dist/mcp-server/tools/definitions/index.d.ts +20 -2
  7. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts +12 -1
  9. package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/search-assays.tool.js +31 -4
  11. package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +6 -0
  13. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
  14. package/dist/mcp-server/tools/definitions/search-compounds.tool.js +94 -22
  15. package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
  16. package/manifest.json +1 -1
  17. package/package.json +3 -3
  18. package/server.json +3 -3
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.3.0-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-0.3.1-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-xrefs.tool.d.ts CHANGED
@@ -17,5 +17,7 @@ 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, undefined>;
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+ }, z.core.$strip>, undefined, {
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+ readonly notice: z.ZodOptional<z.ZodString>;
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+ }>;
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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 @@
1
- {"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"}
1
+ {"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;;;;;;;;;;;;;;;;EAsI3B,CAAC"}
package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js CHANGED
@@ -55,6 +55,15 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
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  .describe('Cross-reference group for one type.'))
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  .describe('Cross-references grouped by type.'),
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  }),
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+ // Agent-facing context — an empty-result notice distinguishing a nonexistent CID from a
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+ // real compound that simply has none of the requested xref types. Reaches structuredContent
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+ // and content[]; keys disjoint from output (cid/xrefs live there).
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+ enrichment: {
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+ notice: z
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+ .string()
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+ .optional()
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+ .describe('Recovery guidance when every requested xref type returned zero IDs — hints to verify the CID. Absent when any cross-references were found.'),
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+ },
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  async handler(input, ctx) {
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  const client = getPubChemClient();
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  // Sequential per type to avoid rate limit spikes
@@ -75,6 +84,11 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
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  types: input.xrefTypes,
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  totalIds: xrefs.reduce((sum, x) => sum + x.ids.length, 0),
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  });
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+ // Empty-result signal (#30): every requested type came back empty — either the CID
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+ // doesn't exist or it genuinely has none of these xref types. Point at CID verification.
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+ if (xrefs.every((x) => x.totalAvailable === 0)) {
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+ ctx.enrich.notice(`No cross-references found for CID ${input.cid} across the requested type(s): ${input.xrefTypes.join(', ')}. The compound may have none of these xref types, or verify the CID with pubchem_search_compounds.`);
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+ }
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  return { cid: input.cid, xrefs };
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  },
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  format(result) {
package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"get-compound-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,UAA8C,CAAC,CAAC;AAE5E,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,6MAA6M;IAC/M,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,SAAS,EAAE,CAAC;aACT,KAAK,CAAC,YAAY,CAAC;aACnB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iNAAiN,CAClN;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,wIAAwI,CACzI;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC;iBACJ,MAAM,EAAE;iBACR,QAAQ,CACP,6FAA6F,CAC9F;YACH,GAAG,EAAE,CAAC;iBACH,KAAK,CACJ,CAAC;iBACE,KAAK,CAAC;gBACL,CAAC;qBACE,MAAM,EAAE;qBACR,QAAQ,CAAC,2DAA2D,CAAC;gBACxE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uDAAuD,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,kEAAkE,CAAC,CAChF;iBACA,QAAQ,CAAC,6CAA6C,CAAC;YAC1D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;YAC7E,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;SACnE,CAAC;aACD,QAAQ,CAAC,qCAAqC,CAAC,CACnD;aACA,QAAQ,CAAC,mCAAmC,CAAC;KACjD,CAAC;IACF,wFAAwF;IACxF,4FAA4F;IAC5F,mEAAmE;IACnE,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,4IAA4I,CAC7I;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,iDAAiD;QACjD,MAAM,KAAK,GAKN,EAAE,CAAC;QAER,KAAK,MAAM,QAAQ,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YACvC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;YAC1D,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC;YACrC,MAAM,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;YAE9C,KAAK,CAAC,IAAI,CAAC;gBACT,IAAI,EAAE,QAAQ;gBACd,GAAG;gBACH,cAAc;gBACd,SAAS,EAAE,cAAc,GAAG,KAAK,CAAC,UAAU;aAC7C,CAAC,CAAC;QACL,CAAC;QAED,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE;YAC5B,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,SAAS;YACtB,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;SAC1D,CAAC,CAAC;QAEH,mFAAmF;QACnF,yFAAyF;QACzF,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,KAAK,CAAC,CAAC,EAAE,CAAC;YAC/C,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,qCAAqC,KAAK,CAAC,GAAG,kCAAkC,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,oGAAoG,CAC/M,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACnC,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QAEvE,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAChC,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS;gBAC9B,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,OAAO,IAAI,CAAC,cAAc,oBAAoB;gBAClE,CAAC,CAAC,GAAG,IAAI,CAAC,cAAc,QAAQ,CAAC;YACnC,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,IAAI,OAAO,SAAS,GAAG,CAAC,CAAC;YAE9C,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxB,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACtC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,WAAW,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;gBACjF,KAAK,CAAC,IAAI,CAAC,KAAK,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAC/C,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YAC7B,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,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
@@ -221,7 +221,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
221
221
  totalAvailable: import("zod").ZodNumber;
222
222
  truncated: import("zod").ZodBoolean;
223
223
  }, import("zod/v4/core").$strip>>;
224
- }, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
224
+ }, import("zod/v4/core").$strip>, undefined, {
225
+ readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
226
+ }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
225
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  entityType: import("zod").ZodEnum<{
226
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  assay: "assay";
227
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  gene: "gene";
@@ -268,7 +270,17 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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  maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
269
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  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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  aids: import("zod").ZodArray<import("zod").ZodNumber>;
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- }, import("zod/v4/core").$strip>, undefined, {
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+ }, import("zod/v4/core").$strip>, readonly [{
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+ readonly reason: "blank_target_query";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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+ readonly when: "targetQuery is empty or whitespace-only";
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+ readonly recovery: "Provide a non-empty target identifier, e.g. \"EGFR\" for genesymbol or \"1956\" for geneid.";
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+ }, {
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+ readonly reason: "invalid_geneid_query";
280
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
281
+ readonly when: "targetType is \"geneid\" but targetQuery is not a positive integer";
282
+ readonly recovery: "Pass a numeric NCBI Gene ID (e.g. \"1956\"), or switch targetType to genesymbol/proteinname for text queries.";
283
+ }], {
272
284
  readonly targetType: import("zod").ZodString;
273
285
  readonly targetQuery: import("zod").ZodString;
274
286
  readonly totalFound: import("zod").ZodNumber;
@@ -308,6 +320,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
308
320
  identifier: import("zod").ZodOptional<import("zod").ZodString>;
309
321
  properties: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
310
322
  }, import("zod/v4/core").$strip>>;
323
+ unresolvedIdentifiers: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
311
324
  }, import("zod/v4/core").$strip>, readonly [{
312
325
  readonly reason: "missing_identifier_args";
313
326
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
@@ -323,6 +336,11 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
323
336
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
324
337
  readonly when: "substructure/superstructure/similarity search missing query or queryType";
325
338
  readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
339
+ }, {
340
+ readonly reason: "invalid_cid_query";
341
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
342
+ readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
343
+ readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
326
344
  }], {
327
345
  readonly searchType: import("zod").ZodString;
328
346
  readonly totalFound: 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/mcp-server/tools/definitions/search-assays.tool.d.ts CHANGED
@@ -4,6 +4,7 @@
4
4
  * @module mcp-server/tools/definitions/search-assays
5
5
  */
6
6
  import { z } from '@cyanheads/mcp-ts-core';
7
+ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
7
8
  export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
8
9
  targetType: z.ZodEnum<{
9
10
  proteinaccession: "proteinaccession";
@@ -15,7 +16,17 @@ export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefiniti
15
16
  maxResults: z.ZodDefault<z.ZodNumber>;
16
17
  }, z.core.$strip>, z.ZodObject<{
17
18
  aids: z.ZodArray<z.ZodNumber>;
18
- }, z.core.$strip>, undefined, {
19
+ }, z.core.$strip>, readonly [{
20
+ readonly reason: "blank_target_query";
21
+ readonly code: JsonRpcErrorCode.ValidationError;
22
+ readonly when: "targetQuery is empty or whitespace-only";
23
+ readonly recovery: "Provide a non-empty target identifier, e.g. \"EGFR\" for genesymbol or \"1956\" for geneid.";
24
+ }, {
25
+ readonly reason: "invalid_geneid_query";
26
+ readonly code: JsonRpcErrorCode.ValidationError;
27
+ readonly when: "targetType is \"geneid\" but targetQuery is not a positive integer";
28
+ readonly recovery: "Pass a numeric NCBI Gene ID (e.g. \"1956\"), or switch targetType to genesymbol/proteinname for text queries.";
29
+ }], {
19
30
  readonly targetType: z.ZodString;
20
31
  readonly targetQuery: z.ZodString;
21
32
  readonly totalFound: z.ZodNumber;
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;;;;;;;;;;;;;;;;;;;EAyFvB,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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2HvB,CAAC"}
package/dist/mcp-server/tools/definitions/search-assays.tool.js CHANGED
@@ -4,6 +4,7 @@
4
4
  * @module mcp-server/tools/definitions/search-assays
5
5
  */
6
6
  import { tool, z } from '@cyanheads/mcp-ts-core';
7
+ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
7
8
  import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
8
9
  export const searchAssays = tool('pubchem_search_assays', {
9
10
  title: 'Search Assays',
@@ -49,21 +50,47 @@ export const searchAssays = tool('pubchem_search_assays', {
49
50
  .optional()
50
51
  .describe('Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.'),
51
52
  },
53
+ errors: [
54
+ {
55
+ reason: 'blank_target_query',
56
+ code: JsonRpcErrorCode.ValidationError,
57
+ when: 'targetQuery is empty or whitespace-only',
58
+ recovery: 'Provide a non-empty target identifier, e.g. "EGFR" for genesymbol or "1956" for geneid.',
59
+ },
60
+ {
61
+ reason: 'invalid_geneid_query',
62
+ code: JsonRpcErrorCode.ValidationError,
63
+ when: 'targetType is "geneid" but targetQuery is not a positive integer',
64
+ recovery: 'Pass a numeric NCBI Gene ID (e.g. "1956"), or switch targetType to genesymbol/proteinname for text queries.',
65
+ },
66
+ ],
52
67
  async handler(input, ctx) {
53
68
  const client = getPubChemClient();
54
- const allAids = await client.searchAssaysByTarget(input.targetType, input.targetQuery);
69
+ // Reject inputs that cannot represent a useful target before the upstream call (#26).
70
+ const targetQuery = input.targetQuery.trim();
71
+ if (targetQuery.length === 0) {
72
+ throw ctx.fail('blank_target_query', undefined, {
73
+ ...ctx.recoveryFor('blank_target_query'),
74
+ });
75
+ }
76
+ // geneid targets are numeric NCBI Gene IDs — a non-numeric value otherwise hits a raw
77
+ // PubChem 400 (searchAssaysByTarget only special-cases 404).
78
+ if (input.targetType === 'geneid' && !/^\d+$/.test(targetQuery)) {
79
+ throw ctx.fail('invalid_geneid_query', `targetType is "geneid" but targetQuery "${input.targetQuery}" is not a positive integer Gene ID.`, { ...ctx.recoveryFor('invalid_geneid_query') });
80
+ }
81
+ const allAids = await client.searchAssaysByTarget(input.targetType, targetQuery);
55
82
  const totalFound = allAids.length;
56
83
  const aids = allAids.slice(0, input.maxResults);
57
84
  ctx.log.info('Assay search completed', {
58
85
  targetType: input.targetType,
59
- targetQuery: input.targetQuery,
86
+ targetQuery,
60
87
  totalFound,
61
88
  returned: aids.length,
62
89
  });
63
90
  // Agent-facing context: target echo, total, and empty-result notice.
64
- ctx.enrich({ targetType: input.targetType, targetQuery: input.targetQuery, totalFound });
91
+ ctx.enrich({ targetType: input.targetType, targetQuery, totalFound });
65
92
  if (aids.length === 0) {
66
- 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.`);
93
+ ctx.enrich.notice(`No assays found for "${targetQuery}" (${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.`);
67
94
  }
68
95
  else if (totalFound > aids.length) {
69
96
  ctx.enrich.truncated({ shown: aids.length, cap: input.maxResults });
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,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,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;QAC1F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QAChF,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,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;aAAM,IAAI,UAAU,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC;YACpC,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC;QACtE,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"}
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,+BAA+B,CAAC;AACjE,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,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;QAC1F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QAChF,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,uIAAuI,CACxI;KACJ;IACD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,oBAAoB;YAC5B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,yCAAyC;YAC/C,QAAQ,EACN,yFAAyF;SAC5F;QACD;YACE,MAAM,EAAE,sBAAsB;YAC9B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,kEAAkE;YACxE,QAAQ,EACN,6GAA6G;SAChH;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,sFAAsF;QACtF,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,EAAE,CAAC;QAC7C,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,oBAAoB,EAAE,SAAS,EAAE;gBAC9C,GAAG,GAAG,CAAC,WAAW,CAAC,oBAAoB,CAAC;aACzC,CAAC,CAAC;QACL,CAAC;QACD,sFAAsF;QACtF,6DAA6D;QAC7D,IAAI,KAAK,CAAC,UAAU,KAAK,QAAQ,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC;YAChE,MAAM,GAAG,CAAC,IAAI,CACZ,sBAAsB,EACtB,2CAA2C,KAAK,CAAC,WAAW,sCAAsC,EAClG,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,sBAAsB,CAAC,EAAE,CAC/C,CAAC;QACJ,CAAC;QAED,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,KAAK,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC;QAEjF,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;YACX,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,UAAU,EAAE,CAAC,CAAC;QACtE,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACtB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,WAAW,MAAM,KAAK,CAAC,UAAU,yKAAyK,CACnO,CAAC;QACJ,CAAC;aAAM,IAAI,UAAU,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC;YACpC,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC;QACtE,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
@@ -37,6 +37,7 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
37
37
  identifier: z.ZodOptional<z.ZodString>;
38
38
  properties: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
39
39
  }, z.core.$strip>>;
40
+ unresolvedIdentifiers: z.ZodOptional<z.ZodArray<z.ZodString>>;
40
41
  }, z.core.$strip>, readonly [{
41
42
  readonly reason: "missing_identifier_args";
42
43
  readonly code: JsonRpcErrorCode.ValidationError;
@@ -52,6 +53,11 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
52
53
  readonly code: JsonRpcErrorCode.ValidationError;
53
54
  readonly when: "substructure/superstructure/similarity search missing query or queryType";
54
55
  readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
56
+ }, {
57
+ readonly reason: "invalid_cid_query";
58
+ readonly code: JsonRpcErrorCode.ValidationError;
59
+ readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
60
+ readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
55
61
  }], {
56
62
  readonly searchType: z.ZodString;
57
63
  readonly totalFound: z.ZodNumber;
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqR1B,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW1B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED
@@ -87,6 +87,10 @@ export const searchCompounds = tool('pubchem_search_compounds', {
87
87
  })
88
88
  .describe('Matching compound entry.'))
89
89
  .describe('Matching compounds.'),
90
+ unresolvedIdentifiers: z
91
+ .array(z.string())
92
+ .optional()
93
+ .describe('Identifier-mode only: input identifiers that resolved to no CID. Omitted when every identifier resolved and for non-identifier searches.'),
90
94
  }),
91
95
  // Agent-facing context — search strategy echo, total before cap, and an empty-result
92
96
  // notice. Reaches structuredContent and content[] automatically; not in the domain return.
@@ -125,11 +129,21 @@ export const searchCompounds = tool('pubchem_search_compounds', {
125
129
  when: 'substructure/superstructure/similarity search missing query or queryType',
126
130
  recovery: 'Provide both query (SMILES string or CID as string) and queryType ("smiles" or "cid").',
127
131
  },
132
+ {
133
+ reason: 'invalid_cid_query',
134
+ code: JsonRpcErrorCode.ValidationError,
135
+ when: 'structure/similarity search with queryType "cid" but query is not a positive integer CID',
136
+ recovery: 'Pass a positive integer CID string (e.g. "2244"), or set queryType "smiles" with a SMILES query.',
137
+ },
128
138
  ],
129
139
  async handler(input, ctx) {
130
140
  const client = getPubChemClient();
131
141
  let allCids = [];
132
142
  const identifierMap = new Map();
143
+ // Identifier-mode resolution tracking (#29): inputs that resolved to no CID, and
144
+ // CIDs claimed by more than one distinct input (the output row can echo only one).
145
+ const unresolvedIdentifiers = [];
146
+ const collisions = [];
133
147
  switch (input.searchType) {
134
148
  case 'identifier': {
135
149
  const { identifierType, identifiers } = input;
@@ -151,12 +165,35 @@ export const searchCompounds = tool('pubchem_search_compounds', {
151
165
  cids = await client.searchByInchiKey(id);
152
166
  break;
153
167
  }
154
- for (const cid of cids)
155
- identifierMap.set(cid, id);
156
- return cids;
168
+ return { id, cids };
157
169
  });
158
- const results = await Promise.all(lookups);
159
- allCids = results.flat();
170
+ const resolutions = await Promise.all(lookups);
171
+ // Track resolution per input in request order: a CID's echo goes to its first
172
+ // requester (deterministic, unlike the prior last-write-wins), unresolved inputs
173
+ // are collected, and any CID with multiple distinct requesters is a collision.
174
+ const cidToIdentifiers = new Map();
175
+ for (const { id, cids } of resolutions) {
176
+ if (cids.length === 0) {
177
+ unresolvedIdentifiers.push(id);
178
+ continue;
179
+ }
180
+ for (const cid of cids) {
181
+ const owners = cidToIdentifiers.get(cid);
182
+ if (owners) {
183
+ if (!owners.includes(id))
184
+ owners.push(id);
185
+ }
186
+ else {
187
+ cidToIdentifiers.set(cid, [id]);
188
+ identifierMap.set(cid, id);
189
+ }
190
+ }
191
+ }
192
+ for (const [cid, owners] of cidToIdentifiers) {
193
+ if (owners.length > 1)
194
+ collisions.push({ cid, identifiers: owners });
195
+ }
196
+ allCids = resolutions.flatMap((r) => r.cids);
160
197
  break;
161
198
  }
162
199
  case 'formula': {
@@ -176,6 +213,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
176
213
  ...ctx.recoveryFor('missing_structure_args'),
177
214
  });
178
215
  }
216
+ // A "cid" query must be a positive integer string — catch it here instead of
217
+ // forwarding a malformed value into a raw PubChem 400 (#26).
218
+ if (input.queryType === 'cid' && !(/^\d+$/.test(input.query) && Number(input.query) > 0)) {
219
+ throw ctx.fail('invalid_cid_query', `queryType is "cid" but query "${input.query}" is not a positive integer CID.`, { ...ctx.recoveryFor('invalid_cid_query') });
220
+ }
179
221
  allCids = await client.searchByStructure(input.searchType, input.query, input.queryType, input.threshold);
180
222
  break;
181
223
  }
@@ -191,11 +233,37 @@ export const searchCompounds = tool('pubchem_search_compounds', {
191
233
  });
192
234
  // Agent-facing context: search strategy echo, total, and empty-result notice.
193
235
  ctx.enrich({ searchType: input.searchType, totalFound });
236
+ // Identifier-mode signals (#29): name inputs that did not resolve and flag CID
237
+ // collisions, so a partial miss is never silent. Empty for other search types.
238
+ const noticeParts = [];
239
+ if (unresolvedIdentifiers.length > 0) {
240
+ const requested = input.identifiers?.length ?? unresolvedIdentifiers.length;
241
+ noticeParts.push(`${unresolvedIdentifiers.length} of ${requested} identifier(s) did not resolve to a CID: ${unresolvedIdentifiers.join(', ')}. Verify spelling and that identifierType="${input.identifierType}" matches the identifier form (name/smiles/inchikey).`);
242
+ }
243
+ for (const c of collisions) {
244
+ noticeParts.push(`Identifiers ${c.identifiers.join(', ')} all resolved to CID ${c.cid}; the result row echoes only "${identifierMap.get(c.cid)}" for it.`);
245
+ }
194
246
  if (cappedCids.length === 0) {
195
- 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.`);
247
+ ctx.enrich.notice(noticeParts.length > 0
248
+ ? noticeParts.join(' ')
249
+ : `No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
196
250
  }
197
251
  else if (totalFound > cappedCids.length) {
198
- ctx.enrich.truncated({ shown: cappedCids.length, cap: input.maxResults });
252
+ // Truncated: fold any identifier notice into the truncation guidance (notice is
253
+ // last-wins, so compose rather than emit two; restate the cap when overriding).
254
+ if (noticeParts.length > 0) {
255
+ ctx.enrich.truncated({
256
+ shown: cappedCids.length,
257
+ cap: input.maxResults,
258
+ guidance: `${noticeParts.join(' ')} Showing ${cappedCids.length} of ${totalFound} matches — raise maxResults (max 200) for more.`,
259
+ });
260
+ }
261
+ else {
262
+ ctx.enrich.truncated({ shown: cappedCids.length, cap: input.maxResults });
263
+ }
264
+ }
265
+ else if (noticeParts.length > 0) {
266
+ ctx.enrich.notice(noticeParts.join(' '));
199
267
  }
200
268
  // Optionally hydrate with properties
201
269
  let propsMap;
@@ -215,30 +283,34 @@ export const searchCompounds = tool('pubchem_search_compounds', {
215
283
  }
216
284
  return result;
217
285
  });
218
- return { results };
286
+ return unresolvedIdentifiers.length > 0 ? { results, unresolvedIdentifiers } : { results };
219
287
  },
220
288
  format(result) {
221
289
  const lines = [];
222
290
  if (result.results.length === 0) {
223
291
  lines.push('No results.');
224
- return [{ type: 'text', text: lines.join('\n') }];
225
292
  }
226
- const hasProps = result.results.some((r) => r.properties);
227
- if (hasProps) {
228
- for (const r of result.results) {
229
- const label = r.identifier ? `CID ${r.cid} — ${r.identifier}` : `CID ${r.cid}`;
230
- lines.push(`**${label}**`);
231
- if (r.properties) {
232
- const entries = Object.entries(r.properties);
233
- lines.push(' **Properties:**');
234
- lines.push(entries.map(([k, v]) => ` ${k}: ${v}`).join('\n'));
293
+ else {
294
+ const hasProps = result.results.some((r) => r.properties);
295
+ if (hasProps) {
296
+ for (const r of result.results) {
297
+ const label = r.identifier ? `CID ${r.cid} — ${r.identifier}` : `CID ${r.cid}`;
298
+ lines.push(`**${label}**`);
299
+ if (r.properties) {
300
+ const entries = Object.entries(r.properties);
301
+ lines.push(' **Properties:**');
302
+ lines.push(entries.map(([k, v]) => ` ${k}: ${v}`).join('\n'));
303
+ }
304
+ lines.push('');
235
305
  }
236
- lines.push('');
306
+ }
307
+ else {
308
+ const items = result.results.map((r) => r.identifier ? `${r.cid} (${r.identifier})` : String(r.cid));
309
+ lines.push(`CIDs: ${items.join(', ')}`);
237
310
  }
238
311
  }
239
- else {
240
- const items = result.results.map((r) => r.identifier ? `${r.cid} (${r.identifier})` : String(r.cid));
241
- lines.push(`CIDs: ${items.join(', ')}`);
312
+ if (result.unresolvedIdentifiers && result.unresolvedIdentifiers.length > 0) {
313
+ lines.push(`Unresolved identifiers (${result.unresolvedIdentifiers.length}): ${result.unresolvedIdentifiers.join(', ')}`);
242
314
  }
243
315
  return [{ type: 'text', text: lines.join('\n') }];
244
316
  },
package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map CHANGED
@@ -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": "0.3.0",
4
+ "version": "0.3.1",
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": "0.3.0",
3
+ "version": "0.3.1",
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",
@@ -78,8 +78,8 @@
78
78
  "zod": "^4.4.3"
79
79
  },
80
80
  "devDependencies": {
81
- "@biomejs/biome": "^2.5.1",
82
- "@types/node": "^26.0.1",
81
+ "@biomejs/biome": "^2.5.2",
82
+ "@types/node": "^26.1.0",
83
83
  "depcheck": "^1.4.7",
84
84
  "ignore": "^7.0.5",
85
85
  "tsc-alias": "^1.8.17",
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": "0.3.0",
9
+ "version": "0.3.1",
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": "0.3.0",
22
+ "version": "0.3.1",
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": "0.3.0",
45
+ "version": "0.3.1",
46
46
  "packageArguments": [
47
47
  { "type": "positional", "value": "run" },
48
48
  { "type": "positional", "value": "start:http" }