@cyanheads/pubchem-mcp-server 0.2.2 → 0.2.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (21) hide show
  1. package/Dockerfile +5 -0
  2. package/README.md +1 -1
  3. package/dist/index.js +2 -0
  4. package/dist/index.js.map +1 -1
  5. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts +3 -0
  6. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
  7. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +9 -0
  8. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/index.d.ts +9 -0
  10. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts +3 -0
  12. package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map +1 -1
  13. package/dist/mcp-server/tools/definitions/search-assays.tool.js +9 -0
  14. package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
  15. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +3 -0
  16. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
  17. package/dist/mcp-server/tools/definitions/search-compounds.tool.js +9 -0
  18. package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
  19. package/manifest.json +1 -1
  20. package/package.json +7 -7
  21. package/server.json +3 -3
package/Dockerfile CHANGED
@@ -37,10 +37,12 @@ WORKDIR /usr/src/app
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  ENV NODE_ENV=production
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  # OCI image metadata (https://github.com/opencontainers/image-spec/blob/main/annotations.md)
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+ ARG APP_VERSION
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  LABEL org.opencontainers.image.title="pubchem-mcp-server"
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  LABEL org.opencontainers.image.description="MCP server for the PubChem chemical database."
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  LABEL org.opencontainers.image.source="https://github.com/cyanheads/pubchem-mcp-server"
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  LABEL org.opencontainers.image.licenses="Apache-2.0"
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+ LABEL org.opencontainers.image.version="${APP_VERSION}"
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  # Copy dependency manifests
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  COPY package.json bun.lock ./
@@ -98,5 +100,8 @@ ENV MCP_FORCE_CONSOLE_LOGGING="true"
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  # Expose the port the server listens on
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  EXPOSE ${MCP_HTTP_PORT}
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+ # Health check using a bun-native fetch (slim image ships no curl/wget)
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+ HEALTHCHECK --interval=30s --timeout=5s --start-period=10s --retries=3 CMD bun -e "fetch('http://localhost:'+(process.env.MCP_HTTP_PORT??'3010')+'/healthz').then((r)=>process.exit(r.ok?0:1)).catch(()=>process.exit(1))"
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+
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  # The command to start the server
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  CMD ["bun", "run", "dist/index.js"]
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-0.2.2-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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+ [![Version](https://img.shields.io/badge/Version-0.2.4-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-^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/index.js CHANGED
@@ -9,6 +9,8 @@ import { allResourceDefinitions } from './mcp-server/resources/definitions/index
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  import { allToolDefinitions } from './mcp-server/tools/definitions/index.js';
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  import { initPubChemClient } from './services/pubchem/pubchem-client.js';
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  await createApp({
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+ name: 'pubchem-mcp-server',
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+ title: 'pubchem-mcp-server',
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  tools: allToolDefinitions,
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  resources: allResourceDefinitions,
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  instructions: "Use the pubchem_* tools to query PubChem's chemical database. Compounds are addressed by CID, assays by AID. Most flows start at `pubchem_search_compounds` (name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity → CIDs), then call per-CID tools for details, safety, image, cross-references, bioactivity, interactions (drug-drug/drug-food/target), or 3D structure. For bioassays by biological target, chain `pubchem_search_assays` (gene/protein → AIDs) into `pubchem_get_bioactivity`. `pubchem_get_summary` covers assay/gene/protein/taxonomy entity lookups. Compound and assay records are also exposed as URI-addressable resources (e.g. `pubchem://compound/{cid}`, `pubchem://assay/{aid}`).",
package/dist/index.js.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6CAA6C,CAAC;AACrF,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE,kBAAkB;IACzB,SAAS,EAAE,sBAAsB;IACjC,YAAY,EACV,4sBAA4sB;IAC9sB,OAAO,EAAE;QACP,OAAO,EACL,+FAA+F;QACjG,QAAQ,EAAE,iDAAiD;QAC3D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,mCAAmC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC/E;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;SACF;KACF;IACD,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6CAA6C,CAAC;AACrF,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE,kBAAkB;IACzB,SAAS,EAAE,sBAAsB;IACjC,YAAY,EACV,4sBAA4sB;IAC9sB,OAAO,EAAE;QACP,OAAO,EACL,+FAA+F;QACjG,QAAQ,EAAE,iDAAiD;QAC3D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,mCAAmC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC/E;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;SACF;KACF;IACD,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts CHANGED
@@ -36,6 +36,9 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
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  readonly targetFilter: z.ZodOptional<z.ZodString>;
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  readonly filteredCount: z.ZodNumber;
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  readonly returnedCount: z.ZodNumber;
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+ readonly truncated: z.ZodOptional<z.ZodBoolean>;
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+ readonly shown: z.ZodOptional<z.ZodNumber>;
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+ readonly cap: z.ZodOptional<z.ZodNumber>;
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  readonly notice: z.ZodOptional<z.ZodString>;
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  }>;
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  //# sourceMappingURL=get-bioactivity.tool.d.ts.map
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkNzB,CAAC"}
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js CHANGED
@@ -90,6 +90,12 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
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  .number()
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  .describe('Assays matching the outcome and target filters, before the maxResults cap.'),
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  returnedCount: z.number().describe('Assays returned after the maxResults cap.'),
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+ truncated: z
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+ .boolean()
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+ .optional()
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+ .describe('True when results were capped at maxResults — more matching assays exist.'),
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+ shown: z.number().optional().describe('Assays returned after the maxResults cap.'),
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+ cap: z.number().optional().describe('The maxResults cap that was applied.'),
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  notice: z
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  .string()
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  .optional()
@@ -144,6 +150,9 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
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  ? `CID ${input.cid} has ${allRows.length} assay(s) but none match the target filter (${targetLabel})${input.outcomeFilter !== 'all' ? ` with outcomeFilter="${input.outcomeFilter}"` : ''}. Verify the target identifier appears in this compound's assays, or widen the filter.`
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  : `CID ${input.cid} has ${allRows.length} assay(s) but none match outcomeFilter="${input.outcomeFilter}". Use outcomeFilter="all" to see them.`);
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  }
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+ else if (filtered.length > results.length) {
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+ ctx.enrich.truncated({ shown: results.length, cap: input.maxResults });
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+ }
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  return {
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  cid: input.cid,
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  totalAssays: allRows.length,
package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -34,6 +34,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
34
34
  readonly targetFilter: import("zod").ZodOptional<import("zod").ZodString>;
35
35
  readonly filteredCount: import("zod").ZodNumber;
36
36
  readonly returnedCount: import("zod").ZodNumber;
37
+ readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
38
+ readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
39
+ readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
37
40
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
38
41
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
39
42
  cid: import("zod").ZodNumber;
@@ -267,6 +270,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
267
270
  readonly targetType: import("zod").ZodString;
268
271
  readonly targetQuery: import("zod").ZodString;
269
272
  readonly totalFound: import("zod").ZodNumber;
273
+ readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
274
+ readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
275
+ readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
270
276
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
271
277
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
272
278
  searchType: import("zod").ZodEnum<{
@@ -318,6 +324,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
318
324
  }], {
319
325
  readonly searchType: import("zod").ZodString;
320
326
  readonly totalFound: import("zod").ZodNumber;
327
+ readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
328
+ readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
329
+ readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
321
330
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
322
331
  }>)[];
323
332
  //# sourceMappingURL=index.d.ts.map
package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED
@@ -1 +1 @@
1
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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
@@ -19,6 +19,9 @@ export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefiniti
19
19
  readonly targetType: z.ZodString;
20
20
  readonly targetQuery: z.ZodString;
21
21
  readonly totalFound: z.ZodNumber;
22
+ readonly truncated: z.ZodOptional<z.ZodBoolean>;
23
+ readonly shown: z.ZodOptional<z.ZodNumber>;
24
+ readonly cap: z.ZodOptional<z.ZodNumber>;
22
25
  readonly notice: z.ZodOptional<z.ZodString>;
23
26
  }>;
24
27
  //# sourceMappingURL=search-assays.tool.d.ts.map
package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-assays.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;EAiFvB,CAAC"}
1
+ {"version":3,"file":"search-assays.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;EAyFvB,CAAC"}
package/dist/mcp-server/tools/definitions/search-assays.tool.js CHANGED
@@ -38,6 +38,12 @@ export const searchAssays = tool('pubchem_search_assays', {
38
38
  .describe('Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession.'),
39
39
  targetQuery: z.string().describe('Target identifier searched.'),
40
40
  totalFound: z.number().describe('Total AIDs found before the maxResults cap.'),
41
+ truncated: z
42
+ .boolean()
43
+ .optional()
44
+ .describe('True when AIDs were capped at maxResults — more assays exist than returned.'),
45
+ shown: z.number().optional().describe('AIDs returned after the maxResults cap.'),
46
+ cap: z.number().optional().describe('The maxResults cap that was applied.'),
41
47
  notice: z
42
48
  .string()
43
49
  .optional()
@@ -59,6 +65,9 @@ export const searchAssays = tool('pubchem_search_assays', {
59
65
  if (aids.length === 0) {
60
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.`);
61
67
  }
68
+ else if (totalFound > aids.length) {
69
+ ctx.enrich.truncated({ shown: aids.length, cap: input.maxResults });
70
+ }
62
71
  return { aids };
63
72
  },
64
73
  format(result) {
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,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uIAAuI,CACxI;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,KAAK,CAAC,UAAU,EAAE,KAAK,CAAC,WAAW,CAAC,CAAC;QAEvF,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC;QAClC,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;QAEhD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,wBAAwB,EAAE;YACrC,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,UAAU;YACV,QAAQ,EAAE,IAAI,CAAC,MAAM;SACtB,CAAC,CAAC;QAEH,qEAAqE;QACrE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,WAAW,EAAE,KAAK,CAAC,WAAW,EAAE,UAAU,EAAE,CAAC,CAAC;QACzF,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACtB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,KAAK,CAAC,WAAW,MAAM,KAAK,CAAC,UAAU,yKAAyK,CACzO,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,IAAI,EAAE,CAAC;IAClB,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,SAAS,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;QACrE,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,EAAE,CAAC,CAAC;IACtD,CAAC;CACF,CAAC,CAAC"}
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"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts CHANGED
@@ -55,6 +55,9 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
55
55
  }], {
56
56
  readonly searchType: z.ZodString;
57
57
  readonly totalFound: z.ZodNumber;
58
+ readonly truncated: z.ZodOptional<z.ZodBoolean>;
59
+ readonly shown: z.ZodOptional<z.ZodNumber>;
60
+ readonly cap: z.ZodOptional<z.ZodNumber>;
58
61
  readonly notice: z.ZodOptional<z.ZodString>;
59
62
  }>;
60
63
  //# sourceMappingURL=search-compounds.tool.d.ts.map
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6Q1B,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqR1B,CAAC"}
package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED
@@ -95,6 +95,12 @@ export const searchCompounds = tool('pubchem_search_compounds', {
95
95
  .string()
96
96
  .describe('Search strategy used: identifier, formula, substructure, superstructure, or similarity.'),
97
97
  totalFound: z.number().describe('Total CIDs found before the maxResults cap.'),
98
+ truncated: z
99
+ .boolean()
100
+ .optional()
101
+ .describe('True when CIDs were capped at maxResults — more matches exist than returned.'),
102
+ shown: z.number().optional().describe('CIDs returned after the maxResults cap.'),
103
+ cap: z.number().optional().describe('The maxResults cap that was applied.'),
98
104
  notice: z
99
105
  .string()
100
106
  .optional()
@@ -188,6 +194,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
188
194
  if (cappedCids.length === 0) {
189
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.`);
190
196
  }
197
+ else if (totalFound > cappedCids.length) {
198
+ ctx.enrich.truncated({ shown: cappedCids.length, cap: input.maxResults });
199
+ }
191
200
  // Optionally hydrate with properties
192
201
  let propsMap;
193
202
  if (input.properties && input.properties.length > 0 && cappedCids.length > 0) {
package/dist/mcp-server/tools/definitions/search-compounds.tool.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": "0.2.2",
4
+ "version": "0.2.4",
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": "0.2.2",
3
+ "version": "0.2.4",
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",
@@ -22,7 +22,7 @@
22
22
  "format:unsafe": "biome check --write --unsafe .",
23
23
  "lint:mcp": "bun scripts/lint-mcp.ts",
24
24
  "lint:packaging": "bun scripts/lint-packaging.ts",
25
- "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubchem-mcp-server.mcpb",
25
+ "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubchem-mcp-server.mcpb && bun run scripts/clean-mcpb.ts dist/pubchem-mcp-server.mcpb",
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",
@@ -68,22 +68,22 @@
68
68
  "node": ">=24.0.0",
69
69
  "bun": ">=1.3.0"
70
70
  },
71
- "packageManager": "bun@1.3.2",
71
+ "packageManager": "bun@1.3.11",
72
72
  "publishConfig": {
73
73
  "access": "public"
74
74
  },
75
75
  "dependencies": {
76
- "@cyanheads/mcp-ts-core": "^0.9.21",
76
+ "@cyanheads/mcp-ts-core": "^0.10.9",
77
77
  "pino-pretty": "^13.1.3",
78
78
  "zod": "^4.4.3"
79
79
  },
80
80
  "devDependencies": {
81
- "@biomejs/biome": "^2.4.16",
82
- "@types/node": "^25.9.1",
81
+ "@biomejs/biome": "^2.5.0",
82
+ "@types/node": "^26.0.0",
83
83
  "depcheck": "^1.4.7",
84
84
  "ignore": "^7.0.5",
85
85
  "tsc-alias": "^1.8.17",
86
86
  "typescript": "^6.0.3",
87
- "vitest": "^4.1.8"
87
+ "vitest": "^4.1.9"
88
88
  }
89
89
  }
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": "0.2.2",
9
+ "version": "0.2.4",
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": "0.2.2",
22
+ "version": "0.2.4",
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": "0.2.2",
45
+ "version": "0.2.4",
46
46
  "packageArguments": [
47
47
  { "type": "positional", "value": "run" },
48
48
  { "type": "positional", "value": "start:http" }