@cyanheads/pubchem-mcp-server 0.2.1 → 0.2.3

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Files changed (21) hide show
  1. package/Dockerfile +5 -0
  2. package/README.md +2 -2
  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 +2 -2
  20. package/package.json +8 -7
  21. package/server.json +4 -4
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
@@ -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-0.2.1-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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+ [![Version](https://img.shields.io/badge/Version-0.2.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^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"}
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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,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0MzB,CAAC"}
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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 @@
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
@@ -1,8 +1,8 @@
1
1
  {
2
2
  "manifest_version": "0.3",
3
3
  "name": "pubchem-mcp-server",
4
- "version": "0.2.1",
5
- "description": "Search PubChem compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP.",
4
+ "version": "0.2.3",
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": "0.2.1",
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": "0.2.3",
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",
@@ -22,10 +22,11 @@
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",
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"
@@ -67,18 +68,18 @@
67
68
  "node": ">=24.0.0",
68
69
  "bun": ">=1.3.0"
69
70
  },
70
- "packageManager": "bun@1.3.2",
71
+ "packageManager": "bun@1.3.11",
71
72
  "publishConfig": {
72
73
  "access": "public"
73
74
  },
74
75
  "dependencies": {
75
- "@cyanheads/mcp-ts-core": "^0.9.16",
76
+ "@cyanheads/mcp-ts-core": "^0.10.6",
76
77
  "pino-pretty": "^13.1.3",
77
78
  "zod": "^4.4.3"
78
79
  },
79
80
  "devDependencies": {
80
- "@biomejs/biome": "^2.4.16",
81
- "@types/node": "^25.9.1",
81
+ "@biomejs/biome": "^2.5.0",
82
+ "@types/node": "^25.9.3",
82
83
  "depcheck": "^1.4.7",
83
84
  "ignore": "^7.0.5",
84
85
  "tsc-alias": "^1.8.17",
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": "0.2.1",
9
+ "version": "0.2.3",
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": "0.2.1",
22
+ "version": "0.2.3",
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": "0.2.1",
45
+ "version": "0.2.3",
46
46
  "packageArguments": [
47
47
  { "type": "positional", "value": "run" },
48
48
  { "type": "positional", "value": "start:http" }