@cyanheads/pubchem-mcp-server 0.1.15 → 0.1.17

package/README.md

@@ -6,7 +6,7 @@
 
 <div align="center">
 
-[![Version](https://img.shields.io/badge/Version-0.1.15-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![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-^1.2.0-f472b6.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.1.17-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![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-^1.2.0-f472b6.svg?style=flat-square)](https://bun.sh/)
 
 </div>
 
@@ -171,17 +171,11 @@ No API keys are required — PubChem's API is freely accessible.
 
 ### Local Development
 
-- **Build and run the production version:**
+- **Build and run:**
 
   ```sh
-  bun run build
-  bun run start:http   # or start:stdio
-  ```
-
-- **Run in dev mode (auto-reload):**
-
-  ```sh
-  bun run dev:stdio    # or dev:http
+  bun run rebuild
+  bun run start:stdio   # or start:http
   ```
 
 - **Run checks and tests:**

package/dist/index.js

@@ -9,6 +9,23 @@ import { allToolDefinitions } from './mcp-server/tools/definitions/index.js';
 import { initPubChemClient } from './services/pubchem/pubchem-client.js';
 await createApp({
     tools: allToolDefinitions,
+    landing: {
+        tagline: 'Search PubChem for chemical compounds, properties, safety, bioactivity, and cross-references.',
+        repoRoot: 'https://github.com/cyanheads/pubchem-mcp-server',
+        links: [
+            { label: 'PubChem', href: 'https://pubchem.ncbi.nlm.nih.gov/', external: true },
+            {
+                label: 'PUG REST docs',
+                href: 'https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest',
+                external: true,
+            },
+            {
+                label: 'PUG View docs',
+                href: 'https://pubchem.ncbi.nlm.nih.gov/docs/pug-view',
+                external: true,
+            },
+        ],
+    },
     setup() {
         initPubChemClient();
     },

package/dist/index.js.map

@@ -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,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE,kBAAkB;IACzB,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

@@ -29,5 +29,5 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
             unit: z.ZodOptional<z.ZodString>;
         }, z.core.$strip>>;
     }, z.core.$strip>>;
-}, z.core.$strip>>;
+}, z.core.$strip>, undefined>;
 //# sourceMappingURL=get-bioactivity.tool.d.ts.map

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map

@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;6BAsIzB,CAAC"}

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js

@@ -35,7 +35,8 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
         activeCount: z.number().describe('Assays with "Active" outcome.'),
         inactiveCount: z.number().describe('Assays with "Inactive" outcome.'),
         results: z
-            .array(z.object({
+            .array(z
+            .object({
             aid: z.number().describe('PubChem Assay ID.'),
             assayName: z.string().describe('Assay name/title.'),
             outcome: z
@@ -47,7 +48,8 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
                 .describe('Target protein accession (UniProt/GenBank).'),
             targetGeneId: z.number().optional().describe('Target NCBI Gene ID.'),
             activityValues: z
-                .array(z.object({
+                .array(z
+                .object({
                 name: z
                     .string()
                     .optional()
@@ -57,9 +59,11 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
                     .string()
                     .optional()
                     .describe('Unit of measurement (e.g. uM, nM). Omitted when not reported.'),
-            }))
+            })
+                .describe('Quantitative activity measurement entry.'))
                 .describe('Quantitative activity measurements.'),
-        }))
+        })
+            .describe('Assay result entry.'))
             .describe('Assay results matching the filter.'),
     }),
     async handler(input, ctx) {

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts

@@ -74,5 +74,5 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
             meshClasses: z.ZodArray<z.ZodString>;
         }, z.core.$strip>>;
     }, z.core.$strip>>;
-}, z.core.$strip>>;
+}, z.core.$strip>, undefined>;
 //# sourceMappingURL=get-compound-details.tool.d.ts.map

package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAyGjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAwX7B,CAAC"}
+{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BA4X7B,CAAC"}

package/dist/mcp-server/tools/definitions/get-compound-details.tool.js

@@ -36,10 +36,12 @@ const drugLikenessSchema = z.object({
 });
 const classificationSchema = z.object({
     atcCodes: z
-        .array(z.object({
+        .array(z
+        .object({
         code: z.string().describe('ATC code.'),
         description: z.string().describe('ATC code description.'),
-    }))
+    })
+        .describe('ATC code entry with hierarchical description.'))
         .describe('ATC codes with hierarchical descriptions.'),
     fdaClasses: z.array(z.string()).describe('FDA Established Pharmacologic Classes.'),
     fdaMechanisms: z.array(z.string()).describe('FDA Mechanisms of Action.'),
@@ -147,7 +149,8 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
     }),
     output: z.object({
         compounds: z
-            .array(z.object({
+            .array(z
+            .object({
             cid: z.number().describe('PubChem Compound ID.'),
             found: z
                 .boolean()
@@ -156,13 +159,15 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 .record(z.string(), z.unknown())
                 .describe('Requested physicochemical properties.'),
             descriptions: z
-                .array(z.object({
+                .array(z
+                .object({
                 source: z
                     .string()
                     .optional()
                     .describe('Depositor source (e.g. "DrugBank", "Wikipedia", "ChEBI").'),
                 text: z.string().describe('Description text.'),
-            }))
+            })
+                .describe('Description entry with optional source attribution.'))
                 .optional()
                 .describe('Textual descriptions, deduplicated and capped at maxDescriptions. Each entry carries ' +
                 'optional source attribution.'),
@@ -178,7 +183,8 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             classification: classificationSchema
                 .optional()
                 .describe('Pharmacological classification (FDA, MeSH, ATC).'),
-        }))
+        })
+            .describe('Per-CID compound detail record.'))
             .describe('Compound detail records.'),
     }),
     async handler(input, ctx) {

package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts

@@ -15,5 +15,5 @@ export declare const getCompoundImage: import("@cyanheads/mcp-ts-core").ToolDefi
     mimeType: z.ZodString;
     width: z.ZodNumber;
     height: z.ZodNumber;
-}, z.core.$strip>>;
+}, z.core.$strip>, undefined>;
 //# sourceMappingURL=get-compound-image.tool.d.ts.map

package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAQjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;kBAgD3B,CAAC"}
+{"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;6BAgD3B,CAAC"}

package/dist/mcp-server/tools/definitions/get-compound-image.tool.js

@@ -4,10 +4,6 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
-/** Convert ArrayBuffer to base64 string */
-function arrayBufferToBase64(buffer) {
-    return Buffer.from(buffer).toString('base64');
-}
 export const getCompoundImage = tool('pubchem_get_compound_image', {
     title: 'Get Compound Image',
     description: 'Fetch a 2D structure diagram (PNG image) for a compound by CID.',
@@ -37,7 +33,7 @@ export const getCompoundImage = tool('pubchem_get_compound_image', {
         ctx.log.info('Image fetched', { cid: input.cid, size: input.size, bytes: buffer.byteLength });
         return {
             cid: input.cid,
-            imageBase64: arrayBufferToBase64(buffer),
+            imageBase64: Buffer.from(buffer).toString('base64'),
             mimeType: 'image/png',
             width: dim,
             height: dim,

package/dist/mcp-server/tools/definitions/get-compound-image.tool.js.map

@@ -1 +1 @@
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+{"version":3,"file":"get-compound-image.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EAAE,iEAAiE;IAC9E,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QACjE,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;aACxB,OAAO,CAAC,OAAO,CAAC;aAChB,QAAQ,CAAC,uEAAuE,CAAC;KACrF,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAClE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACjD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACpD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KACvD,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5D,MAAM,GAAG,GAAG,KAAK,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;QAE/C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC;QAE9F,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,WAAW,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC;YACnD,QAAQ,EAAE,WAAW;YACrB,KAAK,EAAE,GAAG;YACV,MAAM,EAAE,GAAG;SACZ,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,OAAO;YACL,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE;YACtE;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,wBAAwB,MAAM,CAAC,GAAG,KAAK,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,MAAM,GAAG;aAC9E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts

@@ -21,5 +21,5 @@ export declare const getCompoundSafety: import("@cyanheads/mcp-ts-core").ToolDef
         }, z.core.$strip>>;
     }, z.core.$strip>>;
     source: z.ZodOptional<z.ZodString>;
-}, z.core.$strip>>;
+}, z.core.$strip>, undefined>;
 //# sourceMappingURL=get-compound-safety.tool.d.ts.map

package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;kBAmG5B,CAAC"}
+{"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;6BAuG5B,CAAC"}

package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js

@@ -27,16 +27,20 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
                 .array(z.string())
                 .describe('GHS pictogram labels (e.g. "Flammable", "Toxic").'),
             hazardStatements: z
-                .array(z.object({
+                .array(z
+                .object({
                 code: z.string().describe('H-code (e.g. "H225").'),
                 statement: z.string().describe('Hazard statement text.'),
-            }))
+            })
+                .describe('GHS hazard statement entry.'))
                 .describe('GHS hazard statements.'),
             precautionaryStatements: z
-                .array(z.object({
+                .array(z
+                .object({
                 code: z.string().describe('P-code (e.g. "P210").'),
                 statement: z.string().describe('Precautionary statement text.'),
-            }))
+            })
+                .describe('GHS precautionary statement entry.'))
                 .describe('GHS precautionary statements.'),
         })
             .optional()

package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map

@@ -1 +1 @@
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+{"version":3,"file":"get-compound-safety.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,6BAA6B,EAAE;IACnE,KAAK,EAAE,qBAAqB;IAC5B,WAAW,EACT,6FAA6F;QAC7F,wGAAwG;QACxG,qEAAqE;IACvE,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,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KAClE,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,yDAAyD,CAAC;QACxF,GAAG,EAAE,CAAC;aACH,MAAM,CAAC;YACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;YACrF,UAAU,EAAE,CAAC;iBACV,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;iBACjB,QAAQ,CAAC,mDAAmD,CAAC;YAChE,gBAAgB,EAAE,CAAC;iBAChB,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;gBAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;aACzD,CAAC;iBACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;iBACA,QAAQ,CAAC,wBAAwB,CAAC;YACrC,uBAAuB,EAAE,CAAC;iBACvB,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;gBAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;aAChE,CAAC;iBACD,QAAQ,CAAC,oCAAoC,CAAC,CAClD;iBACA,QAAQ,CAAC,+BAA+B,CAAC;SAC7C,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CAAC,0BAA0B,CAAC;QACvC,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;KACnE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAEnD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,qBAAqB,EAAE,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,IAAI,KAAK,IAAI,EAAE,CAAC,CAAC;QAEhF,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC;QAC5C,CAAC;QAED,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,OAAO,EAAE,IAAI;YACb,GAAG,EAAE;gBACH,UAAU,EAAE,IAAI,CAAC,UAAU;gBAC3B,UAAU,EAAE,IAAI,CAAC,UAAU;gBAC3B,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,uBAAuB,EAAE,IAAI,CAAC,uBAAuB;aACtD;YACD,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,CAAC,MAAM,CAAC,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC;YACnC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,wCAAwC,MAAM,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC;QACzF,CAAC;QAED,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QACvE,MAAM,CAAC,GAAG,MAAM,CAAC,GAAG,CAAC;QAErB,IAAI,CAAC,CAAC,UAAU;YAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC;QACjE,IAAI,CAAC,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC;YAAE,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAEtF,IAAI,CAAC,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAClC,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,wBAAwB,CAAC,CAAC;YACzC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,gBAAgB,EAAE,CAAC;gBACnC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAC5C,CAAC;QACH,CAAC;QAED,IAAI,CAAC,CAAC,uBAAuB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACzC,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,+BAA+B,CAAC,CAAC;YAChD,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,uBAAuB,EAAE,CAAC;gBAC1C,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAC5C,CAAC;QACH,CAAC;QAED,IAAI,MAAM,CAAC,MAAM,EAAE,CAAC;YAClB,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,YAAY,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC;QAC/C,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/get-compound-xrefs.tool.d.ts

@@ -17,5 +17,5 @@ export declare const getCompoundXrefs: import("@cyanheads/mcp-ts-core").ToolDefi
         totalAvailable: z.ZodNumber;
         truncated: z.ZodBoolean;
     }, z.core.$strip>>;
-}, z.core.$strip>>;
+}, z.core.$strip>, undefined>;
 //# sourceMappingURL=get-compound-xrefs.tool.d.ts.map

package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map

@@ -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;;;;;;;;;;;;;;kBAoG3B,CAAC"}
+{"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;;;;;;;;;;;;;;6BA+G3B,CAAC"}

package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js

@@ -34,14 +34,23 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
     output: z.object({
         cid: z.number().describe('PubChem Compound ID.'),
         xrefs: z
-            .array(z.object({
+            .array(z
+            .object({
             type: z.string().describe('Cross-reference type.'),
             ids: z
-                .array(z.union([z.string(), z.number()]))
+                .array(z
+                .union([
+                z
+                    .string()
+                    .describe('String-form cross-reference ID (e.g. CAS number, patent).'),
+                z.number().describe('Numeric cross-reference ID (e.g. PubMed ID, Gene ID).'),
+            ])
+                .describe('Cross-reference identifier — string or number depending on type.'))
                 .describe('Cross-reference IDs (capped by maxPerType).'),
             totalAvailable: z.number().describe('Total IDs available before truncation.'),
             truncated: z.boolean().describe('Whether results were truncated.'),
-        }))
+        })
+            .describe('Cross-reference group for one type.'))
             .describe('Cross-references grouped by type.'),
     }),
     async handler(input, ctx) {

package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts

@@ -36,5 +36,5 @@ export declare const getSummary: import("@cyanheads/mcp-ts-core").ToolDefinition
             lineage: z.ZodOptional<z.ZodArray<z.ZodString>>;
         }, z.core.$strip>>;
     }, z.core.$strip>>;
-}, z.core.$strip>>;
+}, z.core.$strip>, undefined>;
 //# sourceMappingURL=get-summary.tool.d.ts.map

package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA6FrB,CAAC"}
+{"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BA2GrB,CAAC"}

package/dist/mcp-server/tools/definitions/get-summary.tool.js

@@ -42,7 +42,12 @@ export const getSummary = tool('pubchem_get_summary', {
     input: z.object({
         entityType: entityTypeEnum.describe('Entity type. Determines ID format and returned fields.'),
         identifiers: z
-            .array(z.union([z.string(), z.number()]))
+            .array(z
+            .union([
+            z.string().describe('String identifier (e.g. UniProt accession).'),
+            z.number().describe('Numeric identifier (e.g. AID, Gene ID, Tax ID).'),
+        ])
+            .describe('Entity identifier — string or number depending on entityType.'))
             .min(1)
             .max(10)
             .describe('Entity identifiers (1-10). Type depends on entityType:\n' +
@@ -54,13 +59,20 @@ export const getSummary = tool('pubchem_get_summary', {
     output: z.object({
         entityType: z.string().describe('Entity type queried.'),
         summaries: z
-            .array(z.object({
-            identifier: z.union([z.string(), z.number()]).describe('Queried identifier.'),
+            .array(z
+            .object({
+            identifier: z
+                .union([
+                z.string().describe('String identifier (e.g. UniProt accession).'),
+                z.number().describe('Numeric identifier (e.g. AID, Gene ID, Tax ID).'),
+            ])
+                .describe('Queried identifier.'),
             found: z.boolean().describe('Whether the entity was found.'),
             data: entitySummaryDataSchema
                 .optional()
                 .describe('Entity summary data. Populated fields depend on entityType.'),
-        }))
+        })
+            .describe('Per-identifier summary result.'))
             .describe('Summary results.'),
     }),
     async handler(input, ctx) {

package/dist/mcp-server/tools/definitions/get-summary.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/index.d.ts

@@ -27,7 +27,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
             unit: import("zod").ZodOptional<import("zod").ZodString>;
         }, import("zod/v4/core").$strip>>;
     }, import("zod/v4/core").$strip>>;
-}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     cids: import("zod").ZodArray<import("zod").ZodNumber>;
     properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
         [x: string]: string;
@@ -97,7 +97,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
             meshClasses: import("zod").ZodArray<import("zod").ZodString>;
         }, import("zod/v4/core").$strip>>;
     }, import("zod/v4/core").$strip>>;
-}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     cid: import("zod").ZodNumber;
     size: import("zod").ZodDefault<import("zod").ZodEnum<{
         small: "small";
@@ -109,7 +109,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     mimeType: import("zod").ZodString;
     width: import("zod").ZodNumber;
     height: import("zod").ZodNumber;
-}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     cid: import("zod").ZodNumber;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     cid: import("zod").ZodNumber;
@@ -127,7 +127,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
         }, import("zod/v4/core").$strip>>;
     }, import("zod/v4/core").$strip>>;
     source: import("zod").ZodOptional<import("zod").ZodString>;
-}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     cid: import("zod").ZodNumber;
     xrefTypes: import("zod").ZodArray<import("zod").ZodEnum<{
         [x: string]: string;
@@ -141,7 +141,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
         totalAvailable: import("zod").ZodNumber;
         truncated: import("zod").ZodBoolean;
     }, import("zod/v4/core").$strip>>;
-}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     entityType: import("zod").ZodEnum<{
         assay: "assay";
         gene: "gene";
@@ -173,7 +173,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
             lineage: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
         }, import("zod/v4/core").$strip>>;
     }, import("zod/v4/core").$strip>>;
-}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     targetType: import("zod").ZodEnum<{
         proteinaccession: "proteinaccession";
         genesymbol: "genesymbol";
@@ -187,7 +187,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     targetQuery: import("zod").ZodString;
     totalFound: import("zod").ZodNumber;
     aids: import("zod").ZodArray<import("zod").ZodNumber>;
-}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     searchType: import("zod").ZodEnum<{
         substructure: "substructure";
         superstructure: "superstructure";
@@ -221,5 +221,20 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
         identifier: import("zod").ZodOptional<import("zod").ZodString>;
         properties: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
     }, import("zod/v4/core").$strip>>;
-}, import("zod/v4/core").$strip>>)[];
+}, import("zod/v4/core").$strip>, readonly [{
+    readonly reason: "missing_identifier_args";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.InvalidParams;
+    readonly when: "searchType is \"identifier\" but identifierType or identifiers were omitted";
+    readonly recovery: "Set identifierType (name/smiles/inchikey) and pass a non-empty identifiers array (1-25 entries).";
+}, {
+    readonly reason: "missing_formula";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.InvalidParams;
+    readonly when: "searchType is \"formula\" but the formula field was omitted";
+    readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
+}, {
+    readonly reason: "missing_structure_args";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.InvalidParams;
+    readonly when: "substructure/superstructure/similarity search missing query or queryType";
+    readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
+}]>)[];
 //# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/definitions/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;oCAS9B,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;MAS9B,CAAC"}

package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts

@@ -18,5 +18,5 @@ export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefiniti
     targetQuery: z.ZodString;
     totalFound: z.ZodNumber;
     aids: z.ZodArray<z.ZodNumber>;
-}, z.core.$strip>>;
+}, z.core.$strip>, undefined>;
 //# sourceMappingURL=search-assays.tool.d.ts.map

package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map

@@ -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;;;;;;;;;;;;;;kBAiFvB,CAAC"}
+{"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;;;;;;;;;;;;;;6BAiFvB,CAAC"}

package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts

@@ -4,6 +4,7 @@
  * @module mcp-server/tools/definitions/search-compounds
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     searchType: z.ZodEnum<{
         substructure: "substructure";
@@ -38,5 +39,20 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
         identifier: z.ZodOptional<z.ZodString>;
         properties: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
     }, z.core.$strip>>;
-}, z.core.$strip>>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "missing_identifier_args";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "searchType is \"identifier\" but identifierType or identifiers were omitted";
+    readonly recovery: "Set identifierType (name/smiles/inchikey) and pass a non-empty identifiers array (1-25 entries).";
+}, {
+    readonly reason: "missing_formula";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "searchType is \"formula\" but the formula field was omitted";
+    readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
+}, {
+    readonly reason: "missing_structure_args";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "substructure/superstructure/similarity search missing query or queryType";
+    readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
+}]>;
 //# sourceMappingURL=search-compounds.tool.d.ts.map

package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map

@@ -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;AAgBjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAuO1B,CAAC"}
+{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAuQ1B,CAAC"}

package/dist/mcp-server/tools/definitions/search-compounds.tool.js

@@ -4,6 +4,7 @@
  * @module mcp-server/tools/definitions/search-compounds
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 import { COMPOUND_PROPERTIES } from '../../../services/pubchem/types.js';
 const searchTypeEnum = z.enum([
@@ -84,7 +85,8 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         searchType: z.string().describe('The search strategy used.'),
         totalFound: z.number().describe('Total CIDs found (before maxResults cap).'),
         results: z
-            .array(z.object({
+            .array(z
+            .object({
             cid: z.number().describe('PubChem Compound ID.'),
             identifier: z
                 .string()
@@ -94,9 +96,30 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 .record(z.string(), z.unknown())
                 .optional()
                 .describe('Compound properties when requested.'),
-        }))
+        })
+            .describe('Matching compound entry.'))
             .describe('Matching compounds.'),
     }),
+    errors: [
+        {
+            reason: 'missing_identifier_args',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'searchType is "identifier" but identifierType or identifiers were omitted',
+            recovery: 'Set identifierType (name/smiles/inchikey) and pass a non-empty identifiers array (1-25 entries).',
+        },
+        {
+            reason: 'missing_formula',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'searchType is "formula" but the formula field was omitted',
+            recovery: 'Pass formula in Hill notation, for example "C6H12O6" or "CaH2O2".',
+        },
+        {
+            reason: 'missing_structure_args',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'substructure/superstructure/similarity search missing query or queryType',
+            recovery: 'Provide both query (SMILES string or CID as string) and queryType ("smiles" or "cid").',
+        },
+    ],
     async handler(input, ctx) {
         const client = getPubChemClient();
         let allCids = [];
@@ -105,7 +128,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             case 'identifier': {
                 const { identifierType, identifiers } = input;
                 if (!identifierType || !identifiers) {
-                    throw new Error('identifierType and identifiers are required for identifier search');
+                    throw ctx.fail('missing_identifier_args', undefined, {
+                        ...ctx.recoveryFor('missing_identifier_args'),
+                    });
                 }
                 const lookups = identifiers.map(async (id) => {
                     let cids;
@@ -129,8 +154,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 break;
             }
             case 'formula': {
-                if (!input.formula)
-                    throw new Error('formula is required for formula search');
+                if (!input.formula) {
+                    throw ctx.fail('missing_formula', undefined, {
+                        ...ctx.recoveryFor('missing_formula'),
+                    });
+                }
                 allCids = await client.searchByFormula(input.formula, input.allowOtherElements);
                 break;
             }
@@ -138,7 +166,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             case 'superstructure':
             case 'similarity': {
                 if (!input.query || !input.queryType) {
-                    throw new Error('query and queryType are required for structure/similarity searches');
+                    throw ctx.fail('missing_structure_args', undefined, {
+                        ...ctx.recoveryFor('missing_structure_args'),
+                    });
                 }
                 allCids = await client.searchByStructure(input.searchType, input.query, input.queryType, input.threshold);
                 break;

package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map

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package/dist/services/pubchem/pubchem-client.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAGV,cAAc,EAEd,sBAAsB,EACtB,iBAAiB,EAQlB,MAAM,YAAY,CAAC;AA2MpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IAwBzB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA+BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAYjD,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAKxE,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC;QAAE,MAAM,CAAC,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA8B9E,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IA0E7D,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,sBAAsB,GAAG,IAAI,CAAC;IA8EtE,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA0EjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CA+B3C;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}

package/dist/services/pubchem/pubchem-client.js

@@ -187,6 +187,8 @@ function parsePictogram(text) {
     }
     return text.replace(/.*\//, '').replace(/\..*/, '');
 }
+/** Identity key for bioactivity entry dedup within an AID. */
+const activityKey = (v) => `${v.name ?? ''}|${v.value}|${v.unit ?? ''}`;
 // ── Client ───────────────────────────────────────────────────────────
 export class PubChemClient {
     pugBase = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug';
@@ -623,7 +625,6 @@ export class PubChemClient {
             }
             if (actValueUnit)
                 entry.unit = actValueUnit;
-            const activityKey = (v) => `${v.name ?? ''}|${v.value}|${v.unit ?? ''}`;
             const key = activityKey(entry);
             if (!bucket.activityValues.some((v) => activityKey(v) === key)) {
                 bucket.activityValues.push(entry);

package/dist/services/pubchem/pubchem-client.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubchem-mcp-server",
-  "version": "0.1.15",
+  "version": "0.1.17",
   "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.",
   "mcpName": "io.github.cyanheads/pubchem-mcp-server",
   "type": "module",
@@ -19,8 +19,6 @@
     "format": "biome check --write --unsafe .",
     "lint:mcp": "bun scripts/lint-mcp.ts",
     "test": "vitest run",
-    "dev:stdio": "bun --watch src/index.ts",
-    "dev:http": "MCP_TRANSPORT_TYPE=http bun --watch src/index.ts",
     "start:stdio": "node dist/index.js",
     "start:http": "MCP_TRANSPORT_TYPE=http node dist/index.js"
   },
@@ -62,16 +60,16 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.5.3",
+    "@cyanheads/mcp-ts-core": "^0.8.8",
     "pino-pretty": "^13.1.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.12",
+    "@biomejs/biome": "^2.4.14",
     "@types/node": "^25.6.0",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
-    "tsc-alias": "^1.8.16",
+    "tsc-alias": "^1.8.17",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.4"
+    "vitest": "^4.1.5"
   }
 }

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubchem-mcp-server",
     "source": "github"
   },
-  "version": "0.1.15",
+  "version": "0.1.17",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.1.15",
+      "version": "0.1.17",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -42,7 +42,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.1.15",
+      "version": "0.1.17",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }