PubChem MCP Server

/** * @fileoverview Defines the core logic, schemas, and types for the `pubchem_search_compound_by_identifier` tool. * @module src/mcp-server/tools/searchCompoundByIdentifier/logic */ import { z } from "zod"; import { pubChemApiClient } from "../../../services/pubchem/pubchemApiClient.js"; import { BaseErrorCode, McpError } from "../../../types-global/errors.js"; import { logger, type RequestContext } from "../../../utils/index.js"; // 1. Define and export the Zod schema for input validation export const PubchemSearchCompoundByIdentifierInputSchema = z.object({ identifierType: z .enum(["name", "smiles", "inchikey"]) .describe("The type of chemical identifier being provided."), identifier: z .string() .min(1, "Identifier cannot be empty.") .describe( "The identifier string. Examples: 'aspirin' for name, 'CC(=O)Oc1ccccc1C(=O)O' for SMILES, or a valid InChIKey.", ), }); // 2. Define and export the TypeScript type for the input export type PubchemSearchCompoundByIdentifierInput = z.infer< typeof PubchemSearchCompoundByIdentifierInputSchema >; // 3. Define and export the Zod schema for the tool's output export const PubchemSearchCompoundByIdentifierOutputSchema = z.object({ cids: z .array(z.number().int()) .describe( "A list of matching PubChem Compound IDs (CIDs). This is often a single result but can be multiple for ambiguous names.", ), }); // 4. Define and export the TypeScript type for the output export type PubchemSearchCompoundByIdentifierOutput = z.infer< typeof PubchemSearchCompoundByIdentifierOutputSchema >; /** * Core logic for the `pubchem_search_compound_by_identifier` tool. * It searches for PubChem Compound IDs (CIDs) using a common chemical identifier. * * @param {PubchemSearchCompoundByIdentifierInput} params - The validated input parameters. * @param {RequestContext} context - The request context for logging and tracing. * @returns {Promise<PubchemSearchCompoundByIdentifierOutput>} A promise that resolves with the search results. * @throws {McpError} Throws a structured error if the API request fails, the identifier is not found, or the response is malformed. */ export async function pubchemSearchCompoundByIdentifierLogic( params: PubchemSearchCompoundByIdentifierInput, context: RequestContext, ): Promise<PubchemSearchCompoundByIdentifierOutput> { logger.debug("Processing pubchem_search_compound_by_identifier logic...", { ...context, params, }); const { identifierType, identifier } = params; const path = `/compound/${identifierType}/${encodeURIComponent( identifier, )}/cids/JSON`; const response = await pubChemApiClient.get(path, context); logger.debug( "Raw PubChem response for pubchem_search_compound_by_identifier", { ...context, response, }, ); if (response?.Fault) { logger.error("PubChem API returned a fault for identifier search.", { ...context, fault: response.Fault, }); throw new McpError( BaseErrorCode.EXTERNAL_SERVICE_ERROR, `PubChem API Fault: ${response.Fault.Message}`, { ...context, details: response.Fault.Details }, ); } if ( !response?.IdentifierList?.CID || !Array.isArray(response.IdentifierList.CID) ) { logger.warning( "No CIDs found for the identifier search, or the response format was unexpected. Returning empty list.", { ...context, identifier, response }, ); return { cids: [] }; } const result: PubchemSearchCompoundByIdentifierOutput = { cids: response.IdentifierList.CID, }; logger.info( `Found ${result.cids.length} CIDs for identifier '${identifier}'.`, context, ); return result; }