PubChem MCP Server

# Changelog All notable changes to this project will be documented in this file. ## [1.0.0] - 2025-06-30 ### New Project - **Project Refocus**: The project has been completely refactored from a generic MCP server template into a dedicated `pubchem-mcp-server`. This includes the removal of all previous example tools (`echoTool`, `catFactFetcher`, `imageTest`) and resources. ### Added - **PubChem Tool Suite**: Introduced a comprehensive suite of 10 tools for interacting with the PubChem API. Each tool is organized into its own module under `src/mcp-server/tools/` and follows the mandated "Logic Throws, Handler Catches" pattern. The new tools are: - `pubchem_search_compound_by_identifier`: Find CIDs by name, SMILES, or InChIKey. - `pubchem_fetch_compound_properties`: Retrieve detailed physicochemical properties for CIDs. - `pubchem_get_compound_image`: Fetch a 2D compound image as a blob. - `pubchem_search_compounds_by_structure`: Perform substructure, superstructure, or identity searches. - `pubchem_search_compounds_by_similarity`: Find structurally similar compounds. - `pubchem_search_compounds_by_formula`: Search for CIDs by molecular formula. - `pubchem_fetch_substance_details`: Get details for a specific Substance ID (SID). - `pubchem_fetch_assay_summary`: Retrieve summaries for a BioAssay ID (AID). - `pubchem_search_assays_by_target`: Find assays related to a biological target. - `pubchem_fetch_compound_xrefs`: Fetch external cross-references for a CID. - **PubChem API Client**: Implemented a new singleton `PubChemApiClient` (`src/services/pubchem/pubchemApiClient.ts`) to manage all interactions with the PubChem PUG REST API. It includes rate limiting (5 requests/sec) and centralized error handling. - **Error Types**: Added new error codes to `src/types-global/errors.ts` (`INVALID_INPUT`, `METHOD_NOT_ALLOWED`, `GATEWAY_TIMEOUT`, `EXTERNAL_SERVICE_ERROR`) to better handle specific API error conditions. ### Changed - **Server Registration**: Updated `src/mcp-server/server.ts` to remove old tool registrations and register the new suite of 10 PubChem tools. - **Dependencies**: Updated all dependencies to their latest versions in `package.json` and `package-lock.json`. - **Configuration**: Updated `.ncurc.json` to also reject the `dotenv` package from updates. - **Documentation**: - Updated `README.md` to reflect the project's new focus as a PubChem server. - Regenerated `docs/tree.md` to show the new tool structure. ### Removed - **Example Tools**: Deleted the `echoTool`, `catFactFetcher`, and `imageTest` directories and all associated logic, registration, and index files. - **Example Resources**: Removed the `echoResource` and its related files.