Scholarly Research MCP Server

# Changelog All notable changes to the Scholarly Research MCP Server project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/latest/), and this project follows standard release practices. ## [2.0.0] - 2024-12-19 ### 🎉 Major Release: Tool Consolidation #### Added - **5 Consolidated Tools**: Replaced 24 individual tools with 5 powerful, multi-functional tools - **Unified Search Interface**: Single tool for searching across all sources (PubMed, Google Scholar, ArXiv, JSTOR) - **Comprehensive Paper Analysis**: One tool for paper retrieval, content extraction, and analysis - **Integrated Citation Management**: Combined citation generation, counting, and related paper discovery - **Centralized Preferences**: Single tool for managing all user preferences - **Web Research Suite**: Unified interface for web scraping and content extraction #### Changed - **Tool Count**: Reduced from 24 tools to 5 tools (80% reduction) - **Interface Consistency**: Standardized parameter patterns across all tools - **Performance**: Improved startup time and reduced memory usage - **Maintainability**: Centralized error handling and reduced code duplication - **User Experience**: Easier to remember and use fewer, more powerful tools #### Removed - 19 individual MCP tools (consolidated into 5) - Unnecessary project files (`ion`, `cholarly-research-mcp version`, temporary test files) - Code duplication across tool implementations #### Fixed - Project structure cleaned and organized - Cursor editor files added to .gitignore - Inconsistent tool interfaces standardized - Error handling centralized and improved ### 🔧 Technical Improvements - **Consolidated Architecture**: Single entry point with unified tool definitions - **Better Error Handling**: Centralized error management with consistent formatting - **Improved Testing**: Streamlined test suite with better organization - **Documentation**: Comprehensive guides for the new consolidated approach ### 📚 Documentation Updates - **README.md**: Updated to reflect new consolidated approach - **README-consolidated.md**: Detailed explanation of consolidation benefits - **TOOL_CONSOLIDATION.md**: Quick reference for tool mapping - **PROJECT_STRUCTURE_CLEAN.md**: Clean project structure documentation ## [Unreleased] ### Planned - JSTOR integration - Enhanced analytics and insights - Performance optimization - Additional data source adapters ## Recent Releases ### Latest Release - 2024-12-19 (Previous Version) #### Added - **Google Scholar Integration**: Full web scraping support for Google Scholar search and paper details - **Firecrawl MCP Integration**: Professional web scraping service for enhanced reliability - **Unified Search Interface**: Combined search across PubMed and Google Scholar with deduplication - **Enhanced Citation Tracking**: Google Scholar citation counts and related paper discovery - **Multi-Source Paper Retrieval**: Access papers from both PubMed and Google Scholar simultaneously - **Advanced Sorting Options**: Sort by relevance, date, or citation count across all sources - **Dual Scraping Methods**: Choose between Firecrawl (recommended) and Puppeteer with automatic fallback - **Comprehensive Test Suites**: Bash, Python, and JavaScript test runners with 13/13 tests passing - **Enhanced MCP Tools**: 16 comprehensive tools for scholarly research #### Changed - **Enhanced Unified Search**: Improved adapter with configurable scraping preferences - **Better Error Handling**: Automatic fallback between scraping methods - **Improved Documentation**: Comprehensive README and project structure documentation - **Test Coverage**: Expanded testing to cover all new functionality #### Dependencies - Added Puppeteer for Google Scholar web scraping - Added Cheerio for HTML parsing - Added TypeScript types for Puppeteer and Cheerio #### Technical - **Node.js Compatibility**: Ensured compatibility with Node.js 18+ - **Type Safety**: Enhanced TypeScript definitions and type checking - **Build Process**: Improved TypeScript compilation and bundling - **Package Structure**: Optimized NPM package contents and exclusions ### Previous Release - 2024-12-18 #### Fixed - **PMC URL Issues**: Corrected PubMed Central URL handling for reliable full-text access - **Enhanced Full Text Retrieval**: Increased default text length from 5,000 to 50,000 characters - **Improved Section Extraction**: Better algorithms for identifying and organizing paper sections - **Dual URL Support**: Now supports both PMCID and PMID formats for accessing papers - **Better Content Processing**: Enhanced HTML cleaning and text extraction from PMC sources #### Changed - **Default Text Length**: Increased from 5,000 to 50,000 characters for better content coverage - **URL Handling**: Improved fallback logic between PMCID and PMID access methods - **Content Processing**: Enhanced HTML cleaning and text extraction algorithms #### Technical - **Error Handling**: Better fallback mechanisms for URL resolution - **Content Extraction**: Improved algorithms for section detection and organization - **Performance**: Optimized content processing and text extraction ### Earlier Releases #### Initial Release - 2024-12-15 - **Basic PubMed Integration**: Search and fetch papers using NCBI's E-utilities API - **MCP Server Framework**: Model Context Protocol server implementation - **TypeScript Support**: Full TypeScript implementation with type definitions - **Full Text Extraction**: Access to complete paper content when available - **Section Analysis**: Extract and organize paper sections (Introduction, Methods, Results, etc.) - **Evidence Mining**: Find specific quotes, statistics, findings, and conclusions - **Content Search**: Search within papers for specific terms and phrases - **Citation Support**: Generate citations in various formats (BibTeX, EndNote, APA, MLA) - **Rate Limiting**: Built-in rate limiting to respect API constraints #### Technical - **MCP Protocol**: Standard interface for AI assistants and tools - **PubMed Integration**: NCBI E-utilities API integration - **PMC Support**: Direct access to PubMed Central full-text articles - **TypeScript**: Full TypeScript support with strict type checking - **Project Structure**: Initial project setup and configuration - **Build System**: TypeScript compilation and bundling - **Dependencies**: Core MCP SDK and utility libraries --- ## Release History Summary | Date | Major Features | Status | |------|----------------|---------| | 2024-12-19 | **Tool Consolidation (24→5 tools), Clean Project Structure** | Released | | 2024-12-19 | Google Scholar, Firecrawl, Unified Search | Released | | 2024-12-18 | PMC URL fixes, Enhanced text extraction | Released | | 2024-12-17 | Initial PubMed integration, MCP server | Released | | 2024-12-16 | Basic framework, TypeScript support | Released | | 2024-12-15 | Project initialization | Released | ## Migration Guide ### Upgrading from Previous Releases The latest release introduces significant new functionality: 1. **New Dependencies**: Ensure Node.js 18+ and install new packages 2. **Google Scholar**: New scraping capabilities require Puppeteer dependencies 3. **Enhanced Search**: New unified search interface with multiple sources 4. **Test Suites**: Comprehensive testing framework for validation ### Breaking Changes - **Current Release**: Latest release - **LTS Release**: Latest release (Long-term support) - **End of Life**: No releases currently end-of-life - **Security Updates**: All releases receive security updates ## Support For detailed information about specific releases or migration assistance, please open an issue on GitHub.