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MCP RAG with ChromaDB - Multi-Format Document Support

By BINATI AInalytics </div>

A powerful MCP (Model Context Protocol) server that provides RAG (Retrieval-Augmented Generation) capabilities with support for multiple document formats. Powered by LangChain, ChromaDB, with OpenAI or Ollama embeddings.

Screenshots

Embedding Options

Choose your embedding provider:

• OpenAI (Recommended for Claude Desktop/MCP) - Reliable, fast, cloud-based. See OPENAI_SETUP.md
• Ollama (Free, Local) - No cost, runs locally, may have MCP connection issues

Quick Start with OpenAI:

1. Get API key from https://platform.openai.com/api-keys
2. Copy .env.example to .env
3. Set OPENAI_API_KEY=sk-your-key-here
4. Run python server.py

See OPENAI_SETUP.md for detailed instructions.

Supported Document Formats

• PDF (.pdf) - via PyPDF2
• Microsoft Word (.docx, .doc) - via python-docx
• PowerPoint (.pptx, .ppt) - via python-pptx
• Excel (.xlsx, .xls) - via openpyxl
• OpenDocument Text (.odt) - via odfpy
• HTML (.html, .htm) - via BeautifulSoup4
• Plain Text (.txt)
• Markdown (.md, .markdown)
• CSV (.csv)
• JSON (.json)
• XML (.xml)
• RTF (.rtf)

Features

• Multi-format document ingestion with automatic format detection
• Vector storage using ChromaDB with persistent storage
• Dual embedding support: OpenAI (recommended for MCP) or Ollama (free, local)
• Concurrent document processing for improved performance
• Batch database writes for efficiency (OpenAI processes 100 docs/batch)
• Support for URLs, single files, and entire directories
• Semantic search and retrieval with similarity scoring
• Graceful fallbacks when optional dependencies are missing
• Environment-based configuration via .env file

Installation

1. Clone or download this repository

2. Install Python dependencies:

pip install -r requirements.txt

OR

uv pip install -r requirements.txt

3. Choose your embedding provider:

   Option A: OpenAI (Recommended)

   # Copy environment file
   cp .env.example .env
   
   # Edit .env and add your API key
   # Get key from: https://platform.openai.com/api-keys
   OPENAI_API_KEY=sk-your-key-here
   

   Option B: Ollama (Free, Local)

   # Download from https://ollama.ai
   # Pull the embedding model
   ollama pull nomic-embed-text
   
   # Edit .env
   EMBEDDING_PROVIDER=ollama
   

   Note: Ollama may have connection issues in MCP/Claude Desktop context.

Usage

Running the Server

python server.py

Integration with Claude Desktop

To use this MCP server with Claude Desktop, add the following configuration to your Claude Desktop config file:

For MacOS: ~/Library/Application Support/Claude/claude_desktop_config.json For Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "mcp-rag-chroma": {
      "command": "uv",
      "args": [
        "--directory",
        "/path/to/mcp_rag_server",
        "run",
        "server.py"
      ]
    }
  }
}

Replace /path/to/mcp_rag_server with the actual path to your installation directory.

Alternatively, you can also integrate it directly from Github by updating claude desktop as follows:

"mcp-rag-chroma": {
	"command": "uvx",
	"args": [
		"--from",
		"git+https://github.com/CyprianFusi/MCP-rag-with-Chromadb.git",
		"server.py"
	]
}

If this is your first MCP server then use this instead:

{
  "mcpServers": {
	"mcp-rag-chroma": {
		"command": "uvx",
		"args": [
			"--from",
			"git+https://github.com/CyprianFusi/MCP-rag-with-Chromadb.git",
			"server.py"
		]
	}
  }
}

Available MCP Tools

1. ingest_document

Ingest documents from various sources and formats.

Parameters:

• source (str): URL, file path, or directory path

Examples:

• Ingest from URL: ingest_document("https://example.com/document.pdf")
• Ingest single file: ingest_document("/path/to/document.docx")
• Ingest entire directory: ingest_document("/path/to/documents/")

Supported sources:

• HTTP/HTTPS URLs (downloads file first)
• Local file paths (any supported format)
• Directory paths (processes all supported files)

2. retrieve

Search for relevant document chunks based on a query.

Parameters:

• query (str): Search query
• n (int, optional): Number of results to return (default: 5, max: 100)

Returns: List of chunks with text, metadata, and similarity scores

3. db_info

Get information about the database and its contents.

Returns: Database statistics, configuration, and unique sources

4. clear_db

Clear all data from the database.

Returns: Status message

5. ingest_pdf (Legacy)

Backwards-compatible PDF ingestion tool. Redirects to ingest_document.

Configuration

Edit the configuration section in server.py and .env:

server.py settings:

CHROMA_PATH = "chroma_db"                   # Vector database storage path
CHUNK_SIZE = 4096                           # Text chunk size
CHUNK_OVERLAP = 409                         # Overlap between chunks
COLLECTION_NAME = "documents"               # ChromaDB collection name
DOWNLOAD_DIR = "downloads"                  # Directory for downloaded files

.env settings:

# Embedding Provider (openai or ollama)
EMBEDDING_PROVIDER=openai

# OpenAI settings (if using OpenAI)
OPENAI_API_KEY=sk-your-key-here

# Ollama settings (if using Ollama)
EMBED_MODEL=nomic-embed-text
OLLAMA_BASE_URL=http://localhost:11434

Architecture

Document Processing Pipeline

1. Source Detection: Determines if source is URL, file, or directory
2. Download (if URL): Downloads file to local storage
3. Format Detection: Identifies document format by extension
4. Text Extraction: Uses appropriate extractor for the format
5. Text Chunking: Splits text into overlapping chunks
6. Embedding: Generates vector embeddings using OpenAI or Ollama (configurable)
7. Storage: Stores chunks and embeddings in ChromaDB

Extraction Methods

Each format has a dedicated extraction function:

• extract_text_from_pdf() - Extracts text from PDF pages
• extract_text_from_docx() - Extracts paragraphs and tables from Word docs
• extract_text_from_pptx() - Extracts text from PowerPoint slides
• extract_text_from_xlsx() - Extracts data from Excel sheets
• extract_text_from_odt() - Extracts text from OpenDocument files
• extract_text_from_html() - Parses HTML and extracts clean text
• extract_text_from_markdown() - Processes Markdown files
• And more...

The main extract_text() function routes to the appropriate extractor based on file extension.

Dependencies

Required

• langchain-chroma - ChromaDB integration
• langchain-ollama - Ollama embeddings
• langchain-core - Core LangChain functionality
• langchain-text-splitters - Text chunking
• requests - HTTP downloads
• fastmcp - MCP server framework

Document Format Support

• PyPDF2 - PDF extraction
• python-docx - DOCX extraction
• beautifulsoup4 + lxml - HTML/XML parsing
• python-pptx - PowerPoint extraction
• openpyxl - Excel extraction
• odfpy - OpenDocument extraction
• markdown - Markdown processing (optional)

Error Handling

The server includes comprehensive error handling:

• Graceful degradation when optional dependencies are missing
• Logging of extraction failures without crashing the entire process
• Informative error messages for unsupported file types
• Fallback to text extraction for unknown formats

Performance Optimizations

• Concurrent Processing: Multiple documents processed in parallel using ThreadPoolExecutor
• Batch Writes: All chunks written to database in a single operation
• Async/Await: Non-blocking I/O operations
• Read-Only Mode: Excel files opened in read-only mode for better performance
• Streaming Downloads: Large files downloaded in chunks

Limitations

• .doc (old Word format) support limited - requires python-docx which works best with .docx
• .ppt (old PowerPoint format) support limited - works best with .pptx
• .xls (old Excel format) support limited - works best with .xlsx
• RTF files use basic text extraction
• Scanned PDFs without OCR will not extract text
• Some complex document layouts may not preserve formatting

Troubleshooting

Ollama Connection Issues

Ensure Ollama is running and accessible:

curl http://localhost:11434/api/tags

Empty Text Extraction

• For PDFs: May be scanned images - consider OCR tools
• For other formats: Check file isn't corrupted or password-protected

License

This project is open source and available under the MIT License.

Acknowledgments

This project is built with and depends on several excellent open-source technologies:

Core Framework & Infrastructure:

• FastMCP - MCP server framework
• LangChain - Core LLM application framework
• ChromaDB - Vector database for embeddings storage

Embedding Providers:

• OpenAI - Cloud-based embedding API (recommended)
• Ollama - Local embedding models

Document Processing:

• PyPDF2 - PDF text extraction
• python-docx - Microsoft Word processing
• python-pptx - PowerPoint processing
• openpyxl - Excel spreadsheet processing
• Beautiful Soup - HTML/XML parsing
• odfpy - OpenDocument format support

Special thanks to the developers and maintainers of these projects for making this RAG server possible.

Contributing

Contributions welcome! To add support for new formats:

1. Add extraction function following the pattern extract_text_from_[format]()
2. Add format extension to SUPPORTED_EXTENSIONS
3. Add mapping in extract_text() function
4. Update documentation