iflow-mcp_ferparra_graph-rag-mcp-server 0.1.0

Graph RAG MCP Server for Obsidian vault with unified ChromaDB store and Gemini 2.5 Flash

Graph RAG MCP Server for Obsidian

A powerful local-first Graph-RAG system that combines ChromaDB unified store with metadata-based graph relationships and Gemini 2.5 Flash for intelligent Q&A over your Obsidian vault.

🌟 Features

• 📊 Unified Database Architecture: ChromaDB with metadata-based graph relationships for both semantic search and graph traversal
• 🧠 Intelligent Semantic Chunking: Respects markdown structure (headers, sections, lists, code blocks)
• 🎯 PARA Taxonomy Classification: AI-powered organization using Projects, Areas, Resources, Archive system
• 🤖 RAG-Powered Q&A: Multi-hop retrieval with Gemini 2.5 Flash
• 🕸️ Graph Navigation: Explore backlinks, tags, and semantic relationships
• 🔄 Real-time Sync: File watcher for automatic indexing
• 🏠 Local-First: All processing happens locally (except Gemini API calls)
• 📝 Multi-Client MCP Support: Works with Claude Desktop, Cursor, and Raycast
• ⚡ Dual Transport Modes: stdio for Claude Desktop, HTTP for other clients
• 🛠️ Automated Installation: One-command setup with client detection
• 🔒 Strongly Typed: Pydantic models throughout for reliability

🎯 Supported MCP Clients

• 🤖 Claude Desktop: Full stdio integration with automatic configuration
• 📝 Cursor: HTTP mode with MCP extension support
• ⚡ Raycast: HTTP API with custom extension templates
• 🔌 Any MCP Client: Standard MCP protocol support (stdio/HTTP)

🏗️ Architecture

┌─────────────────┐    ┌─────────────────┐
│   Obsidian      │    │   ChromaDB      │
│     Vault       │───▶│ (Unified Store) │
│                 │    │ Vector + Graph  │
└─────────────────┘    │   Metadata      │
         │              └─────────────────┘
         │                       │
         │                       ▼
         │              ┌─────────────────┐
         │              │      DSPy       │
         └─────────────▶│   RAG Engine    │
                        │  + Gemini 2.5   │
                        │ (Multi-hop      │
                        │  Retrieval)     │
                        └─────────────────┘
                                 │
                                 ▼
                        ┌─────────────────┐
                        │   MCP Server    │
                        │   (FastMCP)     │
                        └─────────────────┘
                                 │
                                 ▼
                        ┌─────────────────┐
                        │ Claude Desktop  │
                        │   Integration   │
                        └─────────────────┘

🚀 Quick Start

Automated Installation (Recommended)

The easiest way to get started with Claude Desktop, Cursor, or Raycast:

# Interactive setup wizard
uv run install.py

# Or non-interactive with your settings
uv run install.py --vault "/path/to/your/vault" --api-key "your_key"

The installer will:

• ✅ Detect your installed MCP clients (Claude Desktop, Cursor, Raycast)
• ⚙️ Configure each client automatically
• 📦 Install all dependencies
• 🧪 Test the installation
• 📝 Create environment configuration

Manual Installation

If you prefer manual setup:

1. Install uv (if not installed)

curl -LsSf https://astral.sh/uv/install.sh | sh  # macOS/Linux

2. Install Dependencies

uv sync

3. Configure Environment

cp configs/.env.example .env
# Edit .env and add your GEMINI_API_KEY and vault paths

4. Index Your Vault

# Full indexing (unified ChromaDB store)
uv run scripts/reindex.py all

# Check indexing status
uv run scripts/reindex.py status

5. Configure Your MCP Client

Claude Desktop (stdio mode):

{
  "mcpServers": {
    "graph-rag-obsidian": {
      "command": "uvx",
      "args": ["--python", "3.13", "--from", ".", "graph-rag-mcp-stdio"],
      "cwd": "/path/to/graph-rag-mcp-server",
      "env": {
        "GEMINI_API_KEY": "your_api_key_here",
        "OBSIDIAN_RAG_VAULTS": "/path/to/your/vault"
      }
    }
  }
}

Cursor (HTTP mode):

# Start HTTP server
uv run graph-rag-mcp-http

# Configure Cursor MCP extension to use http://localhost:8765

Raycast (HTTP mode):

# Start HTTP server  
uv run graph-rag-mcp-http

# Install generated Raycast extension

For detailed configuration instructions, see SETUP.md.

🛠️ Available Commands

MCP Server Modes

# Interactive installer
uv run install.py

# Claude Desktop (stdio mode)
uvx --python 3.13 --from . graph-rag-mcp-stdio

# Cursor/Raycast (HTTP mode)  
uv run graph-rag-mcp-http

# HTTP with custom port
uv run graph-rag-mcp-http --port 9000

# Direct stdio runs (alternative)
uv run main.py                    # stdio mode
uv run src/mcp_server.py         # stdio mode  

Indexing Scripts

# Full indexing
uv run scripts/reindex.py all

# ChromaDB unified store
uv run scripts/reindex.py unified

# Check status
uv run scripts/reindex.py status

Real-time Watching

# Start file watcher
uv run scripts/reindex_watch.py start

# Test file detection
uv run scripts/reindex_watch.py test

PARA Taxonomy Enrichment

Enhance your vault with intelligent PARA system classification using DSPy:

# Analyze current vault taxonomy state
uv run scripts/enrich_para_taxonomy.py analyze --sample 100

# Preview enrichment (dry run) on sample notes
uv run scripts/enrich_para_taxonomy.py enrich --limit 10 --dry-run

# Apply enrichment to specific notes
uv run scripts/enrich_para_taxonomy.py enrich "path/to/note.md" --apply

# Bulk enrichment with filters
uv run scripts/enrich_para_taxonomy.py enrich --limit 50 --folder "Projects" --apply

# FULL VAULT ENRICHMENT (new!)
# Preview entire vault enrichment
uv run scripts/enrich_para_taxonomy.py enrich-all --dry-run

# Apply to entire vault (skips already enriched by default)
uv run scripts/enrich_para_taxonomy.py enrich-all --apply

# Force re-enrichment of entire vault
uv run scripts/enrich_para_taxonomy.py enrich-all --apply --force-all

# Customize batch size for large vaults
uv run scripts/enrich_para_taxonomy.py enrich-all --apply --batch-size 25

PARA Classification Features:

• 🎯 Intelligent Classification: Uses Gemini 2.5 Flash to classify notes into Projects, Areas, Resources, Archive
• 🏷️ Hierarchical Tags: Suggests structured tags like #para/project/ai/automation
• 🔗 Relationship Discovery: Finds potential links between related notes with validation
• 💡 Concept Extraction: Identifies key concepts and themes
• 🛡️ Safe Updates: Only adds frontmatter, never modifies content
• 📊 Confidence Scoring: Provides reasoning and confidence for classifications
• ⚡ Batch Processing: Process entire vaults efficiently with configurable batch sizes
• 🔄 Smart Deduplication: Avoids reprocessing already enriched notes

🔧 MCP Tools

The server exposes these tools for Claude:

Search & Q&A

• search_notes: Vector search across vault
• answer_question: RAG-powered Q&A with citations
• graph_neighbors: Find related notes via graph
• get_subgraph: Extract note subgraphs

Note Operations

• create_note: Create new notes with auto-enriched frontmatter
• list_notes: Browse vault contents
• read_note: Get full note content
• get_note_properties: Read frontmatter
• update_note_properties: Modify frontmatter
• add_content_to_note: Append content

Graph Navigation

• get_backlinks: Find notes linking to target
• get_notes_by_tag: Find notes by tag

Management

• archive_note: Move notes to archive
• create_folder: Create directories
• reindex_vault: Reindex unified ChromaDB store
• enrich_notes: Apply PARA taxonomy enrichment to notes

⚙️ Configuration

Key settings in .env:

# Required
GEMINI_API_KEY=your_key_here

# ChromaDB configuration
OBSIDIAN_RAG_CHROMA_DIR=/custom/path/to/.chroma_db
OBSIDIAN_RAG_COLLECTION=vault_collection

# Optional customization
OBSIDIAN_RAG_EMBEDDING_MODEL=all-MiniLM-L6-v2
OBSIDIAN_RAG_GEMINI_MODEL=gemini-2.5-flash

# Semantic chunking configuration
OBSIDIAN_RAG_CHUNK_STRATEGY=semantic  # or "character" for simple chunking
OBSIDIAN_RAG_SEMANTIC_MIN_CHUNK_SIZE=100
OBSIDIAN_RAG_SEMANTIC_MAX_CHUNK_SIZE=3000
OBSIDIAN_RAG_SEMANTIC_MERGE_THRESHOLD=200

🏃‍♂️ Usage Examples

Search Your Vault

# Vector search
results = search_notes("machine learning algorithms", k=5)

# Q&A with context
answer = answer_question("What did I learn about transformers?")

Explore Relationships

# Find related notes
neighbors = graph_neighbors("Deep Learning", depth=2)

# Get backlinks
backlinks = get_backlinks("Neural Networks")

# Find by tag
tagged_notes = get_notes_by_tag("ai")

Manage Notes

# Create a new note with auto-enrichment
note = create_note(
    title="Machine Learning Breakthrough",
    content="# Key Findings\n\nDiscovered new optimization technique...",
    folder="Research",
    tags=["ml", "optimization"],
    para_type="project",  # Hint for PARA classification
    enrich=True  # Apply AI enrichment
)

# Read note
content = read_note("Research/AI Progress.md")

# Update properties
update_note_properties("Research/AI Progress.md", {
    "status": "completed",
    "tags": ["ai", "research", "finished"]
})

Creating Notes with Auto-Enrichment

The create_note tool creates properly formatted Obsidian notes with:

• Clean YAML frontmatter
• Automatic PARA classification (if content provided)
• Intelligent tag suggestions
• Potential link discovery
• Timestamps and metadata

Example created note:

---
created: '2025-08-23T20:30:00.000000'
modified: '2025-08-23T20:30:00.000000'
para_type: project
para_category: ai/research
para_confidence: 0.85
key_concepts:
- Machine Learning Optimization
- Gradient Descent Improvements
- Performance Benchmarking
tags:
- ml
- optimization
- para/project
- para/project/ai/research
- tech/ai/ml/optimization
potential_links:
- '[[Optimization Techniques]]'
- '[[Research Log 2025]]'
enrichment_version: '1.0'
last_enriched: '2025-08-23T20:30:00.000000'
enrichment_model: gemini-2.5-flash
---

# Machine Learning Breakthrough

Your content here...

PARA Enrichment Workflow

Step 1: Analyze your vault

uv run scripts/enrich_para_taxonomy.py analyze --sample 100

Shows current taxonomy state and enrichment potential.

Step 2: Test on subset (dry run)

uv run scripts/enrich_para_taxonomy.py enrich --limit 5 --dry-run

Preview classifications without making changes.

Step 3: Apply enrichment

# Start small
uv run scripts/enrich_para_taxonomy.py enrich --limit 20 --apply

# Scale up
uv run scripts/enrich_para_taxonomy.py enrich --limit 100 --apply

Example enriched note:

---
para_type: project
para_category: AI/Automation  
para_confidence: 0.9
key_concepts:
  - AI Agent Development
  - Computer Use Automation
  - Grounded AI Systems
tags:
  - "#project/ai/automation"
  - "#area/ai/development"
potential_links:
  - "Related Project Name"
enrichment_version: "1.0"
last_enriched: "2025-08-23T17:59:32"
---
# Your original note content remains unchanged

🔍 How It Works

1. File Parsing: Extracts markdown content, frontmatter, wikilinks, and tags
2. Semantic Chunking: Intelligent chunking based on markdown structure (headers, sections, lists)
3. Vector Indexing: Stores semantic chunks with embeddings in ChromaDB
4. Graph Metadata: Stores notes, links, tags, and chunk relationships as ChromaDB metadata
5. PARA Classification: Uses DSPy + Gemini to classify notes into Projects, Areas, Resources, Archive
6. RAG Pipeline: Multi-hop retrieval combining vector search with graph traversal
7. MCP Interface: Exposes all capabilities via Model Context Protocol

🆕 What's New

Unified ChromaDB Architecture (Latest Update!)

• ⚡ Simplified Architecture: Single database for both vector search and graph relationships
• 🗄️ Metadata-based Graph: Efficient graph storage using ChromaDB's native metadata capabilities
• 🔧 Colocated Data: Vector embeddings and graph relationships stored together for optimal query performance
• 📦 Reduced Dependencies: No need for separate RDF libraries or stores
• 🚀 Performance: Streamlined queries with direct metadata access
• 💾 Efficient Storage: Single store with optimized embedding and metadata storage

Enhanced PARA Taxonomy

• 🤖 AI-Powered Classification: Automatic categorization into Projects, Areas, Resources, Archive
• 🏷️ Smart Tagging: Hierarchical tags like #para/project/ai/automation
• 🔗 Validated Wikilinks: Only suggests links to existing notes in your vault
• 📊 Batch Processing: Process entire vaults with configurable batch sizes
• 🎯 Obsidian-Native: Clean YAML frontmatter without markdown formatting

ChromaDB Metadata Schema

The system stores graph relationships as ChromaDB metadata:

# Note-level metadata
metadata = {
    "note_id": "my_note",
    "title": "My Note Title",
    "path": "/path/to/note.md",
    "tags": "important,ai,project",
    "links_to": "other_note,related_note",
    "backlinks_from": "source_note,another_note",
    "vault": "my_vault"
}

# Chunk-level metadata (semantic chunking)
chunk_metadata = {
    "chunk_id": "my_note#chunk_0",
    "chunk_type": "section",
    "header_text": "Introduction",
    "header_level": 2,
    "importance_score": 0.8,
    "sequential_next": "my_note#chunk_1",
    "sequential_prev": "",
    "parent_chunk": "my_note#header_0",
    "child_chunks": "my_note#chunk_1,my_note#chunk_2",
    "sibling_chunks": "my_note#chunk_3",
    "semantic_chunk": True
}

🛡️ Security & Privacy

• Local-First: All data processing happens on your machine
• API Calls: Only Gemini API for text generation (optional)
• No Data Leakage: Vault content never leaves your control
• Path Validation: Prevents directory traversal attacks

🧪 Testing

Test Suite (pytest)

Install test dependencies and run the suite:

# Using uv (recommended)
uv sync --extra test
uv run pytest -q

# Or using the local virtualenv
PYTHONPATH=. .venv/bin/pytest -q

Common invocations:

# Only unit / integration
PYTHONPATH=. .venv/bin/pytest tests/unit -q
PYTHONPATH=. .venv/bin/pytest tests/integration -q

# Coverage (threshold configured in pytest.ini)
PYTHONPATH=. .venv/bin/pytest --cov -q

# Markers
pytest -m unit
pytest -m integration
pytest -m "not slow"

Notes:

• If you see ModuleNotFoundError: No module named 'tests', prefix commands with PYTHONPATH=..
• Integration tests run without network. Embeddings fall back to a built‑in default and DSPy caches write to .cache/. Override with XDG_CACHE_HOME or DSPY_CACHEDIR if needed.

Operational Smoke Checks

# Test indexing
uv run scripts/reindex.py status

# Test file watching  
uv run scripts/reindex_watch.py test

# Test unified store
uv run python -c "
from src.unified_store import UnifiedStore
from src.config import settings
store = UnifiedStore(
    client_dir=settings.chroma_dir,
    collection_name=settings.collection,
    embed_model=settings.embedding_model
)
stats = store.get_stats()
print(f'Store stats: {stats}')
"

🔍 Smart Search Response Contract

The smart_search MCP tool now returns a typed SmartSearchResponse payload:

• schema_version, status (ok/degraded/error), and composite confidence.
• diagnostics with retrieval method, intent + confidence, mean distance, retry count, circuit-breaker state, and warnings.
• recommendations (up to three actionable suggestions) whenever the response is degraded or fails.
• Legacy keys (hits, total_results, strategy_used) remain for one release to ease migration.

Inspect responses locally with the updated CLI helper:

uv run scripts/dspy_mcp_client.py --vault /path/to/vault --query "My quarterly goals" --json

Additional MCP tools complement the contract:

• health_check — runs registered probes, returning cache stats, rate limiter tokens, circuit-breaker state, and metrics counters.
• get_dspy_optimization_status — surfaces optimizer schedule/lock state and whether a background run is pending.
• force_dspy_optimization — triggers an optimization cycle (guarded by async/file locks, executed via a background thread).

Each smart-search invocation also emits a structured log line (SMART_SEARCH_RESULT { ... }) containing the query, status, confidence, retrieval method, retries, circuit-breaker state, warnings, and duration. Simple in-process counters (smart_search_ok/degraded/error, cb_open_events, embed_fallback_events) are exposed via health_check for quick instrumentation.

🔧 Troubleshooting

ChromaDB Issues

• ChromaDB stores data in .chroma_db/ directory
• Check disk space and permissions
• Try full reindex: uv run scripts/reindex.py unified --full
• Database is automatically created on first run

Unified Store Issues

• Check disk space for .chroma_db/
• Try full reindex: uv run scripts/reindex.py unified --full
• Ensure notes are properly deduplicated (fixed in latest version)

Gemini API Issues

• Verify API key: uv run scripts/reindex.py status
• Check rate limits and quotas
• For enrichment errors, try smaller batch sizes

Enrichment Issues

• Use --dry-run to preview changes first
• Check note has content (empty files are skipped)
• Reduce batch size if hitting API limits: --batch-size 10

📁 Project Structure

graph-rag-mcp-server/
├── src/
│   ├── config.py               # Configuration management
│   ├── fs_indexer.py           # File parsing & metadata extraction
│   ├── semantic_chunker.py     # Intelligent markdown-aware chunking
│   ├── chroma_store.py         # Vector database operations
│   ├── unified_store.py        # ChromaDB unified operations (vectors + graph metadata)
│   ├── dspy_rag.py             # RAG engine with Gemini 2.5 Flash
│   └── mcp_server.py           # FastMCP server & tool definitions
├── scripts/
│   ├── reindex.py              # Database indexing utilities
│   ├── reindex_watch.py        # Real-time file monitoring
│   ├── enrich_para_taxonomy.py # PARA classification & enrichment
│   └── migrate_rdf_store.py    # (removed)
├── configs/
│   ├── claude-desktop.json     # Claude Desktop MCP configuration template
│   ├── cursor-mcp.json         # Cursor MCP configuration template  
│   ├── raycast-config.json     # Raycast extension configuration template
│   └── .env.example            # Environment configuration template
├── install.py                  # Automated installer & configurator
├── main.py                     # Alternate MCP server entry point (stdio)
├── pyproject.toml              # Dependencies & entry points (uv managed)
├── SETUP.md                    # Comprehensive setup guide
└── README.md                   # Project overview & quick start

🤝 Contributing

1. Fork the repository
2. Create a feature branch
3. Add tests for new functionality
4. Submit a pull request

📄 License

MIT License - see LICENSE file for details.

---

Built with modern python stack: Pydantic, ChromaDB, DSPy, FastMCP, and the latest google-genai SDK.

Comprehensive Test Framework & Evaluation Suite

This repo includes a comprehensive test framework with structured fixtures at tests/fixtures/content/ and an evaluation runner that executes deterministic evals for the MCP tools. The evals use distinctive phrases and low-temperature LLM configs so results are stable across embedding and Gemini model choices.

Running Tests:

• Unit tests: uv run python -m pytest tests/unit/ -v
• All tests: uv run python scripts/run_tests.py all
• Evaluation suite: uv run python tests/evals/runner.py

Test Categories:

• Unit Tests (tests/unit/): Query intent detection, fuzzy matching, relationship weighting, URI generation
• Integration Tests (tests/integration/): Full MCP server component integration
• Evaluation Suite (tests/evals/): Performance metrics and quality assessment
• Test Fixtures (tests/fixtures/): Structured test content (planets, health, projects)

The evaluation framework creates temporary test environments, reinitializes app state, reindexes content, and validates:

• search_notes and smart_search with strategy routing
• graph_neighbors, get_subgraph, get_backlinks, get_notes_by_tag
• CRUD operations: create_note, add_content_to_note, archive_note
• Note management: read_note, get_note_properties, update_note_properties, list_notes

Test environments are automatically created and cleaned up. All test content uses structured Pydantic models with proper type validation.