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Neo4j Setup and Configuration Guide

This guide covers Neo4j-specific setup, configuration, and management for the Flexible GraphRAG system.

Neo4j Database Requirements

Neo4j Server Versions Supported:

  • Neo4j >= 2025.01
  • Neo4j >= 5.18.1

You can use:

  • Neo4j Enterprise Edition (Self Hosted)
  • Neo4j Community Edition (Free, Self hosted)
  • Neo4j Desktop (Free, Windows, Mac, Linux)
  • Neo4j AuraDB (free, professional, mission critical tiers) + Graph Analytics Serverless
  • Neo4j AuraDS

Required Neo4j Plugins

APOC Core is Required

Neo4j Desktop:

  • Install APOC core plugin (expand side panel)
  • Restart Neo4j

Neo4j Enterprise:

  • Copy APOC core jar from /product to /plugins dir
  • Restart Neo4j

Neo4j Community:

  • Download APOC core and copy to /plugins dir
  • Restart Neo4j

Neo4j AuraDB/AuraDS:

  • Have subset of APOC core with required features

GDS (Graph Data Science) is Required

Neo4j Desktop:

  • Install GDS plugin (expand side panel)
  • Restart Neo4j

Neo4j Enterprise:

  • Copy GDS jar from /labs to /plugins dir
  • Restart Neo4j

Neo4j Community:

  • Download GDS jar and copy to /plugins dir
  • Restart Neo4j

Neo4j AuraDB:

  • Requires Neo4j Graph Analytics Serverless or Neo4j AuraDS

Neo4j AuraDS:

  • Includes GDS

Neo4j Configuration

Add these settings to your .env file:

# Neo4j Configuration
NEO4J_URI=neo4j://localhost:7687
NEO4J_USER=neo4j
NEO4J_PASSWORD=your-neo4j-password

Neo4j Console Commands

Viewing Data

// View limited nodes
MATCH (n) RETURN n LIMIT 25

// View all nodes
MATCH (n) RETURN n

// Show all indexes
SHOW INDEXES

Cleanup Commands for LlamaIndex (for testing)

⚠️ Warning: These commands will delete data. Use only on test databases.

// 1. Delete all nodes and relationships
MATCH (n) DETACH DELETE n

// 2. Verify deletion
MATCH (n) RETURN n

// 3. Drop LlamaIndex indexes
DROP INDEX hybrid_search_vector IF EXISTS;
DROP INDEX entity IF EXISTS;

// 4. Drop LlamaIndex constraints  
// Entity and Node constraints for faster retrieval
DROP CONSTRAINT constraint_907a464e IF EXISTS;  // __Entity__ id constraint
DROP CONSTRAINT constraint_ec67c859 IF EXISTS;  // __Node__ id constraint

// 5. Show remaining indexes and constraints
SHOW INDEXES
SHOW CONSTRAINTS

// 6. Optional: Reset database completely (requires restart)
// STOP DATABASE neo4j
// DROP DATABASE neo4j IF EXISTS  
// CREATE DATABASE neo4j

🔍 LlamaIndex Database Structure

Node Labels:

  • __Entity__ - Entities with ID constraints
  • __Node__ - Nodes with ID constraints
  • Chunk - Text chunks with vector embeddings
  • Domain-specific entity types (PERSON, ORGANIZATION, etc.)

Indexes:

  • vector - Vector index on Chunk.embedding property (VECTOR type)
  • entity - Entity index for faster entity lookups

Constraints:

  • constraint_907a464e - RANGE constraint on __Entity__.id
  • constraint_ec67c859 - RANGE constraint on __Node__.id

Relationships:

  • MENTIONS - Between text chunks and entities
  • Domain-specific relationships between entities

API Endpoints (Neo4j-specific)

Graph Data

  • GET /api/graph - Get graph data (nodes and relationships)

System Info

  • GET /api/python-info - Get Python environment information

File Structure (Neo4j-specific)

  • neo4j_util.py - Neo4j database and GraphRAG utilities
  • factories.py - Includes Neo4j database factory
  • hybrid_system.py - Neo4j integration for vector and graph storage

Development Notes

  • The system builds knowledge graphs using Neo4j's capabilities
  • Both vector search and graph-based search are supported
  • For production use, configure proper security and authentication
  • Between tests use the LlamaIndex cleanup commands above to reset the database
  • Use on a test Neo4j database no one else is using

Troubleshooting

  1. Neo4j Connection: Ensure Neo4j is running on bolt://localhost:7687
  2. Missing Plugins: Verify APOC and GDS plugins are installed and active
  3. Memory: Large graphs may require increased Neo4j memory settings
  4. Authentication: Check Neo4j credentials in .env file