reorganization

2026-01-31 17:13:27 -05:00
parent 1fd2e860b2
commit ad39904dda
87 changed files with 1019 additions and 237 deletions
--- a/docs/MIGRATIONS.md
+++ b/docs/MIGRATIONS.md
@@ -0,0 +1,54 @@
+# Database Migrations with Aerich
+
+## Initial Setup (Run Once)
+
+1. Install dependencies:
+```bash
+uv pip install -e .
+```
+
+2. Initialize Aerich:
+```bash
+aerich init-db
+```
+
+This will:
+- Create a `migrations/` directory
+- Generate the initial migration based on your models
+- Create all tables in the database
+
+## When You Add/Change Models
+
+1. Generate a new migration:
+```bash
+aerich migrate --name "describe_your_changes"
+```
+
+Example:
+```bash
+aerich migrate --name "add_user_profile_model"
+```
+
+2. Apply the migration:
+```bash
+aerich upgrade
+```
+
+## Common Commands
+
+- `aerich init-db` - Initialize database (first time only)
+- `aerich migrate --name "description"` - Generate new migration
+- `aerich upgrade` - Apply pending migrations
+- `aerich downgrade` - Rollback last migration
+- `aerich history` - Show migration history
+- `aerich heads` - Show current migration heads
+
+## Docker Setup
+
+In Docker, migrations run automatically on container startup via the startup script.
+
+## Notes
+
+- Migration files are stored in `migrations/models/`
+- Always commit migration files to version control
+- Don't modify migration files manually after they're created
--- a/docs/VECTORSTORE.md
+++ b/docs/VECTORSTORE.md
@@ -0,0 +1,97 @@
+# Vector Store Management
+
+This document describes how to manage the ChromaDB vector store used for RAG (Retrieval-Augmented Generation).
+
+## Configuration
+
+The vector store location is controlled by the `CHROMADB_PATH` environment variable:
+
+- **Development (local)**: Set in `.env` to a local path (e.g., `/path/to/chromadb`)
+- **Docker**: Automatically set to `/app/data/chromadb` and persisted via Docker volume
+
+## Management Commands
+
+### CLI (Command Line)
+
+Use the `scripts/manage_vectorstore.py` script for vector store operations:
+
+```bash
+# Show statistics
+python scripts/manage_vectorstore.py stats
+
+# Index documents from Paperless-NGX (incremental)
+python scripts/manage_vectorstore.py index
+
+# Clear and reindex all documents
+python scripts/manage_vectorstore.py reindex
+
+# List documents
+python scripts/manage_vectorstore.py list 10
+python scripts/manage_vectorstore.py list 20 --show-content
+```
+
+### Docker
+
+Run commands inside the Docker container:
+
+```bash
+# Show statistics
+docker compose exec raggr python scripts/manage_vectorstore.py stats
+
+# Reindex all documents
+docker compose exec raggr python scripts/manage_vectorstore.py reindex
+```
+
+### API Endpoints
+
+The following authenticated endpoints are available:
+
+- `GET /api/rag/stats` - Get vector store statistics
+- `POST /api/rag/index` - Trigger indexing of new documents
+- `POST /api/rag/reindex` - Clear and reindex all documents
+
+## How It Works
+
+1. **Document Fetching**: Documents are fetched from Paperless-NGX via the API
+2. **Chunking**: Documents are split into chunks of ~1000 characters with 200 character overlap
+3. **Embedding**: Chunks are embedded using OpenAI's `text-embedding-3-large` model
+4. **Storage**: Embeddings are stored in ChromaDB with metadata (filename, document type, date)
+5. **Retrieval**: User queries are embedded and similar chunks are retrieved for RAG
+
+## Troubleshooting
+
+### "Error creating hnsw segment reader"
+
+This indicates a corrupted index. Solution:
+
+```bash
+python scripts/manage_vectorstore.py reindex
+```
+
+### Empty results
+
+Check if documents are indexed:
+
+```bash
+python scripts/manage_vectorstore.py stats
+```
+
+If count is 0, run:
+
+```bash
+python scripts/manage_vectorstore.py index
+```
+
+### Different results in Docker vs local
+
+Docker and local environments use separate ChromaDB instances. To sync:
+
+1. Index inside Docker: `docker compose exec raggr python scripts/manage_vectorstore.py reindex`
+2. Or mount the same volume for both environments
+
+## Production Considerations
+
+1. **Volume Persistence**: Use Docker volumes or persistent storage for ChromaDB
+2. **Backup**: Regularly backup the ChromaDB data directory
+3. **Reindexing**: Schedule periodic reindexing to keep data fresh
+4. **Monitoring**: Monitor the `/api/rag/stats` endpoint for document counts
--- a/docs/deployment.md
+++ b/docs/deployment.md
@@ -170,11 +170,12 @@ docker compose exec raggr bash -c "sleep 5 && aerich upgrade"

 | File | Purpose |
 |------|---------|
-| `services/raggr/pyproject.toml` | Aerich config (`[tool.aerich]` section) |
-| `services/raggr/migrations/models/` | Migration files |
-| `services/raggr/startup.sh` | Production startup (runs `aerich upgrade`) |
-| `services/raggr/startup-dev.sh` | Dev startup (runs `aerich upgrade` or `init-db`) |
-| `services/raggr/app.py` | Contains `TORTOISE_CONFIG` |
+| `pyproject.toml` | Aerich config (`[tool.aerich]` section) |
+| `migrations/models/` | Migration files |
+| `startup.sh` | Production startup (runs `aerich upgrade`) |
+| `startup-dev.sh` | Dev startup (runs `aerich upgrade` or `init-db`) |
+| `app.py` | Contains `TORTOISE_CONFIG` |
+| `aerich_config.py` | Aerich initialization configuration |

 ## Quick Reference

--- a/docs/development.md
+++ b/docs/development.md
@@ -0,0 +1,258 @@
+# Development Guide
+
+This guide explains how to run SimbaRAG in development mode.
+
+## Quick Start
+
+### Option 1: Local Development (Recommended)
+
+Run PostgreSQL in Docker and the application locally for faster iteration:
+
+```bash
+# 1. Start PostgreSQL
+docker compose -f docker-compose.dev.yml up -d
+
+# 2. Set environment variables
+export DATABASE_URL="postgres://raggr:raggr_dev_password@localhost:5432/raggr"
+export CHROMADB_PATH="./chromadb"
+export $(grep -v '^#' .env | xargs)  # Load other vars from .env
+
+# 3. Install dependencies (first time)
+pip install -r requirements.txt
+cd raggr-frontend && yarn install && yarn build && cd ..
+
+# 4. Run migrations
+aerich upgrade
+
+# 5. Start the server
+python app.py
+```
+
+The application will be available at `http://localhost:8080`.
+
+### Option 2: Full Docker Development
+
+Run everything in Docker with hot reload (slower, but matches production):
+
+```bash
+# Uncomment the raggr service in docker-compose.dev.yml first!
+
+# Start all services
+docker compose -f docker-compose.dev.yml up --build
+
+# View logs
+docker compose -f docker-compose.dev.yml logs -f raggr
+```
+
+## Project Structure
+
+```
+raggr/
+├── app.py                    # Quart application entry point
+├── main.py                   # RAG logic and LangChain agent
+├── llm.py                    # LLM client (Ollama + OpenAI fallback)
+├── aerich_config.py          # Database migration configuration
+│
+├── blueprints/               # API route blueprints
+│   ├── users/               # Authentication (OIDC, JWT, RBAC)
+│   ├── conversation/        # Chat conversations and messages
+│   └── rag/                 # Document indexing (admin only)
+│
+├── config/                   # Configuration modules
+│   └── oidc_config.py       # OIDC authentication settings
+│
+├── utils/                    # Reusable utilities
+│   ├── chunker.py           # Document chunking for embeddings
+│   ├── cleaner.py           # PDF cleaning and summarization
+│   ├── image_process.py     # Image description with LLM
+│   └── request.py           # Paperless-NGX API client
+│
+├── scripts/                  # Administrative scripts
+│   ├── add_user.py          # Create users manually
+│   ├── user_message_stats.py # User message statistics
+│   ├── manage_vectorstore.py # Vector store management
+│   ├── inspect_vector_store.py # Inspect ChromaDB contents
+│   └── query.py             # Query generation utilities
+│
+├── raggr-frontend/          # React frontend
+│   └── src/                # Frontend source code
+│
+├── migrations/              # Database migrations
+└── docs/                    # Documentation
+```
+
+## Making Changes
+
+### Backend Changes
+
+**Local development:**
+1. Edit Python files
+2. Save
+3. Restart `python app.py` (or use a tool like `watchdog` for auto-reload)
+
+**Docker development:**
+1. Edit Python files
+2. Files are synced via Docker watch mode
+3. Container automatically restarts
+
+### Frontend Changes
+
+```bash
+cd raggr-frontend
+
+# Development mode with hot reload
+yarn dev
+
+# Production build (for testing)
+yarn build
+```
+
+The backend serves built files from `raggr-frontend/dist/`.
+
+### Database Model Changes
+
+When you modify Tortoise ORM models:
+
+```bash
+# Generate migration
+aerich migrate --name "describe_your_change"
+
+# Apply migration
+aerich upgrade
+
+# View history
+aerich history
+```
+
+See [deployment.md](deployment.md) for detailed migration workflows.
+
+### Adding Dependencies
+
+**Backend:**
+```bash
+# Add to requirements.txt or use uv
+pip install package-name
+pip freeze > requirements.txt
+```
+
+**Frontend:**
+```bash
+cd raggr-frontend
+yarn add package-name
+```
+
+## Useful Commands
+
+### Database
+
+```bash
+# Connect to PostgreSQL
+docker compose -f docker-compose.dev.yml exec postgres psql -U raggr -d raggr
+
+# Reset database
+docker compose -f docker-compose.dev.yml down -v
+docker compose -f docker-compose.dev.yml up -d
+aerich init-db
+```
+
+### Vector Store
+
+```bash
+# Show statistics
+python scripts/manage_vectorstore.py stats
+
+# Index new documents from Paperless
+python scripts/manage_vectorstore.py index
+
+# Clear and reindex everything
+python scripts/manage_vectorstore.py reindex
+```
+
+See [vectorstore.md](vectorstore.md) for details.
+
+### Scripts
+
+```bash
+# Add a new user
+python scripts/add_user.py
+
+# View message statistics
+python scripts/user_message_stats.py
+
+# Inspect vector store contents
+python scripts/inspect_vector_store.py
+```
+
+## Environment Variables
+
+Copy `.env.example` to `.env` and configure:
+
+| Variable | Description | Example |
+|----------|-------------|---------|
+| `DATABASE_URL` | PostgreSQL connection | `postgres://user:pass@localhost:5432/db` |
+| `CHROMADB_PATH` | ChromaDB storage path | `./chromadb` |
+| `OLLAMA_URL` | Ollama server URL | `http://localhost:11434` |
+| `OPENAI_API_KEY` | OpenAI API key (fallback LLM) | `sk-...` |
+| `PAPERLESS_TOKEN` | Paperless-NGX API token | `...` |
+| `BASE_URL` | Paperless-NGX URL | `https://paperless.example.com` |
+| `OIDC_ISSUER` | OIDC provider URL | `https://auth.example.com` |
+| `OIDC_CLIENT_ID` | OIDC client ID | `simbarag` |
+| `OIDC_CLIENT_SECRET` | OIDC client secret | `...` |
+| `JWT_SECRET_KEY` | JWT signing key | `random-secret` |
+| `TAVILY_KEY` | Tavily web search API key | `tvly-...` |
+
+## Troubleshooting
+
+### Port Already in Use
+
+```bash
+# Find and kill process on port 8080
+lsof -ti:8080 | xargs kill -9
+
+# Or change the port in app.py
+```
+
+### Database Connection Errors
+
+```bash
+# Check if PostgreSQL is running
+docker compose -f docker-compose.dev.yml ps postgres
+
+# View PostgreSQL logs
+docker compose -f docker-compose.dev.yml logs postgres
+```
+
+### Frontend Not Building
+
+```bash
+cd raggr-frontend
+rm -rf node_modules dist
+yarn install
+yarn build
+```
+
+### ChromaDB Errors
+
+```bash
+# Clear and recreate ChromaDB
+rm -rf chromadb/
+python scripts/manage_vectorstore.py reindex
+```
+
+### Import Errors After Reorganization
+
+Ensure you're in the project root directory when running scripts, or use:
+
+```bash
+# Add project root to Python path
+export PYTHONPATH="${PYTHONPATH}:$(pwd)"
+python scripts/your_script.py
+```
+
+## Hot Tips
+
+- Use `python -m pdb app.py` for debugging
+- Enable Quart debug mode in `app.py`: `app.run(debug=True)`
+- Check API logs: They appear in the terminal running `python app.py`
+- Frontend logs: Open browser DevTools console
+- Use `docker compose -f docker-compose.dev.yml down -v` for a clean slate
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,14 +1,203 @@
 # SimbaRAG Documentation

-SimbaRAG is a RAG-powered conversational AI system with enterprise authentication.
+Welcome to the SimbaRAG documentation! This guide will help you understand, develop, and deploy the SimbaRAG conversational AI system.

-## Architecture
+## Getting Started

- **Backend**: Quart (async Python) with Tortoise ORM
- **Vector Store**: LangChain with configurable embeddings
- **Auth Stack**: LLDAP → Authelia → OAuth2/OIDC
- **Database**: PostgreSQL
+New to SimbaRAG? Start here:

-## Sections
+1. Read the main [README](../README.md) for project overview and architecture
+2. Follow the [Development Guide](development.md) to set up your environment
+3. Learn about [Authentication](authentication.md) setup with OIDC and LDAP

- [Authentication](authentication.md) - OIDC flow, user management, and RBAC planning
+## Documentation Structure
+
+### Core Guides
+
+- **[Development Guide](development.md)** - Local development setup, project structure, and workflows
+- **[Deployment Guide](deployment.md)** - Database migrations, deployment workflows, and troubleshooting
+- **[Vector Store Guide](VECTORSTORE.md)** - Managing ChromaDB, indexing documents, and RAG operations
+- **[Migrations Guide](MIGRATIONS.md)** - Database migration reference
+- **[Authentication Guide](authentication.md)** - OIDC, Authelia, LLDAP configuration and user management
+
+### Quick Reference
+
+| Task | Documentation |
+|------|---------------|
+| Set up local dev environment | [Development Guide → Quick Start](development.md#quick-start) |
+| Run database migrations | [Deployment Guide → Migration Workflow](deployment.md#migration-workflow) |
+| Index documents | [Vector Store Guide → Management Commands](VECTORSTORE.md#management-commands) |
+| Configure authentication | [Authentication Guide](authentication.md) |
+| Run administrative scripts | [Development Guide → Scripts](development.md#scripts) |
+
+## Common Tasks
+
+### Development
+
+```bash
+# Start local development
+docker compose -f docker-compose.dev.yml up -d
+export DATABASE_URL="postgres://raggr:raggr_dev_password@localhost:5432/raggr"
+export CHROMADB_PATH="./chromadb"
+python app.py
+```
+
+### Database Migrations
+
+```bash
+# Generate migration
+aerich migrate --name "your_change"
+
+# Apply migrations
+aerich upgrade
+
+# View history
+aerich history
+```
+
+### Vector Store Management
+
+```bash
+# Show statistics
+python scripts/manage_vectorstore.py stats
+
+# Index new documents
+python scripts/manage_vectorstore.py index
+
+# Reindex everything
+python scripts/manage_vectorstore.py reindex
+```
+
+## Architecture Overview
+
+SimbaRAG is built with:
+
+- **Backend**: Quart (async Python), LangChain, Tortoise ORM
+- **Frontend**: React 19, Rsbuild, Tailwind CSS
+- **Database**: PostgreSQL (users, conversations)
+- **Vector Store**: ChromaDB (document embeddings)
+- **LLM**: Ollama (primary), OpenAI (fallback)
+- **Auth**: Authelia (OIDC), LLDAP (user directory)
+
+See the [README](../README.md#system-architecture) for detailed architecture diagram.
+
+## Project Structure
+
+```
+simbarag/
+├── app.py                  # Quart app entry point
+├── main.py                 # RAG & LangChain agent
+├── llm.py                  # LLM client
+├── blueprints/             # API routes
+├── config/                 # Configuration
+├── utils/                  # Utilities
+├── scripts/                # Admin scripts
+├── raggr-frontend/         # React UI
+├── migrations/             # Database migrations
+├── docs/                   # This documentation
+├── docker-compose.yml      # Production Docker setup
+└── docker-compose.dev.yml  # Development Docker setup
+```
+
+## Key Concepts
+
+### RAG (Retrieval-Augmented Generation)
+
+SimbaRAG uses RAG to answer questions about Simba:
+
+1. Documents are fetched from Paperless-NGX
+2. Documents are chunked and embedded using OpenAI
+3. Embeddings are stored in ChromaDB
+4. User queries are embedded and matched against the store
+5. Relevant chunks are passed to the LLM for context
+6. LLM generates an answer using retrieved context
+
+### LangChain Agent
+
+The conversational agent has two tools:
+
+- **simba_search**: Queries the vector store for Simba's documents
+- **web_search**: Searches the web via Tavily API
+
+The agent automatically selects tools based on the query.
+
+### Authentication Flow
+
+1. User initiates OIDC login via Authelia
+2. Authelia authenticates against LLDAP
+3. Backend receives OIDC tokens and issues JWT
+4. Frontend stores JWT in localStorage
+5. Subsequent requests use JWT for authorization
+
+## Environment Variables
+
+Key environment variables (see `.env.example` for complete list):
+
+| Variable | Purpose |
+|----------|---------|
+| `DATABASE_URL` | PostgreSQL connection |
+| `CHROMADB_PATH` | Vector store location |
+| `OLLAMA_URL` | Local LLM server |
+| `OPENAI_API_KEY` | OpenAI for embeddings/fallback |
+| `PAPERLESS_TOKEN` | Document source API |
+| `OIDC_*` | Authentication configuration |
+| `TAVILY_KEY` | Web search API |
+
+## API Endpoints
+
+### Authentication
+- `GET /api/user/oidc/login` - Start OIDC flow
+- `GET /api/user/oidc/callback` - OIDC callback
+- `POST /api/user/refresh` - Refresh JWT
+
+### Conversations
+- `POST /api/conversation/` - Create conversation
+- `GET /api/conversation/` - List conversations
+- `POST /api/conversation/query` - Chat message
+
+### RAG (Admin Only)
+- `GET /api/rag/stats` - Vector store stats
+- `POST /api/rag/index` - Index documents
+- `POST /api/rag/reindex` - Reindex all
+
+## Troubleshooting
+
+### Common Issues
+
+| Issue | Solution |
+|-------|----------|
+| Port already in use | Check if services are running: `lsof -ti:8080` |
+| Database connection error | Ensure PostgreSQL is running: `docker compose ps` |
+| ChromaDB errors | Clear and reindex: `python scripts/manage_vectorstore.py reindex` |
+| Import errors | Check you're in `services/raggr/` directory |
+| Frontend not building | `cd raggr-frontend && yarn install && yarn build` |
+
+See individual guides for detailed troubleshooting.
+
+## Contributing
+
+1. Read the [Development Guide](development.md)
+2. Set up your local environment
+3. Make changes and test locally
+4. Generate migrations if needed
+5. Submit a pull request
+
+## Additional Resources
+
+- [LangChain Documentation](https://python.langchain.com/)
+- [ChromaDB Documentation](https://docs.trychroma.com/)
+- [Quart Documentation](https://quart.palletsprojects.com/)
+- [Tortoise ORM Documentation](https://tortoise.github.io/)
+- [Authelia Documentation](https://www.authelia.com/)
+
+## Need Help?
+
+- Check the relevant guide in this documentation
+- Review troubleshooting sections
+- Check application logs: `docker compose logs -f`
+- Inspect database: `docker compose exec postgres psql -U raggr`
+
+---
+
+**Documentation Version**: 1.0
+**Last Updated**: January 2026