Bloom - Plant Phenotyping Platform

A comprehensive web application for plant phenotyping data management, built with Next.js, Supabase, and MinIO.

Getting Started

Choose your setup:

• Development Setup - For local development
• Production Setup - For production deployment

Prerequisites

Before starting, ensure you have:

• Docker installed
• Python 3.8 or higher

Repository Structure

bloom-v2/
├── web/                    # Next.js frontend application
├── langchain/              # LangChain AI agent (ReAct agent with chat API)
├── bloommcp/               # FastMCP server (Bloom analysis tools)
├── supabase/              # Supabase configuration and migrations
│   └── migrations/        # Database migration files
├── minio/                 # MinIO storage configuration
│   └── init/              # Bucket initialization scripts
├── scripts/               # Utility scripts for data loading
├── test_data/             # Sample data for testing
├── docker-compose.dev.yml # Development stack configuration
├── docker-compose.prod.yml # Production stack configuration
└── Makefile               # Helper commands

Architecture Overview

Development Stack

• Frontend: Next.js (hot reload) - http://localhost:3000
• Database: PostgreSQL via Supabase - localhost:${POSTGRES_HOST_PORT:-5432}
• Storage: MinIO Console - http://localhost:9101
• AI Agent: LangChain agent - http://localhost:5002
• MCP Server: Bloom FastMCP (Bloom tools) - http://localhost:8811
• Swagger UI: PostgREST API browser - http://localhost:8085
• Studio: Supabase Studio - http://localhost:55323

Production Stack

• Frontend: Next.js (optimized build) - http://yourdomain.com
• Database: PostgreSQL via Supabase
• Storage: MinIO S3
• AI Agent: LangChain agent
• MCP Server: Bloom FastMCP (Bloom tools)
• All services behind Nginx reverse proxy

Available Commands

Stack Management

make dev-up              # Start development stack
make dev-down            # Stop development stack
make prod-up             # Start production stack
make prod-down           # Stop production stack
make dev-logs            # View development logs
make prod-logs           # View production logs

Database Operations

make init                # Generate .env.dev from .env.dev.example (fresh secrets)
make migrate-local       # Apply all migrations to the local dev DB
make check               # Verify the stack: roles, schemas, migrations, id sequences
make verify-dev          # Clean reset -> up -> migrate -> check (destructive)
make test-integration    # Run integration tests against the local stack
make reset-storage       # Reset database and storage (DEV only)
make load-test-data      # Load CSV test data into database

The full first-run workflow (WSL2 notes, port overrides, etc.) lives in DEV_SETUP.md — the single source of truth for getting started.

Storage (S3 Buckets) Operations

make upload-images       # Upload test images to MinIO
make create-bucket BUCKET=name [PUBLIC=true]  # Create new bucket
make list-buckets        # List all storage buckets

Getting Started

1. Development Setup

see [DEV_SETUP.md](./DEV_SETUP.md)

2. Production Setup

see [PROD_SETUP.md](./PROD_SETUP.md)

Test Data

The repository includes sample test data:

• 14 CSV files with reference data
• 72 sample plant scan images
• Scripts to load data automatically

Load test data with:

make load-test-data      # Loads CSV data into database
make upload-images       # Uploads images to MinIO/S3

Support

For issues and questions:

1. Review logs with make dev-logs or make prod-logs
2. Open an issue on GitHub

Last Updated: March 2026