Database Setup Guide¶

Quick Start¶

If you just want to get the database running:

Install Docker on your system
Run the setup command:
1
ethopy-setup-djdocker
Enter a password when prompted
Verify the setup:
1
ethopy-db-connection

That's it! The database is ready to use.

Detailed Guide¶

Prerequisites¶

Docker installed and running on your system
Python 3.8 or higher
EthoPy package installed

Understanding the Components¶

The database setup consists of: - A MySQL database running in Docker - DataJoint configuration for EthoPy

Setup Process¶

1. Docker Container Setup¶

ethopy-setup-djdocker [--mysql-path PATH] [--container-name NAME]

Options: - --mysql-path: Custom path to store MySQL data (default: ~/.ethopy/mysql-docker) - --container-name: Custom name for the container (default: ethopy_sql_db)

This command: - Creates a Docker container with MySQL - Sets up initial configuration - Ensures the database is accessible

2. Database Connection Check¶

1	`ethopy-db-connection`

Verifies that EthoPy can connect to the database.

3. Schema Creation¶

1	`ethopy-setup-schema`

Creates all required database tables and structures.

Troubleshooting¶

Container Won't Start¶

Check Docker status:
1
docker ps -a
Check Docker logs:
1
docker logs ethopy_sql_db

Connection Issues¶

Verify port 3306 is available:
1
netstat -an | grep 3306
Check your local configuration file (~/.ethopy/local_conf.json)

Advanced Configuration¶

Custom Database Host¶

Edit your local_conf.json:

{
    "dj_local_conf": {
        "database.host": "YOUR_HOST",
        "database.user": "root",
        "database.password": "YOUR_PASSWORD",
        "database.port": 3306
    }
}

Multiple Environments¶

You can run multiple database instances by using different container names:

ethopy-setup-djdocker --container-name ethopy_dev
ethopy-setup-djdocker --container-name ethopy_prod

Security Considerations¶

Use strong passwords
Don't expose the database port publicly
Regular backups of ~/.ethopy/mysql-docker/data_*

Technical Reference¶

Command Details¶

setup_dj_docker¶

Sets up the Docker container with MySQL configured for EthoPy.

setup_dj_docker(mysql_path: Optional[str], container_name: str)

check_db_connection¶

Verifies database connectivity.

1	`check_db_connection()`

Architecture¶

The setup follows a three-tier approach: 1. Container Management (Docker) 2. Database Configuration (MySQL) 3. Schema Management (DataJoint)

Each tier is independent and can be modified without affecting the others.