Sepal

A botanical collection management system for managing plant accessions, materials, locations, and taxonomic data. Integrates with the World Flora Online Plantlist for taxonomy reference.

Features

• Plant accession tracking
• Material management
• Location management
• Taxonomic data with WFO Plantlist integration
• Media attachments
• Full-text search

Getting Started

Prerequisites

• Clojure 1.12+
• Node.js 22.x (for frontend build)
• sqlite3 (for database operations)
• SpatiaLite extension (for geo-coordinate support)
• sqlite-migrate (optional, for applying new migrations)

Using devbox (recommended): All prerequisites including SpatiaLite are installed automatically via devbox shell.

WFO Plantlist Database

Sepal uses a SQLite version of the World Flora Online Plantlist for taxonomy data.

• Download pre-built database: 10.5281/zenodo.17444674
• Or build your own: wfo-plantlist-sqlite

Environment Variables

Copy .env.local.example to .env.local and configure the following:

Required:

Variable	Description
COOKIE_SECRET	Secret for encrypting cookies
TOKEN_SECRET	Secret for encrypting tokens (password reset, invitations) - min 16 chars
APP_DOMAIN	Domain for email links (e.g., reset password)
SMTP_HOST	SMTP server hostname
SMTP_PORT	SMTP server port (e.g., 587 for STARTTLS, 465 for SSL)
SMTP_USERNAME	SMTP authentication username
SMTP_PASSWORD	SMTP authentication password
SMTP_AUTH	Enable SMTP authentication (true/false)
SMTP_TLS	TLS mode: starttls, ssl, or none

Database:

Variable	Description
WFO_DATABASE_PATH	Path to WFO Plantlist SQLite database (only needed for DB initialization)
SEPAL_DATA_HOME	Data directory for database and config files (defaults to $XDG_DATA_HOME/Sepal or platform equivalent)
EXTENSIONS_LIBRARY_PATH	Path to directory containing SQLite extensions like mod_spatialite (see troubleshooting below)

Optional - Media Uploads:

Variable	Description
MEDIA_UPLOAD_BUCKET	S3 bucket for media uploads
AWS_S3_ENDPOINT	S3-compatible endpoint
AWS_ACCESS_KEY_ID	AWS access key
AWS_SECRET_ACCESS_KEY	AWS secret key
AWS_REGION	AWS region
IMAGE_CACHE_SIZE_MB	Max size for image thumbnail cache in MB (default: 500)

Optional - Email Customization:

Variable	Description
FORGOT_PASSWORD_EMAIL_FROM	Reply-to address for password reset emails
FORGOT_PASSWORD_EMAIL_SUBJECT	Subject line for password reset emails

Development Setup

1. Enter devbox shell: devbox shell (installs all dependencies including SpatiaLite)
2. Download the WFO Plantlist database (see above)
3. Copy .env.local.example to .env.local and configure variables
4. Run bin/reset-db.sh to initialize database with WFO data
5. Create an admin user (see User Management below)
6. Start REPL and run (go) - zodiac-asset handles npm install and Vite automatically

User Management

User registration is disabled. Users must be invited or created via the CLI.

Roles:

• admin - Full access: organization settings, user management, all CRUD operations
• editor - Can create/edit/delete plant records, edit own profile
• reader - View-only access to plant records, edit own profile

Create a user:

clojure -M:dev:cli create-user --email admin@example.com --password secret --role admin

List all users:

clojure -M:dev:cli list-users

Create admin user during database reset:

ADMIN_EMAIL=admin@example.com ADMIN_PASSWORD=secret bin/reset-db.sh

Troubleshooting SQLite extensions: If you encounter errors loading SQLite extensions (like SpatiaLite), set EXTENSIONS_LIBRARY_PATH to the directory containing the extension libraries. With devbox, this is typically ${PWD}/.devbox/nix/profile/default/lib. See .env.local.example for an example.

Production Build

1. Build frontend assets: cd bases/app && npm run build
2. Build uberjar or deploy as appropriate