/ PlantDB.server

Server-side component of the ROMI plant database system.

Provides a robust REST API server implementation for managing plant phenotyping data.

Features include:

• File system database management
• Data synchronization services
• Command-line tools for database management

Overview

PlantDB is a library for the ROMI (Robotics for Microfarms) plant database ecosystem. It is designed for plant and agricultural research facilities and robotics labs that require lightweight plant data management infrastructure.

It consists of three components:

1. plantdb.commons: provides a Python API for interacting with plant data
2. plantdb.server: provides the server-side REST API to interact with plant data
3. plantdb.client: provides the client-side REST API to interact with plant data

For comprehensive documentation of the PlantImager project, visit: https://docs.romi-project.eu/plant_imager/

API documentation for the plantdb library is available at: https://romi.github.io/plantdb/

Environment Setup

We strongly recommend using isolated environments to install ROMI libraries.

Python venv

To create a new Python virtual environment for PlantDB:

python -m venv .venv         # create a pyvenv named `.venv` in the current directory
source .venv/bin/activate    # activate the virtual environment
pip install ipython          # optional interactive workbench

Conda

This documentation uses conda as both an environment and package manager. If you don't have miniconda3 installed, please refer to the official documentation.

To create a new conda environment for PlantDB:

conda create -n plantdb 'python=3.10' ipython

To use it, you need to activate it with:

conda activate plantdb  # activate your environment

Installation

User - Pre Built Packages

Activate your environment and install the packages using pip:

pip install plantdb.commons plantdb.server plantdb.client

Developers - From Sources

To contribute to the development, you will need to install the sources:

git clone https://github.com/romi/plantdb.git
cd plantdb
# Install 'plantdb.commons'...
pip install -e src/commons/.[io]
# Install 'plantdb.server'...
pip install -e src/server/.
# Install 'plantdb.client'...
pip install -e src/client/

Usage

Test with Toy Dataset

To run the server with a temporary test database in debug mode:

fsdb_rest_api --test --debug

Development

To start the REST API server for a local plant database:

fsdb_rest_api -db /path/to/your/database --host 127.0.0.1 --port 8080

Production

To start the REST API server in production:

uwsgi --http :5000 --module plantdb.server.cli.wsgi:application --callable application --master

For detailed usage instructions and a full endpoint reference, see:

• How to Run the REST API
• REST API Endpoints