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Welcome to PlantDBLink

Licence Python Version GitHub branch check runs

Package PyPI Conda
plantdb.commons PyPI - Version Conda - Version
plantdb.server PyPI - Version Conda - Version
plantdb.client PyPI - Version Conda - Version

ROMI_ICON2_greenB.png

OverviewLink

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/

plantdb.commonsLink

Core shared library for the ROMI plant database ecosystem.

This package provides common utilities and base functionality used by both server and client components.

Features include: - Data management - Common data models and schemas - File system operations and validation - Logging and debugging tools - Data format specifications and validators

plantdb.serverLink

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

plantdb.clientLink

Client-side database library for the ROMI plant database ecosystem.

This package provides a Python interface for interacting with ROMI's plant database system, enabling efficient storage, retrieval, and management of plant-related data.

Features include: - REST API integration - Data validation - Streamlined access to plant phenotyping data.

Environment SetupLink

We strongly recommend using isolated environments to install ROMI libraries. This documentation uses conda as both an environment and package manager. If you don't haveminiconda3 installed, please refer to the official documentation.

The plantdb packages are available through:

To create a new conda environment for PlantDB: 

conda create -n plantdb 'python=3.10' ipython

InstallationLink

For UsersLink

Activate your environment and install the packages using either pip or conda:

Using pip:Link

conda activate plantdb  # activate your environment first!
pip install plantdb.commons plantdb.server plantdb.client

Using conda:Link

conda activate plantdb  # activate your environment first!
conda install -c romi-eu plantdb plantdb.server plantdb.client

Getting startedLink

Set up a local databaseLink

  1. You need to create a directory where to put the data, e.g. /data/ROMI_DB and add a file called romidb: 
    mkdir -p /data/ROMI_DB
touch /data/ROMI_DB/romidb
  2. Then define its location in an environment variable ROMI_DB: 
    export ROMI_DB=/data/ROMI_DB

Info:

To make this setting permanent, add the export command to your ~/.bashrc or ~/.profile file.