Working in Alpha

Overview

ro-crate-rs is a rust library, python library and CLI tool for interfacing with Reserach Object Crates. This implementation was specifically created to address the challenges of data handling on automated robotic systems within an automated synthetic biology lab, however it's noted that this could have more general applicability to other environments. It's aim is to provide a robust, portable and scalable solution to dealing with RO-Crates within the varying software environments of a synthetic biology lab stack.

It enforces minimal RO-Crate structure adherence through it's defined data types, but equally allows the crate to be as expansive as needed.

Why a rust library

Rust is an increasingly popular systems programming language that is useful for systems that require performance, robustness and the ability to run in a myriad of different computing environments; be it Windows, Linux or MacOS, or x86, ARM or any other embedded/IOT system. It is a compiled, statically typed language with a strong emphasis on type safety and has started to form the performant core of data libraries, such as Polars and DeltaLake.

In this library, the rust type system and the serde library have been leveraged to provide a structured core for handling RO-Crates with robust data handling, built in constraints as per the RO-Crate specification (v1.1) and sufficient flexibilty to add any metadata required.

The aim is that for regular, automated and consistent robotic experiements, this library can be relied upon to create RO-Crates for years to come.

Why a CLI tool

The CLI tool can be used to immediately interface with RO-Crates within a somewhat constrained and structured environment, however an understanding of RO-Crate is a realistic requirement to conform with schema.org specifications. The CLI tool should not be relied upon as your primary interface to RO-crates, however it does allow the tool to be used on any system with some form of terminal, be it headless or ssh.

Why a python library wrapper

The python library (rocraters) allows the primary rust library to be leveraged in python. It's designed to be maximally flexible with minimal onboarding, allowing you to incorprate it into scrpits/ data pipelines as easily as possible. Python is a ubquitous language among scientists, so this provides an accessible tool to use ro-crate-rs within already developed/new Python based environments. This library relies on you to have an understanding of the structure of an RO-Crate, but focuses more on the fact that some metadata is better than no metadata.

This is not the go-to python libary for RO-Crate interfacing, please see ro-crate-py for a full python implementation.

Libraries

1. ro-crate-rs core
2. rocraters python bindings
3. cli tool

Compatability

RO-Crate v1.1 only