javaDataPipeline #

The javaDataPipeline Java library allows Java modellers to interface with the FAIR Data Pipeline. It is available on Maven Central:

dependencies {
    implementation 'org.fairdatapipeline:api:1.0.0-beta'
}

The main purpose of interfacing with the FAIR Data Pipeline is the recording of Coderuns: a Coderun is a recorded session of your modelling code, all the inputs used and outputs generated will be recorded and a Provenance Report will be generated.

The basic idea behind the FAIR DataPipeline and Coderuns is explained on the Data pipeline page.

Usage #

A useful starting point to get to know the javaDataPipeline is to explore the java Simple Model. This shows example config.yaml files, example main(String[] args) code that allows fair run to call your code, and example Coderun() code for reading/writing input/output Data Products.

The links below give a basic introduction to the javaDataPipeline; these should be read in conjunction with the javaDocs which give more precise specification of the java API.

Basic Coderun
Issues
Parameters
HDF5
Run
Debug

See the package documentation for Javadoc.

License/copyright #

Copyright (c) 2021: Bram Boskamp, Biomathematics and Statistics Scotland and the Scottish COVID-19 Response Consortium

GNU GENERAL PUBLIC LICENSE Version 3

Source code #

See the package’s code repo.