pyDataPipeline

Welcome to pyDataPipeline a Python api to interact with the Fair Data Pipeline.

Full documention of the pyDataPipeline is avaialable at https://www.fairdatapipeline.org/pyDataPipeline/

Installation

pyDataPipeline can be installed from PyPi:

pip3 install data-pipeline-api

Or from the Repository:

git clone https://github.com/FAIRDataPipeline/pythonFDP.git

git checkout dev

pip3 install -e .

NB. PyDataPipeline requires Python3.

Example submission_script

Assume FDP_CONFIG_DIR, storage_locations and objects have been set by CLI tool

import os
import fairdatapipeline as pipeline

token = os.environ['FDP_LOCAL_TOKEN']
config_dir = os.environ['FDP_CONFIG_DIR']
config_path = os.path.join(config_dir, 'config.yaml')
script_path = os.path.join(config_dir, 'script.sh')

handle = pipeline.initialise(token, config_path, script_path)

pipeline.finalise(token, handle)

SEIRS Model Example

The SEIRS Model Example is available at: https://www.fairdatapipeline.org/pyDataPipeline/examples/SEIRS.html