Dorieh Data Platform for population and environmental health

Read the book about Dorieh, published by Springer.

Detailed documentation: Dorieh Documentation

Dorieh overview

Dorieh Data Platform is intended for development and deployment of ETL/ELT pipelines that includes complex data processing and data cleansing workflows. Complex workflows require a workflow language, and we have chosen Common Workflow Language (CWL).

We have tested deployment with the following CWL implementations:

• Toil.
• CWL reference implementation, primarily using cwlref-runner package
• CWL-Airflow that provides a very nice Airflow graphical user interface (GUI) for running workflows.

The data produced by the data processing workflows is eventually stored in either CSV files, a PostgreSQL DBMS or Parquet files. Dorieh also supports storing results in FST and HDF5 files.

Some of the included data processing workflows use “Extract, Load, Transform,” (ELT) paradigm rather than more traditional “Extract, Transform, Load” ETL. It means that these workflows perform calculations, translations, filtering, cleansing, de-duplicating, validating, and data analysis or summarizations inside a DBMS using DBMS internal tools.

The data platform supports tools written in widely used languages such as Python, C/C++ and Java, R and PL/pgSQL.

Setting up

Python Virtual Environment

Install Toil:

pip install "toil[cwl,aws]"

Install Dorieh (stable version):

pip install dorieh

If you prefer to install the latest version from GitHub:

pip install git+https://github.com/ForomePlatform/dorieh

If FST support is desired, R runtime has to be installed and R_HOME environment variable set up. One of the simples ways of installing R is to use Conda package manager. Once R is set up, install Dorieh with either of the following command:

pip install dorieh[FST]

pip install "git+https://github.com/ForomePlatform/dorieh[FST]"

Docker Container

To build your own Dorieh Docker image see docker directory

A prebuilt docker image with Dorieh is provided:

docker pull forome/dorieh

Built-in Workflows

For examples of data processing workflows, see included data processing workflows