csr2transmart 0.0.4

Script to load CSR data to TranSMART

This package contains a script that transforms Central Subject Registry data to a format that can be loaded into TranSMART platform, an open source data sharing and analytics platform for translational biomedical research.

The output of the transformation is a collection of tab-separated files that can be loaded into a TranSMART database using the transmart-copy tool.

⚠️ Note: this is a very preliminary version, still under development. Issues can be reported at https://github.com/thehyve/python_csr2transmart/issues.

Installation and usage

To install csr2transmart, do:

pip install csr2transmart

or from sources:

git clone https://github.com/thehyve/python_csr2transmart.git
cd python_csr2transmart
pip install .

Usage

TODO: Add example

Python versions

This repository is set up with Python version 3.6

Package management and dependencies

This project uses pip for installing dependencies and package management.

• Dependencies should be added to setup.py in the install_requires list.

Testing and code coverage

• Tests are in the tests folder.

• The tests folder contains:

  • A test if the csr2transmart script starts (file: test_csr2transmart)

  • A test that checks whether your code conforms to the Python style guide (PEP 8) (file: test_lint.py)

• The testing framework used is PyTest

• Tests can be run with python setup.py test

Coding style conventions and code quality

• Check your code style with prospector

• You may need run pip install .[dev] first, to install the required dependencies

License

Copyright (c) 2019 The Hyve B.V.

The CSR to TranSMART loader is licensed under the MIT License. See the file LICENSE.