Script to load CSR data to TranSMART
Project description
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 csr2transmartor 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.
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