TranSMART loader¶
This package contains classes that represent the core domain objects stored in the TranSMART platform, an open source data sharing and analytics platform for translational biomedical research.
It also provides a utility that writes such objects to 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_transmart_loader/issues.
Installation and usage¶
To install transmart_loader, do:
pip install transmart-loader
or from sources:
git clone https://github.com/thehyve/python_transmart_loader.git
cd python_transmart_loader
pip install .
Usage¶
Usage examples can be found in these projects:
- fhir2transmart: a tool that translates core HL7 FHIR resources to the TranSMART data model.
- ontology2transmart: a tool that translates ontologies available from DIMDI to TranSMART ontologies.
Documentation¶
Full documentation of the package is available at Read the Docs.
Known issues¶
- Date values are not correctly translated
Development¶
For a quick reference on software development, we refer to the software guide checklist.
Python versions¶
This repository is set up with Python version 3.6
Add or remove Python versions based on project requirements. The guide contains more information about Python versions and writing Python 2 and 3 compatible code.
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 files for transmart-copy are generated for fake data (file:
test_transmart_loader
) - A test that checks whether your code conforms to the Python style guide (PEP 8) (file:
test_lint.py
)
- A test if files for transmart-copy are generated for fake data (file:
- The testing framework used is PyTest
- Tests can be run with
python setup.py test
Documentation¶
- Documentation should be put in the
docs
folder. - To generate html documentation run
python setup.py build_sphinx
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 TranSMART loader is licensed under the MIT License. See the file LICENSE.
Credits¶
This package was created with Cookiecutter and the NLeSC/python-template.