Python library for loading data to TranSMART using transmart-copy
Project description
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 development version. 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.
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)
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.
Project details
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