transmart-loader 0.1.1

Python library for loading data to TranSMART using transmart-copy

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.

Installation and usage

To install transmart_loader, do:

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

Usage

Usage examples can be found in the examples directory:

• 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.

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

  • PyTest introduction

• 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

  • Alternatively, run make html in the docs folder.

• To put the documentation on Read the Docs, log in to your Read the Docs account, and import the repository (under ‘My Projects’).

  • Include the link to the documentation in this README.

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

Documentation

Include a link to your project’s full documentation here.

License

Copyright (c) 2019, The Hyve

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.

Credits

This package was created with Cookiecutter and the NLeSC/python-template.