transmart-loader 0.1.0

Python library for loading data to TranSMART using transmart-copy

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TranSMART loader
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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.

.. _TranSMART: https://github.com/thehyve/transmart_core
.. _transmart-copy: https://github.com/thehyve/transmart-core/tree/dev/transmart-copy


Installation and usage
**********************

To install transmart_loader, do:

.. code-block:: console

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<https://github.com/thehyve/python_transmart_loader/tree/master/examples>`_ directory:

- `fhir2transmart <https://github.com/thehyve/python_transmart_loader/tree/master/examples/fhir2transmart>`_: a tool that translates core `HL7 FHIR`_ resources to the TranSMART data model.
- `ontology2transmart <https://github.com/thehyve/python_transmart_loader/tree/master/examples/ontology2transmart>`_: a tool that translates ontologies available from DIMDI_
to TranSMART ontologies.

.. _`HL7 FHIR`: http://hl7.org/fhir/
.. _DIMDI: https://www.dimdi.de


Development
*************

For a quick reference on software development, we refer to `the software guide checklist <https://guide.esciencecenter.nl/best_practices/checklist.html>`_.

Python versions
---------------

This repository is set up with Python version 3.6

Add or remove Python versions based on project requirements. `The guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html>`_ 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 <https://pytest.org>`_

- `PyTest introduction <http://pythontesting.net/framework/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 <https://readthedocs.org>`_, 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
*************

.. _README:

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 <https://github.com/audreyr/cookiecutter>`_ and the `NLeSC/python-template <https://github.com/NLeSC/python-template>`_.