Metadata-Version: 2.1
Name: transmart-loader
Version: 1.3.0
Summary: Python library for loading data to TranSMART using transmart-copy
Home-page: https://github.com/thehyve/python_transmart_loader
Author: Gijs Kant
Author-email: gijs@thehyve.nl
License: MIT
Description: TranSMART loader
        ================
        
        |Build status| |codecov| |pypi| |status| |downloads| |license|
        
        .. |Build status| image:: https://travis-ci.org/thehyve/python_transmart_loader.svg?branch=master
           :alt: Build status
           :target: https://travis-ci.org/thehyve/python_transmart_loader/branches
        .. |codecov| image:: https://codecov.io/gh/thehyve/python_transmart_loader/branch/master/graph/badge.svg
           :alt: codecov
           :target: https://codecov.io/gh/thehyve/python_transmart_loader
        .. |pypi| image:: https://img.shields.io/pypi/v/transmart_loader.svg
           :alt: PyPI
           :target: https://pypi.org/project/transmart_loader/
        .. |status| image:: https://img.shields.io/pypi/status/transmart-loader.svg
           :alt: PyPI - Status
        .. |downloads| image:: https://img.shields.io/pypi/dm/transmart-loader.svg
           :alt: PyPI - Downloads
        .. |license| image:: https://img.shields.io/pypi/l/transmart_loader.svg
           :alt: MIT license
           :target: LICENSE
        
        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
        
        ⚠️ 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:
        
        .. code-block:: console
        
          pip install transmart-loader
        
        or from sources:
        
        .. 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 these projects: 
        
        - `fhir2transmart <https://github.com/thehyve/python_fhir2transmart>`_: a tool that translates core `HL7 FHIR`_ resources to the TranSMART data model.  
        - `ontology2transmart <https://github.com/thehyve/python_ontology2transmart>`_: a tool that translates ontologies available from DIMDI_
          to TranSMART ontologies.
        
        .. _`HL7 FHIR`: http://hl7.org/fhir/
        .. _DIMDI: https://www.dimdi.de
        
        
        Documentation
        *************
        
        Full documentation of the package is available at `Read the Docs`_.
        
        .. _Read the Docs: https://transmart-loader.readthedocs.io
        
        
        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``
        
        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 <https://github.com/audreyr/cookiecutter>`_ and the `NLeSC/python-template <https://github.com/NLeSC/python-template>`_.
        
        
        
Keywords: transmart_loader
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3.6.0
Provides-Extra: dev
