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        "author": "Gijs Kant",
        "author_email": "gijs@thehyve.nl",
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            "Development Status :: 3 - Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "TranSMART loader\n================\n\n|Build status| |codecov| |pypi| |status| |downloads| |license|\n\n.. |Build status| image:: https://travis-ci.org/thehyve/python_transmart_loader.svg?branch=master\n   :alt: Build status\n   :target: https://travis-ci.org/thehyve/python_transmart_loader/branches\n.. |codecov| image:: https://codecov.io/gh/thehyve/python_transmart_loader/branch/master/graph/badge.svg\n   :alt: codecov\n   :target: https://codecov.io/gh/thehyve/python_transmart_loader\n.. |pypi| image:: https://img.shields.io/pypi/v/transmart_loader.svg\n   :alt: PyPI\n   :target: https://pypi.org/project/transmart_loader/\n.. |status| image:: https://img.shields.io/pypi/status/transmart-loader.svg\n   :alt: PyPI - Status\n.. |downloads| image:: https://img.shields.io/pypi/dm/transmart-loader.svg\n   :alt: PyPI - Downloads\n.. |license| image:: https://img.shields.io/pypi/l/transmart_loader.svg\n   :alt: MIT license\n   :target: LICENSE\n\nThis package contains classes that represent the core domain objects stored in the TranSMART_ platform,\nan open source data sharing and analytics platform for translational biomedical research.\n\nIt also provides a utility that writes such objects to tab-separated files that can be loaded into\na TranSMART database using the transmart-copy_ tool.\n\n.. _TranSMART: https://github.com/thehyve/transmart-core\n.. _transmart-copy: https://github.com/thehyve/transmart-core/tree/dev/transmart-copy\n\n\u26a0\ufe0f Note: this is a development version.\nIssues can be reported at https://github.com/thehyve/python_transmart_loader/issues.\n\n\nInstallation and usage\n**********************\n\nTo install transmart_loader, do:\n\n.. code-block:: console\n\n  pip install transmart-loader\n\nor from sources:\n\n.. code-block:: console\n\n  git clone https://github.com/thehyve/python_transmart_loader.git\n  cd python_transmart_loader\n  pip install .\n\n\nUsage\n------\n\nDefine a TranSMART data collection, using the classes in `transmart_loader/transmart.py`_, e.g.,\n\n.. _`transmart_loader/transmart.py`: https://github.com/thehyve/python_transmart_loader/blob/master/transmart_loader/transmart.py\n\n.. code-block:: python\n\n  # Create the dimension elements\n  age_concept = Concept('test:age', 'Age', '\\\\Test\\\\age', ValueType.Numeric)\n  concepts = [age_concept]\n  studies = [Study('test', 'Test study')]\n  trial_visits = [TrialVisit(studies[0], 'Week 1', 'Week', 1)]\n  patients = [Patient('SUBJ0', 'male', [])]\n  visits = [Visit(patients[0], 'visit1', None, None, None, None, None, None, [])]\n  # Create the observations\n  observations = [\n      Observation(patients[0], age_concept, visits[0], trial_visits[0],\n                  date(2019, 3, 28), None, NumericalValue(28))]\n\nCreate a hierarchical ontology for the concepts, e.g., to create the following structure:\n\n::\n\n  \u2514 Ontology\n    \u2514 Age\n\n\n.. code-block:: python\n\n  # Create an ontology with one top node and a concept node\n  top_node = TreeNode('Ontology')\n  top_node.add_child(ConceptNode(concepts[0]))\n  ontology = [top_node]\n\nWrite the data collection to a format that can be loaded using ``transmart-copy``:\n\n.. code-block:: python\n\n  collection = DataCollection(concepts, [], [], studies,\n                              trial_visits, visits, ontology, patients, observations)\n\n  # Write collection to a temporary directory\n  # The generated files can be loaded into TranSMART with transmart-copy.\n  output_dir = mkdtemp()\n  copy_writer = TransmartCopyWriter(output_dir)\n  copy_writer.write_collection(collection)\n\n\nCheck `examples/data_collection.py`_ for a complete example.\n\n.. _`examples/data_collection.py`: https://github.com/thehyve/python_transmart_loader/blob/master/examples/data_collection.py\n\nUsage examples can be found in these projects: \n\n- `fhir2transmart <https://github.com/thehyve/python_fhir2transmart>`_: a tool that translates core `HL7 FHIR`_ resources to the TranSMART data model.  \n- `claml2transmart <https://github.com/thehyve/python_claml2transmart>`_: a tool that translates ontologies in ClaML_ format (e.g., ICD-10, available from DIMDI_)\n  to TranSMART ontologies.\n- `csr2transmart <https://github.com/thehyve/python_csr2transmart>`_: a custom data transformation\n  and loading pipeline for a Dutch center for pediatric oncology.\n- `transmart-hyper-dicer <https://github.com/thehyve/transmart-hyper-dicer>`_: a tool that reads a selection of data from a TranSMART instance using its REST API\n  and loads it into another TranSMART instance.\n\n.. _`HL7 FHIR`: http://hl7.org/fhir/\n.. _DIMDI: https://www.dimdi.de\n.. _ClaML: https://www.iso.org/standard/69318.html\n\n\nDocumentation\n*************\n\nFull documentation of the package is available at `Read the Docs`_.\n\n.. _Read the Docs: https://transmart-loader.readthedocs.io\n\n\nDevelopment\n*************\n\nFor a quick reference on software development, we refer to `the software guide checklist <https://guide.esciencecenter.nl/best_practices/checklist.html>`_.\n\nPython versions\n---------------\n\nThis packages is tested with Python versions 3.6 and 3.7.\n\nPackage management and dependencies\n-----------------------------------\n\nThis project uses `pip` for installing dependencies and package management.\n\n* Dependencies should be added to `setup.py` in the `install_requires` list.\n\nTesting and code coverage\n-------------------------\n\n* Tests are in the ``tests`` folder.\n* The ``tests`` folder contains:\n\n  - A test if files for `transmart-copy` are generated for fake data (file: ``test_transmart_loader``)\n  - A test that checks whether your code conforms to the Python style guide (PEP 8) (file: ``test_lint.py``)\n\n* The testing framework used is `PyTest <https://pytest.org>`_\n\n  - `PyTest introduction <http://pythontesting.net/framework/pytest/pytest-introduction/>`_\n\n* Tests can be run with ``python setup.py test``\n\nDocumentation\n-------------\n\n* Documentation should be put in the ``docs`` folder.\n\n* To generate html documentation run ``python setup.py build_sphinx``\n\nCoding style conventions and code quality\n-----------------------------------------\n\n* Check your code style with ``prospector``\n* You may need run ``pip install .[dev]`` first, to install the required dependencies\n\n\nLicense\n*******\n\nCopyright (c) 2019 The Hyve B.V.\n\nThe TranSMART loader is licensed under the MIT License. See the file `<LICENSE>`_.\n\n\nCredits\n*******\n\nThis package was created with `Cookiecutter <https://github.com/audreyr/cookiecutter>`_ and the `NLeSC/python-template <https://github.com/NLeSC/python-template>`_.\n\n\n\n\n",
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