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        "author": "Gijs Kant",
        "author_email": "gijs@thehyve.nl",
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        "classifiers": [
            "Development Status :: 2 - Pre-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": "################################################################################\nExample FHIR to TranSMART loader\n################################################################################\n\n|Build status| |codecov| |pypi| |downloads|\n\n.. |Build status| image:: https://travis-ci.org/thehyve/python_fhir2transmart.svg?branch=master\n   :alt: Build status\n   :target: https://travis-ci.org/thehyve/python_fhir2transmart/branches\n.. |codecov| image:: https://codecov.io/gh/thehyve/python_fhir2transmart/branch/master/graph/badge.svg\n   :alt: codecov\n   :target: https://codecov.io/gh/thehyve/python_fhir2transmart\n.. |pypi| image:: https://img.shields.io/pypi/v/fhir2transmart.svg\n   :alt: PyPI\n   :target: https://pypi.org/project/fhir2transmart/\n.. |downloads| image:: https://img.shields.io/pypi/dm/fhir2transmart.svg\n   :alt: PyPI - Downloads\n   :target: https://pypi.org/project/fhir2transmart/\n\nThis package contains a mapper that reads data from `HL7 FHIR`_ (STU 3 or R4) resources\nand translates them to the data model of the TranSMART_ platform,\nan open source data sharing and analytics platform for translational biomedical research.\n\nIt also provides a utility that applies the mapper and writes the translated data to tab-separated files\nthat can be loaded into a TranSMART database using the transmart-copy_ tool.\n\nThe FHIR reader is based on the fhirclient_ package, writing to TranSMART is based on transmart-loader_.\n\n\u26a0\ufe0f Note: this is a very preliminary version, still under development.\nIssues can be reported at https://github.com/thehyve/python_fhir2transmart/issues.\n\n.. _`HL7 FHIR`: https://hl7.org/fhir\n.. _TranSMART: https://github.com/thehyve/transmart-core\n.. _transmart-copy: https://github.com/thehyve/transmart-core/tree/dev/transmart-copy\n.. _fhirclient: https://pypi.org/project/fhirclient\n.. _transmart-loader: https://pypi.org/project/transmart-loader\n\n\nInstallation\n------------\n\nThe package requires Python 3.6.\n\nTo install ``fhir2transmart``, do:\n\n.. code-block:: bash\n\n  pip install fhir2transmart\n\nOr from source:\n\n.. code-block:: bash\n\n  git clone https://github.com/thehyve/python_fhir2transmart.git\n  cd python_fhir2transmart\n  pip install .\n\n\nRun tests (including coverage) with:\n\n.. code-block:: console\n\n  python setup.py test\n\n\nUsage\n-----\n\nRead input from a JSON file ``input.json`` and write the output in transmart-copy\nformat to ``/path/to/output``. The output directory should be\nempty of not existing (then it will be created).\n\n.. code-block:: bash\n\n  # Translate one json file\n  fhir2transmart [--with-ontology] input.json /path/to/output\n  # Translate all json files in a directory\n  fhir2transmart [--with-ontology] input_dir /path/to/output\n\nWith the ``--with-ontology`` option, concepts and ontology nodes\nare created based on the input data. Do not use this option when ontologies\nhave already been loaded separately.\n\nExample data is available at `MITRE SyntheticMass`_. Instructions:\n\n.. _`MITRE SyntheticMass`: https://syntheticmass.mitre.org/download.html\n\n.. code-block:: bash\n\n  # Download 1K Sample Synthetic Patient Records, FHIR STU3 : 20MB\n  wget https://syntheticmass.mitre.org/downloads/2017_11_06/synthea_sample_data_fhir_stu3_nov2017.zip\n  # unzip creates a directory 'fhir' containing 282MB of json files\n  unzip synthea_sample_data_fhir_stu3_nov2017.zip\n  # create an output directory\n  mkdir output\n  # apply the mapping\n  fhir2transmart fhir output\n\nThis generates the directories ``i2b2metadata`` and ``i2b2demodata`` in the ``output`` directory.\nThe generated data can be loaded using transmart-copy_:\n\n.. code-block:: console\n\n  # Download transmart-copy:\n  curl -f -L https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-copy/17.1-HYVE-5.9-RC3/transmart-copy-17.1-HYVE-5.9-RC3.jar -o transmart-copy.jar\n  # Load data\n  PGUSER=tm_cz PGPASSWORD=tm_cz java -jar transmart-copy.jar -d output\n\n\nMapping\n-------\n\nThe following mapping table shows how FHIR resources are mapped to the\nTranSMART data model.\n\n============= =================  ============== ============== ============ =========\nFIHR                             TranSMART\n-------------------------------  ----------------------------------------------------\nResource type attribute          Class          attribute      concept      modifier\n============= =================  ============== ============== ============ =========\nPatient_      identifier         PatientMapping identifier\nPatient_      gender             Patient        sex\nPatient_      gender             Observation    value          Gender\nPatient_      birthDate          Observation    value          BirthDate\nPatient_      deceased           Observation    value          Deceased\nPatient_      deceasedDate       Observation    value          DeceasedDate\n------------- -----------------  -------------- -------------- ------------ ---------\nCondition_    subject            Observation    patient\nCondition_    code               Observation    conceptCode\nCondition_    onsetDateTime      Observation    startDate\nCondition_    abatementDateTime  Observation    endDate\nCondition_    recordedDate       Observation\nCondition_    category\n------------- -----------------  -------------- -------------- ------------ ---------\nEncounter_    identifier         Visit\nEncounter_    period.start       Visit          startDate\nEncounter_    period.end         Visit          endDate\nEncounter_    status             Visit          activeStatusCd\nEncounter_    class              Visit          inoutCd\nEncounter_    hospitalization    Visit          locationCd\n============= =================  ============== ============== ============ =========\n\n.. _Patient: https://www.hl7.org/fhir/patient.html\n.. _Condition: https://www.hl7.org/fhir/condition.html\n.. _Encounter: https://www.hl7.org/fhir/encounter.html\n\n\nLicense\n-------\n\nCopyright (c) 2019 The Hyve B.V.\n\nThe FHIR to TranSMART loader is licensed under the MIT License. See the file `<LICENSE>`_.\n\n\n\n\n",
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