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    "info": {
        "author": "Ewelina Grudzien",
        "author_email": "ewelina@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",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "################################################################################\ntransmart-hyper-dicer slicing tool for tranSMART\n################################################################################\n\n|Build status| |codecov| |pypi| |downloads|\n\n.. |Build status| image:: https://travis-ci.org/thehyve/transmart-hyper-dicer.svg?branch=master\n   :alt: Build status\n   :target: https://travis-ci.org/thehyve/transmart-hyper-dicer/branches\n.. |codecov| image:: https://codecov.io/gh/thehyve/transmart-hyper-dicer/branch/master/graph/badge.svg\n   :alt: codecov\n   :target: https://codecov.io/gh/thehyve/transmart-hyper-dicer\n.. |pypi| image:: https://img.shields.io/pypi/v/transmart-hyper-dicer.svg\n   :alt: PyPI\n   :target: https://pypi.org/project/transmart-hyper-dicer/\n.. |downloads| image:: https://img.shields.io/pypi/dm/transmart-hyper-dicer.svg\n   :alt: PyPI - Downloads\n   :target: https://pypi.org/project/transmart-hyper-dicer/\n\ntransmart-hyper-dicer is a data slicing tool that reads data from one TranSMART_ instance and uploads it to another. \n\n\u26a0\ufe0f Note: this is a very preliminary version, still under development.\nIssues can be reported at https://github.com/thehyve/transmart-hyper-dicer/issues.\n\n.. _TranSMART: https://github.com/thehyve/transmart_core\n\nConfiguration\n-------------\n\nConnection to Keycloak identity provider and tranSMART is configured by setting the environment variables below:\n\n+---------------------+--------------------------------------------------------------------------------------+\n| Variable            | Description                                                                          |\n+=====================+======================================================================================+\n| TRANSMART_URL       | URL of the TranSMART back-end application e.g. `https://transmart.example.com`       |\n+---------------------+--------------------------------------------------------------------------------------+\n| KEYCLOAK_SERVER_URL | URL of the Keycloak identity provider e.g. `https://keycloak.example.com`            |\n+---------------------+--------------------------------------------------------------------------------------+\n| KEYCLOAK_REALM      | Keycloak realm, e.g. `dev`                                                           |\n+---------------------+--------------------------------------------------------------------------------------+\n| KEYCLOAK_CLIENT_ID  | Keycloak client ID, e.g. `transmart-client`                                          |\n+---------------------+--------------------------------------------------------------------------------------+\n| OFFLINE_TOKEN       | An offline token used used as a refresh token in order to communicate with TranSMART |\n+---------------------+--------------------------------------------------------------------------------------+\n| VERIFY_CERT         | Either a boolean, in which case it controls whether the server\u2019s                     |\n|                     | TLS certificate is verified, or a string, in which case it must be a path            |\n|                     | to a CA bundle to use. Defaults to True.                                             |\n+---------------------+--------------------------------------------------------------------------------------+\n\nIn order to generate an offline token for ``USERNAME`` user, the following ``curl`` command can be used.\nTo get the token the user needs to have the role mapping for the realm-level: ``offline_access``.\nBefore using the command you have to substitute words in uppercase with proper ones.\n\n.. code-block:: bash\n\n    curl \\\n      -d 'client_id=KEYCLOAK_CLIENT_ID' \\\n      -d 'username=USERNAME' \\\n      -d 'password=PASSWORD' \\\n      -d 'grant_type=password' \\\n      -d 'scope=offline_access' \\\n      'https://KEYCLOAK_SERVER_URL/auth/realms/KEYCLOAK_REALM/protocol/openid-connect/token'\n\n\nThe value of the `refresh_token` field in the response is the offline token.\n\nAll the variables can be specified in the ``.env`` file as key-value pairs. They will be automatically set as environment variables, when starting the application. Example of the ``.env`` file:\n\n.. code-block:: bash\n\n   KEYCLOAK_CLIENT_ID=transmart-client\n   KEYCLOAK_SERVER_URL=https://keycloak.example.com\n   KEYCLOAK_REALM=dev\n   OFFLINE_TOKEN=<refresh_token value from the curl response>\n   TRANSMART_URL=https://transmart.example.com\n\n\nInstallation\n------------\n\nThe package requires Python 3.6+.\n\nTo install ``transmart-hyper-dicer``, do:\n\n.. code-block:: bash\n\n  pip install transmart-hyper-dicer\n\nOr from source:\n\n.. code-block:: bash\n\n  git clone https://github.com/thehyve/transmart-hyper-dicer.git\n  cd transmart-hyper-dicer\n  pip install .\n\n\nRun tests (including coverage) with:\n\n.. code-block:: bash\n\n  python setup.py test\n\n\nUsage\n-----\n\nRead subset of data from the configured tranSMART instance, based on the constraint specified in an input JSON file\nand write the output in transmart-copy_ format to /path/to/output.\nThe output directory should be empty of not existing (then it will be created).\n\nInput constraint has to be a `valid tranSMART constraint`_. Example of <input.json> file content:\n\n.. code-block:: JSON\n\n  {\n    \"type\": \"study_name\",\n    \"studyId\": \"EHR\"\n  }\n\n\nRun:\n\n.. code-block:: bash\n\n  transmart-hyper-dicer <input.json> /path/to/output\n\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-6.2/transmart-copy-17.1-HYVE-6.2.jar -o transmart-copy.jar\n  # Load data\n  PGUSER=tm_cz PGPASSWORD=tm_cz java -jar transmart-copy.jar -d output\n\n\n.. _transmart-copy: https://github.com/thehyve/transmart-core/tree/dev/transmart-copy\n.. _`valid tranSMART constraint`: https://transmart.thehyve.net/open-api/index.html\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\n\nLicense\n-------\n\nCopyright (c) 2019 The Hyve B.V.\n\nThe Transmart Hyper Dicer is licensed under the MIT License. See the file `<LICENSE>`_.\n\n\n\n\n",
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