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        "author": "Human Cell Atlas contributors",
        "author_email": "akislyuk@chanzuckerberg.com",
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        "description": "DEPRECATED\n==========\nThis repository has been deprecated. For information about accessing Human Cell Atlas data please refer to the `Data Browser quick start guide. <https://data.humancellatlas.org/guides/quick-start-guide>`_\n\nHCA CLI\n=======\nThis repository is a pip installable Command Line Interface (CLI) and Python library (API) for interacting with the\nData Coordination Platform (DCP) of the Human Cell Atlas (HCA).\n\nCurrently the `hca` package supports interaction with the `Upload Service <https://github.com/HumanCellAtlas/upload-service>`_ and `Data Storage Service (DSS) <https://github.com/HumanCellAtlas/data-store>`_ for services such as uploading, downloading,\nand querying data.\n\nThe HCA CLI is compatible with Python versions 3.5+ (we are no longer compatible with Python 2.7, and our last compatible Python 2.7 version was `hca==6.4.0`).\n\nInstallation\n------------\n:code:`pip install hca`.\n\nUsage\n-----\n\nDocumentation on readthedocs.io:\n\n* `CLI documentation <https://hca.readthedocs.io/en/latest/cli.html>`_\n\n* `Python API documentation <https://hca.readthedocs.io/en/latest/api.html>`_\n\nExample CLI/API usage:\n\n* `CLI examples (open endpoints) <https://github.com/HumanCellAtlas/dcp-cli/tree/master/docs/OpenCLIExamples.rst>`_\n\n* `CLI examples (restricted endpoints) <https://github.com/HumanCellAtlas/dcp-cli/tree/master/docs/RestrictedCLIExamples.rst>`_\n\n* `Python API examples (open endpoints) <https://github.com/HumanCellAtlas/dcp-cli/tree/master/docs/OpenAPIExamples.rst>`_\n\n* `Python API examples (restricted endpoints) <https://github.com/HumanCellAtlas/dcp-cli/tree/master/docs/OpenAPIExamples.rst>`_\n\nTo see the list of commands you can use, type :code:`hca --help`.\n\nConfiguration management\n~~~~~~~~~~~~~~~~~~~~~~~~\nThe HCA CLI supports ingesting configuration from a configurable array of sources. Each source is a JSON file.\nConfiguration sources that follow the first source update the configuration using recursive dictionary merging. Sources\nare enumerated in the following order (i.e., in order of increasing priority):\n\n- Site-wide configuration source, ``/etc/hca/config.json``\n- User configuration source, ``~/.config/hca/config.json``\n- Any sources listed in the colon-delimited variable ``HCA_CONFIG_FILE``\n- Command line options\n\n**Array merge operators**: When loading a chain of configuration sources, the HCA CLI uses recursive dictionary merging\nto combine the sources. Additionally, when the original config value is a list, the package supports array manipulation\noperators, which let you extend and modify arrays defined in underlying configurations. See\nhttps://github.com/kislyuk/tweak#array-merge-operators for a list of these operators.\n\nService to Service Authorization\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nGoogle service credentials must be whitelisted before they will authenticate with the HCA CLI.\n\nSet the environment variable `GOOGLE_APPLICATION_CREDENTIALS` to the path of your Google service credentials file to\nauthenticate.\n\nOne can also use: ``hca dss login``.\n\nSee `Google service credentials <https://cloud.google.com/iam/docs/understanding-service-accounts>`_ \nfor more information about service accounts. Use the `Google Cloud IAM web console\n<https://console.cloud.google.com/iam-admin/serviceaccounts>`_ to manage service accounts.\n\nDevelopment\n-----------\nTo develop on the CLI, first run ``pip install -r requirements-dev.txt``. You can install your locally modified copy of \nthe hca package by running ``make install`` in the repository root directory.\n\nTo use the command line interface with a local or test DSS, first run ``hca`` (or ``scripts/hca`` if you want to use the\npackage in-place from the repository root directory). This will create the file ``~/.config/hca/config.json``, which you\ncan modify to update the value of ``DSSClient.swagger_url`` to point to the URL of the Swagger definition served by your\nDSS deployment. Lastly, the CLI enforces HTTPS connection to the DSS API. If you are connecting to a local DSS, make\nthis change in ``dcp-cli/hca/util/__init__.py`` in the ``SwaggerClient`` object::\n\n    scheme = \"http\"\n\nTo use the Python interface with a local or test DSS, pass the URL of the Swagger definition to the ``DSSClient``\nconstructor via the ``swagger_url`` parameter::\n\n    client = DSSClient(swagger_url=\"https://dss.example.com/v1/swagger.json\")\n\nYou can also layer a minimal config file on top of the default ``config.json`` using the ``HCA_CONFIG_FILE`` environment\nvariable, for example::\n\n    export SWAGGER_URL=\"https://dss.staging.data.humancellatlas.org/v1/swagger.json\"\n    jq -n .DSSClient.swagger_url=env.SWAGGER_URL > ~/.config/hca/config.staging.json\n    export HCA_CONFIG_FILE=~/.config/hca/config.staging.json\n\nTesting\n-------\nBefore you run tests, first run ``hca dss login``.  This will open a browser where you can log in to authenticate\nwith Google. Use an email address from one of the whitelisted domains (in ``DSS_SUBSCRIPTION_AUTHORIZED_DOMAINS_ARRAY``\nfrom `here <https://github.com/HumanCellAtlas/data-store/blob/master/environment#L55>`_).\n\nThen :code:`make test`.\n\nPrimary CI testing is through Travis CI; there is also additional testing with the\n`Gitlab Allspark instance <https://allspark.dev.data.humancellatlas.org/HumanCellAtlas/dcp-cli/>`_ that runs tests for Windows.\n(Note that Allspark is not open to the public, members of the Human Cell Atlas project can access the Allspark cluster using the Github account\nassociated with the Human Cell Atlas organization on Github.) If submitting PRs that have the potential of being platform-dependent, please ensure \nthe status of \"Windows Testing\" is verified before merging.\n\nBugs\n~~~~\nPlease report bugs, issues, feature requests, etc. in the \n`HumanCellAtlas/dcp-cli repository on GitHub <https://github.com/HumanCellAtlas/dcp-cli/issues>`_.\n\n\nSecurity Policy\n---------------\nSee our `Security Policy <https://github.com/HumanCellAtlas/.github/blob/master/SECURITY.md>`_.\n\nLicense\n-------\nLicensed under the terms of the `MIT License <https://opensource.org/licenses/MIT>`_.\n\n.. image:: https://img.shields.io/travis/HumanCellAtlas/dcp-cli.svg?branch=master\n        :target: https://travis-ci.org/HumanCellAtlas/dcp-cli?branch=master\n.. image:: https://codecov.io/github/HumanCellAtlas/dcp-cli/coverage.svg?branch=master\n        :target: https://codecov.io/github/HumanCellAtlas/dcp-cli?branch=master\n.. image:: https://img.shields.io/pypi/v/hca.svg\n        :target: https://pypi.python.org/pypi/hca\n.. image:: https://img.shields.io/pypi/l/hca.svg\n        :target: https://pypi.python.org/pypi/hca\n.. image:: https://readthedocs.org/projects/hca/badge/?version=latest\n        :target: https://hca.readthedocs.io/",
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