{
    "info": {
        "author": "Tom G. Close",
        "author_email": "tom.g.close@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Healthcare Industry",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Medical Science Apps."
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        "description": "XnatUtils\n=========\n\nXnat-utils is a collection of scripts for conveniently up/downloading and\nlisting data on/from XNAT.\n\nOptional Dependencies\n---------------------\n\nThe following converters are required for automatic conversions of downloaded images (using the\n'--convert_to' and '--converter' options)\n\n* dcm2niix (https://github.com/rordenlab/dcm2niix)\n* MRtrix 3 (http://mrtrix.readthedocs.io/en/latest/)\n\nInstallation\n------------\n\nInstall Python (>=3.4)\n~~~~~~~~~~~~~~~~~~~~~~\n\nmacOS\n^^^^^\n\nmacOS ships with it's own, slightly modified, version of Python, which it uses\nin some applications/services. For the most part it is okay for general use\nbut in some cases, such as with `xnat-utils`, the modifications can cause\nproblems. To avoid these I recommend installing an unmodified version of Python\nfor use in your scientific programs using Homebrew (http://brew.sh). To do this\nfirst install Homebrew::\n\n    /usr/bin/ruby -e \"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)\"\n\nthen install Python with::\n\n    brew install python3\n\nIf everything has gone well, when you type::\n\n    which python3\n\nit should come back with::\n\n    /usr/local/bin/python3\n\nIf it doesn't or your run into any problems follow the instructions you receive\nwhen you run::\n\n    brew doctor\n\nNote that these instructions are just recommendations so you don't have to\nfollow all of them, just the ones that are likely to be related to your\nproblem.\n\nWindows\n^^^^^^^\n\nDownload the version of Python for Windows using the most appropriate installer\nfor Python (>=3.4), here https://www.python.org/downloads/windows/.\n\nLinux/Unix\n^^^^^^^^^^\n\nPython is most likely already installed but if it isn't it is best to install\nit using your package manager.\n\nInstall pip\n~~~~~~~~~~~\n\nPip is probably already be installed by default with your Python package so\ncheck whether it is installed first::\n\n    pip3 --version\n\nNoting that it should be in /usr/local/bin if you are using Homebrew on macOS.\n\nIf pip is not installed you can install it by downloading the following script,\nhttps://bootstrap.pypa.io/get-pip.py and::\n\n    python3 <path-to-downloaded-file>\n\n\nInstall XnatUtils package\n~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe XnatUtils source code can be downloaded (or cloned using git) from\nhttps://github.com/MonashBI/xnatutils.git. To install it\n``cd`` to to the directory you have downloaded and run::\n\n    pip3 install xnatutils\n\nIf you get permission denied errors and you may need to use ``sudo``,\nor if you don't have admin access to the box then you can install it in your\nuser directory with the ``--user`` flag.::\n\n    pip3 install --user xnatutils\n\nwhich should install XnatPy for you. If ``pip`` is not installed you should can\ninstall it with `easy_install pip` (you may need to use ``sudo`` for both these\ncommands).\n\nI have had some difficulty with the installation of ``progressbar2`` as there is a\nconflict with the ``progressbar`` package (they both produce packages called\n``progressbar``). In this case it is probably a good idea to install xnat-utils\nin a virtual environment (https://virtualenv.readthedocs.io/en/latest/).\n\nAuthentication\n--------------\n\nThe first time you use one of the utilities you will be prompted for the address\nof the server would like to connect to, in addition to your username and\npassword. By default a alias token for these credentials will be stored in\na ~/.netrc file with the following format (with permissions set to 600 on the file)::\n\n    machine <your-server-url>\n    user <your-alias-token>\n    password <your-alias-secret>\n\nIf you don't want these credentials stored, then pass the '--no_netrc'\n(or '-n') option.\n\nIf you have saved your credentials in the ~/.netrc file, subsequent calls won't require\nyou to provide the server address or username/password until the token\nexpires (if you don't want deal with expiring tokens you can just save your username/password\nin the ~/.netrc file instead, however, please be careful with important passwords). To reset\nthe saved credentials provide ``--server`` option again with the full server address\nincluding the protocol (e.g. 'https://') or edit the ~/.netrc file directly.\n\nTo connect to an additional XNAT server, provide the new server address via the ``--server`` option.\nCredentials for this server will be saved alongside the credentials for your previously saved\nservers. If the ``--server`` option is not provided the first server in the file will be used. To\nused the save credentials for a secondary server you only need to provide as of the secondary server\naddress to ``--server`` to distinguish it from the other saved servers. For example given the following\nsaved credentials in a ~/.netrc file::\n\n    machine xnat.myuni.edu\n    user myusername\n    password mypassword\n    machine xnat-dev.myuni.edu\n    user mydevusername\n    password mydevpassword\n\nthen::\n\n    $ xnat-ls -s dev MYPROJECT\n\nwill be enough to select the development server from the saved credentials list.\n\nUsage\n-----\n\nSix commands will be installed \n\n* xnat-get - download scans and resources\n* xnat-put - upload scans and resources (requires write privileges to project)\n* xnat-ls - list projects/subjects/sessions/scans\n* xnat-rename - renames an XNAT session\n* xnat-varget - set a metadata field (including \"custom variables\")\n* xnat-varput - retrieve a metadata field (including \"custom variables\")\n\nPlease see the help for each tool by passing it the '-h' option.\n\nHelp on Regular Expressions\n---------------------------\n\nThe regular expression syntax used by ``xnat-get`` and ``xnat-ls`` is fully defined\nhere, https://docs.python.org/2/library/re.html. 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