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   "source": [
    "# Flyhweel Software Developer Kit (SDK) Basics and Helpful Hints\n",
    "\n",
    "**Date modified:** 28-July-2022 <br>\n",
    "**Authors:** Amy Hegarty, Lena Sherbakov, Intermountain Neuroimaging Consortium\n",
    "\n",
    "**Description:** <br>\n",
    "The following includes a set of basic SDK commands for Flywheel. Examples included below:\n",
    "\n",
    " - Basic Flywheel Heirarchy (finding a session)\n",
    "\n",
    "**Links** <br>\n",
    "\n",
    " - Flywheel SDK documentation [here](https://flywheel-io.gitlab.io/product/backend/sdk/branches/master/python/index.html)\n",
    " - Flywheel python SDK examples [here](https://gitlab.com/flywheel-io/public/flywheel-tutorials/-/blob/master/python/)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
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     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Welcome to Intermountain Neuroimaging Consortium!\n"
     ]
    }
   ],
   "source": [
    "print(\"Welcome to Intermountain Neuroimaging Consortium!\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Import Python Dependencies"
   ]
  },
  {
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   "execution_count": null,
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     "name": "#%%\n"
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   "outputs": [],
   "source": [
    "import os\n",
    "import logging\n",
    "import flywheel"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Define Supporting Functions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Flywheel API Key and Client\n",
    "An API Key is required to interact with the datasets on flywheel db. More on this in the Flywheel SDK doc [here](https://flywheel-io.gitlab.io/product/backend/sdk/branches/master/python/getting_started.html#api-key). Here we pull the API key directly from the user's os enviornment, set within the flywheel command line interface.  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
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   "outputs": [],
   "source": [
    "# Instantiate a logger\n",
    "logging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s %(message)s')\n",
    "log = logging.getLogger('root')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
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   "outputs": [],
   "source": [
    "# Create client, using CLI credentials\n",
    "fw = flywheel.Client()\n",
    "\n",
    "# who am I logged in as?\n",
    "log.info('You are now logged in as %s to %s', fw.get_current_user()['email'], fw.get_config()['site']['api_url'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Viewing a Flywheel Project\n",
    "The `fw.lookup` function can be used to find any container in flywheel by path. This is an easy way to find projects, subjects, or sessions. Lets view a Flywheel project and list all sessions and their scan date."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
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   "outputs": [],
   "source": [
    "project = fw.lookup('<group>/<project>')\n",
    "\n",
    "# lookup function pulls a lite version of the project object. Get the actual project object...\n",
    "project = fw.get(project.id)\n",
    "\n",
    "# loop through all project sessions\n",
    "for session in project.sessions.find():\n",
    "\n",
    "    # Loop through all sessions in the project container.\n",
    "    dt = session.timestamp\n",
    "    if not dt:\n",
    "        dt = \"NAN\"\n",
    "    else:\n",
    "        dt = dt.strftime(\" %x %X\")\n",
    "    print('%s: Subject: %s Session: %s\\tScanning Date: %s' % (session.id, session.subject.label, session.label, dt))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Viewing a Flywheel Analysis \n",
    "Similarly, we can view analyses that have been either uploaded to Flywheel or generated by running flywheel gears. Here, lets look for all analyses attached to a single session."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
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   "outputs": [],
   "source": [
    "# start by finding a session of interest\n",
    "session = fw.lookup('<group>/<project>/<subject>/<session>')\n",
    "\n",
    "# we need to take an extra step to get the full session object, not just basic info \n",
    "session_object = fw.get_session(session.id)\n",
    "\n",
    "# print all the analyses for this session\n",
    "for analysis in session_object.analyses:\n",
    "    if hasattr(analysis.job,'state'):\n",
    "        print('%s: %s %s' % (analysis.id, analysis.label, analysis.job.state))\n",
    "    else:\n",
    "        print('%s: %s' % (analysis.id, analysis.label))"
   ]
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Update Metadata In Flywheel\n",
    "In this example, lets rename an acquisition to add an \"include-BIDS\" suffix used to indicate to skip BIDS curation for that acquisition."
   ],
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    "pycharm": {
     "name": "#%% md\n"
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   "cell_type": "code",
   "execution_count": null,
   "outputs": [],
   "source": [
    "for acq in session_object.acquisitions():\n",
    "    # get the full acquisition object\n",
    "    acq = fw.get(acq.id)\n",
    "    acq.update({'label':acq.label+\"_ignore-BIDS\"})"
   ],
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   "cell_type": "markdown",
   "source": [
    "<br>\n",
    "\n",
    "Looking for more? Check out our github repository with some commonly used SDK examples! (here)<>\n",
    "\n",
    "### *Thats all Folks!*"
   ],
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    "collapsed": false,
    "pycharm": {
     "name": "#%% md\n"
    }
   }
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