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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Running GEMMA from GN3\n",
    "\n",
    "This document outlines how to use gemma from Genenetwork3."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If you are running gn3 through a development environment, ensure that it is up and running by running the command:\n",
    "\n",
    "```sh\n",
    "env FLASK_APP=\"main.py\" flask run --port 8080\n",
    "```\n",
    "\n",
    "To ensure that things are working, run:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'code': 0, 'output': 'gemma-wrapper 0.98.1 (Ruby 2.6.5) by Pjotr Prins 2017,2018\\n'}\n"
     ]
    }
   ],
   "source": [
    "import requests\n",
    "r = requests.get(\"http://127.0.0.1:8080/api/gemma/version\")\n",
    "print(r.json())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Uploading data\n",
    "\n",
    "Before you perform any computation, you need to ensure you have your data uploaded\n",
    "\n",
    "TODO"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## K-Computation\n",
    "\n",
    "Make sure that your metadata file is up to date!\n",
    "You need the genofile, traitfile, and snpsfile. You also need a token provided when you first uploaded your metadata file."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Computing K-Values (no loco, no cavariates): \n",
    "##### POST /gemma/k-compute/:token\n",
    "The end command will look something like:\n",
    "\n",
    "```\n",
    "gemma-wrapper --json -- -debug \\\n",
    "                -g genotype-file -p traitfile \\\n",
    "                -a genotypte-snps -gk > input-hash-k-output-filename\"\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Demo\n",
    "import requests\n",
    "r = requests.post(\"localhost:8080/api/gemma/k-compute/abcde-abcde\")\n",
    "print(r.json())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### POST /gemma/k-compute/:chromosomes/:token\n",
    "\n",
    "Cqmpute K values with chromosomes. The end command will look similar to:\n",
    "\n",
    "```\n",
    "  gemma-wrapper --json --loco 1,2,3,4 \\\n",
    "                -debug -g genotypefile -p traitfile \\\n",
    "                -a genotype-snps -gk > k_output_filename.json\n",
    "```"
   ]
  }
 ],
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