{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Wherever the current working directory is move to `~/cerebmodels`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/main-dev/cerebtests/docs/notebooks\r\n"
     ]
    }
   ],
   "source": [
    "!pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/main-dev/cerebtests/docs\n"
     ]
    }
   ],
   "source": [
    "cd .."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/main-dev/cerebtests\n"
     ]
    }
   ],
   "source": [
    "cd .."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/main-dev\n"
     ]
    }
   ],
   "source": [
    "cd .."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/main-dev/cerebmodels\n"
     ]
    }
   ],
   "source": [
    "cd cerebmodels/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Load executive control"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "from executive import ExecutiveControl as ec"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "#ec.list_modelscales()\n",
    "#ec.list_models( modelscale=\"cells\" )\n",
    "exc = ec()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1.1. Load desired model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%capture\n",
    "desired_model = ec.choose_model( modelscale=\"cells\", modelname=\"PC2003Khaliq\" )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. Load dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import requests\n",
    "import json"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "datasetlink = \"https://raw.githubusercontent.com/cerebunit/cerebdata/master/expdata/cells/PurkinjeCell/Llinas_Sugimori_1980_soma_restVm.json\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset = json.loads( requests.get(datasetlink).text )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3. Load desired validation test"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cerebunit.validation_tests.cells.Purkinje import SomaRestingVmTest as srvt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3.1. Instantiate test class"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Validate Observation ...\n",
      "Validated.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/envs/py3-cerebmodels/lib/python3.5/site-packages/scipy/stats/stats.py:1450: UserWarning: kurtosistest only valid for n>=20 ... continuing anyway, n=10\n",
      "  \"anyway, n=%i\" % int(n))\n"
     ]
    }
   ],
   "source": [
    "vtest = srvt(dataset)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3.2. Run validation test"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Testing ...\n",
      "Sim produce_soma v_restingVm starting ...\n",
      "Simulation produce_voltage_response starting ...\n",
      "--- 0.11563400000000001 seconds ---\n",
      "File saving ...\n",
      "File saved.\n",
      "Simulation produce_voltage_response Done.\n",
      "--- 0.19566200000000045 seconds ---\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/envs/py3-cerebmodels/lib/python3.5/site-packages/pynwb/file.py:619: UserWarning: Date is missing timezone information. Updating to local timezone.\n",
      "  warn(\"Date is missing timezone information. Updating to local timezone.\")\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Simulation produce_soma v_restingVm Done.\n",
      "--- 3.605861 seconds ---\n",
      "Computing score ...\n",
      "Done.\n",
      "eta0 = -63.99954201896992 mV, eta = -66.5 mV, n = 10\n",
      "H0: eta = eta0\n",
      "Ha: eta =/= eta0\n",
      "Test statistic: z = 2.5298221281347035\n",
      "Assuming H0 is true, p-value = 0.011412036386001651\n"
     ]
    }
   ],
   "source": [
    "test_statistic = vtest.judge(desired_model)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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