HowBadIsMyBatch/HowBadIsMyBatch.ipynb

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   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "\n",
    "pd.set_option('display.max_rows', 100)\n",
    "pd.set_option('display.max_columns', None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "233bc590",
   "metadata": {},
   "outputs": [],
   "source": [
    "def createDataFrame(dataDir, manufacturer):\n",
    "    def read_csv(file, usecols):\n",
    "        return pd.read_csv(file, index_col = 'VAERS_ID', encoding = 'latin1', low_memory = False, usecols = usecols)\n",
    "\n",
    "    def createDataFrameForYear(year):\n",
    "        folder = dataDir + \"/\" + year + \"VAERSData/\"\n",
    "        return pd.merge(\n",
    "            read_csv(folder + year + \"VAERSDATA.csv\", ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE']),\n",
    "            read_csv(folder + year + \"VAERSVAX.csv\", ['VAERS_ID', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT']),\n",
    "            left_index = True,\n",
    "            right_index = True)\n",
    "\n",
    "    df = pd.concat([createDataFrameForYear(\"2021\"), createDataFrameForYear(\"2022\")])\n",
    "    return df[(df[\"VAX_TYPE\"] == \"COVID19\") & (df[\"VAX_MANU\"] == manufacturer)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "99945ca8",
   "metadata": {},
   "outputs": [],
   "source": [
    "def createBatchCodeTable(df):\n",
    "    def filter(df, col):\n",
    "        return df[df[col] == 'Y'][['VAX_LOT']]\n",
    "\n",
    "    batchCodeTableDict = {\n",
    "        'ADRs': df[['VAX_LOT']].value_counts(),\n",
    "        'DEATHS': filter(df, 'DIED').value_counts(),\n",
    "        'DISABILITIES': filter(df, 'DISABLE').value_counts(),\n",
    "        'LIFE THREATENING ILLNESSES': filter(df, 'L_THREAT').value_counts()\n",
    "    }\n",
    "    return pd.concat(batchCodeTableDict, axis=1).replace(to_replace=np.nan, value=0)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "86e0e4f2",
   "metadata": {},
   "outputs": [],
   "source": [
    "def saveBatchCodeTable(manufacturer, excelFile):\n",
    "    createBatchCodeTable(createDataFrame(\"VAERS\", manufacturer)).to_excel(excelFile)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ab170c16",
   "metadata": {},
   "outputs": [],
   "source": [
    "saveBatchCodeTable(\"MODERNA\", \"results/moderna.xlsx\")\n",
    "saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n",
    "saveBatchCodeTable(\"JANSSEN\", \"results/janssen.xlsx\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9f506ac8",
   "metadata": {},
   "outputs": [],
   "source": [
    "import unittest"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e14465d7",
   "metadata": {},
   "outputs": [],
   "source": [
    "from pandas.testing import assert_frame_equal\n",
    "\n",
    "\n",
    "class HowBadIsMyBatchTest(unittest.TestCase):\n",
    "\n",
    "    def test_createBatchCodeTable(self):\n",
    "        # Given\n",
    "        dataFrame = createDataFrame(\"test/VAERS\", \"MODERNA\")\n",
    "        display(\"dataFrame:\", dataFrame)\n",
    "        batchCodeTable = createBatchCodeTable(dataFrame)\n",
    "\n",
    "        # When\n",
    "        batchCodeTableExpected = pd.DataFrame(\n",
    "            {\n",
    "                'ADRs': [2, 1],\n",
    "                'DEATHS': [0, 1],\n",
    "                'DISABILITIES': [2, 0],\n",
    "                'LIFE THREATENING ILLNESSES': [0.0, 0.0]\n",
    "            },\n",
    "            index = pd.MultiIndex.from_arrays([['025L20A', '037K20A']], names = ('VAX_LOT',)))\n",
    "        display(\"batchCodeTable:\", batchCodeTable)\n",
    "        display(\"batchCodeTableExpected:\", batchCodeTableExpected)\n",
    "\n",
    "        # Then\n",
    "        assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ef8f99c4",
   "metadata": {},
   "outputs": [],
   "source": [
    "unittest.main(argv=[''], verbosity=2, exit=False)"
   ]
  }
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