refactoring

HowBadIsMyBatch.ipynb

@@ -14,30 +14,6 @@
     "pd.set_option('display.max_columns', None)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b136967b",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "class DataFrameNormalizer:\n",
-    "    \n",
-    "    @staticmethod\n",
-    "    def convertVAX_LOTColumnToUpperCase(dataFrame):\n",
-    "        dataFrame['VAX_LOT'] = dataFrame['VAX_LOT'].str.upper()\n",
-    "\n",
-    "    @staticmethod\n",
-    "    def convertColumnsOfDataFrameToNumerics(dataFrame, columns):\n",
-    "        for column in columns:\n",
-    "            DataFrameNormalizer._convertColumnOfDataFrameToNumeric(dataFrame, column)\n",
-    "\n",
-    "    @staticmethod\n",
-    "    def _convertColumnOfDataFrameToNumeric(dataFrame, column):\n",
-    "        dataFrame[column] = np.where(dataFrame[column] == 'Y', 1, 0)\n",
-    "    "
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -66,23 +42,17 @@
     "               }\n",
     "\n",
     "    def _readVAERSDATA(self, file):\n",
-    "        VAERSDATA = self._read_csv(\n",
+    "        return self._read_csv(\n",
     "            file = file,\n",
     "            usecols = ['VAERS_ID', 'RECVDATE', 'DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
     "            parse_dates = ['RECVDATE'],\n",
     "            date_parser = lambda dateStr: pd.to_datetime(dateStr, format = \"%m/%d/%Y\"))\n",
-    "        DataFrameNormalizer.convertColumnsOfDataFrameToNumerics(\n",
-    "            VAERSDATA,\n",
-    "            ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'])\n",
-    "        return VAERSDATA\n",
     "\n",
     "    def _readVAERSVAX(self, file):\n",
-    "        VAERSVAX = self._read_csv(\n",
+    "        return self._read_csv(\n",
     "            file = file,\n",
     "            usecols = ['VAERS_ID', 'VAX_DOSE_SERIES', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT'],\n",
     "            dtype = {\"VAX_DOSE_SERIES\": \"string\"})\n",
-    "        DataFrameNormalizer.convertVAX_LOTColumnToUpperCase(VAERSVAX)\n",
-    "        return VAERSVAX\n",
     "\n",
     "    def _read_csv(self, file, **kwargs):\n",
     "        return pd.read_csv(\n",
@@ -120,6 +90,37 @@
     "        return pd.concat(dataFrames)\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6b639196",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "class DataFrameNormalizer:\n",
+    "    \n",
+    "    @staticmethod\n",
+    "    def normalize(dataFrame):\n",
+    "        DataFrameNormalizer.convertVAX_LOTColumnToUpperCase(dataFrame)\n",
+    "        DataFrameNormalizer.convertColumnsOfDataFrameToNumerics(\n",
+    "            dataFrame,\n",
+    "            ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'])\n",
+    "\n",
+    "    @staticmethod\n",
+    "    def convertVAX_LOTColumnToUpperCase(dataFrame):\n",
+    "        dataFrame['VAX_LOT'] = dataFrame['VAX_LOT'].str.upper()\n",
+    "\n",
+    "    @staticmethod\n",
+    "    def convertColumnsOfDataFrameToNumerics(dataFrame, columns):\n",
+    "        for column in columns:\n",
+    "            DataFrameNormalizer._convertColumnOfDataFrameToNumeric(dataFrame, column)\n",
+    "\n",
+    "    @staticmethod\n",
+    "    def _convertColumnOfDataFrameToNumeric(dataFrame, column):\n",
+    "        dataFrame[column] = np.where(dataFrame[column] == 'Y', 1, 0)\n",
+    "    "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -179,7 +180,7 @@
     "class BatchCodeTableHelper:\n",
     "    \n",
     "    def __init__(self, dataFrame : pd.DataFrame):\n",
-    "        self.dataFrame = dataFrame        \n",
+    "        self.dataFrame = dataFrame\n",
     "\n",
     "    def createBatchCodeTable(self):\n",
     "        batchCodeTable = AggregationHelper.aggregateAndFlattenColumnsAndRenameColumns(\n",
@@ -244,8 +245,8 @@
     "    @staticmethod\n",
     "    def createBatchCodeTable(dataFrame : pd.DataFrame, manufacturer, dose):\n",
     "        dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
-    "        filteredDataFrame = DataFrameFilter().filterBy(dataFrame, manufacturer = manufacturer, dose = dose)\n",
+    "        dataFrame = DataFrameFilter().filterBy(dataFrame, manufacturer = manufacturer, dose = dose)\n",
-    "        return BatchCodeTableHelper(filteredDataFrame).createBatchCodeTable()\n",
+    "        return BatchCodeTableHelper(dataFrame).createBatchCodeTable()\n",
     "\n",
     "    # create table from https://www.howbadismybatch.com/combined.html\n",
     "    @staticmethod\n",
@@ -630,6 +631,7 @@
     "    def test_createBatchCodeTable(self):\n",
     "        dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
     "            VaersDescrReader(dataDir = \"test/VAERS\").readAllVaersDescrs())\n",
+    "        DataFrameNormalizer.normalize(dataFrame)\n",
     "        self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1')\n",
     "\n",
     "    def _test_createBatchCodeTable(self, dataFrame, manufacturer, dose):\n",
@@ -751,6 +753,7 @@
     "def saveBatchCodeTable(manufacturer, excelFile):\n",
     "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
     "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
+    "    DataFrameNormalizer.normalize(dataFrame)\n",
     "    batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, manufacturer = manufacturer, dose = '1')\n",
     "    display(batchCodeTable)\n",
     "    batchCodeTable.to_excel(excelFile)"
@@ -831,6 +834,7 @@
     "def saveSevereEffectsBatchCodeTable(excelFile):\n",
     "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
     "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
+    "    DataFrameNormalizer.normalize(dataFrame)\n",
     "    severeEffectsBatchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrame, dose = '1')\n",
     "    display(severeEffectsBatchCodeTable)\n",
     "    severeEffectsBatchCodeTable.to_excel(excelFile)"
@@ -866,11 +870,13 @@
     "def getDoseTable():\n",
     "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
     "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
+    "    DataFrameNormalizer.normalize(dataFrame)\n",
     "    return DoseAnalysis.getDoseTable(dataFrame)\n",
     "\n",
     "def getDoseByMonthTable():\n",
     "    vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
     "    dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
+    "    DataFrameNormalizer.normalize(dataFrame)\n",
     "    return DoseAnalysis.getDoseByMonthTable(dataFrame)"
    ]
   },