diff --git a/HowBadIsMyBatch.ipynb b/HowBadIsMyBatch.ipynb index c3ffaa9df6a..7188477e2d3 100644 --- a/HowBadIsMyBatch.ipynb +++ b/HowBadIsMyBatch.ipynb @@ -126,11 +126,12 @@ "import pandas as pd\n", "\n", "class BatchCodeTableFactory:\n", - " \n", - " @staticmethod\n", - " # FK-TODO: make DataFrame parameter an instance variable\n", - " def createBatchCodeTable(df : pd.DataFrame, manufacturer, dose):\n", - " df = DataFrameFilter(df).filterBy(manufacturer = manufacturer, dose = dose)\n", + "\n", + " def __init__(self, dataFrame : pd.DataFrame):\n", + " self.dataFrame = dataFrame \n", + "\n", + " def createBatchCodeTable(self, manufacturer, dose):\n", + " df = DataFrameFilter(self.dataFrame).filterBy(manufacturer = manufacturer, dose = dose)\n", " return BatchCodeTableFactory._asDataFrame(\n", " {\n", " 'ADRs': BatchCodeTableFactory._getADRs(df),\n", @@ -140,10 +141,8 @@ " })\n", "\n", " # create table from https://www.howbadismybatch.com/combined.html\n", - " @staticmethod\n", - " # FK-TODO: make DataFrame parameter an instance variable\n", - " def createSevereEffectsBatchCodeTable(df : pd.DataFrame, dose):\n", - " df = DataFrameFilter(df).filterForSevereEffects(dose = '1')\n", + " def createSevereEffectsBatchCodeTable(self, dose):\n", + " df = DataFrameFilter(self.dataFrame).filterForSevereEffects(dose)\n", " return BatchCodeTableFactory._addCompanyColumn(\n", " BatchCodeTableFactory._asDataFrame(\n", " {\n", @@ -412,30 +411,30 @@ "\n", " def test_createSevereEffectsBatchCodeTable(self):\n", " # Given\n", - " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n", - " [\n", - " {\n", - " 'VAERSDATA': self.createDataFrame(\n", - " columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n", - " data = [ ['Y', 'Y', np.NaN, 'Y', 'Y'],\n", - " [np.NaN, np.NaN, 'Y', np.NaN, 'Y']],\n", - " index = [\n", - " \"0916600\",\n", - " \"0916601\"]),\n", - " 'VAERSVAX': self.createDataFrame(\n", - " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", - " data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n", - " ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n", - " index = [\n", - " \"0916600\",\n", - " \"0916601\"],\n", - " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", - " }\n", - " ]\n", - " )\n", - " \n", + " batchCodeTableFactory = BatchCodeTableFactory(\n", + " VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n", + " [\n", + " {\n", + " 'VAERSDATA': self.createDataFrame(\n", + " columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n", + " data = [ ['Y', 'Y', np.NaN, 'Y', 'Y'],\n", + " [np.NaN, np.NaN, 'Y', np.NaN, 'Y']],\n", + " index = [\n", + " \"0916600\",\n", + " \"0916601\"]),\n", + " 'VAERSVAX': self.createDataFrame(\n", + " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", + " data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n", + " ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n", + " index = [\n", + " \"0916600\",\n", + " \"0916601\"],\n", + " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", + " }\n", + " ]))\n", + "\n", " # When\n", - " batchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrame, '1')\n", + " batchCodeTable = batchCodeTableFactory.createSevereEffectsBatchCodeTable('1')\n", "\n", " # Then\n", " batchCodeTableExpected = pd.DataFrame(\n", @@ -489,7 +488,7 @@ " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " }\n", " ])\n", - " self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1');\n", + " self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1')\n", "\n", " def test_createBatchCodeTable(self):\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n", @@ -497,8 +496,11 @@ " self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1')\n", "\n", " def _test_createBatchCodeTable(self, dataFrame, manufacturer, dose):\n", + " # Given\n", + " batchCodeTableFactory = BatchCodeTableFactory(dataFrame)\n", + "\n", " # When\n", - " batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, manufacturer, dose)\n", + " batchCodeTable = batchCodeTableFactory.createBatchCodeTable(manufacturer, dose)\n", "\n", " # Then\n", " batchCodeTableExpected = pd.DataFrame(\n", @@ -535,7 +537,8 @@ "def saveBatchCodeTable(manufacturer, excelFile):\n", " vaersDescrs = VaersDescrReader(\"VAERS\").readAllVaersDescrs()\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n", - " batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, manufacturer = manufacturer, dose = '1')\n", + " batchCodeTableFactory = BatchCodeTableFactory(dataFrame)\n", + " batchCodeTable = batchCodeTableFactory.createBatchCodeTable(manufacturer = manufacturer, dose = '1')\n", " display(manufacturer, batchCodeTable)\n", " batchCodeTable.to_excel(excelFile)" ] @@ -562,7 +565,8 @@ "def saveSevereEffectsBatchCodeTable(excelFile):\n", " vaersDescrs = VaersDescrReader(\"VAERS\").readAllVaersDescrs()\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n", - " severeEffectsBatchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrame, dose = '1')\n", + " batchCodeTableFactory = BatchCodeTableFactory(dataFrame)\n", + " severeEffectsBatchCodeTable = batchCodeTableFactory.createSevereEffectsBatchCodeTable(dose = '1')\n", " display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n", " severeEffectsBatchCodeTable.to_excel(excelFile)" ]