diff --git a/HowBadIsMyBatch.ipynb b/HowBadIsMyBatch.ipynb index fb9f35fd4e7..a6af80f8c9d 100644 --- a/HowBadIsMyBatch.ipynb +++ b/HowBadIsMyBatch.ipynb @@ -125,11 +125,14 @@ "\n", "class DataFrameFilter:\n", " \n", - " def filterByCovid19And(self, dataFrame, manufacturer = None, dose = None):\n", - " return dataFrame[self._isCovid19(dataFrame) & self._isManufacturer(dataFrame, manufacturer) & self._isDose(dataFrame, dose)]\n", + " def filterByCovid19(self, dataFrame):\n", + " return dataFrame[self._isCovid19(dataFrame)]\n", + "\n", + " def filterBy(self, dataFrame, manufacturer = None, dose = None):\n", + " return dataFrame[self._isManufacturer(dataFrame, manufacturer) & self._isDose(dataFrame, dose)]\n", "\n", " def filterForSevereEffects(self, dataFrame, dose):\n", - " return self.filterByCovid19And(dataFrame, dose = dose)\n", + " return self.filterBy(self.filterByCovid19(dataFrame), dose = dose)\n", "\n", " def _isCovid19(self, dataFrame):\n", " return dataFrame[\"VAX_TYPE\"] == \"COVID19\"\n", @@ -237,7 +240,8 @@ "\n", " @staticmethod\n", " def createBatchCodeTable(dataFrame : pd.DataFrame, manufacturer, dose):\n", - " filteredDataFrame = DataFrameFilter().filterByCovid19And(dataFrame, manufacturer = manufacturer, dose = dose)\n", + " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n", + " filteredDataFrame = DataFrameFilter().filterBy(dataFrame, manufacturer = manufacturer, dose = dose)\n", " return BatchCodeTableHelper(filteredDataFrame).createBatchCodeTable()\n", "\n", " # create table from https://www.howbadismybatch.com/combined.html\n", @@ -313,7 +317,7 @@ "\n", "class DataFrameFilterTest(unittest.TestCase):\n", "\n", - " def test_filterByCovid19And(self):\n", + " def test_filterByCovid19_filterBy(self):\n", " # Given\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n", " [\n", @@ -321,14 +325,14 @@ " 'VAERSDATA': self.createDataFrame(\n", " columns = ['DIED', 'L_THREAT', 'DISABLE'],\n", " data = [ [1, 0, 0],\n", - " [0, 0, 1]],\n", + " [0, 0, 1]],\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', 'MODERNA', '025L20A', '1']],\n", + " ['COVID19', 'MODERNA', '025L20A', '1']],\n", " index = [\n", " \"0916600\",\n", " \"0916601\"],\n", @@ -338,14 +342,14 @@ " 'VAERSDATA': self.createDataFrame(\n", " columns = ['DIED', 'L_THREAT', 'DISABLE'],\n", " data = [ [0, 0, 0],\n", - " [0, 0, 1]],\n", + " [0, 0, 1]],\n", " index = [\n", " \"1996873\",\n", " \"1996874\"]),\n", " 'VAERSVAX': self.createDataFrame(\n", " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", " data = [ ['HPV9', 'MERCK & CO. INC.', 'R017624', 'UNK'],\n", - " ['COVID19', 'MODERNA', '025L20A', '1']],\n", + " ['COVID19', 'MODERNA', '025L20A', '1']],\n", " index = [\n", " \"1996873\",\n", " \"1996874\"],\n", @@ -355,7 +359,8 @@ " dataFrameFilter = DataFrameFilter()\n", " \n", " # When\n", - " dataFrame = dataFrameFilter.filterByCovid19And(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n", + " dataFrame = dataFrameFilter.filterByCovid19(dataFrame)\n", + " dataFrame = dataFrameFilter.filterBy(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n", " \n", " # Then\n", " dataFrameExpected = self.createDataFrame(\n", @@ -378,14 +383,14 @@ " 'VAERSDATA': self.createDataFrame(\n", " columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n", " data = [ [1, 1, 0, 1, 1],\n", - " [0, 0, 1, 0, 1]],\n", + " [0, 0, 1, 0, 1]],\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", + " ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n", " index = [\n", " \"0916600\",\n", " \"0916601\"],\n", @@ -421,7 +426,7 @@ " 'VAERSVAX': self.createDataFrame(\n", " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", " data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n", - " ['COVID19', 'MODERNA', '030L20A', '1']],\n", + " ['COVID19', 'MODERNA', '030L20A', '1']],\n", " index = [\n", " \"1048786\",\n", " \"1048786\"],\n", @@ -431,7 +436,8 @@ " dataFrameFilter = DataFrameFilter()\n", " \n", " # When\n", - " dataFrame = dataFrameFilter.filterByCovid19And(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n", + " dataFrame = dataFrameFilter.filterByCovid19(dataFrame)\n", + " dataFrame = dataFrameFilter.filterBy(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n", " \n", " # Then\n", " dataFrameExpected = self.createDataFrame(\n", @@ -455,7 +461,7 @@ " 'VAERSVAX': self.createDataFrame(\n", " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", " data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n", - " ['COVID19', 'MODERNA', '030L20A', '1']],\n", + " ['COVID19', 'MODERNA', '030L20A', '1']],\n", " index = [\n", " \"1048786\",\n", " \"1048786\"],\n", @@ -465,7 +471,8 @@ " dataFrameFilter = DataFrameFilter()\n", "\n", " # When\n", - " dataFrame = dataFrameFilter.filterByCovid19And(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n", + " dataFrame = dataFrameFilter.filterByCovid19(dataFrame)\n", + " dataFrame = dataFrameFilter.filterBy(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n", " \n", " # Then\n", " dataFrameExpected = self.createDataFrame(\n", @@ -618,7 +625,7 @@ " \"1048786\",\n", " \"4711\"],\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", - " dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n", + " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n", " \n", " # When\n", " doseTable = DoseAnalysis.getDoseTable(dataFrame)\n", @@ -649,7 +656,7 @@ " \"1048786\",\n", " \"4711\"],\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", - " dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n", + " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n", " \n", " # When\n", " doseByMonthTable = DoseAnalysis.getDoseByMonthTable(dataFrame)\n", @@ -812,13 +819,13 @@ "def getDoseTable():\n", " vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n", - " dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n", + " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n", " return DoseAnalysis.getDoseTable(dataFrame)\n", "\n", "def getDoseByMonthTable():\n", " vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n", - " dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n", + " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n", " return DoseAnalysis.getDoseByMonthTable(dataFrame)" ] },