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refactoring

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frankknoll
2022-02-06 11:13:38 +01:00
parent 90d26d518d
commit 6c9755ad62
1 changed files with 27 additions and 20 deletions
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HowBadIsMyBatch.ipynb
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@@ -125,11 +125,14 @@
"\n", "\n",
"class DataFrameFilter:\n", "class DataFrameFilter:\n",
" \n", " \n",
" def filterByCovid19And(self, dataFrame, manufacturer = None, dose = None):\n", " def filterByCovid19(self, dataFrame):\n",
" return dataFrame[self._isCovid19(dataFrame) & self._isManufacturer(dataFrame, manufacturer) & self._isDose(dataFrame, dose)]\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", "\n",
" def filterForSevereEffects(self, dataFrame, dose):\n", " def filterForSevereEffects(self, dataFrame, dose):\n",
" return self.filterByCovid19And(dataFrame, dose = dose)\n", " return self.filterBy(self.filterByCovid19(dataFrame), dose = dose)\n",
"\n", "\n",
" def _isCovid19(self, dataFrame):\n", " def _isCovid19(self, dataFrame):\n",
" return dataFrame[\"VAX_TYPE\"] == \"COVID19\"\n", " return dataFrame[\"VAX_TYPE\"] == \"COVID19\"\n",
@@ -237,7 +240,8 @@
"\n", "\n",
" @staticmethod\n", " @staticmethod\n",
" def createBatchCodeTable(dataFrame : pd.DataFrame, manufacturer, dose):\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", " return BatchCodeTableHelper(filteredDataFrame).createBatchCodeTable()\n",
"\n", "\n",
" # create table from https://www.howbadismybatch.com/combined.html\n", " # create table from https://www.howbadismybatch.com/combined.html\n",
@@ -313,7 +317,7 @@
"\n", "\n",
"class DataFrameFilterTest(unittest.TestCase):\n", "class DataFrameFilterTest(unittest.TestCase):\n",
"\n", "\n",
" def test_filterByCovid19And(self):\n", " def test_filterByCovid19_filterBy(self):\n",
" # Given\n", " # Given\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" [\n", " [\n",
@@ -321,14 +325,14 @@
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n", " columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
" data = [ [1, 0, 0],\n", " data = [ [1, 0, 0],\n",
" [0, 0, 1]],\n", " [0, 0, 1]],\n",
" index = [\n", " index = [\n",
" \"0916600\",\n", " \"0916600\",\n",
" \"0916601\"]),\n", " \"0916601\"]),\n",
" 'VAERSVAX': self.createDataFrame(\n", " 'VAERSVAX': self.createDataFrame(\n",
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n", " data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
" ['COVID19', 'MODERNA', '025L20A', '1']],\n", " ['COVID19', 'MODERNA', '025L20A', '1']],\n",
" index = [\n", " index = [\n",
" \"0916600\",\n", " \"0916600\",\n",
" \"0916601\"],\n", " \"0916601\"],\n",
@@ -338,14 +342,14 @@
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n", " columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
" data = [ [0, 0, 0],\n", " data = [ [0, 0, 0],\n",
" [0, 0, 1]],\n", " [0, 0, 1]],\n",
" index = [\n", " index = [\n",
" \"1996873\",\n", " \"1996873\",\n",
" \"1996874\"]),\n", " \"1996874\"]),\n",
" 'VAERSVAX': self.createDataFrame(\n", " 'VAERSVAX': self.createDataFrame(\n",
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
" data = [ ['HPV9', 'MERCK & CO. INC.', 'R017624', 'UNK'],\n", " data = [ ['HPV9', 'MERCK & CO. INC.', 'R017624', 'UNK'],\n",
" ['COVID19', 'MODERNA', '025L20A', '1']],\n", " ['COVID19', 'MODERNA', '025L20A', '1']],\n",
" index = [\n", " index = [\n",
" \"1996873\",\n", " \"1996873\",\n",
" \"1996874\"],\n", " \"1996874\"],\n",
@@ -355,7 +359,8 @@
" dataFrameFilter = DataFrameFilter()\n", " dataFrameFilter = DataFrameFilter()\n",
" \n", " \n",
" # When\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", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -378,14 +383,14 @@
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n", " columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
" data = [ [1, 1, 0, 1, 1],\n", " data = [ [1, 1, 0, 1, 1],\n",
" [0, 0, 1, 0, 1]],\n", " [0, 0, 1, 0, 1]],\n",
" index = [\n", " index = [\n",
" \"0916600\",\n", " \"0916600\",\n",
" \"0916601\"]),\n", " \"0916601\"]),\n",
" 'VAERSVAX': self.createDataFrame(\n", " 'VAERSVAX': self.createDataFrame(\n",
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n", " data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
" ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n", " ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n",
" index = [\n", " index = [\n",
" \"0916600\",\n", " \"0916600\",\n",
" \"0916601\"],\n", " \"0916601\"],\n",
@@ -421,7 +426,7 @@
" 'VAERSVAX': self.createDataFrame(\n", " 'VAERSVAX': self.createDataFrame(\n",
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
" data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n", " data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n",
" ['COVID19', 'MODERNA', '030L20A', '1']],\n", " ['COVID19', 'MODERNA', '030L20A', '1']],\n",
" index = [\n", " index = [\n",
" \"1048786\",\n", " \"1048786\",\n",
" \"1048786\"],\n", " \"1048786\"],\n",
@@ -431,7 +436,8 @@
" dataFrameFilter = DataFrameFilter()\n", " dataFrameFilter = DataFrameFilter()\n",
" \n", " \n",
" # When\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", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -455,7 +461,7 @@
" 'VAERSVAX': self.createDataFrame(\n", " 'VAERSVAX': self.createDataFrame(\n",
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n", " columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
" data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n", " data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n",
" ['COVID19', 'MODERNA', '030L20A', '1']],\n", " ['COVID19', 'MODERNA', '030L20A', '1']],\n",
" index = [\n", " index = [\n",
" \"1048786\",\n", " \"1048786\",\n",
" \"1048786\"],\n", " \"1048786\"],\n",
@@ -465,7 +471,8 @@
" dataFrameFilter = DataFrameFilter()\n", " dataFrameFilter = DataFrameFilter()\n",
"\n", "\n",
" # When\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", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -618,7 +625,7 @@
" \"1048786\",\n", " \"1048786\",\n",
" \"4711\"],\n", " \"4711\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n", " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" \n", " \n",
" # When\n", " # When\n",
" doseTable = DoseAnalysis.getDoseTable(dataFrame)\n", " doseTable = DoseAnalysis.getDoseTable(dataFrame)\n",
@@ -649,7 +656,7 @@
" \"1048786\",\n", " \"1048786\",\n",
" \"4711\"],\n", " \"4711\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n", " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" \n", " \n",
" # When\n", " # When\n",
" doseByMonthTable = DoseAnalysis.getDoseByMonthTable(dataFrame)\n", " doseByMonthTable = DoseAnalysis.getDoseByMonthTable(dataFrame)\n",
@@ -812,13 +819,13 @@
"def getDoseTable():\n", "def getDoseTable():\n",
" vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n", " vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n", " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" return DoseAnalysis.getDoseTable(dataFrame)\n", " return DoseAnalysis.getDoseTable(dataFrame)\n",
"\n", "\n",
"def getDoseByMonthTable():\n", "def getDoseByMonthTable():\n",
" vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n", " vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n", " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" return DoseAnalysis.getDoseByMonthTable(dataFrame)" " return DoseAnalysis.getDoseByMonthTable(dataFrame)"
] ]
}, },