francois/HowBadIsMyBatch
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refactoring

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frankknoll
2022-02-06 10:56:33 +01:00
parent fa55ac1da4
commit 90d26d518d
1 changed files with 112 additions and 115 deletions
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67
HowBadIsMyBatch.ipynb
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@@ -125,23 +125,20 @@
"\n", "\n",
"class DataFrameFilter:\n", "class DataFrameFilter:\n",
" \n", " \n",
" def __init__(self, dataFrame):\n", " def filterByCovid19And(self, dataFrame, manufacturer = None, dose = None):\n",
" self.dataFrame = dataFrame\n", " return dataFrame[self._isCovid19(dataFrame) & self._isManufacturer(dataFrame, manufacturer) & self._isDose(dataFrame, dose)]\n",
"\n", "\n",
" def filterByCovid19And(self, manufacturer = None, dose = None):\n", " def filterForSevereEffects(self, dataFrame, dose):\n",
" return self.dataFrame[self._isCovid19() & self._isManufacturer(manufacturer) & self._isDose(dose)]\n", " return self.filterByCovid19And(dataFrame, dose = dose)\n",
"\n", "\n",
" def filterForSevereEffects(self, dose):\n", " def _isCovid19(self, dataFrame):\n",
" return self.filterByCovid19And(dose = dose)\n", " return dataFrame[\"VAX_TYPE\"] == \"COVID19\"\n",
"\n", "\n",
" def _isCovid19(self):\n", " def _isManufacturer(self, dataFrame, manufacturer):\n",
" return self.dataFrame[\"VAX_TYPE\"] == \"COVID19\"\n", " return dataFrame[\"VAX_MANU\"] == manufacturer if manufacturer is not None else True\n",
"\n", "\n",
" def _isManufacturer(self, manufacturer):\n", " def _isDose(self, dataFrame, dose):\n",
" return self.dataFrame[\"VAX_MANU\"] == manufacturer if manufacturer is not None else True\n", " return dataFrame[\"VAX_DOSE_SERIES\"].str.contains(dose) if dose is not None else True\n"
"\n",
" def _isDose(self, dose):\n",
" return self.dataFrame[\"VAX_DOSE_SERIES\"].str.contains(dose) if dose is not None else True\n"
] ]
}, },
{ {
@@ -240,13 +237,13 @@
"\n", "\n",
" @staticmethod\n", " @staticmethod\n",
" def createBatchCodeTable(dataFrame : pd.DataFrame, manufacturer, dose):\n", " def createBatchCodeTable(dataFrame : pd.DataFrame, manufacturer, dose):\n",
" filteredDataFrame = DataFrameFilter(dataFrame).filterByCovid19And(manufacturer = manufacturer, dose = dose)\n", " filteredDataFrame = DataFrameFilter().filterByCovid19And(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",
" @staticmethod\n", " @staticmethod\n",
" def createSevereEffectsBatchCodeTable(dataFrame : pd.DataFrame, dose):\n", " def createSevereEffectsBatchCodeTable(dataFrame : pd.DataFrame, dose):\n",
" severeEffectsDataFrame = DataFrameFilter(dataFrame).filterForSevereEffects(dose)\n", " severeEffectsDataFrame = DataFrameFilter().filterForSevereEffects(dataFrame, dose)\n",
" return BatchCodeTableHelper(severeEffectsDataFrame).createSevereEffectsBatchCodeTable()\n" " return BatchCodeTableHelper(severeEffectsDataFrame).createSevereEffectsBatchCodeTable()\n"
] ]
}, },
@@ -318,8 +315,7 @@
"\n", "\n",
" def test_filterByCovid19And(self):\n", " def test_filterByCovid19And(self):\n",
" # Given\n", " # Given\n",
" dataFrameFilter = DataFrameFilter(\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" [\n", " [\n",
" {\n", " {\n",
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
@@ -355,10 +351,11 @@
" \"1996874\"],\n", " \"1996874\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ]))\n", " ])\n",
" dataFrameFilter = DataFrameFilter()\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = dataFrameFilter.filterByCovid19And(manufacturer = \"MODERNA\", dose = '1')\n", " dataFrame = dataFrameFilter.filterByCovid19And(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
" \n", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -375,8 +372,7 @@
"\n", "\n",
" def test_filterForSevereEffects(self):\n", " def test_filterForSevereEffects(self):\n",
" # Given\n", " # Given\n",
" dataFrameFilter = DataFrameFilter(\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" [\n", " [\n",
" {\n", " {\n",
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
@@ -395,10 +391,11 @@
" \"0916601\"],\n", " \"0916601\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ]))\n", " ])\n",
" dataFrameFilter = DataFrameFilter()\n",
"\n", "\n",
" # When\n", " # When\n",
" dataFrame = dataFrameFilter.filterForSevereEffects(dose = '1')\n", " dataFrame = dataFrameFilter.filterForSevereEffects(dataFrame, dose = '1')\n",
" \n", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -413,8 +410,7 @@
"\n", "\n",
" def test_filterByFirstDose(self):\n", " def test_filterByFirstDose(self):\n",
" # Given\n", " # Given\n",
" dataFrameFilter = DataFrameFilter(\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" [\n", " [\n",
" {\n", " {\n",
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
@@ -431,10 +427,11 @@
" \"1048786\"],\n", " \"1048786\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ]))\n", " ])\n",
" dataFrameFilter = DataFrameFilter()\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = dataFrameFilter.filterByCovid19And(manufacturer = \"MODERNA\", dose = '1')\n", " dataFrame = dataFrameFilter.filterByCovid19And(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
" \n", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -447,8 +444,7 @@
"\n", "\n",
" def test_filterBySecondDose(self):\n", " def test_filterBySecondDose(self):\n",
" # Given\n", " # Given\n",
" dataFrameFilter = DataFrameFilter(\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" [\n", " [\n",
" {\n", " {\n",
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
@@ -465,10 +461,11 @@
" \"1048786\"],\n", " \"1048786\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ]))\n", " ])\n",
" dataFrameFilter = DataFrameFilter()\n",
"\n", "\n",
" # When\n", " # When\n",
" dataFrame = dataFrameFilter.filterByCovid19And(manufacturer = \"MODERNA\", dose = '2')\n", " dataFrame = dataFrameFilter.filterByCovid19And(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n",
" \n", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -621,7 +618,7 @@
" \"1048786\",\n", " \"1048786\",\n",
" \"4711\"],\n", " \"4711\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" dataFrame = DataFrameFilter(dataFrame).filterByCovid19And()\n", " dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n",
" \n", " \n",
" # When\n", " # When\n",
" doseTable = DoseAnalysis.getDoseTable(dataFrame)\n", " doseTable = DoseAnalysis.getDoseTable(dataFrame)\n",
@@ -652,7 +649,7 @@
" \"1048786\",\n", " \"1048786\",\n",
" \"4711\"],\n", " \"4711\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" dataFrame = DataFrameFilter(dataFrame).filterByCovid19And()\n", " dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n",
" \n", " \n",
" # When\n", " # When\n",
" doseByMonthTable = DoseAnalysis.getDoseByMonthTable(dataFrame)\n", " doseByMonthTable = DoseAnalysis.getDoseByMonthTable(dataFrame)\n",
@@ -815,13 +812,13 @@
"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(dataFrame).filterByCovid19And()\n", " dataFrame = DataFrameFilter().filterByCovid19And(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(dataFrame).filterByCovid19And()\n", " dataFrame = DataFrameFilter().filterByCovid19And(dataFrame)\n",
" return DoseAnalysis.getDoseByMonthTable(dataFrame)" " return DoseAnalysis.getDoseByMonthTable(dataFrame)"
] ]
}, },