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refactoring

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frankknoll
2022-02-20 17:26:15 +01:00
parent fac3961ea6
commit aa18911c32
1 changed files with 73 additions and 28 deletions
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101
src/HowBadIsMyBatch.ipynb
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@@ -410,17 +410,18 @@
"source": [
"class InternationalLotTableFactory:\n",
" \n",
" @staticmethod\n",
" def createInternationalLotTable(dataFrame):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" internationalLotTable = InternationalLotTableFactory._createInternationalLotTable(dataFrame)\n",
" def __init__(self, dataFrame : pd.DataFrame):\n",
" self.dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" self.countryBatchCodeTable = None\n",
"\n",
" def createInternationalLotTable(self):\n",
" internationalLotTable = self._createInternationalLotTable()\n",
" return internationalLotTable.sort_values(by = 'Severe reports', ascending = False)\n",
"\n",
" @staticmethod\n",
" def createBatchCodeTableByCountry(dataFrame : pd.DataFrame, country):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" batchCodeTable = InternationalLotTableFactory._createBatchCodeTableByCountry(dataFrame, country)\n",
" batchCodeTable = CompanyColumnAdder.addCompanyColumn(batchCodeTable, CompanyColumnAdder.createCompanyByBatchCodeTable(dataFrame))\n",
" # FK-TODO: move this and dependent methods to another class\n",
" def createBatchCodeTableByCountry(self, country):\n",
" batchCodeTable = self._createBatchCodeTableByCountry(country)\n",
" batchCodeTable = CompanyColumnAdder.addCompanyColumn(batchCodeTable, CompanyColumnAdder.createCompanyByBatchCodeTable(self.dataFrame))\n",
" batchCodeTable = batchCodeTable[\n",
" [\n",
" 'Adverse Reaction Reports',\n",
@@ -433,18 +434,31 @@
" ]]\n",
" return batchCodeTable.sort_values(by = 'Severe reports', ascending = False)\n",
"\n",
" @staticmethod\n",
" def _createInternationalLotTable(dataFrame):\n",
" def _createInternationalLotTable(self):\n",
" countryColumnName = 'Country'\n",
" dataFrame = CountryColumnAdder.addCountryColumn(dataFrame, countryColumnName = countryColumnName)\n",
" dataFrame = CountryColumnAdder.addCountryColumn(self.dataFrame, countryColumnName = countryColumnName)\n",
" return SummationTableFactory.createSummationTableHavingSevereReportsColumn(dataFrame.groupby(dataFrame[countryColumnName]))\n",
"\n",
" @staticmethod\n",
" def _createBatchCodeTableByCountry(dataFrame : pd.DataFrame, country):\n",
" def _createBatchCodeTableByCountry(self, country):\n",
" if self.countryBatchCodeTable is None:\n",
" self.countryBatchCodeTable = self._getCountryBatchCodeTable()\n",
" return self._getCountry(self.countryBatchCodeTable, country)\n",
"\n",
" def _getCountryBatchCodeTable(self):\n",
" countryColumnName = 'Country'\n",
" dataFrame = CountryColumnAdder.addCountryColumn(dataFrame, countryColumnName = countryColumnName)\n",
" dataFrame = DataFrameFilter().filterByCountry(dataFrame, country = country, countryColumnName = countryColumnName)\n",
" return SummationTableFactory.createSummationTableHavingSevereReportsColumn(dataFrame.groupby('VAX_LOT'))\n"
" dataFrame = CountryColumnAdder.addCountryColumn(self.dataFrame, countryColumnName = countryColumnName)\n",
" return SummationTableFactory.createSummationTableHavingSevereReportsColumn(\n",
" dataFrame.groupby(\n",
" [\n",
" dataFrame[countryColumnName],\n",
" dataFrame['VAX_LOT']\n",
" ]))\n",
"\n",
" def _getCountry(self, countryBatchCodeTable, country):\n",
" return countryBatchCodeTable.loc[country] if country in countryBatchCodeTable.index else self._getEmptyBatchCodeTable(countryBatchCodeTable)\n",
" \n",
" def _getEmptyBatchCodeTable(self, countryBatchCodeTable):\n",
" return countryBatchCodeTable[0:0].droplevel(0)\n"
]
},
{
@@ -1109,9 +1123,10 @@
" \"0815\",\n",
" \"0816\"])\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" internationalLotTableFactory = InternationalLotTableFactory(dataFrame)\n",
" \n",
" # When\n",
" internationalLotTable = InternationalLotTableFactory.createInternationalLotTable(dataFrame)\n",
" internationalLotTable = internationalLotTableFactory.createInternationalLotTable()\n",
"\n",
" # Then\n",
" assert_frame_equal(\n",
@@ -1133,20 +1148,21 @@
" def test_createBatchCodeTableByCountry(self):\n",
" # Given\n",
" dataFrame = TestHelper.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT'],\n",
" data = [ [1, 0, 0, 'COVID19', 'MODERNA', '016M20A', '2', 'GBPFIZER INC2020486806', 0, 0],\n",
" [0, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1', 'FRMODERNATX, INC.MOD20224', 0, 0],\n",
" [1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0],\n",
" [0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0]],\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT'],\n",
" data = [ [1, 0, 0, 'COVID19', 'PFIZER\\BIONTECH', '016M20A', '2', 'GBPFIZER INC2020486806', 0, 0],\n",
" [0, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1', 'FRMODERNATX, INC.MOD20224', 0, 0],\n",
" [1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0],\n",
" [0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0]],\n",
" index = [\n",
" \"1048786\",\n",
" \"1048786\",\n",
" \"4711\",\n",
" \"0815\"])\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" internationalLotTableFactory = InternationalLotTableFactory(dataFrame)\n",
" \n",
" # When\n",
" batchCodeTable = InternationalLotTableFactory.createBatchCodeTableByCountry(dataFrame, 'France')\n",
" batchCodeTable = internationalLotTableFactory.createBatchCodeTableByCountry('France')\n",
"\n",
" # Then\n",
" assert_frame_equal(\n",
@@ -1161,6 +1177,34 @@
" '030L20A'\n",
" ],\n",
" name = 'VAX_LOT')),\n",
" check_dtype = False)\n",
"\n",
" def test_createBatchCodeTableByNonExistingCountry(self):\n",
" # Given\n",
" dataFrame = TestHelper.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT'],\n",
" data = [ [1, 0, 0, 'COVID19', 'PFIZER\\BIONTECH', '016M20A', '2', 'GBPFIZER INC2020486806', 0, 0],\n",
" [0, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1', 'FRMODERNATX, INC.MOD20224', 0, 0],\n",
" [1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0],\n",
" [0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0]],\n",
" index = [\n",
" \"1048786\",\n",
" \"1048786\",\n",
" \"4711\",\n",
" \"0815\"])\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" internationalLotTableFactory = InternationalLotTableFactory(dataFrame)\n",
" \n",
" # When\n",
" batchCodeTable = internationalLotTableFactory.createBatchCodeTableByCountry('non existing country')\n",
"\n",
" # Then\n",
" assert_frame_equal(\n",
" batchCodeTable,\n",
" TestHelper.createDataFrame(\n",
" columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality'],\n",
" data = [ ],\n",
" index = pd.Index([], name = 'VAX_LOT')),\n",
" check_dtype = False)\n"
]
},
@@ -1366,7 +1410,7 @@
"metadata": {},
"outputs": [],
"source": [
"internationalLotTable = InternationalLotTableFactory.createInternationalLotTable(nonDomesticVaers)"
"internationalLotTable = InternationalLotTableFactory(nonDomesticVaers).createInternationalLotTable()"
]
},
{
@@ -1388,8 +1432,8 @@
"metadata": {},
"outputs": [],
"source": [
"def createAndSaveAndDisplayBatchCodeTableByCountry(nonDomesticVaers, country, minADRsForLethality = None):\n",
" batchCodeTable = InternationalLotTableFactory.createBatchCodeTableByCountry(nonDomesticVaers, country)\n",
"def createAndSaveAndDisplayBatchCodeTableByCountry(internationalLotTableFactory, country, minADRsForLethality = None):\n",
" batchCodeTable = internationalLotTableFactory.createBatchCodeTableByCountry(country)\n",
" batchCodeTable.index.set_names(\"Batch\", inplace = True)\n",
" if minADRsForLethality is not None:\n",
" batchCodeTable.loc[batchCodeTable['Adverse Reaction Reports'] < minADRsForLethality, ['Severe reports', 'Lethality']] = [np.nan, np.nan]\n",
@@ -1397,8 +1441,9 @@
" display(country + \":\", batchCodeTable)\n",
"\n",
"def createAndSaveAndDisplayBatchCodeTablesByCountry(nonDomesticVaers, countries, minADRsForLethality = None):\n",
" internationalLotTableFactory = InternationalLotTableFactory(nonDomesticVaers)\n",
" for country in countries:\n",
" createAndSaveAndDisplayBatchCodeTableByCountry(nonDomesticVaers, country, minADRsForLethality)"
" createAndSaveAndDisplayBatchCodeTableByCountry(internationalLotTableFactory, country, minADRsForLethality)"
]
},
{